"Fossies" - the Fresh Open Source Software Archive  

Source code changes of the file "layer3/Executive.h" 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.h  (pymol-v1.8.6.0.tar.bz2):Executive.h  (pymol-v2.1.0.tar.bz2)
skipping to change at line 137 skipping to change at line 137
SpecRec *rec; SpecRec *rec;
public: public:
ObjectIterator(PyMOLGlobals * G) : G(G) { ObjectIterator(PyMOLGlobals * G) : G(G) {
reset(); reset();
}; };
void reset(); void reset();
bool next(); bool next();
CObject * getObject(); CObject * getObject();
SpecRec * getSpecRec() { return rec; }
}; };
const char * ExecutiveMapGenerate(PyMOLGlobals * G, const char * name, const cha r * reflection_file, const char * tempFile, const char * ExecutiveMapGenerate(PyMOLGlobals * G, const char * name, const cha r * reflection_file, const char * tempFile,
char * amplitudes, const char * phases, const c har * weights, double reso_low, char * amplitudes, const char * phases, const c har * weights, double reso_low,
double reso_high, const char * space_group, dou ble cell[6], int quiet, int zoom); double reso_high, const char * space_group, dou ble cell[6], int quiet, int zoom);
int ExecutiveReference(PyMOLGlobals * G, int action, const char *sele, int state , int quiet); int ExecutiveReference(PyMOLGlobals * G, int action, const char *sele, int state , int quiet);
int ExecutiveGetExpandedGroupList(PyMOLGlobals * G, const char *name); int ExecutiveGetExpandedGroupList(PyMOLGlobals * G, const char *name);
int ExecutiveGetExpandedGroupListFromPattern(PyMOLGlobals * G, const char *name) ; int ExecutiveGetExpandedGroupListFromPattern(PyMOLGlobals * G, const char *name) ;
void ExecutiveFreeGroupList(PyMOLGlobals * G, int list_id); void ExecutiveFreeGroupList(PyMOLGlobals * G, int list_id);
skipping to change at line 186 skipping to change at line 187
const ExecutiveObjectOffset * ExecutiveUniqueIDAtomDictGet(PyMOLGlobals * G, int i); const ExecutiveObjectOffset * ExecutiveUniqueIDAtomDictGet(PyMOLGlobals * G, int i);
void ExecutiveUniqueIDAtomDictInvalidate(PyMOLGlobals * G); void ExecutiveUniqueIDAtomDictInvalidate(PyMOLGlobals * G);
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, const char *object_name,
int state, int zoom, int state, int zoom,
int discrete, int finish, int multiplex, int quiet, const char *plugin, int discrete, int finish, int multiplex, int quiet, const char *plugin,
const char * object_props=NULL, const char * atom_props=NULL); const char * object_props=NULL, const char * atom_props=NULL,
bool mimic=true);
int ExecutiveDebug(PyMOLGlobals * G, const char *name); int ExecutiveDebug(PyMOLGlobals * G, const char *name);
typedef struct { typedef struct {
int n_residues_aligned; int n_residues_aligned;
float raw_alignment_score; float raw_alignment_score;
int initial_n_atom; int initial_n_atom;
float initial_rms; float initial_rms;
int n_cycles_run; int n_cycles_run;
int final_n_atom; int final_n_atom;
skipping to change at line 295 skipping to change at line 297
int index, const char *value, CObject * obj , int index, const char *value, CObject * obj ,
int state, int quiet, int updates); int state, int quiet, int updates);
int ExecutiveRay(PyMOLGlobals * G, int width, int height, int mode, int ExecutiveRay(PyMOLGlobals * G, int width, int height, int mode,
float angle, float shift, int quiet, int defer, int antialias); float angle, float shift, int quiet, int defer, int antialias);
int ExecutiveGetDistance(PyMOLGlobals * G, const char *s0, const char *s1, float *value, int state); int ExecutiveGetDistance(PyMOLGlobals * G, const char *s0, const char *s1, float *value, int state);
int ExecutiveGetAngle(PyMOLGlobals * G, const char *s0, const char *s1, const ch ar *s2, float *value, int ExecutiveGetAngle(PyMOLGlobals * G, const char *s0, const char *s1, const ch ar *s2, float *value,
int state); int state);
int ExecutiveGetDihe(PyMOLGlobals * G, const char *s0, const char *s1, const cha r *s2, const char *s3, int ExecutiveGetDihe(PyMOLGlobals * G, const char *s0, const char *s1, const cha r *s2, const char *s3,
float *value, int state); float *value, int state);
int ExecutiveSetDihe(PyMOLGlobals * G, const char *s0, const char *s1, const cha r *s2, const char *s3, int ExecutiveSetDihe(PyMOLGlobals * G, const char *s0, const char *s1, const cha r *s2, const char *s3,
float value, int state, int quiet); float value, int state=0, int quiet=1);
int ExecutiveRMS(PyMOLGlobals * G, const char *sele1, const char *sele2, int mod e, float refine, int ExecutiveRMS(PyMOLGlobals * G, const char *sele1, const char *sele2, int mod e, float refine,
int max_cyc, int quiet, const char *oname, int state1, int stat e2, int max_cyc, int quiet, const char *oname, int state1, int stat e2,
int ordered_selections, int matchmaker, ExecutiveRMSInfo * rms_ info); int ordered_selections, int matchmaker, ExecutiveRMSInfo * rms_ info);
void ExecutiveUpdateCmd(PyMOLGlobals * G, const char *sele1, const char *sele2, int sta1, int sta2, void ExecutiveUpdateCmd(PyMOLGlobals * G, const char *sele1, const char *sele2, int sta1, int sta2,
int method, int quiet); int method, int quiet);
float ExecutiveRMSPairs(PyMOLGlobals * G, WordType * sele, int pairs, int mode); float ExecutiveRMSPairs(PyMOLGlobals * G, WordType * sele, int pairs, int mode);
float *ExecutiveRMSStates(PyMOLGlobals * G, const char *s1, int target, int mode , int quiet, float *ExecutiveRMSStates(PyMOLGlobals * G, const char *s1, int target, int mode , int quiet,
int mix); int mix);
int *ExecutiveIdentify(PyMOLGlobals * G, const char *s1, int mode); int *ExecutiveIdentify(PyMOLGlobals * G, const char *s1, int mode);
int ExecutiveIndex(PyMOLGlobals * G, const char *s1, int mode, int **indexVLA, int ExecutiveIndex(PyMOLGlobals * G, const char *s1, int mode, int **indexVLA,
ObjectMolecule *** objVLA); ObjectMolecule *** objVLA);
int ExecutiveReset(PyMOLGlobals * G, int cmd, const char *name); int ExecutiveReset(PyMOLGlobals * G, int cmd, const char *name);
void ExecutiveResetMatrix(PyMOLGlobals * G, void ExecutiveResetMatrix(PyMOLGlobals * G,
const char *name, int mode, int state, int log, int qu iet); const char *name, int mode, int state, int log, int qu iet);
void ExecutiveDrawNow(PyMOLGlobals * G); void ExecutiveDrawNow(PyMOLGlobals * G);
int ExecutiveDrawCmd(PyMOLGlobals * G, int width, int height, int antialias, int ExecutiveDrawCmd(PyMOLGlobals * G, int width, int height, int antialias,
int entire_window, int quiet); int entire_window, int quiet);
int ExecutiveCartoon(PyMOLGlobals * G, int type, const char *sele); int ExecutiveCartoon(PyMOLGlobals * G, int type, const char *sele);
void ExecutiveSetAllVisib(PyMOLGlobals * G, int state);
void ExecutiveSetRepVisib(PyMOLGlobals * G, const char *name, int rep, int state ); void ExecutiveSetRepVisib(PyMOLGlobals * G, const char *name, int rep, int state );
void ExecutiveSetRepVisMask(PyMOLGlobals * G, const char *name, int repmask, int state);
int ExecutiveToggleRepVisib(PyMOLGlobals * G, const char *name, int rep); int ExecutiveToggleRepVisib(PyMOLGlobals * G, const char *name, int rep);
int ExecutiveSetObjVisib(PyMOLGlobals * G, const char *name, int onoff, int pare nts); int ExecutiveSetObjVisib(PyMOLGlobals * G, const char *name, int onoff, int pare nts);
int ExecutiveOrigin(PyMOLGlobals * G, const char *name, int preserve, const char *oname, float *pos, int ExecutiveOrigin(PyMOLGlobals * G, const char *name, int preserve, const char *oname, float *pos,
int state); int state);
int ExecutiveCenter(PyMOLGlobals * G, const char *name, int state, int inclusive , float animate, int ExecutiveCenter(PyMOLGlobals * G, const char *name, int state, int inclusive , float animate,
float *pos, int quiet); float *pos, int quiet);
void ExecutiveDoZoom(PyMOLGlobals * G, CObject * obj, int is_new, int zoom, int quiet); void ExecutiveDoZoom(PyMOLGlobals * G, CObject * obj, int is_new, int zoom, int quiet);
int ExecutiveWindowZoom(PyMOLGlobals * G, const char *name, float buffer, int ExecutiveWindowZoom(PyMOLGlobals * G, const char *name, float buffer,
skipping to change at line 359 skipping to change at line 361
int ExecutiveGetCameraExtent(PyMOLGlobals * G, const char *name, float *mn, floa t *mx, int ExecutiveGetCameraExtent(PyMOLGlobals * G, const char *name, float *mn, floa t *mx,
int transformed, int state); int transformed, int state);
int ExecutiveSeleToObject(PyMOLGlobals * G, const char *name, const char *s1, in t source, int target, int ExecutiveSeleToObject(PyMOLGlobals * G, const char *name, const char *s1, in t source, int target,
int discrete, int zoom, int quiet, int singletons, int copy_properties=0); int discrete, int zoom, int quiet, int singletons, int copy_properties=0);
PyObject *ExecutiveSeleToChemPyModel(PyMOLGlobals * G, const char *s1, int state , PyObject *ExecutiveSeleToChemPyModel(PyMOLGlobals * G, const char *s1, int state ,
const char *ref_object, int ref_state); const char *ref_object, int ref_state);
void ExecutiveInvalidateRep(PyMOLGlobals * G, const char *name, int rep, int lev el); void ExecutiveInvalidateRep(PyMOLGlobals * G, const char *name, int rep, int lev el);
void ExecutiveFlag(PyMOLGlobals * G, int flag, const char *s1, int action, int q uiet); void ExecutiveFlag(PyMOLGlobals * G, int flag, const char *s1, int action, int q uiet);
void ExecutiveRemoveAtoms(PyMOLGlobals * G, const char *s1, int quiet); void ExecutiveRemoveAtoms(PyMOLGlobals * G, const char *s1, int quiet);
void ExecutiveProtect(PyMOLGlobals * G, const char *s1, int mode, int quiet); void ExecutiveProtect(PyMOLGlobals * G, const char *s1, int mode, int quiet);
void ExecutiveMask(PyMOLGlobals * G, const char *s1, int mode, int quiet); void ExecutiveMask(PyMOLGlobals * G, const char *s1, int mode=1, int quiet=1);
void ExecutiveRebuildAll(PyMOLGlobals * G); void ExecutiveRebuildAll(PyMOLGlobals * G);
void ExecutiveSpheroid(PyMOLGlobals * G, const char *name, int average); void ExecutiveSpheroid(PyMOLGlobals * G, const char *name, int average);
void ExecutiveAddHydrogens(PyMOLGlobals * G, const char *s1, int quiet); void ExecutiveAddHydrogens(PyMOLGlobals * G, const char *s1="(all)", int quiet=1 , int state=-1, bool legacy=false);
void ExecutiveFixHydrogens(PyMOLGlobals * G, const char *s1, int quiet); void ExecutiveFixHydrogens(PyMOLGlobals * G, const char *s1, int quiet);
void ExecutiveFuse(PyMOLGlobals * G, const char *s0, const char *s1, int mode, i void ExecutiveFuse(PyMOLGlobals * G, const char *s0="(pk1)", const char *s1="(pk
nt recolor, 2)", int mode=0, int recolor=1,
int move_flag); int move_flag=1);
void ExecutiveRenameObjectAtoms(PyMOLGlobals * G, const char *name, int force, i nt quiet); void ExecutiveRenameObjectAtoms(PyMOLGlobals * G, const char *name, int force, i nt quiet);
int ExecutiveInvert(PyMOLGlobals * G, int quiet); int ExecutiveInvert(PyMOLGlobals * G, int quiet);
char *ExecutiveGetNames(PyMOLGlobals * G, int mode, int enabled_only, const char *s0); char *ExecutiveGetNames(PyMOLGlobals * G, int mode, int enabled_only, const char *s0);
bool ExecutiveIsMoleculeOrSelection(PyMOLGlobals * G, const char *name); bool ExecutiveIsMoleculeOrSelection(PyMOLGlobals * G, const char *name);
int ExecutiveGetType(PyMOLGlobals * G, const char *name, WordType type); int ExecutiveGetType(PyMOLGlobals * G, const char *name, WordType type);
float ExecutiveGetArea(PyMOLGlobals * G, const char *s0, int sta0, int load_b); float ExecutiveGetArea(PyMOLGlobals * G, const char *s0, int sta0, int load_b);
void ExecutiveInvalidateSelectionIndicators(PyMOLGlobals *G); void ExecutiveInvalidateSelectionIndicators(PyMOLGlobals *G);
void ExecutiveInvalidateSelectionIndicatorsCGO(PyMOLGlobals *G); void ExecutiveInvalidateSelectionIndicatorsCGO(PyMOLGlobals *G);
void ExecutiveRenderSelections(PyMOLGlobals * G, int curState, int slot, GridInf o *grid); void ExecutiveRenderSelections(PyMOLGlobals * G, int curState, int slot, GridInf o *grid);
skipping to change at line 433 skipping to change at line 435
int quiet); int quiet);
int ExecutiveGetObjectMatrix(PyMOLGlobals * G, const char *name, int state, doub le **matrix, int ExecutiveGetObjectMatrix(PyMOLGlobals * G, const char *name, int state, doub le **matrix,
int incl_ttt); int incl_ttt);
int ExecutiveSetObjectMatrix(PyMOLGlobals * G, const char *name, int state, doub le *matrix); int ExecutiveSetObjectMatrix(PyMOLGlobals * G, const char *name, int state, doub le *matrix);
int ExecutiveSetGeometry(PyMOLGlobals * G, const char *s1, int geom, int valence ); int ExecutiveSetGeometry(PyMOLGlobals * G, const char *s1, int geom, int valence );
int ExecutiveSculptIterateAll(PyMOLGlobals * G); int ExecutiveSculptIterateAll(PyMOLGlobals * G);
int ExecutiveSmooth(PyMOLGlobals * G, const char *name, int cycles, int window, int ExecutiveSmooth(PyMOLGlobals * G, const char *name, int cycles, int window,
int first, int last, int ends, int quiet); int first, int last, int ends, int quiet);
int ExecutiveSculptDeactivate(PyMOLGlobals * G, const char *name); int ExecutiveSculptDeactivate(PyMOLGlobals * G, const char *name);
int ExecutiveSculptActivate(PyMOLGlobals * G, const char *name, int state, int m int ExecutiveSculptActivate(PyMOLGlobals * G, const char *name, int state=-1, in
atch_state, t match_state=-2,
int match_by_segment); int match_by_segment=0);
float ExecutiveSculptIterate(PyMOLGlobals * G, const char *name, int state, int float ExecutiveSculptIterate(PyMOLGlobals * G, const char *name, int state=-1, i
n_cycle); nt n_cycle=10);
int ExecutiveMapNew(PyMOLGlobals * G, const char *name, int type, float *grid, c onst char *sele, int ExecutiveMapNew(PyMOLGlobals * G, const char *name, int type, float *grid, c onst char *sele,
float buffer, float *minCorner, float *maxCorner, float buffer, float *minCorner, float *maxCorner,
int state, int have_corners, int quiet, int zoom, int normal ize, int state, int have_corners, int quiet, int zoom, int normal ize,
float clamp_floor, float clamp_ceiling, float resolution); float clamp_floor, float clamp_ceiling, float resolution);
int ***ExecutiveGetBondPrint(PyMOLGlobals * G, const char *name, int max_bond, i nt max_type, int ***ExecutiveGetBondPrint(PyMOLGlobals * G, const char *name, int max_bond, i nt max_type,
int *dim); int *dim);
int ExecutiveGetSymmetry(PyMOLGlobals * G, const char *sele, int state, float *a , float *b, float *c, int ExecutiveGetSymmetry(PyMOLGlobals * G, const char *sele, int state, float *a , float *b, float *c,
float *alpha, float *beta, float *gamma, char *sgroup, float *alpha, float *beta, float *gamma, char *sgroup,
int *defined); int *defined);
 End of changes. 9 change blocks. 
13 lines changed or deleted 15 lines changed or added
To the Header Files section of the PyMOL source changes report or the top of this page
Mainly generated by pkgdiff using rfcdiff
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