"Fossies" - the Fresh Open Source Software Archive  

Source code changes of the file "layer2/ObjectAlignment.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.

ObjectAlignment.cpp  (pymol-v1.8.6.0.tar.bz2)	:	ObjectAlignment.cpp  (pymol-v2.1.0.tar.bz2)
skipping to change at line 789		skipping to change at line 789
return (ok);		return (ok);
}		}
int ObjectAlignmentNewFromPyList(PyMOLGlobals * G, PyObject * list,		int ObjectAlignmentNewFromPyList(PyMOLGlobals * G, PyObject * list,
ObjectAlignment ** result, int version)		ObjectAlignment ** result, int version)
{		{
int ok = true;		int ok = true;
ObjectAlignment *I = NULL;		ObjectAlignment *I = NULL;
(*result) = NULL;		(*result) = NULL;
if(ok)		if(ok)
ok = (list != Py_None);		ok = (list != NULL);
if(ok)		if(ok)
ok = PyList_Check(list);		ok = PyList_Check(list);
I = ObjectAlignmentNew(G);		I = ObjectAlignmentNew(G);
if(ok)		if(ok)
ok = (I != NULL);		ok = (I != NULL);
if(ok)		if(ok)
ok = ObjectFromPyList(G, PyList_GetItem(list, 0), &I->Obj);		ok = ObjectFromPyList(G, PyList_GetItem(list, 0), &I->Obj);
if(ok)		if(ok)
skipping to change at line 915		skipping to change at line 915
if(oas->alignVLA) {		if(oas->alignVLA) {
int id, b = 0, c;		int id, b = 0, c;
int *vla = oas->alignVLA;		int *vla = oas->alignVLA;
int n_id = VLAGetSize(vla);		int n_id = VLAGetSize(vla);
float mean[3], vert[3], gvert[3];		float mean[3], vert[3], gvert[3];
int n_coord = 0;		int n_coord = 0;
int tag = SELECTOR_BASE_TAG + 1;		int tag = SELECTOR_BASE_TAG + 1;
OVOneToAny *id2tag = oas->id2tag;		OVOneToAny *id2tag = oas->id2tag;
		CGOBegin(cgo, GL_LINES);
while(b < n_id) {		while(b < n_id) {
int gvert_valid;		int gvert_valid;
while((b < n_id) && (!vla[b]))		while((b < n_id) && (!vla[b]))
b++;		b++;
if(!(b < n_id))		if(!(b < n_id))
break;		break;
c = b;		c = b;
skipping to change at line 949		skipping to change at line 951
}		}
}		}
}		}
if(n_coord > 2) { /* >2 points, then draw to mean or guide vertex */		if(n_coord > 2) { /* >2 points, then draw to mean or guide vertex */
float scale = 1.0F / n_coord;		float scale = 1.0F / n_coord;
scale3f(mean, scale, mean);		scale3f(mean, scale, mean);
c = b;		c = b;
CGOBegin(cgo, GL_LINES);
while((id = vla[c++])) {		while((id = vla[c++])) {
auto eoo = ExecutiveUniqueIDAtomDictGet(G, id);		auto eoo = ExecutiveUniqueIDAtomDictGet(G, id);
if (eoo) {		if (eoo) {
if(ObjectMoleculeGetAtomVertex(eoo->obj, a,		if(ObjectMoleculeGetAtomVertex(eoo->obj, a,
eoo->atm, vert)) {		eoo->atm, vert)) {
if(gvert_valid) {		if(gvert_valid) {
if(eoo->obj != guide_obj) {		if(eoo->obj != guide_obj) {
CGOVertexv(cgo, gvert);		CGOVertexv(cgo, gvert);
CGOVertexv(cgo, vert);		CGOVertexv(cgo, vert);
}		}
} else {		} else {
CGOVertexv(cgo, mean);		CGOVertexv(cgo, mean);
CGOVertexv(cgo, vert);		CGOVertexv(cgo, vert);
}		}
}		}
}		}
}		}
CGOEnd(cgo);
} else if(n_coord) { /* if 2 points, then simply draw a line */		} else if(n_coord) { /* if 2 points, then simply draw a line */
float first[3];		float first[3];
int first_flag = true;		int first_flag = true;
c = b;		c = b;
CGOBegin(cgo, GL_LINES);
while((id = vla[c++])) {		while((id = vla[c++])) {
auto eoo = ExecutiveUniqueIDAtomDictGet(G, id);		auto eoo = ExecutiveUniqueIDAtomDictGet(G, id);
if (eoo) {		if (eoo) {
if(ObjectMoleculeGetAtomVertex(eoo->obj, a,		if(ObjectMoleculeGetAtomVertex(eoo->obj, a,
eoo->atm, vert)) {		eoo->atm, vert)) {
if(first_flag) {		if(first_flag) {
copy3f(vert, first);		copy3f(vert, first);
first_flag = false;		first_flag = false;
} else {		} else {
CGOVertexv(cgo, first);		CGOVertexv(cgo, first);
CGOVertexv(cgo, vert);		CGOVertexv(cgo, vert);
}		}
}		}
}		}
}		}
CGOEnd(cgo);
}		}
/* update the it2tag dictionary */		/* update the it2tag dictionary */
tag++;		tag++;
while((b < n_id) && vla[b]) {		while((b < n_id) && vla[b]) {
OVOneToAny_SetKey(id2tag, vla[b], tag);		OVOneToAny_SetKey(id2tag, vla[b], tag);
b++;		b++;
}		}
}		}
		CGOEnd(cgo);
}		}
CGOStop(cgo);		CGOStop(cgo);
/* simplify if necessary */		/* simplify if necessary */
{		{
int est = CGOCheckComplex(cgo);		int est = CGOCheckComplex(cgo);
{		{
CGO *convertcgo = NULL;		CGO *convertcgo = NULL;
skipping to change at line 1042		skipping to change at line 1041
if(I->SelectionState < 0) {		if(I->SelectionState < 0) {
int state = -1;		int state = -1;
if(I->ForceState >= 0) {		if(I->ForceState >= 0) {
state = I->ForceState;		state = I->ForceState;
I->ForceState = 0;		I->ForceState = 0;
}		}
if(state < 0)		if(state < 0)
state = SettingGet_i(I->Obj.G, NULL, I->Obj.Setting, cSetting_state) - 1;		state = SettingGet_i(I->Obj.G, NULL, I->Obj.Setting, cSetting_state) - 1;
if(state < 0)		if(state < 0)
state = SceneGetState(G);		state = SceneGetState(G);
if(state > I->NState)		if(state >= I->NState)
state = I->NState - 1;		state = I->NState - 1;
if(state < 0)		if(state < 0)
state = 0;		state = 0;
if(state < I->NState) {		if(state < I->NState) {
ObjectAlignmentState *oas = I->State + state;		ObjectAlignmentState *oas = I->State + state;
if(oas->id2tag) {		if(oas->id2tag) {
SelectorDelete(G, I->Obj.Name);		SelectorDelete(G, I->Obj.Name);
SelectorCreateFromTagDict(G, I->Obj.Name, oas->id2tag, false);		SelectorCreateFromTagDict(G, I->Obj.Name, oas->id2tag, false);
I->SelectionState = state;		I->SelectionState = state;
}		}
End of changes. 8 change blocks.
6 lines changed or deleted		5 lines changed or added

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