"Fossies" - the Fresh Open Source Software Archive  

Source code changes of the file "layer2/ObjectMolecule.h" between
pymol-open-source-2.2.0.tar.gz and pymol-open-source-2.3.0.tar.gz

About: PyMOL is a Python-enhanced molecular graphics tool. It excels at 3D visualization of proteins, small molecules, density, surfaces, and trajectories. It also includes molecular editing, ray tracing, and movies. Open Source version.

[ To the main PyMOL source changes report ]

ObjectMolecule.h  (pymol-open-source-2.2.0):ObjectMolecule.h  (pymol-open-source-2.3.0)
/**
* @file
*/
/* /*
A* ------------------------------------------------------------------- A* -------------------------------------------------------------------
B* This file contains source code for the PyMOL computer program B* This file contains source code for the PyMOL computer program
C* copyright 1998-2000 by Warren Lyford Delano of DeLano Scientific. C* copyright 1998-2000 by Warren Lyford Delano of DeLano Scientific.
D* ------------------------------------------------------------------- D* -------------------------------------------------------------------
E* It is unlawful to modify or remove this copyright notice. E* It is unlawful to modify or remove this copyright notice.
F* ------------------------------------------------------------------- F* -------------------------------------------------------------------
G* Please see the accompanying LICENSE file for further information. G* Please see the accompanying LICENSE file for further information.
H* ------------------------------------------------------------------- H* -------------------------------------------------------------------
I* Additional authors of this source file include: I* Additional authors of this source file include:
skipping to change at line 30 skipping to change at line 32
#include"os_python.h" #include"os_python.h"
#include"PyMOLObject.h" #include"PyMOLObject.h"
#include"AtomInfo.h" #include"AtomInfo.h"
#include"Vector.h" #include"Vector.h"
#include"Color.h" #include"Color.h"
#include"Symmetry.h" #include"Symmetry.h"
#include"DistSet.h" #include"DistSet.h"
#include "Executive_pre.h" #include "Executive_pre.h"
#include "CifFile.h" #include "CifFile.h"
#include "vla.h"
#include <memory> #include <memory>
#ifdef _WEBGL #ifdef _WEBGL
#endif #endif
#define cKeywordAll "all" #define cKeywordAll "all"
#define cKeywordNone "none" #define cKeywordNone "none"
#define cKeywordSame "same" #define cKeywordSame "same"
#define cKeywordCenter "center" #define cKeywordCenter "center"
skipping to change at line 64 skipping to change at line 67
/* base Object class */ /* base Object class */
CObject Obj; CObject Obj;
/* array of pointers to coordinate sets; one set per state */ /* array of pointers to coordinate sets; one set per state */
struct CoordSet **CSet; struct CoordSet **CSet;
/* number of coordinate sets */ /* number of coordinate sets */
int NCSet; int NCSet;
struct CoordSet *CSTmpl; /* template for trajectories, etc. */ struct CoordSet *CSTmpl; /* template for trajectories, etc. */
/* array of bonds */ /* array of bonds */
BondType *Bond; BondType *Bond;
/* array of atoms (infos) */ /* array of atoms (infos) */
AtomInfoType *AtomInfo; pymol::vla<AtomInfoType> AtomInfo;
/* number of atoms and bonds */ /* number of atoms and bonds */
int NAtom, prevNAtom; int NAtom, prevNAtom;
int NBond, prevNBond; int NBond, prevNBond;
/* is this object loaded as a discrete object? if so, number of states */ /* is this object loaded as a discrete object? if so, number of states */
int DiscreteFlag; int DiscreteFlag;
int *DiscreteAtmToIdx; int *DiscreteAtmToIdx;
struct CoordSet **DiscreteCSet; struct CoordSet **DiscreteCSet;
/* proposed, for storing uniform trajectory data more efficiently: /* proposed, for storing uniform trajectory data more efficiently:
int *UniformAtmToIdx, *UniformIdxToAtm; */ int *UniformAtmToIdx, *UniformIdxToAtm; */
int CurCSet; /* Current state number */ int CurCSet; /* Current state number */
skipping to change at line 91 skipping to change at line 94
int UndoIter; int UndoIter;
CGO *UnitCellCGO; CGO *UnitCellCGO;
int BondCounter; int BondCounter;
int AtomCounter; int AtomCounter;
/* not stored */ /* not stored */
struct CSculpt *Sculpt; struct CSculpt *Sculpt;
int RepVisCacheValid; int RepVisCacheValid;
int RepVisCache; /* for transient storage during updates */ int RepVisCache; /* for transient storage during updates */
// 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
std::shared_ptr<cif_file> m_ciffile; std::shared_ptr<cif_file> m_ciffile;
#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() const; int getState() const;
bool setNDiscrete(int natom); bool setNDiscrete(int natom);
bool updateAtmToIdx(); bool updateAtmToIdx();
} ObjectMolecule; } ObjectMolecule;
skipping to change at line 164 skipping to change at line 165
inline bool is_pqr_file() const { inline bool is_pqr_file() const {
return variant == PDB_VARIANT_PQR; return variant == PDB_VARIANT_PQR;
} }
} PDBInfoRec; } PDBInfoRec;
/* these four letter code are left over from an /* these four letter code are left over from an
earlier multicharacter constant implementation earlier multicharacter constant implementation
and should be replaced with something more verbose */ and should be replaced with something more verbose */
#define OMOP_PDB1 1
#define OMOP_AVRT 2 #define OMOP_AVRT 2
#define OMOP_SFIT 3 #define OMOP_SFIT 3
#define OMOP_COLR 4 #define OMOP_COLR 4
#define OMOP_VISI 5 #define OMOP_VISI 5
#define OMOP_TTTF 6 #define OMOP_TTTF 6
#define OMOP_ALTR 7 #define OMOP_ALTR 7
#define OMOP_CSOC 8
#define OMOP_SUMC 9 #define OMOP_SUMC 9
#define OMOP_VERT 10 #define OMOP_VERT 10
#define OMOP_SVRT 11 #define OMOP_SVRT 11
#define OMOP_MOME 12 #define OMOP_MOME 12
#define OMOP_INVA 13 #define OMOP_INVA 13
#define OMOP_MDST 14
#define OMOP_MNMX 15 #define OMOP_MNMX 15
#define OMOP_AlterState 16 #define OMOP_AlterState 16
#define OMOP_Flag 17 #define OMOP_Flag 17
#define OMOP_LABL 18 #define OMOP_LABL 18
#define OMOP_Identify 19 #define OMOP_Identify 19
#define OMOP_Remove 20 #define OMOP_Remove 20
#define OMOP_Protect 21 #define OMOP_Protect 21
#define OMOP_Mask 22 #define OMOP_Mask 22
#define OMOP_AddHydrogens 23 #define OMOP_AddHydrogens 23
#define OMOP_SetB 24 #define OMOP_SetB 24
skipping to change at line 220 skipping to change at line 218
#define OMOP_Spectrum 47 #define OMOP_Spectrum 47
#if 0 #if 0
#define OMOP_GetBFactors 48 #define OMOP_GetBFactors 48
#define OMOP_GetOccupancies 49 #define OMOP_GetOccupancies 49
#define OMOP_GetPartialCharges 50 #define OMOP_GetPartialCharges 50
#endif #endif
#define OMOP_StateVRT 51 #define OMOP_StateVRT 51
#define OMOP_CheckVis 52 #define OMOP_CheckVis 52
#define OMOP_OnOff 53 #define OMOP_OnOff 53
#define OMOP_Pop 54 #define OMOP_Pop 54
#define OMOP_TransformR44f 55
#define OMOP_FixHydrogens 56 #define OMOP_FixHydrogens 56
#define OMOP_Sort 57 #define OMOP_Sort 57
#define OMOP_SetAtomicSetting 58 #define OMOP_SetAtomicSetting 58
#define OMOP_CSetSumSqDistToPt 59 #define OMOP_CSetSumSqDistToPt 59
#define OMOP_RevalenceFromSource 60 #define OMOP_RevalenceFromSource 60
#define OMOP_RevalenceByGuessing 61 #define OMOP_RevalenceByGuessing 61
#define OMOP_ReferenceStore 62 #define OMOP_ReferenceStore 62
#define OMOP_ReferenceRecall 63 #define OMOP_ReferenceRecall 63
#define OMOP_ReferenceValidate 64 #define OMOP_ReferenceValidate 64
#define OMOP_ReferenceSwap 65 #define OMOP_ReferenceSwap 65
skipping to change at line 282 skipping to change at line 279
M4XContextType *context; M4XContextType *context;
int xname_flag; int xname_flag;
ObjectNameType xname; ObjectNameType xname;
M4XAlignType *align; M4XAlignType *align;
} M4XAnnoType; } M4XAnnoType;
typedef struct { typedef struct {
ObjectNameType name; ObjectNameType name;
} ObjMolMultiplexType; } ObjMolMultiplexType;
/* loop iterators for the ObjectMolecule::Neighbor array /**
* loop iterators for the ObjectMolecule::Neighbor array
* *
* Arguments: (Neighbor array, const int atom-index, int neighbor-atom-or-bond-i ndex, int used-internally) * Arguments: (Neighbor array, const int atom-index, int neighbor-atom-or-bond-i ndex, int used-internally)
* *
* Example: * Example:
* // iterate over neighbors of obj->AtomInfo[at] * @verbatim
* int neighbor_at, tmp; // iterate over neighbors of obj->AtomInfo[at]
* ITERNEIGHBORATOMS(obj->Neighbor, at, neighbor_at, tmp) { int neighbor_at, tmp;
* // do something with obj->AtomInfo[neighbor_at] ITERNEIGHBORATOMS(obj->Neighbor, at, neighbor_at, tmp) {
* } // do something with obj->AtomInfo[neighbor_at]
}
@endverbatim
*/ */
#define ITERNEIGHBORATOMS(N, a, n, i) for(i = N[a] + 1; (n = N[i]) > -1; i += 2) #define ITERNEIGHBORATOMS(N, a, n, i) for(i = N[a] + 1; (n = N[i]) > -1; i += 2)
#define ITERNEIGHBORBONDS(N, a, b, i) for(i = N[a] + 1; (b = N[i + 1]), N[i] > - 1; i += 2) #define ITERNEIGHBORBONDS(N, a, b, i) for(i = N[a] + 1; (b = N[i + 1]), N[i] > - 1; i += 2)
void M4XAnnoInit(M4XAnnoType * m4x); void M4XAnnoInit(M4XAnnoType * m4x);
void M4XAnnoPurge(M4XAnnoType * m4x); void M4XAnnoPurge(M4XAnnoType * m4x);
void M4XAlignInit(M4XAlignType * align); void M4XAlignInit(M4XAlignType * align);
void M4XAlignPurge(M4XAlignType * align); void M4XAlignPurge(M4XAlignType * align);
skipping to change at line 327 skipping to change at line 327
int match_colors, int nbr_sele); int match_colors, int nbr_sele);
/* */ /* */
int ObjectMoleculeAreAtomsBonded2(ObjectMolecule * obj0, int a0, ObjectMolecule * obj1, int ObjectMoleculeAreAtomsBonded2(ObjectMolecule * obj0, int a0, ObjectMolecule * obj1,
int a1); int a1);
int ObjectMoleculeIsAtomBondedToName(ObjectMolecule * obj, int a0, const char *n ame, int); int ObjectMoleculeIsAtomBondedToName(ObjectMolecule * obj, int a0, const char *n ame, int);
void ObjectMoleculeOpRecInit(ObjectMoleculeOpRec * op); void ObjectMoleculeOpRecInit(ObjectMoleculeOpRec * op);
int ObjectMoleculeNewFromPyList(PyMOLGlobals * G, PyObject * list, int ObjectMoleculeNewFromPyList(PyMOLGlobals * G, PyObject * list,
ObjectMolecule ** result); ObjectMolecule ** result);
PyObject *ObjectMoleculeAsPyList(ObjectMolecule * I); PyObject *ObjectMoleculeAsPyList(ObjectMolecule * I);
int ObjectMoleculeGetSerial(ObjectMolecule * I);
int ObjectMoleculeSetStateTitle(ObjectMolecule * I, int state, const char *text) ; int ObjectMoleculeSetStateTitle(ObjectMolecule * I, int state, const char *text) ;
const char *ObjectMoleculeGetStateTitle(ObjectMolecule * I, int state); const char *ObjectMoleculeGetStateTitle(ObjectMolecule * I, int state);
int ObjectMoleculeCheckFullStateSelection(ObjectMolecule * I, int sele, int stat e); int ObjectMoleculeCheckFullStateSelection(ObjectMolecule * I, int sele, int stat e);
void ObjectMoleculeFree(ObjectMolecule * I); /* only for friends of ObjectMol ecule */ void ObjectMoleculeFree(ObjectMolecule * I); /* only for friends of ObjectMol ecule */
int ObjectMoleculeSetStateOrder(ObjectMolecule * I, int * order, int len); int ObjectMoleculeSetStateOrder(ObjectMolecule * I, int * order, int len);
int ObjectMoleculeAddPseudoatom(ObjectMolecule * I, int sele_index, const char * name, int ObjectMoleculeAddPseudoatom(ObjectMolecule * I, int sele_index, const char * name,
const char *resn, const char *resi, const char * chain, const char *resn, const char *resi, const char * chain,
const char *segi, const char *elem, float vdw, const char *segi, const char *elem, float vdw,
skipping to change at line 368 skipping to change at line 367
ObjectMolecule *ObjectMoleculeLoadCoords(PyMOLGlobals * G, ObjectMolecule * I, ObjectMolecule *ObjectMoleculeLoadCoords(PyMOLGlobals * G, ObjectMolecule * I,
PyObject * coords, int frame); PyObject * coords, int frame);
ObjectMolecule *ObjectMoleculeLoadCoords(PyMOLGlobals * G, ObjectMolecule * I, ObjectMolecule *ObjectMoleculeLoadCoords(PyMOLGlobals * G, ObjectMolecule * I,
const float * coords, int coords_len, i nt frame=-1); const float * coords, int coords_len, i nt frame=-1);
ObjectMolecule *ObjectMoleculeLoadCoords(PyMOLGlobals * G, const char * name, ObjectMolecule *ObjectMoleculeLoadCoords(PyMOLGlobals * G, const char * name,
const float * coords, int coords_len, i nt frame=-1); const float * coords, int coords_len, i nt frame=-1);
ObjectMolecule *ObjectMoleculeReadStr(PyMOLGlobals * G, ObjectMolecule * I, ObjectMolecule *ObjectMoleculeReadStr(PyMOLGlobals * G, ObjectMolecule * I,
const char **next_entry, const char **next_entry,
int content_format, int frame, cLoadType_t content_format, int frame,
int discrete, int quiet, int multiplex, int discrete, int quiet, int multiplex,
char *new_name, char *new_name,
short loadpropertiesall=false, OVLexicon *l oadproplex=NULL); short loadpropertiesall=false, OVLexicon *l oadproplex=NULL);
ObjectMolecule *ObjectMoleculeReadPDBStr(PyMOLGlobals * G, ObjectMolecule * obj, ObjectMolecule *ObjectMoleculeReadPDBStr(PyMOLGlobals * G, ObjectMolecule * obj,
const char *molstr, int frame, int disc rete, const char *molstr, int frame, int disc rete,
M4XAnnoType * m4x, char *pdb_name, M4XAnnoType * m4x, char *pdb_name,
const char **next_pdb, PDBInfoRec * pdb _info, const char **next_pdb, PDBInfoRec * pdb _info,
int quiet, int *model_number); int quiet, int *model_number);
int ObjectMoleculeExtendIndices(ObjectMolecule * I, int state); int ObjectMoleculeExtendIndices(ObjectMolecule * I, int state);
void ObjectMoleculeInvalidate(ObjectMolecule * I, int rep, int level, int state) ; void ObjectMoleculeInvalidate(ObjectMolecule * I, int rep, int level, int state) ;
void ObjectMoleculeInvalidateAtomType(ObjectMolecule *I, int state); void ObjectMoleculeInvalidateAtomType(ObjectMolecule *I, int state);
void ObjectMoleculeRenderSele(ObjectMolecule * I, int curState, int sele, int vi s_only SELINDICATORARG); void ObjectMoleculeRenderSele(ObjectMolecule * I, int curState, int sele, int vi s_only SELINDICATORARG);
void ObjectMoleculeSeleOp(ObjectMolecule * I, int sele, ObjectMoleculeOpRec * op ); void ObjectMoleculeSeleOp(ObjectMolecule * I, int sele, ObjectMoleculeOpRec * op );
struct CoordSet *ObjectMoleculeGetCoordSet(ObjectMolecule * I, int setIndex); struct CoordSet *ObjectMoleculeGetCoordSet(ObjectMolecule * I, int setIndex);
void ObjectMoleculeBlindSymMovie(ObjectMolecule * I); int ObjectMoleculeMerge(ObjectMolecule * I, pymol::vla<AtomInfoType>&& ai,
int ObjectMoleculeMerge(ObjectMolecule * I, AtomInfoType * ai,
struct CoordSet *cs, int bondSearchFlag, struct CoordSet *cs, int bondSearchFlag,
int aic_mask, int invalidate); int aic_mask, int invalidate);
void ObjectMoleculeUpdateNonbonded(ObjectMolecule * I); void ObjectMoleculeUpdateNonbonded(ObjectMolecule * I);
int ObjectMoleculeUpdateNeighbors(ObjectMolecule * I); int ObjectMoleculeUpdateNeighbors(ObjectMolecule * I);
int ObjectMoleculeMoveAtom(ObjectMolecule * I, int state, int index, float *v, i nt mode, int ObjectMoleculeMoveAtom(ObjectMolecule * I, int state, int index, float *v, i nt mode,
int log); int log);
int ObjectMoleculeMoveAtomLabel(ObjectMolecule * I, int state, int index, float *v, int log, float *diff); int ObjectMoleculeMoveAtomLabel(ObjectMolecule * I, int state, int index, float *v, int log, float *diff);
int ObjectMoleculeGetAtomVertex(ObjectMolecule * I, int state, int index, float *v); int ObjectMoleculeGetAtomVertex(ObjectMolecule * I, int state, int index, float *v);
int ObjectMoleculeGetAtomTxfVertex(ObjectMolecule * I, int state, int index, flo at *v); int ObjectMoleculeGetAtomTxfVertex(ObjectMolecule * I, int state, int index, flo at *v);
int ObjectMoleculeGetAtomIndex(ObjectMolecule * I, int sele); int ObjectMoleculeGetAtomIndex(ObjectMolecule * I, int sele);
skipping to change at line 423 skipping to change at line 421
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, bool uniquefy=true); 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);
int ObjectMoleculeAdjustBonds(ObjectMolecule * I, int sele0, int sele1, int mode , int ObjectMoleculeAdjustBonds(ObjectMolecule * I, int sele0, int sele1, int mode ,
int order); int order);
int ObjectMoleculeAttach(ObjectMolecule * I, int index, AtomInfoType * nai); int ObjectMoleculeAttach(ObjectMolecule * I, int index,
pymol::vla<AtomInfoType>&& nai);
int ObjectMoleculeFuse(ObjectMolecule * I, int index0, ObjectMolecule * src, int index1, int ObjectMoleculeFuse(ObjectMolecule * I, int index0, ObjectMolecule * src, int index1,
int mode, int move_flag); int mode, int move_flag);
int ObjectMoleculeRenameAtoms(ObjectMolecule * I, int *flag, int force); int ObjectMoleculeRenameAtoms(ObjectMolecule * I, int *flag, int force);
int ObjectMoleculeAreAtomsBonded(ObjectMolecule * I, int i0, int i1); int ObjectMoleculeAreAtomsBonded(ObjectMolecule * I, int i0, int i1);
void ObjectGotoState(ObjectMolecule * I, int state); void ObjectGotoState(ObjectMolecule * I, int state);
float ObjectMoleculeGetAvgHBondVector(ObjectMolecule * I, int atom, int state, f loat *v, float ObjectMoleculeGetAvgHBondVector(ObjectMolecule * I, int atom, int state, f loat *v,
float *incoming); float *incoming);
int ObjectMoleculeCheckBondSep(ObjectMolecule * I, int a0, int a1, int dist); int ObjectMoleculeCheckBondSep(ObjectMolecule * I, int a0, int a1, int dist);
int ObjectMoleculeGetPhiPsi(ObjectMolecule * I, int ca, float *phi, float *psi, int ObjectMoleculeGetPhiPsi(ObjectMolecule * I, int ca, float *phi, float *psi,
int state); int state);
skipping to change at line 463 skipping to change at line 462
int match_by_segment); int match_by_segment);
float ObjectMoleculeSculptIterate(ObjectMolecule * I, int state, int n_cycle, float ObjectMoleculeSculptIterate(ObjectMolecule * I, int state, int n_cycle,
float *center); float *center);
void ObjectMoleculeSculptClear(ObjectMolecule * I); void ObjectMoleculeSculptClear(ObjectMolecule * I);
/* bond paths */ /* bond paths */
int ObjectMoleculeGetBondPaths(ObjectMolecule * I, int atom, int max, int ObjectMoleculeGetBondPaths(ObjectMolecule * I, int atom, int max,
ObjectMoleculeBPRec * bp); ObjectMoleculeBPRec * bp);
int ObjectMoleculeInitBondPath(ObjectMolecule * I, ObjectMoleculeBPRec * bp); int ObjectMoleculeInitBondPath(ObjectMolecule * I, ObjectMoleculeBPRec * bp);
int ObjectMoleculePurgeBondPath(ObjectMolecule * I, ObjectMoleculeBPRec * bp); int ObjectMoleculePurgeBondPath(ObjectMolecule * I, ObjectMoleculeBPRec * bp);
int ObjectMoleculeGetBondPath(ObjectMolecule * I, int atom, int max,
ObjectMoleculeBPRec * bp);
int ***ObjectMoleculeGetBondPrint(ObjectMolecule * I, int max_bond, int max_type , int ***ObjectMoleculeGetBondPrint(ObjectMolecule * I, int max_bond, int max_type ,
int *dim); int *dim);
int ObjectMoleculeConnect(ObjectMolecule * I, int *nbond, BondType ** bond, Atom InfoType * ai, int ObjectMoleculeConnect(ObjectMolecule * I, int *nbond, BondType ** bond, Atom InfoType * ai,
struct CoordSet *cs, int searchFlag, int connectModeOv erride); struct CoordSet *cs, int searchFlag, int connectModeOv erride);
int ObjectMoleculeSetDiscrete(PyMOLGlobals * G, ObjectMolecule * I, int discrete ); int ObjectMoleculeSetDiscrete(PyMOLGlobals * G, ObjectMolecule * I, int discrete );
float ObjectMoleculeGetMaxVDW(ObjectMolecule * I); float ObjectMoleculeGetMaxVDW(ObjectMolecule * I);
int ObjectMoleculeGetCheckHBond(AtomInfoType **h_real, int ObjectMoleculeGetCheckHBond(AtomInfoType **h_real,
float *h_crd_ret, float *h_crd_ret,
 End of changes. 17 change blocks. 
22 lines changed or deleted 19 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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