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 {lvalue},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 {lvalue},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 {lvalue},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 {lvalue},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 {lvalue},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)