parmed.amber.offlib module

Tool for parsing and writing OFF library files to and from dictionaries of ResidueTemplate objects

class parmed.amber.offlib.AmberOFFLibrary

Bases: object

Class containing static methods responsible for parsing and writing OFF libraries

Methods

id_format(filename)	Sees if an open file is an OFF library file.
parse(filename)	Parses an Amber OFF library
write(lib, dest)	Writes a dictionary of ResidueTemplate units to a file in OFF format

static id_format(filename)

Sees if an open file is an OFF library file.

Parameters

filenamestr

The name of the file to see if it is an OFF file format

Returns

is_fmtbool

True if it is recognized as OFF, False otherwise

static parse(filename)

Parses an Amber OFF library

Parameters

filenamestr or file-like iterable

The file name or file object to parse. If it is an iterable, it will be exhausted

Returns

residuesOrderedDict {str

Dictionary pairing residue names with their ResidueTemplate objects

Raises

ValueError if the first line does not match the file format. This line

will be consumed

IOError if filename is the name of a file that does not exist

RuntimeError if EOF is reached prematurely or other formatting issues

found

static write(lib, dest)

Writes a dictionary of ResidueTemplate units to a file in OFF format

Parameters

libdict {str

Items can be either ResidueTemplate or ResidueTemplateContainer instances

deststr or file-like

Either a file name or a file-like object to write the file to