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Module containing functions to handle force fields
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__package__ = None hash(x) |
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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( (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( (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( (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( (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( (Mol)mol, (MMFFMolProperties)pyMMFFMolProperties [, (float)nonBondedThresh=100.0 [, (int)confId=-1 [, (bool)ignoreInterfragInteractions=True]]]) -> ForceField : 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( (Mol)mol [, (str)mmffVariant='MMFF94' [, (int)mmffVerbosity=0]]) -> MMFFMolProperties : 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::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> >='MMFF94' [,unsigned int=0]]) |
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( (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::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> >='MMFF94' [,int=200 [,double=100.0 [,int=-1 [,bool=True]]]]]) |
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::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> >='MMFF94' [,double=10.0 [,int=-1 [,bool=True]]]]]]) |
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( (Mol)mol [, (float)vdwThresh=10.0 [, (int)confId=-1 [, (bool)ignoreInterfragInteractions=True]]]) -> ForceField : 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( (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( (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( (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]]]]]) |
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