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.
| CoordSet.h (pymol-v2.1.0.tar.bz2) | : | CoordSet.h (pymol-open-source-2.2.0) |
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| skipping to change at line 29 | | skipping to change at line 29 |
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| | |
| #include"os_python.h" | | #include"os_python.h" |
| #include"Rep.h" | | #include"Rep.h" |
| #include"Symmetry.h" | | #include"Symmetry.h" |
| #include"Word.h" | | #include"Word.h" |
| #include"Setting.h" | | #include"Setting.h" |
| #include"ObjectMolecule.h" | | #include"ObjectMolecule.h" |
| | |
| #define COORD_SET_HAS_ANISOU 0x01 | | #define COORD_SET_HAS_ANISOU 0x01 |
| | |
|
| | enum mmpymolx_prop_state_t { |
| | MMPYMOLX_PROP_STATE_NULL = 0, // invalidated |
| | MMPYMOLX_PROP_STATE_AUTO, // auto-assigned (libmmpymolx) |
| | MMPYMOLX_PROP_STATE_USER, // user-assigned (cmd.alter) |
| | }; |
| | |
| typedef struct CoordSet { | | typedef struct CoordSet { |
| // methods (not fully refactored yet) | | // methods (not fully refactored yet) |
| void fFree(); | | void fFree(); |
| | |
| // methods | | // methods |
| void update(int state); | | void update(int state); |
| void render(RenderInfo * info); | | void render(RenderInfo * info); |
| void enumIndices(); | | void enumIndices(); |
| void appendIndices(int offset); | | void appendIndices(int offset); |
| int extendIndices(int nAtom); | | int extendIndices(int nAtom); |
| | |
| skipping to change at line 111 | | skipping to change at line 117 |
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| byres/bychain actions which assume such atoms to be adjancent... | | byres/bychain actions which assume such atoms to be adjancent... |
| */ | | */ |
| | |
| CGO *SculptCGO, *SculptShaderCGO; | | CGO *SculptCGO, *SculptShaderCGO; |
| MapType *Coord2Idx; | | MapType *Coord2Idx; |
| float Coord2IdxReq, Coord2IdxDiv; | | float Coord2IdxReq, Coord2IdxDiv; |
| | |
| /* temporary / optimization */ | | /* temporary / optimization */ |
| | |
| int objMolOpInvalidated; | | int objMolOpInvalidated; |
|
| #ifndef NO_MMLIBS | | #ifdef _PYMOL_IP_EXTRAS |
| bool validMMStereo; | | mmpymolx_prop_state_t validMMStereo; |
| bool validTextType; | | mmpymolx_prop_state_t validTextType; |
| #endif | | #endif |
| | |
|
| #ifdef _PYMOL_IP_EXTRAS | | #ifdef _PYMOL_IP_PROPERTIES |
| #endif | | #endif |
|
| | |
| | /* Atom-state Settings */ |
| | int *atom_state_setting_id; |
| | char *has_atom_state_settings; |
| } CoordSet; | | } CoordSet; |
| | |
| typedef void (*fUpdateFn) (CoordSet *, int); | | typedef void (*fUpdateFn) (CoordSet *, int); |
| | |
| #define cCSet_NoPeriodicity 0 | | #define cCSet_NoPeriodicity 0 |
| #define cCSet_Orthogonal 1 | | #define cCSet_Orthogonal 1 |
| #define cCSet_Octahedral 2 | | #define cCSet_Octahedral 2 |
| | |
| int BondInOrder(BondType * a, int b1, int b2); | | int BondInOrder(BondType * a, int b1, int b2); |
| int BondCompare(BondType * a, BondType * b); | | int BondCompare(BondType * a, BondType * b); |
| | |
| skipping to change at line 139 | | skipping to change at line 149 |
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| PyObject *CoordSetAsNumPyArray(CoordSet * cs, short copy); | | PyObject *CoordSetAsNumPyArray(CoordSet * cs, short copy); |
| PyObject *CoordSetAsPyList(CoordSet * I); | | PyObject *CoordSetAsPyList(CoordSet * I); |
| int CoordSetFromPyList(PyMOLGlobals * G, PyObject * list, CoordSet ** cs); | | int CoordSetFromPyList(PyMOLGlobals * G, PyObject * list, CoordSet ** cs); |
| | |
| CoordSet *CoordSetNew(PyMOLGlobals * G); | | CoordSet *CoordSetNew(PyMOLGlobals * G); |
| void CoordSetAtomToPDBStrVLA(PyMOLGlobals * G, char **charVLA, int *c, | | void CoordSetAtomToPDBStrVLA(PyMOLGlobals * G, char **charVLA, int *c, |
| const AtomInfoType * ai, | | const AtomInfoType * ai, |
| const float *v, int cnt, | | const float *v, int cnt, |
| const PDBInfoRec * pdb_info, | | const PDBInfoRec * pdb_info, |
| const double *matrix); | | const double *matrix); |
|
| void CoordSetAtomToTERStrVLA(PyMOLGlobals * G, char **charVLA, int *c, AtomInfoT | | |
| ype * ai, | | |
| int cnt); | | |
| CoordSet *CoordSetCopy(const CoordSet * cs); | | CoordSet *CoordSetCopy(const CoordSet * cs); |
| | |
| void CoordSetTransform44f(CoordSet * I, const float *mat); | | void CoordSetTransform44f(CoordSet * I, const float *mat); |
| void CoordSetTransform33f(CoordSet * I, const float *mat); | | void CoordSetTransform33f(CoordSet * I, const float *mat); |
| void CoordSetRealToFrac(CoordSet * I, const CCrystal * cryst); | | void CoordSetRealToFrac(CoordSet * I, const CCrystal * cryst); |
| void CoordSetFracToReal(CoordSet * I, const CCrystal * cryst); | | void CoordSetFracToReal(CoordSet * I, const CCrystal * cryst); |
| | |
| bool CoordSetInsureOrthogonal(PyMOLGlobals * G, | | bool CoordSetInsureOrthogonal(PyMOLGlobals * G, |
| CoordSet * cset, | | CoordSet * cset, |
| const float * sca, | | const float * sca, |
| const CCrystal *cryst=NULL, | | const CCrystal *cryst=NULL, |
| bool quiet=true); | | bool quiet=true); |
| | |
| void CoordSetGetAverage(CoordSet * I, float *v0); | | void CoordSetGetAverage(CoordSet * I, float *v0); |
| PyObject *CoordSetAtomToChemPyAtom(PyMOLGlobals * G, AtomInfoType * ai, const fl
oat *v, | | PyObject *CoordSetAtomToChemPyAtom(PyMOLGlobals * G, AtomInfoType * ai, const fl
oat *v, |
| const float *ref, int index, const double *ma
trix); | | const float *ref, int index, const double *ma
trix); |
| int CoordSetGetAtomVertex(CoordSet * I, int at, float *v); | | int CoordSetGetAtomVertex(CoordSet * I, int at, float *v); |
| int CoordSetGetAtomTxfVertex(CoordSet * I, int at, float *v); | | int CoordSetGetAtomTxfVertex(CoordSet * I, int at, float *v); |
| int CoordSetSetAtomVertex(CoordSet * I, int at, const float *v); | | int CoordSetSetAtomVertex(CoordSet * I, int at, const float *v); |
| int CoordSetMoveAtom(CoordSet * I, int at, const float *v, int mode); | | int CoordSetMoveAtom(CoordSet * I, int at, const float *v, int mode); |
|
| int CoordSetMoveAtomLabel(CoordSet * I, int at, const float *v, int mode); | | int CoordSetMoveAtomLabel(CoordSet * I, int at, const float *v, const float *dif
f); |
| | |
| int CoordSetTransformAtomTTTf(CoordSet * I, int at, const float *TTT); | | int CoordSetTransformAtomTTTf(CoordSet * I, int at, const float *TTT); |
| int CoordSetTransformAtomR44f(CoordSet * I, int at, const float *matrix); | | int CoordSetTransformAtomR44f(CoordSet * I, int at, const float *matrix); |
| | |
| int CoordSetValidateRefPos(CoordSet * I); | | int CoordSetValidateRefPos(CoordSet * I); |
| | |
| void CoordSetPurge(CoordSet * I); | | void CoordSetPurge(CoordSet * I); |
| void CoordSetAdjustAtmIdx(CoordSet * I, int *lookup, int nAtom); | | void CoordSetAdjustAtmIdx(CoordSet * I, int *lookup, int nAtom); |
| int CoordSetMerge(ObjectMolecule *OM, CoordSet * I, CoordSet * cs); /* mu
st be non-overlapping */ | | int CoordSetMerge(ObjectMolecule *OM, CoordSet * I, CoordSet * cs); /* mu
st be non-overlapping */ |
| void CoordSetRecordTxfApplied(CoordSet * I, const float *TTT, int homogenous); | | void CoordSetRecordTxfApplied(CoordSet * I, const float *TTT, int homogenous); |
| void CoordSetUpdateCoord2IdxMap(CoordSet * I, float cutoff); | | void CoordSetUpdateCoord2IdxMap(CoordSet * I, float cutoff); |
| | |
| typedef struct _CCoordSetUpdateThreadInfo CCoordSetUpdateThreadInfo; | | typedef struct _CCoordSetUpdateThreadInfo CCoordSetUpdateThreadInfo; |
| | |
| void CoordSetUpdateThread(CCoordSetUpdateThreadInfo * T); | | void CoordSetUpdateThread(CCoordSetUpdateThreadInfo * T); |
| | |
| void LabPosTypeCopy(const LabPosType * src, LabPosType * dst); | | void LabPosTypeCopy(const LabPosType * src, LabPosType * dst); |
| void RefPosTypeCopy(const RefPosType * src, RefPosType * dst); | | void RefPosTypeCopy(const RefPosType * src, RefPosType * dst); |
| | |
|
| | #ifndef _PYMOL_NOPY |
| | int CoordSetSetSettingFromPyObject(PyMOLGlobals * G, CoordSet *cs, int at, int s |
| | etting_id, PyObject *val); |
| | #endif |
| | int CoordSetCheckSetting(PyMOLGlobals * G, CoordSet *cs, int at, int setting_id) |
| | ; |
| | PyObject *SettingGetIfDefinedPyObject(PyMOLGlobals * G, CoordSet *cs, int at, in |
| | t setting_id); |
| | int CoordSetCheckUniqueID(PyMOLGlobals * G, CoordSet *cs, int at); |
| | |
| | #define AtomStateGetSetting_b AtomStateGetSetting |
| | #define AtomStateGetSetting_i AtomStateGetSetting |
| | #define AtomStateGetSetting_f AtomStateGetSetting |
| | #define AtomStateGetSetting_s AtomStateGetSetting |
| | #define AtomStateGetSetting_color AtomStateGetSetting |
| | |
| | #define ATOMSTATEGETSETTINGARGS PyMOLGlobals * G, \ |
| | const ObjectMolecule * obj, \ |
| | const CoordSet * cs, int idx, \ |
| | const AtomInfoType * ai, \ |
| | int setting_id |
| | |
| | template <typename V> void AtomStateGetSetting(ATOMSTATEGETSETTINGARGS, V * out) |
| | ; |
| | |
| | // atom-state level setting |
| | template <typename V> void SettingSet(int index, V value, CoordSet *cs, int idx) |
| | { |
| | auto& G = cs->State.G; |
| | CoordSetCheckUniqueID(G, cs, idx); |
| | cs->has_atom_state_settings[idx] = true; |
| | SettingUniqueSet(G, cs->atom_state_setting_id[idx], index, value); |
| | } |
| | |
| // object-state level setting | | // object-state level setting |
| template <typename V> void SettingSet(int index, V value, CoordSet *cs) { | | template <typename V> void SettingSet(int index, V value, CoordSet *cs) { |
| SettingSet(cs->State.G, &cs->Setting, index, value); | | SettingSet(cs->State.G, &cs->Setting, index, value); |
| } | | } |
| | |
| #endif | | #endif |
| | | |
| End of changes. 7 change blocks. |
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| 8 lines changed or deleted | | 49 lines changed or added |
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