void RepLabelFree(RepLabel * I)
{
FreeP(I->R.P);
FreeP(I->V);
FreeP(I->L);
OOFreeP(I);
}
void RepLabelFree(RepLabel * I)
{
FreeP(I->R.P);
FreeP(I->V);
FreeP(I->L);
if (I->shaderCGO){
CGOFree(I->shaderCGO);
}
OOFreeP(I);
}
void MSKContextFree(MSKContext * G)
{
if (G) {
SphereFree(G);
//ColorFree(G);
FreeP(G);
}
}
void DeferredFree(CDeferred * I)
{
while(I) {
CDeferred *next = I->next;
FreeP(I);
I = next;
}
}
void MemoryCacheDone(PyMOLGlobals * G)
{
int a, b;
register CMemoryCache *I = G->MemoryCache;
for(a = 0; a < cMemoryCache_max_group; a++) {
for(b = 0; b < cMemoryCache_max_block; b++) {
MemoryCacheRec *rec = &I->Cache[a][b];
if(rec->ptr)
mfree(rec->ptr);
}
}
FreeP(G->MemoryCache);
}
CDeferred *DeferredExec(CDeferred * I)
{
while(I) { /* executes all deferred actions */
CDeferred *next = I->next;
if(I->fn) {
if(!I->fn(I)) {
break;
}
}
FreeP(I);
I = next;
}
return I;
}
/*========================================================================*/
void ControlFree(PyMOLGlobals * G)
{
register CControl *I = G->Control;
OrthoFreeBlock(G, I->Block);
FreeP(G->Control);
}
Rep *RepWireBondNew(CoordSet * cs, int state)
{
PyMOLGlobals *G = cs->State.G;
ObjectMolecule *obj = cs->Obj;
int a1, a2;
unsigned int b1, b2;
int a, c1, c2, ord;
bool s1, s2;
BondType *b;
int half_bonds, *other = NULL;
float valence;
float *v1, *v2;
int visFlag;
float line_width;
int valence_flag = false;
AtomInfoType *ai1;
int cartoon_side_chain_helper = 0;
int ribbon_side_chain_helper = 0;
int line_stick_helper = 0;
int na_mode;
bool *marked = NULL;
int valence_found = false;
int variable_width = false;
float last_line_width = -1.f;
int line_color;
int hide_long = false;
int fancy;
const float _0p9 = 0.9F;
int ok = true;
unsigned int line_counter = 0;
OOAlloc(G, RepWireBond);
CHECKOK(ok, I);
PRINTFD(G, FB_RepWireBond)
" RepWireBondNew-Debug: entered.\n" ENDFD;
visFlag = false;
b = obj->Bond;
ai1 = obj->AtomInfo;
if(ok && GET_BIT(obj->RepVisCache,cRepLine)){
for(a = 0; a < obj->NBond; a++) {
b1 = b->index[0];
b2 = b->index[1];
if((cRepLineBit & ai1[b1].visRep & ai1[b2].visRep)) {
visFlag = true;
break;
}
b++;
}
}
if(!visFlag) {
OOFreeP(I);
return (NULL); /* skip if no dots are visible */
}
marked = pymol::calloc<bool>(obj->NAtom);
CHECKOK(ok, marked);
if (!ok){
OOFreeP(I);
return (NULL);
}
valence_flag = SettingGet_b(G, cs->Setting, obj->Obj.Setting, cSetting_valence);
valence = SettingGet_f(G, cs->Setting, obj->Obj.Setting, cSetting_valence_size);
cartoon_side_chain_helper = SettingGet_b(G, cs->Setting, obj->Obj.Setting,
cSetting_cartoon_side_chain_helper);
ribbon_side_chain_helper = SettingGet_b(G, cs->Setting, obj->Obj.Setting,
cSetting_ribbon_side_chain_helper);
line_stick_helper = SettingGet_b(G, cs->Setting, obj->Obj.Setting,
cSetting_line_stick_helper);
line_color = SettingGet_color(G, cs->Setting, obj->Obj.Setting, cSetting_line_color);
line_width = SettingGet_f(G, cs->Setting, obj->Obj.Setting, cSetting_line_width);
if(line_stick_helper && (SettingGet_f(G, cs->Setting, obj->Obj.Setting,
cSetting_stick_transparency) > R_SMALL4))
line_stick_helper = false;
half_bonds = SettingGet_i(G, cs->Setting, obj->Obj.Setting, cSetting_half_bonds);
hide_long = SettingGet_b(G, cs->Setting, obj->Obj.Setting, cSetting_hide_long_bonds);
na_mode =
SettingGet_i(G, cs->Setting, obj->Obj.Setting, cSetting_cartoon_nucleic_acid_mode);
int na_mode_ribbon =
SettingGet_i(G, cs->Setting, obj->Obj.Setting, cSetting_ribbon_nucleic_acid_mode);
fancy = SettingGet_i(G, cs->Setting, obj->Obj.Setting, cSetting_valence_mode) == 1;
auto valence_zero_mode =
SettingGet_i(G, cs->Setting, obj->Obj.Setting, cSetting_valence_zero_mode);
b = obj->Bond;
for(a = 0; a < obj->NBond; a++) {
b1 = b->index[0];
b2 = b->index[1];
if(obj->DiscreteFlag) {
if((cs == obj->DiscreteCSet[b1]) && (cs == obj->DiscreteCSet[b2])) {
a1 = obj->DiscreteAtmToIdx[b1];
a2 = obj->DiscreteAtmToIdx[b2];
} else {
a1 = -1;
a2 = -1;
}
} else {
a1 = cs->AtmToIdx[b1];
a2 = cs->AtmToIdx[b2];
}
if((a1 >= 0) && (a2 >= 0)) {
if(!variable_width)
if (AtomInfoCheckBondSetting(G, b, cSetting_line_width)){
variable_width = true;
if (valence_found) break;
}
auto bd_valence_flag = BondSettingGetWD(G, b, cSetting_valence, valence_flag);
if(bd_valence_flag) {
valence_found = true;
if (variable_width) break;
}
}
b++;
}
RepInit(G, &I->R);
I->R.fRender = (void (*)(struct Rep *, RenderInfo * info)) RepWireBondRender;
I->R.fFree = (void (*)(struct Rep *)) RepWireBondFree;
I->shaderCGO = 0;
I->shaderCGO_has_cylinders = 0;
I->R.P = NULL;
I->R.fRecolor = NULL;
I->R.context.object = (void *) obj;
I->R.context.state = state;
I->R.cs = cs;
I->primitiveCGO = CGONew(G);
CGOSpecialWithArg(I->primitiveCGO, LINE_LIGHTING, 0.f);
CGOSpecial(I->primitiveCGO, LINEWIDTH_FOR_LINES);
CGOBegin(I->primitiveCGO, GL_LINES);
if(obj->NBond) {
if(valence_found) /* build list of up to 2 connected atoms for each atom */
other = ObjectMoleculeGetPrioritizedOtherIndexList(obj, cs);
if(ok && (cartoon_side_chain_helper || ribbon_side_chain_helper)) {
SideChainHelperMarkNonCartoonBonded(marked, obj, cs,
cartoon_side_chain_helper,
ribbon_side_chain_helper);
}
b = obj->Bond;
for(a = 0; ok && a < obj->NBond; ++a, ++b) {
b1 = b->index[0];
b2 = b->index[1];
ord = b->order;
if (ord == 0 && valence_zero_mode == 0)
continue;
if(obj->DiscreteFlag) {
if((cs == obj->DiscreteCSet[b1]) && (cs == obj->DiscreteCSet[b2])) {
a1 = obj->DiscreteAtmToIdx[b1];
a2 = obj->DiscreteAtmToIdx[b2];
} else {
a1 = -1;
a2 = -1;
}
} else {
a1 = cs->AtmToIdx[b1];
a2 = cs->AtmToIdx[b2];
}
if((a1 >= 0) && (a2 >= 0)) {
AtomInfoType *ati1 = obj->AtomInfo + b1;
AtomInfoType *ati2 = obj->AtomInfo + b2;
s1 = (ati1->visRep & cRepLineBit);
s2 = (ati2->visRep & cRepLineBit);
if(s1 ^ s2){
if(!half_bonds) {
if(line_stick_helper &&
(((!s1) && (cRepCylBit & ati1->visRep) && !(cRepCylBit & ati2->visRep)) ||
((!s2) && (cRepCylBit & ati2->visRep) && !(cRepCylBit & ati1->visRep))))
s1 = s2 = 1; /* turn on line when both stick and line are alternately shown */
else {
s1 = 0;
s2 = 0;
}
}
}
if(hide_long && (s1 || s2)) {
float cutoff = (ati1->vdw + ati2->vdw) * _0p9;
v1 = cs->Coord + 3 * a1;
v2 = cs->Coord + 3 * a2;
ai1 = obj->AtomInfo + b1;
if(!within3f(v1, v2, cutoff)) /* atoms separated by more than 90% of the sum of their vdw radii */
s1 = s2 = 0;
}
if(s1 || s2) {
float rgb1[3], rgb2[3];
int terminal = false;
auto bd_valence_flag = BondSettingGetWD(G, b, cSetting_valence, valence_flag);
auto bd_line_color = BondSettingGetWD(G, b, cSetting_line_color, line_color);
if(fancy && bd_valence_flag && (b->order > 1)) {
terminal = IsBondTerminal(obj, b1, b2);
}
if(variable_width) {
auto bd_line_width = BondSettingGetWD(G, b, cSetting_line_width, line_width);
if (last_line_width!=bd_line_width){
CGOSpecialWithArg(I->primitiveCGO, LINEWIDTH_FOR_LINES, bd_line_width);
last_line_width = bd_line_width;
}
}
if(bd_line_color < 0) {
if(bd_line_color == cColorObject) {
c1 = (c2 = obj->Obj.Color);
} else if(ColorCheckRamped(G, bd_line_color)) {
c1 = (c2 = bd_line_color);
} else {
c1 = ati1->color;
c2 = ati2->color;
}
} else {
c1 = (c2 = bd_line_color);
}
v1 = cs->Coord + 3 * a1;
v2 = cs->Coord + 3 * a2;
if (line_stick_helper && (ati1->visRep & ati2->visRep & cRepCylBit)) {
s1 = s2 = 0;
} else if ((ati1->flags & ati2->flags & cAtomFlag_polymer)) {
// side chain helpers
if ((cRepCartoonBit & ati1->visRep & ati2->visRep)) {
bool sc_helper = AtomSettingGetWD(G, ati1,
cSetting_cartoon_side_chain_helper, cartoon_side_chain_helper);
if (!sc_helper)
AtomSettingGetIfDefined(G, ati2, cSetting_cartoon_side_chain_helper, &sc_helper);
if (sc_helper &&
SideChainHelperFilterBond(G, marked, ati1, ati2, b1, b2, na_mode, &c1, &c2))
s1 = s2 = 0;
}
if ((s1 || s2) && (cRepRibbonBit & ati1->visRep & ati2->visRep)) {
bool sc_helper = AtomSettingGetWD(G, ati1,
cSetting_ribbon_side_chain_helper, ribbon_side_chain_helper);
if (!sc_helper)
AtomSettingGetIfDefined(G, ati2, cSetting_ribbon_side_chain_helper, &sc_helper);
if (sc_helper &&
SideChainHelperFilterBond(G, marked, ati1, ati2, b1, b2, na_mode_ribbon, &c1, &c2))
s1 = s2 = 0;
}
}
bool isRamped = false;
isRamped = ColorGetCheckRamped(G, c1, v1, rgb1, state);
isRamped = ColorGetCheckRamped(G, c2, v2, rgb2, state) | isRamped;
if (s1 || s2){
if (ord == 0 && valence_zero_mode == 2) {
ord = 1;
}
if (!ord){
RepWireZeroOrderBond(I->primitiveCGO, s1, s2, v1, v2, rgb1, rgb2, b1, b2, a, .15f, .15f, ati1->masked, ati2->masked);
} else if (!bd_valence_flag || ord <= 1){
RepLine(I->primitiveCGO, s1, s2, isRamped, v1, v2, rgb1, b1, b2, a, rgb2, ati1->masked, ati2->masked);
} else {
if (ord == 4){
RepAromatic(I->primitiveCGO, s1, s2, isRamped, v1, v2, other, a1, a2, cs->Coord, rgb1, rgb2, valence, 0, b1, b2, a, ati1->masked, ati2->masked);
} else {
RepValence(I->primitiveCGO, s1, s2, isRamped, v1, v2, other, a1, a2, cs->Coord, rgb1, rgb2, ord, valence, fancy && !terminal, b1, b2, a, ati1->masked, ati2->masked);
}
}
line_counter++;
}
}
}
ok &= !G->Interrupt;
}
}
CGOEnd(I->primitiveCGO);
CGOSpecialWithArg(I->primitiveCGO, LINE_LIGHTING, 1.f);
CGOStop(I->primitiveCGO);
FreeP(marked);
FreeP(other);
if (!ok || !line_counter){
RepWireBondFree(I);
I = NULL;
}
return (Rep *) I;
}
void QueueFree(CQueue * I)
{
FreeP(I->ptr);
OOFreeP(I);
}
void UtilFree(PyMOLGlobals *G)
{
FreeP(G->Util);
}
/*========================================================================*/
void PopFree(PyMOLGlobals * G)
{
register CPop *I = G->Pop;
OrthoFreeBlock(G, I->Block);
FreeP(G->Pop);
}
