First stable release (squashed 50 commits)

LICENSE

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+The MIT License (MIT)
+
+Copyright (c) 2015 João Rodrigues
+
+Permission is hereby granted, free of charge, to any person obtaining a copy of
+this software and associated documentation files (the "Software"), to deal in
+the Software without restriction, including without limitation the rights to
+use, copy, modify, merge, publish, distribute, sublicense, and/or sell copies of
+the Software, and to permit persons to whom the Software is furnished to do so,
+subject to the following conditions:
+
+The above copyright notice and this permission notice shall be included in all
+copies or substantial portions of the Software.
+
+THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
+IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, FITNESS
+FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR
+COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY, WHETHER
+IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, OUT OF OR IN
+CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE SOFTWARE.

README.md

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+pdb-tools
+================================================
+Set of utility scripts in python to manipulate PDB files as streams. Given the generic name, there
+was already another set of scripts named 'pdb-tools', which perform a very different variety of
+operations on PDB files. You can find them [here](https://github.com/harmslab/pdbtools).
+
+About
+---------
+
+Manipulating PDB files is a pain. Extracting chains, renumbering residues, splitting or merging
+models or chains, modifying b-factors and occupancies, or extracting the sequence of a PDB file, are
+examples of operations that can be done using any decent parsing library but it takes 1) scripting
+knowledge, 2) time, and 3) almost surely a set of external dependencies installed.
+
+The scripts in this repository simplify most of these tasks. They are the descendant of a set of old
+FORTRAN77 programs in use in our lab at Utrecht that had the particular advantage of working with
+streams, i.e. the output of one script could be piped into another. Since FORTRAN77 is a pain too, I
+rewrote the scripts in Python and added a few more.
+
+Requests for new scripts will be taken into consideration, depending on the effort and general
+usability of the script.
+
+Features
+------------
+* Simple: one script, one job.
+* Written using Python (stdlib): no compilation, cross-platform, no external dependencies
+* Read data from file, or from the output of another script.
+
+Requirements
+------------
+* Python 2.7 (might work on earlier versions, not really tested.)
+
+Installation
+------------
+Download the zip archive or clone the repository with git. This last is the recommended option as it
+is then extremely simple to get updates.
+
+```bash
+# To download
+git clone https://github.com/JoaoRodrigues/pdb-tools
+
+# To update
+cd pdb-tools && git pull origin master
+```
+
+Usage
+------------
+All the scripts have a short description of their purpose and their usage. Just run them without any
+arguments:
+```bash
+$ ./pdb_selchain.py
+
+Extracts a chain from a PDB file.
+
+usage: python pdb_selchain.py -<chain> <pdb file>
+example: python pdb_selchain.py -A 1CTF.pdb
+
+Author: Joao Rodrigues ([email protected])
+
+This program is part of the PDB tools distributed with HADDOCK
+or with the HADDOCK tutorial. The utilities in this package
+can be used to quickly manipulate PDB files, with the benefit
+of 'piping' several different commands. This is a rewrite of old
+FORTRAN77 code that was taking too much effort to compile. RIP.
+```
+
+Examples
+------------
+
+* Downloading a structure
+   ```bash
+   ./pdb_fetch.py 1ctf > 1ctf.pdb
+   ./pdb_fetch.py -biounit 1brs > 1brs_biounit.pdb
+   ```
+
+* Renumbering a structure
+   ```bash
+   ./pdb_reres.py -1 1ctf.pdb > 1ctf_renumbered.pdb
+   ```
+
+* Extracting a particular chain
+   ```bash
+   ./pdb_selchain.py -A 1brs_biounit.pdb > 1brs_A.pdb
+   ```
+
+* Downloading, extracting a chain, and extracting its aa sequence
+  ```bash
+  ./pdb_fetch.py 1brs | ./pdb_selchain.py -A | ./pdb_toseq.py > 1brs_A.fasta
+  ```
+
+* Getting general information on a PDB file
+   ```bash
+   $ ./pdb_fetch.py 1brs | ./pdb_wc.py
+   No. atoms:	4640	(4640.0 per model)
+   No. residues:	588	(588.0 per model)
+   No. chains:	6	( 6.0 per model)
+   No. models:	1
+   Hetero Atoms:	Yes
+   Has seq. gaps:	Yes
+   Double Occ.:	Yes
+   Insertions:	No
+
+   $ ./pdb_fetch.py -biounit 1brs | ./pdb_wc.py
+   No. atoms:	1559	(1559.0 per model)
+   No. residues:	195	(195.0 per model)
+   No. chains:	2	( 2.0 per model)
+   No. models:	2
+   Hetero Atoms:	Yes
+   Has seq. gaps:	Yes
+   Double Occ.:	Yes
+   Insertions:	No
+   ```
+
+* Finding gaps in a PDB file
+   ```bash
+   $ ./pdb_fetch.py -biounit 1brs | ./pdb_gap.py
+   D:THR63 <    4.88A > D:GLY66
+   ```
+
+License
+---------
+MIT. See LICENSE file.

pdb_b.py

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+#!/usr/bin/env python
+
+"""
+Modifies the b-factor of a PDB file (default 10.0).
+
+usage: python pdb_b.py -<bfactor> <pdb file>
+example: python pdb_b.py -10.0 1CTF.pdb
+
+Author: {0} ({1})
+
+This program is part of the PDB tools distributed with HADDOCK
+or with the HADDOCK tutorial. The utilities in this package
+can be used to quickly manipulate PDB files, with the benefit
+of 'piping' several different commands. This is a rewrite of old
+FORTRAN77 code that was taking too much effort to compile. RIP.
+"""
+
+import os
+import re
+import sys
+
+__author__ = "Joao Rodrigues"
+__email__ = "[email protected]"
+
+USAGE = __doc__.format(__author__, __email__)
+
+def check_input(args):
+    """Checks whether to read from stdin/file and validates user input/options."""
+
+    if not len(args):
+        # No bfactor, from pipe
+        if not sys.stdin.isatty():
+            pdbfh = sys.stdin
+            bfactor = 10.0
+        else:
+            sys.stderr.write(USAGE)
+            sys.exit(1)
+    elif len(args) == 1:
+        # bfactor & Pipe _or_ file & no bfactor
+        if re.match('\-[0-9\.]+', args[0]):
+            bfactor = float(args[0][1:])
+            if not sys.stdin.isatty():
+                pdbfh = sys.stdin
+            else:
+                sys.stderr.write(USAGE)
+                sys.exit(1)
+        else:
+            if not os.path.isfile(args[0]):
+                sys.stderr.write('File not found: ' + args[0] + '\n')
+                sys.stderr.write(USAGE)
+                sys.exit(1)
+            pdbfh = open(args[0], 'r')
+            bfactor = 10.0
+    elif len(args) == 2:
+        # bfactor & File
+        if not re.match('\-[0-9\.]+', args[0]):
+            sys.stderr.write('Invalid b-factor value: ' + args[0] + '\n')
+            sys.stderr.write(USAGE)
+            sys.exit(1)
+        if not os.path.isfile(args[1]):
+            sys.stderr.write('File not found: ' + args[1] + '\n')
+            sys.stderr.write(USAGE)
+            sys.exit(1)
+        bfactor = float(args[0][1:])
+        pdbfh = open(args[1], 'r')
+    else:
+        sys.stderr.write(USAGE)
+        sys.exit(1)
+
+    return (bfactor, pdbfh)
+
+def _alter_bfactor(fhandle, bfactor):
+    """Enclosing logic in a function to speed up a bit"""
+
+    coord_re = re.compile('^(ATOM|HETATM)')
+    #bfactor = str(round(bfactor, 2)).rjust(6)
+    bfactor = "{0:>6.2f}".format(bfactor)
+    for line in fhandle:
+        line = line.strip()
+        if coord_re.match(line):
+            yield line[:60] + bfactor + line[66:] + '\n'
+        else:
+            yield line + '\n'
+
+if __name__ == '__main__':
+
+    # Check Input
+    bfactor, pdbfh = check_input(sys.argv[1:])
+
+    # Do the job
+    new_pdb = _alter_bfactor(pdbfh, bfactor)
+
+    try:
+        sys.stdout.write(''.join(new_pdb))
+        sys.stdout.flush()
+    except IOError:
+        # This is here to catch Broken Pipes
+        # for example to use 'head' or 'tail' without
+        # the error message showing up
+        pass
+
+    # last line of the script
+    # We can close it even if it is sys.stdin
+    pdbfh.close()
+    sys.exit(0)

pdb_chain.py

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+#!/usr/bin/env python
+
+"""
+Sets the chain ID for a PDB file.
+
+usage: python pdb_chain.py -<chain> <pdb file>
+example: python pdb_chain.py -A 1CTF.pdb
+
+Author: {0} ({1})
+
+This program is part of the PDB tools distributed with HADDOCK
+or with the HADDOCK tutorial. The utilities in this package
+can be used to quickly manipulate PDB files, with the benefit
+of 'piping' several different commands. This is a rewrite of old
+FORTRAN77 code that was taking too much effort to compile. RIP.
+"""
+
+import os
+import re
+import sys
+
+__author__ = "Joao Rodrigues"
+__email__ = "[email protected]"
+
+USAGE = __doc__.format(__author__, __email__)
+
+def check_input(args):
+    """Checks whether to read from stdin/file and validates user input/options."""
+
+    if not len(args):
+        # No chain, from pipe
+        if not sys.stdin.isatty():
+            pdbfh = sys.stdin
+            chain = ' '
+        else:
+            sys.stderr.write(USAGE)
+            sys.exit(1)
+    elif len(args) == 1:
+        # Chain & Pipe _or_ file & no chain
+        if re.match('\-[A-Za-z0-9]', args[0]):
+            chain = args[0][1:]
+            if not sys.stdin.isatty():
+                pdbfh = sys.stdin
+            else:
+                sys.stderr.write(USAGE)
+                sys.exit(1)
+        else:
+            if not os.path.isfile(args[0]):
+                sys.stderr.write('File not found: ' + args[0] + '\n')
+                sys.stderr.write(USAGE)
+                sys.exit(1)
+            pdbfh = open(args[0], 'r')
+            chain = ' '
+    elif len(args) == 2:
+        # Chain & File
+        if not re.match('\-[A-Za-z0-9]', args[0]):
+            sys.stderr.write('Invalid chain ID: ' + args[0] + '\n')
+            sys.stderr.write(USAGE)
+            sys.exit(1)
+
+        if not os.path.isfile(args[1]):
+            sys.stderr.write('File not found: ' + args[1] + '\n')
+            sys.stderr.write(USAGE)
+            sys.exit(1)
+        chain = args[0][1:]
+        pdbfh = open(args[1], 'r')
+    else:
+        sys.stderr.write(USAGE)
+        sys.exit(1)
+
+    return (chain, pdbfh)
+
+def _alter_chain(fhandle, chain_id):
+    """Enclosing logic in a function to speed up a bit"""
+
+    coord_re = re.compile('^(ATOM|HETATM)')
+    fhandle = fhandle
+    chain_id = chain_id
+
+    for line in fhandle:
+        line = line.strip()
+        if coord_re.match(line):
+            yield line[:21] + chain_id[0] + line[22:] + '\n'
+        else:
+            yield line + '\n'
+
+if __name__ == '__main__':
+    # Check Input
+    chain, pdbfh = check_input(sys.argv[1:])
+
+    # Do the job
+    new_pdb = _alter_chain(pdbfh, chain)
+
+    try:
+        sys.stdout.write(''.join(new_pdb))
+        sys.stdout.flush()
+    except IOError:
+        # This is here to catch Broken Pipes
+        # for example to use 'head' or 'tail' without
+        # the error message showing up
+        pass
+
+    # last line of the script
+    # We can close it even if it is sys.stdin
+    pdbfh.close()
+    sys.exit(0)