pub_soft/pymol-open-source
3
0
Fork 0
mirror of https://github.com/schrodinger/pymol-open-source.git synced 2026-06-04 20:04:21 +08:00
Code Issues Packages Projects Releases Wiki Activity
Files
master
pymol-open-source/layer2/RepDot.cpp
Jarrett Johnson 7b10fa0e84 PYMOL-5089: MapType refactor
2025-09-26 12:07:26 -04:00

475 lines
12 KiB
C++
Raw Permalink Blame History

/*
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* -------------------------------------------------------------------
*/
#include"os_python.h"
#include"os_predef.h"
#include"os_std.h"
#include"os_gl.h"
#include"Base.h"
#include"Err.h"
#include"RepDot.h"
#include"Color.h"
#include"Sphere.h"
#include"Map.h"
#include"Setting.h"
#include"main.h"
#include"ObjectMolecule.h"
#include"Scene.h"
#include"ShaderMgr.h"
#include"CGO.h"
#include "pymol/algorithm.h"
RepDot::~RepDot()
{
auto I = this;
if (I->shaderCGO){
CGOFree(I->shaderCGO);
I->shaderCGO = 0;
}
FreeP(I->VC);
FreeP(I->V);
FreeP(I->T);
FreeP(I->F);
FreeP(I->VN);
FreeP(I->A);
FreeP(I->Atom);
}
static int RepDotCGOGenerate(RepDot * I)
{
PyMOLGlobals *G = I->G;
float *v = I->V;
int c = I->N;
int cc = 0;
int ok = true;
CGO *cgo = nullptr;
int normals =
SettingGet_i(G, I->cs->Setting.get(), I->obj->Setting.get(), cSetting_dot_normals);
bool const dot_as_spheres = SettingGet<bool>(
G, I->cs->Setting.get(), I->obj->Setting.get(), cSetting_dot_as_spheres);
cgo = CGONew(G);
CHECKOK(ok, cgo);
if (dot_as_spheres){
while(ok && c--) {
if(!cc) { /* load up the current vertex color */
cc = (int) (*(v++));
ok &= CGOColorv(cgo, v);
v += 3;
}
if(ok && normals)
ok &= CGONormalv(cgo, v);
v += 3;
if (ok)
ok &= CGOSphere(cgo, v, 1.f);
v += 3;
cc--;
}
} else {
if (ok)
ok &= CGOBegin(cgo, GL_POINTS);
while(ok && c--) {
if(!cc) { /* load up the current vertex color */
cc = (int) (*(v++));
ok &= CGOColorv(cgo, v);
v += 3;
}
if(normals)
CGONormalv(cgo, v);
v += 3;
if (ok)
ok &= CGOVertexv(cgo, v);
v += 3;
cc--;
}
if (ok)
ok &= CGOEnd(cgo);
}
if (ok)
ok &= CGOStop(cgo);
if (ok) {
if (dot_as_spheres){
CGO *tmpCGO = CGONew(G);
if (ok) ok &= CGOEnable(tmpCGO, GL_SPHERE_SHADER);
if (ok) ok &= CGOEnable(tmpCGO, GL_DOT_LIGHTING);
if (ok) ok &= CGOSpecial(tmpCGO, DOT_WIDTH_FOR_DOT_SPHERES);
if (ok) {
tmpCGO->free_append(CGOOptimizeSpheresToVBONonIndexedNoShader(cgo,
CGO_BOUNDING_BOX_SZ + fsizeof<cgo::draw::sphere_buffers>() + 2));
}
if (ok) ok &= CGODisable(tmpCGO, GL_SPHERE_SHADER);
if (ok) ok &= CGOStop(tmpCGO);
I->shaderCGO = tmpCGO;
} else {
CGO *tmpCGO = CGONew(G);
if (ok) ok &= CGOEnable(tmpCGO, GL_DEFAULT_SHADER);
if (ok) ok &= CGOEnable(tmpCGO, GL_DOT_LIGHTING);
if (ok) ok &= CGOSpecial(tmpCGO, DOT_WIDTH_FOR_DOTS);
if (ok) {
tmpCGO->free_append(CGOOptimizeToVBONotIndexedNoShader(cgo));
}
if (ok) ok &= CGODisable(tmpCGO, GL_DEFAULT_SHADER);
if (ok) ok &= CGOStop(tmpCGO);
I->shaderCGO = tmpCGO;
}
}
if (ok){
I->shaderCGO->use_shader = true;
I->shaderCGO_as_spheres = dot_as_spheres;
}
CGOFree(cgo);
return ok;
}
void RepDot::render(RenderInfo * info)
{
auto I = this;
CRay *ray = info->ray;
auto pick = info->pick;
float *v = I->V;
int c = I->N;
int cc = 0;
int ok = true;
if(ray) {
#ifndef _PYMOL_NO_RAY
float radius;
if(I->dotSize <= 0.0F) {
radius = ray->PixelRadius * I->Width / 1.4142F;
} else {
radius = I->dotSize;
}
while(ok && c--) {
if(!cc) { /* load up the current vertex color */
cc = (int) (*(v++));
ray->color3fv(v);
v += 3;
}
v += 3;
ok &= ray->sphere3fv(v, radius);
v += 3;
cc--;
}
#endif
} else if(G->HaveGUI && G->ValidContext) {
if(pick) {
} else { /* else not pick, i.e., when rendering */
int normals =
SettingGet_i(G, I->cs->Setting.get(), I->obj->Setting.get(), cSetting_dot_normals);
bool const dot_as_spheres = SettingGet<bool>(
G, cs->Setting.get(), obj->Setting.get(), cSetting_dot_as_spheres);
bool const use_shader = SettingGet<bool>(G, cSetting_dot_use_shader) &&
SettingGet<bool>(G, cSetting_use_shaders);
if (I->shaderCGO && ((!use_shader || CGOCheckWhetherToFree(G, I->shaderCGO)) ||
I->shaderCGO_as_spheres!= dot_as_spheres)){
CGOFree(I->shaderCGO);
I->shaderCGO = 0;
}
if (use_shader){
if (!I->shaderCGO){
ok &= RepDotCGOGenerate(I);
}
if (ok) {
const float *color;
color = ColorGet(G, I->obj->Color);
CGORender(I->shaderCGO, color, nullptr, nullptr, info, I);
return; /* should not do any other rendering after shaderCGO has
been rendered */
}
} else {
if(!normals)
SceneResetNormal(G, true);
int lighting =
SettingGet_i(G, I->cs->Setting.get(), I->obj->Setting.get(), cSetting_dot_lighting);
if(!lighting) {
if(!info->line_lighting)
glDisable(GL_LIGHTING);
}
if(info->width_scale_flag)
glPointSize(I->Width * info->width_scale);
else
glPointSize(I->Width);
glBegin(GL_POINTS);
while(c--) {
if(!cc) { /* load up the current vertex color */
cc = (int) (*(v++));
glColor3fv(v);
v += 3;
}
if(normals)
glNormal3fv(v);
v += 3;
glVertex3fv(v);
v += 3;
cc--;
}
glEnd();
if(!lighting)
glEnable(GL_LIGHTING);
}
}
}
if (!ok){
CGOFree(I->shaderCGO);
I->invalidate(cRepInvPurge);
I->cs->Active[cRepDot] = false;
}
}
Rep *RepDotNew(CoordSet * cs, int state)
{
return (RepDotDoNew(cs, cRepDotNormal, state));
}
/**
* This routine does double duty - generating the dot representation, but also
* acting as our surface area computation routine.
*
* @param mode cRepDotNormal for dot representation, or cRepDotAreaType for
* `cmd.get_area()` computation.
* @param state Object state for ramped coloring
*/
Rep *RepDotDoNew(CoordSet * cs, cRepDot_t mode, int state)
{
PyMOLGlobals *G = cs->G;
float *v, *vn;
float *aa = nullptr;
int *tp = nullptr;
int *tf = nullptr;
float *countPtr = nullptr;
int* ati = nullptr;
auto obj = cs->Obj;
// skip if no dots are visible (assume all atoms "visible" for area comp.)
if (mode != cRepDotAreaType && !cs->hasRep(cRepDotBit)) {
return nullptr;
}
// are we using flags 24 & 25
auto cullByFlag =
SettingGet<bool>(G, cs->Setting.get(), obj->Setting.get(), cSetting_trim_dots);
auto dot_color =
SettingGet_color(G, cs->Setting.get(), obj->Setting.get(), cSetting_dot_color);
// are we ignoring hydrogens?
auto inclH =
SettingGet<bool>(G, cs->Setting.get(), obj->Setting.get(), cSetting_dot_hydrogens);
float solv_rad = 0.f;
if(SettingGet_b(G, cs->Setting.get(), obj->Setting.get(), cSetting_dot_solvent)) { /* are we generating a solvent surface? */
solv_rad = SettingGet_f(G, cs->Setting.get(), obj->Setting.get(), cSetting_solvent_radius); /* if so, get solvent radius */
}
std::unique_ptr<MapType> map(
new MapType(G, MAX_VDW + solv_rad, cs->Coord, cs->NIndex, nullptr));
if (!map) {
return nullptr;
}
// get current dot sampling
// Note: significantly affects the accuracy of our area comp.
auto ds = SettingGet<int>(G, cs->Setting.get(), obj->Setting.get(), cSetting_dot_density);
SphereRec const* sp = G->Sphere->Sphere[std::clamp(ds, 0, 4)];
int lastColor = cColorDefault;
int colorCnt = 0;
auto I = new RepDot(cs, state);
I->dotSize = SettingGet_f(G, cs->Setting.get(), obj->Setting.get(), cSetting_dot_radius);
I->Width = SettingGet_f(G, cs->Setting.get(), obj->Setting.get(), cSetting_dot_width);
I->V = pymol::malloc<float>(cs->NIndex * sp->nDot * 10);
ok_assert(1, I->V);
v = I->V;
// in area mode, we need to save additional info such as the normal vectors,
// the partial area, the originating atom, etc.
if (mode == cRepDotAreaType) {
I->A = pymol::malloc<float>(cs->NIndex * sp->nDot);
ok_assert(1, I->A);
I->T = pymol::malloc<int>(cs->NIndex * sp->nDot);
ok_assert(1, I->T);
I->F = pymol::malloc<int>(cs->NIndex * sp->nDot);
ok_assert(1, I->F);
I->VN = pymol::malloc<float>(cs->NIndex * sp->nDot * 3);
ok_assert(1, I->VN);
I->Atom = pymol::malloc<int>(cs->NIndex * sp->nDot);
ok_assert(1, I->Atom);
aa = I->A;
tp = I->T;
tf = I->F;
vn = I->VN;
ati = I->Atom;
inclH = true;
cullByFlag = true;
}
for (int a = 0; a < cs->NIndex; ++a) {
auto const atm = cs->IdxToAtm[a];
auto const& ai1 = obj->AtomInfo[atm];
if (mode != cRepDotAreaType && !(ai1.visRep & cRepDotBit)) {
continue;
}
if (!inclH && ai1.isHydrogen()) {
continue;
}
// If we are culling, flags control which atoms will have dot surfaces
// generated for them.
if (cullByFlag && (ai1.flags & (cAtomFlag_exfoliate | cAtomFlag_ignore))) {
continue;
}
auto c1 = AtomSettingGetWD(G, &ai1, cSetting_dot_color, dot_color);
if (c1 == cColorDefault) {
c1 = ai1.color;
}
const float* v0 = cs->coordPtr(a);
const float vdw = ai1.vdw + solv_rad;
for (int b = 0; b < sp->nDot; b++) {
const float v1[] = {
v0[0] + vdw * sp->dot[b][0],
v0[1] + vdw * sp->dot[b][1],
v0[2] + vdw * sp->dot[b][2],
};
bool flag = true;
for (int j : MapEIter(*map, v1, false)) {
if (j == a) {
continue;
}
auto const& ai2 = obj->AtomInfo[cs->IdxToAtm[j]];
if (!inclH && ai2.isHydrogen()) {
continue;
}
// If we are cullilng, flag 25 controls which atoms are considered
// "present" in the surface area calculation (i.e. able to occlude
// surface)
if (cullByFlag && (ai2.flags & cAtomFlag_ignore)) {
continue;
}
if (within3f(cs->coordPtr(j), v1, ai2.vdw + solv_rad)) {
flag = false;
break;
}
}
if (!flag) {
continue;
}
switch (mode) {
case cRepDotNormal:
if (c1 == lastColor && !ColorCheckRamped(G, c1)) {
colorCnt++;
} else {
/* new color */
if (countPtr) /* after first pass */
*countPtr = (float) colorCnt; /* save count */
colorCnt = 1;
countPtr = v++;
lastColor = c1;
// save new color
if (ColorCheckRamped(G, c1)) {
ColorGetRamped(G, c1, v1, v, state);
} else {
copy3(ColorGet(G, c1), v);
}
v += 3;
}
*(v++) = sp->dot[b][0];
*(v++) = sp->dot[b][1];
*(v++) = sp->dot[b][2];
*(v++) = v1[0];
*(v++) = v1[1];
*(v++) = v1[2];
I->N++;
break;
case cRepDotAreaType:
*(v++) = v1[0];
*(v++) = v1[1];
*(v++) = v1[2];
*(aa++) = vdw * vdw * sp->area[b]; /* area */
*(tp++) = ai1.customType; /* numeric type */
*(tf++) = ai1.flags; /* flags */
*(vn++) = sp->dot[b][0];
*(vn++) = sp->dot[b][1];
*(vn++) = sp->dot[b][2];
*(ati++) = atm;
I->N++;
break;
default:
assert(false);
}
}
ok_assert(1, !G->Interrupt);
}
// save count
if (countPtr)
*countPtr = (float) colorCnt;
I->V = ReallocForSure(I->V, float, (v - I->V));
ok_assert(1, I->V);
if (mode == cRepDotAreaType) {
I->A = ReallocForSure(I->A, float, (aa - I->A));
ok_assert(1, I->A);
I->T = ReallocForSure(I->T, int, (tp - I->T));
ok_assert(1, I->T);
I->F = ReallocForSure(I->F, int, (tf - I->F));
ok_assert(1, I->F);
I->VN = ReallocForSure(I->VN, float, (vn - I->VN));
ok_assert(1, I->VN);
I->Atom = ReallocForSure(I->Atom, int, (ati - I->Atom));
ok_assert(1, I->Atom);
}
return (Rep*) I;
ok_except1:
delete I;
return nullptr;
}
Reference in New Issue View Git Blame Copy Permalink