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