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Module containing functions to compute atomic coordinates in 3D using distance geometry
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__package__ = None hash(x) |
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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 is we have this more 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]]]]]]]]]]]]]]) |
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 is we have this more 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]]]]]]]]]]]]]]]]]) |
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]]) |
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