def add_new_elements(cgmodel):
"""
Add coarse grained particle types to OpenMM.
:param cgmodel: CGModel object (contains all attributes for a coarse grained model).
:type cgmodel: class
:returns:
- particle_list (list) - a list of the particles 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.
"""
element_index = 117
cg_particle_index = 1
particle_list = []
for monomer_type in cgmodel.monomer_types:
for backbone_bead in range(monomer_type['backbone_length']):
particle_name = str("X" + str(cg_particle_index))
particle_symbol = str("X" + str(cg_particle_index))
if particle_symbol not in elem.Element._elements_by_symbol:
mass = cgmodel.get_particle_mass(cg_particle_index - 1)
elem.Element(element_index, particle_name, particle_symbol,
mass)
particle_list.append(particle_symbol)
element_index = element_index + 1
cg_particle_index = cg_particle_index + 1
if type(monomer_type['sidechain_positions']) == int:
sidechain_positions = [monomer_type['sidechain_positions']]
else:
sidechain_positions = monomer_type['sidechain_positions']
if backbone_bead in sidechain_positions:
for sidechain in range(monomer_type['sidechain_length']):
particle_name = str("A" + str(cg_particle_index))
particle_symbol = str("A" + str(cg_particle_index))
if particle_symbol not in elem.Element._elements_by_symbol:
mass = cgmodel.get_particle_mass(cg_particle_index - 1)
elem.Element(element_index, particle_name,
particle_symbol, mass)
particle_list.append(particle_symbol)
element_index = element_index + 1
cg_particle_index = cg_particle_index + 1
return (particle_list)
def add_new_elements(cgmodel):
"""
Add coarse grained particle types to OpenMM.
:param cgmodel: CGModel object (contains all attributes for a coarse grained model).
:type cgmodel: class
: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.
"""
element_index = 117
new_particles = []
for particle in cgmodel.particle_list:
particle_name = particle["name"]
if particle_name.upper() not in elem.Element._elements_by_symbol:
elem.Element(element_index, particle_name, particle_name,
cgmodel.get_particle_mass(particle))
element_index = element_index + 1
new_particles.append(particle_name)
return new_particles
def _create_element(self, element, mass):
if not isinstance(element, elem.Element):
try:
element = elem.get_by_symbol(element)
except KeyError:
# Enables support for non-atomistic "element types"
if element not in self.non_element_types:
warnings.warn('Non-atomistic element type detected. '
'Creating custom element for {}'.format(element))
element = elem.Element(number=0,
mass=mass,
name=element,
symbol=element)
return element
def registerAtomType(self, parameters):
"""Register a new atom type. """
name = parameters['name']
if name in self._atomTypes:
raise ValueError('Found multiple definitions for atom type: ' +
name)
atomClass = parameters['class']
mass = _convertParameterToNumber(parameters['mass'])
element = None
if 'element' in parameters:
element = parameters['element']
if not isinstance(element, elem.Element):
try:
element = elem.get_by_symbol(element)
except KeyError:
# Enables support for non-atomistic "element types"
if element not in self.non_element_types:
warnings.warn(
'Non-atomistic element type detected. '
'Creating custom element for {}'.format(element))
element = elem.Element(number=0,
mass=parameters['mass'],
name=element,
symbol=element)
self.non_element_types[element.name] = element
self._atomTypes[name] = self.__class__._AtomType(
name, atomClass, mass, element)
if atomClass in self._atomClasses:
typeSet = self._atomClasses[atomClass]
else:
typeSet = set()
self._atomClasses[atomClass] = typeSet
typeSet.add(name)
self._atomClasses[''].add(name)
name = parameters['name']
if 'def' in parameters:
self._atomTypeDefinitions[name] = parameters['def']
if 'overrides' in parameters:
overrides = set(parameters['overrides'].split(","))
if overrides:
self._atomTypeOverrides[name] = overrides
if 'des' in parameters:
self._atomTypeDesc[name] = parameters['desc']