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# NAME

RDKitUtil

# SYNOPSIS

import RDKitUtil

# DESCRIPTION

RDKitUtil module provides the following functions:

GetInlineSVGForMolecule, GetInlineSVGForMolecules, GetMolName, GetSVGForMolecule, GetSVGForMolecules, IsMolEmpty, MoleculesWriter, ReadAndValidateMolecules, ReadMolecules, ReadMoleculesFromMol2File, ReadMoleculesFromMolFile, ReadMoleculesFromPDBFile, ReadMoleculesFromSDFile, ReadMoleculesFromSMILESFile, WriteMolecules

# FUNCTIONS

GetInlineSVGForMolecule
  GetInlineSVGForMolecule(Mol, Width, Height, Legend = None, AtomListToHighlight = None, BondListToHighlight = None, BoldText = 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.

  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>
GetInlineSVGForMolecules
  GetInlineSVGForMolecules(Mols, MolsPerRow, MolWidth, MolHeight, Legends = None, AtomListsToHighlight = None, BondListsToHighLight = None, BoldText = 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.

  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>
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.
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.
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.
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.

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 molecule from a Tripos Mol2 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.
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.
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) 2018 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.

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