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NAME

AssignAtomTypes.pl - Assign atom types for SD files

SYNOPSIS

AssignAtomTypes.pl SDFile(s)...

AtomTypesFingerprints.pl [--AromaticityModel AromaticityModelType] [-a, --AtomIdentifierType AtomicInvariantsAtomTypes | DREIDINGAtomTypes | EStateAtomTypes | MMFF94AtomTypes | SLogPAtomTypes | SYBYLAtomTypes | TPSAAtomTypes | UFFAtomTypes] [--AtomicInvariantsToUse "AtomicInvariant, AtomicInvariant..."] [--FunctionalClassesToUse "FunctionalClass1,FunctionalClass2..."] [--AtomTypesSetToUse ArbitrarySize | FixedSize] [--BitsOrder Ascending | Descending] [-b, --BitStringFormat BinaryString | HexadecimalString] [--CompoundID DataFieldName or LabelPrefixString] [--CompoundIDLabel text] [--CompoundIDMode DataField | MolName | LabelPrefix | MolNameOrLabelPrefix] [--DataFields "FieldLabel1,FieldLabel2,..."] [-d, --DataFieldsMode All | Common | Specify | CompoundID] [-f, --Filter Yes | No] [--FingerprintsLabelMode FingerprintsLabelOnly | FingerprintsLabelWithIDs] [--FingerprintsLabel text] [-h, --help] [-k, --KeepLargestComponent Yes | No] [-m, --mode AtomTypesCount | AtomTypesBits] [-i, --IgnoreHydrogens Yes | No] [--OutDelim comma | tab | semicolon] [--output SD |FP | text | all] [-o, --overwrite] [-q, --quote Yes | No] [-r, --root RootName] [-s, --size number] [--ValuesPrecision number] [-v, --VectorStringFormat IDsAndValuesString | IDsAndValuesPairsString | ValuesAndIDsString | ValuesAndIDsPairsString] [-w, --WorkingDir DirName]

DESCRIPTION

Generate atom types for SDFile(s) and create appropriate SD, or CSV/TSV text file(s) containing atom types assigned to atoms in molecules.

Multiple SDFile names are separated by spaces. The valid file extensions are .sdf and .sd. All other file names are ignored. All the SD files in a current directory can be specified either by *.sdf or the current directory name.

The current release of MayaChemTools supports generation of atom types corresponding to following -a, --AtomIdentifierTypes:

AtomicInvariantsAtomTypes, DREIDINGAtomTypes, EStateAtomTypes,
FunctionalClassAtomTypes, MMFF94AtomTypes, SLogPAtomTypes,
SYBYLAtomTypes, TPSAAtomTypes, UFFAtomTypes

Based on the values specified for -a, --AtomIdentifierType along with other specified parameters such as --AtomicInvariantsToUse and --FunctionalClassesToUse, atom ypes are assigned to all non-hydrogen atoms or all atoms in a molecule

OPTIONS

--AromaticityModel MDLAromaticityModel | TriposAromaticityModel | MMFFAromaticityModel | ChemAxonBasicAromaticityModel | ChemAxonGeneralAromaticityModel | DaylightAromaticityModel | MayaChemToolsAromaticityModel

Specify aromaticity model to use during detection of aromaticity. Possible values in the current release are: MDLAromaticityModel, TriposAromaticityModel, MMFFAromaticityModel, ChemAxonBasicAromaticityModel, ChemAxonGeneralAromaticityModel, DaylightAromaticityModel or MayaChemToolsAromaticityModel. Default value: MayaChemToolsAromaticityModel.

The supported aromaticity model names along with model specific control parameters are defined in AromaticityModelsData.csv, which is distributed with the current release and is available under lib/data directory. Molecule.pm module retrieves data from this file during class instantiation and makes it available to method DetectAromaticity for detecting aromaticity corresponding to a specific model.

--AtomicInvariantsToUse "AtomicInvariant,AtomicInvariant..."

This value is used during AtomicInvariantsAtomTypes value of m, --mode option. It's a list of comma separated valid atomic invariant atom types.

Possible values for atomic invariants are: AS, X, BO, LBO, SB, DB, TB, H, Ar, RA, FC, MN, SM. Default value: AS,X,BO,H,FC.

The atomic invariants abbreviations correspond to:

AS = Atom symbol corresponding to element symbol

X<n> = Number of non-hydrogen atom neighbors or heavy atoms
BO<n> = Sum of bond orders to non-hydrogen atom neighbors or heavy atoms
LBO<n> = Largest bond order of non-hydrogen atom neighbors or heavy atoms
SB<n> = Number of single bonds to non-hydrogen atom neighbors or heavy atoms
DB<n> = Number of double bonds to non-hydrogen atom neighbors or heavy atoms
TB<n> = Number of triple bonds to non-hydrogen atom neighbors or heavy atoms
H<n> = Number of implicit and explicit hydrogens for atom
Ar = Aromatic annotation indicating whether atom is aromatic
RA = Ring atom annotation indicating whether atom is a ring
FC<+n/-n> = Formal charge assigned to atom
MN<n> = Mass number indicating isotope other than most abundant isotope
SM<n> = Spin multiplicity of atom. Possible values: 1 (singlet), 2 (doublet) or 3 (triplet)

Atom type generated by AtomTypes::AtomicInvariantsAtomTypes class corresponds to:

AS.X<n>.BO<n>.LBO<n>.<SB><n>.<DB><n>.<TB><n>.H<n>.Ar.RA.FC<+n/-n>.MN<n>.SM<n>

Except for AS which is a required atomic invariant in atom types, all other atomic invariants are optional. Atom type specification doesn't include atomic invariants with zero or undefined values.

In addition to usage of abbreviations for specifying atomic invariants, the following descriptive words are also allowed:

X : NumOfNonHydrogenAtomNeighbors or NumOfHeavyAtomNeighbors
BO : SumOfBondOrdersToNonHydrogenAtoms or SumOfBondOrdersToHeavyAtoms
LBO : LargestBondOrderToNonHydrogenAtoms or LargestBondOrderToHeavyAtoms
SB : NumOfSingleBondsToNonHydrogenAtoms or NumOfSingleBondsToHeavyAtoms
DB : NumOfDoubleBondsToNonHydrogenAtoms or NumOfDoubleBondsToHeavyAtoms
TB : NumOfTripleBondsToNonHydrogenAtoms or NumOfTripleBondsToHeavyAtoms
H : NumOfImplicitAndExplicitHydrogens
Ar : Aromatic
RA : RingAtom
FC : FormalCharge
MN : MassNumber
SM : SpinMultiplicity

AtomTypes::AtomicInvariantsAtomTypes module is used to assign atomic invariant atom types.

--FunctionalClassesToUse "FunctionalClass1,FunctionalClass2..."

This value is used during FunctionalClassAtomTypes value of m, --mode option. It's a list of comma separated valid functional classes.

Possible values for atom functional classes are: Ar, CA, H, HBA, HBD, Hal, NI, PI, RA. Default value [ Ref 24 ]: HBD,HBA,PI,NI,Ar,Hal.

The functional class abbreviations correspond to:

HBD: HydrogenBondDonor
HBA: HydrogenBondAcceptor
PI : PositivelyIonizable
NI : NegativelyIonizable
Ar : Aromatic
Hal : Halogen
H : Hydrophobic
RA : RingAtom
CA : ChainAtom
Functional class atom type specification for an atom corresponds to:

Ar.CA.H.HBA.HBD.Hal.NI.PI.RA

AtomTypes::FunctionalClassAtomTypes module is used to assign functional class atom types. It uses following definitions [ Ref 60-61, Ref 65-66 ]:

HydrogenBondDonor: NH, NH2, OH
HydrogenBondAcceptor: N[!H], O
PositivelyIonizable: +, NH2
NegativelyIonizable: -, C(=O)OH, S(=O)OH, P(=O)OH
--CompoundID DataFieldName or LabelPrefixString

This value is --CompoundIDMode specific and indicates how compound ID is generated.

For DataField value of --CompoundIDMode option, it corresponds to datafield label name whose value is used as compound ID; otherwise, it's a prefix string used for generating compound IDs like LabelPrefixString<Number>. Default value, Cmpd, generates compound IDs which look like Cmpd<Number>.

Examples for DataField value of --CompoundIDMode:

MolID
ExtReg

Examples for LabelPrefix or MolNameOrLabelPrefix value of --CompoundIDMode:

Compound

The value specified above generates compound IDs which correspond to Compound<Number> instead of default value of Cmpd<Number>.

--CompoundIDLabel text

Specify compound ID column label for FP or CSV/TSV text file(s) used during CompoundID value of --DataFieldsMode option. Default: CompoundID.

--CompoundIDMode DataField | MolName | LabelPrefix | MolNameOrLabelPrefix

Specify how to generate compound IDs and write to FP or CSV/TSV text file(s) along with generated fingerprints for FP | text | all values of --output option: use a SDFile(s) datafield value; use molname line from SDFile(s); generate a sequential ID with specific prefix; use combination of both MolName and LabelPrefix with usage of LabelPrefix values for empty molname lines.

Possible values: DataField | MolName | LabelPrefix | MolNameOrLabelPrefix. Default: LabelPrefix.

For MolNameAndLabelPrefix value of --CompoundIDMode, molname line in SDFile(s) takes precedence over sequential compound IDs generated using LabelPrefix and only empty molname values are replaced with sequential compound IDs.

This is only used for CompoundID value of --DataFieldsMode option.

--DataFields "FieldLabel1,FieldLabel2,..."

Comma delimited list of SDFiles(s) data fields to extract and write to CSV/TSV text file(s) along with generated atom types for text | all values of --output option.

This is only used for Specify value of --DataFieldsMode option.

Examples:

Extreg
MolID,CompoundName
-d, --DataFieldsMode All | Common | Specify | CompoundID

Specify how data fields in SDFile(s) are transferred to output CSV/TSV text file(s) along with generated fingerprints for text | all values of --output option: transfer all SD data field; transfer SD data files common to all compounds; extract specified data fields; generate a compound ID using molname line, a compound prefix, or a combination of both. Possible values: All | Common | specify | CompoundID. Default value: CompoundID.

-f, --Filter Yes | No

Specify whether to check and filter compound data in SDFile(s). Possible values: Yes or No. Default value: Yes.

By default, compound data is checked before calculating fingerprints and compounds containing atom data corresponding to non-element symbols or no atom data are ignored.

-h, --help

Print this help message.

-i, --IgnoreHydrogens Yes | No

Ignore hydrogens during fingerprints generation. Possible values: Yes or No. Default value: Yes.

For yes value of -i, --IgnoreHydrogens, any explicit hydrogens are also used for generation of atom type fingerprints; implicit hydrogens are still ignored.

-k, --KeepLargestComponent Yes | No

Generate fingerprints for only the largest component in molecule. Possible values: Yes or No. Default value: Yes.

For molecules containing multiple connected components, fingerprints can be generated in two different ways: use all connected components or just the largest connected component. By default, all atoms except for the largest connected component are deleted before generation of fingerprints.

-m, --mode AtomicInvariantsAtomTypes | DREIDINGAtomTypes | EStateAtomTypes | FunctionalClassAtomTypes | MMFF94AtomTypes | SLogPAtomTypes | SYBYLAtomTypes | TPSAAtomTypes | UFFAtomTypes | All

Specify atom identifier type to use for assignment of atom types to hydrogen and/or non-hydrogen atoms during calculation of atom types fingerprints. Possible values in the current release are: AtomicInvariantsAtomTypes, DREIDINGAtomTypes, EStateAtomTypes, FunctionalClassAtomTypes, MMFF94AtomTypes, SLogPAtomTypes, SYBYLAtomTypes, TPSAAtomTypes, UFFAtomTypes or All. Default value: AtomicInvariantsAtomTypes.

--OutDelim comma | tab | semicolon

Delimiter for output CSV/TSV text file(s). Possible values: comma, tab, or semicolon Default value: comma.

--output SD | text | all

Type of output files to generate. Possible values: SD, text, or all. Default value: text.

-o, --overwrite

Overwrite existing files.

-q, --quote Yes | No

Put quote around column values in output CSV/TSV text file(s). Possible values: Yes or No. Default value: Yes.

-r, --root RootName

New file name is generated using the root: <Root>.<Ext>. Default for new file names: <SDFileName><AtomTypes>.<Ext>. The file type determines <Ext> value. The sdf, csv, and tsv <Ext> values are used for SD, comma/semicolon, and tab delimited text files, respectively.This option is ignored for multiple input files.

-w, --WorkingDir DirName

Location of working directory. Default: current directory.

EXAMPLES

To generate atomic invariants atom types count fingerprints of arbitrary size in vector string format and create a SampleATFP.csv file containing sequential compound IDs along with fingerprints vector strings data, type:

% AtomTypesFingerprints.pl -r SampleATFP -o Sample.sdf demo:

AUTHOR

Manish Sud

SEE ALSO

AtomTypesFingerprints.pl

COPYRIGHT

Copyright (C) 2018 Manish Sud. All rights reserved.

This file is part of MayaChemTools.

MayaChemTools is free software; you can redistribute it and/or modify it under the terms of the GNU Lesser General Public License as published by the Free Software Foundation; either version 3 of the License, or (at your option) any later version.

 

 

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