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.
| MmtfMoleculeReader.cpp (pymol-v2.1.0.tar.bz2) | : | MmtfMoleculeReader.cpp (pymol-open-source-2.2.0) |
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| skipping to change at line 25 | | skipping to change at line 25 |
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| #include <algorithm> | | #include <algorithm> |
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| #include "AssemblyHelpers.h" | | #include "AssemblyHelpers.h" |
| #include "AtomInfo.h" | | #include "AtomInfo.h" |
| #include "Err.h" | | #include "Err.h" |
| #include "Lex.h" | | #include "Lex.h" |
| #include "MemoryDebug.h" | | #include "MemoryDebug.h" |
| #include "Rep.h" | | #include "Rep.h" |
| | |
|
| const int ss_map[] = { | | const char ss_map[] = { |
| | // indices shifted by +1 w.r.t. spec |
| | 0, // undefined |
| 'H', // pi helix | | 'H', // pi helix |
| 'L', // bend | | 'L', // bend |
| 'H', // alpha helix | | 'H', // alpha helix |
| 'S', // extended | | 'S', // extended |
| 'H', // 3-10 helix | | 'H', // 3-10 helix |
| 'S', // bridge | | 'S', // bridge |
| 'L', // turn | | 'L', // turn |
| 'L', // coil | | 'L', // coil |
| 0 | | 0 |
| }; | | }; |
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| skipping to change at line 210 | | skipping to change at line 212 |
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| LexAssign(G, tai.segi, container->chainIdList[chainIndex]); | | LexAssign(G, tai.segi, container->chainIdList[chainIndex]); |
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| int chainGroupCount = container->groupsPerChain[chainIndex]; | | int chainGroupCount = container->groupsPerChain[chainIndex]; |
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| // groups (residues) | | // groups (residues) |
| for (int k = 0; k < chainGroupCount; ++k, ++groupIndex) { | | for (int k = 0; k < chainGroupCount; ++k, ++groupIndex) { |
| const MMTF_GroupType * group = | | const MMTF_GroupType * group = |
| container->groupList + | | container->groupList + |
| container->groupTypeList[groupIndex]; | | container->groupTypeList[groupIndex]; |
| | |
|
| if (container->secStructList) | | if (container->secStructList) { |
| tai.ssType[0] = ss_map[container->secStructList[groupIndex]]; | | size_t i = container->secStructList[groupIndex] + 1; |
| | tai.ssType[0] = ss_map[std::min(i, sizeof(ss_map) - 1)]; |
| | } |
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| LexAssign(G, tai.resn, group->groupName); | | LexAssign(G, tai.resn, group->groupName); |
| tai.hetatm = group->singleLetterCode == '?'; | | tai.hetatm = group->singleLetterCode == '?'; |
| tai.flags = tai.hetatm ? cAtomFlag_ignore : 0; | | tai.flags = tai.hetatm ? cAtomFlag_ignore : 0; |
| | |
| if (use_auth) { | | if (use_auth) { |
| tai.resv = container->groupIdList[groupIndex]; | | tai.resv = container->groupIdList[groupIndex]; |
| if (container->insCodeList) | | if (container->insCodeList) |
| tai.setInscode(container->insCodeList[groupIndex]); | | tai.setInscode(container->insCodeList[groupIndex]); |
| } else if (container->sequenceIndexList) { | | } else if (container->sequenceIndexList) { |
| tai.resv = container->sequenceIndexList[groupIndex]; | | tai.resv = container->sequenceIndexList[groupIndex]; |
| } | | } |
| | |
| // bonds | | // bonds |
| for (int l = 0, offset = atomIndex; l < group->bondAtomListCount / 2; ++
l) { | | for (int l = 0, offset = atomIndex; l < group->bondAtomListCount / 2; ++
l) { |
|
| | VLACheck(I->Bond, BondType, I->NBond); // PYMOL-3026 |
| BondTypeInit2(I->Bond + (I->NBond++), | | BondTypeInit2(I->Bond + (I->NBond++), |
| offset + group->bondAtomList[l * 2], | | offset + group->bondAtomList[l * 2], |
| offset + group->bondAtomList[l * 2 + 1], | | offset + group->bondAtomList[l * 2 + 1], |
| group->bondOrderListCount ? group->bondOrderList[l] : 1); | | group->bondOrderListCount ? group->bondOrderList[l] : 1); |
| } | | } |
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| int groupAtomCount = group->atomNameListCount; | | int groupAtomCount = group->atomNameListCount; |
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| // atoms | | // atoms |
| for (int l = 0; l < groupAtomCount; ++l, ++atomIndex) { | | for (int l = 0; l < groupAtomCount; ++l, ++atomIndex) { |
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| skipping to change at line 292 | | skipping to change at line 297 |
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| if (atomIndex != I->NAtom) { | | if (atomIndex != I->NAtom) { |
| PRINTFB(G, FB_ObjectMolecule, FB_Warnings) | | PRINTFB(G, FB_ObjectMolecule, FB_Warnings) |
| " MMTF-Inconsistency-Warning: atom count mismatch (%d != numAtoms=%d)\n", | | " MMTF-Inconsistency-Warning: atom count mismatch (%d != numAtoms=%d)\n", |
| atomIndex, I->NAtom ENDFB(G); | | atomIndex, I->NAtom ENDFB(G); |
| } | | } |
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| AtomInfoPurge(G, &tai); | | AtomInfoPurge(G, &tai); |
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| for (int l = 0; l < container->bondAtomListCount / 2; ++l) { | | for (int l = 0; l < container->bondAtomListCount / 2; ++l) { |
|
| | VLACheck(I->Bond, BondType, I->NBond); // PYMOL-3026 |
| BondTypeInit2(I->Bond + (I->NBond++), | | BondTypeInit2(I->Bond + (I->NBond++), |
| container->bondAtomList[l * 2], | | container->bondAtomList[l * 2], |
| container->bondAtomList[l * 2 + 1], | | container->bondAtomList[l * 2 + 1], |
| container->bondOrderListCount ? container->bondOrderList[l] : 1); | | container->bondOrderListCount ? container->bondOrderList[l] : 1); |
| } | | } |
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| if (container->numBonds != I->NBond) { | | if (container->numBonds != I->NBond) { |
| PRINTFB(G, FB_ObjectMolecule, FB_Warnings) | | PRINTFB(G, FB_ObjectMolecule, FB_Warnings) |
| " MMTF-Inconsistency-Warning: bond count mismatch (%d != numBonds=%d)\n", | | " MMTF-Inconsistency-Warning: bond count mismatch (%d != numBonds=%d)\n", |
| I->NBond, container->numBonds ENDFB(G); | | I->NBond, container->numBonds ENDFB(G); |
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| End of changes. 4 change blocks. |
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| 3 lines changed or deleted | | 9 lines changed or added |
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