is a Python-enhanced molecular graphics tool. It excels at 3D visualization of proteins, small molecules, density, surfaces, and trajectories. It also includes molecular editing, ray tracing, and movies. Open Source version.
| HydrogenAdder.cpp (pymol-open-source-2.2.0) | : | HydrogenAdder.cpp (pymol-open-source-2.3.0) |
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| skipping to change at line 243 | | skipping to change at line 243 |
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| break; | | break; |
| } | | } |
| | |
| if (n_missing > n_system - n_present) { | | if (n_missing > n_system - n_present) { |
| n_missing = n_system - n_present; | | n_missing = n_system - n_present; |
| } | | } |
| | |
| // adding coordinates will invalidate pointer | | // adding coordinates will invalidate pointer |
| float center_coord_copy[3]; | | float center_coord_copy[3]; |
| copy3f(center_coord, center_coord_copy); | | copy3f(center_coord, center_coord_copy); |
|
| center_coord = NULL; | | center_coord = nullptr; |
| | |
| for (int i = 0; i < n_missing; ++i) { | | for (int i = 0; i < n_missing; ++i) { |
| float bondlength = AtomInfoGetBondLength(G, | | float bondlength = AtomInfoGetBondLength(G, |
| I->AtomInfo + atm, | | I->AtomInfo + atm, |
| I->AtomInfo + missing_atm[i]); | | I->AtomInfo + missing_atm[i]); |
| float* coord = cbuf + (n_present + i) * 3; | | float* coord = cbuf + (n_present + i) * 3; |
| scale3f(coord, bondlength, coord); | | scale3f(coord, bondlength, coord); |
| add3f(coord, center_coord_copy, coord); | | add3f(coord, center_coord_copy, coord); |
| | |
| if (h_fix && (idx = cs->atmToIdx(missing_atm[i])) != -1) { | | if (h_fix && (idx = cs->atmToIdx(missing_atm[i])) != -1) { |
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| skipping to change at line 325 | | skipping to change at line 325 |
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| // atom | | // atom |
| auto atom = I->AtomInfo + I->NAtom++; | | auto atom = I->AtomInfo + I->NAtom++; |
| atom->protons = cAN_H; | | atom->protons = cAN_H; |
| atom->geom = cAtomInfoSingle; | | atom->geom = cAtomInfoSingle; |
| atom->valence = 1; | | atom->valence = 1; |
| ObjectMoleculePrepareAtom(I, atm, atom, /* uniquefy */ false); | | ObjectMoleculePrepareAtom(I, atm, atom, /* uniquefy */ false); |
| } | | } |
| } | | } |
| | |
| // grow index arrays | | // grow index arrays |
|
| for (StateIterator iter(G, NULL, cSelectorUpdateTableAllStates, I->NCSet); | | for (StateIterator iter(G, nullptr, cSelectorUpdateTableAllStates, I->NCSet); |
| iter.next();) { | | iter.next();) { |
| CoordSet* cs = I->CSet[iter.state]; | | CoordSet* cs = I->CSet[iter.state]; |
| if (cs) | | if (cs) |
| cs->extendIndices(I->NAtom); | | cs->extendIndices(I->NAtom); |
| } | | } |
| | |
| ObjectMoleculeInvalidate(I, cRepAll, cRepInvBonds, state); | | ObjectMoleculeInvalidate(I, cRepAll, cRepInvBonds, state); |
| ObjectMoleculeUpdateNeighbors(I); | | ObjectMoleculeUpdateNeighbors(I); |
| | |
| AtomInfoUniquefyNames(G, | | AtomInfoUniquefyNames(G, |
| I->AtomInfo, n_atom_old, | | I->AtomInfo, n_atom_old, |
|
| I->AtomInfo + n_atom_old, NULL, | | I->AtomInfo + n_atom_old, nullptr, |
| I->NAtom - n_atom_old); | | I->NAtom - n_atom_old); |
| | |
| // fill coordinates | | // fill coordinates |
| for (StateIterator iter(G, I->Obj.Setting, state, I->NCSet); iter.next();) { | | for (StateIterator iter(G, I->Obj.Setting, state, I->NCSet); iter.next();) { |
| CoordSet* cs = I->CSet[iter.state]; | | CoordSet* cs = I->CSet[iter.state]; |
| if (!cs) | | if (!cs) |
| continue; | | continue; |
| | |
| for (unsigned idx = 0; idx < cs->NIndex; ++idx) { | | for (unsigned idx = 0; idx < cs->NIndex; ++idx) { |
| auto atm = cs->IdxToAtm[idx]; | | auto atm = cs->IdxToAtm[idx]; |
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| End of changes. 3 change blocks. |
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| 3 lines changed or deleted | | 3 lines changed or added |
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"Fossies" - the Fresh Open Source Software Archive 