--- /dev/null
- * Copyright (c) 2013,2014,2015,2016, by the GROMACS development team, led by
+/*
+ * This file is part of the GROMACS molecular simulation package.
+ *
+ * Copyright (c) 1991-2000, University of Groningen, The Netherlands.
+ * Copyright (c) 2001-2004, The GROMACS development team.
- rvec_inc(xref[index[i]], xcm);
++ * Copyright (c) 2013,2014,2015,2016,2017, 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.
+ *
+ * GROMACS is free software; you can redistribute it and/or
+ * modify it under the terms of the GNU Lesser General Public License
+ * as published by the Free Software Foundation; either version 2.1
+ * of the License, or (at your option) any later version.
+ *
+ * GROMACS is distributed in the hope that it will be useful,
+ * but WITHOUT ANY WARRANTY; without even the implied warranty of
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
+ * Lesser General Public License for more details.
+ *
+ * You should have received a copy of the GNU Lesser General Public
+ * License along with GROMACS; if not, see
+ * http://www.gnu.org/licenses, or write to the Free Software Foundation,
+ * Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301 USA.
+ *
+ * If you want to redistribute modifications to GROMACS, please
+ * consider that scientific software is very special. Version
+ * control is crucial - bugs must be traceable. We will be happy to
+ * consider code for inclusion in the official distribution, but
+ * derived work must not be called official GROMACS. Details are found
+ * in the README & COPYING files - if they are missing, get the
+ * official version at http://www.gromacs.org.
+ *
+ * To help us fund GROMACS development, we humbly ask that you cite
+ * the research papers on the package. Check out http://www.gromacs.org.
+ */
+#include "gmxpre.h"
+
+#include <cmath>
+#include <cstring>
+
+#include "gromacs/commandline/pargs.h"
+#include "gromacs/commandline/viewit.h"
+#include "gromacs/fileio/confio.h"
+#include "gromacs/fileio/pdbio.h"
+#include "gromacs/fileio/trxio.h"
+#include "gromacs/fileio/xvgr.h"
+#include "gromacs/gmxana/gmx_ana.h"
+#include "gromacs/gmxana/princ.h"
+#include "gromacs/linearalgebra/eigensolver.h"
+#include "gromacs/math/do_fit.h"
+#include "gromacs/math/functions.h"
+#include "gromacs/math/utilities.h"
+#include "gromacs/math/vec.h"
+#include "gromacs/pbcutil/rmpbc.h"
+#include "gromacs/topology/index.h"
+#include "gromacs/topology/topology.h"
+#include "gromacs/utility/arraysize.h"
+#include "gromacs/utility/cstringutil.h"
+#include "gromacs/utility/futil.h"
+#include "gromacs/utility/smalloc.h"
+
+static real find_pdb_bfac(const t_atoms *atoms, t_resinfo *ri, char *atomnm)
+{
+ char rresnm[8];
+ int i;
+
+ std::strcpy(rresnm, *ri->name);
+ rresnm[3] = '\0';
+ for (i = 0; (i < atoms->nr); i++)
+ {
+ if ((ri->nr == atoms->resinfo[atoms->atom[i].resind].nr) &&
+ (ri->ic == atoms->resinfo[atoms->atom[i].resind].ic) &&
+ (std::strcmp(*atoms->resinfo[atoms->atom[i].resind].name, rresnm) == 0) &&
+ (std::strstr(*atoms->atomname[i], atomnm) != NULL))
+ {
+ break;
+ }
+ }
+ if (i == atoms->nr)
+ {
+ fprintf(stderr, "\rCan not find %s%d-%s in pdbfile\n",
+ rresnm, ri->nr, atomnm);
+ fflush(stderr);
+ return 0.0;
+ }
+
+ return atoms->pdbinfo[i].bfac;
+}
+
+void correlate_aniso(const char *fn, t_atoms *ref, t_atoms *calc,
+ const gmx_output_env_t *oenv)
+{
+ FILE *fp;
+ int i, j;
+
+ fp = xvgropen(fn, "Correlation between X-Ray and Computed Uij", "X-Ray",
+ "Computed", oenv);
+ for (i = 0; (i < ref->nr); i++)
+ {
+ if (ref->pdbinfo[i].bAnisotropic)
+ {
+ for (j = U11; (j <= U23); j++)
+ {
+ fprintf(fp, "%10d %10d\n", ref->pdbinfo[i].uij[j], calc->pdbinfo[i].uij[j]);
+ }
+ }
+ }
+ xvgrclose(fp);
+}
+
+static void average_residues(double f[], double **U, int uind,
+ int isize, int index[], real w_rls[],
+ const t_atoms *atoms)
+{
+ int i, j, start;
+ double av, m;
+
+ start = 0;
+ av = 0;
+ m = 0;
+ for (i = 0; i < isize; i++)
+ {
+ av += w_rls[index[i]]*(f != NULL ? f[i] : U[i][uind]);
+ m += w_rls[index[i]];
+ if (i+1 == isize ||
+ atoms->atom[index[i]].resind != atoms->atom[index[i+1]].resind)
+ {
+ av /= m;
+ if (f != NULL)
+ {
+ for (j = start; j <= i; j++)
+ {
+ f[i] = av;
+ }
+ }
+ else
+ {
+ for (j = start; j <= i; j++)
+ {
+ U[j][uind] = av;
+ }
+ }
+ start = i+1;
+ av = 0;
+ m = 0;
+ }
+ }
+}
+
+void print_dir(FILE *fp, real *Uaver)
+{
+ real eigvec[DIM*DIM];
+ real tmp[DIM*DIM];
+ rvec eigval;
+ int d, m;
+
+ fprintf(fp, "MSF X Y Z\n");
+ for (d = 0; d < DIM; d++)
+ {
+ fprintf(fp, " %c ", 'X'+d-XX);
+ for (m = 0; m < DIM; m++)
+ {
+ fprintf(fp, " %9.2e", Uaver[3*m+d]);
+ }
+ fprintf(fp, "%s\n", m == DIM ? " (nm^2)" : "");
+ }
+
+ for (m = 0; m < DIM*DIM; m++)
+ {
+ tmp[m] = Uaver[m];
+ }
+
+
+ eigensolver(tmp, DIM, 0, DIM, eigval, eigvec);
+
+ fprintf(fp, "\n Eigenvectors\n\n");
+ fprintf(fp, "Eigv %-8.2e %-8.2e %-8.2e (nm^2)\n\n",
+ eigval[2], eigval[1], eigval[0]);
+ for (d = 0; d < DIM; d++)
+ {
+ fprintf(fp, " %c ", 'X'+d-XX);
+ for (m = DIM-1; m >= 0; m--)
+ {
+ fprintf(fp, "%7.4f ", eigvec[3*m+d]);
+ }
+ fprintf(fp, "\n");
+ }
+}
+
+int gmx_rmsf(int argc, char *argv[])
+{
+ const char *desc[] = {
+ "[THISMODULE] computes the root mean square fluctuation (RMSF, i.e. standard ",
+ "deviation) of atomic positions in the trajectory (supplied with [TT]-f[tt])",
+ "after (optionally) fitting to a reference frame (supplied with [TT]-s[tt]).[PAR]",
+ "With option [TT]-oq[tt] the RMSF values are converted to B-factor",
+ "values, which are written to a [REF].pdb[ref] file with the coordinates, of the",
+ "structure file, or of a [REF].pdb[ref] file when [TT]-q[tt] is specified.",
+ "Option [TT]-ox[tt] writes the B-factors to a file with the average",
+ "coordinates.[PAR]",
+ "With the option [TT]-od[tt] the root mean square deviation with",
+ "respect to the reference structure is calculated.[PAR]",
+ "With the option [TT]-aniso[tt], [THISMODULE] will compute anisotropic",
+ "temperature factors and then it will also output average coordinates",
+ "and a [REF].pdb[ref] file with ANISOU records (corresonding to the [TT]-oq[tt]",
+ "or [TT]-ox[tt] option). Please note that the U values",
+ "are orientation-dependent, so before comparison with experimental data",
+ "you should verify that you fit to the experimental coordinates.[PAR]",
+ "When a [REF].pdb[ref] input file is passed to the program and the [TT]-aniso[tt]",
+ "flag is set",
+ "a correlation plot of the Uij will be created, if any anisotropic",
+ "temperature factors are present in the [REF].pdb[ref] file.[PAR]",
+ "With option [TT]-dir[tt] the average MSF (3x3) matrix is diagonalized.",
+ "This shows the directions in which the atoms fluctuate the most and",
+ "the least."
+ };
+ static gmx_bool bRes = FALSE, bAniso = FALSE, bFit = TRUE;
+ t_pargs pargs[] = {
+ { "-res", FALSE, etBOOL, {&bRes},
+ "Calculate averages for each residue" },
+ { "-aniso", FALSE, etBOOL, {&bAniso},
+ "Compute anisotropic termperature factors" },
+ { "-fit", FALSE, etBOOL, {&bFit},
+ "Do a least squares superposition before computing RMSF. Without this you must make sure that the reference structure and the trajectory match." }
+ };
+ int natom;
+ int i, m, teller = 0;
+ real t, *w_rls;
+
+ t_topology top;
+ int ePBC;
+ t_atoms *pdbatoms, *refatoms;
+
+ matrix box, pdbbox;
+ rvec *x, *pdbx, *xref;
+ t_trxstatus *status;
+ const char *label;
+
+ FILE *fp; /* the graphics file */
+ const char *devfn, *dirfn;
+ int resind;
+
+ gmx_bool bReadPDB;
+ int *index;
+ int isize;
+ char *grpnames;
+
+ real bfac, pdb_bfac, *Uaver;
+ double **U, *xav;
+ int aid;
+ rvec *rmsd_x = NULL;
+ double *rmsf, invcount, totmass;
+ int d;
+ real count = 0;
+ rvec xcm;
+ gmx_rmpbc_t gpbc = NULL;
+
+ gmx_output_env_t *oenv;
+
+ const char *leg[2] = { "MD", "X-Ray" };
+
+ t_filenm fnm[] = {
+ { efTRX, "-f", NULL, ffREAD },
+ { efTPS, NULL, NULL, ffREAD },
+ { efNDX, NULL, NULL, ffOPTRD },
+ { efPDB, "-q", NULL, ffOPTRD },
+ { efPDB, "-oq", "bfac", ffOPTWR },
+ { efPDB, "-ox", "xaver", ffOPTWR },
+ { efXVG, "-o", "rmsf", ffWRITE },
+ { efXVG, "-od", "rmsdev", ffOPTWR },
+ { efXVG, "-oc", "correl", ffOPTWR },
+ { efLOG, "-dir", "rmsf", ffOPTWR }
+ };
+#define NFILE asize(fnm)
+
+ if (!parse_common_args(&argc, argv, PCA_CAN_TIME | PCA_CAN_VIEW,
+ NFILE, fnm, asize(pargs), pargs, asize(desc), desc, 0, NULL,
+ &oenv))
+ {
+ return 0;
+ }
+
+ bReadPDB = ftp2bSet(efPDB, NFILE, fnm);
+ devfn = opt2fn_null("-od", NFILE, fnm);
+ dirfn = opt2fn_null("-dir", NFILE, fnm);
+
+ read_tps_conf(ftp2fn(efTPS, NFILE, fnm), &top, &ePBC, &xref, NULL, box, TRUE);
+ const char *title = *top.name;
+ snew(w_rls, top.atoms.nr);
+
+ fprintf(stderr, "Select group(s) for root mean square calculation\n");
+ get_index(&top.atoms, ftp2fn_null(efNDX, NFILE, fnm), 1, &isize, &index, &grpnames);
+
+ /* Set the weight */
+ for (i = 0; i < isize; i++)
+ {
+ w_rls[index[i]] = top.atoms.atom[index[i]].m;
+ }
+
+ /* Malloc the rmsf arrays */
+ snew(xav, isize*DIM);
+ snew(U, isize);
+ for (i = 0; i < isize; i++)
+ {
+ snew(U[i], DIM*DIM);
+ }
+ snew(rmsf, isize);
+ if (devfn)
+ {
+ snew(rmsd_x, isize);
+ }
+
+ if (bReadPDB)
+ {
+ t_topology *top_pdb;
+ snew(top_pdb, 1);
+ /* Read coordinates twice */
+ read_tps_conf(opt2fn("-q", NFILE, fnm), top_pdb, NULL, NULL, NULL, pdbbox, FALSE);
+ snew(pdbatoms, 1);
+ *pdbatoms = top_pdb->atoms;
+ read_tps_conf(opt2fn("-q", NFILE, fnm), top_pdb, NULL, &pdbx, NULL, pdbbox, FALSE);
++ /* TODO Should this assert that top_pdb->atoms.nr == top.atoms.nr?
++ * See discussion at https://gerrit.gromacs.org/#/c/6430/1 */
+ title = *top_pdb->name;
+ snew(refatoms, 1);
+ *refatoms = top_pdb->atoms;
+ sfree(top_pdb);
+ }
+ else
+ {
+ pdbatoms = &top.atoms;
+ refatoms = &top.atoms;
+ pdbx = xref;
+ snew(pdbatoms->pdbinfo, pdbatoms->nr);
+ copy_mat(box, pdbbox);
+ }
+
+ if (bFit)
+ {
+ sub_xcm(xref, isize, index, top.atoms.atom, xcm, FALSE);
+ }
+
+ natom = read_first_x(oenv, &status, ftp2fn(efTRX, NFILE, fnm), &t, &x, box);
+
+ if (bFit)
+ {
+ gpbc = gmx_rmpbc_init(&top.idef, ePBC, natom);
+ }
+
+ /* Now read the trj again to compute fluctuations */
+ teller = 0;
+ do
+ {
+ if (bFit)
+ {
+ /* Remove periodic boundary */
+ gmx_rmpbc(gpbc, natom, box, x);
+
+ /* Set center of mass to zero */
+ sub_xcm(x, isize, index, top.atoms.atom, xcm, FALSE);
+
+ /* Fit to reference structure */
+ do_fit(natom, w_rls, xref, x);
+ }
+
+ /* Calculate Anisotropic U Tensor */
+ for (i = 0; i < isize; i++)
+ {
+ aid = index[i];
+ for (d = 0; d < DIM; d++)
+ {
+ xav[i*DIM + d] += x[aid][d];
+ for (m = 0; m < DIM; m++)
+ {
+ U[i][d*DIM + m] += x[aid][d]*x[aid][m];
+ }
+ }
+ }
+
+ if (devfn)
+ {
+ /* Calculate RMS Deviation */
+ for (i = 0; (i < isize); i++)
+ {
+ aid = index[i];
+ for (d = 0; (d < DIM); d++)
+ {
+ rmsd_x[i][d] += gmx::square(x[aid][d]-xref[aid][d]);
+ }
+ }
+ }
+ count += 1.0;
+ teller++;
+ }
+ while (read_next_x(oenv, status, &t, x, box));
+ close_trj(status);
+
+ if (bFit)
+ {
+ gmx_rmpbc_done(gpbc);
+ }
+
+
+ invcount = 1.0/count;
+ snew(Uaver, DIM*DIM);
+ totmass = 0;
+ for (i = 0; i < isize; i++)
+ {
+ for (d = 0; d < DIM; d++)
+ {
+ xav[i*DIM + d] *= invcount;
+ }
+ for (d = 0; d < DIM; d++)
+ {
+ for (m = 0; m < DIM; m++)
+ {
+ U[i][d*DIM + m] = U[i][d*DIM + m]*invcount
+ - xav[i*DIM + d]*xav[i*DIM + m];
+ Uaver[3*d+m] += top.atoms.atom[index[i]].m*U[i][d*DIM + m];
+ }
+ }
+ totmass += top.atoms.atom[index[i]].m;
+ }
+ for (d = 0; d < DIM*DIM; d++)
+ {
+ Uaver[d] /= totmass;
+ }
+
+ if (bRes)
+ {
+ for (d = 0; d < DIM*DIM; d++)
+ {
+ average_residues(NULL, U, d, isize, index, w_rls, &top.atoms);
+ }
+ }
+
+ if (bAniso)
+ {
+ for (i = 0; i < isize; i++)
+ {
+ aid = index[i];
+ pdbatoms->pdbinfo[aid].bAnisotropic = TRUE;
+ pdbatoms->pdbinfo[aid].uij[U11] = static_cast<int>(1e6*U[i][XX*DIM + XX]);
+ pdbatoms->pdbinfo[aid].uij[U22] = static_cast<int>(1e6*U[i][YY*DIM + YY]);
+ pdbatoms->pdbinfo[aid].uij[U33] = static_cast<int>(1e6*U[i][ZZ*DIM + ZZ]);
+ pdbatoms->pdbinfo[aid].uij[U12] = static_cast<int>(1e6*U[i][XX*DIM + YY]);
+ pdbatoms->pdbinfo[aid].uij[U13] = static_cast<int>(1e6*U[i][XX*DIM + ZZ]);
+ pdbatoms->pdbinfo[aid].uij[U23] = static_cast<int>(1e6*U[i][YY*DIM + ZZ]);
+ }
+ }
+ if (bRes)
+ {
+ label = "Residue";
+ }
+ else
+ {
+ label = "Atom";
+ }
+
+ for (i = 0; i < isize; i++)
+ {
+ rmsf[i] = U[i][XX*DIM + XX] + U[i][YY*DIM + YY] + U[i][ZZ*DIM + ZZ];
+ }
+
+ if (dirfn)
+ {
+ fprintf(stdout, "\n");
+ print_dir(stdout, Uaver);
+ fp = gmx_ffopen(dirfn, "w");
+ print_dir(fp, Uaver);
+ gmx_ffclose(fp);
+ }
+
+ for (i = 0; i < isize; i++)
+ {
+ sfree(U[i]);
+ }
+ sfree(U);
+
+ /* Write RMSF output */
+ if (bReadPDB)
+ {
+ bfac = 8.0*M_PI*M_PI/3.0*100;
+ fp = xvgropen(ftp2fn(efXVG, NFILE, fnm), "B-Factors",
+ label, "(A\\b\\S\\So\\N\\S2\\N)", oenv);
+ xvgr_legend(fp, 2, leg, oenv);
+ for (i = 0; (i < isize); i++)
+ {
+ if (!bRes || i+1 == isize ||
+ top.atoms.atom[index[i]].resind != top.atoms.atom[index[i+1]].resind)
+ {
+ resind = top.atoms.atom[index[i]].resind;
+ pdb_bfac = find_pdb_bfac(pdbatoms, &top.atoms.resinfo[resind],
+ *(top.atoms.atomname[index[i]]));
+
+ fprintf(fp, "%5d %10.5f %10.5f\n",
+ bRes ? top.atoms.resinfo[top.atoms.atom[index[i]].resind].nr : index[i]+1, rmsf[i]*bfac,
+ pdb_bfac);
+ }
+ }
+ xvgrclose(fp);
+ }
+ else
+ {
+ fp = xvgropen(ftp2fn(efXVG, NFILE, fnm), "RMS fluctuation", label, "(nm)", oenv);
+ for (i = 0; i < isize; i++)
+ {
+ if (!bRes || i+1 == isize ||
+ top.atoms.atom[index[i]].resind != top.atoms.atom[index[i+1]].resind)
+ {
+ fprintf(fp, "%5d %8.4f\n",
+ bRes ? top.atoms.resinfo[top.atoms.atom[index[i]].resind].nr : index[i]+1, std::sqrt(rmsf[i]));
+ }
+ }
+ xvgrclose(fp);
+ }
+
+ for (i = 0; i < isize; i++)
+ {
+ pdbatoms->pdbinfo[index[i]].bfac = 800*M_PI*M_PI/3.0*rmsf[i];
+ }
+
+ if (devfn)
+ {
+ for (i = 0; i < isize; i++)
+ {
+ rmsf[i] = (rmsd_x[i][XX]+rmsd_x[i][YY]+rmsd_x[i][ZZ])/count;
+ }
+ if (bRes)
+ {
+ average_residues(rmsf, NULL, 0, isize, index, w_rls, &top.atoms);
+ }
+ /* Write RMSD output */
+ fp = xvgropen(devfn, "RMS Deviation", label, "(nm)", oenv);
+ for (i = 0; i < isize; i++)
+ {
+ if (!bRes || i+1 == isize ||
+ top.atoms.atom[index[i]].resind != top.atoms.atom[index[i+1]].resind)
+ {
+ fprintf(fp, "%5d %8.4f\n",
+ bRes ? top.atoms.resinfo[top.atoms.atom[index[i]].resind].nr : index[i]+1, std::sqrt(rmsf[i]));
+ }
+ }
+ xvgrclose(fp);
+ }
+
+ if (opt2bSet("-oq", NFILE, fnm))
+ {
+ /* Write a .pdb file with B-factors and optionally anisou records */
+ for (i = 0; i < isize; i++)
+ {
- /* Misuse xref as a temporary array */
++ rvec_inc(pdbx[index[i]], xcm);
+ }
+ write_sto_conf_indexed(opt2fn("-oq", NFILE, fnm), title, pdbatoms, pdbx,
+ NULL, ePBC, pdbbox, isize, index);
+ }
+ if (opt2bSet("-ox", NFILE, fnm))
+ {
- xref[index[i]][d] = xcm[d] + xav[i*DIM + d];
++ rvec *bFactorX;
++ snew(bFactorX, top.atoms.nr);
+ for (i = 0; i < isize; i++)
+ {
+ for (d = 0; d < DIM; d++)
+ {
- write_sto_conf_indexed(opt2fn("-ox", NFILE, fnm), title, pdbatoms, xref, NULL,
++ bFactorX[index[i]][d] = xcm[d] + xav[i*DIM + d];
+ }
+ }
+ /* Write a .pdb file with B-factors and optionally anisou records */
++ write_sto_conf_indexed(opt2fn("-ox", NFILE, fnm), title, pdbatoms, bFactorX, NULL,
+ ePBC, pdbbox, isize, index);
++ sfree(bFactorX);
+ }
+ if (bAniso)
+ {
+ correlate_aniso(opt2fn("-oc", NFILE, fnm), refatoms, pdbatoms, oenv);
+ do_view(oenv, opt2fn("-oc", NFILE, fnm), "-nxy");
+ }
+ do_view(oenv, opt2fn("-o", NFILE, fnm), "-nxy");
+ if (devfn)
+ {
+ do_view(oenv, opt2fn("-od", NFILE, fnm), "-nxy");
+ }
+
+ return 0;
+}
biod.pnpi.spb.ru / alexxy / gromacs.git / commitdiff