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443 lines
11 KiB
C
443 lines
11 KiB
C
/*
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* Copyright (C) 1992-1994 Dmitrij Frishman <d.frishman at wzw.tum.de>
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*
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* Permission is hereby granted, free of charge, to any person obtaining a copy
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* of this software and associated documentation files (the "Software"), to deal
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* in the Software without restriction, including without limitation the rights
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* to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
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* copies of the Software, and to permit persons to whom the Software is
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* furnished to do so, subject to the following conditions:
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*
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* The above copyright notice and this permission notice shall be included in
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* all copies or substantial portions of the Software.
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*
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* THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
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* IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
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* FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
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* AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
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* LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
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* OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN
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* THE SOFTWARE.
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*/
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#include "stride.h"
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void Report(CHAIN **Chain, int NChain, HBOND **HBond, COMMAND *Cmd)
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{
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FILE *Out;
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if( !strlen(Cmd->OutFile) )
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Out = stdout;
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else
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if( !(Out = fopen(Cmd->OutFile,"w")) )
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die("Can not open output file %s\n",Cmd->OutFile);
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if( !Cmd->ReportSummaryOnly )
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ReportGeneral(Chain,Out);
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ReportSummary(Chain,NChain,Out,Cmd);
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ReportShort(Chain,NChain,Out,Cmd);
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ReportTurnTypes(Chain,NChain,Out,Cmd);
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ReportSSBonds(Chain,Out);
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if( !Cmd->ReportSummaryOnly )
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ReportDetailed(Chain,NChain,Out,Cmd);
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if( Cmd->ReportBonds )
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ReportHydrBonds(Chain,NChain,HBond,Out,Cmd);
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if( Cmd->Measure ) {
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Measure(Chain,NChain,0,Cmd,Out);
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Measure(Chain,NChain,1,Cmd,Out);
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}
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if( Out != stdout )
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fclose(Out);
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}
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void ReportGeneral(CHAIN **Chain, FILE *Out)
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{
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register int i;
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BUFFER Bf, Tmp;
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if( !Chain[0]->NInfo )
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return;
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PrepareBuffer(Bf,Chain);
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Glue(Bf,"REM --------------------------------------------------------------------",Out);
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Glue(Bf,"REM",Out);
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Glue(Bf,"REM STRIDE: Knowledge-based secondary structure assignment",Out);
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Glue(Bf,"REM Please cite: D.Frishman & P.Argos, Proteins XX, XXX-XXX, 1995",Out);
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Glue(Bf,"REM",Out);
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Glue(Bf,"REM Residue accessible surface area calculation",Out);
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Glue(Bf,"REM Please cite: F.Eisenhaber & P.Argos, J.Comp.Chem. 14, 1272-1280, 1993 ",Out);
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Glue(Bf,"REM F.Eisenhaber et al., J.Comp.Chem., 1994, submitted",Out);
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Glue(Bf,"REM",Out);
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sprintf(Tmp,"REM ------------------------ ");
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strcat(Tmp,"General information");
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strcat(Tmp," -----------------------");
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Glue(Bf,Tmp,Out);
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Glue(Bf,"REM",Out);
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for( i=0; i<Chain[0]->NInfo; i++ ) {
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strcpy(Tmp,Chain[0]->Info[i]);
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Tmp[66] = '\0';
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Replace(Tmp,'\n',' ');
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Glue(Bf,Tmp,Out);
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}
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Glue(Bf,"REM",Out);
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}
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void ReportSummary(CHAIN **Chain, int NChain, FILE *Out, COMMAND *Cmd)
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{
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int Cn, Width, CurrWidth, NBlocks, Tail, i, j, From, To;
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BUFFER Bf, Tmp, Tmp1;
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PrepareBuffer(Bf,Chain);
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sprintf(Tmp,"REM -------------------- ");
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strcat(Tmp,"Secondary structure summary");
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strcat(Tmp," -------------------");
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Glue(Bf,Tmp,Out);
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for( Cn=0; Cn<NChain; Cn++ ) {
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if( !Chain[Cn]->Valid )
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continue;
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Width = 50;
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Glue(Bf,"REM",Out);
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strncpy(Tmp1,Chain[Cn]->File,40);
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Tmp1[40] = '\0';
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sprintf(Tmp,"CHN %s %c",Tmp1,SpaceToDash(Chain[Cn]->Id));
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Glue(Bf,Tmp,Out);
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NBlocks = Chain[Cn]->NRes/Width;
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Tail = Chain[Cn]->NRes % Width;
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if( Tail ) NBlocks++;
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for( i=0; i<NBlocks; i++ ) {
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Glue(Bf,"REM",Out);
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From = i*Width;
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if( i == NBlocks-1 && Tail )
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CurrWidth = Tail;
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else
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CurrWidth = Width;
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To = From+CurrWidth;
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sprintf(Tmp,"REM ");
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for( j=0; j<CurrWidth; j++ )
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if( j && (j+1)%10 == 0 )
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strcat(Tmp,".");
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else
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strcat(Tmp," ");
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Glue(Bf,Tmp,Out);
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sprintf(Tmp,"SEQ %-4d ",From+1);
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for( j=From; j<From+Width; j++ ) {
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if( j < To )
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sprintf(Tmp1,"%c",ThreeToOne(Chain[Cn]->Rsd[j]->ResType));
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else
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sprintf(Tmp1," ");
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strcat(Tmp,Tmp1);
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}
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sprintf(Tmp1," %4d",To);
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strcat(Tmp,Tmp1);
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Glue(Bf,Tmp,Out);
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sprintf(Tmp,"STR ");
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for( j=From; j<To; j++ ) {
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if( Chain[Cn]->Rsd[j]->Prop->Asn == 'C' )
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sprintf(Tmp1," ");
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else
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sprintf(Tmp1,"%c",Chain[Cn]->Rsd[j]->Prop->Asn);
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strcat(Tmp,Tmp1);
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}
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strcat(Tmp," ");
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Glue(Bf,Tmp,Out);
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}
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}
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}
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void ReportDetailed(CHAIN **Chain, int NChain, FILE *Out, COMMAND *Cmd)
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{
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register int i, Cn;
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RESIDUE *p;
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BUFFER Bf, Tmp, Tmp1;
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PrepareBuffer(Bf,Chain);
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Glue(Bf,"REM",Out);
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sprintf(Tmp,"REM --------------- ");
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strcat(Tmp,"Detailed secondary structure assignment");
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strcat(Tmp,"-------------");
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Glue(Bf,Tmp,Out);
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Glue(Bf,"REM",Out);
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Glue(Bf,"REM |---Residue---| |--Structure--| |-Phi-| |-Psi-| |-Area-| ",Out);
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for( Cn=0; Cn<NChain; Cn++ ) {
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if( !Chain[Cn]->Valid )
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continue;
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for( i=0; i<Chain[Cn]->NRes; i++ ) {
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p = Chain[Cn]->Rsd[i];
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sprintf(Tmp,"ASG %3s %c %4s %4d %c %11s %7.2f %7.2f %7.1f",
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p->ResType,SpaceToDash(Chain[Cn]->Id),p->PDB_ResNumb,i+1,
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p->Prop->Asn,Translate(p->Prop->Asn),p->Prop->Phi,
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p->Prop->Psi,p->Prop->Solv);
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if( Cmd->BrookhavenAsn ) {
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Tmp[26] = p->Prop->PdbAsn;
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Tmp[25] = ' ';
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Tmp[27] = ' ';
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}
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if( Cmd->DsspAsn ) {
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Tmp[28] = p->Prop->DsspAsn;
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Tmp[27] = ' ';
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Tmp[29] = ' ';
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sprintf(Tmp1," %6.1f ",p->Prop->DsspSolv);
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strcat(Tmp,Tmp1);
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}
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Glue(Bf,Tmp,Out);
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}
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}
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}
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void ReportHydrBonds(CHAIN **Chain, int NChain, HBOND **HBond, FILE *Out,
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COMMAND *Cmd)
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{
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register int i, k, Cn;
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int Cnt, Res;
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BUFFER Bf, Tmp, Tmp1;
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HBOND *p;
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RESIDUE *r;
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PrepareBuffer(Bf,Chain);
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Glue(Bf,"REM",Out);
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sprintf(Tmp,"REM ------------------ ");
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strcat(Tmp,"Mainchain hydrogen bonds");
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strcat(Tmp," ------------------------");
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Glue(Bf,Tmp,Out);
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Glue(Bf,"REM",Out);
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Glue(Bf,"REM Definition of Stickle et al., J.Mol.Biol. 226:1143-1159, 1992",Out);
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Glue(Bf,"REM A1 is the angle between the planes of donor complex and O..N-C",Out);
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Glue(Bf,"REM A2 is the angle between the planes of acceptor complex and N..O=C",Out);
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Glue(Bf,"REM",Out);
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sprintf(Tmp,"HBT %-6d",Chain[0]->NHydrBondTotal);
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Glue(Bf,Tmp,Out);
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sprintf(Tmp,"HBI %-6d",Chain[0]->NHydrBondInterchain);
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Glue(Bf,Tmp,Out);
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for( Cn=0; Cn<NChain; Cn++ )
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if( Chain[Cn]->Valid ) {
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sprintf(Tmp,"HBC %-6d %s %c %4d",
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Chain[Cn]->NHydrBond,Chain[Cn]->File,SpaceToDash(Chain[Cn]->Id),Chain[Cn]->NRes);
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Glue(Bf,Tmp,Out);
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}
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Glue(Bf,"REM",Out);
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Glue(Bf,"REM |--Residue 1--| |--Residue 2--| N-O N..O=C O..N-C A1 A2",Out);
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for( Cn=0; Cn<NChain; Cn++ ) {
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if( !Chain[Cn]->Valid )
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continue;
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for( i=0; i<Chain[Cn]->NRes; i++ ) {
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r = Chain[Cn]->Rsd[i];
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Cnt = 0;
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for( k=0; k<r->Inv->NBondDnr; k++ ) {
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p = HBond[r->Inv->HBondDnr[k]];
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if( p->ExistHydrBondRose ) {
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Res = p->Acc->A_Res;
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sprintf(Tmp,"DNR %4s %c %4s %4d -> ",
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r->ResType,SpaceToDash(Chain[Cn]->Id),r->PDB_ResNumb,i);
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sprintf(Tmp1,"%4s %c %4s %4d %4.1f %6.1f %6.1f %6.1f %6.1f ",
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p->Acc->Chain->Rsd[Res]->ResType,
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/* patch replace SpaceToDash(Chain[Cn]->Id), */
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SpaceToDash(p->Acc->Chain->Id),
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p->Acc->Chain->Rsd[Res]->PDB_ResNumb,Res,p->AccDonDist,p->AccAng,
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p->DonAng,p->AccDonAng,p->DonAccAng);
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strcat(Tmp,Tmp1);
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Glue(Bf,Tmp,Out);
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Cnt++;
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}
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}
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Cnt = 0;
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for( k=0; k<r->Inv->NBondAcc; k++ ) {
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p = HBond[r->Inv->HBondAcc[k]];
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if( p->ExistHydrBondRose ) {
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Res = p->Dnr->D_Res;
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sprintf(Tmp,"ACC %4s %c %4s %4d -> ",
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r->ResType,SpaceToDash(Chain[Cn]->Id),r->PDB_ResNumb,i);
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sprintf(Tmp1,"%4s %c %4s %4d %4.1f %6.1f %6.1f %6.1f %6.1f ",
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p->Dnr->Chain->Rsd[Res]->ResType,
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/* patch replace SpaceToDash(Chain[Cn]->Id), */
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SpaceToDash(p->Dnr->Chain->Id),
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p->Dnr->Chain->Rsd[Res]->PDB_ResNumb,Res,p->AccDonDist,
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p->AccAng,p->DonAng,p->AccDonAng,p->DonAccAng);
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strcat(Tmp,Tmp1);
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Glue(Bf,Tmp,Out);
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Cnt++;
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}
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}
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}
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}
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}
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void ReportSSBonds(CHAIN **Chain, FILE *Out)
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{
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register int i;
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BUFFER Bf, Tmp;
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SSBOND *s;
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if( !Chain[0]->NBond ) return;
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PrepareBuffer(Bf,Chain);
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for( i=0; i<Chain[0]->NBond; i++ ) {
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s = Chain[0]->SSbond[i];
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sprintf(Tmp,"LOC Disulfide CYS %4s %c CYS %4s %c ",
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s->PDB_ResNumb1,SpaceToDash(s->ChainId1),
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s->PDB_ResNumb2,SpaceToDash(s->ChainId2));
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if( s->AsnSource == Pdb )
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strcat(Tmp," PDB");
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else
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strcat(Tmp,"STRIDE\n");
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Glue(Bf,Tmp,Out);
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}
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}
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void ReportTurnTypes(CHAIN **Chain, int NChain, FILE *Out, COMMAND *Cmd)
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{
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register int Cn, Tn;
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BUFFER Bf, Tmp;
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TURN *t;
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Tn = 0;
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for( Cn=0; Cn<NChain; Cn++ )
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if( Chain[Cn]->Valid )
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Tn += Chain[Cn]->NAssignedTurn;
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if( !Tn ) return;
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PrepareBuffer(Bf,Chain);
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for( Cn=0; Cn<NChain; Cn++ ) {
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if( !Chain[Cn]->Valid )
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continue;
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for( Tn=0; Tn<Chain[Cn]->NAssignedTurn; Tn++ ) {
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t = Chain[Cn]->AssignedTurn[Tn];
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sprintf(Tmp,"LOC %-11s %3s %4s %c %3s %4s %c",
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Translate(t->TurnType),t->Res1,t->PDB_ResNumb1,
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SpaceToDash(Chain[Cn]->Id),t->Res2,
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t->PDB_ResNumb2,SpaceToDash(Chain[Cn]->Id));
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Glue(Bf,Tmp,Out);
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}
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}
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}
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void ReportShort(CHAIN **Chain, int NChain, FILE *Out, COMMAND *Cmd)
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{
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register int Cn, i;
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BUFFER Bf, Tmp;
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char *Asn;
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static char *StrTypes = "HGIE";
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int Bound[MAX_ASSIGN][2], NStr;
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if( !ExistsSecStr(Chain,NChain) )
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return;
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PrepareBuffer(Bf,Chain);
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Glue(Bf,"REM",Out);
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Glue(Bf,"REM",Out);
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Glue(Bf,"REM",Out);
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for( ; *StrTypes!= '\0'; StrTypes++ ) {
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for( Cn=0; Cn<NChain; Cn++ ) {
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if( !Chain[Cn]->Valid )
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continue;
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Asn = (char *)ckalloc(Chain[Cn]->NRes*sizeof(char));
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ExtractAsn(Chain,Cn,Asn);
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NStr = Boundaries(Asn,Chain[Cn]->NRes,(*StrTypes),Bound);
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for( i=0; i<NStr; i++ ) {
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sprintf(Tmp,"LOC %-10s %3s %4s %c %3s %4s %c",Translate(*StrTypes),
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Chain[Cn]->Rsd[Bound[i][0]]->ResType,
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Chain[Cn]->Rsd[Bound[i][0]]->PDB_ResNumb,
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SpaceToDash(Chain[Cn]->Id),
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Chain[Cn]->Rsd[Bound[i][1]]->ResType,
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Chain[Cn]->Rsd[Bound[i][1]]->PDB_ResNumb,
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SpaceToDash(Chain[Cn]->Id));
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Glue(Bf,Tmp,Out);
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}
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free(Asn);
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}
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}
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}
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void PrepareBuffer(BUFFER Bf, CHAIN **Chain)
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{
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memset(Bf,' ',OUTPUTWIDTH);
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strcpy(Bf+OUTPUTWIDTH-5,Chain[0]->PdbIdent);
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Bf[OUTPUTWIDTH] = '\0';
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Bf[OUTPUTWIDTH-1] = '\n';
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}
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void Glue(char *String1, char *String2, FILE *Out)
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{
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BUFFER Bf;
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strcpy(Bf,String1);
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strncpy(Bf,String2,(int)strlen(String2));
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fprintf(Out,"%s",Bf);
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}
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