def pdb_fix_pdbfixer(pdbid, file_pathway, ph, chains_to_remove):
"""
Args:
pdbid: 4 letter string specifying the PDB ID of the file yoou want to fix
file_pathway: a string containing the pathway specifying how you want to organize the PDB files once written
ph: the pH at which hydrogens will be determined and added
chains_to_remove: dictionary containing pdbs with chains to remove
Returns: nothing, but it does right PDB files
"""
print(pdbid)
# Download the topology from rcsb based on pdbod
fixer = PDBFixer(pdbid=pdbid)
# Remove chains based on hand curated .csv file
if pdbid in chains_to_remove['pdbid']:
chains = chains_to_remove['chain_to_remove'][chain_to_remove['pdbid'].index(pdbid)]
chains_list = chains.split()
fixer.removeChains(chainIds=chains_list)
# Determine the first and last residue resolved in chain 0
chains = [chain for chain in fixer.topology.chains()]
resindices = [residue.index for residue in chains[0].residues()]
resindices = natsorted(resindices)
first_resindex = resindices[0]
last_resindex = resindices[-1]
# Find Missing residues and determine if they are C or N terminal fragments (which will be removed)
fixer.findMissingResidues()
if len(fixer.missingResidues) > 0:
if sorted(fixer.missingResidues.keys())[0][-1] <= first_resindex:
fixer.missingResidues.pop((sorted(fixer.missingResidues.keys())[0]))
if sorted(fixer.missingResidues.keys())[-1][-1] >= last_resindex:
fixer.missingResidues.pop((sorted(fixer.missingResidues.keys())[-1]))
fixer.findNonstandardResidues()
fixer.replaceNonstandardResidues()
fixer.findMissingAtoms()
fixer.addMissingAtoms()
fixer.addMissingHydrogens(ph)
# Write fixed PDB file, with all of the waters and ligands
PDBFile.writeFile(fixer.topology, fixer.positions, open(os.path.join(file_pathway,
'%s_fixed_ph%s.pdb' % (pdbid, ph)), 'w'),
keepIds=keepNumbers)
# Remove the ligand and write a pdb file
fixer.removeHeterogens(True)
PDBFile.writeFile(fixer.topology, fixer.positions, open(os.path.join(file_pathway,
'%s_fixed_ph%s_apo.pdb' % (pdbid, ph)), 'w'),
keepIds=keepNumbers)
# Remove the waters and write a pdb file
fixer.removeHeterogens(False)
PDBFile.writeFile(fixer.topology, fixer.positions, open(os.path.join(file_pathway,
'%s_fixed_ph%s_apo_nowater.pdb' % (pdbid, ph)),
'w'), keepIds=keepNumbers)
def fix_pdb(pdb_id, pdb_file, pdb_group):
chains_to_retain = get_required_chains(pdb_group)
chains_to_remove = []
for chain in PDBParser().get_structure(pdb_id, pdb_file)[0]:
if chain.get_id() not in chains_to_retain:
chains_to_remove.append(chain.get_id())
fixer = PDBFixer(filename=pdb_file)
fixer.removeChains(chainIds=chains_to_remove)
fixer.findMissingResidues()
fixer.findMissingAtoms()
fixer.addMissingAtoms()
fixer.removeHeterogens(True)
# KeepIds flag is critical here, otherwise we loose all information binding
pdb_file = dirname(pdb_file) + '/' + pdb_id + '.pdb'
PDBFile.writeFile(fixer.topology,
fixer.positions,
open(pdb_file, 'w'),
keepIds=True)
return pdb_file
def cleanPdb(pdb_list, chain=None, fromFolder=None, toFolder="cleaned_pdbs"):
os.system(f"mkdir -p {toFolder}")
for pdb_id in pdb_list:
# print(chain)
pdb = f"{pdb_id.lower()[:4]}"
pdbFile = pdb + ".pdb"
if fromFolder is None:
fromFile = os.path.join("original_pdbs", pdbFile)
elif fromFolder[:4] == ".pdb":
fromFile = fromFolder
else:
fromFile = os.path.join(fromFolder, pdbFile)
if chain is None: # None mean deafult is chain A unless specified.
if len(pdb_id) == 5:
Chosen_chain = pdb_id[4].upper()
else:
assert (len(pdb_id) == 4)
Chosen_chain = "A"
elif chain == "-1" or chain == -1:
Chosen_chain = getAllChains(fromFile)
else:
Chosen_chain = chain
# clean pdb
fixer = PDBFixer(filename=fromFile)
# remove unwanted chains
chains = list(fixer.topology.chains())
chains_to_remove = [
i for i, x in enumerate(chains) if x.id not in Chosen_chain
]
fixer.removeChains(chains_to_remove)
fixer.findMissingResidues()
# add missing residues in the middle of a chain, not ones at the start or end of the chain.
chains = list(fixer.topology.chains())
keys = fixer.missingResidues.keys()
# print(keys)
for key in list(keys):
chain_tmp = chains[key[0]]
if key[1] == 0 or key[1] == len(list(chain_tmp.residues())):
del fixer.missingResidues[key]
fixer.findNonstandardResidues()
fixer.replaceNonstandardResidues()
fixer.removeHeterogens(keepWater=False)
fixer.findMissingAtoms()
fixer.addMissingAtoms()
fixer.addMissingHydrogens(7.0)
PDBFile.writeFile(fixer.topology, fixer.positions,
open(os.path.join(toFolder, pdbFile), 'w'))
def fix_peptide(pdb_file, seq_dict, pH=7.4, remove_water=True, remove_small_mols=True):
global ONE_THREE_CODE
fixer = PDBFixer(filename=pdb_file)
fixer.sequences.clear()
for chain in fixer.topology.chains():
seq = pdbfixer.pdbfixer.Sequence(chain.id, [r.name for r in list(chain.residues())])
fixer.sequences.append(seq)
if remove_small_mols:
fixer.removeHeterogens(not remove_water)
delete_chains = []
# Convert single AA codes to three letter code
for key, value in seq_dict.items():
if not value or value is None:
delete_chains.append(key)
else:
three_letter = []
for item in value:
three_letter.append(ONE_THREE_CODE[item])
seq_dict[key] = three_letter
for chain in fixer.topology.chains():
if chain.index in seq_dict:
if seq_dict[chain.index] is not None:
fixer.sequences[chain.index].residues = seq_dict[chain.index]
fixer.findMissingResidues()
fixer.findNonstandardResidues()
fixer.replaceNonstandardResidues()
fixer.findMissingAtoms()
fixer.addMissingAtoms()
fixer.addMissingHydrogens(pH)
fixer.removeChains(delete_chains)
dummy = tempfile.NamedTemporaryFile(suffix=".pdb")
app.PDBFile.writeFile(fixer.topology, fixer.positions, open(dummy.name, 'w'))
product = mdtraj.load(dummy.name)
problem_cis = ChiralityCheck.check_cispeptide_bond(product)
problem_chiral = ChiralityCheck.check_chirality(product)
print("The following problems have been detected:")
print(problem_cis)
print(problem_chiral)
print("Either rerun or find a tool to solve. Perhaps VMD?")
return product
def fix_pdb(pdb_id, pdb_file, pdb_group):
chains_to_retain = get_required_chains(pdb_group)
chains_to_remove = []
for chain in PDBParser().get_structure(pdb_id, pdb_file)[0]:
if chain.get_id() not in chains_to_retain:
chains_to_remove.append(chain.get_id())
fixer = PDBFixer(filename=pdb_file)
fixer.removeChains(chainIds=chains_to_remove)
fixer.findMissingResidues()
fixer.findMissingAtoms()
fixer.addMissingAtoms()
fixer.removeHeterogens(True)
# KeepIds flag is critical here, otherwise we loose all information binding
pdb_file = dirname(pdb_file) + '/' + pdb_id + '.pdb'
PDBFile.writeFile(fixer.topology, fixer.positions, open(pdb_file, 'w'), keepIds=True)
return pdb_file
c.id = "Z"
chains_to_remove.append(i)
elif num_residues <= 15:
if not found_C:
found_C = True
c.id = "C"
else:
c.id = "Z"
chains_to_remove.append(i)
else:
c.id = "Z"
chains_to_remove.append(i)
#print "ERROR: Found chains with weird number of residues:", num_residues
#sys.exit(0)
fixer.removeChains(chains_to_remove)
chains = fixer.topology.chains()
print chains
chain_lengths = []
for c in chains:
num_residues = len(list(c.residues()))
chain_lengths.append(num_residues)
PDBFile.writeFile(fixer.topology, fixer.positions, open(pdbcode + ".pdb", 'w'))
call(["rm temp.pdb"], shell=True)
if chain_lengths[1] < chain_lengths[2]:
call(["grep \"[A-Z] B \" " + pdbcode + ".pdb > temp.pdb"], shell=True)
call(["sed -i \"/[A-Z] B /d\" " + pdbcode + ".pdb"], shell=True)
call(["sed -i \"/END/d\" " + pdbcode + ".pdb"], shell=True)
# SET UP SYSTEM
################################################################################
# Load forcefield.
forcefield = app.ForceField(*forcefields_to_use)
# Retrieve structure from PDB.
print('Retrieving %s from PDB...' % pdbid)
fixer = PDBFixer(pdbid=pdbid)
# Build a list of chains to remove.
print('Removing all chains but %s' % chain_ids_to_keep)
all_chains = list(fixer.topology.chains())
chain_id_list = [c.chain_id for c in fixer.structure.models[0].chains]
chain_ids_to_remove = set(chain_id_list) - set(chain_ids_to_keep)
fixer.removeChains(chainIds=chain_ids_to_remove)
# Find missing residues.
print('Finding missing residues...')
fixer.findMissingResidues()
# Replace nonstandard residues.
print('Replacing nonstandard residues...')
fixer.findNonstandardResidues()
fixer.replaceNonstandardResidues()
# Add missing atoms.
print('Adding missing atoms...')
fixer.findMissingAtoms()
fixer.addMissingAtoms()
app.PDBFile.writeFile(fixer.topology, fixer.positions, outfile)
outfile.close()
if chain_ids_to_keep is not None:
# Hack to get chain id to chain number mapping.
chain_id_list = [c.chain_id for c in fixer.structure.models[0].chains]
# Build list of chains to remove
chain_numbers_to_remove = list()
for (chain_number, chain_id) in enumerate(chain_id_list):
if chain_id not in chain_ids_to_keep:
chain_numbers_to_remove.append(chain_number)
# Remove all but desired chains.
logger.info("Removing chains...")
fixer.removeChains(chain_numbers_to_remove)
# DEBUG
print "fixer.topology.chains(): %s" % str([ chain.id for chain in fixer.topology.chains() ])
# Add missing atoms and residues.
logger.info("Adding missing atoms and residues...")
fixer.findMissingResidues()
fixer.findMissingAtoms()
fixer.addMissingAtoms()
#fixer.addMissingHydrogens(pH) # DEBUG
fixer.removeHeterogens(keepWater=keep_crystallographic_water)
# Write PDB file for completed output.
logger.info("Writing pdbfixer output...")
pdb_filename = os.path.join(workdir, 'pdbfixer.pdb')
def cleanPdb(pdb_list,
chain=None,
source=None,
toFolder="cleaned_pdbs",
formatName=False,
removeDNAchains=True,
verbose=False,
removeTwoEndsMissingResidues=True,
addMissingResidues=True,
removeHeterogens=True,
keepIds=False):
os.system(f"mkdir -p {toFolder}")
for pdb_id in pdb_list:
# print(chain)
print(pdb_id)
# pdb = f"{pdb_id.lower()[:4]}"
# pdbFile = pdb+".pdb"
if formatName:
pdb = f"{pdb_id.lower()[:4]}"
else:
pdb = pdb_id
pdbFile = pdb + ".pdb"
if source is None:
fromFile = os.path.join("original_pdbs", pdbFile)
elif source[-4:] == ".pdb":
fromFile = source
else:
fromFile = os.path.join(source, pdbFile)
# clean pdb
try:
fixer = PDBFixer(filename=fromFile)
except Exception as inst:
print(inst)
print(f"{fromFile} not found. skipped")
continue
# remove unwanted chains
chains = list(fixer.topology.chains())
print(chains)
if chain is None: # 'None' means deafult is chain A unless specified.
if len(pdb_id) >= 5:
Chosen_chain = pdb_id[4]
# Chosen_chain = pdb_id[4].upper()
else:
assert (len(pdb_id) == 4)
Chosen_chain = "A"
elif chain == "-1" or chain == -1:
Chosen_chain = getAllChains(fromFile,
removeDNAchains=removeDNAchains)
print(f"Chains: {Chosen_chain}")
elif chain == "first":
Chosen_chain = chains[0].id
else:
Chosen_chain = chain
chains_to_remove = [
i for i, x in enumerate(chains) if x.id not in Chosen_chain
]
fixer.removeChains(chains_to_remove)
fixer.findMissingResidues()
# add missing residues in the middle of a chain, not ones at the start or end of the chain.
chains = list(fixer.topology.chains())
keys = fixer.missingResidues.keys()
if verbose:
print("chains to remove", chains_to_remove)
print("missing residues: ", keys)
if not addMissingResidues:
for key in list(keys):
del fixer.missingResidues[key]
else:
if removeTwoEndsMissingResidues:
for key in list(keys):
chain_tmp = chains[key[0]]
if key[1] == 0 or key[1] == len(list(
chain_tmp.residues())):
del fixer.missingResidues[key]
fixer.findNonstandardResidues()
fixer.replaceNonstandardResidues()
if removeHeterogens:
fixer.removeHeterogens(keepWater=False)
fixer.findMissingAtoms()
try:
fixer.addMissingAtoms()
except:
print("Unable to add missing atoms")
continue
fixer.addMissingHydrogens(7.0)
PDBFile.writeFile(fixer.topology,
fixer.positions,
open(os.path.join(toFolder, pdbFile), 'w'),
keepIds=keepIds)
from pdbfixer import PDBFixer
from simtk.openmm.app import PDBFile
fixer = PDBFixer(filename='3UE4.pdb')
fixer.removeChains(chainIds=['B'])
# Without fixer.missingResidues = {}, fixer.addMissingAtoms() throw an exception
# and if I call fixer.findMissingResidues() several terminal residues are added
fixer.missingResidues = {}
fixer.findMissingAtoms()
fixer.addMissingAtoms()
fixer.removeHeterogens(keepWater=False)
fixer.addMissingHydrogens(7.0)
PDBFile.writeFile(fixer.topology, fixer.positions, open('3UE4-pdbfixer.pdb', 'w'))
from simtk.openmm import app
from pdbfixer import PDBFixer
fixer = PDBFixer(pdbid="2z9j")
fixer.removeChains(chainIds=['B'])
fixer.removeHeterogens(keepWater=False)
app.PDBFile.writeFile(fixer.topology, fixer.positions,
open("input/2z9j_clean.pdb", "w"))
# SET UP SYSTEM
################################################################################
# Load forcefield.
forcefield = app.ForceField(*forcefields_to_use)
# Retrieve structure from PDB.
print('Retrieving %s from PDB...' % pdbid)
fixer = PDBFixer(pdbid=pdbid)
# Build a list of chains to remove.
print('Removing all chains but %s' % chain_ids_to_keep)
all_chains = list(fixer.topology.chains())
chain_id_list = [c.chain_id for c in fixer.structure.models[0].chains]
chain_ids_to_remove = set(chain_id_list) - set(chain_ids_to_keep)
fixer.removeChains(chainIds=chain_ids_to_remove)
# Find missing residues.
print('Finding missing residues...')
fixer.findMissingResidues()
# Replace nonstandard residues.
print('Replacing nonstandard residues...')
fixer.findNonstandardResidues()
fixer.replaceNonstandardResidues()
# Add missing atoms.
print('Adding missing atoms...')
fixer.findMissingAtoms()
fixer.addMissingAtoms()
app.PDBFile.writeFile(fixer.topology, fixer.positions, outfile)
outfile.close()
if chain_ids_to_keep is not None:
# Hack to get chain id to chain number mapping.
chain_id_list = [c.chain_id for c in fixer.structure.models[0].chains]
# Build list of chains to remove
chain_numbers_to_remove = list()
for (chain_number, chain_id) in enumerate(chain_id_list):
if chain_id not in chain_ids_to_keep:
chain_numbers_to_remove.append(chain_number)
# Remove all but desired chains.
logger.info("Removing chains...")
fixer.removeChains(chain_numbers_to_remove)
# DEBUG
print "fixer.topology.chains(): %s" % str([ chain.id for chain in fixer.topology.chains() ])
# Add missing atoms and residues.
logger.info("Adding missing atoms and residues...")
fixer.findMissingResidues()
fixer.findMissingAtoms()
fixer.addMissingAtoms()
#fixer.addMissingHydrogens(pH) # DEBUG
fixer.removeHeterogens(keepWater=keep_crystallographic_water)
# Write PDB file for completed output.
logger.info("Writing pdbfixer output...")
pdb_filename = os.path.join(workdir, 'pdbfixer.pdb')
def prepare_pdb(pdb,
chains='A',
ff=('amber99sbildn.xml', 'tip3p.xml'),
ph=7,
pad=10 * unit.angstroms,
nbonded=app.PME,
constraints=app.HBonds,
crystal_water=True):
"""
Fetch, solvate and minimize a protein PDB structure.
Parameters
----------
pdb : str
PDB Id.
chains : str or list
Chain(s) to keep in the system.
ff : tuple of xml ff files.
Forcefields for parametrization.
ph : float
pH value for adding missing hydrogens.
pad: Quantity object
Padding around macromolecule for filling box with water.
nbonded : object
The method to use for nonbonded interactions. Allowed values are
NoCutoff, CutoffNonPeriodic, CutoffPeriodic, Ewald, PME, or LJPME.
constraints : object
Specifies which bonds and angles should be implemented with
constraints. Allowed values are None, HBonds, AllBonds, or HAngles.
crystal_water : bool
Keep crystal water.
"""
# Load forcefield.
logger.info('Retrieving %s from PDB...', pdb)
ff = app.ForceField(*ff)
# Retrieve structure from PDB.
fixer = PDBFixer(pdbid=pdb)
# Remove unselected chains.
logger.info('Removing all chains but %s', chains)
all_chains = [c.id for c in fixer.topology.chains()]
fixer.removeChains(chainIds=set(all_chains) - set(chains))
# Find missing residues.
logger.info('Finding missing residues...')
fixer.findMissingResidues()
# Replace nonstandard residues.
logger.info('Replacing nonstandard residues...')
fixer.findNonstandardResidues()
fixer.replaceNonstandardResidues()
# Add missing atoms.
logger.info('Adding missing atoms...')
fixer.findMissingAtoms()
fixer.addMissingAtoms()
# Remove heterogens.
logger.info('Removing heterogens...')
fixer.removeHeterogens(keepWater=crystal_water)
# Add missing hydrogens.
logger.info('Adding missing hydrogens appropriate for pH %s', ph)
fixer.addMissingHydrogens(ph)
if nbonded in [app.PME, app.CutoffPeriodic, app.Ewald]:
# Add solvent.
logger.info('Adding solvent...')
fixer.addSolvent(padding=pad)
# Write PDB file.
logger.info('Writing PDB file to "%s"...', '%s-pdbfixer.pdb' % pdb)
app.PDBFile.writeFile(fixer.topology, fixer.positions,
open('%s-pdbfixer.pdb' % pdb, 'w'))
# Create OpenMM System.
logger.info('Creating OpenMM system...')
system = ff.createSystem(fixer.topology,
nonbondedMethod=nbonded,
constraints=constraints,
rigidWater=True,
removeCMMotion=False)
# Minimimze to update positions.
logger.info('Minimizing...')
integrator = mm.VerletIntegrator(1.0 * unit.femtosecond)
context = mm.Context(system, integrator)
context.setPositions(fixer.positions)
mm.LocalEnergyMinimizer.minimize(context)
# pylint: disable=unexpected-keyword-arg, no-value-for-parameter
state = context.getState(getPositions=True)
fixer.positions = state.getPositions()
# Write final coordinates.
logger.info('Writing PDB file to "%s"...', '%s-minimized.pdb' % pdb)
with open('%s-minimized.pdb' % pdb, 'w') as fp:
app.PDBFile.writeFile(fixer.topology, fixer.positions, fp)
# Serialize final coordinates.
logger.info('Serializing to XML...')
serialize_system(context, system, integrator)
def main(args):
pdbcode = args[0]
if len(pdbcode) != 4:
print("Please enter a correct 4 letter pdbid")
sys.exit(0)
call("pdbfixer --pdbid " + pdbcode + " --output=temp.pdb --add-atoms=heavy --keep-heterogens=none", shell=True)
fixer = PDBFixer(filename="temp.pdb")
found_A = False
found_B = False
found_C = False
num_chains = len(list(fixer.topology.chains()))
chains = fixer.topology.chains()
chains_to_remove = []
for i, c in enumerate(chains):
num_residues = len(list(c.residues()))
if num_residues > 250:
if not found_A:
found_A = True
c.id = "A"
else:
c.id = "Z"
chains_to_remove.append(i)
elif num_residues > 50 and num_residues < 150:
if not found_B:
found_B = True
c.id = "B"
else:
c.id = "Z"
chains_to_remove.append(i)
elif num_residues <= 15:
if not found_C:
found_C = True
c.id = "C"
else:
c.id = "Z"
chains_to_remove.append(i)
else:
c.id = "Z"
chains_to_remove.append(i)
#print "ERROR: Found chains with weird number of residues:", num_residues
#sys.exit(0)
fixer.removeChains(chains_to_remove)
chains = fixer.topology.chains()
chain_lengths = []
for c in chains:
num_residues = len(list(c.residues()))
chain_lengths.append(num_residues)
PDBFile.writeFile(fixer.topology, fixer.positions, open(pdbcode + ".pdb", 'w'))
call(["rm temp.pdb"], shell=True)
if chain_lengths[1] < chain_lengths[2]:
call(["grep \"[A-Z] B \" " + pdbcode + ".pdb > temp.pdb"], shell=True)
call(["sed -i \"/[A-Z] B /d\" " + pdbcode + ".pdb"], shell=True)
call(["sed -i \"/END/d\" " + pdbcode + ".pdb"], shell=True)
call(["sed -i \"/CONECT/d\" " + pdbcode + ".pdb"], shell=True)
call(["less temp.pdb >> " + pdbcode + ".pdb"], shell=True)
fixer = PDBFixer(filename=pdbcode + ".pdb")
PDBFile.writeFile(fixer.topology, fixer.positions, open(pdbcode + ".pdb", 'w'))
call(["rm temp.pdb"], shell=True)
