*ip = -1;
}
}
-#if PIATOM
- if (mol->piconnects != NULL) {
- for (i = mol->piconnects[idx]; i < mol->piconnects[idx + 1]; i++) {
- n = mol->piconnects[i];
- for (ip = results; *ip >= 0; ip++) {
- if (n == *ip)
- break;
- }
- if (*ip < 0) {
- *ip++ = n;
- *ip = -1;
- }
- }
- }
-#endif
for (ip = results; *ip >= 0; ip++)
;
return ip - results;
#define SWAP_INT(_i, _j) do { Int _k; _k = _i; _i = _j; _j = _k; } while (0)
-#if PIATOM
-/* Check whether i1-i2 is included in the pi-bond list */
-static int
-s_check_pi_bond(MDArena *arena, Int i1, Int i2)
-{
- Molecule *mol = arena->mol;
- PiAtom *pp;
- Int i, j, n1, n2, *cp;
- for (i = 0; i < mol->npibonds; i++) {
- if (mol->pibonds[i * 4 + 2] >= 0)
- continue; /* Not a bond */
- n1 = mol->pibonds[i * 4];
- n2 = mol->pibonds[i * 4 + 1];
- if (n2 == i1) {
- SWAP_INT(n1, n2);
- } else if (n2 == i2) {
- SWAP_INT(n1, n2);
- SWAP_INT(i1, i2);
- } else if (n1 == i2) {
- SWAP_INT(i1, i2);
- } else if (n1 != i1)
- continue; /* No match with this bond */
- /* Now n1 == i1, so check whether pi-atom "n2" includes i2 */
- if (n2 < ATOMS_MAX_NUMBER)
- continue;
- pp = mol->piatoms + (n2 - ATOMS_MAX_NUMBER);
- cp = AtomConnectData(&pp->connect);
- for (j = pp->connect.count - 1; j >= 0; j--) {
- if (cp[j] == i2)
- return 1;
- }
- }
- return 0;
-}
-#endif
-
/* Find vdw parameters and build the in-use list */
static int
s_find_vdw_parameters(MDArena *arena)
Atom *ap1, *ap2;
i1 = mol->bonds[i * 2];
i2 = mol->bonds[i * 2 + 1];
-#if PIATOM
- if (s_check_pi_bond(arena, i1, i2)) {
- /* Skip this bond */
- arena->bond_par_i[i] = -1;
- continue;
- }
-#endif
ap1 = ATOM_AT_INDEX(mol->atoms, i1);
ap2 = ATOM_AT_INDEX(mol->atoms, i2);
type1 = ap1->type;
i1 = mol->angles[i * 3];
i2 = mol->angles[i * 3 + 1];
i3 = mol->angles[i * 3 + 2];
-#if PIATOM
- if (s_check_pi_bond(arena, i1, i2) || s_check_pi_bond(arena, i2, i3)) {
- /* Skip this angle */
- arena->angle_par_i[i] = -1;
- continue;
- }
-#endif
type1 = ATOM_AT_INDEX(mol->atoms, i1)->type;
type2 = ATOM_AT_INDEX(mol->atoms, i2)->type;
type3 = ATOM_AT_INDEX(mol->atoms, i3)->type;
i2 = mol->dihedrals[i * 4 + 1];
i3 = mol->dihedrals[i * 4 + 2];
i4 = mol->dihedrals[i * 4 + 3];
-#if PIATOM
- if (s_check_pi_bond(arena, i1, i2) || s_check_pi_bond(arena, i2, i3) || s_check_pi_bond(arena, i3, i4)) {
- /* Skip this dihedral */
- arena->dihedral_par_i[i] = -1;
- continue;
- }
-#endif
type1 = ATOM_AT_INDEX(mol->atoms, i1)->type;
type2 = ATOM_AT_INDEX(mol->atoms, i2)->type;
type3 = ATOM_AT_INDEX(mol->atoms, i3)->type;
return nmissing;
}
-#if PIATOM
-/* Find pi-bond parameters */
-static int
-s_find_pibond_parameters(MDArena *arena)
-{
- Int i, j, ii, types[4], idx[4], ptype, psize, nmissing = 0;
- Molecule *mol = arena->mol;
- UnionPar upar, *up;
-
- if (mol->npibonds == 0)
- return 0;
-
- for (i = 0; i < mol->npibonds; i++) {
- ptype = kDihedralParType;
- memset(&upar, 0, sizeof(UnionPar));
- for (j = 0; j < 4; j++) {
- ii = mol->pibonds[i * 4 + j];
- if (ii < 0) {
- if (j < 2)
- ptype = -1;
- else if (j == 2)
- ptype = kBondParType;
- else
- ptype = kAngleParType;
- break;
- }
- if (ii >= ATOMS_MAX_NUMBER) {
- ii -= ATOMS_MAX_NUMBER;
- idx[j] = -1;
- if (ii >= mol->npiatoms) {
- types[j] = -1;
- ptype = -1;
- break;
- } else
- types[j] = mol->piatoms[ii].type;
- } else if (ii < mol->natoms) {
- idx[j] = ii;
- types[j] = ATOM_AT_INDEX(mol->atoms, ii)->type;
- } else {
- ptype = -1;
- break;
- }
- }
- if (ptype == kBondParType) {
- up = (UnionPar *)ParameterLookupBondPar(mol->par, types[0], types[1], idx[0], idx[1], 0);
- if (up == NULL)
- up = (UnionPar *)ParameterLookupBondPar(gBuiltinParameters, types[0], types[1], idx[0], idx[1], 0);
- psize = sizeof(BondPar);
- } else if (ptype == kAngleParType) {
- up = (UnionPar *)ParameterLookupAnglePar(mol->par, types[0], types[1], types[2], idx[0], idx[1], idx[2], 0);
- if (up == NULL)
- up = (UnionPar *)ParameterLookupAnglePar(gBuiltinParameters, types[0], types[1], types[2], idx[0], idx[1], idx[2], 0);
- psize = sizeof(AnglePar);
- } else if (ptype == kDihedralParType) {
- up = (UnionPar *)ParameterLookupDihedralPar(mol->par, types[0], types[1], types[2], types[3], idx[0], idx[1], idx[2], idx[3], 0);
- if (up == NULL)
- up = (UnionPar *)ParameterLookupDihedralPar(gBuiltinParameters, types[0], types[1], types[2], types[3], idx[0], idx[1], idx[2], idx[3], 0);
- psize = sizeof(TorsionPar);
- } else {
- up = NULL;
- psize = 0;
- }
- if (up != NULL)
- memmove(&upar, up, psize);
- else {
- upar.bond.src = -1;
- nmissing++;
- }
-
- if (arena->debug_result != NULL && arena->debug_output_level > 0) {
- char s1[8];
- if (i == 0) {
- fprintf(arena->debug_result, "\n Pi anchor parameters\n");
- fprintf(arena->debug_result, " No. atom1 atom2 atom3 atom4 type1 type2 type3 type4 mult r0/a0/phi0 k per\n");
- }
- fprintf(arena->debug_result, "%5d ", i + 1);
- for (j = 0; j < 4; j++) {
- ii = mol->pibonds[i * 4 + j];
- if (ii >= 0) {
- fprintf(arena->debug_result, "%5d ", (ii >= ATOMS_MAX_NUMBER ? -(ii - ATOMS_MAX_NUMBER) - 1 : ii));
- } else {
- fprintf(arena->debug_result, "----- ");
- }
- }
- for (j = 0; j < 4; j++) {
- if (types[j] != -1)
- AtomTypeDecodeToString(types[j], s1);
- else
- strcpy(s1, "-----");
- fprintf(arena->debug_result, "%-6s ", s1);
- }
- if (ptype == kBondParType)
- fprintf(arena->debug_result, " %7.3f %7.3f", upar.bond.r0, upar.bond.k*INTERNAL2KCAL);
- else if (ptype == kAngleParType)
- fprintf(arena->debug_result, " %7.3f %7.3f", upar.angle.a0*180/PI, upar.angle.k*INTERNAL2KCAL);
- else if (ptype == kDihedralParType)
- fprintf(arena->debug_result, "%4d %7.3f %7.3f %1d", upar.torsion.mult, upar.torsion.phi0[0]*180/PI, upar.torsion.k[0]*INTERNAL2KCAL, upar.torsion.period[0]);
- fprintf(arena->debug_result, "\n");
- }
-
- memmove(arena->pi_pars + i, &upar, sizeof(UnionPar));
- }
-
- arena->nmissing += nmissing;
- return nmissing;
-}
-#endif
-
/* Find one fragment, starting from start_index */
static void
s_find_fragment_sub(MDArena *arena, Int start_index, Int fragment_index)
ParameterRelease(arena->par);
arena->par = ParameterNew();
-#if PIATOM
- if (arena->pi_pars != NULL)
- free(arena->pi_pars);
- if (arena->mol->npibonds > 0)
- arena->pi_pars = (UnionPar *)malloc(sizeof(UnionPar) * arena->mol->npibonds);
- else arena->pi_pars = NULL;
-#endif
-
arena->nmissing = arena->nsuspicious = 0;
s_find_vdw_parameters(arena);
s_find_bond_parameters(arena);
s_find_angle_parameters(arena);
s_find_dihedral_parameters(arena);
s_find_improper_parameters(arena);
-#if PIATOM
- s_find_pibond_parameters(arena);
-#endif
if (arena->nmissing > 0) {
/* for (i = 0; i < nmissing; i++) {
memmove(mol->impropers, xmol->impropers, sizeof(Int) * 4 * xmol->nimpropers);
NewArray(&mol->syms, &mol->nsyms, sizeof(Transform), xmol->nsyms);
memmove(mol->syms, xmol->syms, sizeof(Transform) * xmol->nsyms);
-#if PIATOM
- NewArray(&mol->piatoms, &mol->npiatoms, sizeof(PiAtom), xmol->npiatoms);
- for (i = 0; i < xmol->npiatoms; i++) {
- PiAtomDuplicate(mol->piatoms + i, xmol->piatoms + i);
- }
- NewArray(&mol->pibonds, &mol->npibonds, sizeof(Int) * 4, xmol->npibonds);
- memmove(mol->pibonds, xmol->pibonds, sizeof(Int) * 4 * xmol->npibonds);
-#endif
if (xmol->cell != NULL) {
mol->cell = (XtalCell *)malloc(sizeof(XtalCell));
memmove(mol->cell, xmol->cell, sizeof(XtalCell));
s_calc_dihedral_force_sub(arena, mol->atoms, mol->nimpropers, mol->impropers, arena->improper_par_i, par->improperPars, NULL/*arena->sym_improper_uniq*/, energies, forces);
}
-#if PIATOM
-static void
-s_calc_pibond_force(MDArena *arena)
-{
- Atom *ap = arena->mol->atoms;
- Int npibonds = arena->mol->npibonds;
- Int *pibonds = arena->mol->pibonds;
- UnionPar *pars = arena->pi_pars;
- Double energy, val, valk1;
- Int idx;
-// Double *energies = &arena->energies[kAngleIndex];
-// Vector *forces = &arena->forces[kAngleIndex * arena->mol->natoms];
- Int i;
- for (i = 0; i < arena->mol->npiatoms; i++) {
- MoleculeCalculatePiAtomPosition(arena->mol, i);
- }
- for (i = 0; i < npibonds; i++, pibonds += 4, pars++) {
- Vector r[4];
- Vector f[4], *forces;
- PiAtom *pp[4];
- Int j, k, n;
- for (j = 0; j < 4; j++) {
- n = pibonds[j];
- if (n < 0)
- break;
- else if (n < ATOMS_MAX_NUMBER) {
- r[j] = ATOM_AT_INDEX(ap, n)->r;
- pp[j] = NULL;
- } else {
- n -= ATOMS_MAX_NUMBER;
- pp[j] = arena->mol->piatoms + n;
- r[j] = pp[j]->r;
- }
- }
- if (j == 2) { /* Bond */
- Vector r12;
- Double w1, w2, k0, k1;
- VecSub(r12, r[1], r[0]);
- w1 = VecLength(r12);
- w2 = w1 - pars->bond.r0;
- k0 = pars->bond.k * w2 * w2; /* Energy */
- k1 = -2.0 * pars->bond.k * w2 / w1; /* Force / r */
- VecScaleSelf(r12, k1);
- energy = k0;
- VecScale(f[0], r12, -1);
- f[1] = r12;
- if (arena->debug_result && arena->debug_output_level > 1) {
- fprintf(arena->debug_result, "pi bond force %d-%d: r=%f, r0=%f, k1=%f, {%f %f %f}\n", pibonds[0]+1, pibonds[1]+1, w1, pars->bond.r0, k1, r12.x, r12.y, r12.z);
- }
- idx = kBondIndex;
- } else if (j == 3) { /* Angle */
- if (s_calc_angle_force_one(&r[0], &r[1], &r[2], &pars->angle, &val, &energy, &valk1, &f[0], &f[1], &f[2]) != 0)
- continue;
- if (arena->debug_result && arena->debug_output_level > 1) {
- fprintf(arena->debug_result, "pi angle force %d-%d-%d: a=%f, a0=%f, k1=%f, {%f %f %f}, {%f %f %f}\n", pibonds[0]+1, pibonds[1]+1, pibonds[2]+1, val*180/PI, pars->angle.a0*180/PI, energy, f[0].x, f[0].y, f[0].z, f[1].x, f[1].y, f[1].z);
- }
- idx = kAngleIndex;
- } else if (j == 4) { /* Dihedral */
- if (s_calc_dihedral_force_one(&r[0], &r[1], &r[2], &r[3], &pars->torsion, &val, &energy, &valk1, &f[0], &f[1], &f[2], &f[3]) != 0)
- continue;
- if (arena->debug_result && arena->debug_output_level > 1) {
- fprintf(arena->debug_result, "pi dihedral force %d-%d-%d-%d: phi=%f, k1=%f, {%f %f %f}, {%f %f %f}, {%f %f %f}\n", pibonds[0]+1, pibonds[1]+1, pibonds[2]+1, pibonds[3]+1, val*180/PI, energy, f[0].x, f[0].y, f[0].z, f[1].x, f[1].y, f[1].z, f[2].x, f[2].y, f[2].z);
- }
- idx = kDihedralIndex;
- } else continue; /* j == 0 or 1? (Cannot happen) */
- arena->energies[idx] += energy;
- forces = &arena->forces[idx * arena->mol->natoms];
- for (k = 0; k < j; k++) {
- n = pibonds[k];
- if (n < 0)
- break; /* Cannot happen */
- else if (n < ATOMS_MAX_NUMBER) {
- VecInc(forces[n], f[k]);
- } else {
- Int *ip = AtomConnectData(&pp[k]->connect);
- Int kk;
- for (kk = pp[k]->connect.count - 1; kk >= 0; kk--) {
- Int an = ip[kk]; /* Index of the ring atom */
- Double co = pp[k]->coeffs[kk];
- VecScaleInc(forces[an], f[k], co);
- }
- }
- }
- }
-}
-#endif /* PIATOM */
-
/* ==================================================================== */
/* md_check_verlet_list: only for debugging the verlet list generation */
/* ==================================================================== */
s_calc_angle_force(arena);
s_calc_dihedral_force(arena);
s_calc_improper_force(arena);
-#if PIATOM
- s_calc_pibond_force(arena);
-#endif
s_calc_nonbonded_force(arena);
s_calc_auxiliary_force(arena);
free(selectFlags);
}
-#if PIATOM
-static void
-drawPiAtoms(MainView *mview)
-{
- Int i, j, *cp, nrp;
- Vector cen;
- PiAtom *pp;
- Double rad;
- GLfloat fval[12];
- Vector r, *rp;
- Double d;
-// static GLfloat sLightGreenColor[] = {0, 1, 0.50, 1};
- static GLfloat sLightGreenTransColor[] = {0, 1, 0.50, 0.75};
- Molecule *mol = mview->mol;
-// Vector *vp = (Vector *)malloc(sizeof(Vector) * mol->npiatoms);
- nrp = 0;
- rp = NULL;
- glMaterialfv(GL_FRONT_AND_BACK, GL_DIFFUSE, sLightGreenTransColor);
- for (i = 0, pp = mol->piatoms; i < mol->npiatoms; i++, pp++) {
- /* The pi atom position should be explicitly calculated
- (because the base atom(s) may be dragged) */
- VecZero(cen);
- cp = AtomConnectData(&pp->connect);
- AssignArray(&rp, &nrp, sizeof(Vector), pp->connect.count - 1, NULL);
- for (j = 0; j < pp->connect.count; j++) {
- r = ATOM_AT_INDEX(mol->atoms, cp[j])->r;
- if (mview->draggingMode == kMainViewDraggingSelectedAtoms) {
- if (MoleculeIsAtomSelected(mol, cp[j]))
- VecInc(r, mview->dragOffset);
- }
- d = (j < pp->ncoeffs ? pp->coeffs[j] : 0.0);
- VecScaleInc(cen, r, d);
- rp[j] = r;
- }
- pp->r = cen;
- rad = 0.1;
- fval[0] = cen.x;
- fval[1] = cen.y;
- fval[2] = cen.z;
- fval[3] = fval[7] = fval[11] = rad;
- fval[4] = fval[5] = fval[6] = fval[8] = fval[9] = fval[10] = 0.0;
- drawEllipsoid(fval, fval + 3, fval + 6, fval + 9, 8);
- for (j = 0; j < pp->connect.count; j++) {
- fval[3] = rp[j].x;
- fval[4] = rp[j].y;
- fval[5] = rp[j].z;
- drawCylinder(fval, fval + 3, 0.05, 6, 0);
- }
- }
- for (i = 0, cp = mol->pibonds; i < mol->npibonds; i++, cp += 4) {
- if (cp[2] >= 0)
- continue; /* Angle or dihedral */
- for (j = 0; j < 2; j++) {
- if (cp[j] >= 0 && cp[j] < mol->natoms) {
- r = ATOM_AT_INDEX(mol->atoms, cp[j])->r;
- if (mview->draggingMode == kMainViewDraggingSelectedAtoms) {
- if (MoleculeIsAtomSelected(mol, cp[j]))
- VecInc(r, mview->dragOffset);
- }
- } else if (cp[j] >= ATOMS_MAX_NUMBER && cp[j] < ATOMS_MAX_NUMBER + mol->npiatoms) {
- r = mol->piatoms[cp[j] - ATOMS_MAX_NUMBER].r;
- } else break;
- fval[j * 3] = r.x;
- fval[j * 3 + 1] = r.y;
- fval[j * 3 + 2] = r.z;
- }
- if (j == 2)
- drawCylinder(fval, fval + 3, 0.05, 6, 0);
- }
-// free(vp);
- free(rp);
-}
-#endif
-
static void
drawGraphics(MainView *mview)
{
MainViewCallback_clearLabels(mview);
drawModel(mview);
-#if PIATOM
- drawPiAtoms(mview);
-#endif
drawUnitCell(mview);
drawRotationCenter(mview);
drawGraphics(mview);
const char *gMolActionAddParameters = "addParameters:iGU";
const char *gMolActionDeleteParameters = "deleteParameters:iG";
const char *gMolActionAmendBySymmetry = "amendBySymmetry:G;G";
-#if PIATOM
-const char *gMolActionInsertOnePiAtom = "insertOnePiAtom:iCiID";
-const char *gMolActionReplaceOnePiAtom = "replaceOnePiAtom:iCiID";
-const char *gMolActionRemoveOnePiAtom = "removeOnePiAtom:i";
-const char *gMolActionInsertPiBonds = "insertPiBonds:GI";
-const char *gMolActionRemovePiBonds = "removePiBonds:G";
-#endif
/* A Ruby array to retain objects used in MolActionArg */
static VALUE sMolActionArgValues = Qfalse;
return 0;
}
-#if PIATOM
-static int
-s_MolActionInsertPiBonds(Molecule *mol, MolAction *action, MolAction **actp)
-{
- IntGroup *ig;
- Int i, j, n, *ip1;
- ig = action->args[0].u.igval;
- ip1 = action->args[1].u.arval.ptr;
- if (ig == NULL || (n = IntGroupGetCount(ig)) == 0)
- return 0;
- for (i = 0; i < n; i++) {
- j = IntGroupGetNthPoint(ig, i);
- InsertArray(&mol->pibonds, &mol->npibonds, sizeof(Int) * 4, j, 1, ip1 + i * 4);
- }
- *actp = MolActionNew(gMolActionRemovePiBonds, ig);
- MoleculeInvalidatePiConnectionTable(mol);
- return 0;
-}
-
-static int
-s_MolActionRemovePiBonds(Molecule *mol, MolAction *action, MolAction **actp)
-{
- IntGroup *ig;
- Int i, j, n, *ip1;
- ig = action->args[0].u.igval;
- if (ig == NULL || (n = IntGroupGetCount(ig)) == 0)
- return 0;
- ip1 = (Int *)malloc(sizeof(Int) * 4 * n);
- for (i = n - 1; i >= 0; i--) {
- j = IntGroupGetNthPoint(ig, i);
- DeleteArray(&mol->pibonds, &mol->npibonds, sizeof(Int) * 4, j, 1, ip1 + i * 4);
- }
- *actp = MolActionNew(gMolActionInsertPiBonds, ig, n * 4, ip1);
- free(ip1);
- MoleculeInvalidatePiConnectionTable(mol);
- return 0;
-}
-
-static int
-s_MolActionInsertOnePiAtom(Molecule *mol, MolAction *action, MolAction **actp, int willReplace)
-{
- Int idx, atype, nconnects, *connects, i;
- char *aname;
- Double *coeffs;
- PiAtom *pp;
- idx = action->args[0].u.ival;
- if (idx < 0 || idx > mol->npiatoms)
- return 1;
- if (willReplace) {
- if (idx == mol->npiatoms)
- return 1;
- pp = mol->piatoms + idx;
- nconnects = pp->connect.count;
- connects = AtomConnectData(&pp->connect);
- *actp = MolActionNew(gMolActionReplaceOnePiAtom, idx, 4, pp->aname, pp->type, nconnects, connects, pp->ncoeffs, pp->coeffs);
- } else {
- *actp = MolActionNew(gMolActionRemoveOnePiAtom, idx);
- }
- aname = action->args[1].u.arval.ptr;
- atype = action->args[2].u.ival;
- nconnects = action->args[3].u.arval.nitems;
- connects = action->args[3].u.arval.ptr;
- coeffs = action->args[4].u.arval.ptr;
- if (willReplace) {
- pp = mol->piatoms + idx;
- PiAtomClean(pp);
- } else {
- pp = (PiAtom *)InsertArray(&mol->piatoms, &mol->npiatoms, sizeof(PiAtom), idx, 1, NULL);
- memset(pp, 0, sizeof(PiAtom));
- }
- memmove(pp->aname, aname, 4);
- pp->type = atype;
- AtomConnectResize(&pp->connect, nconnects);
- memmove(AtomConnectData(&pp->connect), connects, sizeof(Int) * nconnects);
- NewArray(&pp->coeffs, &pp->ncoeffs, sizeof(Double), nconnects);
- memmove(pp->coeffs, coeffs, sizeof(Double) * nconnects);
- if (!willReplace) {
- for (i = 0; i < mol->npibonds * 4; i++) {
- if (mol->pibonds[i] >= ATOMS_MAX_NUMBER + idx)
- mol->pibonds[i]++;
- }
- }
- MoleculeInvalidatePiConnectionTable(mol);
- return 0;
-}
-
-static int
-s_MolActionRemoveOnePiAtom(Molecule *mol, MolAction *action, MolAction **actp)
-{
- Int idx, i, nconnects, *ip;
- IntGroup *ig = NULL;
- PiAtom *pp;
- idx = action->args[0].u.ival;
- if (idx < 0 || idx >= mol->npiatoms)
- return 1;
- /* Look for the pibonds entry to be removed */
- for (i = 0; i < mol->npibonds * 4; i++) {
- if (mol->pibonds[i] == idx + ATOMS_MAX_NUMBER) {
- if (ig == NULL)
- ig = IntGroupNew();
- IntGroupAdd(ig, i / 4, 1);
- }
- }
- if (ig != NULL) {
- MolActionCreateAndPerform(mol, gMolActionRemovePiBonds, ig);
- IntGroupRelease(ig);
- }
- pp = mol->piatoms + idx;
- nconnects = pp->connect.count;
- ip = AtomConnectData(&pp->connect);
- *actp = MolActionNew(gMolActionInsertOnePiAtom, idx, 4, pp->aname, pp->type, nconnects, ip, pp->ncoeffs, pp->coeffs);
- PiAtomClean(pp);
- DeleteArray(&mol->piatoms, &mol->npiatoms, sizeof(PiAtom), idx, 1, NULL);
- for (i = 0; i < mol->npibonds * 4; i++) {
- if (mol->pibonds[i] > ATOMS_MAX_NUMBER + idx)
- mol->pibonds[i]--;
- }
- MoleculeInvalidatePiConnectionTable(mol);
- return 0;
-}
-#endif /* PIATOM */
-
int
MolActionPerform(Molecule *mol, MolAction *action)
{
if ((result = s_MolActionDeleteParameters(mol, action, &act2)) != 0)
return result;
needsRebuildMDArena = 1;
-#if PIATOM
- } else if (strcmp(action->name, gMolActionInsertOnePiAtom) == 0) {
- if ((result = s_MolActionInsertOnePiAtom(mol, action, &act2, 0)) != 0)
- return result;
- needsRebuildMDArena = 1;
- } else if (strcmp(action->name, gMolActionReplaceOnePiAtom) == 0) {
- if ((result = s_MolActionInsertOnePiAtom(mol, action, &act2, 1)) != 0)
- return result;
- needsRebuildMDArena = 1;
- } else if (strcmp(action->name, gMolActionRemoveOnePiAtom) == 0) {
- if ((result = s_MolActionRemoveOnePiAtom(mol, action, &act2)) != 0)
- return result;
- needsRebuildMDArena = 1;
- } else if (strcmp(action->name, gMolActionInsertPiBonds) == 0) {
- if ((result = s_MolActionInsertPiBonds(mol, action, &act2)) != 0)
- return result;
- needsRebuildMDArena = 1;
- } else if (strcmp(action->name, gMolActionRemovePiBonds) == 0) {
- if ((result = s_MolActionRemovePiBonds(mol, action, &act2)) != 0)
- return result;
- needsRebuildMDArena = 1;
-#endif /* PIATOM */
} else if (strcmp(action->name, gMolActionNone) == 0) {
/* Do nothing */
} else {
extern const char *gMolActionAddParameters;
extern const char *gMolActionDeleteParameters;
extern const char *gMolActionAmendBySymmetry;
-#if PIATOM
-extern const char *gMolActionInsertOnePiAtom;
-extern const char *gMolActionReplaceOnePiAtom;
-extern const char *gMolActionRemoveOnePiAtom;
-extern const char *gMolActionInsertPiBonds;
-extern const char *gMolActionRemovePiBonds;
-#endif
/* Special action signatures to invoke the Ruby script. Used as follows:
* MolActionCreateAndPerform(mol, SCRIPT_ACTION("vd"), "rotate", vec, angle);
return 0;
}
-#if PIATOM
-void
-PiAtomDuplicate(PiAtom *pa, const PiAtom *cpa)
-{
- memmove(pa, cpa, sizeof(PiAtom));
- pa->connect.count = 0;
- AtomConnectResize(&(pa->connect), cpa->connect.count);
- memmove(AtomConnectData(&(pa->connect)), AtomConnectData((AtomConnect *)&(cpa->connect)), sizeof(Int) * cpa->connect.count);
- pa->ncoeffs = 0;
- pa->coeffs = NULL;
- if (cpa->ncoeffs > 0) {
- NewArray(&(pa->coeffs), &(pa->ncoeffs), sizeof(Double), cpa->ncoeffs);
- memmove(pa->coeffs, cpa->coeffs, sizeof(Double) * cpa->ncoeffs);
- }
-}
-
-void
-PiAtomClean(PiAtom *pa)
-{
- AtomConnectResize(&(pa->connect), 0);
- pa->ncoeffs = 0;
- if (pa->coeffs != NULL) {
- free(pa->coeffs);
- pa->coeffs = NULL;
- }
-}
-#endif
-
#pragma mark ====== Accessor types ======
MolEnumerable *
NewArray(&(mp2->syms), &(mp2->nsyms), sizeof(Transform), mp->nsyms);
memmove(mp2->syms, mp->syms, sizeof(Transform) * mp2->nsyms);
}
-#if PIATOM
- if (mp->npiatoms > 0) {
- NewArray(&(mp2->piatoms), &(mp2->npiatoms), sizeof(PiAtom), mp->npiatoms);
- for (i = 0; i < mp->npiatoms; i++)
- PiAtomDuplicate(mp2->piatoms + i, mp->piatoms + i);
- }
- if (mp->npibonds > 0) {
- NewArray(&(mp2->pibonds), &(mp2->npibonds), sizeof(Int) * 4, mp->npibonds);
- memmove(mp2->pibonds, mp->pibonds, sizeof(Int) * 4 * mp->npibonds);
- }
- if (mp->npiconnects > 0) {
- NewArray(&(mp2->piconnects), &(mp2->npiconnects), sizeof(Int), mp->npiconnects);
- memmove(mp2->piconnects, mp->piconnects, sizeof(Int) * mp->npiconnects);
- }
-#endif
-
-/* mp2->useFlexibleCell = mp->useFlexibleCell; */
+
+ /* mp2->useFlexibleCell = mp->useFlexibleCell; */
if (mp->nframe_cells > 0) {
if (NewArray(&mp2->frame_cells, &mp2->nframe_cells, sizeof(Vector) * 4, mp->nframe_cells) == NULL)
goto error;
mp->syms = NULL;
mp->nsyms = 0;
}
-#if PIATOM
- if (mp->piatoms != NULL) {
- for (i = 0; i < mp->npiatoms; i++) {
- PiAtomClean(mp->piatoms + i);
- }
- free(mp->piatoms);
- mp->piatoms = NULL;
- mp->npiatoms = 0;
- }
- if (mp->pibonds != NULL) {
- free(mp->pibonds);
- mp->pibonds = NULL;
- mp->npibonds = 0;
- }
- if (mp->piconnects != NULL) {
- free(mp->piconnects);
- mp->piconnects = NULL;
- mp->npiconnects = 0;
- }
-#endif
if (mp->selection != NULL) {
IntGroupRelease(mp->selection);
mp->selection = NULL;
}
}
continue;
-#if PIATOM
- } else if (strcmp(buf, "!:pi_atoms") == 0) {
- PiAtom *pp;
- while (ReadLine(buf, sizeof buf, fp, &lineNumber) > 0) {
- if (buf[0] == '!')
- continue;
- if (buf[0] == '\n')
- break;
- if (sscanf(buf, "%6s %6s %d", cbuf[0], cbuf[1], &ibuf[0]) < 3) {
- s_append_asprintf(errbuf, "line %d: pi atoms info cannot be read", lineNumber);
- goto err_exit;
- }
- pp = (PiAtom *)AssignArray(&mp->piatoms, &mp->npiatoms, sizeof(PiAtom), mp->npiatoms, NULL);
- memset(pp, 0, sizeof(PiAtom));
- strncpy(pp->aname, cbuf[0], 4);
- pp->type = AtomTypeEncodeToUInt(cbuf[1]);
- if (ibuf[0] <= 0)
- continue;
- AtomConnectResize(&pp->connect, ibuf[0]);
- ip = AtomConnectData(&pp->connect);
- NewArray(&pp->coeffs, &pp->ncoeffs, sizeof(Double), ibuf[0]);
- for (i = 0; i < ibuf[0]; i++) {
- if (ReadLine(buf, sizeof buf, fp, &lineNumber) <= 0) {
- s_append_asprintf(errbuf, "line %d: unexpected end of file during reading pi atoms info", lineNumber);
- goto err_exit;
- }
- if (sscanf(buf, "%d %lf", &ibuf[1], &dbuf[0]) < 2) {
- s_append_asprintf(errbuf, "line %d: bad format during pi atoms info", lineNumber);
- goto err_exit;
- }
- ip[i] = ibuf[1];
- pp->coeffs[i] = dbuf[0];
- }
- }
- continue;
- } else if (strcmp(buf, "!:pi_atom_constructs") == 0) {
- while (ReadLine(buf, sizeof buf, fp, &lineNumber) > 0) {
- if (buf[0] == '!')
- continue;
- if (buf[0] == '\n')
- break;
- /* a1 b1 c1 d1 a2 b2 c2 d2 */
- i = sscanf(buf, "%d %d %d %d %d %d %d %d", &ibuf[0], &ibuf[1], &ibuf[2], &ibuf[3], &ibuf[4], &ibuf[5], &ibuf[6], &ibuf[7]);
- if (i == 0 || i % 4 != 0)
- goto pi_atom_constructs_bad_format;
- for (j = 0; j < i; j++) {
- if (ibuf[j] <= -2) {
- ibuf[j] = (-ibuf[j] - 2) + ATOMS_MAX_NUMBER;
- if (ibuf[j] - ATOMS_MAX_NUMBER >= mp->npiatoms)
- goto pi_atom_constructs_bad_format;
- } else if (ibuf[j] >= mp->natoms) {
- goto pi_atom_constructs_bad_format;
- }
- if (j % 4 == 3) {
- AssignArray(&mp->pibonds, &mp->npibonds, sizeof(Int) * 4, mp->npibonds, &ibuf[j - 3]);
- }
- }
- }
- continue;
- pi_atom_constructs_bad_format:
- s_append_asprintf(errbuf, "line %d: bad format in pi_atom_constructs", lineNumber);
- goto err_exit;
-#endif /* PIATOM */
} else if (strcmp(buf, "!:anisotropic_thermal_parameters") == 0) {
i = 0;
while (ReadLine(buf, sizeof buf, fp, &lineNumber) > 0) {
fprintf(fp, "\n");
}
-#if PIATOM
- if (mp->npiatoms > 0) {
- PiAtom *pp;
- fprintf(fp, "!:pi_atoms\n");
- fprintf(fp, "! name type n; a1 coeff1; a2 coeff2; ...; a_n coeff_n\n");
- for (i = 0, pp = mp->piatoms; i < mp->npiatoms; i++, pp++) {
- strncpy(bufs[0], pp->aname, 4);
- bufs[0][4] = 0;
- AtomTypeDecodeToString(pp->type, bufs[1]);
- bufs[1][6] = 0;
- for (j = 0; j < 2; j++) {
- if (bufs[j][0] == 0) {
- bufs[j][0] = '_';
- bufs[j][1] = 0;
- }
- }
- fprintf(fp, "%s %s %d\n", bufs[0], bufs[1], pp->connect.count);
- ip = AtomConnectData(&pp->connect);
- for (j = 0; j < pp->connect.count; j++) {
- fprintf(fp, "%d %g\n", ip[j], (j < pp->ncoeffs ? pp->coeffs[j] : 0.0));
- }
- }
- fprintf(fp, "\n");
- }
-
- if (mp->npibonds > 0) {
- fprintf(fp, "!:pi_atom_constructs\n");
- fprintf(fp, "! a1 b1 c1 d1 a2 b2 c2 d2\n");
- for (i = 0; i < mp->npibonds * 4; i++) {
- j = mp->pibonds[i];
- if (j >= ATOMS_MAX_NUMBER)
- j = -2 - (j - ATOMS_MAX_NUMBER);
- else if (j < 0)
- j = -1;
- fprintf(fp, "%d%c", j, (i % 8 == 7 || i == mp->npibonds * 4 - 1 ? '\n' : ' '));
- }
- fprintf(fp, "\n");
- }
-#endif /* PIATOM */
-
if (n_aniso > 0) {
fprintf(fp, "!:anisotropic_thermal_parameters\n");
fprintf(fp, "! b11 b22 b33 b12 b13 b23 [sigma; sb11 sb22 sb33 sb12 sb13 sb23]\n");
}
ptr += sizeof(Int) * (2 + n) + sizeof(Double) * n;
}
-#if PIATOM
- } else if (strcmp(data, "PIATOM") == 0) {
- const char *ptr2 = ptr + len;
- mp->piatoms = NULL;
- mp->npiatoms = 0;
- while (ptr < ptr2) {
- PiAtom pa;
- memset(&pa, 0, sizeof(pa));
- n = offsetof(PiAtom, connect);
- memmove(&pa, ptr, n);
- ptr += n;
- n = *((Int *)ptr);
- if (n > 0) {
- AtomConnectResize(&pa.connect, n);
- memmove(AtomConnectData(&pa.connect), ptr + sizeof(Int), n * sizeof(Int));
- }
- ptr += sizeof(Int) * (n + 1);
- n = *((Int *)ptr);
- if (n > 0) {
- NewArray(&pa.coeffs, &pa.ncoeffs, sizeof(Double), n);
- memmove(pa.coeffs, ptr + sizeof(Int), n * sizeof(Double));
- }
- ptr += sizeof(Int) + sizeof(Double) * n;
- AssignArray(&mp->piatoms, &mp->npiatoms, sizeof(PiAtom), mp->npiatoms, &pa);
- }
- } else if (strcmp(data, "PIBOND") == 0) {
- n = len / (sizeof(Int) * 4);
- NewArray(&mp->pibonds, &mp->npibonds, sizeof(Int) * 4, n);
- memmove(mp->pibonds, ptr, len);
-#endif /* PIATOM */
} else if (strcmp(data, "TIME") == 0) {
if (timep != NULL)
*timep = *((Int *)ptr);
len_all += len;
}
-#if PIATOM
- /* Pi-atoms */
- if (mp->npiatoms > 0) {
- /* Estimate the necessary storage first */
- len = 8 + sizeof(Int);
- for (i = 0; i < mp->npiatoms; i++) {
- len += offsetof(PiAtom, connect); /* Members before 'connect' is stored as they are */
- len += sizeof(Int) * (1 + mp->piatoms[i].connect.count); /* Array of Int's */
- len += sizeof(Int) + sizeof(Double) * mp->piatoms[i].ncoeffs; /* Array of Double's */
- }
- ptr = (char *)realloc(ptr, len_all + len);
- if (ptr == NULL)
- goto out_of_memory;
- p = ptr + len_all;
- memmove(p, "PIATOM\0\0", 8);
- *((Int *)(p + 8)) = len - (8 + sizeof(Int));
- p += 8 + sizeof(Int);
- for (i = 0; i < mp->npiatoms; i++) {
- int len0;
- PiAtom *pp = &(mp->piatoms[i]);
- len0 = offsetof(PiAtom, connect);
- memmove(p, pp, len0);
- p += len0;
- len0 = pp->connect.count * sizeof(Int);
- *((Int *)p) = pp->connect.count;
- if (len0 > 0)
- memmove(p + sizeof(Int), AtomConnectData(&(pp->connect)), len0);
- p += sizeof(Int) + len0;
- len0 = pp->ncoeffs * sizeof(Double);
- *((Int *)p) = pp->ncoeffs;
- if (len0 > 0)
- memmove(p + sizeof(Int), pp->coeffs, len0);
- p += sizeof(Int) + len0;
- }
- len_all += len;
- }
-
- /* Pi-atom constructs */
- if (mp->npibonds > 0) {
- len = 8 + sizeof(Int) + sizeof(Int) * 4 * mp->npibonds;
- ptr = (char *)realloc(ptr, len_all + len);
- if (ptr == NULL)
- goto out_of_memory;
- p = ptr + len_all;
- memmove(p, "PIBOND\0\0", 8);
- *((Int *)(p + 8)) = sizeof(Int) * 4 * mp->npibonds;
- p += 8 + sizeof(Int);
- memmove(p, mp->pibonds, sizeof(Int) * 4 * mp->npibonds);
- len_all += len;
- }
-#endif /* PIATOM */
-
/* Parameters */
if (mp->par != NULL) {
int type;
return -2;
/* Create atoms, with avoiding duplicates */
-#if PIATOM
- MoleculeInvalidatePiConnectionTable(mp);
-#endif
n0 = n1 = mp->natoms;
table = (int *)malloc(sizeof(int) * n0);
if (table == NULL)
if (mp->impropers[i] >= pos)
mp->impropers[i]++;
}
-#if PIATOM
- MoleculeInvalidatePiConnectionTable(mp);
-#endif
}
mp->nframes = -1; /* Should be recalculated later */
MoleculeIncrementModifyCount(mp);
act = NULL;
__MoleculeLock(dst);
-#if PIATOM
- MoleculeInvalidatePiConnectionTable(dst);
-#endif
+
nsrc = src->natoms;
ndst = dst->natoms;
if (resSeqOffset < 0)
}
}
-#if PIATOM
- /* Renumber the existing pi-atoms */
- if (dst->npiatoms > 0) {
- for (i = 0; i < dst->npiatoms; i++) {
- PiAtom *pp;
- pp = &dst->piatoms[i];
- cp = AtomConnectData(&pp->connect);
- for (j = 0; j < pp->connect.count; j++) {
- cp[j] = old2new[cp[j]];
- }
- }
- if (dst->npibonds > 0) {
- cp = dst->pibonds;
- for (i = 0; i < dst->npibonds * 4; i++) {
- if (cp[i] < 0)
- continue;
- else if (cp[i] >= ATOMS_MAX_NUMBER)
- continue;
- else {
- cp[i] = old2new[cp[i]];
- }
- }
- }
- }
-
- /* Copy the pi-atoms */
- if (src->npiatoms > 0 && forUndo == 0) {
- int nsrcp, ndstp;
- nsrcp = src->npiatoms;
- ndstp = dst->npiatoms;
- if (AssignArray(&dst->piatoms, &dst->npiatoms, sizeof(PiAtom), nsrcp + ndstp - 1, NULL) == NULL)
- goto panic;
- for (i = 0; i < nsrcp; i++) {
- PiAtom *pp;
- pp = &dst->piatoms[ndstp + i];
- PiAtomDuplicate(pp, &src->piatoms[i]);
- cp = AtomConnectData(&pp->connect);
- for (j = 0; j < pp->connect.count; j++) {
- cp[j] = old2new[ndst + cp[j]];
- }
- if (nactions != NULL) {
- /* This is very inefficient, yet should not cause big problems
- because the number of piatoms in the molecule is usually limited. */
- act = MolActionNew(gMolActionRemoveOnePiAtom, ndstp + i);
- AssignArray(actions, nactions, sizeof(MolAction *), *nactions, &act);
- act = NULL;
- }
- }
- if (src->npibonds > 0) {
- n1 = src->npibonds;
- n2 = dst->npibonds;
- if (AssignArray(&dst->pibonds, &dst->npibonds, sizeof(Int) * 4, n1 + n2 - 1, NULL) == NULL)
- goto panic;
- cp = &dst->pibonds[n2 * 4];
- memmove(cp, src->pibonds, sizeof(Int) * 4 * n1);
- for (i = 0; i < 4 * n1; i++) {
- /* Renumber the pi-atom constructs */
- if (cp[i] < 0)
- continue;
- else if (cp[i] < ATOMS_MAX_NUMBER)
- cp[i] = old2new[ndst + cp[i]]; /* Ordinary atoms */
- else
- cp[i] += ndstp; /* pi-atoms */
- }
- if (nactions != NULL) {
- ig = IntGroupNewWithPoints(n2, n1, -1);
- act = MolActionNew(gMolActionRemovePiBonds, ig);
- AssignArray(actions, nactions, sizeof(MolAction *), *nactions, &act);
- act = NULL;
- IntGroupRelease(ig);
- }
- }
- }
-#endif /* PIATOM */
-
MoleculeCleanUpResidueTable(dst);
free(new2old);
return 1; /* Bad parameter */
__MoleculeLock(src);
-#if PIATOM
- MoleculeInvalidatePiConnectionTable(src);
-#endif
act = NULL;
}
}
-#if PIATOM
- /* Copy the pi-atoms */
- if (src->npiatoms > 0) {
- PiAtom *pp1, *pp2;
- Int *patoms_old2new;
- n1 = src->npiatoms;
- patoms_old2new = (Int *)calloc(sizeof(Int), src->npiatoms);
- if (patoms_old2new == NULL)
- goto panic;
- for (i = 0, pp1 = src->piatoms; i < src->npiatoms; i++, pp1++) {
- /* Is this entry to be copied to dst? */
- cp = AtomConnectData(&pp1->connect);
- for (j = pp1->connect.count - 1; j >= 0; j--) {
- if (old2new[cp[j]] < nsrcnew)
- break;
- }
- if (j < 0) {
- /* Copy this entry */
- patoms_old2new[i] = dst->npiatoms;
- pp2 = AssignArray(&dst->piatoms, &dst->npiatoms, sizeof(PiAtom), dst->npiatoms, NULL);
- PiAtomDuplicate(pp2, pp1);
- cp = AtomConnectData(&pp2->connect);
- for (j = 0; j < pp2->connect.count; j++)
- cp[j] = old2new[cp[j]] - nsrcnew;
- } else {
- patoms_old2new[i] = -1;
- }
- }
- /* Copy the piatom constructs to dst */
- for (i = 0; i < src->npibonds; i++) {
- for (j = 0; j < 4; j++) {
- n2 = src->pibonds[i * 4 + j];
- if (n2 >= ATOMS_MAX_NUMBER) {
- if (patoms_old2new[n2 - ATOMS_MAX_NUMBER] < 0)
- break;
- } else if (n2 >= 0) {
- if (old2new[n2] < nsrcnew)
- break;
- }
- }
- if (j >= 4) {
- /* Copy this entry */
- cp = (Int *)AssignArray(&dst->pibonds, &dst->npibonds, sizeof(Int) * 4, dst->npibonds, &src->pibonds[i * 4]);
- for (j = 0; j < 4; j++) {
- if (cp[j] >= ATOMS_MAX_NUMBER) {
- cp[j] = patoms_old2new[cp[j] - ATOMS_MAX_NUMBER] + ATOMS_MAX_NUMBER;
- } else if (cp[j] >= 0) {
- cp[j] = old2new[cp[j]] - nsrcnew;
- }
- }
- }
- }
- if (moveFlag) {
- Int npibonds_to_go, *pibonds_to_go;
- IntGroup *pibonds_group;
-
- /* Remove the piatom entries containing non-remaining atoms. Note: the piatom
- entries that do not remain in src and not copied to dst will disappear. */
- n2 = 0;
- for (i = 0; i < src->npiatoms; i++) {
- /* Is this entry to be removed? */
- pp1 = &src->piatoms[i];
- cp = AtomConnectData(&pp1->connect);
- for (j = pp1->connect.count - 1; j >= 0; j--) {
- if (old2new[cp[j]] >= nsrcnew)
- break;
- }
- patoms_old2new[i] = (j < 0 ? n2++ : -1);
- }
-
- /* Remove pibonds first (necessary for undo) */
- npibonds_to_go = 0;
- pibonds_to_go = NULL;
- pibonds_group = NULL;
- for (i = src->npibonds - 1; i >= 0; i--) {
- for (j = 0; j < 4; j++) {
- n3 = src->pibonds[i * 4 + j];
- if (n3 >= ATOMS_MAX_NUMBER) {
- if (patoms_old2new[n3 - ATOMS_MAX_NUMBER] < 0)
- break;
- } else if (n3 >= 0) {
- if (old2new[n3] >= nsrcnew)
- break;
- }
- }
- if (j < 4) {
- /* Remove */
- if (nactions != NULL) {
- /* Since we are scanning pibonds[] from the end, the new entry should be inserted
- at the top of the pibonds_to_go[] array. */
- InsertArray(&pibonds_to_go, &npibonds_to_go, sizeof(Int) * 4, 0, 1, src->pibonds + i * 4);
- if (pibonds_group == NULL)
- pibonds_group = IntGroupNew();
- IntGroupAdd(pibonds_group, i, 1);
- }
- DeleteArray(&src->pibonds, &src->npibonds, sizeof(Int) * 4, i, 1, NULL);
- } else {
- /* Renumber */
- cp = &src->pibonds[i * 4];
- for (j = 0; j < 4; j++) {
- n3 = cp[j];
- if (n3 >= ATOMS_MAX_NUMBER)
- cp[j] = patoms_old2new[n3 - ATOMS_MAX_NUMBER] + ATOMS_MAX_NUMBER;
- else if (n3 >= 0)
- cp[j] = old2new[n3];
- }
- }
- }
- if (nactions != NULL && pibonds_to_go != NULL) {
- act = MolActionNew(gMolActionInsertPiBonds, pibonds_group, npibonds_to_go * 4, pibonds_to_go);
- AssignArray(actions, nactions, sizeof(MolAction *), *nactions, &act);
- act = NULL;
- free(pibonds_to_go);
- }
- if (pibonds_group != NULL)
- IntGroupRelease(pibonds_group);
-
- for (i = src->npiatoms - 1; i >= 0; i--) {
- pp1 = &src->piatoms[i];
- if (patoms_old2new[i] < 0) {
- /* Remove the entries */
- /* (If forUndo is true, these entries should already have been removed.) */
- if (nactions != NULL) {
- act = MolActionNew(gMolActionInsertOnePiAtom, i, 4, pp1->aname, pp1->type, pp1->connect.count, AtomConnectData(&pp1->connect), pp1->ncoeffs, pp1->coeffs);
- AssignArray(actions, nactions, sizeof(MolAction *), *nactions, &act);
- act = NULL;
- }
- PiAtomClean(pp1);
- DeleteArray(&src->piatoms, &src->npiatoms, sizeof(PiAtom), i, 1, NULL);
- } else {
- /* Renumber */
- cp = AtomConnectData(&pp1->connect);
- for (j = 0; j < pp1->connect.count; j++) {
- cp[j] = old2new[cp[j]];
- }
- }
- }
- }
-
- free(patoms_old2new);
- }
-#endif /* PIATOM */
-
/* Clean up */
IntGroupRelease(remain_g);
MoleculeCleanUpResidueTable(src);
free(newAtoms);
free(old2new);
free(apArray);
-
-#if PIATOM
- MoleculeInvalidatePiConnectionTable(mp);
-#endif
}
/* Renumber atoms */
}
}
-#if PIATOM
- if (mp->npiatoms) {
- /* Renumber the pi-atoms */
- for (i = 0; i < mp->npiatoms; i++) {
- PiAtom *pp = &mp->piatoms[i];
- Int *cp = AtomConnectData(&pp->connect);
- for (j = 0; j < pp->connect.count; j++)
- cp[j] = old2new[cp[j]];
- }
- }
-
- if (mp->npibonds) {
- /* Renumber the pi-atom constructs */
- for (i = 0; i < mp->npibonds * 4; i++) {
- j = mp->pibonds[i];
- if (j >= 0 && j < mp->natoms)
- mp->pibonds[i] = old2new[j];
- }
- }
-#endif /* PIATOM */
-
/* Renumber the atoms */
for (i = 0; i < mp->natoms; i++)
memmove(ATOM_AT_INDEX(mp->atoms, old2new[i]), ATOM_AT_INDEX(saveAtoms, i), gSizeOfAtomRecord);
retval = 0;
-#if PIATOM
- MoleculeInvalidatePiConnectionTable(mp);
-#endif
MoleculeIncrementModifyCount(mp);
mp->needsMDRebuild = 1;
sMoleculeFragmentSub(mp, idx2, result, exatoms);
}
}
-#if PIATOM
- if (mp->piconnects != NULL) {
- for (i = mp->piconnects[idx]; i < mp->piconnects[idx + 1]; i++) {
- idx2 = mp->piconnects[i];
- if (IntGroupLookup(result, idx2, NULL))
- continue;
- sMoleculeFragmentSub(mp, idx2, result, exatoms);
- }
- }
-#endif
}
/* The molecular fragment (= interconnected atoms) containing the atom n1 and
if (mp == NULL || mp->natoms == 0 || n1 < 0 || n1 >= mp->natoms)
return NULL;
result = IntGroupNew();
-#if PIATOM
- MoleculeValidatePiConnectionTable(mp);
-#endif
sMoleculeFragmentSub(mp, n1, result, exatoms);
return result;
}
for (i = 0; i < argc; i++)
IntGroupAdd(exatoms, argv[i], 1);
result = IntGroupNew();
-#if PIATOM
- MoleculeValidatePiConnectionTable(mp);
-#endif
sMoleculeFragmentSub(mp, n1, result, exatoms);
IntGroupRelease(exatoms);
return result;
return NULL;
IntGroupIteratorInit(inatoms, &iter);
result = IntGroupNew();
-#if PIATOM
- MoleculeValidatePiConnectionTable(mp);
-#endif
while ((i = IntGroupIteratorNext(&iter)) >= 0) {
sMoleculeFragmentSub(mp, i, result, exatoms);
}
Atom *ap;
if (mp == NULL || mp->natoms == 0 || group == NULL)
return 0; /* Invalid arguments */
-#if PIATOM
- MoleculeValidatePiConnectionTable(mp);
-#endif
bond_count = 0;
for (i = 0; (i1 = IntGroupGetStartPoint(group, i)) >= 0; i++) {
i2 = IntGroupGetEndPoint(group, i);
}
}
}
-#if PIATOM
- if (mp->piconnects != NULL) {
- for (k = mp->piconnects[j]; k < mp->piconnects[j + 1]; k++) {
- k2 = mp->piconnects[k];
- if (IntGroupLookup(group, k2, NULL) == 0) {
- bond_count++;
- nval1 = j;
- nval2 = k2;
- if (bond_count > 1)
- return 0; /* Too many bonds */
- }
- }
- }
-#endif
}
}
if (bond_count == 1) {
#pragma mark ====== Pi Atoms ======
-#if !defined(PIATOM)
-
void
MoleculeCalculatePiAnchorPosition(Molecule *mol, int idx)
{
return 0;
}
-#endif
-
-#if PIATOM
-int
-MoleculeCalculatePiAtomPosition(Molecule *mol, int idx)
-{
- PiAtom *pp;
- Int i, *cp;
- if (mol == NULL || idx < 0 || idx >= mol->npiatoms)
- return -1;
- pp = mol->piatoms + idx;
- cp = AtomConnectData(&pp->connect);
- VecZero(pp->r);
- for (i = pp->connect.count - 1; i >= 0; i--) {
- Vector rr = ATOM_AT_INDEX(mol->atoms, cp[i])->r;
- VecScaleInc(pp->r, rr, pp->coeffs[i]);
- }
- return idx;
-}
-
-int
-MoleculeValidatePiConnectionTable(Molecule *mol)
-{
- Int pass, i, j, k, m;
-
- if (mol == NULL || mol->pibonds == NULL)
- return -1; /* No need to process */
- if (mol->piconnects != NULL)
- return 0; /* Already valid */
-
- /* Allocate index table */
- NewArray(&mol->piconnects, &mol->npiconnects, sizeof(Int), mol->natoms + 1);
- memset(mol->piconnects, 0, sizeof(Int) * (mol->natoms + 1));
-
- /* Pass 1: count connections for each atom */
- /* Pass 2: store connection info */
- for (pass = 0; pass < 2; pass++) {
- Int n[2], *ip[2], c[2];
- for (i = 0; i < mol->npibonds; i++) {
- AtomConnect *ac;
- if (mol->pibonds[i * 4 + 2] >= 0)
- continue; /* Skip angle or dihedral entries */
- for (j = 0; j < 2; j++) {
- n[j] = mol->pibonds[i * 4 + j];
- if (n[j] >= ATOMS_MAX_NUMBER) {
- ac = &(mol->piatoms[n[j] - ATOMS_MAX_NUMBER].connect);
- ip[j] = AtomConnectData(ac);
- c[j] = ac->count;
- } else if (n[j] >= 0 && n[j] < mol->natoms) {
- ip[j] = &n[j];
- c[j] = 1;
- } else break;
- }
- if (j < 2)
- continue; /* Ignore the invalid entry */
- for (j = 0; j < c[0]; j++) {
- for (k = 0; k < c[1]; k++) {
- Int a1 = ip[0][j];
- Int a2 = ip[1][k];
- if (pass == 0) {
- /* Count */
- mol->piconnects[a1]++;
- mol->piconnects[a2]++;
- } else {
- /* Store the entry (at the first empty slot) */
- for (m = mol->piconnects[a1]; m < mol->piconnects[a1 + 1]; m++) {
- if (mol->piconnects[m] == -1) {
- mol->piconnects[m] = a2;
- break;
- }
- }
- for (m = mol->piconnects[a2]; m < mol->piconnects[a2 + 1]; m++) {
- if (mol->piconnects[m] == -1) {
- mol->piconnects[m] = a1;
- break;
- }
- }
- }
- }
- }
- }
- if (pass == 0) {
- /* Expand the table, and store the position numbers */
- m = mol->natoms + 1;
- for (i = 0; i <= mol->natoms; i++) {
- j = mol->piconnects[i];
- mol->piconnects[i] = m;
- m += j;
- }
- AssignArray(&mol->piconnects, &mol->npiconnects, sizeof(Int), m - 1, NULL);
- for (j = mol->natoms + 1; j < m; j++)
- mol->piconnects[j] = -1;
- }
- }
- return (mol->npiconnects - mol->natoms - 1); /* Returns the number of entries */
-}
-
-void
-MoleculeInvalidatePiConnectionTable(Molecule *mol)
-{
- if (mol == NULL)
- return;
- if (mol->piconnects != NULL) {
- free(mol->piconnects);
- mol->piconnects = NULL;
- }
- mol->npiconnects = 0;
-}
-#endif /* PIATOM */
-
#pragma mark ====== MO calculation ======
/* Calculate an MO value for a single point. */
Double cellsigma[6]; /* For crystallographic data; sigma for the cell parameters */
} XtalCell;
-#if PIATOM
-/* Dummy atoms to represent metal-pi bonds */
-typedef struct PiAtom {
- char aname[4];
- UInt type;
- AtomConnect connect;
- Int ncoeffs;
- Double *coeffs; /* The piatom position is given by sum(i, atoms[connect.data[i]] * coeffs[i]) */
- Vector r; /* Current position (cache) */
-} PiAtom;
-#endif
-
/* 3-Dimensional distribution */
typedef struct Cube {
Int idn; /* Integer identifier (such as MO number) */
Int nsyms; /* Symmetry operations; syms are always described in crystallographic units (even when the unit cell is not defined) */
Transform *syms;
-#if PIATOM
- Int npiatoms; /* Number of "dummy" atoms to represent pi-metal bonds */
- PiAtom *piatoms;
- Int npibonds;
- Int *pibonds; /* Array to represent bond/angle/dihedral including piatoms. */
- /* [n1, n2, -1, -1]: bonds,
- [n1, n2, n3, -1]: angle,
- [n1, n2, n3, n4]: dihedral,
- where n# is atom index if it is <ATOMS_MAX_NUMBER and
- is piatom index + ATOMS_MAX_NUMBER otherwise.
- The size of array is 4*npibonds. */
- Int npiconnects; /* Connection table for pi-metal bonds */
- Int *piconnects; /* The first (natoms + 1) entries are for lookup table, and
- the connection data (indices of connected atoms) follow.
- The connected atoms (only by pi-bonds) for atom i are listed in
- piconnects[piconnects[i]]...piconnects[piconnects[i+1]] */
-#endif
-
IntGroup *selection;
Int nframes; /* The number of frames (>= 1). This is a cached value, and should be
recalculated from the atoms if it is -1 */
int MoleculeSelectFrame(Molecule *mp, int frame, int copyback);
int MoleculeFlushFrames(Molecule *mp);
-#if !defined(PIATOM)
void MoleculeCalculatePiAnchorPosition(Molecule *mol, int idx);
int MoleculeSetPiAnchorList(Molecule *mol, Int idx, Int nentries, Int *entries, Double *weights, Int *nUndoActions, struct MolAction ***undoActions);
-#endif
-
-#if PIATOM
-int MoleculeCalculatePiAtomPosition(Molecule *mol, int idx);
-int MoleculeValidatePiConnectionTable(Molecule *mol);
-void MoleculeInvalidatePiConnectionTable(Molecule *mol);
-#endif
int MoleculeCalcMO(Molecule *mp, Int mono, const Vector *op, const Vector *dxp, const Vector *dyp, const Vector *dzp, Int nx, Int ny, Int nz, int (*callback)(double progress, void *ref), void *ref);
int MoleculeGetDefaultMOGrid(Molecule *mp, Int npoints, Vector *op, Vector *xp, Vector *yp, Vector *zp, Int *nx, Int *ny, Int *nz);
return val;
}
-#if PIATOM
-static int
-s_Molecule_AtomOrPiAtomIndexFromValue(Molecule *mol, VALUE val)
-{
- int n, i;
- char *p;
- if (FIXNUM_P(val)) {
- n = FIX2INT(val);
- if (n >= 0 && n < mol->natoms)
- return n;
- else if (n < 0 && -n - 1 < mol->npiatoms)
- return ATOMS_MAX_NUMBER + (-n - 1); /* PiAtom */
- n = -1; /* No such atom */
- val = rb_inspect(val);
- } else {
- n = MoleculeAtomIndexFromString(mol, StringValuePtr(val));
- }
- if (n >= 0 && n < mol->natoms)
- return n;
- p = StringValuePtr(val);
- for (i = 0; i < mol->npiatoms; i++) {
- if (strcmp(p, mol->piatoms[i].aname) == 0)
- return ATOMS_MAX_NUMBER + i; /* PiAtom; should be looked up after normal atoms */
- }
- if (n == -1)
- rb_raise(rb_eMolbyError, "no such atom: %s", p);
- else if (n == -2)
- rb_raise(rb_eMolbyError, "bad format of atom specification: %s", p);
- else
- rb_raise(rb_eMolbyError, "error in converting value to atom index: %s", p);
- return 0; /* Not reached */
-}
-
-static int
-s_Molecule_AtomIndexFromValue(Molecule *mol, VALUE val)
-{
- int n = s_Molecule_AtomOrPiAtomIndexFromValue(mol, val);
- if (n >= ATOMS_MAX_NUMBER) {
- val = rb_inspect(val);
- rb_raise(rb_eMolbyError, "no such atom: %s", StringValuePtr(val));
- }
- return n;
-}
-#else
static int
s_Molecule_AtomIndexFromValue(Molecule *mol, VALUE val)
{
rb_raise(rb_eMolbyError, "error in converting value to atom index: %s", p);
return 0; /* Not reached */
}
-#endif /* _not_ PIATOM */
static IntGroup *
s_Molecule_AtomGroupFromValue(VALUE self, VALUE val)
return val;
}
-#if !defined(PIATOM)
/*
* call-seq:
* create_pi_anchor(name, group [, type] [, weights] [, index]) -> AtomRef
return Data_Wrap_Struct(rb_cAtomRef, 0, (void (*)(void *))AtomRefRelease, aref);
}
-#endif
-
-#if PIATOM
-/*
- * call-seq:
- * create_pi_anchor(name, type, group [, weights]) -> index
- * insert_pi_anchor(index, name, type, group [, weights]) -> index
- * replace_pi_anchor(index, name, type, group [, weights]) -> index
- *
- * Create or replace a "pi anchor", which is an anchor point to define a metal-pi bond.
- * If index is negative or no less than the current number of pi anchors, create
- * a new anchor. Otherwise, replace the existing anchor.
- * Name and type are Strings, and are similar to those in atoms.
- * Group is a group of atoms to define a pi system to be bound to the metal.
- * Weights (optional) is an Array of Floats, which determine the significance
- * of the component atoms. If not given, then 1.0/N (N is the number of atoms
- * in the group) is assumed for all atoms.
- */
-static VALUE
-s_Molecule_CreateOrReplacePiAnchor(int func, int argc, VALUE *argv, VALUE self)
-{
- Molecule *mol;
- Int idx, i, j, atype, *ip;
- VALUE ival, nval, tval, gval, wval;
- char *np, *tp, aname[6];
- Double *dp;
- IntGroup *ig;
- Data_Get_Struct(self, Molecule, mol);
- if (func == 0) { /* create */
- rb_scan_args(argc, argv, "31", &nval, &tval, &gval, &wval);
- idx = mol->npiatoms;
- } else {
- rb_scan_args(argc, argv, "41", &ival, &nval, &tval, &gval, &wval);
- idx = NUM2INT(rb_Integer(ival));
- if (idx < 0)
- idx = mol->npiatoms;
- if (idx > mol->npiatoms || (func == 2 && idx == mol->npiatoms))
- rb_raise(rb_eMolbyError, "pi anchor index out of range");
- }
- np = StringValuePtr(nval);
- strncpy(aname, np, 4);
- tp = StringValuePtr(tval);
- atype = AtomTypeEncodeToUInt(tp);
- ig = IntGroupFromValue(gval);
- if ((i = IntGroupGetCount(ig)) < 2)
- rb_raise(rb_eMolbyError, "too few atoms are given (at least 2 are needed)");
- ip = (Int *)malloc(sizeof(Int) * i);
- for (i = 0; (j = IntGroupGetNthPoint(ig, i)) >= 0; i++) {
- ip[i] = j;
- if (j < 0 || j >= mol->natoms) {
- free(ip);
- rb_raise(rb_eMolbyError, "the atom index (%d) is out of range", j);
- }
- }
- dp = (Double *)malloc(sizeof(Double) * i);
- if (wval != Qnil) {
- wval = rb_ary_to_ary(wval);
- if (RARRAY_LEN(wval) < i) {
- free(ip);
- free(dp);
- rb_raise(rb_eMolbyError, "the number of floats is not sufficient (%d needed but only %d given)", i, RARRAY_LEN(wval));
- }
- for (j = 0; j < i; j++) {
- dp[j] = NUM2DBL(rb_Float(RARRAY_PTR(wval)[j]));
- }
- } else {
- for (j = 0; j < i; j++) {
- dp[j] = 1.0 / i;
- }
- }
- if (func == 0 || func == 1) /* Create or insert */
- MolActionCreateAndPerform(mol, gMolActionInsertOnePiAtom, idx, 4, aname, atype, i, ip, i, dp);
- else /* Replace */
- MolActionCreateAndPerform(mol, gMolActionReplaceOnePiAtom, idx, 4, aname, atype, i, ip, i, dp);
- free(ip);
- free(dp);
- return INT2NUM(idx);
-}
-
-static VALUE
-s_Molecule_CreatePiAnchor(int argc, VALUE *argv, VALUE self)
-{
- return s_Molecule_CreateOrReplacePiAnchor(0, argc, argv, self);
-}
-
-static VALUE
-s_Molecule_InsertPiAnchor(int argc, VALUE *argv, VALUE self)
-{
- return s_Molecule_CreateOrReplacePiAnchor(1, argc, argv, self);
-}
-
-static VALUE
-s_Molecule_ReplacePiAnchor(int argc, VALUE *argv, VALUE self)
-{
- return s_Molecule_CreateOrReplacePiAnchor(2, argc, argv, self);
-}
-
-/*
- * call-seq:
- * remove_pi_anchor(idx) -> Molecule
- *
- * Remove the pi-anchor at the given index.
- */
-static VALUE
-s_Molecule_RemovePiAnchor(VALUE self, VALUE ival)
-{
- Molecule *mol;
- Int idx = NUM2INT(rb_Integer(ival));
- Data_Get_Struct(self, Molecule, mol);
- if (idx < 0 || idx >= mol->npiatoms)
- rb_raise(rb_eMolbyError, "pi-anchor index (%d) is out of range (should be 0 <= index < %d)", idx, mol->npiatoms);
- MolActionCreateAndPerform(mol, gMolActionRemoveOnePiAtom, idx);
- return self;
-}
-
-/*
- * call-seq:
- * pi_anchor(idx) -> nil or [name, type, group, weights]
- *
- * Return the attributes of the idx-th pi anchor if present, otherwise nil.
- */
-static VALUE
-s_Molecule_PiAnchorAtIndex(VALUE self, VALUE ival)
-{
- Molecule *mol;
- PiAtom *pp;
- char aname[6], atype[8];
- Int i, *connects;
- VALUE cval, wval, rval;
- Int idx = NUM2INT(rb_Integer(ival));
- Data_Get_Struct(self, Molecule, mol);
- if (idx < 0 || idx >= mol->npiatoms)
- return Qnil;
- pp = mol->piatoms + idx;
- strncpy(aname, pp->aname, 4);
- aname[4] = 0;
- AtomTypeDecodeToString(pp->type, atype);
- cval = rb_ary_new2(pp->connect.count);
- connects = AtomConnectData(&pp->connect);
- for (i = 0; i < pp->connect.count; i++)
- rb_ary_store(cval, i, INT2NUM(connects[i]));
- wval = rb_ary_new2(pp->ncoeffs);
- for (i = 0; i < pp->ncoeffs; i++)
- rb_ary_store(wval, i, rb_float_new(pp->coeffs[i]));
- rval = rb_ary_new3(4, rb_str_new2(aname), rb_str_new2(atype), cval, wval);
- return rval;
-}
-
-/*
- * call-seq:
- * pi_anchor_r(idx) -> Vector3D
- *
- * Calculate the cartesian coordinate of the idx-th pi anchor if present.
- */
-static VALUE
-s_Molecule_PiAnchorR(VALUE self, VALUE ival)
-{
- Molecule *mol;
- Vector v;
- Int idx = NUM2INT(rb_Integer(ival));
- Data_Get_Struct(self, Molecule, mol);
- if (idx < 0 || idx >= mol->npiatoms)
- rb_raise(rb_eMolbyError, "no pi anchor present: %d", idx);
- MoleculeCalculatePiAtomPosition(mol, idx);
- v = mol->piatoms[idx].r;
- return ValueFromVector(&v);
-}
-
-/*
- * call-seq:
- * pi_anchor_fract_r(idx) -> Vector3D
- *
- * Calculate the fractional coordinate of the idx-th pi anchor if present.
- */
-static VALUE
-s_Molecule_PiAnchorFractR(VALUE self, VALUE ival)
-{
- Molecule *mol;
- Vector v;
- Int idx = NUM2INT(rb_Integer(ival));
- Data_Get_Struct(self, Molecule, mol);
- if (idx < 0 || idx >= mol->npiatoms)
- rb_raise(rb_eMolbyError, "no pi anchor present: %d", idx);
- MoleculeCalculatePiAtomPosition(mol, idx);
- v = mol->piatoms[idx].r;
- if (mol->cell != NULL)
- TransformVec(&v, mol->cell->rtr, &v);
- return ValueFromVector(&v);
-}
-
-/*
- * call-seq:
- * count_pi_anchors -> Integer
- *
- * Return the number of defined pi anchors.
- */
-static VALUE
-s_Molecule_CountPiAnchors(VALUE self)
-{
- Molecule *mol;
- Data_Get_Struct(self, Molecule, mol);
- return INT2NUM(mol->npiatoms);
-}
-
-/*
- * call-seq:
- * create_pi_anchor_construct(n1, n2, n3 = nil, n4 = nil) -> Integer
- *
- * Create a bond, angle, or dihedral including one or more pi anchor points.
- * The arguments can either be an atom representation (atom index, atom name, res_seq:name)
- * or a pi-anchor representation (pi-anchor index, pi-anchor name).
- * The pi-anchor index is represented by a negative integer -N, which corresponds to
- * the (N-1)-th pi anchor.
- * Returns the index for the newly created construct.
- * This operation is undoable.
- */
-static VALUE
-s_Molecule_CreatePiAnchorConstruct(int argc, VALUE *argv, VALUE self)
-{
- Molecule *mol;
- VALUE vals[4];
- Int ivals[4], i;
- IntGroup *ig;
- Data_Get_Struct(self, Molecule, mol);
- rb_scan_args(argc, argv, "22", vals, vals + 1, vals + 2, vals + 3);
- for (i = 0; i < 4; i++) {
- if (vals[i] == Qnil)
- ivals[i] = -1;
- else ivals[i] = s_Molecule_AtomOrPiAtomIndexFromValue(mol, vals[i]);
- }
- for (i = 0; i < 4; i++) {
- if (ivals[i] >= ATOMS_MAX_NUMBER)
- break;
- }
- if (i == 4)
- rb_raise(rb_eMolbyError, "No pi anchor is specified");
- ig = IntGroupNewWithPoints(mol->npibonds, 1, -1);
- MolActionCreateAndPerform(mol, gMolActionInsertPiBonds, ig, 4, ivals);
- IntGroupRelease(ig);
- return INT2NUM(mol->npibonds);
-}
-
-/*
- * call-seq:
- * remove_pi_anchor_constructs(IntGroup) -> self
- *
- * Remove pi anchor constructs (bond, angle, dihedral) with indices specified in IntGroup.
- * This operation is undoable.
- */
-static VALUE
-s_Molecule_RemovePiAnchorConstructs(VALUE self, VALUE igval)
-{
- Molecule *mol;
- IntGroup *ig;
- Data_Get_Struct(self, Molecule, mol);
- ig = IntGroupFromValue(igval);
- MolActionCreateAndPerform(mol, gMolActionRemovePiBonds, ig);
- IntGroupRelease(ig);
- return self;
-}
-
-/*
- * call-seq:
- * count_pi_anchor_constructs -> Integer
- *
- * Returns the number of pi anchor constructs.
- */
-static VALUE
-s_Molecule_CountPiAnchorConstructs(VALUE self)
-{
- Molecule *mol;
- Data_Get_Struct(self, Molecule, mol);
- return INT2NUM(mol->npibonds);
-}
-
-/*
- * call-seq:
- * pi_anchor_construct(index) -> Array of Integers
- *
- * Returns the elements representing the index-th pi anchor constructs.
- */
-static VALUE
-s_Molecule_PiAnchorConstructAtIndex(VALUE self, VALUE ival)
-{
- Molecule *mol;
- Int idx, i, n;
- VALUE vals[4];
- Data_Get_Struct(self, Molecule, mol);
- idx = NUM2INT(rb_Integer(ival));
- if (idx < 0 || idx >= mol->npibonds)
- rb_raise(rb_eMolbyError, "index of pi anchor constructs out of range (%d)", idx);
- for (i = 0; i < 4; i++) {
- n = mol->pibonds[idx * 4 + i];
- if (n < 0)
- break;
- if (n >= ATOMS_MAX_NUMBER)
- n = -(n - ATOMS_MAX_NUMBER) - 1;
- vals[i] = INT2NUM(n);
- }
- return rb_ary_new4(i, vals);
-}
-#endif /* PIATOM */
-
/*
* call-seq:
* current -> Molecule
rb_define_method(rb_cMolecule, "create_pi_anchor", s_Molecule_CreatePiAnchor, -1);
-#if PIATOM
- rb_define_method(rb_cMolecule, "replace_pi_anchor", s_Molecule_ReplacePiAnchor, -1);
- rb_define_method(rb_cMolecule, "insert_pi_anchor", s_Molecule_InsertPiAnchor, -1);
- rb_define_method(rb_cMolecule, "remove_pi_anchor", s_Molecule_RemovePiAnchor, 1);
- rb_define_method(rb_cMolecule, "pi_anchor", s_Molecule_PiAnchorAtIndex, 1);
- rb_define_method(rb_cMolecule, "pi_anchor_r", s_Molecule_PiAnchorR, 1);
- rb_define_method(rb_cMolecule, "pi_anchor_fract_r", s_Molecule_PiAnchorFractR, 1);
- rb_define_method(rb_cMolecule, "count_pi_anchors", s_Molecule_CountPiAnchors, 0);
- rb_define_method(rb_cMolecule, "create_pi_anchor_construct", s_Molecule_CreatePiAnchorConstruct, -1);
- rb_define_method(rb_cMolecule, "remove_pi_anchor_constructs", s_Molecule_RemovePiAnchorConstructs, 1);
- rb_define_alias(rb_cMolecule, "remove_pi_anchor_construct", "remove_pi_anchor_constructs");
- rb_define_method(rb_cMolecule, "count_pi_anchor_constructs", s_Molecule_CountPiAnchorConstructs, 0);
- rb_define_method(rb_cMolecule, "pi_anchor_construct", s_Molecule_PiAnchorConstructAtIndex, 1);
-#endif
-
rb_define_singleton_method(rb_cMolecule, "current", s_Molecule_Current, 0);
rb_define_singleton_method(rb_cMolecule, "[]", s_Molecule_MoleculeAtIndex, -1);
rb_define_singleton_method(rb_cMolecule, "open", s_Molecule_Open, -1);
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