def to_pdbfixer_PDBFixer(item,
atom_indices='all',
structure_indices='all',
check=True):
if check:
digest_item(item, 'molsysmt.MolSys')
atom_indices = digest_atom_indices(atom_indices)
structure_indices = digest_structure_indices(structure_indices)
try:
from pdbfixer.pdbfixer import PDBFixer
except:
raise LibraryNotFound('pdbfixer')
from . import to_string_pdb_text
from io import StringIO
tmp_item = to_string_pdb_text(item,
atom_indices=atom_indices,
structure_indices=structure_indices,
check=False)
tmp_item = StringIO(tmp_item)
tmp_item = PDBFixer(pdbfile=tmp_item)
return tmp_item
def configureFiles():
fileType = session['fileType']
if fileType == 'pdb':
if 'file' not in request.files or request.files['file'].filename == '':
# They didn't select a file. Send them back.
return showConfigureFiles()
saveUploadedFiles()
session['forcefield'] = request.form.get('forcefield', '')
session['waterModel'] = request.form.get('waterModel', '')
session['cleanup'] = request.form.get('cleanup', '')
file, name = uploadedFiles['file'][0]
file.seek(0, 0)
session['pdbType'] = _guessFileFormat(file, name)
if session['cleanup'] == 'yes':
global fixer
if session['pdbType'] == 'pdb':
fixer = PDBFixer(pdbfile=file)
else:
fixer = PDBFixer(pdbxfile=StringIO(file.read().decode()))
return showSelectChains()
elif fileType == 'amber':
if 'prmtopFile' not in request.files or request.files[
'prmtopFile'].filename == '' or 'inpcrdFile' not in request.files or request.files[
'inpcrdFile'].filename == '':
# They didn't select a file. Send them back.
return showConfigureFiles()
saveUploadedFiles()
elif fileType == 'charmm':
if 'psfFile' not in request.files or request.files[
'psfFile'].filename == '' or 'crdFile' not in request.files or request.files[
'crdFile'].filename == '':
# They didn't select a file. Send them back.
return showConfigureFiles()
saveUploadedFiles()
elif fileType == 'gromacs':
if 'topFile' not in request.files or request.files[
'topFile'].filename == '' or 'groFile' not in request.files or request.files[
'groFile'].filename == '':
# They didn't select a file. Send them back.
return showConfigureFiles()
saveUploadedFiles()
session['gromacsIncludeDir'] = request.form.get(
'gromacsIncludeDir', '')
configureDefaultOptions()
return showSimulationOptions()
def to_pdbfixer_PDBFixer(item, atom_indices='all', structure_indices='all', check=True):
if check:
digest_item(item, 'string:pdb_text')
atom_indices = digest_atom_indices(atom_indices)
structure_indices = digest_structure_indices(structure_indices)
from io import StringIO
from pdbfixer.pdbfixer import PDBFixer
from . import extract
tmp_item = extract(item, atom_indices=atom_indices, structure_indices=structure_indices, check=False)
tmp_io = StringIO()
tmp_io.write(tmp_item)
tmp_io.close()
tmp_item = PDBFixer(pdbfile=tmp_item)
return tmp_item
def to_pdbfixer_PDBFixer(item,
atom_indices='all',
structure_indices='all',
check=True):
if check:
digest_item(item, 'file:pdb')
atom_indices = digest_atom_indices(atom_indices)
structure_indices = digest_structure_indices(structure_indices)
from pdbfixer.pdbfixer import PDBFixer
from ..pdbfixer_PDBFixer import extract as extract_pdbfixer_PDBFixer
tmp_item = PDBFixer(item)
tmp_item = extract_pdbfixer_PDBFixer(tmp_item,
atom_indices=atom_indices,
structure_indices=structure_indices,
copy_if_all=False,
check=False)
return tmp_item
def test_build_and_simulate():
# 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']
# DEBUG: 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', '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']
# impossible cases
pdbcodes_to_build = [
'1AO9', # contains residue DOP, which is not resolved in the ATOM records and does not appear to have a machine-readable definition anywhere
]
# 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', '1AOO']
# Don't simulate any.
pdbcodes_to_simulate = []
# Keep track of list of failures.
failures = list()
for pdbcode in pdbcodes_to_build:
print("------------------------------------------------")
print(pdbcode)
output_pdb_filename = 'output.pdb'
# PDB setup parameters.
# TODO: Try several combinations?
from simtk import unit
pH = 7.0
ionic = 50.0 * unit.millimolar
box = 10.0 * unit.angstrom
positiveIon = 'Na+'
negativeIon = 'Cl-'
outfile = tempfile.NamedTemporaryFile(mode='w', delete=False)
output_pdb_filename = outfile.name
timeout_seconds = 30
watchdog = Watchdog(timeout_seconds)
build_successful = False
try:
from pdbfixer.pdbfixer import PDBFixer
from simtk.openmm import app
stage = "Creating PDBFixer..."
fixer = PDBFixer(pdbid=pdbcode)
stage = "Finding missing residues..."
fixer.findMissingResidues()
stage = "Finding nonstandard residues..."
fixer.findNonstandardResidues()
stage = "Replacing nonstandard residues..."
fixer.replaceNonstandardResidues()
stage = "Finding missing atoms..."
fixer.findMissingAtoms()
stage = "Adding missing atoms..."
fixer.addMissingAtoms()
stage = "Removing heterogens..."
fixer.removeHeterogens(False)
stage = "Adding missing hydrogens..."
fixer.addMissingHydrogens(pH)
stage = "Writing PDB file..."
app.PDBFile.writeFile(fixer.topology, fixer.positions, outfile)
stage = "Done."
outfile.close()
build_successful = True
except Watchdog:
message = "timed out in stage %s" % stage
print(message)
failures.append((pdbcode, Exception(message)))
except Exception as e:
print("EXCEPTION DURING BUILD")
#import traceback
#print traceback.print_exc()
print(str(e))
failures.append((pdbcode, e))
watchdog.stop()
del watchdog
# Test simulating this with OpenMM.
if (pdbcode in pdbcodes_to_simulate) and (build_successful):
watchdog = Watchdog(timeout_seconds)
try:
simulate(pdbcode, output_pdb_filename)
except Watchdog:
message = "timed out in simulation"
print(message)
failures.append((pdbcode, Exception(message)))
except Exception as e:
print("EXCEPTION DURING SIMULATE")
#import traceback
#print traceback.print_exc()
print(str(e))
failures.append((pdbcode, e))
watchdog.stop()
del watchdog
# Clean up.
os.remove(output_pdb_filename)
print("------------------------------------------------")
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.")
pdbfix_mutation = '{:s}-{:s}-{:s}'.format(orig, resno, final)
pdbfix_mutations.append(pdbfix_mutation)
return pdbfix_mutations
input_pdbfile = 'cAbl.pdb'
chain = "A"
sequences = [
['q252h'],
['y253f'],
['e255k'],
['f317i'],
['f317l'],
['m351t'],
]
for mutations in sequences:
mutation_list = convert_mutation_list(mutations)
fixer = PDBFixer(filename=input_pdbfile)
fixer.applyMutations(mutation_list, chain)
prefix = os.path.splitext(input_pdbfile)[0]
out_filename = "{:s}_{:s}.pdb".format(prefix, '-'.join(mutations))
outfile = open(out_filename, 'w')
app.PDBFile.writeFile(fixer.topology, fixer.positions, outfile)
outfile.close()
def test_build_and_simulate():
# 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'
]
# DEBUG: 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', '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'
]
# impossible cases
pdbcodes_to_build = [
'1AO9', # contains residue DOP, which is not resolved in the ATOM records and does not appear to have a machine-readable definition anywhere
]
# 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', '1AOO'
]
# Don't simulate any.
pdbcodes_to_simulate = []
# Keep track of list of failures.
failures = list()
for pdbcode in pdbcodes_to_build:
print("------------------------------------------------")
print(pdbcode)
output_pdb_filename = 'output.pdb'
# PDB setup parameters.
# TODO: Try several combinations?
from simtk import unit
pH = 7.0
ionic = 50.0 * unit.millimolar
box = 10.0 * unit.angstrom
positiveIon = 'Na+'
negativeIon = 'Cl-'
outfile = tempfile.NamedTemporaryFile(mode='w', delete=False)
output_pdb_filename = outfile.name
timeout_seconds = 30
watchdog = Watchdog(timeout_seconds)
build_successful = False
try:
from pdbfixer.pdbfixer import PDBFixer
from simtk.openmm import app
stage = "Creating PDBFixer..."
fixer = PDBFixer(pdbid=pdbcode)
stage = "Finding missing residues..."
fixer.findMissingResidues()
stage = "Finding nonstandard residues..."
fixer.findNonstandardResidues()
stage = "Replacing nonstandard residues..."
fixer.replaceNonstandardResidues()
stage = "Removing heterogens..."
fixer.removeHeterogens(False)
stage = "Finding missing atoms..."
fixer.findMissingAtoms()
stage = "Adding missing atoms..."
fixer.addMissingAtoms()
stage = "Adding missing hydrogens..."
fixer.addMissingHydrogens(pH)
stage = "Writing PDB file..."
app.PDBFile.writeFile(fixer.topology, fixer.positions, outfile)
stage = "Done."
outfile.close()
build_successful = True
except Watchdog:
message = "timed out in stage %s" % stage
print(message)
failures.append((pdbcode, Exception(message)))
except Exception as e:
print("EXCEPTION DURING BUILD")
#import traceback
#print traceback.print_exc()
print(str(e))
failures.append((pdbcode, e))
watchdog.stop()
del watchdog
# Test simulating this with OpenMM.
if (pdbcode in pdbcodes_to_simulate) and (build_successful):
watchdog = Watchdog(timeout_seconds)
try:
simulate(pdbcode, output_pdb_filename)
except Watchdog:
message = "timed out in simulation"
print(message)
failures.append((pdbcode, Exception(message)))
except Exception as e:
print("EXCEPTION DURING SIMULATE")
#import traceback
#print traceback.print_exc()
print(str(e))
failures.append((pdbcode, e))
watchdog.stop()
del watchdog
# Clean up.
os.remove(output_pdb_filename)
print("------------------------------------------------")
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.")
def run(options):
fixer = PDBFixer(options['pdb'])
fixer.addMissingHydrogens(7.0)
fixer.addSolvent(boxSize=Vec3(2.62,2.62,2.62)*nanometers, padding=None,
positiveIon='Na+', negativeIon='Cl-', ionicStrength=0.0*molar)
PDBFile.writeFile(fixer.topology, fixer.positions, open(options['outfile'], 'w'))
def fix_complexes(self, complex_list):
fixed_complexes = []
for complex in complex_list:
for residue in complex.residues:
atoms = residue._atoms
for i in range(len(atoms) - 1, -1, -1):
if atoms[i].molecular.is_het == True:
del atoms[i]
complex.io.to_pdb("tmp.pdb", pdb_options)
fixer = PDBFixer(filename="tmp.pdb")
fixer.findMissingResidues()
fixer.findNonstandardResidues()
fixer.replaceNonstandardResidues()
fixer.findMissingAtoms()
fixer.addMissingAtoms()
fixer.removeHeterogens(False)
fixer.addMissingHydrogens(7.0)
(topology, positions) = self.delete_alternate_atoms(fixer.topology, fixer.positions)
with open('tmp.pdb', 'w') as pdb_file:
PDBFile.writeFile(topology, positions, pdb_file)
fixed_complex = nanome.structure.Complex.io.from_pdb(path="tmp.pdb")
fixed_complex.index = complex.index
fixed_complex.position = complex.position
fixed_complex.rotation = complex.rotation
fixed_complex.molecular.name = complex.molecular.name
fixed_complex.rendering.visible = True
fixed_complexes.append(fixed_complex)
return fixed_complexes