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#!/usr/bin/env python
# -*- coding: utf-8 -*-
#
# Copyright 2018 João Pedro Rodrigues
#
# Licensed under the Apache License, Version 2.0 (the "License");
# you may not use this file except in compliance with the License.
# You may obtain a copy of the License at
#
# http://www.apache.org/licenses/LICENSE-2.0
#
# Unless required by applicable law or agreed to in writing, software
# distributed under the License is distributed on an "AS IS" BASIS,
# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
# See the License for the specific language governing permissions and
# limitations under the License.
"""The pdb-tools library.
A Swiss army knife for manipulating and editing PDB files.
You can use pdb-tools as a library or as a series of convenient
command-line applications. The complete documentation is available at:
http://www.bonvinlab.org/pdb-tools/
Examples at the command-line
----------------------------
$ pdb_fetch 1brs > 1brs.pdb
$ pdb_reres -1 1ctf.pdb > 1ctf_renumbered.pdb
$ pdb_selchain -A,D 1brs.pdb | pdb_delhetatm | pdb_tidy > 1brs_AD_noHET.pdb
Examples using pdb-tools as library
-----------------------------------
You can import according to your needs:
>>> import pdbtools
>>> from pdbtools import *
>>> from pdbtools import MODULE
>>> from pdbtools import pdb_selchain
Chain the different functionalities conveniently:
>>> from pdbtools import pdb_selchain, pdb_selatom, pdb_keepcoord
>>> with open('dummy.pdb') as fh:
>>> chain_a = pdb_selchain.run(fh, ['A'])
>>> only_N = pdb_selatom.run(chain_a, ['N'])
>>> coords = pdb_keepcoord.run(only_N)
>>> final = pdb_reres.run(coords, 5)
>>> print(''.join(final))
The list of MODULEs is specified bellow.
All packages have three functions: `check_input`, `main`, and `run`.
The latter executes the logic of each package. `check_input` checks and
prepares potential input parameters to feed `run`. Use `check_input` in
case you are not sure the received input is correct. You can chain both
functions:
>>> MODULE.run(**MODULE.check_input(*args))
If you control the input parameters use `run` directly. In general,
`run` functions are generators yielding the modified PDB data
line-by-line. `main` is used solely in the context of the command-line
interface.
All MODULEs and `run` functions provide comprehensive documentation.
>>> help(MODULE)
>>> help(MODULE.run)
"""
__all__ = [
'pdb_b',
'pdb_chainbows',
'pdb_chain',
'pdb_chainxseg',
'pdb_chkensemble',
'pdb_delchain',
'pdb_delelem',
'pdb_delhetatm',
'pdb_delinsertion',
'pdb_delresname',
'pdb_delres',
'pdb_element',
'pdb_fetch',
'pdb_fixinsert',
'pdb_fromcif',
'pdb_gap',
'pdb_head',
'pdb_intersect',
'pdb_keepcoord',
'pdb_merge',
'pdb_mkensemble',
'pdb_occ',
'pdb_reatom',
'pdb_reres',
'pdb_rplchain',
'pdb_rplresname',
'pdb_seg',
'pdb_segxchain',
'pdb_selaltloc',
'pdb_selatom',
'pdb_selchain',
'pdb_selelem',
'pdb_selhetatm',
'pdb_selresname',
'pdb_selres',
'pdb_selseg',
'pdb_shiftres',
'pdb_sort',
'pdb_splitchain',
'pdb_splitmodel',
'pdb_splitseg',
'pdb_tidy',
'pdb_tocif',
'pdb_tofasta',
'pdb_uniqname',
'pdb_validate',
'pdb_wc',
]
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