def writeHeader(topology, file=sys.stdout, entry=None):
"""Write out the header for a PDBx/mmCIF file.
Parameters
----------
topology : Topology
The Topology defining the molecular system being written
file : file=stdout
A file to write the file to
entry : str=None
The entry ID to assign to the CIF file
"""
if entry is not None:
print('data_%s' % entry, file=file)
else:
print('data_cell', file=file)
print("# Created with OpenMM %s, %s" %
(Platform.getOpenMMVersion(), str(date.today())),
file=file)
print('#', file=file)
vectors = topology.getPeriodicBoxVectors()
if vectors is not None:
a, b, c, alpha, beta, gamma = computeLengthsAndAngles(vectors)
RAD_TO_DEG = 180 / math.pi
print('_cell.length_a %10.4f' % (a * 10), file=file)
print('_cell.length_b %10.4f' % (b * 10), file=file)
print('_cell.length_c %10.4f' % (c * 10), file=file)
print('_cell.angle_alpha %10.4f' % (alpha * RAD_TO_DEG),
file=file)
print('_cell.angle_beta %10.4f' % (beta * RAD_TO_DEG), file=file)
print('_cell.angle_gamma %10.4f' % (gamma * RAD_TO_DEG),
file=file)
print('##', file=file)
print('loop_', file=file)
print('_atom_site.group_PDB', file=file)
print('_atom_site.id', file=file)
print('_atom_site.type_symbol', file=file)
print('_atom_site.label_atom_id', file=file)
print('_atom_site.label_alt_id', file=file)
print('_atom_site.label_comp_id', file=file)
print('_atom_site.label_asym_id', file=file)
print('_atom_site.label_entity_id', file=file)
print('_atom_site.label_seq_id', file=file)
print('_atom_site.pdbx_PDB_ins_code', file=file)
print('_atom_site.Cartn_x', file=file)
print('_atom_site.Cartn_y', file=file)
print('_atom_site.Cartn_z', file=file)
print('_atom_site.occupancy', file=file)
print('_atom_site.B_iso_or_equiv', file=file)
print('_atom_site.Cartn_x_esd', file=file)
print('_atom_site.Cartn_y_esd', file=file)
print('_atom_site.Cartn_z_esd', file=file)
print('_atom_site.occupancy_esd', file=file)
print('_atom_site.B_iso_or_equiv_esd', file=file)
print('_atom_site.pdbx_formal_charge', file=file)
print('_atom_site.auth_seq_id', file=file)
print('_atom_site.auth_comp_id', file=file)
print('_atom_site.auth_asym_id', file=file)
print('_atom_site.auth_atom_id', file=file)
print('_atom_site.pdbx_PDB_model_num', file=file)
def writeHeader(topology, file=sys.stdout, entry=None):
"""Write out the header for a PDBx/mmCIF file.
Parameters
----------
topology : Topology
The Topology defining the molecular system being written
file : file=stdout
A file to write the file to
entry : str=None
The entry ID to assign to the CIF file
"""
if entry is not None:
print('data_%s' % entry, file=file)
else:
print('data_cell', file=file)
print("# Created with OpenMM %s, %s" % (Platform.getOpenMMVersion(), str(date.today())), file=file)
print('#', file=file)
vectors = topology.getPeriodicBoxVectors()
if vectors is not None:
a, b, c, alpha, beta, gamma = computeLengthsAndAngles(vectors)
RAD_TO_DEG = 180/math.pi
print('_cell.length_a %10.4f' % (a*10), file=file)
print('_cell.length_b %10.4f' % (b*10), file=file)
print('_cell.length_c %10.4f' % (c*10), file=file)
print('_cell.angle_alpha %10.4f' % (alpha*RAD_TO_DEG), file=file)
print('_cell.angle_beta %10.4f' % (beta*RAD_TO_DEG), file=file)
print('_cell.angle_gamma %10.4f' % (gamma*RAD_TO_DEG), file=file)
print('##', file=file)
print('loop_', file=file)
print('_atom_site.group_PDB', file=file)
print('_atom_site.id', file=file)
print('_atom_site.type_symbol', file=file)
print('_atom_site.label_atom_id', file=file)
print('_atom_site.label_alt_id', file=file)
print('_atom_site.label_comp_id', file=file)
print('_atom_site.label_asym_id', file=file)
print('_atom_site.label_entity_id', file=file)
print('_atom_site.label_seq_id', file=file)
print('_atom_site.pdbx_PDB_ins_code', file=file)
print('_atom_site.Cartn_x', file=file)
print('_atom_site.Cartn_y', file=file)
print('_atom_site.Cartn_z', file=file)
print('_atom_site.occupancy', file=file)
print('_atom_site.B_iso_or_equiv', file=file)
print('_atom_site.Cartn_x_esd', file=file)
print('_atom_site.Cartn_y_esd', file=file)
print('_atom_site.Cartn_z_esd', file=file)
print('_atom_site.occupancy_esd', file=file)
print('_atom_site.B_iso_or_equiv_esd', file=file)
print('_atom_site.pdbx_formal_charge', file=file)
print('_atom_site.auth_seq_id', file=file)
print('_atom_site.auth_comp_id', file=file)
print('_atom_site.auth_asym_id', file=file)
print('_atom_site.auth_atom_id', file=file)
print('_atom_site.pdbx_PDB_model_num', file=file)
def writeHeader(topology, file=sys.stdout):
"""Write out the header for a PDB file.
Parameters:
- topology (Topology) The Topology defining the molecular system being written
- file (file=stdout) A file to write the file to
"""
print >>file, "REMARK 1 CREATED WITH OPENMM %s, %s" % (Platform.getOpenMMVersion(), str(date.today()))
boxSize = topology.getUnitCellDimensions()
if boxSize is not None:
size = boxSize.value_in_unit(angstroms)
print >>file, "CRYST1%9.3f%9.3f%9.3f 90.00 90.00 90.00 P 1 1 " % size
def writeHeader(topology, file=sys.stdout):
"""Write out the header for a PDB file.
Parameters:
- topology (Topology) The Topology defining the molecular system being written
- file (file=stdout) A file to write the file to
"""
print >>file, "REMARK 1 CREATED WITH OPENMM %s, %s" % (Platform.getOpenMMVersion(), str(date.today()))
boxSize = topology.getUnitCellDimensions()
if boxSize is not None:
size = boxSize.value_in_unit(angstroms)
print >>file, "CRYST1%9.3f%9.3f%9.3f 90.00 90.00 90.00 P 1 1 " % size
def writeHeader(topology, file=sys.stdout):
"""Write out the header for a PDB file.
Parameters
----------
topology : Topology
The Topology defining the molecular system being written
file : file=stdout
A file to write the file to
"""
print("REMARK 1 CREATED WITH OPENMM %s, %s" % (Platform.getOpenMMVersion(), str(date.today())), file=file)
vectors = topology.getPeriodicBoxVectors()
if vectors is not None:
a, b, c, alpha, beta, gamma = computeLengthsAndAngles(vectors)
RAD_TO_DEG = 180/math.pi
print("CRYST1%9.3f%9.3f%9.3f%7.2f%7.2f%7.2f P 1 1 " % (
a*10, b*10, c*10, alpha*RAD_TO_DEG, beta*RAD_TO_DEG, gamma*RAD_TO_DEG), file=file)
def writeHeader(topology, file=sys.stdout):
"""Write out the header for a PDB file.
Parameters
----------
topology : Topology
The Topology defining the molecular system being written
file : file=stdout
A file to write the file to
"""
print("REMARK 1 CREATED WITH OPENMM %s, %s" % (Platform.getOpenMMVersion(), str(date.today())), file=file)
vectors = topology.getPeriodicBoxVectors()
if vectors is not None:
a, b, c, alpha, beta, gamma = computeLengthsAndAngles(vectors)
RAD_TO_DEG = 180/math.pi
print("CRYST1%9.3f%9.3f%9.3f%7.2f%7.2f%7.2f P 1 1 " % (
a*10, b*10, c*10, alpha*RAD_TO_DEG, beta*RAD_TO_DEG, gamma*RAD_TO_DEG), file=file)
def writeHeader(topology, file=sys.stdout):
"""Write out the header for a PDB file.
Parameters:
- topology (Topology) The Topology defining the molecular system being written
- file (file=stdout) A file to write the file to
"""
print >> file, "REMARK 1 CREATED WITH OPENMM %s, %s" % (
Platform.getOpenMMVersion(), str(date.today()))
vectors = topology.getPeriodicBoxVectors()
if vectors is not None:
(a, b, c) = vectors.value_in_unit(angstroms)
a_length = norm(a)
b_length = norm(b)
c_length = norm(c)
alpha = math.acos(dot(b, c) /
(b_length * c_length)) * 180.0 / math.pi
beta = math.acos(dot(c, a) /
(c_length * a_length)) * 180.0 / math.pi
gamma = math.acos(dot(a, b) /
(a_length * b_length)) * 180.0 / math.pi
print >> file, "CRYST1%9.3f%9.3f%9.3f%7.2f%7.2f%7.2f P 1 1 " % (
a_length, b_length, c_length, alpha, beta, gamma)
def writeHeader(topology, file=sys.stdout, entry=None, keepIds=False):
"""Write out the header for a PDBx/mmCIF file.
Parameters
----------
topology : Topology
The Topology defining the molecular system being written
file : file=stdout
A file to write the file to
entry : str=None
The entry ID to assign to the CIF file
keepIds : bool=False
If True, keep the residue and chain IDs specified in the Topology
rather than generating new ones. Warning: It is up to the caller to
make sure these are valid IDs that satisfy the requirements of the
PDBx/mmCIF format. Otherwise, the output file will be invalid.
"""
if entry is not None:
print('data_%s' % entry, file=file)
else:
print('data_cell', file=file)
print("# Created with OpenMM %s, %s" % (Platform.getOpenMMVersion(), str(date.today())), file=file)
print('#', file=file)
vectors = topology.getPeriodicBoxVectors()
if vectors is not None:
a, b, c, alpha, beta, gamma = computeLengthsAndAngles(vectors)
RAD_TO_DEG = 180/math.pi
print('_cell.length_a %10.4f' % (a*10), file=file)
print('_cell.length_b %10.4f' % (b*10), file=file)
print('_cell.length_c %10.4f' % (c*10), file=file)
print('_cell.angle_alpha %10.4f' % (alpha*RAD_TO_DEG), file=file)
print('_cell.angle_beta %10.4f' % (beta*RAD_TO_DEG), file=file)
print('_cell.angle_gamma %10.4f' % (gamma*RAD_TO_DEG), file=file)
print('#', file=file)
# Identify bonds that should be listed in the file.
bonds = []
for atom1, atom2 in topology.bonds():
if atom1.residue.name not in PDBFile._standardResidues or atom2.residue.name not in PDBFile._standardResidues:
bonds.append((atom1, atom2))
elif atom1.name == 'SG' and atom2.name == 'SG' and atom1.residue.name == 'CYS' and atom2.residue.name == 'CYS':
bonds.append((atom1, atom2))
if len(bonds) > 0:
# Write the bond information.
print('loop_', file=file)
print('_struct_conn.id', file=file)
print('_struct_conn.conn_type_id', file=file)
print('_struct_conn.ptnr1_label_asym_id', file=file)
print('_struct_conn.ptnr1_label_comp_id', file=file)
print('_struct_conn.ptnr1_label_seq_id', file=file)
print('_struct_conn.ptnr1_label_atom_id', file=file)
print('_struct_conn.ptnr2_label_asym_id', file=file)
print('_struct_conn.ptnr2_label_comp_id', file=file)
print('_struct_conn.ptnr2_label_seq_id', file=file)
print('_struct_conn.ptnr2_label_atom_id', file=file)
chainIds = {}
resIds = {}
if keepIds:
for chain in topology.chains():
chainIds[chain] = chain.id
for res in topology.residues():
resIds[res] = res.id
else:
for (chainIndex, chain) in enumerate(topology.chains()):
chainIds[chain] = chr(ord('A')+chainIndex%26)
for (resIndex, res) in enumerate(chain.residues()):
resIds[res] = resIndex+1
for i, (atom1, atom2) in enumerate(bonds):
if atom1.residue.name == 'CYS' and atom2.residue.name == 'CYS':
bondType = 'disulf'
else:
bondType = 'covale'
line = "bond%d %s %s %-4s %5s %-4s %s %-4s %5s %-4s"
print(line % (i+1, bondType, chainIds[atom1.residue.chain], atom1.residue.name, resIds[atom1.residue], atom1.name,
chainIds[atom2.residue.chain], atom2.residue.name, resIds[atom2.residue], atom2.name), file=file)
print('#', file=file)
# Write the header for the atom coordinates.
print('loop_', file=file)
print('_atom_site.group_PDB', file=file)
print('_atom_site.id', file=file)
print('_atom_site.type_symbol', file=file)
print('_atom_site.label_atom_id', file=file)
print('_atom_site.label_alt_id', file=file)
print('_atom_site.label_comp_id', file=file)
print('_atom_site.label_asym_id', file=file)
print('_atom_site.label_entity_id', file=file)
print('_atom_site.label_seq_id', file=file)
print('_atom_site.pdbx_PDB_ins_code', file=file)
print('_atom_site.Cartn_x', file=file)
print('_atom_site.Cartn_y', file=file)
print('_atom_site.Cartn_z', file=file)
print('_atom_site.occupancy', file=file)
print('_atom_site.B_iso_or_equiv', file=file)
print('_atom_site.Cartn_x_esd', file=file)
print('_atom_site.Cartn_y_esd', file=file)
print('_atom_site.Cartn_z_esd', file=file)
print('_atom_site.occupancy_esd', file=file)
print('_atom_site.B_iso_or_equiv_esd', file=file)
print('_atom_site.pdbx_formal_charge', file=file)
print('_atom_site.auth_seq_id', file=file)
print('_atom_site.auth_comp_id', file=file)
print('_atom_site.auth_asym_id', file=file)
print('_atom_site.auth_atom_id', file=file)
print('_atom_site.pdbx_PDB_model_num', file=file)
def check_openmm_version():
from simtk.openmm import Platform
if not Platform.getOpenMMVersion() >= '5.1':
raise ValueError('MSMAccelerator requires OpenMM >= 5.1')
def writeHeader(topology, file=sys.stdout, entry=None, keepIds=False):
"""Write out the header for a PDBx/mmCIF file.
Parameters
----------
topology : Topology
The Topology defining the molecular system being written
file : file=stdout
A file to write the file to
entry : str=None
The entry ID to assign to the CIF file
keepIds : bool=False
If True, keep the residue and chain IDs specified in the Topology
rather than generating new ones. Warning: It is up to the caller to
make sure these are valid IDs that satisfy the requirements of the
PDBx/mmCIF format. Otherwise, the output file will be invalid.
"""
if entry is not None:
print('data_%s' % entry, file=file)
else:
print('data_cell', file=file)
print("# Created with OpenMM %s, %s" %
(Platform.getOpenMMVersion(), str(date.today())),
file=file)
print('#', file=file)
vectors = topology.getPeriodicBoxVectors()
if vectors is not None:
a, b, c, alpha, beta, gamma = computeLengthsAndAngles(vectors)
RAD_TO_DEG = 180 / math.pi
print('_cell.length_a %10.4f' % (a * 10), file=file)
print('_cell.length_b %10.4f' % (b * 10), file=file)
print('_cell.length_c %10.4f' % (c * 10), file=file)
print('_cell.angle_alpha %10.4f' % (alpha * RAD_TO_DEG),
file=file)
print('_cell.angle_beta %10.4f' % (beta * RAD_TO_DEG), file=file)
print('_cell.angle_gamma %10.4f' % (gamma * RAD_TO_DEG),
file=file)
print('#', file=file)
# Identify bonds that should be listed in the file.
bonds = []
for atom1, atom2 in topology.bonds():
if atom1.residue.name not in PDBFile._standardResidues or atom2.residue.name not in PDBFile._standardResidues:
bonds.append((atom1, atom2))
elif atom1.name == 'SG' and atom2.name == 'SG' and atom1.residue.name == 'CYS' and atom2.residue.name == 'CYS':
bonds.append((atom1, atom2))
if len(bonds) > 0:
# Write the bond information.
print('loop_', file=file)
print('_struct_conn.id', file=file)
print('_struct_conn.conn_type_id', file=file)
print('_struct_conn.ptnr1_label_asym_id', file=file)
print('_struct_conn.ptnr1_label_comp_id', file=file)
print('_struct_conn.ptnr1_label_seq_id', file=file)
print('_struct_conn.ptnr1_label_atom_id', file=file)
print('_struct_conn.ptnr2_label_asym_id', file=file)
print('_struct_conn.ptnr2_label_comp_id', file=file)
print('_struct_conn.ptnr2_label_seq_id', file=file)
print('_struct_conn.ptnr2_label_atom_id', file=file)
chainIds = {}
resIds = {}
if keepIds:
for chain in topology.chains():
chainIds[chain] = chain.id
for res in topology.residues():
resIds[res] = res.id
else:
for (chainIndex, chain) in enumerate(topology.chains()):
chainIds[chain] = chr(ord('A') + chainIndex % 26)
for (resIndex, res) in enumerate(chain.residues()):
resIds[res] = resIndex + 1
for i, (atom1, atom2) in enumerate(bonds):
if atom1.residue.name == 'CYS' and atom2.residue.name == 'CYS':
bondType = 'disulf'
else:
bondType = 'covale'
line = "bond%d %s %s %-4s %5s %-4s %s %-4s %5s %-4s"
print(line %
(i + 1, bondType, chainIds[atom1.residue.chain],
atom1.residue.name, resIds[atom1.residue], atom1.name,
chainIds[atom2.residue.chain], atom2.residue.name,
resIds[atom2.residue], atom2.name),
file=file)
print('#', file=file)
# Write the header for the atom coordinates.
print('loop_', file=file)
print('_atom_site.group_PDB', file=file)
print('_atom_site.id', file=file)
print('_atom_site.type_symbol', file=file)
print('_atom_site.label_atom_id', file=file)
print('_atom_site.label_alt_id', file=file)
print('_atom_site.label_comp_id', file=file)
print('_atom_site.label_asym_id', file=file)
print('_atom_site.label_entity_id', file=file)
print('_atom_site.label_seq_id', file=file)
print('_atom_site.pdbx_PDB_ins_code', file=file)
print('_atom_site.Cartn_x', file=file)
print('_atom_site.Cartn_y', file=file)
print('_atom_site.Cartn_z', file=file)
print('_atom_site.occupancy', file=file)
print('_atom_site.B_iso_or_equiv', file=file)
print('_atom_site.Cartn_x_esd', file=file)
print('_atom_site.Cartn_y_esd', file=file)
print('_atom_site.Cartn_z_esd', file=file)
print('_atom_site.occupancy_esd', file=file)
print('_atom_site.B_iso_or_equiv_esd', file=file)
print('_atom_site.pdbx_formal_charge', file=file)
print('_atom_site.auth_seq_id', file=file)
print('_atom_site.auth_comp_id', file=file)
print('_atom_site.auth_asym_id', file=file)
print('_atom_site.auth_atom_id', file=file)
print('_atom_site.pdbx_PDB_model_num', file=file)
def check_openmm_version():
from simtk.openmm import Platform
if not Platform.getOpenMMVersion() >= '5.1':
raise ValueError('MSMAccelerator requires OpenMM >= 5.1')
