# ******************************************************************************
# pysimm.forcefield module
# ******************************************************************************
#
# ******************************************************************************
# License
# ******************************************************************************
# The MIT License (MIT)
#
# Copyright (c) 2016 Michael E. Fortunato, Coray M. Colina
#
# Permission is hereby granted, free of charge, to any person obtaining a copy
# of this software and associated documentation files (the "Software"), to deal
# in the Software without restriction, including without limitation the rights
# to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
# copies of the Software, and to permit persons to whom the Software is
# furnished to do so, subject to the following conditions:
#
# The above copyright notice and this permission notice shall be included in
# all copies or substantial portions of the Software.
#
# THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
# IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
# FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
# AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
# LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
# OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN
# THE SOFTWARE.
import os
import json
from xml.dom import minidom
from xml.etree import ElementTree as Et
from itertools import permutations, combinations
from .. import error_print
from .. import warning_print
from .. import debug_print
from . import gasteiger
from ..utils import PysimmError, Item, ItemContainer, compare
from ..system import ParticleType, BondType, AngleType
from ..system import Angle, Dihedral, Improper
from ..system import DihedralType, ImproperType
[docs]element_names_by_mass = {1: 'H', 4: 'He', 7: 'Li', 9: 'Be', 11: 'B', 12: 'C',
14: 'N', 16: 'O', 19: 'F', 20: 'Ne', 23: 'Na',
24: 'Mg', 27: 'Al', 28: 'Si', 31: 'P', 32: 'S',
35: 'Cl', 39: 'K', 40: 'Ca', 80: 'Br', 127: 'I'}
[docs]class Forcefield(object):
"""pysimm.forcefield.Forcefield
Base Forcefield class definition.
Initialize with force field xml file.
Attributes:
ff_class: force field class (1 or 2)
ff_name: force field name
particle_types: :class:`~pysimm.utils.ItemContainer` for particle_types
bond_types: :class:`~pysimm.utils.ItemContainer` for bond_types
angle_types: :class:`~pysimm.utils.ItemContainer` for angle_types
dihedral_types: :class:`~pysimm.utils.ItemContainer` for dihedral_types
improper_types: :class:`~pysimm.utils.ItemContainer` for improper_types
"""
def __init__(self, file_=None, format=None):
self.ff_class = 0
self.ff_name = ''
self.pair_style = None
self.particle_types = ItemContainer()
self.bond_style = None
self.bond_types = ItemContainer()
self.angle_style = None
self.angle_types = ItemContainer()
self.dihedral_style = None
self.dihedral_types = ItemContainer()
self.improper_style = None
self.improper_types = ItemContainer()
if file_:
if format == 'json' or file_.split('.')[-1] == 'json':
self.from_json(file_)
elif format == 'xml' or file_.split('.')[-1] == 'xml':
self.from_xml(file_)
[docs] def from_xml(self, file_):
tree = Et.parse(file_)
root = tree.getroot()
ptypes = root.find('ParticleTypes')
btypes = root.find('BondTypes')
atypes = root.find('AngleTypes')
dtypes = root.find('DihedralTypes')
itypes = root.find('ImproperTypes')
for ptype in ptypes:
pt = ParticleType()
for k, v in ptype.attrib.items():
try:
v = float(v)
except ValueError:
pass
setattr(pt, k, v)
pt.tag = pt.name
self.particle_types.add(pt)
for btype in btypes:
bt = BondType()
for k, v in btype.attrib.items():
try:
v = float(v)
except ValueError:
pass
setattr(bt, k, v)
bt.tag = bt.name
bt.rname = ','.join(reversed(bt.name.split(',')))
self.bond_types.add(bt)
for atype in atypes:
at = AngleType()
for k, v in atype.attrib.items():
try:
v = float(v)
except ValueError:
pass
setattr(at, k, v)
at.tag = at.name
at.rname = ','.join(reversed(at.name.split(',')))
self.angle_types.add(at)
for dtype in dtypes:
dt = DihedralType()
for k, v in dtype.attrib.items():
if k != 'd' and k != 'n':
try:
v = float(v)
except ValueError:
pass
elif k == 'd' or k == 'n':
try:
v = int(v)
except ValueError:
pass
setattr(dt, k, v)
dt.tag = dt.name
dt.rname = ','.join(reversed(dt.name.split(',')))
self.dihedral_types.add(dt)
for itype in itypes:
it = ImproperType()
for k, v in itype.attrib.items():
try:
v = float(v)
except ValueError:
pass
setattr(it, k, v)
it.tag = it.name
it.rname = ','.join(reversed(it.name.split(',')))
self.improper_types.add(it)
[docs] def from_json(self, json_file):
with open(json_file) as f:
j = json.loads(f.read())
self.ff_name = j.get('ff_name')
self.ff_class = j.get('ff_class')
self.pair_style = j.get('pair_style')
self.bond_style = j.get('bond_style')
self.angle_style = j.get('angle_style')
self.dihedral_style = j.get('dihedral_style')
self.improper_style = j.get('improper_style')
for pt in j.get('particle_types'):
self.particle_types.add(ParticleType(**pt))
for bt in j.get('bond_types'):
self.bond_types.add(BondType(**bt))
for at in j.get('angle_types'):
self.angle_types.add(AngleType(**at))
for dt in j.get('dihedral_types'):
self.dihedral_types.add(DihedralType(**dt))
for it in j.get('improper_types'):
self.improper_types.add(ImproperType(**it))
[docs] def write_json(self, out):
f = {}
f['ff_name'] = self.ff_name
f['ff_class'] = self.ff_class
f['pair_style'] = self.pair_style
f['bond_style'] = self.bond_style
f['angle_style'] = self.angle_style
f['dihedral_style'] = self.dihedral_style
f['improper_style'] = self.improper_style
f['particle_types'] = [vars(pt) for pt in self.particle_types]
f['bond_types'] = [vars(bt) for bt in self.bond_types]
f['angle_types'] = [vars(at) for at in self.angle_types]
f['dihedral_types'] = [vars(dt) for dt in self.dihedral_types]
f['improper_types'] = [vars(it) for it in self.improper_types]
with file(out, 'w') as _file:
_file.write(json.dumps(f, indent=4))
[docs] def write_xml(self, out):
"""pysimm.forcefield.Forcefield.write
Write Forcefield object to xml format.
Args:
out: file name to write
Returns:
None
"""
ff_elem = Et.Element('Forcefield')
ff_elem.set('name', self.ff_name)
ff_elem.set('class', self.ff_class)
ptypes = Et.SubElement(ff_elem, 'ParticleTypes')
for pt in self.particle_types:
ptype = Et.SubElement(ptypes, 'Type')
for k, v in vars(pt).items():
ptype.set(k, str(v))
btypes = Et.SubElement(ff_elem, 'BondTypes')
for bt in self.bond_types:
btype = Et.SubElement(btypes, 'Type')
for k, v in vars(bt).items():
btype.set(k, str(v))
atypes = Et.SubElement(ff_elem, 'AngleTypes')
for at in self.angle_types:
atype = Et.SubElement(atypes, 'Type')
for k, v in vars(at).items():
atype.set(k, str(v))
dtypes = Et.SubElement(ff_elem, 'DihedralTypes')
for dt in self.dihedral_types:
dtype = Et.SubElement(dtypes, 'Type')
for k, v in vars(dt).items():
dtype.set(k, str(v))
itypes = Et.SubElement(ff_elem, 'ImproperTypes')
for it in self.improper_types:
itype = Et.SubElement(itypes, 'Type')
for k, v in vars(it).items():
itype.set(k, str(v))
with open(out, 'w') as f:
f.write(
minidom.parseString(Et.tostring(ff_elem, 'utf-8')).toprettyxml(
indent=" "))