Package rdkit :: Package Chem :: Module rdDistGeom
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Module rdDistGeom

Module containing functions to compute atomic coordinates in 3D using distance geometry

Classes [hide private]
  EmbedParameters
Parameters controlling embedding
Functions [hide private]
EmbedParameters :

ETDG()
Returns an EmbedParameters object for the ETDG method.
EmbedParameters :

ETKDG()
Returns an EmbedParameters object for the ETKDG method.
 
EmbedMolecule(...)
EmbedMolecule( (Mol)mol [, (int)maxAttempts=0 [, (int)randomSeed=-1 [, (bool)clearConfs=True [, (bool)useRandomCoords=False [, (float)boxSizeMult=2.0 [, (bool)randNegEig=True [, (int)numZeroFail=1 [, (dict)coordMap={} [, (float)forceTol=0.001 [, (bool)ignoreSmoothingFailures=False [, (bool)enforceChirality=True [, (bool)useExpTorsionAnglePrefs=False [, (bool)useBasicKnowledge=False [, (bool)printExpTorsionAngles=False]]]]]]]]]]]]]]) -> int : Use distance geometry to obtain intial coordinates for a molecule
 
EmbedMultipleConfs(...)
EmbedMultipleConfs( (Mol)mol [, (int)numConfs=10 [, (int)maxAttempts=0 [, (int)randomSeed=-1 [, (bool)clearConfs=True [, (bool)useRandomCoords=False [, (float)boxSizeMult=2.0 [, (bool)randNegEig=True [, (int)numZeroFail=1 [, (float)pruneRmsThresh=-1.0 [, (dict)coordMap={} [, (float)forceTol=0.001 [, (bool)ignoreSmoothingFailures=False [, (bool)enforceChirality=True [, (int)numThreads=1 [, (bool)useExpTorsionAnglePrefs=False [, (bool)useBasicKnowledge=False [, (bool)printExpTorsionAngles=False]]]]]]]]]]]]]]]]]) -> _vecti : Use distance geometry to obtain multiple sets of coordinates for a molecule
 
GetMoleculeBoundsMatrix(...)
GetMoleculeBoundsMatrix( (Mol)mol [, (bool)set15bounds=True [, (bool)scaleVDW=False]]) -> object : Returns the distance bounds matrix for a molecule
EmbedParameters :

KDG()
Returns an EmbedParameters object for the KDG method.
Variables [hide private]
  __package__ = None
hash(x)
Function Details [hide private]

ETDG()

 
    Returns an EmbedParameters object for the ETDG method.

    C++ signature :
        RDKit::DGeomHelpers::EmbedParameters* ETDG()

Returns:
EmbedParameters :

ETKDG()

 
    Returns an EmbedParameters object for the ETKDG method.

    C++ signature :
        RDKit::DGeomHelpers::EmbedParameters* ETKDG()

Returns:
EmbedParameters :

EmbedMolecule(...)

 

EmbedMolecule( (Mol)mol [, (int)maxAttempts=0 [, (int)randomSeed=-1 [, (bool)clearConfs=True [, (bool)useRandomCoords=False [, (float)boxSizeMult=2.0 [, (bool)randNegEig=True [, (int)numZeroFail=1 [, (dict)coordMap={} [, (float)forceTol=0.001 [, (bool)ignoreSmoothingFailures=False [, (bool)enforceChirality=True [, (bool)useExpTorsionAnglePrefs=False [, (bool)useBasicKnowledge=False [, (bool)printExpTorsionAngles=False]]]]]]]]]]]]]]) -> int :
    Use distance geometry to obtain intial 
     coordinates for a molecule
    
     
     ARGUMENTS:
    
        - mol : the molecule of interest
        - maxAttempts : the maximum number of attempts to try embedding 
        - randomSeed : provide a seed for the random number generator 
                       so that the same coordinates can be obtained 
                       for a molecule on multiple runs. The default 
                       (-1) uses a random seed 
        - clearConfs : clear all existing conformations on the molecule
        - useRandomCoords : Start the embedding from random coordinates instead of
                            using eigenvalues of the distance matrix.
        - boxSizeMult    Determines the size of the box that is used for
                         random coordinates. If this is a positive number, the 
                         side length will equal the largest element of the distance
                         matrix times boxSizeMult. If this is a negative number,
                         the side length will equal -boxSizeMult (i.e. independent
                         of the elements of the distance matrix).
        - randNegEig : If the embedding yields a negative eigenvalue, 
                       pick coordinates that correspond 
                       to this component at random 
        - numZeroFail : fail embedding if we have at least this many zero eigenvalues 
        - coordMap : a dictionary mapping atom IDs->coordinates. Use this to 
                     require some atoms to have fixed coordinates in the resulting 
                     conformation.
        - forceTol : tolerance to be used during the force-field minimization with 
                     the distance geometry force field.
        - ignoreSmoothingFailures : try to embed the molecule even if triangle smoothing
                     of the bounds matrix fails.
        - enforceChirality : enforce the correct chirality if chiral centers are present.
        - useExpTorsionAnglePrefs : impose experimental torsion angle preferences
        - useBasicKnowledge : impose basic knowledge such as flat rings
        - printExpTorsionAngles : print the output from the experimental torsion angles
    
     RETURNS:
    
        ID of the new conformation added to the molecule 
    
    

    C++ signature :
        int EmbedMolecule(RDKit::ROMol {lvalue} [,unsigned int=0 [,int=-1 [,bool=True [,bool=False [,double=2.0 [,bool=True [,unsigned int=1 [,boost::python::dict {lvalue}={} [,double=0.001 [,bool=False [,bool=True [,bool=False [,bool=False [,bool=False]]]]]]]]]]]]]])

EmbedMolecule( (Mol)mol, (EmbedParameters)params) -> int :
    Use distance geometry to obtain multiple sets of 
     coordinates for a molecule
     
     ARGUMENTS:
    
      - mol : the molecule of interest
      - numConfs : the number of conformers to generate 
      - maxAttempts : the maximum number of attempts to try embedding 
      - randomSeed : provide a seed for the random number generator 
                     so that the same coordinates can be obtained 
                     for a molecule on multiple runs. The default 
                     (-1) uses a random seed 
      - clearConfs : clear all existing conformations on the molecule
      - useRandomCoords : Start the embedding from random coordinates instead of
                          using eigenvalues of the distance matrix.
      - boxSizeMult    Determines the size of the box that is used for
                       random coordinates. If this is a positive number, the 
                       side length will equal the largest element of the distance
                       matrix times boxSizeMult. If this is a negative number,
                       the side length will equal -boxSizeMult (i.e. independent
                       of the elements of the distance matrix).
      - randNegEig : If the embedding yields a negative eigenvalue, 
                     pick coordinates that correspond 
                     to this component at random 
      - numZeroFail : fail embedding if we have at least this many zero eigenvalues 
      - pruneRmsThresh : Retain only the conformations out of 'numConfs' 
                        after embedding that are at least 
                        this far apart from each other. 
              RMSD is computed on the heavy atoms. 
              Pruning is greedy; i.e. the first embedded conformation
              is retained and from then on only those that are at
              least pruneRmsThresh away from all retained conformations
              are kept. The pruning is done after embedding and 
              bounds violation minimization. No pruning by default.
        - coordMap : a dictionary mapping atom IDs->coordinates. Use this to 
                     require some atoms to have fixed coordinates in the resulting 
                     conformation.
        - forceTol : tolerance to be used during the force-field minimization with 
                     the distance geometry force field.
        - ignoreSmoothingFailures : try to embed the molecule even if triangle smoothing
                     of the bounds matrix fails.
        - enforceChirality : enforce the correct chirality if chiral centers are present.
        - numThreads : number of threads to use while embedding. This only has an effect if the RDKit
                     was built with multi-thread support.
                    If set to zero, the max supported by the system will be used.
        - useExpTorsionAnglePrefs : impose experimental torsion angle preferences
        - useBasicKnowledge : impose basic knowledge such as flat rings
        - printExpTorsionAngles : print the output from the experimental torsion angles
     RETURNS:
    
        List of new conformation IDs 
    
    

    C++ signature :
        int EmbedMolecule(RDKit::ROMol {lvalue},RDKit::DGeomHelpers::EmbedParameters {lvalue})

EmbedMultipleConfs(...)

 

EmbedMultipleConfs( (Mol)mol [, (int)numConfs=10 [, (int)maxAttempts=0 [, (int)randomSeed=-1 [, (bool)clearConfs=True [, (bool)useRandomCoords=False [, (float)boxSizeMult=2.0 [, (bool)randNegEig=True [, (int)numZeroFail=1 [, (float)pruneRmsThresh=-1.0 [, (dict)coordMap={} [, (float)forceTol=0.001 [, (bool)ignoreSmoothingFailures=False [, (bool)enforceChirality=True [, (int)numThreads=1 [, (bool)useExpTorsionAnglePrefs=False [, (bool)useBasicKnowledge=False [, (bool)printExpTorsionAngles=False]]]]]]]]]]]]]]]]]) -> _vecti :
    Use distance geometry to obtain multiple sets of 
     coordinates for a molecule
     
     ARGUMENTS:
    
      - mol : the molecule of interest
      - numConfs : the number of conformers to generate 
      - maxAttempts : the maximum number of attempts to try embedding 
      - randomSeed : provide a seed for the random number generator 
                     so that the same coordinates can be obtained 
                     for a molecule on multiple runs. The default 
                     (-1) uses a random seed 
      - clearConfs : clear all existing conformations on the molecule
      - useRandomCoords : Start the embedding from random coordinates instead of
                          using eigenvalues of the distance matrix.
      - boxSizeMult    Determines the size of the box that is used for
                       random coordinates. If this is a positive number, the 
                       side length will equal the largest element of the distance
                       matrix times boxSizeMult. If this is a negative number,
                       the side length will equal -boxSizeMult (i.e. independent
                       of the elements of the distance matrix).
      - randNegEig : If the embedding yields a negative eigenvalue, 
                     pick coordinates that correspond 
                     to this component at random 
      - numZeroFail : fail embedding if we have at least this many zero eigenvalues 
      - pruneRmsThresh : Retain only the conformations out of 'numConfs' 
                        after embedding that are at least 
                        this far apart from each other. 
              RMSD is computed on the heavy atoms. 
              Pruning is greedy; i.e. the first embedded conformation
              is retained and from then on only those that are at
              least pruneRmsThresh away from all retained conformations
              are kept. The pruning is done after embedding and 
              bounds violation minimization. No pruning by default.
        - coordMap : a dictionary mapping atom IDs->coordinates. Use this to 
                     require some atoms to have fixed coordinates in the resulting 
                     conformation.
        - forceTol : tolerance to be used during the force-field minimization with 
                     the distance geometry force field.
        - ignoreSmoothingFailures : try to embed the molecule even if triangle smoothing
                     of the bounds matrix fails.
        - enforceChirality : enforce the correct chirality if chiral centers are present.
        - numThreads : number of threads to use while embedding. This only has an effect if the RDKit
                     was built with multi-thread support.
                    If set to zero, the max supported by the system will be used.
        - useExpTorsionAnglePrefs : impose experimental torsion angle preferences
        - useBasicKnowledge : impose basic knowledge such as flat rings
        - printExpTorsionAngles : print the output from the experimental torsion angles
     RETURNS:
    
        List of new conformation IDs 
    
    

    C++ signature :
        std::vector<int, std::allocator<int> > EmbedMultipleConfs(RDKit::ROMol {lvalue} [,unsigned int=10 [,unsigned int=0 [,int=-1 [,bool=True [,bool=False [,double=2.0 [,bool=True [,unsigned int=1 [,double=-1.0 [,boost::python::dict {lvalue}={} [,double=0.001 [,bool=False [,bool=True [,int=1 [,bool=False [,bool=False [,bool=False]]]]]]]]]]]]]]]]])

EmbedMultipleConfs( (Mol)mol, (int)numConfs, (EmbedParameters)params) -> _vecti :
    Use distance geometry to obtain multiple sets of 
     coordinates for a molecule
     
     ARGUMENTS:
    
      - mol : the molecule of interest
      - numConfs : the number of conformers to generate 
      - maxAttempts : the maximum number of attempts to try embedding 
      - randomSeed : provide a seed for the random number generator 
                     so that the same coordinates can be obtained 
                     for a molecule on multiple runs. The default 
                     (-1) uses a random seed 
      - clearConfs : clear all existing conformations on the molecule
      - useRandomCoords : Start the embedding from random coordinates instead of
                          using eigenvalues of the distance matrix.
      - boxSizeMult    Determines the size of the box that is used for
                       random coordinates. If this is a positive number, the 
                       side length will equal the largest element of the distance
                       matrix times boxSizeMult. If this is a negative number,
                       the side length will equal -boxSizeMult (i.e. independent
                       of the elements of the distance matrix).
      - randNegEig : If the embedding yields a negative eigenvalue, 
                     pick coordinates that correspond 
                     to this component at random 
      - numZeroFail : fail embedding if we have at least this many zero eigenvalues 
      - pruneRmsThresh : Retain only the conformations out of 'numConfs' 
                        after embedding that are at least 
                        this far apart from each other. 
              RMSD is computed on the heavy atoms. 
              Pruning is greedy; i.e. the first embedded conformation
              is retained and from then on only those that are at
              least pruneRmsThresh away from all retained conformations
              are kept. The pruning is done after embedding and 
              bounds violation minimization. No pruning by default.
        - coordMap : a dictionary mapping atom IDs->coordinates. Use this to 
                     require some atoms to have fixed coordinates in the resulting 
                     conformation.
        - forceTol : tolerance to be used during the force-field minimization with 
                     the distance geometry force field.
        - ignoreSmoothingFailures : try to embed the molecule even if triangle smoothing
                     of the bounds matrix fails.
        - enforceChirality : enforce the correct chirality if chiral centers are present.
        - numThreads : number of threads to use while embedding. This only has an effect if the RDKit
                     was built with multi-thread support.
                    If set to zero, the max supported by the system will be used.
        - useExpTorsionAnglePrefs : impose experimental torsion angle preferences
        - useBasicKnowledge : impose basic knowledge such as flat rings
        - printExpTorsionAngles : print the output from the experimental torsion angles
     RETURNS:
    
        List of new conformation IDs 
    
    

    C++ signature :
        std::vector<int, std::allocator<int> > EmbedMultipleConfs(RDKit::ROMol {lvalue},unsigned int,RDKit::DGeomHelpers::EmbedParameters {lvalue})

GetMoleculeBoundsMatrix(...)

 

GetMoleculeBoundsMatrix( (Mol)mol [, (bool)set15bounds=True [, (bool)scaleVDW=False]]) -> object :
    Returns the distance bounds matrix for a molecule
     
     ARGUMENTS:
    
        - mol : the molecule of interest
        - set15bounds : set bounds for 1-5 atom distances based on 
                        topology (otherwise stop at 1-4s)
        - scaleVDW : scale down the sum of VDW radii when setting the 
                     lower bounds for atoms less than 5 bonds apart 
     RETURNS:
    
        the bounds matrix as a Numeric array with lower bounds in 
        the lower triangle and upper bounds in the upper triangle
    
    

    C++ signature :
        _object* GetMoleculeBoundsMatrix(RDKit::ROMol {lvalue} [,bool=True [,bool=False]])

KDG()

 
    Returns an EmbedParameters object for the KDG method.

    C++ signature :
        RDKit::DGeomHelpers::EmbedParameters* KDG()

Returns:
EmbedParameters :