mmLib.FileIO

Package mmLib :: Module FileIO

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Module mmLib.FileIO

Load and save mmLib.Structure objects from/to mmLib supported formats. The mmCIF and PDB file formats are currently supported.

Classes
`ZCat`

Exceptions
`FileIOUnsupportedFormat`

Function Summary
	`get_file_arg(args)`
	`get_file_extension(path, default_extension)` Returns the 3-letter extension of the filename.
	`LoadStructure(**args)` Loads a mmCIF file(.cif) or PDB file(.pdb) into a Structure class and returns it.
	`open_fileobj(fil, file_mode)`
	`OpenFile(path, mode)` Right now this only supports opening GZip'ed files, in the future it might be extended for URLs.
	`SaveStructure(**args)` Saves a Structure object into a supported file type.
	`test_module()`

Function Details

get_file_extension(path, default_extension='PDB')

Returns the 3-letter extension of the filename.

LoadStructure(**args)

Loads a mmCIF file(.cif) or PDB file(.pdb) into a Structure class and returns it. The function takes 5 named arguments, one is required:

file = <file object or path; required> format = <'PDB'|'CIF'; defaults to 'PDB'> structure = <mmLib.Structure object to build on; defaults to createing new> sequence_from_structure = [True|False] <infer sequence from structure file, default False> library_bonds = [True|False] <build bonds from monomer library, default False> distance_bonds = [True|False] <build bonds from covalent distance calculations, default False>

OpenFile(path, mode)

Right now this only supports opening GZip'ed files, in the future it might be extended for URLs.

SaveStructure(**args)

Saves a Structure object into a supported file type. file = <file object or path; required> structure = <mmLib.Structure object to save; required> format = <'PDB' or 'CIF'; defaults to 'PDB'>

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