| File: | gromacs/gmxpreprocess/genhydro.c |
| Location: | line 733, column 9 |
| Description: | Value stored to 'nadd' is never read |
| 1 | /* |
| 2 | * This file is part of the GROMACS molecular simulation package. |
| 3 | * |
| 4 | * Copyright (c) 1991-2000, University of Groningen, The Netherlands. |
| 5 | * Copyright (c) 2001-2004, The GROMACS development team. |
| 6 | * Copyright (c) 2013,2014, by the GROMACS development team, led by |
| 7 | * Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl, |
| 8 | * and including many others, as listed in the AUTHORS file in the |
| 9 | * top-level source directory and at http://www.gromacs.org. |
| 10 | * |
| 11 | * GROMACS is free software; you can redistribute it and/or |
| 12 | * modify it under the terms of the GNU Lesser General Public License |
| 13 | * as published by the Free Software Foundation; either version 2.1 |
| 14 | * of the License, or (at your option) any later version. |
| 15 | * |
| 16 | * GROMACS is distributed in the hope that it will be useful, |
| 17 | * but WITHOUT ANY WARRANTY; without even the implied warranty of |
| 18 | * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU |
| 19 | * Lesser General Public License for more details. |
| 20 | * |
| 21 | * You should have received a copy of the GNU Lesser General Public |
| 22 | * License along with GROMACS; if not, see |
| 23 | * http://www.gnu.org/licenses, or write to the Free Software Foundation, |
| 24 | * Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301 USA. |
| 25 | * |
| 26 | * If you want to redistribute modifications to GROMACS, please |
| 27 | * consider that scientific software is very special. Version |
| 28 | * control is crucial - bugs must be traceable. We will be happy to |
| 29 | * consider code for inclusion in the official distribution, but |
| 30 | * derived work must not be called official GROMACS. Details are found |
| 31 | * in the README & COPYING files - if they are missing, get the |
| 32 | * official version at http://www.gromacs.org. |
| 33 | * |
| 34 | * To help us fund GROMACS development, we humbly ask that you cite |
| 35 | * the research papers on the package. Check out http://www.gromacs.org. |
| 36 | */ |
| 37 | #ifdef HAVE_CONFIG_H1 |
| 38 | #include <config.h> |
| 39 | #endif |
| 40 | |
| 41 | #include <string.h> |
| 42 | #include <time.h> |
| 43 | |
| 44 | #include "typedefs.h" |
| 45 | #include "gromacs/utility/smalloc.h" |
| 46 | #include "gromacs/fileio/confio.h" |
| 47 | #include "symtab.h" |
| 48 | #include "gromacs/math/vec.h" |
| 49 | #include "gromacs/utility/futil.h" |
| 50 | #include "gromacs/utility/fatalerror.h" |
| 51 | #include "physics.h" |
| 52 | #include "calch.h" |
| 53 | #include "genhydro.h" |
| 54 | #include "h_db.h" |
| 55 | #include "ter_db.h" |
| 56 | #include "resall.h" |
| 57 | #include "pgutil.h" |
| 58 | #include "network.h" |
| 59 | #include "macros.h" |
| 60 | |
| 61 | static void copy_atom(t_atoms *atoms1, int a1, t_atoms *atoms2, int a2) |
| 62 | { |
| 63 | atoms2->atom[a2] = atoms1->atom[a1]; |
| 64 | snew(atoms2->atomname[a2], 1)(atoms2->atomname[a2]) = save_calloc("atoms2->atomname[a2]" , "/home/alexxy/Develop/gromacs/src/gromacs/gmxpreprocess/genhydro.c" , 64, (1), sizeof(*(atoms2->atomname[a2]))); |
| 65 | *atoms2->atomname[a2] = strdup(*atoms1->atomname[a1])(__extension__ (__builtin_constant_p (*atoms1->atomname[a1 ]) && ((size_t)(const void *)((*atoms1->atomname[a1 ]) + 1) - (size_t)(const void *)(*atoms1->atomname[a1]) == 1) ? (((const char *) (*atoms1->atomname[a1]))[0] == '\0' ? (char *) calloc ((size_t) 1, (size_t) 1) : ({ size_t __len = strlen (*atoms1->atomname[a1]) + 1; char *__retval = (char *) malloc (__len); if (__retval != ((void*)0)) __retval = (char *) memcpy (__retval, *atoms1->atomname[a1], __len); __retval ; })) : __strdup (*atoms1->atomname[a1]))); |
| 66 | } |
| 67 | |
| 68 | static atom_id pdbasearch_atom(const char *name, int resind, t_atoms *pdba, |
| 69 | const char *searchtype, gmx_bool bAllowMissing) |
| 70 | { |
| 71 | int i; |
| 72 | |
| 73 | for (i = 0; (i < pdba->nr) && (pdba->atom[i].resind != resind); i++) |
| 74 | { |
| 75 | ; |
| 76 | } |
| 77 | |
| 78 | return search_atom(name, i, pdba, |
| 79 | searchtype, bAllowMissing); |
| 80 | } |
| 81 | |
| 82 | static void hacksearch_atom(int *ii, int *jj, char *name, |
| 83 | int nab[], t_hack *ab[], |
| 84 | int resind, t_atoms *pdba) |
| 85 | { |
| 86 | int i, j; |
| 87 | |
| 88 | *ii = -1; |
| 89 | if (name[0] == '-') |
| 90 | { |
| 91 | name++; |
| 92 | resind--; |
| 93 | } |
| 94 | for (i = 0; (i < pdba->nr) && (pdba->atom[i].resind != resind); i++) |
| 95 | { |
| 96 | ; |
| 97 | } |
| 98 | for (; (i < pdba->nr) && (pdba->atom[i].resind == resind) && (*ii < 0); i++) |
| 99 | { |
| 100 | for (j = 0; (j < nab[i]) && (*ii < 0); j++) |
| 101 | { |
| 102 | if (ab[i][j].nname && strcmp(name, ab[i][j].nname)__extension__ ({ size_t __s1_len, __s2_len; (__builtin_constant_p (name) && __builtin_constant_p (ab[i][j].nname) && (__s1_len = strlen (name), __s2_len = strlen (ab[i][j].nname ), (!((size_t)(const void *)((name) + 1) - (size_t)(const void *)(name) == 1) || __s1_len >= 4) && (!((size_t)(const void *)((ab[i][j].nname) + 1) - (size_t)(const void *)(ab[i] [j].nname) == 1) || __s2_len >= 4)) ? __builtin_strcmp (name , ab[i][j].nname) : (__builtin_constant_p (name) && ( (size_t)(const void *)((name) + 1) - (size_t)(const void *)(name ) == 1) && (__s1_len = strlen (name), __s1_len < 4 ) ? (__builtin_constant_p (ab[i][j].nname) && ((size_t )(const void *)((ab[i][j].nname) + 1) - (size_t)(const void * )(ab[i][j].nname) == 1) ? __builtin_strcmp (name, ab[i][j].nname ) : (__extension__ ({ const unsigned char *__s2 = (const unsigned char *) (const char *) (ab[i][j].nname); int __result = (((const unsigned char *) (const char *) (name))[0] - __s2[0]); if (__s1_len > 0 && __result == 0) { __result = (((const unsigned char *) (const char *) (name))[1] - __s2[1]); if (__s1_len > 1 && __result == 0) { __result = (((const unsigned char *) (const char *) (name))[2] - __s2[2]); if (__s1_len > 2 && __result == 0) __result = (((const unsigned char * ) (const char *) (name))[3] - __s2[3]); } } __result; }))) : ( __builtin_constant_p (ab[i][j].nname) && ((size_t)(const void *)((ab[i][j].nname) + 1) - (size_t)(const void *)(ab[i] [j].nname) == 1) && (__s2_len = strlen (ab[i][j].nname ), __s2_len < 4) ? (__builtin_constant_p (name) && ((size_t)(const void *)((name) + 1) - (size_t)(const void *) (name) == 1) ? __builtin_strcmp (name, ab[i][j].nname) : (- ( __extension__ ({ const unsigned char *__s2 = (const unsigned char *) (const char *) (name); int __result = (((const unsigned char *) (const char *) (ab[i][j].nname))[0] - __s2[0]); if (__s2_len > 0 && __result == 0) { __result = (((const unsigned char *) (const char *) (ab[i][j].nname))[1] - __s2[1]); if ( __s2_len > 1 && __result == 0) { __result = (((const unsigned char *) (const char *) (ab[i][j].nname))[2] - __s2[ 2]); if (__s2_len > 2 && __result == 0) __result = (((const unsigned char *) (const char *) (ab[i][j].nname))[3 ] - __s2[3]); } } __result; })))) : __builtin_strcmp (name, ab [i][j].nname)))); }) == 0) |
| 103 | { |
| 104 | *ii = i; |
| 105 | *jj = j; |
| 106 | } |
| 107 | } |
| 108 | } |
| 109 | |
| 110 | return; |
| 111 | } |
| 112 | |
| 113 | void dump_ab(FILE *out, int natom, int nab[], t_hack *ab[], gmx_bool bHeader) |
| 114 | { |
| 115 | int i, j; |
| 116 | |
| 117 | #define SS(s) (s) ? (s) : "-" |
| 118 | /* dump ab */ |
| 119 | if (bHeader) |
| 120 | { |
| 121 | fprintf(out, "ADDBLOCK (t_hack) natom=%d\n" |
| 122 | "%4s %2s %-4s %-4s %2s %-4s %-4s %-4s %-4s %1s %s\n", |
| 123 | natom, "atom", "nr", "old", "new", "tp", "ai", "aj", "ak", "al", "a", "x"); |
| 124 | } |
| 125 | for (i = 0; i < natom; i++) |
| 126 | { |
| 127 | for (j = 0; j < nab[i]; j++) |
| 128 | { |
| 129 | fprintf(out, "%4d %2d %-4s %-4s %2d %-4s %-4s %-4s %-4s %s %g %g %g\n", |
| 130 | i+1, ab[i][j].nr, SS(ab[i][j].oname), SS(ab[i][j].nname), |
| 131 | ab[i][j].tp, |
| 132 | SS(ab[i][j].AIa[0]), SS(ab[i][j].AJa[1]), |
| 133 | SS(ab[i][j].AKa[2]), SS(ab[i][j].ALa[3]), |
| 134 | ab[i][j].atom ? "+" : "", |
| 135 | ab[i][j].newx[XX0], ab[i][j].newx[YY1], ab[i][j].newx[ZZ2]); |
| 136 | } |
| 137 | } |
| 138 | #undef SS |
| 139 | } |
| 140 | |
| 141 | static t_hackblock *get_hackblocks(t_atoms *pdba, int nah, t_hackblock ah[], |
| 142 | int nterpairs, |
| 143 | t_hackblock **ntdb, t_hackblock **ctdb, |
| 144 | int *rN, int *rC) |
| 145 | { |
| 146 | int i, rnr; |
| 147 | t_hackblock *hb, *ahptr; |
| 148 | |
| 149 | /* make space */ |
| 150 | snew(hb, pdba->nres)(hb) = save_calloc("hb", "/home/alexxy/Develop/gromacs/src/gromacs/gmxpreprocess/genhydro.c" , 150, (pdba->nres), sizeof(*(hb))); |
| 151 | /* first the termini */ |
| 152 | for (i = 0; i < nterpairs; i++) |
| 153 | { |
| 154 | if (ntdb[i] != NULL((void*)0)) |
| 155 | { |
| 156 | copy_t_hackblock(ntdb[i], &hb[rN[i]]); |
| 157 | } |
| 158 | if (ctdb[i] != NULL((void*)0)) |
| 159 | { |
| 160 | merge_t_hackblock(ctdb[i], &hb[rC[i]]); |
| 161 | } |
| 162 | } |
| 163 | /* then the whole hdb */ |
| 164 | for (rnr = 0; rnr < pdba->nres; rnr++) |
| 165 | { |
| 166 | ahptr = search_h_db(nah, ah, *pdba->resinfo[rnr].rtp); |
| 167 | if (ahptr) |
| 168 | { |
| 169 | if (hb[rnr].name == NULL((void*)0)) |
| 170 | { |
| 171 | hb[rnr].name = strdup(ahptr->name)(__extension__ (__builtin_constant_p (ahptr->name) && ((size_t)(const void *)((ahptr->name) + 1) - (size_t)(const void *)(ahptr->name) == 1) ? (((const char *) (ahptr-> name))[0] == '\0' ? (char *) calloc ((size_t) 1, (size_t) 1) : ({ size_t __len = strlen (ahptr->name) + 1; char *__retval = (char *) malloc (__len); if (__retval != ((void*)0)) __retval = (char *) memcpy (__retval, ahptr->name, __len); __retval ; })) : __strdup (ahptr->name))); |
| 172 | } |
| 173 | merge_hacks(ahptr, &hb[rnr]); |
| 174 | } |
| 175 | } |
| 176 | return hb; |
| 177 | } |
| 178 | |
| 179 | static void expand_hackblocks_one(t_hackblock *hbr, char *atomname, |
| 180 | int *nabi, t_hack **abi, gmx_bool bN, gmx_bool bC) |
| 181 | { |
| 182 | int j, k, l, d; |
| 183 | gmx_bool bIgnore; |
| 184 | |
| 185 | /* we'll recursively add atoms to atoms */ |
| 186 | for (j = 0; j < hbr->nhack; j++) |
| 187 | { |
| 188 | /* first check if we're in the N- or C-terminus, then we should ignore |
| 189 | all hacks involving atoms from resp. previous or next residue |
| 190 | (i.e. which name begins with '-' (N) or '+' (C) */ |
| 191 | bIgnore = FALSE0; |
| 192 | if (bN) /* N-terminus: ignore '-' */ |
| 193 | { |
| 194 | for (k = 0; k < 4 && hbr->hack[j].a[k] && !bIgnore; k++) |
| 195 | { |
| 196 | bIgnore = hbr->hack[j].a[k][0] == '-'; |
| 197 | } |
| 198 | } |
| 199 | if (bC) /* C-terminus: ignore '+' */ |
| 200 | { |
| 201 | for (k = 0; k < 4 && hbr->hack[j].a[k] && !bIgnore; k++) |
| 202 | { |
| 203 | bIgnore = hbr->hack[j].a[k][0] == '+'; |
| 204 | } |
| 205 | } |
| 206 | /* must be either hdb entry (tp>0) or add from tdb (oname==NULL) |
| 207 | and first control aton (AI) matches this atom or |
| 208 | delete/replace from tdb (oname!=NULL) and oname matches this atom */ |
| 209 | if (debug) |
| 210 | { |
| 211 | fprintf(debug, " %s", hbr->hack[j].oname ? hbr->hack[j].oname : hbr->hack[j].AIa[0]); |
| 212 | } |
| 213 | |
| 214 | if (!bIgnore && |
| 215 | ( ( ( hbr->hack[j].tp > 0 || hbr->hack[j].oname == NULL((void*)0) ) && |
| 216 | strcmp(atomname, hbr->hack[j].AI)__extension__ ({ size_t __s1_len, __s2_len; (__builtin_constant_p (atomname) && __builtin_constant_p (hbr->hack[j]. a[0]) && (__s1_len = strlen (atomname), __s2_len = strlen (hbr->hack[j].a[0]), (!((size_t)(const void *)((atomname) + 1) - (size_t)(const void *)(atomname) == 1) || __s1_len >= 4) && (!((size_t)(const void *)((hbr->hack[j].a[0 ]) + 1) - (size_t)(const void *)(hbr->hack[j].a[0]) == 1) || __s2_len >= 4)) ? __builtin_strcmp (atomname, hbr->hack [j].a[0]) : (__builtin_constant_p (atomname) && ((size_t )(const void *)((atomname) + 1) - (size_t)(const void *)(atomname ) == 1) && (__s1_len = strlen (atomname), __s1_len < 4) ? (__builtin_constant_p (hbr->hack[j].a[0]) && ((size_t)(const void *)((hbr->hack[j].a[0]) + 1) - (size_t )(const void *)(hbr->hack[j].a[0]) == 1) ? __builtin_strcmp (atomname, hbr->hack[j].a[0]) : (__extension__ ({ const unsigned char *__s2 = (const unsigned char *) (const char *) (hbr-> hack[j].a[0]); int __result = (((const unsigned char *) (const char *) (atomname))[0] - __s2[0]); if (__s1_len > 0 && __result == 0) { __result = (((const unsigned char *) (const char *) (atomname))[1] - __s2[1]); if (__s1_len > 1 && __result == 0) { __result = (((const unsigned char *) (const char *) (atomname))[2] - __s2[2]); if (__s1_len > 2 && __result == 0) __result = (((const unsigned char *) (const char *) (atomname))[3] - __s2[3]); } } __result; }))) : (__builtin_constant_p (hbr->hack[j].a[0]) && ((size_t)(const void *)((hbr ->hack[j].a[0]) + 1) - (size_t)(const void *)(hbr->hack [j].a[0]) == 1) && (__s2_len = strlen (hbr->hack[j ].a[0]), __s2_len < 4) ? (__builtin_constant_p (atomname) && ((size_t)(const void *)((atomname) + 1) - (size_t)(const void *)(atomname) == 1) ? __builtin_strcmp (atomname, hbr->hack [j].a[0]) : (- (__extension__ ({ const unsigned char *__s2 = ( const unsigned char *) (const char *) (atomname); int __result = (((const unsigned char *) (const char *) (hbr->hack[j]. a[0]))[0] - __s2[0]); if (__s2_len > 0 && __result == 0) { __result = (((const unsigned char *) (const char *) ( hbr->hack[j].a[0]))[1] - __s2[1]); if (__s2_len > 1 && __result == 0) { __result = (((const unsigned char *) (const char *) (hbr->hack[j].a[0]))[2] - __s2[2]); if (__s2_len > 2 && __result == 0) __result = (((const unsigned char *) (const char *) (hbr->hack[j].a[0]))[3] - __s2[3]); } } __result; })))) : __builtin_strcmp (atomname, hbr->hack[j ].a[0])))); }) == 0 ) || |
| 217 | ( hbr->hack[j].oname != NULL((void*)0) && |
| 218 | strcmp(atomname, hbr->hack[j].oname)__extension__ ({ size_t __s1_len, __s2_len; (__builtin_constant_p (atomname) && __builtin_constant_p (hbr->hack[j]. oname) && (__s1_len = strlen (atomname), __s2_len = strlen (hbr->hack[j].oname), (!((size_t)(const void *)((atomname ) + 1) - (size_t)(const void *)(atomname) == 1) || __s1_len >= 4) && (!((size_t)(const void *)((hbr->hack[j].oname ) + 1) - (size_t)(const void *)(hbr->hack[j].oname) == 1) || __s2_len >= 4)) ? __builtin_strcmp (atomname, hbr->hack [j].oname) : (__builtin_constant_p (atomname) && ((size_t )(const void *)((atomname) + 1) - (size_t)(const void *)(atomname ) == 1) && (__s1_len = strlen (atomname), __s1_len < 4) ? (__builtin_constant_p (hbr->hack[j].oname) && ((size_t)(const void *)((hbr->hack[j].oname) + 1) - (size_t )(const void *)(hbr->hack[j].oname) == 1) ? __builtin_strcmp (atomname, hbr->hack[j].oname) : (__extension__ ({ const unsigned char *__s2 = (const unsigned char *) (const char *) (hbr-> hack[j].oname); int __result = (((const unsigned char *) (const char *) (atomname))[0] - __s2[0]); if (__s1_len > 0 && __result == 0) { __result = (((const unsigned char *) (const char *) (atomname))[1] - __s2[1]); if (__s1_len > 1 && __result == 0) { __result = (((const unsigned char *) (const char *) (atomname))[2] - __s2[2]); if (__s1_len > 2 && __result == 0) __result = (((const unsigned char *) (const char *) (atomname))[3] - __s2[3]); } } __result; }))) : (__builtin_constant_p (hbr->hack[j].oname) && ((size_t)(const void *)(( hbr->hack[j].oname) + 1) - (size_t)(const void *)(hbr-> hack[j].oname) == 1) && (__s2_len = strlen (hbr->hack [j].oname), __s2_len < 4) ? (__builtin_constant_p (atomname ) && ((size_t)(const void *)((atomname) + 1) - (size_t )(const void *)(atomname) == 1) ? __builtin_strcmp (atomname, hbr->hack[j].oname) : (- (__extension__ ({ const unsigned char *__s2 = (const unsigned char *) (const char *) (atomname ); int __result = (((const unsigned char *) (const char *) (hbr ->hack[j].oname))[0] - __s2[0]); if (__s2_len > 0 && __result == 0) { __result = (((const unsigned char *) (const char *) (hbr->hack[j].oname))[1] - __s2[1]); if (__s2_len > 1 && __result == 0) { __result = (((const unsigned char *) (const char *) (hbr->hack[j].oname))[2] - __s2[2] ); if (__s2_len > 2 && __result == 0) __result = ( ((const unsigned char *) (const char *) (hbr->hack[j].oname ))[3] - __s2[3]); } } __result; })))) : __builtin_strcmp (atomname , hbr->hack[j].oname)))); }) == 0) ) ) |
| 219 | { |
| 220 | /* now expand all hacks for this atom */ |
| 221 | if (debug) |
| 222 | { |
| 223 | fprintf(debug, " +%dh", hbr->hack[j].nr); |
| 224 | } |
| 225 | srenew(*abi, *nabi + hbr->hack[j].nr)(*abi) = save_realloc("*abi", "/home/alexxy/Develop/gromacs/src/gromacs/gmxpreprocess/genhydro.c" , 225, (*abi), (*nabi + hbr->hack[j].nr), sizeof(*(*abi))); |
| 226 | for (k = 0; k < hbr->hack[j].nr; k++) |
| 227 | { |
| 228 | copy_t_hack(&hbr->hack[j], &(*abi)[*nabi + k]); |
| 229 | (*abi)[*nabi + k].bXSet = FALSE0; |
| 230 | /* if we're adding (oname==NULL) and don't have a new name (nname) |
| 231 | yet, build it from atomname */ |
| 232 | if ( (*abi)[*nabi + k].nname == NULL((void*)0)) |
| 233 | { |
| 234 | if ( (*abi)[*nabi + k].oname == NULL((void*)0)) |
| 235 | { |
| 236 | (*abi)[*nabi + k].nname = strdup(atomname)(__extension__ (__builtin_constant_p (atomname) && (( size_t)(const void *)((atomname) + 1) - (size_t)(const void * )(atomname) == 1) ? (((const char *) (atomname))[0] == '\0' ? (char *) calloc ((size_t) 1, (size_t) 1) : ({ size_t __len = strlen (atomname) + 1; char *__retval = (char *) malloc (__len ); if (__retval != ((void*)0)) __retval = (char *) memcpy (__retval , atomname, __len); __retval; })) : __strdup (atomname))); |
| 237 | (*abi)[*nabi + k].nname[0] = 'H'; |
| 238 | } |
| 239 | } |
| 240 | else |
| 241 | { |
| 242 | if (gmx_debug_at) |
| 243 | { |
| 244 | fprintf(debug, "Hack '%s' %d, replacing nname '%s' with '%s' (old name '%s')\n", |
| 245 | atomname, j, |
| 246 | (*abi)[*nabi + k].nname, hbr->hack[j].nname, |
| 247 | (*abi)[*nabi + k].oname ? (*abi)[*nabi + k].oname : ""); |
| 248 | } |
| 249 | sfree((*abi)[*nabi + k].nname)save_free("(*abi)[*nabi + k].nname", "/home/alexxy/Develop/gromacs/src/gromacs/gmxpreprocess/genhydro.c" , 249, ((*abi)[*nabi + k].nname)); |
| 250 | (*abi)[*nabi + k].nname = strdup(hbr->hack[j].nname)(__extension__ (__builtin_constant_p (hbr->hack[j].nname) && ((size_t)(const void *)((hbr->hack[j].nname) + 1) - (size_t )(const void *)(hbr->hack[j].nname) == 1) ? (((const char * ) (hbr->hack[j].nname))[0] == '\0' ? (char *) calloc ((size_t ) 1, (size_t) 1) : ({ size_t __len = strlen (hbr->hack[j]. nname) + 1; char *__retval = (char *) malloc (__len); if (__retval != ((void*)0)) __retval = (char *) memcpy (__retval, hbr-> hack[j].nname, __len); __retval; })) : __strdup (hbr->hack [j].nname))); |
| 251 | } |
| 252 | |
| 253 | if (hbr->hack[j].tp == 10 && k == 2) |
| 254 | { |
| 255 | /* This is a water virtual site, not a hydrogen */ |
| 256 | /* Ugly hardcoded name hack */ |
| 257 | (*abi)[*nabi + k].nname[0] = 'M'; |
| 258 | } |
| 259 | else if (hbr->hack[j].tp == 11 && k >= 2) |
| 260 | { |
| 261 | /* This is a water lone pair, not a hydrogen */ |
| 262 | /* Ugly hardcoded name hack */ |
| 263 | srenew((*abi)[*nabi + k].nname, 4)((*abi)[*nabi + k].nname) = save_realloc("(*abi)[*nabi + k].nname" , "/home/alexxy/Develop/gromacs/src/gromacs/gmxpreprocess/genhydro.c" , 263, ((*abi)[*nabi + k].nname), (4), sizeof(*((*abi)[*nabi + k].nname))); |
| 264 | (*abi)[*nabi + k].nname[0] = 'L'; |
| 265 | (*abi)[*nabi + k].nname[1] = 'P'; |
| 266 | (*abi)[*nabi + k].nname[2] = '1' + k - 2; |
| 267 | (*abi)[*nabi + k].nname[3] = '\0'; |
| 268 | } |
| 269 | else if (hbr->hack[j].nr > 1) |
| 270 | { |
| 271 | /* adding more than one atom, number them */ |
| 272 | l = strlen((*abi)[*nabi + k].nname); |
| 273 | srenew((*abi)[*nabi + k].nname, l+2)((*abi)[*nabi + k].nname) = save_realloc("(*abi)[*nabi + k].nname" , "/home/alexxy/Develop/gromacs/src/gromacs/gmxpreprocess/genhydro.c" , 273, ((*abi)[*nabi + k].nname), (l+2), sizeof(*((*abi)[*nabi + k].nname))); |
| 274 | (*abi)[*nabi + k].nname[l] = '1' + k; |
| 275 | (*abi)[*nabi + k].nname[l+1] = '\0'; |
| 276 | } |
| 277 | } |
| 278 | (*nabi) += hbr->hack[j].nr; |
| 279 | |
| 280 | /* add hacks to atoms we've just added */ |
| 281 | if (hbr->hack[j].tp > 0 || hbr->hack[j].oname == NULL((void*)0)) |
| 282 | { |
| 283 | for (k = 0; k < hbr->hack[j].nr; k++) |
| 284 | { |
| 285 | expand_hackblocks_one(hbr, (*abi)[*nabi-hbr->hack[j].nr+k].nname, |
| 286 | nabi, abi, bN, bC); |
| 287 | } |
| 288 | } |
| 289 | } |
| 290 | } |
| 291 | } |
| 292 | |
| 293 | static void expand_hackblocks(t_atoms *pdba, t_hackblock hb[], |
| 294 | int nab[], t_hack *ab[], |
| 295 | int nterpairs, int *rN, int *rC) |
| 296 | { |
| 297 | int i, j; |
| 298 | gmx_bool bN, bC; |
| 299 | |
| 300 | for (i = 0; i < pdba->nr; i++) |
| 301 | { |
| 302 | bN = FALSE0; |
| 303 | for (j = 0; j < nterpairs && !bN; j++) |
| 304 | { |
| 305 | bN = pdba->atom[i].resind == rN[j]; |
| 306 | } |
| 307 | bC = FALSE0; |
| 308 | for (j = 0; j < nterpairs && !bC; j++) |
| 309 | { |
| 310 | bC = pdba->atom[i].resind == rC[j]; |
| 311 | } |
| 312 | |
| 313 | /* add hacks to this atom */ |
| 314 | expand_hackblocks_one(&hb[pdba->atom[i].resind], *pdba->atomname[i], |
| 315 | &nab[i], &ab[i], bN, bC); |
| 316 | } |
| 317 | if (debug) |
| 318 | { |
| 319 | fprintf(debug, "\n"); |
| 320 | } |
| 321 | } |
| 322 | |
| 323 | static int check_atoms_present(t_atoms *pdba, int nab[], t_hack *ab[]) |
| 324 | { |
| 325 | int i, j, k, d, rnr, nadd; |
| 326 | |
| 327 | nadd = 0; |
| 328 | for (i = 0; i < pdba->nr; i++) |
| 329 | { |
| 330 | rnr = pdba->atom[i].resind; |
| 331 | for (j = 0; j < nab[i]; j++) |
| 332 | { |
| 333 | if (ab[i][j].oname == NULL((void*)0)) |
| 334 | { |
| 335 | /* we're adding */ |
| 336 | if (ab[i][j].nname == NULL((void*)0)) |
| 337 | { |
| 338 | gmx_incons("ab[i][j].nname not allocated")_gmx_error("incons", "ab[i][j].nname not allocated", "/home/alexxy/Develop/gromacs/src/gromacs/gmxpreprocess/genhydro.c" , 338); |
| 339 | } |
| 340 | /* check if the atom is already present */ |
| 341 | k = pdbasearch_atom(ab[i][j].nname, rnr, pdba, "check", TRUE1); |
| 342 | if (k != -1) |
| 343 | { |
| 344 | /* We found the added atom. */ |
| 345 | ab[i][j].bAlreadyPresent = TRUE1; |
| 346 | if (debug) |
| 347 | { |
| 348 | fprintf(debug, "Atom '%s' in residue '%s' %d is already present\n", |
| 349 | ab[i][j].nname, |
| 350 | *pdba->resinfo[rnr].name, pdba->resinfo[rnr].nr); |
| 351 | } |
| 352 | } |
| 353 | else |
| 354 | { |
| 355 | ab[i][j].bAlreadyPresent = FALSE0; |
| 356 | /* count how many atoms we'll add */ |
| 357 | nadd++; |
| 358 | } |
| 359 | } |
| 360 | else if (ab[i][j].nname == NULL((void*)0)) |
| 361 | { |
| 362 | /* we're deleting */ |
| 363 | nadd--; |
| 364 | } |
| 365 | } |
| 366 | } |
| 367 | |
| 368 | return nadd; |
| 369 | } |
| 370 | |
| 371 | static void calc_all_pos(t_atoms *pdba, rvec x[], int nab[], t_hack *ab[], |
| 372 | gmx_bool bCheckMissing) |
| 373 | { |
| 374 | int i, j, ii, jj, m, ia, d, rnr, l = 0; |
| 375 | #define MAXH4 4 |
| 376 | rvec xa[4]; /* control atoms for calc_h_pos */ |
| 377 | rvec xh[MAXH4]; /* hydrogen positions from calc_h_pos */ |
| 378 | gmx_bool bFoundAll; |
| 379 | |
| 380 | jj = 0; |
| 381 | |
| 382 | for (i = 0; i < pdba->nr; i++) |
| 383 | { |
| 384 | rnr = pdba->atom[i].resind; |
| 385 | for (j = 0; j < nab[i]; j += ab[i][j].nr) |
| 386 | { |
| 387 | /* check if we're adding: */ |
| 388 | if (ab[i][j].oname == NULL((void*)0) && ab[i][j].tp > 0) |
| 389 | { |
| 390 | bFoundAll = TRUE1; |
| 391 | for (m = 0; (m < ab[i][j].nctl && bFoundAll); m++) |
| 392 | { |
| 393 | ia = pdbasearch_atom(ab[i][j].a[m], rnr, pdba, |
| 394 | bCheckMissing ? "atom" : "check", |
| 395 | !bCheckMissing); |
| 396 | if (ia < 0) |
| 397 | { |
| 398 | /* not found in original atoms, might still be in t_hack (ab) */ |
| 399 | hacksearch_atom(&ii, &jj, ab[i][j].a[m], nab, ab, rnr, pdba); |
| 400 | if (ii >= 0) |
| 401 | { |
| 402 | copy_rvec(ab[ii][jj].newx, xa[m]); |
| 403 | } |
| 404 | else |
| 405 | { |
| 406 | bFoundAll = FALSE0; |
| 407 | if (bCheckMissing) |
| 408 | { |
| 409 | gmx_fatal(FARGS0, "/home/alexxy/Develop/gromacs/src/gromacs/gmxpreprocess/genhydro.c" , 409, "Atom %s not found in residue %s %d" |
| 410 | ", rtp entry %s" |
| 411 | " while adding hydrogens", |
| 412 | ab[i][j].a[m], |
| 413 | *pdba->resinfo[rnr].name, |
| 414 | pdba->resinfo[rnr].nr, |
| 415 | *pdba->resinfo[rnr].rtp); |
| 416 | } |
| 417 | } |
| 418 | } |
| 419 | else |
| 420 | { |
| 421 | copy_rvec(x[ia], xa[m]); |
| 422 | } |
| 423 | } |
| 424 | if (bFoundAll) |
| 425 | { |
| 426 | for (m = 0; (m < MAXH4); m++) |
| 427 | { |
| 428 | for (d = 0; d < DIM3; d++) |
| 429 | { |
| 430 | if (m < ab[i][j].nr) |
| 431 | { |
| 432 | xh[m][d] = 0; |
| 433 | } |
| 434 | else |
| 435 | { |
| 436 | xh[m][d] = NOTSET-12345; |
| 437 | } |
| 438 | } |
| 439 | } |
| 440 | calc_h_pos(ab[i][j].tp, xa, xh, &l); |
| 441 | for (m = 0; m < ab[i][j].nr; m++) |
| 442 | { |
| 443 | copy_rvec(xh[m], ab[i][j+m].newx); |
| 444 | ab[i][j+m].bXSet = TRUE1; |
| 445 | } |
| 446 | } |
| 447 | } |
| 448 | } |
| 449 | } |
| 450 | } |
| 451 | |
| 452 | static void free_ab(int natoms, int *nab, t_hack **ab) |
| 453 | { |
| 454 | int i; |
| 455 | |
| 456 | for (i = 0; i < natoms; i++) |
| 457 | { |
| 458 | free_t_hack(nab[i], &ab[i]); |
| 459 | } |
| 460 | sfree(nab)save_free("nab", "/home/alexxy/Develop/gromacs/src/gromacs/gmxpreprocess/genhydro.c" , 460, (nab)); |
| 461 | sfree(ab)save_free("ab", "/home/alexxy/Develop/gromacs/src/gromacs/gmxpreprocess/genhydro.c" , 461, (ab)); |
| 462 | } |
| 463 | |
| 464 | static int add_h_low(t_atoms **pdbaptr, rvec *xptr[], |
| 465 | int nah, t_hackblock ah[], |
| 466 | int nterpairs, t_hackblock **ntdb, t_hackblock **ctdb, |
| 467 | int *rN, int *rC, gmx_bool bCheckMissing, |
| 468 | int **nabptr, t_hack ***abptr, |
| 469 | gmx_bool bUpdate_pdba, gmx_bool bKeep_old_pdba) |
| 470 | { |
| 471 | t_atoms *newpdba = NULL((void*)0), *pdba = NULL((void*)0); |
| 472 | int nadd; |
| 473 | int i, newi, j, d, natoms, nalreadypresent; |
| 474 | int *nab = NULL((void*)0); |
| 475 | t_hack **ab = NULL((void*)0); |
| 476 | t_hackblock *hb; |
| 477 | rvec *xn; |
| 478 | gmx_bool bKeep_ab; |
| 479 | |
| 480 | /* set flags for adding hydrogens (according to hdb) */ |
| 481 | pdba = *pdbaptr; |
| 482 | natoms = pdba->nr; |
| 483 | |
| 484 | if (nabptr && abptr) |
| 485 | { |
| 486 | /* the first time these will be pointers to NULL, but we will |
| 487 | return in them the completed arrays, which we will get back |
| 488 | the second time */ |
| 489 | nab = *nabptr; |
| 490 | ab = *abptr; |
| 491 | bKeep_ab = TRUE1; |
| 492 | if (debug) |
| 493 | { |
| 494 | fprintf(debug, "pointer to ab found\n"); |
| 495 | } |
| 496 | } |
| 497 | else |
| 498 | { |
| 499 | bKeep_ab = FALSE0; |
| 500 | } |
| 501 | |
| 502 | if (nab && ab) |
| 503 | { |
| 504 | /* WOW, everything was already figured out */ |
| 505 | bUpdate_pdba = FALSE0; |
| 506 | if (debug) |
| 507 | { |
| 508 | fprintf(debug, "pointer to non-null ab found\n"); |
| 509 | } |
| 510 | } |
| 511 | else |
| 512 | { |
| 513 | /* We'll have to do all the hard work */ |
| 514 | bUpdate_pdba = TRUE1; |
| 515 | /* first get all the hackblocks for each residue: */ |
| 516 | hb = get_hackblocks(pdba, nah, ah, nterpairs, ntdb, ctdb, rN, rC); |
| 517 | if (debug) |
| 518 | { |
| 519 | dump_hb(debug, pdba->nres, hb); |
| 520 | } |
| 521 | |
| 522 | /* expand the hackblocks to atom level */ |
| 523 | snew(nab, natoms)(nab) = save_calloc("nab", "/home/alexxy/Develop/gromacs/src/gromacs/gmxpreprocess/genhydro.c" , 523, (natoms), sizeof(*(nab))); |
| 524 | snew(ab, natoms)(ab) = save_calloc("ab", "/home/alexxy/Develop/gromacs/src/gromacs/gmxpreprocess/genhydro.c" , 524, (natoms), sizeof(*(ab))); |
| 525 | expand_hackblocks(pdba, hb, nab, ab, nterpairs, rN, rC); |
| 526 | free_t_hackblock(pdba->nres, &hb); |
| 527 | } |
| 528 | |
| 529 | if (debug) |
| 530 | { |
| 531 | fprintf(debug, "before calc_all_pos\n"); |
| 532 | dump_ab(debug, natoms, nab, ab, TRUE1); |
| 533 | } |
| 534 | |
| 535 | /* Now calc the positions */ |
| 536 | calc_all_pos(pdba, *xptr, nab, ab, bCheckMissing); |
| 537 | |
| 538 | if (debug) |
| 539 | { |
| 540 | fprintf(debug, "after calc_all_pos\n"); |
| 541 | dump_ab(debug, natoms, nab, ab, TRUE1); |
| 542 | } |
| 543 | |
| 544 | if (bUpdate_pdba) |
| 545 | { |
| 546 | /* we don't have to add atoms that are already present in pdba, |
| 547 | so we will remove them from the ab (t_hack) */ |
| 548 | nadd = check_atoms_present(pdba, nab, ab); |
| 549 | if (debug) |
| 550 | { |
| 551 | fprintf(debug, "removed add hacks that were already in pdba:\n"); |
| 552 | dump_ab(debug, natoms, nab, ab, TRUE1); |
| 553 | fprintf(debug, "will be adding %d atoms\n", nadd); |
| 554 | } |
| 555 | |
| 556 | /* Copy old atoms, making space for new ones */ |
| 557 | snew(newpdba, 1)(newpdba) = save_calloc("newpdba", "/home/alexxy/Develop/gromacs/src/gromacs/gmxpreprocess/genhydro.c" , 557, (1), sizeof(*(newpdba))); |
| 558 | init_t_atoms(newpdba, natoms+nadd, FALSE0); |
| 559 | newpdba->nres = pdba->nres; |
| 560 | sfree(newpdba->resinfo)save_free("newpdba->resinfo", "/home/alexxy/Develop/gromacs/src/gromacs/gmxpreprocess/genhydro.c" , 560, (newpdba->resinfo)); |
| 561 | newpdba->resinfo = pdba->resinfo; |
| 562 | } |
| 563 | else |
| 564 | { |
| 565 | nadd = 0; |
| 566 | } |
| 567 | if (debug) |
| 568 | { |
| 569 | fprintf(debug, "snew xn for %d old + %d new atoms %d total)\n", |
| 570 | natoms, nadd, natoms+nadd); |
| 571 | } |
| 572 | |
| 573 | if (nadd == 0) |
| 574 | { |
| 575 | /* There is nothing to do: return now */ |
| 576 | if (!bKeep_ab) |
| 577 | { |
| 578 | free_ab(natoms, nab, ab); |
| 579 | } |
| 580 | |
| 581 | return natoms; |
| 582 | } |
| 583 | |
| 584 | snew(xn, natoms+nadd)(xn) = save_calloc("xn", "/home/alexxy/Develop/gromacs/src/gromacs/gmxpreprocess/genhydro.c" , 584, (natoms+nadd), sizeof(*(xn))); |
| 585 | newi = 0; |
| 586 | for (i = 0; (i < natoms); i++) |
| 587 | { |
| 588 | /* check if this atom wasn't scheduled for deletion */ |
| 589 | if (nab[i] == 0 || (ab[i][0].nname != NULL((void*)0)) ) |
| 590 | { |
| 591 | if (newi >= natoms+nadd) |
| 592 | { |
| 593 | /*gmx_fatal(FARGS,"Not enough space for adding atoms");*/ |
| 594 | nadd += 10; |
| 595 | srenew(xn, natoms+nadd)(xn) = save_realloc("xn", "/home/alexxy/Develop/gromacs/src/gromacs/gmxpreprocess/genhydro.c" , 595, (xn), (natoms+nadd), sizeof(*(xn))); |
| 596 | if (bUpdate_pdba) |
| 597 | { |
| 598 | srenew(newpdba->atom, natoms+nadd)(newpdba->atom) = save_realloc("newpdba->atom", "/home/alexxy/Develop/gromacs/src/gromacs/gmxpreprocess/genhydro.c" , 598, (newpdba->atom), (natoms+nadd), sizeof(*(newpdba-> atom))); |
| 599 | srenew(newpdba->atomname, natoms+nadd)(newpdba->atomname) = save_realloc("newpdba->atomname", "/home/alexxy/Develop/gromacs/src/gromacs/gmxpreprocess/genhydro.c" , 599, (newpdba->atomname), (natoms+nadd), sizeof(*(newpdba ->atomname))); |
| 600 | } |
| 601 | debug_gmx(); |
| 602 | } |
| 603 | if (debug) |
| 604 | { |
| 605 | fprintf(debug, "(%3d) %3d %4s %4s%3d %3d", |
| 606 | i+1, newi+1, *pdba->atomname[i], |
| 607 | *pdba->resinfo[pdba->atom[i].resind].name, |
| 608 | pdba->resinfo[pdba->atom[i].resind].nr, nab[i]); |
| 609 | } |
| 610 | if (bUpdate_pdba) |
| 611 | { |
| 612 | copy_atom(pdba, i, newpdba, newi); |
| 613 | } |
| 614 | copy_rvec((*xptr)[i], xn[newi]); |
| 615 | /* process the hacks for this atom */ |
| 616 | nalreadypresent = 0; |
| 617 | for (j = 0; j < nab[i]; j++) |
| 618 | { |
| 619 | if (ab[i][j].oname == NULL((void*)0)) /* add */ |
| 620 | { |
| 621 | newi++; |
| 622 | if (newi >= natoms+nadd) |
| 623 | { |
| 624 | /* gmx_fatal(FARGS,"Not enough space for adding atoms");*/ |
| 625 | nadd += 10; |
| 626 | srenew(xn, natoms+nadd)(xn) = save_realloc("xn", "/home/alexxy/Develop/gromacs/src/gromacs/gmxpreprocess/genhydro.c" , 626, (xn), (natoms+nadd), sizeof(*(xn))); |
| 627 | if (bUpdate_pdba) |
| 628 | { |
| 629 | srenew(newpdba->atom, natoms+nadd)(newpdba->atom) = save_realloc("newpdba->atom", "/home/alexxy/Develop/gromacs/src/gromacs/gmxpreprocess/genhydro.c" , 629, (newpdba->atom), (natoms+nadd), sizeof(*(newpdba-> atom))); |
| 630 | srenew(newpdba->atomname, natoms+nadd)(newpdba->atomname) = save_realloc("newpdba->atomname", "/home/alexxy/Develop/gromacs/src/gromacs/gmxpreprocess/genhydro.c" , 630, (newpdba->atomname), (natoms+nadd), sizeof(*(newpdba ->atomname))); |
| 631 | } |
| 632 | debug_gmx(); |
| 633 | } |
| 634 | if (bUpdate_pdba) |
| 635 | { |
| 636 | newpdba->atom[newi].resind = pdba->atom[i].resind; |
| 637 | } |
| 638 | if (debug) |
| 639 | { |
| 640 | fprintf(debug, " + %d", newi+1); |
| 641 | } |
| 642 | } |
| 643 | if (ab[i][j].nname != NULL((void*)0) && |
| 644 | (ab[i][j].oname == NULL((void*)0) || |
| 645 | strcmp(ab[i][j].oname, *newpdba->atomname[newi])__extension__ ({ size_t __s1_len, __s2_len; (__builtin_constant_p (ab[i][j].oname) && __builtin_constant_p (*newpdba-> atomname[newi]) && (__s1_len = strlen (ab[i][j].oname ), __s2_len = strlen (*newpdba->atomname[newi]), (!((size_t )(const void *)((ab[i][j].oname) + 1) - (size_t)(const void * )(ab[i][j].oname) == 1) || __s1_len >= 4) && (!((size_t )(const void *)((*newpdba->atomname[newi]) + 1) - (size_t) (const void *)(*newpdba->atomname[newi]) == 1) || __s2_len >= 4)) ? __builtin_strcmp (ab[i][j].oname, *newpdba->atomname [newi]) : (__builtin_constant_p (ab[i][j].oname) && ( (size_t)(const void *)((ab[i][j].oname) + 1) - (size_t)(const void *)(ab[i][j].oname) == 1) && (__s1_len = strlen ( ab[i][j].oname), __s1_len < 4) ? (__builtin_constant_p (*newpdba ->atomname[newi]) && ((size_t)(const void *)((*newpdba ->atomname[newi]) + 1) - (size_t)(const void *)(*newpdba-> atomname[newi]) == 1) ? __builtin_strcmp (ab[i][j].oname, *newpdba ->atomname[newi]) : (__extension__ ({ const unsigned char * __s2 = (const unsigned char *) (const char *) (*newpdba->atomname [newi]); int __result = (((const unsigned char *) (const char *) (ab[i][j].oname))[0] - __s2[0]); if (__s1_len > 0 && __result == 0) { __result = (((const unsigned char *) (const char *) (ab[i][j].oname))[1] - __s2[1]); if (__s1_len > 1 && __result == 0) { __result = (((const unsigned char *) (const char *) (ab[i][j].oname))[2] - __s2[2]); if (__s1_len > 2 && __result == 0) __result = (((const unsigned char *) (const char *) (ab[i][j].oname))[3] - __s2[3]); } } __result ; }))) : (__builtin_constant_p (*newpdba->atomname[newi]) && ((size_t)(const void *)((*newpdba->atomname[newi]) + 1) - (size_t)(const void *)(*newpdba->atomname[newi]) == 1) && (__s2_len = strlen (*newpdba->atomname[newi]), __s2_len < 4) ? (__builtin_constant_p (ab[i][j].oname) && ((size_t )(const void *)((ab[i][j].oname) + 1) - (size_t)(const void * )(ab[i][j].oname) == 1) ? __builtin_strcmp (ab[i][j].oname, * newpdba->atomname[newi]) : (- (__extension__ ({ const unsigned char *__s2 = (const unsigned char *) (const char *) (ab[i][j ].oname); int __result = (((const unsigned char *) (const char *) (*newpdba->atomname[newi]))[0] - __s2[0]); if (__s2_len > 0 && __result == 0) { __result = (((const unsigned char *) (const char *) (*newpdba->atomname[newi]))[1] - __s2 [1]); if (__s2_len > 1 && __result == 0) { __result = (((const unsigned char *) (const char *) (*newpdba->atomname [newi]))[2] - __s2[2]); if (__s2_len > 2 && __result == 0) __result = (((const unsigned char *) (const char *) (* newpdba->atomname[newi]))[3] - __s2[3]); } } __result; })) )) : __builtin_strcmp (ab[i][j].oname, *newpdba->atomname[ newi])))); }) == 0)) |
| 646 | { |
| 647 | /* add or replace */ |
| 648 | if (ab[i][j].oname == NULL((void*)0) && ab[i][j].bAlreadyPresent) |
| 649 | { |
| 650 | /* This atom is already present, copy it from the input. */ |
| 651 | nalreadypresent++; |
| 652 | if (bUpdate_pdba) |
| 653 | { |
| 654 | copy_atom(pdba, i+nalreadypresent, newpdba, newi); |
| 655 | } |
| 656 | copy_rvec((*xptr)[i+nalreadypresent], xn[newi]); |
| 657 | } |
| 658 | else |
| 659 | { |
| 660 | if (bUpdate_pdba) |
| 661 | { |
| 662 | if (gmx_debug_at) |
| 663 | { |
| 664 | fprintf(debug, "Replacing %d '%s' with (old name '%s') %s\n", |
| 665 | newi, |
| 666 | (newpdba->atomname[newi] && *newpdba->atomname[newi]) ? *newpdba->atomname[newi] : "", |
| 667 | ab[i][j].oname ? ab[i][j].oname : "", |
| 668 | ab[i][j].nname); |
| 669 | } |
| 670 | snew(newpdba->atomname[newi], 1)(newpdba->atomname[newi]) = save_calloc("newpdba->atomname[newi]" , "/home/alexxy/Develop/gromacs/src/gromacs/gmxpreprocess/genhydro.c" , 670, (1), sizeof(*(newpdba->atomname[newi]))); |
| 671 | *newpdba->atomname[newi] = strdup(ab[i][j].nname)(__extension__ (__builtin_constant_p (ab[i][j].nname) && ((size_t)(const void *)((ab[i][j].nname) + 1) - (size_t)(const void *)(ab[i][j].nname) == 1) ? (((const char *) (ab[i][j].nname ))[0] == '\0' ? (char *) calloc ((size_t) 1, (size_t) 1) : ({ size_t __len = strlen (ab[i][j].nname) + 1; char *__retval = (char *) malloc (__len); if (__retval != ((void*)0)) __retval = (char *) memcpy (__retval, ab[i][j].nname, __len); __retval ; })) : __strdup (ab[i][j].nname))); |
| 672 | if (ab[i][j].oname != NULL((void*)0) && ab[i][j].atom) /* replace */ |
| 673 | { /* newpdba->atom[newi].m = ab[i][j].atom->m; */ |
| 674 | /* newpdba->atom[newi].q = ab[i][j].atom->q; */ |
| 675 | /* newpdba->atom[newi].type = ab[i][j].atom->type; */ |
| 676 | } |
| 677 | } |
| 678 | if (ab[i][j].bXSet) |
| 679 | { |
| 680 | copy_rvec(ab[i][j].newx, xn[newi]); |
| 681 | } |
| 682 | } |
| 683 | if (bUpdate_pdba && debug) |
| 684 | { |
| 685 | fprintf(debug, " %s %g %g", *newpdba->atomname[newi], |
| 686 | newpdba->atom[newi].m, newpdba->atom[newi].q); |
| 687 | } |
| 688 | } |
| 689 | } |
| 690 | newi++; |
| 691 | i += nalreadypresent; |
| 692 | if (debug) |
| 693 | { |
| 694 | fprintf(debug, "\n"); |
| 695 | } |
| 696 | } |
| 697 | } |
| 698 | if (bUpdate_pdba) |
| 699 | { |
| 700 | newpdba->nr = newi; |
| 701 | } |
| 702 | |
| 703 | if (bKeep_ab) |
| 704 | { |
| 705 | *nabptr = nab; |
| 706 | *abptr = ab; |
| 707 | } |
| 708 | else |
| 709 | { |
| 710 | /* Clean up */ |
| 711 | free_ab(natoms, nab, ab); |
| 712 | } |
| 713 | |
| 714 | if (bUpdate_pdba) |
| 715 | { |
| 716 | if (!bKeep_old_pdba) |
| 717 | { |
| 718 | for (i = 0; i < natoms; i++) |
| 719 | { |
| 720 | /* Do not free the atomname string itself, it might be in symtab */ |
| 721 | /* sfree(*(pdba->atomname[i])); */ |
| 722 | /* sfree(pdba->atomname[i]); */ |
| 723 | } |
| 724 | sfree(pdba->atomname)save_free("pdba->atomname", "/home/alexxy/Develop/gromacs/src/gromacs/gmxpreprocess/genhydro.c" , 724, (pdba->atomname)); |
| 725 | sfree(pdba->atom)save_free("pdba->atom", "/home/alexxy/Develop/gromacs/src/gromacs/gmxpreprocess/genhydro.c" , 725, (pdba->atom)); |
| 726 | sfree(pdba->pdbinfo)save_free("pdba->pdbinfo", "/home/alexxy/Develop/gromacs/src/gromacs/gmxpreprocess/genhydro.c" , 726, (pdba->pdbinfo)); |
| 727 | sfree(pdba)save_free("pdba", "/home/alexxy/Develop/gromacs/src/gromacs/gmxpreprocess/genhydro.c" , 727, (pdba)); |
| 728 | } |
| 729 | *pdbaptr = newpdba; |
| 730 | } |
| 731 | else |
| 732 | { |
| 733 | nadd = newi-natoms; |
Value stored to 'nadd' is never read | |
| 734 | } |
| 735 | |
| 736 | sfree(*xptr)save_free("*xptr", "/home/alexxy/Develop/gromacs/src/gromacs/gmxpreprocess/genhydro.c" , 736, (*xptr)); |
| 737 | *xptr = xn; |
| 738 | |
| 739 | return newi; |
| 740 | } |
| 741 | |
| 742 | void deprotonate(t_atoms *atoms, rvec *x) |
| 743 | { |
| 744 | int i, j; |
| 745 | |
| 746 | j = 0; |
| 747 | for (i = 0; i < atoms->nr; i++) |
| 748 | { |
| 749 | if ( (*atoms->atomname[i])[0] != 'H') |
| 750 | { |
| 751 | atoms->atomname[j] = atoms->atomname[i]; |
| 752 | atoms->atom[j] = atoms->atom[i]; |
| 753 | copy_rvec(x[i], x[j]); |
| 754 | j++; |
| 755 | } |
| 756 | } |
| 757 | atoms->nr = j; |
| 758 | } |
| 759 | |
| 760 | int add_h(t_atoms **pdbaptr, rvec *xptr[], |
| 761 | int nah, t_hackblock ah[], |
| 762 | int nterpairs, t_hackblock **ntdb, t_hackblock **ctdb, |
| 763 | int *rN, int *rC, gmx_bool bAllowMissing, |
| 764 | int **nabptr, t_hack ***abptr, |
| 765 | gmx_bool bUpdate_pdba, gmx_bool bKeep_old_pdba) |
| 766 | { |
| 767 | int nold, nnew, niter; |
| 768 | |
| 769 | /* Here we loop to be able to add atoms to added atoms. |
| 770 | * We should not check for missing atoms here. |
| 771 | */ |
| 772 | niter = 0; |
| 773 | nnew = 0; |
| 774 | do |
| 775 | { |
| 776 | nold = nnew; |
| 777 | nnew = add_h_low(pdbaptr, xptr, nah, ah, nterpairs, ntdb, ctdb, rN, rC, FALSE0, |
| 778 | nabptr, abptr, bUpdate_pdba, bKeep_old_pdba); |
| 779 | niter++; |
| 780 | if (niter > 100) |
| 781 | { |
| 782 | gmx_fatal(FARGS0, "/home/alexxy/Develop/gromacs/src/gromacs/gmxpreprocess/genhydro.c" , 782, "More than 100 iterations of add_h. Maybe you are trying to replace an added atom (this is not supported)?"); |
| 783 | } |
| 784 | } |
| 785 | while (nnew > nold); |
| 786 | |
| 787 | if (!bAllowMissing) |
| 788 | { |
| 789 | /* Call add_h_low once more, now only for the missing atoms check */ |
| 790 | add_h_low(pdbaptr, xptr, nah, ah, nterpairs, ntdb, ctdb, rN, rC, TRUE1, |
| 791 | nabptr, abptr, bUpdate_pdba, bKeep_old_pdba); |
| 792 | } |
| 793 | |
| 794 | return nnew; |
| 795 | } |
| 796 | |
| 797 | int protonate(t_atoms **atomsptr, rvec **xptr, t_protonate *protdata) |
| 798 | { |
| 799 | #define NTERPAIRS 1 |
| 800 | t_atoms *atoms; |
| 801 | gmx_bool bUpdate_pdba, bKeep_old_pdba; |
| 802 | int nntdb, nctdb, nt, ct; |
| 803 | int nadd; |
| 804 | |
| 805 | atoms = NULL((void*)0); |
| 806 | if (!protdata->bInit) |
| 807 | { |
| 808 | if (debug) |
| 809 | { |
| 810 | fprintf(debug, "protonate: Initializing protdata\n"); |
| 811 | } |
| 812 | |
| 813 | /* set forcefield to use: */ |
| 814 | strcpy(protdata->FF, "oplsaa.ff"); |
| 815 | |
| 816 | /* get the databases: */ |
| 817 | protdata->nah = read_h_db(protdata->FF, &protdata->ah); |
| 818 | open_symtab(&protdata->tab); |
| 819 | protdata->atype = read_atype(protdata->FF, &protdata->tab); |
| 820 | nntdb = read_ter_db(protdata->FF, 'n', &protdata->ntdb, protdata->atype); |
| 821 | if (nntdb < 1) |
| 822 | { |
| 823 | gmx_fatal(FARGS0, "/home/alexxy/Develop/gromacs/src/gromacs/gmxpreprocess/genhydro.c" , 823, "no N-terminus database"); |
| 824 | } |
| 825 | nctdb = read_ter_db(protdata->FF, 'c', &protdata->ctdb, protdata->atype); |
| 826 | if (nctdb < 1) |
| 827 | { |
| 828 | gmx_fatal(FARGS0, "/home/alexxy/Develop/gromacs/src/gromacs/gmxpreprocess/genhydro.c" , 828, "no C-terminus database"); |
| 829 | } |
| 830 | |
| 831 | /* set terminus types: -NH3+ (different for Proline) and -COO- */ |
| 832 | atoms = *atomsptr; |
| 833 | snew(protdata->sel_ntdb, NTERPAIRS)(protdata->sel_ntdb) = save_calloc("protdata->sel_ntdb" , "/home/alexxy/Develop/gromacs/src/gromacs/gmxpreprocess/genhydro.c" , 833, (NTERPAIRS), sizeof(*(protdata->sel_ntdb))); |
| 834 | snew(protdata->sel_ctdb, NTERPAIRS)(protdata->sel_ctdb) = save_calloc("protdata->sel_ctdb" , "/home/alexxy/Develop/gromacs/src/gromacs/gmxpreprocess/genhydro.c" , 834, (NTERPAIRS), sizeof(*(protdata->sel_ctdb))); |
| 835 | |
| 836 | if (nntdb >= 4 && nctdb >= 2) |
| 837 | { |
| 838 | /* Yuk, yuk, hardcoded default termini selections !!! */ |
| 839 | if (strncmp(*atoms->resinfo[atoms->atom[atoms->nr-1].resind].name, "PRO", 3)(__extension__ (__builtin_constant_p (3) && ((__builtin_constant_p (*atoms->resinfo[atoms->atom[atoms->nr-1].resind].name ) && strlen (*atoms->resinfo[atoms->atom[atoms-> nr-1].resind].name) < ((size_t) (3))) || (__builtin_constant_p ("PRO") && strlen ("PRO") < ((size_t) (3)))) ? __extension__ ({ size_t __s1_len, __s2_len; (__builtin_constant_p (*atoms-> resinfo[atoms->atom[atoms->nr-1].resind].name) && __builtin_constant_p ("PRO") && (__s1_len = strlen ( *atoms->resinfo[atoms->atom[atoms->nr-1].resind].name ), __s2_len = strlen ("PRO"), (!((size_t)(const void *)((*atoms ->resinfo[atoms->atom[atoms->nr-1].resind].name) + 1 ) - (size_t)(const void *)(*atoms->resinfo[atoms->atom[ atoms->nr-1].resind].name) == 1) || __s1_len >= 4) && (!((size_t)(const void *)(("PRO") + 1) - (size_t)(const void *)("PRO") == 1) || __s2_len >= 4)) ? __builtin_strcmp (*atoms ->resinfo[atoms->atom[atoms->nr-1].resind].name, "PRO" ) : (__builtin_constant_p (*atoms->resinfo[atoms->atom[ atoms->nr-1].resind].name) && ((size_t)(const void *)((*atoms->resinfo[atoms->atom[atoms->nr-1].resind ].name) + 1) - (size_t)(const void *)(*atoms->resinfo[atoms ->atom[atoms->nr-1].resind].name) == 1) && (__s1_len = strlen (*atoms->resinfo[atoms->atom[atoms->nr-1]. resind].name), __s1_len < 4) ? (__builtin_constant_p ("PRO" ) && ((size_t)(const void *)(("PRO") + 1) - (size_t)( const void *)("PRO") == 1) ? __builtin_strcmp (*atoms->resinfo [atoms->atom[atoms->nr-1].resind].name, "PRO") : (__extension__ ({ const unsigned char *__s2 = (const unsigned char *) (const char *) ("PRO"); int __result = (((const unsigned char *) (const char *) (*atoms->resinfo[atoms->atom[atoms->nr-1].resind ].name))[0] - __s2[0]); if (__s1_len > 0 && __result == 0) { __result = (((const unsigned char *) (const char *) ( *atoms->resinfo[atoms->atom[atoms->nr-1].resind].name ))[1] - __s2[1]); if (__s1_len > 1 && __result == 0 ) { __result = (((const unsigned char *) (const char *) (*atoms ->resinfo[atoms->atom[atoms->nr-1].resind].name))[2] - __s2[2]); if (__s1_len > 2 && __result == 0) __result = (((const unsigned char *) (const char *) (*atoms->resinfo [atoms->atom[atoms->nr-1].resind].name))[3] - __s2[3]); } } __result; }))) : (__builtin_constant_p ("PRO") && ((size_t)(const void *)(("PRO") + 1) - (size_t)(const void * )("PRO") == 1) && (__s2_len = strlen ("PRO"), __s2_len < 4) ? (__builtin_constant_p (*atoms->resinfo[atoms-> atom[atoms->nr-1].resind].name) && ((size_t)(const void *)((*atoms->resinfo[atoms->atom[atoms->nr-1].resind ].name) + 1) - (size_t)(const void *)(*atoms->resinfo[atoms ->atom[atoms->nr-1].resind].name) == 1) ? __builtin_strcmp (*atoms->resinfo[atoms->atom[atoms->nr-1].resind].name , "PRO") : (- (__extension__ ({ const unsigned char *__s2 = ( const unsigned char *) (const char *) (*atoms->resinfo[atoms ->atom[atoms->nr-1].resind].name); int __result = (((const unsigned char *) (const char *) ("PRO"))[0] - __s2[0]); if ( __s2_len > 0 && __result == 0) { __result = (((const unsigned char *) (const char *) ("PRO"))[1] - __s2[1]); if ( __s2_len > 1 && __result == 0) { __result = (((const unsigned char *) (const char *) ("PRO"))[2] - __s2[2]); if ( __s2_len > 2 && __result == 0) __result = (((const unsigned char *) (const char *) ("PRO"))[3] - __s2[3]); } } __result ; })))) : __builtin_strcmp (*atoms->resinfo[atoms->atom [atoms->nr-1].resind].name, "PRO")))); }) : strncmp (*atoms ->resinfo[atoms->atom[atoms->nr-1].resind].name, "PRO" , 3))) == 0) |
| 840 | { |
| 841 | nt = 3; |
| 842 | } |
| 843 | else |
| 844 | { |
| 845 | nt = 1; |
| 846 | } |
| 847 | ct = 1; |
| 848 | } |
| 849 | else |
| 850 | { |
| 851 | nt = 0; |
| 852 | ct = 0; |
| 853 | } |
| 854 | protdata->sel_ntdb[0] = &(protdata->ntdb[nt]); |
| 855 | protdata->sel_ctdb[0] = &(protdata->ctdb[ct]); |
| 856 | |
| 857 | /* set terminal residue numbers: */ |
| 858 | snew(protdata->rN, NTERPAIRS)(protdata->rN) = save_calloc("protdata->rN", "/home/alexxy/Develop/gromacs/src/gromacs/gmxpreprocess/genhydro.c" , 858, (NTERPAIRS), sizeof(*(protdata->rN))); |
| 859 | snew(protdata->rC, NTERPAIRS)(protdata->rC) = save_calloc("protdata->rC", "/home/alexxy/Develop/gromacs/src/gromacs/gmxpreprocess/genhydro.c" , 859, (NTERPAIRS), sizeof(*(protdata->rC))); |
| 860 | protdata->rN[0] = 0; |
| 861 | protdata->rC[0] = atoms->atom[atoms->nr-1].resind; |
| 862 | |
| 863 | /* keep unprotonated topology: */ |
| 864 | protdata->upatoms = atoms; |
| 865 | /* we don't have these yet: */ |
| 866 | protdata->patoms = NULL((void*)0); |
| 867 | bUpdate_pdba = TRUE1; |
| 868 | bKeep_old_pdba = TRUE1; |
| 869 | |
| 870 | /* clear hackblocks: */ |
| 871 | protdata->nab = NULL((void*)0); |
| 872 | protdata->ab = NULL((void*)0); |
| 873 | |
| 874 | /* set flag to show we're initialized: */ |
| 875 | protdata->bInit = TRUE1; |
| 876 | } |
| 877 | else |
| 878 | { |
| 879 | if (debug) |
| 880 | { |
| 881 | fprintf(debug, "protonate: using available protdata\n"); |
| 882 | } |
| 883 | /* add_h will need the unprotonated topology again: */ |
| 884 | atoms = protdata->upatoms; |
| 885 | bUpdate_pdba = FALSE0; |
| 886 | bKeep_old_pdba = FALSE0; |
| 887 | } |
| 888 | |
| 889 | /* now protonate */ |
| 890 | nadd = add_h(&atoms, xptr, protdata->nah, protdata->ah, |
| 891 | NTERPAIRS, protdata->sel_ntdb, protdata->sel_ctdb, |
| 892 | protdata->rN, protdata->rC, TRUE1, |
| 893 | &protdata->nab, &protdata->ab, bUpdate_pdba, bKeep_old_pdba); |
| 894 | if (!protdata->patoms) |
| 895 | { |
| 896 | /* store protonated topology */ |
| 897 | protdata->patoms = atoms; |
| 898 | } |
| 899 | *atomsptr = protdata->patoms; |
| 900 | if (debug) |
| 901 | { |
| 902 | fprintf(debug, "natoms: %d -> %d (nadd=%d)\n", |
| 903 | protdata->upatoms->nr, protdata->patoms->nr, nadd); |
| 904 | } |
| 905 | return nadd; |
| 906 | #undef NTERPAIRS |
| 907 | } |