"Fossies" - the Fresh Open Source Software Archive  

Source code changes of the file "layer3/Executive.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 ]

Executive.cpp  (pymol-v1.8.6.0.tar.bz2):Executive.cpp  (pymol-v2.1.0.tar.bz2)
skipping to change at line 24 skipping to change at line 24
Z* ------------------------------------------------------------------- Z* -------------------------------------------------------------------
*/ */
#include"os_python.h" #include"os_python.h"
#include"os_predef.h" #include"os_predef.h"
#include"os_std.h" #include"os_std.h"
#include"os_gl.h" #include"os_gl.h"
#include <set> #include <set>
#include <algorithm> #include <algorithm>
#include <map> #include <map>
#include <clocale>
#include"Version.h" #include"Version.h"
#include"main.h" #include"main.h"
#include"Base.h" #include"Base.h"
#include"OOMac.h" #include"OOMac.h"
#include"Executive.h" #include"Executive.h"
#include"SpecRec.h"
#include"ObjectMesh.h" #include"ObjectMesh.h"
#include"ObjectDist.h" #include"ObjectDist.h"
#include"ObjectSurface.h" #include"ObjectSurface.h"
#include"ObjectSlice.h" #include"ObjectSlice.h"
#include"ObjectAlignment.h" #include"ObjectAlignment.h"
#include"ObjectGroup.h" #include"ObjectGroup.h"
#include"ObjectVolume.h" #include"ObjectVolume.h"
#include"ObjectCallback.h" #include"ObjectCallback.h"
#include"ObjectMap.h" #include"ObjectMap.h"
#include"ListMacros.h" #include"ListMacros.h"
skipping to change at line 102 skipping to change at line 104
#endif #endif
#define cExecObject 0 #define cExecObject 0
#define cExecSelection 1 #define cExecSelection 1
#define cExecAll 2 #define cExecAll 2
#define cTempRectSele "_rect" #define cTempRectSele "_rect"
#define cLeftButSele "lb" #define cLeftButSele "lb"
#define cIndicateSele "indicate" #define cIndicateSele "indicate"
/*
* Specification record (a row in the object menu panel)
*/
class SpecRec {
public:
/* NOTE: must zero-init with CALLOC */
int type;
WordType name; /*only used for selections */
CObject *obj;
SpecRec *next;
int visible; /* This is actually when object is "Enabled", not visi
ble */
ObjectNameType group_name;
/* not pickled */
int sele_color;
int hilight; /* 0 = none, 1 = name, 2 = group control (if any
) */
int previous;
int cand_id;
SpecRec *group;
int group_member_list_id;
int in_scene, is_hidden;
int in_panel;
int grid_slot;
CGO *gridSlotSelIndicatorsCGO;
};
typedef struct PanelRec { typedef struct PanelRec {
SpecRec *spec; SpecRec *spec;
int nest_level; int nest_level;
int is_group; int is_group;
int is_open; int is_open;
struct PanelRec *next; struct PanelRec *next;
} PanelRec; } PanelRec;
typedef struct { typedef struct {
int list_id; int list_id;
skipping to change at line 199 skipping to change at line 174
ExecutiveSculptDeactivate ExecutiveSculptDeactivate
ExecutiveRenameObjectAtoms ExecutiveRenameObjectAtoms
ExecutiveSpheroid ExecutiveSpheroid
*/ */
static int ExecutiveGetNamesListFromPattern(PyMOLGlobals * G, const char *name, static int ExecutiveGetNamesListFromPattern(PyMOLGlobals * G, const char *name,
int allow_partial, int expand_groups ); int allow_partial, int expand_groups );
static void ExecutiveSpecEnable(PyMOLGlobals * G, SpecRec * rec, int parents, in t log); static void ExecutiveSpecEnable(PyMOLGlobals * G, SpecRec * rec, int parents, in t log);
static void ExecutiveSetAllRepVisib(PyMOLGlobals * G, int rep, int state); static void ExecutiveSetAllRepVisMask(PyMOLGlobals * G, int repmask, int state);
static SpecRec *ExecutiveFindSpec(PyMOLGlobals * G, const char *name); static SpecRec *ExecutiveFindSpec(PyMOLGlobals * G, const char *name);
static int ExecutiveDrag(Block * block, int x, int y, int mod); static int ExecutiveDrag(Block * block, int x, int y, int mod);
static void ExecutiveSpecSetVisibility(PyMOLGlobals * G, SpecRec * rec, static void ExecutiveSpecSetVisibility(PyMOLGlobals * G, SpecRec * rec,
int new_vis, int mod, int parents); int new_vis, int mod, int parents);
static int ExecutiveSetObjectMatrix2(PyMOLGlobals * G, CObject * obj, int state, static int ExecutiveSetObjectMatrix2(PyMOLGlobals * G, CObject * obj, int state,
double *matrix); double *matrix);
static int ExecutiveGetObjectMatrix2(PyMOLGlobals * G, CObject * obj, int state, static int ExecutiveGetObjectMatrix2(PyMOLGlobals * G, CObject * obj, int state,
double **matrix, int incl_ttt); double **matrix, int incl_ttt);
int ExecutiveTransformObjectSelection2(PyMOLGlobals * G, CObject * obj, int stat e, int ExecutiveTransformObjectSelection2(PyMOLGlobals * G, CObject * obj, int stat e,
const char *s1, int log, float *matrix, i nt homogenous, const char *s1, int log, float *matrix, i nt homogenous,
skipping to change at line 237 skipping to change at line 212
if (rec->type != cExecObject) if (rec->type != cExecObject)
return next(); return next();
return true; return true;
} }
CObject * ObjectIterator::getObject() { CObject * ObjectIterator::getObject() {
return rec->obj; return rec->obj;
} }
/*
* True if `rec` and all its parent groups are enabled
*/
static bool SpecRecIsEnabled(const SpecRec * rec) {
while (rec->visible && (rec = rec->group)) {}
return !rec;
}
/* ======================================================= */ /* ======================================================= */
static void ReportEnabledChange(PyMOLGlobals * G, SpecRec *rec){ static void ReportEnabledChange(PyMOLGlobals * G, SpecRec *rec){
#ifdef _PYMOL_LIB #ifdef _PYMOL_LIB
if (G->CallbackObject && G->enabledCallback){ if (G->CallbackObject && G->enabledCallback){
G->enabledCallback(G->CallbackObject, rec->name, rec->visible); G->enabledCallback(G->CallbackObject, rec->name, rec->visible);
} }
#endif #endif
OrthoInvalidateDoDraw(G); OrthoInvalidateDoDraw(G);
ExecutiveInvalidateSelectionIndicatorsCGO(G); ExecutiveInvalidateSelectionIndicatorsCGO(G);
skipping to change at line 2012 skipping to change at line 1995
CWordMatchOptions options; CWordMatchOptions options;
CTracker *I_Tracker = I->Tracker; CTracker *I_Tracker = I->Tracker;
const char *wildcard = SettingGetGlobal_s(G, cSetting_wildcard); const char *wildcard = SettingGetGlobal_s(G, cSetting_wildcard);
int iter_id = TrackerNewIter(I_Tracker, 0, I->all_names_list_id); int iter_id = TrackerNewIter(I_Tracker, 0, I->all_names_list_id);
int cand_id; int cand_id;
int group_found = false; int group_found = false;
SpecRec *rec; SpecRec *rec;
if (!name) if (!name)
return -1; return -1;
// sanity check: name patterns are not object selections, bail if
// parenthesis or operators in pattern
if (strchr(name, '(') || strchr(name, ')') || strchr(name, '|')) {
PRINTFB(G, FB_Executive, FB_Errors)
" Names-Pattern-Error: Pattern looks like an atom selection"
" (has parenthesis or operators), this is not supported for"
" object name patterns.\n" ENDFB(G);
return -1;
}
// special case: allow "not ..."
bool match_not = false;
if (WordMatchNoWild(G, "not ", name, false)) {
match_not = true;
name += 4;
} else if (name[0] == '!') {
match_not = true;
name += 1;
}
// skip whitespace
while (name[0] == ' ') {
++name;
}
bool match_enabled = WordMatchExact(G, "enabled", name, false);
// ignore % and ? prefixes // ignore % and ? prefixes
while(name[0] && (name[0] == '%' || name[0] == '?')) while(name[0] && (name[0] == '%' || name[0] == '?'))
name++; name++;
WordMatchOptionsConfigNameList(&options, WordMatchOptionsConfigNameList(&options,
*wildcard, SettingGetGlobal_b(G, cSetting_ignor e_case)); *wildcard, SettingGetGlobal_b(G, cSetting_ignor e_case));
matcher = WordMatcherNew(G, name, &options, false); matcher = WordMatcherNew(G, name, &options, /* force= */ match_not);
if(matcher) { if(matcher || match_enabled) {
if(iter_id) { if(iter_id) {
while((cand_id = TrackerIterNextCandInList(I_Tracker, iter_id, while((cand_id = TrackerIterNextCandInList(I_Tracker, iter_id,
(TrackerRef **) (void *) &rec)) ) { (TrackerRef **) (void *) &rec)) ) {
if(rec && !(rec->type == cExecAll)) { if(rec && !(rec->type == cExecAll)) {
if(WordMatcherMatchAlpha(matcher, rec->name)) { bool test = match_enabled ? SpecRecIsEnabled(rec) :
WordMatcherMatchAlpha(matcher, rec->name);
if(test ^ match_not) {
if((rec->type == cExecObject) && (rec->obj->type == cObjectGroup)) if((rec->type == cExecObject) && (rec->obj->type == cObjectGroup))
group_found = true; group_found = true;
if(!result) if(!result)
result = TrackerNewList(I_Tracker, NULL); result = TrackerNewList(I_Tracker, NULL);
if(result) { if(result) {
TrackerLink(I_Tracker, cand_id, result, 1); TrackerLink(I_Tracker, cand_id, result, 1);
} }
} }
} }
} }
skipping to change at line 3156 skipping to change at line 3169
op.obj1VLA = (ObjectMolecule **) VLAlloc(ObjectMolecule *, 10); op.obj1VLA = (ObjectMolecule **) VLAlloc(ObjectMolecule *, 10);
op.i1 = 0; op.i1 = 0;
ExecutiveObjMolSeleOp(G, s1, &op); ExecutiveObjMolSeleOp(G, s1, &op);
result = (ObjectMolecule **) op.obj1VLA; result = (ObjectMolecule **) op.obj1VLA;
VLASize(result, ObjectMolecule *, op.i1); VLASize(result, ObjectMolecule *, op.i1);
} }
return result; return result;
} }
/* #define ExecLineHeight 18 */ /* #define ExecLineHeight 18 */
#define ExecClickMargin 2 #define ExecClickMargin DIP2PIXEL(2)
#define ExecTopMargin 0 #define ExecTopMargin 0
#define ExecToggleMargin 2 #define ExecToggleMargin DIP2PIXEL(2)
#define ExecLeftMargin 1 #define ExecLeftMargin DIP2PIXEL(1)
#define ExecRightMargin 0 #define ExecRightMargin 0
#define ExecToggleWidth 17 #define ExecToggleWidth DIP2PIXEL(17)
#define ExecToggleSize 16 #define ExecToggleSize DIP2PIXEL(16)
#define ExecToggleTextShift 4 #define ExecToggleTextShift DIP2PIXEL(4)
typedef struct { typedef struct {
M4XAnnoType m4x; M4XAnnoType m4x;
ObjectMolecule *obj; ObjectMolecule *obj;
} ProcPDBRec; } ProcPDBRec;
int ExecutiveSetDrag(PyMOLGlobals * G, const char *name, int quiet,int mode) int ExecutiveSetDrag(PyMOLGlobals * G, const char *name, int quiet,int mode)
{ {
char drag_name[] = cEditorDrag; char drag_name[] = cEditorDrag;
int set_flag = false; int set_flag = false;
skipping to change at line 3560 skipping to change at line 3573
* atom_props: names of atom properties to load * atom_props: names of atom properties to load
*/ */
int ExecutiveLoad(PyMOLGlobals * G, int ExecutiveLoad(PyMOLGlobals * G,
const char *content, int content_length, const char *content, int content_length,
int content_format, int content_format,
const char *object_name_proposed, const char *object_name_proposed,
int state, int zoom, int state, int zoom,
int discrete, int finish, int multiplex, int quiet, int discrete, int finish, int multiplex, int quiet,
const char * plugin_arg, const char * plugin_arg,
const char * object_props, const char * object_props,
const char * atom_props) const char * atom_props,
bool mimic)
{ {
int ok = true; int ok = true;
const char * fname = content; const char * fname = content;
char * buffer = NULL; char * buffer = NULL;
long size = (long) content_length; long size = (long) content_length;
OrthoLineType buf = ""; OrthoLineType buf = "";
char plugin[16] = ""; char plugin[16] = "";
CObject *obj = NULL; CObject *obj = NULL;
CObject *origObj = NULL; CObject *origObj = NULL;
int pdb_variant = PDB_VARIANT_DEFAULT; int pdb_variant = PDB_VARIANT_DEFAULT;
// validate proposed object name // validate proposed object name
ObjectNameType object_name = ""; ObjectNameType object_name = "";
ExecutiveProcessObjectName(G, object_name_proposed, object_name); ExecutiveProcessObjectName(G, object_name_proposed, object_name);
// Ensure correct float parsing with scanf. It's possible to change this from
// Python, so don't rely on a persistent global value.
std::setlocale(LC_NUMERIC, "C");
if (!object_props) object_props = SettingGetGlobal_s(G, cSetting_load_object_p
rops_default);
if (!atom_props) atom_props = SettingGetGlobal_s(G, cSetting_load_atom_pro
ps_default);
// multiplex -2 -> "multiplex" setting // multiplex -2 -> "multiplex" setting
// multiplex -1 -> file type dependant default // multiplex -1 -> file type dependant default
// multiplex 1 -> split entries (don't try to load into existing object) // multiplex 1 -> split entries (don't try to load into existing object)
if(multiplex == -2) { if(multiplex == -2) {
multiplex = SettingGetGlobal_i(G, cSetting_multiplex); multiplex = SettingGetGlobal_i(G, cSetting_multiplex);
} }
switch (content_format) { switch (content_format) {
// string loading functions // string loading functions
case cLoadTypePDBStr: case cLoadTypePDBStr:
skipping to change at line 3673 skipping to change at line 3694
} }
if (plugin[0]) { if (plugin[0]) {
content_format = cLoadTypePlugin; content_format = cLoadTypePlugin;
} }
if (multiplex != 1) { if (multiplex != 1) {
origObj = ExecutiveGetExistingCompatible(G, object_name, content_format); origObj = ExecutiveGetExistingCompatible(G, object_name, content_format);
} }
#ifndef PYMOL_EDU #ifndef _PYMOL_NO_UNDO
#endif #endif
// file type dependent multiplex and discrete default // file type dependent multiplex and discrete default
if(discrete < 0) { if(discrete < 0) {
if(multiplex == 1) { if(multiplex == 1) {
discrete = 0; discrete = 0;
} else { } else {
switch (content_format) { switch (content_format) {
case cLoadTypeMOL2: case cLoadTypeMOL2:
case cLoadTypeMOL2Str: case cLoadTypeMOL2Str:
skipping to change at line 3885 skipping to change at line 3906
sprintf(buf, " CmdLoad: loaded as \"%s\".\n", obj->Name); sprintf(buf, " CmdLoad: loaded as \"%s\".\n", obj->Name);
} }
mfree(buffer); mfree(buffer);
if(!quiet && buf[0]) { if(!quiet && buf[0]) {
PRINTFB(G, FB_Executive, FB_Actions) PRINTFB(G, FB_Executive, FB_Actions)
"%s", buf ENDFB(G); "%s", buf ENDFB(G);
} }
#ifndef PYMOL_EDU #ifndef _PYMOL_NO_UNDO
#endif #endif
return (ok); return (ok);
} }
/* ExecutiveGetExistingCompatible /* ExecutiveGetExistingCompatible
* *
* PARAMS * PARAMS
* oname -- object name * oname -- object name
skipping to change at line 4848 skipping to change at line 4869
op.i3 = 0; op.i3 = 0;
op.i4 = byres; op.i4 = byres;
op.ii1 = color_index; op.ii1 = color_index;
op.ff1 = value; op.ff1 = value;
op.f1 = min; op.f1 = min;
op.f2 = range; op.f2 = range;
ExecutiveObjMolSeleOp(G, sele1, &op); ExecutiveObjMolSeleOp(G, sele1, &op);
op.code = OMOP_INVA; op.code = OMOP_INVA;
op.i1 = cRepAll; op.i1 = cRepBitmask;
op.i2 = cRepInvColor; op.i2 = cRepInvColor;
ExecutiveObjMolSeleOp(G, sele1, &op); ExecutiveObjMolSeleOp(G, sele1, &op);
} }
} }
ok_except1: ok_except1:
FreeP(color_index); FreeP(color_index);
FreeP(value); FreeP(value);
} }
skipping to change at line 5459 skipping to change at line 5480
Py_XDECREF(tmp); Py_XDECREF(tmp);
tmp = MovieAsPyList(G); tmp = MovieAsPyList(G);
PyDict_SetItemString(dict, "movie", tmp); PyDict_SetItemString(dict, "movie", tmp);
Py_XDECREF(tmp); Py_XDECREF(tmp);
tmp = EditorAsPyList(G); tmp = EditorAsPyList(G);
PyDict_SetItemString(dict, "editor", tmp); PyDict_SetItemString(dict, "editor", tmp);
Py_XDECREF(tmp); Py_XDECREF(tmp);
#ifndef _PYMOL_NO_MAIN
tmp = MainAsPyList(); tmp = MainAsPyList();
PyDict_SetItemString(dict, "main", tmp); PyDict_SetItemString(dict, "main", tmp);
Py_XDECREF(tmp); Py_XDECREF(tmp);
#endif
#ifdef PYMOL_EVAL #ifdef PYMOL_EVAL
ExecutiveEvalMessage(G, dict); ExecutiveEvalMessage(G, dict);
#endif #endif
} }
if(Feedback(G, FB_Executive, FB_Errors)) { if(Feedback(G, FB_Executive, FB_Errors)) {
if(PyErr_Occurred()) { if(PyErr_Occurred()) {
PRINTF PRINTF
skipping to change at line 5607 skipping to change at line 5626
} }
if(ok) { if(ok) {
tmp = PyDict_GetItemString(session, "version"); tmp = PyDict_GetItemString(session, "version");
if(tmp) { if(tmp) {
ok = PConvPyIntToInt(tmp, &version); ok = PConvPyIntToInt(tmp, &version);
if(ok) { if(ok) {
version_full = version; version_full = version;
while (version_full < 210) /* any version less than 2.1 (account for nex t major version 2) should be 4 digits, otherwise 3 */ while (version_full < 210) /* any version less than 2.1 (account for nex t major version 2) should be 4 digits, otherwise 3 */
version_full *= 10; version_full *= 10;
float version_float = version_full / (version >= 1000000 ? 1000000.f : 1 000.f);
if(version > _PyMOL_VERSION_int) { if(version > _PyMOL_VERSION_int) {
if(!quiet) { if(!quiet) {
PRINTFB(G, FB_Executive, FB_Errors) PRINTFB(G, FB_Executive, FB_Errors)
"Warning: This session was created with a newer version of PyMOL ( "Warning: This session was created with a newer version of PyMOL (
%1.3f).\n", %1.6f).\n",
version_full / 1000. ENDFB(G); version_float ENDFB(G);
if(SettingGetGlobal_i(G, cSetting_session_version_check)) { if(SettingGetGlobal_i(G, cSetting_session_version_check)) {
PRINTFB(G, FB_Executive, FB_Errors) PRINTFB(G, FB_Executive, FB_Errors)
"Error: Please update first -- see http://www.pymol.org\n" ENDFB (G); "Error: Please update first -- see http://www.pymol.org\n" ENDFB (G);
ok = false; ok = false;
} else { } else {
PRINTFB(G, FB_Executive, FB_Errors) PRINTFB(G, FB_Executive, FB_Errors)
"Warning: Some content may not load completely.\n" ENDFB(G); "Warning: Some content may not load completely.\n" ENDFB(G);
} }
} }
} else { } else {
if(!quiet) { if(!quiet) {
PRINTFB(G, FB_Executive, FB_Details) PRINTFB(G, FB_Executive, FB_Details)
" Executive: Loading version %1.3f session...\n", version_full / 1 000.0 ENDFB(G); " Executive: Loading version %1.6f session...\n", version_float EN DFB(G);
} }
} }
} }
} }
} }
#ifndef PYMOL_EVAL #ifndef PYMOL_EVAL
if(ok) { if(ok) {
tmp = PyDict_GetItemString(session, "eval_nag"); tmp = PyDict_GetItemString(session, "eval_nag");
if(tmp) { if(tmp) {
ok = PyString_Check(tmp); ok = PyString_Check(tmp);
if(ok) { if(ok) {
char *st = PyString_AsString(tmp); const char *st = PyString_AsString(tmp);
if(st) { if(st) {
if(Feedback(G, FB_Nag, FB_Warnings)) { if(Feedback(G, FB_Nag, FB_Warnings)) {
OrthoAddOutput(G, st); OrthoAddOutput(G, st);
} }
} }
} }
} }
} }
#endif #endif
skipping to change at line 5860 skipping to change at line 5880
incomplete = true; incomplete = true;
ok = true; /* keep trying...don't give up */ ok = true; /* keep trying...don't give up */
} }
} }
} }
if(ok) { /* update mouse in GUI */ if(ok) { /* update mouse in GUI */
PParse(G, "cmd.mouse(quiet=1)"); PParse(G, "cmd.mouse(quiet=1)");
if(!G->Option->presentation && !SettingGetGlobal_b(G, cSetting_suspend_updat es)) if(!G->Option->presentation && !SettingGetGlobal_b(G, cSetting_suspend_updat es))
PParse(G, "viewport"); /* refresh window/internal_gui status */ PParse(G, "viewport"); /* refresh window/internal_gui status */
} }
#ifndef _PYMOL_NO_MAIN
// Do not load viewport size when we have a GUI // Do not load viewport size when we have a GUI
if(ok && !G->HaveGUI) { if(ok) {
tmp = PyDict_GetItemString(session, "main"); tmp = PyDict_GetItemString(session, "main");
if(tmp) { if(tmp) {
ok = MainFromPyList(tmp); /* main just stores the viewport size */ if (!G->HaveGUI &&
/* PYMOL-775 added suspend_updates check, but does it make sense? */
!SettingGetGlobal_b(G, cSetting_suspend_updates) &&
!partial_restore) {
ok = MainFromPyList(tmp);
#ifndef _PYMOL_NOPY
} else if (!quiet) {
int viewport[2];
PConvPyListToIntArrayInPlace(tmp, viewport, 2);
PRINTFB(G, FB_Executive, FB_Actions)
" Session was saved with: viewport %d, %d\n",
viewport[0], viewport[1] ENDFB(G);
#endif
}
} }
if(tmp || (!(partial_restore | partial_session))) { /* ignore missing if par tial restore */ if(tmp || (!(partial_restore | partial_session))) { /* ignore missing if par tial restore */
if(PyErr_Occurred()) { if(PyErr_Occurred()) {
PyErr_Print(); PyErr_Print();
ok = false; ok = false;
} }
if(!ok) { if(!ok) {
PRINTFB(G, FB_Executive, FB_Errors) PRINTFB(G, FB_Executive, FB_Errors)
"ExectiveSetSession-Error: after main.\n" ENDFB(G); "ExectiveSetSession-Error: after main.\n" ENDFB(G);
} }
if(!ok) { if(!ok) {
incomplete = true; incomplete = true;
ok = true; /* keep trying...don't give up */ ok = true; /* keep trying...don't give up */
} }
} }
} }
#endif
if(ok && migrate_sessions) { /* migrate sessions */ if(ok && migrate_sessions) { /* migrate sessions */
tmp = PyDict_GetItemString(session, "version"); tmp = PyDict_GetItemString(session, "version");
if(tmp) { if(tmp) {
ok = PConvPyIntToInt(tmp, &version); ok = PConvPyIntToInt(tmp, &version);
if(ok) { if(ok) {
ExecutiveMigrateSession(G, version); ExecutiveMigrateSession(G, version);
} }
} }
} }
skipping to change at line 5911 skipping to change at line 5942
PRINTFB(G, FB_Executive, FB_Warnings) PRINTFB(G, FB_Executive, FB_Warnings)
"ExectiveSetSession-Warning: restore may be incomplete.\n" ENDFB(G); "ExectiveSetSession-Warning: restore may be incomplete.\n" ENDFB(G);
} }
CShaderMgr_Set_Reload_Bits(G, RELOAD_SHADERS_UPDATE_FOR_BACKGROUND); CShaderMgr_Set_Reload_Bits(G, RELOAD_SHADERS_UPDATE_FOR_BACKGROUND);
OrthoBackgroundTextureNeedsUpdate(G); OrthoBackgroundTextureNeedsUpdate(G);
ExecutiveInvalidateSelectionIndicatorsCGO(G); ExecutiveInvalidateSelectionIndicatorsCGO(G);
SceneChanged(G); SceneChanged(G);
return (ok); return (ok);
} }
#define ExecScrollBarMargin 1 #define ExecScrollBarMargin DIP2PIXEL(1)
#define ExecScrollBarWidth 13 #define ExecScrollBarWidth DIP2PIXEL(13)
void ExecutiveObjMolSeleOp(PyMOLGlobals * G, int sele, ObjectMoleculeOpRec * op) ; void ExecutiveObjMolSeleOp(PyMOLGlobals * G, int sele, ObjectMoleculeOpRec * op) ;
static CObject **ExecutiveSeleToObjectVLA(PyMOLGlobals * G, const char *s1) static CObject **ExecutiveSeleToObjectVLA(PyMOLGlobals * G, const char *s1)
{ {
/* return VLA containing list of atoms references by selection */ /* return VLA containing list of atoms references by selection */
CObject **result = NULL; CObject **result = NULL;
CExecutive *I = G->Executive; CExecutive *I = G->Executive;
SpecRec *rec = NULL; SpecRec *rec = NULL;
skipping to change at line 8076 skipping to change at line 8107
op1.i1 = cRepCartoon; op1.i1 = cRepCartoon;
op1.i2 = cRepInvRep; op1.i2 = cRepInvRep;
ExecutiveObjMolSeleOp(G, sele1, &op1); ExecutiveObjMolSeleOp(G, sele1, &op1);
op1.code = OMOP_Cartoon; op1.code = OMOP_Cartoon;
op1.i1 = type; op1.i1 = type;
op1.i2 = 0; op1.i2 = 0;
op1.i3 = 0; op1.i3 = 0;
ExecutiveObjMolSeleOp(G, sele1, &op1); ExecutiveObjMolSeleOp(G, sele1, &op1);
if (op1.i3>0){ if (op1.i3>0){
op1.code = OMOP_INVA; op1.code = OMOP_INVA;
op1.i1 = cRepCartoon; op1.i1 = cRepCartoonBit;
op1.i2 = cRepInvRep; op1.i2 = cRepInvRep;
ExecutiveObjMolSeleOp(G, sele1, &op1); ExecutiveObjMolSeleOp(G, sele1, &op1);
} }
} else { } else {
ErrMessage(G, "Cartoon", "Invalid selection."); ErrMessage(G, "Cartoon", "Invalid selection.");
} }
return (op1.i2); return (op1.i2);
} }
/*========================================================================*/ /*========================================================================*/
skipping to change at line 8488 skipping to change at line 8519
CShaderPrg *shaderPrg; CShaderPrg *shaderPrg;
float text_texture_dim = TextureGetTextTextureSize(G); float text_texture_dim = TextureGetTextTextureSize(G);
float textureScale; float textureScale;
int no_depth = (int) SettingGetGlobal_f(G, cSetting_selection_overlay); int no_depth = (int) SettingGetGlobal_f(G, cSetting_selection_overlay);
shaderPrg = CShaderPrg_Enable_IndicatorShader(G); shaderPrg = CShaderPrg_Enable_IndicatorShader(G);
if (!shaderPrg)return; if (!shaderPrg)return;
glEnable(GL_POINT_SPRITE); glEnable(GL_POINT_SPRITE);
glEnable(GL_VERTEX_PROGRAM_POINT_SIZE); glEnable(GL_VERTEX_PROGRAM_POINT_SIZE);
CShaderPrg_SetLightingEnabled(shaderPrg, 0); CShaderPrg_SetLightingEnabled(shaderPrg, 0);
CShaderPrg_SetAttrib4fLocation(shaderPrg, "a_Color", 1.f, 1.f, 1.f, 1.f); CShaderPrg_SetAttrib4fLocation(shaderPrg, "a_Color", 1.f, 1.f, 1.f, 1.f);
CShaderPrg_Set1f(shaderPrg, "g_pointSize", I->selectorTextureSize); CShaderPrg_Set1f(shaderPrg, "g_pointSize", DIP2PIXEL(I->selectorTextureSize));
CShaderPrg_Set2f(shaderPrg, "textureLookup", I->selectorTexturePosX/text_textu re_dim, I->selectorTexturePosY/text_texture_dim); CShaderPrg_Set2f(shaderPrg, "textureLookup", I->selectorTexturePosX/text_textu re_dim, I->selectorTexturePosY/text_texture_dim);
textureScale = I->selectorTextureSize/text_texture_dim ; textureScale = I->selectorTextureSize/text_texture_dim ;
CShaderPrg_Set2f(shaderPrg, "textureScale", textureScale, textureScale); CShaderPrg_Set2f(shaderPrg, "textureScale", textureScale, textureScale);
if(no_depth) if(no_depth)
glDisable(GL_DEPTH_TEST); glDisable(GL_DEPTH_TEST);
CGORenderGL(selIndicatorsCGO, NULL, NULL, NULL, NULL, NULL); CGORenderGL(selIndicatorsCGO, NULL, NULL, NULL, NULL, NULL);
if(no_depth) if(no_depth)
glEnable(GL_DEPTH_TEST); glEnable(GL_DEPTH_TEST);
glDisable(GL_VERTEX_PROGRAM_POINT_SIZE); glDisable(GL_VERTEX_PROGRAM_POINT_SIZE);
glDisable(GL_POINT_SPRITE); glDisable(GL_POINT_SPRITE);
skipping to change at line 9236 skipping to change at line 9267
#define tmp_fuse_sele "tmp_fuse_sele" #define tmp_fuse_sele "tmp_fuse_sele"
SelectorTmp tmpsele0(G, s0); SelectorTmp tmpsele0(G, s0);
SelectorTmp tmpsele1(G, s1); SelectorTmp tmpsele1(G, s1);
sele0 = tmpsele0.getIndex(); sele0 = tmpsele0.getIndex();
sele1 = tmpsele1.getIndex(); sele1 = tmpsele1.getIndex();
if(sele0 < 0 || sele1 < 0) { if(sele0 < 0 || sele1 < 0) {
ErrMessage(G, "Fuse", "Need two selections"); ErrMessage(G, "Fuse", "Need two selections");
} else { } else {
#ifndef PYMOL_EDU #ifndef _PYMOL_NO_UNDO
#endif #endif
{ {
EditorInactivate(G); EditorInactivate(G);
obj0 = SelectorGetSingleObjectMolecule(G, sele0); obj0 = SelectorGetSingleObjectMolecule(G, sele0);
obj1 = SelectorGetSingleObjectMolecule(G, sele1); obj1 = SelectorGetSingleObjectMolecule(G, sele1);
if(obj0) if(obj0)
i0 = ObjectMoleculeGetAtomIndex(obj0, sele0); i0 = ObjectMoleculeGetAtomIndex(obj0, sele0);
if(obj1) if(obj1)
i1 = ObjectMoleculeGetAtomIndex(obj1, sele1); i1 = ObjectMoleculeGetAtomIndex(obj1, sele1);
if(obj0 && obj1 && (i0 >= 0) && (i1 >= 0) && (obj0 != obj1)) { if(obj0 && obj1 && (i0 >= 0) && (i1 >= 0) && (obj0 != obj1)) {
skipping to change at line 9431 skipping to change at line 9462
if((rec->type == cExecObject) && (rec->obj->type == cObjectMolecule) ) { if((rec->type == cExecObject) && (rec->obj->type == cObjectMolecule) ) {
obj = (ObjectMolecule *) rec->obj; obj = (ObjectMolecule *) rec->obj;
if (ok) if (ok)
ok &= ObjectMoleculeSort(obj); ok &= ObjectMoleculeSort(obj);
if (ok){ if (ok){
changed = true; changed = true;
sele = SelectorIndexByName(G, rec->name); sele = SelectorIndexByName(G, rec->name);
if(sele >= 0) { if(sele >= 0) {
ObjectMoleculeOpRecInit(&op); ObjectMoleculeOpRecInit(&op);
op.code = OMOP_INVA; op.code = OMOP_INVA;
op.i1 = cRepAll; op.i1 = cRepCartoonBit | cRepRibbonBit;
op.i2 = cRepInvRep; op.i2 = cRepInvRep;
ExecutiveObjMolSeleOp(G, sele, &op); ExecutiveObjMolSeleOp(G, sele, &op);
} }
} }
} }
} }
break; break;
case cExecSelection: case cExecSelection:
sele = SelectorIndexByName(G, rec->name); sele = SelectorIndexByName(G, rec->name);
if(sele >= 0) { if(sele >= 0) {
op.code = OMOP_Sort; op.code = OMOP_Sort;
ExecutiveObjMolSeleOp(G, sele, &op); ExecutiveObjMolSeleOp(G, sele, &op);
ObjectMoleculeOpRecInit(&op); ObjectMoleculeOpRecInit(&op);
op.code = OMOP_INVA; op.code = OMOP_INVA;
op.i1 = cRepAll; op.i1 = cRepCartoonBit | cRepRibbonBit;
op.i2 = cRepInvRep; op.i2 = cRepInvRep;
ExecutiveObjMolSeleOp(G, sele, &op); ExecutiveObjMolSeleOp(G, sele, &op);
ObjectMoleculeOpRecInit(&op); ObjectMoleculeOpRecInit(&op);
} }
break; break;
case cExecObject: case cExecObject:
if(rec->obj->type == cObjectMolecule) { if(rec->obj->type == cObjectMolecule) {
obj = (ObjectMolecule *) rec->obj; obj = (ObjectMolecule *) rec->obj;
if (ok) if (ok)
ok &= ObjectMoleculeSort(obj); ok &= ObjectMoleculeSort(obj);
changed = true; changed = true;
sele = SelectorIndexByName(G, rec->name); sele = SelectorIndexByName(G, rec->name);
if(sele >= 0) { if(sele >= 0) {
ObjectMoleculeOpRecInit(&op); ObjectMoleculeOpRecInit(&op);
op.code = OMOP_INVA; op.code = OMOP_INVA;
op.i1 = cRepAll; op.i1 = cRepCartoonBit | cRepRibbonBit;
op.i2 = cRepInvRep; op.i2 = cRepInvRep;
ExecutiveObjMolSeleOp(G, sele, &op); ExecutiveObjMolSeleOp(G, sele, &op);
} }
} }
break; break;
} }
} }
} }
TrackerDelList(I_Tracker, list_id); TrackerDelList(I_Tracker, list_id);
TrackerDelIter(I_Tracker, iter_id); TrackerDelIter(I_Tracker, iter_id);
skipping to change at line 9518 skipping to change at line 9549
op.i1, obj->Obj.Name ENDFB(G); op.i1, obj->Obj.Name ENDFB(G);
} }
} }
} }
} }
} }
} }
} }
/*========================================================================*/ /*========================================================================*/
void ExecutiveAddHydrogens(PyMOLGlobals * G, const char *s1, int quiet) void ExecutiveAddHydrogens(PyMOLGlobals * G, const char *s1, int quiet, int stat e, bool legacy)
{ {
ObjectMoleculeOpRec op; ObjectMoleculeOpRec op;
/* Needs 4 passes */ /* Needs 4 passes */
for (int cnt = 0; cnt < 4; ++cnt) { int passes = legacy ? 4 : 1;
for (int cnt = 0; cnt < passes; ++cnt) {
SelectorTmp tmpsele1(G, s1); SelectorTmp tmpsele1(G, s1);
int sele1 = tmpsele1.getIndex(); int sele1 = tmpsele1.getIndex();
ObjectMoleculeOpRecInit(&op); ObjectMoleculeOpRecInit(&op);
op.code = OMOP_AddHydrogens; /* 4 passes completes the job */ op.code = OMOP_AddHydrogens; /* 4 passes completes the job */
op.i1 = state;
op.i2 = legacy;
ExecutiveObjMolSeleOp(G, sele1, &op); ExecutiveObjMolSeleOp(G, sele1, &op);
} }
} }
/*========================================================================*/ /*========================================================================*/
void ExecutiveFixHydrogens(PyMOLGlobals * G, const char *s1, int quiet) void ExecutiveFixHydrogens(PyMOLGlobals * G, const char *s1, int quiet)
{ {
int sele1; int sele1;
ObjectMoleculeOpRec op; ObjectMoleculeOpRec op;
skipping to change at line 9682 skipping to change at line 9716
if(mode) { if(mode) {
PRINTF " Mask: %d atoms masked (cannot be picked or selected).\n", PRINTF " Mask: %d atoms masked (cannot be picked or selected).\n",
op.i2 ENDF(G); op.i2 ENDF(G);
} else { } else {
PRINTF " Mask: %d atoms unmasked.\n", op.i2 ENDF(G); PRINTF " Mask: %d atoms unmasked.\n", op.i2 ENDF(G);
} }
} }
} }
} }
op.code = OMOP_INVA; /* need to invalidate all pickable representatio ns */ op.code = OMOP_INVA; /* need to invalidate all pickable representatio ns */
op.i1 = cRepAll; op.i1 = cRepsAtomMask;
op.i2 = cRepInvPick; op.i2 = cRepInvPick;
ExecutiveObjMolSeleOp(G, sele1, &op); ExecutiveObjMolSeleOp(G, sele1, &op);
} }
} }
/*========================================================================*/ /*========================================================================*/
int ExecutiveStereo(PyMOLGlobals * G, int flag) int ExecutiveStereo(PyMOLGlobals * G, int flag)
{ {
int ok = 1; int ok = 1;
int stereo_mode; int stereo_mode;
skipping to change at line 9704 skipping to change at line 9738
switch (flag) { switch (flag) {
case -1: case -1:
SettingSetGlobal_f(G, cSetting_stereo_shift, -SettingGetGlobal_f(G, cSetting _stereo_shift)); SettingSetGlobal_f(G, cSetting_stereo_shift, -SettingGetGlobal_f(G, cSetting _stereo_shift));
break; break;
default: /* -2 */ default: /* -2 */
if(G->HaveGUI) { if(G->HaveGUI) {
stereo_mode = SettingGetGlobal_i(G, cSetting_stereo_mode); stereo_mode = SettingGetGlobal_i(G, cSetting_stereo_mode);
switch (stereo_mode) { switch (stereo_mode) {
case 0: /* off */ case 0: /* off */
break; break;
case 1: /* hardware stereo-in-a-window */ case cStereo_quadbuffer: /* hardware stereo-in-a-window * /
SceneSetStereo(G, flag); SceneSetStereo(G, flag);
#ifndef _PYMOL_NOPY #ifndef _PYMOL_NOPY
PSGIStereo(G, flag); /* does this have any effect anymore? */ PSGIStereo(G, flag); /* does this have any effect anymore? */
#endif #endif
break; break;
default: default:
SceneSetStereo(G, flag); SceneSetStereo(G, flag);
break; break;
} }
} }
skipping to change at line 10492 skipping to change at line 10526
sele1 = SelectorIndexByName(G, s1); sele1 = SelectorIndexByName(G, s1);
if(sele1 >= 0) { if(sele1 >= 0) {
ObjectMoleculeOpRecInit(&op1); ObjectMoleculeOpRecInit(&op1);
op1.code = OMOP_LABL; op1.code = OMOP_LABL;
op1.s1 = expr; op1.s1 = expr;
op1.i1 = 0; op1.i1 = 0;
op1.i2 = eval_mode; op1.i2 = eval_mode;
ExecutiveObjMolSeleOp(G, sele1, &op1); ExecutiveObjMolSeleOp(G, sele1, &op1);
cnt = op1.i1; cnt = op1.i1;
op1.code = OMOP_VISI; op1.code = OMOP_VISI;
op1.i1 = cRepLabel; op1.i1 = cRepLabelBit;
op1.i2 = 1; op1.i2 = cVis_SHOW;
ExecutiveObjMolSeleOp(G, sele1, &op1); ExecutiveObjMolSeleOp(G, sele1, &op1);
op1.code = OMOP_INVA; op1.code = OMOP_INVA;
op1.i1 = cRepLabel;
op1.i2 = cRepInvVisib; op1.i2 = cRepInvVisib;
ExecutiveObjMolSeleOp(G, sele1, &op1); ExecutiveObjMolSeleOp(G, sele1, &op1);
if(!quiet) { if(!quiet) {
{ {
const char *unlabelledstr = ""; const char *unlabelledstr = "";
if (cnt<0){ /* if negative, say unlabelled */ if (cnt<0){ /* if negative, say unlabelled */
cnt = -cnt; cnt = -cnt;
unlabelledstr = "un"; unlabelledstr = "un";
} }
skipping to change at line 10724 skipping to change at line 10757
int sele0 = SelectorIndexByName(G, name); int sele0 = SelectorIndexByName(G, name);
PyObject *entry = NULL; PyObject *entry = NULL;
ObjectMolecule *obj = NULL; ObjectMolecule *obj = NULL;
if(sele0 >= 0) if(sele0 >= 0)
obj = SelectorGetSingleObjectMolecule(G, sele0); obj = SelectorGetSingleObjectMolecule(G, sele0);
if(obj) { if(obj) {
int n_atom = obj->NAtom; int n_atom = obj->NAtom;
int list_len = 0; int list_len = 0;
int a; int a;
int index = 0; int index = 0;
char *expr = NULL; const char *expr = NULL;
if(ok) if(ok)
ok = PyList_Check(list); ok = PyList_Check(list);
if(ok) { if(ok) {
list_len = PyList_Size(list); list_len = PyList_Size(list);
for(a = 0; a < list_len; a++) { for(a = 0; a < list_len; a++) {
if(ok) if(ok)
entry = PyList_GetItem(list, a); entry = PyList_GetItem(list, a);
if(ok) if(ok)
ok = PyList_Check(entry); ok = PyList_Check(entry);
if(ok) if(ok)
skipping to change at line 11360 skipping to change at line 11393
f1 += 3; f1 += 3;
f2 += 3; f2 += 3;
if(ai1 && ai2) { /* make sure we keep track of which atom s are aligned */ if(ai1 && ai2) { /* make sure we keep track of which atom s are aligned */
*(ai1++) = op1.ai1VLA[a]; *(ai1++) = op1.ai1VLA[a];
*(ai2++) = op2.ai1VLA[a]; *(ai2++) = op2.ai1VLA[a];
} }
} }
} }
if(!quiet && (n_next != n_pair)) { if(!quiet && (n_next != n_pair)) {
PRINTFB(G, FB_Executive, FB_Actions) PRINTFB(G, FB_Executive, FB_Actions)
" ExecutiveRMS: %d atoms rejected during cycle %d (RMS=%0.2f ).\n", " ExecutiveRMS: %d atoms rejected during cycle %d (RMSD=%0.2 f).\n",
n_pair - n_next, b, rms ENDFB(G); n_pair - n_next, b, rms ENDFB(G);
} }
n_pair = n_next; n_pair = n_next;
FreeP(flag); FreeP(flag);
if(n_pair) { if(n_pair) {
rms = MatrixFitRMSTTTf(G, n_pair, op1.vv1, op2.vv1, NULL, op2. ttt); rms = MatrixFitRMSTTTf(G, n_pair, op1.vv1, op2.vv1, NULL, op2. ttt);
if(rms_info) { if(rms_info) {
rms_info->n_cycles_run = b; rms_info->n_cycles_run = b;
rms_info->final_n_atom = n_pair; rms_info->final_n_atom = n_pair;
rms_info->final_rms = rms; rms_info->final_rms = rms;
skipping to change at line 11394 skipping to change at line 11427
} }
if(!n_pair) { if(!n_pair) {
PRINTFB(G, FB_Executive, FB_Results) PRINTFB(G, FB_Executive, FB_Results)
" Executive: Error -- no atoms left after refinement!\n" ENDFB(G); " Executive: Error -- no atoms left after refinement!\n" ENDFB(G);
ok = false; ok = false;
} }
if(ok) { if(ok) {
if(!quiet) { if(!quiet) {
PRINTFB(G, FB_Executive, FB_Results) PRINTFB(G, FB_Executive, FB_Results)
" Executive: RMS = %8.3f (%d to %d atoms)\n", rms, n_pair, n_pair EN DFB(G); " Executive: RMSD = %8.3f (%d to %d atoms)\n", rms, n_pair, n_pair E NDFB(G);
} }
if(oname && oname[0]) { if(oname && oname[0]) {
int align_state = state2; int align_state = state2;
ObjectMolecule *trg_obj = SelectorGetSingleObjectMolecule(G, sele2); ObjectMolecule *trg_obj = SelectorGetSingleObjectMolecule(G, sele2);
if(align_state < 0) { if(align_state < 0) {
align_state = SceneGetState(G); align_state = SceneGetState(G);
} }
/* we're going to create/update an alignment object */ /* we're going to create/update an alignment object */
skipping to change at line 11701 skipping to change at line 11734
if(op1.nvv1 != op2.nvv1) { if(op1.nvv1 != op2.nvv1) {
sprintf(buffer, "Atom counts between selection sets don't match (%d != %d) .", sprintf(buffer, "Atom counts between selection sets don't match (%d != %d) .",
op1.nvv1, op2.nvv1); op1.nvv1, op2.nvv1);
ErrMessage(G, "ExecutiveRMS", buffer); ErrMessage(G, "ExecutiveRMS", buffer);
} else if(op1.nvv1) { } else if(op1.nvv1) {
if(mode != 0) if(mode != 0)
rms = MatrixFitRMSTTTf(G, op1.nvv1, op1.vv1, op2.vv1, NULL, op2.ttt); rms = MatrixFitRMSTTTf(G, op1.nvv1, op1.vv1, op2.vv1, NULL, op2.ttt);
else else
rms = MatrixGetRMS(G, op1.nvv1, op1.vv1, op2.vv1, NULL); rms = MatrixGetRMS(G, op1.nvv1, op1.vv1, op2.vv1, NULL);
PRINTFB(G, FB_Executive, FB_Results) PRINTFB(G, FB_Executive, FB_Results)
" ExecutiveRMS: RMS = %8.3f (%d to %d atoms)\n", rms, op1.nvv1, op2.nvv1 ENDFB(G); " ExecutiveRMS: RMSD = %8.3f (%d to %d atoms)\n", rms, op1.nvv1, op2.nvv 1 ENDFB(G);
op2.code = OMOP_TTTF; op2.code = OMOP_TTTF;
SelectorGetTmp(G, combi, s1); SelectorGetTmp(G, combi, s1);
sele1 = SelectorIndexByName(G, s1); sele1 = SelectorIndexByName(G, s1);
ExecutiveObjMolSeleOp(G, sele1, &op2); ExecutiveObjMolSeleOp(G, sele1, &op2);
SelectorFreeTmp(G, s1); SelectorFreeTmp(G, s1);
} else { } else {
ErrMessage(G, "ExecutiveRMS", "No atoms selected."); ErrMessage(G, "ExecutiveRMS", "No atoms selected.");
} }
} }
skipping to change at line 12101 skipping to change at line 12134
(SelectorIsMember(G, ai2->selEntry, sele1) && (SelectorIsMember(G, ai2->selEntry, sele1) &&
SelectorIsMember(G, ai1->selEntry, sele2))) { SelectorIsMember(G, ai1->selEntry, sele2))) {
PyObject *pyBondInfo = PyList_New(3); PyObject *pyBondInfo = PyList_New(3);
PyObject *bond_setting_value = NULL; PyObject *bond_setting_value = NULL;
if (!pyObjList){ if (!pyObjList){
pyObjList = PyList_New(2); pyObjList = PyList_New(2);
pyBondList = PyList_New(0); pyBondList = PyList_New(0);
PyList_SetItem(pyObjList, 0, PyString_FromString(obj->Obj.Name)); PyList_SetItem(pyObjList, 0, PyString_FromString(obj->Obj.Name));
PyList_SetItem(pyObjList, 1, pyBondList); PyList_SetItem(pyObjList, 1, pyBondList);
PyList_Append(result, pyObjList); PyList_Append(result, pyObjList);
Py_DECREF(pyObjList);
} }
PyList_SetItem(pyBondInfo, 0, PyInt_FromLong((long)bi->index[0]+1)) ; PyList_SetItem(pyBondInfo, 0, PyInt_FromLong((long)bi->index[0]+1)) ;
PyList_SetItem(pyBondInfo, 1, PyInt_FromLong((long)bi->index[1]+1)) ; PyList_SetItem(pyBondInfo, 1, PyInt_FromLong((long)bi->index[1]+1)) ;
if (bi->has_setting){ if (bi->has_setting){
int uid = AtomInfoCheckUniqueBondID(G, bi); int uid = AtomInfoCheckUniqueBondID(G, bi);
bond_setting_value = SettingUniqueGetPyObject(G, uid, index); bond_setting_value = SettingUniqueGetPyObject(G, uid, index);
} }
PyList_SetItem(pyBondInfo, 2, PConvAutoNone(bond_setting_value)); PyList_SetItem(pyBondInfo, 2, PConvAutoNone(bond_setting_value));
PyList_Append(pyBondList, pyBondInfo); PyList_Append(pyBondList, pyBondInfo);
Py_DECREF(pyBondInfo);
nSet++; nSet++;
} }
bi++; bi++;
} }
if(nSet && !quiet) { if(nSet && !quiet) {
SettingGetName(G, index, name); SettingGetName(G, index, name);
PRINTF PRINTF
" Getting: %s for %d bonds in object \"%s\".\n", " Getting: %s for %d bonds in object \"%s\".\n",
name, nSet, obj->Obj.Name ENDF(G); name, nSet, obj->Obj.Name ENDF(G);
} }
skipping to change at line 12328 skipping to change at line 12363
SpecRec *rec = NULL; SpecRec *rec = NULL;
ObjectMolecule *obj = NULL; ObjectMolecule *obj = NULL;
int sele1; int sele1;
ObjectMoleculeOpRec op; ObjectMoleculeOpRec op;
OrthoLineType value; OrthoLineType value;
CSetting **handle = NULL; CSetting **handle = NULL;
SettingName name = ""; SettingName name = "";
int nObj = 0; int nObj = 0;
int unblock; int unblock;
int ok = true; int ok = true;
PRINTFD(G, FB_Executive) PRINTFD(G, FB_Executive)
" ExecutiveSetSetting: entered. sele \"%s\" updates=%d index=%d\n", sele, up dates, index ENDFD; " ExecutiveSetSetting: entered. sele \"%s\" updates=%d index=%d\n", sele, up dates, index ENDFD;
if(!quiet) { if(!quiet) {
SettingGetName(G, index, name); SettingGetName(G, index, name);
} }
unblock = PAutoBlock(G); unblock = PAutoBlock(G);
if((!sele) || (sele[0] == 0)) { /* global setting */ if((!sele) || (sele[0] == 0)) { /* global setting */
ok = SettingSetFromTuple(G, NULL, index, tuple); ok = SettingSetFromTuple(G, NULL, index, tuple);
skipping to change at line 13012 skipping to change at line 13048
ObjectMoleculeOpRec op; ObjectMoleculeOpRec op;
if(sele >= 0) { if(sele >= 0) {
ok = true; ok = true;
ObjectMoleculeOpRecInit(&op); ObjectMoleculeOpRecInit(&op);
op.code = OMOP_COLR; op.code = OMOP_COLR;
op.i1 = col_ind; op.i1 = col_ind;
op.i2 = n_atm; op.i2 = n_atm;
ExecutiveObjMolSeleOp(G, sele, &op); ExecutiveObjMolSeleOp(G, sele, &op);
n_atm = op.i2; n_atm = op.i2;
op.code = OMOP_INVA; op.code = OMOP_INVA;
op.i1 = cRepAll; op.i1 = cRepBitmask;
op.i2 = cRepInvColor; op.i2 = cRepInvColor;
ExecutiveObjMolSeleOp(G, sele, &op); ExecutiveObjMolSeleOp(G, sele, &op);
} }
} }
} }
break; break;
} }
switch (rec->type) { /* sets object color */ switch (rec->type) { /* sets object color */
case cExecObject: case cExecObject:
skipping to change at line 13881 skipping to change at line 13917
tRec->visible = !tRec->visible; tRec->visible = !tRec->visible;
ReportEnabledChange(G, rec); ReportEnabledChange(G, rec);
} else { } else {
if((!suppress_hidden) || (!hide_underscore) || (!tRec->is_hi dden)) { if((!suppress_hidden) || (!hide_underscore) || (!tRec->is_hi dden)) {
tRec->in_scene = SceneObjectAdd(G, tRec->obj); tRec->in_scene = SceneObjectAdd(G, tRec->obj);
ExecutiveInvalidateSceneMembers(G); ExecutiveInvalidateSceneMembers(G);
tRec->visible = !tRec->visible; tRec->visible = !tRec->visible;
ReportEnabledChange(G, rec); ReportEnabledChange(G, rec);
} }
} }
} else if((tRec->type != cExecSelection) || (!onoff)) /* hide all selections, but show all */ } else if((tRec->type != cExecSelection) || (!onoff)) { /* hide all selections, but show all */
tRec->visible = !tRec->visible; tRec->visible = !tRec->visible;
ReportEnabledChange(G, rec); ReportEnabledChange(G, rec);
}
} }
} }
} }
break; break;
case cExecObject: case cExecObject:
/* /*
if(rec->visible!=onoff) { if(rec->visible!=onoff) {
if(rec->visible) { if(rec->visible) {
rec->in_scene = SceneObjectDel(G,rec->obj); rec->in_scene = SceneObjectDel(G,rec->obj);
ExecutiveInvalidateSceneMembers(G); ExecutiveInvalidateSceneMembers(G);
skipping to change at line 14023 skipping to change at line 14060
#endif #endif
} }
} }
#endif #endif
PyMOL_NeedReshape(G->PyMOL, flag, 0, 0, 0, 0); PyMOL_NeedReshape(G->PyMOL, flag, 0, 0, 0, 0);
SceneChanged(G); SceneChanged(G);
} }
/*========================================================================*/ /*========================================================================*/
void ExecutiveSetAllVisib(PyMOLGlobals * G, int state) static
{ void fInvalidateRepMask(CObject * obj, int repmask, int state=-1) {
ObjectMoleculeOpRec op; if(obj->fInvalidate) {
ObjectMolecule *obj; for(int a = 0; a < cRepCnt; a++) {
int rep; if ((1 << a) & repmask)
int sele; obj->fInvalidate(obj, a, cRepInvVisib, state);
CExecutive *I = G->Executive;
SpecRec *rec = NULL;
PRINTFD(G, FB_Executive)
" ExecutiveSetAllVisib: entered.\n" ENDFD;
while(ListIterate(I->Spec, rec, next)) {
if(rec->type == cExecObject) {
switch (rec->obj->type) {
case cObjectMolecule:
obj = (ObjectMolecule *) rec->obj;
sele = SelectorIndexByName(G, obj->Obj.Name);
ObjectMoleculeOpRecInit(&op);
op.code = OMOP_VISI;
op.i1 = -1;
op.i2 = state;
ObjectMoleculeSeleOp(obj, sele, &op);
op.code = OMOP_INVA;
op.i1 = -1;
op.i2 = cRepInvVisib;
ObjectMoleculeSeleOp(obj, sele, &op);
break;
default:
for(rep = 0; rep < cRepCnt; rep++) {
ObjectSetRepVis(rec->obj, rep, state);
if(rec->obj->fInvalidate)
rec->obj->fInvalidate(rec->obj, rep, cRepInvVisib, state);
}
SceneInvalidate(G);
break;
}
} }
} }
PRINTFD(G, FB_Executive)
" ExecutiveSetAllVisib: leaving...\n" ENDFD;
} }
/*========================================================================*/ /*========================================================================*/
int ExecutiveToggleRepVisib(PyMOLGlobals * G, const char *name, int rep) int ExecutiveToggleRepVisib(PyMOLGlobals * G, const char *name, int rep)
{ {
int ok = true; int ok = true;
int sele = -1; int sele = -1;
SpecRec *tRec; SpecRec *tRec;
ObjectMoleculeOpRec op; ObjectMoleculeOpRec op;
OrthoLineType tmpname; OrthoLineType tmpname;
skipping to change at line 14093 skipping to change at line 14095
// special case: toggle object visibility (should that be in this function?) // special case: toggle object visibility (should that be in this function?)
if(tRec) { if(tRec) {
ExecutiveSetObjVisib(G, name, !tRec->visible, 0); ExecutiveSetObjVisib(G, name, !tRec->visible, 0);
} else { } else {
PRINTFB(G, FB_Executive, FB_Errors) PRINTFB(G, FB_Executive, FB_Errors)
" ExecutiveToggleRepVisib-Error: '%s' not found\n", name ENDFB(G); " ExecutiveToggleRepVisib-Error: '%s' not found\n", name ENDFB(G);
} }
} else if(tRec && tRec->type == cExecObject && } else if(tRec && tRec->type == cExecObject &&
tRec->obj->type != cObjectMolecule) { tRec->obj->type != cObjectMolecule) {
// non-atom object // non-atom object
ObjectToggleRepVis(tRec->obj, rep); tRec->obj->visRep ^= rep;
if(tRec->obj->fInvalidate) fInvalidateRepMask(tRec->obj, rep, 0);
tRec->obj->fInvalidate(tRec->obj, rep, cRepInvVisib, 0);
SceneChanged(G); SceneChanged(G);
} else if(SelectorGetTmp(G, name, tmpname) >= 0) { } else if(SelectorGetTmp(G, name, tmpname) >= 0) {
// atom selection // atom selection
sele = SelectorIndexByName(G, tmpname); sele = SelectorIndexByName(G, tmpname);
if(sele >= 0) { if(sele >= 0) {
ObjectMoleculeOpRecInit(&op); ObjectMoleculeOpRecInit(&op);
op.code = OMOP_CheckVis; op.code = OMOP_CheckVis;
op.i1 = rep; op.i1 = rep;
op.i2 = false; op.i2 = false;
ExecutiveObjMolSeleOp(G, sele, &op); ExecutiveObjMolSeleOp(G, sele, &op);
op.i2 = !op.i2; op.i2 = !op.i2;
if(tRec && tRec->type == cExecObject)
ObjectSetRepVis(tRec->obj, rep, op.i2);
op.code = OMOP_VISI; op.code = OMOP_VISI;
op.i1 = rep; op.i1 = rep;
ExecutiveObjMolSeleOp(G, sele, &op); ExecutiveObjMolSeleOp(G, sele, &op);
op.code = OMOP_INVA; op.code = OMOP_INVA;
op.i2 = cRepInvVisib; op.i2 = cRepInvVisib;
ExecutiveObjMolSeleOp(G, sele, &op); ExecutiveObjMolSeleOp(G, sele, &op);
} }
SelectorFreeTmp(G, tmpname); SelectorFreeTmp(G, tmpname);
} }
PRINTFD(G, FB_Executive) PRINTFD(G, FB_Executive)
" ExecutiveToggleRepVisib: leaving...\n" ENDFD; " ExecutiveToggleRepVisib: leaving...\n" ENDFD;
return (ok); return (ok);
} }
/*========================================================================*/ /*========================================================================*/
void ExecutiveSetRepVisib(PyMOLGlobals * G, const char *name, int rep, int state ) void ExecutiveSetRepVisib(PyMOLGlobals * G, const char *name, int rep, int state )
{ {
int repmask = (rep == cRepAll) ? cRepBitmask : (1 << rep);
ExecutiveSetRepVisMask(G, name, repmask, state);
}
void ExecutiveSetRepVisMask(PyMOLGlobals * G, const char *name, int repmask, int
state)
{
PRINTFD(G, FB_Executive) PRINTFD(G, FB_Executive)
" ExecutiveSetRepVisib: entered.\n" ENDFD; " ExecutiveSetRepVisib: entered.\n" ENDFD;
{ {
CExecutive *I = G->Executive; CExecutive *I = G->Executive;
CTracker *I_Tracker = I->Tracker; CTracker *I_Tracker = I->Tracker;
SpecRec *rec = NULL; SpecRec *rec = NULL;
int list_id = ExecutiveGetNamesListFromPattern(G, name, true, true); int list_id = ExecutiveGetNamesListFromPattern(G, name, true, true);
int iter_id = TrackerNewIter(I_Tracker, 0, list_id); int iter_id = TrackerNewIter(I_Tracker, 0, list_id);
while(TrackerIterNextCandInList(I_Tracker, iter_id, (TrackerRef **) (void *) &rec)) { while(TrackerIterNextCandInList(I_Tracker, iter_id, (TrackerRef **) (void *) &rec)) {
skipping to change at line 14152 skipping to change at line 14156
switch (rec->type) { switch (rec->type) {
case cExecSelection: case cExecSelection:
case cExecObject: case cExecObject:
{ {
int sele = SelectorIndexByName(G, rec->name); int sele = SelectorIndexByName(G, rec->name);
if(sele >= 0) { if(sele >= 0) {
ObjectMoleculeOpRec op; ObjectMoleculeOpRec op;
ObjectMoleculeOpRecInit(&op); ObjectMoleculeOpRecInit(&op);
op.code = OMOP_VISI; op.code = OMOP_VISI;
op.i1 = rep; op.i1 = repmask;
op.i2 = state; op.i2 = state;
ExecutiveObjMolSeleOp(G, sele, &op); ExecutiveObjMolSeleOp(G, sele, &op);
op.code = OMOP_INVA; op.code = OMOP_INVA;
if (state == cVis_AS)
op.i1 = cRepBitmask;
op.i2 = cRepInvVisib; op.i2 = cRepInvVisib;
ExecutiveObjMolSeleOp(G, sele, &op); ExecutiveObjMolSeleOp(G, sele, &op);
} }
} }
break; break;
} }
/* per-object/name */ /* per-object/name */
switch (rec->type) { switch (rec->type) {
case cExecObject: case cExecObject:
if(rep >= 0) { ObjectSetRepVisMask(rec->obj, repmask, state);
ObjectSetRepVis(rec->obj, rep, state); fInvalidateRepMask(rec->obj, repmask, 0);
if(rec->obj->fInvalidate)
rec->obj->fInvalidate(rec->obj, rep, cRepInvVisib, 0);
} else {
int a;
for(a = 0; a < cRepCnt; a++) {
ObjectSetRepVis(rec->obj, a, state);
if(rec->obj->fInvalidate)
rec->obj->fInvalidate(rec->obj, a, cRepInvVisib, 0);
}
}
SceneChanged(G); SceneChanged(G);
break; break;
case cExecAll: case cExecAll:
ExecutiveSetAllRepVisib(G, rep, state); ExecutiveSetAllRepVisMask(G, repmask, state);
break; break;
} }
} }
} }
TrackerDelList(I_Tracker, list_id); TrackerDelList(I_Tracker, list_id);
TrackerDelIter(I_Tracker, iter_id); TrackerDelIter(I_Tracker, iter_id);
} }
PRINTFD(G, FB_Executive) PRINTFD(G, FB_Executive)
" ExecutiveSetRepVisib: leaving...\n" ENDFD; " ExecutiveSetRepVisib: leaving...\n" ENDFD;
skipping to change at line 14220 skipping to change at line 14216
op.code = OMOP_OnOff; op.code = OMOP_OnOff;
op.i1 = onoff; op.i1 = onoff;
ExecutiveObjMolSeleOp(G, sele, &op); ExecutiveObjMolSeleOp(G, sele, &op);
} }
} }
return 1; return 1;
} }
/*========================================================================*/ /*========================================================================*/
static void ExecutiveSetAllRepVisib(PyMOLGlobals * G, int rep, int state) /*
* repmask: rep bit mask
* state: 0 (hide), 1 (show), 2 (as)
*/
static void ExecutiveSetAllRepVisMask(PyMOLGlobals * G, int repmask, int state)
{ {
ObjectMoleculeOpRec op; ObjectMoleculeOpRec op;
ObjectMolecule *obj; ObjectMolecule *obj;
int sele; int sele;
int a;
CExecutive *I = G->Executive; CExecutive *I = G->Executive;
SpecRec *rec = NULL; SpecRec *rec = NULL;
PRINTFD(G, FB_Executive) PRINTFD(G, FB_Executive)
" ExecutiveSetAllRepVisib: entered.\n" ENDFD; " ExecutiveSetAllRepVisib: entered.\n" ENDFD;
while(ListIterate(I->Spec, rec, next)) { while(ListIterate(I->Spec, rec, next)) {
if(rec->type == cExecObject) { if(rec->type == cExecObject) {
if(rec->type == cExecObject) { if(rec->type == cExecObject) {
switch (rec->obj->type) { switch (rec->obj->type) {
case cObjectMolecule: case cObjectMolecule:
obj = (ObjectMolecule *) rec->obj; obj = (ObjectMolecule *) rec->obj;
sele = SelectorIndexByName(G, obj->Obj.Name); sele = SelectorIndexByName(G, obj->Obj.Name);
ObjectMoleculeOpRecInit(&op); ObjectMoleculeOpRecInit(&op);
op.code = OMOP_VISI; op.code = OMOP_VISI;
op.i1 = rep; op.i1 = repmask;
op.i2 = state; op.i2 = state;
ObjectMoleculeSeleOp(obj, sele, &op); ObjectMoleculeSeleOp(obj, sele, &op);
op.code = OMOP_INVA; op.code = OMOP_INVA;
if (state == cVis_AS)
op.i1 = cRepBitmask;
op.i2 = cRepInvVisib; op.i2 = cRepInvVisib;
ObjectMoleculeSeleOp(obj, sele, &op); ObjectMoleculeSeleOp(obj, sele, &op);
break; break;
default: default:
if(rep >= 0) { ObjectSetRepVisMask(rec->obj, repmask, state);
ObjectSetRepVis(rec->obj, rep, state); fInvalidateRepMask(rec->obj, repmask, -1);
if(rec->obj->fInvalidate)
rec->obj->fInvalidate(rec->obj, rep, cRepInvVisib, state);
} else {
for(a = 0; a < cRepCnt; a++) {
ObjectSetRepVis(rec->obj, a, state);
if(rec->obj->fInvalidate)
rec->obj->fInvalidate(rec->obj, rep, cRepInvVisib, state);
}
}
SceneInvalidate(G); SceneInvalidate(G);
break; break;
} }
} }
} }
} }
PRINTFD(G, FB_Executive) PRINTFD(G, FB_Executive)
" ExecutiveSetAllRepVisib: leaving...\n" ENDFD; " ExecutiveSetAllRepVisib: leaving...\n" ENDFD;
} }
skipping to change at line 14294 skipping to change at line 14286
while(TrackerIterNextCandInList(I_Tracker, iter_id, (TrackerRef **) (void *) &rec)) { while(TrackerIterNextCandInList(I_Tracker, iter_id, (TrackerRef **) (void *) &rec)) {
if(rec) { if(rec) {
switch (rec->type) { switch (rec->type) {
case cExecSelection: case cExecSelection:
case cExecObject: case cExecObject:
{ {
int sele = SelectorIndexByName(G, rec->name); int sele = SelectorIndexByName(G, rec->name);
if(sele >= 0) { if(sele >= 0) {
ObjectMoleculeOpRecInit(&op); ObjectMoleculeOpRecInit(&op);
op.code = OMOP_INVA; op.code = OMOP_INVA;
op.i1 = rep; op.i1 = (rep == cRepAll) ? cRepBitmask : (1 << rep);
op.i2 = level; op.i2 = level;
ExecutiveObjMolSeleOp(G, sele, &op); ExecutiveObjMolSeleOp(G, sele, &op);
} else if(rec->obj->fInvalidate) { } else if(rec->obj->fInvalidate) {
rec->obj->fInvalidate(rec->obj, rep, level, -1); rec->obj->fInvalidate(rec->obj, rep, level, -1);
} }
} }
break; break;
case cExecAll: case cExecAll:
rec = NULL; rec = NULL;
while(ListIterate(I->Spec, rec, next)) { while(ListIterate(I->Spec, rec, next)) {
skipping to change at line 14737 skipping to change at line 14729
} }
PRINTFD(G, FB_Executive) PRINTFD(G, FB_Executive)
" ExecutiveSymExp: leaving...\n" ENDFD; " ExecutiveSymExp: leaving...\n" ENDFD;
SettingSetGlobal_i(G, cSetting_auto_zoom, auto_save); SettingSetGlobal_i(G, cSetting_auto_zoom, auto_save);
} }
static void ExecutivePurgeSpec(PyMOLGlobals * G, SpecRec * rec) static void ExecutivePurgeSpec(PyMOLGlobals * G, SpecRec * rec)
{ {
CExecutive *I = G->Executive; CExecutive *I = G->Executive;
if (rec->gridSlotSelIndicatorsCGO){
CGOFree(rec->gridSlotSelIndicatorsCGO); CGOFree(rec->gridSlotSelIndicatorsCGO);
rec->gridSlotSelIndicatorsCGO = NULL;
}
if(rec->group_name[0]) { if(rec->group_name[0]) {
/* cascade group members up to the surrounding group */ /* cascade group members up to the surrounding group */
SpecRec *rec2 = NULL; SpecRec *rec2 = NULL;
while(ListIterate(I->Spec, rec2, next)) { while(ListIterate(I->Spec, rec2, next)) {
if((rec2->group == rec) || WordMatchExact(G, rec->name, rec2->group_name, true)) { if((rec2->group == rec) || WordMatchExact(G, rec->name, rec2->group_name, true)) {
strcpy(rec2->group_name, rec->group_name); strcpy(rec2->group_name, rec->group_name);
} }
} }
} else if((rec->type == cExecObject) && (rec->obj->type == cObjectGroup)) { } else if((rec->type == cExecObject) && (rec->obj->type == cObjectGroup)) {
/* and/or delete their group membership */ /* and/or delete their group membership */
skipping to change at line 14833 skipping to change at line 14823
break; break;
} }
} }
SelectorDefragment(G); SelectorDefragment(G);
break; break;
} }
} }
} }
TrackerDelList(I_Tracker, list_id); TrackerDelList(I_Tracker, list_id);
TrackerDelIter(I_Tracker, iter_id); TrackerDelIter(I_Tracker, iter_id);
// fix for PYMOL-757 - Note: This should probably go somewhere else, but we
// couldn't figure out the correct place so far
ExecutiveUpdateGroups(G, false); ExecutiveUpdateGroups(G, false);
} }
/*========================================================================*/ /*========================================================================*/
void ExecutiveDump(PyMOLGlobals * G, const char *fname, const char *obj) void ExecutiveDump(PyMOLGlobals * G, const char *fname, const char *obj)
{ {
SpecRec *rec = NULL; SpecRec *rec = NULL;
CExecutive *I = G->Executive; CExecutive *I = G->Executive;
SceneUpdate(G, false); SceneUpdate(G, false);
skipping to change at line 15128 skipping to change at line 15121
static int ExecutiveClick(Block * block, int button, int x, int y, int mod) static int ExecutiveClick(Block * block, int button, int x, int y, int mod)
{ {
PyMOLGlobals *G = block->G; PyMOLGlobals *G = block->G;
CExecutive *I = G->Executive; CExecutive *I = G->Executive;
int n, a; int n, a;
SpecRec *rec = NULL; SpecRec *rec = NULL;
PanelRec *panel = NULL; PanelRec *panel = NULL;
int t, xx; int t, xx;
int pass = false; int pass = false;
int skip; int skip;
int ExecLineHeight = SettingGetGlobal_i(G, cSetting_internal_gui_control_size) ; int ExecLineHeight = DIP2PIXEL(SettingGetGlobal_i(G, cSetting_internal_gui_con trol_size));
int hide_underscore = SettingGetGlobal_b(G, cSetting_hide_underscore_names); int hide_underscore = SettingGetGlobal_b(G, cSetting_hide_underscore_names);
int op_cnt = get_op_cnt(G); int op_cnt = get_op_cnt(G);
if(y < I->HowFarDown) { if(y < I->HowFarDown) {
if(SettingGetGlobal_b(G, cSetting_internal_gui_mode) == 1) if(SettingGetGlobal_b(G, cSetting_internal_gui_mode) == 1)
return SceneDeferClick(SceneGetBlock(G), button, x, y, mod); return SceneDeferClick(SceneGetBlock(G), button, x, y, mod);
} }
n = ((I->Block->rect.top - y) - (ExecTopMargin + ExecClickMargin)) / ExecLineH eight; n = ((I->Block->rect.top - y) - (ExecTopMargin + ExecClickMargin)) / ExecLineH eight;
a = n; a = n;
xx = (x - I->Block->rect.left); xx = (x - I->Block->rect.left);
skipping to change at line 15391 skipping to change at line 15384
case cObjectMesh: case cObjectMesh:
MenuActivate(G, mx, my, x, y, false, "obj_motion", namesele) ; MenuActivate(G, mx, my, x, y, false, "obj_motion", namesele) ;
break; break;
} }
break; break;
} }
break; break;
} }
} else { /* clicked in variable area */ } else { /* clicked in variable area */
if(((panel->is_group) && (((xx) - 1) / 8) > (panel->nest_level + 1 if(((panel->is_group) && (((xx) - 1) / DIP2PIXEL(8)) > (panel->nes
)) || t_level + 1)) ||
((!panel->is_group) && (((xx) - 1) / 8) > panel->nest_level)) { ((!panel->is_group) && (((xx) - 1) / DIP2PIXEL(8)) > panel->nes
t_level)) {
/* clicked on name */ /* clicked on name */
rec->hilight = 1; rec->hilight = 1;
switch (button) { switch (button) {
case P_GLUT_LEFT_BUTTON: case P_GLUT_LEFT_BUTTON:
I->Pressed = n; I->Pressed = n;
I->OldVisibility = rec->visible; I->OldVisibility = rec->visible;
I->Over = n; I->Over = n;
I->DragMode = 1; I->DragMode = 1;
I->ToggleMode = 0; I->ToggleMode = 0;
skipping to change at line 15669 skipping to change at line 15662
/*while(ListIterate(I->Spec,rec,next)) { */ /*while(ListIterate(I->Spec,rec,next)) { */
while(ListIterate(I->Panel, panel, next)) { while(ListIterate(I->Panel, panel, next)) {
rec = panel->spec; rec = panel->spec;
if((rec->name[0] != '_') || (!hide_underscore)) { if((rec->name[0] != '_') || (!hide_underscore)) {
if(skip) { if(skip) {
skip--; skip--;
} else { } else {
if((I->PressedWhat == 1) && if((I->PressedWhat == 1) &&
(((panel->is_group) && ((xx - 1) / 8) > (panel->nest_level + 1)) (((panel->is_group) && ((xx - 1) / DIP2PIXEL(8)) > (panel->nest_l
|| evel + 1)) ||
((!panel->is_group) && ((xx - 1) / 8) > panel->nest_level))) { ((!panel->is_group) && ((xx - 1) / DIP2PIXEL(8)) > panel->nest_l
evel))) {
/* over name */ /* over name */
if(rec->hilight == 1) { if(rec->hilight == 1) {
if(rec->type == cExecSelection) { if(rec->type == cExecSelection) {
ExecutiveSpecSetVisibility(G, rec, !I->OldVisibility, 0, false ); ExecutiveSpecSetVisibility(G, rec, !I->OldVisibility, 0, false );
} else { } else {
ExecutiveSpecSetVisibility(G, rec, !I->OldVisibility, mod, tru e); ExecutiveSpecSetVisibility(G, rec, !I->OldVisibility, mod, tru e);
} }
} }
} else if((I->PressedWhat == 2) && (panel->is_group)) { } else if((I->PressedWhat == 2) && (panel->is_group)) {
if(rec->hilight == 2) { if(rec->hilight == 2) {
skipping to change at line 15726 skipping to change at line 15719
PyMOL_NeedRedisplay(G->PyMOL); PyMOL_NeedRedisplay(G->PyMOL);
return (1); return (1);
} }
/*========================================================================*/ /*========================================================================*/
static int ExecutiveDrag(Block * block, int x, int y, int mod) static int ExecutiveDrag(Block * block, int x, int y, int mod)
{ {
PyMOLGlobals *G = block->G; PyMOLGlobals *G = block->G;
CExecutive *I = G->Executive; CExecutive *I = G->Executive;
int xx, t; int xx, t;
int ExecLineHeight = SettingGetGlobal_i(G, cSetting_internal_gui_control_size) ; int ExecLineHeight = DIP2PIXEL(SettingGetGlobal_i(G, cSetting_internal_gui_con trol_size));
int hide_underscore = SettingGetGlobal_b(G, cSetting_hide_underscore_names); int hide_underscore = SettingGetGlobal_b(G, cSetting_hide_underscore_names);
int op_cnt = get_op_cnt(G); int op_cnt = get_op_cnt(G);
ExecutiveUpdateGroups(G, false); ExecutiveUpdateGroups(G, false);
ExecutiveUpdatePanelList(G); ExecutiveUpdatePanelList(G);
if(y < I->HowFarDown) { if(y < I->HowFarDown) {
if(SettingGetGlobal_b(G, cSetting_internal_gui_mode) == 1) if(SettingGetGlobal_b(G, cSetting_internal_gui_mode) == 1)
return SceneDeferDrag(SceneGetBlock(G), x, y, mod); return SceneDeferDrag(SceneGetBlock(G), x, y, mod);
} }
skipping to change at line 15774 skipping to change at line 15767
int row = 0; int row = 0;
while(ListIterate(I->Panel, panel, next)) { while(ListIterate(I->Panel, panel, next)) {
rec = panel->spec; rec = panel->spec;
if((rec->name[0] != '_') || (!hide_underscore)) { if((rec->name[0] != '_') || (!hide_underscore)) {
if(skip) { if(skip) {
skip--; skip--;
} else { } else {
if(rec == I->RecoverPressed) { if(rec == I->RecoverPressed) {
I->Pressed = row; I->Pressed = row;
I->RecoverPressed = false; I->RecoverPressed = NULL;
} }
row++; row++;
} }
} }
} }
} }
if(I->PressedWhat == 2) { if(I->PressedWhat == 2) {
I->OverWhat = 0; I->OverWhat = 0;
} }
skipping to change at line 15807 skipping to change at line 15800
if((rec->name[0] != '_') || (!hide_underscore)) { if((rec->name[0] != '_') || (!hide_underscore)) {
if(skip) { if(skip) {
skip--; skip--;
} else { } else {
rec->hilight = 0; rec->hilight = 0;
if((I->PressedWhat == 1) && /* name button */ if((I->PressedWhat == 1) && /* name button */
(((row >= I->Over) && (row <= I->Pressed)) || (((row >= I->Over) && (row <= I->Pressed)) ||
((row >= I->Pressed) && (row <= I->Over)))) { ((row >= I->Pressed) && (row <= I->Over)))) {
if(((panel->is_group) && ((xx - 1) / 8) > (panel->nest_level + if(((panel->is_group) && ((xx - 1) / DIP2PIXEL(8)) > (panel->n
1)) || est_level + 1)) ||
((!panel->is_group) && ((xx - 1) / 8) > panel->nest_level)) ((!panel->is_group) && ((xx - 1) / DIP2PIXEL(8)) > panel->n
{ est_level)) {
/* dragged over name */ /* dragged over name */
I->OverWhat = 1; I->OverWhat = 1;
switch (I->ToggleMode) { switch (I->ToggleMode) {
case 0: case 0:
if(row || (row == I->Pressed)) if(row || (row == I->Pressed))
rec->hilight = 1; rec->hilight = 1;
break; break;
case 1: case 1:
skipping to change at line 15843 skipping to change at line 15836
if(rec != I->LastZoomed) if(rec != I->LastZoomed)
ExecutiveWindowZoom(G, rec->name, 0.0F, -1, false, - 1.0F, ExecutiveWindowZoom(G, rec->name, 0.0F, -1, false, - 1.0F,
true); true);
I->LastZoomed = rec; I->LastZoomed = rec;
} }
} }
break; break;
} }
} }
} else if((row == I->Pressed) && (I->PressedWhat == 2)) { } else if((row == I->Pressed) && (I->PressedWhat == 2)) {
if(!((panel->is_group) && ((xx - 1) / 8) > (panel->nest_level + 1))) { if(!((panel->is_group) && ((xx - 1) / DIP2PIXEL(8)) > (panel-> nest_level + 1))) {
/* on group control */ /* on group control */
I->OverWhat = 2; I->OverWhat = 2;
if(I->PressedWhat == I->OverWhat) { if(I->PressedWhat == I->OverWhat) {
rec->hilight = 2; rec->hilight = 2;
} }
} else { } else {
I->OverWhat = 0; I->OverWhat = 0;
} }
skipping to change at line 16168 skipping to change at line 16161
float toggleColor3[3] = { 0.6F, 0.6F, 0.8F }; float toggleColor3[3] = { 0.6F, 0.6F, 0.8F };
#endif #endif
SpecRec *rec = NULL; SpecRec *rec = NULL;
PanelRec *panel = NULL; PanelRec *panel = NULL;
CExecutive *I = G->Executive; CExecutive *I = G->Executive;
int n_ent; int n_ent;
int n_disp; int n_disp;
int skip = 0; int skip = 0;
int row = -1; int row = -1;
int ExecLineHeight = SettingGetGlobal_i(G, cSetting_internal_gui_control_size) int ExecLineHeight = DIP2PIXEL(SettingGetGlobal_i(G, cSetting_internal_gui_con
; trol_size));
int text_lift = (ExecLineHeight / 2) - 5; int text_lift = (ExecLineHeight / 2) - DIP2PIXEL(5);
int hide_underscore = SettingGetGlobal_b(G, cSetting_hide_underscore_names); int hide_underscore = SettingGetGlobal_b(G, cSetting_hide_underscore_names);
int op_cnt = get_op_cnt(G); int op_cnt = get_op_cnt(G);
int full_names = SettingGetGlobal_b(G, cSetting_group_full_member_names); int full_names = SettingGetGlobal_b(G, cSetting_group_full_member_names);
int arrows = SettingGetGlobal_b(G, cSetting_group_arrow_prefix); int arrows = SettingGetGlobal_b(G, cSetting_group_arrow_prefix);
ExecutiveUpdatePanelList(G); ExecutiveUpdatePanelList(G);
/* if we're running with a GUI and have a valid panel */ /* if we're running with a GUI and have a valid panel */
if(G->HaveGUI && G->ValidContext && ((block->rect.right - block->rect.left) > 6) if(G->HaveGUI && G->ValidContext && ((block->rect.right - block->rect.left) > 6)
&& I->ValidPanel) { && I->ValidPanel) {
skipping to change at line 16228 skipping to change at line 16221
I->NSkip = 0; I->NSkip = 0;
} }
/* determination of longest string based on internal_gui_size, etc... */ /* determination of longest string based on internal_gui_size, etc... */
max_char = max_char =
(((I->Block->rect.right - I->Block->rect.left) - (((I->Block->rect.right - I->Block->rect.left) -
(ExecLeftMargin + ExecRightMargin + 4)) - (op_cnt * ExecToggleWidth)); (ExecLeftMargin + ExecRightMargin + 4)) - (op_cnt * ExecToggleWidth));
if(I->ScrollBarActive) { if(I->ScrollBarActive) {
max_char -= (ExecScrollBarMargin + ExecScrollBarWidth); max_char -= (ExecScrollBarMargin + ExecScrollBarWidth);
} }
max_char /= 8; max_char /= DIP2PIXEL(8);
/* fill and outline the entire block */ /* fill and outline the entire block */
if(SettingGetGlobal_b(G, cSetting_internal_gui_mode) == 0) { if(SettingGetGlobal_b(G, cSetting_internal_gui_mode) == 0) {
if (orthoCGO) if (orthoCGO)
CGOColorv(orthoCGO, I->Block->BackColor); CGOColorv(orthoCGO, I->Block->BackColor);
else else
glColor3fv(I->Block->BackColor); glColor3fv(I->Block->BackColor);
BlockFill(I->Block ORTHOCGOARGVAR); BlockFill(I->Block ORTHOCGOARGVAR);
BlockDrawLeftEdge(I->Block ORTHOCGOARGVAR); BlockDrawLeftEdge(I->Block ORTHOCGOARGVAR);
} }
skipping to change at line 16370 skipping to change at line 16363
} }
} }
/* end ASHLC */ /* end ASHLC */
#endif #endif
{ {
int x3 = x; int x3 = x;
int hidden_prefix = false; int hidden_prefix = false;
TextSetColor(G, I->Block->TextColor); TextSetColor(G, I->Block->TextColor);
TextSetPos2i(G, x3 + 2, y2 + text_lift); TextSetPos2i(G, x3 + DIP2PIXEL(2), y2 + text_lift);
if((rec->type == cExecObject) || if((rec->type == cExecObject) ||
(rec->type == cExecAll) || (rec->type == cExecSelection)) { (rec->type == cExecAll) || (rec->type == cExecSelection)) {
y2 = y; y2 = y;
x2 = xx; x2 = xx;
if((x - ExecToggleMargin) - (xx - ExecToggleMargin) > -10) { if((x - ExecToggleMargin) - (xx - ExecToggleMargin) > DIP2PIXEL(-1
x2 = x + 10; 0)) {
x2 = x + DIP2PIXEL(10);
} }
x3 += panel->nest_level * 8; x3 += panel->nest_level * DIP2PIXEL(8);
TextSetPos2i(G, x3 + 2, y2 + text_lift); TextSetPos2i(G, x3 + DIP2PIXEL(2), y2 + text_lift);
nChar -= panel->nest_level; nChar -= panel->nest_level;
{ {
int but_width = (x2 - x3) - 1; int but_width = (x2 - x3) - 1;
/* drawing a group +/- NAME */ /* drawing a group +/- NAME */
if(panel->is_group) { if(panel->is_group) {
const int button_width = DIP2PIXEL(15);
if((rec->hilight == 2) && (I->Over == I->Pressed)) { if((rec->hilight == 2) && (I->Over == I->Pressed)) {
draw_button(x3, y2, 15, (ExecLineHeight - 1), lightEdge, dar kEdge, draw_button(x3, y2, button_width, (ExecLineHeight - 1), ligh tEdge, darkEdge,
pressedColor ORTHOCGOARGVAR); pressedColor ORTHOCGOARGVAR);
} else if(panel->is_open) { } else if(panel->is_open) {
draw_button(x3, y2, 15, (ExecLineHeight - 1), lightEdge, dar kEdge, draw_button(x3, y2, button_width, (ExecLineHeight - 1), ligh tEdge, darkEdge,
disabledColor ORTHOCGOARGVAR); disabledColor ORTHOCGOARGVAR);
} else { } else {
draw_button(x3, y2, 15, (ExecLineHeight - 1), lightEdge, dar kEdge, draw_button(x3, y2, button_width, (ExecLineHeight - 1), ligh tEdge, darkEdge,
disabledColor ORTHOCGOARGVAR); disabledColor ORTHOCGOARGVAR);
} }
TextSetPos2i(G, x3 + DIP2PIXEL(4), y2 + text_lift);
#define cControlBoxSize 17
#define cControlLeftMargin 8
#define cControlTopMargin 2
#define cControlSpacing 2
#define cControlInnerMargin 4
#define cControlSpread 6
#define cControlSize 160
TextSetPos2i(G, x3 + 4, y2 + text_lift);
if(panel->is_open) { if(panel->is_open) {
TextDrawChar(G, '-' ORTHOCGOARGVAR); TextDrawChar(G, '-' ORTHOCGOARGVAR);
} else { } else {
TextDrawChar(G, '+' ORTHOCGOARGVAR); TextDrawChar(G, '+' ORTHOCGOARGVAR);
} }
but_width -= 16; but_width -= DIP2PIXEL(16);
x3 += 16; x3 += DIP2PIXEL(16);
nChar -= 2; nChar -= 2;
TextSetPos2i(G, x3 + 2, y2 + text_lift); TextSetPos2i(G, x3 + DIP2PIXEL(2), y2 + text_lift);
} }
if((rec->hilight == 1) || ((row == I->Over) && (I->OverWhat == 1 ))) { if((rec->hilight == 1) || ((row == I->Over) && (I->OverWhat == 1 ))) {
/* button hull */ /* button hull */
draw_button(x3, y2, but_width, (ExecLineHeight - 1), lightEdge , draw_button(x3, y2, but_width, (ExecLineHeight - 1), lightEdge ,
darkEdge, pressedColor ORTHOCGOARGVAR); darkEdge, pressedColor ORTHOCGOARGVAR);
} else if(rec->visible) { } else if(rec->visible) {
int enabled = true; int enabled = true;
SpecRec *group_rec = rec->group; SpecRec *group_rec = rec->group;
while(enabled && group_rec) { while(enabled && group_rec) {
skipping to change at line 16480 skipping to change at line 16465
if((nChar--) > 0) { if((nChar--) > 0) {
TextDrawChar(G, '(' ORTHOCGOARGVAR); TextDrawChar(G, '(' ORTHOCGOARGVAR);
} }
} }
if(c) { if(c) {
if(hidden_prefix) { if(hidden_prefix) {
/* ^.name */ /* ^.name */
if(arrows && ((nChar--) > 0)) { if(arrows && ((nChar--) > 0)) {
TextDrawChar(G, '^' ORTHOCGOARGVAR); TextDrawChar(G, '^' ORTHOCGOARGVAR);
TextSetPos2i(G, x3 + 2, y2 + text_lift); TextSetPos2i(G, x3 + DIP2PIXEL(2), y2 + text_lift);
TextDrawChar(G, '|' ORTHOCGOARGVAR); TextDrawChar(G, '|' ORTHOCGOARGVAR);
} }
} }
/* draw the object name, char by char */ /* draw the object name, char by char */
while(*c) { while(*c) {
if((nChar--) > 0) { if((nChar--) > 0) {
TextDrawChar(G, *(c++) ORTHOCGOARGVAR); TextDrawChar(G, *(c++) ORTHOCGOARGVAR);
} }
else else
skipping to change at line 16513 skipping to change at line 16498
/* OBJECTS: output any label captions, like state number, state title */ /* OBJECTS: output any label captions, like state number, state title */
if(rec->type == cExecObject) { if(rec->type == cExecObject) {
if(rec->obj->fGetCaption) { if(rec->obj->fGetCaption) {
/* get this object's "caption" that goes on its title line, /* get this object's "caption" that goes on its title line,
* currently, this is "state-title [curState/nState]" */ * currently, this is "state-title [curState/nState]" */
c = rec->obj->fGetCaption(rec->obj, ch, WordLength); c = rec->obj->fGetCaption(rec->obj, ch, WordLength);
} }
/* now print the caption */ /* now print the caption */
if(c && c[0] && nChar > 1 && strcmp(c, rec->obj->Name) != 0) { if(c && c[0] && nChar > 1 && strcmp(c, rec->obj->Name) != 0) {
TextSetColor(G, captionColor); TextSetColor(G, captionColor);
TextSetPos2i(G, x + 2 + 8 * (max_char - nChar), y2 + text_lift); TextSetPos2i(G, x + DIP2PIXEL(2) + DIP2PIXEL(8) * (max_char - nC har), y2 + text_lift);
if((nChar--) > 0) if((nChar--) > 0)
TextDrawChar(G, ' ' ORTHOCGOARGVAR); TextDrawChar(G, ' ' ORTHOCGOARGVAR);
while(*c) while(*c && nChar > 0) {
if((nChar--) > 0) {
/* allow color encoding for names */ /* allow color encoding for names */
if((*c == '\\') && (*(c + 1)) && (*(c + 2)) && (*(c + 3))) { if((*c == '\\') && (*(c + 1)) && (*(c + 2)) && (*(c + 3))) {
TextSetColor3f(G, (*(c + 1) - '0') / 9.0F, (*(c + 2) - '0') / 9.0F, TextSetColor3f(G, (*(c + 1) - '0') / 9.0F, (*(c + 2) - '0') / 9.0F,
(*(c + 3) - '0') / 9.0F); (*(c + 3) - '0') / 9.0F);
c += 4; c += 4;
} } else {
TextDrawChar(G, *(c++) ORTHOCGOARGVAR); TextDrawChar(G, *(c++) ORTHOCGOARGVAR);
--nChar;
} }
else }
break;
} }
/* I added this to fix a string clearing problem,
* but it then caused an issue with groups. Interestingly,
* removing this fixes the bug and no longer makes the other bug */
/* c[0] = 0; */
} }
} }
y -= ExecLineHeight; y -= ExecLineHeight;
if(y < (I->Block->rect.bottom)) if(y < (I->Block->rect.bottom))
break; break;
} }
} }
} }
I->HowFarDown = y; I->HowFarDown = y;
skipping to change at line 16761 skipping to change at line 16741
} else } else
return 0; return 0;
} }
/*========================================================================*/ /*========================================================================*/
void ExecutiveFree(PyMOLGlobals * G) void ExecutiveFree(PyMOLGlobals * G)
{ {
CExecutive *I = G->Executive; CExecutive *I = G->Executive;
SpecRec *rec = NULL; SpecRec *rec = NULL;
if (I->selIndicatorsCGO)
CGOFree(I->selIndicatorsCGO); CGOFree(I->selIndicatorsCGO);
I->selIndicatorsCGO = NULL;
while(ListIterate(I->Spec, rec, next)) { while(ListIterate(I->Spec, rec, next)) {
if(rec->type == cExecObject) if(rec->type == cExecObject)
rec->obj->fFree(rec->obj); rec->obj->fFree(rec->obj);
} }
ListFree(I->Spec, next, SpecRec); ListFree(I->Spec, next, SpecRec);
ListFree(I->Panel, next, PanelRec); ListFree(I->Panel, next, PanelRec);
if(I->Tracker) if(I->Tracker)
TrackerFree(I->Tracker); TrackerFree(I->Tracker);
if(I->ScrollBar) if(I->ScrollBar)
ScrollBarFree(I->ScrollBar); ScrollBarFree(I->ScrollBar);
 End of changes. 97 change blocks. 
208 lines changed or deleted 190 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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