1 /* mkbioseq.h 2 * 3 * =========================================================================== 4 * 5 * PUBLIC DOMAIN NOTICE 6 * National Center for Biotechnology Information (NCBI) 7 * 8 * This software/database is a "United States Government Work" under the 9 * terms of the United States Copyright Act. It was written as part of 10 * the author's official duties as a United States Government employee and 11 * thus cannot be copyrighted. This software/database is freely available 12 * to the public for use. The National Library of Medicine and the U.S. 13 * Government do not place any restriction on its use or reproduction. 14 * We would, however, appreciate having the NCBI and the author cited in 15 * any work or product based on this material 16 * 17 * Although all reasonable efforts have been taken to ensure the accuracy 18 * and reliability of the software and data, the NLM and the U.S. 19 * Government do not and cannot warrant the performance or results that 20 * may be obtained by using this software or data. The NLM and the U.S. 21 * Government disclaim all warranties, express or implied, including 22 * warranties of performance, merchantability or fitness for any particular 23 * purpose. 24 * 25 * =========================================================================== 26 * 27 * File Name: mkbioseq.h 28 * 29 * Author: Ken Addess 30 * 31 * $Log: mkbioseq.h,v $ 32 * Revision 6.1 1998/07/17 18:56:01 madej 33 * Created by Ken Addess. 34 * 35 */ 36 37 /***************************************************************************** 38 * 39 * mkbioseq.h 40 * 41 *****************************************************************************/ 42 43 #ifndef _MKBIOSEQ_ 44 #define _MKBIOSEQ_ 45 46 #include <ncbi.h> 47 #include <asn.h> 48 #include <mmdbapi.h> 49 50 #include "strimprt.h" 51 #define MAXNUM 50 52 53 SeqEntryPtr LIBCALL CreateSeqEntry PROTO 54 ((BiostrucSourcePtr bssp, BiostrucGraphPtr bsgp, BiostrucModelPtr bsmp, ValNodePtr descr, Int4 nchn)); 55 SeqIdPtr LIBCALL MakePDBId PROTO((BiostrucSourcePtr bssp, MoleculeGraphPtr mgp, DbtagPtr dtp)); 56 SeqIdPtr LIBCALL MakeLocalID PROTO((Int4 mid, MoleculeGraphPtr mgp, DbtagPtr dtp)); 57 SeqIdPtr LIBCALL MakeGId PROTO((Int4 gi)); 58 BiostrucPtr LIBCALL readBiostruc PROTO((CharPtr filename, Int2 mode, Int4 mdlLvl)); 59 ValNodePtr LIBCALL MakeBioseqDescr PROTO((MoleculeGraphPtr mgp, ValNodePtr bioseq_descr)); 60 Uint1 LIBCALL MakeBioseqMol PROTO((MoleculeGraphPtr mgp)); 61 Int4 LIBCALL CountNumOfResidues PROTO((MoleculeGraphPtr mgp)); 62 Boolean LIBCALL isBiopoly PROTO((Int4 molecule_id, MoleculeGraphPtr currentbp)); 63 Boolean LIBCALL isHet PROTO((Int4 molecule_id, MoleculeGraphPtr currenthet)); 64 Int4 LIBCALL getHetIdx PROTO((Int4 molecule_id, MoleculeGraphPtr currenthet)); 65 ByteStorePtr LIBCALL AddSeqData PROTO((MoleculeGraphPtr mgp, Uint1 mol, Int4 length, BiostrucGraphPtr bsgp, BiostrucResidueGraphSetPtr stdDictionary)); 66 CharPtr LIBCALL getStdOlcode PROTO 67 ((Int4 standard_graphs_id, Int4 residue_graph_id, BiostrucResidueGraphSetPtr std)); 68 CharPtr LIBCALL getNstdOlcode PROTO((ResidueGraphPtr nrg)); 69 ResidueGraphPtr LIBCALL getNstdResGraph PROTO((Int4 rgid, BiostrucGraphPtr bsgp)); 70 CharPtr LIBCALL rmvSpace PROTO((CharPtr str)); 71 SeqAnnotPtr LIBCALL AddNstdSeqAnnot PROTO((MoleculeGraphPtr mgp, SeqIdPtr id, BiostrucGraphPtr bsgp)); 72 Boolean LIBCALL isNstd PROTO((ResidueGraphPtr rgp)); 73 SeqAnnotPtr LIBCALL AddSecDomToSeqAnnot PROTO((BiostrucFeaturePtr bsfp, CharPtr name, SeqAnnotPtr seq_annot, SeqIdPtr id, Int4 num)); 74 Int4 LIBCALL findChnidx PROTO((Int4 mol_id, Int4 nbp, MoleculeGraphPtr bp)); 75 ValNodePtr LIBCALL MakeHetValNode PROTO((MoleculeGraphPtr nhet, BiostrucResidueGraphSetPtr stdDictionary, ResidueGraphPtr rg)); 76 CharPtr LIBCALL getResNam PROTO((ResidueGraphPntrPtr rgpp, BiostrucResidueGraphSetPtr stdDictionary, ResidueGraphPtr rg)); 77 CharPtr LIBCALL getResComm PROTO((ResidueGraphPntrPtr rgpp, BiostrucResidueGraphSetPtr stdDictionary, ResidueGraphPtr rg)); 78 SeqAnnotPtr LIBCALL AddHetToSeqAnnot 79 PROTO((SeqAnnotPtr seq_annot, SeqIdPtr id, ValNodePtr hetval, ValNodePtr pvnThePoints, Int4 rescount)); 80 SeqAnnotPtr LIBCALL AddDisulToSeqAnnot PROTO((SeqAnnotPtr seq_annot, Int4 residx1, Int4 residx2, SeqIdPtr id1, SeqIdPtr id2)); 81 Int4 LIBCALL 82 getAtomElementIdx PROTO ((Int4 molecule_id, Int4 residue_id, Int4 atom_id, BiostrucGraphPtr bsgp, BiostrucResidueGraphSetPtr stdDictionary)); 83 ResidueGraphPtr LIBCALL getResGraph PROTO((ResidueGraphPntrPtr rgpp, BiostrucGraphPtr bsgp, BiostrucResidueGraphSetPtr stdDictionary)); 84 85 86 #endif 87