def __init__(self, *filenames):
super(AmberParameterSet, self).__init__()
self.default_scee = 1.2
self.default_scnb = 2.0
self.titles = []
for filename in filenames:
if isinstance(filename, string_types):
if AmberOFFLibrary.id_format(filename):
self.residues.update(AmberOFFLibrary.parse(filename))
else:
self.load_parameters(filename)
elif isinstance(filename, Sequence):
for fname in filename:
if AmberOFFLibrary.id_format(fname):
self.residues.update(AmberOFFLibrary.parse(fname))
else:
self.load_parameters(fname)
else:
# Assume open file object
self.load_parameters(filename)
def from_leaprc(cls, fname):
""" Load a parameter set from a leaprc file
Parameters
----------
fname : str or file-like
Name of the file or open file-object from which a leaprc-style file
will be read
Notes
-----
This does not read all parts of a leaprc file -- only those pertinent to
defining force field information. For instance, the following sections
and commands are processed:
- addAtomTypes
- loadAmberParams
- loadOFF
"""
params = cls()
if isinstance(fname, string_types):
f = genopen(fname, 'r')
own_handle = True
else:
f = fname
own_handle = False
# To make parsing easier, and because leaprc files are usually quite
# short, I'll read the whole file into memory
text = f.read()
if own_handle: f.close()
lowertext = text.lower() # commands are case-insensitive
try:
idx = lowertext.index('addatomtypes')
except ValueError:
# Does not exist in this file
atom_types_str = ''
else:
# Now process the addAtomTypes
i = idx + len('addatomtypes')
while i < len(text) and text[i] != '{':
if text[i] not in '\r\n\t ':
raise ParameterError('Unsupported addAtomTypes syntax in '
'leaprc file')
i += 1
if i == len(text):
raise ParameterError('Unsupported addAtomTypes syntax in '
'leaprc file')
# We are at our first brace
chars = []
nopen = 1
i += 1
while i < len(text):
char = text[i]
if char == '{':
nopen += 1
elif char == '}':
nopen -= 1
if nopen == 0: break
elif char == '\n':
char = ' '
chars.append(char)
i += 1
atom_types_str = ''.join(chars).strip()
for _, name, symb, hyb in _atomtypere.findall(atom_types_str):
if symb not in AtomicNum:
raise ParameterError('%s is not a recognized element' % symb)
if name in params.atom_types:
params.atom_types[name].atomic_number = AtomicNum[symb]
else:
params.atom_types[name] = \
AtomType(name, len(params.atom_types)+1, Mass[symb],
AtomicNum[symb])
# Now process the parameter files
for fname in _loadparamsre.findall(text):
params.load_parameters(_find_amber_file(fname))
# Now process the library file
for fname in _loadoffre.findall(text):
params.residues.update(
AmberOFFLibrary.parse(_find_amber_file(fname))
)
return params
def from_leaprc(cls, fname, search_oldff=False):
""" Load a parameter set from a leaprc file
Parameters
----------
fname : str or file-like
Name of the file or open file-object from which a leaprc-style file
will be read
search_oldff : bool, optional, default=False
If True, search the oldff directories in the main Amber leap
folders. Default is False
Notes
-----
This does not read all parts of a leaprc file -- only those pertinent to
defining force field information. For instance, the following sections
and commands are processed:
- addAtomTypes
- loadAmberParams
- loadOFF
- loadMol2
- loadMol3
"""
params = cls()
if isinstance(fname, string_types):
f = genopen(fname, 'r')
own_handle = True
else:
f = fname
own_handle = False
# To make parsing easier, and because leaprc files are usually quite
# short, I'll read the whole file into memory
def joinlines(lines):
newlines = []
composite = []
for line in lines:
if line.endswith('\\\n'):
composite.append(line[:-2])
continue
else:
composite.append(line)
newlines.append(''.join(composite))
composite = []
if composite:
newlines.append(''.join(composite))
return newlines
lines = joinlines(map(lambda line:
line if '#' not in line else line[:line.index('#')], f))
text = ''.join(lines)
if own_handle: f.close()
lowertext = text.lower() # commands are case-insensitive
# Now process the parameter files
def process_fname(fname):
if fname[0] in ('"', "'"):
fname = fname[1:-1]
fname = fname.replace('_BSTOKEN_', r'\ ').replace(r'\ ', ' ')
return fname
for line in lines:
line = line.replace(r'\ ', '_BSTOKEN_')
if _loadparamsre.findall(line):
fname = process_fname(_loadparamsre.findall(line)[0])
params.load_parameters(_find_amber_file(fname, search_oldff))
elif _loadoffre.findall(line):
fname = process_fname(_loadoffre.findall(line)[0])
params.residues.update(
AmberOFFLibrary.parse(_find_amber_file(fname, search_oldff))
)
elif _loadmol2re.findall(line):
(resname, fname), = _loadmol2re.findall(line)
residue = Mol2File.parse(_find_amber_file(fname, search_oldff))
if isinstance(residue, ResidueTemplateContainer):
warnings.warn('Multi-residue mol2 files not supported by '
'tleap. Loading anyway using names in mol2',
AmberWarning)
for res in residue:
params.residues[res.name] = res
else:
params.residues[resname] = residue
# Now process the addAtomTypes
try:
idx = lowertext.index('addatomtypes')
except ValueError:
# Does not exist in this file
atom_types_str = ''
else:
i = idx + len('addatomtypes')
while i < len(text) and text[i] != '{':
if text[i] not in '\r\n\t ':
raise ParameterError('Unsupported addAtomTypes syntax in '
'leaprc file')
i += 1
if i == len(text):
raise ParameterError('Unsupported addAtomTypes syntax in '
'leaprc file')
# We are at our first brace
chars = []
nopen = 1
i += 1
while i < len(text):
char = text[i]
if char == '{':
nopen += 1
elif char == '}':
nopen -= 1
if nopen == 0: break
elif char == '\n':
char = ' '
chars.append(char)
i += 1
atom_types_str = ''.join(chars).strip()
for _, name, symb, hyb in _atomtypere.findall(atom_types_str):
if symb not in AtomicNum:
raise ParameterError('%s is not a recognized element' % symb)
if name in params.atom_types:
params.atom_types[name].atomic_number = AtomicNum[symb]
return params
""" Standard residue templates for biomolecular residues """ import os from parmed.amber.offlib import AmberOFFLibrary as _parser StandardBiomolecularResidues = _parser.parse(os.path.join(os.path.split(__file__)[0], "data", "standard_residues.lib"))
""" Standard residue templates for biomolecular residues """
import os
from parmed.amber.offlib import AmberOFFLibrary as _parser
StandardBiomolecularResidues = _parser.parse(
os.path.join(os.path.split(__file__)[0], 'data', 'standard_residues.lib'))
