def read(self, filename, format='auto'):
"""Load structure from a file, any original data may become lost.
filename -- file to be loaded
format -- all structure formats are defined in Parsers submodule,
when format == 'auto' all Parsers are tried one by one
Return instance of data Parser used to process file. This
can be inspected for information related to particular format.
"""
from Parsers import getParser
p = getParser(format)
new_structure = p.parseFile(filename)
# reinitialize data after successful parsing
# avoid calling __init__ from a derived class
Structure.__init__(self)
if new_structure is not None:
self.__dict__.update(new_structure.__dict__)
self[:] = new_structure
if not self.description:
self.generateDescription()
# import os.path
# tailname = os.path.basename(filename)
# tailbase = os.path.splitext(tailname)[0]
# self.description = tailbase
return p
def read(self, filename, format='auto'):
"""Load structure from a file, any original data may become lost.
filename -- file to be loaded
format -- all structure formats are defined in Parsers submodule,
when format == 'auto' all Parsers are tried one by one
Return instance of data Parser used to process file. This
can be inspected for information related to particular format.
"""
from Parsers import getParser
p = getParser(format)
new_structure = p.parseFile(filename)
# reinitialize data after successful parsing
# avoid calling __init__ from a derived class
Molecule.__init__(self)
if new_structure is not None:
self.__dict__.update(new_structure.__dict__)
self[:] = new_structure
if not self.description:
self.generateDescription()
# import os.path
# tailname = os.path.basename(filename)
# tailbase = os.path.splitext(tailname)[0]
# self.description = tailbase
return p
def writeStr(self, format, **kwds):
"""return string representation of the structure in specified format
Note: available structure formats can be obtained by:
from Parsers import formats
"""
from Parsers import getParser
p = getParser(format)
s = p.tostring(self, **kwds)
return s
def writeStr(self, format, **kwds):
"""return string representation of the structure in specified format
Note: available structure formats can be obtained by:
from Parsers import formats
"""
from Parsers import getParser
p = getParser(format)
s = p.tostring(self,**kwds)
return s
def write(self, filename, format, **kwds):
"""Save structure to file in the specified format
No return value.
Note: available structure formats can be obtained by:
from Parsers import formats
"""
from Parsers import getParser
p = getParser(format)
p.filename = filename
s = p.tostring(self, **kwds)
f = open(filename, 'wb')
f.write(s)
f.close()
return
def write(self, filename, format):
"""Save molecule to file in the specified format
No return value.
Note: available structure formats can be obtained by:
from Parsers import formats
"""
from Parsers import getParser
p = getParser(format)
p.filename = filename
s = p.tostring(self)
f = open(filename, 'wb')
f.write(s)
f.close()
return
def readStr(self, s, format='auto'):
"""Load structure from a string, any original data become lost.
s -- string with structure definition
format -- all structure formats are defined in Parsers submodule,
when format == 'auto' all Parsers are tried one by one
Return instance of data Parser used to process input string. This
can be inspected for information related to particular format.
"""
from Parsers import getParser
p = getParser(format)
new_structure = p.parse(s)
# reinitialize data after successful parsing
# avoid calling __init__ from a derived class
Structure.__init__(self)
if new_structure is not None:
self.__dict__.update(new_structure.__dict__)
self[:] = new_structure
return p
def readStr(self, s, format='auto'):
"""Load structure from a string, any original data become lost.
s -- string with structure definition
format -- all structure formats are defined in Parsers submodule,
when format == 'auto' all Parsers are tried one by one
Return instance of data Parser used to process input string. This
can be inspected for information related to particular format.
"""
from Parsers import getParser
p = getParser(format)
new_structure = p.parse(s)
# reinitialize data after successful parsing
# avoid calling __init__ from a derived class
Molecule.__init__(self)
if new_structure is not None:
self.__dict__.update(new_structure.__dict__)
self[:] = new_structure
return p
def loadStructure(filename, format=None, **kwds):
if format is None:
format = 'auto'
from Parsers import getParser
p = getParser(format)
return p.parseFile(filename)
