rdkit.Chem.rdForceFieldHelpers module

Module containing functions to handle force fields

rdkit.Chem.rdForceFieldHelpers.CreateEmptyForceFieldForMol((Mol)mol[, (int)confId=-1]) → ForceField :

Get An empty Force Field, with only the positions of the atoms but no Contributions.

ARGUMENTS :

  • mol : the molecule of interest

  • confId: the conformer which positions should be added to the force field.

C++ signature :

ForceFields::PyForceField* CreateEmptyForceFieldForMol(RDKit::ROMol {lvalue} [,int=-1])

rdkit.Chem.rdForceFieldHelpers.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)

rdkit.Chem.rdForceFieldHelpers.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)

rdkit.Chem.rdForceFieldHelpers.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)

rdkit.Chem.rdForceFieldHelpers.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)

rdkit.Chem.rdForceFieldHelpers.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)

rdkit.Chem.rdForceFieldHelpers.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

  • pyMMFFMolPropertiesPyMMFFMolProperties object as returned

    by MMFFGetMoleculeProperties()

  • nonBondedThreshused to exclude long-range non-bonded

    interactions (defaults to 100.0)

  • confId : indicates which conformer to optimize

  • ignoreInterfragInteractionsif 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]]])

rdkit.Chem.rdForceFieldHelpers.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]])

rdkit.Chem.rdForceFieldHelpers.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)

rdkit.Chem.rdForceFieldHelpers.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)

  • nonBondedThreshused to exclude long-range non-bonded

    interactions (defaults to 100.0)

  • confId : indicates which conformer to optimize

  • ignoreInterfragInteractionsif 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]]]]])

rdkit.Chem.rdForceFieldHelpers.MMFFOptimizeMoleculeConfs((Mol)self[, (int)numThreads=1[, (int)maxIters=200[, (str)mmffVariant='MMFF94'[, (float)nonBondedThresh=100.0[, (bool)ignoreInterfragInteractions=True]]]]]) → object :

uses MMFF to optimize all of a molecule’s conformations

ARGUMENTS:

  • mol : the molecule of interest

  • numThreadsthe 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”

  • nonBondedThreshused to exclude long-range non-bonded

    interactions (defaults to 100.0)

  • ignoreInterfragInteractionsif true, nonbonded terms between

    fragments will not be added to the forcefield.

RETURNS: a list of (not_converged, energy) 2-tuples.

If not_converged is 0 the optimization converged for that conformer.

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=100.0 [,bool=True]]]]])

rdkit.Chem.rdForceFieldHelpers.MMFFSanitizeMolecule((Mol)mol) → int :

sanitizes a molecule according to MMFF requirements.

  • mol : the molecule of interest.

C++ signature :

unsigned int MMFFSanitizeMolecule(RDKit::ROMol {lvalue})

rdkit.Chem.rdForceFieldHelpers.OptimizeMolecule((ForceField)ff[, (int)maxIters=200]) → int :

uses the supplied force field to optimize a molecule’s structure

ARGUMENTS:

  • ff : the force field

  • maxIters : the maximum number of iterations (defaults to 200)

RETURNS: 0 if the optimization converged, 1 if more iterations are required.

C++ signature :

int OptimizeMolecule(ForceFields::PyForceField {lvalue} [,int=200])

rdkit.Chem.rdForceFieldHelpers.OptimizeMoleculeConfs((Mol)mol, (ForceField)ff[, (int)numThreads=1[, (int)maxIters=200]]) → object :

uses the supplied force field to optimize all of a molecule’s conformations

ARGUMENTS:

  • mol : the molecule of interest

  • ff : the force field

  • numThreadsthe 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)

RETURNS: a list of (not_converged, energy) 2-tuples.

If not_converged is 0 the optimization converged for that conformer.

C++ signature :

boost::python::api::object OptimizeMoleculeConfs(RDKit::ROMol {lvalue},ForceFields::PyForceField {lvalue} [,int=1 [,int=200]])

rdkit.Chem.rdForceFieldHelpers.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

  • vdwThreshused to exclude long-range van der Waals interactions

    (defaults to 10.0)

  • confId : indicates which conformer to optimize

  • ignoreInterfragInteractionsif 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]]])

rdkit.Chem.rdForceFieldHelpers.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)

rdkit.Chem.rdForceFieldHelpers.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)

  • vdwThreshused to exclude long-range van der Waals interactions

    (defaults to 10.0)

  • confId : indicates which conformer to optimize

  • ignoreInterfragInteractionsif 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]]]])

rdkit.Chem.rdForceFieldHelpers.UFFOptimizeMoleculeConfs((Mol)self[, (int)numThreads=1[, (int)maxIters=200[, (float)vdwThresh=10.0[, (bool)ignoreInterfragInteractions=True]]]]) → object :

uses UFF to optimize all of a molecule’s conformations

ARGUMENTS:

  • mol : the molecule of interest

  • numThreadsthe 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)

  • vdwThreshused to exclude long-range van der Waals interactions

    (defaults to 10.0)

  • ignoreInterfragInteractionsif true, nonbonded terms between

    fragments will not be added to the forcefield.

RETURNS: a list of (not_converged, energy) 2-tuples.

If not_converged is 0 the optimization converged for that conformer.

C++ signature :

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