Chem.rdDistGeom

Package Chem :: Module rdDistGeom |
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# Module rdDistGeom

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

Functions | [hide private]
EmbedMolecule(...) 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. | source code
EmbedMultipleConfs(...) 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. | source code
GetMoleculeBoundsMatrix(...) Returns the distance bounds matrix for a molecule... | source code

Function Details | [hide private]

### EmbedMolecule(...) | source code
    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

     RETURNS:

        ID of the new conformation added to the molecule

    C++ signature:
        EmbedMolecule(RDKit::ROMol {lvalue} mol, unsigned int maxAttempts=30, int randomSeed=-1, bool clearConfs=True, bool useRandomCoords=False, double boxSizeMult=2.0, bool randNegEig=True, unsigned int numZeroFail=1) -> int

### EmbedMultipleConfs(...) | source code
    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.
     RETURNS:

        List of new conformation IDs

    C++ signature:
        EmbedMultipleConfs(RDKit::ROMol {lvalue} mol, unsigned int numConfs=10, unsigned int maxAttempts=10, int randomSeed=-1, bool clearConfs=True, bool useRandomCoords=False, double boxSizeMult=2.0, bool randNegEig=True, unsigned int numZeroFail=1, double pruneRmsThresh=-1.0) -> std::vector<int, std::allocator<int> >

### GetMoleculeBoundsMatrix(...) | source code
    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:
        GetMoleculeBoundsMatrix(RDKit::ROMol {lvalue} mol, bool set15bounds=True, bool scaleVDW=False) -> _object*