class CifAtom(object):
"""
This is a class to write cifatom files. These are partial cif files that
contain all atoms, including those created by symmetry operations. These
files differ from normal cif files in that they only contain the atom_site
block and this block differs from that in the standard cif files.
1. This file conatins all atoms, even those produced by rotations.
2. All label_* and auth_* fields will be the same and will the values used
to copute the unit id of the atom.
3. Entity id is '?'.
4. All *_esd, charge, *_esi, occupancy and such entries are '?'.
5. We have a final field which the component unit id for each atom.
"""
def __init__(self, handle):
self.writer = Writer(handle)
def atom_container(self, structure):
atoms = DataCategory('atom_site')
fields = ['group_PDB', 'id', 'type_symbol', 'label_atom_id',
'label_alt_id', 'label_comp_id', 'label_asym_id',
'label_entity_id', 'label_seq_id', 'pdbx_PDB_ins_code',
'Cartn_x', 'Cartn_y', 'Cartn_z', 'occupancy',
'B_iso_or_equiv', 'Cartn_x_esd', 'Cartn_y_esd',
'Cartn_z_esd', 'occupancy_ies', 'B_iso_or_equiv_esd',
'pdbx_formal_charge', 'auth_seq_id', 'auth_comp_id',
'auth_asym_id', 'auth_atom_id', 'pdbx_PDB_model_num',
'unit_id']
for field in fields:
atoms.appendAttribute(field)
def key(atom):
return (atom.symmetry, atom.model, atom.chain,
atom.component_number, atom.insertion_code)
all_atoms = it.imap(lambda r: r.atoms(),
structure.residues(polymeric=None))
all_atoms = it.chain.from_iterable(all_atoms)
for index, atom in enumerate(sorted(all_atoms, key=key)):
alt_id = getattr(atom, 'alt_id', '.')
data = [atom.group, index, atom.type, atom.name,
alt_id, atom.component_id, atom.chain,
'?', atom.component_number, atom.insertion_code,
atom.x, atom.y, atom.z, '?',
'?', '?', '?',
'?', '?', '?',
'.', atom.component_number, atom.component_id,
atom.chain, atom.name, atom.model,
atom.component_unit_id()]
atoms.append(data)
return atoms
def __call__(self, structure):
atoms = self.atom_container(structure)
container = DataContainer(structure.pdb)
container.append(atoms)
self.writer.writeContainer(container)
class CifAtom(object):
"""
This is a class to write cifatom files. These are partial cif files that
contain all atoms, including those created by symmetry operations. These
files differ from normal cif files in that they only contain the atom_site
block and this block differs from that in the standard cif files.
1. This file conatins all atoms, even those produced by rotations.
2. All label_* and auth_* fields will be the same and will the values used
to copute the unit id of the atom.
3. Entity id is '?'.
4. All *_esd, charge, *_esi, occupancy and such entries are '?'.
5. We have a final field which the component unit id for each atom.
"""
def __init__(self, handle):
self.writer = Writer(handle)
def atom_container(self, structure):
atoms = DataCategory('atom_site')
fields = [
'group_PDB', 'id', 'type_symbol', 'label_atom_id', 'label_alt_id',
'label_comp_id', 'label_asym_id', 'label_entity_id',
'label_seq_id', 'pdbx_PDB_ins_code', 'Cartn_x', 'Cartn_y',
'Cartn_z', 'occupancy', 'B_iso_or_equiv', 'Cartn_x_esd',
'Cartn_y_esd', 'Cartn_z_esd', 'occupancy_ies',
'B_iso_or_equiv_esd', 'pdbx_formal_charge', 'auth_seq_id',
'auth_comp_id', 'auth_asym_id', 'auth_atom_id',
'pdbx_PDB_model_num', 'unit_id'
]
for field in fields:
atoms.appendAttribute(field)
def key(atom):
return (atom.symmetry, atom.model, atom.chain,
atom.component_number, atom.insertion_code)
all_atoms = it.imap(lambda r: r.atoms(),
structure.residues(polymeric=None))
all_atoms = it.chain.from_iterable(all_atoms)
for index, atom in enumerate(sorted(all_atoms, key=key)):
alt_id = getattr(atom, 'alt_id', '.')
data = [
atom.group, index, atom.type, atom.name, alt_id,
atom.component_id, atom.chain, '?', atom.component_number,
atom.insertion_code, atom.x, atom.y, atom.z, '?', '?', '?',
'?', '?', '?', '?', '.', atom.component_number,
atom.component_id, atom.chain, atom.name, atom.model,
atom.component_unit_id()
]
atoms.append(data)
return atoms
def __call__(self, structure):
atoms = self.atom_container(structure)
container = DataContainer(structure.pdb)
container.append(atoms)
self.writer.writeContainer(container)
def write_cif(container, ocif):
ofh = open(ocif, 'w')
pdbxW = PdbxWriter(ofh)
pdbxW.writeContainer(curContainer)
ofh.close()
class CifAtom(object):
"""
This is a class to write cifatom files. These are partial cif files that
contain all atoms, including those created by symmetry operations. These
files differ from normal cif files in that they only contain the atom_site
block and this block differs from that in the standard cif files.
1. This file conatins all atoms, even those produced by rotations.
2. All label_* and auth_* fields will be the same and will contain the
values used to compute the unit id of the atom.
3. The entity id is '?'.
4. All *_esd, charge, *_esi, occupancy and such entries are '?'.
5. An additional final field contains the component unit id for each atom.
"""
def __init__(self, handle, unit_ids=True, protect_lists_of_lists=False):
self.writer = Writer(handle)
self.unit_ids = unit_ids
self.protect_lists_of_lists = protect_lists_of_lists
def atom_container(self, structure, protect_lists_of_lists):
atoms = DataCategory('atom_site')
fields = ['group_PDB', 'id', 'type_symbol', 'label_atom_id',
'label_alt_id', 'label_comp_id', 'label_asym_id',
'label_entity_id', 'label_seq_id', 'pdbx_PDB_ins_code',
'Cartn_x', 'Cartn_y', 'Cartn_z', 'occupancy',
'B_iso_or_equiv', 'Cartn_x_esd', 'Cartn_y_esd',
'Cartn_z_esd', 'occupancy_ies', 'B_iso_or_equiv_esd',
'pdbx_formal_charge', 'auth_seq_id', 'auth_comp_id',
'auth_asym_id', 'auth_atom_id', 'pdbx_PDB_model_num']
if self.unit_ids:
fields.append('unit_id')
for field in fields:
atoms.appendAttribute(field)
def key(atom):
return (atom.symmetry, atom.model, atom.chain,
atom.component_number, atom.insertion_code)
all_atoms = it.imap(lambda r: r.atoms(),
structure.residues(polymeric=None))
all_atoms = it.chain.from_iterable(all_atoms)
for index, atom in enumerate(sorted(all_atoms, key=key)):
alt_id = getattr(atom, 'alt_id', '.')
data = [atom.group, index, atom.type, atom.name,
alt_id, atom.component_id, atom.chain,
'?', atom.component_number, atom.insertion_code,
atom.x, atom.y, atom.z, '?',
'?', '?', '?',
'?', '?', '?',
'.', atom.component_number, atom.component_id,
atom.chain, atom.name, atom.model]
# atoms added by infer_hydrogens don't have information to make
# the unit_id and should not be written out anyway
# So if the next line fails, don't write the atom out.
try:
unit_id = atom.component_unit_id()
if self.unit_ids:
data.append(atom.component_unit_id())
atoms.append(data)
except:
continue
if protect_lists_of_lists is True:
# Kludge fix for single atom residues.
# Handles cases where single atom residues are not handled
# correctly as lists of lists, but as simple lists instead,
# which has downstream implications in units.coordinates.
#
# Here, we force a fix, using the line-skipping logic from
# units.coordinates to keep the kludge line out of the output
# data.
dummy = [ 'loop_foo', 'foo', 'foo', 'foo', 'foo', 'foo', 'foo',
'?', 'foo', 'foo', 'foo', 'foo', 'foo', '?',
'?', '?', '?', '?', '?', '?',
'.', 'foo', 'foo', 'foo', 'foo', 'foo']
atoms.append(dummy)
return atoms
def __call__(self, structure):
atoms = self.atom_container(structure, self.protect_lists_of_lists)
container = DataContainer(structure.pdb)
container.append(atoms)
self.writer.writeContainer(container)
