"Fossies" - the Fresh Open Source Software Archive  

Source code changes of the file "layer2/RepCartoon.cpp" 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 ]

RepCartoon.cpp  (pymol-open-source-2.2.0):RepCartoon.cpp  (pymol-open-source-2.3.0)
skipping to change at line 66 skipping to change at line 66
Rep R; /* must be first! */ Rep R; /* must be first! */
CGO *ray, *std, *preshader; CGO *ray, *std, *preshader;
char *LastVisib; char *LastVisib;
unsigned char renderWithShaders, hasTransparency; unsigned char renderWithShaders, hasTransparency;
} RepCartoon; } RepCartoon;
#include"ObjectMolecule.h" #include"ObjectMolecule.h"
#define ESCAPE_MAX 500 #define ESCAPE_MAX 500
void RepCartoonFree(RepCartoon * I); static
void RepCartoonFree(RepCartoon * I) void RepCartoonFree(RepCartoon * I)
{ {
if (I->ray != I->preshader) if (I->ray != I->preshader)
CGOFree(I->preshader); CGOFree(I->preshader);
CGOFree(I->ray); CGOFree(I->ray);
CGOFree(I->std); CGOFree(I->std);
FreeP(I->LastVisib); FreeP(I->LastVisib);
RepPurge(&I->R); RepPurge(&I->R);
OOFreeP(I); OOFreeP(I);
} }
skipping to change at line 106 skipping to change at line 105
} }
static int RepCartoonCGOGenerate(RepCartoon * I, RenderInfo * info) static int RepCartoonCGOGenerate(RepCartoon * I, RenderInfo * info)
{ {
PyMOLGlobals *G = I->R.G; PyMOLGlobals *G = I->R.G;
int ok = true; int ok = true;
int use_shaders, has_cylinders_to_optimize; int use_shaders, has_cylinders_to_optimize;
float alpha = 1.0F - SettingGet_f(G, I->R.cs->Setting, I->R.obj->Setting, cSet ting_cartoon_transparency); float alpha = 1.0F - SettingGet_f(G, I->R.cs->Setting, I->R.obj->Setting, cSet ting_cartoon_transparency);
auto hasAtomLevelAlpha = [](RepCartoon * I){
for(CoordSetAtomIterator iter(I->R.cs); iter.next();){
auto ai = iter.getAtomInfo();
if(AtomSettingGetWD(I->R.G, ai, cSetting_cartoon_transparency, 0.0f)){
return true;
}
}
return false;
}(I);
use_shaders = SettingGetGlobal_b(G, cSetting_use_shaders) && SettingGetGlobal_ b(G, cSetting_cartoon_use_shader); use_shaders = SettingGetGlobal_b(G, cSetting_use_shaders) && SettingGetGlobal_ b(G, cSetting_cartoon_use_shader);
has_cylinders_to_optimize = G->ShaderMgr->Get_CylinderShader(info->pass, 0) && has_cylinders_to_optimize = G->ShaderMgr->Get_CylinderShader(info->pass, 0) &&
SettingGetGlobal_i(G, cSetting_cartoon_nucleic_aci d_as_cylinders) && SettingGetGlobal_i(G, cSetting_cartoon_nucleic_aci d_as_cylinders) &&
SettingGetGlobal_b(G, cSetting_render_as_cylinders ) && SettingGetGlobal_b(G, cSetting_render_as_cylinders ) &&
CGOHasCylinderOperations(I->preshader); CGOHasCylinderOperations(I->preshader);
if (I->std && if (I->std &&
(use_shaders ^ I->renderWithShaders)){ (use_shaders ^ I->renderWithShaders)){
// if renderWithShaders doesn't match use_shader, clear CGO and re-generate // if renderWithShaders doesn't match use_shader, clear CGO and re-generate
CGOFree(I->std); CGOFree(I->std);
I->std = 0; I->std = 0;
} }
I->hasTransparency = 0; I->hasTransparency = 0;
if (use_shaders){ if (use_shaders){
CGO *convertcgo = NULL, *tmpCGO = NULL, *tmp2CGO = NULL; CGO *convertcgo = NULL, *tmpCGO = NULL, *tmp2CGO = NULL;
if ((alpha < 1.f) && (SettingGetGlobal_i(G, cSetting_transparency_mode) != 3 if (((alpha < 1.f) || hasAtomLevelAlpha) &&
)){ (SettingGetGlobal_i(G, cSetting_transparency_mode) != 3)){
// some transparency // some transparency
const float *color; const float *color;
float colorWithA[4]; float colorWithA[4];
CGO *convertcgo2; CGO *convertcgo2;
convertcgo2 = CGOSimplify(I->preshader, 0) ; convertcgo2 = CGOSimplify(I->preshader, 0) ;
convertcgo = CGOCombineBeginEnd(convertcgo2, 0); convertcgo = CGOCombineBeginEnd(convertcgo2, 0);
CGOFree(convertcgo2); CGOFree(convertcgo2);
CHECKOK(ok, convertcgo); CHECKOK(ok, convertcgo);
color = ColorGet(G, I->R.obj->Color); color = ColorGet(G, I->R.obj->Color);
copy3f(color, colorWithA); copy3f(color, colorWithA);
skipping to change at line 209 skipping to change at line 218
CHECKOK(ok, tmpCGO); CHECKOK(ok, tmpCGO);
CGOFree(leftOverCGOCombined); CGOFree(leftOverCGOCombined);
if (ok) if (ok)
ok &= CGOAppend(convertcgo, tmpCGO); ok &= CGOAppend(convertcgo, tmpCGO);
CGOFreeWithoutVBOs(tmpCGO); CGOFreeWithoutVBOs(tmpCGO);
tmpCGO = NULL; tmpCGO = NULL;
I->std = CGOAddTwoSidedBackfaceSpecialOps(G, convertcgo); I->std = CGOAddTwoSidedBackfaceSpecialOps(G, convertcgo);
} }
} else { } else {
if (ok){ if (ok){
if (alpha < 1.f){ auto simplifiedCGO = CGOSimplify(I->preshader, 0);
CGO *tmpCGO = NULL; if (alpha < 1.f || hasAtomLevelAlpha){
tmpCGO = CGOConvertTrianglesToAlpha(I->preshader); auto convertedCGO = CGOConvertTrianglesToAlpha(simplifiedCGO);
I->std = tmpCGO; CGOFree(simplifiedCGO);
I->std->render_alpha = 1; // CGORenderGL should call CGOSetZVector/CGORe I->std = convertedCGO;
nderGLAlpha only if(I->std){
I->std->render_alpha = 1; // CGORenderGL should call CGOSetZVector/CGO
RenderGLAlpha only
}
} else { } else {
I->std = CGOSimplify(I->preshader, 0); I->std = simplifiedCGO;
CHECKOK(ok, I->std); CHECKOK(ok, I->std);
} }
I->std = CGOAddTwoSidedBackfaceSpecialOps(G, I->std); if(I->std) {
I->std = CGOAddTwoSidedBackfaceSpecialOps(G, I->std);
}
} }
} }
if(I->preshader && (I->ray!=I->preshader)){ if(I->preshader && (I->ray!=I->preshader)){
CGOFree(I->preshader); CGOFree(I->preshader);
} }
I->preshader = NULL; I->preshader = NULL;
I->renderWithShaders = use_shaders; I->renderWithShaders = use_shaders;
return ok; return ok;
} }
static void RepCartoonRender(RepCartoon * I, RenderInfo * info) static void RepCartoonRender(RepCartoon * I, RenderInfo * info)
{ {
CRay *ray = info->ray; CRay *ray = info->ray;
Picking **pick = info->pick; auto pick = info->pick;
PyMOLGlobals *G = I->R.G; PyMOLGlobals *G = I->R.G;
int ok = true; int ok = true;
if (!ray && I->preshader) { if (!ray && I->preshader) {
ok &= RepCartoonCGOGenerate(I, info); ok &= RepCartoonCGOGenerate(I, info);
} }
if(ray) { if(ray) {
#ifndef _PYMOL_NO_RAY #ifndef _PYMOL_NO_RAY
int try_std = false; int try_std = false;
skipping to change at line 1025 skipping to change at line 1039
color1 = color2 = ColorGet(G, ladder_color); color1 = color2 = ColorGet(G, ladder_color);
} else { } else {
color1 = ColorGet(G, g1_ai->color); color1 = ColorGet(G, g1_ai->color);
color2 = ColorGet(G, g2_ai->color); color2 = ColorGet(G, g2_ai->color);
} }
CGOPickColor(cgo, g1, g1_ai->masked ? cPickableNoPick : cPic kableAtom); CGOPickColor(cgo, g1, g1_ai->masked ? cPickableNoPick : cPic kableAtom);
Pickable pickcolor2 = { g2, g2_ai->masked ? cPickableNoPick : cPickableAtom }; Pickable pickcolor2 = { g2, g2_ai->masked ? cPickableNoPick : cPickableAtom };
float axis[3]; float axis[3];
subtract3f(g2p, g1p, axis); subtract3f(g2p, g1p, axis);
CGOColorv(cgo, color1); CGOColorv(cgo, color1);
cgo->add<cgo::draw::shadercylinder2ndcolor>(cgo, g1p, axis, float ladder_alpha = 1.0f - AtomSettingGetWD(G, ai_i[i], cSe
glyco_radius, 0x1f, color2, &pickcolor2); tting_cartoon_transparency, 1.0f - alpha);
} cgo->add<cgo::draw::shadercylinder2ndcolor>(cgo, g1p, axis,
glyco_radius, 0x1f, color2, &pickcolor2, ladder_alpha);
}
} }
} }
} }
} }
} }
} }
/* see if any of the neighbors are confirmed nucleic acids... */ /* see if any of the neighbors are confirmed nucleic acids... */
if(sugar_at >= 0) { if(sugar_at >= 0) {
if(!nf) { if(!nf) {
skipping to change at line 1081 skipping to change at line 1096
color1 = color2 = ColorGet(G, ladder_color); color1 = color2 = ColorGet(G, ladder_color);
} else { } else {
color1 = ColorGet(G, sug_ai->color); color1 = ColorGet(G, sug_ai->color);
color2 = ColorGet(G, bas_ai->color); color2 = ColorGet(G, bas_ai->color);
} }
CGOPickColor(cgo, sugar_at, sug_ai->masked ? cPickableNoPi ck : cPickableAtom); CGOPickColor(cgo, sugar_at, sug_ai->masked ? cPickableNoPi ck : cPickableAtom);
Pickable pickcolor2 = { base_at, bas_ai->masked ? cPickabl eNoPick : cPickableAtom }; Pickable pickcolor2 = { base_at, bas_ai->masked ? cPickabl eNoPick : cPickableAtom };
float axis[3]; float axis[3];
subtract3f(cs->Coord + 3 * bas, cs->Coord + 3 * sug, axis) ; subtract3f(cs->Coord + 3 * bas, cs->Coord + 3 * sug, axis) ;
CGOColorv(cgo, color1); CGOColorv(cgo, color1);
cgo->add<cgo::draw::shadercylinder2ndcolor>(cgo, cs->Coord float ladder_alpha = 1.0f - AtomSettingGetWD(G, ai_i[i], c
+ 3 * sug, axis, ladder_radius, 0x1f, color2, &pickcolor2); Setting_cartoon_transparency, 1.0f - alpha);
} cgo->add<cgo::draw::shadercylinder2ndcolor>(cgo, cs->Coord
+ 3 * sug, axis, ladder_radius, 0x1f, color2, &pickcolor2, ladder_alpha);
}
} }
} }
} }
base_at = save_at; base_at = save_at;
sugar_at = save_at; sugar_at = save_at;
} }
} }
if((base_at >= 0) && (sugar_at >= 0)) { if((base_at >= 0) && (sugar_at >= 0)) {
AtomInfoType *sug_ai = atomInfo + sugar_at; AtomInfoType *sug_ai = atomInfo + sugar_at;
AtomInfoType *bas_ai = atomInfo + base_at; AtomInfoType *bas_ai = atomInfo + base_at;
skipping to change at line 1160 skipping to change at line 1176
} else { } else {
color1 = ColorGet(G, sug_ai->color); color1 = ColorGet(G, sug_ai->color);
color2 = ColorGet(G, bas_ai->color); color2 = ColorGet(G, bas_ai->color);
} }
CGOPickColor(cgo, sugar_at, sug_ai->masked ? cPickableNoPick : cPickableAtom); CGOPickColor(cgo, sugar_at, sug_ai->masked ? cPickableNoPick : cPickableAtom);
Pickable pickcolor2 = { base_at, bas_ai->masked ? cPickableNoP ick : cPickableAtom }; Pickable pickcolor2 = { base_at, bas_ai->masked ? cPickableNoP ick : cPickableAtom };
float axis[3]; float axis[3];
subtract3f(cs->Coord + 3 * bas, v_outer, axis); subtract3f(cs->Coord + 3 * bas, v_outer, axis);
CGOColorv(cgo, color1); CGOColorv(cgo, color1);
cgo->add<cgo::draw::shadercylinder2ndcolor>(cgo, v_outer, axis float ladder_alpha = 1.0f - AtomSettingGetWD(G, sug_ai, cSetti
, ladder_radius, 0x1f, color2, &pickcolor2); ng_cartoon_transparency, 1.0f - alpha);
} cgo->add<cgo::draw::shadercylinder2ndcolor>(cgo, v_outer, axis
, ladder_radius, 0x1f, color2, &pickcolor2, ladder_alpha);
}
} }
} }
} }
} }
} }
} }
if((!ring_mode) || (finder == 2)) { if((!ring_mode) || (finder == 2)) {
if(ladder_mode) { /* mark sure all rings traversed are mark */ if(ladder_mode) { /* mark sure all rings traversed are mark */
int i; int i;
for(i = 0; i <= n_atom; i++) { for(i = 0; i <= n_atom; i++) {
skipping to change at line 1222 skipping to change at line 1239
float *v_moved = moved + atix[i] * 3; float *v_moved = moved + atix[i] * 3;
copy3f(avg, v_moved); /* store ring center for later use */ copy3f(avg, v_moved); /* store ring center for later use */
} }
if((nf || (!ladder_mode) || (finder >= 3)) && if((nf || (!ladder_mode) || (finder >= 3)) &&
ring_mode && ring_mode &&
(((finder == 1) && ((have_C4 >= 0) || (have_C4_prime >= 0))) || (((finder == 1) && ((have_C4 >= 0) || (have_C4_prime >= 0))) ||
((finder == 2) && ((have_C4 >= 0))) || ((finder == 2) && ((have_C4 >= 0))) ||
((finder == 3) && ((have_C_number >= 0))) || ((finder == 4)))) { ((finder == 3) && ((have_C_number >= 0))) || ((finder == 4)))) {
if((alpha != 1.0F) || (ring_alpha != alpha)) auto atom_alpha = 1.0f - AtomSettingGetWD(G, ai_i[i], cSetting_cartoon_t
CGOAlpha(cgo, ring_alpha); ransparency, 1.0f - ring_alpha);
if((alpha != 1.0F) || (ring_alpha != alpha) || atom_alpha != 1.0){
if(atom_alpha != ring_alpha){
CGOAlpha(cgo, atom_alpha);
} else {
CGOAlpha(cgo, ring_alpha);
}
}
if(ring_color >= 0) { if(ring_color >= 0) {
color = ColorGet(G, ring_color); color = ColorGet(G, ring_color);
} else { } else {
color = avg_col; color = avg_col;
} }
CGOColorv(cgo, color); CGOColorv(cgo, color);
if((ring_mode == 4) || (ring_mode == 5)) { /* spherical ring */ if((ring_mode == 4) || (ring_mode == 5)) { /* spherical ring */
skipping to change at line 1397 skipping to change at line 1420
color1 = col[i]; color1 = col[i];
color2 = col[ii]; color2 = col[ii];
} else { } else {
color1 = color2 = color; color1 = color2 = color;
} }
CGOPickColor(cgo, atix[i], ai_i[i]->masked ? cPickableNoPick : cPickableAtom); CGOPickColor(cgo, atix[i], ai_i[i]->masked ? cPickableNoPick : cPickableAtom);
Pickable pickcolor2 = { atix[ii], ai_i[ii]->masked ? cPickable NoPick : cPickableAtom }; Pickable pickcolor2 = { atix[ii], ai_i[ii]->masked ? cPickable NoPick : cPickableAtom };
float axis[3]; float axis[3];
subtract3f(v_i[ii], v_i[i], axis); subtract3f(v_i[ii], v_i[i], axis);
CGOColorv(cgo, color1); CGOColorv(cgo, color1);
cgo->add<cgo::draw::shadercylinder2ndcolor>(cgo, v_i[i], axis, float ladder_alpha = 1.0f - AtomSettingGetWD(G, ai_i[i], cSett
ring_width_for_mode, 0x1f, color2, &pickcolor2); ing_cartoon_transparency, 1.0f - alpha);
} cgo->add<cgo::draw::shadercylinder2ndcolor>(cgo, v_i[i], axis,
ring_width_for_mode, 0x1f, color2, &pickcolor2, ladder_alpha);
}
} }
} }
} }
} }
} }
} }
} }
} }
/* /*
skipping to change at line 1626 skipping to change at line 1650
#ifndef PURE_OPENGL_ES_2 #ifndef PURE_OPENGL_ES_2
if (ok) if (ok)
ok &= CGOEnable(cgo, GL_LIGHTING); ok &= CGOEnable(cgo, GL_LIGHTING);
#endif #endif
return ok; return ok;
} }
static static
int GenerateRepCartoonProcessCylindricalHelices(PyMOLGlobals * G, ObjectMolecule * obj, CoordSet *cs, CGO *cgo, CExtrude *ex, int nAt, int *seg, float *pv, floa t *tv, float *pvo, int GenerateRepCartoonProcessCylindricalHelices(PyMOLGlobals * G, ObjectMolecule * obj, CoordSet *cs, CGO *cgo, CExtrude *ex, int nAt, int *seg, float *pv, floa t *tv, float *pvo,
const CCInOut *cc, const CCInOut *cc,
int *at, float *dl, int cartoon_color, int discrete_colors, float loop_radiu s){ int *at, float *dl, int cartoon_color, int discrete_colors, float loop_radiu s, const float objAlpha){
int ok = true; int ok = true;
int n_p, n_pm1, n_pm2; int n_p, n_pm1, n_pm2;
const float *v0; const float *v0;
float *v, *v1, *v2, *vo, *d; float *v, *v1, *v2, *vo, *d;
float *valpha;
float *vc = NULL; float *vc = NULL;
int atom_index1, atom_index2, *s, int atom_index1, atom_index2, *s,
*atp, a, cur_car; *atp, a, cur_car;
unsigned *vi; unsigned *vi;
int last_color, uniform_color; int last_color, uniform_color;
bool hasAtomLevelTrans = false;
int contFlag, extrudeFlag; int contFlag, extrudeFlag;
int b, c1, c2; int b, c1, c2;
float *h_start = NULL, *h_end = NULL; float *h_start = NULL, *h_end = NULL;
float t0[3], t1[3], t2[3], t3[3]; float t0[3], t1[3], t2[3], t3[3];
float t4[3]; float t4[3];
float helix_radius; float helix_radius;
CGOPickColor(cgo, 0, cPickableNoPick); CGOPickColor(cgo, 0, cPickableNoPick);
helix_radius = helix_radius =
SettingGet_f(G, cs->Setting, obj->Obj.Setting, cSetting_cartoon_helix_radius ); SettingGet_f(G, cs->Setting, obj->Obj.Setting, cSetting_cartoon_helix_radius );
/* this is confusing because we're borrowing Extrude's arrays /* this is confusing because we're borrowing Extrude's arrays
* for convenient storage, but not actually calling Extrude */ * for convenient storage, but not actually calling Extrude */
n_p = 0; n_p = 0;
v = ex->p; v = ex->p;
vc = ex->c; vc = ex->c;
valpha = ex->alpha;
vi = ex->i; vi = ex->i;
last_color = -1; last_color = -1;
uniform_color = true; uniform_color = true;
v1 = pv; /* points */ v1 = pv; /* points */
v2 = tv; /* tangents */ v2 = tv; /* tangents */
vo = pvo; vo = pvo;
d = dl; d = dl;
s = seg; s = seg;
skipping to change at line 1676 skipping to change at line 1703
while(contFlag) { while(contFlag) {
if((*cc) != cur_car) { /* new cartoon type */ if((*cc) != cur_car) { /* new cartoon type */
if(n_p) { /* any cartoon points? */ if(n_p) { /* any cartoon points? */
extrudeFlag = true; extrudeFlag = true;
} else { } else {
cur_car = *(cc); /* now: go ahead and switch cartoons */ cur_car = *(cc); /* now: go ahead and switch cartoons */
n_p = 0; n_p = 0;
v = ex->p; v = ex->p;
vc = ex->c; vc = ex->c;
valpha = ex->alpha;
vi = ex->i; vi = ex->i;
last_color = -1; last_color = -1;
uniform_color = true; uniform_color = true;
} }
} }
if(a && !extrudeFlag) { if(a && !extrudeFlag) {
if((*s) != *(s - 1)) { /* new segment */ if((*s) != *(s - 1)) { /* new segment */
if(n_p) { /* any cartoon points? */ if(n_p) { /* any cartoon points? */
extrudeFlag = true; extrudeFlag = true;
} else { } else {
n_p = 0; n_p = 0;
v = ex->p; v = ex->p;
vc = ex->c; vc = ex->c;
valpha = ex->alpha;
vi = ex->i; vi = ex->i;
last_color = -1; last_color = -1;
uniform_color = true; uniform_color = true;
} }
} }
} }
if(!extrudeFlag) { if(!extrudeFlag) {
if((a < (nAt - 1)) && (*s == *(s + 1))) { /* working in the same seg ment... */ if((a < (nAt - 1)) && (*s == *(s + 1))) { /* working in the same seg ment... */
AtomInfoType *ai1, *ai2; AtomInfoType *ai1, *ai2;
atom_index1 = cs->IdxToAtm[*atp]; atom_index1 = cs->IdxToAtm[*atp];
atom_index2 = cs->IdxToAtm[*(atp + 1)]; atom_index2 = cs->IdxToAtm[*(atp + 1)];
ai1 = obj->AtomInfo + atom_index1; ai1 = obj->AtomInfo + atom_index1;
ai2 = obj->AtomInfo + atom_index2; ai2 = obj->AtomInfo + atom_index2;
c1 = AtomSettingGetWD(G, ai1, cSetting_cartoon_color, cartoon_color); c1 = AtomSettingGetWD(G, ai1, cSetting_cartoon_color, cartoon_color);
c2 = AtomSettingGetWD(G, ai2, cSetting_cartoon_color, cartoon_color); c2 = AtomSettingGetWD(G, ai2, cSetting_cartoon_color, cartoon_color);
float alpha1 = 1.0f - AtomSettingGetWD(G, ai1, cSetting_cartoon_transpar
ency, 1.0f - objAlpha);
float alpha2 = 1.0f - AtomSettingGetWD(G, ai2, cSetting_cartoon_transpar
ency, 1.0f - objAlpha);
if (!hasAtomLevelTrans && (alpha1 != objAlpha || alpha2 != objAlpha)) {
hasAtomLevelTrans = true;
}
if (c1 < 0) c1 = ai1->color; if (c1 < 0) c1 = ai1->color;
if (c2 < 0) c2 = ai2->color; if (c2 < 0) c2 = ai2->color;
if((*(cc) == *(cc + 1)) && (c1 != c2)) if((*(cc) == *(cc + 1)) && (c1 != c2))
uniform_color = false; uniform_color = false;
if(last_color >= 0) { if(last_color >= 0) {
if(c1 != last_color) if(c1 != last_color)
uniform_color = false; uniform_color = false;
} }
last_color = c1; last_color = c1;
v0 = ColorGet(G, c1); v0 = ColorGet(G, c1);
*(vc++) = *(v0++); *(vc++) = *(v0++);
*(vc++) = *(v0++); *(vc++) = *(v0++);
*(vc++) = *(v0++); *(vc++) = *(v0++);
*(valpha++) = alpha1;
*(vi++) = ai1->masked ? -1 : atom_index1; *(vi++) = ai1->masked ? -1 : atom_index1;
v0 = ColorGet(G, c2); /* kludge */ v0 = ColorGet(G, c2); /* kludge */
*(vc) = *(v0++); *(vc) = *(v0++);
*(vc + 1) = *(v0++); *(vc + 1) = *(v0++);
*(vc + 2) = *(v0++); *(vc + 2) = *(v0++);
*(valpha) = alpha2;
*(vi) = ai2->masked ? -1 : atom_index2; *(vi) = ai2->masked ? -1 : atom_index2;
} else { } else {
vc += 3; /* part of kludge */ vc += 3; /* part of kludge */
valpha++;
vi++; vi++;
} }
if(cur_car == cCartoon_skip_helix) { if(cur_car == cCartoon_skip_helix) {
if(!n_p) { if(!n_p) {
h_start = v1; h_start = v1;
h_end = v1; h_end = v1;
} else { } else {
h_end = v1; h_end = v1;
} }
copy3f(v1, v); /* just store coordinates until we have a complete cylinder */ copy3f(v1, v); /* just store coordinates until we have a complete cylinder */
skipping to change at line 1764 skipping to change at line 1802
if(n_p) if(n_p)
extrudeFlag = true; extrudeFlag = true;
} }
if(extrudeFlag) { /* generate cylinder */ if(extrudeFlag) { /* generate cylinder */
if(n_p > 1) { if(n_p > 1) {
atom_index1 = cs->IdxToAtm[*(atp - 1)]; atom_index1 = cs->IdxToAtm[*(atp - 1)];
c1 = AtomSettingGetWD(G, obj->AtomInfo + atom_index1, c1 = AtomSettingGetWD(G, obj->AtomInfo + atom_index1,
cSetting_cartoon_color, cartoon_color); cSetting_cartoon_color, cartoon_color);
auto ai1 = obj->AtomInfo + atom_index1;
auto ai2 = obj->AtomInfo + atom_index2;
float alpha1 = 1.0f - AtomSettingGetWD(G, ai1, cSetting_cartoon_transpar
ency, 1.0f - objAlpha);
float alpha2 = 1.0f - AtomSettingGetWD(G, ai2, cSetting_cartoon_transpar
ency, 1.0f - objAlpha);
if(!hasAtomLevelTrans && (alpha1 != objAlpha || alpha2 != objAlpha)){
hasAtomLevelTrans = true;
}
if (c1 < 0) c1 = (obj->AtomInfo + atom_index1)->color; if (c1 < 0) c1 = (obj->AtomInfo + atom_index1)->color;
if(n_p < 5) { if(n_p < 5) {
copy3f(ex->p, t3); copy3f(ex->p, t3);
copy3f(v - 3, t4); copy3f(v - 3, t4);
} else { } else {
add3f(ex->p, ex->p + 9, t0); add3f(ex->p, ex->p + 9, t0);
add3f(ex->p + 3, ex->p + 6, t1); add3f(ex->p + 3, ex->p + 6, t1);
scale3f(t0, 0.2130F, t0); scale3f(t0, 0.2130F, t0);
scale3f(t1, 0.2870F, t1); scale3f(t1, 0.2870F, t1);
skipping to change at line 1817 skipping to change at line 1863
} }
} }
} }
/* push helix out a tad to consume loop */ /* push helix out a tad to consume loop */
subtract3f(t4, t3, t0); subtract3f(t4, t3, t0);
normalize3f(t0); normalize3f(t0);
scale3f(t0, loop_radius * 2, t0); scale3f(t0, loop_radius * 2, t0);
add3f(t0, t4, t4); add3f(t0, t4, t4);
invert3f(t0); invert3f(t0);
add3f(t0, t3, t3); add3f(t0, t3, t3);
if(uniform_color && !hasAtomLevelTrans) {
if(uniform_color) { cgo->add<cgo::draw::cylinder>(t3, t4, helix_radius, ex->c, ex->c);
CGOCylinderv(cgo, t3, t4, helix_radius, ex->c, ex->c);
} else { } else {
subtract3f(t4, t3, t0); subtract3f(t4, t3, t0);
n_pm1 = n_p - 1; n_pm1 = n_p - 1;
n_pm2 = n_p - 2; n_pm2 = n_p - 2;
for(b = 0; ok && b < n_pm1; b++) { for(b = 0; ok && b < n_pm1; b++) {
if(!b) { scale3f(t0, ((float) b) / n_pm1, t1);
scale3f(t0, ((float) b - 0.005F) / n_pm1, t1); /* add small overl scale3f(t0, ((float) b + 1) / n_pm1, t2);
ap */
} else {
scale3f(t0, ((float) b) / n_pm1, t1);
}
if(b < n_pm2) {
scale3f(t0, ((float) b + 1.005F) / n_pm1, t2);
} else {
scale3f(t0, ((float) b + 1) / n_pm1, t2);
}
add3f(t3, t1, t1); add3f(t3, t1, t1);
add3f(t3, t2, t2); add3f(t3, t2, t2);
CGOCustomCylinderv(cgo, t1, t2, helix_radius, ex->c + (b * 3), if(hasAtomLevelTrans){
cgo->add<cgo::draw::custom_cylinder_alpha>(t1, t2, helix_radius, e
x->c + (b * 3),
ex->c + (b + 1) * 3, ex->alpha[b], ex->alph
a[b + 1], (float) (b ? 0 : cCylCapFlat),
(float) (b == n_pm2 ? cCylCapFlat : 0));
} else {
cgo->add<cgo::draw::custom_cylinder>(t1, t2, helix_radius, ex->c +
(b * 3),
ex->c + (b + 1) * 3, (float) (b ? 0 : cCylC apFlat), ex->c + (b + 1) * 3, (float) (b ? 0 : cCylC apFlat),
(float) (b == n_pm2 ? cCylCapFlat : 0)); (float) (b == n_pm2 ? cCylCapFlat : 0));
}
} }
} }
} }
a--; /* undo above... */ a--; /* undo above... */
extrudeFlag = false; extrudeFlag = false;
n_p = 0; n_p = 0;
v = ex->p; v = ex->p;
vc = ex->c; vc = ex->c;
valpha = ex->alpha;
vi = ex->i; vi = ex->i;
uniform_color = true; uniform_color = true;
last_color = -1; last_color = -1;
} }
} }
return ok; return ok;
} }
static static
int GenerateRepCartoonDrawRings(PyMOLGlobals * G, nuc_acid_data *ndata, ObjectMo lecule * obj, int GenerateRepCartoonDrawRings(PyMOLGlobals * G, nuc_acid_data *ndata, ObjectMo lecule * obj,
skipping to change at line 2002 skipping to change at line 2048
} }
escape: escape:
escape_count = ESCAPE_MAX; /* don't get bogged down with structures escape_count = ESCAPE_MAX; /* don't get bogged down with structures
that have unreasonable connectivity */ that have unreasonable connectivity */
} }
FreeP(marked); FreeP(marked);
FreeP(moved); FreeP(moved);
return ok; return ok;
} }
#define EXTRUDE_TRUNCATE() { ExtrudeTruncate(ex, 0); n_p = 0; v = ex->p;
\
vc = ex->c; vn = ex->n; vi = ex->i; }
/* /*
* skip > dash > loop * skip > dash > loop
*/ */
inline int prioritize(int a, int b) { inline int prioritize(int a, int b) {
if (a == b) if (a == b)
return a; return a;
if (a == cCartoon_skip || b == cCartoon_skip) if (a == cCartoon_skip || b == cCartoon_skip)
return cCartoon_skip; return cCartoon_skip;
if (a == cCartoon_dash || b == cCartoon_dash) if (a == cCartoon_dash || b == cCartoon_dash)
return cCartoon_dash; return cCartoon_dash;
skipping to change at line 2050 skipping to change at line 2093
truncate = true; truncate = true;
} }
} }
return truncate; return truncate;
} }
static static
void ComputeCartoonAtomColors(PyMOLGlobals *G, ObjectMolecule *obj, CoordSet *cs , int *nuc_flag, int atom_index1, int atom_index2, int *c1a, int *c2a, int *atp, void ComputeCartoonAtomColors(PyMOLGlobals *G, ObjectMolecule *obj, CoordSet *cs , int *nuc_flag, int atom_index1, int atom_index2, int *c1a, int *c2a, int *atp,
const CCInOut *cc, const CCInOut *cc,
int cur_car, int cartoon_color, int nucleic_color, int discrete_colors, int n_p, int contigFlag){ int cur_car, int cartoon_color, float& alpha1, float& alpha2, int nucleic_co lor, int discrete_colors, int n_p, int contigFlag){
int c1, c2; int c1, c2;
if (nucleic_color >= 0 && (nuc_flag[*atp] || nuc_flag[*(atp + 1)])) { if (nucleic_color >= 0 && (nuc_flag[*atp] || nuc_flag[*(atp + 1)])) {
c1 = c2 = nucleic_color; c1 = c2 = nucleic_color;
} else { } else {
c1 = c2 = cartoon_color; c1 = c2 = cartoon_color;
} }
auto ai1 = obj->AtomInfo + atom_index1; auto ai1 = obj->AtomInfo + atom_index1;
auto ai2 = obj->AtomInfo + atom_index2; auto ai2 = obj->AtomInfo + atom_index2;
AtomSettingGetIfDefined(G, ai1, cSetting_cartoon_color, &c1); AtomSettingGetIfDefined(G, ai1, cSetting_cartoon_color, &c1);
AtomSettingGetIfDefined(G, ai2, cSetting_cartoon_color, &c2); AtomSettingGetIfDefined(G, ai2, cSetting_cartoon_color, &c2);
alpha1 = 1.0f - AtomSettingGetWD(G, ai1, cSetting_cartoon_transparency, 1.0f -
alpha1);
alpha2 = 1.0f - AtomSettingGetWD(G, ai2, cSetting_cartoon_transparency, 1.0f -
alpha2);
if (c1 < 0) c1 = ai1->color; if (c1 < 0) c1 = ai1->color;
if (c2 < 0) c2 = ai2->color; if (c2 < 0) c2 = ai2->color;
if(discrete_colors) { if(discrete_colors) {
int next_car = *(cc + 1); int next_car = *(cc + 1);
// end of loop or dash segment // end of loop or dash segment
if (cur_car != next_car) { if (cur_car != next_car) {
if (cur_car == cCartoon_dash) { if (cur_car == cCartoon_dash) {
c2 = c1; c2 = c1;
skipping to change at line 2095 skipping to change at line 2140
c1 = c2; c1 = c2;
} }
} }
*c1a = c1; *c1a = c1;
*c2a = c2; *c2a = c2;
} }
static static
void CartoonGenerateSample(PyMOLGlobals *G, int sampling, int *n_p, float dev, f loat *vo, void CartoonGenerateSample(PyMOLGlobals *G, int sampling, int *n_p, float dev, f loat *vo,
float *v1, float *v1,
float *v2, int c1, int c2, int atom_index1, int atom_ float *v2, int c1, int c2, float alpha1, float alpha2
index2, ,
float power_a, float power_b, float **vc_p, unsigned int atom_index1, int atom_index2,
int **vi_p, float power_a, float power_b, float **vc_p, float **v
float **v_p, float **vn_p){ alpha_p,
unsigned int **vi_p, float **v_p, float **vn_p){
int b, i0; int b, i0;
float f0, f1, f2, f3, f4; float f0, f1, f2, f3, f4;
float a0;
const float *v0; const float *v0;
unsigned int *vi = *vi_p; unsigned int *vi = *vi_p;
float *valpha = *valpha_p;
float *vc = *vc_p, *v = *v_p, *vn = *vn_p; float *vc = *vc_p, *v = *v_p, *vn = *vn_p;
for(b = 0; b < sampling; b++) { /* needs optimization */ for(b = 0; b < sampling; b++) { /* needs optimization */
if(*n_p == 0) { if(*n_p == 0) {
/* provide starting point on first point in segment only... */ /* provide starting point on first point in segment only... */
f0 = ((float) b) / sampling; /* fraction of completion */ f0 = ((float) b) / sampling; /* fraction of completion */
if(f0 <= 0.5) { if(f0 <= 0.5) {
v0 = ColorGet(G, c1); v0 = ColorGet(G, c1);
i0 = atom_index1; i0 = atom_index1;
a0 = alpha1;
} else { } else {
v0 = ColorGet(G, c2); v0 = ColorGet(G, c2);
i0 = atom_index2; i0 = atom_index2;
a0 = alpha2;
} }
f0 = smooth(f0, power_a); /* bias sampling towards the center of the curve */ f0 = smooth(f0, power_a); /* bias sampling towards the center of the curve */
/* store colors */ /* store colors and alpha*/
*(vc++) = *(v0++); *(vc++) = *(v0++);
*(vc++) = *(v0++); *(vc++) = *(v0++);
*(vc++) = *(v0++); *(vc++) = *(v0++);
*(valpha++) = a0;
*(vi++) = i0; *(vi++) = i0;
/* start of line/cylinder */ /* start of line/cylinder */
f1 = 1.0F - f0; f1 = 1.0F - f0;
f2 = smooth(f0, power_b); f2 = smooth(f0, power_b);
f3 = smooth(f1, power_b); f3 = smooth(f1, power_b);
f4 = dev * f2 * f3; /* displacement magnitude */ f4 = dev * f2 * f3; /* displacement magnitude */
*(v++) = f1 * v1[0] + f0 * v1[3] + f4 * (f3 * v2[0] - f2 * v2[3]); *(v++) = f1 * v1[0] + f0 * v1[3] + f4 * (f3 * v2[0] - f2 * v2[3]);
*(v++) = f1 * v1[1] + f0 * v1[4] + f4 * (f3 * v2[1] - f2 * v2[4]); *(v++) = f1 * v1[1] + f0 * v1[4] + f4 * (f3 * v2[1] - f2 * v2[4]);
*(v++) = f1 * v1[2] + f0 * v1[5] + f4 * (f3 * v2[2] - f2 * v2[5]); *(v++) = f1 * v1[2] + f0 * v1[5] + f4 * (f3 * v2[2] - f2 * v2[5]);
vn += 9; vn += 9;
copy3f(vo, vn - 6); /* starter... */ copy3f(vo, vn - 6); /* starter... */
(*n_p)++; (*n_p)++;
} }
f0 = ((float) b + 1) / sampling; f0 = ((float) b + 1) / sampling;
if(f0 <= 0.5) { if(f0 <= 0.5) {
v0 = ColorGet(G, c1); v0 = ColorGet(G, c1);
i0 = atom_index1; i0 = atom_index1;
a0 = alpha1;
} else { } else {
v0 = ColorGet(G, c2); v0 = ColorGet(G, c2);
i0 = atom_index2; i0 = atom_index2;
a0 = alpha2;
} }
f0 = smooth(f0, power_a); /* bias sampling towards the center of the curve */ f0 = smooth(f0, power_a); /* bias sampling towards the center of the curve */
/* store colors */ /* store colors and alpha*/
*(vc++) = *(v0++); *(vc++) = *(v0++);
*(vc++) = *(v0++); *(vc++) = *(v0++);
*(vc++) = *(v0++); *(vc++) = *(v0++);
*(valpha++) = a0;
*(vi++) = i0; *(vi++) = i0;
/* end of line/cylinder */ /* end of line/cylinder */
f1 = 1.0F - f0; f1 = 1.0F - f0;
f2 = smooth(f0, power_b); f2 = smooth(f0, power_b);
f3 = smooth(f1, power_b); f3 = smooth(f1, power_b);
f4 = dev * f2 * f3; /* displacement magnitude */ f4 = dev * f2 * f3; /* displacement magnitude */
*(v++) = f1 * v1[0] + f0 * v1[3] + f4 * (f3 * v2[0] - f2 * v2[3]); *(v++) = f1 * v1[0] + f0 * v1[3] + f4 * (f3 * v2[0] - f2 * v2[3]);
*(v++) = f1 * v1[1] + f0 * v1[4] + f4 * (f3 * v2[1] - f2 * v2[4]); *(v++) = f1 * v1[1] + f0 * v1[4] + f4 * (f3 * v2[1] - f2 * v2[4]);
skipping to change at line 2171 skipping to change at line 2225
*(vn++) = f1 * (vo[0] * f2) + f0 * (vo[3] * f3); *(vn++) = f1 * (vo[0] * f2) + f0 * (vo[3] * f3);
*(vn++) = f1 * (vo[1] * f2) + f0 * (vo[4] * f3); *(vn++) = f1 * (vo[1] * f2) + f0 * (vo[4] * f3);
*(vn++) = f1 * (vo[2] * f2) + f0 * (vo[5] * f3); *(vn++) = f1 * (vo[2] * f2) + f0 * (vo[5] * f3);
vn += 3; vn += 3;
if(b == sampling - 1) if(b == sampling - 1)
copy3f(vo + 3, vn - 6); /* starter... */ copy3f(vo + 3, vn - 6); /* starter... */
(*n_p)++; (*n_p)++;
} }
(*vc_p) = vc; (*vc_p) = vc;
(*valpha_p) = valpha;
(*vi_p) = vi; (*vi_p) = vi;
(*v_p) = v; (*v_p) = v;
(*vn_p) = vn; (*vn_p) = vn;
} }
static static
void CartoonGenerateRefine(int refine, int sampling, float *v, float *vn, float *vo, float *sampling_tmp){ void CartoonGenerateRefine(int refine, int sampling, float *v, float *vn, float *vo, float *sampling_tmp){
int b, c; int b, c;
float t0[3], t1[3]; float t0[3], t1[3];
float *p0, *p1, *p2, *p3; float *p0, *p1, *p2, *p3;
skipping to change at line 2327 skipping to change at line 2382
ExtrudeCircle(ex,loop_quality,loop_radius); ExtrudeCircle(ex,loop_quality,loop_radius);
ExtrudeBuildNormals1f(ex); ExtrudeBuildNormals1f(ex);
ExtrudeCGOSurfaceTube(ex,cgo,loop_cap,NULL); ExtrudeCGOSurfaceTube(ex,cgo,loop_cap,NULL);
*/ */
return ok; return ok;
} }
static static
int CartoonExtrudeDumbbell(PyMOLGlobals *G, CExtrude *ex, CGO *cgo, int sampling , float dumbbell_width, float dumbbell_length, int highlight_color, int loop_qua lity, float dumbbell_radius, short use_cylinders_for_strands){ int CartoonExtrudeDumbbell(PyMOLGlobals *G, CExtrude *ex, CGO *cgo, int sampling , float dumbbell_width, float dumbbell_length, int highlight_color, int loop_qua lity, float dumbbell_radius, short use_cylinders_for_strands){
int ok; int ok;
CExtrude *ex1; CExtrude *ex1 = nullptr;
if(highlight_color < 0) { if(highlight_color < 0) {
ok = ExtrudeDumbbell1(ex, dumbbell_width, dumbbell_length, 0); ok = ExtrudeDumbbell1(ex, dumbbell_width, dumbbell_length, 0);
if (ok) if (ok)
ExtrudeBuildNormals2f(ex); ExtrudeBuildNormals2f(ex);
if (ok) if (ok)
ok &= ExtrudeCGOSurfacePolygonTaper(ex, cgo, sampling, NULL); ok &= ExtrudeCGOSurfacePolygonTaper(ex, cgo, sampling, NULL);
} else { } else {
ok = ExtrudeDumbbell1(ex, dumbbell_width, dumbbell_length, 1); ok = ExtrudeDumbbell1(ex, dumbbell_width, dumbbell_length, 1);
if (ok) if (ok)
ExtrudeBuildNormals2f(ex); ExtrudeBuildNormals2f(ex);
skipping to change at line 2423 skipping to change at line 2478
PyMOLGlobals *G = cs->State.G; PyMOLGlobals *G = cs->State.G;
int ok = true; int ok = true;
CGO *cgo; CGO *cgo;
int contigFlag, contFlag, extrudeFlag, n_p; int contigFlag, contFlag, extrudeFlag, n_p;
CExtrude *ex = NULL; CExtrude *ex = NULL;
float dev; float dev;
unsigned int *vi; unsigned int *vi;
int atom_index1, atom_index2; int atom_index1, atom_index2;
float *v, *v1, *v2, *vo; float *v, *v1, *v2, *vo;
float *d, *vc = NULL, *vn; float *d, *vc = NULL, *vn;
float *valpha = nullptr;
int *atp; int *atp;
int c1, c2; int c1, c2;
int a; int a;
int sampling; int sampling;
float *sampling_tmp; float *sampling_tmp;
int *segptr; int *segptr;
const CCInOut *cc; const CCInOut *cc;
int cur_car; int cur_car;
float loop_radius; float loop_radius;
int nucleic_color = 0; int nucleic_color = 0;
skipping to change at line 2445 skipping to change at line 2501
float power_b = 5; float power_b = 5;
int refine; int refine;
float tube_radius; float tube_radius;
float putty_radius; float putty_radius;
int cartoon_debug, cylindrical_helices, cartoon_color, highlight_color, int cartoon_debug, cylindrical_helices, cartoon_color, highlight_color,
discrete_colors, loop_quality, oval_quality, tube_quality, putty_quality, lo op_cap, tube_cap; discrete_colors, loop_quality, oval_quality, tube_quality, putty_quality, lo op_cap, tube_cap;
float length, width; float length, width;
float oval_width, oval_length; float oval_width, oval_length;
float dumbbell_radius, dumbbell_width, dumbbell_length; float dumbbell_radius, dumbbell_width, dumbbell_length;
float ring_width; float ring_width;
auto EXTRUDE_TRUNCATE = [&ex, &n_p, &v, &vc, &valpha, &vn, &vi]() {
ExtrudeTruncate(ex, 0);
n_p = 0;
v = ex->p;
vc = ex->c;
valpha = ex->alpha;
vn = ex->n;
vi = ex->i;
};
cartoon_color = cartoon_color =
SettingGet_color(G, cs->Setting, obj->Obj.Setting, cSetting_cartoon_color); SettingGet_color(G, cs->Setting, obj->Obj.Setting, cSetting_cartoon_color);
ring_width = ring_width =
SettingGet_f(G, cs->Setting, obj->Obj.Setting, cSetting_cartoon_ring_width); SettingGet_f(G, cs->Setting, obj->Obj.Setting, cSetting_cartoon_ring_width);
if(ring_width < 0.0F) { if(ring_width < 0.0F) {
ring_width = ring_width =
fabs(SettingGet_f(G, cs->Setting, obj->Obj.Setting, cSetting_stick_radius) ) * 0.5F; fabs(SettingGet_f(G, cs->Setting, obj->Obj.Setting, cSetting_stick_radius) ) * 0.5F;
} }
length = SettingGet_f(G, cs->Setting, obj->Obj.Setting, cSetting_cartoon_rect_ length); length = SettingGet_f(G, cs->Setting, obj->Obj.Setting, cSetting_cartoon_rect_ length);
width = SettingGet_f(G, cs->Setting, obj->Obj.Setting, cSetting_cartoon_rect_w idth); width = SettingGet_f(G, cs->Setting, obj->Obj.Setting, cSetting_cartoon_rect_w idth);
skipping to change at line 2538 skipping to change at line 2605
/* okay, we now have enough info to generate smooth interpolations */ /* okay, we now have enough info to generate smooth interpolations */
if(nAt > 1) { if(nAt > 1) {
ex = ExtrudeNew(G); ex = ExtrudeNew(G);
CHECKOK(ok, ex); CHECKOK(ok, ex);
if (ok) if (ok)
ok &= ExtrudeAllocPointsNormalsColors(ex, cs->NIndex * (3 * sampling + 3)) ; ok &= ExtrudeAllocPointsNormalsColors(ex, cs->NIndex * (3 * sampling + 3)) ;
} }
/* process cylindrical helices first */ /* process cylindrical helices first */
if(ok && (nAt > 1) && cylindrical_helices) { if(ok && (nAt > 1) && cylindrical_helices) {
ok = GenerateRepCartoonProcessCylindricalHelices(G, obj, cs, cgo, ex, nAt, s eg, pv, tv, ok = GenerateRepCartoonProcessCylindricalHelices(G, obj, cs, cgo, ex, nAt, s eg, pv, tv,
pvo, car, at, dl, cartoon_c olor, discrete_colors, loop_radius); pvo, car, at, dl, cartoon_c olor, discrete_colors, loop_radius, alpha);
} }
if(ok && nAt > 1) { if(ok && nAt > 1) {
EXTRUDE_TRUNCATE(); EXTRUDE_TRUNCATE();
v1 = pv; /* points */ v1 = pv; /* points */
v2 = tv; /* tangents */ v2 = tv; /* tangents */
vo = pvo; vo = pvo;
d = dl; d = dl;
segptr = seg; segptr = seg;
cc = car; cc = car;
atp = at; /* cs index pointer */ atp = at; /* cs index pointer */
skipping to change at line 2567 skipping to change at line 2634
EXTRUDE_TRUNCATE(); EXTRUDE_TRUNCATE();
} }
if(ok && !extrudeFlag) { if(ok && !extrudeFlag) {
if((a < (nAt - 1)) && (*segptr == *(segptr + 1))) { /* working in the same segment... */ if((a < (nAt - 1)) && (*segptr == *(segptr + 1))) { /* working in the same segment... */
AtomInfoType *ai1, *ai2; AtomInfoType *ai1, *ai2;
atom_index1 = cs->IdxToAtm[*atp]; atom_index1 = cs->IdxToAtm[*atp];
atom_index2 = cs->IdxToAtm[*(atp + 1)]; atom_index2 = cs->IdxToAtm[*(atp + 1)];
ai1 = obj->AtomInfo + atom_index1; ai1 = obj->AtomInfo + atom_index1;
ai2 = obj->AtomInfo + atom_index2; ai2 = obj->AtomInfo + atom_index2;
ComputeCartoonAtomColors(G, obj, cs, nuc_flag, atom_index1, atom_index 2, &c1, &c2, atp, cc, cur_car, cartoon_color, nucleic_color, discrete_colors, n_ p, contigFlag);
float alpha1 = alpha;
float alpha2 = alpha;
ComputeCartoonAtomColors(G, obj, cs, nuc_flag, atom_index1, atom_index
2, &c1, &c2, atp, cc, cur_car, cartoon_color, alpha1, alpha2, nucleic_color, dis
crete_colors, n_p, contigFlag);
dev = throw_ * (*d); dev = throw_ * (*d);
CartoonGenerateSample(G, sampling, &n_p, dev, vo, v1, v2, c1, c2, CartoonGenerateSample(G, sampling, &n_p, dev, vo, v1, v2, c1, c2, alph
ai1->masked ? -1 : atom_index1, ai2->masked ? -1 a1, alpha2,
: atom_index2, power_a, power_b, &vc, &vi, &v, &vn); ai1->masked ? -1 : atom_index1, ai2->masked ? -1
: atom_index2, power_a, power_b, &vc, &valpha, &vi, &v, &vn);
/* now do a smoothing pass along orientation /* now do a smoothing pass along orientation
vector to smooth helices, etc... */ vector to smooth helices, etc... */
CartoonGenerateRefine(refine, sampling, v, vn, vo, sampling_tmp); CartoonGenerateRefine(refine, sampling, v, vn, vo, sampling_tmp);
} }
v1 += 3; v1 += 3;
v2 += 3; v2 += 3;
vo += 3; vo += 3;
d++; d++;
atp += 1; atp += 1;
 End of changes. 50 change blocks. 
61 lines changed or deleted 145 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
Home  |  About  |  Features  |  All  |  Newest  |  Dox  |  Diffs  |  RSS Feeds  |  Screenshots  |  Comments  |  Imprint  |  Privacy  |  HTTP(S)