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from mmtf.codecs import decode_array
from mmtf.utils import decoder_utils
import sys
class MMTFDecoder(object):
"""Class to decode raw mmtf data into a parsed data model that can be fed into other data model"""
model_counter = 0
chain_counter = 0
group_counter = 0
atom_counter = 0
def get_coords(self):
"""Utility function to get the coordinates as a single list of tuples."""
out_list = []
for i in range(len(self.x_coord_list)):
out_list.append((self.x_coord_list[i],self.y_coord_list[i],self.z_coord_list[i],))
return out_list
def get_bonds(self):
"""Utility function to get all the inter group bonds for the structure in pairs."""
return decoder_utils.get_bonds(self)
def decode_data(self, input_data):
"""Function to decode the input data and place it onto the class.
:param input_data: the input data as a dict"""
self.group_type_list = decode_array(input_data["groupTypeList"])
self.x_coord_list = decode_array(input_data["xCoordList"])
self.y_coord_list = decode_array(input_data["yCoordList"])
self.z_coord_list = decode_array(input_data["zCoordList"])
if "bFactorList" in input_data:
self.b_factor_list = decode_array(input_data["bFactorList"])
else:
self.b_factor_list = []
if "occupancyList" in input_data:
self.occupancy_list = decode_array(input_data["occupancyList"])
else:
self.occupancy_list = []
if "atomIdList" in input_data:
self.atom_id_list = decode_array(input_data["atomIdList"])
else:
self.atom_id_list = []
if "altLocList" in input_data:
self.alt_loc_list = decode_array(input_data["altLocList"])
else:
self.alt_loc_list = []
if "insCodeList" in input_data:
self.ins_code_list = decode_array(input_data["insCodeList"])
else:
self.ins_code_list = []
self.group_id_list = decode_array(input_data["groupIdList"])
self.group_list = input_data["groupList"]
if "sequenceIndexList" in input_data:
self.sequence_index_list = decode_array(input_data["sequenceIndexList"])
else:
self.sequence_index_list = []
self.chains_per_model = input_data["chainsPerModel"]
self.groups_per_chain = input_data["groupsPerChain"]
if "chainNameList" in input_data:
self.chain_name_list = decode_array(input_data["chainNameList"])
else:
self.chain_name_list = []
self.chain_id_list = decode_array(input_data["chainIdList"])
if "spaceGroup" in input_data:
self.space_group = input_data["spaceGroup"]
else:
self.space_group = None
if "bondAtomList" in input_data:
self.bond_atom_list = decode_array(input_data["bondAtomList"])
else:
self.bond_atom_list = None
if "bondOrderList" in input_data:
self.bond_order_list = decode_array(input_data["bondOrderList"])
else:
self.bond_order_list = None
if "mmtfVersion" in input_data:
self.mmtf_version = input_data["mmtfVersion"]
else:
self.mmtf_version = None
if "mmtfProducer" in input_data:
self.mmtf_producer = input_data["mmtfProducer"]
else:
self.mmtf_producer = None
if "structureId" in input_data:
self.structure_id = input_data["structureId"]
else:
self.structure_id = None
if "title" in input_data:
self.title = input_data["title"]
else:
self.title = None
if "experimentalMethods" in input_data:
self.experimental_methods = input_data["experimentalMethods"]
else:
self.experimental_methods = None
if "depositionDate" in input_data:
self.deposition_date = input_data["depositionDate"]
else:
self.deposition_date = None
if "releaseDate" in input_data:
self.release_date = input_data["releaseDate"]
else:
self.release_date = None
if "entityList" in input_data:
self.entity_list = input_data["entityList"]
else:
self.entity_list = []
if "bioAssemblyList" in input_data:
self.bio_assembly = input_data["bioAssemblyList"]
else:
self.bio_assembly = []
if "rFree" in input_data:
self.r_free = input_data["rFree"]
else:
self.r_free = None
if "rWork" in input_data:
self.r_work = input_data["rWork"]
else:
self.r_work = None
if "resolution" in input_data:
self.resolution = input_data["resolution"]
else:
self.resolution = None
if "unitCell" in input_data:
self.unit_cell = input_data["unitCell"]
else:
self.unit_cell = None
if "secStructList" in input_data:
self.sec_struct_list = decode_array(input_data["secStructList"])
# Now all the numbers to defien the
self.num_bonds = int(input_data["numBonds"])
self.num_chains = int(input_data["numChains"])
self.num_models = int(input_data["numModels"])
self.num_atoms = int(input_data["numAtoms"])
self.num_groups = int(input_data["numGroups"])
def pass_data_on(self, data_setters):
"""Write the data from the getters to the setters.
:param data_setters: a series of functions that can fill a chemical
data structure
:type data_setters: DataTransferInterface
"""
data_setters.init_structure(self.num_bonds, len(self.x_coord_list), len(self.group_type_list),
len(self.chain_id_list), len(self.chains_per_model), self.structure_id)
decoder_utils.add_entity_info(self, data_setters)
decoder_utils.add_atomic_information(self, data_setters)
decoder_utils.add_header_info(self, data_setters)
decoder_utils.add_xtalographic_info(self, data_setters)
decoder_utils.generate_bio_assembly(self, data_setters)
decoder_utils.add_inter_group_bonds(self, data_setters)
data_setters.finalize_structure()
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