Merge pull request #96 from jchodera/master

Added --pdbid, --url, and --verbose flags.

Manual.html

@@ -98,6 +98,8 @@ When run with no arguments, it launches the user interface.  If any arguments ar
 
 Options:
   -h, --help            show this help message and exit
+  --pdbid=PDBID         PDB id to retrieve from RCSB [default: None]
+  --url=URL             URL to retrieve PDB from [default: None]
   --output=FILENAME     output pdb file [default: output.pdb]
   --add-atoms=ATOMS     which missing atoms to add: all, heavy, hydrogen, or
                         none [default: all]

README.md

-[![Build Status](https://travis-ci.org/pandegroup/pdbfixer.svg)](https://travis-ci.org/pandegroup/pdbfixer)
+[![Build Status](https://travis-ci.org/pandegroup/pdbfixer.svg?branch=master)](https://travis-ci.org/pandegroup/pdbfixer)
 
 PDBFixer
 ========

devtools/conda-recipe/meta.yaml

@@ -2,6 +2,10 @@ package:
   name: pdbfixer-dev
   version: dev
 
+build:
+  entry_points:
+    - pdbfixer = pdbfixer.pdbfixer:main
+
 requirements:
   build:
     - python
@@ -18,6 +22,9 @@ test:
   requires:
     - nose
 
+  imports:
+    - pdbfixer
+
   commands:
     - nosetests pdbfixer --nocapture --verbosity=2 --with-doctest
 

pdbfixer/pdbfixer.py

@@ -1036,6 +1036,8 @@ def main():
         
         from optparse import OptionParser
         parser = OptionParser(usage="Usage: %prog\n       %prog [options] filename\n\nWhen run with no arguments, it launches the user interface.  If any arguments are specified, it runs in command line mode.")
+        parser.add_option('--pdbid', default=None, dest='pdbid', metavar='PDBID', help='PDB id to retrieve from RCSB [default: None]')
+        parser.add_option('--url', default=None, dest='url', metavar='URL', help='URL to retrieve PDB from [default: None]')
         parser.add_option('--output', default='output.pdb', dest='output', metavar='FILENAME', help='output pdb file [default: output.pdb]')
         parser.add_option('--add-atoms', default='all', dest='atoms', choices=('all', 'heavy', 'hydrogen', 'none'), help='which missing atoms to add: all, heavy, hydrogen, or none [default: all]')
         parser.add_option('--keep-heterogens', default='all', dest='heterogens', choices=('all', 'water', 'none'), metavar='OPTION', help='which heterogens to keep: all, water, or none [default: all]')
@@ -1046,37 +1048,54 @@ def main():
         parser.add_option('--positive-ion', default='Na+', dest='positiveIon', choices=('Cs+', 'K+', 'Li+', 'Na+', 'Rb+'), metavar='ION', help='positive ion to include in the water box: Cs+, K+, Li+, Na+, or Rb+ [default: Na+]')
         parser.add_option('--negative-ion', default='Cl-', dest='negativeIon', choices=('Cl-', 'Br-', 'F-', 'I-'), metavar='ION', help='negative ion to include in the water box: Cl-, Br-, F-, or I- [default: Cl-]')
         parser.add_option('--ionic-strength', type='float', default=0.0, dest='ionic', metavar='STRENGTH', help='molar concentration of ions to add to the water box [default: 0.0]')
+        parser.add_option('--verbose', default=False, action='store_true', dest='verbose', metavar='VERBOSE', help='Print verbose output')
         (options, args) = parser.parse_args()
-        if len(args) == 0:
+        if (len(args) == 0) and (options.pdbid==None) and (options.url==None):
             parser.error('No filename specified')
         if len(args) > 1:
-            parser.error('Must specify a single filename')
-        fixer = PDBFixer(filename=sys.argv[1])
+            parser.error('Must specify a single filename or --pdbid or --url')
+        if options.pdbid != None:
+            if options.verbose: print('Retrieving PDB "' + options.pdbid + '" from RCSB...')
+            fixer = PDBFixer(pdbid=options.pdbid)
+        elif options.url != None:
+            if options.verbose: print('Retrieving PDB from URL "' + options.url + '"...')
+            fixer = PDBFixer(url=options.url)
+        else:
+            fixer = PDBFixer(filename=sys.argv[1])
         if options.residues:
+            if options.verbose: print('Finding missing residues...')
             fixer.findMissingResidues()
         else:
             fixer.missingResidues = {}
         if options.nonstandard:
+            if options.verbose: print('Finding nonstandard residues...')
             fixer.findNonstandardResidues()
+            if options.verbose: print('Replacing nonstandard residues...')
             fixer.replaceNonstandardResidues()
+        if options.verbose: print('Finding missing atoms...')
         fixer.findMissingAtoms()
         if options.atoms not in ('all', 'heavy'):
             fixer.missingAtoms = {}
             fixer.missingTerminals = {}
+        if options.verbose: print('Adding missing atoms...')
         fixer.addMissingAtoms()
         if options.heterogens == 'none':
             fixer.removeHeterogens(False)
         elif options.heterogens == 'water':
             fixer.removeHeterogens(True)
         if options.atoms in ('all', 'hydrogen'):
+            if options.verbose: print('Adding missing hydrogens...')
             fixer.addMissingHydrogens(options.ph)
         if options.box is not None:
-            fixer.addSolvent(boxSize=options.box*unit.nanometer, positiveIon=options.positiveIon, 
+            if options.verbose: print('Adding solvent...')
+            fixer.addSolvent(boxSize=options.box*unit.nanometer, positiveIon=options.positiveIon,
                 negativeIon=options.negativeIon, ionicStrength=options.ionic*unit.molar)
         with open(options.output, 'w') as f:
+            if options.verbose: print('Writing output...')
             if fixer.source is not None:
                 f.write("REMARK   1 PDBFIXER FROM: %s\n" % fixer.source)
             app.PDBFile.writeFile(fixer.topology, fixer.positions, f, True)
+        if options.verbose: print('Done.')
 
 if __name__ == '__main__':
     main()

pdbfixer/tests/test_cli.py

+#!/usr/bin/python
+
+#=============================================================================================
+# MODULE DOCSTRING
+#=============================================================================================
+
+"""
+Test command-line interface.
+
+"""
+
+#=============================================================================================
+# GLOBAL IMPORTS
+#=============================================================================================
+
+import subprocess
+from subprocess import CalledProcessError
+
+from nose.plugins.skip import Skip, SkipTest
+
+#=============================================================================================
+# UNIT TESTS
+#=============================================================================================
+
+def run_cli(arguments, expected_output=None):
+    try:
+        output = subprocess.check_output('pdbfixer ' + arguments, shell=True)
+    except CalledProcessError as e:
+        message  = "An error return value (%s) was obtained:\n" % str(e.returncode)
+        message += "\n"
+        message += str(e.output)
+        message += "\n"
+        raise Exception(message)
+
+    if expected_output:
+        if output != expected_output:
+            message  = "Output differs from expected output.\n"
+            message += "\n"
+            message += "Expected output:\n"
+            message += expected_output
+            message += "\n"
+            message += "Actual output:\n"
+            message += output
+            message += "\n"
+            raise Exception(message)
+
+def test_help():
+    run_cli('--help')
+
+def test_pdbid():
+    run_cli('--pdbid 1LE1')
+
+def test_url():
+    run_cli('--url "http://www.rcsb.org/pdb/download/downloadFile.do?fileFormat=pdb&compression=NO&structureId=1LE1"')

pdbfixer/tests/test_removechains.py

@@ -2,6 +2,7 @@ from nose.tools import ok_, eq_, raises, assert_list_equal
 import simtk.openmm.app as app
 import pdbfixer
 import tempfile
+import time
 
 def remove_chain_ids_and_verify(pdbid, chain_ids_to_remove, expected_chain_ids_remaining):
     # Create a PDBFixer instance for the given pdbid
@@ -11,6 +12,8 @@ def remove_chain_ids_and_verify(pdbid, chain_ids_to_remove, expected_chain_ids_r
     # Check to make sure asserted chains remain.
     chain_ids_remaining = [c.id for c in fixer.topology.chains()]
     assert_list_equal(chain_ids_remaining, expected_chain_ids_remaining)
+    # Slow down to prevent rapid URL retrievals
+    time.sleep(2)
 
 def test_removechain_ids():
     remove_chain_ids_and_verify('4JSV', [], ['B', 'D', 'A', 'C', 'B', 'A'])
@@ -27,6 +30,8 @@ def remove_chain_indices_and_verify(pdbid, chain_indices_to_remove, expected_cha
     # Check to make sure asserted chains remain.
     chain_ids_remaining = [c.id for c in fixer.topology.chains()]
     assert_list_equal(chain_ids_remaining, expected_chain_ids_remaining)
+    # Slow down to prevent rapid URL retrievals
+    time.sleep(2)
 
 def test_removechain_indices():
     remove_chain_indices_and_verify('4JSV', [], ['B', 'D', 'A', 'C', 'B', 'A'])