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 sys.version_info[0] < 3: 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 else: 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: if sys.version_info[0] < 3: self.title = input_data["title"] else: self.title = input_data["title"] 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()