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/*
A* -------------------------------------------------------------------
B* This file contains source code for the PyMOL computer program
C* copyright 1998-2000 by Warren Lyford Delano of DeLano Scientific.
D* -------------------------------------------------------------------
E* It is unlawful to modify or remove this copyright notice.
F* -------------------------------------------------------------------
G* Please see the accompanying LICENSE file for further information.
H* -------------------------------------------------------------------
I* Additional authors of this source file include:
-*
-*
-*
Z* -------------------------------------------------------------------
*/
#ifndef _H_CoordSet
#define _H_CoordSet
#include"os_python.h"
#include"Rep.h"
#include"Symmetry.h"
#include"Word.h"
#include"Setting.h"
#include"ObjectMolecule.h"
#define COORD_SET_HAS_ANISOU 0x01
typedef struct CoordSet {
void (*fUpdate) (struct CoordSet * I, int state);
void (*fRender) (struct CoordSet * I, RenderInfo * info);
void (*fFree) (struct CoordSet * I);
void (*fEnumIndices) (struct CoordSet * I);
void (*fAppendIndices) (struct CoordSet * I, int existingAtoms);
int (*fExtendIndices) (struct CoordSet * I, int nAtom);
void (*fInvalidateRep) (struct CoordSet * I, int type, int level);
CObjectState State;
ObjectMolecule *Obj;
float *Coord;
int *Color;
int *IdxToAtm;
int *AtmToIdx;
int NIndex, NAtIndex, prevNIndex, prevNAtIndex;
Rep *Rep[cRepCnt]; /* an array of pointers to representations */
int Active[cRepCnt]; /* active flags */
int NTmpBond; /* optional, temporary (for coord set transfers) */
BondType *TmpBond; /* actual bond info is stored in ObjectMolecule */
int NTmpLinkBond; /* optional, temporary storage of linkage info. */
BondType *TmpLinkBond; /* first atom is in obj, second is in cset */
CSymmetry *Symmetry;
WordType Name;
float *Spheroid;
float *SpheroidNormal;
int NSpheroid;
int SpheroidSphereSize;
CSetting *Setting;
/* for periodic MD boxes -- may be merge into symmetry lattice later... */
CCrystal *PeriodicBox;
int PeriodicBoxType;
int tmp_index; /* for saving */
int NMatrix; /* number of matrices for this coordinate set */
double *MatrixVLA; /* end-to-end array of 16x16 matrices */
LabPosType *LabPos;
/* not saved in state */
RefPosType *RefPos;
/* idea:
int start_atix, stop_atix <-- for discrete objects, we need
something like this that would enable pymol to skip atoms not in the
discrete state...question is: are these atoms sorted together right
now or not? probably not, and if not then we need to change sorting
for discrete objects to be state-dependent, but this could screw up
byres/bychain actions which assume such atoms to be adjancent...
*/
CGO *SculptCGO, *SculptShaderCGO;
MapType *Coord2Idx;
float Coord2IdxReq, Coord2IdxDiv;
/* temporary / optimization */
int objMolOpInvalidated;
short int noInvalidateMMStereoAndTextType;
} CoordSet;
typedef void (*fUpdateFn) (CoordSet *, int);
#define cCSet_NoPeriodicity 0
#define cCSet_Orthogonal 1
#define cCSet_Octahedral 2
int BondInOrder(BondType * a, int b1, int b2);
int BondCompare(BondType * a, BondType * b);
PyObject *CoordSetAsPyList(CoordSet * I);
int CoordSetFromPyList(PyMOLGlobals * G, PyObject * list, CoordSet ** cs);
CoordSet *CoordSetNew(PyMOLGlobals * G);
void CoordSetAtomToPDBStrVLA(PyMOLGlobals * G, char **charVLA, int *c, AtomInfoType * ai,
float *v, int cnt, PDBInfoRec * pdb_info, double *matrix);
void CoordSetAtomToTERStrVLA(PyMOLGlobals * G, char **charVLA, int *c, AtomInfoType * ai,
int cnt);
CoordSet *CoordSetCopy(CoordSet * cs);
void CoordSetTransform44f(CoordSet * I, float *mat);
void CoordSetTransform33f(CoordSet * I, float *mat);
void CoordSetRealToFrac(CoordSet * I, CCrystal * cryst);
void CoordSetFracToReal(CoordSet * I, CCrystal * cryst);
void CoordSetGetAverage(CoordSet * I, float *v0);
PyObject *CoordSetAtomToChemPyAtom(PyMOLGlobals * G, AtomInfoType * ai, float *v,
float *ref, int index, double *matrix);
int CoordSetGetAtomVertex(CoordSet * I, int at, float *v);
int CoordSetGetAtomTxfVertex(CoordSet * I, int at, float *v);
int CoordSetSetAtomVertex(CoordSet * I, int at, float *v);
int CoordSetMoveAtom(CoordSet * I, int at, float *v, int mode);
int CoordSetMoveAtomLabel(CoordSet * I, int at, float *v, int mode);
int CoordSetTransformAtomTTTf(CoordSet * I, int at, float *TTT);
int CoordSetTransformAtomR44f(CoordSet * I, int at, float *matrix);
int CoordSetValidateRefPos(CoordSet * I);
void CoordSetPurge(CoordSet * I);
void CoordSetAdjustAtmIdx(CoordSet * I, int *lookup, int nAtom);
int CoordSetMerge(ObjectMolecule *OM, CoordSet * I, CoordSet * cs); /* must be non-overlapping */
void CoordSetRecordTxfApplied(CoordSet * I, float *TTT, int homogenous);
void CoordSetUpdateCoord2IdxMap(CoordSet * I, float cutoff);
typedef struct _CCoordSetUpdateThreadInfo CCoordSetUpdateThreadInfo;
void CoordSetUpdateThread(CCoordSetUpdateThreadInfo * T);
void LabPosTypeCopy(LabPosType * src, LabPosType * dst);
void RefPosTypeCopy(RefPosType * src, RefPosType * dst);
void CoordSetFree(CoordSet * I);
#endif
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