def save(self, fname, format=None, overwrite=False, **kwargs):
"""
Saves the current ResidueTemplate in the requested file format.
Supported formats can be specified explicitly or determined by file-name
extension. The following formats are supported, with the recognized
suffix shown in parentheses:
- MOL2 (.mol2)
- MOL3 (.mol3)
- OFF (.lib/.off)
- PDB (.pdb)
- PQR (.pqr)
Parameters
----------
fname : str
Name of the file to save. If ``format`` is ``None`` (see below), the
file type will be determined based on the filename extension. If the
type cannot be determined, a ValueError is raised.
format : str, optional
The case-insensitive keyword specifying what type of file ``fname``
should be saved as. If ``None`` (default), the file type will be
determined from filename extension of ``fname``
overwrite : bool, optional
If True, allow the target file to be overwritten. Otherwise, an
IOError is raised if the file exists. Default is False
kwargs : keyword-arguments
Remaining arguments are passed on to the file writing routines that
are called by this function
Raises
------
ValueError if either filename extension or ``format`` are not recognized
TypeError if the structure cannot be converted to the desired format for
whatever reason
"""
from parmed.amber.offlib import AmberOFFLibrary
from parmed.formats.mol2 import Mol2File
extmap = {".mol2": "MOL2", ".mol3": "MOL3", ".off": "OFFLIB", ".lib": "OFFLIB", ".pdb": "PDB", ".pqr": "PQR"}
if format is not None:
format = format.upper()
else:
base, ext = os.path.splitext(fname)
if ext in (".bz2", ".gz"):
ext = os.path.splitext(base)[1]
if ext in extmap:
format = extmap[ext]
else:
raise ValueError("Could not determine file type of %s" % fname)
if format == "MOL2":
Mol2File.write(self, fname, mol3=False, **kwargs)
elif format == "MOL3":
Mol2File.write(self, fname, mol3=True, **kwargs)
elif format in ("OFFLIB", "OFF"):
AmberOFFLibrary.write({self.name: self}, fname, **kwargs)
elif format in ("PDB", "PQR"):
self.to_structure().save(fname, format=format, overwrite=overwrite, **kwargs)
else:
raise ValueError("Unrecognized format for ResidueTemplate save")
def save(self, fname, format=None, **kwargs):
"""
Saves the current ResidueTemplateContainer in the requested file format.
Supported formats can be specified explicitly or determined by file-name
extension. The following formats are supported, with the recognized
suffix and ``format`` keyword shown in parentheses:
- MOL2 (.mol2)
- MOL3 (.mol3)
- OFF (.lib/.off)
Parameters
----------
fname : str
Name of the file to save. If ``format`` is ``None`` (see below), the
file type will be determined based on the filename extension. If the
type cannot be determined, a ValueError is raised.
format : str, optional
The case-insensitive keyword specifying what type of file ``fname``
should be saved as. If ``None`` (default), the file type will be
determined from filename extension of ``fname``
kwargs : keyword-arguments
Remaining arguments are passed on to the file writing routines that
are called by this function
Raises
------
ValueError if either filename extension or ``format`` are not recognized
TypeError if the structure cannot be converted to the desired format for
whatever reason
Notes
-----
Mol2 and Mol3 files are saved as concatenated multiple @<MOLECULE>s. By
contrast, ``Structure.save`` will save a single @<MOLECULE> mol2 file
with multiple residues if the mol2 format is requested.
"""
from parmed.amber.offlib import AmberOFFLibrary
from parmed.formats.mol2 import Mol2File
extmap = {".mol2": "MOL2", ".mol3": "MOL3", ".off": "OFFLIB", ".lib": "OFFLIB"}
if format is not None:
format = format.upper()
else:
base, ext = os.path.splitext(fname)
if ext in (".bz2", ".gz"):
ext = os.path.splitext(base)[1]
if ext in extmap:
format = extmap[ext]
else:
raise ValueError("Could not determine file type of %s" % fname)
if format == "MOL2":
Mol2File.write(self, fname, mol3=False, split=True, **kwargs)
elif format == "MOL3":
Mol2File.write(self, fname, mol3=True, split=True, **kwargs)
elif format in ("OFFLIB", "OFF"):
AmberOFFLibrary.write(self.to_library(), fname, **kwargs)
else:
raise ValueError("Unrecognized format for ResidueTemplate save")
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 save(self, fname, format=None, **kwargs):
"""
Saves the current ResidueTemplateContainer in the requested file format.
Supported formats can be specified explicitly or determined by file-name
extension. The following formats are supported, with the recognized
suffix and ``format`` keyword shown in parentheses:
- MOL2 (.mol2)
- MOL3 (.mol3)
- OFF (.lib/.off)
Parameters
----------
fname : str
Name of the file to save. If ``format`` is ``None`` (see below), the
file type will be determined based on the filename extension. If the
type cannot be determined, a ValueError is raised.
format : str, optional
The case-insensitive keyword specifying what type of file ``fname``
should be saved as. If ``None`` (default), the file type will be
determined from filename extension of ``fname``
kwargs : keyword-arguments
Remaining arguments are passed on to the file writing routines that
are called by this function
Raises
------
ValueError if either filename extension or ``format`` are not recognized
TypeError if the structure cannot be converted to the desired format for
whatever reason
Notes
-----
Mol2 and Mol3 files are saved as concatenated multiple @<MOLECULE>s. By
contrast, ``Structure.save`` will save a single @<MOLECULE> mol2 file
with multiple residues if the mol2 format is requested.
"""
from parmed.amber.offlib import AmberOFFLibrary
from parmed.formats.mol2 import Mol2File
extmap = {
'.mol2': 'MOL2',
'.mol3': 'MOL3',
'.off': 'OFFLIB',
'.lib': 'OFFLIB',
}
if format is not None:
format = format.upper()
else:
base, ext = os.path.splitext(fname)
if ext in ('.bz2', '.gz'):
ext = os.path.splitext(base)[1]
if ext in extmap:
format = extmap[ext]
else:
raise ValueError('Could not determine file type of %s' % fname)
if format == 'MOL2':
Mol2File.write(self, fname, mol3=False, split=True, **kwargs)
elif format == 'MOL3':
Mol2File.write(self, fname, mol3=True, split=True, **kwargs)
elif format in ('OFFLIB', 'OFF'):
AmberOFFLibrary.write(self.to_library(), fname, **kwargs)
else:
raise ValueError('Unrecognized format for ResidueTemplate save')
def save(self, fname, format=None, overwrite=False, **kwargs):
"""
Saves the current ResidueTemplate in the requested file format.
Supported formats can be specified explicitly or determined by file-name
extension. The following formats are supported, with the recognized
suffix shown in parentheses:
- MOL2 (.mol2)
- MOL3 (.mol3)
- OFF (.lib/.off)
- PDB (.pdb)
- PQR (.pqr)
Parameters
----------
fname : str
Name of the file to save. If ``format`` is ``None`` (see below), the
file type will be determined based on the filename extension. If the
type cannot be determined, a ValueError is raised.
format : str, optional
The case-insensitive keyword specifying what type of file ``fname``
should be saved as. If ``None`` (default), the file type will be
determined from filename extension of ``fname``
overwrite : bool, optional
If True, allow the target file to be overwritten. Otherwise, an
IOError is raised if the file exists. Default is False
kwargs : keyword-arguments
Remaining arguments are passed on to the file writing routines that
are called by this function
Raises
------
ValueError if either filename extension or ``format`` are not recognized
TypeError if the structure cannot be converted to the desired format for
whatever reason
"""
from parmed.amber.offlib import AmberOFFLibrary
from parmed.formats.mol2 import Mol2File
extmap = {
'.mol2': 'MOL2',
'.mol3': 'MOL3',
'.off': 'OFFLIB',
'.lib': 'OFFLIB',
'.pdb': 'PDB',
'.pqr': 'PQR',
}
if format is not None:
format = format.upper()
else:
base, ext = os.path.splitext(fname)
if ext in ('.bz2', '.gz'):
ext = os.path.splitext(base)[1]
if ext in extmap:
format = extmap[ext]
else:
raise ValueError('Could not determine file type of %s' % fname)
if format == 'MOL2':
Mol2File.write(self, fname, mol3=False, **kwargs)
elif format == 'MOL3':
Mol2File.write(self, fname, mol3=True, **kwargs)
elif format in ('OFFLIB', 'OFF'):
AmberOFFLibrary.write({self.name: self}, fname, **kwargs)
elif format in ('PDB', 'PQR'):
self.to_structure().save(fname,
format=format,
overwrite=overwrite,
**kwargs)
else:
raise ValueError('Unrecognized format for ResidueTemplate save')
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'))
