Package rdkit :: Package Chem :: Module AllChem

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# Module AllChem

source code

    Import all RDKit chemistry modules

Functions | [hide private]

TransformMol(mol, tform, confId=-1, keepConfs=False) Applies the transformation (usually a 4x4 double matrix) to a molecule... | source code

ComputeMolShape(mol, confId=-1, boxDim=(20,20,20), spacing=0.5, **kwargs) returns a grid representation of the molecule's shape... | source code

ComputeMolVolume(mol, confId=-1, gridSpacing=0.2, boxMargin=2.0) Calculates the volume of a particular conformer of a molecule based on a grid-encoding of the molecular shape. | source code

GenerateDepictionMatching2DStructure(mol, reference, confId=-1, referencePattern=None, acceptFailure=False, **kwargs) Generates a depiction for a molecule where a piece of the molecule is constrained to have the same coordinates as a reference. | source code

GenerateDepictionMatching3DStructure(mol, reference, confId=-1, **kwargs) Generates a depiction for a molecule where a piece of the molecule is constrained to have coordinates similar to those of a 3D reference structure. | source code

GetBestRMS(ref, probe, refConfId=-1, probeConfId=-1, maps=None) Returns the optimal RMS for aligning two molecules, taking symmetry into account. | source code

GetConformerRMS(mol, confId1, confId2, atomIds=None, prealigned=False) Returns the RMS between two conformations. | source code

GetConformerRMSMatrix(mol, atomIds=None, prealigned=False) Returns the RMS matrix of the conformers of a molecule. | source code

EnumerateLibraryFromReaction(reaction, sidechainSets) Returns a generator for the virtual library defined by a reaction and a sequence of sidechain sets | source code

ConstrainedEmbed(mol, core, useTethers=True, coreConfId=-1, randomseed=2342, getForceField=UFFGetMoleculeForceField, **kwargs) generates an embedding of a molecule where part of the molecule is constrained to have particular coordinates | source code

AssignBondOrdersFromTemplate(refmol, mol) assigns bond orders to a molecule based on the bond orders in a template molecule | source code

_test() | source code

Variables | [hide private]

| logger = `logger()`

Imports: rdBase, RDConfig, DataStructs, rdGeometry, ForceField, numpy, os, warnings

Function Details | [hide private]

### TransformMol(mol, tform, confId=-1, keepConfs=False)

source code

    Applies the transformation (usually a 4x4 double matrix) to a molecule
    if keepConfs is False then all but that conformer are removed

### ComputeMolShape(mol, confId=-1, boxDim=(20,20,20), spacing=0.5, **kwargs)

source code

    returns a grid representation of the molecule's shape

### GenerateDepictionMatching2DStructure(mol, reference, confId=-1, referencePattern=None, acceptFailure=False, **kwargs)

source code

    Generates a depiction for a molecule where a piece of the molecule
       is constrained to have the same coordinates as a reference.

       This is useful for, for example, generating depictions of SAR data
       sets so that the cores of the molecules are all oriented the same
       way.

    Arguments:
      - mol:          the molecule to be aligned, this will come back
                      with a single conformer.
      - reference:    a molecule with the reference atoms to align to;
                      this should have a depiction.
      - confId:       (optional) the id of the reference conformation to use
      - referencePattern:  (optional) an optional molecule to be used to
                           generate the atom mapping between the molecule
                           and the reference.
      - acceptFailure: (optional) if True, standard depictions will be generated
                       for molecules that don't have a substructure match to the
                       reference; if False, a ValueError will be raised

### GenerateDepictionMatching3DStructure(mol, reference, confId=-1, **kwargs)

source code

    Generates a depiction for a molecule where a piece of the molecule
       is constrained to have coordinates similar to those of a 3D reference
       structure.

    Arguments:
      - mol:          the molecule to be aligned, this will come back
                      with a single conformer.
      - reference:    a molecule with the reference atoms to align to;
                      this should have a depiction.
      - confId:       (optional) the id of the reference conformation to use

### GetBestRMS(ref, probe, refConfId=-1, probeConfId=-1, maps=None)

source code

    Returns the optimal RMS for aligning two molecules, taking
    symmetry into account. As a side-effect, the probe molecule is
    left in the aligned state.

    Arguments:
      - ref: the reference molecule
      - probe: the molecule to be aligned to the reference
      - refConfId: (optional) reference conformation to use
      - probeConfId: (optional) probe conformation to use
      - maps: (optional) a list of lists of (probeAtomId,refAtomId)
        tuples with the atom-atom mappings of the two molecules.
        If not provided, these will be generated using a substructure
        search.

    Note:
    This function will attempt to align all permutations of matching atom
    orders in both molecules, for some molecules it will lead to 'combinatorial
    explosion' especially if hydrogens are present.
    Use 'rdkit.Chem.AllChem.AlignMol' to align molecules without changing the
    atom order.

### GetConformerRMS(mol, confId1, confId2, atomIds=None, prealigned=False)

source code

    Returns the RMS between two conformations.
    By default, the conformers will be aligned to the first conformer
    of the molecule (i.e. the reference) before RMS calculation and,
    as a side-effect, will be left in the aligned state.

    Arguments:
      - mol:        the molecule
      - confId1:    the id of the first conformer
      - confId2:    the id of the second conformer
      - atomIds:    (optional) list of atom ids to use a points for
                    alingment - defaults to all atoms
      - prealigned: (optional) by default the conformers are assumed
                    be unaligned and will therefore be aligned to the
                    first conformer

### GetConformerRMSMatrix(mol, atomIds=None, prealigned=False)

source code

    Returns the RMS matrix of the conformers of a molecule.
    As a side-effect, the conformers will be aligned to the first
    conformer (i.e. the reference) and will left in the aligned state.

    Arguments:
      - mol:     the molecule
      - atomIds: (optional) list of atom ids to use a points for
                 alingment - defaults to all atoms
      - prealigned: (optional) by default the conformers are assumed
                    be unaligned and will therefore be aligned to the
                    first conformer

    Note that the returned RMS matrix is symmetrically, i.e. it is the
    lower half of the matrix, e.g. for 5 conformers:
    rmsmatrix = [ a,
                  b, c,
                  d, e, f,
                  g, h, i, j]
    This way it can be directly used as distance matrix in e.g. Butina
    clustering.

### EnumerateLibraryFromReaction(reaction, sidechainSets)

source code

    Returns a generator for the virtual library defined by
     a reaction and a sequence of sidechain sets

    >>> from rdkit import Chem
    >>> from rdkit.Chem import AllChem
    >>> s1=[Chem.MolFromSmiles(x) for x in ('NC','NCC')]
    >>> s2=[Chem.MolFromSmiles(x) for x in ('OC=O','OC(=O)C')]
    >>> rxn = AllChem.ReactionFromSmarts('[O:2]=[C:1][OH].[N:3]>>[O:2]=[C:1][N:3]')
    >>> r = AllChem.EnumerateLibraryFromReaction(rxn,[s2,s1])
    >>> [Chem.MolToSmiles(x[0]) for x in list(r)]
    ['CNC=O', 'CCNC=O', 'CNC(C)=O', 'CCNC(C)=O']

    Note that this is all done in a lazy manner, so "infinitely" large libraries can
    be done without worrying about running out of memory. Your patience will run out first:

    Define a set of 10000 amines:
    >>> amines = (Chem.MolFromSmiles('N'+'C'*x) for x in range(10000))

    ... a set of 10000 acids
    >>> acids = (Chem.MolFromSmiles('OC(=O)'+'C'*x) for x in range(10000))

    ... now the virtual library (1e8 compounds in principle):
    >>> r = AllChem.EnumerateLibraryFromReaction(rxn,[acids,amines])

    ... look at the first 4 compounds:
    >>> [Chem.MolToSmiles(next(r)[0]) for x in range(4)]
    ['NC=O', 'CNC=O', 'CCNC=O', 'CCCNC=O']

### ConstrainedEmbed(mol, core, useTethers=True, coreConfId=-1, randomseed=2342, getForceField=UFFGetMoleculeForceField, **kwargs)

source code

    generates an embedding of a molecule where part of the molecule
    is constrained to have particular coordinates

    Arguments
      - mol: the molecule to embed
      - core: the molecule to use as a source of constraints
      - useTethers: (optional) 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: (optional) id of the core conformation to use
      - randomSeed: (optional) seed for the random number generator

      An example, start by generating a template with a 3D structure:
      >>> from rdkit.Chem import AllChem
      >>> template = AllChem.MolFromSmiles("c1nn(Cc2ccccc2)cc1")
      >>> AllChem.EmbedMolecule(template)
      0
      >>> AllChem.UFFOptimizeMolecule(template)
      0

      Here's a molecule:
      >>> mol = AllChem.MolFromSmiles("c1nn(Cc2ccccc2)cc1-c3ccccc3")

      Now do the constrained embedding
      >>> newmol=AllChem.ConstrainedEmbed(mol, template)

      Demonstrate that the positions are the same:
      >>> newp=newmol.GetConformer().GetAtomPosition(0)
      >>> molp=mol.GetConformer().GetAtomPosition(0)
      >>> list(newp-molp)==[0.0,0.0,0.0]
      True
      >>> newp=newmol.GetConformer().GetAtomPosition(1)
      >>> molp=mol.GetConformer().GetAtomPosition(1)
      >>> list(newp-molp)==[0.0,0.0,0.0]
      True

### AssignBondOrdersFromTemplate(refmol, mol)

source code

    assigns bond orders to a molecule based on the
        bond orders in a template molecule

    Arguments
      - refmol: the template molecule
      - mol: the molecule to assign bond orders to

      An example, start by generating a template from a SMILES
      and read in the PDB structure of the molecule
      >>> from rdkit.Chem import AllChem
      >>> template = AllChem.MolFromSmiles("CN1C(=NC(C1=O)(c2ccccc2)c3ccccc3)N")
      >>> mol = AllChem.MolFromPDBFile(os.path.join(RDConfig.RDCodeDir, 'Chem', 'test_data', '4DJU_lig.pdb'))
      >>> len([1 for b in template.GetBonds() if b.GetBondTypeAsDouble() == 1.0])
      8
      >>> len([1 for b in mol.GetBonds() if b.GetBondTypeAsDouble() == 1.0])
      22

      Now assign the bond orders based on the template molecule
      >>> newMol = AllChem.AssignBondOrdersFromTemplate(template, mol)
      >>> len([1 for b in newMol.GetBonds() if b.GetBondTypeAsDouble() == 1.0])
      8

      Note that the template molecule should have no explicit hydrogens
      else the algorithm will fail.

      It also works if there are different formal charges (this was github issue 235):
      >>> template=AllChem.MolFromSmiles('CN(C)C(=O)Cc1ccc2c(c1)NC(=O)c3ccc(cc3N2)c4ccc(c(c4)OC)[N+](=O)[O-]')
      >>> mol = AllChem.MolFromMolFile(os.path.join(RDConfig.RDCodeDir, 'Chem', 'test_data', '4FTR_lig.mol'))
      >>> AllChem.MolToSmiles(mol)
      'COC1CC(C2CCC3C(O)NC4CC(CC(O)N(C)C)CCC4NC3C2)CCC1N(O)O'
      >>> newMol = AllChem.AssignBondOrdersFromTemplate(template, mol)
      >>> AllChem.MolToSmiles(newMol)
      'COc1cc(-c2ccc3c(c2)Nc2ccc(CC(=O)N(C)C)cc2NC3=O)ccc1[N+](=O)[O-]'