cg_openmm.build.cg_build

Functions

add_force(cgmodel[, force_type, ...])	Given a 'cgmodel' and 'force_type' as input, this function adds the OpenMM force corresponding to 'force_type' to 'cgmodel.system'.
add_new_elements(cgmodel)	Add coarse grained particle types to OpenMM.
add_rosetta_exception_parameters(cgmodel, ...)
build_system(cgmodel[, ...])	Builds an OpenMM System() object, given a CGModel() as input.
build_topology(cgmodel[, use_pdbfile, pdbfile])	Construct an OpenMM Topology() class object for our coarse grained model,
check_force(cgmodel, force[, force_type])	Given an OpenMM Force(), this function determines if there are any problems with its configuration.
check_forces(cgmodel)	Given a cgmodel that contains positions and an an OpenMM System() object, this function tests the forces for cgmodel.system.
get_num_forces(cgmodel)	Given a CGModel() class object, this function determines how many forces we are including when evaluating the energy.
verify_system(cgmodel)	Given a CGModel() class object, this function confirms that its OpenMM System() object is configured correctly.
verify_topology(cgmodel)	Given a coarse grained model that contains a Topology() (cgmodel.topology), this function verifies the validity of the topology.
write_xml_file(cgmodel, xml_file_name)	Write an XML-formatted forcefield file for a coarse grained model.