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213 lines
7.0 KiB
C
213 lines
7.0 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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int CheckChain(CHAIN *Chain, COMMAND *Cmd)
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{
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int Res, HelAlp, HelPI, Hel310, Sheet, Turn, Bound[300][2];
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int i, j, AsnNumb=0, At, SuspCnt, Beg, End;
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float Content;
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if( Cmd->NProcessed && !ChInStr(Cmd->Processed,SpaceToDash(Chain->Id)) ) {
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Chain->Valid = NO;
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return(FAILURE);
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}
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if( Chain->NRes < 5 )
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return(NotValid(Chain,"less than 5 residues"));
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if( !Cmd->Stringent )
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return(SUCCESS);
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for( Res=0; Res<Chain->NRes; Res++ ){
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if( !CheckRes(Chain->Rsd[Res]->ResType) )
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Chain->NonStandRes++;
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for( At=0; At<Chain->Rsd[Res]->NAtom; At++) {
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if( !CheckAtom(Chain->Rsd[Res]->AtomType[At]) )
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Chain->NonStandAtom++;
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if(Chain->Rsd[Res]->Coord[At][0] < MIN_X || Chain->Rsd[Res]->Coord[At][0] > MAX_X ||
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Chain->Rsd[Res]->Coord[At][1] < MIN_Y || Chain->Rsd[Res]->Coord[At][1] > MAX_Y ||
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Chain->Rsd[Res]->Coord[At][2] < MIN_Z || Chain->Rsd[Res]->Coord[At][2] > MAX_Z ||
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Chain->Rsd[Res]->Occupancy[At] < MIN_Occupancy ||
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Chain->Rsd[Res]->Occupancy[At] > MAX_Occupancy ||
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Chain->Rsd[Res]->TempFactor[At] < MIN_TempFactor ||
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Chain->Rsd[Res]->TempFactor[At] > MAX_TempFactor )
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break;
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}
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if( At < Chain->Rsd[Res]->NAtom )
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break;
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}
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if( Res < Chain->NRes )
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return(NotValid(Chain,"suspicious coordinates, occupancy or temperature factor"));
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if( 100.0*(float)Chain->NonStandRes/(float)Chain->NRes > MAXNONSTAND )
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return(NotValid(Chain,"too many non-standard residues"));
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if( Chain->NRes < Cmd->MinLength )
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return(NotValid(Chain,"Short chain"));
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if( Chain->NRes > Cmd->MaxLength )
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return(NotValid(Chain,"Long chain"));
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if( Chain->Method == XRay &&
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(Chain->Resolution < Cmd->MinResolution || Chain->Resolution > Cmd->MaxResolution ) )
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return(NotValid(Chain,"Resolution out of range"));
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if( (int)strlen(Cmd->Cond) != 0 ) {
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if( ChInStr(Cmd->Cond,'c') ) {
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for( Res=0; Res<Chain->NRes; Res++ )
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if( FindAtom(Chain,Res,"N",&At) ||
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FindAtom(Chain,Res,"O",&At) ||
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FindAtom(Chain,Res,"C",&At) )
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break;
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if( Res == Chain->NRes )
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return(NotValid(Chain,"only CA"));
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}
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if( Chain->Method == NMR && !ChInStr(Cmd->Cond,'n') )
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return(NotValid(Chain,"NMR chain"));
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if( Chain->Method == XRay && !ChInStr(Cmd->Cond,'x') )
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return(NotValid(Chain,"XRay chain"));
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if( Chain->Method == Model && !ChInStr(Cmd->Cond,'m') )
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return(NotValid(Chain,"Model chain"));
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if( Chain->Published == NO && ChInStr(Cmd->Cond,'p') )
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return(NotValid(Chain,"Not published"));
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if( Chain->DsspAssigned == YES && ChInStr(Cmd->Cond,'d') )
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return(NotValid(Chain,"Assigned according to DSSP"));
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if( ChInStr(Cmd->Cond,'a') ) {
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if( Chain->Valid && Chain->NHelix == 0 && Chain->NSheet == -1 && Chain->NTurn == 0 )
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return(NotValid(Chain,"No assignment"));
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if( (Content = SecStrContent(Chain,&HelAlp,&HelPI,&Hel310,&Sheet,&Turn)) < 0.4 ||
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Content > 0.9 )
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return(NotValid(Chain,"Suspicious content"));
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SuspCnt = 0;
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for( Res=1; Res<Chain->NRes-1; Res++ ) {
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if( ( Chain->Rsd[Res]->Prop->PdbAsn != 'H' && Chain->Rsd[Res]->Prop->PdbAsn != 'T' &&
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Chain->Rsd[Res]->Prop->Phi > -150.0 && Chain->Rsd[Res]->Prop->Phi < 0.0 &&
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Chain->Rsd[Res]->Prop->Psi > -100.0 && Chain->Rsd[Res]->Prop->Psi < 10.0) )
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SuspCnt++;
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}
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if( (float)SuspCnt/(float)Chain->NRes > 0.4 )
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return(NotValid(Chain,"Suspicious assignment"));
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for( i=0; i<Chain->NHelix; i++ ) {
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if( !PdbN2SeqN(Chain,Chain->Helix[i]->PDB_ResNumb1,&Beg) ||
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!PdbN2SeqN(Chain,Chain->Helix[i]->PDB_ResNumb2,&End) ||
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/* !CheckRes(Chain->Helix[i]->PDB_ResNumb1) ||
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!CheckRes(Chain->Helix[i]->PDB_ResNumb2) || */
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Chain->Helix[i]->Class > 10 ||
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Chain->Helix[i]->Class < 1 ||
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End-Beg > 100 || End-Beg < 0 )
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break;
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else
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if( Chain->Helix[i]->Class == 1 ) {
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Bound[AsnNumb][0] = Beg;
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Bound[AsnNumb][1] = End;
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AsnNumb++;
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}
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}
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if( i < Chain->NHelix )
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return(NotValid(Chain,"Erraneous helix assignment"));
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for( i=0; i<Chain->NSheet; i++ )
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for( j=0; j<Chain->Sheet[i]->NStrand; j++ ) {
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if( !PdbN2SeqN(Chain,Chain->Sheet[i]->PDB_ResNumb1[j],&Beg) ||
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!PdbN2SeqN(Chain,Chain->Sheet[i]->PDB_ResNumb2[j],&End) ||
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/* !CheckRes(Chain->Sheet[i]->PDB_ResNumb1[j]) ||
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!CheckRes(Chain->Sheet[i]->PDB_ResNumb2[j]) || */
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End-Beg > 100 || End-Beg < 0 )
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break;
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else
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if( Chain->Sheet[i]->Sence[j] != 0 ) {
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Bound[AsnNumb][0] = Beg;
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Bound[AsnNumb][1] = End;
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AsnNumb++;
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}
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if( j < Chain->Sheet[i]->NStrand )
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break;
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}
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if( i < Chain->NSheet )
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return(NotValid(Chain,"Erraneous sheet assignment"));
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for( i=0; i<Chain->NTurn; i++ )
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if( !PdbN2SeqN(Chain,Chain->Turn[i]->PDB_ResNumb1,&Beg) ||
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!PdbN2SeqN(Chain,Chain->Turn[i]->PDB_ResNumb2,&End) ||
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End-Beg > 100 || End-Beg < 0 )
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break;
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if( i < Chain->NTurn )
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NotValid(Chain,"Erraneous turn assignment");
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for( i=0; i<AsnNumb-1; i++ ) {
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for( j=i+1; j<AsnNumb; j++ ) {
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if( Bound[i][0] == Bound[j][0] && Bound[i][1] == Bound[j][1] ) continue;
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if( (Bound[j][0] > Bound[i][0] && Bound[j][0] < Bound[i][1]) ||
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(Bound[j][1] > Bound[i][0] && Bound[j][1] < Bound[i][1]) ||
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(Bound[i][0] > Bound[j][0] && Bound[i][0] < Bound[j][1]) ||
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(Bound[i][1] > Bound[j][0] && Bound[i][1] < Bound[j][1]) )
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break;
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}
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if( j < AsnNumb )
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break;
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}
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if( i < AsnNumb-1 )
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return(NotValid(Chain,"Assignment overlap"));
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}
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}
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fprintf(stderr,"ACCEPTED %s %c %4d %7.3f\n",
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Chain->File,Chain->Id,Chain->NRes,Chain->Resolution);
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return(SUCCESS);
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}
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int NotValid(CHAIN *Chain, char *Message)
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{
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fprintf(stderr,"IGNORED %s %c ",Chain->File,SpaceToDash(Chain->Id));
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fprintf(stderr,"(%s)\n",Message);
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Chain->Valid = NO;
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return(FAILURE);
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}
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