*
* Copyright (c) 1991-2000, University of Groningen, The Netherlands.
* Copyright (c) 2001-2004, The GROMACS development team.
- * Copyright (c) 2013,2014,2015,2016,2017,2018, by the GROMACS development team, led by
+ * Copyright (c) 2013,2014,2015,2016,2017,2018,2019, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
#include "gromacs/utility/futil.h"
#include "gromacs/utility/smalloc.h"
-int gmx_helix(int argc, char *argv[])
+int gmx_helix(int argc, char* argv[])
{
- const char *desc[] = {
+ const char* desc[] = {
"[THISMODULE] computes all kinds of helix properties. First, the peptide",
"is checked to find the longest helical part, as determined by",
"hydrogen bonds and [GRK]phi[grk]/[GRK]psi[grk] angles.",
"",
" * Helix radius (file [TT]radius.xvg[tt]). This is merely the",
" RMS deviation in two dimensions for all C[GRK]alpha[grk] atoms.",
- " it is calculated as [SQRT]([SUM][sum][SUB]i[sub] (x^2(i)+y^2(i)))/N[sqrt] where N is the number",
- " of backbone atoms. For an ideal helix the radius is 0.23 nm.",
+ " it is calculated as [SQRT]([SUM][sum][SUB]i[sub] (x^2(i)+y^2(i)))/N[sqrt] where N is ",
+ " the number of backbone atoms. For an ideal helix the radius is 0.23 nm.",
" * Twist (file [TT]twist.xvg[tt]). The average helical angle per",
" residue is calculated. For an [GRK]alpha[grk]-helix it is 100 degrees,",
" for 3-10 helices it will be smaller, and ",
" * Average [GRK]phi[grk] and [GRK]psi[grk] angles (file [TT]phipsi.xvg[tt]).",
" * Ellipticity at 222 nm according to Hirst and Brooks."
};
- 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" },
- { "-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" }
- };
+ 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" },
+ { "-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 { //NOLINT(clang-analyzer-optin.performance.Padding)
- FILE *fp, *fp2;
+ typedef struct
+ { //NOLINT(clang-analyzer-optin.performance.Padding)
+ FILE * fp, *fp2;
gmx_bool bfp2;
- const char *filenm;
- const char *title;
- const char *xaxis;
- const char *yaxis;
+ const char* filenm;
+ const char* title;
+ const char* xaxis;
+ const char* yaxis;
real val;
} t_xvgrfile;
- t_xvgrfile xf[efhNR] = {
- { nullptr, nullptr, TRUE, "radius", "Helix radius", nullptr, "r (nm)", 0.0 },
- { nullptr, nullptr, TRUE, "twist", "Twist per residue", nullptr, "Angle (deg)", 0.0 },
- { nullptr, nullptr, TRUE, "rise", "Rise per residue", nullptr, "Rise (nm)", 0.0 },
- { nullptr, nullptr, FALSE, "len-ahx", "Length of the Helix", nullptr, "Length (nm)", 0.0 },
- { nullptr, nullptr, FALSE, "dip-ahx", "Helix Backbone Dipole", nullptr, "rq (nm e)", 0.0 },
- { nullptr, nullptr, TRUE, "rms-ahx", "RMS Deviation from Ideal Helix", nullptr, "RMS (nm)", 0.0 },
- { nullptr, nullptr, FALSE, "rmsa-ahx", "Average RMSD per Residue", "Residue", "RMS (nm)", 0.0 },
- { nullptr, nullptr, FALSE, "cd222", "Ellipticity at 222 nm", nullptr, "nm", 0.0 },
- { nullptr, nullptr, TRUE, "pprms", "RMS Distance from \\8a\\4-helix", nullptr, "deg", 0.0 },
- { nullptr, nullptr, TRUE, "caphi", "Average Ca-Ca Dihedral", nullptr, "\\8F\\4(deg)", 0.0 },
- { nullptr, nullptr, TRUE, "phi", "Average \\8F\\4 angles", nullptr, "deg", 0.0 },
- { nullptr, nullptr, TRUE, "psi", "Average \\8Y\\4 angles", nullptr, "deg", 0.0 },
- { nullptr, nullptr, TRUE, "hb3", "Average n-n+3 hbond length", nullptr, "nm", 0.0 },
- { nullptr, nullptr, TRUE, "hb4", "Average n-n+4 hbond length", nullptr, "nm", 0.0 },
- { nullptr, nullptr, TRUE, "hb5", "Average n-n+5 hbond length", nullptr, "nm", 0.0 },
- { nullptr, nullptr, FALSE, "JCaHa", "J-Coupling Values", "Residue", "Hz", 0.0 },
- { nullptr, nullptr, FALSE, "helicity", "Helicity per Residue", "Residue", "% of time", 0.0 }
+ t_xvgrfile xf[efhNR] = {
+ { nullptr, nullptr, TRUE, "radius", "Helix radius", nullptr, "r (nm)", 0.0 },
+ { nullptr, nullptr, TRUE, "twist", "Twist per residue", nullptr, "Angle (deg)", 0.0 },
+ { nullptr, nullptr, TRUE, "rise", "Rise per residue", nullptr, "Rise (nm)", 0.0 },
+ { nullptr, nullptr, FALSE, "len-ahx", "Length of the Helix", nullptr, "Length (nm)", 0.0 },
+ { nullptr, nullptr, FALSE, "dip-ahx", "Helix Backbone Dipole", nullptr, "rq (nm e)", 0.0 },
+ { nullptr, nullptr, TRUE, "rms-ahx", "RMS Deviation from Ideal Helix", nullptr, "RMS (nm)", 0.0 },
+ { nullptr, nullptr, FALSE, "rmsa-ahx", "Average RMSD per Residue", "Residue", "RMS (nm)", 0.0 },
+ { nullptr, nullptr, FALSE, "cd222", "Ellipticity at 222 nm", nullptr, "nm", 0.0 },
+ { nullptr, nullptr, TRUE, "pprms", "RMS Distance from \\8a\\4-helix", nullptr, "deg", 0.0 },
+ { nullptr, nullptr, TRUE, "caphi", "Average Ca-Ca Dihedral", nullptr, "\\8F\\4(deg)", 0.0 },
+ { nullptr, nullptr, TRUE, "phi", "Average \\8F\\4 angles", nullptr, "deg", 0.0 },
+ { nullptr, nullptr, TRUE, "psi", "Average \\8Y\\4 angles", nullptr, "deg", 0.0 },
+ { nullptr, nullptr, TRUE, "hb3", "Average n-n+3 hbond length", nullptr, "nm", 0.0 },
+ { nullptr, nullptr, TRUE, "hb4", "Average n-n+4 hbond length", nullptr, "nm", 0.0 },
+ { nullptr, nullptr, TRUE, "hb5", "Average n-n+5 hbond length", nullptr, "nm", 0.0 },
+ { nullptr, nullptr, FALSE, "JCaHa", "J-Coupling Values", "Residue", "Hz", 0.0 },
+ { nullptr, nullptr, FALSE, "helicity", "Helicity per Residue", "Residue", "% of time", 0.0 }
};
- gmx_output_env_t *oenv;
+ gmx_output_env_t* oenv;
char buf[54];
- t_trxstatus *status;
+ t_trxstatus* status;
int natoms, nres;
- t_bb *bb;
+ t_bb* bb;
int i, j, nall, nbb, nca, teller;
- int *bbindex, *caindex, *allindex;
- t_topology *top;
+ int * bbindex, *caindex, *allindex;
+ t_topology* top;
int ePBC;
- rvec *x, *xref;
+ rvec * x, *xref;
real t;
real rms;
matrix box;
gmx_rmpbc_t gpbc = nullptr;
gmx_bool bRange;
t_filenm fnm[] = {
- { efTPR, nullptr, nullptr, ffREAD },
- { efNDX, nullptr, nullptr, ffREAD },
- { efTRX, "-f", nullptr, ffREAD },
+ { efTPR, nullptr, nullptr, ffREAD },
+ { efNDX, nullptr, nullptr, ffREAD },
+ { efTRX, "-f", nullptr, ffREAD },
{ efSTO, "-cz", "zconf", ffWRITE },
};
#define NFILE asize(fnm)
- if (!parse_common_args(&argc, argv, PCA_CAN_VIEW | PCA_CAN_TIME,
- NFILE, fnm, asize(pa), pa, asize(desc), desc, 0, nullptr, &oenv))
+ if (!parse_common_args(&argc, argv, PCA_CAN_VIEW | PCA_CAN_TIME, NFILE, fnm, asize(pa), pa,
+ asize(desc), desc, 0, nullptr, &oenv))
{
return 0;
}
- bRange = (opt2parg_bSet("-ahxstart", asize(pa), pa) &&
- opt2parg_bSet("-ahxend", asize(pa), pa));
+ bRange = (opt2parg_bSet("-ahxstart", asize(pa), pa) && opt2parg_bSet("-ahxend", asize(pa), pa));
top = read_top(ftp2fn(efTPR, NFILE, fnm), &ePBC);
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)",
+ 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);
+ 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);
{
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);
+ 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);
/* Read reference frame from tpx file to compute helix length */
snew(xref, top->atoms.nr);
- read_tpx(ftp2fn(efTPR, NFILE, fnm),
- nullptr, nullptr, nullptr, xref, nullptr, nullptr);
+ read_tpx(ftp2fn(efTPR, NFILE, fnm), nullptr, nullptr, nullptr, xref, nullptr, nullptr);
calc_hxprops(nres, bb, xref);
do_start_end(nres, bb, &nbb, bbindex, &nca, caindex, bRange, rStart, rEnd);
sfree(xref);
if (teller == 1)
{
- write_sto_conf(opt2fn("-cz", NFILE, fnm), "Helix fitted to Z-Axis",
- &(top->atoms), x, nullptr, ePBC, box);
+ write_sto_conf(opt2fn("-cz", NFILE, fnm), "Helix fitted to Z-Axis", &(top->atoms),
+ x, nullptr, ePBC, box);
}
xf[efhRAD].val = radius(xf[efhRAD].fp2, nca, caindex, x);
for (j = 0; (j <= efhCPHI); j++)
{
- fprintf(xf[j].fp, "%10g %10g\n", t, xf[j].val);
+ 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);
+ 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);
}
- }
- while (read_next_x(oenv, status, &t, x, box));
+ } while (read_next_x(oenv, status, &t, x, box));
fprintf(stderr, "\n");
gmx_rmpbc_done(gpbc);
{
if (bb[i].nrms > 0)
{
- fprintf(xf[efhRMSA].fp, "%10d %10g\n", r0+i, bb[i].rmsa/bb[i].nrms);
+ 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)/static_cast<real>(teller));
- fprintf(xf[efhJCA].fp, "%10d %10g\n",
- r0+i, 140.3+(bb[i].jcaha/static_cast<double>(teller)));
+ fprintf(xf[efhAHX].fp, "%10d %10g\n", r0 + i, (bb[i].nhx * 100.0) / static_cast<real>(teller));
+ fprintf(xf[efhJCA].fp, "%10d %10g\n", r0 + i,
+ 140.3 + (bb[i].jcaha / static_cast<double>(teller)));
}
for (i = 0; (i < efhNR); i++)
biod.pnpi.spb.ru / alexxy / gromacs.git / blobdiff