"Fossies" - the Fresh Open Source Software Archive  

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

ObjectMolecule.h  (pymol-v1.8.6.0.tar.bz2)	:	ObjectMolecule.h  (pymol-v2.1.0.tar.bz2)
skipping to change at line 100		skipping to change at line 100
// for reporting available assembly ids after mmCIF loading - SUBJECT TO CHANG E		// for reporting available assembly ids after mmCIF loading - SUBJECT TO CHANG E
#ifndef _PYMOL_NO_CXX11		#ifndef _PYMOL_NO_CXX11
std::shared_ptr<cif_file> m_ciffile;		std::shared_ptr<cif_file> m_ciffile;
#endif		#endif
const cif_data * m_cifdata;		const cif_data * m_cifdata;
// hetatm and ignore-flag by non-polymer classification		// hetatm and ignore-flag by non-polymer classification
bool need_hetatm_classification;		bool need_hetatm_classification;
// methods		// methods
int getState();		int getState() const;
bool setNDiscrete(int natom);		bool setNDiscrete(int natom);
bool updateAtmToIdx();		bool updateAtmToIdx();
} ObjectMolecule;		} ObjectMolecule;
/* this is a record that holds information for specific types of Operatations on Molecules, eg. translation/rotation/etc */		/* this is a record that holds information for specific types of Operatations on Molecules, eg. translation/rotation/etc */
typedef struct ObjectMoleculeOpRec {		typedef struct ObjectMoleculeOpRec {
unsigned int code;		unsigned int code;
Vector3f v1, v2;		Vector3f v1, v2;
int cs1, cs2;		int cs1, cs2;
int i1, i2, i3, i4, i5, i6, *vc1, *i1VLA, *ii1, *vp1;		int i1, i2, i3, i4, i5, i6, *vc1, *i1VLA, *ii1, *vp1;
skipping to change at line 423		skipping to change at line 423
int source_state, int quiet);		int source_state, int quiet);
void ObjectMoleculeGuessValences(ObjectMolecule * I, int state, int *flag1, int *flag2,		void ObjectMoleculeGuessValences(ObjectMolecule * I, int state, int *flag1, int *flag2,
int reset);		int reset);
int ObjectMoleculeAddBond(ObjectMolecule * I, int sele0, int sele1, int order);		int ObjectMoleculeAddBond(ObjectMolecule * I, int sele0, int sele1, int order);
int ObjectMoleculeRemoveBonds(ObjectMolecule * I, int sele1, int sele2);		int ObjectMoleculeRemoveBonds(ObjectMolecule * I, int sele1, int sele2);
int ObjectMoleculeAutoDisableAtomNameWildcard(ObjectMolecule * I);		int ObjectMoleculeAutoDisableAtomNameWildcard(ObjectMolecule * I);
void ObjectMoleculeSaveUndo(ObjectMolecule * I, int state, int log);		void ObjectMoleculeSaveUndo(ObjectMolecule * I, int state, int log);
void ObjectMoleculeUndo(ObjectMolecule * I, int dir);		void ObjectMoleculeUndo(ObjectMolecule * I, int dir);
int ObjectMoleculePrepareAtom(ObjectMolecule * I, int index, AtomInfoType * ai);		int ObjectMoleculePrepareAtom(ObjectMolecule * I, int index, AtomInfoType * ai, bool uniquefy=true);
void ObjectMoleculeReplaceAtom(ObjectMolecule * I, int index, AtomInfoType * ai) ;		void ObjectMoleculeReplaceAtom(ObjectMolecule * I, int index, AtomInfoType * ai) ;
int ObjectMoleculePreposReplAtom(ObjectMolecule * I, int index, AtomInfoType * a i);		int ObjectMoleculePreposReplAtom(ObjectMolecule * I, int index, AtomInfoType * a i);
void ObjectMoleculeCreateSpheroid(ObjectMolecule * I, int average);		void ObjectMoleculeCreateSpheroid(ObjectMolecule * I, int average);
int ObjectMoleculeSetAtomVertex(ObjectMolecule * I, int state, int index, float *v);		int ObjectMoleculeSetAtomVertex(ObjectMolecule * I, int state, int index, float *v);
int ObjectMoleculeVerifyChemistry(ObjectMolecule * I, int state);		int ObjectMoleculeVerifyChemistry(ObjectMolecule * I, int state);
int ObjectMoleculeFindOpenValenceVector(ObjectMolecule * I, int state,		int ObjectMoleculeFindOpenValenceVector(ObjectMolecule * I, int state,
int index, float *v, float *seek,		int index, float *v, float *seek,
int ignore_index);		int ignore_index);
int ObjectMoleculeFillOpenValences(ObjectMolecule * I, int index);		int ObjectMoleculeFillOpenValences(ObjectMolecule * I, int index);
int ObjectMoleculeGetTotalAtomValence(ObjectMolecule * I, int atom);		int ObjectMoleculeGetTotalAtomValence(ObjectMolecule * I, int atom);
skipping to change at line 506		skipping to change at line 506
const char *buffer,		const char *buffer,
AtomInfoType ** atInfoPtr,		AtomInfoType ** atInfoPtr,
const char **restart_model,		const char **restart_model,
char *segi_override,		char *segi_override,
M4XAnnoType * m4x,		M4XAnnoType * m4x,
char *pdb_name,		char *pdb_name,
const char **next_pdb,		const char **next_pdb,
PDBInfoRec * pdb_info,		PDBInfoRec * pdb_info,
int quiet, int *model_number);		int quiet, int *model_number);
		#ifndef NO_MMLIBS
int ObjectMoleculeUpdateAtomTypeInfoForState(PyMOLGlobals * G, ObjectMolecule * obj, int state, int initialize, int format);		int ObjectMoleculeUpdateAtomTypeInfoForState(PyMOLGlobals * G, ObjectMolecule * obj, int state, int initialize, int format);
		#endif
		#ifndef _PYMOL_NO_UNDO
void ObjectMoleculeSetAtomBondInfoTypeOldId(PyMOLGlobals * G, ObjectMolecule * o bj);		void ObjectMoleculeSetAtomBondInfoTypeOldId(PyMOLGlobals * G, ObjectMolecule * o bj);
void ObjectMoleculeSetAtomBondInfoTypeOldIdToNegOne(PyMOLGlobals * G, ObjectMole cule * obj);		void ObjectMoleculeSetAtomBondInfoTypeOldIdToNegOne(PyMOLGlobals * G, ObjectMole cule * obj);
		#endif
void ObjectMoleculeAdjustDiscreteAtmIdx(ObjectMolecule *I, int *lookup, int nAto m);		void ObjectMoleculeAdjustDiscreteAtmIdx(ObjectMolecule *I, int *lookup, int nAto m);
void AtomInfoSettingGenerateSideEffects(PyMOLGlobals * G, ObjectMolecule *obj, i nt index, int id);		void AtomInfoSettingGenerateSideEffects(PyMOLGlobals * G, ObjectMolecule *obj, i nt index, int id);
int *AtomInfoGetSortedIndex(PyMOLGlobals * G, ObjectMolecule * obj, AtomInfoType * rec, int n,		int *AtomInfoGetSortedIndex(PyMOLGlobals * G, ObjectMolecule * obj, AtomInfoType * rec, int n,
int **outdex);		int **outdex);
ObjectMolecule *ObjectMoleculeReadMmtfStr(PyMOLGlobals * G, ObjectMolecule * I,		ObjectMolecule *ObjectMoleculeReadMmtfStr(PyMOLGlobals * G, ObjectMolecule * I,
const char *st, int st_len, int frame, int discrete, int quiet, int multiple x, int zoom);		const char *st, int st_len, int frame, int discrete, int quiet, int multiple x, int zoom);
ObjectMolecule *ObjectMoleculeReadCifStr(PyMOLGlobals * G, ObjectMolecule * I,		ObjectMolecule *ObjectMoleculeReadCifStr(PyMOLGlobals * G, ObjectMolecule * I,
End of changes. 5 change blocks.
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