"Fossies" - the Fresh Open Source Software Archive  

Source code changes of the file "layer1/P.cpp" between
pymol-open-source-2.2.0.tar.gz and pymol-open-source-2.3.0.tar.gz

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 ]

P.cpp  (pymol-open-source-2.2.0):P.cpp  (pymol-open-source-2.3.0)
skipping to change at line 442 skipping to change at line 442
} }
auto G = wobj->G; auto G = wobj->G;
if ((setting_id = get_and_check_setting_index(G, key)) == -1) { if ((setting_id = get_and_check_setting_index(G, key)) == -1) {
return NULL; return NULL;
} }
if (wobj->idx >= 0){ if (wobj->idx >= 0){
// atom-state level // atom-state level
// (not supported in Open-Source PyMOL, skip to atom level setting) ret = SettingGetIfDefinedPyObject(G, wobj->cs, wobj->idx, setting_id);
} }
if (!ret){ if (!ret){
// atom level // atom level
ret = SettingGetIfDefinedPyObject(G, wobj->atomInfo, setting_id); ret = SettingGetIfDefinedPyObject(G, wobj->atomInfo, setting_id);
if (!ret) { if (!ret) {
// object-state, object, or global // object-state, object, or global
ret = SettingGetPyObject(G, ret = SettingGetPyObject(G,
wobj->cs ? wobj->cs->Setting : NULL, wobj->cs ? wobj->cs->Setting : NULL,
skipping to change at line 493 skipping to change at line 493
PyErr_SetString(PyExc_TypeError, "Use alter/alter_state to modify settings") ; PyErr_SetString(PyExc_TypeError, "Use alter/alter_state to modify settings") ;
return -1; return -1;
} }
if ((setting_id = get_and_check_setting_index(G, key)) == -1) { if ((setting_id = get_and_check_setting_index(G, key)) == -1) {
return -1; return -1;
} }
if (wobj->idx >= 0) { if (wobj->idx >= 0) {
// atom-state level // atom-state level
PyErr_SetString(PyExc_NotImplementedError, if(!SettingLevelCheck(G, setting_id, cSettingLevel_astate)) {
"atom-state-level settings not supported in Open-Source PyMOL"); PyErr_SetString(PyExc_TypeError,
return -1; // failure "only atom-state level settings can be set in alter_state function");
return -1; // failure
} else if (CoordSetSetSettingFromPyObject(G, wobj->cs, wobj->idx, setting_id
, val)) {
}
} else { } else {
// atom level // atom level
if(!SettingLevelCheck(G, setting_id, cSettingLevel_atom)) { if(!SettingLevelCheck(G, setting_id, cSettingLevel_atom)) {
PyErr_SetString(PyExc_TypeError, PyErr_SetString(PyExc_TypeError,
"only atom-level settings can be set in alter function"); "only atom-level settings can be set in alter function");
return -1; // failure return -1; // failure
} else if (AtomInfoSetSettingFromPyObject(G, wobj->atomInfo, setting_id, val )) { } else if (AtomInfoSetSettingFromPyObject(G, wobj->atomInfo, setting_id, val )) {
AtomInfoSettingGenerateSideEffects(G, wobj->obj, setting_id, wobj->atm); AtomInfoSettingGenerateSideEffects(G, wobj->obj, setting_id, wobj->atm);
} }
} }
skipping to change at line 524 skipping to change at line 527
{ {
auto& wobj = reinterpret_cast<SettingPropertyWrapperObject*>(self)->wobj; auto& wobj = reinterpret_cast<SettingPropertyWrapperObject*>(self)->wobj;
if (!check_wrapper_scope(wobj)) { if (!check_wrapper_scope(wobj)) {
return NULL; return NULL;
} }
int unique_id = wobj->atomInfo->unique_id; int unique_id = wobj->atomInfo->unique_id;
if (wobj->idx >= 0) { if (wobj->idx >= 0) {
PyErr_SetString(PyExc_NotImplementedError, unique_id =
"atom-state-level settings not supported in Open-Source PyMOL"); wobj->cs->atom_state_setting_id ?
return NULL; wobj->cs->atom_state_setting_id[wobj->idx] : 0;
} }
PyObject * items = SettingUniqueGetIndicesAsPyList(wobj->G, unique_id); PyObject * items = SettingUniqueGetIndicesAsPyList(wobj->G, unique_id);
PyObject * iter = PyObject_GetIter(items); PyObject * iter = PyObject_GetIter(items);
Py_XDECREF(items); Py_XDECREF(items);
return iter; return iter;
} }
/* /*
skipping to change at line 980 skipping to change at line 983
static void PUnlockGLUT(PyMOLGlobals * G) static void PUnlockGLUT(PyMOLGlobals * G)
{ /* assumes we have the GIL */ { /* assumes we have the GIL */
PXDecRef(PYOBJECT_CALLFUNCTION(G->P_inst->unlock_glut, "O", G->P_inst->cmd)); PXDecRef(PYOBJECT_CALLFUNCTION(G->P_inst->unlock_glut, "O", G->P_inst->cmd));
} }
static long P_glut_thread_id = -1; static long P_glut_thread_id = -1;
/* enables us to keep glut out if by chance it grabs the API /* enables us to keep glut out if by chance it grabs the API
* in the middle of a nested API based operation */ * in the middle of a nested API based operation */
static
void PCatchInit(void); void PCatchInit(void);
void my_interrupt(int a);
/* /*
PyObject *GetBondsDict(PyMOLGlobals *G) PyObject *GetBondsDict(PyMOLGlobals *G)
{ {
PyObject *result = NULL; PyObject *result = NULL;
result = PyObject_GetAttrString(P_chempy,"bonds"); result = PyObject_GetAttrString(P_chempy,"bonds");
if(!result) ErrMessage(G,"PyMOL","can't find 'chempy.bonds.bonds'"); if(!result) ErrMessage(G,"PyMOL","can't find 'chempy.bonds.bonds'");
return(result); return(result);
} }
*/ */
skipping to change at line 1108 skipping to change at line 1111
obj = Py_None; obj = Py_None;
Py_XINCREF(obj); Py_XINCREF(obj);
return obj; return obj;
} }
void PXDecRef(PyObject * obj) void PXDecRef(PyObject * obj)
{ {
Py_XDECREF(obj); Py_XDECREF(obj);
} }
OV_STATIC ov_status CacheCreateEntry(PyObject ** result, PyObject * input) static ov_status CacheCreateEntry(PyObject ** result, PyObject * input)
{ {
ov_status status = OV_STATUS_FAILURE; ov_status status = OV_STATUS_FAILURE;
if(input && PyTuple_Check(input)) { if(input && PyTuple_Check(input)) {
ov_size tuple_size = PyTuple_Size(input); ov_size tuple_size = PyTuple_Size(input);
ov_size tot_size = tuple_size; ov_size tot_size = tuple_size;
PyObject *hash_code = PyTuple_New(tuple_size); PyObject *hash_code = PyTuple_New(tuple_size);
PyObject *entry = PyList_New(6); PyObject *entry = PyList_New(6);
if(hash_code && entry) { if(hash_code && entry) {
/* compute hash codes & total input size */ /* compute hash codes & total input size */
ov_size i; ov_size i;
skipping to change at line 1280 skipping to change at line 1283
PXDecRef(PYOBJECT_CALLFUNCTION(P_sleep, "f", usec / 1000000.0)); PXDecRef(PYOBJECT_CALLFUNCTION(P_sleep, "f", usec / 1000000.0));
PLockAPIAndUnblock(G); PLockAPIAndUnblock(G);
/* END PROPRIETARY CODE SEGMENT */ /* END PROPRIETARY CODE SEGMENT */
#endif #endif
} }
static PyObject *PCatchWrite(PyObject * self, PyObject * args); static PyObject *PCatchWrite(PyObject * self, PyObject * args);
static PyObject *PCatch_install(PyObject * self, PyObject * args); static PyObject *PCatch_install(PyObject * self, PyObject * args);
static
void my_interrupt(int a) void my_interrupt(int a)
{ {
exit(EXIT_FAILURE); exit(EXIT_FAILURE);
} }
void PDumpTraceback(PyObject * err) void PDumpTraceback(PyObject * err)
{ {
PYOBJECT_CALLMETHOD(P_traceback, "print_tb", "O", err); PYOBJECT_CALLMETHOD(P_traceback, "print_tb", "O", err);
} }
void PDumpException() void PDumpException()
{ {
PYOBJECT_CALLMETHOD(P_traceback, "print_exc", ""); PYOBJECT_CALLMETHOD(P_traceback, "print_exc", "");
} }
static static
WrapperObject * WrapperObjectNew() { WrapperObject * WrapperObjectNew() {
auto wobj = (WrapperObject *)PyType_GenericNew(&Wrapper_Type, Py_None, Py_None ); auto wobj = (WrapperObject *)PyType_GenericNew(&Wrapper_Type, Py_None, Py_None );
wobj->dict = NULL; wobj->dict = NULL;
wobj->settingWrapperObject = NULL; wobj->settingWrapperObject = NULL;
#ifdef _PYMOL_IP_EXTRAS #ifdef _PYMOL_IP_PROPERTIES
wobj->propertyWrapperObject = NULL; wobj->propertyWrapperObject = NULL;
#endif #endif
return wobj; return wobj;
} }
int PAlterAtomState(PyMOLGlobals * G, PyCodeObject *expr_co, int read_only, int PAlterAtomState(PyMOLGlobals * G, PyCodeObject *expr_co, int read_only,
ObjectMolecule *obj, CoordSet *cs, int atm, int idx, ObjectMolecule *obj, CoordSet *cs, int atm, int idx,
int state, PyObject * space) int state, PyObject * space)
/* assumes Blocked python interpreter */ /* assumes Blocked python interpreter */
skipping to change at line 1606 skipping to change at line 1610
void init_pyomm(void); void init_pyomm(void);
#endif #endif
#ifdef __cplusplus #ifdef __cplusplus
} }
#endif #endif
#endif #endif
#endif #endif
/* BEGIN PROPRIETARY CODE SEGMENT (see disclaimer in "os_proprietary.h") */ /* BEGIN PROPRIETARY CODE SEGMENT (see disclaimer in "os_proprietary.h") */
#ifdef WIN32 #if 0 // def WIN32
static int IsSecurityRequired() static int IsSecurityRequired()
{ {
DWORD WindowsVersion = GetVersion(); DWORD WindowsVersion = GetVersion();
DWORD WindowsMajorVersion = (DWORD) (LOBYTE(LOWORD(WindowsVersion))); DWORD WindowsMajorVersion = (DWORD) (LOBYTE(LOWORD(WindowsVersion)));
DWORD WindowsMinorVersion = (DWORD) (HIBYTE(LOWORD(WindowsVersion))); DWORD WindowsMinorVersion = (DWORD) (HIBYTE(LOWORD(WindowsVersion)));
if(WindowsVersion >= 0x80000000) if(WindowsVersion >= 0x80000000)
return FALSE; return FALSE;
return TRUE; return TRUE;
skipping to change at line 1628 skipping to change at line 1632
#endif #endif
/* END PROPRIETARY CODE SEGMENT */ /* END PROPRIETARY CODE SEGMENT */
void PSetupEmbedded(PyMOLGlobals * G, int argc, char **argv) void PSetupEmbedded(PyMOLGlobals * G, int argc, char **argv)
{ {
/* This routine is called if we are running with an embedded Python interprete r */ /* This routine is called if we are running with an embedded Python interprete r */
PyObject *args; PyObject *args;
/* BEGIN PROPRIETARY CODE SEGMENT (see disclaimer in "os_proprietary.h") */ /* BEGIN PROPRIETARY CODE SEGMENT (see disclaimer in "os_proprietary.h") */
#ifdef WIN32 #if 0 // def WIN32
/* Windows PyMOL now ships with Python 2.5 for both /* Windows PyMOL now ships with Python 2.5 for both
32 and 64 bit */ 32 and 64 bit */
#ifndef EMBEDDED_PYTHONHOME #ifndef EMBEDDED_PYTHONHOME
#define EMBEDDED_PYTHONHOME "\\py27" #define EMBEDDED_PYTHONHOME "\\py27"
#endif #endif
{ /* Automatically hide the window if this process was started as a { /* Automatically hide the window if this process was started as a
vanilla console application (by double-clicki ng). vanilla console application (by double-clicki ng).
skipping to change at line 2094 skipping to change at line 2098
void PRunStringInstance(PyMOLGlobals * G, const char *str) void PRunStringInstance(PyMOLGlobals * G, const char *str)
{ /* runs a string in the namespace of the pymol i nstance */ { /* runs a string in the namespace of the pymol i nstance */
PXDecRef(PYOBJECT_CALLFUNCTION(G->P_inst->exec, "Os", G->P_inst->obj, str)); PXDecRef(PYOBJECT_CALLFUNCTION(G->P_inst->exec, "Os", G->P_inst->obj, str));
} }
void WrapperObjectReset(WrapperObject *wo){ void WrapperObjectReset(WrapperObject *wo){
if (wo->settingWrapperObject) { if (wo->settingWrapperObject) {
reinterpret_cast<SettingPropertyWrapperObject *>(wo->settingWrapperObject)-> wobj = NULL; reinterpret_cast<SettingPropertyWrapperObject *>(wo->settingWrapperObject)-> wobj = NULL;
Py_DECREF(wo->settingWrapperObject); Py_DECREF(wo->settingWrapperObject);
} }
#ifdef _PYMOL_IP_EXTRAS #ifdef _PYMOL_IP_PROPERTIES
if (wo->propertyWrapperObject) { if (wo->propertyWrapperObject) {
reinterpret_cast<SettingPropertyWrapperObject *>(wo->propertyWrapperObject)- >wobj = NULL; reinterpret_cast<SettingPropertyWrapperObject *>(wo->propertyWrapperObject)- >wobj = NULL;
Py_DECREF(wo->propertyWrapperObject); Py_DECREF(wo->propertyWrapperObject);
} }
#endif #endif
Py_XDECREF(wo->dict); Py_XDECREF(wo->dict);
Py_DECREF(wo); Py_DECREF(wo);
} }
void PInit(PyMOLGlobals * G, int global_instance) void PInit(PyMOLGlobals * G, int global_instance)
skipping to change at line 2325 skipping to change at line 2329
PBlock(G); PBlock(G);
result = result =
PYOBJECT_CALLMETHOD(P_povray, "render_from_string", "sssiii", header, inp, f ile, PYOBJECT_CALLMETHOD(P_povray, "render_from_string", "sssiii", header, inp, f ile,
width, height, antialias); width, height, antialias);
ok = PyObject_IsTrue(result); ok = PyObject_IsTrue(result);
Py_DECREF(result); Py_DECREF(result);
PUnblock(G); PUnblock(G);
return (ok); return (ok);
} }
void PSGIStereo(PyMOLGlobals * G, int flag)
{
int blocked;
blocked = PAutoBlock(G);
if(flag)
PRunStringModule(G, "cmd._sgi_stereo(1)");
else
PRunStringModule(G, "cmd._sgi_stereo(0)");
if(blocked)
PUnblock(G);
}
void PFree(PyMOLGlobals * G) void PFree(PyMOLGlobals * G)
{ {
PXDecRef(G->P_inst->parse); PXDecRef(G->P_inst->parse);
PXDecRef(G->P_inst->complete); PXDecRef(G->P_inst->complete);
PXDecRef(G->P_inst->colortype); PXDecRef(G->P_inst->colortype);
} }
void PExit(PyMOLGlobals * G, int code) void PExit(PyMOLGlobals * G, int code)
{ {
ExecutiveDelete(G, "all"); ExecutiveDelete(G, "all");
skipping to change at line 2490 skipping to change at line 2482
int PFlush(PyMOLGlobals * G) int PFlush(PyMOLGlobals * G)
{ {
/* NOTE: ASSUMES unblocked Python threads and a locked API */ /* NOTE: ASSUMES unblocked Python threads and a locked API */
PyObject *err; PyObject *err;
int did_work = false; int did_work = false;
if(OrthoCommandWaiting(G)) { if(OrthoCommandWaiting(G)) {
did_work = true; did_work = true;
PBlock(G); PBlock(G);
if(!(PIsGlutThread() && G->P_inst->glut_thread_keep_out)) { if(!(PIsGlutThread() && G->P_inst->glut_thread_keep_out)) {
/* don't run if we're currently banned */ /* don't run if we're currently banned */
char *buffer = 0; auto ortho = G->Ortho;
int size; while(!OrthoCommandIsEmpty(*ortho)){
while((size = OrthoCommandOutSize(G))){ auto buffer = OrthoCommandOut(*ortho);
if (!buffer){ OrthoCommandSetBusy(G, true);
buffer = VLACalloc(char, size);
} else {
VLACheck(buffer, char, size);
}
OrthoCommandSetBusy(G, true);
OrthoCommandOut(G, buffer);
OrthoCommandNest(G, 1); OrthoCommandNest(G, 1);
PUnlockAPIWhileBlocked(G); PUnlockAPIWhileBlocked(G);
if(PyErr_Occurred()) { if(PyErr_Occurred()) {
PyErr_Print(); PyErr_Print();
PRINTFB(G, FB_Python, FB_Errors) PRINTFB(G, FB_Python, FB_Errors)
" PFlush: Uncaught exception. PyMOL may have a bug.\n" ENDFB(G); " PFlush: Uncaught exception. PyMOL may have a bug.\n" ENDFB(G);
} }
PXDecRef(PYOBJECT_CALLFUNCTION(G->P_inst->parse, "si", buffer, 0)); PXDecRef(PYOBJECT_CALLFUNCTION(G->P_inst->parse, "si", buffer.c_str(), 0 ));
err = PyErr_Occurred(); err = PyErr_Occurred();
if(err) { if(err) {
PyErr_Print(); PyErr_Print();
PRINTFB(G, FB_Python, FB_Errors) PRINTFB(G, FB_Python, FB_Errors)
" PFlush: Uncaught exception. PyMOL may have a bug.\n" ENDFB(G); " PFlush: Uncaught exception. PyMOL may have a bug.\n" ENDFB(G);
} }
PLockAPIWhileBlocked(G); PLockAPIWhileBlocked(G);
OrthoCommandSetBusy(G, false); OrthoCommandSetBusy(G, false);
/* make sure no commands left at this level */ /* make sure no commands left at this level */
while(OrthoCommandWaiting(G)) while(OrthoCommandWaiting(G))
PFlushFast(G); PFlushFast(G);
OrthoCommandNest(G, -1); OrthoCommandNest(G, -1);
} }
if (buffer)
VLAFreeP(buffer);
} }
PUnblock(G); PUnblock(G);
} }
return did_work; return did_work;
} }
int PFlushFast(PyMOLGlobals * G) int PFlushFast(PyMOLGlobals * G)
{ {
/* NOTE: ASSUMES we currently have blocked Python threads and an unlocked API */ /* NOTE: ASSUMES we currently have blocked Python threads and an unlocked API */
PyObject *err; PyObject *err;
int did_work = false; int did_work = false;
char *buffer = 0; auto ortho = G->Ortho;
int size; while(!OrthoCommandIsEmpty(*ortho)){
while((size = OrthoCommandOutSize(G))){ auto buffer = OrthoCommandOut(*ortho);
if (!buffer){
buffer = VLACalloc(char, size);
} else {
VLACheck(buffer, char, size);
}
OrthoCommandSetBusy(G, true); OrthoCommandSetBusy(G, true);
OrthoCommandOut(G, buffer);
OrthoCommandNest(G, 1); OrthoCommandNest(G, 1);
did_work = true; did_work = true;
PRINTFD(G, FB_Threads) PRINTFD(G, FB_Threads)
" PFlushFast-DEBUG: executing '%s' as thread %ld\n", buffer, " PFlushFast-DEBUG: executing '%s' as thread %ld\n", buffer.c_str(),
PyThread_get_thread_ident() PyThread_get_thread_ident()
ENDFD; ENDFD;
if(PyErr_Occurred()) { if(PyErr_Occurred()) {
PyErr_Print(); PyErr_Print();
PRINTFB(G, FB_Python, FB_Errors) PRINTFB(G, FB_Python, FB_Errors)
" PFlushFast: Uncaught exception. PyMOL may have a bug.\n" ENDFB(G); " PFlushFast: Uncaught exception. PyMOL may have a bug.\n" ENDFB(G);
} }
PXDecRef(PYOBJECT_CALLFUNCTION(G->P_inst->parse, "si", buffer, 0)); PXDecRef(PYOBJECT_CALLFUNCTION(G->P_inst->parse, "si", buffer.c_str(), 0));
err = PyErr_Occurred(); err = PyErr_Occurred();
if(err) { if(err) {
PyErr_Print(); PyErr_Print();
PRINTFB(G, FB_Python, FB_Errors) PRINTFB(G, FB_Python, FB_Errors)
" PFlushFast: Uncaught exception. PyMOL may have a bug.\n" ENDFB(G); " PFlushFast: Uncaught exception. PyMOL may have a bug.\n" ENDFB(G);
} }
OrthoCommandSetBusy(G, false); OrthoCommandSetBusy(G, false);
/* make sure no commands left at this level */ /* make sure no commands left at this level */
while(OrthoCommandWaiting(G)) while(OrthoCommandWaiting(G))
PFlushFast(G); PFlushFast(G);
OrthoCommandNest(G, -1); OrthoCommandNest(G, -1);
} }
if (buffer)
VLAFreeP(buffer);
return did_work; return did_work;
} }
void PBlockLegacy() void PBlockLegacy()
{ {
PBlock(SingletonPyMOLGlobals); PBlock(SingletonPyMOLGlobals);
} }
void PUnblockLegacy() void PUnblockLegacy()
{ {
 End of changes. 21 change blocks. 
53 lines changed or deleted 29 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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