"Fossies" - the Fresh Open Source Software Archive  

Source code changes of the file "layer2/DistSet.cpp" between
pymol-v1.8.6.0.tar.bz2 and pymol-v2.1.0.tar.bz2

About: PyMOL 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.

[ To the main PyMOL source changes report ]

DistSet.cpp  (pymol-v1.8.6.0.tar.bz2):DistSet.cpp  (pymol-v2.1.0.tar.bz2)
skipping to change at line 157 skipping to change at line 157
ok_except1: ok_except1:
return rVal; return rVal;
} }
static CMeasureInfo * MeasureInfoListFromPyList(PyMOLGlobals * G, PyObject * lis t) static CMeasureInfo * MeasureInfoListFromPyList(PyMOLGlobals * G, PyObject * lis t)
{ {
int i, ll, N; int i, ll, N;
CMeasureInfo *item = NULL, *I= NULL; CMeasureInfo *item = NULL, *I= NULL;
CPythonVal *val, *tmp; CPythonVal *val, *tmp;
ok_assert(1, list && CPythonVal_PyList_Check(list)); ok_assert(1, list && PyList_Check(list));
ll = CPythonVal_PyList_Size(list); ll = PyList_Size(list);
for (i = 0; i < ll; i++) { for (i = 0; i < ll; i++) {
ok_assert(1, item = Alloc(CMeasureInfo, 1)); ok_assert(1, item = Alloc(CMeasureInfo, 1));
ListPrepend(I, item, next); ListPrepend(I, item, next);
val = CPythonVal_PyList_GetItem(G, list, i); val = CPythonVal_PyList_GetItem(G, list, i);
if(val && CPythonVal_PyList_Check(val) && if(val && PyList_Check(val) &&
CPythonVal_PyList_Size(val) > 2) { PyList_Size(val) > 2) {
tmp = CPythonVal_PyList_GetItem(G, val, 1); tmp = CPythonVal_PyList_GetItem(G, val, 1);
N = CPythonVal_PyList_Size(tmp); N = PyList_Size(tmp);
ok_assert(1, N < 5); ok_assert(1, N < 5);
item->measureType = (N == 2) ? cRepDash : item->measureType = (N == 2) ? cRepDash :
(N == 3) ? cRepAngle : cRepDihedral; (N == 3) ? cRepAngle : cRepDihedral;
CPythonVal_PConvPyIntToInt_From_List(G, val, 0, &item->offset); CPythonVal_PConvPyIntToInt_From_List(G, val, 0, &item->offset);
CPythonVal_PConvPyListToIntArrayInPlace(G, tmp, item->id, N); CPythonVal_PConvPyListToIntArrayInPlace(G, tmp, item->id, N);
CPythonVal_PConvPyListToIntArrayInPlace_From_List(G, val, 2, item->state, N); CPythonVal_PConvPyListToIntArrayInPlace_From_List(G, val, 2, item->state, N);
CPythonVal_Free(tmp); CPythonVal_Free(tmp);
skipping to change at line 193 skipping to change at line 193
} }
CPythonVal_Free(val); CPythonVal_Free(val);
} }
ok_except1: ok_except1:
return I; return I;
} }
static PyObject *MeasureInfoListAsPyList(CMeasureInfo * I) static PyObject *MeasureInfoListAsPyList(CMeasureInfo * I)
{ {
#ifdef _PYMOL_NOPY
return NULL;
#else
int N; int N;
PyObject *item, *result = PyList_New(0); PyObject *item, *result = PyList_New(0);
ok_assert(1, result); ok_assert(1, result);
while (I) { while (I) {
switch(I->measureType) { switch(I->measureType) {
case cRepDash: N = 2; break; case cRepDash: N = 2; break;
case cRepAngle: N = 3; break; case cRepAngle: N = 3; break;
default: N = 4; default: N = 4;
} }
ok_assert(1, item = PyList_New(3)); ok_assert(1, item = PyList_New(3));
PyList_Append(result, item);
PyList_SetItem(item, 0, PyInt_FromLong(I->offset)); PyList_SetItem(item, 0, PyInt_FromLong(I->offset));
PyList_SetItem(item, 1, PConvIntArrayToPyList(I->id, N)); PyList_SetItem(item, 1, PConvIntArrayToPyList(I->id, N));
PyList_SetItem(item, 2, PConvIntArrayToPyList(I->state, N)); PyList_SetItem(item, 2, PConvIntArrayToPyList(I->state, N));
PyList_Append(result, item);
Py_DECREF(item);
I = I->next; I = I->next;
} }
ok_except1: ok_except1:
return PConvAutoNone(result); return PConvAutoNone(result);
#endif
} }
int DistSetFromPyList(PyMOLGlobals * G, PyObject * list, DistSet ** cs) int DistSetFromPyList(PyMOLGlobals * G, PyObject * list, DistSet ** cs)
{ {
DistSet *I = NULL; DistSet *I = NULL;
int ll = 0; int ll = 0;
CPythonVal *val; CPythonVal *val;
if(*cs) { if(*cs) {
(*cs)->fFree(); (*cs)->fFree();
*cs = NULL; *cs = NULL;
} }
if(list == Py_None) { /* allow None for CSet */ if(list == Py_None) { /* allow None for CSet */
*cs = NULL; *cs = NULL;
return true; return true;
} }
ok_assert(1, list && CPythonVal_PyList_Check(list)); ok_assert(1, list && PyList_Check(list));
ok_assert(1, I = DistSetNew(G)); ok_assert(1, I = DistSetNew(G));
ll = PyList_Size(list); ll = PyList_Size(list);
/* TO SUPPORT BACKWARDS COMPATIBILITY... /* TO SUPPORT BACKWARDS COMPATIBILITY...
Always check ll when adding new PyList_GetItem's */ Always check ll when adding new PyList_GetItem's */
ok_assert(1, CPythonVal_PConvPyIntToInt_From_List(G, list, 0, &I->NIndex)); ok_assert(1, CPythonVal_PConvPyIntToInt_From_List(G, list, 0, &I->NIndex));
ok_assert(1, CPythonVal_PConvPyListToFloatVLANoneOkay_From_List(G, list, 1, &I ->Coord)); ok_assert(1, CPythonVal_PConvPyListToFloatVLANoneOkay_From_List(G, list, 1, &I ->Coord));
ok_assert(2, ll > 2); ok_assert(2, ll > 2);
I->LabCoord = NULL; // will be calculated in RepDistLabelNew I->LabCoord = NULL; // will be calculated in RepDistLabelNew
ok_assert(1, CPythonVal_PConvPyIntToInt_From_List(G, list, 3, &I->NAngleIndex) ); ok_assert(1, CPythonVal_PConvPyIntToInt_From_List(G, list, 3, &I->NAngleIndex) );
ok_assert(1, CPythonVal_PConvPyListToFloatVLANoneOkay_From_List(G, list, 4, &I ->AngleCoord)); ok_assert(1, CPythonVal_PConvPyListToFloatVLANoneOkay_From_List(G, list, 4, &I ->AngleCoord));
ok_assert(1, CPythonVal_PConvPyIntToInt_From_List(G, list, 5, &I->NDihedralInd ex)); ok_assert(1, CPythonVal_PConvPyIntToInt_From_List(G, list, 5, &I->NDihedralInd ex));
ok_assert(1, CPythonVal_PConvPyListToFloatVLANoneOkay_From_List(G, list, 6, &I ->DihedralCoord)); ok_assert(1, CPythonVal_PConvPyListToFloatVLANoneOkay_From_List(G, list, 6, &I ->DihedralCoord));
ok_assert(2, ll > 7); ok_assert(2, ll > 7);
val = CPythonVal_PyList_GetItem(G, list, 7); // DistSet->Setting never gets set (removed BB 11/14), was state settings?
I->Setting = SettingNewFromPyList(G, val); /* state settings */ /* val = CPythonVal_PyList_GetItem(G, list, 7);
CPythonVal_Free(val); I->Setting = SettingNewFromPyList(G, val);
CPythonVal_Free(val); */
ok_assert(2, ll > 8); ok_assert(2, ll > 8);
val = CPythonVal_PyList_GetItem(G, list, 8); val = CPythonVal_PyList_GetItem(G, list, 8);
ok_assert(1, CPythonVal_PConvPyListToLabPosVLA(G, val, &I->LabPos)); ok_assert(1, CPythonVal_PConvPyListToLabPosVLA(G, val, &I->LabPos));
CPythonVal_Free(val); CPythonVal_Free(val);
ok_assert(2, ll > 9); ok_assert(2, ll > 9);
val = CPythonVal_PyList_GetItem(G, list, 9); val = CPythonVal_PyList_GetItem(G, list, 9);
skipping to change at line 284 skipping to change at line 282
ok_except2: ok_except2:
*cs = I; *cs = I;
return true; return true;
ok_except1: ok_except1:
I->fFree(); I->fFree();
return false; return false;
} }
PyObject *DistSetAsPyList(DistSet * I) PyObject *DistSetAsPyList(DistSet * I)
{ {
#ifdef _PYMOL_NOPY
return NULL;
#else
PyObject *result = NULL; PyObject *result = NULL;
if(I) { if(I) {
result = PyList_New(9); result = PyList_New(10);
PyList_SetItem(result, 0, PyInt_FromLong(I->NIndex)); PyList_SetItem(result, 0, PyInt_FromLong(I->NIndex));
PyList_SetItem(result, 1, PConvFloatArrayToPyListNullOkay(I->Coord, I->NInde x * 3)); PyList_SetItem(result, 1, PConvFloatArrayToPyListNullOkay(I->Coord, I->NInde x * 3));
PyList_SetItem(result, 2, PConvAutoNone(NULL)); // I->LabCoord recalculated in RepDistLabelNew PyList_SetItem(result, 2, PConvAutoNone(NULL)); // I->LabCoord recalculated in RepDistLabelNew
PyList_SetItem(result, 3, PyInt_FromLong(I->NAngleIndex)); PyList_SetItem(result, 3, PyInt_FromLong(I->NAngleIndex));
PyList_SetItem(result, 4, PyList_SetItem(result, 4,
PConvFloatArrayToPyListNullOkay(I->AngleCoord, I->NAngleIndex * 3)); PConvFloatArrayToPyListNullOkay(I->AngleCoord, I->NAngleIndex * 3));
PyList_SetItem(result, 5, PyInt_FromLong(I->NDihedralIndex)); PyList_SetItem(result, 5, PyInt_FromLong(I->NDihedralIndex));
PyList_SetItem(result, 6, PyList_SetItem(result, 6,
PConvFloatArrayToPyListNullOkay(I->DihedralCoord, PConvFloatArrayToPyListNullOkay(I->DihedralCoord,
I->NDihedralIndex * 3)); I->NDihedralIndex * 3));
PyList_SetItem(result, 7, SettingAsPyList(I->Setting)); // DistSet->Setting never gets set (removed BB 11/14), was state settings?
PyList_SetItem(result, 7, PConvAutoNone(NULL) /* SettingAsPyList(I->Setting)
*/);
if(I->LabPos) { if(I->LabPos) {
PyList_SetItem(result, 8, PConvLabPosVLAToPyList(I->LabPos, VLAGetSize(I-> LabPos))); PyList_SetItem(result, 8, PConvLabPosVLAToPyList(I->LabPos, VLAGetSize(I-> LabPos)));
} else { } else {
PyList_SetItem(result, 8, PConvAutoNone(NULL)); PyList_SetItem(result, 8, PConvAutoNone(NULL));
} }
PyList_Append(result, MeasureInfoListAsPyList(I->MeasureInfo)); PyList_SetItem(result, 9, MeasureInfoListAsPyList(I->MeasureInfo));
/* TODO setting ... */ /* TODO setting ... */
} }
return (PConvAutoNone(result)); return (PConvAutoNone(result));
#endif
} }
/*========================================================================*/ /*========================================================================*/
int DistSetGetExtent(DistSet * I, float *mn, float *mx) int DistSetGetExtent(DistSet * I, float *mn, float *mx)
{ {
float *v; float *v;
int a; int a;
int c; int c;
v = I->Coord; v = I->Coord;
for(a = 0; a < I->NIndex; a++) { for(a = 0; a < I->NIndex; a++) {
skipping to change at line 436 skipping to change at line 431
} }
/*========================================================================*/ /*========================================================================*/
void DistSet::render(RenderInfo * info) void DistSet::render(RenderInfo * info)
{ {
DistSet * I = this; DistSet * I = this;
CRay *ray = info->ray; CRay *ray = info->ray;
int pass = info->pass; int pass = info->pass;
Picking **pick = info->pick; Picking **pick = info->pick;
int float_labels = SettingGet_i(I->State.G, int float_labels = SettingGet_i(I->State.G,
I->Setting, NULL,
I->Obj->Obj.Setting, I->Obj->Obj.Setting,
cSetting_float_labels); cSetting_float_labels);
int a; int a;
::Rep *r; ::Rep *r;
for(a = 0; a < I->NRep; a++) for(a = 0; a < I->NRep; a++)
{ {
if(!GET_BIT(I->Obj->Obj.visRep, a)) if(!GET_BIT(I->Obj->Obj.visRep, a))
continue; continue;
if(!I->Rep[a]) { if(!I->Rep[a]) {
switch(a) { switch(a) {
skipping to change at line 499 skipping to change at line 494
/*========================================================================*/ /*========================================================================*/
DistSet *DistSetNew(PyMOLGlobals * G) DistSet *DistSetNew(PyMOLGlobals * G)
{ {
int a; int a;
OOAlloc(G, DistSet); OOAlloc(G, DistSet);
ObjectStateInit(G, &I->State); ObjectStateInit(G, &I->State);
I->NIndex = 0; I->NIndex = 0;
I->Coord = NULL; I->Coord = NULL;
I->Rep = VLAlloc(Rep *, cRepCnt); I->Rep = VLAlloc(Rep *, cRepCnt);
I->NRep = cRepCnt; I->NRep = cRepCnt;
I->Setting = NULL;
I->LabPos = NULL; I->LabPos = NULL;
I->LabCoord = NULL; I->LabCoord = NULL;
I->AngleCoord = NULL; I->AngleCoord = NULL;
I->NAngleIndex = 0; I->NAngleIndex = 0;
I->DihedralCoord = NULL; I->DihedralCoord = NULL;
I->NDihedralIndex = 0; I->NDihedralIndex = 0;
I->NLabel = 0; I->NLabel = 0;
for(a = 0; a < I->NRep; a++) for(a = 0; a < I->NRep; a++)
I->Rep[a] = NULL; I->Rep[a] = NULL;
I->MeasureInfo = NULL; I->MeasureInfo = NULL;
skipping to change at line 548 skipping to change at line 542
VLAFreeP(I->Coord); VLAFreeP(I->Coord);
VLAFreeP(I->Rep); VLAFreeP(I->Rep);
ptr = I->MeasureInfo; ptr = I->MeasureInfo;
while((target = ptr)) { while((target = ptr)) {
ptr = target->next; ptr = target->next;
ListElemFree(target); ListElemFree(target);
} }
/* need to find and decrement the number of dist sets on the objects */ /* need to find and decrement the number of dist sets on the objects */
SettingFreeP(I->Setting);
OOFreeP(I); OOFreeP(I);
} }
} }
 End of changes. 17 change blocks. 
24 lines changed or deleted 18 lines changed or added
To the C++ Programs section of the PyMOL source changes report or the top of this page
Mainly generated by pkgdiff using rfcdiff
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