Chem.rdMolTransforms

Package Chem :: Module rdMolTransforms |
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# Module rdMolTransforms

    Module containing functions to perform 3D operations like rotate and translate conformations

Functions | [hide private]
CanonicalizeConformer(...) CanonicalizeConformer( (Conformer)conf [, (Point3D)center=None [, (bool)normalizeCovar=False [, (bool)ignoreHs=True]]]) -> None :... | source code
CanonicalizeMol(...) CanonicalizeMol( (Mol)mol [, (bool)normalizeCovar=False [, (bool)ignoreHs=True]]) -> None :... | source code
ComputeCanonicalTransform(...) ComputeCanonicalTransform( (Conformer)conf [, (Point3D)center=None [, (bool)normalizeCovar=False [, (bool)ignoreHs=True]]]) -> object :... | source code
ComputeCentroid(...) ComputeCentroid( (Conformer)conf [, (bool)ignoreHs=True]) -> Point3D :... | source code
TransformConformer(...) TransformConformer( (Conformer)arg1, (AtomPairsParameters)arg2) -> None :... | source code

Function Details | [hide private]

### CanonicalizeConformer(...) | source code
    CanonicalizeConformer( (Conformer)conf [, (Point3D)center=None [, (bool)normalizeCovar=False [, (bool)ignoreHs=True]]]) -> None :
        Canonicalize the orientation of a conformer so that its principal axes
                       around the specified center point coincide with the x, y, z axes

          ARGUMENTS:
            - conf : conformer of interest
            - center : optionally center point about which the principal axes are computed
                                  if not specified the centroid of the conformer will be used
            - normalizeCovar : Optionally normalize the covariance matrix by the number of atoms

        C++ signature :
            void CanonicalizeConformer(RDKit::Conformer {lvalue} [,RDGeom::Point3D const*=None [,bool=False [,bool=True]]])

### CanonicalizeMol(...) | source code
    CanonicalizeMol( (Mol)mol [, (bool)normalizeCovar=False [, (bool)ignoreHs=True]]) -> None :
        Loop over the conformers in a molecule and canonicalize their orientation

        C++ signature :
            void CanonicalizeMol(RDKit::ROMol {lvalue} [,bool=False [,bool=True]])

### ComputeCanonicalTransform(...) | source code
    ComputeCanonicalTransform( (Conformer)conf [, (Point3D)center=None [, (bool)normalizeCovar=False [, (bool)ignoreHs=True]]]) -> object :
        Compute the transformation required aligna conformer so that
                       the the principal axes align up with the x,y, z axes
                       The conformer itself is left unchanged
          ARGUMENTS:
            - conf : the conformer of interest
            - center : optional center point to compute the principal axes around (defaults to the centroid)
            - normalizeCovar : optionally normalize the covariance matrix by the number of atoms

        C++ signature :
            _object* ComputeCanonicalTransform(RDKit::Conformer [,RDGeom::Point3D const*=None [,bool=False [,bool=True]]])

### ComputeCentroid(...) | source code
    ComputeCentroid( (Conformer)conf [, (bool)ignoreHs=True]) -> Point3D :
        Compute the centroid of the conformation - hydrogens are ignored and no attention
                                   if paid to the difference in sizes of the heavy atoms

        C++ signature :
            RDGeom::Point3D ComputeCentroid(RDKit::Conformer [,bool=True])

### TransformConformer(...) | source code
    TransformConformer( (Conformer)arg1, (AtomPairsParameters)arg2) -> None :
        Transform the coordinates of a conformer

        C++ signature :
            void TransformConformer(RDKit::Conformer {lvalue},boost::python::api::object)