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Source code changes of the file "layer2/ObjectMolecule.cpp" between
pymol-v2.1.0.tar.bz2 and pymol-open-source-2.2.0.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.

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ObjectMolecule.cpp  (pymol-v2.1.0.tar.bz2):ObjectMolecule.cpp  (pymol-open-source-2.2.0)
skipping to change at line 77 skipping to change at line 77
#define ntrim ParseNTrim #define ntrim ParseNTrim
#define nextline ParseNextLine #define nextline ParseNextLine
#define ncopy ParseNCopy #define ncopy ParseNCopy
#define nskip ParseNSkip #define nskip ParseNSkip
#ifndef NO_MMLIBS #ifndef NO_MMLIBS
#include "mmpymolx.h" #include "mmpymolx.h"
#endif #endif
int ObjectMoleculeUpdateMMStereoInfoForState(PyMOLGlobals * G, ObjectMolecule *
obj, int state, int initialize);
void ObjectMoleculeCylinders(ObjectMolecule * I); void ObjectMoleculeCylinders(ObjectMolecule * I);
static static
CoordSet *ObjectMoleculeMMDStr2CoordSet(PyMOLGlobals * G, const char *buffer, CoordSet *ObjectMoleculeMMDStr2CoordSet(PyMOLGlobals * G, const char *buffer,
AtomInfoType ** atInfoPtr, const char ** restart); AtomInfoType ** atInfoPtr, const char ** restart);
int ObjectMoleculeDoesAtomNeighborSele(ObjectMolecule * I, int index, int sele); int ObjectMoleculeDoesAtomNeighborSele(ObjectMolecule * I, int index, int sele);
void ObjectMoleculeAppendAtoms(ObjectMolecule * I, AtomInfoType * atInfo, void ObjectMoleculeAppendAtoms(ObjectMolecule * I, AtomInfoType * atInfo,
CoordSet * cset); CoordSet * cset);
skipping to change at line 6813 skipping to change at line 6811
if(atom < I->NAtom) { if(atom < I->NAtom) {
ITERNEIGHBORBONDS(I->Neighbor, atom, b, i) { ITERNEIGHBORBONDS(I->Neighbor, atom, b, i) {
result += I->Bond[b].order; result += I->Bond[b].order;
} }
} else { } else {
result = -1; /* error */ result = -1; /* error */
} }
return result; return result;
} }
/*
* Generate I->Neighbor from I->Bond, but only if I->Neighbor is not NULL.
*
* Changed in PyMOL 2.1.1: Ignore zero-order bonds (PYMOL-3025)
*
* To force the update, call ObjectMoleculeInvalidate(level=cRepInvBonds) first.
*
*/
/*========================================================================*/ /*========================================================================*/
int ObjectMoleculeUpdateNeighbors(ObjectMolecule * I) int ObjectMoleculeUpdateNeighbors(ObjectMolecule * I)
{ {
/* neighbor storage structure: VERY COMPLICATED... /* neighbor storage structure: VERY COMPLICATED...
0 list offset for atom 0 = n 0 list offset for atom 0 = n
1 list offset for atom 1 = n + m + 1 1 list offset for atom 1 = n + m + 1
... ...
n-1 list offset for atom n-1 n-1 list offset for atom n-1
skipping to change at line 6884 skipping to change at line 6890
if (!ok) if (!ok)
return ok; return ok;
/* initialize; zero out neighbors */ /* initialize; zero out neighbors */
l = I->Neighbor; l = I->Neighbor;
for(a = 0; a < I->NAtom; a++) for(a = 0; a < I->NAtom; a++)
(*l++) = 0; (*l++) = 0;
/* count neighbors for each atom */ /* count neighbors for each atom */
bnd = I->Bond; bnd = I->Bond;
for(b = 0; b < I->NBond; b++) { for(b = 0; b < I->NBond; b++) {
I->Neighbor[bnd->index[0]]++; if (bnd->order) {
I->Neighbor[bnd->index[1]]++; I->Neighbor[bnd->index[0]]++;
I->Neighbor[bnd->index[1]]++;
}
bnd++; bnd++;
} }
/* set up offsets and list terminators */ /* set up offsets and list terminators */
c = I->NAtom; c = I->NAtom;
for(a = 0; a < I->NAtom; a++) { for(a = 0; a < I->NAtom; a++) {
d = I->Neighbor[a]; /* get number of neighbors */ d = I->Neighbor[a]; /* get number of neighbors */
I->Neighbor[c] = d; /* store neighbor count */ I->Neighbor[c] = d; /* store neighbor count */
I->Neighbor[a] = c + d + d + 1; /* set initial position to end of list, we'll fill backwards */ I->Neighbor[a] = c + d + d + 1; /* set initial position to end of list, we'll fill backwards */
I->Neighbor[I->Neighbor[a]] = -1; /* store terminator */ I->Neighbor[I->Neighbor[a]] = -1; /* store terminator */
c += d + d + 2; c += d + d + 2;
} }
/* now load neighbors in a sequential list for each atom (reverse order) */ /* now load neighbors in a sequential list for each atom (reverse order) */
bnd = I->Bond; bnd = I->Bond;
for(b = 0; b < I->NBond; b++) { for(b = 0; b < I->NBond; b++, ++bnd) {
l0 = bnd->index[0]; l0 = bnd->index[0];
l1 = bnd->index[1]; l1 = bnd->index[1];
bnd++;
if (!bnd->order)
continue;
I->Neighbor[l0]--; I->Neighbor[l0]--;
I->Neighbor[I->Neighbor[l0]] = b; /* store bond indices (for I->Bond) */ I->Neighbor[I->Neighbor[l0]] = b; /* store bond indices (for I->Bond) */
I->Neighbor[l0]--; I->Neighbor[l0]--;
I->Neighbor[I->Neighbor[l0]] = l1; /* store neighbor references (I- >AtomInfo, etc.) */ I->Neighbor[I->Neighbor[l0]] = l1; /* store neighbor references (I- >AtomInfo, etc.) */
I->Neighbor[l1]--; I->Neighbor[l1]--;
I->Neighbor[I->Neighbor[l1]] = b; /* store bond indices (for I->Bond) */ I->Neighbor[I->Neighbor[l1]] = b; /* store bond indices (for I->Bond) */
I->Neighbor[l1]--; I->Neighbor[l1]--;
I->Neighbor[I->Neighbor[l1]] = l0; /* store neighbor references (I- >AtomInfo, etc.) */ I->Neighbor[I->Neighbor[l1]] = l0; /* store neighbor references (I- >AtomInfo, etc.) */
skipping to change at line 10331 skipping to change at line 10341
cs->objMolOpInvalidated = false; cs->objMolOpInvalidated = false;
} }
break; break;
} }
use_matrices = SettingGet_i(I->Obj.G, I->Obj.Setting, NULL, cSetting_mat rix_mode); use_matrices = SettingGet_i(I->Obj.G, I->Obj.Setting, NULL, cSetting_mat rix_mode);
if(use_matrices<0) use_matrices = 0; if(use_matrices<0) use_matrices = 0;
ai = I->AtomInfo; ai = I->AtomInfo;
#ifdef _PYMOL_IP_EXTRAS #ifdef _PYMOL_IP_EXTRAS
// use stereo or text_type ? // use stereo or text_type ?
switch (op->code){ // only do this for "label2" command (better logic in WrapperObjectSubSc
case OMOP_AlterState: ript)
case OMOP_LABL: if (op->code == OMOP_LABL && op->i2 == cExecutiveLabelEvalAlt) {
case OMOP_ALTR:
use_stereo = PLabelExprUsesVariable(G, op->s1, "stereo"); use_stereo = PLabelExprUsesVariable(G, op->s1, "stereo");
use_text_type = PLabelExprUsesVariable(G, op->s1, "text_type"); use_text_type = PLabelExprUsesVariable(G, op->s1, "text_type");
} }
#ifdef NO_MMLIBS #ifdef NO_MMLIBS
if (use_stereo) { if (use_stereo) {
PRINTFB(G, FB_ObjectMolecule, FB_Warnings) PRINTFB(G, FB_ObjectMolecule, FB_Warnings)
" NO_MMLIBS-Warning: stereochemistry not supported in this PyMOL bui ld.\n" ENDFB(G); " NO_MMLIBS-Warning: stereochemistry not supported in this PyMOL bui ld.\n" ENDFB(G);
} }
if (use_text_type) { if (use_text_type) {
skipping to change at line 11290 skipping to change at line 11298
start = state; start = state;
stop = state + 1; stop = state + 1;
} }
if(stop > I->NCSet) if(stop > I->NCSet)
stop = I->NCSet; stop = I->NCSet;
for(a = start; a < stop; a++) { for(a = start; a < stop; a++) {
CoordSet *cset = 0; CoordSet *cset = 0;
cset = I->CSet[a]; cset = I->CSet[a];
if(cset) { if(cset) {
cset->invalidateRep(rep, level); cset->invalidateRep(rep, level);
#ifndef NO_MMLIBS
if (level >= cRepInvProp) {
cset->validMMStereo = false;
cset->validTextType = false;
}
#endif
} }
} }
} }
PRINTFD(I->Obj.G, FB_ObjectMolecule) PRINTFD(I->Obj.G, FB_ObjectMolecule)
" ObjectMoleculeInvalidate: leaving...\n" ENDFD; " ObjectMoleculeInvalidate: leaving...\n" ENDFD;
} }
void ObjectMoleculeInvalidateAtomType(ObjectMolecule *I, int state){ void ObjectMoleculeInvalidateAtomType(ObjectMolecule *I, int state){
skipping to change at line 11361 skipping to change at line 11363
ObjectMoleculeGetAtomSele(I, index, buffer); ObjectMoleculeGetAtomSele(I, index, buffer);
sprintf(line, "cmd.translate_atom(\"%s\",%15.9f,%15.9f,%15.9f,%d,%d,%d)\n" , sprintf(line, "cmd.translate_atom(\"%s\",%15.9f,%15.9f,%15.9f,%d,%d,%d)\n" ,
buffer, v[0], v[1], v[2], state + 1, mode, 0); buffer, v[0], v[1], v[2], state + 1, mode, 0);
PLog(G, line, cPLog_no_flush); PLog(G, line, cPLog_no_flush);
} }
} }
return (result); return (result);
} }
/*========================================================================*/ /*========================================================================*/
int ObjectMoleculeMoveAtomLabel(ObjectMolecule * I, int state, int index, float int ObjectMoleculeMoveAtomLabel(ObjectMolecule * I, int state, int index, float
*v, *v, int log, float *diff)
int mode, int log)
{ {
int result = 0; int result = 0;
CoordSet *cs; CoordSet *cs;
if(!(I->AtomInfo[index].protekted == 1)) { if(!(I->AtomInfo[index].protekted == 1)) {
if(state < 0) if(state < 0)
state = 0; state = 0;
if(I->NCSet == 1) if(I->NCSet == 1)
state = 0; state = 0;
state = state % I->NCSet; state = state % I->NCSet;
if((!I->CSet[state]) if((!I->CSet[state])
&& (SettingGet_b(I->Obj.G, I->Obj.Setting, NULL, cSetting_all_states))) && (SettingGet_b(I->Obj.G, I->Obj.Setting, NULL, cSetting_all_states)))
state = 0; state = 0;
cs = I->CSet[state]; cs = I->CSet[state];
if(cs) { if(cs) {
result = CoordSetMoveAtomLabel(I->CSet[state], index, v, mode); result = CoordSetMoveAtomLabel(I->CSet[state], index, v, diff);
cs->invalidateRep(cRepLabel, cRepInvCoord); cs->invalidateRep(cRepLabel, cRepInvCoord);
} }
} }
return (result); return (result);
} }
/*========================================================================*/ /*========================================================================*/
int ObjectMoleculeInitBondPath(ObjectMolecule * I, ObjectMoleculeBPRec * bp) int ObjectMoleculeInitBondPath(ObjectMolecule * I, ObjectMoleculeBPRec * bp)
{ {
int a; int a;
skipping to change at line 11657 skipping to change at line 11658
CRay *ray = info->ray; CRay *ray = info->ray;
Picking **pick = info->pick; Picking **pick = info->pick;
int pass = info->pass; int pass = info->pass;
CoordSet *cs; CoordSet *cs;
int pop_matrix = false; int pop_matrix = false;
int use_matrices = SettingGet_i(I->Obj.G, I->Obj.Setting, NULL, cSetting_matri x_mode); int use_matrices = SettingGet_i(I->Obj.G, I->Obj.Setting, NULL, cSetting_matri x_mode);
if(use_matrices<0) use_matrices = 0; if(use_matrices<0) use_matrices = 0;
PRINTFD(I->Obj.G, FB_ObjectMolecule) PRINTFD(I->Obj.G, FB_ObjectMolecule)
" ObjectMolecule: rendering %s pass %d...\n", I->Obj.Name, pass ENDFD; " ObjectMolecule: rendering %s pass %d...\n", I->Obj.Name, pass ENDFD;
ObjectPrepareContext(&I->Obj, ray); ObjectPrepareContext(&I->Obj, info);
if(I->UnitCellCGO && (I->Obj.visRep & cRepCellBit)) { if(I->UnitCellCGO && (I->Obj.visRep & cRepCellBit)) {
if(ray) { if(ray) {
/* need to apply object state matrix here */ /* need to apply object state matrix here */
int ok = CGORenderRay(I->UnitCellCGO, ray, ColorGet(I->Obj.G, I->Obj.Color int ok = CGORenderRay(I->UnitCellCGO, ray, info, ColorGet(I->Obj.G, I->Obj
), .Color),
I->Obj.Setting, NULL); NULL, I->Obj.Setting, NULL);
if (!ok){ if (!ok){
CGOFree(I->UnitCellCGO); CGOFree(I->UnitCellCGO);
} }
} else if(G->HaveGUI && G->ValidContext) { } else if(G->HaveGUI && G->ValidContext) {
if(pick) { if(pick) {
} else { } else {
/* need to apply object state matrix here */ /* need to apply object state matrix here */
ObjectUseColor(&I->Obj); ObjectUseColor(&I->Obj);
CGORenderGL(I->UnitCellCGO, ColorGet(I->Obj.G, I->Obj.Color), CGORenderGL(I->UnitCellCGO, ColorGet(I->Obj.G, I->Obj.Color),
I->Obj.Setting, NULL, info, NULL); I->Obj.Setting, NULL, info, NULL);
skipping to change at line 11942 skipping to change at line 11943
ok_except1: ok_except1:
ErrMessage(I->Obj.G, "ObjectMoleculeSetStateOrder", "failed"); ErrMessage(I->Obj.G, "ObjectMoleculeSetStateOrder", "failed");
VLAFreeP(csets); VLAFreeP(csets);
return false; return false;
} }
/*========================================================================*/ /*========================================================================*/
void ObjectMoleculeFree(ObjectMolecule * I) void ObjectMoleculeFree(ObjectMolecule * I)
{ {
int a; int a;
SceneObjectDel(I->Obj.G, (CObject *) I, false);
SelectorPurgeObjectMembers(I->Obj.G, I); SelectorPurgeObjectMembers(I->Obj.G, I);
for(a = 0; a < I->NCSet; a++){ for(a = 0; a < I->NCSet; a++){
if(I->CSet[a]) { if(I->CSet[a]) {
I->CSet[a]->fFree(); I->CSet[a]->fFree();
I->CSet[a] = NULL; I->CSet[a] = NULL;
} }
} }
/* RemoveAllUndosForObjectMolecule(I); */ /* RemoveAllUndosForObjectMolecule(I); */
if(I->Symmetry) if(I->Symmetry)
SymmetryFree(I->Symmetry); SymmetryFree(I->Symmetry);
skipping to change at line 12035 skipping to change at line 12035
atInfo = I->AtomInfo; atInfo = I->AtomInfo;
isNew = true; isNew = true;
} else { } else {
atInfo = (AtomInfoType*) VLAMalloc(10, sizeof(AtomInfoType), 2, true); /* autozero here is important */ atInfo = (AtomInfoType*) VLAMalloc(10, sizeof(AtomInfoType), 2, true); /* autozero here is important */
CHECKOK(ok, atInfo); CHECKOK(ok, atInfo);
isNew = false; isNew = false;
} }
if(ok && isNew) { if(ok && isNew) {
I->Obj.Color = AtomInfoUpdateAutoColor(G); I->Obj.Color = AtomInfoUpdateAutoColor(G);
if (pdb_info->variant == PDB_VARIANT_VDB) { if (pdb_info->variant == PDB_VARIANT_VDB ||
pdb_info->variant == PDB_VARIANT_PQR) {
// pqr files have no chain identifier by default
// vdb files have same chain identifiers in all symmetry copies // vdb files have same chain identifiers in all symmetry copies
SettingSet(cSetting_retain_order, 1, (CObject *) I); SettingSet(cSetting_retain_order, 1, (CObject *) I);
} }
} }
if (ok) if (ok)
cset = ObjectMoleculePDBStr2CoordSet(G, start, &atInfo, &restart, cset = ObjectMoleculePDBStr2CoordSet(G, start, &atInfo, &restart,
segi_override, m4x, pdb_name, segi_override, m4x, pdb_name,
next_pdb, pdb_info, quiet, model_num ber); next_pdb, pdb_info, quiet, model_num ber);
if (isNew && atInfo != I->AtomInfo){ if (isNew && atInfo != I->AtomInfo){
I->AtomInfo = atInfo; I->AtomInfo = atInfo;
skipping to change at line 12395 skipping to change at line 12397
I->DiscreteAtmToIdx[a0] = I->DiscreteAtmToIdx[a]; I->DiscreteAtmToIdx[a0] = I->DiscreteAtmToIdx[a];
I->DiscreteCSet[a0] = I->DiscreteCSet[a]; I->DiscreteCSet[a0] = I->DiscreteCSet[a];
} }
} }
} }
} }
void AtomInfoSettingGenerateSideEffects(PyMOLGlobals * G, ObjectMolecule *obj, i nt index, int id){ void AtomInfoSettingGenerateSideEffects(PyMOLGlobals * G, ObjectMolecule *obj, i nt index, int id){
switch(index){ switch(index){
case cSetting_label_position: case cSetting_label_position:
case cSetting_label_placement_offset:
case cSetting_label_screen_point:
case cSetting_label_relative_mode:
ObjectMoleculeInvalidate(obj, cRepLabel, cRepInvCoord, -1); ObjectMoleculeInvalidate(obj, cRepLabel, cRepInvCoord, -1);
} }
} }
static int AtomInfoInOrder(PyMOLGlobals * G, AtomInfoType * atom, int atom1, int atom2) static int AtomInfoInOrder(PyMOLGlobals * G, AtomInfoType * atom, int atom1, int atom2)
{ {
return (AtomInfoCompare(G, atom + atom1, atom + atom2) <= 0); return (AtomInfoCompare(G, atom + atom1, atom + atom2) <= 0);
} }
static int AtomInfoInOrderIgnoreHet(PyMOLGlobals * G, AtomInfoType * atom, static int AtomInfoInOrderIgnoreHet(PyMOLGlobals * G, AtomInfoType * atom,
 End of changes. 14 change blocks. 
27 lines changed or deleted 32 lines changed or added
To the C++ Programs section of the PyMOL source changes report or the top of this page
Mainly generated by pkgdiff using rfcdiff
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