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 save(self, fname, format=None, **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 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
"""
from parmed.modeller.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, **kwargs)
elif format == 'MOL3':
Mol2File.write(self, fname, mol3=True, **kwargs)
elif format in ('OFFLIB', 'OFF'):
AmberOFFLibrary.write({self.name : self}, fname, **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 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')
