Cactvs Toolkit Standard Property Definition Summary
| Name | Datatype | Description | Literature | Enumerations | Fields | Parameters | Computation | Dependencies | Invalidation | CompModule |
|---|---|---|---|---|---|---|---|---|---|---|
| A_3D_BONDING_VECTOR | floatvector | 3D bonding vector (i.e. next open ligand shell position in VSEPR model to attach a ligand to). The length of this vector is always 1.0 regardless of the elements involved - this value is only to be used for directions, not as a bond length. Currently, the implementatiion is limited to s/sp/sp2/sp3 geometries. |
Compiled C module | A_XYZ | atomchange bondchange merge 3drelative 3dabsolute hadd | mod_a_3d_bonding_vector.so | ||||
| A_ALCHEMY_TYPE | shortstring | Atom type as used in the Alchemy program | Tcl script | A_TYPE A_ELEMENT A_ISAROMATIC | atomchange bondchange | a_alchemy_type.xpd | ||||
| A_ALIHETERO_SUBSTITUENT_COUNT | int | Count the number of hetero (not C or H) ligands around a central atom which are not part of an aroamtic system | Compiled C module | A_ELEMENT A_TYPE B_TYPE B_ISAROMATIC | atomchange bondchange | mod_a_alihetero_substituent_count.so | ||||
| A_ALIRING_COUNT | short | Number of aliphatic rings the atom is member of | countenvelopes: { value: 0 description: If set, also count envelope rings. By default, the triple ring set is used. datatype: boolean}
|
Compiled C module | R_AROMATIC R_TYPE | atomchange bondchange ring | mod_a_aliring_count.so | |||
| A_ALKYL_SUBSTITUENT_COUNT | short | Number of alkyl substituents (carbon sp3 ligand with no hetero atoms except possibly the atom for which this property is computed). This follows the Lhasa definition of alkyl substituent groups. | CHMTRN Reference Manual, Lhasa Group, Harvard University, November 2002, Version 19.1, p. 36 | Compiled C module | A_TYPE A_ELEMENT B_TYPE B_ORDER A_HETERO_SUBSTITUENT_COUNT | atomchange bondchange atom bond | mod_a_alkyl_substituent_count.so | |||
| A_ALLENE | byte | Flag for atoms in allenic system | no:terminal:odd:even |
(builtin) | A_VALENCE B_TYPE B_ORDER | atomchange bondchange | ||||
| A_ALLYLIC | byte | An allylic atom according to the Lhasa definition. These are saturated carbon atoms that are alpha to a carbon-carbon double bond. | CHMTRN Reference Manual, Lhasa Group, Harvard University, November 2002, Version 19.1, p. 47 | Compiled C module | A_ELEMENT A_TYPE B_TYPE B_ORDER B_ARORING_COUNT | atomchange bondchange atom bond | mod_a_allylic.so | |||
| A_ALPHA_ARO_COUNT | int | Number of aromatic systems in alpha position, without the atom being a member of these. | Compiled C module | A_ISAROMATIC B_TYPE | atomchange bondchange | mod_a_alpha_aro_count.so | ||||
| A_ALPHA_UNSAT_COUNT | int | Number of vinyl, aliphatic systems in alpha position, without the atom being a member of these. This corresponds to the Lilly SMARTS extension "AG>0" and is used to implement the /IWVy extension. | Compiled C module | A_ARORING_COUNT A_UNSATURATION B_TYPE B_ORDER | atomchange bondchange | mod_a_alpha_unsat_count.so | ||||
| A_ANNOTATION | string | Atom annotation string for 2D rendering, containing, for example, charge and radical information | chargerepeatlimit: { value: 2 datatype: string} stereogroups: { value: 1 datatype: string} stereo: { value: 7 datatype: string} isotope: { value: 1 datatype: string} radical: { value: 1 datatype: string} mapping: { value: 1 datatype: string} query: { value: 1 datatype: string} flags: { value: 1 datatype: string} nostereo: { value: 0 datatype: string} auxproperty: { value: {} datatype: string} auxfilter: { value: {} datatype: string} auxpropertyprefix: { value: {} datatype: string} auxpropertysuffix: { value: {} datatype: string} style: { value: default datatype: string} label: { value: 0 datatype: string} |
(builtin) | A_TYPE A_ISOTOPE A_FORMAL_CHARGE A_FREE_ELECTRONS A_ELEMENT A_LABEL_STEREO A_CIP_STEREO A_FLAGS A_DL_STEREO A_QUERY A_HASH_STEREO A_MAP_STEREO A_RADICAL A_STEREO_GROUP | atomchange bondchange stereochange | ||||
| A_AROBOND_COUNT | byte | Number of aromatic bonds atom participates in | Compiled C module | B_ISAROMATIC | atomchange bondchange | mod_a_arobond_count.so | ||||
| A_AROCONDENSED | boolean | Flags for atoms in condensed aromatic ring systems (i.e. atoms which are member in two or more aromatic rings that are connected by an overlapping ring portion, or share an annealed aromatic bond) | Compiled C module | R_TYPE R_AROMATIC | atomchange bondchange | mod_a_arocondensed.so | ||||
| A_ARORING_COUNT | short | Number of aromatic rings the atom is member of | countenvelopes: { value: 0 datatype: string}
|
(builtin) | R_AROMATIC R_TYPE | atomchange bondchange ring | ||||
| A_ARORING_SIZE_BITS | bitset | Bit mask for aromatic ring sizes the atom participates in | ringset: { value: full enumeration: sssr:esssr,triple:k:full datatype: string}
|
Compiled C module | R_SIZE R_TYPE B_TYPE A_ARORING_COUNT R_AROMATIC | bondchange ring | mod_a_aroring_size_bits.so | |||
| A_AUTODOCK4_TYPE | shortstring | Atom type as used in the Autodock 4 program | Tcl script | A_TYPE A_ELEMENT A_ISAROMATIC | atomchange bondchange | a_autodock4_type.xpd | ||||
| A_BENZYLIC | byte | A benzylic atom according to the Lhasa definition. These are saturated carbon atoms that are alpha to an aromatic carbon atom. | CHMTRN Reference Manual, Lhasa Group, Harvard University, November 2002, Version 19.1, p. 47 | Compiled C module | A_ELEMENT A_TYPE B_TYPE B_ORDER A_ARORING_COUNT | atomchange bondchange atom bond | mod_a_benzylic.so | |||
| A_BONDORDER_COUNT | bytevector | Count of different bond orders around an atom (array). | (builtin) | B_ORDER | atomchange bondchange | |||||
| A_BOND_RANGE | intpair | Ids of first and last bond atom is bonded to | (builtin) | B_SEQUENCE_NUMBER | atomchange bondchange merge shuffle hadd mol | |||||
| A_BRICS_LINKER_TYPE | short | BRICS fragmentation scheme linker type | ChemMedChem 2008, 3, 1503-1507 | none:C-R1:N-R2:O-R3:C-R4:N-R5:C-R6:C-R7:C-R8:n-R9:N-R10:S-R11:S-R12:C-R13:C-R14:C-R15:C-R16 |
never | |||||
| A_BRIDGEHEAD | boolean | Flag indicating atom is a ring system bridgehead | Compiled C module | A_RING_COUNT | atomchange bondchange | mod_a_bridgehead.so | ||||
| A_C13_NMRSHIFT | float | C13 NMR shift, measured in ppm. | atomchange bondchange stereochange atom bond | |||||||
| A_CARBOCYCLE | boolean | Flag indicating an atom in a carbocycle ESSSR ring | Compiled C module | R_TYPE R_HETEROATOM_COUNT | atomchange bondchange atom bond | mod_a_carbocycle.so | ||||
| A_CARBON_FRAGMENT_SIZE | int | Size of the carbon skeleton the atom looked at is member of | Compiled C module | B_TYPE A_ELEMENT A_TYPE | atomchange bondchange | mod_a_carbon_fragment_size.so | ||||
| A_CENTRALITY | double | Centrality rating of the atom (scaled to 1 for most central, 0 for most peripheral, computed from A_TOPO_DISTANCE and M_SPAN) | Compiled C module | A_TOPO_DISTANCE M_SPAN | atomchange bondchange atom bond | mod_a_centrality.so | ||||
| A_CGR_CHANGE | intpair | Atom change when interpreting a CGR-encoded structure. The values are a flag for addition/removal (-1: delete in product, 0: no change, 1:add in product) and the formal charge delta when going from reagent to product | presence int charge int |
atomchange bondchange 3dabsolute atom bond reaction | ||||||
| A_CH2_CHAIN_LENGTH | int | The length of the unbranched CH2/CH3 chain the atom is a member of. Hetero or carbon atoms that do not have 2 or more hydrogen neighbors have a 0 value. Hydrogen atoms are assigned the value of their bonding partner. | Compiled C module | A_TYPE A_ELEMENT B_TYPE A_RING_COUNT A_HEAVY_SUBSTITUENT_COUNT | atomchange bondchange atom bond | mod_a_ch2_chain_length.so | ||||
| A_CHAIN_LENGTH | int | The size of the chain-heavy-atoms-only fragment the atom is a member of. Ring atoms have value 0. Hydrogen atoms inherit the value of their bond partner. | Compiled C module | A_TYPE A_RING_COUNT B_TYPE | atomchange bondchange atom bond | mod_a_chain_length.so | ||||
| A_CHARGE_STABILIZATION | shortvector | Stabilization for negative charges, radicals and positive charges (in this order) on carbon atom (potentially after cutting a bond which is not the source of a stabilizing effect) according to the Lhasa formula | CHMTRN Reference Manual, Lhasa Group, Harvard University, November 2002, Version 19.1, p. 43 | minus int plus int radical int |
Compiled C module | atomchange bondchange atom bond | mod_a_charge_stabilization.so | |||
| A_CIP_STEREO | byte | Stereo descriptor for atoms, based on CIP (R/S) rules | SS=-2:S=-1:undef=0:R=1:RR=2 |
(builtin) | atomchange bondchange | |||||
| A_CL_COUNT | int | Count the number of chlorine substituents around the atoms | Tcl script | A_ELEMENT A_TYPE | atomchange bondchange | a_cl_count.xpd | ||||
| A_COLOR | color | Atom rendering color | mode: { value: light datatype: string} labellist: { value: 1 datatype: string} colorlist: { value: green datatype: string} defaultcolor: { value: gray20 datatype: string} |
(builtin) | A_ELEMENT A_TYPE | never | ||||
| A_COLOR_SCALE | color | Get color values in different coloration models useing some atom property as data | property: { value: A_SIGMA_CHARGE datatype: string constraints: property} maxintensity: { value: 255 datatype: int} minintensity: { value: 0 datatype: int} maxvalue: { value: auto datatype: string} minvalue: { value: auto datatype: string} colorspace: { value: rgb enumeration: red:green:blue:grey,gray:rgb:fixed datatype: int} invert: { value: 0 datatype: boolean} rootscale: { value: 0 datatype: boolean} zerobalance: { value: 0 datatype: boolean} filter: { value: {} datatype: string constraints: filterlist} rangecolors: { value: red 1 green 0 blue datatype: string} |
Tcl script | atomchange bondchange | a_color_scale.xpd | ||||
| A_COMMENT | string | free-form atom comment. This is used for exampole in reading PubChem ASN.1 structure data. | never | |||||||
| A_CONFORMER | xyzvector | Conformers of the ensemble, created by various methods | maxconformers: { value: 10 description: Maximum number of conformers to generate or store minvalue: 1 maxvalue: 99999 datatype: int}
|
Tcl script | A_ELEMENT A_MOL_NUMBER A_TYPE B_TYPE A_FREE_ELECTRONS A_LABEL_STEREO B_LABEL_STEREO B_ORDER A_FLAGS A_FORMAL_CHARGE | atomchange bondchange merge | a_conformer.xpd | |||
| A_CONJUGATED | boolean | A conjugated atom according to the Lhasa definition. Conjugated atoms are those alpha to a multiply bonded atom. | CHMTRN Reference Manual, Lhasa Group, Harvard University, November 2002, Version 19.1, p. 47 | Compiled C module | A_TYPE B_TYPE A_FG_PARTICIPATION B_ORDER | atomchange bondchange atom bond | mod_a_conjugated.so | |||
| A_CONJUGATED_SYSTEM_SIZE | int | The size of the conjugated system the atom participates in according to the Shoichet definition (see literature reference). Atoms not in such a system get value 0. | J. Med. Chem. 2003, 46, 4477-4486 | Compiled C module | A_TYPE A_SP2 A_INAMIDE A_ARORING_COUNT B_TYPE | atomchange bondchange atom bond | mod_a_conjugated_system_size.so | |||
| A_COVALENCY_RADIUS | float | Default covalence radius | (builtin) | A_ELEMENT A_TYPE | atomchange | |||||
| A_CSP2_0H | boolean | Flag for carbon atoms with sp2 hybridization and no hydrogen substituents | Tcl script | A_ELEMENT A_HCOUNT A_VB_NEIGHBOR_COUNT | atomchange bondchange | a_csp2_0h.xpd | ||||
| A_CSP2_1H | boolean | Flag for carbon atoms with sp2 hybridization and one hydrogen substituent | Tcl script | A_HCOUNT A_VB_NEIGHBOR_COUNT | atomchange bondchange | a_csp2_1h.xpd | ||||
| A_CSP2_2H | boolean | Flag for carbon atoms with sp2 hybridization and two hydrogen substituents | Tcl script | A_ELEMENT A_HCOUNT A_VB_NEIGHBOR_COUNT | atomchange bondchange | a_csp2_2h.xpd | ||||
| A_CSPECIAL | boolean | Flag for carbon atoms plotted with symbols by common agreement | triplebond: { value: 1 datatype: string} allene: { value: 1 datatype: string} charged: { value: 1 datatype: string} isotope: { value: 1 datatype: string} specialbonds: { value: 1 datatype: string} onlyhligands: { value: 1 datatype: string} onlyterminalxligands: { value: 1 datatype: string} never: { value: 0 datatype: string} |
(builtin) | B_TYPE A_ELEMENT A_FORMAL_CHARGE B_ORDER A_TERMINAL_DISTANCE A_ISOTOPE A_TEXTLABEL | atomchange bondchange merge hadd | ||||
| A_CSP_0H | boolean | Flag for carbon atoms with sp hybridization and no hydrogen substituents | Tcl script | A_HCOUNT A_VB_NEIGHBOR_COUNT | atomchange bondchange | a_csp_0h.xpd | ||||
| A_CSP_1H | boolean | Flag for carbon atoms with sp hybridization and one hydrogen substituent | Tcl script | A_HCOUNT A_VB_NEIGHBOR_COUNT | atomchange bondchange | a_csp_1h.xpd | ||||
| A_DAYLIGHT_ALIRING_COUNT | short | Number of aliphatic rings the atom is member of, with Daylight definition of aromaticity | countenvelopes: { value: 0 description: If set, also count envelope rings. By default, the triple ring set is used. datatype: boolean}
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Compiled C module | R_DAYLIGHT_AROMATIC R_TYPE | atomchange bondchange ring | mod_a_daylight_aliring_count.so | |||
| A_DAYLIGHT_ARORING_COUNT | short | Number of aromatic rings the atom is member of, using Daylight aromaticity from R_DAYLIGHT_AROMATIC instead of globally configurable R_AROMATIC | countenvelopes: { value: 0 description: If set, also count envelope rings. By default, the triple ring set is used. datatype: boolean}
|
Compiled C module | R_DAYLIGHT_AROMATIC R_TYPE | atomchange bondchange ring | mod_a_daylight_aroring_count.so | |||
| A_DAYLIGHT_ARORING_SIZE_BITS | bitset | Bit mask for aromatic ring sizes the atom participates in, using always Daylight aromaticity | ringset: { value: full enumeration: sssr:esssr,triple:k:full datatype: string}
|
Compiled C module | R_SIZE R_TYPE B_TYPE A_DAYLIGHT_ARORING_COUNT R_DAYLIGHT_AROMATIC | bondchange ring | mod_a_daylight_aroring_size_bits.so | |||
| A_DEGREE | byte | Number of explicit valences around atom. This corresponds to the absurdly impractical and dangerous 'D' attribute in SMILES and should be avoided to be used for anything else. | ignorequeryatoms: { value: 0 description: If set, query atoms are not counted to the degree value in the atom neighbor sphere datatype: boolean} ignorestereoh: { value: 1 description: If set, non-implicit H at stereo centers is treated as implicit, assuming it was only added for stereochemistry encoding, not to make a structural statement datatype: boolean} |
Compiled C module | A_TYPE B_TYPE B_ORDER A_ELEMENT A_LABEL_STEREO | atomchange bondchange | mod_a_degree.so | |||
| A_DISTANCE | floatvector | Interatomic 3D distances | (builtin) | A_XYZ | atomchange bondchange stereochange 3drelative shuffle hadd | |||||
| A_DL_STEREO | byte | Stereo descriptor for atoms, based on D/L nomenclature rules | L=-1:undef=0:D=1 |
(builtin) | atomchange bondchange | |||||
| A_EC_FRAGMENTS | dataset | Structure fragments associated with the different spheres of the EC hashcode Optionally, the last sphere of included atoms on each level can be simplified in modes "tohetero" (H/C/X atom distinction) and "toheavy" (H/notH atom distinction) |
diameter: { value: 4 description: Maximum neighbor distance to consider minvalue: 1 maxvalue: 15 datatype: int} debug: { value: 0 description: If set, print debug info datatype: boolean} usebondorder: { value: 0 description: If set, use sphere expansion bond order as additional factor datatype: boolean} includehydrogens: { value: 0 description: If set, include hydrogens as computation atoms datatype: boolean} lastspheregeneralization: { value: none description: Atom type generalization for last sphere (inner spheres use full atom identity) enumeration: none:tohetero:toheavy datatype: string} |
Compiled C module | A_TYPE A_ELEMENT B_TYPE B_ORDER | atomchange bondchange atom bond | mod_a_ec_fragments.so | |||
| A_EC_HASH | uint64vector | Base atoms hashcodes for ECFP-style fingerprints. Optionally, the last sphere of included atoms on each level can be simplified in modes "tohetero" (H/C/X atom distinction) and "toheavy" (H/notH atom distinction) |
diameter: { value: 4 description: Maximum neighbor distance to consider minvalue: 1 maxvalue: 15 datatype: int} debug: { value: 0 description: If set, print debug info datatype: boolean} usebondorder: { value: 0 description: If set, use sphere expansion bond order as additional factor datatype: boolean} includeh: { value: 0 description: If set, include hydrogens as computation atoms datatype: boolean} properties: { value: A_ELEMENT A_SUBSTITUENT_COUNT A_HCOUNT description: List of properties to use in the atom seed, values cast to integer datatype: string constraints: propertylist} boolproperties: { value: A_RING_COUNT description: List of properties to use in the atom seed, values cast to boolean datatype: string constraints: propertylist} exprproperties: { value: A_EQUILIBRATED_CHARGE*10 description: List of property expressions to use in the atom seed, values cast to int datatype: string constraints: list} lastspheregeneralization: { value: none description: Atom type generalization for last sphere (inner spheres use full atom identity) enumeration: none:tohetero:toheavy datatype: string} |
Compiled C module | A_TYPE A_ELEMENT B_TYPE B_ORDER | atomchange bondchange atom bond | mod_a_ec_hash.so | |||
| A_ELEMENT | byte | Atomic number (periodic table of elements index, H=1) | (builtin) | A_SYMBOL | never | |||||
| A_ENOLIZABLE | boolean | An enolizable atom by the Lhasa definition. An enolizable atom must be saturated, non-bridgehead, have at least one hydrogen and be activated by a withdrawing bond. | CHMTRN Reference Manual, Lhasa Group, Harvard University, November 2002, Version 19.1, p. 48 | Compiled C module | A_TYPE A_ELEMENT A_BRIDGEHEAD A_HCOUNT B_TYPE B_ORDER A_FG_SUBSTITUENTS | atomchange bondchange atom bond | mod_a_enolizable.so | |||
| A_EQUILIBRATED_CHARGE | float | Equilibrated nominal charge | fixnoxides: { value: 1 datatype: string}
|
(builtin) | B_TYPE A_FORMAL_CHARGE A_PICENTER | atomchange bondchange hadd | ||||
| A_EXPLICIT_VALENCE | byte | Sum of bond orders of bonds which do not lead to implicit atoms (property A_IMPLICIT). Use with extreme caution, this is not a generally useful property. This maps to the "nbonds" property in Bruns/Watson query processing. | ignoreallh: { value: 1 description: If set, all hydrogens are assumed to be implicit datatype: boolean}
|
Compiled C module | B_TYPE B_ORDER A_IMPLICIT A_TYPE A_ELEMENT | atomchange bondchange atom bond | mod_a_explicit_valence.so | |||
| A_EXTENDED_GROUPHASH | uint64 | Perturbed group hashcode | usebondorder: { value: aro description: Whether to mix in bond orders within group: none: no, simple: direct bond order, aro: aro bonds have special mix-in value, otherwise mix in straight bond order enumeration: none:simple:aro,aromatic datatype: string} usesubstitution: { value: none description: none: pure group, location: mix in location of non-h substituents, hetero: mix in location and hetero vs. carbon character of first substituent atom, element: mix in location and element of first substituent atom enumeration: none:location:hetero:element datatype: string} |
Compiled C module | A_TYPE A_FRAMEWORK A_ELEMENT | atomchange bondchange groupchange hadd group | mod_a_extended_grouphash.so | |||
| A_EXTENDED_GROUPHASH_GROUP | index | Hash group id index for atom group hash code. The index data structure is somewhat abused: The molecule part (as in A_HASHGROUP) is used for *group* indexing, the ensemble part is used as in A_HASHGROUP for global grouping. | Compiled C module | A_GROUP_NUMBER A_EXTENDED_GROUPHASH | atomchange bondchange groupchange merge hadd group | mod_a_extended_grouphash_group.so | ||||
| A_EXTENDED_RINGHASH | uint64 | Perturbed ringsystem hashcode | usebondorder: { value: aro description: Whether to mix in bond orders within ring: none: no, simple: direct bond order, aro: aro bonds have special mix-in value, otherwise mix in straight bond order enumeration: none:simple:aro,aromatic datatype: string} usesubstitution: { value: none description: none: pure ring system, location: mix in location of non-h substituents, hetero: mix in location and hetero vs. carbon character of first substituent atom, element: mix in location and element of first substituent atom enumeration: none:location:hetero:element datatype: string} |
Compiled C module | A_TYPE A_FRAMEWORK A_ELEMENT | atomchange bondchange hadd ring | mod_a_extended_ringhash.so | |||
| A_EXTENDED_RINGHASH_GROUP | index | Hash group id index for atom ring hash code. The index data structure is somewhat abused: The molecule part (as in A_HASHGROUP) is used for *ringsystem* indexing, the ensemble part is used as in A_HASHGROUP for global grouping. | Compiled C module | A_RINGSYSTEM_NUMBER A_EXTENDED_RINGHASH | atomchange bondchange merge hadd ring | mod_a_extended_ringhash_group.so | ||||
| A_FG_CHECK | bitvector | Functional group test (for example, in Patran FGS/FGNOT clauses) of atoms as per the LHASA definition, If the atom is a carbon atom and the FG is carbon-centric, this is the A_FG_PARTICIPATION flag, otherwise a test for A_FG_SUBSTITUIENTS>1 |
none:ketone:aldehyde:acid:thioacid:ester:amide*1,amide1:amide*2,amide2:amide*3,amide3:sulfonamide*1,sulphonamide*1,sulfonamide1,sulphonamide 1:sulfonamide*2,sulphonamide*2,sulfonamide2,sulphonamide2:sulfonamide*3,sulphonamide*3,sulfonamide3,sulphonamide3:carbonium:isocyanate:acid*halide,acidhalide:thioester:amine*3,amine3:aziridine:amine*2,amine2:amine*1,amine1:nitroso:diazo:haloamine:hydrazone:oxime:imine:thiocyanate:isocyanide:nitrile,cyano,cyanide:azo:hydroxylamine:nitro:enamine:amine*oxide,amineoxide:thiol:episulfide,episulphide:sulfide,sulphide:sulfoxide,sulphoxide:sulfone,sulphone:c*sulfonate,c*sulphonate,csulfonate,csulphonate:anhydride:lactam:phosphine:phosphonate:epoxide:ether:peroxide:alcohol,hydroxyl:enol*ether,enolether:nitrite:o*sulfonate,o*sulphonate,osulfonate,osulphonate:fluoride:chloride:bromide:iodide:gem*dihalide,gemdihalide,dihalide:trihalide:acetylene:olefin:vic*dihalide,vicdihalide:halohydrin:glycol:hydrate:hemiketal:ketal:hemiacetal:acetal:azide:disulfide,disulphide:allene:vinylsilane:lactone:vinylw:vinyld:esterx:amidz,amidez:methylene:carbonyl:carboxyl:halide:amine:amide:sulfonamide:selenide:trialkylsilyl:trialkylsiloxy:silylenolether:n*urea*h,nureah:n*urea*c,nureac:carbamate*h,carbamateh:carbamate*c,carbamatec:o*carbamate,ocarbamate:n*carbamate,ncarbamate:o*carbonate,ocarbonate:dithioacetal:dithioketal:requested:withdrawing,w:expandable*withdrawing,expandablewithdrawing,xwithdrawing:nonexpandable*withdrawing,nonexpandablewithdrawing:donating,d:leaving:good*leaving,goodleaving |
ketone boolean aldehyde boolean acid boolean thioacid boolean ester boolean amide*1 boolean amide*2 boolean amide*3 boolean sulfonamide*1 boolean sulfonamide*2 boolean sulfonamide*3 boolean carbonium boolean isocyanate boolean acid*halide boolean thioester boolean amine*3 boolean aziridine boolean amine*2 boolean amine*1 boolean nitroso boolean diazo boolean haloamine boolean hydrazone boolean oxime boolean imine boolean thiocyanate boolean isocyanide boolean nitrile boolean azo boolean hydroxylamine boolean nitro boolean enamine boolean amine*oxide boolean thiol boolean episulfide boolean sulfide boolean sulfoxide boolean sulfone boolean c*sulfonate boolean anhydride boolean lactam boolean phosphine boolean phosphonate boolean epoxide boolean ether boolean peroxide boolean alcohol boolean enol*ether boolean nitrite boolean o*sulfonate boolean fluoride boolean chloride boolean bromide boolean iodide boolean gem*dihalide boolean trihalide boolean acetylene boolean olefin boolean vic*dihalide boolean halohydrin boolean glycol boolean hydrate boolean hemiketal boolean ketal boolean hemiacetal boolean acetal boolean azide boolean disulfide boolean allene boolean vinylsilane boolean lactone boolean vinylw boolean vinyld boolean esterx boolean amidz boolean methylene boolean carbonyl boolean carboxyl boolean halide boolean amine boolean amide boolean sulfonamide boolean selenide boolean trialkylsilyl boolean trialkylsiloxy boolean silylenolether boolean n*urea*h boolean n*urea*c boolean carbamate*h boolean carbamate*c boolean o*carbamate boolean n*carbamate boolean o*carbonate boolean dithioacetal boolean dithioketal boolean requested boolean withdrawing boolean expandable*withdrawing boolean nonexpandable*withdrawing boolean donating boolean leaving boolean good*leaving boolean |
Compiled C module | A_FG_PARTICIPATION A_FG_SUBSTITUENTS A_ELEMENT A_TYPE | atomchange bondchange atom bond | mod_a_fg_check.so | ||
| A_FG_PARTICIPATION | bitvector | Functional group participation of atoms as per the LHASA definition | none:ketone:aldehyde:acid:thioacid:ester:amide*1,amide1:amide*2,amide2:amide*3,amide3:sulfonamide*1,sulphonamide*1,sulfonamide1,sulphonamide1:sulfonamide*2,sulphonamide*2,sulfonamide2,sulphonamide2:sulfonamide*3,sulphonamide*3,sulfonamide3,sulphonamide3:carbonium:isocyanate:acid*halide,acidhalide:thioester:amine*3,amine3:aziridine:amine*2,amine2:amine*1,amine1:nitroso:diazo:haloamine:hydrazone:oxime:imine:thiocyanate:isocyanide:nitrile,cyano,cyanide:azo:hydroxylamine:nitro:enamine:amine*oxide,amineoxide:thiol:episulfide,episulphide:sulfide,sulphide:sulfoxide,sulphoxide:sulfone,sulphone:c*sulfonate,c*sulphonate,csulfonate,csulphonate:anhydride:lactam:phosphine:phosphonate:epoxide:ether:peroxide:alcohol,hydroxyl:enol*ether,enolether:nitrite:o*sulfonate,o*sulphonate,osulfonate,osulphonate:fluoride:chloride:bromide:iodide:gem*dihalide,gemdihalide,dihalide:trihalide:acetylene:olefin:vic*dihalide,vicdihalide:halohydrin:glycol:hydrate:hemiketal:ketal:hemiacetal:acetal:azide:disulfide,disulphide:allene:vinylsilane:lactone:vinylw:vinyld:esterx:amidz,amidez:methylene:carbonyl:carboxyl:halide:amine:amide:sulfonamide,sulphonamide:selenide:trialkylsilyl:trialkylsiloxy:silylenolether:n*urea*h,nureah:n*urea*c,nureac:carbamate*h,carbamateh:carbamate*c,carbamatec:o*carbamate,ocarbamate:n*carbamate,ncarbamate:o*carbonate,ocarbonate:dithioacetal:dithioketal:requested:withdrawing,w:expandable*withdrawing,expandablewithdrawing,xwithdrawing:nonexpandable*withdrawing,nonexpandablewithdrawing:donating,d:leaving:good*leaving,goodleaving:origin |
ketone boolean aldehyde boolean acid boolean thioacid boolean ester boolean amide*1 boolean amide*2 boolean amide*3 boolean sulfonamide*1 boolean sulfonamide*2 boolean sulfonamide*3 boolean carbonium boolean isocyanate boolean acid*halide boolean thioester boolean amine*3 boolean aziridine boolean amine*2 boolean amine*1 boolean nitroso boolean diazo boolean haloamine boolean hydrazone boolean oxime boolean imine boolean thiocyanate boolean isocyanide boolean nitrile boolean azo boolean hydroxylamine boolean nitro boolean enamine boolean amine*oxide boolean thiol boolean episulfide boolean sulfide boolean sulfoxide boolean sulfone boolean c*sulfonate boolean anhydride boolean lactam boolean phosphine boolean phosphonate boolean epoxide boolean ether boolean peroxide boolean alcohol boolean enol*ether boolean nitrite boolean o*sulfonate boolean fluoride boolean chloride boolean bromide boolean iodide boolean gem*dihalide boolean trihalide boolean acetylene boolean olefin boolean vic*dihalide boolean halohydrin boolean glycol boolean hydrate boolean hemiketal boolean ketal boolean hemiacetal boolean acetal boolean azide boolean disulfide boolean allene boolean vinylsilane boolean lactone boolean vinylw boolean vinyld boolean esterx boolean amidz boolean methylene boolean carbonyl boolean carboxyl boolean halide boolean amine boolean amide boolean sulfonamide boolean selenide boolean trialkylsilyl boolean trialkylsiloxy boolean silylenolether boolean n*urea*h boolean n*urea*c boolean carbamate*h boolean carbamate*c boolean o*carbamate boolean n*carbamate boolean o*carbonate boolean dithioacetal boolean dithioketal boolean requested boolean withdrawing boolean expandable*withdrawing boolean nonexpandable*withdrawing boolean donating boolean leaving boolean good*leaving boolean origin boolean |
Compiled C module | A_ELEMENT A_TYPE B_TYPE B_ORDER A_FORMAL_CHARGE | atomchange bondchange atom bond | mod_a_fg_participation.so | ||
| A_FG_SUBSTITUENTS | shortvector | Functional group substituents on carbon as per the LHASA definition | ketone short aldehyde short acid short thioacid boolean ester short amide*1 short amide*2 short amide*3 short sulfonamide*1 boolean sulfonamide*2 boolean sulfonamide*3 boolean carbonium short isocyanate short acid*halide short thioester short amine*3 short aziridine short amine*2 short amine*1 short nitroso short diazo short haloamine short hydrazone short oxime short imine short thiocyanate short isocyanide short nitrile short azo short hydroxylamine short nitro short enamine short amine*oxide short thiol short episulfide short sulfide short sulfoxide short sulfone short c*sulfonate short anhydride short lactam short phosphine short phosphonate short epoxide short ether short peroxide short alcohol short enol*ether short nitrite short o*sulfonate short fluoride short chloride short bromide short iodide short gem*dihalide short trihalide short acetylene short olefin short vic*dihalide short halohydrin short glycol short hydrate short hemiketal short ketal short hemiacetal short acetal short azide short disulfide short allene short vinylsilane short lactone short vinylw short vinyld short esterx short amidz short methylene short carbonyl short carboxyl short halide short amine short amide short sulfonamide boolean selenide short trialkylsilyl short trialkylsiloxy short silylenolether short n*urea*h short n*urea*c short carbamate*h short carbamate*c short o*carbamate short n*carbamate short o*carbonate short dithioacetal short dithioketal short requested short withdrawing short expandable*withdrawing short nonexpandable*withdrawing short donating short leaving short good*leaving short |
Compiled C module | A_FG_PARTICIPATION A_ELEMENT A_TYPE B_TYPE | atomchange bondchange atom bond | mod_a_fg_substituents.so | |||
| A_FLAGS | bitset | Display attributes for atom like boxing, marks, Fisher center | ^none:starred,star:inverted,inverse,invert:boxed:groupbox1,gbox1:groupbox2,gbox2:invisible,invis:secondary:bold,dgrey,dgray,dark:greyed,mgrey,mgray,medium:italic,light,lgrey,lgray:fischer,fischercenter,fisher:nosym,nosymbol:circled,circle:alpha:beta:gamma:label:top:bottom:left:right:core:ligand,coreligand:highlight:diamond:triangle:cross:active:nostereo:protected:interfering:participating:hshowhetero:hshowterminal:hshowall:ballstick:capped:spacefill:wireframe:selected:expanded:spare1:spare2:spare3:node:symbol:insuperatom,insuper:hidden:firsthidden:groupsymbol |
starred boolean inverted boolean boxed boolean groupbox1 boolean groupbox2 boolean invisible boolean secondary boolean bold boolean greyed boolean italic boolean fischercenter boolean nosymbol boolean circled boolean alpha boolean beta boolean gamma boolean label boolean top boolean bottom boolean left boolean right boolean core boolean ligand boolean highlight boolean diamon boolean triangle boolean cross boolean active boolean nostereo boolean protected boolean interfering boolean participating boolean hshowheterolboolean boolean hshowterminal boolean hshowall boolean ballstick boolean capped boolean spacefill boolean wireframe boolean selected boolean expanded boolean spare1 boolean spare2 boolean spare3 boolean node boolean symbol boolean insuperatom boolean hidden boolean firsthidden boolean groupsymbol boolean |
(builtin) | never | ||||
| A_FMC0 | float | Fragment molecular connectivity level #0 | Compiled C module | atomchange bondchange | mod_a_fmc0.so | |||||
| A_FMC1 | float | Fragment molecular connectivity level #1 | Compiled C module | atomchange bondchange | mod_a_fmc1.so | |||||
| A_FMC2 | float | Fragment molecular connectivity level #2 | Compiled C module | B_TYPE A_SUBSTITUENT_COUNT | atomchange bondchange | mod_a_fmc2.so | ||||
| A_FMC3 | float | Fragment molecular connectivity level #3 | Compiled C module | B_TYPE A_SUBSTITUENT_COUNT | atomchange bondchange | mod_a_fmc3.so | ||||
| A_FMC4 | float | Fragment molecular connectivity level #4 | Compiled C module | B_TYPE A_SUBSTITUENT_COUNT | atomchange bondchange | mod_a_fmc4.so | ||||
| A_FMC5 | float | Fragment molecular connectivity level #5 | Compiled C module | B_TYPE A_SUBSTITUENT_COUNT | atomchange bondchange | mod_a_fmc5.so | ||||
| A_FORMAL_CHARGE | byte | Nominal atom charge | (builtin) | A_FREE_ELECTRONS | never | |||||
| A_FRACTIONAL_XYZ | floatvector | Fractional/reciprocal atomic 3D-coordinates. This is used in the CIF I/O module. | x float y float z float |
A_XYZ E_UNIT_CELL | atomchange bondchange stereochange merge 3drelative 3dabsolute | |||||
| A_FRAGMENT_ID | string | Fragment identifier for original atom source. This is used in D_CHEMDRAW_PAGE. | never | |||||||
| A_FRAMEWORK | byte | Framework classification 0=ring, 1=sidechain, 2=linker | ring:sidechain,chain:linker,bridge |
(builtin) | B_TYPE | atomchange bondchange hadd ring | ||||
| A_FREE_ELECTRONS | byte | Number of free electrons | (builtin) | A_FORMAL_CHARGE | never | |||||
| A_FREE_VALENCE | byte | Number of free valences | (builtin) | A_ELEMENT A_FORMAL_CHARGE A_VALENCE | atomchange bondchange hadd | |||||
| A_F_COUNT | int | Count the number of fluorine substituents around a central atom | Tcl script | A_ELEMENT A_TYPE | atomchange bondchange | a_f_count.xpd | ||||
| A_GENERIC_FORCEFIELD_TYPE | string | Generic Force Field atom type- Used in the IFF I/O module. Computation of this property is linked to various program-specific variants, which can be selected by a parameter. | forcefield: { value: none description: If set to none, use the first type alread present on structure, or fallback to Sybyl2 as last resort enumeration: tinker:macromodel:sybyl2:sybyl:alchemy:babel datatype: string}
|
Tcl script | A_TYPE A_ELEMENT A_ISAROMATIC A_FORMAL_CHARGE | atomchange bondchange | a_generic_forcefield_type.xpd | |||
| A_GEOMETRY | byte | Enumerated value of the geometry of an atom (terminal, tetrahedral, etc.) | none:terminal,end,s:linear,sp:trigonalplanar,planar,sp2:tetrahedral,tetraeder,sp3:bipyramidal,tbp,trigonalbipyramidal,bipyramid,sp3d,dsp3:sawhorse,seesaw:tshaped,t-shaped:octahedral,octaeder,sp3d2,d2sp3:squarepyramidal:squareplanar,sp2d,dsp2:other |
Compiled C module | A_VERTEX_DEGREE A_FREE_ELECTRONS A_TYPE B_TYPE A_FORMAL_CHARGE A_ISAROMATIC A_PICENTER A_IUPAC_GROUP | atomchange bondchange | mod_a_geometry.so | |||
| A_GROUP_FRAMEWORK | byte | Framework classification 0=group, 1=sidechain, 2=linker, using groups as core elements instead of rings as in standard A_FRAMEWORK | group:sidechain:linker |
Compiled C module | B_TYPE | atomchange bondchange groupchange hadd group | mod_a_group_framework.so | |||
| A_GROUP_NUMBER | int | Number (1-indexed group list position) of atoms, with 0 for atoms which are not in a group. This property assumes that an atom is only a member in a single group, if any. | Compiled C module | atomchange bondchange groupchange atom bond group | mod_a_group_number.so | |||||
| A_H1_NMRSHIFT | float | Proton NMR shift, measured in ppm. | atomchange bondchange stereochange atom bond | |||||||
| A_HAMMET_ABSOLUTE_ELECTROPHILIC_REACTIVITY | double | The absolute electrophilic reactivity as computed by a simple Hammet calculation. Used in Lhasa transforms. | delta: { value: 1 datatype: double} rho: { value: -5 datatype: double} |
Compiled C module | A_HUCKEL_PI_ELECTRON_DENSITY | atomchange bondchange pi | mod_a_hammet_absolute_electrophilic_reactivity.so | |||
| A_HAMMET_ABSOLUTE_NUCLEOPHILIC_REACTIVITY | double | The absolute nucleophilic reactivity as computed by a simple Hammet calculation. Used in Lhasa transforms. | delta: { value: 1 datatype: double} rho: { value: -5 datatype: double} |
Compiled C module | A_HUCKEL_PI_ELECTRON_DENSITY | atomchange bondchange pi | mod_a_hammet_absolute_nucleophilic_reactivity.so | |||
| A_HAMMET_DIFFERENTIAL_ELECTROPHILIC_REACTIVITY | double | The differential electrophilic reactivity as computed by a simple Huckel calculation. Used in Lhasa transforms. | Compiled C module | A_HAMMET_ABSOLUTE_ELECTROPHILIC_REACTIVITY | atomchange bondchange pi | mod_a_hammet_differential_electrophilic_reactivity.so | ||||
| A_HAMMET_RELATIVE_ELECTROPHILIC_REACTIVITY | double | The relative electrophilic reactivity as computed by a simple Huckel calculation, expressed as percent of max reactivity in the structure. Used in Lhasa transforms. | Compiled C module | A_HAMMET_ABSOLUTE_ELECTROPHILIC_REACTIVITY | atomchange bondchange pi | mod_a_hammet_relative_electrophilic_reactivity.so | ||||
| A_HAMMET_RELATIVE_NUCLEOPHILIC_REACTIVITY | double | The relative nucleophilic reactivity as computed by a simple Huckel calculation, expressed as percent of max reactivity in the structure. Used in Lhasa transforms. | Compiled C module | A_HAMMET_ABSOLUTE_NUCLEOPHILIC_REACTIVITY | atomchange bondchange pi | mod_a_hammet_relative_nucleophilic_reactivity.so | ||||
| A_HASH | uint64 | Basic atomic hashcode | usebondorder: { value: 0 datatype: string} seedproperty: { value: {} datatype: string} filter: { value: {} datatype: string} useisotope: { value: 0 datatype: string} usesubstitution: { value: 0 datatype: string} usesuperatom: { value: 0 datatype: string} uselocalcharge: { value: 0 datatype: string} useenantiomer: { value: 0 datatype: string} usering: { value: 1 datatype: string} usequery: { value: 0 datatype: string} ignoreh: { value: 0 datatype: string} usecharge: { value: 1 datatype: string} useradical: { value: 0 datatype: string} useringelectrons: { value: 0 datatype: string} excludebonds: { value: {} datatype: string} printseed: { value: 0 datatype: string} seedmodulo: { value: 0 datatype: string} seedoffset: { value: 0 datatype: string} |
(builtin) | A_MOL_NUMBER A_ELEMENT A_HCOUNT A_VB_NEIGHBOR_COUNT A_FORMAL_CHARGE | atomchange bondchange hadd | ||||
| A_HASHGROUP | index | Hash group id index for basic hash code | (builtin) | A_MOL_NUMBER A_HASH | atomchange bondchange merge hadd | |||||
| A_HASH_STEREO | byte | Stereo descriptor for atoms, based on atomic hashcodes | M=-1:undef=0:P=1 |
useisotope: { value: 0 datatype: string}
|
(builtin) | A_LABEL A_HASH A_LABEL_STEREO B_LABEL_STEREO | atomchange bondchange hadd | |||
| A_HCOUNT | byte | Number of classically bonded hydrogen atoms | useimplicith: { value: 0 datatype: string}
|
(builtin) | B_TYPE A_ELEMENT | atomchange bondchange hadd | ||||
| A_HEAVY_SUBSTITUENT_COUNT | byte | Number of classically bonded non-hydrogen atoms | (builtin) | B_TYPE A_ELEMENT | atomchange bondchange | |||||
| A_HETERO_SUBSTITUENT_COUNT | byte | Count the number of hetero (not C or H) ligands around a central atom | Compiled C module | A_ELEMENT A_TYPE B_TYPE | atomchange bondchange | mod_a_hetero_substituent_count.so | ||||
| A_HSPECIAL | byte | Flag for hydrogen atoms plotted with symbols by common agreement: 0: no, 1:yes, 2:at cis/trans db, 3:at stereocenter, but not wedge | never: { value: 0 datatype: string}
|
(builtin) | B_STEREOINFO A_STEREOINFO A_ELEMENT A_TERMINAL_DISTANCE B_ORDER A_CSPECIAL B_FLAGS A_FLAGS A_ISOTOPE A_RING_COUNT | atomchange bondchange merge hadd | ||||
| A_HUCKEL_ELECTROPHILIC_LOCALIZATION_ENERGY | double | The electrophilic localization energy as computed by a simple Huckel calculation. Used in Lhasa transforms. | Compiled C module | P_HUCKEL_MO_OCCUPANCY | atomchange bondchange pi | mod_a_huckel_electrophilic_localization_energy.so | ||||
| A_HUCKEL_HOMO_COEFFICIENT | double | The HOMO coefficient as computed by a simple Huckel method. Used in Lhasa transforms. | P_HUCKEL_MO_OCCUPANCY | atomchange bondchange pi | ||||||
| A_HUCKEL_HOMO_ENERGY | double | The LUMO energy of the pi system on this atom as computed by a simple Huckel method | Compiled C module | P_HUCKEL_HOMO_ENERGY | atomchange bondchange pi | mod_a_huckel_homo_energy.so | ||||
| A_HUCKEL_LUMO_COEFFICIENT | double | The LUMO coefficient as computed by a simple Huckel method. Used in Lhasa transforms. | P_HUCKEL_MO_OCCUPANCY | atomchange bondchange pi | ||||||
| A_HUCKEL_LUMO_ENERGY | double | The LUMO energy of the pi system on this atom as computed by a simple Huckel method | Compiled C module | P_HUCKEL_LUMO_ENERGY | atomchange bondchange pi | mod_a_huckel_lumo_energy.so | ||||
| A_HUCKEL_NUCLEOPHILIC_LOCALIZATION_ENERGY | double | The nucleophilic localization energy as computed by a simple Huckel calculation. Used in Lhasa transforms. | Compiled C module | P_HUCKEL_MO_OCCUPANCY | atomchange bondchange pi | mod_a_huckel_nucleophilic_localization_energy.so | ||||
| A_HUCKEL_PI_ELECTRON_DENSITY | double | Pi elektron density (sum of electron count in occupied orbitals multiplied with atomic MO coefficient) according to plain Huckel model | P_HUCKEL_MO_OCCUPANCY | atomchange bondchange atom bond pi | ||||||
| A_HYBRIDIZATION | byte | Hybridization of atom | none:s:sp3:sp2:sp:sp3d:sp3d2 |
Compiled C module | never | mod_a_hybridization.so | ||||
| A_HYDROGENS_NEEDED | byte | Number of hydrogen atoms missing to fill up to standard valency | maxsulphurvalence: { value: 2 datatype: string} maxchlorinevalence: { value: 1 datatype: string} maxphosphorvalence: { value: 3 datatype: string} hypervalentaddition: { value: 0 datatype: string} |
(builtin) | B_TYPE A_IUPAC_GROUP A_FORMAL_CHARGE A_FREE_ELECTRONS A_VALENCE A_RADICAL | atomchange bondchange shuffle | ||||
| A_HYDROGEN_BONDING | byte | Classification of H-Bonding Donor/Acceptor Potential | none:acidic:donor:acceptor:basic |
Compiled C module | A_FORMAL_CHARGE A_ELEMENT B_TYPE B_ORDER A_FREE_ELECTRONS A_SIGMA_CHARGE A_ISAROMATIC R_AROMATIC A_IUPAC_GROUP | atomchange bondchange | mod_a_hydrogen_bonding.so | |||
| A_IMPLICIT | boolean | Flag for implicitly added atoms. This information is internally maintained by hydrogen addition etc. subroutines. The compute function copies this internal data into a property. | Compiled C module | atomchange | mod_a_implicit.so | |||||
| A_IMPLICIT_HCOUNT | byte | Number of implicit (automatically added) hydrogens around atom. This is computed from the internal hydrogen origin memory of structures. If this information has been deleted, the result is always zero. | Compiled C module | A_ELEMENT A_TYPE B_TYPE | atomchange bondchange | mod_a_implicit_hcount.so | ||||
| A_INAMIDE | boolean | Flags for atoms in amide-type system (set for n,o,c). Or'ed bits 'extended 1' allow C=S, 'extended 2' allow C=N | extended: { value: 1 datatype: string}
|
(builtin) | A_ELEMENT B_TYPE B_ORDER | atomchange bondchange | ||||
| A_INDEX | int | Index of atom in internal atom list, not ordered into blocked molecules | Compiled C module | atomchange bondchange merge shuffle hadd atom | mod_a_index.so | |||||
| A_ISAROMATIC | boolean | Flag whether atom is member of aromatic ring or not | (builtin) | R_AROMATIC R_TYPE | atomchange bondchange ring | |||||
| A_ISMETAL | boolean | Flag for metal atoms, as determined by the column in the built-in element table, where the criterion could be modified if necessary. | Compiled C module | A_ELEMENT | atomchange bondchange | mod_a_ismetal.so | ||||
| A_ISOLATED_RING | boolean | Flag indicating atom is part of an isolated ring | Compiled C module | Y_RING_COUNT | atomchange bondchange atom bond | mod_a_isolated_ring.so | ||||
| A_ISOTOPE | short | Absolute isotopic mass (12C=12.0000) | never | |||||||
| A_ISOTOPE_HASH | uint64 | Atomic hashcode with isotopes | usebondorder: { value: 0 datatype: string} seedproperty: { value: {} datatype: string} filter: { value: {} datatype: string} useisotope: { value: 1 datatype: string} usesubstitution: { value: 0 datatype: string} usesuperatom: { value: 0 datatype: string} uselocalcharge: { value: 0 datatype: string} usering: { value: 1 datatype: string} usequery: { value: 0 datatype: string} ignoreh: { value: 0 datatype: string} usecharge: { value: 1 datatype: string} useradical: { value: 0 datatype: string} useringelectrons: { value: 0 datatype: string} useenantiomer: { value: 0 datatype: string} excludebonds: { value: {} datatype: string} printseed: { value: 0 datatype: string} seedmodulo: { value: 0 datatype: string} seedoffset: { value: 0 datatype: string} |
(builtin) | A_MOL_NUMBER A_ELEMENT A_HCOUNT A_VB_NEIGHBOR_COUNT A_FORMAL_CHARGE A_ISOTOPE | atomchange bondchange hadd | ||||
| A_ISOTOPE_HASHGROUP | index | Hash group id index for isotope hash code | (builtin) | A_MOL_NUMBER A_ISOTOPE_HASH | atomchange bondchange merge | |||||
| A_ISOTOPE_LABELLING_DEGREE | float | Isotope labelling degree (0.0..1.0) | A_ISOTOPE | atomchange | ||||||
| A_ISOTOPE_STEREO_HASH | uint64 | Stereospecific and isotope-aware atomic hashcode | usebondorder: { value: 0 datatype: string} seedproperty: { value: {} datatype: string} filter: { value: {} datatype: string} useisotope: { value: 1 datatype: string} usesubstitution: { value: 0 datatype: string} usesuperatom: { value: 0 datatype: string} uselocalcharge: { value: 0 datatype: string} usering: { value: 1 datatype: string} usequery: { value: 0 datatype: string} ignoreh: { value: 0 datatype: string} usecharge: { value: 1 datatype: string} useradical: { value: 0 datatype: string} useringelectrons: { value: 0 datatype: string} useenantiomer: { value: 0 datatype: string} excludebonds: { value: {} datatype: string} printseed: { value: 0 datatype: string} seedmodulo: { value: 0 datatype: string} seedoffset: { value: 0 datatype: string} |
(builtin) | A_HASH_STEREO B_HASH_STEREO A_MOL_NUMBER A_ELEMENT A_HCOUNT A_VB_NEIGHBOR_COUNT A_FORMAL_CHARGE A_ISOTOPE | atomchange bondchange stereochange hadd | ||||
| A_ISOTOPE_STEREO_HASHGROUP | index | Hash group id index for stereospecific isotope hash code | (builtin) | A_MOL_NUMBER A_ISOTOPE_STEREO_HASH | atomchange bondchange merge | |||||
| A_IS_CHARGED_METAL_ION | boolean | Boolean flag indicating an unbonded, charged metal ion | Tcl script | A_TYPE A_ELEMENT A_FORMAL_CHARGE | atomchange bondchange | a_is_charged_metal_ion.xpd | ||||
| A_IUPAC_GROUP | byte | New IUPAC group number in range 1-18, 19=lanthanides, 20=actinides | (builtin) | A_ELEMENT A_TYPE | atomchange | |||||
| A_JSTDATA | intquad | Extended fields in JST-type molfile | atomchange bondchange stereochange merge | |||||||
| A_LABEL | int | Arbitrary atom label | (builtin) | never | ||||||
| A_LABELCOLOR | color | X11 style color name of atom labels | Tcl script | never | a_labelcolor.xpd | |||||
| A_LABEL_STEREO | byte | Stereo descriptor for atoms, based on atomic labels | M,-=-1:undef=0:P,+=1:U,C=2:Z,N=3:X=4 |
(builtin) | never | |||||
| A_LHASA_PATH_LABEL | byte | Path atom label (1-based) for matched Lhasa patterns | X_LHASA_SCORE | atomchange bondchange atom bond | ||||||
| A_LIGAND_ANGLE_SUM | float | Allred/Rochow ligand angle sum for phosphor atoms | Tcl script | atomchange bondchange 3drelative | a_ligand_angle_sum.xpd | |||||
| A_LIGAND_ENEG_SUM | float | Tcl script | atomchange bondchange | a_ligand_eneg_sum.xpd | ||||||
| A_LIGAND_RANK | intvector | Priority-sorted list of ligands around stereocenters according to CIP rules. The vector fields are label values of the stereo-defining root substituents (which may be distand in case of atom-stereogenic allenes). The ligand with highest priority is listed first. Stereogenic electron pairs are not listed, and for such compounds there are only three listed ligands on the stereo atom. Atoms without stereo potential have an empty vector. | Compiled C module | A_TYPE A_ELEMENT B_TYPE B_ORDER A_CIP_STEREO B_CIP_STEREO A_LABEL A_ALLENE | atomchange bondchange stereochange hadd | mod_a_ligand_rank.so | ||||
| A_LILLY_SPINACH | boolean | Boolean flag whether the atom is part of what in Eli Lilly lingo is defined "molecular spinach". Atoms which are a ring atom, a ring bridge atom, or connected via a multiple bond to a ring or ring bridge are part of the scaffold and not spinach. | J. Med. Chem. 2012, 55, 9763-9772 | Compiled C module | A_FRAMEWORK B_TYPE B_ORDER | atomchange bondchange atom bond ring | mod_a_lilly_spinach.so | |||
| A_LINEAR_CHAIN_LENGTH | int | The size of the linear-chain-heavy-atoms-only fragment the atom is a member of. Ring atoms or branch atoms have value 0. Hydrogen atoms inherit the value of their bond partner. | Compiled C module | A_TYPE A_RING_COUNT B_TYPE A_SUBSTITUENT_COUNT | atomchange bondchange atom bond | mod_a_linear_chain_length.so | ||||
| A_MACROMODEL_TYPE | short | MacroModel atom type. Used for example in the MMD and MAESTRO I/O modules. | none:C1:C2:C3:CA:CB:CC:CD:CE:CF:CM:CP:CR:unused:C0:O2:O3:OA:OM:OW:OP:OQ:unused:O0:N1:N2:N3:NA:NB:NC:ND:N4:N5:NE:NF:NG:NH:NI:NM:NP:N0:H1:H2:H3:H4:H5:unused:unused:unused:H0:S1:SA:SM:S0:P0:B2:B3:F0:Cl:Br:I0:Si:Z0:Lp:00:Li:Na:K0:Rb:Cs:Ca:Ba:Mg:M2:M3:M4:M5:M6:M7:f2:f3:o2:o3:n2:n3:c1:c2:Zn:m3:m4:m5:m6:unused:unused:unused:unused:unused:unused:unused:unused:SP:S2:Cm:unused:unused:unused:unused:unused:unused:unused:unused:unused:unused:unused:unused:unused:unused:unused:unused:unused:unused:unused:unused:unused:unused:unused:unused:unused:unused:unused:unused:unused:unused:unused:unused:unused:unused:unused:unused:unused:unused:unused:unused:unused:unused:unused:unused:unused:unused:unused:PI |
Tcl script | A_TYPE A_ELEMENT B_TYPE B_ORDER | atomchange bondchange | a_macromodel_type.xpd | |||
| A_MAPPING | int | Atom mapping (for example for reactions), linking to same-value A_MAPPING atoms of complementary structure (reagent <-> product), 0 for unmapped atoms. A_MAPPING has no direct relationship to atom labels A_LABEL. | ignoreexpandedcarbon: { value: 0 datatype: string} ignoreexpandedhetero: { value: 0 datatype: string} ignoreexpandedhydrogen: { value: 0 datatype: string} ignoreexpandedalicarbon: { value: 0 datatype: string} ignoreexpandedarocarbon: { value: 0 datatype: string} |
(builtin) | atomchange bondchange merge atom bond reaction | |||||
| A_MAP_STEREO | byte | Atom stereo descriptor based on reaction mapping | M,-=-1:undef=0:P,+=1 |
(builtin) | A_MAPPING | never | ||||
| A_MDL_VALUE | string | Custom atom value in MDL files ('V' data lines in Molfiles) | never | |||||||
| A_MOL_LABEL | int | Label of molecule atom belongs to | (builtin) | A_MOL_NUMBER M_LABEL | atomchange bondchange merge shuffle hadd mol | |||||
| A_MOL_NUMBER | short | Number (index+1) of molecule atom belongs to | (builtin) | B_TYPE | atomchange bondchange merge shuffle hadd | |||||
| A_MORGAN | uint64 | Morgan numbering value (not the atom rank in the Morgan number, this is the full raw value) | includeh: { value: 1 datatype: boolean} useelement: { value: 0 datatype: boolean} |
Compiled C module | A_TYPE B_TYPE A_ELEMENT A_VERTEX_DEGREE | atomchange bondchange hadd bond | mod_a_morgan.so | |||
| A_MORGAN_RANK | int | Ranking of atoms according to Morgan code value (rank 1 has highest rating) | Tcl script | A_MORGAN | atomchange bondchange merge hadd atom bond | a_morgan_rank.xpd | ||||
| A_N15_NMRSHIFT | float | Proton NMR shift, measured in ppm. | atomchange bondchange stereochange atom bond | |||||||
| A_NCBI_MMDB | compound | MMDB source information | mmdb-id int molecule-id int molecule-name stringvector residue-id int residue-name string atom-id int atom-name string |
never | ||||||
| A_NCICADD_NORM_CHARGE | boolean | Sitzmann, M., Fillipov, I.V., Nicklaus, M.C., SAR and QSAR in Environmental Research, 19:1, 1-9, 2008 (DOI 10.1080/10629360701843540) | atomchange bondchange stereochange atom bond | |||||||
| A_NCICADD_RESONANCE_STEREO_DELETED | boolean | Sitzmann, M., Fillipov, I.V., Nicklaus, M.C., SAR and QSAR in Environmental Research, 19:1, 1-9, 2008 (DOI 10.1080/10629360701843540) | atomchange bondchange stereochange atom bond | |||||||
| A_NCICADD_TAUTO_STEREO_DELETED | boolean | Sitzmann, M., Fillipov, I.V., Nicklaus, M.C., SAR and QSAR in Environmental Research, 19:1, 1-9, 2008 (DOI 10.1080/10629360701843540) | atomchange bondchange stereochange atom bond | |||||||
| A_NEIGHBOR_COUNT | byte | Number of ALL bonded neighbor atoms | (builtin) | bondchange hadd | ||||||
| A_NH2_COUNT | int | Count the number of -NH2 substituents around an atom | Tcl script | A_ELEMENT A_HCOUNT | atomchange bondchange | a_nh2_count.xpd | ||||
| A_NMRSHIFT | float | True shift values, computed from shielding parameters and method string | Tcl script | A_SHIELDING | atomchange bondchange stereochange 3drelative | a_nmrshift.xpd | ||||
| A_NORMAL_VIBRATIONS | xyzvector | Raman and IR normal vibrations of the structure | A_XYZ | atomchange bondchange stereochange merge 3drelative mol atom bond | ||||||
| A_OSAWA_C13_NMRSHIFT | float | C13 NMR spectrum chemical shift., as computed by a simple QSAR function. This is defined only for simple alkanes and more a demo property than of practical use. | Osawa, FMC wo mochiita 13C-NMR kagakushifto no yosoku ni kan suru kenkyuu; master thesis; TUT 1993 | Tcl script | A_FMC0 A_FMC1 A_FMC2 A_FMC3 A_FMC4 A_FMC5 | atomchange bondchange | a_osawa_c13_nmrshift.xpd | |||
| A_P31_NMRSHIFT | float | P31 NMR shift values, by default computed from A_SHIELDING shielding parameters | Tcl script | A_SHIELDING | atomchange bondchange stereochange 3drelative | a_p31_nmrshift.xpd | ||||
| A_PATTY_TYPE | string | Programmable atom typer | patternfile: { value: patty.sma datatype: diskfile constraints: readable} trace: { value: 0 datatype: boolean} |
Tcl script | A_TYPE B_TYPE B_ORDER A_ELEMENT A_FORMAL_CHARGE A_ISOTOPE | atomchange bondchange hadd atom bond | a_patty_type.xpd | |||
| A_PHENYL_COUNT | int | Count for the number or ESSSR phenyl rings the atom is part of | Compiled C module | R_TYPE R_AROMATIC R_HETEROATOM_COUNT | atomchange bondchange atom bond ring | mod_a_phenyl_count.so | ||||
| A_PICENTER | byte | Flag for atoms with pi system (1:free electrons, 2:multibond or epair) | (builtin) | A_PSE_ROW A_FREE_ELECTRONS B_TYPE A_FORMAL_CHARGE B_ORDER | atomchange bondchange hadd | |||||
| A_PISYSTEM_ELECTRON_COUNT | short | Number of pi electrons in largest pi system the atom is a member of | Compiled C module | P_ELECTRON_COUNT | atomchange bondchange atom bond pi | mod_a_pisystem_electron_count.so | ||||
| A_PISYSTEM_SIZE | short | Size (atom count) of the largest pi system the atom is a member of | Compiled C module | atomchange bondchange atom bond pi | mod_a_pisystem_size.so | |||||
| A_PI_CHARGE | float | Gasteiger Pi charges | A_TYPE A_SIGMA_CHARGE | atomchange bondchange hadd | ||||||
| A_PI_ELECTRONEGATIVITY | float | Gasteiger Pi Eneg value | A_TYPE A_PI_CHARGE | atomchange bondchange hadd | ||||||
| A_POLARIZABILITY | float | Atom polarizablities by the Kang & Jhon (sic) algorithm | Y. K. Kang, M. S. Jhon, Theor. Chim. Acta 61, 41 (1982) | Compiled C module | A_VB_NEIGHBOR_COUNT A_ELEMENT A_FREE_ELECTRONS A_FORMAL_CHARGE A_ISAROMATIC A_AROCONDENSED | atomchange bondchange | mod_a_polarizability.so | |||
| A_PSE_ROW | byte | Row number in PSE (1 for H,He, 2 for Li ..) | (builtin) | A_ELEMENT A_TYPE | atomchange | |||||
| A_QNA_DESCRIPTORS | floatpair | Filimonov/Zakharov/Lagunin/Poroikov QNA atomic descriptors. The p value correlates with partial atomic hardness, and q with electronegativity. The use of the matrix exponent of the adjaceny matrix ensures a decreasing neighbor influence with increasing topological distance. Further literature references: Chemical Research in Toxicology, 2012, 25, 2378-2385, DOI 10.1021/tx300247r SAR and QSAR in Environmental Research, 2009, 20, 679-709, DOI 10.1080/10629360903438370 |
Molecular Informatics 30, 2011, 241-250 | p double q double |
Compiled C module | A_TYPE A_ELEMENT E_EXP_CONNECTIVITY_MATRIX | atomchange bondchange atom bond | mod_a_qna_descriptors.so | ||
| A_QUERY | compound | Atom query attributes | element,std,normal,standard:any,*,?:list,whitelist:excllist,neglist,blacklist:hetero,q:halogen,x:noth,noh:heteroh,qh,notc,noc:metal,m:pull1,y:pull2,z:hdonor,hd:hacceptor,ha:insulator,r:terminator,t,ref,reference:anyh,ah:metalh,mh:halogenh,xh:g,group:gh,grouph:g*,groupx:gh*,grouphx:acy:ach:abc:abh:ayl:ayh:alk:alh:ael:aeh:ahc:ahh:aox:aoh:aam:aah:amox:amoxh:cyc:cyh:cbc:cbh:ary:arh:cal:cah:cel:ceh:chc:chh:har:hah:cxx:cxh:1a:2a:3a:4a:5a:6a:7a:8a:1b:2b:3b:4b:5b:6b:7b:8b:8x:8y:8z:1m:2m:3m:tr:ln:ac,an:4m:nm:alk*,*alk,allalk:alh*,*alh,allalh:chk:hea:hef:het:spinach:spinachh:xspinach:xspinachh:cspinach:cspinachh:spinach2:spinach2h:xspinach2:xspinach2h:cspinach2:cspinach2h ^none:stereo:charge:unsaturated,unsat,insaturated,insat:dontmatch,exclude:aromatic:aliphatic,inaromatic:mustmap:picenter:aroneighbor,aroneighbour:noaroneighbor,noaroneighbour:substituted:unsubstituted:fgneighbor,fgneighbor:nofgneighbor,nofgneighbour:aroneighbor_unmatched,aroneighbour_unmatched:noaroneighbor_unmatched,noaroneighbour_unmatched:substituted_unmatched:unsubstituted_unmatched:fgneighbor_unmatched,fgneighbor_unmatched:nofgneighbor_unmatched,nofgneighbour_unmatched:nostereook:nomappingok:nooverlap:exactchange:noextrah:noextrac:noextrax:stereoinversion,inversion:stereoretention,retention:saturated:branched:linear,chain:nochargeok:explicitzerocharge:noextrarings:filledvalence:unfilledvalence:stereochangeofpresence,changeofpresence:noisotopeok:offpath:rgroup:groupsaturated,gsaturated:groupunsaturated,groupinsaturated,gunsaturated,ginsaturated:groupacyclic,gacyclic:groupmonocyclic,gmonocyclic:grouppolycyclic,gpolycyclic:groupcyclic,gcyclic:groupsimple,groupnotpolycyclic,gsimple,gnotpolycyclic:wbond,withdrawingbond:nowbond,nowithdrawingbond,no_withdrawing_bond,no_wbond:branched:unbranched:tertbranched,tbranched:heterocyclic:carbocylic none:H:He:Li:Be:B:C:N:O:F:Ne:Na:Mg:Al:Si:P:S:Cl:Ar:K:Ca:Sc:Ti:V:Cr:Mn:Fe:Co:Ni:Cu:Zn:Ga:Ge:As:Se:Br:Kr:Rb:Sr:Y:Zr:Nb:Mo:Tc:Ru:Rh:Pd:Ag:Cd:In:Sn:Sb:Te:I:Xe:Cs:Ba:La:Ce:Pr:Nd:Pm:Sm:Eu:Gd:Tb:Dy:Ho:Er:Tm:Yb:Lu:Hf:Ta:W:Re:Os:Ir:Pt:Au:Hg:Tl:Pb:Bi:Po:At:Rn:Fr:Ra:Ac:Th:Pa:U:Np:Pu:Am:Cm:Bk:Cf:Es:Fm:Md:No:Lr |
type byte flags bitset list intvector substituentcount bitset valencecount bitset neighborcount bitset hydrogencount bitset ringsize bitset ringcount bitset rganchor int rgmember int rginstance int rgattach int tclproc string fuzz int query querytree component int heterosubstituentcount bitset rbcount bitset repeat bitset charge bitset pyfunction string ringid int ringsystemid int fgs bitvector fgnot bitvector aliheterosubstituentcount bitset freeelectroncount bitset pielectroncount bitset rgroupid int pathid int altpathid int formula formulamatch piformula formulamatch |
never | |||||
| A_RACEMATE | byte | Racemate distribution of stereocenter | undefined,undef:rac,racemat:pure |
atomchange bondchange | ||||||
| A_RADICAL | byte | Flag for radical center | none,no:singlet:doublet,yes:triplet:quartet:quintet |
(builtin) | A_FREE_ELECTRONS | never | ||||
| A_RADIOACTIVE | boolean | Marker for radioactive isotope labels. | Tcl script | A_ISOTOPE A_ELEMENT | atomchange bondchange atom bond | a_radioactive.xpd | ||||
| A_RECAP_LINKER_TYPE | byte | Connection type on this placeholder atom in the RECAP algorithm. The original paper abuses isotope labels for this. | J. Chem. Inf. Comput. Sci. 1998, 38, 511-522 | none:urea:amide:ester:amines:cyclicamines:ether:olefin:aronitroalicarbon:lactam:arocarbonarocarbon:sulphonamide:aronitroarocarbon |
never | |||||
| A_RENDER_XY | floatpair | Render coordinate of atoms on images, etc. Only set by render functions is specifically requested. | A_XY E_STDBLE A_FLAGS | atomchange bondchange groupchange mol atom bond ring group | ||||||
| A_RESIDUE | compound | Residue information, esp. for proteins from PDB | atomtag string grouptag string groupindex int segmentid string resid string chain string weight double hetatm boolean |
atomchange bondchange | ||||||
| A_RINGHASH | uint64 | Atom hash code for atoms which are part of ring systems | usebondorder: { value: none datatype: string}
|
(builtin) | A_TYPE A_FRAMEWORK A_ELEMENT B_TYPE | atomchange bondchange 3drelative 3dabsolute ring | ||||
| A_RINGHASH_GROUP | index | Hash group id index for atom ring hash code. The index data structure is somewhat abused: The molecule part (as in A_HASHGROUP) is used for *ringsystem* indexing, the ensemble part is used as in A_HASHGROUP for global grouping. | Compiled C module | A_RINGSYSTEM_NUMBER A_RINGHASH | atomchange bondchange merge hadd ring | mod_a_ringhash_group.so | ||||
| A_RINGLABEL | int | Renumbered labels of atoms in ring system- Atoms not in ring get label 0, the ring atoms start with one. The order of the labelled atoms follows their standard atom label rank. | Tcl script | A_LABEL | ring | a_ringlabel.xpd | ||||
| A_RINGS | intvector | Labels of the rings the atom is member in | (builtin) | R_LABEL A_RING_COUNT R_TYPE | atomchange bondchange merge ring | |||||
| A_RINGSYSTEM_NUMBER | int | Number (1-indexed ringsystem list position) of atoms, with 0 for atoms which are not in a ringsystem. | Compiled C module | Y_LABEL | atomchange bondchange atom bond ring | mod_a_ringsystem_number.so | ||||
| A_RINGSYSTEM_SIZE | short | Number of ESSSR rings in the ringsystem the atom is a member of, 0 for chain atoms | Compiled C module | atomchange bondchange ring | mod_a_ringsystem_size.so | |||||
| A_RING_BOND_COUNT | byte | Number of ring bonds atom is participating in | Compiled C module | B_RING_COUNT | bondchange ring | mod_a_ring_bond_count.so | ||||
| A_RING_COUNT | short | Number of simple (non-envelope) rings an atom is member of | countenvelopes: { value: 0 datatype: string}
|
(builtin) | R_TYPE | atomchange bondchange ring | ||||
| A_RING_HETEROATOM_COUNT_BITS | bitset | A bit is set at bit position n for any ESSSR ring the atom is a member of which has n hetero atoms. Chain atoms have value 0. If the atom is a member of a carbocyclic ESSSR ring, bit position 0 is set. | Compiled C module | R_HETEROATOM_COUNT R_TYPE | atomchange bondchange atom bond | mod_a_ring_heteroatom_count_bits.so | ||||
| A_RING_SIZE_BITS | bitset | Bit mask for ring sizes the atom participates in | ringset: { value: full enumeration: sssr:esssr,triple:k:full datatype: string}
|
Compiled C module | R_SIZE R_TYPE B_TYPE A_RING_COUNT | bondchange ring | mod_a_ring_size_bits.so | |||
| A_RING_SUBSTITUENT_SIZE | intpair | Number of atoms and maximum bond distance in ring substituent | size int depth int |
(builtin) | A_FRAMEWORK | ring | ||||
| A_SCIDEX_DATA | dictionary | Scidex-specific atom attribute support for MDL SD-files. Handles data encoded in "S SDX" lines. | atomchange bondchange atom bond | |||||||
| A_SEQUENCE_NUMBER | int | Sequential atom number (trad. atoms only) | (builtin) | A_MOL_NUMBER M_ATOM_RANGE A_TYPE | atomchange bondchange merge shuffle hadd mol | |||||
| A_SHELL_ELECTRONS | byte | Number of shell electrons in unbonded atom | (builtin) | A_ELEMENT A_TYPE | atomchange bondchange | |||||
| A_SHIELDING | float | Isotropic magnetic shielding (NMR spectroscopy). This is a field in the SHARC spectroscopy archive format. | atomchange bondchange stereochange merge 3drelative hadd | |||||||
| A_SHIELD_TENSOR | tensor | Anisotropic magnetic shielding tensor. Used as data field in the SHARC NMR archive format. | atomchange bondchange stereochange merge 3drelative hadd | |||||||
| A_SIGMA_CHARGE | float | Gasteiger sigma charges | Compiled C module | A_EQUILIBRATED_CHARGE R_SIZE B_TYPE A_ELEMENT A_VB_NEIGHBOR_COUNT A_FORMAL_CHARGE A_FREE_ELECTRONS A_SP A_SP2 | atomchange bondchange | mod_a_sigma_charge.so | ||||
| A_SIGMA_ELECTRONEGATIVITY | float | Gasteiger sigma electronegativities | A_EQUILIBRATED_CHARGE R_SIZE B_TYPE A_ELEMENT A_VB_NEIGHBOR_COUNT A_SP A_SP2 | atomchange bondchange | ||||||
| A_SIMILARITY_PATTERN | float | Quantitative evaluation of fragment-bit similarity | cmplist: { value: {} datatype: string}
|
Tcl script | A_TYPE A_ELEMENT B_TYPE B_ORDER | atomchange bondchange | a_similarity_pattern.xpd | |||
| A_SMALLEST_RING | int | Size of smallest ESSSR ring the atom is a member of (0 for non-ring atoms) | Compiled C module | R_SIZE | ring | mod_a_smallest_ring.so | ||||
| A_SMILES_INDEX | int | Atom index in SMILES string (-1 for implicit atoms not explicitly encoded in the SMILES string). The result data is automatically set when computing E_SMILES, which has many options which influence the atom sequence in the string. | E_SMILES A_SYMBOL A_TYPE B_TYPE B_ORDER A_ELEMENT A_FORMAL_CHARGE A_LABEL_STEREO B_LABEL_STEREO A_ISOTOPE A_MAPPING A_QUERY B_QUERY | atomchange bondchange merge hadd mol | ||||||
| A_SMILES_RANK | int | Unique SMILES ranking of atoms | Compiled C module | A_ELEMENT B_TYPE A_TYPE B_ORDER A_FORMAL_CHARGE | atomchange bondchange merge hadd | mod_a_smiles_rank.so | ||||
| A_SP | boolean | Flags for atoms forced into sp hybridisation by charge equilibration or aromaticity | useimplicith: { value: 1 datatype: boolean}
|
Compiled C module | A_ELEMENT B_TYPE B_ORDER A_HYDROGENS_NEEDED | atomchange bondchange | mod_a_sp.so | |||
| A_SP2 | boolean | Flags for atoms forced into sp2 hybridisation by charge equilibration or aromaticity | useimplicith: { value: 1 datatype: boolean}
|
Compiled C module | A_FORMAL_CHARGE B_ORDER B_TYPE A_HYDROGENS_NEEDED A_ELEMENT | atomchange bondchange | mod_a_sp2.so | |||
| A_SPAN | float | Largest distance of this atom to any atom in molecule, divided by molecule span | Compiled C module | B_TYPE M_SPAN A_TOPO_DISTANCE | atomchange bondchange hadd atom bond | mod_a_span.so | ||||
| A_SPIRO | byte | Number of spiro ring joins atom is participating in ESSSR ring set | (builtin) | A_RING_COUNT R_TYPE | atomchange bondchange ring | |||||
| A_SSMATCH | int | Ensemble is structure, property data encodes labels of matching substructure atoms, 0 for unmatched parts | sshandle: { value: {} description: Handle of substructure-side ensemble datatype: substructure}
|
Tcl script | never | a_ssmatch.xpd | ||||
| A_SSMATCH_COUNT | int | Atom match count for structure matching. This is set on the *structure* ensemble when specific match flags are set in the substructure match routine. | sshandle: { value: {} datatype: substructure}
|
Tcl script | never | a_ssmatch_count.xpd | ||||
| A_SSMATCH_ENVIRONMENT | datatree | Classigied unmatched structure environment of the substructure atoms, i.e. data on the characteristics of the unmatched structure atoms sprouting from the structure atom matched by this substructure atom. Set by a substructure hit option, not directly computable. | atomchange bondchange atom bond | |||||||
| A_STANDARD_GROUP_LABEL | int | Label of group which contains the atoms which form a standard group | A_TYPE A_ELEMENT B_TYPE B_ORDER | atomchange bondchange | ||||||
| A_STEREOGENIC | byte | Can this atom be a stereocenter ? | no:maybe:checkno:yes,checkyes:ringct |
(builtin) | atomchange bondchange hadd | |||||
| A_STEREOINFO | byte | Stereo descriptor availability info: 1:Label,2:R/S,4:D/L:8:hash,16:map | ^none,st_none:label,st_label:cip,st_cip:dl,st_dl:hash,st_hash:map,st_map |
(builtin) | A_HASH_STEREO A_LABEL_STEREO A_CIP_STEREO A_DL_STEREO A_MAP_STEREO | atomchange bondchange stereochange | ||||
| A_STEREO_CHANGE | byte | Stereo change during course of reaction | unknown:inversion:retention:changeofpresence |
atomchange bondchange atom bond | ||||||
| A_STEREO_GROUP | short | MDL-style stereo group. The enumeration values correspond to the official MDL names of these groups. They are read and set by SDF3000/RXN3000 file format modules, and also used in PubChem I/O via ASN. | abs=99:or15=-15:or14=-14:or13=-31:or12=-12:or11=-11:or10=-10:or9=-9:or8=-8:or7=-7:or6=-6:or5=-5:or4=-4:or3=-3:or2=-2:or1=-1:none=0:&1,and1=1:&2,and2=2:&3,and3=3:&4,and4=4:&5,and5=5:&6,and6=6:&7,and7=7:&8,and8=8:&9,and9=9:&10,and10=10:&11,and11=11:&12,and12=12:&13,and13=13:&14,and14=14:&15,and15=15 |
A_TYPE B_TYPE | atomchange bondchange stereochange | |||||
| A_STEREO_HASH | uint64 | Stereospecific basic atomic hashcode | usebondorder: { value: 0 datatype: string} seedproperty: { value: {} datatype: string} filter: { value: {} datatype: string} useisotope: { value: 0 datatype: string} usesubstitution: { value: 0 datatype: string} usesuperatom: { value: 0 datatype: string} uselocalcharge: { value: 0 datatype: string} usering: { value: 1 datatype: string} usequery: { value: 0 datatype: string} ignoreh: { value: 0 datatype: string} usecharge: { value: 1 datatype: string} useradical: { value: 0 datatype: string} useringelectrons: { value: 0 datatype: string} useenantiomer: { value: 0 datatype: string} excludebonds: { value: {} datatype: string} printseed: { value: 0 datatype: string} seedmodulo: { value: 0 datatype: string} seedoffset: { value: 0 datatype: string} |
(builtin) | A_HASH_STEREO B_HASH_STEREO A_MOL_NUMBER A_ELEMENT A_HCOUNT A_VB_NEIGHBOR_COUNT A_FORMAL_CHARGE | atomchange bondchange stereochange hadd | ||||
| A_STEREO_HASHGROUP | index | Hash group id index for basic stereospecific hash code | (builtin) | A_MOL_NUMBER A_STEREO_HASH | atomchange bondchange merge hadd | |||||
| A_STMATCH | int | Ensemble is substructure, property data encodes labels of matching structure atoms, 0 for unmatched parts | sthandle: { value: {} description: Handle of structure-side ensemble datatype: structure}
|
Tcl script | never | a_stmatch.xpd | ||||
| A_STMATCH_COUNT | int | Atom match count for structure matching. This is set on the *substructure* ensemble when specific match flags are set in the substructure match routine. | sthandle: { value: {} datatype: structure}
|
Tcl script | never | a_stmatch_count.xpd | ||||
| A_SUBSTITUENT_COUNT | int | Count the number of non-H neighbors around a central atom | Compiled C module | A_ELEMENT A_TYPE B_TYPE | atomchange bondchange | mod_a_substituent_count.so | ||||
| A_SUBSTITUENT_VECTOR | float | Angle of the mid of the largest gap in the 2D layout of the substituent sphere | excludeatoms: { value: {} datatype: string}
|
(builtin) | A_XY | atomchange bondchange hadd | ||||
| A_SUPERATOMSTRING | string | Descriptive string for atoms and especially superatoms | never | |||||||
| A_SUPERATOM_SSMATCH | string | A_SUPERATOMSTRING of matching substructure superatom, empty for unmatched parts. This is set by the substructure match routine if suitable flags are set. | sshandle: { value: {} datatype: structure}
|
Tcl script | never | a_superatom_ssmatch.xpd | ||||
| A_SURFACE_AREA | double | Estimated surface area from simple intersection of bonded VdW spheres on A_XYZ coordinates | P. Labute, Methods in Molecular Biology, 275, 261ff | vdwscale: { value: 0.8 description: scaling parameter for VdW radii datatype: double} bondsonly: { value: 1 description: if set, only compute sphere intersections of bonded atoms datatype: boolean} |
Compiled C module | A_XYZ A_TYPE A_ELEMENT A_ISAROMATIC A_VDW_RADIUS | atomchange bondchange 3dabsolute hadd atom bond | mod_a_surface_area.so | ||
| A_SURFACE_SPHERE_RADIUS | float | Radius of sphere used for surface calculation | A_XYZ | atomchange bondchange stereochange 3drelative | ||||||
| A_SYBYL2_TYPE | shortstring | Atom type as used in the Sybyl mol2 format | Tcl script | A_TYPE A_ELEMENT A_ISAROMATIC A_FORMAL_CHARGE | atomchange bondchange | a_sybyl2_type.xpd | ||||
| A_SYBYL_TYPE | byte | Atom type as used in the Sybyl mol format (version 1, not mol2) | Tcl script | A_TYPE A_ELEMENT A_ISAROMATIC A_FORMAL_CHARGE | atomchange bondchange | a_sybyl_type.xpd | ||||
| A_SYMBOL | shortstring | Atomic symbol | querysymbol: { value: ? datatype: string}
|
(builtin) | A_ISOTOPE A_ELEMENT A_QUERY | never | ||||
| A_SYMVISIBLE | boolean | Flag for atoms typically plotted with symbol | (builtin) | A_HSPECIAL A_CSPECIAL A_TYPE A_ELEMENT A_FLAGS | atomchange bondchange | |||||
| A_TAUTOMER_SYSTEM | int | Tautomer system ID of the atoms. Atoms outside any tautomer system receive ID 0, the rest of the systems are numbered starting with one. | Compiled C module | B_ISTAUTOMERIC | atomchange bondchange atom bond | mod_a_tautomer_system.so | ||||
| A_TERMINAL_DISTANCE | short | Number of bonds from terminal atom (0 if itself terminal) | (builtin) | B_TYPE | atomchange bondchange | |||||
| A_TEXTLABEL | compound | Arbitrary textual atom label plus alignment info for plots | {} @above:left:center:right:below |
label string align byte |
level: { value: 0 datatype: string}
|
(builtin) | never | |||
| A_TINKER_TYPE | short | Atom type as used in the Tinker xyz format | forcefield: { value: none datatype: string}
|
Tcl script | A_TYPE A_ELEMENT A_ISAROMATIC A_FORMAL_CHARGE | atomchange bondchange | a_tinker_type.xpd | |||
| A_TOPO_DISTANCE | shortvector | Topological distance matrix (minimum number of bonds between atoms) | bondclasses: { value: VB datatype: string}
|
Compiled C module | B_TYPE | bondchange | mod_a_topo_distance.so | |||
| A_TOTAL_CHARGE | float | Atomic charge on Sigma and Pi systems | (builtin) | A_TYPE A_ELEMENT B_TYPE B_ORDER A_SIGMA_CHARGE A_PI_CHARGE | atomchange bondchange | |||||
| A_TRAJECTORY | xyzvector | 3D atomic path trajectory, for example from a molecular modelling study. This property is for example used in the I/O modules for the GROMACS, XBSA, XYZ and GHEMICAL formats. | A_TYPE B_TYPE B_ORDER A_ELEMENT | atomchange | ||||||
| A_TRANSFORM_STATUS | byte | Atom status as result of SMIRKS transformation. None: not matched in transform, matched: matched, but unchanged, changed: element or attribute changed, new: fragment introduced by transform | none:matched:changed:new |
atomchange bondchange atom bond | ||||||
| A_TYPE | short | Classification, 0:Undef,1:Normal,2:Search,4:Epair,8:3DPoint,16:Super,32:Deloc,64:Polymer,128:Annotation,256:Open,512:Enzyme,1024:Unspecified | ^undef:normal,element:search,query:epair,electron,ep,lp:3dpoint,bq,du:super,superatom:anchor,delocalized,deloc,@:polymer,poly:annotation,annot:open:enzyme,e,protein:unspecified |
never | ||||||
| A_UNDEF_FLOAT1 | float | Some undefined atom property read from file formats with anonymous atom data | atomchange bondchange stereochange merge 3drelative 3dabsolute | |||||||
| A_UNSATURATION | byte | Sum of bond orders in excess of one of all non-aromatic bonds atom is participating in | aroisunsaturated: { value: 1 description: If set, aromatic bonds count as unsaturated datatype: boolean}
|
Compiled C module | A_TYPE B_TYPE B_ORDER B_ISAROMATIC | atomchange bondchange | mod_a_unsaturation.so | |||
| A_VALD | double | Molconn-Z atom value parameter | never | |||||||
| A_VALENCE | byte | Number of classical bond valences | (builtin) | B_ORDER B_TYPE | bondchange hadd | |||||
| A_VAMP_CHARGE | float | Atomic Charge as computed by the Vamp program. This is computed indireclty by requesting computation of heat for formation via Vamp (property E_HEAT_OF_FORMATION). | A_XYZ | atomchange bondchange | ||||||
| A_VB_NEIGHBOR_COUNT | byte | Number of classically bonded neighbor atoms | (builtin) | B_TYPE | bondchange hadd | |||||
| A_VDW_INTERACTION | floatvector | Atom-by-atom nonbonding interaction coefficients, dependent on the elements of an atom pair. The result s a float vector on each atom. The vector length is the number of atoms. The element value at each index is computed by formula hardness(a1)*hardness(a2).pow(VdwBumperRad(element1)+VdWBumperRad(element2),12). The atom hardness value is either the standard atom hardness (default 0.3) or a special hydrogen hardness (default 0.09). The diagonals are set to 0, and interactions to non-standrd atoms to -1. Note that is is only a helper property. it is not dependen on the actual atomic coordinates. It is used by the computation functions of properties E_NONBONDING_ENERGY and E_CONFORMER_ENERGY. |
stdhardness: { value: 0.30 datatype: double} hydrogenhardness: { value: 0.09 datatype: double} |
Compiled C module | A_TYPE A_ELEMENT | atomchange atom | mod_a_vdw_interaction.so | |||
| A_VDW_RADIUS | float | Default van-der-Waals radius | (builtin) | A_ELEMENT A_TYPE | atomchange | |||||
| A_VECTOR | floatvector | Directional 3D vector originating from atoms, generic purpose | atomchange bondchange 3drelative 3dabsolute | |||||||
| A_VERTEX_DEGREE | byte | Number of neighbors which are real atoms and are connected by vb or complex bonds | Compiled C module | A_TYPE B_TYPE | atomchange bondchange hadd | mod_a_vertex_degree.so | ||||
| A_VIRTUAL_HCOUNT | byte | Sum of actual hydrogen count (A_HCOUNT) and hydrogens needed for full set (A_HYDROGENS_NEEDED) | Compiled C module | A_HCOUNT A_HYDROGENS_NEEDED | atomchange bondchange atom bond | mod_a_virtual_hcount.so | ||||
| A_VORONOI_COLOR | color | Color of Voronoi background cells in 2D structure plots | Tcl script | atomchange bondchange atom bond | a_voronoi_color.xpd | |||||
| A_VORONOI_POLYGON | xyvector | Voronoi polygon around 2D display of atom | polygonsonly: { value: 1 datatype: boolean} adddummies: { value: 1 datatype: boolean} extradummies: { value: 1 datatype: boolean} debug: { value: 0 datatype: boolean} |
Compiled C module | A_XY | never | mod_a_voronoi_polygon.so | |||
| A_WATERMARK_SENSITIVITY | float | Guestimated sensitivity of overall compound energy on atom movement for watermarking | datafile: { value: a_watermark_sensitivity.dat datatype: diskfile constraints: readable}
|
Tcl script | A_ELEMENT A_TYPE B_ORDER B_TYPE | atomchange bondchange atom bond ring | a_watermark_sensitivity.xpd | |||
| A_WATERMARK_XYZ | floatvector | Atomic 3D-coordinates with watermarking | x float y float z float |
key: { value: LNTSCSWW datatype: string} message: { value: CACTVS Watermark datatype: string} scale: { value: 100 datatype: double} sigma: { value: 1.0 datatype: double} spread: { value: 1 datatype: boolean} markhydrogens: { value: 0 datatype: boolean} alignpmi: { value: 1 datatype: boolean} usesensitivity: { value: 0 datatype: boolean} |
Compiled C module | A_XYZ A_TYPE A_ELEMENT A_WATERMARK_SENSITIVITY | atomchange bondchange stereochange | mod_a_watermark_xyz.so | ||
| A_WEIGHT | float | Atomic weight | allisotopes: { value: 0 datatype: string}
|
(builtin) | A_TYPE A_ISOTOPE A_ELEMENT | atomchange | ||||
| A_WILDMAN_CRIPPEN_TYPE | shortstring | Atom classification according to the Wildman-Crippen scheme (see litref) | J. Chem. Inf. Comput. Sci 1999, 39, 868-873 | Compiled C module | A_TYPE A_ELEMENT A_ISAROMATIC A_FORMAL_CHARGE B_TYPE B_ORDER B_ISAROMATIC A_IUPAC_GROUP | atomchange bondchange atom bond | mod_a_wildman_crippen_type.so | |||
| A_XSYMBOL | string | Expanded element symbol, lists contain all elements | (builtin) | A_ISOTOPE A_SYMBOL A_ELEMENT A_QUERY | atomchange | |||||
| A_XY | floatpair | Atomic 2D display coordinates | x float y float |
fixbridgeheadstereo: { value: 1 datatype: string} align: { value: none datatype: string} optimize: { value: 1 datatype: string} ringalignment: { value: 1 datatype: string} heteroringalignment: { value: 1 datatype: string} bondlength: { value: 1.0 datatype: string} wedgepairs: { value: none datatype: string} wedgestyle: { value: default datatype: string} pseudo3d: { value: 0 datatype: string} template: { value: {} datatype: string} aspectratio: { value: 1.2 datatype: string} ignorewiggleh: { value: 0 datatype: string} ignoreatoms: { value: {} datatype: string} templatefile: { value: 2dtpl.cbin datatype: string} maxops: { value: 210000 datatype: string} usertemplatefiles: { value: {} datatype: string} hbondfactor: { value: 0.62 datatype: string} hwedgefactor: { value: 0.85 datatype: string} |
(builtin) | never | ||||
| A_XYDISTANCE | floatvector | Atomic distance in 2D plot coordinates | Tcl script | A_XY | atomchange bondchange | a_xydistance.xpd | ||||
| A_XYZ | floatvector | Atomic 3D-coordinates | J. Gasteiger, C. Rudolph, J. Sadowsky, <Automatic Generation of 3D Atomic Coordinates for Organic Molecules>, Tetrahedron Computer Methodol. (1992) | x float y float z float |
usechembiogrid: { value: 0 datatype: string} usepubchem: { value: 1 datatype: string} usecorina: { value: 1 datatype: string} usepubchemqc: { value: 0 datatype: string} maxconformers: { value: 1 datatype: string} corinaoptions: { value: preserve,stergen,r2d,ori,rc,flapn,msc=32,msi=1024,v3000 datatype: string} |
Compiled C module | A_ELEMENT A_TYPE B_TYPE B_ORDER A_FREE_ELECTRONS | atomchange bondchange stereochange | mod_a_xyz.so | |
| B_1ST_ATOM | int | First atom of a bond | Tcl script | A_LABEL | atomchange bondchange merge | b_1st_atom.xpd | ||||
| B_2ND_ATOM | int | Second atom of a bond | Tcl script | A_LABEL | atomchange bondchange merge | b_2nd_atom.xpd | ||||
| B_3RING | boolean | Flag indicating bond is part of 3-membered ring | Tcl script | atomchange bondchange | b_3ring.xpd | |||||
| B_4RING | boolean | Flag indicating bond is part of 4-membered ring | Tcl script | atomchange bondchange | b_4ring.xpd | |||||
| B_5RING | boolean | Flag indicating bond is part of 5-membered ring | Tcl script | atomchange bondchange | b_5ring.xpd | |||||
| B_6RING | boolean | Flag indicating bond is part of 6-membered ring | Tcl script | atomchange bondchange | b_6ring.xpd | |||||
| B_7RING | boolean | Flag indicating bond is part of 7-membered ring | Tcl script | atomchange bondchange | b_7ring.xpd | |||||
| B_ALLYLIC | boolean | A allylic bond according to the Lhasa definition. These are bonds on saturated carbon atoms that are alpha to a carbon-carbon double bond, excluding bonds that lead back to the C=C double bond. | CHMTRN Reference Manual, Lhasa Group, Harvard University, November 2002, Version 19.1, p. 47 | A_ALLYLIC | atomchange bondchange atom bond | |||||
| B_ANGLE | float | Angle of atom triples, encoded as pseudo-bond | (builtin) | A_XYZ | atomchange bondchange 3drelative | |||||
| B_ANNOTATION | string | Bond annoations (stereo information etc.), primarily for 2D plots | style: { value: default datatype: string} stereo: { value: 1 datatype: string} query: { value: 1 datatype: string} label: { value: 0 datatype: string} |
(builtin) | B_FLAGS B_CISTRANS_STEREO B_CIP_STEREO B_LABEL_STEREO B_QUERY | atomchange bondchange stereochange | ||||
| B_ARORING_COUNT | short | Number of aromatic rings the bond is member of | countenvelopes: { value: 0 datatype: string}
|
(builtin) | R_AROMATIC R_TYPE B_TYPE | atomchange bondchange ring | ||||
| B_ATOMS | intpair | Sequence numbers of atoms of traditional bond, with lower number listed first | property: { value: A_SEQUENCE_NUMBER datatype: string}
|
(builtin) | A_SEQUENCE_NUMBER | atomchange bondchange merge hadd | ||||
| B_BENZYLIC | boolean | A benzylic bond according to the Lhasa definition. These are bonds on saturated carbon atoms that are alpha to an aromatic carbon, excluding bonds that lead back to an aromatic atom. | CHMTRN Reference Manual, Lhasa Group, Harvard University, November 2002, Version 19.1, p. 47 | A_BENZYLIC | atomchange bondchange atom bond | |||||
| B_BRICS_FRAGMENTATION | boolean | Bond which would be cut in the BRICS fragmentation method | ChemMedChem 2008, 3, 1503 | atomchange bondchange atom bond | ||||||
| B_BUGGY1 | int | Test case of buggy property computation to test recovery mechanisms | Compiled C module | atomchange bondchange | mod_b_buggy1.so | |||||
| B_BUGGY2 | int | Test case of buggy property computation to test recovery mechanisms | Compiled C module | atomchange bondchange | mod_b_buggy2.so | |||||
| B_BUGGY3 | int | Test case of buggy property computation to test recovery mechanisms | Compiled C module | B_BUGGY1 | atomchange bondchange | mod_b_buggy3.so | ||||
| B_CENTRALITY | double | Centrality rating of the bond (scaled to 1 for most central, 0 for most peripheral, computed from A_TOPO_DISTANCE and M_SPAN) | Compiled C module | A_TOPO_DISTANCE M_SPAN B_TYPE | atomchange bondchange atom bond | mod_b_centrality.so | ||||
| B_CGR_CHANGE | intpair | Bond change when interpreting a CGR-encoded structure. The value are the bond orders on the reagent and product sides. Bonds which are created have a zero value on the reagent side. Bonds which are broken have a zero value on the product side. Bonds which change during CGR interpretation are encoded as 'link' type in B_TYPE, while constant bonds retain their original bond type. This property is set as windfall when computing property X_CGR. | Hoonakker, F.; Lachiche, N.; Varnek, A. Condensed Graph of Reaction: Considas one single pseudo molecule. Int. J. Artif. Intell. Tools 2011, 20, 253–270. | reagent int product int |
atomchange bondchange 3dabsolute atom bond reaction | |||||
| B_CIP_STEREO | byte | Bond chirality descriptor based on CIP (E/Z) rules | E=-1:undef=0:Z=1 |
(builtin) | atomchange bondchange | |||||
| B_CISTRANS_STEREO | byte | Bond chirality descriptor based on cis/trans rules | cis=-1:undef=0:trans=1 |
(builtin) | atomchange bondchange | |||||
| B_CLASSIFICATION | bitset | Simple bond classification bits | ^none:ccbond:chbond:cxbond:xhbond:xxbond:single:double:triple:multiple:aromatic:xaromatic:caromatic:ring:smallring:mediumring:bigring:a-ring:a-aromatic:a-multiple:a-cxbond:b-ring:b-aromatic:b-multiple:b-cxbond |
Compiled C module | B_TYPE B_ORDER A_TYPE A_ELEMENT B_ISAROMATIC B_RINGS R_HETEROATOM_COUNT R_AROMATIC | atom bond ring | mod_b_classification.so | |||
| B_COLOR | colorvector | Bond rendering color | color: { value: white datatype: string}
|
(builtin) | never | |||||
| B_CONJUGATED | boolean | A conjugated bond according to the Lhasa definition. These are bonds which have a spanning atom alpha to a multiply bonded atom. | CHMTRN Reference Manual, Lhasa Group, Harvard University, November 2002, Version 19.1, p. 47 | A_CONJUGATED | atomchange bondchange atom bond | |||||
| B_DAYLIGHT_ARORING_COUNT | short | Number of aromatic rings the bond is member of, using explicit Daylight aromaticity in R_DAYLIGHT_AROMATIC instead of aromodel-configurable R_AROMATIC | Compiled C module | R_DAYLIGHT_AROMATIC R_TYPE B_TYPE | atomchange bondchange ring | mod_b_daylight_aroring_count.so | ||||
| B_DELTA_PI_CHARGE | float | Difference of Gasteiger pi-charges of the bond atoms | Tcl script | A_PI_CHARGE B_TYPE | atomchange bondchange | b_delta_pi_charge.xpd | ||||
| B_DELTA_PI_ELECTRONEGATIVITY | float | Difference of Gasteiger pi-electronegativity of the bond atoms. The value is dependent on the order of the atoms in the bond. | Tcl script | A_PI_ELECTRONEGATIVITY B_TYPE | atomchange bondchange | b_delta_pi_electronegativity.xpd | ||||
| B_DELTA_SIGMA_CHARGE | float | Difference of Gasteiger sigma charges of the bond atoms | Tcl script | A_SIGMA_CHARGE B_TYPE | atomchange bondchange | b_delta_sigma_charge.xpd | ||||
| B_DELTA_SIGMA_ELECTRONEGATIVITY | float | Difference of Gasteiger sigma electronegativity of the bond atoms | Tcl script | A_SIGMA_ELECTRONEGATIVITY B_TYPE | atomchange bondchange | b_delta_sigma_electronegativity.xpd | ||||
| B_DELTA_TOTAL_CHARGE | float | Difference of Gasteiger charges (sum of pi and sigma parts) of the bond atoms | Tcl script | A_TOTAL_CHARGE B_TYPE | atomchange bondchange | b_delta_total_charge.xpd | ||||
| B_DELTA_TOTAL_WALK_COUNT | double | Difference in total walk count E_TOTAL_WALK_COUNT if bond is cut | J. Chem. Inf. Comput. Sci. 2000, 40, 99-106 | usexatoms: { value: 1 description: If set, use heteroatom vs. carbon for additional differentiation. By default, non-hydrogen atoms are anonymous datatype: boolean} usebo: { value: 1 description: If set, use bond order for additional walks datatype: boolean} |
Compiled C module | M_HEAVY_ATOM_COUNT B_TYPE B_ORDER B_ISAROMATIC B_RING_COUNT A_TYPE A_ELEMENT E_TOTAL_WALK_COUNT | atomchange bondchange mol atom bond | mod_b_delta_total_walk_count.so | ||
| B_FG_SUBSTITUENTS | bitvector | Functional group substituents on bonds as per the LHASA definition | ketone boolean aldehyde boolean acid boolean ester boolean amide*1 boolean amide*2 boolean amide*3 boolean carbonium boolean isocyanate boolean acid*halide boolean thioester boolean amine*3 boolean aziridine boolean amine*2 boolean amine*1 boolean nitroso boolean diazo boolean haloamine boolean hydrazone boolean oxime boolean imine boolean thiocyanate boolean isocyanide boolean nitrile boolean azo boolean hydroxylamine boolean nitro boolean enamine boolean amine*oxide boolean thiol boolean episulfide boolean sulfide boolean sulfoxide boolean sulfone boolean c*sulfonate boolean anhydride boolean lactam boolean phosphine boolean phosphonate boolean epoxide boolean ether boolean peroxide boolean alcohol boolean enol*ether boolean nitrite boolean o*sulfonate boolean fluoride boolean chloride boolean bromide boolean iodide boolean gem*dihalide boolean trihalide boolean acetylene boolean olefin boolean vic*dihalide boolean halohydrin boolean glycol boolean hydrate boolean hemiketal boolean ketal boolean hemiacetal boolean acetal boolean azide boolean disulfide boolean allene boolean vinylsilane boolean lactone boolean vinylw boolean vinyld boolean esterx boolean amidz boolean methylene boolean carbonyl boolean carboxyl boolean halide boolean amine boolean amide boolean selenide boolean trialkylsilyl boolean trialkylsiloxy boolean silylenolether boolean n*urea*h boolean n*urea*c boolean carbamate*h boolean carbamate*c boolean o*carbamate boolean n*carbamate boolean o*carbonate boolean dithioacetal boolean dithioketal boolean requested boolean withdrawing boolean expandable*withdrawing boolean nonexpandable*withdrawing boolean donating boolean leaving boolean good*leaving boolean |
Compiled C module | A_FG_PARTICIPATION A_ELEMENT A_TYPE B_TYPE | atomchange bondchange atom bond | mod_b_fg_substituents.so | |||
| B_FLAGS | bitset | Display attributes for bond | ^none:bold,fat:dotted:dashed:lowarrowtip,lowarrow:higharrowtip,higharrow:highwedgetip,highwedge,hightip,lowbase:lowwedgetip,lowwedge,lowtip,lowbase:slash,intersect,intersection:split,wintersect,wslash,wavyslash,wavyintersect,wavyintersection:lowparallelarrow,lowparallel,lowarrow:highparallelarrow,highparallel,higharrow:right:left:crossed:wavy,zigzag:circle,mark1:square,mark2:cross,mark3:anchor,mark4:wedgelocation,wedgehere,wedgeposition:selected:front:back:protected:colorsplit:highlight:doubleslash:hash:resonance:aromatic:invisible:secondary:edge |
bold boolean dotted boolean dashed boolean lowarrowtip boolean higharrowtip boolean highwedgetip boolean lowwedgetip boolean slash boolean split boolean lowparallelarrow boolean highparallelarrow boolean right boolean left boolean crossed boolean wavy boolean circle boolean square boolean cross boolean anchor boolean wedgelocation boolean selected boolean front boolean back boolean protected boolean colorsplit boolean highlight boolean doubleslash boolean hash boolean resonance boolean aromatic boolean invisible boolean secondary boolean edge boolean |
(builtin) | never | ||||
| B_FRAGMENT_CARBON_CHAIN_LENGTH | int | Maximum length of linked carbon atoms in the fragments containing the respective bond atoms as first path atom if the bond were cut. | Compiled C module | B_TYPE A_TYPE A_ELEMENT | atomchange bondchange mol atom bond ring | mod_b_fragment_carbon_chain_length.so | ||||
| B_FRAGMENT_CARBON_COUNT | int | Number of carbon atoms in the fragments containing the respective bond atoms if the bond were cut. In case of a ring bond, this is the same as M_ELEMENT_COUNT(carbon). For a bond to hydrogen, one value is zero and the other the molecule carbon count. The fragment size values are in the same order as the bond atoms, i.e. the first property value is the fragment which contains the first bond atom. | Compiled C module | B_TYPE A_TYPE A_ELEMENT | atomchange bondchange mol atom bond ring | mod_b_fragment_carbon_count.so | ||||
| B_FRAGMENT_COMPLEXITY | double | The fragment complexity (M_COMPLEXITY equivalent) of the fragment containing the first and second atom after cutting the bond | B_TYPE A_TYPE A_ELEMENT | atomchange bondchange mol atom bond ring | ||||||
| B_FRAGMENT_DIRECTION | short | Indicator whether the bond, as seen from its first atom to its second atom, is the principal substituent connection (i.e. if the bond is cut, the second atom is in the smaller substituent, and the first atom in the core). | magic=-1:none:asstored:symmetrical:reversed:ringbond |
criteria: { value: B_FRAGMENT_CARBON_COUNT B_FRAGMENT_HEAVY_ATOM_COUNT B_FRAGMENT_COMPLEXITY B_HASH description: Properties used as criteria to determine the core-side and substituent atoms of the bond, in order of decreasing significance datatype: string constraints: propertylist}
|
Compiled C module | B_TYPE B_FRAGMENT_CARBON_COUNT B_FRAGMENT_HEAVY_ATOM_COUNT B_FRAGMENT_COMPLEXITY B_HASH B_RING_COUNT | atomchange bondchange atom bond | mod_b_fragment_direction.so | ||
| B_FRAGMENT_ELEMENT_COUNT | shortvector | Element counts in the fragments containing the respective bond atoms if the bond were cut. In case of a ring bond, this is the same as M_ELEMENT_COUNT. The fragment values are in the same order as the bond atoms, i.e. the first property value is the fragment which contains the first bond atom. | Compiled C module | B_TYPE A_TYPE A_ELEMENT | atomchange bondchange mol atom bond ring | mod_b_fragment_element_count.so | ||||
| B_FRAGMENT_FORMULA | string | Hill formula of the fragments containing the respective bond atoms if the bond were cut. In case of a ring bond, this is the same as M_FORMULA. The fragment values are in the same order as the bond atoms, i.e. the first property value is the fragment which contains the first bond atom. | format: { value: ascii enumeration: ascii:html datatype: string} usequeryatoms: { value: 0 datatype: string} |
Compiled C module | B_FRAGMENT_ELEMENT_COUNT | atomchange bondchange mol atom bond ring | mod_b_fragment_formula.so | |||
| B_FRAGMENT_HASH | uint64 | The hashcode (M_HASHY equivalent) of the fragment containing the first and second atom after cutting the bond | Compiled C module | B_TYPE B_ORDER B_ISAROMATIC B_HASHGROUP A_TYPE A_ELEMENT | atomchange bondchange mol atom bond ring | mod_b_fragment_hash.so | ||||
| B_FRAGMENT_HEAVY_ATOM_COUNT | int | Number of heavy atoms in the fragments containing the respective bond atoms if the bond were cut. In case of a ring bond, this is the same as M_HEAVY_ATOM_COUNT. For a bond to hydrogen, one value is zero and the other the molecule heavy atom count. The fragment size values are in the same order as the bond atoms, i.e. the first property value is the fragment which contains the first bond atom. | Compiled C module | B_TYPE A_TYPE A_ELEMENT | atomchange bondchange mol atom bond ring | mod_b_fragment_heavy_atom_count.so | ||||
| B_FRAGMENT_HETEROATOM_COUNT | int | Number of heteroatoms in the fragments containing the respective bond atoms if the bond were cut. In case of a ring bond, this is the same as M_HETEROATOM_COUNT. For a bond to hydrogen, one value is zero and the other the molecule heteroatom count. The fragment size values are in the same order as the bond atoms, i.e. the first property value is the fragment which contains the first bond atom. | Compiled C module | B_TYPE A_TYPE A_ELEMENT | atomchange bondchange mol atom bond ring | mod_b_fragment_heteroatom_count.so | ||||
| B_FRAGMENT_STEREO_HASH | uint64 | The hashcode (M_HASHSY equivalent) of the fragment containing the first and second atom after cutting the bond | Compiled C module | B_TYPE A_TYPE B_ISAROMATIC B_STEREO_HASHGROUP A_ELEMENT A_LABEL_STEREO B_LABEL_STEREO | atomchange bondchange stereochange mol atom bond ring | mod_b_fragment_stereo_hash.so | ||||
| B_FRAMEWORK | byte | Framework classification 0=ring, 1=sidechain, 2=linker | ring:sidechain,chain:linker,bridge |
(builtin) | A_FRAMEWORK | atomchange bondchange | ||||
| B_HASH | uint64 | Bond hashcode | pathlength: { value: 30 datatype: string}
|
(builtin) | A_FRAMEWORK A_HASH B_TYPE B_FRAMEWORK | atomchange bondchange | ||||
| B_HASHGROUP | index | Hash group id index for bond hash code | (builtin) | B_MOL_NUMBER B_HASH | atomchange bondchange merge | |||||
| B_HASH_STEREO | byte | Hashcode-based bond chirality descriptor | M=-1:undef=0:P=1 |
useisotope: { value: 0 datatype: string}
|
(builtin) | A_LABEL A_HASH A_LABEL_STEREO B_LABEL_STEREO | atomchange bondchange | |||
| B_HETERO_AROMAT_COUNT | short | Count for the number of heteroaromatic rings the bond participates in | Tcl script | B_ISAROMATIC R_HETEROATOM_COUNT R_AROMATIC | atomchange bondchange ring | b_hetero_aromat_count.xpd | ||||
| B_ISALPHAARO | boolean | Flag for bonds which are not aromatic themselves but linked to aromatic atom | (builtin) | A_ARORING_COUNT B_TYPE B_ARORING_COUNT | atomchange bondchange ring | |||||
| B_ISAROMATIC | boolean | Flag whether bond is aromatic or not | (builtin) | R_AROMATIC R_TYPE B_TYPE | atomchange bondchange ring | |||||
| B_ISAROTAUTOMERIC | short | Tautosytem-number for bonds which are in a potentially tautomeric system, including those which would destroy an aromatic system | useimplicith: { value: 0 datatype: string} maxpathlen: { value: 18 datatype: string} arotautomers: { value: 1 datatype: boolean} |
Compiled C module | A_ELEMENT B_ORDER B_TYPE A_TYPE A_FREE_ELECTRONS B_ISAROMATIC B_RING_COUNT | atomchange bondchange hadd | mod_b_isarotautomeric.so | |||
| B_ISTAUTOMERIC | short | Tautosystem number for bonds which are in a potentially tautomeric system | useimplicith: { value: 0 datatype: string} maxpathlen: { value: 18 datatype: string} arotautomers: { value: 0 datatype: string} |
(builtin) | A_ELEMENT B_ORDER B_TYPE A_TYPE A_FREE_ELECTRONS B_ISAROMATIC B_RING_COUNT | atomchange bondchange hadd | ||||
| B_LABEL | int | Arbitrary bond label | (builtin) | never | ||||||
| B_LABELCOLOR | string | X11 style color name of bond labels | color: { value: black datatype: color}
|
Tcl script | never | b_labelcolor.xpd | ||||
| B_LABEL_STEREO | byte | Label-based bond chirality descriptor | M,MI,-=-1:undef=0:P,PL,+=1 |
(builtin) | never | |||||
| B_LENGTH | float | Bond length (taken from 3D-coordinates) | (builtin) | A_XYZ | atomchange bondchange stereochange 3drelative | |||||
| B_MAPPING | int | Bond map computed from A_MAPPING. The compute ensemble must be part of a reaction, with corresponding A_MAPPING for reagent and product ensemble. Unmapped bonds (those not having mapped atoms on both sides) have value 0. | Tcl script | atomchange bondchange atom bond reaction | b_mapping.xpd | |||||
| B_MAP_STEREO | byte | Bond stereo descriptor based on reaction mapping | M,MI,-=-1:undef=0:P,PL,+=1 |
(builtin) | A_MAPPING | never | ||||
| B_MOL_LABEL | int | Label of molecule bond belongs to | (builtin) | A_MOL_LABEL | atomchange bondchange merge shuffle hadd mol | |||||
| B_MOL_NUMBER | short | Number of molecule bond belongs to | (builtin) | A_MOL_NUMBER | atomchange bondchange merge shuffle hadd mol | |||||
| B_MOVED_SIGMA_CHARGE | float | Charge moved during PEOE equilibration during Gasteiger sigma charge/eneg iternation | A_EQUILIBRATED_CHARGE R_SIZE B_TYPE A_ELEMENT A_VB_NEIGHBOR_COUNT A_FORMAL_CHARGE A_FREE_ELECTRONS A_SP A_SP2 | atomchange bondchange | ||||||
| B_NCICADD_RESONANCE_CROSSED | boolean | Sitzmann, M., Fillipov, I.V., Nicklaus, M.C., SAR and QSAR in Environmental Research, 19:1, 1-9, 2008 (DOI 10.1080/10629360701843540) | atomchange bondchange stereochange atom bond | |||||||
| B_NCICADD_TAUTO_CROSSED | boolean | Sitzmann, M., Fillipov, I.V., Nicklaus, M.C., SAR and QSAR in Environmental Research, 19:1, 1-9, 2008 (DOI 10.1080/10629360701843540) | atomchange bondchange stereochange atom bond | |||||||
| B_ORDER | byte | Bond order | never | |||||||
| B_ORDER_ESTIMATE | float | Estimation of fractional bond order from 3D coordinates via element pair plus base length/exponent table. Uses external data file b_order_estimate.dat (usually located in ${data_directory}/propdata/b_order_estimate directory) for the atom pair parameters. Bonds perceived from close atom distances are created as type "link" if not yet present, and their frational bond order is larger than the threshold parameter. | threshold: { value: 0.25 description: Minimal found bond order to act upon datatype: double} patternfile: { value: b_order_estimate.dat datatype: diskfile constraints: readable} |
Tcl script | A_XYZ A_ELEMENT | never | b_order_estimate.xpd | |||
| B_POLARIZABILITY | float | Average of atom polarizabilities involved in bond | Compiled C module | A_TYPE A_POLARIZABILITY | atomchange bondchange | mod_b_polarizability.so | ||||
| B_QUERY | compound | Bond attributes for structure queries | ^none:stereo:aromatic,aro:aliphatic,ali,nonaromatic,inaromatic,unaromatic:ringsystem,ringcount:doublearo,doubleoraro,da,d/a:singlearo,singleoraro,sa,s/a:mustmap:nostereook:symmetric,symmetry:asymmetric,asymmetry:nooverlap:implicitbondorder,implicit,implicitbo:kekulecmp:any:multiaro,multioraro,ma,m/a:multiple,m:offpath:daylightaromatic,daylightaro:singledouble,s/d:singledoublearo,s/d/a |
flags bitset order bitset ringsize bitset ringcount bitset aroringcount bitset tclproc string query querytree varbo double pyfunction string |
never | |||||
| B_RACEMATE | byte | Racemate distribution of stereobond | undefined,undef:rac,racemat:pure |
atomchange bondchange | ||||||
| B_REACTION_CENTER | int | Reaction Center information from MDL rxn/rdf file, can also be computed from a reaction with atom mapping information | nocenter=-1:unmarked=0:center=1:nochange=2:madebroken=4:madebrokencenter=5:orderchange=8:orderchangecenter=9:madebrokenorderchange=12:madebrokenorderchangecenter=13 |
(builtin) | B_TYPE A_MAPPING B_ORDER B_ISAROMATIC | atomchange bondchange reaction | ||||
| B_RECAP_FRAGMENTATION | boolean | Bond which would be cut in the RECAP fragmentation method | J. Chem. Inf. Comput. Sci. 38, 1998, 511-522 | atomchange bondchange atom bond | ||||||
| B_RINGS | intvector | Labels of the rings the bond is member in | (builtin) | R_LABEL R_TYPE B_TYPE | atomchange bondchange merge ring | |||||
| B_RINGSIZE | uint64 | Bits indicate membership in ring of size N | ringset: { value: esssr datatype: string}
|
(builtin) | R_TYPE B_TYPE | atomchange bondchange ring | ||||
| B_RING_COUNT | short | Number of simple (non-enevelope) rings a bond is member of | countenvelopes: { value: 0 datatype: string}
|
(builtin) | B_TYPE R_TYPE | atomchange bondchange ring | ||||
| B_RING_HETEROATOM_COUNT_BITS | bitset | A bit is set at bit position n for any ESSSR ring the bond is a member of which has n hetero atoms. Chain and bridge bonds have value 0. If the bond is a member of a carbocyclic ESSSR ring, bit position 0 is set. | Compiled C module | R_HETEROATOM_COUNT R_TYPE B_TYPE | atomchange bondchange atom bond | mod_b_ring_heteroatom_count_bits.so | ||||
| B_RING_SIZE_BITS | bitset | Bit mask for ring sizes the bond participates in | Compiled C module | R_SIZE R_TYPE B_TYPE | bondchange ring | mod_b_ring_size_bits.so | ||||
| B_RING_SUBSTITUENT_PATTERN | compound | Compute relative alignment of ring atom substituents in cases where the ring plane is the stereo-defining anchor, This is done both for ring substituents which are on directly connected ring atoms and those which are distant (for example, 1.4 cis/trans relationships in six-membered rings) and where the ring acts as a pseudo-doublebond. In the first case, the property is set on the ring bond between the substituted ring atoms. In the second case, all bonds which are on one of the shortest paths between two same-ring atoms where the A_STEREOGENIC value is "ringct" get the descriptor. For a simple 1.4 cyclohexane, these are all ring atoms. Note that a 1.3-substituted cyclohexane gets no descriptors in this property: Neither share the substituted ring atoms a bond, nor is the ring acting as a pseudo doublebond. Across-ring stereodescriptors are not set if other ring substituents impress normal atom stereogenicity on the substituted ring atoms, which is for example the case in any 1.x.4 substituent pattern. Field descriptor is the label-based stereo decriptor for the bond(s). Value 1/P: low-label off-ring substituents on different sides of ring plane, 1.2-substituents Value -1/M: Low-label off-ring substituents on same side of ring plane, 1.2-substituents Value 2/p: low-label off-ring substituents on different sides of ring plane, distant substituents Value -2/m: Low-label off-ring substituents on same side of ring plane, distant substituents Value 0: no ring substituent stereo Fields ligatom1a/ligatom2a are the low-label off-ring substitituent atoms. Fields ligatom1b/ligatom2b are the secondary off-ring substituent atoms. |
@m:M:none:P:p |
descriptor byte ligatom1a int ligatom1b int ligatom2a int ligatom2b int |
Compiled C module | A_LABEL_STEREO R_TYPE A_LABEL B_TYPE A_STEREOGENIC | atomchange bondchange stereochange ring | mod_b_ring_substituent_pattern.so | ||
| B_ROTATABILITY | byte | Classification of bond rotatability. Ring bond flag must have precedence over multi-bond flag for E_EFFECTIVE_ROTOR_COUNT | undef:terminal:ring:multiple:spheric,round,roundligand:linear,linearligand:yes:locked:forced |
Compiled C module | B_TYPE B_ORDER A_TYPE A_ELEMENT A_INAMIDE A_TERMINAL_DISTANCE | atomchange bondchange hadd | mod_b_rotatability.so | |||
| B_SEQUENCE_NUMBER | int | Sequential bond number for CTX output | (builtin) | B_MOL_NUMBER A_SEQUENCE_NUMBER A_TYPE | atomchange bondchange merge shuffle hadd mol | |||||
| B_SSMATCH | int | Ensemble is structure, property data encodes labels of matching substructure bonds, 0 for unmatched parts | sshandle: { value: {} description: Handle of substructure-side ensemble datatype: substructure}
|
Tcl script | never | b_ssmatch.xpd | ||||
| B_SSMATCH_ENVIRONMENT | datatree | Classigied unmatched structure environment of the substructure bonds, i.e. data on the characteristics of the unmatched structure bonds sprouting from the structure bond matched by this substructure bond. Set by a substructure hit option, not directly computable. | atomchange bondchange atom bond | |||||||
| B_STEREOGENIC | byte | Can this bond be a stereocenter ? | no:maybe:checkno:yes,checkyes:ringct |
simple: { value: 0 datatype: string} ringsizecheck: { value: 1 datatype: string} electronegativitycheck: { value: 1 datatype: string} |
(builtin) | atomchange bondchange hadd | ||||
| B_STEREOINFO | byte | Stereo descriptor availability info: 1:Label,2:E/Z,4:cis/trans,8:hash,16:map | ^none:label:cip:cistrans:hash:map |
(builtin) | B_CISTRANS_STEREO B_LABEL_STEREO B_HASH_STEREO B_CIP_STEREO B_MAP_STEREO | atomchange bondchange stereochange | ||||
| B_STEREO_HASH | uint64 | Stereospecific bond hashcode | (builtin) | A_FRAMEWORK A_STEREO_HASH B_FRAMEWORK B_TYPE | atomchange bondchange | |||||
| B_STEREO_HASHGROUP | index | Hash group id index for stereospecific bond hash code | (builtin) | B_MOL_NUMBER B_HASH A_HASH_STEREO B_HASH_STEREO | atomchange bondchange merge | |||||
| B_STMATCH | int | Ensemble is substructure, property data encodes labels of matching structure bonds, 0 for unmatched parts | sthandle: { value: {} description: Handle of structure-side ensemble datatype: structure}
|
Tcl script | never | b_stmatch.xpd | ||||
| B_STRAINED | boolean | Flags for strained bonds according to the Lhasa definition. These are: endocylic 3/4-membered ring bonds endocyclic 5-membered ring bonds which are part of a [2.1.1], [2.2.1] or [3.2.1] bicyclic system trans C=C double bonds in rings smaller than size 10 C=C double bonds exocyclic to 3/4-membered rings |
Compiled C module | R_TYPE B_TYPE B_ORDER A_TYPE A_LABEL A_ELEMENT B_LABEL_STEREO A_RING_COUNT | bondchange ring | mod_b_strained.so | ||||
| B_TEXTLABEL | compound | Arbitrary textual bond label plus alignment info for plots | left=-1:center=0:right=1 |
label string align byte |
never | |||||
| B_TORSION_ANGLE | float | Torsion angle of atom quartets, encoded as pseudo bond | (builtin) | A_XYZ | atomchange bondchange 3drelative | |||||
| B_TRANSFORM_STATUS | byte | Bond status as result of SMIRKS transformation. Possible values are none: not matched in transform, matched: matched, but unchanged, changed: bond order or attribute changed, new: bond introduced by transform | none:matched:changed:new |
atomchange bondchange atom bond | ||||||
| B_TYPE | int | Bond type | ^none:link:normal,valence,vb:hbond,hydrogen:dative:3center:angle,dihedral,3atom:torsion,torsional,4atom:rgroup,rg:nobond,searchnot,not:deloc,delocalized:complex:ionic |
never | ||||||
| C_COMMENT | string | Connection (edge) comment in free format | never | |||||||
| C_DIRECTED | boolean | Flag indicating whether connection/edge is directed. Global default is given in N_DIRECTED. | Compiled C module | atomchange bondchange atom bond | mod_c_directed.so | |||||
| C_GRAPHICS | compound | Connection (edge) graphics | none:arc:bitmap:image:line:oval,ellipse,ellipsis:polygon:rectangle,rect:text:box:circle:rhombus,diamond:ver_ellipsis:hor_ellipsis:triangle:pentagon:hexagon:octagon:roundedrectangle,roundrectangle,roundrect,roundedrect |
type int attributes dictionary |
usehtml: { value: 0 description: Whether to use HTML encoding of the text annotation datatype: boolean} fontsize: { value: -1 description: Font size (negative value: unset) datatype: int} font: { value: Verdana description: Font name datatype: string} fontcolor: { value: black description: Font color (empty is unset) datatype: color constraints: emptycolor} color: { value: black description: Connection line color (empty is unset) datatype: color constraints: emptycolor} |
Tcl script | C_NAME | never | c_graphics.xpd | |
| C_IDENT | string | Connection (edge) ident string | Compiled C module | never | mod_c_ident.so | |||||
| C_LABEL | int | Connection (edge) label of connections in network objects | Compiled C module | never | mod_c_label.so | |||||
| C_LABEL_GRAPHICS | compound | Connection (edge) label graphics | none:arc:bitmap:image:line:oval,ellipsis,ellipse:polygon:rectangle:text:box:circle:rhombus:ver_ellipsis:hor_ellipsis:rhombus:trinagle:pentagon:hexagon:octagon |
type int attributes dictionary |
never | |||||
| C_NAME | string | Connection (edge) name in free format | never | |||||||
| C_ONTOLOGY_LINK | int | Ontology link type | none:is_a:has_part:is_conjugate_base_of:is_conjugate_acid_of:is_tautomer_of:is_enantiomer_of:has_functional_parent:has_parent_hydride:is_substituent_group_from:has_role |
never | ||||||
| C_PARTITION | int | Partition code for connections (edges). If a symbolic name is available, I/O modules modify the enumeration field of the property. | atomchange bondchange atom bond | |||||||
| C_TEXT | string | Connection (edge) text label | never | |||||||
| C_TYPE | string | Connection (edge) type in free format | never | |||||||
| C_URL | url | Connection reference URL | atomchange bondchange atom bond | |||||||
| C_WEIGHT | double | Graph connection (edge) weight | Compiled C module | never | mod_c_weight.so | |||||
| D_AUTHOR | compound | Dataset author data, computation copies these from the internal object author fields | name string author string email string phone string orcid string authorurl url date date version string affiliation string affiliationurl url affiliationduns string doi string infourl url street string city string zip string state string country string literature string keywords string comment string license string licenseurl url category string repopath string baseuuid string versionuuid string |
Tcl script | never | d_author.xpd | ||||
| D_CHEMDRAW_PAGE | diskfile (switchable between blob diskfile) |
Tabular display of structure collection in ChemDraw page | ncols: { value: 3 minvalue: 1 maxvalue: 20 datatype: int} nrows: { value: 4 minvalue: 1 maxvalue: 20 datatype: int} offset: { value: 0 minvalue: 0 datatype: int} filename: { value: {} datatype: string constraints: writeable} format: { value: cdx enumeration: cdx:cdxml datatype: int} grid: { value: 1 datatype: boolean} gridcolor: { value: black datatype: color} gridselectcolor: { value: orange datatype: color} papersize: { value: a4 enumeration: a3:a4:a5:a6:a7:b3:b4:b5:b6:letter:legal:executive datatype: int} border: { value: 12.0 minvalue: 0 maxvalue: 99 datatype: double} boxspacing: { value: 6.0 minvalue: 0 maxvalue: 99 datatype: double} bonds: { value: 8 minvalue: 1 maxvalue: 25 datatype: int} boxborder: { value: 3.0 minvalue: 0 maxvalue: 99 datatype: double} orientation: { value: portrait enumeration: portrait:landscape datatype: int} cdxversion: { value: 8.0 datatype: double} journalstyle: { value: acs enumeration: default:acs,jacs datatype: int} multipage: { value: 0 datatype: boolean} headerproperty: { value: {} datatype: string constraints: propertylist} headerformat: { value: {} datatype: string} headerfont: { value: Arial datatype: string} headercolor: { value: black datatype: color} headerhighlightcolor: { value: red datatype: color} headerhighlightfilter: { value: {} datatype: string constraints: filtername} headerfontstyle: { value: none datatype: string} headerfontsize: { value: 9 minvalue: 7 maxvalue: 30 datatype: int} header2property: { value: {} datatype: string constraints: propertylist} header2format: { value: {} datatype: string} header2font: { value: Arial datatype: string} header2color: { value: black datatype: color} header2highlightcolor: { value: red datatype: color} header2highlightfilter: { value: {} datatype: string constraints: filtername} header2fontstyle: { value: none datatype: string} header2fontsize: { value: 9 minvalue: 7 maxvalue: 30 datatype: int} footerproperty: { value: E_NAME datatype: string constraints: propertylist} footerformat: { value: {} datatype: string} footerfont: { value: Arial datatype: string} footerfontsize: { value: 9 minvalue: 7 maxvalue: 30 datatype: int} footercolor: { value: black datatype: color} footerhighlightcolor: { value: red datatype: color} footerhighlightfilter: { value: {} datatype: string constraints: filtername} footerfontstyle: { value: none datatype: string} footer2property: { value: {} datatype: string constraints: propertylist} footer2format: { value: {} datatype: string} footer2font: { value: Arial datatype: string} footer2fontsize: { value: 9 minvalue: 7 maxvalue: 30 datatype: int} footer2color: { value: black datatype: color} footer2highlightcolor: { value: red datatype: color} footer2highlightfilter: { value: {} datatype: string constraints: filtername} footer2fontstyle: { value: none datatype: string} headercols: { value: 1 minvalue: 1 maxvalue: 3 datatype: int} footercols: { value: 1 minvalue: 1 maxvalue: 3 datatype: int} |
Tcl script | atomchange bondchange stereochange groupchange dataset | d_chemdraw_page.xpd | ||||
| D_COPYRIGHT | string | Copyright information | never | |||||||
| D_CREATION_TIME | datetime | Date of dataset generation | Tcl script | never | d_creation_time.xpd | |||||
| D_DATE | date | Dataset creation date | atomchange bondchange atom bond | |||||||
| D_DESCRIPTION | string | Free-form description of dataset | never | |||||||
| D_DIVERSITY_SET | dataset | Select a diverse subset from the source dataset. | property: { value: E_SCREEN description: Property to base diversity selection on datatype: string constraints: property} query: { value: all description: Structure filter query expression datatype: string} size: { value: 50 description: Target size minvalue: 1 datatype: int} startindex: { value: -1 description: First structure source index, -1 is random datatype: int} minsimilarity: { value: 0 description: Required minimum similarity of tested structure to start structure to be eligible for inclusion datatype: int} |
Tcl script | atomchange bondchange atom bond | d_diversity_set.xpd | ||||
| D_EMF_IMAGE | diskfile | Dataset rendered as WMF/EMF image, from assembled E_EMF_IMAGE structure renderings | ncols: { value: 3 minvalue: 1 datatype: int} nrows: { value: 4 minvalue: 1 datatype: int} bgcolor: { value: white datatype: color} framecolor: { value: black datatype: color} framewidth: { value: 1 datatype: int} boxwidth: { value: 200 minvalue: 10 maxvalue: 2048 datatype: int} boxheight: { value: 200 minvalue: 10 maxvalue: 2048 datatype: int} header: { value: {} datatype: string} footer: { value: {} datatype: string} headerheight: { value: 0 minvalue: 0 datatype: int} footerheight: { value: 0 minvalue: 0 datatype: int} comment: { value: {} datatype: string} commenttype: { value: text enumeration: none:text:property,prop datatype: int} filename: { value: {} datatype: diskfile constraints: writeable} format: { value: pwmf enumeration: emf:wmf:placeablewmf,pwmf,placeable datatype: int} httpheader: { value: 0 minvalue: 0 maxvalue: 2 datatype: int} headercolor: { value: black datatype: color} footercolor: { value: black datatype: color} font: { value: arialn datatype: string} annotationfontsize: { value: -1 datatype: double} offset: { value: 0 datatype: int} imgproperty: { value: E_EMF_IMAGE datatype: string constraints: property} padding: { value: 1 datatype: int} boxbgcolor: { value: transparent datatype: color} boxhighlightcolor: { value: red datatype: string} selectlist: { value: {} datatype: intvector} colormode: { value: color enumeration: mono,bw,b/w,black,monochrome:gray,grey,grayscale,greyscale:color,colour datatype: int} downloadfilename: { value: {} datatype: string} |
Compiled C module | E_EMF_IMAGE | dataset | mod_d_emf_image.so | |||
| D_FRAGMENT_NETWORK | network | Set of fragments generated by systematic bond cutting of all structures in the dataset, filtered by minimum and maximum occurrence counts and frequencies. | trace: { value: 0 description: If set, print trace information on the progress of the process datatype: boolean} mincount: { value: -1 description: Minimum count for inclusion in table minvalue: -1 datatype: int} maxcount: { value: -1 description: Maximum count for inclusion in table minvalue: -1 datatype: int} minfrequency: { value: 0.01 description: Minimum frequency for inclusion in table minvalue: -1 maxvalue: 1 datatype: double} maxfrequency: { value: 0.80 description: Maximum frequency for inclusion in table minvalue: -1 maxvalue: 1 datatype: double} maxgeneration: { value: -1 description: Maximum number of generations to run minvalue: -1 datatype: int} bondfilter: { value: !ringbond !hydrogen !multibond datatype: string constraints: list} |
Tcl script | dataset | d_fragment_network.xpd | ||||
| D_FRAGMENT_TABLE | table | Set of fragments generated by systematic bond cutting of all structures in the dataset, filtered by minimum and maximum occurrence counts and frequencies. | mincount: { value: -1 description: Minimum count for inclusion in table minvalue: -1 datatype: int} maxcount: { value: -1 description: Maximum count for inclusion in table minvalue: -1 datatype: int} minfrequency: { value: 0.01 description: Minimum frequency for inclusion in table minvalue: -1 maxvalue: 1 datatype: double} maxfrequency: { value: 0.80 description: Maximum frequency for inclusion in table minvalue: -1 maxvalue: 1 datatype: double} columns: { value: E_SMILES E_HASHY count frequency source destination description: Result table columns datatype: string constraints: list} maxgeneration: { value: -1 description: Maximum number of generations to run minvalue: -1 datatype: int} bondfilter: { value: !ringbond !hydrogen !multibond datatype: string constraints: list} |
Tcl script | dataset | d_fragment_table.xpd | ||||
| D_FUZZY_MCSS | structure | Maximum common substructure of dataset, determined by non-deterministic fuzzy matching | maxfuzz: { value: 5 datatype: string}
|
Compiled C module | atomchange bondchange stereochange dataset | mod_d_fuzzy_mcss.so | ||||
| D_GIF | diskfile (switchable between string blob diskfile url) |
GIF image table of the contents of a dataset, assembled by tiles of E_GIF structure images | ncols: { value: 3 datatype: int} nrows: { value: 4 datatype: int} bgcolor: { value: white datatype: color} framecolor: { value: black datatype: color} framewidth: { value: 1 datatype: int} boxwidth: { value: 200 datatype: int} boxheight: { value: 200 datatype: int} header: { value: {} datatype: string} footer: { value: {} datatype: string} headerheight: { value: 0 datatype: int} footerheight: { value: 0 datatype: int} comment: { value: {} datatype: string} commenttype: { value: text enumeration: none:text:property datatype: string} filename: { value: {} datatype: diskfile constraints: writeable} format: { value: gif enumeration: gif:png,png24:png8 datatype: string} httpheader: { value: 0 minvalue: 0 maxvalue: 2 datatype: int} headercolor: { value: black datatype: string} footercolor: { value: black datatype: string} antialiasing: { value: 3 minvalue: 0 maxvalue: 3 datatype: string} font: { value: arialn datatype: string} annotationfontsize: { value: -1 datatype: double} interlace: { value: 0 datatype: boolean} offset: { value: 0 description: First dataset object to use datatype: int} imgproperty: { value: E_GIF datatype: string constraints: property} padding: { value: 1 datatype: int} boxbgcolor: { value: transparent datatype: color} boxhighlightcolor: { value: red datatype: color} selectlist: { value: {} description: Indices of dataset objects to draw with highlight background datatype: intvector} downloadfilename: { value: {} description: Save file name if http header is used datatype: string} fixiepngsize: { value: 1 description: Circumvent Windows bug in older releases datatype: boolean} checkimgsize: { value: 1 datatype: boolean} |
Compiled C module | E_GIF | dataset | mod_d_gif.so | |||
| D_HASHISY | uint64 | Stereospecific and isotope-sensitive dataset hashcode, computed from the individual hashcodes of all ensemble (and only ensemble) objects in the dataset | Compiled C module | E_HASHISY | dataset | mod_d_hashisy.so | ||||
| D_HASHIY | uint64 | Non-stereospecific but isotope-sensitive dataset hashcode, computed from the individual hashcodes of all ensemble (and only ensemble) objects in the dataset | Compiled C module | E_HASHIY | dataset | mod_d_hashiy.so | ||||
| D_HASHSY | uint64 | Stereospecific dataset hashcode, computed from the individual hashcodes of all ensemble (and only ensemble) objects in the dataset | Compiled C module | E_HASHSY | dataset | mod_d_hashsy.so | ||||
| D_HASHY | uint64 | Non-stereospecific dataset hashcode, computed from the individual hashcodes of all ensemble (and only ensemble) objects in the dataset | Compiled C module | E_HASHY | dataset | mod_d_hashy.so | ||||
| D_HTML_PAGE | blob (switchable between blob diskfile) |
filename: { value: {} description: Output file name, empty for tmp file datatype: string} htmlpage: { value: 0 description: If set, write complete HTML page, otherwise write only ExtJS generator statements. datatype: boolean} title: { value: {} description: Graph title datatype: string} |
Tcl script | atomchange bondchange atom bond dataset | d_html_page.xpd | |||||
| D_IDENT | string | Ident string of dataset | Tcl script | atomchange bondchange atom bond | d_ident.xpd | |||||
| D_MATCHED_PAIRS | compoundvector | Identify matched pair molecules, or matched series molecules, in a dataset. | id int datasetindex int bond int centrality double size int setindex int structure structure |
mode: { value: pairs description: In pairs mode, always find molecule pairs under any ID. In series mode, if there are more than 2 structures linked, group them all under a common ID. Example: F/Cl/Br-benzene, In pairs mode, find 3 structure pairs, in series mode, find one series with 3 members enumeration: pairs:series datatype: string} copystructures: { value: 0 description: If set, duplicate the matched pair/set structures with highlighted bonds in B_FLAGS into the "structure" field of this property. If it is not set, only the id/dataset index/bond fields are filled and the structure field is set to NULL datatype: boolean} cutxhbonds: { value: 1 description: If set, allow bonds between hydrogen and heteroatom to be part of a pair or set definition datatype: boolean} cutchbonds: { value: 1 description: If set, allow bonds between hydrogen and carbon to be part of a pair or set definition datatype: boolean} cutcxbonds: { value: 1 description: If set, allow bonds between carbon and heteroatom to be part of a pair or set definition datatype: boolean} cutccbonds: { value: 1 description: If set, allow bonds between carbon to be part of a pair or set definition datatype: boolean} cutxxbonds: { value: 1 description: If set, allow bonds between heteroatoms to be part of a pair or set definition datatype: boolean} cutchainchainbonds: { value: 1 description: If set, allow bonds between two chain atoms to be part of a pair or set definition datatype: boolean} cutringchainbonds: { value: 1 description: If set, allow bonds between a ring and a chain atom to be part of a pair or set definition datatype: boolean} cutringringbonds: { value: 1 description: If set, allow non-ring bonds between ring atoms to be part of a pair or set definition datatype: boolean} cutpreference: { value: first description: Define which bonds should be preferred if there a multiple possibilities to define a pair or set. All: report all possibilities, first: report first possibility found, core: report most central cut, peripheral: report most peripheral cut for any given set or series enumeration: all:first:core,central:peripheral datatype: string} minheavyatoms: { value: 0 description: Minimum number of heavy atoms which must be present in the R-group part datatype: int} maxheavyatoms: { value: 999 description: Maximum number of heavy atoms which must be present in the R-group part datatype: int} formulafilter: { value: {} description: A formula match expression which possible R-groups must match datatype: formulamatch} removesubsets: { value: 0 description: If set, remove (in series mode) sets which are a subset of a larger set datatype: boolean} |
Compiled C module | B_FRAGMENT_HASH B_FRAGMENT_DIRECTION B_FRAGMENT_ELEMENT_COUNT B_FRAGMENT_HEAVY_ATOM_COUNT B_CENTRALITY B_STEREO_HASHGROUP A_RING_COUNT A_TYPE A_ELEMENT | atomchange bondchange atom bond dataset | mod_d_matched_pairs.so | ||
| D_MCSS | structure | Maximum common substructure of dataset | cmpflags: { value: bondorder datatype: string} hitflags: { value: {} datatype: string} exclflags: { value: st_h|ss_h datatype: string} |
Compiled C module | atomchange bondchange stereochange dataset | mod_d_mcss.so | ||||
| D_METADATA | dictionary | Dublin Core metadata for dataset | never | |||||||
| D_NAME | string | Free-form user-defined dataset name | never | |||||||
| D_NEW_FLAG | boolean | Dataset flag for new compounds. THis is primarily used in the CHAI file format. | never | |||||||
| D_PROGRAM | string | Program source of dataset | never | |||||||
| D_PS_PAGES | diskfile | Postscript dataset rendering | filename: { value: {} datatype: diskfile constraints: writeable} httpheader: { value: 0 datatype: boolean} ncols: { value: 2 datatype: int} nrows: { value: 3 datatype: int} papersize: { value: A4 enumeration: none:a3:a4:a5:a6:a7:b3:b4:b5:b6:letter,usletter:legal,uslegal:executive,exec,usexecutive,usexec datatype: string} border: { value: 10 datatype: int} title: { value: {} datatype: string} comment: { value: {} datatype: string} space: { value: 5 datatype: int} frame: { value: line enumeration: none:line:shadow datatype: string} boxproperty: { value: E_NAME datatype: string constraints: property} orientation: { value: portrait enumeration: none:landscape,wide,quer,querformat:portrait,tall,hoch,hochformat datatype: string} colormode: { value: bow enumeration: bow,bw:wob:cow,color:cob datatype: string} headerfontsize: { value: 12 datatype: double} footerfontsize: { value: 12 datatype: double} labelfontsize: { value: 10 datatype: double} pagelimit: { value: 100 minvalue: 1 maxvalue: 9999 datatype: int} pageoffset: { value: 0 minvalue: 0 maxvalue: 9999 datatype: int} psheader: { value: all enumeration: all:none:prolog:trailer datatype: string} pagecount: { value: 0 minvalue: -1 maxvalue: 9999 datatype: int} shadow: { value: 3 datatype: int} eps: { value: 0 datatype: boolean} binder: { value: none enumeration: none:left:top:right:bottom datatype: string} binderwidth: { value: 30 datatype: int} logotext: { value: {} datatype: string} printpagecount: { value: -1 datatype: int} headerheight: { value: 14 datatype: int} footerheight: { value: 14 datatype: int} labelheight: { value: 12 datatype: int} nameheight: { value: 12 datatype: int} namefontsize: { value: 10 datatype: int} atomcolor: { value: {} description: A color name, the magic value "element", or a atom color property. "element" uses the default color defined in the element table datatype: string constraints: emptycolor} downloadfilename: { value: {} datatype: string} |
Compiled C module | E_EPS_IMAGE | atomchange bondchange stereochange groupchange dataset | mod_d_ps_pages.so | |||
| D_SCAFFOLD_TABLE | table | A list of Ertl-type scaffolds extracted from a file. The table contains the counts and SMILES strings as columns, plus row-attached structures. | maxrecs: { value: -1 description: The maximum number of records to process, -1 is infinite datatype: int} maxscaffolds: { value: -1 description: The maximum number of scaffolds to record, -1 is infinite datatype: int} maxsimplification: { value: 1 description: The maximum number of scaffolds simplification steps to perform, -1 is infinite datatype: int} compoundfilter: { value: all description: A compound filter expression (see 'ens scan' command) scaffolds must match datatype: string} |
Tcl script | E_SMILES E_SCAFFOLD_TREE_STRUCTURE | atomchange bondchange stereochange atom bond | d_scaffold_table.xpd | |||
| D_SCAFFOLD_TREE | datatree | The scaffolds of the structures in the dataset in sorted, hierarchical order. The first node a an empty root node, and its children are the irreducible scaffolds. The individual scaffold nodes of the tree contain SMILES strings as value and the (non-stereo/non-isotope) ensemble hashcode as name, followed by all more complex scaffolds which are reduced to the current scaffold by one simplification step. | J. Chem. Inf. Model. 2007, 47, 47-58 | maxlevel: { value: -1 description: Maximum tree depth to generate, -1 for unlimited datatype: int} includeoriginals: { value: 0 description: If set, include the base structures. By default, only the scaffolds are included datatype: boolean} hashcode: { value: E_HASHY description: The hashcode property to be used to check structure identity datatype: string constraints: property} nodenameproperty: { value: E_HASHY description: Instance values of this property are stored as node names. datatype: string constraints: property} auxproperties: { value: {} description: Instance data of these properties is appended to the right of the SMILES data in the nodes datatype: string constraints: propertylist} |
Tcl script | atomchange bondchange atom bond dataset | d_scaffold_tree.xpd | |||
| D_SIMILARITY_MATRIX | intmatrix | Similarity matrix between structures in dataset, with dataset element indices as matrix indices | property: { value: E_SCREEN datatype: string constraints: property} method: { value: tanimoto datatype: string} |
Tcl script | E_SCREEN | atomchange bondchange merge atom bond dataset | d_similarity_matrix.xpd | |||
| D_SIZE | int | Dataset size | Tcl script | dataset | d_size.xpd | |||||
| D_SMALLWORLD_NETWORK | network | Sample implementation of R. Sayles SmallWorld network for accelerated MCSS searching | useelements: { value: 1 datatype: boolean} usebondorders: { value: 1 datatype: boolean} addsingleatomfragments: { value: 0 datatype: boolean} |
Compiled C module | E_HASHY B_HASHGROUP A_ELEMENT A_LABEL B_LABEL A_TYPE B_TYPE B_ISAROMATIC B_RING_COUNT A_SUBSTITUENT_COUNT E_NMOLECULES E_HEAVY_ATOM_COUNT | atomchange bondchange atom bond dataset | mod_d_smallworld_network.so | |||
| D_SOURCE | string | Free-form dataset source description | never | |||||||
| D_SUBSTRUCTURE_HIERARCHY | network | A tree-style network of substructure hierarchies of the structures in the dataset. | storestructures: { value: 0 description: If set, store the structures in the nodes in property V_STRUCTURE datatype: boolean} storeimages: { value: 0 description: If set, store an image of the structures in the nodes in property V_GRAPHICS datatype: boolean} directory: { value: img description: Image directory datatype: string constraints: directory} imgparameters: { value: width 100 height 100 bgcolor black atomcolor element bondcolor white format png frame 0 bonds 6 description: Image parameters datatype: dictionary} ssmatchflags: { value: -excludeh all description: Extra flags to pass to the substructure matcher datatype: string} auxlinks: { value: 0 description: if set, create additional links to alternative matches in the same level datatype: boolean} |
Tcl script | atomchange bondchange atom bond dataset | d_substructure_hierarchy.xpd | ||||
| D_SVG_IMAGE | diskfile (switchable between string blob diskfile url xmlstring) |
SVG image table of the contents of a dataset, assembled by tiles of E_SVG_IMAGE structure images | ncols: { value: 3 datatype: int} nrows: { value: 4 datatype: int} bgcolor: { value: white datatype: color} framecolor: { value: black datatype: color} framewidth: { value: 1 datatype: int} boxwidth: { value: 200 datatype: int} boxheight: { value: 200 datatype: int} header: { value: {} datatype: string} footer: { value: {} datatype: string} headerheight: { value: 0 datatype: int} footerheight: { value: 0 datatype: int} comment: { value: {} datatype: string} commenttype: { value: text enumeration: none:text:property datatype: string} filename: { value: {} datatype: diskfile constraints: writeable} httpheader: { value: 0 minvalue: 0 maxvalue: 2 datatype: int} headercolor: { value: black datatype: string} footercolor: { value: black datatype: string} font: { value: arialn datatype: string} usewebfont: { value: 0 datatype: boolean} annotationfontsize: { value: -1 datatype: double} offset: { value: 0 description: First dataset object to use datatype: int} imgproperty: { value: E_SVG_IMAGE datatype: string constraints: property} padding: { value: 1 datatype: int} boxbgcolor: { value: transparent datatype: color} boxhighlightcolor: { value: red datatype: color} selectlist: { value: {} description: Indices of dataset objects to include, if empty, use all datatype: intvector} downloadfilename: { value: {} description: Save file name if http header is used datatype: string} id: { value: {} datatype: string} title: { value: {} datatype: string} standalone: { value: 1 datatype: boolean} xmlheader: { value: 1 datatype: boolean} metadata: { value: 1 datatype: boolean} footerproperty: { value: {} datatype: string constraints: property} headerproperty: { value: {} datatype: string constraints: property} checkimgsize: { value: 1 datatype: boolean} |
Compiled C module | E_SVG_IMAGE | dataset | mod_d_svg_image.so | |||
| D_TREE_DATA_GIF | diskfile (switchable between string blob diskfile url) |
Rendering of tree-style property data (must be of property datatype "datatree") as a GIF/PNG image using a modified Reingold-Tilford tree layout algorithm. | property: { value: D_SCAFFOLD_TREE description: Property to read rendered data from datatype: string constraints: property} treeindex: { value: 0 datatype: string} maxlevel: { value: -1 datatype: int} boxwidth: { value: 100 datatype: int} boxheight: { value: 100 datatype: int} treedistance: { value: 10 description: Minimum horizontal distance between boxes on a level which do not have the same parent datatype: int} siblingdistance: { value: 5 description: Minimum horizontal distance between boxes on a level which do have the same parent datatype: int} leveldistance: { value: 25 description: Distance between lower box Y of parent level and upper box Y of child level datatype: int} border: { value: 5 description: Unused pixels around tree datatype: int} decodestructures: { value: 1 description: If set, assume that the data is a structure encoding like SMILES, and decode it datatype: boolean} showname: { value: 0 description: If set, include the node name in rendering datatype: boolean} showcount: { value: 0 description: If set, include non-negative count node fields in rendering datatype: boolean} interlace: { value: 0 description: For GIF format, enable or disable interlacing datatype: boolean} alignstructures: { value: 1 description: If structures are rendered, align them hierarchically datatype: boolean} excluderoot: { value: 0 description: If set, do not render root node datatype: boolean} framewidth: { value: 0 datatype: int} bgcolor: { value: white datatype: color} framecolor: { value: black datatype: color} linecolor: { value: red datatype: color} boxframecolor: { value: blue datatype: color} boxbgcolor: { value: grey90 datatype: color} format: { value: png enumeration: gif:png,png24:png8 datatype: string} font: { value: arialn datatype: string} fontsize: { value: 8.0 datatype: double} filename: { value: {} description: Output file name, if data type is diskfile. If empty, generate /tmp file datatype: diskfile constraints: writeable} httpheader: { value: 0 minvalue: 0 maxvalue: 2 datatype: int} |
Compiled C module | atomchange bondchange atom bond dataset | mod_d_tree_data_gif.so | ||||
| D_WATERMARK | double | Watermark detection in a set of structures with 3D coordinates | key: { value: LNTSCSWW description: Message encoder key datatype: string} message: { value: CACTVS Watermark description: Encoded message datatype: string} scale: { value: 100 datatype: double} sigma: { value: 1.0 datatype: double} spread: { value: 1 datatype: int} markhydrogens: { value: 0 description: Include hydrogens in atoms encoding the message datatype: boolean} alignpmi: { value: 1 description: Align 3D atomic coordinates to PMI datatype: boolean} usesensitivity: { value: 0 description: If set, use A_WATERMARK_SENSITITIVY data to tune coordiante shifts to minimize energy distortions datatype: boolean} |
Compiled C module | A_XYZ A_ELEMENT A_TYPE A_SMILES_RANK A_WATERMARK_SENSITIVITY E_HASHY | dataset | mod_d_watermark.so | |||
| D_XYPLOTENERGY | double | Plot pseudo energy - debug property, not intended for production use | maximprove: { value: 100 datatype: int} maxcycle: { value: 100 datatype: int} uselast: { value: 0 datatype: boolean} |
Compiled C module | A_XY A_ELEMENT A_TYPE B_TYPE | dataset | mod_d_xyplotenergy.so | |||
| E_ACROS_URL | url | Catalog URL of structure for Acros Organics/Fisher Scientific | Tcl script | atomchange bondchange atom bond | e_acros_url.xpd | |||||
| E_ACTIVE_AIDSET | intvector | Set of PubChem assay IDs testing this compound as active | Tcl script | E_CID | atomchange bondchange stereochange | e_active_aidset.xpd | ||||
| E_ADJACENCY_MATRIX | intmatrix | Standard non-canonical adjacency matrix for the representation of compounds, with bond orders in i/j elements and free electrons in i/i elements. If there is no bond, the matrix element value is zero. | Tcl script | A_ELEMENT A_TYPE B_TYPE B_ORDER A_FREE_ELECTRONS | atomchange bondchange atom bond | e_adjacency_matrix.xpd | ||||
| E_AIDSET | intvector | Set of PubChem assay IDs where this compoundwas tested | Tcl script | E_CID | atomchange bondchange stereochange | e_aidset.xpd | ||||
| E_AIDSET_URL | url | PubChem assay database URL | Tcl script | E_AIDSET | atomchange bondchange stereochange merge | e_aidset_url.xpd | ||||
| E_ALFA_AESAR_ID | string | Structure ID in the AlfaAesar catalog(www.alfa.com) | Tcl script | E_SMILES | atomchange bondchange stereochange atom bond | e_alfa_aesar_id.xpd | ||||
| E_ALFA_AESAR_URL | url | Data page in the AlfaAesar catalog (www.alfa.com) | Tcl script | E_ALFA_AESAR_ID | atomchange bondchange atom bond | e_alfa_aesar_url.xpd | ||||
| E_ALIRING_COUNT | short | Number of aliphatic rings the ensemble contains | ringtypes: { value: esssr description: Ringset to perform count on enumeration: ^none:sssr:esssr,triple:k:envelope datatype: int}
|
Compiled C module | R_AROMATIC R_TYPE | atomchange bondchange atom bond ring | mod_e_aliring_count.so | |||
| E_AMINO_ACID_SEQUENCE | string | Amino acid sequence in 1- or 3-letter letter code. Can be computed from molecular structure with standard amino acid set. | nomenclature: { value: a description: Whether to use single-letter amino acid codes (a) or 3-letter codes (aaa) enumeration: a,letter1=1:aaa,letter3=3 datatype: int} encodeterminals: { value: 0 description: If set, include H- and -OH terminal encodings datatype: boolean} encodebridges: { value: 0 description: If set, encode SS disulfide bridges in (x) format datatype: boolean} separator: { value: {} description: Separator character between AA encodings (can be empty) datatype: string} |
Compiled C module | M_AMINO_ACID_SEQUENCE | atomchange bondchange mol atom bond | mod_e_amino_acid_sequence.so | |||
| E_ANNOTATION | choicevector | Graphical annotation objects of an ensemble. Thre various graphicsl objects supported by this property are described as separate proerties referred as choice variant fields. | text compound rectangle compound ellipse compound roundedrectangle compound polyline compound bracket compound |
A_XY | never | |||||
| E_AOPWIKI_URL | url | Display URL in the AOP Wiki (Adverse Outcome Pathway, https://aopwiki.org) | Tcl script | E_CAS | atomchange bondchange stereochange atom bond | e_aopwiki_url.xpd | ||||
| E_ARORING_COUNT | short | Count of aromatic rings in ESSSR | ringtypes: { value: esssr description: Ringset to perform count on enumeration: ^none:sssr:esssr,triple:k:envelope datatype: int}
|
Compiled C module | R_AROMATIC R_TYPE | atomchange bondchange atom bond ring | mod_e_aroring_count.so | |||
| E_ASCII_IMAGE | string (switchable between string unicode) |
ASCII (or Unicode) rendering of a chemical structure. Useful to use as a quick command-line check tool, or for console SQL queries. Contains embedded newlines, but not for the last line. |
width: { value: 40 minvalue: 25 maxvalue: 256 datatype: int} height: { value: 30 minvalue: 25 maxvalue: 256 datatype: int} showcharge: { value: 0 datatype: boolean} useunicode: { value: 1 datatype: boolean} bonds: { value: 10 minvalue: 3 maxvalue: 25 datatype: double} usecolor: { value: 0 datatype: boolean} usefontstyle: { value: 0 datatype: boolean} showradical: { value: 0 datatype: boolean} asymbol: { value: xsymbol enumeration: none,no:symbol,sym,normal:xsymbol,xsym,exten ded,expanded:label:index,idx:box:compact,text,super,superatom:residue datatype: int} hsymbol: { value: special enumeration: none,no,suppress:special,normal,hetero:all,y es datatype: int} csymbol: { value: all enumeration: none,no:special,normal:all,yes datatype: int} bgcolor: { value: white datatype: color} highlightcolor: { value: red datatype: string} atomcolor: { value: black description: A color name, the magic value "element", or a atom color property. "element" uses the default color defined in the element table datatype: string} frame: { value: 0 datatype: boolean} contractgroups: { value: 0 datatype: boolean} crop: { value: left|right|top|bottom enumeration: ^none:left:right:top:bottom datatype: bitset} bondcolor: { value: black comment: Cannot be color datatype because we recognize 'atomsplit' value datatype: string} usealtcharset: { value: 0 datatype: boolean} leadnewline: { value: 0 datatype: boolean} tailnewline: { value: 0 datatype: boolean} framecolor: { value: black datatype: color} hcolor: { value: {} datatype: string} headerproperty: { value: {} datatype: string constraints: property} footerproperty: { value: {} datatype: string constraints: property} header: { value: {} datatype: string} footer: { value: {} datatype: string} headercolor: { value: black datatype: color} footercolor: { value: black datatype: color} unicodeforringbonds: { value: macrocycles enumeration: no,never:macrocycles,largerings:yes,always datatype: int} badunicodechars: { value: 0x2571 0x2572 0x2573 0x2afd description: Codes of Unicode chars which should not be used, for example because they are missing in the terminal font comment: 0x2afd: double slash, 0x244a: double backslash, 0x2500: horizontal single line, 0x2501: horizontal bold single line, 0x2502: vertical single line, 0x2504: vertical bold single line, 0x2504: horizontal dotted line, 0x2506: vertical dotted line, 0x250c: corner lower right, 0x2510: corner lower left, 0x2514: corner upper right, 0x2518: corner upper left, 0x2550: horizontal double line, 0x2551: vertical double line, 0x2554: double corner lower right, 0x2557: double corner lower left, 0x255A: double corner upper right, 0x255D: double corner upper left, 0x2571: diagonal lower left to upper right, 0x2572: diagonal upper left to lower right, 0x2573: cross, 0x2630: horizontal triple line datatype: string constraints: list} lineprefix: { value: {} description: Characters to add to the 2nd and later lines, for example to compensate for database table formatting datatype: string} |
Compiled C module | A_TYPE A_ELEMENT A_FLAGS B_FLAGS A_QUERY B_QUERY A_FORMAL_CHARGE A_RESIDUE A_SYMBOL A_XSYMBOL A_XY A_HSPECIAL A_CSPECIAL A_COLOR A_ANNOTATION B_TYPE B_LABEL B_ORDER B_COLOR R_TYPE | atomchange bondchange stereochange merge mol atom bond | mod_e_ascii_image.so | |||
| E_ASTATECH_ID | string | Catalog ID from AstaTech (astatechinc.om) | Tcl script | E_SMILES | atomchange bondchange stereochange atom bond | e_astatech_id.xpd | ||||
| E_ASTATECH_URL | url | Catalog display URL for AstaTech catalog (astatechinc.om) | Tcl script | E_ASTATECH_ID | atomchange bondchange stereochange atom bond | e_astatech_url.xpd | ||||
| E_ASYNCSERVER | string | Dummy property to test asynchronous client/server property computation/communication | never | |||||||
| E_ATOMHASH_COUNT | int | Number of different basic atom hash codes | (builtin) | E_HASHGROUP_COUNT_A | atomchange bondchange merge | |||||
| E_AUTHOR | compound | Information about the original author of a structure or related document | name string author string email string phone string orcid string authorurl url date date version string affiliation string affiliationurl url affiliationduns string doi string infourl url street string city string zip string state string country string literature string keywords string comment string license string licenseurl url category string repopath string baseuuid string versionuuid string |
never | ||||||
| E_AUTODOCK4_TORSIONAL_FREEDOM | byte | Torsional freedom parameter for Audock 4. Used in the I/O modules for the Autodoc4 PDBQT file format. | atomchange bondchange stereochange 3drelative | |||||||
| E_AUXILIARY_SCREEN | bitvector | Auxiliary custom structure search screens, configurable via pattern parameter or file | patternfile: { value: {} datatype: diskfile constraints: readable} patterns: { value: N=[N+]=[N-] datatype: string} aromode: { value: strict enumeration: strict:lenient:default datatype: int} |
Tcl script | atomchange bondchange stereochange hadd | e_auxiliary_screen.xpd | ||||
| E_BARCODE | blob (switchable between string blob diskfile) |
Barcodes in various formats as image data, returned either as a blob or disk file | code: { value: qrcode description: barcode encoding standard enumeration: code39,39:code39x,39x:code128,128:ucc,ean,ucc/ean,ean/ucc:qrcode,qr,qrc datatype: int} format: { value: png description: image format enumeration: gif:png,png24:png8 datatype: string} mode: { value: property description: encode either property data or directly specified data value enumeration: property:value datatype: int} value: { value: E_IDENT datatype: string} filename: { value: {} datatype: string constraints: writeable} httpheader: { value: 0 description: whether to prefix HTTP header (0=no,1:standard,2=with 200 result code) minvalue: 0 maxvalue: 2 datatype: int} width: { value: -1 minvalue: -1 maxvalue: 512 datatype: int} height: { value: 15 minvalue: 8 maxvalue: 50 datatype: int} checksum: { value: 1 datatype: boolean} bgcolor: { value: white datatype: color} fgcolor: { value: black datatype: color} showtext: { value: default description: Whether to also print ASCII text on the label enumeration: no:default:yes datatype: int} font: { value: arialn datatype: string} fontsize: { value: 8 minvalue: 7 maxvalue: 24 datatype: int} antialias: { value: 1 datatype: boolean} widebarfactor: { value: 3 description: Multiplier for 'wide' bars for codes which support that minvalue: 2 maxvalue: 5 datatype: int} linewidth: { value: 1 description: Minimum line width minvalue: 1 maxvalue: 3 datatype: int} downloadfilename: { value: {} description: If http header is generated, default download filename at client side datatype: string} eclevel: { value: Q description: error correction level for qr encoding enumeration: L:M:Q:H datatype: int} |
Compiled C module | never | mod_e_barcode.so | ||||
| E_BARCODE_ID | string | Barcode tracking ID | never | |||||||
| E_BEILSTEIN_NUMBER | int | Beilstein registry number for structure ensemble | Tcl script | atomchange bondchange stereochange merge | ||||||
| E_BENZENOID_INDEX | double | The count of benzene ESSSR rings divided by the total number of aromatic ESSSR rings. Zero in case there are no aromatic rings. | Roughley and Jordan, J. Med. Chem. 2011, 54, 3451-3479 | Compiled C module | R_TYPE R_AROMATIC R_HETEROATOM_COUNT | atomchange bondchange atom bond | mod_e_benzenoid_index.so | |||
| E_BINDINGDB_URL | url | Structure display URL for BindingDB database (www.bindingdb.org) | Tcl script | atomchange bondchange atom bond | e_bindingdb_url.xpd | |||||
| E_BINDING_AFFINITY | qualifiedfloat | General binding affinity descriptor | atomchange bondchange stereochange atom bond | |||||||
| E_BIOCYC_ID | string | Database identifier in the BioCyc database (biocyc.org) | Tcl script | E_CID | atomchange bondchange stereochange atom bond | e_biocyc_id.xpd | ||||
| E_BIOCYC_URL | url | Display URL for a compound in the BioCyc database (biocyc.org) | Tcl script | E_BIOCYC_ID | atomchange bondchange stereochange atom bond | e_biocyc_url.xpd | ||||
| E_BOND_ORDER_COUNT | intvector | Count of bond orders (index 5==aromatic, other bond orders are index to count vector, bond order 0 for non-standard bonds) | special int single int double int triple int quadruple int aromatic int |
excludeh: { value: 0 datatype: boolean}
|
Compiled C module | B_TYPE B_ORDER A_TYPE A_ELEMENT | atomchange bondchange | mod_e_bond_order_count.so | ||
| E_BP | floatpair | Boiling point in Kelvin, with optional temperature range | value float range float |
pressure: { value: 760 datatype: double} pressureunit: { value: Torr datatype: string} |
A_TYPE A_ELEMENT A_FORMAL_CHARGE B_ORDER B_TYPE | atomchange bondchange | ||||
| E_BRACKET_ANNOTATION | compound | Bracket as structure drawing annotation. This is one of the choice variants of property E_ANNOTATION. | {} {} {} ROUND:SQUARE:BRACES:CHEVRONS SINGLE:DOUBLE |
coords floatvector linecolor color linewidth float type int orientation int |
A_XY | never | ||||
| E_BRENDA_ID | int | Ligand ID in the BRENDA database (www.brenda-enzymes.org) | Tcl script | E_STDINCHIKEY | atomchange bondchange stereochange atom bond | e_brenda_id.xpd | ||||
| E_BRENDA_URL | url | Ligand display URL in the BRENDA database (www.brenda-enzymes.org) | Tcl script | E_BRENDA_ID | atomchange bondchange stereochange atom bond | e_brenda_url.xpd | ||||
| E_BRENK_ALERTS | stringvector | Structural alerts as per Brenk et al. (see literature reference) | Brenk, R. et al., ChemMedChem 3, 435 (2008) | Tcl script | A_FORMAL_CHARGE A_ELEMENT B_ORDER B_ARORING_COUNT A_ARORING_COUNT | atomchange bondchange atom bond | e_brenk_alerts.xpd | |||
| E_BRICS_FRAGMENTS | structure | Fragmentation of the structure according to the Raray BRICS rules. | ChemMedChem 2008, 3, 1503 | shredderpatternfile: { value: brics_shred.smarts datatype: diskfile constraints: readable} excludepatternfile: { value: brics_exclude.smarts datatype: diskfile constraints: readable} trace: { value: 0 datatype: boolean} |
Tcl script | A_TYPE A_ELEMENT B_TYPE B_ORDER B_FRAGMENT_CARBON_COUNT B_FRAGMENT_CARBON_CHAIN_LENGTH | atomchange bondchange atom bond | e_brics_fragments.xpd | ||
| E_BRUNS_WATSON_DEMERIT | compound | An implementaton of the Bruns/Watson structural MedChem filters as published in J. Med. Chem. 2012, 55, 9763-9772. The return value is a score between 0 (nothing found) up to an integer >= 100. 100 is the threshold where a comoiund should be rejected, values inbetween are scaled demerits. By default the check stops after the threshold has been reached - it can happen that the sum of demerits at that time has reached exactly 100 or a higher value. It is possible to force the use of the complete rule set by a parameter to tally up the complete set of disagreeable features. The rule set is editable and can be user-expanded. The query files are located at $DATADIR/propdata/e_bruns_watson_demerit. | J. Med. Chem. 2012, 55, 9763-9772 | demerit int features dictionary |
useallrules: { value: 0 description: If set, force the application of the full rules set. By default, as soon as the demerit threshold has been reached, the evaluation stops. datatype: boolean} reportallrules: { value: 0 description: If set, report on the match scores of all applied rules, not just the ones which change the demerit score datatype: boolean} threshold: { value: 100 description: The threshold after which to stop further computation datatype: int} |
Compiled C module | E_BRUNS_WATSON_INITIAL_DEMERIT | atomchange bondchange atom bond | mod_e_bruns_watson_demerit.so | |
| E_BRUNS_WATSON_INITIAL_DEMERIT | compound | Bruns/Watson non-substructural filters as published in J. Med. Chem. 2012, 55, 9763-9772. The return value is a value between 0 and 100, where 100 is outright rejection, 0 no problems found, and values inbetween for demerit points. |
J. Med. Chem. 2012, 55, 9763-9772 | demerit int features dictionary |
heavy_atom_lower_cutoff: { value: 7 description: Reject compound if fewer heavy atoms found datatype: int} heavy_atom_upper_cutoff: { value: 40 description: Reject compound if more heavy atoms found datatype: int} heavy_atom_demerit_threshold: { value: 25 description: Demerit compound if more heavy atoms found datatype: string} use_formal_charge: { value: 0 description: If set, use A_FORMAL_CHARGE for plus(minus rules. By default, use E_CHARGED_GROUP_COUNTS datatype: boolean} useallrules: { value: 0 description: If set, force the application of the full rules set. By default, as soon as the demerit threshold of 100 has been reached, the evaluation stops. datatype: boolean} threshold: { value: 100 description: The threshold after which to stop further computation datatype: int} |
Compiled C module | A_TYPE B_TYPE B_ORDER A_ELEMENT A_MOL_NUMBER A_HEAVY_SUBSTITUENT_COUNT A_RING_COUNT A_FORMAL_CHARGE A_ISOTOPE R_TYPE A_UNSATURATION A_CH2_CHAIN_LENGTH E_NSSSR | atomchange bondchange atom bond | mod_e_bruns_watson_initial_demerit.so | |
| E_CAMEO_ID | int | Registration ID in Cameo Chemicals safety database (https://cameochemicals.noaa.gov). | Tcl script | E_CAS | atomchange bondchange stereochange atom bond | e_cameo_id.xpd | ||||
| E_CAMEO_URL | url | Data display URL in Cameo Chemicals safety database (https://cameochemicals.noaa.gov). | Tcl script | E_CAMEO_ID | atomchange bondchange stereochange atom bond | e_cameo_url.xpd | ||||
| E_CANONIC_TAUTOMER | structure | Canonic tautomer form of ensemble, selected from a rated collection of generated tautomers. | maxtautomers: { value: 500 description: Maximum number of tautomers to generate and rate datatype: int} maxtransforms: { value: -1 description: Maximum number of tautomer transforms to apply datatype: int} useneutralform: { value: 0 description: If set, compute on E_NEUTRALIZED_STRUCTURE instead of current structure datatype: boolean} preservegroups: { value: 0 datatype: boolean} |
Compiled C module | A_TYPE B_TYPE A_ELEMENT B_ORDER | atomchange bondchange merge mol atom bond | mod_e_canonic_tautomer.so | |||
| E_CARBON_COUNT | int | Number of carbon atoms in ensemble - the same as E_ELEMENT_COUNT(6) | Compiled C module | A_TYPE A_ELEMENT | atomchange bondchange atom bond | mod_e_carbon_count.so | ||||
| E_CAS | string | Chemical Abstracts registry number for structure ensemble | useresolver: { value: 1 datatype: string} usepubchem: { value: 1 datatype: string} uselookchem: { value: 0 datatype: string} |
Tcl script | atomchange bondchange stereochange merge | |||||
| E_CAS_URL | url | CommonChemistry URL linked via CAS number. By default the validity of the target is not verified - set parameter to perform this check. | verify: { value: 0 datatype: boolean}
|
Tcl script | E_CAS | atomchange bondchange stereochange merge | e_cas_url.xpd | |||
| E_CATALOG | compound | Catalog data | producer stringvector catnum stringvector country stringvector packsize intvector purity shortvector price intvector |
atomchange bondchange stereochange merge | ||||||
| E_CATALOG_CAS | stringvector | CAS numbers of compound in catalog | never | |||||||
| E_CATALOG_NAMES | stringvector | Names of compound in a catalog | never | |||||||
| E_CCRIS_URL | url | Display URL in EPA CCRIS (Chemical Carcinogenesis Research Information System, https://toxnet.nlm.nih.gov/newtoxnet/ccris.htm) | Tcl script | E_CAS | atomchange bondchange stereochange atom bond | e_ccris_url.xpd | ||||
| E_CDXML_IMAGE | diskfile (switchable between blob diskfile xmlstring) |
A standard structure rendering in the ChemDraw XML format. This is not a complete file which could be loaded into ChemDraw, but a building block to assemble CDXML files. | width: { value: 180 minvalue: 32 maxvalue: 1024 datatype: int} height: { value: 180 minvalue: 32 maxvalue: 1024 datatype: int} bonds: { value: 8 minvalue: 2 maxvalue: 32 datatype: int} filename: { value: {} datatype: string constraints: writeable} border: { value: 12 minvalue: 0 maxvalue: 256 datatype: int} idstart: { value: -1 minvalue: -1 datatype: int} frame: { value: 0 datatype: boolean} xoffset: { value: 8 datatype: double} yoffset: { value: 8 datatype: double} framecolor: { value: black datatype: color} markcolor: { value: blue datatype: color} |
Compiled C module | A_TYPE B_TYPE B_ORDER A_ELEMENT B_FLAGS A_FLAGS | atomchange bondchange stereochange merge mol atom bond | mod_e_cdxml_image.so | |||
| E_CDXML_STRING | xmlstring | Structure encoded in CDXML (CambridgeSoft) | Tcl script | atomchange bondchange stereochange merge hadd atom bond | e_cdxml_string.xpd | |||||
| E_CENTER | compound | Box, geometric and mass-weighted ensemble center | box floatvector geo floatvector mass floatvector |
coordinateproperty: { value: A_XYZ datatype: string} useh: { value: 1 datatype: string} |
(builtin) | E_XYZEXTENT A_WEIGHT A_XYZ | atomchange bondchange 3drelative 3dabsolute | |||
| E_CHANGEDATE | date | Change data time stamp for molecule | Tcl script | never | e_changedate.xpd | |||||
| E_CHARGE | short | Sum of charges in ensemble | (builtin) | A_FORMAL_CHARGE | atomchange | |||||
| E_CHARGED_ATOM_COUNT | int | Number of atoms which are formally charged and not direclty adjacent to an atom of opposite formal charge (such as in ionic nitro groups). | Compiled C module | A_TYPE A_FORMAL_CHARGE B_TYPE | atomchange bondchange atom bond | mod_e_charged_atom_count.so | ||||
| E_CHARGED_GROUP_COUNTS | intpair | Counts of groups charged positively or negatively under neutral conditions in protic solvents. This is a simple guestimate from A_HYDROGEN_BONDING, using acidic and basic groups as starting points and combining close centers (i.e. a P(=O)(OH)2 group with 2 acidic protons only gets a single positive charge count). | positive int negative int |
Compiled C module | M_CHARGED_GROUP_COUNTS | atomchange bondchange atom bond | mod_e_charged_group_counts.so | |||
| E_CHEBI_ID | string | ChEBI ID (www.ebi.ac.uk/chebi) | Tcl script | E_STDINCHI | atomchange bondchange stereochange merge | e_chebi_id.xpd | ||||
| E_CHEBI_URL | url | ChEBI structure data display URL | urlencoding: { value: 1 datatype: boolean}
|
Tcl script | E_CHEBI_ID | atomchange bondchange stereochange merge | e_chebi_url.xpd | |||
| E_CHECKDATE | date | Check data time stamp for molecule | Tcl script | never | e_checkdate.xpd | |||||
| E_CHEMAGORA_URL | url | Display link for ChemAogra (chemagora.jrc.ec.europa.eu) | Tcl script | E_STDINCHIKEY | atomchange bondchange stereochange atom bond | e_chemagora_url.xpd | ||||
| E_CHEMBASE_ID | int | Record ID in Chembase (en.chembase.cn) | matchatomstereo: { value: 1 datatype: boolean} matchbondstereo: { value: 1 datatype: boolean} matchisotopes: { value: 1 datatype: boolean} matchcharges: { value: 1 datatype: boolean} matchradicals: { value: 1 datatype: boolean} |
Tcl script | atomchange bondchange atom bond | e_chembase_id.xpd | ||||
| E_CHEMBASE_URL | url | Display URL in ChemBase database (en.chembase.cn) | Tcl script | E_CHEMBASE_ID | atomchange bondchange atom bond | e_chembase_url.xpd | ||||
| E_CHEMBL_ASSAY_IDS | stringvector | ChEMBL assay IDs which test the substance | limit: { value: 5000 description: Maximum number of assay IDs to retrieve minvalue: 1 datatype: int}
|
Tcl script | atomchange bondchange atom bond | e_chembl_assay_ids.xpd | ||||
| E_CHEMBL_ID | string | ChEMBL ID (https://www.ebi.ac.uk/chembl/) | Tcl script | E_STDINCHIKEY | atomchange bondchange stereochange merge | e_chembl_id.xpd | ||||
| E_CHEMBL_MEDCHEM_FRIENDLY | boolean | Implementation of the simple CHEMBL MedChemFriendly filter, a simple substructure-based exclusion list. | Tcl script | atomchange bondchange atom bond | e_chembl_medchem_friendly.xpd | |||||
| E_CHEMBL_URL | url | ChEMBL compound data display URL (https://www.ebi.ac.uk/chembl) | Tcl script | E_CHEMBL_ID | atomchange bondchange stereochange merge | e_chembl_url.xpd | ||||
| E_CHEMBUYERSGUIDE_IDS | compoundvector | Get company name and their catalog number by querying chembuyersguide.com via full-structure search. | name string catalogno string |
Tcl script | atomchange bondchange atom bond | e_chembuyersguide_ids.xpd | ||||
| E_CHEMDB_ID | string | Structure ID in the NIH NIAID ChemDB database (https://chemdb.niaid.nih.gov) | Tcl script | E_CAS | atomchange bondchange atom bond | e_chemdb_id.xpd | ||||
| E_CHEMDB_URL | url | Data display URL for the NIH NIAID ChemDB database | Tcl script | E_CHEMDB_ID | atomchange bondchange stereochange atom bond | e_chemdb_url.xpd | ||||
| E_CHEMDIV_ID | string | ID of structure in ChemDiv (chemistryondemand.com) database | Tcl script | E_SMILES | atomchange bondchange atom bond | e_chemdiv_id.xpd | ||||
| E_CHEMDIV_URL | url | Data display URL for structure in catalog of chemdiv.com/chemistryondemand.com | atomchange bondchange stereochange atom bond | |||||||
| E_CHEMEO_ID | string | ID in the Chemeo properties database (www.chemeo.com) | Tcl script | atomchange bondchange atom bond | e_chemeo_id.xpd | |||||
| E_CHEMEO_URL | url | Display URL for the Chemeo properties database (www.chemeo.com) | Tcl script | atomchange bondchange atom bond | e_chemeo_url.xpd | |||||
| E_CHEMEXPER_URL | url | ChemExper data display URL (chemexper.com) | querytype: { value: fs enumeration: fs:ss datatype: int}
|
Tcl script | E_CHEMEXPER_URL | mol atom bond | e_chemexper_url.xpd | |||
| E_CHEMICALBOOK_ID | string | Database ID for the chemicalbook.com site | Tcl script | E_CAS | atomchange bondchange stereochange atom bond | e_chemicalbook_id.xpd | ||||
| E_CHEMICALBOOK_URL | url | Data display URL for the chemicalbook.com site | Tcl script | E_CAS | atomchange bondchange stereochange atom bond | e_chemicalbook_url.xpd | ||||
| E_CHEMICALIZE_URL | url | URL to submit compound to chemicalize.org computational service by ChemAxon | Tcl script | E_SMILES | atomchange bondchange stereochange merge | e_chemicalize_url.xpd | ||||
| E_CHEMICAL_BEAUTY | double | Chemical beauty score (aka QED, quantitative estimate of drug likeness). Because we are using different logP and HA/HD algorithms, the results are not exactly identical to those from the publication, but close. | Bickerton et al., Nature Chemistry, 4, 90 (2012) | weightingscheme: { value: max enumeration: max:mo:u datatype: int}
|
Tcl script | E_BRENK_ALERTS E_WEIGHT E_XLOGP2 E_NHDONORS E_NHACCEPTORS E_NROTBONDS E_TPSA E_ARORING_COUNT | atomchange bondchange stereochange atom bond | e_chemical_beauty.xpd | ||
| E_CHEMIDPLUS_ID | string | ChemIDPlus structure id (from http://chem.sis.nlm.nih.gov) | Tcl script | E_STDINCHIKEY | mol atom bond | e_chemidplus_id.xpd | ||||
| E_CHEMIDPLUS_URL | url | ChemIDPlus URL | Tcl script | E_CHEMIDPLUS_ID | mol atom bond | e_chemidplus_url.xpd | ||||
| E_CHEMSPIDER_ID | string | chemspider.com structure record ID | Tcl script | E_STDINCHI | atomchange bondchange stereochange merge | e_chemspider_id.xpd | ||||
| E_CHEMSPIDER_URL | url | chemspider.com structure data display URL | Tcl script | E_CHEMSPIDER_ID | atomchange bondchange stereochange merge | e_chemspider_url.xpd | ||||
| E_CHEMSYNTHESIS_ID | int | ID of structure in ChemSynthesis database (www.chemsynthesis.com) | Tcl script | atomchange bondchange merge mol | e_chemsynthesis_id.xpd | |||||
| E_CHEMSYNTHESIS_URL | url | Data sccess URL of structure in ChemSynthesis database (www.chemsynthesis.com) | Tcl script | E_CHEMSYNTHESIS_ID | atomchange bondchange merge mol | e_chemsynthesis_url.xpd | ||||
| E_CHIRALITY | byte | Stereo status and potential of ensemble | none:meso:unspecified:chiral:contradictory |
Compiled C module | M_CHIRALITY | atomchange bondchange stereochange mol atom bond | mod_e_chirality.so | |||
| E_CHIRAL_POTENTIAL | intpair | Number of possible chiral atom and bond centers | Tcl script | A_STEREOGENIC B_STEREOGENIC A_TYPE | atomchange merge atom bond | e_chiral_potential.xpd | ||||
| E_CID | int | PubChem CID structure identifier | trace: { value: 0 datatype: boolean}
|
Tcl script | E_STDINCHIKEY | atomchange bondchange stereochange merge hadd | e_cid.xpd | |||
| E_CIF_BLOCK | table | _loop dataset of a CIF file | never | |||||||
| E_CLASSIFIED_BOND_COUNT | intvector | Counts of used-defined classes of bonds | bondtypes: { value: C-C C=C C*C C-X C=X C*X X-X X=X X*X C-H X-H description: The bond types to look for, in element/bondordersymbol/element notation datatype: string constraints: list}
|
Compiled C module | A_ELEMENT A_TYPE B_TYPE B_ORDER | atomchange bondchange merge | mod_e_classfied_bond_count.so | |||
| E_CLASSIFIED_SURFACE_AREA | doublevector | Estimated surface area classified by atom type | P. Labute, Methods in Molecular Biology, 275, 261ff | total_double double carbon double hydrogen double hetero double aromatic double aliphatic double ring double chain double |
Compiled C module | A_SURFACE_AREA A_ISAROMATIC A_ELEMENT A_TYPE A_RING_COUNT | atomchange bondchange 3dabsolute hadd atom bond | mod_e_classified_surface_area.so | ||
| E_CLASSYFIRE_CLASSIFICATION | jsonstring | ClassyFire classification (http://classyfire.wishartlab.com) | Djoumbou Feunang Y, Eisner R, Knox C, Chepelev L, Hastings J, Owen G, Fahy E, Steinbeck C, Subramanian S, Bolton E, Greiner R, and Wishart DS. ClassyFire: Automated Chemical Classification With A Comprehensive, Computable Taxonomy. Journal of Cheminformatics, 2016, 8:61. | Tcl script | atomchange bondchange stereochange merge | e_classyfire_classification.xpd | ||||
| E_CLASSYFIRE_URL | url | ClassyFire display URL (http://classyfire.wishartlab.com) | Djoumbou Feunang Y, Eisner R, Knox C, Chepelev L, Hastings J, Owen G, Fahy E, Steinbeck C, Subramanian S, Bolton E, Greiner R, and Wishart DS. ClassyFire: Automated Chemical Classification With A Comprehensive, Computable Taxonomy. Journal of Cheminformatics, 2016, 8:61. | Tcl script | E_STDINCHIKEY | atomchange bondchange stereochange merge | e_classyfire_url.xpd | |||
| E_CLEANNAME | string | Name cleaned from purity info and miscellaneous remarks | keeppurity: { value: 1 datatype: boolean} keepstereo: { value: 1 datatype: boolean} keepisotope: { value: 1 datatype: boolean} keepsalt: { value: 1 datatype: boolean} trace: { value: 0 datatype: boolean} watch: { value: {} description: String to watch out for, output notification if found datatype: string} |
Tcl script | E_NAME | never | e_cleanname.xpd | |||
| E_CML_STRING | string | CML structure record as string | pedantic: { value: 1 datatype: boolean}
|
Tcl script | atomchange bondchange stereochange merge 3drelative 3dabsolute hadd atom bond | e_cml_string.xpd | ||||
| E_CMSSPECTRUM | compound | Continuous mass spectrum. Filled by reading JCAMP spectrum file of CMS type. | experimental boolean origin string author string date int spectrometer string parameters string specificparams dictionary page string reference string purity float source string description string solvent string procedure string resolution double firstx double lastx double xfactor double yfactor double xunit string yunit string {#points} int coding string spectrum floatvector |
atomchange bondchange | ||||||
| E_COCONUT_ID | string | Structure key for the Coconut natural products database (http://coconut.naturalproducts.net) | Tcl script | E_STDINCHI | atomchange bondchange stereochange atom bond | e_coconut_id.xpd | ||||
| E_COCONUT_URL | url | Display URL for a natural product entry in the COCNUT database (coconut.naturalproducts.net) | Tcl script | atomchange bondchange atom bond | e_coconut_url.xpd | |||||
| E_COD_ID | int | ID of structure in the Crystallography Open Database (www.crystallography.net) | Tcl script | atomchange bondchange atom bond | e_cod_id.xpd | |||||
| E_COD_URL | url | URL to the Crystallography Open Database (www.crystallography.net) | Tcl script | E_COD_ID | atomchange bondchange atom bond | e_cod_url.xpd | ||||
| E_COLOR | color | Background color to use in plots | never | |||||||
| E_COMMENT | stringvector | Free form comment for ensemble | never | |||||||
| E_COMMONCHEMISTRY_URL | url | Display URL in the ACS CommonChemistry database (commonchemistryy.org) | Tcl script | E_CAS | atomchange bondchange stereochange atom bond | e_commonchemistry_url.xpd | ||||
| E_COMPLEXITY | float | Ensemble complexity according to modified Bertz/Hendrickson algorithm | W. D. Ihlenfeldt, Ph.D. Thesis, TU Munich 1991 | Compiled C module | M_COMPLEXITY M_HASH | atomchange bondchange merge mol | mod_e_complexity.so | |||
| E_COMPOSITION | string | Elemental composition | useimplicith: { value: 1 datatype: boolean}
|
Tcl script | A_WEIGHT A_SYMBOL A_HYDROGENS_NEEDED | atomchange | e_composition.xpd | |||
| E_CONFORMER_ENERGY | floatvector | Estimation of energy of conformer | Compiled C module | A_CONFORMER A_TYPE A_TOPO_DISTANCE A_VDW_INTERACTION | atomchange bondchange stereochange merge 3drelative hadd | mod_e_conformer_energy.so | ||||
| E_CONNECTIVITY | boolean | Pseudo property for connectivity reconstruction | (builtin) | never | ||||||
| E_CONNECTIVITY_MATRIX | floatmatrix | Connectivity matrix, configurable in several variants | usefe: { value: 0 description: If set, the diagonal contains the atom free electron count datatype: boolean} usebo: { value: 0 description: If set, atom pair matrix elements contain the VB bond order, not just 1 for an existing bond datatype: boolean} usearo: { value: 0 description: If set, and bond orders are use, the bond order for aromatic bonds is 1.5 (Kekule VB otherwise) datatype: boolean} |
Compiled C module | B_ORDER B_TYPE B_ISAROMATIC A_FREE_ELECTRONS | atomchange bondchange atom bond | mod_e_connectivity_matrix.so | |||
| E_CONSENSUSPATHDB_URL | url | Display URL in MPG ConsensusPathDB (http://consensuspathdb.org/) | Tcl script | E_CAS | atomchange bondchange stereochange atom bond | e_consensuspathdb_url.xpd | ||||
| E_CONVENTION | string | Free-form description of structure encoding convention | never | |||||||
| E_COSMO_DATA | dictionary | COSMO runtime information | atomchange bondchange stereochange merge 3drelative | |||||||
| E_CREST_URL | url | Display URL in the CREST (Chemical attributes, Regulatory approaches and Experimental STudies, http://www.rmeonline.net/CREST/r1/start.php) database | Tcl script | E_STDINCHIKEY | atomchange bondchange stereochange atom bond | e_crest_url.xpd | ||||
| E_CTDBASE_ID | string | CTD database ID (ctdbase.org) | Tcl script | E_CAS | atomchange bondchange atom bond | e_ctdbase_id.xpd | ||||
| E_CTDBASE_URL | url | CTD database (ctdbase.org) data display URL | Tcl script | E_CTDBASE_ID | atomchange bondchange atom bond | e_ctdbase_url.xpd | ||||
| E_DATABASE | compound | Info about the database the molecule was read from | dbtype string database string host string port int table string id int time date |
atomchange bondchange stereochange merge | ||||||
| E_DAYLIGHT_ARORING_COUNT | short | Count of aromatic rings in ESSSR, always using Daylight aromaticity definition | Compiled C module | R_DAYLIGHT_AROMATIC R_TYPE | atomchange bondchange atom bond ring | mod_e_daylight_aroring_count.so | ||||
| E_DBREFERENCE | stringvector | Generic free-form database references associated with ensemble | never | |||||||
| E_DECORATED_STRUCTURES | dataset | Exhaustive set of structures generated by decorating a core with any combination of user-supplied substituents. | substituents: { value: {} description: Substituent fragments in line notation. The first atom of these is their attachment point datatype: string constraints: list} coreatomfilters: { value: hydrogen chbond description: These atoms on the core will be replaced by combinations of fragments datatype: string constraints: filterlist} duphash: { value: E_HASHY description: Hash code used to remove duplicates datatype: string constraints: property} |
Tcl script | atomchange bondchange atom bond | e_decorated_structures.xpd | ||||
| E_DEGLYCOSILATED_STRUCTURE | structure | Structure with glycolisation fragments removed | spinach1: { value: C1-2O0-1H3- datatype: string} spinach2: { value: O0-2N0-1C0-2H+ datatype: string} |
Tcl script | atomchange bondchange stereochange shuffle atom bond | e_deglycosilated_structure.xpd | ||||
| E_DENSITY | float | Density of compound at room temperature in kg/L | Tcl script | A_ELEMENT A_ISOTOPE | atomchange bondchange | e_density.xpd | ||||
| E_DICTIONARY_OF_NATURAL_PRODUCTS_ID | string | Entry ID in dictionary of natural products (dnp.chemnetbase.com) | Tcl script | E_MRV_STRING | atomchange bondchange stereochange atom bond | e_dictionary_of_natural_products_id.xpd | ||||
| E_DICTIONARY_OF_NATURAL_PRODUCTS_URL | url | Display URL in dictionary of natrual products (dnp.chemnetbase.com) | Tcl script | E_DICTIONARY_OF_NATURAL_PRODUCTS_ID | atomchange bondchange atom bond | e_dictionary_of_natural_products_url.xpd | ||||
| E_DIPOLEMOMENT | compound | Dipole Moment. The computation links indirectly vie E_HEAT_OF_FORMATION to a VAMP run. | pointcharge floatvector hybrid floatvector sum floatvector |
A_XYZ | atomchange bondchange stereochange 3drelative | |||||
| E_DOTSURFACE | xyzvector | Coordinates of points on dot-surface | distance: { value: 0 description: dot distance to VDW surface (nm) datatype: double} density: { value: 30 description: average number of dots per atom datatype: int} |
A_XYZ A_ELEMENT | atomchange bondchange stereochange 3drelative 3dabsolute | |||||
| E_DRUGBANK_ID | string | Drugbank ID, looked up over the Internet | Tcl script | E_SMILES | atomchange bondchange stereochange merge | e_drugbank_id.xpd | ||||
| E_DRUGBANK_URL | url | Drugbank data display URL | Tcl script | E_DRUGBANK_ID | atomchange bondchange stereochange merge | e_drugbank_url.xpd | ||||
| E_DRUGINFO_URL | url | Display URL for the NIH DrugInfo prtal (druginfo.nlm.nih.gov) | Tcl script | E_UNII | atomchange bondchange atom bond | e_druginfo_url.xpd | ||||
| E_EC50 | compound | EC50 aids screen data | concentration float concunit shortstring flag shortstring ecconc float nexperiments short |
atomchange bondchange merge | ||||||
| E_ECHA_URL | url | Display number for a structure in the EU ECHA (European Chemicals Agency) registration system. | E_CAS | atomchange bondchange stereochange atom bond | ||||||
| E_ECHEMPORTAL_URL | url | Link into the OECD echemportal.org site | Tcl script | E_CAS | atomchange bondchange atom bond | e_echemportal_url.xpd | ||||
| E_EC_FINGERPRINT | bitvector (switchable between bitvector bytevector shortvector intvector) |
An ECFP-style fingerprint implementation. This property merges atomic enviroment hash codes from property A_EC_HASH for different numbers of spheres into a fingerprint or count vector. The number of enviroment spheres used is controlled by the settings of A_EC_HASH - this is a vector, and each element is the hashed atom enviroment including an additional sphere. If changed from default data type bitvector to bytevector, shortvector or intvector, the number of found atom environments in A_EC_HASH is counted. |
diameter: { value: -1 description: Maximum neighbor distance to consider. Must be <= length of A_EC_HASH vector, use -1 to use vector length minvalue: -1 maxvalue: 15 datatype: int} length: { value: 1024 description: Folded bitvector length minvalue: 16 maxvalue: 32768 datatype: int} counts: { value: 0 description: Whether to use counts enumeration: no:linear:exponential datatype: int} debug: { value: 0 description: If set, print debug info datatype: boolean} |
Compiled C module | A_EC_HASH | atomchange bondchange atom bond | mod_e_ec_fingerprint.so | |||
| E_EC_NUMBER | string | The European Community registration number for a compound with the European Chemicals Agency (ECHA, echa.europa.eu). This replaces the EINECS system (property E_EINECS_ID). Note that this identifier is very different from the enzyme commission EC number for proteins. | usepubchem: { value: 0 datatype: boolean} useecha: { value: 1 datatype: boolean} |
Tcl script | E_CID E_CAS | atomchange bondchange stereochange atom bond | e_ec_number.xpd | |||
| E_EEROS_URL | url | Data display URL for compound in Wiley Electronic Encyclopedia of Reagents for Organic Synthesis (https://onlinelibrary.wiley.com/doi/book/10.1002/047084289X) | Tcl script | E_STDINCHIKEY | atomchange bondchange atom bond | e_eeros_url.xpd | ||||
| E_EFFECTIVE_ROTOR_COUNT | double | Effective rotor count, computed from rotatable bonds (B_ROTATABILITY) and fractional values for ring flexibility. | usecanonictautomer: { value: 0 description: If set, compute on standard tautomer instead of current structure datatype: boolean}
|
Tcl script | B_ROTATABILITY | atomchange bondchange | e_effective_rotor_count.xpd | |||
| E_EGAN_BIOAVAILABILITY_FLAG | boolean | Veber bioavailability flag (E_XLOGP2<=5.88 && E_TPSA<=131.6) | Journal of Medicinal Chemistry, Vol. 43, pp. 3867-3877, 2000 | Compiled C module | E_XLOGP2 E_TPSA | atomchange bondchange atom bond | mod_e_egan_bioavailability_flag.so | |||
| E_EIGENVALUES | floatvector | MO Eigenvalues | A_XYZ | atomchange bondchange | ||||||
| E_EINECS_ID | string | EINECS ID. Note that this is now an outdated identifier with the launch of the EU REACH system. It should be replaced by the ECHA (https://echa.europa.eu) European Commission EC number (property E_EC_NUMBER, this is not the same as the Enzyme Commission protein EC number). | Tcl script | E_SDF_STRING | atomchange bondchange stereochange merge | e_einecs_id.xpd | ||||
| E_ELECTRONIC_ENERGY | float | Measured or computed electronic energy, as returned by, for example, a QM program. This property currently is used for reading VAMP data. | atomchange bondchange | |||||||
| E_ELEMENT_COUNT | shortvector | Count of element types of atoms of ensemble | ? short h short he short li short be short b short c short n short o short f short ne short na short mg short al short si short p short s short cl short ar short k short ca short sc short ti short v short cr short mn short fe short co short ni short cu short zn short ga short ge short as short se short br short kr short rb short sr short y short zr short nb short mo short tc short ru short rh short pd short ag short cd short in short sn short sb short te short i short xe short cs short ba short la short ce short pr short nd short pm short sm short eu short gd short tb short dy short ho short er short tm short yb short lu short hf short ta short w short re short os short ir short pt short au short hg short tl short pb short bi short po short at short rn short fr short ra short ac short th short pa short u short np short pu short am short cm short bk short cf short es short fm short md short no short lr short rf short db short sg short bh short hs short mt short ds short |
(builtin) | A_ELEMENT A_TYPE | atomchange merge hadd | ||||
| E_ELLIPSE_ANNOTATION | compound | Ellipse as structure drawing annotation. This is one of the choice variants of property E_ANNOTATION. | {} {} {} {} ^none:round:shadow:shaded:filled:dashed:bold |
coords floatvector linecolor color linewidth float bgcolor color style bitset |
A_XY | never | ||||
| E_EMBL_SIDER_URL | url | Data display link in the EMBL Sider database (http://sideeffects.embl.de) | Tcl script | E_CID | atomchange bondchange stereochange atom bond | e_embl_sider_url.xpd | ||||
| E_EMBL_STITCH_URL | url | Data display URL in the STITCH database (http://stitch.embl.de) | Tcl script | E_CID | atomchange bondchange stereochange atom bond | e_embl_stitch_url.xpd | ||||
| E_EMF_IMAGE | diskfile (switchable between blob diskfile url) |
Metafile WIN32 structure drawing | width: { value: 180 minvalue: 1 maxvalue: 65535 datatype: int} height: { value: 180 minvalue: 1 maxvalue: 65535 datatype: int} asymbol: { value: xsymbol enumeration: none,no:symbol,sym,normal:xsymbol,xsym,extended,ex panded:label:index,idx:box:compact,text,super,superatom:residue" datatype: int} bonds: { value: 8 datatype: int} hsymbol: { value: special enumeration: none,no,suppress:special,normal,hetero:all,yes datatype: int} csymbol: { value: special enumeration: none,no:special,normal:all,yes datatype: int} bgcolor: { value: transparent datatype: string} border: { value: 12 datatype: int} bondcolor: { value: black comment: Cannot be color datatype because we recognize 'atomsplit' value datatype: string} atomcolor: { value: black description: A color name, the magic value "element", or a atom color property. "element" uses the default color defined in the element table datatype: string} hcolor: { value: {} datatype: color constraints: emptycolor} header: { value: {} datatype: string} footer: { value: {} datatype: string} headercolor: { value: black datatype: color} footercolor: { value: black datatype: color} commenttype: { value: property enumeration: none:text:property,prop datatype: int} comment: { value: E_NAME datatype: string} structure: { value: smiles datatype: string} metadata: { value: 1 datatype: boolean constraints: writeable} filename: { value: {} datatype: diskfile} highlightcolor: { value: red datatype: color} highlightbonds: { value: {} datatype: intvector} httpheader: { value: 0 minvalue: 0 maxvalue: 2 datatype: int} wedges: { value: 1 datatype: boolean} wiggles: { value: all enumeration: none:sp3:sp2:all datatype: int} markcolor: { value: blue datatype: color} logofile: { value: {} datatype: diskfile constraints: readable} logoscale: { value: 1 datatype: double} dashes: { value: 1 datatype: boolean} headerproperty: { value: {} datatype: string constraints: property} footerproperty: { value: {} datatype: string constraints: property} bead: { value: 1 datatype: boolean} beadcolor1: { value: black datatype: color} beadcolor2: { value: gray60 datatype: color} linewidth: { value: 1.4 datatype: double} colormode: { value: color enumeration: mono,bw,b/w,black,monochrome:gray,grey,gr ayscale,greyscale:color,colour datatype: int} showcharge: { value: 1 datatype: boolean} showradical: { value: 1 datatype: boolean} showstereo: { value: 1 datatype: boolean} highlightgroups: { value: {} datatype: intvector} boxgroups: { value: {} datatype: intvector} groupcolor: { value: purple datatype: color} symbolfontsize: { value: -1 datatype: double} annotationfontsize: { value: -1 datatype: double} isotopemapping: { value: none datatype: string} showisotope: { value: 1 datatype: boolean} showstereoh: { value: 1 datatype: boolean} showmapping: { value: 0 datatype: boolean} usehatch: { value: 0 datatype: boolean} format: { value: wmf enumeration: emf:wmf:placeablewmf,pwmf,placeable datatype: int} frame: { value: 1 datatype: boolean} showchirality: { value: none enumeration: none:simple:extended datatype: int} linespacing: { value: 2.0 datatype: double} headerfontsize: { value: -1 datatype: double} footerfontsize: { value: -1 datatype: double} voronoicolorproperty: { value: {} datatype: string constraints: property} voronoifilter: { value: {} datatype: string constraints: filtername} circlecolor: { value: {} description: A property name or a color name datatype: string constraints: colorproperty} circleatoms: { value: {} datatype: intvector} circlefilter: { value: {} datatype: string constraints: filtername} wigglecount: { value: 6 datatype: int} wiggleamplitude: { value: 1.5 datatype: double} checkintersection: { value: 0 datatype: boolean} annotationcolor: { value: {} datatype: color constraints: emptycolor} crop: { value: -1 datatype: int} showstereogroups: { value: 0 datatype: boolean} font: { value: Arial datatype: string} usesubscripts: { value: 1 datatype: boolean} contractgroups: { value: 0 datatype: boolean} downloadfilename: { value: {} datatype: string} labelproperty: { value: {} datatype: string constraints: property} labelfilterset: { value: !hydrogen datatype: string constraints: filterlist} labelcolor: { value: darkgreen datatype: color} labelformat: { value: <%s> datatype: string} usegrouplabels: { value: 0 datatype: boolean} forcecarbonsymbol: { value: 1 description: If set, an element symbol is rendered if a carbon atom has a circle background highlight, etc. datatype: boolean} |
Compiled C module | A_XY A_TYPE B_TYPE B_ORDER A_COLOR A_ANNOTATION B_FLAGS A_FLAGS | atomchange bondchange stereochange merge hadd mol | mod_e_emf_image.so | |||
| E_EMOLECULES_ID | string | EMolecules Web database ID (www.emolecules.com) | catalog: { value: all enumeration: SC:BB:all datatype: string}
|
Tcl script | E_SMILES | atomchange bondchange stereochange merge | e_emolecules_id.xpd | |||
| E_EMOLECULES_URL | url | EMolecules (www.emolecules.com) Web database display URL | Tcl script | E_EMOLECULES_ID | atomchange bondchange stereochange merge | e_emolecules_url.xpd | ||||
| E_ENAMINE_ID | string | Catalog ID for the Enamine catalog (enaminestore.com) | Tcl script | atomchange bondchange stereochange atom bond | e_enamine_id.xpd | |||||
| E_ENAMINE_URL | url | Data display URL for the Enamine catalog (enaminestore.com) | Tcl script | E_ENAMINE_ID | atomchange bondchange stereochange atom bond | e_enamine_url.xpd | ||||
| E_ENANTIOMER | structure | Enantiomer of ensemble (i.e. all tetrahedral stereochemistry is reversed) | Tcl script | A_TYPE A_ELEMENT B_TYPE B_ORDER A_LABEL_STEREO B_LABEL_STEREO | atomchange bondchange stereochange merge | e_enantiomer.xpd | ||||
| E_ENERGY | float | Ensemble energy | A_TYPE A_ELEMENT B_TYPE B_ORDER | atomchange bondchange stereochange merge 3drelative | ||||||
| E_ENS_COUNT | int | Pseudo-property: Number of ens in ensemble - always 1, needed for generality in processing bind sets in "scan" queries | Compiled C module | atomchange bondchange atom bond | mod_e_ens_count.so | |||||
| E_EPA_ACTOR_URL | url | EPA Actor data access | Tcl script | E_CAS | atomchange bondchange stereochange | e_epa_actor_url.xpd | ||||
| E_EPA_COMPTOX_URL | url | Data display URL for the new EPA CompTox portal | Tcl script | E_STDINCHIKEY | atomchange bondchange atom bond | e_epa_comptox_url.xpd | ||||
| E_EPA_HPVIS_URL | url | Data display URL in US EPA High Production Volume Information System (HPVIS), https://www.epa.gov/hpvis | Tcl script | E_CAS | atomchange bondchange atom bond | e_epa_hpvis_url.xpd | ||||
| E_EPRSPECTRUM | compound | EPR spectrum, usually read from JCAMP file | experimental boolean origin string author string date int spectrometer string parameters string specificparams dictionary page string reference string purity float source string description string solvent string procedure string resolution double firstx double lastx double xfactor double yfactor double xunit string yunit string {#points} int coding string spectrum floatvector |
atomchange bondchange stereochange | ||||||
| E_EPS_IMAGE | diskfile (switchable between blob diskfile) |
A 2D-plot of the structure as EPS image file | width: { value: 180 datatype: int} height: { value: 180 datatype: int} asymbol: { value: xsymbol enumeration: none,no:symbol,sym,normal:xsymbol,xsym,extended,expanded:label:index,idx:box:compact,text,super,superatom:residue datatype: string} bonds: { value: 8 datatype: int} hsymbol: { value: special enumeration: none,no,suppress:special,normal,hetero:all,yes datatype: string} csymbol: { value: special enumeration: none,no:special,normal:all,yes datatype: string} bgcolor: { value: transparent datatype: color} border: { value: 12 datatype: int} bondcolor: { value: black comment: Cannot be color datatype because we recognize 'atomsplit' value datatype: string} atomcolor: { value: black description: A color name, the magic value "element", or a atom color property. "element" uses the default color defined in the element table datatype: string} hcolor: { value: {} datatype: color} header: { value: {} datatype: string} footer: { value: {} datatype: string} headercolor: { value: black datatype: color} footercolor: { value: black datatype: color} commenttype: { value: property enumeration: none:text:property,prop datatype: string} comment: { value: E_NAME datatype: string} structure: { value: none enumeration: none:smiles:stdinchi:cactvs:molfile datatype: string} metadata: { value: 1 datatype: boolean} filename: { value: {} datatype: diskfile constraints: writeable} highlightcolor: { value: red datatype: color} highlightbonds: { value: {} datatype: intvector} httpheader: { value: 0 datatype: int} wedges: { value: 1 datatype: boolean} wiggles: { value: all enumeration: none:sp3,tetrahedral:sp2,planar:all datatype: string} markcolor: { value: blue datatype: color} logofile: { value: {} datatype: diskfile constraints: readable} logoscale: { value: 1 datatype: double} dashes: { value: 1 datatype: boolean} headerproperty: { value: {} datatype: string constraints: property} footerproperty: { value: {} datatype: string constraints: property} bead: { value: 1 datatype: boolean} beadcolor1: { value: black datatype: color} beadcolor2: { value: gray60 datatype: color} linewidth: { value: 1.3 datatype: double} colormode: { value: mono datatype: string} showcharge: { value: 1 datatype: boolean} showradical: { value: 1 datatype: boolean} showstereo: { value: 1 datatype: boolean} highlightgroups: { value: {} datatype: intvector} boxgroups: { value: {} datatype: intvector} groupcolor: { value: purple datatype: color} symbolfontsize: { value: -1 datatype: double} annotationfontsize: { value: -1 datatype: double} isotopemapping: { value: none datatype: string} showisotope: { value: 1 datatype: boolean} showstereoh: { value: 1 datatype: boolean} showmapping: { value: 0 datatype: boolean} showchirality: { value: none enumeration: none:simple:extended datatype: string} frame: { value: 0 datatype: boolean} linespacing: { value: 2.5 datatype: double} headerfontsize: { value: -1 datatype: double} footerfontsize: { value: -1 datatype: double} voronoicolorproperty: { value: {} datatype: string constraints: property} voronoifilter: { value: {} datatype: string constraints: filterlist} circlecolor: { value: {} description: A property name or a color name datatype: string constraints: colorproperty} circleatoms: { value: {} datatype: intvector} circlefilter: { value: {} datatype: string constraints: filterlist} wigglecount: { value: 10 datatype: int} wiggleamplitude: { value: 3.0 datatype: double} checkintersection: { value: 0 datatype: boolean} annotationcolor: { value: {} datatype: color constraints: emptycolor} showstereogroups: { value: 0 datatype: boolean} font: { value: Helvetica datatype: string} contractgroups: { value: 0 datatype: boolean} framecolor: { value: black datatype: color} downloadfilename: { value: {} datatype: string constraints: writeable} labelproperty: { value: {} datatype: string constraints: property} labelfilterset: { value: !hydrogen datatype: string constraints: filterlist} labelcolor: { value: darkgreen datatype: color} labelformat: { value: <%s> datatype: string} usegrouplabels: { value: 0 datatype: boolean} forcecarbonsymbol: { value: 1 description: If set, an element symbol is rendered if a carbon atom has a circle background highlight, etc. datatype: boolean} |
Compiled C module | A_XY A_TYPE B_TYPE B_ORDER A_COLOR B_FLAGS A_FLAGS A_ANNOTATION | atomchange bondchange stereochange merge hadd | mod_e_eps_image.so | |||
| E_EXACT_MASS | floatpair | Exact mass of most abundant compound isotope combination, assuming natural abundance | weight double abundance double |
useimplicith: { value: 1 description: Whether to include implicit hydrogens in the computation datatype: boolean}
|
Compiled C module | atomchange merge atom | mod_e_exact_mass.so | |||
| E_EXPANDED_QUERY_STRUCTURES | dataset | Tcl script | atomchange bondchange stereochange atom bond | e_expanded_query_structures.xpd | ||||||
| E_EXPERIMENT | string | Experimental setup used to obtain structure data | never | |||||||
| E_EXP_CONNECTIVITY_MATRIX | floatmatrix | Exponent of the connectivity matrix, as per the work of Alexey Lagunin | Molecular Informatics 30, 2011, 241-250 | multiplier: { value: -0.5 description: multiplier for all matrix elements applied before exponent computation datatype: double}
|
Compiled C module | E_CONNECTIVITY_MATRIX | atomchange bondchange atom bond | mod_e_exp_connectivity_matrix.so | ||
| E_FDA_OBJECT_CODE | compound | FDA data code triple from SPL file, identiying for example the type of structure extracted | code string codesystem string displayname string |
atomchange bondchange atom bond | ||||||
| E_FDA_SPL_URL | url | Tcl script | E_UNII | atomchange bondchange atom bond | e_fda_spl_url.xpd | |||||
| E_FDA_SRS_URL | url | Link into FDA SRS (structure registration system) database | Tcl script | E_UNII | atomchange bondchange atom bond | e_fda_srs_url.xpd | ||||
| E_FEATURES | bytevector | Count of structural features defined as parameters by SMARTS expressions | carboxylic_acid byte acid_halogenide byte aldehyde byte ketone byte amine byte primary_amine byte secondary_amine byte tertiary_amine byte quarternary_amine byte hydrazine byte urea byte 12diamine byte pyridine byte thp byte piperidine byte piperazine byte morpholine byte thiomorpholine byte amide byte ester byte alpha_aminoacid byte betaaminoacid byte alpha_ketoacid byte betaketoacid byte alcohol byte phenol byte thiol byte thiophenol byte ether byte thioether byte epoxide byte acetal byte enol byte lactone byte oxime byte nitro byte isocyanate byte thioisocyanate byte anhydride byte cyanide byte sulfonic_acid byte sulfonic_acid_halogenide byte sulfonamide byte phosphoric_acid byte boronic_ester byte silyl_hydride byte siloxyl byte aliphatic_halogen byte aromatic_halogen byte trifluoromethyl byte 11_diphenyl_methyl byte alpha_haloketone byte chalcone byte aromatic_nitrogen byte aromatic_oxygen byte aromatic_sulphur byte cc_doublebond byte cc_triplebond byte phenyl byte |
patterns: { value: {{carboxylic acid} C(=O)O[#1]} {{acid halogenide} C(=O)[Cl,Br,I,F]} {aldehyde CC(=O)[#1]} {ketone CC(=O)C} {amine N([Cx1,cx1,#1])([Cx1,cx1,#1])[Cx1,cx1,#1]} {{primary amine} [Cx1,cx1][NH2;v3]} {{secondary amine} [NH;v3]([Cx1,cx1])([Cx1,cx1])} {{tertiary amine} [N;v3]([Cx1,cx1])([Cx1,cx1])[Cx1,cx1]} {{quarternary amine} [N;v4](C)(C)(C)C} {hydrazine [N;R0][N;R0]} {urea [N;x0]C(=O)[N;x0]} {{1.2-diamine} [NH2]CC[NH2]} {pyridine n1ccccc1} {tetrahydropyrrole N1CCCC1} {piperidine [N;A]1CCCCC1} {piperazine N1CCNCC1} {morpholine N1CCOCC1} {thiomorpholine S1CCOCC1} {amide CC(=O)N([C,c,#1])[C,c,#1]} {ester CC(=O)[O;R0]C} {{alpha-aminoacid} NCC(=O)O} {{beta-aminoacid} NCCC(=O)O} {{alpha-ketoacid} O=CC(=O)O} {{beta-ketoacid} O=CCC(=O)O} {alcohol [C;X4;A]O[#1]} {phenol [c]O[#1]} {thiol [C;X4;A]S[#1]} {thiophenol [c]S[#1]} {ether [Cx1,cx1][O;!r3][Cx1,cx1]} {thioether [Cx1,cx1][S;!r3][Cx1,cx1]} {epoxide C1OC1} {acetal [Cx1,cx1]O[Cx2]O[Cx1,cx1]} {enol C=CO} {lactone [C;R](=O)[O;R]} {oxime C=NO} {nitro N(=O)O} {isocyanate N=C=O} {thioisocyanate N=C=S} {anhydride {C(=O)OC(=O)C}} {cyanide C#N} {{sulfonic acid} S(=O)(=O)O[#1]} {{sulfonic acid halogenide} S(=O)(=O)[F,Cl,Br,I]} {sulfonamide S(=O)(=O)N} {{phosphoric acid derivative} P(=[O,S,N])[N,O,S,F,Cl,Br,I]} {{boronic ester} C[B](O[C,#1])O[C,#1]} {{silyl hydride} [SiH]} {{siloxyl} [Si]O} {{aliphatic halogen} [C;A][F,Cl,Br,I]} {{aromatic halogen} [c][F,Cl,Br,I]} {trifluoromethyl C(F)(F)F} {{1.1-diphenyl-methyl} c1ccccc1C(c1ccccc1)[!C;!c;!#1]} {{alpha-haloketone} CC(=O)C[F,Cl,Br,I]} {chalcone CC(=O)[C;A]=[C;A]} {{aromatic nitrogen} [n]} {{aromatic oxygen} [o]} {{aromatic sulphur} [s]} {{C-C double bond} [C;A]=[C;A]} {{C-C triple bond} C#C} {{phenyl ring} c1ccccc1} datatype: string}
|
Tcl script | A_ELEMENT B_ORDER B_TYPE | atomchange bondchange merge hadd atom bond ring | e_features.xpd | ||
| E_FELDMAN_FINGERPRINT | bitvector | Feldman and Hodes, JCICS 1975 15(3) 147-152 | Python script | atomchange bondchange atom bond | e_feldman_fingerprint.xpd | |||||
| E_FG_COUNT | shortvector | Count of functional groups in ensemble, summed up from molecular FG counts in M_FG_COUNT | Compiled C module | M_FG_COUNT | atomchange bondchange | mod_e_fg_count.so | ||||
| E_FICTS_ID | string | Sitzmann, M., Fillipov, I.V., Nicklaus, M.C., SAR and QSAR in Environmental Research, 19:1, 1-9, 2008 (DOI 10.1080/10629360701843540) | primarytag: { value: FICTS datatype: string} scope: { value: public datatype: string} addsecondarytag: { value: 1 datatype: string} addtag: { value: 1 datatype: string} tagseparator: { value: - datatype: string} debug: { value: 0 datatype: string} forcemagic: { value: 0 datatype: string} test: { value: parameters {partialStereo 1 neutralSalt 1 singleMetalAtoms 1 inorganic 1 enantiomer 1 unspecifiedStereo 1 singleAtom 1 diastereomer 1 radical 1 noAtoms 1 pseudoOrganic 1 organoMetallic 1 organic 1 metalComplex 1 isotopes 1 clusterCompound 1 metalAtoms 1 sizeLimit 1 meso 1 noStereo 1 empty 1 fullStereo 1 singleHydrogenAtoms 1 specialAtomTypes 1} order {list: noAtoms singleAtom empty organic pseudoOrganic inorganic specialAtomTypes isotopes metalAtoms singleMetalAtoms singleHydrogenAtoms sizeLimit clusterCompound noStereo unspecifiedStereo partialStereo fullStereo meso enantiomer diastereomer neutralSalt organoMetallic metalComplex radical} exec 1 datatype: string} addprimarytag: { value: 1 datatype: string} structurepropname: { value: E_FICTS_STRUCTURE datatype: string} norm: { value: order {list: singleMetalAtoms singleHydrogenAtoms singleHalogenAtoms deleteSearchInfo radical functionalGroups hsaturation metalLigandBonds desalt deleteMetalComplexCenter resonance grabLargestFragment uncharge tautomer stereo deleteStereoInfo deleteIsotopeLabels} parameters {desalt 0 hsaturation 1 tautomer 0 singleHalogenAtoms 0 uncharge 0 deleteMetalComplexCenter 0 deleteSearchInfo 1 functionalGroups 1 singleMetalAtoms 0 radical 0 stereo 1 singleHydrogenAtoms 0 metalLigandBonds 1 resonance 1 deleteStereoInfo 0 deleteIsotopeLabels 0 grabLargestFragment 0} args {functionalGroups {} deleteMetalComplexCenter {} stereo {list: 1 1 0 0 0 0} singleMetalAtoms {} metalLigandBonds {} resonance {list: 1000 0 E_HASHY 1 1} deleteStereoInfo {} desalt {} tautomer {list: 1000 0 E_HASHY 0 0 0 0 1 0} uncharge {list: 0 E_HASHY} singleHalogenAtoms {} singleHydrogenAtoms {} radical {} deleteSearchInfo {} hsaturation {list: 0 0 {} !normal {noatoms nometals nospecial} {}} deleteIsotopeLabels {} grabLargestFragment {}} exec 1 datatype: string} secondarytag: { value: 01-xx datatype: string} csbasehash: { value: E_HASHISY datatype: string} post: { value: norm {parameters {deleteSearchInfo 1 functionalGroups 1 singleMetalAtoms 0 singleHalogenAtoms 0 radical 0 metalLigandBonds 1 tautomer 0 stereo 1 uncharge 0 deleteMetalComplexCenter 0 deleteStereoInfo 0 hsaturation 1 singleHydrogenAtoms 0 desalt 0 resonance 1 deleteIsotopeLabels 0 grabLargestFragment 0} exec 1} test {parameters {metalAtoms 1 organic 1 inorganic 1 pseudoOrganic 1 fullStereo 1 metalComplex 1 neutralSalt 1 specialAtomTypes 1 isotopes 1 enantiomer 1 sizeLimit 1 singleAtom 1 clusterCompound 1 organoMetallic 1 singleMetalAtoms 1 singleHydrogenAtoms 1 unspecifiedStereo 1 partialStereo 1 noStereo 1 radical 1 noAtoms 1 meso 1 empty 1 diastereomer 1} exec 1 switches {norm {parameters {deleteStereoInfo 0 desalt 0 radical 0 singleHydrogenAtoms 0 tautomer 0 singleHalogenAtoms 0 uncharge 0 resonance 0 deleteMetalComplexCenter 0 deleteIsotopeLabels 0 grabLargestFragment 0 deleteSearchInfo 0 functionalGroups 0 singleMetalAtoms 0 stereo 0 hsaturation 0 metalLigandBonds 0} exec 0} forcemagic 0 unreliable 0}} norm {cmds {true {resonance {} deleteStereoInfo {} desalt {} tautomer tautomer uncharge uncharge singleHalogenAtoms {} singleHydrogenAtoms {} radical {} deleteSearchInfo {} hsaturation {} deleteIsotopeLabels {} grabLargestFragment grabLargestFragment functionalGroups {} deleteMetalComplexCenter deleteMetalComplexCenter stereo {} singleMetalAtoms {} metalLigandBonds {}} false {deleteSearchInfo {} functionalGroups {} deleteIsotopeLabels {} grabLargestFragment {} singleMetalAtoms {} resonance {} metalLigandBonds {} radical {} hsaturation {} stereo {} deleteStereoInfo {} singleHalogenAtoms {} tautomer {} uncharge {} desalt {} singleHydrogenAtoms {} deleteMetalComplexCenter {}}}} test {cmds {true {enantiomer {} singleAtom {} meso {} metalComplex metalComplex specialAtomTypes specialAtomTypes radical radical noAtoms noAtoms singleMetalAtoms singleMetalAtoms pseudoOrganic {} empty empty inorganic inorganic metalAtoms {} organic {} isotopes {} fullStereo {} singleHydrogenAtoms singleHydrogenAtoms neutralSalt {} unspecifiedStereo {} noStereo noStereo clusterCompound clusterCompound diastereomer {} partialStereo {} organoMetallic {} sizeLimit sizeLimit} false {isotopes {} sizeLimit {} fullStereo {} organic {} clusterCompound {} neutralSalt {} diastereomer {} organoMetallic {} noStereo {} pseudoOrganic {} enantiomer {} specialAtomTypes {} singleAtom {} metalComplex metalComplex inorganic {} unspecifiedStereo {} singleMetalAtoms {} empty {} meso {} partialStereo {} metalAtoms metalAtoms radical radical noAtoms {} singleHydrogenAtoms {}}}} datatype: string} |
Tcl script | A_ELEMENT A_TYPE B_TYPE A_FORMAL_CHARGE A_ISOTOPE A_LABEL_STEREO B_LABEL_STEREO | atomchange bondchange stereochange atom bond | e_ficts_id.xpd | |||
| E_FICTS_STRUCTURE | structure | Sitzmann, M., Fillipov, I.V., Nicklaus, M.C., SAR and QSAR in Environmental Research, 19:1, 1-9, 2008 (DOI 10.1080/10629360701843540) | A_ELEMENT A_TYPE B_TYPE A_FORMAL_CHARGE A_ISOTOPE A_LABEL_STEREO B_LABEL_STEREO | atomchange bondchange stereochange atom bond | ||||||
| E_FICTU_ID | string | Sitzmann, M., Fillipov, I.V., Nicklaus, M.C., SAR and QSAR in Environmental Research, 19:1, 1-9, 2008 (DOI 10.1080/10629360701843540) | primarytag: { value: FICTu datatype: string} scope: { value: public datatype: string} addsecondarytag: { value: 1 datatype: string} addtag: { value: 1 datatype: string} tagseparator: { value: - datatype: string} debug: { value: 0 datatype: string} forcemagic: { value: 0 datatype: string} test: { value: parameters {partialStereo 1 neutralSalt 1 singleMetalAtoms 1 inorganic 1 enantiomer 1 unspecifiedStereo 1 singleAtom 1 diastereomer 1 radical 1 noAtoms 1 pseudoOrganic 1 organoMetallic 1 organic 1 metalComplex 1 isotopes 1 clusterCompound 1 metalAtoms 1 sizeLimit 1 meso 1 noStereo 1 empty 1 fullStereo 1 singleHydrogenAtoms 1 specialAtomTypes 1} order {list: noAtoms singleAtom empty organic pseudoOrganic inorganic specialAtomTypes isotopes metalAtoms singleMetalAtoms singleHydrogenAtoms sizeLimit clusterCompound noStereo unspecifiedStereo partialStereo fullStereo meso enantiomer diastereomer neutralSalt organoMetallic metalComplex radical} exec 1 datatype: string} addprimarytag: { value: 1 datatype: string} structurepropname: { value: E_FICTU_STRUCTURE datatype: string} norm: { value: order {list: singleMetalAtoms singleHydrogenAtoms singleHalogenAtoms deleteSearchInfo radical functionalGroups hsaturation metalLigandBonds desalt deleteMetalComplexCenter resonance grabLargestFragment uncharge tautomer stereo deleteStereoInfo deleteIsotopeLabels} parameters {desalt 0 hsaturation 1 tautomer 0 singleHalogenAtoms 0 uncharge 0 deleteMetalComplexCenter 0 deleteSearchInfo 1 functionalGroups 1 singleMetalAtoms 0 radical 0 stereo 1 singleHydrogenAtoms 0 metalLigandBonds 1 resonance 1 deleteStereoInfo 1 deleteIsotopeLabels 0 grabLargestFragment 0} args {functionalGroups {} deleteMetalComplexCenter {} stereo {list: 1 1 0 0 0 0} singleMetalAtoms {} metalLigandBonds {} resonance {list: 1000 0 E_HASHY 1 1} deleteStereoInfo {} desalt {} tautomer {list: 1000 0 E_HASHY 0 0 0 0 1 0} uncharge {list: 0 E_HASHY} singleHalogenAtoms {} singleHydrogenAtoms {} radical {} deleteSearchInfo {} hsaturation {list: 0 0 {} !normal {noatoms nometals nospecial} {}} deleteIsotopeLabels {} grabLargestFragment {}} exec 1 datatype: string} secondarytag: { value: 01-xx datatype: string} csbasehash: { value: E_HASHIY datatype: string} post: { value: norm {parameters {deleteSearchInfo 1 functionalGroups 1 singleMetalAtoms 0 singleHalogenAtoms 0 radical 0 metalLigandBonds 1 tautomer 0 stereo 1 uncharge 0 deleteMetalComplexCenter 0 deleteStereoInfo 1 hsaturation 1 singleHydrogenAtoms 0 desalt 0 resonance 1 deleteIsotopeLabels 0 grabLargestFragment 0} exec 1} test {parameters {metalAtoms 1 organic 1 inorganic 1 pseudoOrganic 1 fullStereo 1 metalComplex 1 neutralSalt 1 specialAtomTypes 1 isotopes 1 enantiomer 1 sizeLimit 1 singleAtom 1 clusterCompound 1 organoMetallic 1 singleMetalAtoms 1 singleHydrogenAtoms 1 unspecifiedStereo 1 partialStereo 1 noStereo 1 radical 1 noAtoms 1 meso 1 empty 1 diastereomer 1} exec 1 switches {norm {parameters {deleteStereoInfo 0 desalt 0 radical 0 singleHydrogenAtoms 0 tautomer 0 singleHalogenAtoms 0 uncharge 0 resonance 0 deleteMetalComplexCenter 0 deleteIsotopeLabels 0 grabLargestFragment 0 deleteSearchInfo 0 functionalGroups 0 singleMetalAtoms 0 stereo 0 hsaturation 0 metalLigandBonds 0} exec 0} forcemagic 0 unreliable 0}} norm {cmds {true {resonance {} deleteStereoInfo {} desalt {} tautomer tautomer uncharge uncharge singleHalogenAtoms {} singleHydrogenAtoms {} radical {} deleteSearchInfo {} hsaturation {} deleteIsotopeLabels {} grabLargestFragment grabLargestFragment functionalGroups {} deleteMetalComplexCenter deleteMetalComplexCenter stereo {} singleMetalAtoms {} metalLigandBonds {}} false {deleteSearchInfo {} functionalGroups {} deleteIsotopeLabels {} grabLargestFragment {} singleMetalAtoms {} resonance {} metalLigandBonds {} radical {} hsaturation {} stereo {} deleteStereoInfo {} singleHalogenAtoms {} tautomer {} uncharge {} desalt {} singleHydrogenAtoms {} deleteMetalComplexCenter {}}}} test {cmds {true {enantiomer {} singleAtom {} meso {} metalComplex metalComplex specialAtomTypes specialAtomTypes radical radical noAtoms noAtoms singleMetalAtoms singleMetalAtoms pseudoOrganic {} empty empty inorganic inorganic metalAtoms {} organic {} isotopes {} fullStereo {} singleHydrogenAtoms singleHydrogenAtoms neutralSalt {} unspecifiedStereo {} noStereo noStereo clusterCompound clusterCompound diastereomer {} partialStereo {} organoMetallic {} sizeLimit sizeLimit} false {isotopes {} sizeLimit {} fullStereo {} organic {} clusterCompound {} neutralSalt {} diastereomer {} organoMetallic {} noStereo {} pseudoOrganic {} enantiomer {} specialAtomTypes {} singleAtom {} metalComplex metalComplex inorganic {} unspecifiedStereo {} singleMetalAtoms {} empty {} meso {} partialStereo {} metalAtoms metalAtoms radical radical noAtoms {} singleHydrogenAtoms {}}}} datatype: string} |
Tcl script | A_ELEMENT A_TYPE B_TYPE A_FORMAL_CHARGE A_ISOTOPE A_LABEL_STEREO B_LABEL_STEREO | atomchange bondchange stereochange atom bond | e_fictu_id.xpd | |||
| E_FICTU_STRUCTURE | structure | Sitzmann, M., Fillipov, I.V., Nicklaus, M.C., SAR and QSAR in Environmental Research, 19:1, 1-9, 2008 (DOI 10.1080/10629360701843540) | A_ELEMENT A_TYPE B_TYPE A_FORMAL_CHARGE A_ISOTOPE A_LABEL_STEREO B_LABEL_STEREO | atomchange bondchange stereochange atom bond | ||||||
| E_FICUS_ID | string | Sitzmann, M., Fillipov, I.V., Nicklaus, M.C., SAR and QSAR in Environmental Research, 19:1, 1-9, 2008 (DOI 10.1080/10629360701843540) | primarytag: { value: FICuS datatype: string} scope: { value: public datatype: string} addsecondarytag: { value: 1 datatype: string} addtag: { value: 1 datatype: string} tagseparator: { value: - datatype: string} debug: { value: 0 datatype: string} forcemagic: { value: 0 datatype: string} test: { value: parameters {partialStereo 1 neutralSalt 1 singleMetalAtoms 1 inorganic 1 enantiomer 1 unspecifiedStereo 1 singleAtom 1 diastereomer 1 radical 1 noAtoms 1 pseudoOrganic 1 organoMetallic 1 organic 1 metalComplex 1 isotopes 1 clusterCompound 1 metalAtoms 1 sizeLimit 1 meso 1 noStereo 1 empty 1 fullStereo 1 singleHydrogenAtoms 1 specialAtomTypes 1} order {list: noAtoms singleAtom empty organic pseudoOrganic inorganic specialAtomTypes isotopes metalAtoms singleMetalAtoms singleHydrogenAtoms sizeLimit clusterCompound noStereo unspecifiedStereo partialStereo fullStereo meso enantiomer diastereomer neutralSalt organoMetallic metalComplex radical} exec 1 datatype: string} addprimarytag: { value: 1 datatype: string} structurepropname: { value: E_FICUS_STRUCTURE datatype: string} norm: { value: order {list: singleMetalAtoms singleHydrogenAtoms singleHalogenAtoms deleteSearchInfo radical functionalGroups hsaturation metalLigandBonds desalt deleteMetalComplexCenter resonance grabLargestFragment uncharge tautomer stereo deleteStereoInfo deleteIsotopeLabels} parameters {desalt 0 hsaturation 1 tautomer 1 singleHalogenAtoms 0 uncharge 0 deleteMetalComplexCenter 0 deleteSearchInfo 1 functionalGroups 1 singleMetalAtoms 0 radical 0 stereo 1 singleHydrogenAtoms 0 metalLigandBonds 1 resonance 1 deleteStereoInfo 0 deleteIsotopeLabels 0 grabLargestFragment 0} args {functionalGroups {} deleteMetalComplexCenter {} stereo {list: 1 1 0 0 0 0} singleMetalAtoms {} metalLigandBonds {} resonance {list: 1000 0 E_HASHY 1 1} deleteStereoInfo {} desalt {} tautomer {list: 1000 0 E_HASHY 0 0 0 0 1 0} uncharge {list: 0 E_HASHY} singleHalogenAtoms {} singleHydrogenAtoms {} radical {} deleteSearchInfo {} hsaturation {list: 0 0 {} !normal {noatoms nometals nospecial} {}} deleteIsotopeLabels {} grabLargestFragment {}} exec 1 datatype: string} secondarytag: { value: 01-xx datatype: string} csbasehash: { value: E_HASHISY datatype: string} post: { value: norm {parameters {deleteSearchInfo 1 functionalGroups 1 singleMetalAtoms 0 singleHalogenAtoms 0 radical 0 metalLigandBonds 1 tautomer 1 stereo 1 uncharge 0 deleteMetalComplexCenter 0 deleteStereoInfo 0 hsaturation 1 singleHydrogenAtoms 0 desalt 0 resonance 1 deleteIsotopeLabels 0 grabLargestFragment 0} exec 1} test {parameters {metalAtoms 1 organic 1 inorganic 1 pseudoOrganic 1 fullStereo 1 metalComplex 1 neutralSalt 1 specialAtomTypes 1 isotopes 1 enantiomer 1 sizeLimit 1 singleAtom 1 clusterCompound 1 organoMetallic 1 singleMetalAtoms 1 singleHydrogenAtoms 1 unspecifiedStereo 1 partialStereo 1 noStereo 1 radical 1 noAtoms 1 meso 1 empty 1 diastereomer 1} exec 1 switches {norm {parameters {deleteStereoInfo 0 desalt 0 radical 0 singleHydrogenAtoms 0 tautomer 0 singleHalogenAtoms 0 uncharge 0 resonance 0 deleteMetalComplexCenter 0 deleteIsotopeLabels 0 grabLargestFragment 0 deleteSearchInfo 0 functionalGroups 0 singleMetalAtoms 0 stereo 0 hsaturation 0 metalLigandBonds 0} exec 0} forcemagic 0 unreliable 0}} norm {cmds {true {resonance {} deleteStereoInfo {} desalt {} tautomer tautomer uncharge uncharge singleHalogenAtoms {} singleHydrogenAtoms {} radical {} deleteSearchInfo {} hsaturation {} deleteIsotopeLabels {} grabLargestFragment grabLargestFragment functionalGroups {} deleteMetalComplexCenter deleteMetalComplexCenter stereo {} singleMetalAtoms {} metalLigandBonds {}} false {deleteSearchInfo {} functionalGroups {} deleteIsotopeLabels {} grabLargestFragment {} singleMetalAtoms {} resonance {} metalLigandBonds {} radical {} hsaturation {} stereo {} deleteStereoInfo {} singleHalogenAtoms {} tautomer {} uncharge {} desalt {} singleHydrogenAtoms {} deleteMetalComplexCenter {}}}} test {cmds {true {enantiomer {} singleAtom {} meso {} metalComplex metalComplex specialAtomTypes specialAtomTypes radical radical noAtoms noAtoms singleMetalAtoms singleMetalAtoms pseudoOrganic {} empty empty inorganic inorganic metalAtoms {} organic {} isotopes {} fullStereo {} singleHydrogenAtoms singleHydrogenAtoms neutralSalt {} unspecifiedStereo {} noStereo noStereo clusterCompound clusterCompound diastereomer {} partialStereo {} organoMetallic {} sizeLimit sizeLimit} false {isotopes {} sizeLimit {} fullStereo {} organic {} clusterCompound {} neutralSalt {} diastereomer {} organoMetallic {} noStereo {} pseudoOrganic {} enantiomer {} specialAtomTypes {} singleAtom {} metalComplex metalComplex inorganic {} unspecifiedStereo {} singleMetalAtoms {} empty {} meso {} partialStereo {} metalAtoms metalAtoms radical radical noAtoms {} singleHydrogenAtoms {}}}} datatype: string} |
Tcl script | A_ELEMENT A_TYPE B_TYPE A_FORMAL_CHARGE A_ISOTOPE A_LABEL_STEREO B_LABEL_STEREO | atomchange bondchange stereochange atom bond | e_ficus_id.xpd | |||
| E_FICUS_STRUCTURE | structure | Standardized structure for FICUS computations. | Sitzmann, M., Fillipov, I.V., Nicklaus, M.C., SAR and QSAR in Environmental Research, 19:1, 1-9, 2008 (DOI 10.1080/10629360701843540) | A_ELEMENT A_TYPE B_TYPE A_FORMAL_CHARGE A_ISOTOPE A_LABEL_STEREO B_LABEL_STEREO | atomchange bondchange stereochange atom bond | |||||
| E_FICUU_ID | string | Sitzmann, M., Fillipov, I.V., Nicklaus, M.C., SAR and QSAR in Environmental Research, 19:1, 1-9, 2008 (DOI 10.1080/10629360701843540) | primarytag: { value: FICuu datatype: string} scope: { value: public datatype: string} addsecondarytag: { value: 1 datatype: string} addtag: { value: 1 datatype: string} tagseparator: { value: - datatype: string} debug: { value: 0 datatype: string} forcemagic: { value: 0 datatype: string} test: { value: parameters {partialStereo 1 neutralSalt 1 singleMetalAtoms 1 inorganic 1 enantiomer 1 unspecifiedStereo 1 singleAtom 1 diastereomer 1 radical 1 noAtoms 1 pseudoOrganic 1 organoMetallic 1 organic 1 metalComplex 1 isotopes 1 clusterCompound 1 metalAtoms 1 sizeLimit 1 meso 1 noStereo 1 empty 1 fullStereo 1 singleHydrogenAtoms 1 specialAtomTypes 1} order {list: noAtoms singleAtom empty organic pseudoOrganic inorganic specialAtomTypes isotopes metalAtoms singleMetalAtoms singleHydrogenAtoms sizeLimit clusterCompound noStereo unspecifiedStereo partialStereo fullStereo meso enantiomer diastereomer neutralSalt organoMetallic metalComplex radical} exec 1 datatype: string} addprimarytag: { value: 1 datatype: string} structurepropname: { value: E_FICUU_STRUCTURE datatype: string} norm: { value: order {list: singleMetalAtoms singleHydrogenAtoms singleHalogenAtoms deleteSearchInfo radical functionalGroups hsaturation metalLigandBonds desalt deleteMetalComplexCenter resonance grabLargestFragment uncharge tautomer stereo deleteStereoInfo deleteIsotopeLabels} parameters {desalt 0 hsaturation 1 tautomer 1 singleHalogenAtoms 0 uncharge 0 deleteMetalComplexCenter 0 deleteSearchInfo 1 functionalGroups 1 singleMetalAtoms 0 radical 0 stereo 1 singleHydrogenAtoms 0 metalLigandBonds 1 resonance 1 deleteStereoInfo 1 deleteIsotopeLabels 0 grabLargestFragment 0} args {functionalGroups {} deleteMetalComplexCenter {} stereo {list: 1 1 0 0 0 0} singleMetalAtoms {} metalLigandBonds {} resonance {list: 1000 0 E_HASHY 1 1} deleteStereoInfo {} desalt {} tautomer {list: 1000 0 E_HASHY 0 0 0 0 1 0} uncharge {list: 0 E_HASHY} singleHalogenAtoms {} singleHydrogenAtoms {} radical {} deleteSearchInfo {} hsaturation {list: 0 0 {} !normal {noatoms nometals nospecial} {}} deleteIsotopeLabels {} grabLargestFragment {}} exec 1 datatype: string} secondarytag: { value: 01-xx datatype: string} csbasehash: { value: E_HASHIY datatype: string} post: { value: norm {parameters {deleteSearchInfo 1 functionalGroups 1 singleMetalAtoms 0 singleHalogenAtoms 0 radical 0 metalLigandBonds 1 tautomer 1 stereo 1 uncharge 0 deleteMetalComplexCenter 0 deleteStereoInfo 1 hsaturation 1 singleHydrogenAtoms 0 desalt 0 resonance 1 deleteIsotopeLabels 0 grabLargestFragment 0} exec 1} test {parameters {metalAtoms 1 organic 1 inorganic 1 pseudoOrganic 1 fullStereo 1 metalComplex 1 neutralSalt 1 specialAtomTypes 1 isotopes 1 enantiomer 1 sizeLimit 1 singleAtom 1 clusterCompound 1 organoMetallic 1 singleMetalAtoms 1 singleHydrogenAtoms 1 unspecifiedStereo 1 partialStereo 1 noStereo 1 radical 1 noAtoms 1 meso 1 empty 1 diastereomer 1} exec 1 switches {norm {parameters {deleteStereoInfo 0 desalt 0 radical 0 singleHydrogenAtoms 0 tautomer 0 singleHalogenAtoms 0 uncharge 0 resonance 0 deleteMetalComplexCenter 0 deleteIsotopeLabels 0 grabLargestFragment 0 deleteSearchInfo 0 functionalGroups 0 singleMetalAtoms 0 stereo 0 hsaturation 0 metalLigandBonds 0} exec 0} forcemagic 0 unreliable 0}} norm {cmds {true {resonance {} deleteStereoInfo {} desalt {} tautomer tautomer uncharge uncharge singleHalogenAtoms {} singleHydrogenAtoms {} radical {} deleteSearchInfo {} hsaturation {} deleteIsotopeLabels {} grabLargestFragment grabLargestFragment functionalGroups {} deleteMetalComplexCenter deleteMetalComplexCenter stereo {} singleMetalAtoms {} metalLigandBonds {}} false {deleteSearchInfo {} functionalGroups {} deleteIsotopeLabels {} grabLargestFragment {} singleMetalAtoms {} resonance {} metalLigandBonds {} radical {} hsaturation {} stereo {} deleteStereoInfo {} singleHalogenAtoms {} tautomer {} uncharge {} desalt {} singleHydrogenAtoms {} deleteMetalComplexCenter {}}}} test {cmds {true {enantiomer {} singleAtom {} meso {} metalComplex metalComplex specialAtomTypes specialAtomTypes radical radical noAtoms noAtoms singleMetalAtoms singleMetalAtoms pseudoOrganic {} empty empty inorganic inorganic metalAtoms {} organic {} isotopes {} fullStereo {} singleHydrogenAtoms singleHydrogenAtoms neutralSalt {} unspecifiedStereo {} noStereo noStereo clusterCompound clusterCompound diastereomer {} partialStereo {} organoMetallic {} sizeLimit sizeLimit} false {isotopes {} sizeLimit {} fullStereo {} organic {} clusterCompound {} neutralSalt {} diastereomer {} organoMetallic {} noStereo {} pseudoOrganic {} enantiomer {} specialAtomTypes {} singleAtom {} metalComplex metalComplex inorganic {} unspecifiedStereo {} singleMetalAtoms {} empty {} meso {} partialStereo {} metalAtoms metalAtoms radical radical noAtoms {} singleHydrogenAtoms {}}}} datatype: string} |
Tcl script | A_ELEMENT A_TYPE B_TYPE A_FORMAL_CHARGE A_ISOTOPE A_LABEL_STEREO B_LABEL_STEREO | atomchange bondchange stereochange atom bond | e_ficuu_id.xpd | |||
| E_FICUU_STRUCTURE | structure | Sitzmann, M., Fillipov, I.V., Nicklaus, M.C., SAR and QSAR in Environmental Research, 19:1, 1-9, 2008 (DOI 10.1080/10629360701843540) | A_ELEMENT A_TYPE B_TYPE A_FORMAL_CHARGE A_ISOTOPE A_LABEL_STEREO B_LABEL_STEREO | atomchange bondchange stereochange atom bond | ||||||
| E_FICXX_ID | string | Sitzmann, M., Fillipov, I.V., Nicklaus, M.C., SAR and QSAR in Environmental Research, 19:1, 1-9, 2008 (DOI 10.1080/10629360701843540) | primarytag: { value: FICxx datatype: string} scope: { value: private datatype: string} addsecondarytag: { value: 1 datatype: string} addtag: { value: 1 datatype: string} tagseparator: { value: - datatype: string} debug: { value: 0 datatype: string} forcemagic: { value: 0 datatype: string} test: { value: parameters {partialStereo 1 neutralSalt 1 singleMetalAtoms 1 inorganic 1 enantiomer 1 unspecifiedStereo 1 singleAtom 1 diastereomer 1 radical 1 noAtoms 1 pseudoOrganic 1 organoMetallic 1 organic 1 metalComplex 1 isotopes 1 clusterCompound 1 metalAtoms 1 sizeLimit 1 meso 1 noStereo 1 empty 1 fullStereo 1 singleHydrogenAtoms 1 specialAtomTypes 1} order {list: noAtoms singleAtom empty organic pseudoOrganic inorganic specialAtomTypes isotopes metalAtoms singleMetalAtoms singleHydrogenAtoms sizeLimit clusterCompound noStereo unspecifiedStereo partialStereo fullStereo meso enantiomer diastereomer neutralSalt organoMetallic metalComplex radical} exec 1 datatype: string} addprimarytag: { value: 1 datatype: string} structurepropname: { value: E_FICXX_STRUCTURE datatype: string} norm: { value: order {list: singleMetalAtoms singleHydrogenAtoms singleHalogenAtoms deleteSearchInfo radical functionalGroups hsaturation metalLigandBonds desalt deleteMetalComplexCenter resonance grabLargestFragment uncharge tautomer stereo deleteStereoInfo deleteIsotopeLabels} parameters {desalt 0 hsaturation 1 tautomer 0 singleHalogenAtoms 0 uncharge 0 deleteMetalComplexCenter 0 deleteSearchInfo 1 functionalGroups 1 singleMetalAtoms 0 radical 0 stereo 1 singleHydrogenAtoms 0 metalLigandBonds 1 resonance 1 deleteStereoInfo 0 deleteIsotopeLabels 0 grabLargestFragment 0} args {functionalGroups {} deleteMetalComplexCenter {} stereo {list: 1 1 0 0 0 0} singleMetalAtoms {} metalLigandBonds {} resonance {list: 1000 0 E_HASHY 1 1} deleteStereoInfo {} desalt {} tautomer {list: 1000 0 E_HASHY 0 0 0 0 1 0} uncharge {list: 0 E_HASHY} singleHalogenAtoms {} singleHydrogenAtoms {} radical {} deleteSearchInfo {} hsaturation {list: 0 0 {} !normal {noatoms nometals nospecial} {}} deleteIsotopeLabels {} grabLargestFragment {}} exec 1 datatype: string} secondarytag: { value: 01-xx datatype: string} csbasehash: { value: E_HASHIY datatype: string} post: { value: norm {parameters {deleteSearchInfo 1 functionalGroups 1 singleMetalAtoms 0 singleHalogenAtoms 0 radical 0 metalLigandBonds 1 tautomer 0 stereo 1 uncharge 0 deleteMetalComplexCenter 0 deleteStereoInfo 0 hsaturation 1 singleHydrogenAtoms 0 desalt 0 resonance 1 deleteIsotopeLabels 0 grabLargestFragment 0} exec 1} test {parameters {metalAtoms 1 organic 1 inorganic 1 pseudoOrganic 1 fullStereo 1 metalComplex 1 neutralSalt 1 specialAtomTypes 1 isotopes 1 enantiomer 1 sizeLimit 1 singleAtom 1 clusterCompound 1 organoMetallic 1 singleMetalAtoms 1 singleHydrogenAtoms 1 unspecifiedStereo 1 partialStereo 1 noStereo 1 radical 1 noAtoms 1 meso 1 empty 1 diastereomer 1} exec 1 switches {norm {parameters {deleteStereoInfo 0 desalt 0 radical 0 singleHydrogenAtoms 0 tautomer 0 singleHalogenAtoms 0 uncharge 0 resonance 0 deleteMetalComplexCenter 0 deleteIsotopeLabels 0 grabLargestFragment 0 deleteSearchInfo 0 functionalGroups 0 singleMetalAtoms 0 stereo 0 hsaturation 0 metalLigandBonds 0} exec 0} forcemagic 0 unreliable 0}} norm {cmds {true {resonance {} deleteStereoInfo {} desalt {} tautomer tautomer uncharge uncharge singleHalogenAtoms {} singleHydrogenAtoms {} radical {} deleteSearchInfo {} hsaturation {} deleteIsotopeLabels {} grabLargestFragment grabLargestFragment functionalGroups {} deleteMetalComplexCenter deleteMetalComplexCenter stereo {} singleMetalAtoms {} metalLigandBonds {}} false {deleteSearchInfo {} functionalGroups {} deleteIsotopeLabels {} grabLargestFragment {} singleMetalAtoms {} resonance {} metalLigandBonds {} radical {} hsaturation {} stereo {} deleteStereoInfo {} singleHalogenAtoms {} tautomer {} uncharge {} desalt {} singleHydrogenAtoms {} deleteMetalComplexCenter {}}}} test {cmds {true {enantiomer {} singleAtom {} meso {} metalComplex metalComplex specialAtomTypes specialAtomTypes radical radical noAtoms noAtoms singleMetalAtoms singleMetalAtoms pseudoOrganic {} empty empty inorganic inorganic metalAtoms {} organic {} isotopes {} fullStereo {} singleHydrogenAtoms singleHydrogenAtoms neutralSalt {} unspecifiedStereo {} noStereo noStereo clusterCompound clusterCompound diastereomer {} partialStereo {} organoMetallic {} sizeLimit sizeLimit} false {isotopes {} sizeLimit {} fullStereo {} organic {} clusterCompound {} neutralSalt {} diastereomer {} organoMetallic {} noStereo {} pseudoOrganic {} enantiomer {} specialAtomTypes {} singleAtom {} metalComplex metalComplex inorganic {} unspecifiedStereo {} singleMetalAtoms {} empty {} meso {} partialStereo {} metalAtoms metalAtoms radical radical noAtoms {} singleHydrogenAtoms {}}}} datatype: string} |
Tcl script | A_ELEMENT A_TYPE B_TYPE A_FORMAL_CHARGE A_ISOTOPE A_LABEL_STEREO B_LABEL_STEREO | atomchange bondchange stereochange atom bond | e_ficxx_id.xpd | |||
| E_FICXX_STRUCTURE | structure | Sitzmann, M., Fillipov, I.V., Nicklaus, M.C., SAR and QSAR in Environmental Research, 19:1, 1-9, 2008 (DOI 10.1080/10629360701843540) | A_ELEMENT A_TYPE B_TYPE A_FORMAL_CHARGE A_ISOTOPE A_LABEL_STEREO B_LABEL_STEREO | atomchange bondchange stereochange atom bond | ||||||
| E_FILE | compound | Info about the file the molecule was read from | filename string startrecord int endrecord int line int format string offset int64 length int |
atomchange bondchange merge | ||||||
| E_FLEXNOVO_FILTER | boolean | Test whether structure passes the FlexNovo smarts pattern filter (which removes reactive or non-druglike componds) | patternfile: { value: flexnovo_exclude.sma datatype: diskfile constraints: readable} trace: { value: 0 datatype: boolean} |
Tcl script | atomchange bondchange atom bond | e_flexnovo_filter.xpd | ||||
| E_FLG_FICTS_UNRELIABLE | boolean | Sitzmann, M., Fillipov, I.V., Nicklaus, M.C., SAR and QSAR in Environmental Research, 19:1, 1-9, 2008 (DOI 10.1080/10629360701843540) | atomchange bondchange stereochange atom bond | |||||||
| E_FLG_FICTU_UNRELIABLE | boolean | Sitzmann, M., Fillipov, I.V., Nicklaus, M.C., SAR and QSAR in Environmental Research, 19:1, 1-9, 2008 (DOI 10.1080/10629360701843540) | atomchange bondchange stereochange atom bond | |||||||
| E_FLG_FICUS_UNRELIABLE | boolean | Sitzmann, M., Fillipov, I.V., Nicklaus, M.C., SAR and QSAR in Environmental Research, 19:1, 1-9, 2008 (DOI 10.1080/10629360701843540) | atomchange bondchange stereochange atom bond | |||||||
| E_FLG_FICUU_UNRELIABLE | boolean | Sitzmann, M., Fillipov, I.V., Nicklaus, M.C., SAR and QSAR in Environmental Research, 19:1, 1-9, 2008 (DOI 10.1080/10629360701843540) | atomchange bondchange stereochange atom bond | |||||||
| E_FLG_UUUTS_UNRELIABLE | boolean | Sitzmann, M., Fillipov, I.V., Nicklaus, M.C., SAR and QSAR in Environmental Research, 19:1, 1-9, 2008 (DOI 10.1080/10629360701843540) | atomchange bondchange stereochange atom bond | |||||||
| E_FLG_UUUTU_UNRELIABLE | boolean | Sitzmann, M., Fillipov, I.V., Nicklaus, M.C., SAR and QSAR in Environmental Research, 19:1, 1-9, 2008 (DOI 10.1080/10629360701843540) | atomchange bondchange stereochange atom bond | |||||||
| E_FLG_UUUUS_UNRELIABLE | boolean | Sitzmann, M., Fillipov, I.V., Nicklaus, M.C., SAR and QSAR in Environmental Research, 19:1, 1-9, 2008 (DOI 10.1080/10629360701843540) | atomchange bondchange stereochange atom bond | |||||||
| E_FLG_UUUUU_UNRELIABLE | boolean | Sitzmann, M., Fillipov, I.V., Nicklaus, M.C., SAR and QSAR in Environmental Research, 19:1, 1-9, 2008 (DOI 10.1080/10629360701843540) | atomchange bondchange stereochange atom bond | |||||||
| E_FORMAT | string | Original format in data file (I/O module name) | never | |||||||
| E_FORMULA | string | Molecular formula of ensemble | usecharges: { value: 0 datatype: string} format: { value: ascii datatype: string} useimplicith: { value: 1 datatype: string} usequeryatoms: { value: 0 datatype: string} |
(builtin) | A_ISOTOPE | atomchange merge | ||||
| E_FRAGMENT_COMPOSITION | intvector | Get composition of structure using a user-defined hierarchical fragment database with SMILES/SMARTS fragment definition. Larger fragments, and fragments with more specialized attributes have precedence. Multiple solutions may be found and are attached as E_FRAGMENT_COMPOSITION/n. The result is an int vector with the counts for each fragment in their definition file order. The default fragment set is for the UNIFAC method. Various other fragment files for Joback, Lyderson, Sedlbaur methods are also supplied in the data directory. |
fragfile: { value: unifac.sma datatype: diskfile constraints: readable} explicith: { value: 0 datatype: boolean} debug: { value: 0 datatype: boolean} |
Tcl script | A_TYPE A_ELEMENT B_TYPE B_ORDER | atomchange bondchange merge hadd | e_fragment_composition.xpd | |||
| E_FRAGMENT_COUNT | dictionary | Counts of all (filtered) fragments the structure, The result is a dictionary with SMARTS keys, and occurence count values. | minsize: { value: 3 minvalue: 1 maxvalue: 99 datatype: int} maxsize: { value: 3 minvalue: 1 maxvalue: 99 datatype: int} hydrogen: { value: 0 datatype: boolean} mode: { value: absolute description: In relative mode, scale to total count 1 enumeration: absolute:relative datatype: int} keeparo: { value: 0 description: If set, lock A_ISAROMATIC datatype: boolean} aroquery: { value: 0 description: If set, rewrite SMARTS to match only aromatic fragments where applicable datatype: boolean} |
Tcl script | A_TYPE A_ELEMENT B_TYPE B_ORDER | atomchange bondchange merge atom bond | e_fragment_count.xpd | |||
| E_FRAGMENT_TREE_CUTS | datatree | Topological fragment hierarchy tree - cut bond classification | A_TYPE A_ELEMENT B_TYPE B_ORDER | atomchange bondchange | ||||||
| E_FRAGMENT_TREE_HASH | datatree | Topological fragment hierarchy tree - hashcodes | maxcuts: { value: 3 datatype: int} minsize: { value: 2 datatype: int} cutphenyl: { value: 0 datatype: boolean} queryhash: { value: 0 datatype: boolean} dupcheck: { value: hierarchical enumeration: hierarchical:global datatype: string} |
Compiled C module | A_TYPE A_ELEMENT B_TYPE B_ORDER | atomchange bondchange | mod_e_fragment_tree_hash.so | |||
| E_FRAGMENT_TREE_LABELS | datatree | Topological fragment hierarchy tree - atom labels of fragments | A_TYPE A_ELEMENT B_TYPE B_ORDER | atomchange bondchange | ||||||
| E_FRAGMENT_TREE_SMARTS | datatree | Topological fragment hierarchy tree - SMARTS of fragments | A_TYPE A_ELEMENT B_TYPE B_ORDER | atomchange bondchange | ||||||
| E_FRAGMENT_TREE_TABLE | table | Summary of fragmentation routes | Tcl script | E_FRAGMENT_TREE_HASH E_FRAGMENT_TREE_CUTS E_FRAGMENT_TREE_LABELS | atomchange bondchange | e_fragment_tree_table.xpd | ||||
| E_FREQUENCY | string | Generic computed frequencies. Used in Gaussian Archive I/O module | atomchange bondchange merge 3drelative hadd | |||||||
| E_FSP3 | double | Carbon flatness score - the ratio of SP3 hybridized carbon atoms to total carbon atom count | Lovering, F. et al., J.Med.Chem. 2009, 52, 6752-6756 | Compiled C module | A_TYPE A_ELEMENT A_HYBRIDIZATION | atomchange bondchange atom bond | mod_e_fsp3.so | |||
| E_GC | compound | Measured gas-chromatograph spectrum. Used for example in JCAMP I/O module | experimental boolean origin string author string date int spectrometer string parameters string reference string purity float source string procedure string resolution double firstx double lastx double xfactor double yfactor double xunit string yunit string {#points} int spectrum floatvector |
atomchange bondchange | ||||||
| E_GDL_ID | int | Substance ID in German hazardous chemicals database (http://www.gefahrstoff-info.de) | Tcl script | E_CAS | atomchange bondchange atom bond | e_gdl_id.xpd | ||||
| E_GDL_URL | url | Data display URL in German hazardous chemicals database (http://www.gefahrstoff-info.de) | Tcl script | E_GDL_ID | atomchange bondchange atom bond | e_gdl_url.xpd | ||||
| E_GENETOX_URL | url | Display URL in EPA GENE-TOX (Genetic Toxicology Data Bank, https://toxnet.nlm.nih.gov/newtoxnet/genetox.htm) | Tcl script | E_CAS | atomchange bondchange stereochange atom bond | e_genetox_url.xpd | ||||
| E_GENOTOXIC_ALERTS | shortvector | Check for problematic potentially genotoxic groups | CE&N Sep 27, 2010 p16ff | patternfile: { value: genotoxic.sma datatype: diskfile constraints: readable}
|
Tcl script | atomchange bondchange merge hadd mol atom bond ring | e_genotoxic_alerts.xpd | |||
| E_GEOOPT_METHOD | string | Geometry optimization method description string. Used for example in the Gaussian Input, Gaussian Archive and Sharc file forms. | atomchange bondchange 3drelative 3dabsolute | |||||||
| E_GI50 | compound | GI50 tumor screen data | concunit shortstring lcconc float panel shortstring cell string panelnumber short cellnumber short nlog_gi50 float ntest_this short ntest_max short |
atomchange bondchange merge | ||||||
| E_GIF | diskfile (switchable between string blob diskfile url) |
A 2D-plot of the structure as a GIF or PNG file | width: { value: 180 datatype: int} height: { value: 180 datatype: int} asymbol: { value: xsymbol enumeration: none,no:symbol,sym,normal:xsymbol,xsym,extended,expanded:label:index,idx:box:compact,text,super,superatom:residue datatype: int} bonds: { value: 8 datatype: int} hsymbol: { value: special enumeration: none,no,suppress:special,normal,hetero:all,yes datatype: int} csymbol: { value: special enumeration: none,no:special,normal:all,yes datatype: int} bgcolor: { value: transparent datatype: color} border: { value: 12 datatype: int} bondcolor: { value: black comment: Cannot be color datatype because we recognize 'atomsplit' value datatype: string} atomcolor: { value: black description: A color name, the magic value "element", or a atom color property. "element" uses the default color defined in the element table datatype: string} hcolor: { value: {} datatype: color constraints: emptycolor} header: { value: {} datatype: string} footer: { value: {} datatype: string} headercolor: { value: black datatype: color} footercolor: { value: black datatype: color} interlace: { value: 1 datatype: boolean} commenttype: { value: property enumeration: none:text:property,prop datatype: int} comment: { value: E_NAME datatype: string} structure: { value: none datatype: string} metadata: { value: 1 datatype: boolean} filename: { value: {} datatype: diskfile constraints: writeable} highlightcolor: { value: red datatype: color} secondarycolor: { value: #00D000 datatype: color} highlightbonds: { value: {} datatype: intvector} highlightatoms: { value: {} datatype: intvector} httpheader: { value: 0 description: whether to prefix HTTP header (0=no,1:standard,2=with 200 result code) minvalue: 0 maxvalue: 2 datatype: int} crop: { value: -1 datatype: int} wedges: { value: 1 datatype: boolean} wiggles: { value: all enumeration: none:sp3:sp2:all datatype: int} format: { value: gif enumeration: gif:png:png8:bmp datatype: int} markcolor: { value: blue datatype: color} logofile: { value: {} datatype: diskfile constraints: existing readable} logoscale: { value: 1 datatype: double} dashes: { value: 1 datatype: boolean} headerproperty: { value: {} datatype: string} footerproperty: { value: {} datatype: string} bead: { value: 1 datatype: boolean} beadcolor1: { value: black datatype: color} beadcolor2: { value: gray60 datatype: color} showcharge: { value: 1 datatype: boolean} showradical: { value: 1 datatype: boolean} showstereo: { value: 1 datatype: boolean} font: { value: arialn datatype: string} symbolfontsize: { value: -1 datatype: int} annotationfontsize: { value: -1 datatype: int} antialiasing: { value: 3 minvalue: 0 maxvalue: 3 datatype: int} highlightgroups: { value: {} datatype: intvector} boxgroups: { value: {} datatype: intvector} groupcolor: { value: purple datatype: color} showisotope: { value: 1 datatype: boolean} isotopemapping: { value: none datatype: string} showstereoh: { value: 1 datatype: boolean} suppressedmols: { value: {} datatype: intvector} linewidth: { value: 1.4 datatype: double} showempty: { value: 0 datatype: boolean} voronoicolorproperty: { value: {} datatype: string constraints: property} voronoifilter: { value: {} datatype: string constraints: filtername} showmapping: { value: 0 datatype: boolean} showstereogroups: { value: 0 datatype: boolean} annotationcolor: { value: {} datatype: color} showchirality: { value: none enumeration: none:simple:extended datatype: int} frame: { value: 0 datatype: boolean} framecolor: { value: black datatype: diskfile} linespacing: { value: 2.0 datatype: double} headerfontsize: { value: -1 datatype: int} footerfontsize: { value: -1 datatype: int} circlecolor: { value: {} description: A property name or a color name datatype: string constraints: colorproperty} circlefilter: { value: {} datatype: string} circleatoms: { value: {} datatype: intvector} atomselectionmapping: { value: none enumeration: none:highlight:circle datatype: int} wigglecount: { value: 6 datatype: int} wiggleamplitude: { value: 2.0 datatype: double} fixiepngsize: { value: 1 datatype: string} rawcoordinates: { value: 0 datatype: boolean} checkintersection: { value: 0 datatype: boolean} usegrouplabels: { value: 0 datatype: boolean} usesubscripts: { value: 1 datatype: boolean} contractgroups: { value: 0 datatype: boolean} downloadfilename: { value: {} datatype: string} colormode: { value: color datatype: string} leftfooter: { value: {} datatype: string} rightfooter: { value: {} datatype: string} leftheader: { value: {} datatype: string} rightheader: { value: {} datatype: string} saverendercoordinates: { value: 0 datatype: boolean} labelproperty: { value: {} datatype: string} labelfilterset: { value: !hydrogen datatype: string constraints: filterlist} labelcolor: { value: darkgreen datatype: color} labelformat: { value: <%s> datatype: string} forcecarbonsymbol: { value: 1 description: If set, an element symbol is rendered if a carbon atom has a circle background highlight, etc. datatype: boolean} |
Compiled C module | A_XY A_TYPE B_TYPE B_ORDER A_COLOR B_FLAGS A_FLAGS A_ANNOTATION | atomchange bondchange stereochange groupchange merge hadd | mod_e_gif.so | |||
| E_GOLM_URL | url | Data display link into the GOLM metabolome database (http://gmd.mpimp-golm.mpg.de) | Tcl script | E_STDINCHIKEY | atomchange bondchange stereochange atom bond | e_golm_url.xpd | ||||
| E_GOOGLE_SCHOLAR_URL | url | URL for data in the Google Scholar search engine | Tcl script | E_STDINCHI E_STDINCHIKEY E_CAS | atomchange bondchange stereochange atom bond | e_google_scholar_url.xpd | ||||
| E_GPCR_LIGAND_LIKENESS | compound | GPCR ligand structural likeness, computed as maximum similarity score with standard similarity property E_SCREEN on a diverse 1K cpds subset of the GLL database. | Gatica, Cavasotto, J. Chem. Inf. Model. 2011, 52, 1 | similarity byte structure structure |
Tcl script | E_SCREEN | atomchange bondchange atom bond | e_gpcr_ligand_likeness.xpd | ||
| E_GRAPHICS_TEXT | stringvector | Head- and footline for graphics plots | never | |||||||
| E_GRID_VOLUME | floatvolume | Generic floating-point volume grid data. Used for exmapl ein the STF and Gausscube file I/O modules. | atomchange bondchange stereochange merge 3drelative hadd atom bond ring | |||||||
| E_GROUP_COUNT | int | Number of groups defined for the ensemble | Compiled C module | atomchange bondchange groupchange atom bond | mod_e_group_count.so | |||||
| E_GUIDETOPHARMACOLOGY_ID | int | Guide to Pharmacology database ID (www.guidetopharmacology.org, www..iuphar-db.org) | Tcl script | E_SMILES | atomchange bondchange stereochange merge | e_guidetopharmacology_id.xpd | ||||
| E_GUIDETOPHARMACOLOGY_URL | url | Guide to Pharmacology database record display URL (www.guidetopharmacology.org, was www.iuphar-db.org) | Tcl script | E_GUIDETOPHARMACOLOGY_ID | atomchange bondchange stereochange merge | e_guidetopharmacology_url.xpd | ||||
| E_HALIDE_FRACTION | double | Fraction of molecular weight contributed by halogen atoms | Compiled C module | A_TYPE A_ELEMENT | atomchange bondchange atom bond | mod_e_halide_fraction.so | ||||
| E_HASH | uint64 | Basic ensemble hashcode | (builtin) | M_HASHGROUP M_HASH | atomchange bondchange merge | |||||
| E_HASH128 | uint128 | Perturbed ensemble hashcode, extended to 128 bits | Compiled C module | M_HASHGROUP128 M_HASH128 | atomchange bondchange merge hadd | mod_e_hash128.so | ||||
| E_HASHGROUP_COUNT_A | intvector | Population of basic atom hash groups | (builtin) | A_HASH | atomchange bondchange merge hadd | |||||
| E_HASHGROUP_COUNT_AI | intvector | Population of isotope atom hash groups | (builtin) | A_ISOTOPE_HASH | atomchange bondchange merge hadd | |||||
| E_HASHGROUP_COUNT_AIS | intvector | Population of isotopic stereospecific basic atom hash groups | (builtin) | A_ISOTOPE_STEREO_HASH | atomchange bondchange merge hadd | |||||
| E_HASHGROUP_COUNT_AS | intvector | Population of stereospecific basic atom hash groups | (builtin) | A_STEREO_HASH | atomchange bondchange merge hadd | |||||
| E_HASHGROUP_COUNT_B | intvector | Population of bond hash groups | (builtin) | B_HASH | atomchange bondchange merge | |||||
| E_HASHGROUP_COUNT_BS | intvector | Population of stereospecific bond hash groups | (builtin) | B_STEREO_HASH | atomchange bondchange merge | |||||
| E_HASHGROUP_COUNT_M | intvector | Population of perturbed molecule hash groups | (builtin) | M_HASHY | atomchange bondchange merge hadd | |||||
| E_HASHGROUP_COUNT_MI | intvector | Population of isotopic perturbed molecule hash groups | (builtin) | M_HASHIY | atomchange bondchange merge hadd | |||||
| E_HASHGROUP_COUNT_MIS | intvector | Population of isotopic stereospecific perturbed molecule hash groups | (builtin) | M_HASHISY | atomchange bondchange merge hadd | |||||
| E_HASHGROUP_COUNT_MS | intvector | Population of stereospecifc perturbed molecule hash groups | (builtin) | M_HASHSY | atomchange bondchange merge hadd | |||||
| E_HASHISY | uint64 | Perturbed isotope stereo ensemble hashcode | (builtin) | M_ISOTOPE_STEREO_HASHGROUP_Y M_HASHISY | atomchange bondchange merge hadd | |||||
| E_HASHIY | uint64 | Perturbed isotope ensemble hashcode | (builtin) | M_ISOTOPE_HASHGROUP_Y M_HASHIY | atomchange bondchange merge hadd | |||||
| E_HASHS | uint64 | Stereospecific basic ensemble hashcode | (builtin) | M_STEREO_HASHGROUP M_HASHS | atomchange bondchange merge | |||||
| E_HASHSY | uint64 | Perturbed stereospecific ensemble hashcode | useisotope: { value: 0 datatype: string}
|
(builtin) | M_STEREO_HASHGROUP_Y M_HASHSY | atomchange bondchange merge hadd | ||||
| E_HASHY | uint64 | Perturbed ensemble hashcode | useisotope: { value: 0 datatype: string}
|
(builtin) | M_HASHGROUP_Y M_HASHY | atomchange bondchange merge hadd | ||||
| E_HEAT_OF_FORMATION | float | Measured or computed Heat of Formation. The computation procedure tries to run a simple VAMP job. This proeprties acts as the cornerstone for a standard set of QM-related properties via windfall/indirect property definition relationships. | filename: { value: {} datatype: string} prgpath: { value: /usr/local/bin/vamp datatype: string} method: { value: AM1 datatype: string} |
Tcl script | A_XYZ | atomchange bondchange | e_heat_of_formation.xpd | |||
| E_HEAVY_ATOM_COUNT | int | Number of non-hydrogen atoms in the ensemble | Compiled C module | A_ELEMENT A_TYPE | atomchange bondchange mol atom bond | mod_e_heavy_atom_count.so | ||||
| E_HEAVY_BOND_COUNT | int | Count of VB bonds which do not contain hydrogen | Compiled C module | A_TYPE A_ELEMENT B_TYPE | atomchange | mod_e_heavy_bond_count.so | ||||
| E_HETEROATOM_CARBON_RATIO | double | Number of hetero atoms devided by number of carbon atoms | Compiled C module | A_TYPE A_ELEMENT | atomchange bondchange atom bond | mod_e_heteroatom_carbon_ratio.so | ||||
| E_HETEROATOM_COUNT | int | Number of hetero (not C or H) atoms in the ensemble | Compiled C module | A_TYPE A_ELEMENT | atomchange bondchange atom bond | mod_e_heteroatom_count.so | ||||
| E_HISTORY | compoundvector | Record history | program string version string patchlevel string pgmdate date user string date date machine string |
never | ||||||
| E_HIT2LEAD_ID | int | Catalog number from www.hit2lead.com (aka ChemBridge) | database: { value: SC description: Database to query (screening compounds or building blocks) enumeration: SC:BB datatype: int}
|
Tcl script | E_SDF_STRING | atomchange bondchange atom bond | e_hit2lead_id.xpd | |||
| E_HIT2LEAD_URL | url | Display URL for a hit2lead (www.hit2lead.com, aka ChemBridge) database entry | database: { value: SC description: Database to query (screening compounds or building blocks) enumeration: SC:BB datatype: int}
|
Tcl script | E_HIT2LEAD_ID | atomchange bondchange atom bond | e_hit2lead_url.xpd | |||
| E_HMDB_ID | string | ID of structure in the HMDB database (www.hmdb.ca) | Tcl script | E_SMILES | atomchange bondchange atom bond | e_hmdb_id.xpd | ||||
| E_HMDB_URL | url | Display URL of structure in the HMDB database (www.hmdb.ca) | Tcl script | E_HMDB_ID | atomchange bondchange atom bond | e_hmdb_url.xpd | ||||
| E_HSDB_URL | url | Display URL for the HSDB (http://toxnet.nlm.nih.gov/newtoxnet/hsdb.htm) database | Tcl script | E_CAS | atomchange bondchange atom bond | e_hsdb_url.xpd | ||||
| E_HYDROGEN_BOND_CENTER_COUNT | int | Number of heavy atoms that can act as hydrogen donor or acceptor | Tcl script | A_HYDROGEN_BONDING | never | e_hydrogen_bond_center_count.xpd | ||||
| E_HYDROGEN_COMPLETE | boolean | Boolean flag indicating whether there are no open hydrogen sites | Compiled C module | A_HYDROGENS_NEEDED | atomchange bondchange hadd atom bond | mod_e_hydrogen_complete.so | ||||
| E_IC50 | compound | IC50 aids screen data | concentration float concunit shortstring flag shortstring icconc float nexperiments short |
atomchange bondchange merge | ||||||
| E_ICSC_CARD_ID | shortstring | International Chemical Safety Cards ID (from www.ilo.org) | Tcl script | E_CAS | atomchange bondchange atom bond | e_icsc_card_id.xpd | ||||
| E_ICSC_CARD_URL | url | International Chemical Safety Cards display URL (from www.ilo.org) | Tcl script | E_ICSC_CARD_ID | atomchange bondchange atom bond | e_icsc_card_url.xpd | ||||
| E_IDENT | string | Short ensemble identification string | (builtin) | never | ||||||
| E_IDENTIFIER_NORM_DATASET | dataset | Debug property for FICUS suite | atomchange bondchange atom bond | |||||||
| E_IDENTIFIER_NORM_EXEMPTION_LIST | stringvector | Sitzmann, M., Fillipov, I.V., Nicklaus, M.C., SAR and QSAR in Environmental Research, 19:1, 1-9, 2008 (DOI 10.1080/10629360701843540) | atomchange bondchange stereochange atom bond | |||||||
| E_IDTF_MODEL | blob (switchable between blob diskfile mapfile) |
3D structure model in Intel IDTF format | style: { value: spacefill enumeration: ballstick:capped:spacefill:wireframe:all datatype: string} filename: { value: {} datatype: diskfile constraints: writeable} bondradius: { value: 15 datatype: double} ignoreh: { value: 0 datatype: boolean} vdwscaling: { value: 25 datatype: double} atomhighlightcolor: { value: red datatype: color} highlightatoms: { value: {} datatype: intvector} bondhighlightcolor: { value: red datatype: color} highlightbonds: { value: {} datatype: intvector} showbondorder: { value: 0 datatype: boolean} bondcolor: { value: atomsplit datatype: string} structure: { value: 0 datatype: boolean} showlabel: { value: 0 datatype: boolean} labelcolor: { value: purple datatype: color} addlights: { value: 0 datatype: boolean} addview: { value: 0 datatype: boolean} glossfactor: { value: 75 datatype: double} labelsize: { value: 15 datatype: int} tesselation: { value: octahedron 4 20 20 datatype: string} dynamictesselation: { value: 1 datatype: boolean} downloadfilename: { value: {} datatype: string} suppressedatoms: { value: {} datatype: intvector} suppressedbonds: { value: {} datatype: intvector} |
Compiled C module | A_XYZ A_ELEMENT B_TYPE B_ORDER B_FLAGS A_FLAGS A_COLOR B_COLOR | atomchange bondchange stereochange merge 3drelative 3dabsolute hadd | mod_e_idtf_model.so | |||
| E_IMAGEMAP | string | HTML imagemap associated with a GIF/PNG image (property E_GIF) | name: { value: {} datatype: string} mode: { value: mol enumeration: atom:bond:mol datatype: int} target: { value: {} datatype: string} url: { value: {} datatype: string} title: { value: {} datatype: string} |
Tcl script | E_GIF | never | e_imagemap.xpd | |||
| E_IMAGE_SCALING | doublevector | 2D coordinate scaling information (A_XY) for rendering in an image of specified size. The fields are the coordinate scale factor, the x and y offsets (these three values place the drawing into the 0..w/h-1 pixel area), the relative scale factor for the structure needed to fit into the "bonds" size box (1.0 if it fits into the box), and suggested symbol and annotation font sizes in points. | factor double xoffset double yoffset double scale double symbolfontsize double annotationfontsize double |
width: { value: 25ß description: Image width (pixel) datatype: int} height: { value: 250 description: Image height (pixel) datatype: int} border: { value: 10 description: Image border (pixel) minvalue: 0 maxvalue: 100 datatype: int} bonds: { value: 8 description: Number of standard bonds across image minvalue: 1 maxvalue: 20 datatype: int} hidefragment: { value: {} description: Structure fragment to hide and exclude from computation datatype: structure} |
Compiled C module | A_XY | atomchange bondchange atom bond | mod_e_image_scaling.so | ||
| E_INACTIVE_AIDSET | intvector | Set of PubChem assay IDs testing this compound as inactive | Tcl script | E_CID | atomchange bondchange stereochange | e_inactive_aidset.xpd | ||||
| E_INCHI | string | First release InChI identifier (E_STDINCHI following the current standard is preferred) | options: { value: DONOTADDH FIXEDH RECMET NOWARNINGS description: Set of default option words as used in the original NIST software comment: Supported option words: MISMATCHISERROR OUTERRINCHI Key XHash1 XHash2 SNON NEWPSOFF DONOTADDH LooseTSACheck SREL ChiralFlagOFF SUU SLUUD FIXEDH RECMET KET 15T PT_22_00 PT_16_00 PT_06_00 PT_39_00 LargeMolecules Polymers Polymers105 NPZz NoWarnings FoldCRU FoldSRU FrameShift: NoFrameShift NoEdits SATZZ FNUDOFF FixSp3bugOFF FBOFF FB2OFF SPXYZOFF SASXYZOFF Polymers105+. Record processing and output options NOLABELS SAVEOPT AUXNONE NoInCXhI INPAUX START: END: RECORD: MergeHash have no effect. datatype: string constraints: list} fakemetalbonds: { value: 0 description: If set, all bonds to metals are encoded as simple single VB bonds, regardless of their real bond type datatype: boolean} stereoperception: { value: 1 description: If set, perceive stereochemistry, if no, use what is presently set on the structure datatype: boolean} stereomode: { value: sabs enumeration: snon,none:sabs,abs,absolute:srel,rel,relative:srac,rac,racemic,racemate datatype: int} autohadd: { value: 1 description: If set, implicitly add a standard set of hydrogens, without actually modifying the structure datatype: boolean} prefix: { value: 1 description: If set, include InChI= prefix in output datatype: boolean} stripstereolayer: { value: 0 datatype: boolean} stripisotopelayer: { value: 0 datatype: boolean} stripfixedhlayer: { value: 0 description: If set, the /f layer *and* the following /h and /q layers are stripped datatype: boolean} stripreconnectlayer: { value: 0 datatype: boolean} stripchargelayer: { value: 0 datatype: boolean} |
Compiled C module | B_ORDER B_TYPE A_TYPE A_ISOTOPE B_FLAGS A_FORMAL_CHARGE B_STEREOGENIC B_ISAROMATIC A_ALLENE | atomchange bondchange stereochange merge atom bond | mod_e_inchi.so | |||
| E_INCHIKEY | string | Hash of InChI string | prefix: { value: 1 datatype: boolean}
|
Compiled C module | E_INCHI | atomchange bondchange stereochange atom bond | mod_e_inchikey.so | |||
| E_INCHI_AUXINFO | string | InChI auxiliary information, as defined in the InChI file format. This data is also automatically computed as windfall when requesting E_INCHI | B_ORDER B_TYPE A_TYPE A_ISOTOPE B_FLAGS A_FORMAL_CHARGE | atomchange bondchange stereochange hadd atom bond | ||||||
| E_INPUTDATE | date | Time stamp for molecule | Tcl script | never | e_inputdate.xpd | |||||
| E_IONIZATION_POTENTIAL | float | Measured or computed Ionization potential. This can be computed indirectly via E_HEAT_OF_FORMATION by a VAMP run. | A_XYZ | atomchange bondchange | ||||||
| E_IRIS_URL | url | Display URL in EPA IRIS (Integrated Risk Information System, https://toxnet.nlm.nih.gov/newtoxnet/iris.htm) | Tcl script | E_CAS | atomchange bondchange stereochange atom bond | e_iris_url.xpd | ||||
| E_IRSPECTRUM | compound | Measured or computed IR spectrum. The compuation function attempts to get an IR spectrum from the NIST WebBook, or run a simple VAMP job depending on the "source" parameter, which should be set to "NIST" or "VAMP". | experimental boolean origin string author string date datetime spectrometer string parameters string specificparams dictionary page string reference string purity float source string description string solvent string procedure string resolution double firstx double lastx double xfactor double yfactor double xunit string yunit string {#points} int coding string spectrum xyvector peaks floatvector peakshape stringvector peakintensity floatvector peakname stringvector |
filename: { value: {} description: temporary job file datatype: diskfile constraints: writeable} prgpath: { value: /usr/local/bin/vamp datatype: diskfile constraints: existing} method: { value: AM1 datatype: string} freqfactor: { value: 0.98 datatype: string} cofreqfactor: { value: 0.90 datatype: string} source: { value: NIST enumeration: NIST:VAMP datatype: int} |
Tcl script | A_XYZ | atomchange bondchange 3drelative | e_irspectrum.xpd | ||
| E_IRSPECTRUM_IMAGE | diskfile (switchable between string blob diskfile url) |
IR spectrum rendering | height: { value: 250 datatype: int} width: { value: 500 datatype: int} bgcolor: { value: white datatype: color} title: { value: {} datatype: string} filename: { value: {} datatype: string constraints: writeable} format: { value: gif enumeration: png,png24:gif:png8 datatype: string} titlecolor: { value: black datatype: color} framecolor: { value: black datatype: color} signalcolor: { value: #DD0000 datatype: color} ystyle: { value: transmittance enumeration: transmittance:absorbance datatype: int} xdirection: { value: reverse enumeration: normal:reverse datatype: int} xstyle: { value: 1/cm enumeration: 1/cm:um datatype: int} |
Tcl script | E_IRSPECTRUM | atomchange bondchange merge mol | e_irspectrum_image.xpd | |||
| E_ISOTOPE_ATOMHASH_COUNT | int | Number of different isotopic basic atom hash codes | (builtin) | E_HASHGROUP_COUNT_AI | atomchange bondchange merge | |||||
| E_ISOTOPE_COUNT | int | Number of isotopically labelled atoms | Compiled C module | A_TYPE A_ISOTOPE | atomchange merge atom bond | mod_e_isotope_count.so | ||||
| E_ISOTOPE_HASH128 | uint128 | Perturbed isotope-sensitive ensemble hashcode, extended to 128 bits | Compiled C module | M_ISOTOPE_HASHGROUP128 M_ISOTOPE_HASH128 | atomchange bondchange merge hadd | mod_e_isotope_hash128.so | ||||
| E_ISOTOPE_MOLHASH_COUNT | int | Number of different isotopic perturbed molecule hash codes | (builtin) | E_HASHGROUP_COUNT_MI | atomchange bondchange merge hadd | |||||
| E_ISOTOPE_STEREO_ATOMHASH_COUNT | int | Number of different isotopic stereospecific basic atom hash codes | (builtin) | E_HASHGROUP_COUNT_AIS | atomchange bondchange merge | |||||
| E_ISOTOPE_STEREO_HASH128 | uint128 | Perturbed isotope-sensitive and stereo-sensitive ensemble hashcode, extended to 128 bits | Compiled C module | M_ISOTOPE_STEREO_HASHGROUP128 M_ISOTOPE_STEREO_HASH128 | atomchange bondchange merge hadd | mod_e_isotope_stereo_hash128.so | ||||
| E_ISOTOPE_STEREO_MOLHASH_COUNT | int | Number of different isotopic stereospecific perturbed molecule hash codes | (builtin) | E_HASHGROUP_COUNT_MIS | atomchange bondchange merge hadd | |||||
| E_ISOTOPE_STEREO_TAUTO_HASH | uint64 | Perturbed tautomer-tolerant ensemble isotope stereo hashcode | maxtautomers: { value: 250 datatype: int} loghandle: { value: {} datatype: string} scramble: { value: 0 datatype: int} setcanonictautomer: { value: 0 datatype: boolean} usekekuleset: { value: 1 datatype: boolean} stereobondmalus: { value: 1 datatype: boolean} restrictedtransforms: { value: 0 datatype: boolean} setcount: { value: 1 datatype: boolean} useneutralform: { value: 0 description: If set, operate on neutralized structure E_NEUTRALIZED_STRUCTURE instead of original compound datatype: boolean} lockringpielectroncount: { value: 0 datatype: boolean} usetautoset: { value: 0 description: If set, use or compute property E_TAUTOSET instead of using low-level routines to enumerate tautomers datatype: boolean} |
Compiled C module | E_HASHISY | atomchange bondchange stereochange merge | mod_e_isotope_stereo_tauto_hash.so | |||
| E_ISOTOPE_STEREO_TAUTO_HASH128 | uint128 | Perturbed tautomer-tolerant ensemble isotope stereo hashcode, 128 bit version | maxtautomers: { value: 250 datatype: int} loghandle: { value: {} datatype: string} scramble: { value: 0 datatype: int} setcanonictautomer: { value: 0 datatype: boolean} usekekuleset: { value: 1 datatype: boolean} stereobondmalus: { value: 1 datatype: boolean} restrictedtransforms: { value: 0 datatype: boolean} setcount: { value: 1 datatype: boolean} useneutralform: { value: 0 description: If set, operate on neutralized structure E_NEUTRALIZED_STRUCTURE instead of original compound datatype: boolean} lockringpielectroncount: { value: 0 datatype: boolean} usetautoset: { value: 0 description: If set, use or compute property E_TAUTOSET instead of using low-level routines to enumerate tautomers datatype: boolean} |
Compiled C module | E_ISOTOPE_STEREO_HASH128 | atomchange bondchange stereochange merge | mod_e_isotope_stereo_tauto_hash128.so | |||
| E_ISOTOPE_TAUTO_HASH | uint64 | Perturbed tautomer-tolerant ensemble stereo hashcode, with isotope labels but without stereochemistry | maxtautomers: { value: 250 datatype: int} loghandle: { value: {} datatype: string} scramble: { value: 0 datatype: int} setcanonictautomer: { value: 0 datatype: boolean} usekekuleset: { value: 1 datatype: boolean} setcount: { value: 1 datatype: boolean} restrictedtransforms: { value: 0 datatype: boolean} stereobondmalus: { value: 0 datatype: boolean} useneutralform: { value: 0 description: If set, operate on neutralized structure E_NEUTRALIZED_STRUCTURE instead of original compound datatype: boolean} lockringpielectroncount: { value: 0 datatype: boolean} usetautoset: { value: 0 description: If set, use or compute property E_TAUTOSET instead of using low-level routines to enumerate tautomers datatype: boolean} |
Compiled C module | E_HASHIY | atomchange bondchange merge | mod_e_isotope_tauto_hash.so | |||
| E_ISOTOPE_TAUTO_HASH128 | uint128 | Perturbed tautomer-tolerant ensemble isotope hashcode, 128 bit version | maxtautomers: { value: 250 datatype: int} loghandle: { value: {} datatype: string} scramble: { value: 0 datatype: int} setcanonictautomer: { value: 0 datatype: boolean} usekekuleset: { value: 1 datatype: boolean} stereobondmalus: { value: 1 datatype: boolean} restrictedtransforms: { value: 0 datatype: boolean} setcount: { value: 1 datatype: boolean} useneutralform: { value: 0 description: If set, operate on neutralized structure E_NEUTRALIZED_STRUCTURE instead of original compound datatype: boolean} lockringpielectroncount: { value: 0 datatype: boolean} usetautoset: { value: 0 description: If set, use or compute property E_TAUTOSET instead of using low-level routines to enumerate tautomers datatype: boolean} |
Compiled C module | E_ISOTOPE_HASH128 | atomchange bondchange stereochange merge | mod_e_isotope_tauto_hash128.so | |||
| E_ITER_URL | url | Display URL in EPA ITER (International Toxicity Estimates for Risk, https://toxnet.nlm.nih.gov/newtoxnet/iter.htm) | Tcl script | E_CAS | atomchange bondchange stereochange atom bond | e_iter_url.xpd | ||||
| E_IUPAC_ALLOWED_NAME | string | Allowed IUPAC name. This can be extracted from PubChem for structures registered there. In Pubchem, the name is computed with OpenEye software and one of the name generator options of that software. | Tcl script | never | e_iupac_allowed_name.xpd | |||||
| E_IUPAC_OECAS_NAME | string | IUPAC name (OEChem CAS-like Style). This is a field in PubChem and used by the ASN I/O module. | atomchange bondchange stereochange | |||||||
| E_IUPAC_PREFERRED_NAME | string | Preferred IUPAC name. This can be extracted from PubChem for structures registered there. In Pubchem, the name is computed with OpenEye software and one of the name generator options of that software. | Tcl script | never | e_iupac_preferred_name.xpd | |||||
| E_IUPAC_SYSTEMATIC_NAME | string | Systematic IUPAC name. This can be extracted from PubChem for structures registered there. In Pubchem, the name is computed with OpenEye software and one of the name generator options of that software. | Tcl script | never | e_iupac_systematic_name.xpd | |||||
| E_IUPAC_TRADITIONAL_NAME | string | Traditional IUPAC name. This can be extracted from PubChem for structures registered there. In Pubchem, the name is computed with OpenEye software and one of the name generator options of that software. | Tcl script | never | e_iupac_traditional_name.xpd | |||||
| E_IUPHAR_ID | int | Guide to Pharmacology database ID (www.guidetopharmacology.org, www..iuphar-db.org) | Tcl script | E_SMILES | atomchange bondchange stereochange merge | e_iuphar_id.xpd | ||||
| E_IUPHAR_URL | url | Guide to Pharmacology database record display URL (www.guidetopharmacology.org, was www.iuphar-db.org) | Tcl script | E_GUIDETOPHARMACOLOGY_ID | atomchange bondchange stereochange merge | e_iuphar_url.xpd | ||||
| E_JCAMP_SPECTRA_BLOCK | compound | Embedded JCAMP spectral data block. Currently only used in E_NMRSPECTRUM to support the newer NTUPLES data table JCAMP style, with real/imaginary spectrum and real/imaginary FID possibly stored all in one file. | name string symbol string {#points} int firstx double lastx double firsty double lasty double xfactor double yfactor double xunit string yunit string data floatvector |
atomchange bondchange atom bond | ||||||
| E_JCHECK_URL | url | Data display URL in Japanese JCHECK databases (www.safe.nite.go.jp) | Tcl script | E_CAS E_MITI_ID | atomchange bondchange atom bond | e_jcheck_url.xpd | ||||
| E_JGLOBAL_ID | string | Database ID for the J-GLOBAL registry (https://jglobal.jst.go.jp) | Tcl script | atomchange bondchange atom bond | e_jglobal_id.xpd | |||||
| E_JGLOBAL_URL | url | Display URL for the J-GLOBAL registry (https://jglobal.jst.go.jp) | Tcl script | atomchange bondchange atom bond | e_jglobal_url.xpd | |||||
| E_JHOTI_FRAGMENTLIKENESS_VIOLATIONS | byte | Congreve, Carr, Murray, Jhoti, Drug. Discov. Today 2003, 8, 876 | Tcl script | E_WEIGHT E_NHDONORS E_NHACCEPTORS E_XLOGP2 | atomchange bondchange atom bond | e_jhoti_fragmentlikeness_violations.xpd | ||||
| E_JME_STRING | string | JME editor structure encoding | Compiled C module | A_ELEMENT B_ORDER B_TYPE A_TYPE A_FORMAL_CHARGE A_ISOTOPE | atomchange bondchange stereochange hadd mol atom bond ring | mod_e_jme_string.so | ||||
| E_JSTDATA | stringvector | JST extended molfile data in skip section | atomchange bondchange stereochange merge | |||||||
| E_KEGG_BRITE_CLASSIFICATION | stringvector | Compound classification codes as per the KEGG BRITE database (http://www.genome.jp/kegg/brite.html). Compounds must be present in KEGG database, i.e. have a KEGG ID. | Tcl script | atomchange bondchange atom bond | e_kegg_brite_classification.xpd | |||||
| E_KEGG_COMPOUND_ID | string | KEGG ID (www.genome.jp) | Tcl script | atomchange bondchange stereochange merge | e_kegg_compound_id.xpd | |||||
| E_KEGG_COMPOUND_URL | url | KEGG compound display URL (www.genome.jp) | Tcl script | E_KEGG_COMPOUND_ID | atomchange bondchange stereochange merge | e_kegg_compound_url.xpd | ||||
| E_KEGG_DRUG_ID | string | KEGG drug ID (www.genome.jp) | Tcl script | atomchange bondchange stereochange merge | e_kegg_drug_id.xpd | |||||
| E_KEGG_DRUG_URL | url | KEGG drug display URL (www.genome.jp) | Tcl script | E_KEGG_DRUG_ID | atomchange bondchange stereochange merge | e_kegg_drug_url.xpd | ||||
| E_KEKULESET | dataset | Generated set of alternative Kekule forms of the structure- The generated forms are duplicate-filtered by symmetry hashcodes - that means there is only a single Kekule form for benzene, pyridine, pyrimidine (1.3-diazine) or pyrazine (1.4-diazine) - but two for pyridazine (1.2-diazine, with a double or single bond between the adjacent nitrogens). | maxkekuleforms: { value: 512 datatype: int}
|
Compiled C module | A_TYPE B_TYPE A_ELEMENT B_ORDER | atomchange bondchange merge atom bond | mod_e_kekuleset.so | |||
| E_KEYWORDS | stringvector | Keywords associated with ensemble | never | |||||||
| E_KLIFS_ID | int | Database ID for the KLIFS database (http://klifs.vu-compmedchem.nl) | Tcl script | E_SMILES | atomchange bondchange stereochange atom bond | e_klifs_id.xpd | ||||
| E_KLIFS_URL | url | Data display URL for the KLIFS database (http://klifs.vu-compmedchem.nl) | Tcl script | E_KLIFS_ID | atomchange bondchange stereochange atom bond | e_klifs_url.xpd | ||||
| E_KNAPSACK_ID | string | Database ID of compund in KNAPSACK database (http://www.knapsackfamily.com) | Tcl script | E_CAS | atomchange bondchange stereochange atom bond | e_knapsack_id.xpd | ||||
| E_KNAPSACK_URL | url | Data display URL for the Knapsack database (www.knapsackfamily.com) | Tcl script | E_KNAPSACK_ID | atomchange bondchange stereochange atom bond | e_knapsack_url.xpd | ||||
| E_LC50 | compound | LC50 tumor screen data | concunit shortstring lcconc float panel shortstring cell string panelnumber short cellnumber short nlog_lc50 float ntest_this short ntest_max short |
atomchange bondchange merge | ||||||
| E_LEVEL | int | Ensemble level | never | |||||||
| E_LHASA_REAGENT_SCAN_VERIFICATION | compound | Test conditions for Lhasa transform reagent scan verification. The value consists of a transform ID this test applies to, and a bit set indicating which starting material reagent condition this structure should match (0 if none) | {} {none:intramolecular:intermolecular1:intermolecular2:intermolecular3:intermolecular4} |
transformid int reagentmatches bitset |
atomchange bondchange stereochange atom bond | |||||
| E_LINCS_ID | string | Dabase ID of small molecule in the LINCS database (http://lincsportal.ccs.miami.edu) | Tcl script | E_SMILES | atomchange bondchange stereochange atom bond | e_lincs_id.xpd | ||||
| E_LINCS_URL | url | Display URL of small molecule in the LINCS database (http://lincsportal.ccs.miami.edu) | Tcl script | E_LINCS_ID | atomchange bondchange stereochange atom bond | e_lincs_url.xpd | ||||
| E_LINKTEXTS | stringvector | Toplevel link texts of HTML URLs leading to this molecule | never | |||||||
| E_LIPIDMAPS_ID | string | Structure ID for the Lipidmaps database | Tcl script | atomchange bondchange stereochange atom bond | e_lipidmaps_id.xpd | |||||
| E_LIPIDMAPS_URL | url | Tcl script | atomchange bondchange atom bond | e_lipidmaps_url.xpd | ||||||
| E_LIPINSKI_ACCEPTOR_COUNT | int | Number of hydrogens on N and O atoms - H-bond acceptors according to simple Lipinski definition. For a more refined definition, use property E_NHACCEPTORS. |
Compiled C module | A_TYPE A_ELEMENT A_FREE_ELECTRONS | atomchange bondchange atom bond | mod_e_lipinski_acceptor_count.so | ||||
| E_LIPINSKI_DONOR_COUNT | int | Number of oxygen and nitrogen atoms according to really simple Lipinski definition. For a more refined definition, use E_NHDONORS. | Compiled C module | A_TYPE A_ELEMENT | atomchange bondchange atom bond | mod_e_lipinski_donor_count.so | ||||
| E_LITERATURE_REFERENCE | stringvector | Auxiliary literature references | never | |||||||
| E_LOOKCHEM_URL | url | PubChem compound database URL | Tcl script | atomchange bondchange stereochange merge | e_lookchem_url.xpd | |||||
| E_MACCS_KEYS | bitvector | MDL MACCS fingerprint (166 bits) | Tcl script | atom bond | e_maccs_keys.xpd | |||||
| E_MANUFACTURERS | compoundvector | Data about manufactorers of a chemical | catno string manufacturer string catalog string price float currency string amount float unit string info string purity string |
atomchange bondchange stereochange merge | ||||||
| E_MAP_ANNOTATION | compoundvector | Map markers to be used in conjuction with D_ANNOTATED_MAP | {} {none:circle:triangle:invtriangle:square:diamond:pentagon:hexagon} |
tag string object string size int outlinecolor color fillcolor color textcolor color header string footer string |
atomchange bondchange stereochange 3drelative atom bond | |||||
| E_MARKED | boolean | Flag for marked structures | never | |||||||
| E_MASSBANK_URL | url | Display URL for MassBank (https://massbank.eu) entry | Tcl script | atomchange bondchange atom bond | e_massbank_url.xpd | |||||
| E_MASS_PATTERN | xyvector | Mass distribution pattern | cutoff: { value: 0.01 description: Minimum abundancy to include in output vector minvalue: 0.00 maxvalue: 1.00 datatype: double} useimplicith: { value: 1 description: Whether to include implicit hydrogen datatype: boolean} |
Compiled C module | A_ELEMENT A_TYPE A_ISOTOPE | atomchange | mod_e_mass_pattern.so | |||
| E_MATRIX_SCIENTIFIC_IDS | stringvector | ID of the compound Matrix Scientific catalog | Tcl script | atomchange bondchange stereochange atom bond | e_matrix_scientific_ids.xpd | |||||
| E_MATRIX_SCIENTIFIC_URLS | urlvector | URL Matrix Scientific catalog entry | Tcl script | E_MATRIX_SCIENTIFIC_IDS | atomchange bondchange atom bond | e_matrix_scientific_urls.xpd | ||||
| E_MAX_CHAIN_FRAGMENT_SIZE | int | The maximum value of A_CHAIN_LENGTH in the structure, i.e. the size of the largest fragment of connected non-ring non-hydrogen atoms. | Compiled C module | A_CHAIN_LENGTH | atomchange bondchange atom bond | mod_e_max_chain_fragment_size.so | ||||
| E_MAX_CONJUGATED_SYSTEM_SIZE | int | The maximum size of a conjugated system in the ensemble according to the Shoichet definition (see literature reference). | J. Med. Chem. 2003, 46, 4477-4486 | Compiled C module | A_CONJUGATED_SYSTEM_SIZE | atomchange bondchange atom bond | mod_e_max_conjugated_system_size.so | |||
| E_MAX_LINEAR_CHAIN_FRAGMENT_SIZE | int | The maximum value of A_LINEAR_CHAIN_LENGTH in the structure, i.e. the size of the largest fragment of connected non-ring non-branching non-hydrogen atoms. | Compiled C module | A_LINEAR_CHAIN_LENGTH | atomchange bondchange atom bond | mod_e_max_linear_chain_fragment_size.so | ||||
| E_MCULE_ID | string | Get database ID of structure in MCULE (mcule.com) database | Tcl script | E_SMILES | atomchange bondchange atom bond | e_mcule_id.xpd | ||||
| E_MCULE_URL | url | Display URL for MCULE (mcule.com) database | Tcl script | E_MCULE_ID | atomchange bondchange atom bond | e_mcule_url.xpd | ||||
| E_MDL_NAME | string | Name as extracted from MDL Molfile header | never | |||||||
| E_MDL_NUMBER | string | MDL substance number |