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.
| Editor.cpp (pymol-v1.8.6.0.tar.bz2) | : | Editor.cpp (pymol-v2.1.0.tar.bz2) |
|---|
| | |
| skipping to change at line 401 | | skipping to change at line 401 |
|---|
| } | | } |
| | |
| int EditorIsBondMode(PyMOLGlobals * G) | | int EditorIsBondMode(PyMOLGlobals * G) |
| { | | { |
| CEditor *I = G->Editor; | | CEditor *I = G->Editor; |
| return (I->BondMode); | | return (I->BondMode); |
| } | | } |
| | |
| PyObject *EditorAsPyList(PyMOLGlobals * G) | | PyObject *EditorAsPyList(PyMOLGlobals * G) |
| { | | { |
|
| #ifdef _PYMOL_NOPY | | |
| return NULL; | | |
| #else | | |
| PyObject *result = NULL; | | PyObject *result = NULL; |
| CEditor *I = G->Editor; | | CEditor *I = G->Editor; |
| | |
| if(!EditorActive(G)) { | | if(!EditorActive(G)) { |
| result = PyList_New(0); /* not editing? return null list */ | | result = PyList_New(0); /* not editing? return null list */ |
| } else { | | } else { |
| result = PyList_New(3); | | result = PyList_New(3); |
| PyList_SetItem(result, 0, PyString_FromString("")); | | PyList_SetItem(result, 0, PyString_FromString("")); |
| PyList_SetItem(result, 1, PyInt_FromLong(I->ActiveState)); | | PyList_SetItem(result, 1, PyInt_FromLong(I->ActiveState)); |
| PyList_SetItem(result, 2, PyInt_FromLong(I->BondMode)); | | PyList_SetItem(result, 2, PyInt_FromLong(I->BondMode)); |
| } | | } |
| return (PConvAutoNone(result)); | | return (PConvAutoNone(result)); |
|
| #endif | | |
| } | | } |
| | |
| int EditorFromPyList(PyMOLGlobals * G, PyObject * list) | | int EditorFromPyList(PyMOLGlobals * G, PyObject * list) |
| { | | { |
|
| #ifdef _PYMOL_NOPY | | |
| return 0; | | |
| #else | | |
| | | |
| int ok = true; | | int ok = true; |
| int active_flag = false; | | int active_flag = false; |
| int active_state; | | int active_state; |
| WordType obj_name; | | WordType obj_name; |
| int ll = 0; | | int ll = 0; |
| int bond_mode = true; | | int bond_mode = true; |
| | |
| if(ok) | | if(ok) |
| ok = (list != NULL); | | ok = (list != NULL); |
| if(ok) | | if(ok) |
| | |
| skipping to change at line 462 | | skipping to change at line 454 |
|---|
| EditorActivate(G, active_state, bond_mode); | | EditorActivate(G, active_state, bond_mode); |
| EditorDefineExtraPks(G); | | EditorDefineExtraPks(G); |
| } else { | | } else { |
| EditorInactivate(G); | | EditorInactivate(G); |
| } | | } |
| } | | } |
| if(!ok) { | | if(!ok) { |
| EditorInactivate(G); | | EditorInactivate(G); |
| } | | } |
| return (ok); | | return (ok); |
|
| #endif | | |
| } | | } |
| | |
| int EditorActive(PyMOLGlobals * G) | | int EditorActive(PyMOLGlobals * G) |
| { | | { |
| CEditor *I = G->Editor; | | CEditor *I = G->Editor; |
| return (I->Active); | | return (I->Active); |
| } | | } |
| | |
| CObject *EditorDragObject(PyMOLGlobals * G) | | CObject *EditorDragObject(PyMOLGlobals * G) |
| { | | { |
| | |
| skipping to change at line 912 | | skipping to change at line 903 |
|---|
| } | | } |
| } | | } |
| } | | } |
| | |
| /*========================================================================*/ | | /*========================================================================*/ |
| void EditorAttach(PyMOLGlobals * G, const char *elem, int geom, int valence, | | void EditorAttach(PyMOLGlobals * G, const char *elem, int geom, int valence, |
| const char *name, int quiet) | | const char *name, int quiet) |
| { | | { |
| int i0; | | int i0; |
| int sele0, sele1; | | int sele0, sele1; |
|
| int state; | | |
| AtomInfoType *ai; | | AtomInfoType *ai; |
| ObjectMolecule *obj0 = NULL, *obj1 = NULL; | | ObjectMolecule *obj0 = NULL, *obj1 = NULL; |
| int ok = true; | | int ok = true; |
| | |
| ai = (AtomInfoType *) VLAMalloc(1, sizeof(AtomInfoType), 1, true); | | ai = (AtomInfoType *) VLAMalloc(1, sizeof(AtomInfoType), 1, true); |
| if(EditorActive(G)) { | | if(EditorActive(G)) { |
| | |
| sele0 = SelectorIndexByName(G, cEditorSele1); | | sele0 = SelectorIndexByName(G, cEditorSele1); |
| if(sele0 >= 0) { | | if(sele0 >= 0) { |
| sele1 = SelectorIndexByName(G, cEditorSele2); | | sele1 = SelectorIndexByName(G, cEditorSele2); |
| obj0 = SelectorGetFastSingleObjectMolecule(G, sele0); | | obj0 = SelectorGetFastSingleObjectMolecule(G, sele0); |
| obj1 = SelectorGetFastSingleObjectMolecule(G, sele1); | | obj1 = SelectorGetFastSingleObjectMolecule(G, sele1); |
| | |
| if(obj0) { | | if(obj0) { |
| if(obj0->DiscreteFlag) { | | if(obj0->DiscreteFlag) { |
| ErrMessage(G, "Remove", "Can't attach atoms onto discrete objects."); | | ErrMessage(G, "Remove", "Can't attach atoms onto discrete objects."); |
| } else { | | } else { |
| ObjectMoleculeVerifyChemistry(obj0, -1); /* remember chemistry fo
r later */ | | ObjectMoleculeVerifyChemistry(obj0, -1); /* remember chemistry fo
r later */ |
|
| state = SceneGetState(G); | | |
| if(obj1) { | | if(obj1) { |
| if(obj0 == obj1) { | | if(obj0 == obj1) { |
| /* bond mode - behave like replace */ | | /* bond mode - behave like replace */ |
| EditorReplace(G, elem, geom, valence, name, quiet); | | EditorReplace(G, elem, geom, valence, name, quiet); |
| } | | } |
| } else { | | } else { |
| /* atom mode */ | | /* atom mode */ |
| i0 = ObjectMoleculeGetAtomIndex(obj0, sele0); /* slow */ | | i0 = ObjectMoleculeGetAtomIndex(obj0, sele0); /* slow */ |
| if(i0 >= 0) { | | if(i0 >= 0) { |
| UtilNCopy(ai->elem, elem, sizeof(ElemName)); | | UtilNCopy(ai->elem, elem, sizeof(ElemName)); |
| | |
| skipping to change at line 1086 | | skipping to change at line 1075 |
|---|
| ExecutiveFixHydrogens(G, sele, quiet); | | ExecutiveFixHydrogens(G, sele, quiet); |
| } | | } |
| } | | } |
| | |
| /*========================================================================*/ | | /*========================================================================*/ |
| void EditorReplace(PyMOLGlobals * G, const char *elem, int geom, int valence, co
nst char *name, | | void EditorReplace(PyMOLGlobals * G, const char *elem, int geom, int valence, co
nst char *name, |
| int quiet) | | int quiet) |
| { | | { |
| int i0; | | int i0; |
| int sele0; | | int sele0; |
|
| int state; | | |
| AtomInfoType ai; | | AtomInfoType ai; |
| ObjectMolecule *obj0 = NULL; | | ObjectMolecule *obj0 = NULL; |
| int ok = true; | | int ok = true; |
| UtilZeroMem(&ai, sizeof(AtomInfoType)); | | UtilZeroMem(&ai, sizeof(AtomInfoType)); |
| if(EditorActive(G)) { | | if(EditorActive(G)) { |
| sele0 = SelectorIndexByName(G, cEditorSele1); | | sele0 = SelectorIndexByName(G, cEditorSele1); |
| obj0 = SelectorGetFastSingleObjectMolecule(G, sele0); | | obj0 = SelectorGetFastSingleObjectMolecule(G, sele0); |
| if(obj0->DiscreteFlag) { | | if(obj0->DiscreteFlag) { |
| ErrMessage(G, "Remove", "Can't attach atoms onto discrete objects."); | | ErrMessage(G, "Remove", "Can't attach atoms onto discrete objects."); |
| } else { | | } else { |
| ObjectMoleculeVerifyChemistry(obj0, -1); /* remember chemistry for later
*/ | | ObjectMoleculeVerifyChemistry(obj0, -1); /* remember chemistry for later
*/ |
|
| | | |
| state = SceneGetState(G); | | |
| | | |
| if(sele0 >= 0) { | | if(sele0 >= 0) { |
| i0 = ObjectMoleculeGetAtomIndex(obj0, sele0); /* slow */ | | i0 = ObjectMoleculeGetAtomIndex(obj0, sele0); /* slow */ |
| if(i0 >= 0) { | | if(i0 >= 0) { |
| UtilNCopy(ai.elem, elem, sizeof(ElemName)); | | UtilNCopy(ai.elem, elem, sizeof(ElemName)); |
| if(name[0]) | | if(name[0]) |
| LexAssign(G, ai.name, name); | | LexAssign(G, ai.name, name); |
| ai.geom = geom; | | ai.geom = geom; |
| ai.valence = valence; | | ai.valence = valence; |
| if (ok) | | if (ok) |
| ok &= ObjectMoleculePrepareAtom(obj0, i0, &ai); | | ok &= ObjectMoleculePrepareAtom(obj0, i0, &ai); |
| | |
| skipping to change at line 1560 | | skipping to change at line 1545 |
|---|
| | |
| if(EditorActive(G)) { | | if(EditorActive(G)) { |
| int use_shader = SettingGetGlobal_b(G, cSetting_use_shaders); | | int use_shader = SettingGetGlobal_b(G, cSetting_use_shaders); |
| if (use_shader){ | | if (use_shader){ |
| if (!I->shaderCGO){ | | if (!I->shaderCGO){ |
| shaderCGO = CGONew(G); | | shaderCGO = CGONew(G); |
| } else { | | } else { |
| CGORenderGL(I->shaderCGO, NULL, NULL, NULL, NULL, NULL); | | CGORenderGL(I->shaderCGO, NULL, NULL, NULL, NULL, NULL); |
| return; | | return; |
| } | | } |
|
| } else if (I->shaderCGO) { | | } else { |
| CGOFree(I->shaderCGO); | | CGOFree(I->shaderCGO); |
|
| I->shaderCGO = NULL; | | |
| } | | } |
| | |
| PRINTFD(G, FB_Editor) | | PRINTFD(G, FB_Editor) |
| " EditorRender-Debug: rendering...\n" ENDFD; | | " EditorRender-Debug: rendering...\n" ENDFD; |
| | |
| if(G->HaveGUI && G->ValidContext) { | | if(G->HaveGUI && G->ValidContext) { |
| | |
| sele1 = SelectorIndexByName(G, cEditorSele1); | | sele1 = SelectorIndexByName(G, cEditorSele1); |
| sele2 = SelectorIndexByName(G, cEditorSele2); | | sele2 = SelectorIndexByName(G, cEditorSele2); |
| sele3 = SelectorIndexByName(G, cEditorSele3); | | sele3 = SelectorIndexByName(G, cEditorSele3); |
| | |
| skipping to change at line 2380 | | skipping to change at line 2364 |
|---|
| /*========================================================================*/ | | /*========================================================================*/ |
| void EditorFree(PyMOLGlobals * G) | | void EditorFree(PyMOLGlobals * G) |
| { | | { |
| CEditor *I = G->Editor; | | CEditor *I = G->Editor; |
| VLAFreeP(I->PosVLA); | | VLAFreeP(I->PosVLA); |
| FreeP(G->Editor); | | FreeP(G->Editor); |
| } | | } |
| | |
| void EditorInvalidateShaderCGO(PyMOLGlobals * G){ | | void EditorInvalidateShaderCGO(PyMOLGlobals * G){ |
| CEditor *I = G->Editor; | | CEditor *I = G->Editor; |
|
| if (I->shaderCGO){ | | CGOFree(I->shaderCGO); |
| CGOFree(I->shaderCGO); | | |
| I->shaderCGO = NULL; | | |
| } | | |
| } | | } |
| | | |
| End of changes. 11 change blocks. |
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| 21 lines changed or deleted | | 2 lines changed or added |
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