def build_structure(atoms):
sb = StructureBuilder()
sb.init_structure('pdb')
sb.init_seg(' ')
sb.init_model(0)
sb.init_chain('A')
i = 1
for atom in atoms:
sb.init_residue('DUM', ' ', i, ' ')
sb.structure[0]['A'].child_list[i - 1].add(atom)
i += 1
return sb.structure
def set_structure(self, pdb_object):
"""Check what the user is providing and build a structure."""
# The idea here is to build missing upstream components of
# the SMCRA object representation. E.g., if the user provides
# a Residue, build Structure/Model/Chain.
if pdb_object.level == "S":
structure = pdb_object
else: # Not a Structure
sb = StructureBuilder()
sb.init_structure("pdb")
sb.init_seg(" ")
if pdb_object.level == "M":
sb.structure.add(pdb_object.copy())
self.structure = sb.structure
else: # Not a Model
sb.init_model(0)
if pdb_object.level == "C":
sb.structure[0].add(pdb_object.copy())
else: # Not a Chain
chain_id = "A" # default
sb.init_chain(chain_id)
if pdb_object.level == "R": # Residue
# Residue extracted from a larger structure?
if pdb_object.parent is not None:
og_chain_id = pdb_object.parent.id
sb.structure[0][chain_id].id = og_chain_id
chain_id = og_chain_id
sb.structure[0][chain_id].add(pdb_object.copy())
else: # Atom
sb.init_residue("DUM", " ", 1, " ") # Dummy residue
sb.structure[0][chain_id].child_list[0].add(
pdb_object.copy())
# Fix chain identifier if Atom has grandparents.
try:
og_chain_id = pdb_object.parent.parent.id
except AttributeError: # pdb_object.parent == None
pass
else:
sb.structure[0][chain_id].id = og_chain_id
# Return structure
structure = sb.structure
self.structure = structure
def pdb_writer(graph, results, dir_name="templates"):
PDB_CODE = graph.protein_name
structure = graph.structure
path = "%s/%s/" % (dir_name, PDB_CODE)
if len(results) > 0:
if not os.path.exists(path):
os.makedirs(path)
else:
print 'No results'
return
top = min(NUM_OF_RESULTS_TO_SAVE, len(results))
i = 0
for key, value in results[:top]:
# TODO - save as different chains
sb = StructureBuilder()
sb.init_structure(PDB_CODE)
sb.init_model(0)
sb.init_chain('X')
for node_id in key[0]:
for res in graph.nodes[node_id].residues:
sb.init_seg(res.get_segid())
sb.init_residue(res.get_resname(),
res.get_id()[0],
res.get_id()[1],
res.get_id()[2])
for atom in res:
sb.init_atom(atom.get_name(), atom.get_coord(),
atom.get_bfactor(), atom.get_occupancy(),
atom.get_altloc(), atom.get_fullname())
sb.init_chain('Y')
for node_id in key[1]:
for res in graph.nodes[node_id].residues:
sb.init_residue(res.get_resname(),
res.get_id()[0],
res.get_id()[1],
res.get_id()[2])
for atom in res:
sb.init_atom(atom.get_name(), atom.get_coord(),
atom.get_bfactor(), atom.get_occupancy(),
atom.get_altloc(), atom.get_fullname())
filename = path + "interface%d.pdb" % (i)
io = PDBIO()
io.set_structure(sb.get_structure())
io.save(filename)
i += 1
return 1
def residues_to_struct(name_residues_list, structID):
"""
Build a structure from a list of (chain name, residues) - each as
a chain.
"""
builder = StructureBuilder()
builder.init_structure(structID)
builder.init_model(0)
for (name, residues) in name_residues_list:
builder.init_chain(name)
for res in residues:
builder.chain.add(res)
return builder.get_structure()
def coarse_grain(self, cg_type="CA_TRACE"):
"""
Reduces the protein structure complexity to a few (pseudo-)atoms per residue.
Parameters:
- cg_type: CA_TRACE (Ca-only) [Default]
ENCAD_3P (CA, O, SC Beads)
MARTINI (CA, O, SC Beads)
Returns a new structure object.
"""
# Import CG Types
import CG_Models
CG_Library = {
"CA_TRACE": CG_Models.CA_TRACE,
"ENCAD_3P": CG_Models.ENCAD_3P,
"MARTINI": CG_Models.MARTINI
}
CG_Method = CG_Library[cg_type]
# Creates a brand new structure object
from Bio.PDB.StructureBuilder import StructureBuilder
structure_builder = StructureBuilder()
cg_id = "CG_" + self.id
structure_builder.init_structure(cg_id)
structure_builder.init_seg(' ') # Empty SEGID
for model in self:
structure_builder.init_model(model.id)
for chain in model:
structure_builder.init_chain(chain.id)
cur_chain = structure_builder.chain
for residue in chain:
cg_residue = CG_Method(residue)
cur_chain.add(cg_residue)
cg_structure = structure_builder.get_structure()
return cg_structure
class XBGFParser:
def __init__(self, PERMISSIVE=1, structure_builder=None):
if structure_builder != None:
self.structure_builder = structure_builder
else:
self.structure_builder = StructureBuilder()
self.PERMISSIVE = PERMISSIVE
# public interface
def parse(self, id, file):
self.structure_builder.init_structure(id)
if isinstance(file, basestring):
file = open(file)
self.charges = dict()
self.chain_suffix = 0
self._parse(file.readlines())
self.structure = self.structure_builder.get_structure()
return self._process_structure()
# private methods
def _parse(self, lines):
self.structure_builder.init_model(0)
self.structure_builder.init_seg("")
self.current_chain_id = None
self.current_residue_id = None
self.current_resname = None
for i in range(0, len(lines)):
self.line_counter = i + 1
self.structure_builder.set_line_counter(self.line_counter)
line = lines[i]
if line[0:6] == 'ATOM ':
self._update_atom(line)
def _update_chain(self, line):
chain_id = self._extract_chain(line)
if self.current_chain_id != chain_id:
try:
self.structure_builder.init_chain(chain_id)
self.current_chain_id = chain_id
self.current_residue_id = None
self.current_resname = None
except PDBConstructionException, message:
self._handle_PDB_exception(message)
class XBGFParser:
def __init__(self, PERMISSIVE=1, structure_builder=None):
if structure_builder != None:
self.structure_builder = structure_builder
else:
self.structure_builder = StructureBuilder()
self.PERMISSIVE = PERMISSIVE
# public interface
def parse(self, id, file):
self.structure_builder.init_structure(id)
if isinstance(file, basestring):
file=open(file)
self.charges = dict()
self.chain_suffix = 0
self._parse(file.readlines())
self.structure = self.structure_builder.get_structure()
return self._process_structure()
# private methods
def _parse(self, lines):
self.structure_builder.init_model(0)
self.structure_builder.init_seg("")
self.current_chain_id = None
self.current_residue_id = None
self.current_resname = None
for i in range(0, len(lines)):
self.line_counter = i + 1
self.structure_builder.set_line_counter(self.line_counter)
line = lines[i]
if line[0:6] == 'ATOM ':
self._update_atom(line)
def _update_chain(self, line):
chain_id = self._extract_chain(line)
if self.current_chain_id != chain_id:
try:
self.structure_builder.init_chain(chain_id)
self.current_chain_id = chain_id
self.current_residue_id = None
self.current_resname = None
except PDBConstructionException, message:
self._handle_PDB_exception(message)
def write_helical_axes(self, filename):
"""Writes helical axes in PDB format."""
sb = StructureBuilder()
sb.init_structure('')
sb.init_model('')
for cpos, chain in enumerate(self.chains):
sb.init_chain(str(cpos))
sb.init_seg('')
for pos, i in enumerate(chain.res[1:-1]):
sb.init_residue('ALA', ' ', pos, ' ')
sb.init_atom('CA', i.O._ar, 0, 0, " ", ' CA ', 1)
io = PDBIO()
io.set_structure(sb.structure)
io.save(filename)
def set_structure(self, pdb_object):
"""Check what the user is providing and build a structure."""
if pdb_object.level == "S":
structure = pdb_object
else:
sb = StructureBuilder()
sb.init_structure("pdb")
sb.init_seg(" ")
# Build parts as necessary
if pdb_object.level == "M":
sb.structure.add(pdb_object.copy())
self.structure = sb.structure
else:
sb.init_model(0)
if pdb_object.level == "C":
sb.structure[0].add(pdb_object.copy())
else:
sb.init_chain("A")
if pdb_object.level == "R":
try:
parent_id = pdb_object.parent.id
sb.structure[0]["A"].id = parent_id
except Exception:
pass
sb.structure[0]["A"].add(pdb_object.copy())
else:
# Atom
sb.init_residue("DUM", " ", 1, " ")
try:
parent_id = pdb_object.parent.parent.id
sb.structure[0]["A"].id = parent_id
except Exception:
pass
sb.structure[0]["A"].child_list[0].add(
pdb_object.copy())
# Return structure
structure = sb.structure
self.structure = structure
def set_structure(self, pdb_object):
"""Check what object the user is providing and build a structure."""
# This is duplicated from the PDBIO class
if pdb_object.level == "S":
structure = pdb_object
else:
sb = StructureBuilder()
sb.init_structure('pdb')
sb.init_seg(' ')
# Build parts as necessary
if pdb_object.level == "M":
sb.structure.add(pdb_object)
self.structure = sb.structure
else:
sb.init_model(0)
if pdb_object.level == "C":
sb.structure[0].add(pdb_object)
else:
sb.init_chain('A')
if pdb_object.level == "R":
try:
parent_id = pdb_object.parent.id
sb.structure[0]['A'].id = parent_id
except ValueError:
pass
sb.structure[0]['A'].add(pdb_object)
else:
# Atom
sb.init_residue('DUM', ' ', 1, ' ')
try:
parent_id = pdb_object.parent.parent.id
sb.structure[0]['A'].id = parent_id
except ValueError:
pass
sb.structure[0]['A'].child_list[0].add(pdb_object)
# Return structure
structure = sb.structure
self.structure = structure
def set_structure(self, pdb_object):
"""Check what object the user is providing and build a structure."""
# This is duplicated from the PDBIO class
if pdb_object.level == "S":
structure = pdb_object
else:
sb = StructureBuilder()
sb.init_structure('pdb')
sb.init_seg(' ')
# Build parts as necessary
if pdb_object.level == "M":
sb.structure.add(pdb_object)
self.structure = sb.structure
else:
sb.init_model(0)
if pdb_object.level == "C":
sb.structure[0].add(pdb_object)
else:
sb.init_chain('A')
if pdb_object.level == "R":
try:
parent_id = pdb_object.parent.id
sb.structure[0]['A'].id = parent_id
except ValueError:
pass
sb.structure[0]['A'].add(pdb_object)
else:
# Atom
sb.init_residue('DUM', ' ', 1, ' ')
try:
parent_id = pdb_object.parent.parent.id
sb.structure[0]['A'].id = parent_id
except ValueError:
pass
sb.structure[0]['A'].child_list[0].add(pdb_object)
# Return structure
structure = sb.structure
self.structure = structure
def set_structure(self, pdb_object):
"""Check what the user is providing and build a structure."""
if pdb_object.level == "S":
structure = pdb_object
else:
sb = StructureBuilder()
sb.init_structure('pdb')
sb.init_seg(' ')
# Build parts as necessary
if pdb_object.level == "M":
sb.structure.add(pdb_object.copy())
self.structure = sb.structure
else:
sb.init_model(0)
if pdb_object.level == "C":
sb.structure[0].add(pdb_object.copy())
else:
sb.init_chain('A')
if pdb_object.level == "R":
try:
parent_id = pdb_object.parent.id
sb.structure[0]['A'].id = parent_id
except Exception:
pass
sb.structure[0]['A'].add(pdb_object.copy())
else:
# Atom
sb.init_residue('DUM', ' ', 1, ' ')
try:
parent_id = pdb_object.parent.parent.id
sb.structure[0]['A'].id = parent_id
except Exception:
pass
sb.structure[0]['A'].child_list[0].add(pdb_object.copy())
# Return structure
structure = sb.structure
self.structure = structure
def set_structure(self, pdb_object):
# Check what the user is providing and build a structure appropriately
if pdb_object.level == "S":
structure = pdb_object
else:
sb = StructureBuilder()
sb.init_structure('pdb')
sb.init_seg(' ')
# Build parts as necessary
if pdb_object.level == "M":
sb.structure.add(pdb_object)
self.structure = sb.structure
else:
sb.init_model(0)
if pdb_object.level == "C":
sb.structure[0].add(pdb_object)
else:
sb.init_chain('A')
if pdb_object.level == "R":
try:
parent_id = pdb_object.parent.id
sb.structure[0]['A'].id = parent_id
except Exception:
pass
sb.structure[0]['A'].add(pdb_object)
else:
# Atom
sb.init_residue('DUM', ' ', 1, ' ')
try:
parent_id = pdb_object.parent.parent.id
sb.structure[0]['A'].id = parent_id
except Exception:
pass
sb.structure[0]['A'].child_list[0].add(pdb_object)
# Return structure
structure = sb.structure
self.structure = structure
def set_structure(self, pdb_object):
# Check what the user is providing and build a structure appropriately
if pdb_object.level == "S":
structure = pdb_object
else:
sb = StructureBuilder()
sb.init_structure("pdb")
sb.init_seg(" ")
# Build parts as necessary
if pdb_object.level == "M":
sb.structure.add(pdb_object)
self.structure = sb.structure
else:
sb.init_model(0)
if pdb_object.level == "C":
sb.structure[0].add(pdb_object)
else:
sb.init_chain("A")
if pdb_object.level == "R":
try:
parent_id = pdb_object.parent.id
sb.structure[0]["A"].id = parent_id
except Exception:
pass
sb.structure[0]["A"].add(pdb_object)
else:
# Atom
sb.init_residue("DUM", " ", 1, " ")
try:
parent_id = pdb_object.parent.parent.id
sb.structure[0]["A"].id = parent_id
except Exception:
pass
sb.structure[0]["A"].child_list[0].add(pdb_object)
# Return structure
structure = sb.structure
self.structure = structure
class StructureDecoder(object):
"""Class to pass the data from mmtf-python into a Biopython data structure."""
def __init__(self):
"""Initialize the class."""
self.this_type = ""
def init_structure(self, total_num_bonds, total_num_atoms,
total_num_groups, total_num_chains, total_num_models,
structure_id):
"""Initialize the structure object.
:param total_num_bonds: the number of bonds in the structure
:param total_num_atoms: the number of atoms in the structure
:param total_num_groups: the number of groups in the structure
:param total_num_chains: the number of chains in the structure
:param total_num_models: the number of models in the structure
:param structure_id: the id of the structure (e.g. PDB id)
"""
self.structure_bulder = StructureBuilder()
self.structure_bulder.init_structure(structure_id=structure_id)
self.chain_index_to_type_map = {}
self.chain_index_to_seq_map = {}
self.chain_index_to_description_map = {}
self.chain_counter = 0
def set_atom_info(self, atom_name, serial_number, alternative_location_id,
x, y, z, occupancy, temperature_factor, element, charge):
"""Create an atom object an set the information.
:param atom_name: the atom name, e.g. CA for this atom
:param serial_number: the serial id of the atom (e.g. 1)
:param alternative_location_id: the alternative location id for the atom, if present
:param x: the x coordiante of the atom
:param y: the y coordinate of the atom
:param z: the z coordinate of the atom
:param occupancy: the occupancy of the atom
:param temperature_factor: the temperature factor of the atom
:param element: the element of the atom, e.g. C for carbon. According to IUPAC. Calcium is Ca
:param charge: the formal atomic charge of the atom
"""
# MMTF uses "\x00" (the NUL character) to indicate to altloc, so convert
# that to the space required by StructureBuilder
if alternative_location_id == "\x00":
alternative_location_id = " "
# Atom_name is in twice - the full_name is with spaces
self.structure_bulder.init_atom(str(atom_name), [x, y, z],
temperature_factor, occupancy,
alternative_location_id, str(atom_name),
serial_number=serial_number,
element=str(element).upper())
def set_chain_info(self, chain_id, chain_name, num_groups):
"""Set the chain information.
:param chain_id: the asym chain id from mmCIF
:param chain_name: the auth chain id from mmCIF
:param num_groups: the number of groups this chain has
"""
# A Bradley - chose to use chain_name (auth_id) as it complies
# with current Biopython. Chain_id might be better.
self.structure_bulder.init_chain(chain_id=chain_name)
if self.chain_index_to_type_map[self.chain_counter] == "polymer":
self.this_type = " "
elif self.chain_index_to_type_map[self.chain_counter] == "non-polymer":
self.this_type = "H"
elif self.chain_index_to_type_map[self.chain_counter] == "water":
self.this_type = "W"
self.chain_counter += 1
def set_entity_info(self, chain_indices, sequence, description, entity_type):
"""Set the entity level information for the structure.
:param chain_indices: the indices of the chains for this entity
:param sequence: the one letter code sequence for this entity
:param description: the description for this entity
:param entity_type: the entity type (polymer,non-polymer,water)
"""
for chain_ind in chain_indices:
self.chain_index_to_type_map[chain_ind] = entity_type
self.chain_index_to_seq_map[chain_ind] = sequence
self.chain_index_to_description_map[chain_ind] = description
def set_group_info(self, group_name, group_number, insertion_code,
group_type, atom_count, bond_count, single_letter_code,
sequence_index, secondary_structure_type):
"""Set the information for a group
:param group_name: the name of this group, e.g. LYS
:param group_number: the residue number of this group
:param insertion_code: the insertion code for this group
:param group_type: a string indicating the type of group (as found in the chemcomp dictionary.
Empty string if none available.
:param atom_count: the number of atoms in the group
:param bond_count: the number of unique bonds in the group
:param single_letter_code: the single letter code of the group
:param sequence_index: the index of this group in the sequence defined by the entity
:param secondary_structure_type: the type of secondary structure used
(types are according to DSSP and number to type mappings are defined in the specification)
"""
# MMTF uses a NUL character to indicate a blank insertion code, but
# StructureBuilder expects a space instead.
if insertion_code == "\x00":
insertion_code = " "
self.structure_bulder.init_seg(' ')
self.structure_bulder.init_residue(group_name, self.this_type,
group_number, insertion_code)
def set_model_info(self, model_id, chain_count):
"""Set the information for a model.
:param model_id: the index for the model
:param chain_count: the number of chains in the model
"""
self.structure_bulder.init_model(model_id)
def set_xtal_info(self, space_group, unit_cell):
"""Set the crystallographic information for the structure.
:param space_group: the space group name, e.g. "P 21 21 21"
:param unit_cell: an array of length 6 with the unit cell parameters in order: a, b, c, alpha, beta, gamma
"""
self.structure_bulder.set_symmetry(space_group, unit_cell)
def set_header_info(self, r_free, r_work, resolution, title,
deposition_date, release_date, experimnetal_methods):
"""Sets the header information.
:param r_free: the measured R-Free for the structure
:param r_work: the measure R-Work for the structure
:param resolution: the resolution of the structure
:param title: the title of the structure
:param deposition_date: the deposition date of the structure
:param release_date: the release date of the structure
:param experimnetal_methods: the list of experimental methods in the structure
"""
pass
def set_bio_assembly_trans(self, bio_assembly_index, input_chain_indices,
input_transform):
"""Set the Bioassembly transformation information. A single bioassembly can have multiple transforms.
:param bio_assembly_index: the integer index of the bioassembly
:param input_chain_indices: the list of integer indices for the chains of this bioassembly
:param input_transform: the list of doubles for the transform of this bioassmbly transform.
"""
pass
def finalize_structure(self):
"""Any functions needed to cleanup the structure."""
pass
def set_group_bond(self, atom_index_one, atom_index_two, bond_order):
"""Add bonds within a group.
:param atom_index_one: the integer atom index (in the group) of the first partner in the bond
:param atom_index_two: the integer atom index (in the group) of the second partner in the bond
:param bond_order: the integer bond order
"""
pass
def set_inter_group_bond(self, atom_index_one, atom_index_two, bond_order):
"""Add bonds between groups.
:param atom_index_one: the integer atom index (in the structure) of the first partner in the bond
:param atom_index_two: the integer atom index (in the structure) of the second partner in the bond
:param bond_order: the bond order
"""
pass
class StructureDecoder(object):
"""Class to pass the data from mmtf-python into a Biopython data structure."""
def __init__(self):
"""Initialize the class."""
self.this_type = ""
def init_structure(self, total_num_bonds, total_num_atoms,
total_num_groups, total_num_chains, total_num_models,
structure_id):
"""Initialize the structure object.
:param total_num_bonds: the number of bonds in the structure
:param total_num_atoms: the number of atoms in the structure
:param total_num_groups: the number of groups in the structure
:param total_num_chains: the number of chains in the structure
:param total_num_models: the number of models in the structure
:param structure_id: the id of the structure (e.g. PDB id)
"""
self.structure_bulder = StructureBuilder()
self.structure_bulder.init_structure(structure_id=structure_id)
self.chain_index_to_type_map = {}
self.chain_index_to_seq_map = {}
self.chain_index_to_description_map = {}
self.chain_counter = 0
def set_atom_info(self, atom_name, serial_number, alternative_location_id,
x, y, z, occupancy, temperature_factor, element, charge):
"""Create an atom object an set the information.
:param atom_name: the atom name, e.g. CA for this atom
:param serial_number: the serial id of the atom (e.g. 1)
:param alternative_location_id: the alternative location id for the atom, if present
:param x: the x coordiante of the atom
:param y: the y coordinate of the atom
:param z: the z coordinate of the atom
:param occupancy: the occupancy of the atom
:param temperature_factor: the temperature factor of the atom
:param element: the element of the atom, e.g. C for carbon. According to IUPAC. Calcium is Ca
:param charge: the formal atomic charge of the atom
"""
# MMTF uses "\x00" (the NUL character) to indicate to altloc, so convert
# that to the space required by StructureBuilder
if alternative_location_id == "\x00":
alternative_location_id = " "
# Atom_name is in twice - the full_name is with spaces
self.structure_bulder.init_atom(str(atom_name),
numpy.array((x, y, z), "f"),
temperature_factor,
occupancy,
alternative_location_id,
str(atom_name),
serial_number=serial_number,
element=str(element).upper())
def set_chain_info(self, chain_id, chain_name, num_groups):
"""Set the chain information.
:param chain_id: the asym chain id from mmCIF
:param chain_name: the auth chain id from mmCIF
:param num_groups: the number of groups this chain has
"""
# A Bradley - chose to use chain_name (auth_id) as it complies
# with current Biopython. Chain_id might be better.
self.structure_bulder.init_chain(chain_id=chain_name)
if self.chain_index_to_type_map[self.chain_counter] == "polymer":
self.this_type = " "
elif self.chain_index_to_type_map[self.chain_counter] == "non-polymer":
self.this_type = "H"
elif self.chain_index_to_type_map[self.chain_counter] == "water":
self.this_type = "W"
self.chain_counter += 1
def set_entity_info(self, chain_indices, sequence, description,
entity_type):
"""Set the entity level information for the structure.
:param chain_indices: the indices of the chains for this entity
:param sequence: the one letter code sequence for this entity
:param description: the description for this entity
:param entity_type: the entity type (polymer,non-polymer,water)
"""
for chain_ind in chain_indices:
self.chain_index_to_type_map[chain_ind] = entity_type
self.chain_index_to_seq_map[chain_ind] = sequence
self.chain_index_to_description_map[chain_ind] = description
def set_group_info(self, group_name, group_number, insertion_code,
group_type, atom_count, bond_count, single_letter_code,
sequence_index, secondary_structure_type):
"""Set the information for a group.
:param group_name: the name of this group, e.g. LYS
:param group_number: the residue number of this group
:param insertion_code: the insertion code for this group
:param group_type: a string indicating the type of group (as found in the chemcomp dictionary.
Empty string if none available.
:param atom_count: the number of atoms in the group
:param bond_count: the number of unique bonds in the group
:param single_letter_code: the single letter code of the group
:param sequence_index: the index of this group in the sequence defined by the entity
:param secondary_structure_type: the type of secondary structure used
(types are according to DSSP and number to type mappings are defined in the specification)
"""
# MMTF uses a NUL character to indicate a blank insertion code, but
# StructureBuilder expects a space instead.
if insertion_code == "\x00":
insertion_code = " "
self.structure_bulder.init_seg(' ')
self.structure_bulder.init_residue(group_name, self.this_type,
group_number, insertion_code)
def set_model_info(self, model_id, chain_count):
"""Set the information for a model.
:param model_id: the index for the model
:param chain_count: the number of chains in the model
"""
self.structure_bulder.init_model(model_id)
def set_xtal_info(self, space_group, unit_cell):
"""Set the crystallographic information for the structure.
:param space_group: the space group name, e.g. "P 21 21 21"
:param unit_cell: an array of length 6 with the unit cell parameters in order: a, b, c, alpha, beta, gamma
"""
self.structure_bulder.set_symmetry(space_group, unit_cell)
def set_header_info(self, r_free, r_work, resolution, title,
deposition_date, release_date, experimnetal_methods):
"""Set the header information.
:param r_free: the measured R-Free for the structure
:param r_work: the measure R-Work for the structure
:param resolution: the resolution of the structure
:param title: the title of the structure
:param deposition_date: the deposition date of the structure
:param release_date: the release date of the structure
:param experimnetal_methods: the list of experimental methods in the structure
"""
pass
def set_bio_assembly_trans(self, bio_assembly_index, input_chain_indices,
input_transform):
"""Set the Bioassembly transformation information. A single bioassembly can have multiple transforms.
:param bio_assembly_index: the integer index of the bioassembly
:param input_chain_indices: the list of integer indices for the chains of this bioassembly
:param input_transform: the list of doubles for the transform of this bioassmbly transform.
"""
pass
def finalize_structure(self):
"""Any functions needed to cleanup the structure."""
pass
def set_group_bond(self, atom_index_one, atom_index_two, bond_order):
"""Add bonds within a group.
:param atom_index_one: the integer atom index (in the group) of the first partner in the bond
:param atom_index_two: the integer atom index (in the group) of the second partner in the bond
:param bond_order: the integer bond order
"""
pass
def set_inter_group_bond(self, atom_index_one, atom_index_two, bond_order):
"""Add bonds between groups.
:param atom_index_one: the integer atom index (in the structure) of the first partner in the bond
:param atom_index_two: the integer atom index (in the structure) of the second partner in the bond
:param bond_order: the bond order
"""
pass
io = PDBIO()
# Parse PDB and run DSSP
pdbf_path = os.path.abspath(sys.argv[1])
aa_model = P.get_structure('aa_model', pdbf_path)
# Convert to MARTINI types
# Assign by chain and build the cg structure already
structure_builder = StructureBuilder()
structure_builder.init_structure("cg_model")
structure_builder.init_seg(' ') # Empty SEGID
nbeads = 0
for model in aa_model:
structure_builder.init_model(model.id)
dssp = DSSP(model, pdbf_path)
for chain in model:
structure_builder.init_chain(chain.id)
# Get SS information and translate it to MARTINI
dssp_ss = []
for residue in chain:
if residue.id[0] != ' ':
continue
if "SS_DSSP" in residue.xtra:
dssp_ss.append(residue.xtra["SS_DSSP"])
else:
dssp_ss.append('-')
def pdb_extract(structure, **kwargs):
# model to extract from pdb
extract_model = None if not 'model' in kwargs else kwargs['model']
new_model_id = -1 if not 'new_model' in kwargs else kwargs['new_model']
extract_chain = None if not 'chain' in kwargs else kwargs['chain']
first_res = None if not 'first_res' in kwargs else kwargs['first_res']
last_res = None if not 'last_res' in kwargs else kwargs['last_res']
new_first_res = None if not 'new_first_res' in kwargs else kwargs[
'new_first_res']
gap_count = 0 if not 'gap_count' in kwargs else kwargs['gap_count']
water_id = None if not 'water' in kwargs else kwargs['water']
model_rebumber_flag = bool((extract_model is not None)
or new_model_id >= 0)
res_renumber_flag = bool(first_res or last_res or new_first_res
or gap_count)
structure_builder = StructureBuilder()
structure_builder.init_structure('pdb_extract')
structure_builder.set_line_counter(0)
line_counter = 0
start_resseq_by_default = 1 if not new_first_res else new_first_res
for model in structure:
if model_rebumber_flag and \
( extract_model is not None ) and model.get_id() != extract_model:
continue
if model_rebumber_flag and new_model_id >= 0:
this_model_id = new_model_id
new_model_id += 1
else:
this_model_id = model.get_id()
structure_builder.init_model(this_model_id, this_model_id)
for chain in model:
if extract_chain and chain.get_id() != extract_chain:
continue
structure_builder.init_seg(' ')
structure_builder.init_chain(chain.get_id())
resdict = {}
if res_renumber_flag:
# first_res = res_range_tuple[0]
# last_res = res_range_tuple[1]
resdict['before'] = select_residues_from_chain(
chain, first_res=first_res, gap_count=gap_count)
resdict['hit'] = select_residues_from_chain(
chain, first_res=first_res, last_res=last_res)
resdict['after'] = select_residues_from_chain(
chain, last_res=last_res, gap_count=gap_count)
else:
resdict['before'] = []
resdict['hit'] = chain.get_list()
resdict['after'] = []
new_resseq = start_resseq_by_default - len(resdict['before'])
resdict['water'] = chain_water_id(chain, water_id)
for key in ['before', 'hit', 'after', 'water']:
for residue in resdict[key]:
if res_renumber_flag:
new_resid = ' ', new_resseq, ' '
else:
new_resid = residue.get_id()
structure_builder.init_residue(residue.get_resname(),
*new_resid)
residue_atoms = None
if key == 'before':
residue_atoms = [atom for atom in residue if \
(atom.get_name() == 'C' or atom.get_name() == 'O')]
elif key == 'hit' or key == 'water':
residue_atoms = residue.get_list()
elif key == 'after':
residue_atoms = [atom for atom in residue if \
(atom.get_name() == 'N' or atom.get_name() == 'HN')]
for atom in residue_atoms:
structure_builder.init_atom(atom.get_name(),
atom.get_coord(),
atom.get_bfactor(),
atom.get_occupancy(),
atom.get_altloc(),
atom.get_fullname())
structure_builder.set_line_counter(line_counter)
line_counter += 1
new_resseq += 1
if key == 'water' and gap_count and len(
resdict['after']) != gap_count:
new_resseq += gap_count - len(resdict['after'])
out_structure = structure_builder.get_structure()
return out_structure