rdkit.Chem.rdMolTransforms

Package rdkit :: 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 : Canonicalize the orientation of a conformer so that its principal axes around the specified center point coincide with the x, y, z axes |
CanonicalizeMol(...) CanonicalizeMol( (Mol)mol [, (bool)normalizeCovar=False [, (bool)ignoreHs=True]]) -> None : Loop over the conformers in a molecule and canonicalize their orientation |
ComputeCanonicalTransform(...) 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 |
ComputeCentroid(...) 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 |
GetAngleDeg(...) GetAngleDeg( (Conformer)conf, (int)iAtomId, (int)jAtomId, (int)kAtomId) -> float : Returns the angle in degrees between atoms i, j, k |
GetAngleRad(...) GetAngleRad( (Conformer)conf, (int)iAtomId, (int)jAtomId, (int)kAtomId) -> float : Returns the angle in radians between atoms i, j, k |
GetBondLength(...) GetBondLength( (Conformer)conf, (int)iAtomId, (int)jAtomId) -> float : Returns the bond length in angstrom between atoms i, j |
GetDihedralDeg(...) GetDihedralDeg( (Conformer)conf, (int)iAtomId, (int)jAtomId, (int)kAtomId, (int)lAtomId) -> float : Returns the dihedral angle in degrees between atoms i, j, k, l |
GetDihedralRad(...) GetDihedralRad( (Conformer)conf, (int)iAtomId, (int)jAtomId, (int)kAtomId, (int)lAtomId) -> float : Returns the dihedral angle in radians between atoms i, j, k, l |
SetAngleDeg(...) SetAngleDeg( (Conformer)conf, (int)iAtomId, (int)jAtomId, (int)kAtomId, (float)value) -> None : Sets the angle in degrees between atoms i, j, k; all atoms bonded to atom k are moved |
SetAngleRad(...) SetAngleRad( (Conformer)conf, (int)iAtomId, (int)jAtomId, (int)kAtomId, (float)value) -> None : Sets the angle in radians between atoms i, j, k; all atoms bonded to atom k are moved |
SetBondLength(...) SetBondLength( (Conformer)conf, (int)iAtomId, (int)jAtomId, (float)value) -> None : Sets the bond length in angstrom between atoms i, j; all atoms bonded to atom j are moved |
SetDihedralDeg(...) SetDihedralDeg( (Conformer)arg1, (int)arg2, (int)arg3, (int)arg4, (int)arg5, (float)arg6) -> None : Sets the dihedral angle in degrees between atoms i, j, k, l; all atoms bonded to atom l are moved |
SetDihedralRad(...) SetDihedralRad( (Conformer)conf, (int)iAtomId, (int)jAtomId, (int)kAtomId, (int)lAtomId, (float)value) -> None : Sets the dihedral angle in radians between atoms i, j, k, l; all atoms bonded to atom l are moved |
TransformConformer(...) TransformConformer( (Conformer)arg1, (AtomPairsParameters)arg2) -> None : Transform the coordinates of a conformer |

Variables | [hide private]
| __package__ = `None` hash(x)

Function Details | [hide private]

### CanonicalizeConformer(...) |
    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(...) |
    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(...) |
    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(...) |
    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])

### GetAngleDeg(...) |
    GetAngleDeg( (Conformer)conf, (int)iAtomId, (int)jAtomId, (int)kAtomId) -> float :
        Returns the angle in degrees between atoms i, j, k

        C++ signature :
            double GetAngleDeg(RDKit::Conformer,unsigned int,unsigned int,unsigned int)

### GetAngleRad(...) |
    GetAngleRad( (Conformer)conf, (int)iAtomId, (int)jAtomId, (int)kAtomId) -> float :
        Returns the angle in radians between atoms i, j, k

        C++ signature :
            double GetAngleRad(RDKit::Conformer,unsigned int,unsigned int,unsigned int)

### GetBondLength(...) |
    GetBondLength( (Conformer)conf, (int)iAtomId, (int)jAtomId) -> float :
        Returns the bond length in angstrom between atoms i, j

        C++ signature :
            double GetBondLength(RDKit::Conformer,unsigned int,unsigned int)

### GetDihedralDeg(...) |
    GetDihedralDeg( (Conformer)conf, (int)iAtomId, (int)jAtomId, (int)kAtomId, (int)lAtomId) -> float :
        Returns the dihedral angle in degrees between atoms i, j, k, l

        C++ signature :
            double GetDihedralDeg(RDKit::Conformer,unsigned int,unsigned int,unsigned int,unsigned int)

### GetDihedralRad(...) |
    GetDihedralRad( (Conformer)conf, (int)iAtomId, (int)jAtomId, (int)kAtomId, (int)lAtomId) -> float :
        Returns the dihedral angle in radians between atoms i, j, k, l

        C++ signature :
            double GetDihedralRad(RDKit::Conformer,unsigned int,unsigned int,unsigned int,unsigned int)

### SetAngleDeg(...) |
    SetAngleDeg( (Conformer)conf, (int)iAtomId, (int)jAtomId, (int)kAtomId, (float)value) -> None :
        Sets the angle in degrees between atoms i, j, k; all atoms bonded to atom k are moved

        C++ signature :
            void SetAngleDeg(RDKit::Conformer {lvalue},unsigned int,unsigned int,unsigned int,double)

### SetAngleRad(...) |
    SetAngleRad( (Conformer)conf, (int)iAtomId, (int)jAtomId, (int)kAtomId, (float)value) -> None :
        Sets the angle in radians between atoms i, j, k; all atoms bonded to atom k are moved

        C++ signature :
            void SetAngleRad(RDKit::Conformer {lvalue},unsigned int,unsigned int,unsigned int,double)

### SetBondLength(...) |
    SetBondLength( (Conformer)conf, (int)iAtomId, (int)jAtomId, (float)value) -> None :
        Sets the bond length in angstrom between atoms i, j; all atoms bonded to atom j are moved

        C++ signature :
            void SetBondLength(RDKit::Conformer {lvalue},unsigned int,unsigned int,double)

### SetDihedralDeg(...) |
    SetDihedralDeg( (Conformer)arg1, (int)arg2, (int)arg3, (int)arg4, (int)arg5, (float)arg6) -> None :
        Sets the dihedral angle in degrees between atoms i, j, k, l; all atoms bonded to atom l are moved

        C++ signature :
            void SetDihedralDeg(RDKit::Conformer {lvalue},unsigned int,unsigned int,unsigned int,unsigned int,double)

### SetDihedralRad(...) |
    SetDihedralRad( (Conformer)conf, (int)iAtomId, (int)jAtomId, (int)kAtomId, (int)lAtomId, (float)value) -> None :
        Sets the dihedral angle in radians between atoms i, j, k, l; all atoms bonded to atom l are moved

        C++ signature :
            void SetDihedralRad(RDKit::Conformer {lvalue},unsigned int,unsigned int,unsigned int,unsigned int,double)

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

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