model.make_chains() -- Fetch sequences from PDB file

file = <str:1>	'default'	partial or complete filename
structure_types = <str:1>	'structure'	'structure structureX structureN structureM structureF structureE structureU'
minimal_resolution = <float:1>	99.0	resolution threshold to select chains
minimal_chain_length = <int:1>	30	length cut-off for selecting chains
max_nonstdres = <int:1>	10	max. number of non-standard residues
chop_nonstd_terminii = <bool:1>	True	whether or not to chop non-standard N- and/or C-terminal residue in MAKE_CHAINS
minimal_stdres = <int:1>	30	min. number of standard residues
alignment_format = <str:1>	'PIR'	format of the alignment file: 'PIR' | 'PAP' | 'QUANTA' | 'INSIGHT' | 'FASTA'

Description:

This command fetches the sequences of the various chains found in the PDB file that has been read into memory (see model.read()).

The sequence of every chain that matches the input criteria is written out to separate files.

structure_types refers to the experimental method used to determine the structure. The following types are recognized: 'structureX' for x-ray, 'structureN' for NMR and 'structureM' for model, 'structureE' for electron microscopy, 'structureF' for fiber diffraction, 'structureU' for neutron diffraction, 'structure' for any structure.

minimal_resolution refers to the cut-off value of the experimental resolution of the structure. Structures with resolutions larger than this threshold are not processed.

minimal_chain_length refers to the lower limit of the chain length. Chains whose lengths are smaller than this value are not processed.

max_nonstdres sets the maximum limit of non-standard residues that is tolerated.

chop_nonstd_terminii removes the non-standard residues found at the terminii of the chains.

minimal_stdres sets the minimum number of standard residues that are required to process the chain. Chains that don't have at least this number of standard residues are not written out.

alignment_format specifies the format of the output file.

Example: examples/commands/make_chains.py

# Example for: model.make_chains()

# This will read a PDB file (segment), and write out all of its chains
# satisfying the listed conditions into separate alignment files in the
# PIR format.

env = environ()
mdl = model(env, file='../atom_files/pdb1lzd.ent')
mdl.make_chains(file='1lzd', minimal_chain_length=30, minimal_resolution=2.0,
                minimal_stdres=30, chop_nonstd_terminii=True,
                structure_types='structureN structureX',
                alignment_format='PIR')