BigDFT.Interop.OpenMMInterop module
This module contains some wrappers for using OpenMM to perform various operations on BigDFT molecules.
http://docs.openmm.org/development/api-python/index.html
- class OMMSystem(system=None, filename=None)[source]
Class of OpenMM binder system which enables functionalities of openMM on a BigDFT system
- Parameters:
- set_forcefields(*ff_list)[source]
Define a set of force fields that will be used in the geometry ops.
- Parameters:
*ff_list – list of the force fields to be included, in priority order. Use the :func:py:`get_available_ff_names` to identify the available force fields
- omm_system(sys, ligand=None, *ff_list, **kwargs)[source]
Instantiate a omm system from a system and a force field.
- Parameters:
*ff_list – list of the force fields to be included, in priority order. Use the :func:py:`get_available_ff_names` to identify the available force fields.
- Returns:
Instance ready to be optimized.
- Return type:
- optimize_system(sys, outfile, *forcefields)[source]
Take a BigDFT system and optimize it according to a set of OMM FFs.
- three_point_energies(sys, subs1, subs2, *forcefields)[source]
Calculate three_point_energies of two portion of a system. :param sys: the system to optimize. :type sys: BigDFT.System :param subs1: list of fragments composing subsystem 1 :type subs1: list :param subs2: list of fragments composing subsystem 2 :type subs2: list :param *forcefields: sequence of forcefields to be employed in the
optimization.
- Returns:
tuple of the three energies, eT, e1, e2.
- Return type:
collections.namedtuple
- get_mutation_name(mut, offset=0)[source]
From a usual mutation notation AXXXB get the PDBfixer-compliant tuple.
- fixed_system(pH=None, mutations=[], system=None, filename=None, pdbid=None, select_chains=None, remove_extremal_missing_residues=True, custom_fixing_function=None, add_missing_residues=True, keepIds=False, convert_from_charmm_format=False, variants={}, **kwargs)[source]
Create a system with the pdbfixer tool.
- Parameters:
pH (float) – the pH of the environment. Add missing hydrogens according to this pH if provided.
mutations (list) – the mutation to be applied to the original structure. should be a list of two-element lists, the first being the list of mutations to be applied to the chain_id, provided by the second.
system (BigDFT.System) – the system to be fixed.
filename (str) – the PDB file from which the system has to be read. If system is provided, this arguments indicate the PDB file in which the system is written, prior to fixing. After fixing, such file may have to be overwritten.
pdbid (str) – the id of the PDB database.
select_chains (list) – if provided indicate the chains to be selected. Useful when pdbid is provided. All the chains will be included if omitted.
remove_extremal_missing_residues (bool) – if True only the internal missing residues are restored.
custom_fixing_function (func) – a function that has a BigDFT.System as an argument and returns the object to be provided.
add_missing_residues (bool) – include missing residues if true.
keepIds (bool) – If True, keep the residue and chain IDs specified in the Topology rather than generating new ones.
convert_from_charmm_format (bool) – Accept the PDB format which is usually provided as the output of charmm-gui. The chain id is provided as the last letter of each line.
variants (dict) – dictionary of
chain_id,res_id: nameof the variants which have to be imposed for the protonation state. Allowed names are ASH, ASP, CYS, CYX, GLH, GLU, HID, HIE, HIP, HIN, LYN, LYS, with obvious meaning of the names (see OpenMM documentation).
Warning
(From OpenMM documentation) When keepIds=True, it is up to the caller to make sure these are valid IDs that satisfy the requirements of the PDB format. Otherwise, the output file will be invalid.
- Returns:
- Fixed system, or returned object of
custom_fixing_function if present.
- Return type: