Package rdkit :: Package Chem :: Module rdForceFieldHelpers
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Module rdForceFieldHelpers

Module containing functions to handle force fields

Functions [hide private]
 
GetUFFAngleBendParams(...)
GetUFFAngleBendParams( (Mol)mol, (int)idx1, (int)idx2, (int)idx3) -> object : Retrieves UFF angle bend parameters for atoms with indexes idx1, idx2, idx3 as a (ka, theta0) tuple, or None if no parameters could be found
 
GetUFFBondStretchParams(...)
GetUFFBondStretchParams( (Mol)mol, (int)idx1, (int)idx2) -> object : Retrieves UFF bond stretch parameters for atoms with indexes idx1, idx2 as a (kb, r0) tuple, or None if no parameters could be found
 
GetUFFInversionParams(...)
GetUFFInversionParams( (Mol)mol, (int)idx1, (int)idx2, (int)idx3, (int)idx4) -> object : Retrieves UFF inversion parameters for atoms with indexes idx1, idx2, idx3, idx4 as a K float value, or None if no parameters could be found
 
GetUFFTorsionParams(...)
GetUFFTorsionParams( (Mol)mol, (int)idx1, (int)idx2, (int)idx3, (int)idx4) -> object : Retrieves UFF torsion parameters for atoms with indexes idx1, idx2, idx3, idx4 as a V float value, or None if no parameters could be found
 
GetUFFVdWParams(...)
GetUFFVdWParams( (Mol)mol, (int)idx1, (int)idx2) -> object : Retrieves UFF van der Waals parameters for atoms with indexes idx1, idx2 as a (x_ij, D_ij) tuple, or None if no parameters could be found
 
MMFFGetMoleculeForceField(...)
MMFFGetMoleculeForceField( (Mol)mol, (object)pyMMFFMolProperties [, (float)nonBondedThresh=100.0 [, (int)confId=-1 [, (bool)ignoreInterfragInteractions=True]]]) -> object : returns a MMFF force field for a molecule
 
MMFFGetMoleculeProperties(...)
MMFFGetMoleculeProperties( (Mol)mol [, (str)mmffVariant='MMFF94' [, (int)mmffVerbosity=0]]) -> object : returns a PyMMFFMolProperties object for a molecule, which is required by MMFFGetMoleculeForceField() and can be used to get/set MMFF properties
 
MMFFHasAllMoleculeParams(...)
MMFFHasAllMoleculeParams( (Mol)mol) -> bool : checks if MMFF parameters are available for all of a molecule's atoms
 
MMFFOptimizeMolecule(...)
MMFFOptimizeMolecule( (Mol)mol [, (str)mmffVariant='MMFF94' [, (int)maxIters=200 [, (float)nonBondedThresh=100.0 [, (int)confId=-1 [, (bool)ignoreInterfragInteractions=True]]]]]) -> int : uses MMFF to optimize a molecule's structure
 
MMFFOptimizeMoleculeConfs(...)
MMFFOptimizeMoleculeConfs( (Mol)self [, (int)numThreads=1 [, (int)maxIters=200 [, (str)mmffVariant='MMFF94' [, (float)nonBondedThresh=10.0 [, (int)confId=-1 [, (bool)ignoreInterfragInteractions=True]]]]]]) -> object : uses MMFF to optimize all of a molecule's conformations
 
MMFFSanitizeMolecule(...)
MMFFSanitizeMolecule( (Mol)mol) -> int : sanitizes a molecule according to MMFF requirements.
 
UFFGetMoleculeForceField(...)
UFFGetMoleculeForceField( (Mol)mol [, (float)vdwThresh=10.0 [, (int)confId=-1 [, (bool)ignoreInterfragInteractions=True]]]) -> object : returns a UFF force field for a molecule
 
UFFHasAllMoleculeParams(...)
UFFHasAllMoleculeParams( (Mol)mol) -> bool : checks if UFF parameters are available for all of a molecule's atoms
 
UFFOptimizeMolecule(...)
UFFOptimizeMolecule( (Mol)self [, (int)maxIters=200 [, (float)vdwThresh=10.0 [, (int)confId=-1 [, (bool)ignoreInterfragInteractions=True]]]]) -> int : uses UFF to optimize a molecule's structure
 
UFFOptimizeMoleculeConfs(...)
UFFOptimizeMoleculeConfs( (Mol)self [, (int)numThreads=1 [, (int)maxIters=200 [, (float)vdwThresh=10.0 [, (int)confId=-1 [, (bool)ignoreInterfragInteractions=True]]]]]) -> object : uses UFF to optimize all of a molecule's conformations
Variables [hide private]
  __package__ = None
hash(x)
Function Details [hide private]

GetUFFAngleBendParams(...)

 

GetUFFAngleBendParams( (Mol)mol, (int)idx1, (int)idx2, (int)idx3) -> object :
    Retrieves UFF angle bend parameters for atoms with indexes idx1, idx2, idx3 as a (ka, theta0) tuple, or None if no parameters could be found

    C++ signature :
        _object* GetUFFAngleBendParams(RDKit::ROMol,unsigned int,unsigned int,unsigned int)

GetUFFBondStretchParams(...)

 

GetUFFBondStretchParams( (Mol)mol, (int)idx1, (int)idx2) -> object :
    Retrieves UFF bond stretch parameters for atoms with indexes idx1, idx2 as a (kb, r0) tuple, or None if no parameters could be found

    C++ signature :
        _object* GetUFFBondStretchParams(RDKit::ROMol,unsigned int,unsigned int)

GetUFFInversionParams(...)

 

GetUFFInversionParams( (Mol)mol, (int)idx1, (int)idx2, (int)idx3, (int)idx4) -> object :
    Retrieves UFF inversion parameters for atoms with indexes idx1, idx2, idx3, idx4 as a K float value, or None if no parameters could be found

    C++ signature :
        _object* GetUFFInversionParams(RDKit::ROMol,unsigned int,unsigned int,unsigned int,unsigned int)

GetUFFTorsionParams(...)

 

GetUFFTorsionParams( (Mol)mol, (int)idx1, (int)idx2, (int)idx3, (int)idx4) -> object :
    Retrieves UFF torsion parameters for atoms with indexes idx1, idx2, idx3, idx4 as a V float value, or None if no parameters could be found

    C++ signature :
        _object* GetUFFTorsionParams(RDKit::ROMol,unsigned int,unsigned int,unsigned int,unsigned int)

GetUFFVdWParams(...)

 

GetUFFVdWParams( (Mol)mol, (int)idx1, (int)idx2) -> object :
    Retrieves UFF van der Waals parameters for atoms with indexes idx1, idx2 as a (x_ij, D_ij) tuple, or None if no parameters could be found

    C++ signature :
        _object* GetUFFVdWParams(RDKit::ROMol,unsigned int,unsigned int)

MMFFGetMoleculeForceField(...)

 

MMFFGetMoleculeForceField( (Mol)mol, (object)pyMMFFMolProperties [, (float)nonBondedThresh=100.0 [, (int)confId=-1 [, (bool)ignoreInterfragInteractions=True]]]) -> object :
    returns a MMFF force field for a molecule
    
     
     ARGUMENTS:
    
        - mol : the molecule of interest
        - pyMMFFMolProperties : PyMMFFMolProperties object as returned
                      by MMFFGetMoleculeProperties()
        - nonBondedThresh : used to exclude long-range non-bonded
                      interactions (defaults to 100.0)
        - confId : indicates which conformer to optimize
        - ignoreInterfragInteractions : if true, nonbonded terms between
                      fragments will not be added to the forcefield
    
    

    C++ signature :
        ForceFields::PyForceField* MMFFGetMoleculeForceField(RDKit::ROMol {lvalue},ForceFields::PyMMFFMolProperties* [,double=100.0 [,int=-1 [,bool=True]]])

MMFFGetMoleculeProperties(...)

 

MMFFGetMoleculeProperties( (Mol)mol [, (str)mmffVariant='MMFF94' [, (int)mmffVerbosity=0]]) -> object :
    returns a PyMMFFMolProperties object for a
      molecule, which is required by MMFFGetMoleculeForceField()
      and can be used to get/set MMFF properties
    
      
      ARGUMENTS:
    
        - mol : the molecule of interest
        - mmffVariant : "MMFF94" or "MMFF94s"
                      (defaults to "MMFF94")
        - mmffVerbosity : 0: none; 1: low; 2: high (defaults to 0).
    
    

    C++ signature :
        ForceFields::PyMMFFMolProperties* MMFFGetMoleculeProperties(RDKit::ROMol {lvalue} [,std::string='MMFF94' [,unsigned int=0]])

MMFFHasAllMoleculeParams(...)

 

MMFFHasAllMoleculeParams( (Mol)mol) -> bool :
    checks if MMFF parameters are available for all of a molecule's atoms
    
     
     ARGUMENTS:
    
        - mol : the molecule of interest
    
    

    C++ signature :
        bool MMFFHasAllMoleculeParams(RDKit::ROMol {lvalue})

MMFFOptimizeMolecule(...)

 

MMFFOptimizeMolecule( (Mol)mol [, (str)mmffVariant='MMFF94' [, (int)maxIters=200 [, (float)nonBondedThresh=100.0 [, (int)confId=-1 [, (bool)ignoreInterfragInteractions=True]]]]]) -> int :
    uses MMFF to optimize a molecule's structure
    
     
     ARGUMENTS:
    
        - mol : the molecule of interest
        - mmffVariant : "MMFF94" or "MMFF94s"
        - maxIters : the maximum number of iterations (defaults to 200)
        - nonBondedThresh : used to exclude long-range non-bonded
                     interactions (defaults to 100.0)
        - confId : indicates which conformer to optimize
        - ignoreInterfragInteractions : if true, nonbonded terms between
                     fragments will not be added to the forcefield
    
     RETURNS: 0 if the optimization converged, -1 if the forcefield could
              not be set up, 1 if more iterations are required.
    
    

    C++ signature :
        int MMFFOptimizeMolecule(RDKit::ROMol {lvalue} [,std::string='MMFF94' [,int=200 [,double=100.0 [,int=-1 [,bool=True]]]]])

MMFFOptimizeMoleculeConfs(...)

 

MMFFOptimizeMoleculeConfs( (Mol)self [, (int)numThreads=1 [, (int)maxIters=200 [, (str)mmffVariant='MMFF94' [, (float)nonBondedThresh=10.0 [, (int)confId=-1 [, (bool)ignoreInterfragInteractions=True]]]]]]) -> object :
    uses MMFF to optimize all of a molecule's conformations
    
     
     ARGUMENTS:
    
        - mol : the molecule of interest
        - numThreads : the number of threads to use, only has an effect if the RDKit
                       was built with thread support (defaults to 1)
                       If set to zero, the max supported by the system will be used.
        - maxIters : the maximum number of iterations (defaults to 200)
        - mmffVariant : "MMFF94" or "MMFF94s"
        - nonBondedThresh : used to exclude long-range non-bonded
                      interactions (defaults to 100.0)
        - confId : indicates which conformer to optimize
        - ignoreInterfragInteractions : if true, nonbonded terms between
                      fragments will not be added to the forcefield.
    
     RETURNS: 0 if the optimization converged, 1 if more iterations are required.
    
    

    C++ signature :
        boost::python::api::object MMFFOptimizeMoleculeConfs(RDKit::ROMol {lvalue} [,int=1 [,int=200 [,std::string='MMFF94' [,double=10.0 [,int=-1 [,bool=True]]]]]])

MMFFSanitizeMolecule(...)

 

MMFFSanitizeMolecule( (Mol)mol) -> int :
    sanitizes a molecule according to MMFF requirements.
    
        - mol : the molecule of interest.
    
    

    C++ signature :
        unsigned int MMFFSanitizeMolecule(RDKit::ROMol {lvalue})

UFFGetMoleculeForceField(...)

 

UFFGetMoleculeForceField( (Mol)mol [, (float)vdwThresh=10.0 [, (int)confId=-1 [, (bool)ignoreInterfragInteractions=True]]]) -> object :
    returns a UFF force field for a molecule
    
     
     ARGUMENTS:
    
        - mol : the molecule of interest
        - vdwThresh : used to exclude long-range van der Waals interactions
                      (defaults to 10.0)
        - confId : indicates which conformer to optimize
        - ignoreInterfragInteractions : if true, nonbonded terms between
                      fragments will not be added to the forcefield.
    
    

    C++ signature :
        ForceFields::PyForceField* UFFGetMoleculeForceField(RDKit::ROMol {lvalue} [,double=10.0 [,int=-1 [,bool=True]]])

UFFHasAllMoleculeParams(...)

 

UFFHasAllMoleculeParams( (Mol)mol) -> bool :
    checks if UFF parameters are available for all of a molecule's atoms
    
     
     ARGUMENTS:
    
        - mol : the molecule of interest.
    
    

    C++ signature :
        bool UFFHasAllMoleculeParams(RDKit::ROMol)

UFFOptimizeMolecule(...)

 

UFFOptimizeMolecule( (Mol)self [, (int)maxIters=200 [, (float)vdwThresh=10.0 [, (int)confId=-1 [, (bool)ignoreInterfragInteractions=True]]]]) -> int :
    uses UFF to optimize a molecule's structure
    
     
     ARGUMENTS:
    
        - mol : the molecule of interest
        - maxIters : the maximum number of iterations (defaults to 200)
        - vdwThresh : used to exclude long-range van der Waals interactions
                      (defaults to 10.0)
        - confId : indicates which conformer to optimize
        - ignoreInterfragInteractions : if true, nonbonded terms between
                      fragments will not be added to the forcefield.
    
     RETURNS: 0 if the optimization converged, 1 if more iterations are required.
    
    

    C++ signature :
        int UFFOptimizeMolecule(RDKit::ROMol {lvalue} [,int=200 [,double=10.0 [,int=-1 [,bool=True]]]])

UFFOptimizeMoleculeConfs(...)

 

UFFOptimizeMoleculeConfs( (Mol)self [, (int)numThreads=1 [, (int)maxIters=200 [, (float)vdwThresh=10.0 [, (int)confId=-1 [, (bool)ignoreInterfragInteractions=True]]]]]) -> object :
    uses UFF to optimize all of a molecule's conformations
    
     
     ARGUMENTS:
    
        - mol : the molecule of interest
        - numThreads : the number of threads to use, only has an effect if the RDKit
                       was built with thread support (defaults to 1)
                       If set to zero, the max supported by the system will be used.
        - maxIters : the maximum number of iterations (defaults to 200)
        - vdwThresh : used to exclude long-range van der Waals interactions
                      (defaults to 10.0)
        - confId : indicates which conformer to optimize
        - ignoreInterfragInteractions : if true, nonbonded terms between
                      fragments will not be added to the forcefield.
    
     RETURNS: 0 if the optimization converged, 1 if more iterations are required.
    
    

    C++ signature :
        boost::python::api::object UFFOptimizeMoleculeConfs(RDKit::ROMol {lvalue} [,int=1 [,int=200 [,double=10.0 [,int=-1 [,bool=True]]]]])