int gmx_helix(int argc,char *argv[]) { const char *desc[] = { "g_helix computes all kind of helix properties. First, the peptide", "is checked to find the longest helical part. This is determined by", "Hydrogen bonds and Phi/Psi angles.", "That bit is fitted", "to an ideal helix around the Z-axis and centered around the origin.", "Then the following properties are computed:[PAR]", "[BB]1.[bb] Helix radius (file radius.xvg). This is merely the", "RMS deviation in two dimensions for all Calpha atoms.", "it is calced as sqrt((SUM i(x^2(i)+y^2(i)))/N), where N is the number", "of backbone atoms. For an ideal helix the radius is 0.23 nm[BR]", "[BB]2.[bb] Twist (file twist.xvg). The average helical angle per", "residue is calculated. For alpha helix it is 100 degrees,", "for 3-10 helices it will be smaller,", "for 5-helices it will be larger.[BR]", "[BB]3.[bb] Rise per residue (file rise.xvg). The helical rise per", "residue is plotted as the difference in Z-coordinate between Ca", "atoms. For an ideal helix this is 0.15 nm[BR]", "[BB]4.[bb] Total helix length (file len-ahx.xvg). The total length", "of the", "helix in nm. This is simply the average rise (see above) times the", "number of helical residues (see below).[BR]", "[BB]5.[bb] Number of helical residues (file n-ahx.xvg). The title says", "it all.[BR]", "[BB]6.[bb] Helix Dipole, backbone only (file dip-ahx.xvg).[BR]", "[BB]7.[bb] RMS deviation from ideal helix, calculated for the Calpha", "atoms only (file rms-ahx.xvg).[BR]", "[BB]8.[bb] Average Calpha-Calpha dihedral angle (file phi-ahx.xvg).[BR]", "[BB]9.[bb] Average Phi and Psi angles (file phipsi.xvg).[BR]", "[BB]10.[bb] Ellipticity at 222 nm according to [IT]Hirst and Brooks[it]", "[PAR]" }; static const char *ppp[efhNR+2] = { NULL, "RAD", "TWIST", "RISE", "LEN", "NHX", "DIP", "RMS", "CPHI", "RMSA", "PHI", "PSI", "HB3", "HB4", "HB5", "CD222", NULL }; static gmx_bool bCheck=FALSE,bFit=TRUE,bDBG=FALSE,bEV=FALSE; static int rStart=0,rEnd=0,r0=1; t_pargs pa [] = { { "-r0", FALSE, etINT, {&r0}, "The first residue number in the sequence" }, { "-q", FALSE, etBOOL,{&bCheck}, "Check at every step which part of the sequence is helical" }, { "-F", FALSE, etBOOL,{&bFit}, "Toggle fit to a perfect helix" }, { "-db", FALSE, etBOOL,{&bDBG}, "Print debug info" }, { "-prop", FALSE, etENUM, {ppp}, "Select property to weight eigenvectors with. WARNING experimental stuff" }, { "-ev", FALSE, etBOOL,{&bEV}, "Write a new 'trajectory' file for ED" }, { "-ahxstart", FALSE, etINT, {&rStart}, "First residue in helix" }, { "-ahxend", FALSE, etINT, {&rEnd}, "Last residue in helix" } }; typedef struct { FILE *fp,*fp2; gmx_bool bfp2; const char *filenm; const char *title; const char *xaxis; const char *yaxis; real val; } t_xvgrfile; t_xvgrfile xf[efhNR] = { { NULL, NULL, TRUE, "radius", "Helix radius", NULL, "r (nm)" , 0.0 }, { NULL, NULL, TRUE, "twist", "Twist per residue", NULL, "Angle (deg)", 0.0 }, { NULL, NULL, TRUE, "rise", "Rise per residue", NULL, "Rise (nm)", 0.0 }, { NULL, NULL, FALSE, "len-ahx", "Length of the Helix", NULL, "Length (nm)", 0.0 }, { NULL, NULL, FALSE, "dip-ahx", "Helix Backbone Dipole", NULL, "rq (nm e)", 0.0 }, { NULL, NULL, TRUE, "rms-ahx", "RMS Deviation from Ideal Helix", NULL, "RMS (nm)", 0.0 }, { NULL, NULL, FALSE, "rmsa-ahx","Average RMSD per Residue", "Residue", "RMS (nm)", 0.0 }, { NULL, NULL,FALSE, "cd222", "Ellipticity at 222 nm", NULL, "nm", 0.0 }, { NULL, NULL, TRUE, "pprms", "RMS Distance from \\8a\\4-helix", NULL, "deg" , 0.0 }, { NULL, NULL, TRUE, "caphi", "Average Ca-Ca Dihedral", NULL, "\\8F\\4(deg)", 0.0 }, { NULL, NULL, TRUE, "phi", "Average \\8F\\4 angles", NULL, "deg" , 0.0 }, { NULL, NULL, TRUE, "psi", "Average \\8Y\\4 angles", NULL, "deg" , 0.0 }, { NULL, NULL, TRUE, "hb3", "Average n-n+3 hbond length", NULL, "nm" , 0.0 }, { NULL, NULL, TRUE, "hb4", "Average n-n+4 hbond length", NULL, "nm" , 0.0 }, { NULL, NULL, TRUE, "hb5", "Average n-n+5 hbond length", NULL, "nm" , 0.0 }, { NULL, NULL,FALSE, "JCaHa", "J-Coupling Values", "Residue", "Hz" , 0.0 }, { NULL, NULL,FALSE, "helicity","Helicity per Residue", "Residue", "% of time" , 0.0 } }; output_env_t oenv; FILE *otrj; char buf[54],prop[256]; t_trxstatus *status; int natoms,nre,nres; t_bb *bb; int i,j,ai,m,nall,nbb,nca,teller,nSel=0; atom_id *bbindex,*caindex,*allindex; t_topology *top; int ePBC; rvec *x,*xref,*xav; real t; real rms,fac; matrix box; gmx_rmpbc_t gpbc=NULL; gmx_bool bRange; t_filenm fnm[] = { { efTPX, NULL, NULL, ffREAD }, { efNDX, NULL, NULL, ffREAD }, { efTRX, "-f", NULL, ffREAD }, { efG87, "-to", NULL, ffOPTWR }, { efSTO, "-cz", "zconf",ffWRITE }, { efSTO, "-co", "waver",ffWRITE } }; #define NFILE asize(fnm) CopyRight(stderr,argv[0]); parse_common_args(&argc,argv,PCA_CAN_VIEW | PCA_CAN_TIME | PCA_BE_NICE, NFILE,fnm,asize(pa),pa,asize(desc),desc,0,NULL,&oenv); bRange=(opt2parg_bSet("-ahxstart",asize(pa),pa) && opt2parg_bSet("-ahxend",asize(pa),pa)); top=read_top(ftp2fn(efTPX,NFILE,fnm),&ePBC); natoms=read_first_x(oenv,&status,opt2fn("-f",NFILE,fnm),&t,&x,box); if (opt2bSet("-to",NFILE,fnm)) { otrj=opt2FILE("-to",NFILE,fnm,"w"); strcpy(prop,ppp[0]); fprintf(otrj,"%s Weighted Trajectory: %d atoms, NO box\n",prop,natoms); } else otrj=NULL; if (natoms != top->atoms.nr) gmx_fatal(FARGS,"Sorry can only run when the number of atoms in the run input file (%d) is equal to the number in the trajectory (%d)", top->atoms.nr,natoms); bb=mkbbind(ftp2fn(efNDX,NFILE,fnm),&nres,&nbb,r0,&nall,&allindex, top->atoms.atomname,top->atoms.atom,top->atoms.resinfo); snew(bbindex,natoms); snew(caindex,nres); fprintf(stderr,"nall=%d\n",nall); /* Open output files, default x-axis is time */ for(i=0; (i<efhNR); i++) { sprintf(buf,"%s.xvg",xf[i].filenm); remove(buf); xf[i].fp=xvgropen(buf,xf[i].title, xf[i].xaxis ? xf[i].xaxis : "Time (ps)", xf[i].yaxis,oenv); if (xf[i].bfp2) { sprintf(buf,"%s.out",xf[i].filenm); remove(buf); xf[i].fp2=ffopen(buf,"w"); } } /* Read reference frame from tpx file to compute helix length */ snew(xref,top->atoms.nr); read_tpx(ftp2fn(efTPX,NFILE,fnm), NULL,NULL,&natoms,xref,NULL,NULL,NULL); calc_hxprops(nres,bb,xref,box); do_start_end(nres,bb,xref,&nbb,bbindex,&nca,caindex,bRange,rStart,rEnd); sfree(xref); if (bDBG) { fprintf(stderr,"nca=%d, nbb=%d\n",nca,nbb); pr_bb(stdout,nres,bb); } gpbc = gmx_rmpbc_init(&top->idef,ePBC,natoms,box); snew(xav,natoms); teller=0; do { if ((teller++ % 10) == 0) fprintf(stderr,"\rt=%.2f",t); gmx_rmpbc(gpbc,natoms,box,x); calc_hxprops(nres,bb,x,box); if (bCheck) do_start_end(nres,bb,x,&nbb,bbindex,&nca,caindex,FALSE,0,0); if (nca >= 5) { rms=fit_ahx(nres,bb,natoms,nall,allindex,x,nca,caindex,box,bFit); if (teller == 1) { write_sto_conf(opt2fn("-cz",NFILE,fnm),"Helix fitted to Z-Axis", &(top->atoms),x,NULL,ePBC,box); } xf[efhRAD].val = radius(xf[efhRAD].fp2,nca,caindex,x); xf[efhTWIST].val = twist(xf[efhTWIST].fp2,nca,caindex,x); xf[efhRISE].val = rise(nca,caindex,x); xf[efhLEN].val = ahx_len(nca,caindex,x,box); xf[efhCD222].val = ellipticity(nres,bb); xf[efhDIP].val = dip(nbb,bbindex,x,top->atoms.atom); xf[efhRMS].val = rms; xf[efhCPHI].val = ca_phi(nca,caindex,x,box); xf[efhPPRMS].val = pprms(xf[efhPPRMS].fp2,nres,bb); for(j=0; (j<=efhCPHI); j++) fprintf(xf[j].fp, "%10g %10g\n",t,xf[j].val); av_phipsi(xf[efhPHI].fp,xf[efhPSI].fp,xf[efhPHI].fp2,xf[efhPSI].fp2, t,nres,bb); av_hblen(xf[efhHB3].fp,xf[efhHB3].fp2, xf[efhHB4].fp,xf[efhHB4].fp2, xf[efhHB5].fp,xf[efhHB5].fp2, t,nres,bb); if (otrj) dump_otrj(otrj,nall,allindex,x,xf[nSel].val,xav); } } while (read_next_x(oenv,status,&t,natoms,x,box)); fprintf(stderr,"\n"); gmx_rmpbc_done(gpbc); close_trj(status); if (otrj) { ffclose(otrj); fac=1.0/teller; for(i=0; (i<nall); i++) { ai=allindex[i]; for(m=0; (m<DIM); m++) xav[ai][m]*=fac; } write_sto_conf_indexed(opt2fn("-co",NFILE,fnm), "Weighted and Averaged conformation", &(top->atoms),xav,NULL,ePBC,box,nall,allindex); } for(i=0; (i<nres); i++) { if (bb[i].nrms > 0) { fprintf(xf[efhRMSA].fp,"%10d %10g\n",r0+i,bb[i].rmsa/bb[i].nrms); } fprintf(xf[efhAHX].fp,"%10d %10g\n",r0+i,(bb[i].nhx*100.0)/(real )teller); fprintf(xf[efhJCA].fp,"%10d %10g\n", r0+i,140.3+(bb[i].jcaha/(double)teller)); } for(i=0; (i<efhNR); i++) { ffclose(xf[i].fp); if (xf[i].bfp2) ffclose(xf[i].fp2); do_view(oenv,xf[i].filenm,"-nxy"); } thanx(stderr); return 0; }
void search(void) { Obj2 *p, *q; int i, j; double t; for(i=0; objlst[i]; i++) { p = objlst[i]; if(p == &oshad) continue; t = rise(p, -.833); if(t >= 0.) event("%s rises at ", p->name, "", t, i==0? PTIME: PTIME|DARK); t = set(p, -.833); if(t >= 0.) event("%s sets at ", p->name, "", t, i==0? PTIME: PTIME|DARK); if(p == &osun) { for(j=0; j<4; j++) { t = solstice(j); if(t >= 0) event("%s at ", solstr[j], "", t, SIGNIF|PTIME); } for(j=0; bettab[j].beta!=0; j++) { t = betcross(bettab[j].beta); if(t >= 0) event("%s meeteeor shouwer", bettab[j].betstr, "", t, SIGNIF); } t = rise(p, -18); if(t >= 0) event("Twilight starts at ", "", "", t, PTIME); t = set(p, -18); if(t >= 0) event("Twilight ends at ", "", "", t, PTIME); } if(p == &omoon) for(j=0; j<NPTS; j++) { if(p->point[j].mag > .75 && p->point[j+1].mag < .25) event("New moon", "", "", 0, 0); if(p->point[j].mag <= .25 && p->point[j+1].mag > .25) event("First quarter moon", "", "", 0, 0); if(p->point[j].mag <= .50 && p->point[j+1].mag > .50) event("Full moon", "", "", 0, 0); if(p->point[j].mag <= .75 && p->point[j+1].mag > .75) event("Last quarter moon", "", "", 0, 0); } if(p == &omerc || p == &ovenus) { t = melong(p); if(t >= 0) { t = rise(p, 0) - rise(&osun, 0); if(t < 0) t += NPTS; if(t > NPTS) t -= NPTS; if(t > NPTS/2) event("Morning elongation of %s", p->name, "", 0, SIGNIF); else event("Evening elongation of %s", p->name, "", 0, SIGNIF); } } for(j=i; objlst[j]; j++) { if(i == j) continue; q = objlst[j]; if(p == &omoon || q == &omoon) { occult(p, q, 0); if(occ.t3 < 0) continue; if(p == &osun || q == &oshad) { if(occ.t1 >= 0) event("Partial eclipse of %s begins at ", p->name, "", occ.t1, SIGNIF|PTIME); if(occ.t2 >= 0) event("Total eclipse of %s begins at ", p->name, "", occ.t2, SIGNIF|PTIME); if(occ.t4 >= 0) event("Total eclipse of %s ends at ", p->name, "", occ.t4, SIGNIF|PTIME); if(occ.t5 >= 0) event("Partial eclipse of %s ends at ", p->name, "", occ.t5, SIGNIF|PTIME); } else { if(occ.t1 >= 0) event("Occultation of %s begins at ", q->name, "", occ.t1, SIGNIF|PTIME); if(occ.t5 >= 0) event("Occultation of %s ends at ", q->name, "", occ.t5, SIGNIF|PTIME); } continue; } if(p == &osun) { if(q != &omerc && q != &ovenus) continue; occult(p, q, -1); if(occ.t3 >= 0.) { if(occ.t1 >= 0) event("Transit of %s begins at ", q->name, "", occ.t1, SIGNIF|LIGHT|PTIME); if(occ.t5 >= 0) event("Transit of %s ends at ", q->name, "", occ.t5, SIGNIF|LIGHT|PTIME); } continue; } t = dist(&p->point[0], &q->point[0]); if(t > 5000) continue; event("%s is in the house of %s", p->name, q->name, 0, 0); } } if(flags['o']) stars(); if(flags['a']) satels(); evflush(); }