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pdbfixer
Commit 264f95c1 by peastman
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Merge pull request #26 from jchodera/master 

Add support for specifying PDB codes, filenames, and file objects [ready to merge]
parents 6e4432c2 10eb76db
Showing with 54 additions and 41 deletions
.travis.yml
...@@ -11,7 +11,7 @@ install: ...@@ -11,7 +11,7 @@ install:
script: script:
- python setup.py install - python setup.py install
- cd tests - cd tests
- nosetests - nosetests --with-doctest
after_script: after_script:
- pyflakes pdbfixer/*.py - pyflakes pdbfixer/*.py
......
setup.py
...@@ -111,6 +111,7 @@ setup( ...@@ -111,6 +111,7 @@ setup(
packages=find_packages(), packages=find_packages(),
package_data={'pdbfixer': find_package_data()}, package_data={'pdbfixer': find_package_data()},
zip_safe=False, zip_safe=False,
install_requires=[],
entry_points={'console_scripts': ['pdbfixer = pdbfixer.pdbfixer:main']}) entry_points={'console_scripts': ['pdbfixer = pdbfixer.pdbfixer:main']})
check_dependencies() check_dependencies()
tests/test_build_and_simulate.py
import pdbfixer import pdbfixer
import simtk.openmm import simtk.openmm
import Bio.PDB
import os import os
import os.path import os.path
import sys import sys
import numpy import numpy
import tempfile
from threading import Timer from threading import Timer
...@@ -37,7 +37,8 @@ def simulate(pdbcode, pdb_filename): ...@@ -37,7 +37,8 @@ def simulate(pdbcode, pdb_filename):
pdb = app.PDBFile(pdb_filename) pdb = app.PDBFile(pdb_filename)
# Set up implicit solvent forcefield. # Set up implicit solvent forcefield.
forcefield = app.ForceField('amber99sbildn.xml') #forcefield = app.ForceField('amber99sbildn.xml')
forcefield = app.ForceField('amber10.xml')
# Create the system. # Create the system.
system = forcefield.createSystem(pdb.topology, nonbondedMethod=app.NoCutoff, constraints=app.HBonds) system = forcefield.createSystem(pdb.topology, nonbondedMethod=app.NoCutoff, constraints=app.HBonds)
...@@ -83,32 +84,24 @@ def simulate(pdbcode, pdb_filename): ...@@ -83,32 +84,24 @@ def simulate(pdbcode, pdb_filename):
return return
def test_build_and_simulate(): def test_build_and_simulate():
# These are tough PDB codes from http://www.umass.edu/microbio/chime/pe_beta/pe/protexpl/badpdbs.htm # DEBUG: These are tough PDB codes from http://www.umass.edu/microbio/chime/pe_beta/pe/protexpl/badpdbs.htm
pdbcodes_to_build = ['1AS5', '1CBN', '1DPO', '1IGY', '1HAG', '1IAO', '4CPA', '1QCQ'] pdbcodes_to_build = ['1AS5', '1CBN', '1DPO', '1IGY', '1HAG', '1IAO', '4CPA', '1QCQ']
pdbcodes_to_simulate = ['1AS5', '1CBN', '1DPO', '1IGY', '1HAG', '1IAO', '4CPA', '1QCQ']
# Set up PDB retrieval. # DEBUG: Small test cases.
from Bio.PDB import PDBList pdbcodes_to_build = ['110D', '116D', '117D', '118D', '134D', '135D', '136D', '138D', '143D', '148D', '151D', '152D', '159D', '177D', '17RA', '183D', '184D', '186D', '187D', '188D', '189D', '1A11', '1A13', '1A1P', '1A3P', '1A51', '1A60', '1A83', '1A9L', '1AAF', '1AB1', '1ABZ', '1AC7', '1ACW', '1AD7', '1ADX', '1AFP', '1AFT', '1AFX', '1AG7', '1AGG', '1AGL', '1AGT', '1AHL', '1AIE', '1AJ1', '1AJF', '1AJJ', '1AJU', '1AKG', '1AKX', '1AL1', '1ALE', '1ALF', '1ALG', '1AM0', '1AMB', '1AMC', '1AML', '1ANP', '1ANR', '1ANS', '1AO9', '1AOO', '1APF', '1APO', '1APQ', '1AQG', '1AQO', '1AQQ', '1AQR', '1AQS', '1ARD', '1ARE', '1ARF', '1ARJ', '1ARK', '1AS5', '1AT4', '1ATO', '1ATV', '1ATW', '1ATX', '1AV3', '1AW4', '1AW6', '1AWY', '1AXH', '1AY3', '1AYJ', '1AZ6', '1AZH', '1AZJ', '1AZK', '1B03', '1B0Q', '1B13', '1B1V', '1B2J', '1B36', '1B45', '1B4G', '1B4I', '1B4Y', '1B5N', '1B8W', '1B9G', '1B9P', '1B9Q', '1B9U', '1BA4', '1BA5', '1BA6', '1BAH', '1BAL', '1BBA', '1BBG', '1BBL', '1BBO', '1BCV', '1BD1', '1BDC', '1BDD', '1BDE', '1BDK', '1BDS', '1BE7', '1BEI', '1BF0', '1BF9', '1BFW', '1BFY', '1BFZ', '1BGK', '1BGZ', '1BH0', '1BH1', '1BH4', '1BH7', '1BHI', '1BHP', '1BIG', '1BJB', '1BJC', '1BJH', '1BK2', '1BK8', '1BKT', '1BKU', '1BL1', '1BM4', '1BMX', '1BN0', '1BNB', '1BNX', '1BOE', '1BOR', '1BPI', '1BPT', '1BQ8', '1BQ9', '1BQF', '1BRF', '1BRV', '1BRZ', '1BTI', '1BTQ', '1BTR', '1BTS', '1BTT', '1BUB', '1BUS', '1BVJ', '1BW6', '1BWX', '1BX7', '1BX8', '1BY0', '1BY6', '1BYJ', '1BYV', '1BYY', '1BZ2', '1BZ3', '1BZB', '1BZG', '1BZK', '1BZT', '1BZU', '1C0O', '1C26', '1C2U', '1C32', '1C34', '1C35', '1C38', '1C49', '1C4B', '1C4E', '1C4S', '1C55', '1C56', '1C6W', '1C98', '1C9A', '1C9Z', '1CAA', '1CAD', '1CAP', '1CB3', '1CB9', '1CBH', '1CBN', '1CCF', '1CCM', '1CCN', '1CCQ', '1CCV', '1CE3', '1CE4', '1CEK', '1CEU', '1CFG', '1CFH', '1CFI', '1CHL', '1CHV', '1CIX', '1CKW', '1CKX', '1CKY', '1CKZ', '1CL4', '1CLF', '1CMR', '1CNL', '1CNN', '1CNR', '1CO4', '1COI', '1CQ0', '1CQ5', '1CQL', '1CQU', '1CR8', '1CRE', '1CRF', '1CRN', '1CS9', '1CSA', '1CT6', '1CTI', '1CV9', '1CVQ', '1CW5', '1CW6', '1CW8', '1CWX', '1CWZ', '1CXN', '1CXO', '1CXR', '1CXW', '1CYA', '1CYB', '1CZ6', '1D0R', '1D0T', '1D0U', '1D0W', '1D10', '1D11', '1D12', '1D13', '1D14', '1D15', '1D16', '1D17', '1D1E', '1D1F', '1D1H', '1D26', '1D2D', '1D2J', '1D2L', '1D33', '1D35', '1D36', '1D37', '1D38', '1D54', '1D58', '1D5Q', '1D61', '1D62', '1D67', '1D6B', '1D6X', '1D78', '1D79', '1D7N', '1D7T', '1D7Z', '1D82', '1D8G', '1D93', '1D9J', '1D9L', '1D9M', '1D9O', '1D9P', '1DA0', '1DA9', '1DB6', '1DEC', '1DEM', '1DEN', '1DEP', '1DF6', '1DFE', '1DFS', '1DFT', '1DFW', '1DFY', '1DFZ']
pdblist = PDBList(server=PDBList.alternative_download_url)
success = True # DEBUG: A few small test cases.
pdbcodes_to_build = ['110D', '116D', '117D', '118D', '134D', '135D', '136D', '138D', '143D', '148D', '151D', '152D', '159D', '177D', '17RA', '183D', '184D', '186D', '187D', '188D', '189D', '1A11', '1A13', '1A1P', '1A3P', '1A51', '1A60', '1A83', '1A9L', '1AAF', '1AB1', '1ABZ', '1AC7', '1ACW', '1AD7', '1ADX', '1AFP', '1AFT', '1AFX', '1AG7', '1AGG', '1AGL', '1AGT', '1AHL', '1AIE', '1AJ1', '1AJF', '1AJJ', '1AJU', '1AKG', '1AKX', '1AL1', '1ALE', '1ALF', '1ALG', '1AM0', '1AMB', '1AMC', '1AML', '1ANP', '1ANR', '1ANS', '1AO9', '1AOO']
for pdbcode in pdbcodes_to_build: # Don't simulate any.
print pdbcode pdbcodes_to_simulate = []
try:
# Remove file if it exists already.
input_pdb_filename = 'pdb' + pdbcode + '.ent'
if os.path.exists(input_pdb_filename):
os.remove(input_pdb_filename)
print "Attempting to retrieve PDB code '%s' from %s..." % (pdbcode, PDBList.alternative_download_url) # Keep track of list of failures.
input_pdb_filename = pdblist.retrieve_pdb_file(pdbcode, pdir='.') failures = list()
except Exception as e: for pdbcode in pdbcodes_to_build:
print str(e) print "------------------------------------------------"
print "Could not download PDB code '%s'" % pdbcode print pdbcode
continue
output_pdb_filename = 'output.pdb' output_pdb_filename = 'output.pdb'
...@@ -121,18 +114,17 @@ def test_build_and_simulate(): ...@@ -121,18 +114,17 @@ def test_build_and_simulate():
positiveIon = 'Na+' positiveIon = 'Na+'
negativeIon = 'Cl-' negativeIon = 'Cl-'
infile = open(input_pdb_filename) outfile = tempfile.NamedTemporaryFile(mode='w', delete=False)
outfile = open(output_pdb_filename, 'w') output_pdb_filename = outfile.name
success = True
timeout_seconds = 0.1 timeout_seconds = 30
watchdog = Watchdog(timeout_seconds) watchdog = Watchdog(timeout_seconds)
build_successful = False
try: try:
from pdbfixer.pdbfixer import PDBFixer, PdbStructure from pdbfixer.pdbfixer import PDBFixer
from simtk.openmm import app from simtk.openmm import app
stage = "Creating PDBFixer..." stage = "Creating PDBFixer..."
fixer = PDBFixer(PdbStructure(infile)) fixer = PDBFixer(pdbid=pdbcode)
stage = "Finding missing residues..." stage = "Finding missing residues..."
fixer.findMissingResidues() fixer.findMissingResidues()
stage = "Finding nonstandard residues..." stage = "Finding nonstandard residues..."
...@@ -150,43 +142,63 @@ def test_build_and_simulate(): ...@@ -150,43 +142,63 @@ def test_build_and_simulate():
stage = "Writing PDB file..." stage = "Writing PDB file..."
app.PDBFile.writeFile(fixer.topology, fixer.positions, outfile) app.PDBFile.writeFile(fixer.topology, fixer.positions, outfile)
stage = "Done." stage = "Done."
infile.close()
outfile.close() outfile.close()
build_successful = True
except Watchdog: except Watchdog:
print "timed out fixing PDB %s" % pdbcode message = "timed out in stage %s" % stage
success = False print message
failures.append((pdbcode, Exception(message)))
except Exception as e: except Exception as e:
print "EXCEPTION DURING BUILD"
#import traceback
#print traceback.print_exc()
print str(e) print str(e)
success = False failures.append((pdbcode, e))
watchdog.stop() watchdog.stop()
del watchdog del watchdog
# Test simulating this with OpenMM. # Test simulating this with OpenMM.
if pdbcode in pdbcodes_to_simulate: if (pdbcode in pdbcodes_to_simulate) and (build_successful):
watchdog = Watchdog(timeout_seconds) watchdog = Watchdog(timeout_seconds)
try: try:
simulate(pdbcode, output_pdb_filename) simulate(pdbcode, output_pdb_filename)
except Watchdog: except Watchdog:
print "PDB code %s timed out in stage '%s'." % (pdbcode, stage) message = "timed out in simulation"
success = False print message
failures.append((pdbcode, Exception(message)))
except Exception as e: except Exception as e:
print "EXCEPTION DURING SIMULATE"
#import traceback
#print traceback.print_exc()
print str(e) print str(e)
success = False failures.append((pdbcode, e))
watchdog.stop() watchdog.stop()
del watchdog del watchdog
# Clean up. # Clean up.
os.remove(input_pdb_filename)
os.remove(output_pdb_filename) os.remove(output_pdb_filename)
if not success: print "------------------------------------------------"
raise Exception("build test failed on one or more PDB files.")
if len(failures) != 0:
print ""
print "SUMMARY OF FAILURES:"
print ""
for failure in failures:
(pdbcode, exception) = failure
print "%6s : %s" % (pdbcode, str(exception))
print ""
raise Exception("Build test failed on one or more PDB files.")
else:
print "All tests succeeded."
if __name__ == '__main__': if __name__ == '__main__':
test_build_and_simulate() test_build_and_simulate()
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