Module rdDistGeom

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

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> >

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*