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367 lines
11 KiB
C
367 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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/* #include <console.h> */ /* For Macintosh only, see readme.mac */
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int main(int argc, char **argv)
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{
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CHAIN **Chain;
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HBOND **HBond;
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COMMAND *Cmd;
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int Cn, NChain=0, NHBond=0, ValidChain=0;
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float **PhiPsiMapHelix, **PhiPsiMapSheet;
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register int i;
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/* argc = ccommand(&argv); */ /* For Macintosh only, see readme.mac */
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Chain = (CHAIN **)ckalloc(MAX_CHAIN*sizeof(CHAIN *));
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HBond = (HBOND **)ckalloc(MAXHYDRBOND*sizeof(HBOND *));
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Cmd = (COMMAND *)ckalloc(sizeof(COMMAND));
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ProcessStrideOptions(argv,argc,Cmd);
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if( !ReadPDBFile(Chain,&NChain,Cmd) || !NChain )
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die("Error reading PDB file %s\n",Cmd->InputFile);
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for( Cn=0; Cn<NChain; Cn++ )
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ValidChain += CheckChain(Chain[Cn],Cmd);
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/* if( Cmd->Stringent )
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* exit(0);
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*/
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if( !ValidChain )
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die("No valid chain in %s\n",Chain[0]->File);
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if( Cmd->BrookhavenAsn )
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GetPdbAsn(Chain,NChain);
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if( Cmd->DsspAsn )
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GetDsspAsn(Chain,NChain,Cmd);
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BackboneAngles(Chain,NChain);
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if( Cmd->OutSeq )
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OutSeq(Chain,NChain,Cmd);
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if( Cmd->ContactOrder )
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ContactOrder(Chain,NChain,Cmd);
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if( Cmd->ContactMap )
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ContactMap(Chain,NChain,Cmd);
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if( !strlen(Cmd->MapFileHelix) )
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PhiPsiMapHelix = DefaultHelixMap(Cmd);
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else
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ReadPhiPsiMap(Cmd->MapFileHelix,&PhiPsiMapHelix,Cmd);
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if( !strlen(Cmd->MapFileSheet) )
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PhiPsiMapSheet = DefaultSheetMap(Cmd);
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else
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ReadPhiPsiMap(Cmd->MapFileSheet,&PhiPsiMapSheet,Cmd);
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for( Cn=0; Cn<NChain; Cn++ )
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PlaceHydrogens(Chain[Cn]);
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if( (NHBond = FindHydrogenBonds(Chain,Cn,HBond,Cmd)) == 0 )
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die("No hydrogen bonds found in %s\n",Cmd->InputFile);
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NoDoubleHBond(HBond,NHBond);
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DiscrPhiPsi(Chain,NChain,Cmd);
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if(Cmd->ExposedArea)
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Area(Chain,NChain,Cmd);
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for( Cn=0; Cn<NChain; Cn++ ) {
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if( Chain[Cn]->Valid ) {
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Helix(Chain,Cn,HBond,Cmd,PhiPsiMapHelix);
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for( i=0; i<NChain; i++ )
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if( Chain[i]->Valid )
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Sheet(Chain,Cn,i,HBond,Cmd,PhiPsiMapSheet);
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BetaTurn(Chain,Cn);
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GammaTurn(Chain,Cn,HBond);
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}
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}
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Report(Chain,NChain,HBond,Cmd);
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if( Cmd->MolScript )
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MolScript(Chain,NChain,Cmd);
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for( i=0; i<Cn; i++ ) free(Chain[i]);
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for( i=0; i<NHBond; i++ ) free(HBond[i]);
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free(Cmd);
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return(0);
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}
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void ProcessStrideOptions(char **List, int ListLength, COMMAND *Cmd)
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{
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int i, InpFile = 0;
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char OPTION;
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BOOLEAN Password = NO;
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if( Uniq(List,ListLength) == 0 ) {
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fprintf(stderr,"All options must be unique\n");
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PrintStrideHelp(Cmd);
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}
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DefaultCmd(Cmd);
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Password = Specified(List,ListLength,'$');
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for( i=1; i<ListLength; i++ ) {
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if( *List[i] == '-' ) {
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OPTION = toupper((*(List[i]+1)));
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/*********************** Process public options ************************/
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if(OPTION == 'M') {
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strcpy(Cmd->MolScriptFile,List[i]+2);
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Cmd->MolScript = YES;
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}
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else if( OPTION == 'O' ) Cmd->ReportSummaryOnly = YES;
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else if( OPTION == 'H' ) Cmd->ReportBonds = YES;
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else if( OPTION == 'R' ) strcpy(Cmd->Active,List[i]+2);
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else if( OPTION == 'C' ) strcpy(Cmd->Processed,List[i]+2);
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else if( OPTION == 'F' ) strcpy(Cmd->OutFile,List[i]+2);
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else if( OPTION == 'Q' ) {
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strcpy(Cmd->SeqFile,List[i]+2);
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Cmd->OutSeq = YES;
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}
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/*********************** Process private options ************************/
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else if( OPTION == 'I' && Password ) Cmd->Info = YES;
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else if( OPTION == 'Z' && Password ) Cmd->Measure = YES;
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else if( OPTION == 'K' && Password ) Cmd->ContactOrder = YES;
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else if( OPTION == 'W' && Password ) Cmd->ContactMap = YES;
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else if( OPTION == 'X' && Password ) strcpy(Cmd->FirstResidue,List[i]+2);
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else if( OPTION == 'Y' && Password ) strcpy(Cmd->LastResidue,List[i]+2);
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else if( OPTION == 'D' && Password ) {
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strcpy(Cmd->DsspFile,List[i]+2);
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Cmd->DsspAsn = YES;
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}
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else if( OPTION == 'B' && Password ) Cmd->BrookhavenAsn = YES;
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else
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if(OPTION == 'P'&& Password ) {
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if( toupper(*(List[i]+2)) == 'H' )
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strcpy(Cmd->MapFileHelix,List[i]+3);
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else
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if( toupper(*(List[i]+2)) == 'E' )
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strcpy(Cmd->MapFileSheet,List[i]+3);
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else
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PrintStrideHelp(Cmd);
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}
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else
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if( OPTION == 'T' && Password ) {
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if( toupper(*(List[i]+2)) == 'H' ) {
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if( toupper(*(List[i]+3)) == 'A' )
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Cmd->Treshold_H1 = atof(List[i]+4);
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else
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if( toupper(*(List[i]+3)) == 'C' )
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Cmd->Treshold_H3 = atof(List[i]+4);
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else
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if( toupper(*(List[i]+3)) == 'D' )
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Cmd->Treshold_H4 = atof(List[i]+4);
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else
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PrintStrideHelp(Cmd);
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}
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else
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if( toupper(*(List[i]+2)) == 'E' ) {
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if( toupper(*(List[i]+3)) == 'A' )
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Cmd->Treshold_E1 = atof(List[i]+4);
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else
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if( toupper(*(List[i]+3)) == 'B' )
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Cmd->Treshold_E2 = atof(List[i]+4);
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else
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if( toupper(*(List[i]+3)) == 'C' )
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Cmd->Treshold_E3 = atof(List[i]+4);
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else
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if( toupper(*(List[i]+3)) == 'D' )
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Cmd->Treshold_E4 = atof(List[i]+4);
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else
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PrintStrideHelp(Cmd);
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}
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}
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else if( OPTION == 'S' && Password ) {
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Cmd->Stringent = YES;
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if( (int)strlen(List[i]+2) > MAXCONDITIONS-1 )
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PrintStrideHelp(Cmd);
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strcpy(Cmd->Cond,List[i]+2);
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}
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else if( OPTION == 'L' && Password ) {
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if( toupper(*(List[i]+2)) == 'L' ) Cmd->MaxLength = atoi(List[i]+3);
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if( toupper(*(List[i]+2)) == 'G' ) Cmd->MinLength = atoi(List[i]+3);
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}
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else if( OPTION == 'U' && Password ) {
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if( toupper(*(List[i]+2)) == 'L' ) Cmd->MaxResolution = atof(List[i]+3);
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if( toupper(*(List[i]+2)) == 'G' ) Cmd->MinResolution = atof(List[i]+3);
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}
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else
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if( OPTION != '$' )
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PrintStrideHelp(Cmd);
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}
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else {
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strcpy(Cmd->InputFile,List[i]);
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InpFile++;
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}
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}
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if( InpFile > 1 ) {
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fprintf(stderr,"\nOnly one input file is allowed\n");
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PrintStrideHelp(Cmd);
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}
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else
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if( !InpFile ) {
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fprintf(stderr,"\nYou must specify input file \n");
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PrintStrideHelp(Cmd);
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}
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Cmd->NActive = (int)strlen(Cmd->Active);
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Cmd->NProcessed = (int)strlen(Cmd->Processed);
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if( Cmd->Measure ) {
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Cmd->BrookhavenAsn = YES;
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Cmd->DsspAsn = YES;
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}
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}
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void PrintStrideHelp(COMMAND *Cmd)
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{
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fprintf(stderr,"\nAction: secondary structure assignment\n");
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fprintf(stderr,"Usage: stride [Options] InputFile [ > file ]\n");
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fprintf(stderr,"Options: \n");
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fprintf(stderr," -fFile Output file\n");
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fprintf(stderr," -mFile MolScript file\n");
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fprintf(stderr," -o Report secondary structure summary Only\n");
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fprintf(stderr," -h Report Hydrogen bonds\n");
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fprintf(stderr," -rId1Id2.. Read only chains Id1, Id2 ...\n");
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fprintf(stderr," -cId1Id2.. Process only Chains Id1, Id2 ...\n");
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fprintf(stderr," -q[File] Generate SeQuence file in FASTA format and die\n");
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fprintf(stderr,"\nOptions are position and case insensitive\n");
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/*************** Private options - not for general use ****************/
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if( Cmd->Info ) {
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fprintf(stderr," -phFile PhiPsiMap file for alpha helix\n");
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fprintf(stderr," -peFile PhiPsiMap file for beta-sheet\n");
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fprintf(stderr," -pgFile PhiPsiMap file for 3-1 helix\n");
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fprintf(stderr," -tha treshold (Ener*Conf*Conf) for H\n");
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fprintf(stderr," -thc treshold (Conf) for H\n");
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fprintf(stderr," -thd treshold (Conf) for H\n");
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fprintf(stderr," -tea treshold (Ener*Conf*Conf) for E\n");
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fprintf(stderr," -teb treshold (Conf) for E\n");
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fprintf(stderr," -dFile Dssp file\n");
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fprintf(stderr," -b Include Brookhaven assignment\n");
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fprintf(stderr," -i Print detailed information\n");
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fprintf(stderr," -llNumber Sequence Length less then Number (with -s)\n");
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fprintf(stderr," -lgNumber Sequence Length greater then Number (with -s)\n");
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fprintf(stderr," -ulNumber ResolUtion less (better) then Number (with -s)\n");
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fprintf(stderr," -ugNumber ResolUtion greater (worse) then Number (with -s)\n");
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fprintf(stderr," -s[xcnmapd] Stringent: discard wrong or suspisious PDB files \n");
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fprintf(stderr," -x Process X-Ray structures\n");
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fprintf(stderr," -n Process NMR structures\n");
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fprintf(stderr," -m Process Model structures\n");
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fprintf(stderr," -c Exlude structures with only Calpha atoms\n");
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fprintf(stderr," -d Exculde structures with automatic secondary structure assignment\n");
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fprintf(stderr," -a Exclude structures without secondary structure assignment\n");
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fprintf(stderr," -p Exlude structures that are not published or in press\n");
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fprintf(stderr," -z Measure differences with PDB and DSSP\n");
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}
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exit(0);
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}
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void DefaultCmd(COMMAND *Cmd)
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{
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Cmd->SideChainHBond = NO;
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Cmd->MainChainHBond = YES;
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Cmd->MainChainPolarInt = YES;
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Cmd->Published = NO;
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Cmd->DsspAssigned = NO;
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Cmd->UseResolution = NO;
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Cmd->Info = NO;
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Cmd->Truncate = YES;
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Cmd->ExposedArea = YES;
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Cmd->ReportSummaryOnly = NO;
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Cmd->ReportBonds = NO;
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Cmd->BrookhavenAsn = NO;
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Cmd->DsspAsn = NO;
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Cmd->MolScript = NO;
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Cmd->OutSeq = NO;
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Cmd->Stringent = NO;
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Cmd->Measure = NO;
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Cmd->EnergyType = 'G';
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Cmd->DistCutOff = 6.0;
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Cmd->PhiPsiStep = 0.0;
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Cmd->C1_H = -1.0;
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Cmd->C2_H = 1.0;
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Cmd->C1_E = -0.2;
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Cmd->C2_E = 0.2;
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Cmd->Treshold_H1 = -230.0;
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Cmd->Treshold_H3 = 0.12;
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Cmd->Treshold_H4 = 0.06;
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Cmd->Treshold_E1 = -240.0;
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Cmd->Treshold_E2 = -310.0;
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Cmd->MinResolution = 0.1;
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Cmd->MaxResolution = 100.0;
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Cmd->MinLength = 0;
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Cmd->MaxLength = MAX_RES;
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Cmd->NPixel = 0;
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Cmd->NActive = 0;
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Cmd->NProcessed = 0;
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strcpy(Cmd->FirstResidue,"");
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strcpy(Cmd->LastResidue,"");
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strcpy(Cmd->MapFileHelix,"");
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strcpy(Cmd->MapFileSheet,"");
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strcpy(Cmd->OutFile,"");
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strcpy(Cmd->Active,"");
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strcpy(Cmd->Processed,"");
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strcpy(Cmd->Cond,"");
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}
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