def preprocess_COMPND(self, compnd_list): entity = self.struct.cifdb.confirm_table("entity") entity_keywords = self.struct.cifdb.confirm_table("entity_keywords") for compnd in compnd_list: erow = mmCIF.mmCIFRow() ekrow = mmCIF.mmCIFRow() setmaps(compnd, "MOLECULE", erow, "pdbx_description") if erow: entity.append(erow) setmaps(compnd, "FRAGMENT", ekrow, "pdbx_fragment") setmaps(compnd, "EC", ekrow, "pdbx_ec") setmaps(compnd, "MUTATION", ekrow, "pdbx_mutation") if ekrow: entity_keywords.append(ekrow)
def preprocess_EXPDTA(self, expdta_list): for technique, details in expdta_list: self.struct.experimental_method = technique break exptl = self.struct.cifdb.confirm_table("exptl") for (technique, details) in expdta_list: row = mmCIF.mmCIFRow({"method": technique}) if details: row["details"] = details exptl.append(row)
def set_single(self, table_name, col_name, val): """Utility function for setting a table where there should only be a single row of data. """ if val == None: return table = self.confirm_table(table_name) if len(table): table[0][col_name] = val else: row = mmCIF.mmCIFRow() table.append(row) row[col_name] = val
def preprocess_AUTHOR(self, author_list): audit_author = self.struct.cifdb.confirm_table("audit_author") for author in author_list: audit_author.append(mmCIF.mmCIFRow({"name": author}))
def preprocess_KEYWDS(self, keywds_list): struct_keywords = self.struct.cifdb.confirm_table("struct_keywords") for keywds in keywds_list: struct_keywords.append(mmCIF.mmCIFRow({"text": keywds}))
def preprocess_SOURCE(self, source_list): entity_src_nat = self.struct.cifdb.confirm_table("entity_src_nat") entity_src_gen = self.struct.cifdb.confirm_table("entity_src_gen") for source in source_list: nrow = mmCIF.mmCIFRow() grow = mmCIF.mmCIFRow() setmaps(source, "FRAGMENT", grow, "pdbx_gene_src_fragment") setmaps(source, "ORGANISM_SCIENTIFIC", grow, "pdbx_gene_src_scientific_name") setmaps(source, "ORGANISM_COMMON", grow, "pdbx_gene_src_common_name") setmaps(source, "GENUS", grow, "pdbx_gene_src_genus") setmaps(source, "GENUS", grow, "pdbx_gene_src_genus") setmaps(source, "SPECIES", grow, "pdbx_gene_src_species") setmaps(source, "STRAIN", grow, "pdbx_gene_src_strain") setmaps(source, "VARIANT", grow, "pdbx_gene_src_variant") setmaps(source, "CELL_LINE", grow, "pdbx_gene_src_cell_line") setmaps(source, "ATCC", grow, "pdbx_gene_src_atcc") setmaps(source, "ORGAN", grow, "pdbx_gene_src_organ") setmaps(source, "TISSUE", grow, "pdbx_gene_src_tissue") setmaps(source, "CELL", grow, "pdbx_gene_src_cell") setmaps(source, "ORGANELLE", grow, "pdbx_gene_src_organelle") setmaps(source, "SECRETION", nrow, "pdbx_secretion") setmaps(source, "CELLULAR_LOCATION", grow, "pdbx_gene_src_cellular_location") setmaps(source, "PLASMID", nrow, "pdbx_plasmid_name") setmaps(source, "GENE", grow, "pdbx_gene_src_gene") setmaps(source, "EXPRESSION_SYSTEM", grow, "pdbx_host_org_scientific_name") setmaps(source, "EXPRESSION_SYSTEM_COMMON", grow, "pdbx_host_org_common_name") setmaps(source, "EXPRESSION_SYSTEM_GENUS", grow, "pdbx_host_org_genus") setmaps(source, "EXPRESSION_SYSTEM_SPECIES", grow, "pdbx_host_org_species") setmaps(source, "EXPRESSION_SYSTEM_STRAIN", grow, "pdbx_host_org_strain") setmaps(source, "EXPRESSION_SYSTEM_VARIANT", grow, "pdbx_host_org_variant") setmaps(source, "EXPRESSION_SYSTEM_CELL_LINE", grow, "pdbx_host_org_cell_line") setmaps(source, "EXPRESSION_SYSTEM_ATCC_NUMBER", grow, "pdbx_host_org_atcc") setmaps(source, "EXPRESSION_SYSTEM_ORGAN", grow, "pdbx_host_org_organ") setmaps(source, "EXPRESSION_SYSTEM_TISSUE", grow, "pdbx_host_org_tissue") setmaps(source, "EXPRESSION_SYSTEM_CELL", grow, "pdbx_host_org_cell") setmaps(source, "EXPRESSION_SYSTEM_ORGANELLE", grow, "pdbx_host_org_organelle") setmaps(source, "EXPRESSION_SYSTEM_CELLULAR_LOCATION", grow, "pdbx_host_org_cellular_location") setmaps(source, "EXPRESSION_SYSTEM_VECTOR_TYPE", grow, "pdbx_host_org_vector_type") setmaps(source, "EXPRESSION_SYSTEM_VECTOR", grow, "pdbx_host_org_vector") setmaps(source, "EXPRESSION_SYSTEM_PLASMID", grow, "plasmid") setmaps(source, "EXPRESSION_SYSTEM_GENE", grow, "pdbx_host_org_gene") setmaps(source, "OTHER_DETAILS", grow, "pdbx_description") if nrow: entity_src_nat.append(nrow) if grow: entity_src_gen.append(grow)