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)