def test_atom(self):
"""Test the lib.structure.pdb_read.atom() function."""
# Parse a PDB record.
record = pdb_read.atom('ATOM 158 CG GLU 11 9.590 -1.041 -11.596 1.00 0.00 C ')
# Test the elements.
self.assertEqual(record[0], 'ATOM')
self.assertEqual(record[1], 158)
self.assertEqual(record[2], 'CG')
self.assertEqual(record[3], None)
self.assertEqual(record[4], 'GLU')
self.assertEqual(record[5], None)
self.assertEqual(record[6], 11)
self.assertEqual(record[7], None)
self.assertEqual(record[8], 9.59)
self.assertEqual(record[9], -1.041)
self.assertEqual(record[10], -11.596)
self.assertEqual(record[11], 1.0)
self.assertEqual(record[12], 0.0)
self.assertEqual(record[13], 'C')
self.assertEqual(record[14], None)
def test_atom(self):
"""Test the lib.structure.pdb_read.atom() function."""
# Parse a PDB record.
record = pdb_read.atom('ATOM 158 CG GLU 11 9.590 -1.041 -11.596 1.00 0.00 C ')
# Test the elements.
self.assertEqual(record[0], 'ATOM')
self.assertEqual(record[1], 158)
self.assertEqual(record[2], 'CG')
self.assertEqual(record[3], None)
self.assertEqual(record[4], 'GLU')
self.assertEqual(record[5], None)
self.assertEqual(record[6], 11)
self.assertEqual(record[7], None)
self.assertEqual(record[8], 9.59)
self.assertEqual(record[9], -1.041)
self.assertEqual(record[10], -11.596)
self.assertEqual(record[11], 1.0)
self.assertEqual(record[12], 0.0)
self.assertEqual(record[13], 'C')
self.assertEqual(record[14], None)
def fill_object_from_pdb(self, records, alt_loc_select=None):
"""Method for generating a complete Structure_container object from the given PDB records.
@param records: A list of structural PDB records.
@type records: list of str
@keyword alt_loc_select: The PDB ATOM record 'Alternate location indicator' field value to select which coordinates to use.
@type alt_loc_select: str or None
"""
# Loop over the records.
for record in records:
# Nothing to do.
if not record or record == '\n':
continue
# Add the atom.
if record[:4] == 'ATOM' or record[:6] == 'HETATM':
# Parse the record.
if record[:4] == 'ATOM':
record_type, serial, name, alt_loc, res_name, chain_id, res_seq, icode, x, y, z, occupancy, temp_factor, element, charge = pdb_read.atom(record)
if record[:6] == 'HETATM':
record_type, serial, name, alt_loc, res_name, chain_id, res_seq, icode, x, y, z, occupancy, temp_factor, element, charge = pdb_read.hetatm(record)
# Handle the alternate locations.
if alt_loc != None:
# Don't know what to do.
if alt_loc_select == None:
raise RelaxError("Multiple alternate location indicators are present in the PDB file, but the desired coordinate set has not been specified.")
# Skip non-matching locations.
if alt_loc != alt_loc_select:
continue
# Attempt at determining the element, if missing.
if not element:
element = self._det_pdb_element(name)
# Add.
self.atom_add(pdb_record=record_type, atom_num=serial, atom_name=name, res_name=res_name, chain_id=chain_id, res_num=res_seq, pos=[x, y, z], element=element)
# Connect atoms.
if record[:6] == 'CONECT':
# Parse the record.
record_type, serial, bonded1, bonded2, bonded3, bonded4 = pdb_read.conect(record)
# Loop over the atoms of the record.
for bonded in [bonded1, bonded2, bonded3, bonded4]:
# Skip if there is no record.
if not bonded:
continue
# Skip broken CONECT records (for when the record points to a non-existent atom).
if self._atom_index(serial) == None or self._atom_index(bonded) == None:
continue
# Make the connection.
self.atom_connect(index1=self._atom_index(serial), index2=self._atom_index(bonded))
def fill_object_from_pdb(self, records, alt_loc_select=None):
"""Method for generating a complete Structure_container object from the given PDB records.
@param records: A list of structural PDB records.
@type records: list of str
@keyword alt_loc_select: The PDB ATOM record 'Alternate location indicator' field value to select which coordinates to use.
@type alt_loc_select: str or None
"""
# Loop over the records.
water = []
missing_connect = []
for record in records:
# Nothing to do.
if not record or record == '\n':
continue
# Add the atom.
if record[:4] == 'ATOM' or record[:6] == 'HETATM':
# Parse the record.
if record[:4] == 'ATOM':
record_type, serial, name, alt_loc, res_name, chain_id, res_seq, icode, x, y, z, occupancy, temp_factor, element, charge = pdb_read.atom(record)
if record[:6] == 'HETATM':
record_type, serial, name, alt_loc, res_name, chain_id, res_seq, icode, x, y, z, occupancy, temp_factor, element, charge = pdb_read.hetatm(record)
# Skip waters.
if res_name == 'HOH':
water.append(res_seq)
continue
# Handle the alternate locations.
if alt_loc != None:
# Don't know what to do.
if alt_loc_select == None:
raise RelaxError("Multiple alternate location indicators are present in the PDB file, but the desired coordinate set has not been specified.")
# Skip non-matching locations.
if alt_loc != alt_loc_select:
continue
# Attempt at determining the element, if missing.
if not element:
element = self._det_pdb_element(name)
# Add.
self.atom_add(pdb_record=record_type, atom_num=serial, atom_name=name, res_name=res_name, chain_id=chain_id, res_num=res_seq, pos=[x, y, z], element=element)
# Connect atoms.
if record[:6] == 'CONECT':
# Parse the record.
record_type, serial, bonded1, bonded2, bonded3, bonded4 = pdb_read.conect(record)
# Loop over the atoms of the record.
for bonded in [bonded1, bonded2, bonded3, bonded4]:
# Skip if there is no record.
if not bonded:
continue
# The atom indices.
serial_index = self._atom_index(serial)
bonded_index = self._atom_index(bonded)
# Skip broken CONECT records (for when the record points to a non-existent atom).
if serial_index == None:
if serial not in missing_connect:
missing_connect.append(serial)
continue
if bonded_index == None:
if bonded not in missing_connect:
missing_connect.append(bonded)
continue
# Make the connection.
self.atom_connect(index1=serial_index, index2=bonded_index)
# Warnings.
if len(missing_connect):
missing_connect.sort()
warn(RelaxWarning("The following atom numbers from the CONECT records cannot be found within the ATOM and HETATM records: %s." % missing_connect))
if len(water):
warn(RelaxWarning("Skipping the water molecules HOH %s." % water))
def fill_object_from_pdb(self,
records,
alt_loc_select=None,
reset_serial=True):
"""Method for generating a complete Structure_container object from the given PDB records.
@param records: A list of structural PDB records.
@type records: list of str
@keyword alt_loc_select: The PDB ATOM record 'Alternate location indicator' field value to select which coordinates to use.
@type alt_loc_select: str or None
@keyword reset_serial: A flag which if True will cause the first serial number (or atom number) to be reset to 1, and all other numbers shifted.
@type reset_serial: bool
"""
# Loop over the records.
water = []
missing_connect = []
number_offset = None
for record in records:
# Nothing to do.
if not record or record == '\n':
continue
# Add the atom.
if record[:4] == 'ATOM' or record[:6] == 'HETATM':
# Parse the record.
if record[:4] == 'ATOM':
record_type, serial, name, alt_loc, res_name, chain_id, res_seq, icode, x, y, z, occupancy, temp_factor, element, charge = pdb_read.atom(
record)
if record[:6] == 'HETATM':
record_type, serial, name, alt_loc, res_name, chain_id, res_seq, icode, x, y, z, occupancy, temp_factor, element, charge = pdb_read.hetatm(
record)
# The serial number.
if reset_serial:
# The first number.
if number_offset == None:
number_offset = serial - 1
# Reset.
serial -= number_offset
# Skip waters.
if res_name == 'HOH':
water.append(res_seq)
continue
# Handle the alternate locations.
if alt_loc != None:
# Don't know what to do.
if alt_loc_select == None:
raise RelaxError(
"Multiple alternate location indicators are present in the PDB file, but the desired coordinate set has not been specified."
)
# Skip non-matching locations.
if alt_loc != alt_loc_select:
continue
# Attempt at determining the element, if missing.
if not element:
element = self._det_pdb_element(name)
# Add.
self.atom_add(pdb_record=record_type,
atom_num=serial,
atom_name=name,
res_name=res_name,
res_num=res_seq,
pos=[x, y, z],
element=element)
# Connect atoms.
if record[:6] == 'CONECT':
# Parse the record.
record_type, serial, bonded1, bonded2, bonded3, bonded4 = pdb_read.conect(
record)
# Reset the serial numbers.
if reset_serial:
serial -= number_offset
bonded1 -= number_offset
if bonded2 != None:
bonded2 -= number_offset
if bonded3 != None:
bonded3 -= number_offset
if bonded4 != None:
bonded4 -= number_offset
# Loop over the atoms of the record.
for bonded in [bonded1, bonded2, bonded3, bonded4]:
# Skip if there is no record.
if not bonded:
continue
# The atom indices.
serial_index = self._atom_index(serial)
bonded_index = self._atom_index(bonded)
# Skip broken CONECT records (for when the record points to a non-existent atom).
if serial_index == None:
if serial not in missing_connect:
missing_connect.append(serial)
continue
if bonded_index == None:
if bonded not in missing_connect:
missing_connect.append(bonded)
continue
# Make the connection.
self.atom_connect(index1=serial_index, index2=bonded_index)
# Warnings.
if len(missing_connect):
missing_connect.sort()
warn(
RelaxWarning(
"The following atom numbers from the CONECT records cannot be found within the ATOM and HETATM records: %s."
% missing_connect))
if len(water):
warn(RelaxWarning("Skipping the water molecules HOH %s." % water))