--- /dev/null
- * Copyright (c) 2013,2014,2015, 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.
- if (is_bond(nsb, sb, pdba, ai, aj, d[i][j], &index_sb, &bSwap))
++ * Copyright (c) 2013,2014,2015,2016, 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 "specbond.h"
+
+#include <ctype.h>
+#include <string.h>
+
+#include <cmath>
+
+#include <algorithm>
+
+#include "gromacs/fileio/pdbio.h"
+#include "gromacs/gmxpreprocess/pdb2top.h"
+#include "gromacs/math/vec.h"
+#include "gromacs/utility/cstringutil.h"
+#include "gromacs/utility/fatalerror.h"
+#include "gromacs/utility/smalloc.h"
+#include "gromacs/utility/strdb.h"
+
+gmx_bool yesno(void)
+{
+ char c;
+
+ do
+ {
+ c = toupper(fgetc(stdin));
+ }
+ while ((c != 'Y') && (c != 'N'));
+
+ return (c == 'Y');
+}
+
+t_specbond *get_specbonds(int *nspecbond)
+{
+ const char *sbfile = "specbond.dat";
+
+ t_specbond *sb = NULL;
+ char r1buf[32], r2buf[32], a1buf[32], a2buf[32], nr1buf[32], nr2buf[32];
+ double length;
+ int nb1, nb2;
+ char **lines;
+ int nlines, i, n;
+
+ nlines = get_lines(sbfile, &lines);
+ if (nlines > 0)
+ {
+ snew(sb, nlines);
+ }
+
+ n = 0;
+ for (i = 0; (i < nlines); i++)
+ {
+ if (sscanf(lines[i], "%s%s%d%s%s%d%lf%s%s",
+ r1buf, a1buf, &nb1, r2buf, a2buf, &nb2, &length, nr1buf, nr2buf) != 9)
+ {
+ fprintf(stderr, "Invalid line '%s' in %s\n", lines[i], sbfile);
+ }
+ else
+ {
+ sb[n].res1 = gmx_strdup(r1buf);
+ sb[n].res2 = gmx_strdup(r2buf);
+ sb[n].newres1 = gmx_strdup(nr1buf);
+ sb[n].newres2 = gmx_strdup(nr2buf);
+ sb[n].atom1 = gmx_strdup(a1buf);
+ sb[n].atom2 = gmx_strdup(a2buf);
+ sb[n].nbond1 = nb1;
+ sb[n].nbond2 = nb2;
+ sb[n].length = length;
+ n++;
+ }
+ sfree(lines[i]);
+ }
+ if (nlines > 0)
+ {
+ sfree(lines);
+ }
+ fprintf(stderr, "%d out of %d lines of %s converted successfully\n",
+ n, nlines, sbfile);
+
+ *nspecbond = n;
+
+ return sb;
+}
+
+void done_specbonds(int nsb, t_specbond sb[])
+{
+ int i;
+
+ for (i = 0; (i < nsb); i++)
+ {
+ sfree(sb[i].res1);
+ sfree(sb[i].res2);
+ sfree(sb[i].atom1);
+ sfree(sb[i].atom2);
+ sfree(sb[i].newres1);
+ sfree(sb[i].newres2);
+ }
+}
+
+static gmx_bool is_special(int nsb, t_specbond sb[], char *res, char *atom)
+{
+ int i;
+
+ for (i = 0; (i < nsb); i++)
+ {
+ if (((strncmp(sb[i].res1, res, 3) == 0) &&
+ (gmx_strcasecmp(sb[i].atom1, atom) == 0)) ||
+ ((strncmp(sb[i].res2, res, 3) == 0) &&
+ (gmx_strcasecmp(sb[i].atom2, atom) == 0)))
+ {
+ return TRUE;
+ }
+ }
+ return FALSE;
+}
+
+static gmx_bool is_bond(int nsb, t_specbond sb[], t_atoms *pdba, int a1, int a2,
+ real d, int *index_sb, gmx_bool *bSwap)
+{
+ int i;
+ char *at1, *at2, *res1, *res2;
+
+ at1 = *pdba->atomname[a1];
+ at2 = *pdba->atomname[a2];
+ res1 = *pdba->resinfo[pdba->atom[a1].resind].name;
+ res2 = *pdba->resinfo[pdba->atom[a2].resind].name;
+
+ if (debug)
+ {
+ fprintf(stderr, "Checking %s-%d %s-%d and %s-%d %s-%d: %g ",
+ res1, pdba->resinfo[pdba->atom[a1].resind].nr, at1, a1+1,
+ res2, pdba->resinfo[pdba->atom[a2].resind].nr, at2, a2+1, d);
+ }
+
+ for (i = 0; (i < nsb); i++)
+ {
+ *index_sb = i;
+ if (((strncmp(sb[i].res1, res1, 3) == 0) &&
+ (gmx_strcasecmp(sb[i].atom1, at1) == 0) &&
+ (strncmp(sb[i].res2, res2, 3) == 0) &&
+ (gmx_strcasecmp(sb[i].atom2, at2) == 0)))
+ {
+ *bSwap = FALSE;
+ if ((0.9*sb[i].length < d) && (1.1*sb[i].length > d))
+ {
+ if (debug)
+ {
+ fprintf(stderr, "%g\n", sb[i].length);
+ }
+ return TRUE;
+ }
+ }
+ if (((strncmp(sb[i].res1, res2, 3) == 0) &&
+ (gmx_strcasecmp(sb[i].atom1, at2) == 0) &&
+ (strncmp(sb[i].res2, res1, 3) == 0) &&
+ (gmx_strcasecmp(sb[i].atom2, at1) == 0)))
+ {
+ *bSwap = TRUE;
+ if ((0.9*sb[i].length < d) && (1.1*sb[i].length > d))
+ {
+ if (debug)
+ {
+ fprintf(stderr, "%g\n", sb[i].length);
+ }
+ return TRUE;
+ }
+ }
+ }
+ if (debug)
+ {
+ fprintf(stderr, "\n");
+ }
+ return FALSE;
+}
+
+static void rename_1res(t_atoms *pdba, int resind, char *newres, gmx_bool bVerbose)
+{
+ if (bVerbose)
+ {
+ printf("Using rtp entry %s for %s %d\n",
+ newres,
+ *pdba->resinfo[resind].name,
+ pdba->resinfo[resind].nr);
+ }
+ /* this used to free *resname, which messes up the symtab! */
+ snew(pdba->resinfo[resind].rtp, 1);
+ *pdba->resinfo[resind].rtp = gmx_strdup(newres);
+}
+
+int mk_specbonds(t_atoms *pdba, rvec x[], gmx_bool bInteractive,
+ t_ssbond **specbonds, gmx_bool bVerbose)
+{
+ t_specbond *sb = NULL;
+ t_ssbond *bonds = NULL;
+ int nsb;
+ int nspec, nbonds;
+ int *specp, *sgp;
+ gmx_bool bDoit, bSwap;
+ int i, j, b, e, e2;
+ int ai, aj, index_sb;
+ real **d;
+ char buf[10];
+
+ nbonds = 0;
+ sb = get_specbonds(&nsb);
+
+ if (nsb > 0)
+ {
+ snew(specp, pdba->nr);
+ snew(sgp, pdba->nr);
+
+ nspec = 0;
+ for (i = 0; (i < pdba->nr); i++)
+ {
+ /* Check if this atom is special and if it is not a double atom
+ * in the input that still needs to be removed.
+ */
+ if (is_special(nsb, sb, *pdba->resinfo[pdba->atom[i].resind].name,
+ *pdba->atomname[i]) &&
+ !(nspec > 0 &&
+ pdba->atom[sgp[nspec-1]].resind == pdba->atom[i].resind &&
+ gmx_strcasecmp(*pdba->atomname[sgp[nspec-1]],
+ *pdba->atomname[i]) == 0))
+ {
+ specp[nspec] = pdba->atom[i].resind;
+ sgp[nspec] = i;
+ nspec++;
+ }
+ }
+ /* distance matrix d[nspec][nspec] */
+ snew(d, nspec);
+ for (i = 0; (i < nspec); i++)
+ {
+ snew(d[i], nspec);
+ }
+
+ for (i = 0; (i < nspec); i++)
+ {
+ ai = sgp[i];
+ for (j = 0; (j < nspec); j++)
+ {
+ aj = sgp[j];
+ d[i][j] = std::sqrt(distance2(x[ai], x[aj]));
+ }
+ }
+ if (nspec > 1)
+ {
+#define MAXCOL 7
+ fprintf(stderr, "Special Atom Distance matrix:\n");
+ for (b = 0; (b < nspec); b += MAXCOL)
+ {
+ /* print resname/number column headings */
+ fprintf(stderr, "%8s%8s", "", "");
+ e = std::min(b+MAXCOL, nspec-1);
+ for (i = b; (i < e); i++)
+ {
+ sprintf(buf, "%s%d", *pdba->resinfo[pdba->atom[sgp[i]].resind].name,
+ pdba->resinfo[specp[i]].nr);
+ fprintf(stderr, "%8s", buf);
+ }
+ fprintf(stderr, "\n");
+ /* print atomname/number column headings */
+ fprintf(stderr, "%8s%8s", "", "");
+ e = std::min(b+MAXCOL, nspec-1);
+ for (i = b; (i < e); i++)
+ {
+ sprintf(buf, "%s%d", *pdba->atomname[sgp[i]], sgp[i]+1);
+ fprintf(stderr, "%8s", buf);
+ }
+ fprintf(stderr, "\n");
+ /* print matrix */
+ e = std::min(b+MAXCOL, nspec);
+ for (i = b+1; (i < nspec); i++)
+ {
+ sprintf(buf, "%s%d", *pdba->resinfo[pdba->atom[sgp[i]].resind].name,
+ pdba->resinfo[specp[i]].nr);
+ fprintf(stderr, "%8s", buf);
+ sprintf(buf, "%s%d", *pdba->atomname[sgp[i]], sgp[i]+1);
+ fprintf(stderr, "%8s", buf);
+ e2 = std::min(i, e);
+ for (j = b; (j < e2); j++)
+ {
+ fprintf(stderr, " %7.3f", d[i][j]);
+ }
+ fprintf(stderr, "\n");
+ }
+ }
+ }
+
+ snew(bonds, nspec);
+
+ for (i = 0; (i < nspec); i++)
+ {
+ ai = sgp[i];
+ for (j = i+1; (j < nspec); j++)
+ {
+ aj = sgp[j];
++ /* Ensure creation of at most nspec special bonds to avoid overflowing bonds[] */
++ if (nbonds < nspec && is_bond(nsb, sb, pdba, ai, aj, d[i][j], &index_sb, &bSwap))
+ {
+ fprintf(stderr, "%s %s-%d %s-%d and %s-%d %s-%d%s",
+ bInteractive ? "Link" : "Linking",
+ *pdba->resinfo[pdba->atom[ai].resind].name,
+ pdba->resinfo[specp[i]].nr,
+ *pdba->atomname[ai], ai+1,
+ *pdba->resinfo[pdba->atom[aj].resind].name,
+ pdba->resinfo[specp[j]].nr,
+ *pdba->atomname[aj], aj+1,
+ bInteractive ? " (y/n) ?" : "...\n");
+ bDoit = bInteractive ? yesno() : TRUE;
+
+ if (bDoit)
+ {
+ /* Store the residue numbers in the bonds array */
+ bonds[nbonds].res1 = specp[i];
+ bonds[nbonds].res2 = specp[j];
+ bonds[nbonds].a1 = gmx_strdup(*pdba->atomname[ai]);
+ bonds[nbonds].a2 = gmx_strdup(*pdba->atomname[aj]);
+ /* rename residues */
+ if (bSwap)
+ {
+ rename_1res(pdba, specp[i], sb[index_sb].newres2, bVerbose);
+ rename_1res(pdba, specp[j], sb[index_sb].newres1, bVerbose);
+ }
+ else
+ {
+ rename_1res(pdba, specp[i], sb[index_sb].newres1, bVerbose);
+ rename_1res(pdba, specp[j], sb[index_sb].newres2, bVerbose);
+ }
+ nbonds++;
+ }
+ }
+ }
+ }
+
+ for (i = 0; (i < nspec); i++)
+ {
+ sfree(d[i]);
+ }
+ sfree(d);
+ sfree(sgp);
+ sfree(specp);
+
+ done_specbonds(nsb, sb);
+ sfree(sb);
+ }
+
+ *specbonds = bonds;
+
+ return nbonds;
+}
biod.pnpi.spb.ru / alexxy / gromacs.git / commitdiff