BioSimSpace.Parameters¶

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

Functions¶

 parameterise(molecule, forcefield[, …]) Parameterise a molecule using a specified force field. ff99(molecule[, work_dir, property_map]) Parameterise using the ff99 force field. ff99SB(molecule[, work_dir, property_map]) Parameterise using the ff99SB force field. ff99SBildn(molecule[, work_dir, property_map]) Parameterise using the ff99SBildn force field. ff14SB(molecule[, work_dir, property_map]) Parameterise using the ff14SB force field. gaff(molecule[, work_dir, net_charge, …]) Parameterise using the gaff force field. gaff2(molecule[, work_dir, net_charge, …]) Parameterise using the gaff force field. Return a list of the supported force fields. 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.

# 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.

# 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.

# 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.

# 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()