def __call__(self, t):
structure = t[1]
structure = structure.set_alt_loc_list()
# print(structure.group_type_list)
bioassemblies = structure.bio_assembly
numBioassembly = len(bioassemblies)
resList = list()
for i in range(numBioassembly):
bioAssembly = MMTFEncoder()
structureId = structure.structure_id + '-BioAssembly' + \
bioassemblies[i][b'name'].decode('utf-8')
totAtoms = 0
totBonds = 0
totGroups = 0
totChains = 0
totModels = structure.num_models
numTrans = len(bioassemblies[i][b'transformList'])
bioChainList = [[]] * numTrans
transMatrix = [[]] * numTrans
for ii in range(numTrans):
bioChainList[ii] = bioassemblies[i][b'transformList'][ii][
b'chainIndexList']
transMatrix[ii] = bioassemblies[i][b'transformList'][ii][
b'matrix']
for j in range(totModels):
totChains = totChains + len(bioChainList[ii])
groupCounter = 0
for k in range(structure.chains_per_model[j]):
adding = False
for currChain in bioChainList[ii]:
if currChain == k:
adding = True
if adding:
totGroups = totGroups + \
structure.groups_per_chain[k]
for h in range(structure.groups_per_chain[k]):
if adding:
groupIndex = structure.group_type_list[
groupCounter]
totAtoms = totAtoms + \
len(structure.group_list[groupIndex]
['atomNameList'])
totBonds = totBonds + \
len(structure.group_list[groupIndex]
['bondOrderList'])
groupCounter = groupCounter + 1
# Set header
bioAssembly.init_structure(totBonds, totAtoms, totGroups,
totChains, totModels, structureId)
decoder_utils.add_xtalographic_info(structure, bioAssembly)
decoder_utils.add_header_info(structure, bioAssembly)
modelIndex = 0
chainIndex = 0
groupIndex = 0
atomIndex = 0
chainCounter = 0
for ii in range(totModels):
numChainsPerModel = structure.chains_per_model[
modelIndex] * numTrans
bioAssembly.set_model_info(modelIndex, numChainsPerModel)
chainToEntityIndex = self._getChainToEntityIndex(structure)
for j in range(structure.chains_per_model[modelIndex]):
currGroupIndex = groupIndex
currAtomIndex = atomIndex
for k in range(numTrans):
currChainList = bioChainList[k]
currMatrix = transMatrix[k]
addThisChain = False
for currChain in currChainList:
if currChain == j:
addThisChain = True
groupIndex = currGroupIndex
atomIndex = currAtomIndex
xCoords = structure.x_coord_list
yCoords = structure.y_coord_list
zCoords = structure.z_coord_list
m = reshape(matrix(currMatrix), (4, 4))
if addThisChain:
entityToChainIndex = chainToEntityIndex[chainIndex]
bioAssembly.set_entity_info(
[chainCounter],
structure.entity_list[entityToChainIndex]
['sequence'],
structure.entity_list[entityToChainIndex]
['description'],
structure.entity_list[entityToChainIndex]
['type'])
bioAssembly.set_chain_info(
structure.chain_id_list[chainIndex],
structure.chain_name_list[chainIndex],
structure.groups_per_chain[chainIndex])
chainCounter = chainCounter + 1
for jj in range(
structure.groups_per_chain[chainIndex]):
# print(structure.group_type_list)
currgroup = structure.group_type_list[groupIndex]
# if ii == 0 and j == 0 and jj < 10:
# print(currgroup)
if addThisChain:
bioAssembly.set_group_info(
structure.group_list[currgroup]
['groupName'],
structure.group_id_list[groupIndex],
structure.ins_code_list[groupIndex],
structure.group_list[currgroup]
['chemCompType'],
len(structure.group_list[currgroup]
['atomNameList']),
len(structure.group_list[currgroup]
['bondOrderList']),
structure.group_list[currgroup]
['singleLetterCode'],
structure.sequence_index_list[groupIndex],
structure.sec_struct_list[groupIndex])
for kk in range(
len(structure.group_list[currgroup]
['atomNameList'])):
if addThisChain:
p1 = array([
xCoords[atomIndex], yCoords[atomIndex],
zCoords[atomIndex], 1
])
p2 = matmul(p1, m)
bioAssembly.set_atom_info(
structure.group_list[currgroup]
['atomNameList'][kk],
structure.atom_id_list[atomIndex],
structure.alt_loc_list[atomIndex],
p2.item(0),
p2.item(1),
p2.item(2),
structure.occupancy_list[atomIndex],
structure.b_factor_list[atomIndex],
structure.group_list[currgroup]
['elementList'][kk],
structure.group_list[currgroup]
['formalChargeList'][kk],
)
atomIndex = atomIndex + 1
# bond not implemented
if addThisChain:
for l in range(
len(structure.group_list[currgroup]
['bondOrderList'])):
bondIndOne = structure.group_list[
currgroup]['bondAtomList'][l * 2]
bondIndTwo = structure.group_list[
currgroup]['bondAtomList'][l * 2 + 1]
bondOrder = structure.group_list[
currgroup]['bondOrderList'][l]
#newChain.set_group_bond(bondIndOne, bondIndTwo, bondOrder)
bioAssembly.current_group.bond_atom_list += [
bondIndOne, bondIndTwo
]
bioAssembly.current_group.bond_order_list.append(
bondOrder)
groupIndex = groupIndex + 1
chainIndex = chainIndex + 1
modelIndex = modelIndex + 1
# print(type(currMatrix))
bioAssembly.finalize_structure()
resList.append((structureId, bioAssembly))
return resList
def __call__(self, t):
structure = t[1]
# Precalculate indices
numChains = structure.chains_per_model[0]
chainToEntityIndex = self._get_chain_to_entity_index(structure)
atomsPerChain, bondsPerChain = self._get_num_atoms_and_bonds(structure)
chainList = list()
seqSet = set()
groupCounter = 0
atomCounter = 0
for i in range(numChains):
polymerChain = MMTFEncoder()
entityToChainIndex = chainToEntityIndex[i]
chain_type = structure.entity_list[entityToChainIndex]['type']
polymer = chain_type == "polymer"
polymerAtomCount = 0
atomMap = {}
structureId = ''
if polymer:
# To avoid of information loss, add chainName/IDs and entity id
# This required by some queries
structureId = structure.structure_id + '.' +\
structure.chain_name_list[i] + '.' +\
structure.chain_id_list[i] + '.' +\
str(entityToChainIndex + 1)
# Set header
polymerChain.init_structure(bondsPerChain[i], atomsPerChain[i],
structure.groups_per_chain[i], 1,
1, structureId)
decoder_utils.add_xtalographic_info(structure, polymerChain)
decoder_utils.add_header_info(structure, polymerChain)
# Set model info (only one model: 0)
polymerChain.set_model_info(0, 1)
# Set entity and chain info
polymerChain.set_entity_info(
[0], structure.entity_list[entityToChainIndex]['sequence'],
structure.entity_list[entityToChainIndex]['description'],
structure.entity_list[entityToChainIndex]['type'])
polymerChain.set_chain_info(structure.chain_id_list[i],
structure.chain_name_list[i],
structure.groups_per_chain[i])
for j in range(structure.groups_per_chain[i]):
groupIndex = structure.group_type_list[groupCounter]
if polymer:
# Set group info
polymerChain.set_group_info(
structure.group_list[groupIndex]['groupName'],
structure.group_id_list[groupCounter],
structure.ins_code_list[groupCounter],
structure.group_list[groupIndex]['chemCompType'],
len(structure.group_list[groupIndex]['atomNameList']),
len(structure.group_list[groupIndex]['bondOrderList']),
structure.group_list[groupIndex]['singleLetterCode'],
structure.sequence_index_list[groupCounter],
structure.sec_struct_list[groupCounter])
for k in range(
len(structure.group_list[groupIndex]['atomNameList'])):
if polymer:
atomMap[atomCounter] = polymerAtomCount
polymerAtomCount += 1
polymerChain.set_atom_info(
structure.group_list[groupIndex]['atomNameList']
[k],
structure.atom_id_list[atomCounter],
structure.alt_loc_list[atomCounter],
structure.x_coord_list[atomCounter],
structure.y_coord_list[atomCounter],
structure.z_coord_list[atomCounter],
structure.occupancy_list[atomCounter],
structure.b_factor_list[atomCounter],
structure.group_list[groupIndex]['elementList'][k],
structure.group_list[groupIndex]
['formalChargeList'][k],
)
atomCounter += 1
if polymer:
# Add intra-group bond info
for l in range(
len(structure.group_list[groupIndex]
['bondOrderList'])):
bondIndOne = structure.group_list[groupIndex][
'bondAtomList'][l * 2]
bondIndTwo = structure.group_list[groupIndex][
'bondAtomList'][l * 2 + 1]
bondOrder = structure.group_list[groupIndex][
'bondOrderList'][l]
polymerChain.set_group_bond(bondIndOne, bondIndTwo,
bondOrder)
groupCounter += 1
if polymer:
# TODO skipping adding inter group bond info for now
polymerChain.finalize_structure()
chId = structure.chain_name_list[i]
if self.useChainIdInsteadOfChainName:
chId = structure.chain_id_list[i]
if self.excludeDuplicates:
if chainToEntityIndex[i] in seqSet:
continue
seqSet.add(chainToEntityIndex[i])
chainList.append(
(structure.structure_id + "." + chId, polymerChain))
return chainList
def _combine_chains(self, s1, s2):
if not s1.alt_loc_set:
s1 = s1.set_alt_loc_list()
if not s2.alt_loc_set:
s2 = s2.set_alt_loc_list()
groupCounter = 0
atomCounter = 0
structureId = s1.structure_id + "_append_" + s2.structure_id
combinedStructure = MMTFEncoder()
# Set header
combinedStructure.init_structure(s1.num_bonds + s2.num_bonds,
s1.num_atoms + s2.num_atoms,
s1.num_groups + s2.num_groups, 2, 1,
structureId)
decoder_utils.add_xtalographic_info(s1, combinedStructure)
decoder_utils.add_header_info(s1, combinedStructure)
# Set model info (only one model: 0)
combinedStructure.set_model_info(0, 2)
chainToEntityIndex = self._get_chain_to_entity_index(s1)[0]
# Set entity and chain info
combinedStructure.set_entity_info(
[0], s1.entity_list[chainToEntityIndex]['sequence'],
s1.entity_list[chainToEntityIndex]['description'],
s1.entity_list[chainToEntityIndex]['type'])
combinedStructure.set_chain_info(s1.chain_id_list[0],
s1.chain_name_list[0],
s1.groups_per_chain[0])
for i in range(s1.groups_per_chain[0]):
groupIndex = s1.group_type_list[groupCounter]
# Set group info
combinedStructure.set_group_info(
s1.group_list[groupIndex]['groupName'],
s1.group_id_list[groupCounter], s1.ins_code_list[groupCounter],
s1.group_list[groupIndex]['chemCompType'],
len(s1.group_list[groupIndex]['atomNameList']),
len(s1.group_list[groupIndex]['bondOrderList']),
s1.group_list[groupIndex]['singleLetterCode'],
s1.sequence_index_list[groupCounter],
s1.sec_struct_list[groupCounter])
for j in range(len(s1.group_list[groupIndex]['atomNameList'])):
combinedStructure.set_atom_info(
s1.group_list[groupIndex]['atomNameList'][j],
s1.atom_id_list[atomCounter], s1.alt_loc_list[atomCounter],
s1.x_coord_list[atomCounter], s1.y_coord_list[atomCounter],
s1.z_coord_list[atomCounter],
s1.occupancy_list[atomCounter],
s1.b_factor_list[atomCounter],
s1.group_list[groupIndex]['elementList'][j],
s1.group_list[groupIndex]['formalChargeList'][j])
atomCounter += 1
# TODO not sure if we should add bonds like this
# TODO bondAtomList == getGroupBondIndices?
for k in range(len(s1.group_list[groupIndex]["bondOrderList"])):
bondIndOne = s1.group_list[groupIndex]["bondAtomList"][k * 2]
bondIndTwo = s1.group_list[groupIndex]["bondAtomList"][k * 2 +
1]
bondOrder = s1.group_list[groupIndex]["bondOrderList"][k]
combinedStructure.set_group_bond(bondIndOne, bondIndTwo,
bondOrder)
groupCounter += 1
# Set entity and chain info for s2
chainToEntityIndex = self._get_chain_to_entity_index(s2)[0]
combinedStructure.set_entity_info(
[1], s2.entity_list[chainToEntityIndex]['sequence'],
s2.entity_list[chainToEntityIndex]['description'],
s2.entity_list[chainToEntityIndex]['type'])
combinedStructure.set_chain_info(s2.chain_id_list[0],
s2.chain_name_list[0],
s2.groups_per_chain[0])
groupCounter = 0
atomCounter = 0
for i in range(s2.groups_per_chain[0]):
groupIndex = s2.group_type_list[groupCounter]
# Set group info
combinedStructure.set_group_info(
s2.group_list[groupIndex]['groupName'],
s2.group_id_list[groupCounter], s2.ins_code_list[groupCounter],
s2.group_list[groupIndex]['chemCompType'],
len(s2.group_list[groupIndex]['atomNameList']),
len(s2.group_list[groupIndex]['bondOrderList']),
s2.group_list[groupIndex]['singleLetterCode'],
s2.sequence_index_list[groupCounter],
s2.sec_struct_list[groupCounter])
for j in range(len(s2.group_list[groupIndex]['atomNameList'])):
combinedStructure.set_atom_info(
s2.group_list[groupIndex]['atomNameList'][j],
s2.atom_id_list[atomCounter], s2.alt_loc_list[atomCounter],
s2.x_coord_list[atomCounter], s2.y_coord_list[atomCounter],
s2.z_coord_list[atomCounter],
s2.occupancy_list[atomCounter],
s2.b_factor_list[atomCounter],
s2.group_list[groupIndex]['elementList'][j],
s2.group_list[groupIndex]['formalChargeList'][j])
atomCounter += 1
# TODO not sure if we should add bonds like this
# TODO bondAtomList == getGroupBondIndices?
for k in range(len(s2.group_list[groupIndex]["bondOrderList"])):
bondIndOne = s2.group_list[groupIndex]["bondAtomList"][k * 2]
bondIndTwo = s2.group_list[groupIndex]["bondAtomList"][k * 2 +
1]
bondOrder = s2.group_list[groupIndex]["bondOrderList"][k]
combinedStructure.set_group_bond(bondIndOne, bondIndTwo,
bondOrder)
groupCounter += 1
combinedStructure.finalize_structure()
return (structureId, combinedStructure)
def _save_structure(self, filepath, select):
count_models, count_chains, count_groups, count_atoms = 0, 0, 0, 0
# If atom serials are missing, renumber atoms starting from 1
atom_serials = [a.serial_number for a in self.structure.get_atoms()]
renumber_atoms = None in atom_serials
encoder = MMTFEncoder()
# The counts are set to 0 here and changed later once we have the values
encoder.init_structure(total_num_bonds=0,
total_num_atoms=0,
total_num_groups=0,
total_num_chains=0,
total_num_models=0,
structure_id=self.structure.id)
encoder.set_xtal_info(space_group="", unit_cell=None)
# The header information is missing for some structure objects
header_dict = defaultdict(str, self.structure.header)
if header_dict["resolution"] == "":
header_dict["resolution"] = None
if header_dict["structure_method"] == "":
header_dict["structure_method"] = []
else:
header_dict["structure_method"] = [header_dict["structure_method"]]
encoder.set_header_info(
r_free=None,
r_work=None,
resolution=header_dict["resolution"],
title=header_dict["name"],
deposition_date=header_dict["deposition_date"],
release_date=header_dict["release_date"],
experimental_methods=header_dict["structure_method"])
# Tracks values to replace them at the end
chains_per_model = []
groups_per_chain = []
for mi, model in enumerate(self.structure.get_models()):
if not select.accept_model(model):
continue
chain_id_iterator = self._chain_id_iterator()
count_models += 1
encoder.set_model_info(
model_id=mi, # According to mmtf-python this is meaningless
chain_count=0 # Set to 0 here and changed later
)
for chain in model.get_chains():
if not select.accept_chain(chain):
continue
seqs = []
seq = ""
prev_residue_type = ""
prev_resname = ""
first_chain = True
for residue in chain.get_unpacked_list():
if not select.accept_residue(residue):
continue
count_groups += 1
hetfield, resseq, icode = residue.get_id()
if hetfield == " ":
residue_type = "ATOM"
entity_type = "polymer"
elif hetfield == "W":
residue_type = "HETATM"
entity_type = "water"
else:
residue_type = "HETATM"
entity_type = "non-polymer"
resname = residue.get_resname()
# Check if the molecule changes within the chain
# This will always increment for the first residue in a
# chain due to the starting values above
# Checking for similar entities is non-trivial from the
# structure object so we treat each molecule as a separate
# entity
if residue_type != prev_residue_type or (
residue_type == "HETATM"
and resname != prev_resname):
encoder.set_entity_info(
chain_indices=[count_chains],
sequence="", # Set to empty here and changed later
description="",
entity_type=entity_type)
encoder.set_chain_info(
chain_id=next(chain_id_iterator),
chain_name="\x00" if len(chain.get_id().strip())
== 0 else chain.get_id(),
num_groups=0 # Set to 0 here and changed later
)
if count_chains > 0:
groups_per_chain.append(count_groups -
sum(groups_per_chain) - 1)
if not first_chain:
seqs.append(seq)
first_chain = False
count_chains += 1
seq = ""
if entity_type == "polymer":
seq += seq1(resname, custom_map=protein_letters_3to1)
prev_residue_type = residue_type
prev_resname = resname
encoder.set_group_info(
group_name=resname,
group_number=residue.id[1],
insertion_code="\x00"
if residue.id[2] == " " else residue.id[2],
group_type=
"", # Value in the chemcomp dictionary, which is unknown here
atom_count=sum(1 for a in residue.get_unpacked_list()
if select.accept_atom(a)),
bond_count=0,
single_letter_code=seq1(
resname, custom_map=protein_letters_3to1),
sequence_index=len(seq) -
1 if entity_type == "polymer" else -1,
secondary_structure_type=-1)
for atom in residue.get_unpacked_list():
if select.accept_atom(atom):
count_atoms += 1
encoder.set_atom_info(
atom_name=atom.name,
serial_number=count_atoms
if renumber_atoms else atom.serial_number,
alternative_location_id="\x00"
if atom.altloc == " " else atom.altloc,
x=atom.coord[0],
y=atom.coord[1],
z=atom.coord[2],
occupancy=atom.occupancy,
temperature_factor=atom.bfactor,
element=atom.element,
charge=0)
seqs.append(seq)
# Now that we have the sequences, edit the entities to add them
start_ind = len(encoder.entity_list) - len(seqs)
for i, seq in enumerate(seqs):
encoder.entity_list[start_ind + i]["sequence"] = seq
chains_per_model.append(count_chains - sum(chains_per_model))
groups_per_chain.append(count_groups - sum(groups_per_chain))
encoder.chains_per_model = chains_per_model
encoder.groups_per_chain = groups_per_chain
encoder.num_atoms = count_atoms
encoder.num_groups = count_groups
encoder.num_chains = count_chains
encoder.num_models = count_models
encoder.finalize_structure()
encoder.write_file(filepath)
def _split_to_chains(self, s):
'''split structure to a list of chains
'''
chains = []
numChains = s.chains_per_model[0]
chainToEntityIndex = self._get_chain_to_entity_index(s)
atomsPerChain, bondsPerChain = self._get_num_atoms_and_bonds(s)
groupCounter = 0
atomCounter = 0
for i in range(numChains):
atomMap = {}
newChain = MMTFEncoder()
entityToChainIndex = chainToEntityIndex[i]
structureId = s.structure_id + '.' +\
s.chain_name_list[i] + '.' +\
s.chain_id_list[i] + '.' +\
str(entityToChainIndex + 1)
# Set header
newChain.init_structure(bondsPerChain[i], atomsPerChain[i],
s.groups_per_chain[i], 1, 1, structureId)
decoder_utils.add_xtalographic_info(s, newChain)
decoder_utils.add_header_info(s, newChain)
# Set model info (only one model: 0)
newChain.set_model_info(0, 1)
# Set entity and chain info
newChain.set_entity_info(
[0], s.entity_list[entityToChainIndex]['sequence'],
s.entity_list[entityToChainIndex]['description'],
s.entity_list[entityToChainIndex]['type'])
newChain.set_chain_info(s.chain_id_list[i], s.chain_name_list[i],
s.groups_per_chain[i])
for j in range(s.groups_per_chain[i]):
groupIndex = s.group_type_list[groupCounter]
# print(s.group_type_list)
# Set group info
newChain.set_group_info(
s.group_list[groupIndex]['groupName'],
s.group_id_list[groupCounter],
s.ins_code_list[groupCounter],
s.group_list[groupIndex]['chemCompType'],
len(s.group_list[groupIndex]['atomNameList']),
len(s.group_list[groupIndex]['bondOrderList']),
s.group_list[groupIndex]['singleLetterCode'],
s.sequence_index_list[groupCounter],
s.sec_struct_list[groupCounter])
for k in range(len(s.group_list[groupIndex]['atomNameList'])):
newChain.set_atom_info(
s.group_list[groupIndex]['atomNameList'][k],
s.atom_id_list[atomCounter],
s.alt_loc_list[atomCounter],
s.x_coord_list[atomCounter],
s.y_coord_list[atomCounter],
s.z_coord_list[atomCounter],
s.occupancy_list[atomCounter],
s.b_factor_list[atomCounter],
s.group_list[groupIndex]['elementList'][k],
s.group_list[groupIndex]['formalChargeList'][k])
atomCounter += 1
for l in range(len(s.group_list[groupIndex]['bondOrderList'])):
bondIndOne = s.group_list[groupIndex]['bondAtomList'][l *
2]
bondIndTwo = s.group_list[groupIndex]['bondAtomList'][l * 2
+ 1]
bondOrder = s.group_list[groupIndex]['bondOrderList'][l]
#newChain.set_group_bond(bondIndOne, bondIndTwo, bondOrder)
newChain.current_group.bond_atom_list += [
bondIndOne, bondIndTwo
]
newChain.current_group.bond_order_list.append(bondOrder)
groupCounter += 1
# TODO skipping adding inter group bond info for now
newChain.finalize_structure()
# TODO double check if just getting from chain 0
chain_type = [chain['type'] for chain in newChain.entity_list]
polymer = "polymer" in chain_type
if polymer:
match = True
for j in range(newChain.groups_per_chain[0]):
#print(newChain.groups_per_chain, newChain.group_type_list)
groupIndex = newChain.group_type_list[j]
if match:
_type = newChain.group_list[groupIndex]["chemCompType"]
match = (_type == "L-PEPTIDE LINKING") or (
_type == "PEPTIDE LINKING")
if match:
chains.append(newChain)
return chains