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47 #include "gromacs/topology/atomprop.h"
48 #include "gromacs/topology/symtab.h"
49 #include "gromacs/utility/compare.h"
50 #include "gromacs/utility/fatalerror.h"
51 #include "gromacs/utility/smalloc.h"
52 #include "gromacs/utility/txtdump.h"
54 const char* ptype_str[eptNR + 1] = { "Atom", "Nucleus", "Shell", "Bond", "VSite", nullptr };
56 void init_atom(t_atoms* at)
61 at->resinfo = nullptr;
62 at->atomname = nullptr;
63 at->atomtype = nullptr;
64 at->atomtypeB = nullptr;
65 at->pdbinfo = nullptr;
67 at->haveCharge = FALSE;
69 at->haveBState = FALSE;
70 at->havePdbInfo = FALSE;
73 void init_atomtypes(t_atomtypes* at)
76 at->atomnumber = nullptr;
79 void done_atom(t_atoms* at)
90 void done_and_delete_atoms(t_atoms* atoms)
96 void done_atomtypes(t_atomtypes* atype)
99 sfree(atype->atomnumber);
102 void add_t_atoms(t_atoms* atoms, int natom_extra, int nres_extra)
108 srenew(atoms->atomname, atoms->nr + natom_extra);
109 srenew(atoms->atom, atoms->nr + natom_extra);
110 if (nullptr != atoms->pdbinfo)
112 srenew(atoms->pdbinfo, atoms->nr + natom_extra);
114 if (nullptr != atoms->atomtype)
116 srenew(atoms->atomtype, atoms->nr + natom_extra);
118 if (nullptr != atoms->atomtypeB)
120 srenew(atoms->atomtypeB, atoms->nr + natom_extra);
122 for (i = atoms->nr; (i < atoms->nr + natom_extra); i++)
124 atoms->atomname[i] = nullptr;
125 memset(&atoms->atom[i], 0, sizeof(atoms->atom[i]));
126 if (nullptr != atoms->pdbinfo)
128 std::memset(&atoms->pdbinfo[i], 0, sizeof(atoms->pdbinfo[i]));
130 if (nullptr != atoms->atomtype)
132 atoms->atomtype[i] = nullptr;
134 if (nullptr != atoms->atomtypeB)
136 atoms->atomtypeB[i] = nullptr;
139 atoms->nr += natom_extra;
143 srenew(atoms->resinfo, atoms->nres + nres_extra);
144 for (i = atoms->nres; (i < atoms->nres + nres_extra); i++)
146 std::memset(&atoms->resinfo[i], 0, sizeof(atoms->resinfo[i]));
148 atoms->nres += nres_extra;
152 void init_t_atoms(t_atoms* atoms, int natoms, gmx_bool bPdbinfo)
156 snew(atoms->atomname, natoms);
157 atoms->atomtype = nullptr;
158 atoms->atomtypeB = nullptr;
159 snew(atoms->resinfo, natoms);
160 snew(atoms->atom, natoms);
161 atoms->haveMass = FALSE;
162 atoms->haveCharge = FALSE;
163 atoms->haveType = FALSE;
164 atoms->haveBState = FALSE;
165 atoms->havePdbInfo = bPdbinfo;
166 if (atoms->havePdbInfo)
168 snew(atoms->pdbinfo, natoms);
172 atoms->pdbinfo = nullptr;
176 void gmx_pdbinfo_init_default(t_pdbinfo* pdbinfo)
178 pdbinfo->type = epdbATOM;
180 pdbinfo->altloc = ' ';
181 pdbinfo->atomnm[0] = '\0';
182 pdbinfo->occup = 1.0;
184 pdbinfo->bAnisotropic = FALSE;
185 std::fill(pdbinfo->uij, pdbinfo->uij + 6, 0.0);
188 t_atoms* copy_t_atoms(const t_atoms* src)
194 init_t_atoms(dst, src->nr, (nullptr != src->pdbinfo));
196 if (nullptr != src->atomname)
198 snew(dst->atomname, src->nr);
200 if (nullptr != src->atomtype)
202 snew(dst->atomtype, src->nr);
204 if (nullptr != src->atomtypeB)
206 snew(dst->atomtypeB, src->nr);
208 for (i = 0; (i < src->nr); i++)
210 dst->atom[i] = src->atom[i];
211 if (nullptr != src->pdbinfo)
213 dst->pdbinfo[i] = src->pdbinfo[i];
215 if (nullptr != src->atomname)
217 dst->atomname[i] = src->atomname[i];
219 if (nullptr != src->atomtype)
221 dst->atomtype[i] = src->atomtype[i];
223 if (nullptr != src->atomtypeB)
225 dst->atomtypeB[i] = src->atomtypeB[i];
228 dst->haveBState = src->haveBState;
229 dst->haveCharge = src->haveCharge;
230 dst->haveMass = src->haveMass;
231 dst->havePdbInfo = src->havePdbInfo;
232 dst->haveType = src->haveType;
233 dst->nres = src->nres;
234 for (i = 0; (i < src->nres); i++)
236 dst->resinfo[i] = src->resinfo[i];
241 void t_atoms_set_resinfo(t_atoms* atoms,
252 ri = &atoms->resinfo[atoms->atom[atom_ind].resind];
253 ri->name = put_symtab(symtab, resname);
257 ri->chainnum = chainnum;
258 ri->chainid = chainid;
261 static void pr_atom(FILE* fp, int indent, const char* title, const t_atom* atom, int n)
265 if (available(fp, atom, indent, title))
267 indent = pr_title_n(fp, indent, title, n);
268 for (i = 0; i < n; i++)
270 pr_indent(fp, indent);
272 "%s[%6d]={type=%3hu, typeB=%3hu, ptype=%8s, m=%12.5e, "
273 "q=%12.5e, mB=%12.5e, qB=%12.5e, resind=%5d, atomnumber=%3d}\n",
274 title, i, atom[i].type, atom[i].typeB, ptype_str[atom[i].ptype], atom[i].m,
275 atom[i].q, atom[i].mB, atom[i].qB, atom[i].resind, atom[i].atomnumber);
280 static void pr_strings2(FILE* fp, int indent, const char* title, char*** nm, char*** nmB, int n, gmx_bool bShowNumbers)
284 if (available(fp, nm, indent, title))
286 indent = pr_title_n(fp, indent, title, n);
287 for (i = 0; i < n; i++)
289 pr_indent(fp, indent);
290 fprintf(fp, "%s[%d]={name=\"%s\",nameB=\"%s\"}\n", title, bShowNumbers ? i : -1,
291 *(nm[i]), *(nmB[i]));
296 static void pr_resinfo(FILE* fp, int indent, const char* title, const t_resinfo* resinfo, int n, gmx_bool bShowNumbers)
300 if (available(fp, resinfo, indent, title))
302 indent = pr_title_n(fp, indent, title, n);
303 for (i = 0; i < n; i++)
305 pr_indent(fp, indent);
306 fprintf(fp, "%s[%d]={name=\"%s\", nr=%d, ic='%c'}\n", title, bShowNumbers ? i : -1,
307 *(resinfo[i].name), resinfo[i].nr, (resinfo[i].ic == '\0') ? ' ' : resinfo[i].ic);
312 void pr_atoms(FILE* fp, int indent, const char* title, const t_atoms* atoms, gmx_bool bShownumbers)
314 if (available(fp, atoms, indent, title))
316 indent = pr_title(fp, indent, title);
317 pr_atom(fp, indent, "atom", atoms->atom, atoms->nr);
318 pr_strings(fp, indent, "atom", atoms->atomname, atoms->nr, bShownumbers);
319 pr_strings2(fp, indent, "type", atoms->atomtype, atoms->atomtypeB, atoms->nr, bShownumbers);
320 pr_resinfo(fp, indent, "residue", atoms->resinfo, atoms->nres, bShownumbers);
325 void pr_atomtypes(FILE* fp, int indent, const char* title, const t_atomtypes* atomtypes, gmx_bool bShowNumbers)
328 if (available(fp, atomtypes, indent, title))
330 indent = pr_title(fp, indent, title);
331 for (i = 0; i < atomtypes->nr; i++)
333 pr_indent(fp, indent);
334 fprintf(fp, "atomtype[%3d]={atomnumber=%4d}\n", bShowNumbers ? i : -1,
335 atomtypes->atomnumber[i]);
340 static void compareAtom(FILE* fp, int index, const t_atom* a1, const t_atom* a2, real relativeTolerance, real absoluteTolerance)
344 cmp_us(fp, "atom.type", index, a1->type, a2->type);
345 cmp_us(fp, "atom.ptype", index, a1->ptype, a2->ptype);
346 cmp_int(fp, "atom.resind", index, a1->resind, a2->resind);
347 cmp_int(fp, "atom.atomnumber", index, a1->atomnumber, a2->atomnumber);
348 cmp_real(fp, "atom.m", index, a1->m, a2->m, relativeTolerance, absoluteTolerance);
349 cmp_real(fp, "atom.q", index, a1->q, a2->q, relativeTolerance, absoluteTolerance);
350 cmp_us(fp, "atom.typeB", index, a1->typeB, a2->typeB);
351 cmp_real(fp, "atom.mB", index, a1->mB, a2->mB, relativeTolerance, absoluteTolerance);
352 cmp_real(fp, "atom.qB", index, a1->qB, a2->qB, relativeTolerance, absoluteTolerance);
353 cmp_str(fp, "elem", index, a1->elem, a2->elem);
357 cmp_us(fp, "atom.type", index, a1->type, a1->typeB);
358 cmp_real(fp, "atom.m", index, a1->m, a1->mB, relativeTolerance, absoluteTolerance);
359 cmp_real(fp, "atom.q", index, a1->q, a1->qB, relativeTolerance, absoluteTolerance);
363 static void compareResinfo(FILE* fp, int residue, const t_resinfo& r1, const t_resinfo& r2)
365 fprintf(fp, "comparing t_resinfo\n");
366 cmp_str(fp, "name", residue, *r1.name, *r2.name);
367 cmp_int(fp, "nr", residue, r1.nr, r2.nr);
368 cmp_uc(fp, "ic", residue, r1.ic, r2.ic);
369 cmp_int(fp, "chainnum", residue, r1.chainnum, r2.chainnum);
370 cmp_uc(fp, "chainid", residue, r1.chainid, r2.chainid);
371 if ((r1.rtp || r2.rtp) && (!r1.rtp || !r2.rtp))
373 fprintf(fp, "rtp info is present in topology %d but not in the other\n", r1.rtp ? 1 : 2);
375 if (r1.rtp && r2.rtp)
377 cmp_str(fp, "rtp", residue, *r1.rtp, *r2.rtp);
381 static void comparePdbinfo(FILE* fp,
383 const t_pdbinfo& pdb1,
384 const t_pdbinfo& pdb2,
385 real relativeTolerance,
386 real absoluteTolerance)
388 fprintf(fp, "comparing t_pdbinfo\n");
389 cmp_int(fp, "type", pdb, pdb1.type, pdb2.type);
390 cmp_int(fp, "atomnr", pdb, pdb1.atomnr, pdb2.atomnr);
391 cmp_uc(fp, "altloc", pdb, pdb1.altloc, pdb2.altloc);
392 cmp_str(fp, "atomnm", pdb, pdb1.atomnm, pdb2.atomnm);
393 cmp_real(fp, "occup", pdb, pdb1.occup, pdb2.occup, relativeTolerance, absoluteTolerance);
394 cmp_real(fp, "bfac", pdb, pdb1.bfac, pdb2.bfac, relativeTolerance, absoluteTolerance);
395 cmp_bool(fp, "bAnistropic", pdb, pdb1.bAnisotropic, pdb2.bAnisotropic);
396 for (int i = 0; i < 6; i++)
398 std::string buf = gmx::formatString("uij[%d]", i);
399 cmp_int(fp, buf.c_str(), pdb, pdb1.uij[i], pdb2.uij[i]);
404 void compareAtoms(FILE* fp, const t_atoms* a1, const t_atoms* a2, real relativeTolerance, real absoluteTolerance)
406 fprintf(fp, "comparing atoms\n");
410 cmp_int(fp, "atoms->nr", -1, a1->nr, a2->nr);
411 cmp_int(fp, "atoms->nres", -1, a1->nres, a2->nres);
412 cmp_bool(fp, "atoms->haveMass", -1, a1->haveMass, a2->haveMass);
413 cmp_bool(fp, "atoms->haveCharge", -1, a1->haveCharge, a2->haveCharge);
414 cmp_bool(fp, "atoms->haveType", -1, a1->haveType, a2->haveType);
415 cmp_bool(fp, "atoms->haveBState", -1, a1->haveBState, a2->haveBState);
416 cmp_bool(fp, "atoms->havePdbInfo", -1, a1->havePdbInfo, a2->havePdbInfo);
417 for (int i = 0; i < std::min(a1->nr, a2->nr); i++)
419 compareAtom(fp, i, &(a1->atom[i]), &(a2->atom[i]), relativeTolerance, absoluteTolerance);
420 if (a1->atomname && a2->atomname)
422 cmp_str(fp, "atomname", i, *a1->atomname[i], *a2->atomname[i]);
424 if (a1->havePdbInfo && a2->havePdbInfo)
426 comparePdbinfo(fp, i, a1->pdbinfo[i], a2->pdbinfo[i], relativeTolerance, absoluteTolerance);
428 if (a1->haveType && a2->haveType)
430 cmp_str(fp, "atomtype", i, *a1->atomtype[i], *a2->atomtype[i]);
432 if (a1->haveBState && a2->haveBState)
434 cmp_str(fp, "atomtypeB", i, *a1->atomtypeB[i], *a2->atomtypeB[i]);
437 for (int i = 0; i < std::min(a1->nres, a2->nres); i++)
439 compareResinfo(fp, i, a1->resinfo[i], a2->resinfo[i]);
444 for (int i = 0; (i < a1->nr); i++)
446 compareAtom(fp, i, &(a1->atom[i]), nullptr, relativeTolerance, absoluteTolerance);
451 void atomsSetMassesBasedOnNames(t_atoms* atoms, gmx_bool printMissingMasses)
455 /* We could decide to anyhow assign then or generate a fatal error,
456 * but it's probably most useful to keep the masses we have.
461 int maxWarn = (printMissingMasses ? 10 : 0);
466 bool haveMass = true;
467 for (int i = 0; i < atoms->nr; i++)
469 if (!aps.setAtomProperty(epropMass, *atoms->resinfo[atoms->atom[i].resind].name,
470 *atoms->atomname[i], &atoms->atom[i].m))
474 if (numWarn < maxWarn)
476 fprintf(stderr, "Can not find mass in database for atom %s in residue %d %s\n",
477 *atoms->atomname[i], atoms->resinfo[atoms->atom[i].resind].nr,
478 *atoms->resinfo[atoms->atom[i].resind].name);
487 atoms->haveMass = haveMass;