def get_minimum_energy_ensemble(topology,replica_energies,replica_positions,ensemble_size=5,file_name=None):
"""
Get an ensemble of low (potential) energy poses, and write the lowest energy structure to a PDB file if a file_name is provided.
:param topology: OpenMM Topology()
:type topology: `Topology() <https://simtk.org/api_docs/openmm/api4_1/python/classsimtk_1_1openmm_1_1app_1_1topology_1_1Topology.html>`_
:param replica_energies: List of dimension num_replicas X simulation_steps, which gives the energies for all replicas at all simulation steps
:type replica_energies: List( List( float * simtk.unit.energy for simulation_steps ) for num_replicas )
:param replica_positions: List of positions for all output frames for all replicas
:type replica_positions: np.array( ( float * simtk.unit.positions for num_beads ) for simulation_steps )
:param file_name: Output destination for PDB coordinates of minimum energy pose, Default = None
:returns:
- ensemble ( List() ) - A list of poses that are in the minimum energy ensemble.
:Example:
>>> from foldamers.cg_model.cgmodel import CGModel
>>> from cg_openmm.simulation.rep_exch import *
>>> cgmodel = CGModel()
>>> replica_energies,replica_positions,replica_state_indices = run_replica_exchange(cgmodel.topology,cgmodel.system,cgmodel.positions)
>>> ensemble_size = 5
>>> file_name = "minimum.pdb"
>>> minimum_energy_ensemble = get_minimum_energy_ensemble(cgmodel.topology,replica_energies,replica_positions,ensemble_size=ensemble_size,file_name=file_name)
"""
# Get the minimum energy structure sampled during the simulation
ensemble = []
ensemble_energies = []
for replica in range(len(replica_energies)):
energies = np.array([energy for energy in replica_energies[replica][replica]])
for energy in range(len(energies)):
if len(ensemble) < ensemble_size:
ensemble.append(replica_positions[replica][energy])
ensemble_energies.append(energies[energy])
else:
for comparison in range(len(ensemble_energies)):
if energies[energy] < ensemble_energies[comparison]:
ensemble_energies[comparison] = energies[energy]
ensemble[comparison] = replica_positions[replica][energy]
if file_name == None:
index = 1
for pose in ensemble:
file = open(str("re_min_"+str(index)+".pdb"),"w")
PDBFile.writeFile(topology,pose,file=file)
else:
file = open(file_name,"w")
for pose in ensemble:
PDBFile.writeFile(topology,pose,file=file)
return(ensemble)
def write_single_pdb(xp, top, target):
"""Dump coordinates to a pdb file `target`."""
try:
target = Path(target)
except TypeError:
if hasattr(target, 'write'):
PDBFile.writeFile(top, xp, target)
else:
raise
else:
with open(target, 'w') as fp:
PDBFile.writeFile(top, xp, fp)
def fix_pdb(pdb_id):
path = os.getcwd()
if len(pdb_id) != 4:
print("Creating PDBFixer...")
fixer = PDBFixer(pdb_id)
print("Finding missing residues...")
fixer.findMissingResidues()
chains = list(fixer.topology.chains())
keys = fixer.missingResidues.keys()
for key in list(keys):
chain = chains[key[0]]
if key[1] == 0 or key[1] == len(list(chain.residues())):
print("ok")
del fixer.missingResidues[key]
print("Finding nonstandard residues...")
fixer.findNonstandardResidues()
print("Replacing nonstandard residues...")
fixer.replaceNonstandardResidues()
print("Removing heterogens...")
fixer.removeHeterogens(keepWater=True)
print("Finding missing atoms...")
fixer.findMissingAtoms()
print("Adding missing atoms...")
fixer.addMissingAtoms()
print("Adding missing hydrogens...")
fixer.addMissingHydrogens(7)
print("Writing PDB file...")
PDBFile.writeFile(
fixer.topology,
fixer.positions,
open(
os.path.join(path,
"%s_fixed_pH_%s.pdb" % (pdb_id.split('.')[0], 7)),
"w"),
keepIds=True)
return "%s_fixed_pH_%s.pdb" % (pdb_id.split('.')[0], 7)