rdkit.Chem.rdForceFieldHelpers

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::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> >='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::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> >='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::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> >='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]]]]])