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-v1.8.6.0.tar.bz2) | : | MmtfMoleculeReader.cpp (pymol-v2.1.0.tar.bz2) |
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| skipping to change at line 132 | | skipping to change at line 132 |
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| MMTF_container * container = MMTF_container_new(); | | MMTF_container * container = MMTF_container_new(); |
| | |
| if (!MMTF_unpack_from_string(st, st_len, container)) { | | if (!MMTF_unpack_from_string(st, st_len, container)) { |
| PRINTFB(G, FB_ObjectMolecule, FB_Errors) | | PRINTFB(G, FB_ObjectMolecule, FB_Errors) |
| " Error: Failed to load MMTF file\n" ENDFB(G); | | " Error: Failed to load MMTF file\n" ENDFB(G); |
| MMTF_container_free(container); | | MMTF_container_free(container); |
| return NULL; | | return NULL; |
| } | | } |
| | |
|
| PRINTFB(G, FB_ObjectMolecule, FB_Details) | | if (!quiet) { |
| " MMTF structureId: '%s', mmtfVersion: '%s'\n", | | PRINTFB(G, FB_ObjectMolecule, FB_Details) |
| (container->structureId ? container->structureId : ""), | | " MMTF structureId: '%s', mmtfVersion: '%s'\n", |
| (container->mmtfVersion ? container->mmtfVersion : "") ENDFB(G); | | (container->structureId ? container->structureId : ""), |
| | (container->mmtfVersion ? container->mmtfVersion : "") ENDFB(G); |
| | |
| | // title "echo tag" |
| | if (container->title && container->title[0] && |
| | strstr(SettingGetGlobal_s(G, cSetting_pdb_echo_tags), "TITLE")) { |
| | PRINTFB(G, FB_ObjectMolecule, FB_Details) |
| | "TITLE %s\n", container->title ENDFB(G); |
| | } |
| | } |
| | |
| int chainIndex = 0; | | int chainIndex = 0; |
| int groupIndex = 0; | | int groupIndex = 0; |
| int atomIndex = 0; | | int atomIndex = 0; |
| | |
| // template atom | | // template atom |
| AtomInfoType tai; | | AtomInfoType tai; |
| memset(&tai, 0, sizeof(AtomInfoType)); | | memset(&tai, 0, sizeof(AtomInfoType)); |
| tai.visRep = RepGetAutoShowMask(G); | | tai.visRep = RepGetAutoShowMask(G); |
|
| | tai.id = -1; |
| | tai.q = 1.0f; |
| | |
| I = ObjectMoleculeNew(G, /* discrete */ 1); | | I = ObjectMoleculeNew(G, /* discrete */ 1); |
| I->Obj.Color = AtomInfoUpdateAutoColor(G); | | I->Obj.Color = AtomInfoUpdateAutoColor(G); |
| I->NAtom = container->numAtoms; | | I->NAtom = container->numAtoms; |
| I->NCSet = container->numModels; | | I->NCSet = container->numModels; |
| I->Bond = VLAlloc(BondType, container->numBonds); | | I->Bond = VLAlloc(BondType, container->numBonds); |
| VLASize(I->AtomInfo, AtomInfoType, I->NAtom); | | VLASize(I->AtomInfo, AtomInfoType, I->NAtom); |
| VLASize(I->CSet, CoordSet *, I->NCSet); | | VLASize(I->CSet, CoordSet *, I->NCSet); |
| | |
| int nindexEstimate = container->numAtoms / std::max(1, container->numModels); | | int nindexEstimate = container->numAtoms / std::max(1, container->numModels); |
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| skipping to change at line 246 | | skipping to change at line 257 |
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| if (container->bFactorList) | | if (container->bFactorList) |
| ai->b = container->bFactorList[atomIndex]; | | ai->b = container->bFactorList[atomIndex]; |
| if (container->occupancyList) | | if (container->occupancyList) |
| ai->q = container->occupancyList[atomIndex]; | | ai->q = container->occupancyList[atomIndex]; |
| if (container->altLocList) | | if (container->altLocList) |
| ai->alt[0] = container->altLocList[atomIndex]; | | ai->alt[0] = container->altLocList[atomIndex]; |
| | |
| AtomInfoAssignParameters(G, ai); | | AtomInfoAssignParameters(G, ai); |
| AtomInfoAssignColors(G, ai); | | AtomInfoAssignColors(G, ai); |
| | |
|
| | if (container->pymolRepsList) { |
| | ai->visRep = container->pymolRepsList[atomIndex]; |
| | ai->flags |= cAtomFlag_inorganic; // suppress auto_show_classified |
| | } |
| | |
| | if (container->pymolColorList) { |
| | ai->color = container->pymolColorList[atomIndex]; |
| | } |
| | |
| VLACheck(cset->IdxToAtm, int, cset->NIndex); | | VLACheck(cset->IdxToAtm, int, cset->NIndex); |
| VLACheck(cset->Coord, float, 3 * cset->NIndex + 2); | | VLACheck(cset->Coord, float, 3 * cset->NIndex + 2); |
| cset->IdxToAtm[cset->NIndex] = atomIndex; | | cset->IdxToAtm[cset->NIndex] = atomIndex; |
| float * coord = cset->coordPtr(cset->NIndex); | | float * coord = cset->coordPtr(cset->NIndex); |
| cset->NIndex++; | | cset->NIndex++; |
| | |
| coord[0] = container->xCoordList[atomIndex]; | | coord[0] = container->xCoordList[atomIndex]; |
| coord[1] = container->yCoordList[atomIndex]; | | coord[1] = container->yCoordList[atomIndex]; |
| coord[2] = container->zCoordList[atomIndex]; | | coord[2] = container->zCoordList[atomIndex]; |
| } | | } |
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| skipping to change at line 291 | | skipping to change at line 311 |
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| I->NBond, container->numBonds ENDFB(G); | | I->NBond, container->numBonds ENDFB(G); |
| } | | } |
| | |
| if (discrete < 1) { | | if (discrete < 1) { |
| ObjectMoleculeSetDiscrete(G, I, 0); | | ObjectMoleculeSetDiscrete(G, I, 0); |
| } else { | | } else { |
| I->updateAtmToIdx(); | | I->updateAtmToIdx(); |
| } | | } |
| | |
| // assemblies | | // assemblies |
|
| if (!I->DiscreteFlag) { | | if (!I->DiscreteFlag && I->NCSet > 0) { |
| CoordSet ** assembly_csets = get_assembly_csets(G, container, | | CoordSet ** assembly_csets = get_assembly_csets(G, container, |
| I->AtomInfo, I->CSet[0]); | | I->AtomInfo, I->CSet[0]); |
| | |
| ObjectMoleculeSetAssemblyCSets(I, assembly_csets); | | ObjectMoleculeSetAssemblyCSets(I, assembly_csets); |
| } | | } |
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| MMTF_container_free(container); | | MMTF_container_free(container); |
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| ObjectMoleculeInvalidate(I, cRepAll, cRepInvAll, -1); | | ObjectMoleculeInvalidate(I, cRepAll, cRepInvAll, -1); |
| ObjectMoleculeUpdateNonbonded(I); | | ObjectMoleculeUpdateNonbonded(I); |
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| End of changes. 4 change blocks. |
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| 5 lines changed or deleted | | 25 lines changed or added |
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