"Fossies" - the Fresh Open Source Software Archive  

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

AtomInfo.h  (pymol-v1.8.6.0.tar.bz2)	:	AtomInfo.h  (pymol-v2.1.0.tar.bz2)
skipping to change at line 55		skipping to change at line 55
/* FLAG 3 - Fixed atoms - no movement allowed */		/* FLAG 3 - Fixed atoms - no movement allowed */
#define cAtomFlag_fix 0x00000008		#define cAtomFlag_fix 0x00000008
/* FLAG 4 - Exclude these atoms when performing simulation, minimization */		/* FLAG 4 - Exclude these atoms when performing simulation, minimization */
#define cAtomFlag_exclude 0x00000010		#define cAtomFlag_exclude 0x00000010
/* FLAG 5 - Study atoms */		/* FLAG 5 - Study atoms */
#define cAtomFlag_study 0x00000020		#define cAtomFlag_study 0x00000020
/* FLAGS 4-7 are reserved for additional molecular modeling tasks */		/* FLAGS 6-7 are for polymer sub-classification */
		#define cAtomFlag_protein 0x00000040
		#define cAtomFlag_nucleic 0x00000080
/* FLAGS 8-15 are free for end users to manipulate */		/* FLAGS 8-15 are free for end users to manipulate */
/* FLAGS 16-21 are reserved for external GUIs and linked applications */		/* FLAGS 16-21 are reserved for external GUIs and linked applications */
/* FLAGS 22-23 are for temporary use only (inside of self-contained loops) */		/* FLAGS 22-23 are for temporary use only (inside of self-contained loops) */
/* FLAGS 24-31 are reserved for PyMOL's internal use */		/* FLAGS 24-31 are reserved for PyMOL's internal use */
/* FLAG 24 - don't surface these atoms (waters, ligands, etc.) */		/* FLAG 24 - don't surface these atoms (waters, ligands, etc.) */
skipping to change at line 171		skipping to change at line 173
#define cAN_Ce 58		#define cAN_Ce 58
#define cAN_Pt 78		#define cAN_Pt 78
#define cAN_Au 79		#define cAN_Au 79
#define cAN_Hg 80		#define cAN_Hg 80
#define cAN_Tl 81		#define cAN_Tl 81
#define cAN_Pb 82		#define cAN_Pb 82
#define cAN_U 92		#define cAN_U 92
		#define SDF_CHIRALITY_ODD 1 // odd / clockwise
		#define SDF_CHIRALITY_EVEN 2 // even / counterclockwise
		#define SDF_CHIRALITY_EITHER 3 // either or unmarked
typedef char Chain[2];		typedef char Chain[2];
typedef char SSType[2];		typedef char SSType[2];
typedef char SegIdent[cSegiLen + 1];		typedef char SegIdent[cSegiLen + 1];
typedef char ResIdent[cResiLen + 1];		typedef char ResIdent[cResiLen + 1];
typedef char ResName[cResnLen + 1];		typedef char ResName[cResnLen + 1];
typedef char AtomName[cAtomNameLen + 1];		typedef char AtomName[cAtomNameLen + 1];
typedef char ElemName[cElemNameLen + 1];		typedef char ElemName[cElemNameLen + 1];
// for customType (not geom)		// for customType (not geom)
skipping to change at line 270		skipping to change at line 276
char inscode;		char inscode;
ElemName elem; // redundant with "protons" ?		ElemName elem; // redundant with "protons" ?
SSType ssType; /* blank or 'L' = turn/loop, 'H' = helix, 'S' = b eta-strand/sheet */		SSType ssType; /* blank or 'L' = turn/loop, 'H' = helix, 'S' = b eta-strand/sheet */
Chain alt;		Chain alt;
// small value optimized bitfields		// small value optimized bitfields
unsigned char stereo : 2; // 0-3 Only for SDF (MOL) format in/out		unsigned char stereo : 2; // 0-3 Only for SDF (MOL) format in/out
unsigned char chemFlag : 2; // 0,1,2		unsigned char chemFlag : 2; // 0,1,2
unsigned char protekted : 2; // 0,1,2		unsigned char protekted : 2; // 0,1,2
		unsigned char mmstereo : 2; // 0/R/S/?
// methods		// methods
bool isHydrogen() const {		bool isHydrogen() const {
return protons == cAN_H;		return protons == cAN_H;
}		}
		bool isMetal() const {
		return (
		(protons > 2 && protons < 5) ||
		(protons > 10 && protons < 14) ||
		(protons > 18 && protons < 32) ||
		(protons > 36 && protons < 51) ||
		(protons > 54 && protons < 85) ||
		protons > 86);
		}
char getInscode(bool space=false) const {		char getInscode(bool space=false) const {
if (space && !inscode)		if (space && !inscode)
return ' ';		return ' ';
return inscode;		return inscode;
}		}
void setInscode(char c) {		void setInscode(char c) {
inscode = makeInscode(c);		inscode = makeInscode(c);
}		}
skipping to change at line 394		skipping to change at line 411
int AtomInfoUniquefyNames(PyMOLGlobals * G, const AtomInfoType * atInfo0, int n0 ,		int AtomInfoUniquefyNames(PyMOLGlobals * G, const AtomInfoType * atInfo0, int n0 ,
AtomInfoType * atInfo1, int *flag1, int n1);		AtomInfoType * atInfo1, int *flag1, int n1);
int AtomInfoGetCarbColor(PyMOLGlobals * G);		int AtomInfoGetCarbColor(PyMOLGlobals * G);
bool AtomResiFromResv(char *resi, size_t size, int resv, char inscode);		bool AtomResiFromResv(char *resi, size_t size, int resv, char inscode);
inline bool AtomResiFromResv(char *resi, size_t size, const AtomInfoType * ai) {		inline bool AtomResiFromResv(char *resi, size_t size, const AtomInfoType * ai) {
return AtomResiFromResv(resi, size, ai->resv, ai->inscode);		return AtomResiFromResv(resi, size, ai->resv, ai->inscode);
}		}
int AtomInfoKnownWaterResName(PyMOLGlobals * G, const char *resn);		int AtomInfoKnownWaterResName(PyMOLGlobals * G, const char *resn);
int AtomInfoKnownPolymerResName(const char *resn);		int AtomInfoKnownPolymerResName(const char *resn);
		int AtomInfoKnownProteinResName(const char *resn);
		int AtomInfoKnownNucleicResName(const char *resn);
void AtomInfoGetPDB3LetHydroName(PyMOLGlobals * G, const char *resn, const char *iname, char *oname);		void AtomInfoGetPDB3LetHydroName(PyMOLGlobals * G, const char *resn, const char *iname, char *oname);
#define cAIC_ct 0x0001		#define cAIC_ct 0x0001
#define cAIC_fc 0x0002		#define cAIC_fc 0x0002
#define cAIC_pc 0x0004		#define cAIC_pc 0x0004
#define cAIC_b 0x0008		#define cAIC_b 0x0008
#define cAIC_q 0x0010		#define cAIC_q 0x0010
#define cAIC_id 0x0020		#define cAIC_id 0x0020
#define cAIC_flags 0x0080		#define cAIC_flags 0x0080
#define cAIC_tt 0x0100		#define cAIC_tt 0x0100
skipping to change at line 475		skipping to change at line 494
return out;		return out;
return default_;		return default_;
}		}
#define BondSettingGetWD AtomSettingGetWD		#define BondSettingGetWD AtomSettingGetWD
// stereochemistry		// stereochemistry
const char * AtomInfoGetStereoAsStr(const AtomInfoType * ai);		const char * AtomInfoGetStereoAsStr(const AtomInfoType * ai);
void AtomInfoSetStereo(AtomInfoType * ai, const char * stereo);		void AtomInfoSetStereo(AtomInfoType * ai, const char * stereo);
		void AtomInfoGetAlignedPDBResidueName(PyMOLGlobals * G,
		const AtomInfoType * ai,
		ResName & resn);
		void AtomInfoGetAlignedPDBAtomName(PyMOLGlobals * G,
		const AtomInfoType * ai,
		const ResName & resn,
		AtomName & name);
#endif		#endif
End of changes. 6 change blocks.
1 lines changed or deleted		28 lines changed or added

---