BioSimSpace.Parameters

The Parameters package contains tools for parameterising molecules with a range of force fields.

Functions

amberForceFields()	Return a list of the supported AMBER force fields.
amberProteinForceFields()	Return a list of the supported AMBER protein force fields.
ff03(molecule[, tolerance, max_distance, ...])	Parameterise a molecule using the named AMBER force field.
ff14SB(molecule[, tolerance, max_distance, ...])	Parameterise a molecule using the named AMBER force field.
ff99(molecule[, tolerance, max_distance, ...])	Parameterise a molecule using the named AMBER force field.
ff99SB(molecule[, tolerance, max_distance, ...])	Parameterise a molecule using the named AMBER force field.
ff99SBildn(molecule[, tolerance, ...])	Parameterise a molecule using the named AMBER force field.
forceFields()	Return a list of the supported force fields.
gaff(molecule[, work_dir, net_charge, ...])	Parameterise using the GAFF force field.
gaff2(molecule[, work_dir, net_charge, ...])	Parameterise using the GAFF2 force field.
openForceFields()	Return a list of the supported force fields from the Open Force Field Initiative.
openff_unconstrained_1_0_0(molecule[, ...])	Parameterise a molecule using the named force field from the Open Force Field initiative.
openff_unconstrained_1_0_0_RC1(molecule[, ...])	Parameterise a molecule using the named force field from the Open Force Field initiative.
openff_unconstrained_1_0_0_RC2(molecule[, ...])	Parameterise a molecule using the named force field from the Open Force Field initiative.
openff_unconstrained_1_0_1(molecule[, ...])	Parameterise a molecule using the named force field from the Open Force Field initiative.
openff_unconstrained_1_1_0(molecule[, ...])	Parameterise a molecule using the named force field from the Open Force Field initiative.
openff_unconstrained_1_1_1(molecule[, ...])	Parameterise a molecule using the named force field from the Open Force Field initiative.
openff_unconstrained_1_2_0(molecule[, ...])	Parameterise a molecule using the named force field from the Open Force Field initiative.
openff_unconstrained_1_2_1(molecule[, ...])	Parameterise a molecule using the named force field from the Open Force Field initiative.
openff_unconstrained_1_3_0(molecule[, ...])	Parameterise a molecule using the named force field from the Open Force Field initiative.
openff_unconstrained_1_3_1(molecule[, ...])	Parameterise a molecule using the named force field from the Open Force Field initiative.
openff_unconstrained_1_3_1_alpha_1(molecule)	Parameterise a molecule using the named force field from the Open Force Field initiative.
openff_unconstrained_2_0_0(molecule[, ...])	Parameterise a molecule using the named force field from the Open Force Field initiative.
openff_unconstrained_2_0_0_rc_1(molecule[, ...])	Parameterise a molecule using the named force field from the Open Force Field initiative.
openff_unconstrained_2_0_0_rc_2(molecule[, ...])	Parameterise a molecule using the named force field from the Open Force Field initiative.
openff_unconstrained_2_1_0(molecule[, ...])	Parameterise a molecule using the named force field from the Open Force Field initiative.
openff_unconstrained_2_1_0_rc_1(molecule[, ...])	Parameterise a molecule using the named force field from the Open Force Field initiative.
openff_unconstrained_2_1_1(molecule[, ...])	Parameterise a molecule using the named force field from the Open Force Field initiative.
openff_unconstrained_2_2_0(molecule[, ...])	Parameterise a molecule using the named force field from the Open Force Field initiative.
openff_unconstrained_2_2_0_rc1(molecule[, ...])	Parameterise a molecule using the named force field from the Open Force Field initiative.
openff_unconstrained_2_2_1(molecule[, ...])	Parameterise a molecule using the named force field from the Open Force Field initiative.
openff_unconstrained_2_2_1_rc1(molecule[, ...])	Parameterise a molecule using the named force field from the Open Force Field initiative.
parameterise(molecule, forcefield[, ...])	Parameterise a molecule using a specified force field.
formalCharge(molecule)	Compute the formal charge on a molecule.

Examples

Print the list of supported force fields.

import BioSimSpace as BSS

print(BSS.Parameters.forceFields())

Parameterise a molecule using GAFF.

import BioSimSpace as BSS

# Load a molecule from file.
molecule = BSS.IO.readMolecules("molecules/benzene.pdb")

# Initialise the parameterisation process. This will run the parameterisation
# in the background. This is useful when you are working interactively and
# wish to continue doing other things while the parameterisation runs.
# (Parameterisation can be slow.)
process = BSS.Parameters.gaff(molecule)

# Get the parameterised molecule. This will now block until the
# parameterisation is finished.
molecule = process.getMolecule()

The same as above, but immediately getting the parameterised molecule from the process object, i.e. not saving it as an intermediate variable.

import BioSimSpace as BSS

# Load a molecule from file.
molecule = BSS.IO.readMolecules("molecules/benzene.pdb")

# Initialise the parameterisation process and block until the molecule is
# ready to be returned.
molecule = BSS.Parameters.gaff(molecule).getMolecule()

The same as above, but instead passing “GAFF” as an argument to the parameterise function. This function should be used in any interoperable workflow Node where the force field is specified as an input requirement by the user.

import BioSimSpace as BSS

# Load a molecule from file.
molecule = BSS.IO.readMolecules("molecules/benzene.pdb")

# Initialise the parameterisation process and block until the molecule is
# ready to be returned.
molecule = BSS.Parameters.parameterise(molecule, "gaff").getMolecule()

Parameterise a molecule using GAFF, passing the net formal charge computed by BioSimSpace. This is useful when your input PDB file has missing or incorrect formal charge information.

import BioSimSpace as BSS

# Load a molecule from file.
molecule = BSS.IO.readMolecules("molecules/benzene.pdb")

# Compute the net formal charge on the molecule.
formal_charge = BSS.Parameters.formalCharge(molecule)

# Initialise the parameterisation process. This will run the parameterisation
# in the background. This is useful when you are working interactively and
# wish to continue doing other things while the parameterisation runs.
# (Parameterisation can be slow.)
process = BSS.Parameters.gaff(molecule, net_charge=formal_charge)

# Get the parameterised molecule. This will now block until the
# parameterisation is finished.
molecule = process.getMolecule()

Parameterise a molecule using GAFF, passing the molecule as a SMILES string.

import BioSimSpace as BSS

# Parameterise directly using a SMILES string.
molecule = BSS.Parameters.gaff("C1=CC=CC=C1").getMolecule()

When parameterising a molecule containing a structural ion with an AMBER force field then it is necessary to pass the name of a water model that will be used for the ion parameters, e.g:

import BioSimSpace as BSS

# Load a molecule from file.
molecule = BSS.IO.readMolecules("molecules/4V2Y_A.pdb")

# Initialise the parameterisation process and block until the molecule is
# ready to be returned.
molecule = BSS.Parameters.ff14SB(molecule, water_model="tip3p").getMolecule()

Additional parameters can be loaded by passing the pre_mol_commands option to any compatible AMBER force field function, e.g.:

import BioSimSpace as BSS

# Load a molecule from file.
molecule = BSS.IO.readMolecules("molecules/peptide.pdb")

# Create a list of the additional commands for the LEaP program. These will
# be run after any default commands.
leap_commands = ["addPath phosphate_params", "source leaprc.phosaa10"]

# Initialise the parameterisation process and block until the molecule is
# ready to be returned.
molecule = BSS.Parameters.ff14SB(molecule, pre_mol_commands=leap_commands).getMolecule()

If you need to apply any additional operations on the loaded molecule, then this can be done using the post_mol_commands option, using mol for the name of the molecule.