# Memory leaks in the legacy code are excluded
# Other problems besides memory leaks should NOT be excluded for legacy code
+# Ugly memory leak that depends on global variables being used to pass
+# information between routines.
+{
+ nsc_dclm_pbc
+ Memcheck:Leak
+ fun:calloc
+ fun:save_calloc
+ fun:ico_dot_dod
+ fun:make_unsp
+ fun:nsc_dclm_pbc
+}
+
+{
+ ctime_r
+ Memcheck:Leak
+ ...
+ fun:ctime_r
+}
+
{
libz
Memcheck:Cond
int
gmx_saltbr(int argc, char *argv[]);
-int
-gmx_sas(int argc, char *argv[]);
-
int
gmx_sham(int argc, char *argv[]);
+++ /dev/null
-/*
- * This file is part of the GROMACS molecular simulation package.
- *
- * Copyright (c) 1991-2000, University of Groningen, The Netherlands.
- * Copyright (c) 2001-2007, The GROMACS development team.
- * Copyright (c) 2013,2014, 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.
- */
-#ifdef HAVE_CONFIG_H
-#include <config.h>
-#endif
-#include <math.h>
-#include <stdlib.h>
-
-#include "sysstuff.h"
-#include <string.h>
-#include "typedefs.h"
-#include "smalloc.h"
-#include "macros.h"
-#include "vec.h"
-#include "xvgr.h"
-#include "pbc.h"
-#include "copyrite.h"
-#include "gromacs/fileio/futil.h"
-#include "gromacs/commandline/pargs.h"
-#include "index.h"
-#include "nsc.h"
-#include "gromacs/fileio/pdbio.h"
-#include "gromacs/fileio/confio.h"
-#include "rmpbc.h"
-#include "names.h"
-#include "atomprop.h"
-#include "physics.h"
-#include "gromacs/fileio/tpxio.h"
-#include "gromacs/fileio/trxio.h"
-#include "gmx_ana.h"
-
-
-typedef struct {
- atom_id aa, ab;
- real d2a, d2b;
-} t_conect;
-
-void add_rec(t_conect c[], atom_id i, atom_id j, real d2)
-{
- if (c[i].aa == NO_ATID)
- {
- c[i].aa = j;
- c[i].d2a = d2;
- }
- else if (c[i].ab == NO_ATID)
- {
- c[i].ab = j;
- c[i].d2b = d2;
- }
- else if (d2 < c[i].d2a)
- {
- c[i].aa = j;
- c[i].d2a = d2;
- }
- else if (d2 < c[i].d2b)
- {
- c[i].ab = j;
- c[i].d2b = d2;
- }
- /* Swap them if necessary: a must be larger than b */
- if (c[i].d2a < c[i].d2b)
- {
- j = c[i].ab;
- c[i].ab = c[i].aa;
- c[i].aa = j;
- d2 = c[i].d2b;
- c[i].d2b = c[i].d2a;
- c[i].d2a = d2;
- }
-}
-
-void do_conect(const char *fn, int n, rvec x[])
-{
- FILE *fp;
- int i, j;
- t_conect *c;
- rvec dx;
- real d2;
-
- fprintf(stderr, "Building CONECT records\n");
- snew(c, n);
- for (i = 0; (i < n); i++)
- {
- c[i].aa = c[i].ab = NO_ATID;
- }
-
- for (i = 0; (i < n); i++)
- {
- for (j = i+1; (j < n); j++)
- {
- rvec_sub(x[i], x[j], dx);
- d2 = iprod(dx, dx);
- add_rec(c, i, j, d2);
- add_rec(c, j, i, d2);
- }
- }
- fp = gmx_ffopen(fn, "a");
- for (i = 0; (i < n); i++)
- {
- if ((c[i].aa == NO_ATID) || (c[i].ab == NO_ATID))
- {
- fprintf(stderr, "Warning dot %d has no conections\n", i+1);
- }
- fprintf(fp, "CONECT%5d%5d%5d\n", i+1, c[i].aa+1, c[i].ab+1);
- }
- gmx_ffclose(fp);
- sfree(c);
-}
-
-void connelly_plot(const char *fn, int ndots, real dots[], rvec x[], t_atoms *atoms,
- t_symtab *symtab, int ePBC, matrix box, gmx_bool bSave)
-{
- static const char *atomnm = "DOT";
- static const char *resnm = "DOT";
- static const char *title = "Connely Dot Surface Generated by g_sas";
-
- int i, i0, r0, ii0, k;
- rvec *xnew;
- t_atoms aaa;
-
- if (bSave)
- {
- i0 = atoms->nr;
- r0 = atoms->nres;
- srenew(atoms->atom, atoms->nr+ndots);
- srenew(atoms->atomname, atoms->nr+ndots);
- srenew(atoms->resinfo, r0+1);
- atoms->atom[i0].resind = r0;
- t_atoms_set_resinfo(atoms, i0, symtab, resnm, r0+1, ' ', 0, ' ');
- srenew(atoms->pdbinfo, atoms->nr+ndots);
- snew(xnew, atoms->nr+ndots);
- for (i = 0; (i < atoms->nr); i++)
- {
- copy_rvec(x[i], xnew[i]);
- }
- for (i = k = 0; (i < ndots); i++)
- {
- ii0 = i0+i;
- atoms->atomname[ii0] = put_symtab(symtab, atomnm);
- atoms->pdbinfo[ii0].type = epdbATOM;
- atoms->pdbinfo[ii0].atomnr = ii0;
- atoms->atom[ii0].resind = r0;
- xnew[ii0][XX] = dots[k++];
- xnew[ii0][YY] = dots[k++];
- xnew[ii0][ZZ] = dots[k++];
- atoms->pdbinfo[ii0].bfac = 0.0;
- atoms->pdbinfo[ii0].occup = 0.0;
- }
- atoms->nr = i0+ndots;
- atoms->nres = r0+1;
- write_sto_conf(fn, title, atoms, xnew, NULL, ePBC, box);
- atoms->nres = r0;
- atoms->nr = i0;
- }
- else
- {
- init_t_atoms(&aaa, ndots, TRUE);
- aaa.atom[0].resind = 0;
- t_atoms_set_resinfo(&aaa, 0, symtab, resnm, 1, ' ', 0, ' ');
- snew(xnew, ndots);
- for (i = k = 0; (i < ndots); i++)
- {
- ii0 = i;
- aaa.atomname[ii0] = put_symtab(symtab, atomnm);
- aaa.pdbinfo[ii0].type = epdbATOM;
- aaa.pdbinfo[ii0].atomnr = ii0;
- aaa.atom[ii0].resind = 0;
- xnew[ii0][XX] = dots[k++];
- xnew[ii0][YY] = dots[k++];
- xnew[ii0][ZZ] = dots[k++];
- aaa.pdbinfo[ii0].bfac = 0.0;
- aaa.pdbinfo[ii0].occup = 0.0;
- }
- aaa.nr = ndots;
- write_sto_conf(fn, title, &aaa, xnew, NULL, ePBC, box);
- do_conect(fn, ndots, xnew);
- free_t_atoms(&aaa, FALSE);
- }
- sfree(xnew);
-}
-
-real calc_radius(char *atom)
-{
- real r;
-
- switch (atom[0])
- {
- case 'C':
- r = 0.16;
- break;
- case 'O':
- r = 0.13;
- break;
- case 'N':
- r = 0.14;
- break;
- case 'S':
- r = 0.2;
- break;
- case 'H':
- r = 0.1;
- break;
- default:
- r = 1e-3;
- }
- return r;
-}
-
-void sas_plot(int nfile, t_filenm fnm[], real solsize, int ndots,
- real qcut, gmx_bool bSave, real minarea, gmx_bool bPBC,
- real dgs_default, gmx_bool bFindex, const output_env_t oenv)
-{
- FILE *fp, *fp2, *fp3 = NULL, *vp;
- const char *flegend[] = {
- "Hydrophobic", "Hydrophilic",
- "Total", "D Gsolv"
- };
- const char *vlegend[] = { "Volume (nm\\S3\\N)", "Density (g/l)" };
- const char *or_and_oa_legend[] = { "Average (nm\\S2\\N)", "Standard deviation (nm\\S2\\N)" };
- const char *vfile;
- real t;
- gmx_atomprop_t aps = NULL;
- gmx_rmpbc_t gpbc = NULL;
- t_trxstatus *status;
- int ndefault;
- int i, j, ii, nfr, natoms, flag, nsurfacedots, res;
- rvec *xtop, *x;
- matrix topbox, box;
- t_topology top;
- char title[STRLEN];
- int ePBC;
- gmx_bool bTop;
- t_atoms *atoms;
- gmx_bool *bOut, *bPhobic;
- gmx_bool bConnelly;
- gmx_bool bResAt, bITP, bDGsol;
- real *radius, *dgs_factor = NULL, *area = NULL, *surfacedots = NULL;
- real at_area, *atom_area = NULL, *atom_area2 = NULL;
- real *res_a = NULL, *res_area = NULL, *res_area2 = NULL;
- real totarea, totvolume, totmass = 0, density, harea, tarea, fluc2;
- atom_id **index, *findex;
- int *nx, nphobic, npcheck, retval;
- char **grpname, *fgrpname;
- real dgsolv;
-
- bITP = opt2bSet("-i", nfile, fnm);
- bResAt = opt2bSet("-or", nfile, fnm) || opt2bSet("-oa", nfile, fnm) || bITP;
-
- bTop = read_tps_conf(ftp2fn(efTPS, nfile, fnm), title, &top, &ePBC,
- &xtop, NULL, topbox, FALSE);
- atoms = &(top.atoms);
-
- if (!bTop)
- {
- fprintf(stderr, "No tpr file, will not compute Delta G of solvation\n");
- bDGsol = FALSE;
- }
- else
- {
- bDGsol = strcmp(*(atoms->atomtype[0]), "?") != 0;
- if (!bDGsol)
- {
- fprintf(stderr, "Warning: your tpr file is too old, will not compute "
- "Delta G of solvation\n");
- }
- else
- {
- printf("In case you use free energy of solvation predictions:\n");
- please_cite(stdout, "Eisenberg86a");
- }
- }
-
- aps = gmx_atomprop_init();
-
- if ((natoms = read_first_x(oenv, &status, ftp2fn(efTRX, nfile, fnm),
- &t, &x, box)) == 0)
- {
- gmx_fatal(FARGS, "Could not read coordinates from statusfile\n");
- }
-
- if ((ePBC != epbcXYZ) || (TRICLINIC(box)))
- {
- fprintf(stderr, "\n\nWARNING: non-rectangular boxes may give erroneous results or crashes.\n"
- "Analysis based on vacuum simulations (with the possibility of evaporation)\n"
- "will certainly crash the analysis.\n\n");
- }
- snew(nx, 2);
- snew(index, 2);
- snew(grpname, 2);
- fprintf(stderr, "Select a group for calculation of surface and a group for output:\n");
- get_index(atoms, ftp2fn_null(efNDX, nfile, fnm), 2, nx, index, grpname);
-
- if (bFindex)
- {
- fprintf(stderr, "Select a group of hydrophobic atoms:\n");
- get_index(atoms, ftp2fn_null(efNDX, nfile, fnm), 1, &nphobic, &findex, &fgrpname);
- }
- snew(bOut, natoms);
- for (i = 0; i < nx[1]; i++)
- {
- bOut[index[1][i]] = TRUE;
- }
-
- /* Now compute atomic readii including solvent probe size */
- snew(radius, natoms);
- snew(bPhobic, nx[0]);
- if (bResAt)
- {
- snew(atom_area, nx[0]);
- snew(atom_area2, nx[0]);
- snew(res_a, atoms->nres);
- snew(res_area, atoms->nres);
- snew(res_area2, atoms->nres);
- }
- if (bDGsol)
- {
- snew(dgs_factor, nx[0]);
- }
-
- /* Get a Van der Waals radius for each atom */
- ndefault = 0;
- for (i = 0; (i < natoms); i++)
- {
- if (!gmx_atomprop_query(aps, epropVDW,
- *(atoms->resinfo[atoms->atom[i].resind].name),
- *(atoms->atomname[i]), &radius[i]))
- {
- ndefault++;
- }
- /* radius[i] = calc_radius(*(top->atoms.atomname[i])); */
- radius[i] += solsize;
- }
- if (ndefault > 0)
- {
- fprintf(stderr, "WARNING: could not find a Van der Waals radius for %d atoms\n", ndefault);
- }
- /* Determine which atom is counted as hydrophobic */
- if (bFindex)
- {
- npcheck = 0;
- for (i = 0; (i < nx[0]); i++)
- {
- ii = index[0][i];
- for (j = 0; (j < nphobic); j++)
- {
- if (findex[j] == ii)
- {
- bPhobic[i] = TRUE;
- if (bOut[ii])
- {
- npcheck++;
- }
- }
- }
- }
- if (npcheck != nphobic)
- {
- gmx_fatal(FARGS, "Consistency check failed: not all %d atoms in the hydrophobic index\n"
- "found in the normal index selection (%d atoms)", nphobic, npcheck);
- }
- }
- else
- {
- nphobic = 0;
- }
-
- for (i = 0; (i < nx[0]); i++)
- {
- ii = index[0][i];
- if (!bFindex)
- {
- bPhobic[i] = fabs(atoms->atom[ii].q) <= qcut;
- if (bPhobic[i] && bOut[ii])
- {
- nphobic++;
- }
- }
- if (bDGsol)
- {
- if (!gmx_atomprop_query(aps, epropDGsol,
- *(atoms->resinfo[atoms->atom[ii].resind].name),
- *(atoms->atomtype[ii]), &(dgs_factor[i])))
- {
- dgs_factor[i] = dgs_default;
- }
- }
- if (debug)
- {
- fprintf(debug, "Atom %5d %5s-%5s: q= %6.3f, r= %6.3f, dgsol= %6.3f, hydrophobic= %s\n",
- ii+1, *(atoms->resinfo[atoms->atom[ii].resind].name),
- *(atoms->atomname[ii]),
- atoms->atom[ii].q, radius[ii]-solsize, dgs_factor[i],
- EBOOL(bPhobic[i]));
- }
- }
- fprintf(stderr, "%d out of %d atoms were classified as hydrophobic\n",
- nphobic, nx[1]);
-
- fp = xvgropen(opt2fn("-o", nfile, fnm), "Solvent Accessible Surface", "Time (ps)",
- "Area (nm\\S2\\N)", oenv);
- xvgr_legend(fp, asize(flegend) - (bDGsol ? 0 : 1), flegend, oenv);
- vfile = opt2fn_null("-tv", nfile, fnm);
- if (vfile)
- {
- if (!bTop)
- {
- gmx_fatal(FARGS, "Need a tpr file for option -tv");
- }
- vp = xvgropen(vfile, "Volume and Density", "Time (ps)", "", oenv);
- xvgr_legend(vp, asize(vlegend), vlegend, oenv);
- totmass = 0;
- ndefault = 0;
- for (i = 0; (i < nx[0]); i++)
- {
- real mm;
- ii = index[0][i];
- /*
- if (!query_atomprop(atomprop,epropMass,
- *(top->atoms.resname[top->atoms.atom[ii].resnr]),
- *(top->atoms.atomname[ii]),&mm))
- ndefault++;
- totmass += mm;
- */
- totmass += atoms->atom[ii].m;
- }
- if (ndefault)
- {
- fprintf(stderr, "WARNING: Using %d default masses for density calculation, which most likely are inaccurate\n", ndefault);
- }
- }
- else
- {
- vp = NULL;
- }
-
- gmx_atomprop_destroy(aps);
-
- if (bPBC)
- {
- gpbc = gmx_rmpbc_init(&top.idef, ePBC, natoms);
- }
-
- nfr = 0;
- do
- {
- if (bPBC)
- {
- gmx_rmpbc(gpbc, natoms, box, x);
- }
-
- bConnelly = (nfr == 0 && opt2bSet("-q", nfile, fnm));
- if (bConnelly)
- {
- if (!bTop)
- {
- gmx_fatal(FARGS, "Need a tpr file for Connelly plot");
- }
- flag = FLAG_ATOM_AREA | FLAG_DOTS;
- }
- else
- {
- flag = FLAG_ATOM_AREA;
- }
- if (vp)
- {
- flag = flag | FLAG_VOLUME;
- }
-
- if (debug)
- {
- write_sto_conf("check.pdb", "pbc check", atoms, x, NULL, ePBC, box);
- }
-
- retval = nsc_dclm_pbc(x, radius, nx[0], ndots, flag, &totarea,
- &area, &totvolume, &surfacedots, &nsurfacedots,
- index[0], ePBC, bPBC ? box : NULL);
- if (retval)
- {
- gmx_fatal(FARGS, "Something wrong in nsc_dclm_pbc");
- }
-
- if (bConnelly)
- {
- connelly_plot(ftp2fn(efPDB, nfile, fnm),
- nsurfacedots, surfacedots, x, atoms,
- &(top.symtab), ePBC, box, bSave);
- }
- harea = 0;
- tarea = 0;
- dgsolv = 0;
- if (bResAt)
- {
- for (i = 0; i < atoms->nres; i++)
- {
- res_a[i] = 0;
- }
- }
- for (i = 0; (i < nx[0]); i++)
- {
- ii = index[0][i];
- if (bOut[ii])
- {
- at_area = area[i];
- if (bResAt)
- {
- atom_area[i] += at_area;
- atom_area2[i] += sqr(at_area);
- res_a[atoms->atom[ii].resind] += at_area;
- }
- tarea += at_area;
- if (bDGsol)
- {
- dgsolv += at_area*dgs_factor[i];
- }
- if (bPhobic[i])
- {
- harea += at_area;
- }
- }
- }
- if (bResAt)
- {
- for (i = 0; i < atoms->nres; i++)
- {
- res_area[i] += res_a[i];
- res_area2[i] += sqr(res_a[i]);
- }
- }
- fprintf(fp, "%10g %10g %10g %10g", t, harea, tarea-harea, tarea);
- if (bDGsol)
- {
- fprintf(fp, " %10g\n", dgsolv);
- }
- else
- {
- fprintf(fp, "\n");
- }
-
- /* Print volume */
- if (vp)
- {
- density = totmass*AMU/(totvolume*NANO*NANO*NANO);
- fprintf(vp, "%12.5e %12.5e %12.5e\n", t, totvolume, density);
- }
- if (area)
- {
- sfree(area);
- area = NULL;
- }
- if (surfacedots)
- {
- sfree(surfacedots);
- surfacedots = NULL;
- }
- nfr++;
- }
- while (read_next_x(oenv, status, &t, x, box));
-
- if (bPBC)
- {
- gmx_rmpbc_done(gpbc);
- }
-
- fprintf(stderr, "\n");
- close_trj(status);
- gmx_ffclose(fp);
- if (vp)
- {
- gmx_ffclose(vp);
- }
-
- /* if necessary, print areas per atom to file too: */
- if (bResAt)
- {
- for (i = 0; i < atoms->nres; i++)
- {
- res_area[i] /= nfr;
- res_area2[i] /= nfr;
- }
- for (i = 0; i < nx[0]; i++)
- {
- atom_area[i] /= nfr;
- atom_area2[i] /= nfr;
- }
- fprintf(stderr, "Printing out areas per atom\n");
- fp = xvgropen(opt2fn("-or", nfile, fnm), "Area per residue over the trajectory", "Residue",
- "Area (nm\\S2\\N)", oenv);
- xvgr_legend(fp, asize(or_and_oa_legend), or_and_oa_legend, oenv);
- fp2 = xvgropen(opt2fn("-oa", nfile, fnm), "Area per atom over the trajectory", "Atom #",
- "Area (nm\\S2\\N)", oenv);
- xvgr_legend(fp2, asize(or_and_oa_legend), or_and_oa_legend, oenv);
- if (bITP)
- {
- fp3 = ftp2FILE(efITP, nfile, fnm, "w");
- fprintf(fp3, "[ position_restraints ]\n"
- "#define FCX 1000\n"
- "#define FCY 1000\n"
- "#define FCZ 1000\n"
- "; Atom Type fx fy fz\n");
- }
- for (i = 0; i < nx[0]; i++)
- {
- ii = index[0][i];
- res = atoms->atom[ii].resind;
- if (i == nx[0]-1 || res != atoms->atom[index[0][i+1]].resind)
- {
- fluc2 = res_area2[res]-sqr(res_area[res]);
- if (fluc2 < 0)
- {
- fluc2 = 0;
- }
- fprintf(fp, "%10d %10g %10g\n",
- atoms->resinfo[res].nr, res_area[res], sqrt(fluc2));
- }
- fluc2 = atom_area2[i]-sqr(atom_area[i]);
- if (fluc2 < 0)
- {
- fluc2 = 0;
- }
- fprintf(fp2, "%d %g %g\n", index[0][i]+1, atom_area[i], sqrt(fluc2));
- if (bITP && (atom_area[i] > minarea))
- {
- fprintf(fp3, "%5d 1 FCX FCX FCZ\n", ii+1);
- }
- }
- if (bITP)
- {
- gmx_ffclose(fp3);
- }
- gmx_ffclose(fp);
- }
-
- /* Be a good citizen, keep our memory free! */
- sfree(x);
- sfree(nx);
- for (i = 0; i < 2; i++)
- {
- sfree(index[i]);
- sfree(grpname[i]);
- }
- sfree(bOut);
- sfree(radius);
- sfree(bPhobic);
-
- if (bResAt)
- {
- sfree(atom_area);
- sfree(atom_area2);
- sfree(res_a);
- sfree(res_area);
- sfree(res_area2);
- }
- if (bDGsol)
- {
- sfree(dgs_factor);
- }
-}
-
-int gmx_sas(int argc, char *argv[])
-{
- const char *desc[] = {
- "[THISMODULE] computes hydrophobic, hydrophilic and total solvent",
- "accessible surface area. See Eisenhaber F, Lijnzaad P, Argos P,",
- "Sander C, & Scharf M (1995) J. Comput. Chem. 16, 273-284.",
- "As a side effect, the Connolly surface can be generated as well in",
- "a [TT].pdb[tt] file where the nodes are represented as atoms and the",
- "vertice connecting the nearest nodes as CONECT records.",
- "The program will ask for a group for the surface calculation",
- "and a group for the output. The calculation group should always",
- "consists of all the non-solvent atoms in the system.",
- "The output group can be the whole or part of the calculation group.",
- "The average and standard deviation of the area over the trajectory can be plotted",
- "per residue and atom as well (options [TT]-or[tt] and [TT]-oa[tt]).",
- "In combination with the latter option an [TT].itp[tt] file can be",
- "generated (option [TT]-i[tt])",
- "which can be used to restrain surface atoms.[PAR]",
-
- "By default, periodic boundary conditions are taken into account,",
- "this can be turned off using the [TT]-nopbc[tt] option.[PAR]",
-
- "With the [TT]-tv[tt] option the total volume and density of the",
- "molecule can be computed.",
- "Please consider whether the normal probe radius is appropriate",
- "in this case or whether you would rather use e.g. 0. It is good",
- "to keep in mind that the results for volume and density are very",
- "approximate. For example, in ice Ih, one can easily fit water molecules in the",
- "pores which would yield a volume that is too low, and surface area and density",
- "that are both too high."
- };
-
- output_env_t oenv;
- static real solsize = 0.14;
- static int ndots = 24;
- static real qcut = 0.2;
- static real minarea = 0.5, dgs_default = 0;
- static gmx_bool bSave = TRUE, bPBC = TRUE, bFindex = FALSE;
- t_pargs pa[] = {
- { "-probe", FALSE, etREAL, {&solsize},
- "Radius of the solvent probe (nm)" },
- { "-ndots", FALSE, etINT, {&ndots},
- "Number of dots per sphere, more dots means more accuracy" },
- { "-qmax", FALSE, etREAL, {&qcut},
- "The maximum charge (e, absolute value) of a hydrophobic atom" },
- { "-f_index", FALSE, etBOOL, {&bFindex},
- "Determine from a group in the index file what are the hydrophobic atoms rather than from the charge" },
- { "-minarea", FALSE, etREAL, {&minarea},
- "The minimum area (nm^2) to count an atom as a surface atom when writing a position restraint file (see help)" },
- { "-pbc", FALSE, etBOOL, {&bPBC},
- "Take periodicity into account" },
- { "-prot", FALSE, etBOOL, {&bSave},
- "Output the protein to the Connelly [TT].pdb[tt] file too" },
- { "-dgs", FALSE, etREAL, {&dgs_default},
- "Default value for solvation free energy per area (kJ/mol/nm^2)" }
- };
- t_filenm fnm[] = {
- { efTRX, "-f", NULL, ffREAD },
- { efTPS, "-s", NULL, ffREAD },
- { efXVG, "-o", "area", ffWRITE },
- { efXVG, "-or", "resarea", ffOPTWR },
- { efXVG, "-oa", "atomarea", ffOPTWR },
- { efXVG, "-tv", "volume", ffOPTWR },
- { efPDB, "-q", "connelly", ffOPTWR },
- { efNDX, "-n", "index", ffOPTRD },
- { efITP, "-i", "surfat", ffOPTWR }
- };
-#define NFILE asize(fnm)
-
- if (!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))
- {
- return 0;
- }
- if (solsize < 0)
- {
- solsize = 1e-3;
- fprintf(stderr, "Probe size too small, setting it to %g\n", solsize);
- }
- if (ndots < 20)
- {
- ndots = 20;
- fprintf(stderr, "Ndots too small, setting it to %d\n", ndots);
- }
-
- please_cite(stderr, "Eisenhaber95");
-
- sas_plot(NFILE, fnm, solsize, ndots, qcut, bSave, minarea, bPBC, dgs_default, bFindex,
- oenv);
-
- do_view(oenv, opt2fn("-o", NFILE, fnm), "-nxy");
- do_view(oenv, opt2fn_null("-or", NFILE, fnm), "-nxy");
- do_view(oenv, opt2fn_null("-oa", NFILE, fnm), "-nxy");
-
- return 0;
-}
//! Returns whether the selection object is initialized.
bool isValid() const { return sel_ != NULL; }
+ //! Returns whether two selection objects wrap the same selection.
+ bool operator==(const Selection &other) const
+ {
+ return sel_ == other.sel_;
+ }
+ //! Returns whether two selection objects wrap different selections.
+ bool operator!=(const Selection &other) const
+ {
+ return !operator==(other);
+ }
+
//! Returns the name of the selection.
const char *name() const { return data().name(); }
//! Returns the string that was parsed to produce this selection.
#
# This file is part of the GROMACS molecular simulation package.
#
-# Copyright (c) 2010,2013, by the GROMACS development team, led by
+# Copyright (c) 2010,2013,2014, 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.
# To help us fund GROMACS development, we humbly ask that you cite
# the research papers on the package. Check out http://www.gromacs.org.
-file(GLOB TRAJECTORYANALYSIS_SOURCES *.cpp modules/*.cpp)
+file(GLOB TRAJECTORYANALYSIS_SOURCES *.cpp modules/*.cpp modules/*.c)
set(LIBGROMACS_SOURCES ${LIBGROMACS_SOURCES} ${TRAJECTORYANALYSIS_SOURCES} PARENT_SCOPE)
set(TRAJECTORYANALYSIS_PUBLIC_HEADERS
#include "modules/angle.h"
#include "modules/distance.h"
#include "modules/freevolume.h"
+#include "modules/sasa.h"
#include "modules/select.h"
namespace gmx
registerModule<AngleInfo>(manager, group);
registerModule<DistanceInfo>(manager, group);
registerModule<FreeVolumeInfo>(manager, group);
+ registerModule<SasaInfo>(manager, group);
registerModule<SelectInfo>(manager, group);
}
//! \endcond
*
* Copyright (c) 1991-2000, University of Groningen, The Netherlands.
* Copyright (c) 2001-2007, The GROMACS development team.
- * Copyright (c) 2013, by the GROMACS development team, led by
+ * Copyright (c) 2013,2014, 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.
real *xpunsp = NULL;
real del_cube;
-int *ico_wk = NULL, *ico_pt = NULL;
int n_dot, ico_cube, last_n_dot = 0, last_densit = 0, last_unsp = 0;
int last_cubus = 0;
int make_unsp(int densit, int mode, int * num_dot, int cubus)
{
+ int *ico_wk, *ico_pt;
int ndot, ico_cube_cb, i, j, k, l, ijk, tn, tl, tl2;
real *xus;
int *work;
{
free(xpunsp);
}
- if (ico_wk)
- {
- free(ico_wk);
- }
k = 1; if (mode < 0)
{
} /* cycle k */
} /* cycle j */
} /* cycle i */
- free(work);
+ sfree(ico_wk);
+ sfree(work);
return 0;
}
real dot;
} Neighb;
-int nsc_dclm_pbc(rvec *coords, real *radius, int nat,
+int nsc_dclm_pbc(const rvec *coords, real *radius, int nat,
int densit, int mode,
real *value_of_area, real **at_area,
real *value_of_vol,
real **lidots, int *nu_dots,
atom_id index[], int ePBC, matrix box)
{
- int iat, i, ii, iii, ix, iy, iz, ixe, ixs, iye, iys, ize, izs, i_ac;
- int jat, j, jj, jjj, jx, jy, jz;
- int distribution;
- int l;
- int maxnei, nnei, last, maxdots = 0;
- int *wkdot = NULL, *wkbox = NULL, *wkat1 = NULL, *wkatm = NULL;
- Neighb *wknb, *ctnb;
- int iii1, iii2, iiat, lfnr = 0, i_at, j_at;
- real dx, dy, dz, dd, ai, aisq, ajsq, aj, as, a;
- real xi, yi, zi, xs = 0., ys = 0., zs = 0.;
- real dotarea, area, vol = 0.;
- real *xus, *dots = NULL, *atom_area = NULL;
- int nxbox, nybox, nzbox, nxy, nxyz;
- real xmin = 0, ymin = 0, zmin = 0, xmax, ymax, zmax, ra2max, d, *pco;
+ int iat, i, ii, iii, ix, iy, iz, ixe, ixs, iye, iys, ize, izs, i_ac;
+ int jat, j, jj, jjj, jx, jy, jz;
+ int distribution;
+ int l;
+ int maxnei, nnei, last, maxdots = 0;
+ int *wkdot = NULL, *wkbox = NULL, *wkat1 = NULL, *wkatm = NULL;
+ Neighb *wknb, *ctnb;
+ int iii1, iii2, iiat, lfnr = 0, i_at, j_at;
+ real dx, dy, dz, dd, ai, aisq, ajsq, aj, as, a;
+ real xi, yi, zi, xs = 0., ys = 0., zs = 0.;
+ real dotarea, area, vol = 0.;
+ real *xus, *dots = NULL, *atom_area = NULL;
+ int nxbox, nybox, nzbox, nxy, nxyz;
+ real xmin = 0, ymin = 0, zmin = 0, xmax, ymax, zmax, ra2max, d;
+ const real *pco;
/* Added DvdS 2006-07-19 */
- t_pbc pbc;
- rvec ddx, *x = NULL;
- int iat_xx, jat_xx;
+ t_pbc pbc;
+ rvec ddx, *x = NULL;
+ int iat_xx, jat_xx;
distribution = unsp_type(densit);
if (distribution != -last_unsp || last_cubus != 4 ||
*
* Copyright (c) 1991-2000, University of Groningen, The Netherlands.
* Copyright (c) 2001-2004, The GROMACS development team.
- * Copyright (c) 2013, by the GROMACS development team, led by
+ * Copyright (c) 2013,2014, 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.
#define FLAG_VOLUME 02
#define FLAG_ATOM_AREA 04
+#ifdef __cplusplus
+extern "C"
+{
+#endif
-
-extern int nsc_dclm_pbc(rvec *coords, real *radius, int nat,
- int densit, int mode,
- real *value_of_area, real **at_area,
- real *value_of_vol,
- real **lidots, int *nu_dots,
- atom_id index[], int ePBC, matrix box);
+int nsc_dclm_pbc(const rvec *coords, real *radius, int nat,
+ int densit, int mode,
+ real *value_of_area, real **at_area,
+ real *value_of_vol,
+ real **lidots, int *nu_dots,
+ atom_id index[], int ePBC, matrix box);
/*
User notes :
}
*/
+
+#ifdef __cplusplus
+}
+#endif
--- /dev/null
+/*
+ * This file is part of the GROMACS molecular simulation package.
+ *
+ * Copyright (c) 1991-2000, University of Groningen, The Netherlands.
+ * Copyright (c) 2001-2006, The GROMACS development team.
+ * Copyright (c) 2008,2009,2010,2011,2012,2013,2014, 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.
+ */
+/*! \internal \file
+ * \brief
+ * Implements gmx::analysismodules::Sasa.
+ *
+ * \author Teemu Murtola <teemu.murtola@gmail.com> (C++ conversion)
+ * \ingroup module_trajectoryanalysis
+ */
+#include "sasa.h"
+
+#include <algorithm>
+#include <string>
+#include <vector>
+
+#include "gromacs/legacyheaders/atomprop.h"
+#include "gromacs/legacyheaders/copyrite.h"
+#include "gromacs/legacyheaders/pbc.h"
+#include "gromacs/legacyheaders/physics.h"
+#include "gromacs/legacyheaders/smalloc.h"
+#include "gromacs/legacyheaders/symtab.h"
+#include "gromacs/legacyheaders/vec.h"
+
+#include "gromacs/analysisdata/analysisdata.h"
+#include "gromacs/analysisdata/modules/average.h"
+#include "gromacs/analysisdata/modules/plot.h"
+#include "gromacs/fileio/confio.h"
+#include "gromacs/fileio/futil.h"
+#include "gromacs/fileio/pdbio.h"
+#include "gromacs/options/basicoptions.h"
+#include "gromacs/options/filenameoption.h"
+#include "gromacs/options/options.h"
+#include "gromacs/selection/selection.h"
+#include "gromacs/selection/selectionoption.h"
+#include "gromacs/trajectoryanalysis/analysismodule.h"
+#include "gromacs/trajectoryanalysis/analysissettings.h"
+#include "gromacs/utility/exceptions.h"
+#include "gromacs/utility/stringutil.h"
+
+#include "nsc.h"
+
+namespace gmx
+{
+
+namespace analysismodules
+{
+
+namespace
+{
+
+//! \addtogroup module_trajectoryanalysis
+//! \{
+
+//! Tracks information on two nearest neighbors of a single surface dot.
+struct t_conect
+{
+ //! Index of the second nearest neighbor dot.
+ atom_id aa;
+ //! Index of the nearest neighbor dot.
+ atom_id ab;
+ //! Squared distance to `aa`.
+ real d2a;
+ //! Squared distance to `ab`.
+ real d2b;
+};
+
+/*! \brief
+ * Updates nearest neighbor information for a surface dot.
+ *
+ * \param[in,out] c Nearest neighbor information array to update.
+ * \param[in] i Index in `c` to update.
+ * \param[in] j Index of the other surface dot to add to the array.
+ * \param[in] d2 Squared distance between `i` and `j`.
+ */
+void add_rec(t_conect c[], atom_id i, atom_id j, real d2)
+{
+ if (c[i].aa == NO_ATID)
+ {
+ c[i].aa = j;
+ c[i].d2a = d2;
+ }
+ else if (c[i].ab == NO_ATID)
+ {
+ c[i].ab = j;
+ c[i].d2b = d2;
+ }
+ else if (d2 < c[i].d2a)
+ {
+ c[i].aa = j;
+ c[i].d2a = d2;
+ }
+ else if (d2 < c[i].d2b)
+ {
+ c[i].ab = j;
+ c[i].d2b = d2;
+ }
+ /* Swap them if necessary: a must be larger than b */
+ if (c[i].d2a < c[i].d2b)
+ {
+ j = c[i].ab;
+ c[i].ab = c[i].aa;
+ c[i].aa = j;
+ d2 = c[i].d2b;
+ c[i].d2b = c[i].d2a;
+ c[i].d2a = d2;
+ }
+}
+
+/*! \brief
+ * Adds CONECT records for surface dots.
+ *
+ * \param[in] fn PDB file to append the CONECT records to.
+ * \param[in] n Number of dots in `x`.
+ * \param[in] x Array of surface dot positions.
+ *
+ * Adds a CONECT record that connects each surface dot to its two nearest
+ * neighbors. The function is copied verbatim from the old gmx_sas.c
+ * implementation.
+ */
+void do_conect(const char *fn, int n, rvec x[])
+{
+ FILE *fp;
+ int i, j;
+ t_conect *c;
+ rvec dx;
+ real d2;
+
+ fprintf(stderr, "Building CONECT records\n");
+ snew(c, n);
+ for (i = 0; (i < n); i++)
+ {
+ c[i].aa = c[i].ab = NO_ATID;
+ }
+
+ for (i = 0; (i < n); i++)
+ {
+ for (j = i+1; (j < n); j++)
+ {
+ rvec_sub(x[i], x[j], dx);
+ d2 = iprod(dx, dx);
+ add_rec(c, i, j, d2);
+ add_rec(c, j, i, d2);
+ }
+ }
+ fp = gmx_ffopen(fn, "a");
+ for (i = 0; (i < n); i++)
+ {
+ if ((c[i].aa == NO_ATID) || (c[i].ab == NO_ATID))
+ {
+ fprintf(stderr, "Warning dot %d has no conections\n", i+1);
+ }
+ fprintf(fp, "CONECT%5d%5d%5d\n", i+1, c[i].aa+1, c[i].ab+1);
+ }
+ gmx_ffclose(fp);
+ sfree(c);
+}
+
+/*! \brief
+ * Plots the surface into a PDB file, optionally including the original atoms.
+ */
+void connolly_plot(const char *fn, int ndots, real dots[], rvec x[], t_atoms *atoms,
+ t_symtab *symtab, int ePBC, const matrix box, gmx_bool bIncludeSolute)
+{
+ const char *const atomnm = "DOT";
+ const char *const resnm = "DOT";
+ const char *const title = "Connolly Dot Surface Generated by gmx sasa";
+
+ int i, i0, r0, ii0, k;
+ rvec *xnew;
+ t_atoms aaa;
+
+ if (bIncludeSolute)
+ {
+ i0 = atoms->nr;
+ r0 = atoms->nres;
+ srenew(atoms->atom, atoms->nr+ndots);
+ memset(&atoms->atom[i0], 0, sizeof(*atoms->atom)*ndots);
+ srenew(atoms->atomname, atoms->nr+ndots);
+ srenew(atoms->resinfo, r0+1);
+ atoms->atom[i0].resind = r0;
+ t_atoms_set_resinfo(atoms, i0, symtab, resnm, r0+1, ' ', 0, ' ');
+ if (atoms->pdbinfo != NULL)
+ {
+ srenew(atoms->pdbinfo, atoms->nr+ndots);
+ }
+ snew(xnew, atoms->nr+ndots);
+ for (i = 0; (i < atoms->nr); i++)
+ {
+ copy_rvec(x[i], xnew[i]);
+ }
+ for (i = k = 0; (i < ndots); i++)
+ {
+ ii0 = i0+i;
+ atoms->atomname[ii0] = put_symtab(symtab, atomnm);
+ atoms->atom[ii0].resind = r0;
+ xnew[ii0][XX] = dots[k++];
+ xnew[ii0][YY] = dots[k++];
+ xnew[ii0][ZZ] = dots[k++];
+ if (atoms->pdbinfo != NULL)
+ {
+ atoms->pdbinfo[ii0].type = epdbATOM;
+ atoms->pdbinfo[ii0].atomnr = ii0;
+ atoms->pdbinfo[ii0].bfac = 0.0;
+ atoms->pdbinfo[ii0].occup = 0.0;
+ }
+ }
+ atoms->nr = i0+ndots;
+ atoms->nres = r0+1;
+ write_sto_conf(fn, title, atoms, xnew, NULL, ePBC, const_cast<rvec *>(box));
+ atoms->nres = r0;
+ atoms->nr = i0;
+ }
+ else
+ {
+ init_t_atoms(&aaa, ndots, TRUE);
+ aaa.atom[0].resind = 0;
+ t_atoms_set_resinfo(&aaa, 0, symtab, resnm, 1, ' ', 0, ' ');
+ snew(xnew, ndots);
+ for (i = k = 0; (i < ndots); i++)
+ {
+ ii0 = i;
+ aaa.atomname[ii0] = put_symtab(symtab, atomnm);
+ aaa.pdbinfo[ii0].type = epdbATOM;
+ aaa.pdbinfo[ii0].atomnr = ii0;
+ aaa.atom[ii0].resind = 0;
+ xnew[ii0][XX] = dots[k++];
+ xnew[ii0][YY] = dots[k++];
+ xnew[ii0][ZZ] = dots[k++];
+ aaa.pdbinfo[ii0].bfac = 0.0;
+ aaa.pdbinfo[ii0].occup = 0.0;
+ }
+ aaa.nr = ndots;
+ write_sto_conf(fn, title, &aaa, xnew, NULL, ePBC, const_cast<rvec *>(box));
+ do_conect(fn, ndots, xnew);
+ free_t_atoms(&aaa, FALSE);
+ }
+ sfree(xnew);
+}
+
+/********************************************************************
+ * Actual analysis module
+ */
+
+/*! \brief
+ * Implements `gmx sas` trajectory analysis module.
+ */
+class Sasa : public TrajectoryAnalysisModule
+{
+ public:
+ Sasa();
+
+ virtual void initOptions(Options *options,
+ TrajectoryAnalysisSettings *settings);
+ virtual void initAnalysis(const TrajectoryAnalysisSettings &settings,
+ const TopologyInformation &top);
+
+ virtual TrajectoryAnalysisModuleDataPointer startFrames(
+ const AnalysisDataParallelOptions &opt,
+ const SelectionCollection &selections);
+ virtual void analyzeFrame(int frnr, const t_trxframe &fr, t_pbc *pbc,
+ TrajectoryAnalysisModuleData *pdata);
+
+ virtual void finishAnalysis(int nframes);
+ virtual void writeOutput();
+
+ private:
+ /*! \brief
+ * Surface areas as a function of time.
+ *
+ * First column is for the calculation group, and the rest for the
+ * output groups. This data is always produced.
+ */
+ AnalysisData area_;
+ /*! \brief
+ * Per-atom surface areas as a function of time.
+ *
+ * Contains one data set for each column in `area_`.
+ * Each column corresponds to a selection position in `surfaceSel_`.
+ * This data is only produced if atom or residue areas have been
+ * requested.
+ */
+ AnalysisData atomArea_;
+ /*! \brief
+ * Per-residue surface areas as a function of time.
+ *
+ * Contains one data set for each column in `area_`.
+ * Each column corresponds to a distinct residue `surfaceSel_`.
+ * For example, if `surfaceSel_` selects residues 2, 5, and 7, there
+ * will be three columns here.
+ * This data is only produced if atom or residue areas have been
+ * requested.
+ */
+ AnalysisData residueArea_;
+ /*! \brief
+ * Free energy estimates as a function of time.
+ *
+ * Column layout is the same as for `area_`.
+ * This data is only produced if the output is requested.
+ */
+ AnalysisData dgSolv_;
+ /*! \brief
+ * Total volume and density of the calculation group as a function of
+ * time.
+ *
+ * The first column is the volume and the second column is the density.
+ * This data is only produced if the output is requested.
+ */
+ AnalysisData volume_;
+
+ /*! \brief
+ * The selection to calculate the surface for.
+ *
+ * Selection::originalId() and Selection::mappedId() store the mapping
+ * from the positions to the columns of `residueArea_`.
+ * The selection is computed with SelectionOption::dynamicMask(), i.e.,
+ * even in the presence of a dynamic selection, the number of returned
+ * positions is fixed, and SelectionPosition::selected() is used.
+ */
+ Selection surfaceSel_;
+ /*! \brief
+ * List of optional additional output groups.
+ *
+ * Each of these must be a subset of the `surfaceSel_`.
+ * Selection::originalId() and Selection::mappedId() store the mapping
+ * from the positions to the corresponsing positions in `surfaceSel_`.
+ */
+ SelectionList outputSel_;
+
+ std::string fnArea_;
+ std::string fnAtomArea_;
+ std::string fnResidueArea_;
+ std::string fnDGSolv_;
+ std::string fnVolume_;
+ std::string fnConnolly_;
+
+ double solsize_;
+ int ndots_;
+ //double minarea_;
+ double dgsDefault_;
+ bool bIncludeSolute_;
+
+ t_topology *top_;
+ //! Combined VdW and probe radii for each atom in the calculation group.
+ std::vector<real> radii_;
+ /*! \brief
+ * Solvation free energy coefficients for each atom in the calculation
+ * group.
+ *
+ * Empty if the free energy output has not been requested.
+ */
+ std::vector<real> dgsFactor_;
+
+ // Copy and assign disallowed by base.
+};
+
+Sasa::Sasa()
+ : TrajectoryAnalysisModule(SasaInfo::name, SasaInfo::shortDescription),
+ solsize_(0.14), ndots_(24), dgsDefault_(0), bIncludeSolute_(true), top_(NULL)
+{
+ //minarea_ = 0.5;
+ registerAnalysisDataset(&area_, "area");
+ registerAnalysisDataset(&atomArea_, "atomarea");
+ registerAnalysisDataset(&residueArea_, "resarea");
+ registerAnalysisDataset(&dgSolv_, "dgsolv");
+ registerAnalysisDataset(&volume_, "volume");
+}
+
+void
+Sasa::initOptions(Options *options, TrajectoryAnalysisSettings *settings)
+{
+ static const char *const desc[] = {
+ "[THISMODULE] computes solvent accessible surface areas.",
+ "See Eisenhaber F, Lijnzaad P, Argos P, Sander C, & Scharf M",
+ "(1995) J. Comput. Chem. 16, 273-284 for the algorithm used.",
+ "With [TT]-q[tt], the Connolly surface can be generated as well",
+ "in a [TT].pdb[tt] file where the nodes are represented as atoms",
+ "and the edges connecting the nearest nodes as CONECT records.",
+ "[TT]-odg[tt] allows for estimation of solvation free energies",
+ "from per-atom solvation energies per exposed surface area.[PAR]",
+
+ "The program requires a selection for the surface calculation to be",
+ "specified with [TT]-surface[tt]. This should always consist of all",
+ "non-solvent atoms in the system. The area of this group is always",
+ "calculated. Optionally, [TT]-output[tt] can specify additional",
+ "selections, which should be subsets of the calculation group.",
+ "The solvent-accessible areas for these groups are also extracted",
+ "from the full surface.[PAR]",
+
+ "The average and standard deviation of the area over the trajectory",
+ "can be calculated per residue and atom (options [TT]-or[tt] and",
+ "[TT]-oa[tt]).[PAR]",
+ //"In combination with the latter option an [TT].itp[tt] file can be",
+ //"generated (option [TT]-i[tt])",
+ //"which can be used to restrain surface atoms.[PAR]",
+
+ "With the [TT]-tv[tt] option the total volume and density of the",
+ "molecule can be computed.",
+ "Please consider whether the normal probe radius is appropriate",
+ "in this case or whether you would rather use, e.g., 0. It is good",
+ "to keep in mind that the results for volume and density are very",
+ "approximate. For example, in ice Ih, one can easily fit water molecules in the",
+ "pores which would yield a volume that is too low, and surface area and density",
+ "that are both too high."
+ };
+
+ options->setDescription(concatenateStrings(desc));
+
+ options->addOption(FileNameOption("o").filetype(eftPlot).outputFile().required()
+ .store(&fnArea_).defaultBasename("area")
+ .description("Total area as a function of time"));
+ options->addOption(FileNameOption("odg").filetype(eftPlot).outputFile()
+ .store(&fnDGSolv_).defaultBasename("dgsolv")
+ .description("Estimated solvation free energy as a function of time"));
+ options->addOption(FileNameOption("or").filetype(eftPlot).outputFile()
+ .store(&fnResidueArea_).defaultBasename("resarea")
+ .description("Average area per residue"));
+ options->addOption(FileNameOption("oa").filetype(eftPlot).outputFile()
+ .store(&fnAtomArea_).defaultBasename("atomarea")
+ .description("Average area per atom"));
+ options->addOption(FileNameOption("tv").filetype(eftPlot).outputFile()
+ .store(&fnVolume_).defaultBasename("volume")
+ .description("Total volume and density as a function of time"));
+ options->addOption(FileNameOption("q").filetype(eftPDB).outputFile()
+ .store(&fnConnolly_).defaultBasename("connolly")
+ .description("PDB file for Connolly surface"));
+ //options->addOption(FileNameOption("i").filetype(eftITP).outputFile()
+ // .store(&fnRestraints_).defaultBasename("surfat")
+ // .description("Topology file for position restraings on surface atoms"));
+
+
+ options->addOption(DoubleOption("probe").store(&solsize_)
+ .description("Radius of the solvent probe (nm)"));
+ options->addOption(IntegerOption("ndots").store(&ndots_)
+ .description("Number of dots per sphere, more dots means more accuracy"));
+ //options->addOption(DoubleOption("minarea").store(&minarea_)
+ // .description("The minimum area (nm^2) to count an atom as a surface atom when writing a position restraint file (see help)"));
+ options->addOption(BooleanOption("prot").store(&bIncludeSolute_)
+ .description("Output the protein to the Connolly [TT].pdb[tt] file too"));
+ options->addOption(DoubleOption("dgs").store(&dgsDefault_)
+ .description("Default value for solvation free energy per area (kJ/mol/nm^2)"));
+
+ // Selections must select atoms for the VdW radii lookup to work.
+ // The calculation group uses dynamicMask() so that the coordinates
+ // match a static array of VdW radii.
+ options->addOption(SelectionOption("surface").store(&surfaceSel_)
+ .required().onlyAtoms().dynamicMask()
+ .description("Surface calculation selection"));
+ options->addOption(SelectionOption("output").storeVector(&outputSel_)
+ .onlyAtoms().multiValue()
+ .description("Output selection(s)"));
+
+ // Atom names etc. are required for the VdW radii lookup.
+ settings->setFlag(TrajectoryAnalysisSettings::efRequireTop);
+}
+
+void
+Sasa::initAnalysis(const TrajectoryAnalysisSettings &settings,
+ const TopologyInformation &top)
+{
+ const t_atoms &atoms = top.topology()->atoms;
+ top_ = top.topology();
+
+ //bITP = opt2bSet("-i", nfile, fnm);
+ const bool bResAt =
+ !fnResidueArea_.empty() || !fnAtomArea_.empty(); // || bITP;
+ const bool bDGsol = !fnDGSolv_.empty();
+
+ if (solsize_ < 0)
+ {
+ solsize_ = 1e-3;
+ fprintf(stderr, "Probe size too small, setting it to %g\n", solsize_);
+ }
+ if (ndots_ < 20)
+ {
+ ndots_ = 20;
+ fprintf(stderr, "Ndots too small, setting it to %d\n", ndots_);
+ }
+
+ please_cite(stderr, "Eisenhaber95");
+ //if ((top.ePBC() != epbcXYZ) || (TRICLINIC(fr.box)))
+ //{
+ // fprintf(stderr, "\n\nWARNING: non-rectangular boxes may give erroneous results or crashes.\n"
+ // "Analysis based on vacuum simulations (with the possibility of evaporation)\n"
+ // "will certainly crash the analysis.\n\n");
+ //}
+
+ if (bDGsol)
+ {
+ if (!top.hasFullTopology())
+ {
+ GMX_THROW(InconsistentInputError("Cannot compute Delta G of solvation without a tpr file"));
+ }
+ else
+ {
+ if (strcmp(*(atoms.atomtype[0]), "?") == 0)
+ {
+ GMX_THROW(InconsistentInputError("Your input tpr file is too old (does not contain atom types). Cannot not compute Delta G of solvation"));
+ }
+ else
+ {
+ printf("Free energy of solvation predictions:\n");
+ please_cite(stdout, "Eisenberg86a");
+ }
+ }
+ }
+
+ // Now compute atomic radii including solvent probe size.
+ // Also, fetch solvation free energy coefficients and
+ // compute the residue indices that map the calculation atoms
+ // to the columns of residueArea_.
+ radii_.reserve(surfaceSel_.posCount());
+ if (bDGsol)
+ {
+ dgsFactor_.reserve(surfaceSel_.posCount());
+ }
+
+ // TODO: Not exception-safe, but nice solution would be to have a C++
+ // atom properties class...
+ gmx_atomprop_t aps = gmx_atomprop_init();
+
+ ConstArrayRef<int> atomIndices = surfaceSel_.atomIndices();
+ int prevResind = atoms.atom[atomIndices[0]].resind;
+ int resCount = 0;
+ int ndefault = 0;
+ for (int i = 0; i < surfaceSel_.posCount(); i++)
+ {
+ const int ii = atomIndices[i];
+ const int resind = atoms.atom[ii].resind;
+ if (resind != prevResind)
+ {
+ ++resCount;
+ prevResind = resind;
+ }
+ surfaceSel_.setOriginalId(i, resCount);
+ real radius;
+ if (!gmx_atomprop_query(aps, epropVDW,
+ *(atoms.resinfo[resind].name),
+ *(atoms.atomname[ii]), &radius))
+ {
+ ndefault++;
+ }
+ radii_.push_back(radius + solsize_);
+ if (bDGsol)
+ {
+ real dgsFactor;
+ if (!gmx_atomprop_query(aps, epropDGsol,
+ *(atoms.resinfo[resind].name),
+ *(atoms.atomtype[ii]), &dgsFactor))
+ {
+ dgsFactor = dgsDefault_;
+ }
+ dgsFactor_.push_back(dgsFactor);
+ }
+ }
+ if (ndefault > 0)
+ {
+ fprintf(stderr, "WARNING: could not find a Van der Waals radius for %d atoms\n", ndefault);
+ }
+ gmx_atomprop_destroy(aps);
+
+ // The loop above doesn't count the last residue.
+ ++resCount;
+
+ // Pre-compute mapping from the output groups to the calculation group,
+ // and store it in the selection ID map for easy lookup.
+ for (size_t g = 0; g < outputSel_.size(); ++g)
+ {
+ ConstArrayRef<int> outputIndices = outputSel_[g].atomIndices();
+ for (int i = 0, j = 0; i < outputSel_[g].posCount(); ++i)
+ {
+ while (j < surfaceSel_.posCount() && outputIndices[i] > atomIndices[j])
+ {
+ ++j;
+ }
+ if (j == surfaceSel_.posCount() || outputIndices[i] != atomIndices[j])
+ {
+ GMX_THROW(InconsistentInputError("Output selection is not a subset of the input selection"));
+ }
+ outputSel_[g].setOriginalId(i, j);
+ }
+ }
+
+ // Initialize all the output data objects and initialize the output plotters.
+
+ area_.setColumnCount(0, 1 + outputSel_.size());
+ {
+ AnalysisDataPlotModulePointer plotm(
+ new AnalysisDataPlotModule(settings.plotSettings()));
+ plotm->setFileName(fnArea_);
+ plotm->setTitle("Solvent Accessible Surface");
+ plotm->setXAxisIsTime();
+ plotm->setYLabel("Area (nm\\S2\\N)");
+ plotm->appendLegend("Total");
+ for (size_t i = 0; i < outputSel_.size(); ++i)
+ {
+ plotm->appendLegend(outputSel_[i].name());
+ }
+ area_.addModule(plotm);
+ }
+
+ if (bResAt)
+ {
+ atomArea_.setDataSetCount(1 + outputSel_.size());
+ residueArea_.setDataSetCount(1 + outputSel_.size());
+ for (size_t i = 0; i <= outputSel_.size(); ++i)
+ {
+ atomArea_.setColumnCount(i, surfaceSel_.posCount());
+ residueArea_.setColumnCount(i, resCount);
+ }
+ {
+ AnalysisDataAverageModulePointer avem(new AnalysisDataAverageModule);
+ for (int i = 0; i < surfaceSel_.posCount(); ++i)
+ {
+ avem->setXAxisValue(i, surfaceSel_.position(i).atomIndices()[0] + 1);
+ }
+ atomArea_.addModule(avem);
+ if (!fnAtomArea_.empty())
+ {
+ AnalysisDataPlotModulePointer plotm(
+ new AnalysisDataPlotModule(settings.plotSettings()));
+ plotm->setFileName(fnAtomArea_);
+ plotm->setTitle("Area per residue over the trajectory");
+ plotm->setXLabel("Atom");
+ plotm->setXFormat(8, 0);
+ plotm->setYLabel("Area (nm\\S2\\N)");
+ plotm->setErrorsAsSeparateColumn(true);
+ plotm->appendLegend("Average (nm\\S2\\N)");
+ plotm->appendLegend("Standard deviation (nm\\S2\\N)");
+ avem->addModule(plotm);
+ }
+ }
+ {
+ AnalysisDataAverageModulePointer avem(new AnalysisDataAverageModule);
+ for (int i = 0; i < surfaceSel_.posCount(); ++i)
+ {
+ const int atomIndex = surfaceSel_.position(i).atomIndices()[0];
+ const int residueIndex = atoms.atom[atomIndex].resind;
+ avem->setXAxisValue(i, atoms.resinfo[residueIndex].nr);
+ }
+ residueArea_.addModule(avem);
+ if (!fnResidueArea_.empty())
+ {
+ AnalysisDataPlotModulePointer plotm(
+ new AnalysisDataPlotModule(settings.plotSettings()));
+ plotm->setFileName(fnResidueArea_);
+ plotm->setTitle("Area per atom over the trajectory");
+ plotm->setXLabel("Residue");
+ plotm->setXFormat(8, 0);
+ plotm->setYLabel("Area (nm\\S2\\N)");
+ plotm->setErrorsAsSeparateColumn(true);
+ plotm->appendLegend("Average (nm\\S2\\N)");
+ plotm->appendLegend("Standard deviation (nm\\S2\\N)");
+ avem->addModule(plotm);
+ }
+ }
+ }
+
+ if (!fnDGSolv_.empty())
+ {
+ dgSolv_.setColumnCount(0, 1 + outputSel_.size());
+ AnalysisDataPlotModulePointer plotm(
+ new AnalysisDataPlotModule(settings.plotSettings()));
+ plotm->setFileName(fnDGSolv_);
+ plotm->setTitle("Free Energy of Solvation");
+ plotm->setXAxisIsTime();
+ plotm->setYLabel("D Gsolv");
+ plotm->appendLegend("Total");
+ for (size_t i = 0; i < outputSel_.size(); ++i)
+ {
+ plotm->appendLegend(outputSel_[i].name());
+ }
+ dgSolv_.addModule(plotm);
+ }
+
+ if (!fnVolume_.empty())
+ {
+ volume_.setColumnCount(0, 2);
+ AnalysisDataPlotModulePointer plotm(
+ new AnalysisDataPlotModule(settings.plotSettings()));
+ plotm->setFileName(fnVolume_);
+ plotm->setTitle("Volume and Density");
+ plotm->setXAxisIsTime();
+ plotm->appendLegend("Volume (nm\\S3\\N)");
+ plotm->appendLegend("Density (g/l)");
+ volume_.addModule(plotm);
+ }
+}
+
+/*! \brief
+ * Temporary memory for use within a single-frame calculation.
+ */
+class SasaModuleData : public TrajectoryAnalysisModuleData
+{
+ public:
+ /*! \brief
+ * Reserves memory for the frame-local data.
+ *
+ * `residueCount` will be zero if per-residue data is not being
+ * calculated.
+ */
+ SasaModuleData(TrajectoryAnalysisModule *module,
+ const AnalysisDataParallelOptions &opt,
+ const SelectionCollection &selections,
+ int atomCount, int residueCount)
+ : TrajectoryAnalysisModuleData(module, opt, selections)
+ {
+ index_.reserve(atomCount);
+ // If the calculation group is not dynamic, pre-calculate
+ // the index, since it is not going to change.
+ for (int i = 0; i < atomCount; ++i)
+ {
+ index_.push_back(i);
+ }
+ atomAreas_.resize(atomCount);
+ res_a_.resize(residueCount);
+ }
+
+ virtual void finish() { finishDataHandles(); }
+
+ //! Indices of the calculation selection positions selected for the frame.
+ std::vector<int> index_;
+ /*! \brief
+ * Atom areas for each calculation selection position for the frame.
+ *
+ * One entry for each position in the calculation group.
+ * Values for atoms not selected are set to zero.
+ */
+ std::vector<real> atomAreas_;
+ /*! \brief
+ * Working array to accumulate areas for each residue.
+ *
+ * One entry for each distinct residue in the calculation group;
+ * indices are not directly residue numbers or residue indices.
+ *
+ * This vector is empty if residue area calculations are not being
+ * performed.
+ */
+ std::vector<real> res_a_;
+};
+
+TrajectoryAnalysisModuleDataPointer Sasa::startFrames(
+ const AnalysisDataParallelOptions &opt,
+ const SelectionCollection &selections)
+{
+ return TrajectoryAnalysisModuleDataPointer(
+ new SasaModuleData(this, opt, selections, surfaceSel_.posCount(),
+ residueArea_.columnCount(0)));
+}
+
+/*! \brief
+ * Helper method to compute the areas for a single selection.
+ *
+ * \param[in] surfaceSel The calculation selection.
+ * \param[in] sel The selection to compute the areas for (can be
+ * `surfaceSel` or one of the output selections).
+ * \param[in] atomAreas Atom areas for each position in `surfaceSel`.
+ * \param[in] dgsFactor Free energy coefficients for each position in
+ * `surfaceSel`. If empty, free energies are not calculated.
+ * \param[out] totalAreaOut Total area of `sel` (sum of atom areas it selects).
+ * \param[out] dgsolvOut Solvation free energy.
+ * Will be zero of `dgsFactor` is empty.
+ * \param atomAreaHandle Data handle to use for storing atom areas for `sel`.
+ * \param resAreaHandle Data handle to use for storing residue areas for `sel`.
+ * \param resAreaWork Work array for accumulating the residue areas.
+ * If empty, atom and residue areas are not calculated.
+ *
+ * `atomAreaHandle` and `resAreaHandle` are not used if `resAreaWork` is empty.
+ */
+void computeAreas(const Selection &surfaceSel, const Selection &sel,
+ const std::vector<real> &atomAreas,
+ const std::vector<real> &dgsFactor,
+ real *totalAreaOut, real *dgsolvOut,
+ AnalysisDataHandle atomAreaHandle,
+ AnalysisDataHandle resAreaHandle,
+ std::vector<real> *resAreaWork)
+{
+ const bool bResAt = !resAreaWork->empty();
+ const bool bDGsolv = !dgsFactor.empty();
+ real totalArea = 0;
+ real dgsolv = 0;
+
+ if (bResAt)
+ {
+ std::fill(resAreaWork->begin(), resAreaWork->end(),
+ static_cast<real>(0.0));
+ }
+ for (int i = 0; i < sel.posCount(); ++i)
+ {
+ // Get the index of the atom in the calculation group.
+ // For the output groups, the mapping has been precalculated in
+ // initAnalysis().
+ const int ii = (sel != surfaceSel ? sel.position(i).mappedId() : i);
+ if (!surfaceSel.position(ii).selected())
+ {
+ // For the calculation group, skip unselected atoms.
+ if (sel == surfaceSel)
+ {
+ continue;
+ }
+ GMX_THROW(InconsistentInputError("Output selection is not a subset of the surface selection"));
+ }
+ // Get the internal index of the matching residue.
+ // These have been precalculated in initAnalysis().
+ const int ri = surfaceSel.position(ii).mappedId();
+ const real atomArea = atomAreas[ii];
+ totalArea += atomArea;
+ if (bResAt)
+ {
+ atomAreaHandle.setPoint(ii, atomArea);
+ (*resAreaWork)[ri] += atomArea;
+ }
+ if (bDGsolv)
+ {
+ dgsolv += atomArea * dgsFactor[ii];
+ }
+ }
+ if (bResAt)
+ {
+ for (size_t i = 0; i < (*resAreaWork).size(); ++i)
+ {
+ resAreaHandle.setPoint(i, (*resAreaWork)[i]);
+ }
+ }
+ *totalAreaOut = totalArea;
+ *dgsolvOut = dgsolv;
+}
+
+void
+Sasa::analyzeFrame(int frnr, const t_trxframe &fr, t_pbc *pbc,
+ TrajectoryAnalysisModuleData *pdata)
+{
+ AnalysisDataHandle ah = pdata->dataHandle(area_);
+ AnalysisDataHandle dgh = pdata->dataHandle(dgSolv_);
+ AnalysisDataHandle aah = pdata->dataHandle(atomArea_);
+ AnalysisDataHandle rah = pdata->dataHandle(residueArea_);
+ AnalysisDataHandle vh = pdata->dataHandle(volume_);
+ const Selection &surfaceSel = pdata->parallelSelection(surfaceSel_);
+ const SelectionList &outputSel = pdata->parallelSelections(outputSel_);
+ SasaModuleData &frameData = *static_cast<SasaModuleData *>(pdata);
+
+ const bool bResAt = !frameData.res_a_.empty();
+ const bool bDGsol = !dgsFactor_.empty();
+ const bool bConnolly = (frnr == 0 && !fnConnolly_.empty());
+
+ // Update indices of selected atoms in the work array.
+ if (surfaceSel.isDynamic())
+ {
+ frameData.index_.clear();
+ for (int i = 0; i < surfaceSel.posCount(); ++i)
+ {
+ if (surfaceSel.position(i).selected())
+ {
+ frameData.index_.push_back(i);
+ }
+ }
+ }
+
+ // Determine what needs to be calculated.
+ int flag = 0;
+ if (bResAt || bDGsol || !outputSel.empty())
+ {
+ flag |= FLAG_ATOM_AREA;
+ }
+ if (bConnolly)
+ {
+ flag |= FLAG_DOTS;
+ }
+ if (volume_.columnCount() > 0)
+ {
+ flag |= FLAG_VOLUME;
+ }
+
+ // Do the low-level calculation.
+ // totarea and totvolume receive the values for the calculation group.
+ // area array contains the per-atom areas for the selected positions.
+ // surfacedots contains nsurfacedots entries, and contains the actual
+ // points.
+ real totarea, totvolume;
+ real *area = NULL, *surfacedots = NULL;
+ int nsurfacedots;
+ int retval = nsc_dclm_pbc(surfaceSel.coordinates().data(), &radii_[0],
+ frameData.index_.size(), ndots_, flag, &totarea,
+ &area, &totvolume, &surfacedots, &nsurfacedots,
+ &frameData.index_[0],
+ pbc != NULL ? pbc->ePBC : epbcNONE,
+ pbc != NULL ? pbc->box : NULL);
+ // Unpack the atomwise areas into the frameData.atomAreas_ array for easier
+ // indexing in the case of dynamic surfaceSel.
+ if (area != NULL)
+ {
+ if (surfaceSel.isDynamic())
+ {
+ std::fill(frameData.atomAreas_.begin(), frameData.atomAreas_.end(),
+ static_cast<real>(0.0));
+ for (size_t i = 0; i < frameData.index_.size(); ++i)
+ {
+ frameData.atomAreas_[frameData.index_[i]] = area[i];
+ }
+ }
+ else
+ {
+ std::copy(area, area + surfaceSel.posCount(),
+ frameData.atomAreas_.begin());
+ }
+ sfree(area);
+ }
+ scoped_ptr_sfree dotsGuard(surfacedots);
+ if (retval != 0)
+ {
+ GMX_THROW(InternalError("nsc_dclm_pbc failed"));
+ }
+
+ if (bConnolly)
+ {
+ // This is somewhat nasty, as it modifies the atoms and symtab
+ // structures. But since it is only used in the first frame, and no
+ // one else uses the topology after initialization, it may just work
+ // even with future parallelization.
+ connolly_plot(fnConnolly_.c_str(),
+ nsurfacedots, surfacedots, fr.x, &top_->atoms,
+ &top_->symtab, fr.ePBC, fr.box, bIncludeSolute_);
+ }
+
+ ah.startFrame(frnr, fr.time);
+ if (bResAt)
+ {
+ aah.startFrame(frnr, fr.time);
+ rah.startFrame(frnr, fr.time);
+ }
+ if (bDGsol)
+ {
+ dgh.startFrame(frnr, fr.time);
+ }
+
+ ah.setPoint(0, totarea);
+
+ real totalArea, dgsolv;
+ if (bResAt || bDGsol)
+ {
+ computeAreas(surfaceSel, surfaceSel, frameData.atomAreas_, dgsFactor_,
+ &totalArea, &dgsolv, aah, rah, &frameData.res_a_);
+ if (bDGsol)
+ {
+ dgh.setPoint(0, dgsolv);
+ }
+ }
+ for (size_t g = 0; g < outputSel.size(); ++g)
+ {
+ if (bResAt)
+ {
+ aah.selectDataSet(g + 1);
+ rah.selectDataSet(g + 1);
+ }
+ computeAreas(surfaceSel, outputSel[g], frameData.atomAreas_, dgsFactor_,
+ &totalArea, &dgsolv, aah, rah, &frameData.res_a_);
+ ah.setPoint(g + 1, totalArea);
+ if (bDGsol)
+ {
+ dgh.setPoint(g + 1, dgsolv);
+ }
+ }
+
+ ah.finishFrame();
+ if (bResAt)
+ {
+ aah.finishFrame();
+ rah.finishFrame();
+ }
+ if (bDGsol)
+ {
+ dgh.finishFrame();
+ }
+
+ if (vh.isValid())
+ {
+ real totmass = 0;
+ for (int i = 0; i < surfaceSel.posCount(); ++i)
+ {
+ totmass += surfaceSel.position(i).mass();
+ }
+ const real density = totmass*AMU/(totvolume*NANO*NANO*NANO);
+ vh.startFrame(frnr, fr.time);
+ vh.setPoint(0, totvolume);
+ vh.setPoint(1, density);
+ vh.finishFrame();
+ }
+}
+
+void
+Sasa::finishAnalysis(int /*nframes*/)
+{
+ //if (bITP)
+ //{
+ // fp3 = ftp2FILE(efITP, nfile, fnm, "w");
+ // fprintf(fp3, "[ position_restraints ]\n"
+ // "#define FCX 1000\n"
+ // "#define FCY 1000\n"
+ // "#define FCZ 1000\n"
+ // "; Atom Type fx fy fz\n");
+ // for (i = 0; i < nx[0]; i++)
+ // {
+ // if (atom_area[i] > minarea)
+ // {
+ // fprintf(fp3, "%5d 1 FCX FCX FCZ\n", ii+1);
+ // }
+ // }
+ // ffclose(fp3);
+ //}
+}
+
+void
+Sasa::writeOutput()
+{
+}
+
+//! \}
+
+} // namespace
+
+const char SasaInfo::name[] = "sasa";
+const char SasaInfo::shortDescription[] =
+ "Compute solvent accessible surface area";
+
+TrajectoryAnalysisModulePointer SasaInfo::create()
+{
+ return TrajectoryAnalysisModulePointer(new Sasa);
+}
+
+} // namespace analysismodules
+
+} // namespace gmx
--- /dev/null
+/*
+ * This file is part of the GROMACS molecular simulation package.
+ *
+ * Copyright (c) 2013,2014, 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.
+ */
+/*! \internal \file
+ * \brief
+ * Declares trajectory analysis module for surface area calculations.
+ *
+ * \author Teemu Murtola <teemu.murtola@gmail.com>
+ * \ingroup module_trajectoryanalysis
+ */
+#ifndef GMX_TRAJECTORYANALYSIS_MODULES_SASA_H
+#define GMX_TRAJECTORYANALYSIS_MODULES_SASA_H
+
+#include "../analysismodule.h"
+
+namespace gmx
+{
+
+namespace analysismodules
+{
+
+class SasaInfo
+{
+ public:
+ static const char name[];
+ static const char shortDescription[];
+ static TrajectoryAnalysisModulePointer create();
+};
+
+} // namespace analysismodules
+
+} // namespace gmx
+
+#endif
angle.cpp
distance.cpp
freevolume.cpp
+ sasa.cpp
select.cpp
$<TARGET_OBJECTS:analysisdata-test-shared>)
--- /dev/null
+First 10 residues from 1AKI
+ 155
+ 1LYS N 1 3.536 2.234 -1.198
+ 1LYS H1 2 3.612 2.288 -1.236
+ 1LYS H2 3 3.470 2.214 -1.270
+ 1LYS H3 4 3.492 2.286 -1.125
+ 1LYS CA 5 3.589 2.107 -1.143
+ 1LYS HA 6 3.633 2.055 -1.216
+ 1LYS CB 7 3.687 2.144 -1.031
+ 1LYS HB1 8 3.763 2.195 -1.070
+ 1LYS HB2 9 3.639 2.201 -0.964
+ 1LYS CG 10 3.745 2.025 -0.956
+ 1LYS HG1 11 3.676 1.989 -0.894
+ 1LYS HG2 12 3.770 1.954 -1.023
+ 1LYS CD 13 3.869 2.065 -0.877
+ 1LYS HD1 14 3.945 2.083 -0.940
+ 1LYS HD2 15 3.849 2.147 -0.824
+ 1LYS CE 16 3.906 1.951 -0.784
+ 1LYS HE1 17 3.841 1.946 -0.708
+ 1LYS HE2 18 3.906 1.864 -0.833
+ 1LYS NZ 19 4.042 1.977 -0.730
+ 1LYS HZ1 20 4.069 1.903 -0.668
+ 1LYS HZ2 21 4.108 1.982 -0.806
+ 1LYS HZ3 22 4.042 2.064 -0.680
+ 1LYS C 23 3.474 2.026 -1.084
+ 1LYS O 24 3.395 2.081 -1.008
+ 2VAL N 25 3.474 1.896 -1.104
+ 2VAL H 26 3.536 1.860 -1.174
+ 2VAL CA 27 3.390 1.800 -1.033
+ 2VAL HA 28 3.317 1.852 -0.990
+ 2VAL CB 29 3.314 1.703 -1.123
+ 2VAL HB 30 3.386 1.652 -1.170
+ 2VAL CG1 31 3.225 1.608 -1.043
+ 2VAL HG11 32 3.177 1.547 -1.106
+ 2VAL HG12 33 3.282 1.555 -0.981
+ 2VAL HG13 34 3.158 1.661 -0.991
+ 2VAL CG2 35 3.229 1.771 -1.229
+ 2VAL HG21 36 3.183 1.702 -1.284
+ 2VAL HG22 37 3.162 1.830 -1.185
+ 2VAL HG23 38 3.288 1.827 -1.288
+ 2VAL C 39 3.480 1.731 -0.929
+ 2VAL O 40 3.576 1.661 -0.966
+ 3PHE N 41 3.449 1.755 -0.804
+ 3PHE H 42 3.375 1.819 -0.784
+ 3PHE CA 43 3.519 1.690 -0.692
+ 3PHE HA 44 3.615 1.697 -0.717
+ 3PHE CB 45 3.497 1.763 -0.559
+ 3PHE HB1 46 3.405 1.802 -0.558
+ 3PHE HB2 47 3.506 1.698 -0.484
+ 3PHE CG 48 3.594 1.874 -0.538
+ 3PHE CD1 49 3.567 2.005 -0.580
+ 3PHE HD1 50 3.481 2.025 -0.627
+ 3PHE CD2 51 3.700 1.856 -0.447
+ 3PHE HD2 52 3.713 1.766 -0.405
+ 3PHE CE1 53 3.658 2.108 -0.557
+ 3PHE HE1 54 3.648 2.195 -0.604
+ 3PHE CE2 55 3.787 1.959 -0.416
+ 3PHE HE2 56 3.866 1.942 -0.357
+ 3PHE CZ 57 3.764 2.087 -0.467
+ 3PHE HZ 58 3.822 2.164 -0.439
+ 3PHE C 59 3.474 1.544 -0.677
+ 3PHE O 60 3.352 1.516 -0.686
+ 4GLY N 61 3.572 1.464 -0.633
+ 4GLY H 62 3.667 1.495 -0.632
+ 4GLY CA 63 3.537 1.328 -0.587
+ 4GLY HA1 64 3.462 1.292 -0.643
+ 4GLY HA2 65 3.616 1.268 -0.594
+ 4GLY C 66 3.492 1.342 -0.442
+ 4GLY O 67 3.530 1.440 -0.378
+ 5ARG N 68 3.405 1.254 -0.397
+ 5ARG H 69 3.371 1.184 -0.460
+ 5ARG CA 70 3.356 1.254 -0.259
+ 5ARG HA 71 3.298 1.334 -0.252
+ 5ARG CB 72 3.276 1.126 -0.233
+ 5ARG HB1 73 3.200 1.122 -0.297
+ 5ARG HB2 74 3.336 1.047 -0.247
+ 5ARG CG 75 3.221 1.120 -0.092
+ 5ARG HG1 76 3.297 1.117 -0.027
+ 5ARG HG2 77 3.165 1.201 -0.075
+ 5ARG CD 78 3.138 1.000 -0.072
+ 5ARG HD1 79 3.104 0.999 0.022
+ 5ARG HD2 80 3.060 1.005 -0.135
+ 5ARG NE 81 3.206 0.875 -0.096
+ 5ARG HE 82 3.202 0.840 -0.189
+ 5ARG CZ 83 3.273 0.801 -0.010
+ 5ARG NH1 84 3.284 0.833 0.119
+ 5ARG HH11 85 3.239 0.916 0.153
+ 5ARG HH12 86 3.336 0.775 0.181
+ 5ARG NH2 87 3.325 0.684 -0.053
+ 5ARG HH21 88 3.311 0.655 -0.147
+ 5ARG HH22 89 3.376 0.626 0.010
+ 5ARG C 90 3.467 1.273 -0.156
+ 5ARG O 91 3.467 1.365 -0.070
+ 6CYS N 92 3.567 1.185 -0.161
+ 6CYS H 93 3.567 1.116 -0.233
+ 6CYS CA 94 3.678 1.187 -0.065
+ 6CYS HA 95 3.631 1.202 0.022
+ 6CYS CB 96 3.749 1.053 -0.062
+ 6CYS HB1 97 3.770 1.034 -0.158
+ 6CYS HB2 98 3.834 1.072 -0.013
+ 6CYS SG 99 3.654 0.920 0.014
+ 6CYS C 100 3.775 1.305 -0.078
+ 6CYS O 101 3.815 1.361 0.026
+ 7GLU N 102 3.786 1.348 -0.202
+ 7GLU H 103 3.740 1.300 -0.276
+ 7GLU CA 104 3.868 1.469 -0.231
+ 7GLU HA 105 3.960 1.455 -0.193
+ 7GLU CB 106 3.878 1.485 -0.382
+ 7GLU HB1 107 3.923 1.402 -0.417
+ 7GLU HB2 108 3.785 1.489 -0.417
+ 7GLU CG 109 3.954 1.605 -0.438
+ 7GLU HG1 110 3.913 1.687 -0.399
+ 7GLU HG2 111 4.049 1.598 -0.407
+ 7GLU CD 112 3.958 1.624 -0.587
+ 7GLU OE1 113 3.867 1.564 -0.649
+ 7GLU OE2 114 4.042 1.695 -0.638
+ 7GLU C 115 3.805 1.593 -0.166
+ 7GLU O 116 3.874 1.673 -0.101
+ 8LEU N 117 3.674 1.605 -0.182
+ 8LEU H 118 3.626 1.535 -0.235
+ 8LEU CA 119 3.596 1.716 -0.125
+ 8LEU HA 120 3.640 1.801 -0.156
+ 8LEU CB 121 3.453 1.717 -0.181
+ 8LEU HB1 122 3.457 1.722 -0.281
+ 8LEU HB2 123 3.406 1.633 -0.153
+ 8LEU CG 124 3.372 1.835 -0.131
+ 8LEU HG 125 3.378 1.842 -0.031
+ 8LEU CD1 126 3.430 1.966 -0.184
+ 8LEU HD11 127 3.376 2.043 -0.150
+ 8LEU HD12 128 3.524 1.975 -0.153
+ 8LEU HD13 129 3.427 1.965 -0.284
+ 8LEU CD2 130 3.225 1.814 -0.160
+ 8LEU HD21 131 3.172 1.893 -0.126
+ 8LEU HD22 132 3.211 1.805 -0.258
+ 8LEU HD23 133 3.193 1.731 -0.114
+ 8LEU C 134 3.605 1.713 0.027
+ 8LEU O 135 3.616 1.817 0.092
+ 9ALA N 136 3.575 1.598 0.083
+ 9ALA H 137 3.546 1.522 0.024
+ 9ALA CA 138 3.584 1.576 0.228
+ 9ALA HA 139 3.508 1.626 0.269
+ 9ALA CB 140 3.566 1.429 0.262
+ 9ALA HB1 141 3.572 1.416 0.361
+ 9ALA HB2 142 3.476 1.398 0.230
+ 9ALA HB3 143 3.637 1.375 0.218
+ 9ALA C 144 3.714 1.631 0.284
+ 9ALA O 145 3.715 1.698 0.390
+ 10ALA N 146 3.827 1.598 0.220
+ 10ALA H 147 3.820 1.539 0.140
+ 10ALA CA 148 3.961 1.643 0.262
+ 10ALA HA 149 3.969 1.619 0.358
+ 10ALA CB 150 4.071 1.571 0.184
+ 10ALA HB1 151 4.160 1.603 0.215
+ 10ALA HB2 152 4.064 1.472 0.201
+ 10ALA HB3 153 4.060 1.589 0.086
+ 10ALA C 154 3.974 1.794 0.246
+ 10ALA O 155 4.019 1.850 0.347
+ 5.90620 6.84510 3.05170
--- /dev/null
+<?xml version="1.0"?>
+<?xml-stylesheet type="text/xsl" href="referencedata.xsl"?>
+<ReferenceData>
+ <String Name="CommandLine">sasa -surface all -output 'name N CA C O H'</String>
+ <OutputData Name="Data">
+ <AnalysisData Name="area">
+ <DataFrame Name="Frame0">
+ <Real Name="X">0</Real>
+ <DataValues>
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+ <DataValue>
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+ </DataValue>
+ <DataValue>
+ <Real Name="Value">2.2198340537623622</Real>
+ </DataValue>
+ </DataValues>
+ </DataFrame>
+ </AnalysisData>
+ <AnalysisData Name="atomarea">
+ <DataFrame Name="Frame0">
+ <Real Name="X">0</Real>
+ <DataValues>
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+TITLE Connolly Dot Surface Generated by gmx sasa
+REMARK THIS IS A SIMULATION BOX
+CRYST1 59.062 68.451 30.517 90.00 90.00 90.00 P 1 1
+MODEL 1
+ATOM 1 N LYS 1 35.360 22.340 -11.980 1.00 0.00
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+ATOM 11 HG1 LYS 1 36.760 19.890 -8.940 1.00 0.00
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+ATOM 16 CE LYS 1 39.060 19.510 -7.840 1.00 0.00
+ATOM 17 HE1 LYS 1 38.410 19.460 -7.080 1.00 0.00
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+ATOM 20 HZ1 LYS 1 40.690 19.030 -6.680 1.00 0.00
+ATOM 21 HZ2 LYS 1 41.080 19.820 -8.060 1.00 0.00
+ATOM 22 HZ3 LYS 1 40.420 20.640 -6.800 1.00 0.00
+ATOM 23 C LYS 1 34.740 20.260 -10.840 1.00 0.00
+ATOM 24 O LYS 1 33.950 20.810 -10.080 1.00 0.00
+ATOM 25 N VAL 2 34.740 18.960 -11.040 1.00 0.00
+ATOM 26 H VAL 2 35.360 18.600 -11.740 1.00 0.00
+ATOM 27 CA VAL 2 33.900 18.000 -10.330 1.00 0.00
+ATOM 28 HA VAL 2 33.170 18.520 -9.900 1.00 0.00
+ATOM 29 CB VAL 2 33.140 17.030 -11.230 1.00 0.00
+ATOM 30 HB VAL 2 33.860 16.520 -11.700 1.00 0.00
+ATOM 31 CG1 VAL 2 32.250 16.080 -10.430 1.00 0.00
+ATOM 32 1HG1 VAL 2 31.770 15.470 -11.060 1.00 0.00
+ATOM 33 2HG1 VAL 2 32.820 15.550 -9.810 1.00 0.00
+ATOM 34 3HG1 VAL 2 31.580 16.610 -9.910 1.00 0.00
+ATOM 35 CG2 VAL 2 32.290 17.710 -12.290 1.00 0.00
+ATOM 36 1HG2 VAL 2 31.830 17.020 -12.840 1.00 0.00
+ATOM 37 2HG2 VAL 2 31.620 18.300 -11.850 1.00 0.00
+ATOM 38 3HG2 VAL 2 32.880 18.270 -12.880 1.00 0.00
+ATOM 39 C VAL 2 34.800 17.310 -9.290 1.00 0.00
+ATOM 40 O VAL 2 35.760 16.610 -9.660 1.00 0.00
+ATOM 41 N PHE 3 34.490 17.550 -8.040 1.00 0.00
+ATOM 42 H PHE 3 33.750 18.190 -7.840 1.00 0.00
+ATOM 43 CA PHE 3 35.190 16.900 -6.920 1.00 0.00
+ATOM 44 HA PHE 3 36.150 16.970 -7.170 1.00 0.00
+ATOM 45 CB PHE 3 34.970 17.630 -5.590 1.00 0.00
+ATOM 46 HB1 PHE 3 34.050 18.020 -5.580 1.00 0.00
+ATOM 47 HB2 PHE 3 35.060 16.980 -4.840 1.00 0.00
+ATOM 48 CG PHE 3 35.940 18.740 -5.380 1.00 0.00
+ATOM 49 CD1 PHE 3 35.670 20.050 -5.800 1.00 0.00
+ATOM 50 HD1 PHE 3 34.810 20.250 -6.270 1.00 0.00
+ATOM 51 CD2 PHE 3 37.000 18.560 -4.470 1.00 0.00
+ATOM 52 HD2 PHE 3 37.130 17.660 -4.050 1.00 0.00
+ATOM 53 CE1 PHE 3 36.580 21.080 -5.570 1.00 0.00
+ATOM 54 HE1 PHE 3 36.480 21.950 -6.040 1.00 0.00
+ATOM 55 CE2 PHE 3 37.870 19.590 -4.160 1.00 0.00
+ATOM 56 HE2 PHE 3 38.660 19.420 -3.570 1.00 0.00
+ATOM 57 CZ PHE 3 37.640 20.870 -4.670 1.00 0.00
+ATOM 58 HZ PHE 3 38.220 21.640 -4.390 1.00 0.00
+ATOM 59 C PHE 3 34.740 15.440 -6.770 1.00 0.00
+ATOM 60 O PHE 3 33.520 15.160 -6.860 1.00 0.00
+ATOM 61 N GLY 4 35.720 14.640 -6.330 1.00 0.00
+ATOM 62 H GLY 4 36.670 14.950 -6.320 1.00 0.00
+ATOM 63 CA GLY 4 35.370 13.280 -5.870 1.00 0.00
+ATOM 64 HA1 GLY 4 34.620 12.920 -6.430 1.00 0.00
+ATOM 65 HA2 GLY 4 36.160 12.680 -5.940 1.00 0.00
+ATOM 66 C GLY 4 34.920 13.420 -4.420 1.00 0.00
+ATOM 67 O GLY 4 35.300 14.400 -3.780 1.00 0.00
+ATOM 68 N ARG 5 34.050 12.540 -3.970 1.00 0.00
+ATOM 69 H ARG 5 33.710 11.840 -4.600 1.00 0.00
+ATOM 70 CA ARG 5 33.560 12.540 -2.590 1.00 0.00
+ATOM 71 HA ARG 5 32.980 13.340 -2.520 1.00 0.00
+ATOM 72 CB ARG 5 32.760 11.260 -2.330 1.00 0.00
+ATOM 73 HB1 ARG 5 32.000 11.220 -2.970 1.00 0.00
+ATOM 74 HB2 ARG 5 33.360 10.470 -2.470 1.00 0.00
+ATOM 75 CG ARG 5 32.210 11.200 -0.920 1.00 0.00
+ATOM 76 HG1 ARG 5 32.970 11.170 -0.270 1.00 0.00
+ATOM 77 HG2 ARG 5 31.650 12.010 -0.750 1.00 0.00
+ATOM 78 CD ARG 5 31.380 10.000 -0.720 1.00 0.00
+ATOM 79 HD1 ARG 5 31.040 9.990 0.220 1.00 0.00
+ATOM 80 HD2 ARG 5 30.600 10.050 -1.350 1.00 0.00
+ATOM 81 NE ARG 5 32.060 8.750 -0.960 1.00 0.00
+ATOM 82 HE ARG 5 32.020 8.400 -1.890 1.00 0.00
+ATOM 83 CZ ARG 5 32.730 8.010 -0.100 1.00 0.00
+ATOM 84 NH1 ARG 5 32.840 8.330 1.190 1.00 0.00
+ATOM 85 1HH1 ARG 5 32.390 9.160 1.530 1.00 0.00
+ATOM 86 2HH1 ARG 5 33.360 7.750 1.810 1.00 0.00
+ATOM 87 NH2 ARG 5 33.250 6.840 -0.530 1.00 0.00
+ATOM 88 1HH2 ARG 5 33.110 6.550 -1.470 1.00 0.00
+ATOM 89 2HH2 ARG 5 33.760 6.260 0.100 1.00 0.00
+ATOM 90 C ARG 5 34.670 12.730 -1.560 1.00 0.00
+ATOM 91 O ARG 5 34.670 13.650 -0.700 1.00 0.00
+ATOM 92 N CYS 6 35.670 11.850 -1.610 1.00 0.00
+ATOM 93 H CYS 6 35.670 11.160 -2.330 1.00 0.00
+ATOM 94 CA CYS 6 36.780 11.870 -0.650 1.00 0.00
+ATOM 95 HA CYS 6 36.310 12.020 0.220 1.00 0.00
+ATOM 96 CB CYS 6 37.490 10.530 -0.620 1.00 0.00
+ATOM 97 HB1 CYS 6 37.700 10.340 -1.580 1.00 0.00
+ATOM 98 HB2 CYS 6 38.340 10.720 -0.130 1.00 0.00
+ATOM 99 SG CYS 6 36.540 9.200 0.140 1.00 0.00
+ATOM 100 C CYS 6 37.750 13.050 -0.780 1.00 0.00
+ATOM 101 O CYS 6 38.150 13.610 0.260 1.00 0.00
+ATOM 102 N GLU 7 37.860 13.480 -2.020 1.00 0.00
+ATOM 103 H GLU 7 37.400 13.000 -2.760 1.00 0.00
+ATOM 104 CA GLU 7 38.680 14.690 -2.310 1.00 0.00
+ATOM 105 HA GLU 7 39.600 14.550 -1.930 1.00 0.00
+ATOM 106 CB GLU 7 38.780 14.850 -3.820 1.00 0.00
+ATOM 107 HB1 GLU 7 39.230 14.020 -4.170 1.00 0.00
+ATOM 108 HB2 GLU 7 37.850 14.890 -4.170 1.00 0.00
+ATOM 109 CG GLU 7 39.540 16.050 -4.380 1.00 0.00
+ATOM 110 HG1 GLU 7 39.130 16.870 -3.990 1.00 0.00
+ATOM 111 HG2 GLU 7 40.490 15.980 -4.070 1.00 0.00
+ATOM 112 CD GLU 7 39.580 16.240 -5.870 1.00 0.00
+ATOM 113 OE1 GLU 7 38.670 15.640 -6.490 1.00 0.00
+ATOM 114 OE2 GLU 7 40.420 16.950 -6.380 1.00 0.00
+ATOM 115 C GLU 7 38.050 15.930 -1.660 1.00 0.00
+ATOM 116 O GLU 7 38.740 16.730 -1.010 1.00 0.00
+ATOM 117 N LEU 8 36.740 16.050 -1.820 1.00 0.00
+ATOM 118 H LEU 8 36.260 15.350 -2.350 1.00 0.00
+ATOM 119 CA LEU 8 35.960 17.160 -1.250 1.00 0.00
+ATOM 120 HA LEU 8 36.400 18.010 -1.560 1.00 0.00
+ATOM 121 CB LEU 8 34.530 17.170 -1.810 1.00 0.00
+ATOM 122 HB1 LEU 8 34.570 17.220 -2.810 1.00 0.00
+ATOM 123 HB2 LEU 8 34.060 16.330 -1.530 1.00 0.00
+ATOM 124 CG LEU 8 33.720 18.350 -1.310 1.00 0.00
+ATOM 125 HG LEU 8 33.780 18.420 -0.310 1.00 0.00
+ATOM 126 CD1 LEU 8 34.300 19.660 -1.840 1.00 0.00
+ATOM 127 1HD1 LEU 8 33.760 20.430 -1.500 1.00 0.00
+ATOM 128 2HD1 LEU 8 35.240 19.750 -1.530 1.00 0.00
+ATOM 129 3HD1 LEU 8 34.270 19.650 -2.840 1.00 0.00
+ATOM 130 CD2 LEU 8 32.250 18.140 -1.600 1.00 0.00
+ATOM 131 1HD2 LEU 8 31.720 18.930 -1.260 1.00 0.00
+ATOM 132 2HD2 LEU 8 32.110 18.050 -2.580 1.00 0.00
+ATOM 133 3HD2 LEU 8 31.930 17.310 -1.140 1.00 0.00
+ATOM 134 C LEU 8 36.050 17.130 0.270 1.00 0.00
+ATOM 135 O LEU 8 36.160 18.170 0.920 1.00 0.00
+ATOM 136 N ALA 9 35.750 15.980 0.830 1.00 0.00
+ATOM 137 H ALA 9 35.460 15.220 0.240 1.00 0.00
+ATOM 138 CA ALA 9 35.840 15.760 2.280 1.00 0.00
+ATOM 139 HA ALA 9 35.080 16.260 2.690 1.00 0.00
+ATOM 140 CB ALA 9 35.660 14.290 2.620 1.00 0.00
+ATOM 141 HB1 ALA 9 35.720 14.160 3.610 1.00 0.00
+ATOM 142 HB2 ALA 9 34.760 13.980 2.300 1.00 0.00
+ATOM 143 HB3 ALA 9 36.370 13.750 2.180 1.00 0.00
+ATOM 144 C ALA 9 37.140 16.310 2.840 1.00 0.00
+ATOM 145 O ALA 9 37.150 16.980 3.900 1.00 0.00
+ATOM 146 N ALA 10 38.270 15.980 2.200 1.00 0.00
+ATOM 147 H ALA 10 38.200 15.390 1.400 1.00 0.00
+ATOM 148 CA ALA 10 39.610 16.430 2.620 1.00 0.00
+ATOM 149 HA ALA 10 39.690 16.190 3.580 1.00 0.00
+ATOM 150 CB ALA 10 40.710 15.710 1.840 1.00 0.00
+ATOM 151 HB1 ALA 10 41.600 16.030 2.150 1.00 0.00
+ATOM 152 HB2 ALA 10 40.640 14.720 2.010 1.00 0.00
+ATOM 153 HB3 ALA 10 40.600 15.890 0.860 1.00 0.00
+ATOM 154 C ALA 10 39.740 17.940 2.460 1.00 0.00
+ATOM 155 O ALA 10 40.190 18.500 3.470 1.00 0.00
+ATOM 156 DOT DOT 11 33.016 20.637 -12.533 1.00 0.00
+ATOM 157 DOT DOT 11 33.225 20.789 -10.661 1.00 0.00
+ATOM 158 DOT DOT 11 32.462 22.340 -11.427 1.00 0.00
+ATOM 159 DOT DOT 11 33.569 22.340 -9.636 1.00 0.00
+ATOM 160 DOT DOT 11 32.721 22.340 -13.299 1.00 0.00
+ATOM 161 DOT DOT 11 33.016 24.043 -12.533 1.00 0.00
+ATOM 162 DOT DOT 11 33.225 23.891 -10.661 1.00 0.00
+ATOM 163 DOT DOT 11 34.545 19.831 -13.299 1.00 0.00
+ATOM 164 DOT DOT 11 34.465 19.584 -11.427 1.00 0.00
+ATOM 165 DOT DOT 11 34.807 20.637 -9.636 1.00 0.00
+ATOM 166 DOT DOT 11 33.911 21.287 -14.324 1.00 0.00
+ATOM 167 DOT DOT 11 33.911 23.393 -14.324 1.00 0.00
+ATOM 168 DOT DOT 11 34.545 24.849 -13.299 1.00 0.00
+ATOM 169 DOT DOT 11 34.465 25.096 -11.427 1.00 0.00
+ATOM 170 DOT DOT 11 34.807 24.043 -9.636 1.00 0.00
+ATOM 171 DOT DOT 11 35.913 20.637 -14.324 1.00 0.00
+ATOM 172 DOT DOT 11 36.255 19.584 -12.533 1.00 0.00
+ATOM 173 DOT DOT 11 36.175 19.831 -10.661 1.00 0.00
+ATOM 174 DOT DOT 11 36.809 21.287 -9.636 1.00 0.00
+ATOM 175 DOT DOT 11 35.360 22.340 -14.930 1.00 0.00
+ATOM 176 DOT DOT 11 36.809 23.393 -9.636 1.00 0.00
+ATOM 177 DOT DOT 11 35.360 22.340 -9.030 1.00 0.00
+ATOM 178 DOT DOT 11 35.913 24.043 -14.324 1.00 0.00
+ATOM 179 DOT DOT 11 36.255 25.096 -12.533 1.00 0.00
+ATOM 180 DOT DOT 11 36.175 24.849 -10.661 1.00 0.00
+ATOM 181 DOT DOT 11 37.495 20.789 -13.299 1.00 0.00
+ATOM 182 DOT DOT 11 37.704 20.637 -11.427 1.00 0.00
+ATOM 183 DOT DOT 11 37.151 22.340 -14.324 1.00 0.00
+ATOM 184 DOT DOT 11 38.258 22.340 -12.533 1.00 0.00
+ATOM 185 DOT DOT 11 37.999 22.340 -10.661 1.00 0.00
+ATOM 186 DOT DOT 11 37.495 23.891 -13.299 1.00 0.00
+ATOM 187 DOT DOT 11 37.704 24.043 -11.427 1.00 0.00
+TER
+ENDMDL
+]]></String>
+ </OutputFiles>
+</ReferenceData>
--- /dev/null
+/*
+ * This file is part of the GROMACS molecular simulation package.
+ *
+ * Copyright (c) 2014, 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.
+ */
+/*! \internal \file
+ * \brief
+ * Tests for functionality of the "sasa" trajectory analysis module.
+ *
+ * These tests test the basic functionality of the tool itself, but currently
+ * the following are missing:
+ * - Tests related to -odg output. This would require a full tpr file, and
+ * some investigation on what kind of tpr it should be to produce reasonable
+ * output.
+ * - Tests for the X axes in the area per atom/residue plots. These could be
+ * added once better X axes are implemented.
+ * - Tests for XVG labels. This is a limitation of the current testing
+ * framework.
+ *
+ * The actual surface area algorithm should be tested separately with a more
+ * extensive set of data, but those fit better as a separate set of unit tests.
+ *
+ * \author Teemu Murtola <teemu.murtola@gmail.com>
+ * \ingroup module_trajectoryanalysis
+ */
+#include <gtest/gtest.h>
+
+#include "gromacs/trajectoryanalysis/modules/sasa.h"
+
+#include "testutils/cmdlinetest.h"
+#include "testutils/testasserts.h"
+
+#include "moduletest.h"
+
+namespace
+{
+
+using gmx::test::CommandLine;
+
+/********************************************************************
+ * Tests for gmx::analysismodules::Sas.
+ */
+
+//! Test fixture for the select analysis module.
+typedef gmx::test::TrajectoryAnalysisModuleTestFixture<gmx::analysismodules::SasaInfo>
+ SasaModuleTest;
+
+TEST_F(SasaModuleTest, BasicTest)
+{
+ const char *const cmdline[] = {
+ "sasa",
+ "-surface", "all",
+ "-output", "name N CA C O H"
+ };
+ setTopology("lysozyme.gro");
+ setOutputFileNoTest("-o", "xvg");
+ setOutputFileNoTest("-or", "xvg");
+ setOutputFileNoTest("-oa", "xvg");
+ setOutputFileNoTest("-tv", "xvg");
+ excludeDataset("dgsolv");
+ setDatasetTolerance("area", gmx::test::ulpTolerance(8));
+ setDatasetTolerance("volume", gmx::test::ulpTolerance(8));
+ runTest(CommandLine(cmdline));
+}
+
+TEST_F(SasaModuleTest, WritesConnollySurfaceWithSolute)
+{
+ const char *const cmdline[] = {
+ "sasa",
+ "-surface", "atomnr 1"
+ };
+ setTopology("lysozyme.gro");
+ setOutputFileNoTest("-o", "xvg");
+ setOutputFile("-q", "connolly.pdb");
+ includeDataset("area");
+ runTest(CommandLine(cmdline));
+}
+
+// The CONECT records written to the output make this very difficult to test
+// without parsing the output file, since by construction, there are a lot of
+// dot pairs that are at exactly the same distance from each other in exact
+// arithmetic, and depending on rounding etc., different pairs get picked into
+// the output for single and double precision.
+#if 0
+TEST_F(SasaModuleTest, WritesConnollySurfaceWithoutSolute)
+{
+ const char *const cmdline[] = {
+ "sasa",
+ "-surface", "atomnr 1",
+ "-noprot"
+ };
+ setTopology("lysozyme.gro");
+ setOutputFileNoTest("-o", "xvg");
+ setOutputFile("-q", "connolly.pdb");
+ includeDataset("area");
+ runTest(CommandLine(cmdline));
+}
+#endif
+
+TEST_F(SasaModuleTest, HandlesDynamicOutputGroup)
+{
+ const char *const cmdline[] = {
+ "sasa",
+ "-surface", "all",
+ "-output", "y > 1.5"
+ };
+ setTopology("lysozyme.gro");
+ setOutputFileNoTest("-o", "xvg");
+ setOutputFileNoTest("-or", "xvg");
+ setOutputFileNoTest("-oa", "xvg");
+ excludeDataset("volume");
+ excludeDataset("dgsolv");
+ setDatasetTolerance("area", gmx::test::ulpTolerance(8));
+ runTest(CommandLine(cmdline));
+}
+
+TEST_F(SasaModuleTest, HandlesDynamicCalculationGroup)
+{
+ const char *const cmdline[] = {
+ "sasa",
+ "-surface", "y > 1.5",
+ "-output", "y > 1.5 and z > 0"
+ };
+ setTopology("lysozyme.gro");
+ setOutputFileNoTest("-o", "xvg");
+ setOutputFileNoTest("-or", "xvg");
+ setOutputFileNoTest("-oa", "xvg");
+ excludeDataset("volume");
+ excludeDataset("dgsolv");
+ setDatasetTolerance("area", gmx::test::ulpTolerance(8));
+ runTest(CommandLine(cmdline));
+}
+
+} // namespace
"Calculate free energy difference estimates through Bennett's acceptance ratio");
registerObsoleteTool(manager, "bond");
registerObsoleteTool(manager, "dist");
+ registerObsoleteTool(manager, "sas");
registerObsoleteTool(manager, "sgangle");
registerModule(manager, &gmx_bundle, "bundle",
"Compute salt bridges");
registerModule(manager, &gmx_sans, "sans",
"Compute small angle neutron scattering spectra");
- registerModule(manager, &gmx_sas, "sas",
- "Compute solvent accessible surface area");
registerModule(manager, &gmx_saxs, "saxs",
"Compute small angle X-ray scattering spectra");
registerModule(manager, &gmx_sham, "sham",
group.addModule("principal");
group.addModule("rdf");
group.addModule("saltbr");
- group.addModule("sas");
group.addModule("sorient");
group.addModule("spol");
}
biod.pnpi.spb.ru / alexxy / gromacs.git / commitdiff