rdkit.Chem.rdDistGeom

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 intial
         coordinates for a molecule

         ARGUMENTS:

            - mol : the molecule of interest
            - params : an EmbedParameters object

         RETURNS:

            ID of the new conformation added to the molecule

        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
          - params : an EmbedParameters object
         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 :