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pdbfixer
Commit 24ca9600 by John Chodera (MSKCC)
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Added simulation test, and cleaned up tests a bit. 

We still only test one PDB file, however.
parent fc191ebd
Showing with 83 additions and 7 deletions
tests/test_build.py
from Bio.PDB import PDBList
from simtk import unit import pdbfixer
from pdbfixer.pdbfixer import * import simtk.openmm
import Bio.PDB
import os import os
import sys import sys
import numpy
def test_build(): def test_build():
# These are tough PDB codes from http://www.umass.edu/microbio/chime/pe_beta/pe/protexpl/badpdbs.htm # These are tough PDB codes from http://www.umass.edu/microbio/chime/pe_beta/pe/protexpl/badpdbs.htm
...@@ -10,6 +13,7 @@ def test_build(): ...@@ -10,6 +13,7 @@ def test_build():
pdbcodes = ['1VII'] # DEBUG: just use one pdbcodes = ['1VII'] # DEBUG: just use one
# Set up PDB retrieval. # Set up PDB retrieval.
from Bio.PDB import PDBList
pdblist = PDBList(server=PDBList.alternative_download_url) pdblist = PDBList(server=PDBList.alternative_download_url)
success = True success = True
...@@ -29,6 +33,7 @@ def test_build(): ...@@ -29,6 +33,7 @@ def test_build():
# PDB setup parameters. # PDB setup parameters.
# TODO: Try several combinations? # TODO: Try several combinations?
from simtk import unit
pH = 7.0 pH = 7.0
ionic = 50.0 * unit.millimolar ionic = 50.0 * unit.millimolar
box = 10.0 * unit.angstrom box = 10.0 * unit.angstrom
...@@ -39,6 +44,8 @@ def test_build(): ...@@ -39,6 +44,8 @@ def test_build():
outfile = open(output_pdb_filename, 'w') outfile = open(output_pdb_filename, 'w')
try: try:
from pdbfixer.pdbfixer import PDBFixer, PdbStructure
from simtk.openmm import app
fixer = PDBFixer(PdbStructure(infile)) fixer = PDBFixer(PdbStructure(infile))
fixer.findMissingResidues() fixer.findMissingResidues()
fixer.findNonstandardResidues() fixer.findNonstandardResidues()
...@@ -63,3 +70,5 @@ def test_build(): ...@@ -63,3 +70,5 @@ def test_build():
if not success: if not success:
raise Exception("build test failed on one or more PDB files.") raise Exception("build test failed on one or more PDB files.")
if __name__ == '__main__':
test_build()
tests/test_simulate.py
from Bio.PDB import PDBList
from simtk import unit import pdbfixer
from pdbfixer.pdbfixer import * import simtk.openmm
import Bio.PDB
import os import os
import sys import sys
import numpy
def simulate(pdbcode, pdb_filename):
from simtk.openmm import app
import simtk.openmm as mm
from simtk import unit
from sys import stdout
# Load the PDB file.
pdb = app.PDBFile(pdb_filename)
# Set up implicit solvent forcefield.
forcefield = app.ForceField('amber99sbildn.xml', 'amber99_obc.xml')
# Create the system.
system = forcefield.createSystem(pdb.topology, nonbondedMethod=app.NoCutoff, constraints=app.HBonds)
# Create an integrator.
integrator = mm.LangevinIntegrator(300*unit.kelvin, 91.0/unit.picoseconds, 1.0*unit.femtoseconds)
# Create a context.
context = mm.Context(system, integrator)
context.setPositions(pdb.positions)
# Check to make sure energy is finite.
state = context.getState(getEnergy=True)
potential = state.getPotentialEnergy() / unit.kilocalories_per_mole
if numpy.isnan(potential):
raise Exception("Initial energy for %s is NaN." % pdbcode)
# Minimize.
tolerance = 1.0 * unit.kilocalories_per_mole / unit.angstroms
maxIterations = 50
mm.LocalEnergyMinimizer.minimize(context, tolerance, maxIterations)
def test_build(): # Check to make sure energy is finite.
state = context.getState(getEnergy=True)
potential = state.getPotentialEnergy() / unit.kilocalories_per_mole
if numpy.isnan(potential):
raise Exception("Energy for %s is NaN after minimization." % pdbcode)
# Simulate.
nsteps = 500
integrator.step(nsteps)
# Check to make sure energy is finite.
state = context.getState(getEnergy=True)
potential = state.getPotentialEnergy() / unit.kilocalories_per_mole
if numpy.isnan(potential):
raise Exception("Energy for %s is NaN after simulation." % pdbcode)
del context, integrator
print "Simulation completed: potential = %.3f kcal/mol" % potential
return
def test_simulate():
# These are tough PDB codes from http://www.umass.edu/microbio/chime/pe_beta/pe/protexpl/badpdbs.htm # These are tough PDB codes from http://www.umass.edu/microbio/chime/pe_beta/pe/protexpl/badpdbs.htm
pdbcodes = ['1AS5', '1CBN', '1DPO', '1IGY', '1HAG', '1IAO', '4CPA', '1QCQ'] pdbcodes = ['1AS5', '1CBN', '1DPO', '1IGY', '1HAG', '1IAO', '4CPA', '1QCQ']
pdbcodes = ['1VII'] # DEBUG: just use one pdbcodes = ['1VII'] # DEBUG: just use one
# Set up PDB retrieval. # Set up PDB retrieval.
from Bio.PDB import PDBList
pdblist = PDBList(server=PDBList.alternative_download_url) pdblist = PDBList(server=PDBList.alternative_download_url)
success = True success = True
...@@ -29,6 +88,7 @@ def test_build(): ...@@ -29,6 +88,7 @@ def test_build():
# PDB setup parameters. # PDB setup parameters.
# TODO: Try several combinations? # TODO: Try several combinations?
from simtk import unit
pH = 7.0 pH = 7.0
ionic = 50.0 * unit.millimolar ionic = 50.0 * unit.millimolar
box = 10.0 * unit.angstrom box = 10.0 * unit.angstrom
...@@ -39,6 +99,8 @@ def test_build(): ...@@ -39,6 +99,8 @@ def test_build():
outfile = open(output_pdb_filename, 'w') outfile = open(output_pdb_filename, 'w')
try: try:
from pdbfixer.pdbfixer import PDBFixer, PdbStructure
from simtk.openmm import app
fixer = PDBFixer(PdbStructure(infile)) fixer = PDBFixer(PdbStructure(infile))
fixer.findMissingResidues() fixer.findMissingResidues()
fixer.findNonstandardResidues() fixer.findNonstandardResidues()
...@@ -52,6 +114,9 @@ def test_build(): ...@@ -52,6 +114,9 @@ def test_build():
infile.close() infile.close()
outfile.close() outfile.close()
# Test simulating this with OpenMM.
simulate(pdbcode, output_pdb_filename)
# Delete input file. # Delete input file.
os.remove(input_pdb_filename) os.remove(input_pdb_filename)
os.remove(output_pdb_filename) os.remove(output_pdb_filename)
...@@ -63,3 +128,5 @@ def test_build(): ...@@ -63,3 +128,5 @@ def test_build():
if not success: if not success:
raise Exception("build test failed on one or more PDB files.") raise Exception("build test failed on one or more PDB files.")
if __name__ == '__main__':
test_simulate()
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