MayaChemTools

Previous  TOC  NextPython/RDKitUtil.pyCode | PDF | PDFA4

NAME

RDKitUtil

SYNOPSIS

import RDKitUtil

DESCRIPTION

RDKitUtil module provides the following functions:

AreAtomIndicesSequentiallyConnected, AreAtomMapNumbersPresentInMol, AreHydrogensMissingInMolecule, CalculateFormalCharge, CalculateSpinMultiplicity, ClearAtomMapNumbers, ConstrainAndEmbed, FilterSubstructureMatchByAtomMapNumbers, FilterSubstructureMatchesByAtomMapNumbers, GenerateBase64EncodedMolStringWithConfIDs, GenerateBase64EncodedMolStrings, GenerateBase64EncodedMolStringsWithIDs, GetAtomIndices, GetAtomMapIndices, GetAtomMapIndicesAndMapNumbers, GetAtomPositions, GetAtomSymbols, GetFormalCharge, GetHeavyAtomNeighbors, GetInlineSVGForMolecule, GetInlineSVGForMolecules, GetMolName, GetNumFragments, GetNumHeavyAtomNeighbors, GetPsi4XYZFormatString, GetSVGForMolecule, GetSVGForMolecules, GetSpinMultiplicity, IsAtomSymbolPresentInMol, IsMolEmpty, IsValidAtomIndex, IsValidElementSymbol, MolFromBase64EncodedMolString, MolFromSubstructureMatch, MolToBase64EncodedMolString, MoleculesWriter, MolsFromSubstructureMatches, ReadAndValidateMolecules, ReadMolecules, ReadMoleculesFromMol2File, ReadMoleculesFromMolFile, ReadMoleculesFromPDBFile, ReadMoleculesFromSDFile, ReadMoleculesFromSMILESFile, ReorderAtomIndicesInSequentiallyConnectedManner, SetAtomPositions, SetWriterMolProps, ValidateElementSymbols, WriteMolecules

FUNCTIONS

AreAtomIndicesSequentiallyConnected
AreAtomIndicesSequentiallyConnected(Mol, AtomIndices)

Check for the presence bonds between sequential pairs of atoms in a molecule.

Arguments:

Mol (object): RDKit molecule object.
AtomIndices (list): List of atom indices.

Returns:

bool : True - Sequentially connected; Otherwise, false.
AreAtomMapNumbersPresentInMol
AreAtomMapNumbersPresentInMol(Mol)

Check for the presence of atom map numbers in a molecue.

Arguments:

Mol (object): RDKit molecule object.

Returns:

bool : True - Atom map numbers present; Otherwise, false.
AreHydrogensMissingInMolecule
AreHydrogensMissingInMolecule(Mol)

Check for any missing hydrogens in in a molecue.

Arguments:

Mol (object): RDKit molecule object.

Returns:

bool : True - Missing hydrogens; Otherwise, false.
CalculateFormalCharge
CalculateFormalCharge(Mol)

Calculate formal charge of a molecule. The formal charge is calculated using RDKit function Chem.GetFormalCharge(Mol).

Arguments:

Mol (object): RDKit molecule object.
     retrieve formal charge.

Returns:

int : Formal charge.
CalculateSpinMultiplicity
CalculateSpinMultiplicity(Mol)

Calculate spin multiplicity of a molecule. The spin multiplicity is calculated from the number of free radical electrons using Hund's rule of maximum multiplicity defined as 2S + 1 where S is the total electron spin. The total spin is 1/2 the number of free radical electrons in a molecule.

Arguments:

Mol (object): RDKit molecule object.

Returns:

int : Spin multiplicity.
ClearAtomMapNumbers
ClearAtomMapNumbers(Mol, AllowImplicitValence = True, ClearRadicalElectrons = True)

Check and clear atom map numbers in a molecule. In addition, allow implicit valence and clear radical electrons for atoms with associated map numbers.

For example, the following atomic properties are assigned by RDKit to atom map number 1 in a molecule corresponding to SMILES C[C:1](C)C:

NoImplicit: True; ImplicitValence: 0; ExplicitValence: 3; NumExplicitHs: 0; NumImplicitHs: 0; NumRadicalElectrons: 1

This function clears atoms map numbers in the molecule leading to SMILES CC(C)C, along with optionally updating atomic properties as shown below:

NoImplicit: False; ImplicitValence: 1; ExplicitValence: 3; NumExplicitHs: 0; NumImplicitHs: 1; NumRadicalElectrons: 0

Arguments:

Mol (object): RDKit molecule object.

Returns:

Mol (object): RDKit molecule object.
ConstrainAndEmbed
ConstrainAndEmbed(mol, core, coreMatchesMol=None, useTethers=True, coreConfId=-1, randomseed=2342, getForceField=AllChem.UFFGetMoleculeForceField, **kwargs)

The function is a local copy of RDKit fucntion AllChem.ConstrainedEmbed(). It has been enhanced to support an explicit list of core matches corresponding to the matched atom indices in the molecule. The number of matched atom indices must be equal to the number of atoms in core molecule.

Arguments:

mol (object): RDKit molecule object to embed.
core (object): RDKit molecule to use as a source of constraints.
coreMatchesMol (list): A list matches atom indices in mol.
useTethers: (bool) if True, the final conformation will be optimized
     subject to a series of extra forces that pull the matching atoms to
     the positions of the core atoms. Otherwise simple distance
     constraints based on the core atoms will be used in the
     optimization.
coreConfId (int): ID of the core conformation to use.
randomSeed (int): Seed for the random number generator

Returns:

mol (object): RDKit molecule object.
FilterSubstructureMatchByAtomMapNumbers
FilterSubstructureMatchByAtomMapNumbers(Mol, PatternMol, AtomIndices)

Filter a list of matched atom indices by map atom numbers present in a pattern molecule. The list of atom indices correspond to a list retrieved by RDKit function GetSubstructureMatches using SMILES/SMARTS pattern. The atom map numbers are mapped to appropriate atom indices during the generation of molecules. For example: [O:1]=[S:2](=[O])[C:3][C:4].

Arguments:

Mol (object): RDKit molecule object.
PatternMol (object): RDKit molecule object for a SMILES/SMARTS pattern.
AtomIndices (list): Atom indices.

Returns:

list : A list of filtered atom indices.
FilterSubstructureMatchesByAtomMapNumbers
FilterSubstructureMatchesByAtomMapNumbers(Mol, PatternMol, AtomIndicesList)

Filter a list of lists containing matched atom indices by map atom numbers present in a pattern molecule. The list of atom indices correspond to a list retrieved by RDKit function GetSubstructureMatches using SMILES/SMARTS pattern. The atom map numbers are mapped to appropriate atom indices during the generation of molecules. For example: [O:1]=[S:2](=[O])[C:3][C:4].

Arguments:

Mol (object): RDKit molecule object.
PatternMol (object): RDKit molecule object for a SMILES/SMARTS pattern.
AtomIndicesList (list): A list of lists containing atom indices.

Returns:

list : A list of lists containing filtered atom indices.
GenerateBase64EncodedMolStringWithConfIDs
GenerateBase64EncodedMolStringWithConfIDs(Mol, MolIndex, ConfIDs, PropertyPickleFlags = Chem.PropertyPickleOptions.AllProps)

Setup an iterator generating base64 encoded molecule string for a molecule. The iterator returns a list containing a molecule index, an encoded molecule string, and conf ID.

The molecules are pickled using RDKit Mol.ToBinary() function before their encoding.

Arguments:

Mol (object): RDKit molecule object.
MolIndex (int): Molecule index.
ConfIDs (list): Conformer IDs.
PropertyFlags: RDKit property pickle options.

Returns:

object : Base64 endcoded molecules iterator. The iterator returns a
     list containing a molecule index, an encoded molecule string, and
     conf ID.

The following property pickle flags are currently available in RDKit:

Chem.PropertyPickleOptions.NoProps
Chem.PropertyPickleOptions.MolProps
Chem.PropertyPickleOptions.AtomProps
Chem.PropertyPickleOptions.BondProps
Chem.PropertyPickleOptions.PrivateProps
Chem.PropertyPickleOptions.AllProps

Example(s):

EncodedMolsInfo = GenerateBase64EncodedMolStringWithConfIDs(Mol, MolIndex, ConfIDs)
for MolIndex, EncodedMol, ConfID in EncodedMolsInfo:
     if EncodeMol is not None:
         Mol = MolFromBase64EncodedMolString(EncodedMol)
GenerateBase64EncodedMolStrings
GenerateBase64EncodedMolStrings(Mols, PropertyPickleFlags = Chem.PropertyPickleOptions.AllProps)

Setup an iterator for generating base64 encoded molecule string from a RDKit molecule iterator. The iterator returns a list containing a molecule index and encoded molecule string or None.

The molecules are pickled using RDKit Mol.ToBinary() function before their encoding.

Arguments:

iterator: RDKit molecules iterator.
PropertyFlags: RDKit property pickle options.

Returns:

object : Base64 endcoded molecules iterator. The iterator returns a
     list containing a molecule index and an encoded molecule string
     or None.

The following property pickle flags are currently available in RDKit:

Chem.PropertyPickleOptions.NoProps
Chem.PropertyPickleOptions.MolProps
Chem.PropertyPickleOptions.AtomProps
Chem.PropertyPickleOptions.BondProps
Chem.PropertyPickleOptions.PrivateProps
Chem.PropertyPickleOptions.AllProps

Example(s):

EncodedMolsInfo = GenerateBase64EncodedMolStrings(Mols)
for MolIndex, EncodedMol in EncodedMolsInfo:
     if EncodeMol is not None:
         Mol = MolFromBase64EncodedMolString(EncodedMol)
GenerateBase64EncodedMolStringsWithIDs
GenerateBase64EncodedMolStringsWithIDs(Mols, MolIDs, PropertyPickleFlags = Chem.PropertyPickleOptions.AllProps)

Setup an iterator for generating base64 encoded molecule string from a RDKit molecule iterator. The iterator returns a list containing a molecule ID and encoded molecule string or None.

The molecules are pickled using RDKit Mol.ToBinary() function before their encoding.

Arguments:

iterator: RDKit molecules iterator.
MolIDs (list): Molecule IDs.
PropertyFlags: RDKit property pickle options.

Returns:

object : Base64 endcoded molecules iterator. The iterator returns a
     list containing a molecule ID and an encoded molecule string
     or None.

The following property pickle flags are currently available in RDKit:

Chem.PropertyPickleOptions.NoProps
Chem.PropertyPickleOptions.MolProps
Chem.PropertyPickleOptions.AtomProps
Chem.PropertyPickleOptions.BondProps
Chem.PropertyPickleOptions.PrivateProps
Chem.PropertyPickleOptions.AllProps

Example(s):

EncodedMolsInfo = GenerateBase64EncodedMolStringsWithIDs(Mols)
for MolID, EncodedMol in EncodedMolsInfo:
     if EncodeMol is not None:
         Mol = MolFromBase64EncodedMolString(EncodedMol)
GetAtomIndices
GetAtomIndices(Mol)

Retrieve a list containing atom indices of all atoms a molecule.

Arguments:

Mol (object): RDKit molecule object.

Returns:

list : List of atom indices.
GetAtomMapIndices
GetAtomMapIndices(Mol)

Get a list of available atom indices corresponding to atom map numbers present in a SMILES/SMARTS pattern used for creating a molecule. The list of atom indices is sorted in ascending order by atom map numbers.

Arguments:

Mol (object): RDKit molecule object.

Returns:

list : List of atom indices sorted in the ascending order of atom map
     numbers or None.
GetAtomMapIndicesAndMapNumbers
GetAtomMapIndicesAndMapNumbers(Mol)

Get lists of available atom indices and atom map numbers present in a SMILES/SMARTS pattern used for creating a molecule. Both lists are sorted in ascending order by atom map numbers.

Arguments:

Mol (object): RDKit molecule object.

Returns:

list : List of atom indices sorted in the ascending order of atom map
     numbers or None.
list : List of atom map numbers sorted in the ascending order or None.
GetAtomPositions
GetAtomPositions(Mol, ConfID = -1)

Retrieve a list of lists containing coordinates of all atoms in a molecule.

Arguments:

Mol (object): RDKit molecule object.
ConfID (int): Conformer number.

Returns:

list : List of lists containing atom positions.

Example(s):

for AtomPosition in RDKitUtil.GetAtomPositions(Mol):
     print("X: %s; Y: %s; Z: %s" % (AtomPosition[0], AtomPosition[1], AtomPosition[2]))
GetAtomSymbols
GetAtomSymbols(Mol)

Retrieve a list containing atom symbols of all atoms a molecule.

Arguments:

Mol (object): RDKit molecule object.

Returns:

list : List of atom symbols.
GetFormalCharge
GetFormalCharge(Mol, CheckMolProp = True)

Get formal charge of a molecule. The formal charge is either retrieved from 'FormalCharge' molecule property or calculated using RDKit function Chem.GetFormalCharge(Mol).

The 'FormalCharge' molecule property may contain multiple space delimited values. The total formal charge corresponds to the sum of the specified formal charge values.

Arguments:

Mol (object): RDKit molecule object.
CheckMolProp (bool): Check 'FormalCharge' molecule property to
     retrieve formal charge.

Returns:

int : Formal charge.
GetHeavyAtomNeighbors
GetHeavyAtomNeighbors(Atom)

Get a list of heavy atom neighbors.

Arguments:

Atom (object): RDKit atom object.

Returns:

list : List of heavy atom neighbors.
GetInlineSVGForMolecule
GetInlineSVGForMolecule(Mol, Width, Height, Legend = None, AtomListToHighlight = None, BondListToHighlight = None, BoldText = True, Base64Encoded = True)

Get SVG image text for a molecule suitable for inline embedding into a HTML page.

Arguments:

Mol (object): RDKit molecule object.
Width (int): Width of a molecule image in pixels.
Height (int): Height of a molecule image in pixels.
Legend (str): Text to display under the image.
AtomListToHighlight (list): List of atoms to highlight.
BondListToHighlight (list): List of bonds to highlight.
BoldText (bool): Flag to make text bold in the image of molecule.
Base64Encoded (bool): Flag to return base64 encoded string.

Returns:

str : SVG image text for inline embedding into a HTML page using "img"
     tag: <img src="data:image/svg+xml;charset=UTF-8,SVGImageText> or
     tag: <img src="data:image/svg+xml;base64,SVGImageText>
GetInlineSVGForMolecules
GetInlineSVGForMolecules(Mols, MolsPerRow, MolWidth, MolHeight, Legends = None, AtomListsToHighlight = None, BondListsToHighLight = None, BoldText = True, Base64Encoded = True)

Get SVG image text for molecules suitable for inline embedding into a HTML page.

Arguments:

Mols (list): List of RDKit molecule objects.
MolsPerRow (int): Number of molecules per row.
Width (int): Width of a molecule image in pixels.
Height (int): Height of a molecule image in pixels.
Legends (list): List containing strings to display under images.
AtomListsToHighlight (list): List of lists containing atoms to highlight
     for molecules.
BondListsToHighlight (list): List of lists containing bonds to highlight
     for molecules
BoldText (bool): Flag to make text bold in the image of molecules.
Base64Encoded (bool): Flag to return base64 encoded string.

Returns:

str : SVG image text for inline embedding into a HTML page using "img"
     tag: <img src="data:image/svg+xml;charset=UTF-8,SVGImageText> or
     tag: <img src="data:image/svg+xml;base64,SVGImageText>
GetMolName
GetMolName(Mol, MolNum = None)

Get molecule name.

Arguments:

Mol (object): RDKit molecule object.
MolNum (int or None): Molecule number in input file.

Returns:

str : Molname corresponding to _Name property of a molecule, generated
     from specieid MolNum using the format "Mol%d" % MolNum, or an
     empty string.
GetNumFragments
GetNumFragments(Mol)

Get number of fragment in a molecule.

Arguments:

Atom (object): RDKit molecule object.

Returns:

int : Number of fragments.
GetNumHeavyAtomNeighbors
GetNumHeavyAtomNeighbors(Atom)

Get number of heavy atom neighbors.

Arguments:

Atom (object): RDKit atom object.

Returns:

int : Number of neighbors.
GetPsi4XYZFormatString
GetPsi4XYZFormatString(Mol, ConfID = -1, FormalCharge = "auto", SpinMultiplicity = "auto", Symmetry = "auto", NoCom = False, NoReorient = False, CheckFragments = False)

Retrieve geometry string of a molecule in Psi4ish XYZ format to perform Psi4 quantum chemistry calculations.

You may explicit specify multiple space delimited values for formal charge and spin multiplicity. Otherwise, these values are either automatically retrieved from 'FormalCharge' and 'SpinMultiplicity' molecule properties or calculated using RDKit. The number of specified values for these properties must match the number of fragments in the molecule during the processing of the fragments.

Arguments:

Mol (object): RDKit molecule object.
ConfID (int): Conformer number.
FormalCharge (str): Specified formal charge or 'auto' to calculate its value by RDKit.
SpinMultiplicity (str): Specified spin multiplicity or 'auto' to calculate its value by RDKit.
Symmetry (str): Specified symmetry or 'auto' to calculate its value by Psi4.
NoCom (bool): Flag to disable recentering of a molecule by Psi4.
NoReorient (bool): Flag to disable reorientation of a molecule by Psi4.
CheckFragments (bool): Check for fragments and setup geometry string using -- separator between fragments.

Returns:

str : Geometry string of a molecule in Psi4ish XYZ format.
GetSVGForMolecule
GetSVGForMolecule(Mol, Width, Height, Legend = None, AtomListToHighlight = None, BondListToHighlight = None, BoldText = True)

Get SVG image text for a molecule suitable for viewing in a browser.

Arguments:

Mol (object): RDKit molecule object.
Width (int): Width of a molecule image in pixels.
Height (int): Height of a molecule image in pixels.
Legend (str): Text to display under the image.
AtomListToHighlight (list): List of atoms to highlight.
BondListToHighlight (list): List of bonds to highlight.
BoldText (bool): Flag to make text bold in the image of molecule.

Returns:

str : SVG image text for writing to a SVG file for viewing in a browser.
GetSVGForMolecules
GetSVGForMolecules(Mols, MolsPerRow, MolWidth, MolHeight, Legends = None, AtomListsToHighlight = None, BondListsToHighlight = None, BoldText = True)

Get SVG image text for molecules suitable for viewing in a browser.

Arguments:

Mols (list): List of RDKit molecule objects.
MolsPerRow (int): Number of molecules per row.
Width (int): Width of a molecule image in pixels.
Height (int): Height of a molecule image in pixels.
Legends (list): List containing strings to display under images.
AtomListsToHighlight (list): List of lists containing atoms to highlight
     for molecules.
BondListsToHighlight (list): List of lists containing bonds to highlight
     for molecules
BoldText (bool): Flag to make text bold in the image of molecules.

Returns:

str : SVG image text for writing to a SVG file for viewing in a browser.
GetSpinMultiplicity
GetSpinMultiplicity(Mol, CheckMolProp = True)

Get spin multiplicity of a molecule. The spin multiplicity is either retrieved from 'SpinMultiplicity' molecule property or calculated from the number of free radical electrons using Hund's rule of maximum multiplicity defined as 2S + 1 where S is the total electron spin. The total spin is 1/2 the number of free radical electrons in a molecule.

The 'SpinMultiplicity' molecule property may contain multiple space delimited values. The total spin multiplicity corresponds to the total number of free radical electrons which are calculated for each specified value.

Arguments:

Mol (object): RDKit molecule object.
CheckMolProp (bool): Check 'SpinMultiplicity' molecule property to
     retrieve spin multiplicity.

Returns:

int : Spin multiplicity.
IsAtomSymbolPresentInMol
IsAtomSymbolPresentInMol(Mol, AtomSymbol, IgnoreCase = True)
Check for the presence of an atom symbol in a molecule.

Arguments:

Mol (object): RDKit molecule object.
AtomSymbol (str): Atom symbol.

Returns:

bool : True - Atom symbol in molecule; Otherwise, false.
IsMolEmpty
IsMolEmpty(Mol)

Check for the presence of atoms in a molecule.

Arguments:

Mol (object): RDKit molecule object.

Returns:

bool : True - No atoms in molecule; Otherwise, false.
IsValidAtomIndex
IsValidAtomIndex(Mol, AtomIndex)

Validate presence atom index in a molecule.

Arguments:

Mol (object): RDKit molecule object.
AtomIndex (int): Atom index.

Returns:

bool : True - Valid atom index; Otherwise, false.
IsValidElementSymbol
IsValidElementSymbol(ElementSymbol)

Validate element symbol.

Arguments:

ElementSymbol (str): Element symbol

Returns:

bool : True - Valid element symbol; Otherwise, false.
MolFromBase64EncodedMolString
MolFromBase64EncodedMolString(EncodedMol)

Generate a RDKit molecule object from a base64 encoded string.

Arguments:

str: Base64 encoded molecule string.

Returns:

object : RDKit molecule object or None.
MolFromSubstructureMatch
MolFromSubstructureMatch(Mol, PatternMol, AtomIndices, FilterByAtomMapNums = False)

Generate a RDKit molecule object for a list of matched atom indices present in a pattern molecule. The list of atom indices correspond to a list retrieved by RDKit function GetSubstructureMatches using SMILES/SMARTS pattern. The atom indices are optionally filtered by mapping atom numbers to appropriate atom indices during the generation of the molecule. For example: [O:1]=[S:2](=[O])[C:3][C:4].

Arguments:

Mol (object): RDKit molecule object.
PatternMol (object): RDKit molecule object for a SMILES/SMARTS pattern.
AtomIndices (list): Atom indices.
FilterByAtomMapNums (bool): Filter matches by atom map numbers.

Returns:

object : RDKit molecule object or None.
MolToBase64EncodedMolString
MolToBase64EncodedMolString(Mol, PropertyPickleFlags = Chem.PropertyPickleOptions.AllProps)

Encode RDkit molecule object into a base64 encoded string. The properties can be optionally excluded.

The molecule is pickled using RDKit Mol.ToBinary() function before their encoding.

Arguments:

Mol (object): RDKit molecule object.
PropertyPickleFlags: RDKit property pickle options.

Returns:

str : Base64 encode molecule string or None.

The following property pickle flags are currently available in RDKit:

Chem.PropertyPickleOptions.NoProps
Chem.PropertyPickleOptions.MolProps
Chem.PropertyPickleOptions.AtomProps
Chem.PropertyPickleOptions.BondProps
Chem.PropertyPickleOptions.PrivateProps
Chem.PropertyPickleOptions.AllProps
MoleculesWriter
MoleculesWriter(FileName, **KeyWordArgs)

Set up a molecule writer.

Arguments:

FileName (str): Name of a file with complete path.
**KeyWordArgs (dictionary) : Parameter name and value pairs for writing and
     processing molecules.

Returns:

RDKit object : Molecule writer.

The file extension is used to determine type of the file and set up an appropriate file writer.

MolsFromSubstructureMatches
MolsFromSubstructureMatches(Mol, PatternMol, AtomIndicesList, FilterByAtomMapNums = False)

Generate a list of RDKit molecule objects for a list containing lists of matched atom indices present in a pattern molecule. The list of atom indices correspond to a list retrieved by RDKit function GetSubstructureMatches using SMILES/SMARTS pattern. The atom indices are optionally filtered by mapping atom numbers to appropriate atom indices during the generation of the molecule. For example: [O:1]=[S:2](=[O])[C:3][C:4].

Arguments:

Mol (object): RDKit molecule object.
PatternMol (object): RDKit molecule object for a SMILES/SMARTS pattern.
AtomIndicesList (list): A list of lists containing atom indices.
FilterByAtomMapNums (bool): Filter matches by atom map numbers.

Returns:

list : A list of lists containg RDKit molecule objects or None.
ReadAndValidateMolecules
ReadAndValidateMolecules(FileName, **KeyWordArgs)

Read molecules from an input file, validate all molecule objects, and return a list of valid and non-valid molecule objects along with their counts.

Arguments:

FileName (str): Name of a file with complete path.
**KeyWordArgs (dictionary) : Parameter name and value pairs for reading and
     processing molecules.

Returns:

list : List of valid RDKit molecule objects.
int : Number of total molecules in input file.
int : Number of valid molecules in input file.

The file extension is used to determine type of the file and set up an appropriate file reader.

ReadMolecules
ReadMolecules(FileName, **KeyWordArgs)

Read molecules from an input file without performing any validation and creation of molecule objects.

Arguments:

FileName (str): Name of a file with complete path.
**KeyWordArgs (dictionary) : Parameter name and value pairs for reading and
     processing molecules.

Returns:

list : List of RDKit molecule objects.

The file extension is used to determine type of the file and set up an appropriate file reader.

ReadMoleculesFromMol2File
ReadMoleculesFromMol2File(FileName, Sanitize = True, RemoveHydrogens = True)

Read molecules from a Tripos Mol2 file. The first call to the function creates and returns a generator object using Python yield statement. The molecules are created during the subsequent iteration by the generator object.

Arguments:

FileName (str): Name of a file with complete path.
Sanitize (bool): Sanitize molecules.
RemoveHydrogens (bool): Remove hydrogens from molecules.

Returns:

list : A Python generator object for iterating over the molecules.
ReadMoleculesFromMolFile
ReadMoleculesFromMolFile(FileName, Sanitize = True, RemoveHydrogens = True, StrictParsing = True)

Read molecule from a MDL Mol file.

Arguments:

FileName (str): Name of a file with complete path.
Sanitize (bool): Sanitize molecules.
RemoveHydrogens (bool): Remove hydrogens from molecules.
StrictParsing (bool): Perform strict parsing.

Returns:

list : List of RDKit molecule objects.
ReadMoleculesFromPDBFile
ReadMoleculesFromPDBFile(FileName, Sanitize = True, RemoveHydrogens = True)

Read molecule from a PDB file.

Arguments:

FileName (str): Name of a file with complete path.
Sanitize (bool): Sanitize molecules.
RemoveHydrogens (bool): Remove hydrogens from molecules.

Returns:

list : List of RDKit molecule objects.
ReadMoleculesFromSDFile
ReadMoleculesFromSDFile(FileName, Sanitize = True, RemoveHydrogens = True, StrictParsing = True)

Read molecules from a SD file.

Arguments:

FileName (str): Name of a file with complete path.
Sanitize (bool): Sanitize molecules.
RemoveHydrogens (bool): Remove hydrogens from molecules.
StrictParsing (bool): Perform strict parsing.

Returns:

list : List of RDKit molecule objects.
ReadMoleculesFromSMILESFile
ReadMoleculesFromSMILESFile(FileName, SMILESDelimiter = ' ', SMILESColIndex = 0, SMILESNameColIndex = 1, SMILESTitleLine = 1, Sanitize = 1)

Read molecules from a SMILES file.

Arguments:

SMILESDelimiter (str): Delimiter for parsing SMILES line
SMILESColIndex (int): Column index containing SMILES string.
SMILESNameColIndex (int): Column index containing molecule name.
SMILESTitleLine (int): Flag to indicate presence of title line.
Sanitize (int): Sanitize molecules.

Returns:

list : List of RDKit molecule objects.
ReorderAtomIndicesInSequentiallyConnectedManner
ReorderAtomIndicesInSequentiallyConnectedManner(Mol, AtomIndices)

Check for the presence of sequentially connected list of atoms in an arbitray list of atoms in molecule.

Arguments:

Mol (object): RDKit molecule object.
AtomIndices (list): List of atom indices.

Returns:

bool : True - Sequentially connected list found; Otherwise, false.
list : List of seqeuntially connected atoms or None.
SetAtomPositions
SetAtomPositions(Mol, AtomPositions, ConfID = -1)

Set atom positions of all atoms in a molecule.

Arguments:

Mol (object): RDKit molecule object.
AtomPositions (object): List of lists containing atom positions.
ConfID (int): Conformer number.

Returns:

object : RDKit molecule object.
SetWriterMolProps
SetWriterMolProps(Writer, Mol)

Setup molecule properties for a writer to output.

Arguments:

Writer (object): RDKit writer object.
Mol (object): RDKit molecule object.

Returns:

object : Writer object.
ValidateElementSymbols
ValidateElementSymbols(ElementSymbols)

Validate element symbols.

Arguments:

ElementSymbols (list): List of element symbols to validate.

Returns:

bool : True - All element symbols are valid; Otherwise, false.
WriteMolecules
WriteMolecules(FileName, Mols, **KeyWordArgs)

Write molecules to an output file.

Arguments:

FileName (str): Name of a file with complete path.
Mols (list): List of RDKit molecule objects.
**KeyWordArgs (dictionary) : Parameter name and value pairs for writing and
     processing molecules.

Returns:

int : Number of total molecules.
int : Number of processed molecules written to output file.

The file extension is used to determine type of the file and set up an appropriate file writer.

AUTHOR

Manish Sud

COPYRIGHT

Copyright (C) 2024 Manish Sud. All rights reserved.

The functionality available in this file is implemented using RDKit, an open source toolkit for cheminformatics developed by Greg Landrum.

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.

 

 

Previous  TOC  NextMarch 27, 2024Python/RDKitUtil.py