build.cg_build submodule

cg_openmm.build.cg_build.add_force(cgmodel, force_type=None, rosetta_functional_form=False)

Given a ‘cgmodel’ and ‘force_type’ as input, this function adds the OpenMM force corresponding to ‘force_type’ to ‘cgmodel.system’.

Parameters

• cgmodel – CGModel() class object.

• type – class

• force_type (str) – Designates the kind of ‘force’ provided. (Valid options include: “Bond”, “Nonbonded”, “Angle”, and “Torsion”)

Returns

• cgmodel (class) - ‘foldamers’ CGModel() class object

• force (class) - An OpenMM Force() object.

Example

>>> from foldamers.cg_model.cgmodel import CGModel
>>> cgmodel = CGModel()
>>> force_type = "Bond"
>>> cgmodel,force = add_force(cgmodel,force_type=force_type)

cg_openmm.build.cg_build.add_new_elements(cgmodel)

Add coarse grained particle types to OpenMM.

Parameters

cgmodel (class) – CGModel object (contains all attributes for a coarse grained model).

Returns

• new_particles (list) - a list of the particle names that were added to OpenMM’s ‘Element’ List.

Example

>>> from foldamers.cg_model.cgmodel import CGModel
>>> cgmodel = CGModel()
>>> particle_types = add_new_elements(cgmodel)

Warning

If the particle names were user defined, and any of the names conflict with existing element names in OpenMM, OpenMM will issue an error exit.

cg_openmm.build.cg_build.add_rosetta_exception_parameters(cgmodel, nonbonded_force, particle_index_1, particle_index_2)

cg_openmm.build.cg_build.build_system(cgmodel, rosetta_functional_form=False, verify=True)

Builds an OpenMM System() object, given a CGModel() as input.

Parameters

cgmodel (class) – CGModel() class object

Returns

• system ( System() ) - OpenMM System() object

Example

>>> from foldamers.cg_model.cgmodel import CGModel
>>> cgmodel = CGModel()
>>> system = build_system(cgmodel)
>>> cgmodel.system = system

cg_openmm.build.cg_build.build_topology(cgmodel, use_pdbfile=False, pdbfile=None)

Construct an OpenMM Topology() class object for our coarse grained model,

Parameters

• cgmodel (class) – CGModel() class object

• use_pdbfile (Logical) – Determines whether or not to use a PDB file in order to generate the Topology().

• pdbfile (str) – Name of a PDB file to use when building the topology.

Returns

• topology (Topology() ) - OpenMM Topology() object

Example

>>> from foldamers.cg_model.cgmodel import CGModel
>>> from foldamers.util.iotools import write_pdbfile_without_topology
>>> input_pdb = "top.pdb"
>>> cgmodel = CGModel()
>>> write_pdbfile_without_topology(cgmodel,input_pdb)
>>> topology = build_topology(cgmodel,use_pdbfile=True,pdbfile=input_pdb)
>>> cgmodel.topology = topology

Warning

When ‘use_pdbfile’=True, this function will use the PDBFile() class object from OpenMM to build the Topology(). In order for this approach to function correctly, the particle names in the PDB file must match the particle names in the coarse grained model.

cg_openmm.build.cg_build.check_force(cgmodel, force, force_type=None)

Given an OpenMM Force(), this function determines if there are any problems with its configuration.

Parameters

• cgmodel (class) – CGModel() class object.

• force – An OpenMM Force() object.

• force_type (str) – Designates the kind of ‘force’ provided. (Valid options include: “Nonbonded”)

Returns

• ‘success’ (Logical) - a variable indicating if the force test passed.

Example

>>> from simtk.openmm.openmm import NonbondedForce
>>> from foldamers.cg_model.cgmodel import CGModel
>>> cgmodel = CGModel()
>>> force = NonbondedForce()
>>> force_type = "Nonbonded"
>>> test_result = check_force(cgmodel,force,force_type="Nonbonded")

cg_openmm.build.cg_build.check_forces(cgmodel)

Given a cgmodel that contains positions and an an OpenMM System() object, this function tests the forces for cgmodel.system.

More specifically, this function confirms that the model does not have any “NaN” or unphysically large forces.

Parameters

• cgmodel – CGModel() class object.

• type – class

Returns

• success (Logical) - Indicates if this cgmodel has unphysical forces.

Example

>>> from foldamers.cg_model.cgmodel import CGModel
>>> cgmodel = CGModel()
>>> pass_forces_test = check_forces(cgmodel)

cg_openmm.build.cg_build.get_num_forces(cgmodel)

Given a CGModel() class object, this function determines how many forces we are including when evaluating the energy.

Parameters

cgmodel (class) – CGModel() class object

Returns

• total_forces (int) - Number of forces in the coarse grained model

Example

>>> from foldamers.cg_model.cgmodel import CGModel
>>> cgmodel = CGModel()
>>> total_number_forces = get_num_forces(cgmodel)

cg_openmm.build.cg_build.verify_system(cgmodel)

Given a CGModel() class object, this function confirms that its OpenMM System() object is configured correctly.

Parameters

cgmodel (class) – CGModel() class object

Example

>>> from foldamers.cg_model.cgmodel import CGModel
>>> cgmodel = CGModel()
>>> verify_system(cgmodel)

Warning

The function will force an error exit if the system is invalid, and will proceed as normal if the system is valid.

cg_openmm.build.cg_build.verify_topology(cgmodel)

Given a coarse grained model that contains a Topology() (cgmodel.topology), this function verifies the validity of the topology.

Parameters

cgmodel (class) – CGModel() class object.

Example

>>> from foldamers.cg_model.cgmodel import CGModel
>>> cgmodel = CGModel()
>>> verify_topology(cgmodel)

Warning

The function will force an error exit if the topology is invalid, and will proceed as normal if the topology is valid.

cg_openmm.build.cg_build.write_xml_file(cgmodel, xml_file_name)

Write an XML-formatted forcefield file for a coarse grained model.

Parameters

• cgmodel (class) – CGModel() class object.

• xml_file_name (str) – Path to XML output file.

Example

>>> from foldamers.cg_model.cgmodel import CGModel
>>> cgmodel = CGModel()
>>> xml_file_name = "openmm_cgmodel.xml"
>>> write_xml_file(cgmodel,xml_file_name)