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.
| View.cpp (pymol-v1.8.6.0.tar.bz2) | : | View.cpp (pymol-v2.1.0.tar.bz2) |
|---|
| | |
| skipping to change at line 70 | | skipping to change at line 70 |
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| dst = target+i; | | dst = target+i; |
| } else { | | } else { |
| src = index+(count-1)-i; | | src = index+(count-1)-i; |
| dst = target+(count-1)-i; | | dst = target+(count-1)-i; |
| } | | } |
| memcpy(vla + dst, vla + src, sizeof(CViewElem)); | | memcpy(vla + dst, vla + src, sizeof(CViewElem)); |
| memset(vla + src, 0, sizeof(CViewElem)); | | memset(vla + src, 0, sizeof(CViewElem)); |
| } | | } |
| } | | } |
| } | | } |
|
| | | |
| } | | } |
| break; | | break; |
| case cViewElemModifyCopy: | | case cViewElemModifyCopy: |
| if((index>=0) && (target>=0) && (index<n_frame) && (target<n_frame)) { | | if((index>=0) && (target>=0) && (index<n_frame) && (target<n_frame)) { |
| if((count>1)||(vla[index].specification_level>1)) { | | if((count>1)||(vla[index].specification_level>1)) { |
| int i; | | int i; |
| for(i=0;i<count;i++) { | | for(i=0;i<count;i++) { |
| if( ((i+index)<n_frame) && ((i+target)<n_frame)) { | | if( ((i+index)<n_frame) && ((i+target)<n_frame)) { |
| int src,dst; | | int src,dst; |
| if(index>target) { | | if(index>target) { |
| | |
| skipping to change at line 99 | | skipping to change at line 98 |
|---|
| } | | } |
| } | | } |
| } | | } |
| break; | | break; |
| } | | } |
| } | | } |
| *handle = vla; | | *handle = vla; |
| return ok; | | return ok; |
| } | | } |
| | |
|
| int ViewElemXtoFrame(PyMOLGlobals *G, CViewElem * view_elem, BlockRect *rect, in
t frames, int x, int nearest) | | int ViewElemXtoFrame(BlockRect *rect, int frames, int x, int nearest) |
| { | | { |
|
| int nDrawn = frames; | | |
| int offset = 0; | | int offset = 0; |
| float width = (float) (rect->right - rect->left); | | float width = (float) (rect->right - rect->left); |
| float extra = (nearest ? 0.4999F : 0.0F); | | float extra = (nearest ? 0.4999F : 0.0F); |
|
| int frame = (int)(extra + (nDrawn * (x - rect->left )) / width + offset); | | int frame = (int)(extra + (frames * (x - rect->left )) / width + offset); |
| return frame; | | return frame; |
| } | | } |
| | |
| void ViewElemDrawBox(PyMOLGlobals *G, BlockRect *rect, int first, int last, | | void ViewElemDrawBox(PyMOLGlobals *G, BlockRect *rect, int first, int last, |
| int frames, float *color4,int fill ORTHOCGOARG) | | int frames, float *color4,int fill ORTHOCGOARG) |
| { | | { |
| if(G->HaveGUI && G->ValidContext && rect) { | | if(G->HaveGUI && G->ValidContext && rect) { |
| int nDrawn = frames; | | int nDrawn = frames; |
| int offset = 0; | | int offset = 0; |
| float width = (float) (rect->right - rect->left); | | float width = (float) (rect->right - rect->left); |
| | |
| skipping to change at line 167 | | skipping to change at line 165 |
|---|
| } | | } |
| } | | } |
| | |
| void ViewElemDraw(PyMOLGlobals *G, CViewElem * view_elem, BlockRect *rect, int f
rames, | | void ViewElemDraw(PyMOLGlobals *G, CViewElem * view_elem, BlockRect *rect, int f
rames, |
| const char *title ORTHOCGOARG) | | const char *title ORTHOCGOARG) |
| { | | { |
| if(G->HaveGUI && G->ValidContext && view_elem) { | | if(G->HaveGUI && G->ValidContext && view_elem) { |
| int size = VLAGetSize(view_elem); | | int size = VLAGetSize(view_elem); |
| float width = (float) (rect->right - rect->left); | | float width = (float) (rect->right - rect->left); |
| float start = 0.0F, stop; | | float start = 0.0F, stop; |
|
| int offset = 0; | | const int last = size; |
| int first = 0; | | |
| int last = size; | | |
| int nDrawn = frames; | | |
| float top = rect->top - 2; | | float top = rect->top - 2; |
| float bot = rect->bottom + 2; | | float bot = rect->bottom + 2; |
| float mid_top = (int)((0.499F + 3 * top + 2 * bot) / 5); | | float mid_top = (int)((0.499F + 3 * top + 2 * bot) / 5); |
| float mid_bot = (int)((0.499F + 2 * top + 3 * bot) / 5); | | float mid_bot = (int)((0.499F + 2 * top + 3 * bot) / 5); |
| float top_color[3] = { 0.6, 0.6, 1.0 }; | | float top_color[3] = { 0.6, 0.6, 1.0 }; |
| float key_color[3] = { 0.4, 0.4, 0.8 }; | | float key_color[3] = { 0.4, 0.4, 0.8 }; |
| float bar_color[3] = { 0.3, 0.3, 0.6 }; | | float bar_color[3] = { 0.3, 0.3, 0.6 }; |
| float bot_color[3] = { 0.2, 0.2, 0.4 }; | | float bot_color[3] = { 0.2, 0.2, 0.4 }; |
| int cur_level = -1, last_level = -1; | | int cur_level = -1, last_level = -1; |
| int cur; | | int cur; |
|
| for(cur = first; cur <= last; cur++) { | | for(cur = 0; cur <= last; cur++) { |
| if(cur < last) { | | if(cur < last) { |
|
| if(cur>=size) | | |
| cur_level = -1; | | |
| else | | |
| cur_level = view_elem->specification_level; | | cur_level = view_elem->specification_level; |
| } else { | | } else { |
| cur_level = -1; | | cur_level = -1; |
| } | | } |
| if(cur_level != last_level) { | | if(cur_level != last_level) { |
|
| stop = (int)(rect->left + (width * (cur - offset)) / nDrawn); | | stop = (int)(rect->left + (width * cur) / frames); |
| switch (last_level) { | | switch (last_level) { |
| case 0: | | case 0: |
| break; | | break; |
| case 1: | | case 1: |
| if (orthoCGO){ | | if (orthoCGO){ |
| CGOColorv(orthoCGO, bar_color); | | CGOColorv(orthoCGO, bar_color); |
| CGOBegin(orthoCGO, GL_TRIANGLE_STRIP); | | CGOBegin(orthoCGO, GL_TRIANGLE_STRIP); |
| CGOVertex(orthoCGO, start, mid_bot, 0.f); | | CGOVertex(orthoCGO, start, mid_bot, 0.f); |
| CGOVertex(orthoCGO, start, mid_top, 0.f); | | CGOVertex(orthoCGO, start, mid_top, 0.f); |
| CGOVertex(orthoCGO, stop, mid_bot, 0.f); | | CGOVertex(orthoCGO, stop, mid_bot, 0.f); |
| | |
| skipping to change at line 303 | | skipping to change at line 295 |
|---|
| glVertex2f(stop,bot-1); | | glVertex2f(stop,bot-1); |
| glVertex2f(stop,bot); | | glVertex2f(stop,bot); |
| glVertex2f(stop,top); | | glVertex2f(stop,top); |
| glColor3fv(top_color); | | glColor3fv(top_color); |
| glVertex2f(start,top); | | glVertex2f(start,top); |
| glVertex2f(stop,top); | | glVertex2f(stop,top); |
| glVertex2f(start,bot); | | glVertex2f(start,bot); |
| glVertex2f(start,top); | | glVertex2f(start,top); |
| glEnd(); | | glEnd(); |
| } | | } |
|
| | | |
| break; | | break; |
| } | | } |
|
| start = (int)(rect->left + (width * (cur - offset)) / nDrawn); | | start = stop; |
| } | | } |
| last_level = cur_level; | | last_level = cur_level; |
| view_elem++; | | view_elem++; |
| } | | } |
| | |
| if(title) | | if(title) |
| TextDrawStrAt(G, title, rect->right + 1, (rect->bottom+rect->top)/2 - 3 OR
THOCGOARGVAR); | | TextDrawStrAt(G, title, rect->right + 1, (rect->bottom+rect->top)/2 - 3 OR
THOCGOARGVAR); |
| } | | } |
| } | | } |
| | |
| | |
| skipping to change at line 433 | | skipping to change at line 424 |
|---|
| } | | } |
| | |
| } | | } |
| | |
| return PConvAutoNone(result); | | return PConvAutoNone(result); |
| #endif | | #endif |
| } | | } |
| | |
| int ViewElemFromPyList(PyMOLGlobals * G, PyObject * list, CViewElem * view) | | int ViewElemFromPyList(PyMOLGlobals * G, PyObject * list, CViewElem * view) |
| { | | { |
|
| #ifdef _PYMOL_NOPY | | |
| return 0; | | |
| #else | | |
| | | |
| int ok = true; | | int ok = true; |
| ov_size ll = 0; | | ov_size ll = 0; |
| | |
| if(ok) | | if(ok) |
| ok = (list != NULL); | | ok = (list != NULL); |
| if(ok) | | if(ok) |
| ok = PyList_Check(list); | | ok = PyList_Check(list); |
| if(ok) | | if(ok) |
| ok = ((ll = PyList_Size(list)) > 11); | | ok = ((ll = PyList_Size(list)) > 11); |
| | |
| | |
| skipping to change at line 491 | | skipping to change at line 478 |
|---|
| | |
| if(ok) | | if(ok) |
| ok = PConvPyIntToInt(PyList_GetItem(list, 11), &view->view_mode); | | ok = PConvPyIntToInt(PyList_GetItem(list, 11), &view->view_mode); |
| if(ok) | | if(ok) |
| ok = PConvPyIntToInt(PyList_GetItem(list, 12), &view->specification_level); | | ok = PConvPyIntToInt(PyList_GetItem(list, 12), &view->specification_level); |
| | |
| if(ok & (ll > 14)) { | | if(ok & (ll > 14)) { |
| if(ok) | | if(ok) |
| ok = PConvPyIntToInt(PyList_GetItem(list, 13), &view->scene_flag); | | ok = PConvPyIntToInt(PyList_GetItem(list, 13), &view->scene_flag); |
| if(ok && view->scene_flag) { | | if(ok && view->scene_flag) { |
|
| char *ptr = NULL; | | const char *ptr = NULL; |
| view->scene_flag = false; | | view->scene_flag = false; |
| if(PConvPyStrToStrPtr(PyList_GetItem(list, 14), &ptr)) { | | if(PConvPyStrToStrPtr(PyList_GetItem(list, 14), &ptr)) { |
| OVreturn_word result = OVLexicon_GetFromCString(G->Lexicon, ptr); | | OVreturn_word result = OVLexicon_GetFromCString(G->Lexicon, ptr); |
| if(OVreturn_IS_OK(result)) { | | if(OVreturn_IS_OK(result)) { |
| view->scene_name = result.word; | | view->scene_name = result.word; |
| view->scene_flag = true; | | view->scene_flag = true; |
| } | | } |
| } | | } |
| } | | } |
| } | | } |
| | |
| skipping to change at line 527 | | skipping to change at line 514 |
|---|
| } | | } |
| if(ok && (ll>20)) { | | if(ok && (ll>20)) { |
| ok = PConvPyIntToInt(PyList_GetItem(list, 19), &view->state_flag); | | ok = PConvPyIntToInt(PyList_GetItem(list, 19), &view->state_flag); |
| if(ok && view->state_flag) { | | if(ok && view->state_flag) { |
| ok = PConvPyIntToInt(PyList_GetItem(list, 20), &view->state); | | ok = PConvPyIntToInt(PyList_GetItem(list, 20), &view->state); |
| } else { | | } else { |
| view->state = 0; | | view->state = 0; |
| } | | } |
| } | | } |
| return ok; | | return ok; |
|
| #endif | | |
| } | | } |
| | |
| int ViewElemVLAFromPyList(PyMOLGlobals * G, PyObject * list, CViewElem ** vla_pt
r, | | int ViewElemVLAFromPyList(PyMOLGlobals * G, PyObject * list, CViewElem ** vla_pt
r, |
| int nFrame) | | int nFrame) |
| { | | { |
|
| #ifdef _PYMOL_NOPY | | |
| return 0; | | |
| #else | | |
| | | |
| int ok = true; | | int ok = true; |
|
| | | |
| CViewElem *vla = NULL; | | CViewElem *vla = NULL; |
|
| | | |
| if(ok) | | if(ok) |
| ok = (list != NULL); | | ok = (list != NULL); |
| if(ok) | | if(ok) |
| ok = PyList_Check(list); | | ok = PyList_Check(list); |
| if(ok) | | if(ok) |
| ok = (PyList_Size(list) == nFrame); | | ok = (PyList_Size(list) == nFrame); |
| if(ok) | | if(ok) |
| ok = ((vla = VLACalloc(CViewElem, nFrame)) != NULL); | | ok = ((vla = VLACalloc(CViewElem, nFrame)) != NULL); |
| if(ok) { | | if(ok) { |
| int a; | | int a; |
| | |
| skipping to change at line 563 | | skipping to change at line 543 |
|---|
| ok = ViewElemFromPyList(G, PyList_GetItem(list, a), vla + a); | | ok = ViewElemFromPyList(G, PyList_GetItem(list, a), vla + a); |
| else | | else |
| break; | | break; |
| } | | } |
| } | | } |
| if(!ok) { | | if(!ok) { |
| VLAFreeP(vla); | | VLAFreeP(vla); |
| } else | | } else |
| *vla_ptr = vla; | | *vla_ptr = vla; |
| return ok; | | return ok; |
|
| #endif | | |
| } | | } |
| | |
| PyObject *ViewElemVLAAsPyList(PyMOLGlobals * G, CViewElem * vla, int nFrame) | | PyObject *ViewElemVLAAsPyList(PyMOLGlobals * G, CViewElem * vla, int nFrame) |
| { | | { |
| #ifdef _PYMOL_NOPY | | #ifdef _PYMOL_NOPY |
| return NULL; | | return NULL; |
| #else | | #else |
| | |
| PyObject *result = NULL; | | PyObject *result = NULL; |
| int a; | | int a; |
| | | |
| End of changes. 17 change blocks. |
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| 28 lines changed or deleted | | 7 lines changed or added |
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