def from_xml(cls, xmls_or_etrees):
"""Create a gmso.Forcefield object from XML File(s)
This class method creates a ForceFiled object from the reference
XML file. This method takes in a single or collection of XML files
with information about gmso.AtomTypes, gmso.BondTypes, gmso.AngleTypes
and gmso.DihedralTypes to create the ForceField object.
Parameters
----------
xmls_or_etrees : Union[str, Iterable[str], etree._ElementTree, Iterable[etree._ElementTree]]
The forcefield XML locations or XML Element Trees
Returns
--------
forcefield : gmso.ForceField
A gmso.Forcefield object with a collection of Potential objects
created using the information in the XML file
"""
if not isinstance(xmls_or_etrees, typing.Iterable) or isinstance(xmls_or_etrees, str):
xmls_or_etrees = [xmls_or_etrees]
should_parse_xml = False
if not (all(map(lambda x: isinstance(x, str), xmls_or_etrees))
or all(map(lambda x: isinstance(x, etree._ElementTree), xmls_or_etrees))):
raise TypeError('Please provide an iterable of strings '
'as locations of the XML files '
'or equivalent element Trees')
if all(map(lambda x: isinstance(x, str), xmls_or_etrees)):
should_parse_xml = True
versions = []
names = []
ff_atomtypes_list = []
ff_bondtypes_list = []
ff_angletypes_list = []
ff_dihedraltypes_list = []
atom_types_dict = ChainMap()
bond_types_dict = {}
angle_types_dict = {}
dihedral_types_dict = {}
improper_types_dict = {}
potential_groups = {}
for loc_or_etree in set(xmls_or_etrees):
validate(loc_or_etree)
ff_tree = loc_or_etree
if should_parse_xml:
ff_tree = etree.parse(loc_or_etree)
ff_el = ff_tree.getroot()
versions.append(ff_el.attrib['version'])
names.append(ff_el.attrib['name'])
ff_meta_tree = ff_tree.find('FFMetaData')
if ff_meta_tree is not None:
ff_meta_map = parse_ff_metadata(ff_meta_tree)
ff_atomtypes_list.extend(ff_tree.findall('AtomTypes'))
ff_bondtypes_list.extend(ff_tree.findall('BondTypes'))
ff_angletypes_list.extend(ff_tree.findall('AngleTypes'))
ff_dihedraltypes_list.extend(ff_tree.findall('DihedralTypes'))
# Consolidate AtomTypes
for atom_types in ff_atomtypes_list:
this_atom_types_group = parse_ff_atomtypes(atom_types, ff_meta_map)
this_atom_group_name = atom_types.attrib.get('name', None)
if this_atom_group_name:
potential_groups[this_atom_group_name] = this_atom_types_group
atom_types_dict.update(this_atom_types_group)
# Consolidate BondTypes
for bond_types in ff_bondtypes_list:
this_bond_types_group = parse_ff_connection_types(
bond_types,
atom_types_dict,
child_tag='BondType'
)
this_bond_types_group_name = bond_types.attrib.get('name', None)
if this_bond_types_group_name:
potential_groups[this_bond_types_group_name] = this_bond_types_group
bond_types_dict.update(this_bond_types_group)
# Consolidate AngleTypes
for angle_types in ff_angletypes_list:
this_angle_types_group = parse_ff_connection_types(
angle_types,
atom_types_dict,
child_tag='AngleType'
)
this_angle_types_group_name = angle_types.attrib.get('name', None)
if this_angle_types_group_name:
potential_groups[this_angle_types_group_name] = this_angle_types_group
angle_types_dict.update(this_angle_types_group)
# Consolidate DihedralTypes
for dihedral_types in ff_dihedraltypes_list:
this_dihedral_types_group = parse_ff_connection_types(
dihedral_types,
atom_types_dict,
child_tag='DihedralType'
)
this_improper_types_group = parse_ff_connection_types(
dihedral_types,
atom_types_dict,
child_tag='ImproperType'
)
this_group_name = dihedral_types.attrib.get('name', None)
dihedral_types_dict.update(this_dihedral_types_group)
improper_types_dict.update(this_improper_types_group)
if this_group_name:
this_dihedral_types_group.update(this_improper_types_group)
potential_groups[this_group_name] = this_dihedral_types_group
ff = cls()
ff.name = names[0]
ff.version = versions[0]
ff.scaling_factors = ff_meta_map['scaling_factors']
ff.units = ff_meta_map['Units']
ff.atom_types = atom_types_dict.maps[0]
ff.bond_types = bond_types_dict
ff.angle_types = angle_types_dict
ff.dihedral_types = dihedral_types_dict
ff.improper_types = improper_types_dict
ff.potential_groups = potential_groups
return ff
def from_xml(cls, xml_locs):
"""Create a gmso.Forcefield object from XML File(s)
This class method creates a ForceFiled object from the reference
XML file. This method takes in a single or collection of XML files
with information about gmso.AtomTypes, gmso.BondTypes, gmso.AngleTypes
and gmso.DihedralTypes to create the ForceField object.
Parameters
----------
xml_locs : str or iterable of str
string or iterable of strings containing the forcefield XML locations
Returns
--------
forcefield : gmso.ForceField
A gmso.Forcefield object with a collection of Potential objects
created using the information in the XML file
"""
if not hasattr(xml_locs, '__iter__'):
xml_locs = [].append(xml_locs)
if isinstance(xml_locs, str):
xml_locs = [xml_locs]
versions = []
names = []
ff_atomtypes_list = []
ff_bondtypes_list = []
ff_angletypes_list = []
ff_dihedraltypes_list = []
atom_types_dict = ChainMap()
bond_types_dict = {}
angle_types_dict = {}
dihedral_types_dict = {}
improper_types_dict = {}
potential_groups = {}
for loc in xml_locs:
validate(loc)
ff_tree = etree.parse(loc)
ff_el = ff_tree.getroot()
versions.append(ff_el.attrib['version'])
names.append(ff_el.attrib['name'])
ff_meta_tree = ff_tree.find('FFMetaData')
if ff_meta_tree is not None:
ff_meta_map = parse_ff_metadata(ff_meta_tree)
ff_atomtypes_list.extend(ff_tree.findall('AtomTypes'))
ff_bondtypes_list.extend(ff_tree.findall('BondTypes'))
ff_angletypes_list.extend(ff_tree.findall('AngleTypes'))
ff_dihedraltypes_list.extend(ff_tree.findall('DihedralTypes'))
# Consolidate AtomTypes
for atom_types in ff_atomtypes_list:
this_atom_types_group = parse_ff_atomtypes(atom_types, ff_meta_map)
this_atom_group_name = atom_types.attrib.get('name', None)
if this_atom_group_name:
potential_groups[this_atom_group_name] = this_atom_types_group
atom_types_dict.update(this_atom_types_group)
# Consolidate BondTypes
for bond_types in ff_bondtypes_list:
this_bond_types_group = parse_ff_connection_types(
bond_types, atom_types_dict, child_tag='BondType')
this_bond_types_group_name = bond_types.attrib.get('name', None)
if this_bond_types_group_name:
potential_groups[
this_bond_types_group_name] = this_bond_types_group
bond_types_dict.update(this_bond_types_group)
# Consolidate AngleTypes
for angle_types in ff_angletypes_list:
this_angle_types_group = parse_ff_connection_types(
angle_types, atom_types_dict, child_tag='AngleType')
this_angle_types_group_name = angle_types.attrib.get('name', None)
if this_angle_types_group_name:
potential_groups[
this_angle_types_group_name] = this_angle_types_group
angle_types_dict.update(this_angle_types_group)
# Consolidate DihedralTypes
for dihedral_types in ff_dihedraltypes_list:
this_dihedral_types_group = parse_ff_connection_types(
dihedral_types, atom_types_dict, child_tag='DihedralType')
this_improper_types_group = parse_ff_connection_types(
dihedral_types, atom_types_dict, child_tag='ImproperType')
this_group_name = dihedral_types.attrib.get('name', None)
dihedral_types_dict.update(this_dihedral_types_group)
improper_types_dict.update(this_improper_types_group)
if this_group_name:
this_dihedral_types_group.update(this_improper_types_group)
potential_groups[this_group_name] = this_dihedral_types_group
ff = cls()
ff.name = names[0]
ff.version = versions[0]
ff.scaling_factors = ff_meta_map['scaling_factors']
ff.units = ff_meta_map['Units']
ff.atom_types = atom_types_dict.maps[0]
ff.bond_types = bond_types_dict
ff.angle_types = angle_types_dict
ff.dihedral_types = dihedral_types_dict
ff.improper_types = improper_types_dict
ff.potential_groups = potential_groups
return ff
def from_xml(cls, xmls_or_etrees, strict=True, greedy=True):
"""Create a gmso.Forcefield object from XML File(s).
This class method creates a ForceField object from the reference
XML file. This method takes in a single or collection of XML files
with information about gmso.AtomTypes, gmso.BondTypes, gmso.AngleTypes
and gmso.DihedralTypes to create the ForceField object.
Parameters
----------
xmls_or_etrees : Union[str, Iterable[str], etree._ElementTree, Iterable[etree._ElementTree]]
The forcefield XML locations or XML Element Trees
strict: bool, default=True
If true, perform a strict validation of the forcefield XML file
greedy: bool, default=True
If True, when using strict mode, fail on the first error/mismatch
Returns
-------
forcefield : gmso.ForceField
A gmso.Forcefield object with a collection of Potential objects
created using the information in the XML file
"""
if not isinstance(xmls_or_etrees, Iterable) or isinstance(
xmls_or_etrees, str
):
xmls_or_etrees = [xmls_or_etrees]
should_parse_xml = False
if not (
all(map(lambda x: isinstance(x, str), xmls_or_etrees))
or all(
map(lambda x: isinstance(x, etree._ElementTree), xmls_or_etrees)
)
):
raise TypeError(
"Please provide an iterable of strings "
"as locations of the XML files "
"or equivalent element Trees"
)
if all(map(lambda x: isinstance(x, str), xmls_or_etrees)):
should_parse_xml = True
versions = []
names = []
ff_atomtypes_list = []
ff_bondtypes_list = []
ff_angletypes_list = []
ff_dihedraltypes_list = []
atom_types_dict = ChainMap()
bond_types_dict = {}
angle_types_dict = {}
dihedral_types_dict = {}
improper_types_dict = {}
potential_groups = {}
for loc_or_etree in set(xmls_or_etrees):
validate(loc_or_etree, strict=strict, greedy=greedy)
ff_tree = loc_or_etree
if should_parse_xml:
ff_tree = etree.parse(loc_or_etree)
ff_el = ff_tree.getroot()
versions.append(ff_el.attrib["version"])
names.append(ff_el.attrib["name"])
ff_meta_tree = ff_tree.find("FFMetaData")
if ff_meta_tree is not None:
ff_meta_map = parse_ff_metadata(ff_meta_tree)
ff_atomtypes_list.extend(ff_tree.findall("AtomTypes"))
ff_bondtypes_list.extend(ff_tree.findall("BondTypes"))
ff_angletypes_list.extend(ff_tree.findall("AngleTypes"))
ff_dihedraltypes_list.extend(ff_tree.findall("DihedralTypes"))
# Consolidate AtomTypes
for atom_types in ff_atomtypes_list:
this_atom_types_group = parse_ff_atomtypes(atom_types, ff_meta_map)
this_atom_group_name = atom_types.attrib.get("name", None)
if this_atom_group_name:
potential_groups[this_atom_group_name] = this_atom_types_group
atom_types_dict.update(this_atom_types_group)
# Consolidate BondTypes
for bond_types in ff_bondtypes_list:
this_bond_types_group = parse_ff_connection_types(
bond_types, child_tag="BondType"
)
this_bond_types_group_name = bond_types.attrib.get("name", None)
if this_bond_types_group_name:
potential_groups[
this_bond_types_group_name
] = this_bond_types_group
bond_types_dict.update(this_bond_types_group)
# Consolidate AngleTypes
for angle_types in ff_angletypes_list:
this_angle_types_group = parse_ff_connection_types(
angle_types, child_tag="AngleType"
)
this_angle_types_group_name = angle_types.attrib.get("name", None)
if this_angle_types_group_name:
potential_groups[
this_angle_types_group_name
] = this_angle_types_group
angle_types_dict.update(this_angle_types_group)
# Consolidate DihedralTypes
for dihedral_types in ff_dihedraltypes_list:
this_dihedral_types_group = parse_ff_connection_types(
dihedral_types, child_tag="DihedralType"
)
this_improper_types_group = parse_ff_connection_types(
dihedral_types, child_tag="ImproperType"
)
this_group_name = dihedral_types.attrib.get("name", None)
dihedral_types_dict.update(this_dihedral_types_group)
improper_types_dict.update(this_improper_types_group)
if this_group_name:
this_dihedral_types_group.update(this_improper_types_group)
potential_groups[this_group_name] = this_dihedral_types_group
ff = cls()
ff.name = names[0]
ff.version = versions[0]
ff.scaling_factors = ff_meta_map["scaling_factors"]
ff.units = ff_meta_map["Units"]
ff.atom_types = atom_types_dict.maps[0]
ff.bond_types = bond_types_dict
ff.angle_types = angle_types_dict
ff.dihedral_types = dihedral_types_dict
ff.improper_types = improper_types_dict
ff.potential_groups = potential_groups
return ff