/** * Get NIPROT IDs from PDB structure */ Map<String, String> chainUniprotIds(Structure pdbStruct) { Map<String, String> chain2uniproId = new HashMap<String, String>(); for (DBRef dbref : pdbStruct.getDBRefs()) { if (debug) Gpr.debug("PDB_DBREF\tchain:" + dbref.getChainName() + "\tdb: " + dbref.getDatabase() + "\tID: " + dbref.getDbAccession()); if (dbref.getDatabase().equals(UNIPROT_DATABASE)) chain2uniproId.put(dbref.getChainName(), dbref.getDbAccession()); } return chain2uniproId; }
DBRef dbref = new DBRef(); String idCode = line.substring(7,11); String chainName = line.substring(12,13); dbinsEnd = " "; dbref.setIdCode(idCode); dbref.setChainName(chainName); dbref.setSeqBegin(intFromString(seqBegin)); dbref.setInsertBegin(insertBegin.charAt(0)); dbref.setSeqEnd(intFromString(seqEnd)); dbref.setInsertEnd(insertEnd.charAt(0)); dbref.setDatabase(database.trim()); dbref.setDbAccession(dbAccession.trim()); dbref.setDbIdCode(dbIdCode.trim()); dbref.setDbSeqBegin(intFromString(dbseqBegin)); dbref.setIdbnsBegin(idbnsBeg.charAt(0)); dbref.setDbSeqEnd(intFromString(dbseqEnd)); dbref.setIdbnsEnd(dbinsEnd.charAt(0));
DBRef r = new DBRef(); r.setIdCode(sref.getPdbx_PDB_id_code()); r.setDbAccession(sref.getPdbx_db_accession()); r.setDbIdCode(sref.getPdbx_db_accession()); r.setChainName(sref.getPdbx_strand_id()); StructRef structRef = getStructRef(sref.getRef_id()); if (structRef == null){ logger.info("could not find StructRef " + sref.getRef_id() + " for StructRefSeq " + sref); } else { r.setDatabase(structRef.getDb_name()); r.setDbIdCode(structRef.getDb_code()); logger.warn("Couldn't parse pdbx_auth_seq_align_beg/end in _struct_ref_seq. Will not store dbref alignment info for accession {}. Error: {}", r.getDbAccession(), e.getMessage()); return; r.setSeqBegin(seqbegin); r.setInsertBegin(begin_ins_code); r.setSeqEnd(seqend); r.setInsertEnd(end_ins_code); r.setDbSeqBegin(dbseqbegin); r.setIdbnsBegin(db_begin_in_code); r.setDbSeqEnd(dbseqend); r.setIdbnsEnd(db_end_in_code);