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520bf2a72a1e092a555c639718ae071ce5e05380
pymol-open-source/layer2/ObjectMesh.cpp
Thomas Holder 520bf2a72a 1.9.0.0 
* use PyMOL 2.0 setting defaults
* L > residues (oneletter)
* fix py3 crash in "A > copy to object"
* fix scene object visibility with hidden groups
* fix "ending" after loading movie session
2017-10-18 17:21:19 +00:00

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/*
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"OOMac.h"
#include"ObjectMesh.h"
#include"Base.h"
#include"MemoryDebug.h"
#include"Map.h"
#include"Debug.h"
#include"Parse.h"
#include"Isosurf.h"
#include"Vector.h"
#include"Color.h"
#include"main.h"
#include"Scene.h"
#include"Setting.h"
#include"Executive.h"
#include"PConv.h"
#include"P.h"
#include"Matrix.h"
#include"ShaderMgr.h"
#include"CGO.h"
#include"ObjectCGO.h"
ObjectMesh *ObjectMeshNew(PyMOLGlobals * G);
static void ObjectMeshFree(ObjectMesh * I);
static void ObjectMeshInvalidate(ObjectMesh * I, int rep, int level, int state);
void ObjectMeshStateInit(PyMOLGlobals * G, ObjectMeshState * ms);
void ObjectMeshRecomputeExtent(ObjectMesh * I);
static PyObject *ObjectMeshStateAsPyList(ObjectMeshState * I)
{
PyObject *result = NULL;
result = PyList_New(17);
PyList_SetItem(result, 0, PyInt_FromLong(I->Active));
PyList_SetItem(result, 1, PyString_FromString(I->MapName));
PyList_SetItem(result, 2, PyInt_FromLong(I->MapState));
PyList_SetItem(result, 3, CrystalAsPyList(&I->Crystal));
PyList_SetItem(result, 4, PyInt_FromLong(I->ExtentFlag));
PyList_SetItem(result, 5, PConvFloatArrayToPyList(I->ExtentMin, 3));
PyList_SetItem(result, 6, PConvFloatArrayToPyList(I->ExtentMax, 3));
PyList_SetItem(result, 7, PConvIntArrayToPyList(I->Range, 6));
PyList_SetItem(result, 8, PyFloat_FromDouble(I->Level));
PyList_SetItem(result, 9, PyFloat_FromDouble(I->Radius));
PyList_SetItem(result, 10, PyInt_FromLong(I->CarveFlag));
PyList_SetItem(result, 11, PyFloat_FromDouble(I->CarveBuffer));
if(I->CarveFlag && I->AtomVertex) {
PyList_SetItem(result, 12, PConvFloatVLAToPyList(I->AtomVertex));
} else {
PyList_SetItem(result, 12, PConvAutoNone(NULL));
}
PyList_SetItem(result, 13, PyInt_FromLong(I->MeshMode));
PyList_SetItem(result, 14, PyFloat_FromDouble(I->AltLevel));
PyList_SetItem(result, 15, PyInt_FromLong(I->quiet));
if(I->Field) {
PyList_SetItem(result, 16, IsosurfAsPyList(I->State.G, I->Field));
} else {
PyList_SetItem(result, 16, PConvAutoNone(NULL));
}
return (PConvAutoNone(result));
}
static int ObjectMeshStateMapExists(ObjectMesh *I, ObjectMeshState *ms){
return ExecutiveFindObjectMapByName(I->Obj.G, ms->MapName) ? 1 : 0;
}
int ObjectMeshAllMapsInStatesExist(ObjectMesh * I)
{
int a;
for(a = 0; a < I->NState; a++) {
if(I->State[a].Active) {
if (!ObjectMeshStateMapExists(I, I->State + a)){
return 0;
}
}
}
return 1;
}
static PyObject *ObjectMeshAllStatesAsPyList(ObjectMesh * I)
{
PyObject *result = NULL;
int a;
result = PyList_New(I->NState);
for(a = 0; a < I->NState; a++) {
if(I->State[a].Active) {
PyList_SetItem(result, a, ObjectMeshStateAsPyList(I->State + a));
} else {
PyList_SetItem(result, a, PConvAutoNone(NULL));
}
}
return (PConvAutoNone(result));
}
static int ObjectMeshStateFromPyList(PyMOLGlobals * G, ObjectMeshState * I,
PyObject * list)
{
int ok = true;
int ll = 0;
PyObject *tmp;
if(ok)
ok = (list != NULL);
if(ok) {
if(!PyList_Check(list))
I->Active = false;
else {
ObjectMeshStateInit(G, I);
if(ok)
ok = (list != NULL);
if(ok)
ok = PyList_Check(list);
if(ok)
ll = PyList_Size(list);
/* TO SUPPORT BACKWARDS COMPATIBILITY...
Always check ll when adding new PyList_GetItem's */
if(ok)
ok = PConvPyIntToInt(PyList_GetItem(list, 0), &I->Active);
if(ok)
ok = PConvPyStrToStr(PyList_GetItem(list, 1), I->MapName, WordLength);
if(ok)
ok = PConvPyIntToInt(PyList_GetItem(list, 2), &I->MapState);
if(ok)
ok = CrystalFromPyList(&I->Crystal, PyList_GetItem(list, 3));
if(ok)
ok = PConvPyIntToInt(PyList_GetItem(list, 4), &I->ExtentFlag);
if(ok)
ok = PConvPyListToFloatArrayInPlace(PyList_GetItem(list, 5), I->ExtentMin, 3);
if(ok)
ok = PConvPyListToFloatArrayInPlace(PyList_GetItem(list, 6), I->ExtentMax, 3);
if(ok)
ok = PConvPyListToIntArrayInPlace(PyList_GetItem(list, 7), I->Range, 6);
if(ok)
ok = PConvPyFloatToFloat(PyList_GetItem(list, 8), &I->Level);
if(ok)
ok = PConvPyFloatToFloat(PyList_GetItem(list, 9), &I->Radius);
if(ok)
ok = PConvPyIntToInt(PyList_GetItem(list, 10), &I->CarveFlag);
if(ok)
ok = PConvPyFloatToFloat(PyList_GetItem(list, 11), &I->CarveBuffer);
if(ok) {
tmp = PyList_GetItem(list, 12);
if(tmp == Py_None)
I->AtomVertex = NULL;
else
ok = PConvPyListToFloatVLA(tmp, &I->AtomVertex);
}
if(ok)
ok = PConvPyIntToInt(PyList_GetItem(list, 13), &I->MeshMode);
if(ok) {
I->RefreshFlag = true;
I->ResurfaceFlag = true;
}
if(ok && (ll > 14)) {
ok = PConvPyFloatToFloat(PyList_GetItem(list, 14), &I->AltLevel);
} else {
I->AltLevel = I->Level;
}
if(ok && (ll > 15)) {
ok = PConvPyIntToInt(PyList_GetItem(list, 15), &I->quiet);
} else {
I->quiet = true;
}
if(ok && (ll > 16)) {
tmp = PyList_GetItem(list, 16);
if(tmp == Py_None)
I->Field = NULL;
else
ok = ((I->Field = IsosurfNewFromPyList(G, tmp)) != NULL);
}
}
}
return (ok);
}
static int ObjectMeshAllStatesFromPyList(ObjectMesh * I, PyObject * list)
{
int ok = true;
int a;
VLACheck(I->State, ObjectMeshState, I->NState);
if(ok)
ok = PyList_Check(list);
if(ok) {
for(a = 0; a < I->NState; a++) {
ok = ObjectMeshStateFromPyList(I->Obj.G, I->State + a, PyList_GetItem(list, a));
if(!ok)
break;
}
}
return (ok);
}
int ObjectMeshNewFromPyList(PyMOLGlobals * G, PyObject * list, ObjectMesh ** result)
{
int ok = true;
int ll;
ObjectMesh *I = NULL;
(*result) = NULL;
if(ok)
ok = (list != NULL);
if(ok)
ok = PyList_Check(list);
if(ok)
ll = PyList_Size(list);
/* TO SUPPORT BACKWARDS COMPATIBILITY...
Always check ll when adding new PyList_GetItem's */
I = ObjectMeshNew(G);
if(ok)
ok = (I != NULL);
if(ok)
ok = ObjectFromPyList(G, PyList_GetItem(list, 0), &I->Obj);
if(ok)
ok = PConvPyIntToInt(PyList_GetItem(list, 1), &I->NState);
if(ok)
ok = ObjectMeshAllStatesFromPyList(I, PyList_GetItem(list, 2));
if(ok) {
(*result) = I;
ObjectMeshRecomputeExtent(I);
} else {
ObjectMeshFree(I);
(*result) = NULL;
}
return (ok);
}
static CGO *ObjectMeshRenderImpl(ObjectMesh * I, RenderInfo * info, int returnCGO, int stateArg);
PyObject *ObjectMeshAsPyList(ObjectMesh * I)
{
PyObject *result = NULL;
int allMapsExist = ObjectMeshAllMapsInStatesExist(I);
if (allMapsExist){
result = PyList_New(3);
PyList_SetItem(result, 0, ObjectAsPyList(&I->Obj));
PyList_SetItem(result, 1, PyInt_FromLong(I->NState));
PyList_SetItem(result, 2, ObjectMeshAllStatesAsPyList(I));
} else {
/* save ObjectMesh as ObjectCGO */
ObjectCGO *retObjectCGO = ObjectCGONew(I->Obj.G);
ObjectCopyHeader(&retObjectCGO->Obj, &I->Obj);
retObjectCGO->Obj.type = cObjectCGO;
int a;
PRINTFB(I->Obj.G, FB_ObjectMesh, FB_Errors)
"ObjectMesh-Warning: map has been deleted, saving as CGO.\n"
ENDFB(I->Obj.G);
for(a = 0; a < I->NState; a++) {
CGO *cgo = ObjectMeshRenderImpl(I, 0, 1, a);
retObjectCGO = ObjectCGOFromCGO(I->Obj.G, retObjectCGO, cgo, a);
}
ObjectSetRepVisMask(&retObjectCGO->Obj, cRepCGOBit, cVis_AS);
result = ObjectCGOAsPyList(retObjectCGO);
ObjectCGOFree(retObjectCGO);
}
return (PConvAutoNone(result));
}
static void ObjectMeshStatePurge(ObjectMeshState * ms)
{
ObjectStatePurge(&ms->State);
if(ms->Field) {
IsosurfFieldFree(ms->State.G, ms->Field);
ms->Field = NULL;
}
VLAFreeP(ms->AtomVertex);
CGOFree(ms->shaderCGO);
CGOFree(ms->shaderUnitCellCGO);
CGOFree(ms->UnitCellCGO);
ms->Active = false;
}
static void ObjectMeshStateFree(ObjectMeshState * ms)
{
ObjectMeshStatePurge(ms);
VLAFreeP(ms->N);
VLAFreeP(ms->V);
FreeP(ms->VC);
FreeP(ms->RC);
}
static void ObjectMeshFree(ObjectMesh * I)
{
int a;
for(a = 0; a < I->NState; a++) {
if(I->State[a].Active)
ObjectMeshStateFree(I->State + a);
}
VLAFreeP(I->State);
ObjectPurge(&I->Obj);
OOFreeP(I);
}
int ObjectMeshInvalidateMapName(ObjectMesh * I, const char *name, const char * new_name)
{
int a;
ObjectMeshState *ms;
int result = false;
for(a = 0; a < I->NState; a++) {
ms = I->State + a;
if(ms->Active) {
if(strcmp(ms->MapName, name) == 0) {
if (new_name)
strcpy(ms->MapName, new_name);
ObjectMeshInvalidate(I, cRepAll, cRepInvAll, a);
result = true;
}
}
}
return result;
}
void ObjectMeshDump(ObjectMesh * I, const char *fname, int state)
{
float *v;
int *n;
int c;
FILE *f;
f = fopen(fname, "wb");
if(!f)
ErrMessage(I->Obj.G, "ObjectMeshDump", "can't open file for writing");
else {
if(state < I->NState) {
n = I->State[state].N;
v = I->State[state].V;
if(n && v)
while(*n) {
c = *(n++);
if(!I->State[state].MeshMode) {
fprintf(f, "\n");
}
while(c--) {
fprintf(f, "%10.4f%10.4f%10.4f\n", v[0], v[1], v[2]);
v += 3;
}
}
}
fclose(f);
PRINTFB(I->Obj.G, FB_ObjectMesh, FB_Actions)
" ObjectMeshDump: %s written to %s\n", I->Obj.Name, fname ENDFB(I->Obj.G);
}
}
static void ObjectMeshInvalidate(ObjectMesh * I, int rep, int level, int state)
{
if(level >= cRepInvExtents) {
I->Obj.ExtentFlag = false;
}
if((rep == cRepMesh) || (rep == cRepAll) || (rep == cRepCell)) {
for(StateIterator iter(I->Obj.G, NULL, state, I->NState); iter.next();) {
ObjectMeshState *ms = I->State + iter.state;
CGOFree(ms->shaderCGO);
CGOFree(ms->shaderUnitCellCGO);
ms->RefreshFlag = true;
if(level >= cRepInvAll) {
ms->ResurfaceFlag = true;
SceneChanged(I->Obj.G);
} else if(level >= cRepInvColor) {
ms->RecolorFlag = true;
SceneChanged(I->Obj.G);
} else {
SceneInvalidate(I->Obj.G);
}
}
}
}
int ObjectMeshGetLevel(ObjectMesh * I, int state, float *result)
{
int ok = true;
ObjectMeshState *ms;
if(state >= I->NState) {
ok = false;
} else {
if(state < 0) {
state = 0;
}
ms = I->State + state;
if(ms->Active && result) {
*result = ms->Level;
} else
ok = false;
}
return (ok);
}
int ObjectMeshSetLevel(ObjectMesh * I, float level, int state, int quiet)
{
int ok = true;
if(state >= I->NState) {
ok = false;
} else {
for(StateIterator iter(I->Obj.G, NULL, state, I->NState); iter.next();) {
ObjectMeshState *ms = I->State + iter.state;
if(ms->Active) {
ms->ResurfaceFlag = true;
ms->RefreshFlag = true;
ms->Level = level;
ms->quiet = quiet;
}
}
}
return (ok);
}
static void ObjectMeshStateUpdateColors(ObjectMesh * I, ObjectMeshState * ms)
{
int one_color_flag = true;
int cur_color = -1;
if(ms->MeshMode == 0) {
cur_color = SettingGet_color(I->Obj.G, I->Obj.Setting, NULL, cSetting_mesh_color);
} else if(ms->MeshMode == 1) {
cur_color = SettingGet_color(I->Obj.G, I->Obj.Setting, NULL, cSetting_dot_color);
}
if(cur_color == -1)
cur_color = I->Obj.Color;
if(ColorCheckRamped(I->Obj.G, cur_color))
one_color_flag = false;
ms->OneColor = cur_color;
if(ms->V) {
int ramped_flag = false;
float *v = ms->V;
float *vc;
int *rc;
int a;
int state = ms - I->State;
int n_vert = VLAGetSize(ms->V) / 3;
int base_n_vert = ms->base_n_V / 3;
if(ms->VC && (ms->VCsize < n_vert)) {
FreeP(ms->VC);
FreeP(ms->RC);
}
if(!ms->VC) {
ms->VCsize = n_vert;
ms->VC = Alloc(float, n_vert * 3);
}
if(!ms->RC) {
ms->RC = Alloc(int, n_vert);
}
rc = ms->RC;
vc = ms->VC;
if(vc) {
for(a = 0; a < n_vert; a++) {
if(a == base_n_vert) {
int new_color = SettingGet_color(I->Obj.G, I->Obj.Setting,
NULL, cSetting_mesh_negative_color);
if(new_color == -1)
new_color = cur_color;
if(new_color != cur_color) {
one_color_flag = false;
cur_color = new_color;
}
}
if(ColorCheckRamped(I->Obj.G, cur_color)) {
ColorGetRamped(I->Obj.G, cur_color, v, vc, state);
*rc = cur_color;
ramped_flag = true;
} else {
float *col = ColorGet(I->Obj.G, cur_color);
copy3f(col, vc);
}
rc++;
vc += 3;
v += 3;
}
}
if(one_color_flag && (!ramped_flag)) {
FreeP(ms->VC);
FreeP(ms->RC);
} else if((!ramped_flag)
||
(!SettingGet_b(I->Obj.G, NULL, I->Obj.Setting, cSetting_ray_color_ramps))) {
FreeP(ms->RC);
}
}
}
static void ObjectMeshUpdate(ObjectMesh * I)
{
PyMOLGlobals *G = I->Obj.G;
int a;
int c;
ObjectMeshState *ms;
ObjectMapState *oms = NULL;
ObjectMap *map = NULL;
int *n;
float *v;
float carve_buffer;
int avoid_flag = false;
int *old_n;
float *old_v;
int n_cur;
int n_seg;
int n_line;
int flag;
int last_flag = 0;
int h, k, l;
int i, j;
int mesh_skip = SettingGet_i(G, I->Obj.Setting, NULL, cSetting_mesh_skip);
MapType *voxelmap; /* this has nothing to do with isosurfaces... */
for(a = 0; a < I->NState; a++) {
ms = I->State + a;
if(ms->Active) {
map = ExecutiveFindObjectMapByName(I->Obj.G, ms->MapName);
if(!map) {
PRINTFB(I->Obj.G, FB_ObjectMesh, FB_Errors)
"ObjectMeshUpdate-Error: map '%s' has been deleted.\n", ms->MapName
ENDFB(I->Obj.G);
ms->ResurfaceFlag = false;
}
if(map) {
oms = ObjectMapGetState(map, ms->MapState);
}
if(oms) {
if(ms->RefreshFlag || ms->ResurfaceFlag) {
if(!ms->Field) {
ms->Crystal = *(oms->Symmetry->Crystal);
}
if((I->Obj.visRep & cRepCellBit)) {
CGOFree(ms->UnitCellCGO);
ms->UnitCellCGO = CrystalGetUnitCellCGO(&ms->Crystal);
}
if(oms->State.Matrix) {
ObjectStateSetMatrix(&ms->State, oms->State.Matrix);
} else if(ms->State.Matrix) {
ObjectStateResetMatrix(&ms->State);
}
ms->RefreshFlag = false;
}
}
if(map && oms && ms->N && ms->V && (I->Obj.visRep & cRepMeshBit)) {
if(ms->ResurfaceFlag) {
Isofield *field = NULL;
ms->RecolorFlag = true;
ms->ResurfaceFlag = false;
if(!ms->quiet) {
PRINTFB(G, FB_ObjectMesh, FB_Details)
" ObjectMesh: updating \"%s\".\n", I->Obj.Name ENDFB(G);
}
if(ms->Field) {
field = ms->Field;
} else if(oms->Field) {
field = oms->Field;
}
if(field) {
{
float *min_ext, *max_ext;
float tmp_min[3], tmp_max[3];
if(MatrixInvTransformExtentsR44d3f(ms->State.Matrix,
ms->ExtentMin, ms->ExtentMax,
tmp_min, tmp_max)) {
min_ext = tmp_min;
max_ext = tmp_max;
} else {
min_ext = ms->ExtentMin;
max_ext = ms->ExtentMax;
}
IsosurfGetRange(I->Obj.G, field, oms->Symmetry->Crystal,
min_ext, max_ext, ms->Range, true);
}
/* printf("Mesh-DEBUG: %d %d %d %d %d %d\n",
ms->Range[0],
ms->Range[1],
ms->Range[2],
ms->Range[3],
ms->Range[4],
ms->Range[5]); */
IsosurfVolume(I->Obj.G, I->Obj.Setting, NULL,
field,
ms->Level,
&ms->N, &ms->V,
ms->Range, ms->MeshMode, mesh_skip, ms->AltLevel);
if(!SettingGet_b
(I->Obj.G, I->Obj.Setting, NULL, cSetting_mesh_negative_visible)) {
ms->base_n_V = VLAGetSize(ms->V);
} else if(ms->MeshMode != 3) {
/* do we want the negative surface too? */
int *N2 = VLAlloc(int, 10000);
float *V2 = VLAlloc(float, 10000);
IsosurfVolume(I->Obj.G, I->Obj.Setting, NULL,
field,
-ms->Level,
&N2, &V2, ms->Range, ms->MeshMode, mesh_skip, ms->AltLevel);
if(N2 && V2) {
int base_n_N = VLAGetSize(ms->N);
int base_n_V = VLAGetSize(ms->V);
int addl_n_N = VLAGetSize(N2);
int addl_n_V = VLAGetSize(V2);
ms->base_n_V = base_n_V;
/* make room */
VLASize(ms->N, int, base_n_N + addl_n_N);
VLASize(ms->V, float, base_n_V + addl_n_V);
/* copy vertex data */
memcpy(((char *) ms->V) + (sizeof(float) * base_n_V),
V2, sizeof(float) * addl_n_V);
/* copy strip counts */
memcpy(((char *) ms->N) + (sizeof(int) * (base_n_N - 1)),
N2, sizeof(int) * addl_n_N);
ms->N[base_n_N + addl_n_N - 1] = 0;
VLAFreeP(N2);
VLAFreeP(V2);
}
}
if(ms->State.Matrix && VLAGetSize(ms->N) && VLAGetSize(ms->V)) {
int count;
/* take map coordinates back to view coordinates if necessary */
v = ms->V;
count = VLAGetSize(ms->V) / 3;
while(count--) {
transform44d3f(ms->State.Matrix, v, v);
v += 3;
}
}
}
if(ms->CarveFlag && ms->AtomVertex && VLAGetSize(ms->N) && VLAGetSize(ms->V)) {
carve_buffer = ms->CarveBuffer;
if(ms->CarveBuffer < 0.0F) {
avoid_flag = true;
carve_buffer = -carve_buffer;
}
/* cull my friend, cull */
voxelmap = MapNew(I->Obj.G,
-carve_buffer, ms->AtomVertex,
VLAGetSize(ms->AtomVertex) / 3, NULL);
if(voxelmap) {
MapSetupExpress(voxelmap);
old_n = ms->N;
old_v = ms->V;
ms->N = VLAlloc(int, VLAGetSize(old_n));
ms->V = VLAlloc(float, VLAGetSize(old_v));
n = old_n;
v = old_v;
n_cur = 0;
n_seg = 0;
n_line = 0;
while(*n) {
last_flag = false;
c = *(n++);
while(c--) {
flag = false;
MapLocus(voxelmap, v, &h, &k, &l);
i = *(MapEStart(voxelmap, h, k, l));
if(i) {
j = voxelmap->EList[i++];
while(j >= 0) {
if(within3f(ms->AtomVertex + 3 * j, v, carve_buffer)) {
flag = true;
break;
}
j = voxelmap->EList[i++];
}
}
if(avoid_flag)
flag = !flag;
if(flag && (!last_flag)) {
VLACheck(ms->V, float, 3 * (n_line + 1));
copy3f(v, ms->V + n_line * 3);
n_cur++;
n_line++;
}
if(flag && last_flag) { /* continue segment */
VLACheck(ms->V, float, 3 * (n_line + 1));
copy3f(v, ms->V + n_line * 3);
n_cur++;
n_line++;
}
if((!flag) && last_flag) { /* terminate segment */
VLACheck(ms->N, int, n_seg);
ms->N[n_seg] = n_cur;
n_seg++;
n_cur = 0;
}
last_flag = flag;
v += 3;
}
if(last_flag) { /* terminate segment */
VLACheck(ms->N, int, n_seg);
ms->N[n_seg] = n_cur;
n_seg++;
n_cur = 0;
}
}
VLACheck(ms->N, int, n_seg);
ms->N[n_seg] = 0;
VLAFreeP(old_n);
VLAFreeP(old_v);
MapFree(voxelmap);
}
}
}
if(ms->RecolorFlag) {
ObjectMeshStateUpdateColors(I, ms);
ms->RecolorFlag = false;
}
}
CGOFree(ms->shaderCGO);
CGOFree(ms->shaderUnitCellCGO);
}
SceneInvalidate(I->Obj.G);
}
if(!I->Obj.ExtentFlag) {
ObjectMeshRecomputeExtent(I);
if(I->Obj.ExtentFlag)
SceneInvalidate(I->Obj.G);
}
}
static void ObjectMeshRender(ObjectMesh * I, RenderInfo * info)
{
ObjectMeshRenderImpl(I, info, 0, 0);
}
static short ObjectMeshStateRenderShader(ObjectMeshState *ms, ObjectMesh *I,
RenderInfo *info, short mesh_as_cylinders, float mesh_width)
{
PyMOLGlobals *G = I->Obj.G;
CShaderPrg *shaderPrg;
if (mesh_as_cylinders) {
shaderPrg = CShaderPrg_Enable_CylinderShader(G);
CShaderPrg_Set1f(shaderPrg, "uni_radius",
SceneGetLineWidthForCylinders(G, info, mesh_width));
} else {
shaderPrg = CShaderPrg_Enable_DefaultShader(G);
CShaderPrg_SetLightingEnabled(shaderPrg, 1);
CShaderPrg_Set1i(shaderPrg, "two_sided_lighting_enabled",
SceneGetTwoSidedLighting(G));
}
if (!shaderPrg)
return false;
CGORenderGL(ms->shaderCGO, NULL, NULL, NULL, info, NULL);
CShaderPrg_Disable(shaderPrg);
if (ms->shaderUnitCellCGO){
shaderPrg = CShaderPrg_Enable_DefaultShader(G);
CShaderPrg_SetLightingEnabled(shaderPrg, 0);
CGORenderGL(ms->shaderUnitCellCGO, NULL, NULL, NULL, info, NULL);
CShaderPrg_Disable(shaderPrg);
}
return true;
}
static CGO *ObjectMeshRenderImpl(ObjectMesh * I, RenderInfo * info, int returnCGO, int stateArg)
{
PyMOLGlobals *G = I->Obj.G;
float *v = NULL;
float *vc;
int *rc;
float radius;
int state = 0;
CRay *ray = 0;
Picking **pick = 0;
int pass = 0;
int *n = NULL;
int c;
float line_width, mesh_width = SettingGet_f(I->Obj.G, I->Obj.Setting, NULL, cSetting_mesh_width);
ObjectMeshState *ms = NULL;
int ok = true;
if (info){
state = info->state;
ray = info->ray;
pick = info->pick;
pass = info->pass;
} else {
state = stateArg;
}
line_width = SceneGetDynamicLineWidth(info, mesh_width);
ObjectPrepareContext(&I->Obj, ray);
for(StateIterator iter(I->Obj.G, I->Obj.Setting, state, I->NState); iter.next();) {
ms = I->State + iter.state;
if(!ms->Active || !ms->V || !ms->N)
continue;
{
v = ms->V;
n = ms->N;
if(ok && ray) {
if(ms->UnitCellCGO && (I->Obj.visRep & cRepCellBit)){
ok &= CGORenderRay(ms->UnitCellCGO, ray, ColorGet(I->Obj.G, I->Obj.Color),
I->Obj.Setting, NULL);
if (!ok){
CGOFree(ms->UnitCellCGO);
break;
}
}
if(ms->MeshMode != 1) {
radius = SettingGet_f(I->Obj.G, I->Obj.Setting, NULL, cSetting_mesh_radius);
if(radius == 0.0F) {
radius = ray->PixelRadius * line_width / 2.0F;
}
} else {
radius = SettingGet_f(I->Obj.G, I->Obj.Setting, NULL, cSetting_dot_radius);
if(radius == 0.0F) {
radius =
ray->PixelRadius * SettingGet_f(I->Obj.G, I->Obj.Setting, NULL,
cSetting_dot_width) / 1.4142F;
}
}
if(ok && n && v && (I->Obj.visRep & cRepMeshBit)) {
float cc[3];
float colA[3], colB[3];
ColorGetEncoded(G, ms->OneColor, cc);
vc = ms->VC;
rc = ms->RC;
if(ms->MeshMode == 1) {
ray->color3fv(cc);
while(ok && *n) {
c = *(n++);
while(ok && c--) {
if(vc) {
float *cA = vc;
if(rc) {
if(rc[0] < -1)
ColorGetEncoded(G, rc[0], (cA = colA));
rc++;
}
ray->color3fv(cA);
ok &= ray->sphere3fv(v, radius);
vc += 3;
} else {
ok &= ray->sphere3fv(v, radius);
}
v += 3;
}
}
} else {
while(ok && *n) {
c = *(n++);
if(c--) {
v += 3;
if(vc) {
vc += 3;
if(rc)
rc++;
}
while(ok && c--) {
if(vc) {
float *cA = vc - 3, *cB = vc;
if(rc) {
if(rc[-1] < -1)
ColorGetEncoded(G, rc[-1], (cA = colA));
if(rc[0] < -1)
ColorGetEncoded(G, rc[0], (cB = colB));
rc++;
}
ok &= ray->sausage3fv(v - 3, v, radius, cA, cB);
vc += 3;
} else {
ok &= ray->sausage3fv(v - 3, v, radius, cc, cc);
}
v += 3;
}
}
}
}
}
} else if((G->HaveGUI && G->ValidContext) || returnCGO) {
if(!pick && !pass) {
short use_shader;
short mesh_as_cylinders ;
CGO *shaderCGO = NULL;
use_shader = ( SettingGetGlobal_b(G, cSetting_mesh_use_shader) & SettingGetGlobal_b(G, cSetting_use_shaders)) | returnCGO;
mesh_as_cylinders = SettingGetGlobal_b(G, cSetting_render_as_cylinders) && SettingGetGlobal_b(G, cSetting_mesh_as_cylinders) && ms->MeshMode != 1;
if (ms->shaderCGO && (!use_shader || (mesh_as_cylinders ^ ms->shaderCGO->has_draw_cylinder_buffers))){
CGOFree(ms->shaderCGO);
CGOFree(ms->shaderUnitCellCGO);
}
if (ms->shaderCGO && !returnCGO) {
ok &= ObjectMeshStateRenderShader(ms, I, info, mesh_as_cylinders, mesh_width);
continue;
}
if (use_shader){
shaderCGO = CGONew(G);
if(!shaderCGO) {
ok = false;
break;
}
shaderCGO->use_shader = true;
}
if(ms->UnitCellCGO && (I->Obj.visRep & cRepCellBit)) {
float *color = ColorGet(I->Obj.G, I->Obj.Color);
if (!use_shader) {
CGORenderGL(ms->UnitCellCGO, color, I->Obj.Setting, NULL, info, NULL);
} else if(!ms->shaderUnitCellCGO) {
CGO *newUnitCellCGO = CGONewSized(G, 0);
CGOColorv(newUnitCellCGO, color);
CGOAppend(newUnitCellCGO, ms->UnitCellCGO);
ms->shaderUnitCellCGO = CGOOptimizeToVBONotIndexed(newUnitCellCGO, 0);
CGOFree(newUnitCellCGO);
ms->shaderUnitCellCGO->use_shader = true;
ms->shaderUnitCellCGO->enable_shaders = false;
}
}
if(info && !info->line_lighting){
if(!use_shader){
glDisable(GL_LIGHTING);
} else if(!mesh_as_cylinders) {
ok &= CGODisable(shaderCGO, GL_LIGHTING);
}
}
if(!ok) break;
if (use_shader){
ok &= CGOResetNormal(shaderCGO, false);
} else {
SceneResetNormal(I->Obj.G, false);
}
if(n && v && (I->Obj.visRep & cRepMeshBit)) {
if(use_shader) {
vc = ms->VC;
if(!vc)
ok &= CGOColorv(shaderCGO, ColorGet(I->Obj.G, ms->OneColor));
if (!mesh_as_cylinders){
if(ms->MeshMode == 1){
ok &= CGODotwidth(shaderCGO, SettingGet_f
(I->Obj.G, I->Obj.Setting, NULL, cSetting_dot_width));
} else {
ok &= CGOLinewidthSpecial(shaderCGO, LINEWIDTH_DYNAMIC_MESH);
}
}
if(!ok) break;
if (mesh_as_cylinders){
if(returnCGO) {
ok &= CGOLinewidthSpecial(shaderCGO, CYLINDERWIDTH_DYNAMIC_MESH);
}
for(; ok && (c = *(n++)); v += 3, vc && (vc += 3)) {
for(; ok && (--c); v += 3) {
float axis[] = {
v[3] - v[0],
v[4] - v[1],
v[5] - v[2]
};
if(vc) {
ok &= CGOColorv(shaderCGO, vc);
vc += 3;
}
if(vc && memcmp(vc - 3, vc, sizeof(float) * 3)) {
ok &= CGOShaderCylinder2ndColor(shaderCGO, v, axis, 1.f, 15, vc);
} else {
ok &= CGOShaderCylinder(shaderCGO, v, axis, 1.f, 15);
}
}
}
} else {
while(ok && *n) {
c = *(n++);
if(ms->MeshMode == 1)
ok &= CGOBegin(shaderCGO, GL_POINTS);
else {
if (c < 2){
while(c--) {
if(vc) {
vc += 3;
}
v += 3;
}
continue;
}
ok &= CGOBegin(shaderCGO, GL_LINE_STRIP);
}
while(ok && c--) {
if(vc) {
ok &= CGOColorv(shaderCGO, vc);
vc += 3;
}
if (ok)
ok &= CGOVertexv(shaderCGO, v);
v += 3;
}
if (ok)
ok &= CGOEnd(shaderCGO);
}
}
} else {
vc = ms->VC;
if(!vc)
glColor3fv(ColorGet(I->Obj.G, ms->OneColor));
if(ms->MeshMode == 1){
glPointSize(SettingGet_f
(I->Obj.G, I->Obj.Setting, NULL, cSetting_dot_width));
} else {
glLineWidth(line_width);
}
while(*n) {
c = *(n++);
if(ms->MeshMode == 1)
glBegin(GL_POINTS);
else
glBegin(GL_LINE_STRIP);
while(c--) {
if(vc) {
glColor3fv(vc);
vc += 3;
}
glVertex3fv(v);
v += 3;
}
glEnd();
}
}
}
if(info && !info->line_lighting){
if(!use_shader){
glEnable(GL_LIGHTING);
} else if (ok && !mesh_as_cylinders){
ok &= CGOEnable(shaderCGO, GL_LIGHTING);
}
}
if (use_shader) {
if (ok){
CGO *convertcgo = NULL;
if (ok)
ok &= CGOStop(shaderCGO);
if (ok)
convertcgo = CGOCombineBeginEnd(shaderCGO, 0);
CHECKOK(ok, convertcgo);
CGOFree(shaderCGO);
shaderCGO = convertcgo;
if (returnCGO){
return (shaderCGO);
} else {
ms->shaderCGO = shaderCGO;
}
if (ok){
if (mesh_as_cylinders){
convertcgo = CGOOptimizeGLSLCylindersToVBOIndexed(ms->shaderCGO, 0);
} else {
convertcgo = CGOOptimizeToVBONotIndexed(ms->shaderCGO, 0);
}
CHECKOK(ok, convertcgo);
}
if (convertcgo){
CGOFree(ms->shaderCGO);
ms->shaderCGO = convertcgo;
}
}
if(!ok) break;
ok &= ObjectMeshStateRenderShader(ms, I, info, mesh_as_cylinders, mesh_width);
}
}
}
}
}
if (!ok){
I->Obj.fInvalidate(&I->Obj, cRepMesh, cRepInvPurge, -1);
I->Obj.fInvalidate(&I->Obj, cRepCGO, cRepInvPurge, -1);
ObjectSetRepVisMask(&I->Obj, 0, cVis_AS);
}
return NULL;
}
/*========================================================================*/
static int ObjectMeshGetNStates(ObjectMesh * I)
{
return (I->NState);
}
/*========================================================================*/
ObjectMesh *ObjectMeshNew(PyMOLGlobals * G)
{
int ok = true;
OOAlloc(G, ObjectMesh);
CHECKOK(ok, I);
if (ok)
ObjectInit(G, (CObject *) I);
if (ok){
I->NState = 0;
I->State = VLACalloc(ObjectMeshState, 10); /* autozero important */
CHECKOK(ok, I->State);
}
if (ok){
I->Obj.type = cObjectMesh;
I->Obj.fFree = (void (*)(CObject *)) ObjectMeshFree;
I->Obj.fUpdate = (void (*)(CObject *)) ObjectMeshUpdate;
I->Obj.fRender = (void (*)(CObject *, RenderInfo *)) ObjectMeshRender;
I->Obj.fInvalidate = (void (*)(CObject *, int, int, int)) ObjectMeshInvalidate;
I->Obj.fGetNFrame = (int (*)(CObject *)) ObjectMeshGetNStates;
}
if (!ok){
ObjectMeshFree(I);
I = NULL;
}
/* I->Obj.fGetCaption = (char *(*)(CObject *))ObjectMeshGetCaption; */
return (I);
}
/*========================================================================*/
void ObjectMeshStateInit(PyMOLGlobals * G, ObjectMeshState * ms)
{
if(ms->Active)
ObjectMeshStatePurge(ms);
ObjectStateInit(G, &ms->State);
if(!ms->V) {
ms->V = VLAlloc(float, 10000);
}
if(!ms->N) {
ms->N = VLAlloc(int, 10000);
}
ms->N[0] = 0;
ms->Active = true;
ms->ResurfaceFlag = true;
ms->RecolorFlag = false;
ms->ExtentFlag = false;
ms->CarveFlag = false;
ms->quiet = true;
ms->CarveBuffer = 0.0;
ms->AtomVertex = NULL;
ms->UnitCellCGO = NULL;
ms->caption[0] = 0;
ms->Field = NULL;
ms->shaderCGO = NULL;
ms->shaderUnitCellCGO = NULL;
}
/*========================================================================*/
ObjectMesh *ObjectMeshFromXtalSym(PyMOLGlobals * G, ObjectMesh * obj, ObjectMap * map,
CSymmetry * sym,
int map_state,
int state, float *mn, float *mx,
float level, int meshMode,
float carve, float *vert_vla,
float alt_level, int quiet)
{
int ok = true;
ObjectMesh *I = NULL;
ObjectMeshState *ms = NULL;
ObjectMapState *oms = NULL;
int created = !obj;
if(created) {
I = ObjectMeshNew(G);
} else {
I = obj;
}
CHECKOK(ok, I);
if (ok){
if(state < 0)
state = I->NState;
if(I->NState <= state) {
VLACheck(I->State, ObjectMeshState, state);
CHECKOK(ok, I->State);
if (ok)
I->NState = state + 1;
}
}
if (ok){
ms = I->State + state;
ObjectMeshStateInit(G, ms);
}
if (ok){
strcpy(ms->MapName, map->Obj.Name);
ms->MapState = map_state;
oms = ObjectMapGetState(map, map_state);
ms->Level = level;
ms->AltLevel = alt_level;
ms->MeshMode = meshMode;
ms->quiet = quiet;
}
if(ok && oms) {
if((meshMode == 3) && (ms->AltLevel < ms->Level)) {
/* gradient object -- need to auto-set range */
if(!ObjectMapStateGetDataRange(G, oms, &ms->Level, &ms->AltLevel)) {
ms->Level = -1.0F;
ms->AltLevel = 1.0F;
}
}
copy3f(mn, ms->ExtentMin); /* this is not exactly correct...should actually take vertex points from range */
copy3f(mx, ms->ExtentMax);
if(oms->State.Matrix) {
ok &= ObjectStateSetMatrix(&ms->State, oms->State.Matrix);
} else if(ms->State.Matrix) {
ObjectStateResetMatrix(&ms->State);
}
if (ok) {
float *min_ext, *max_ext;
float tmp_min[3], tmp_max[3];
if(MatrixInvTransformExtentsR44d3f(ms->State.Matrix,
ms->ExtentMin, ms->ExtentMax,
tmp_min, tmp_max)) {
min_ext = tmp_min;
max_ext = tmp_max;
} else {
min_ext = ms->ExtentMin;
max_ext = ms->ExtentMax;
}
if(sym) {
int eff_range[6];
if(IsosurfGetRange
(G, oms->Field, oms->Symmetry->Crystal, min_ext, max_ext, eff_range, false)) {
int fdim[3];
int expand_result;
/* need to generate symmetry-expanded temporary map */
ms->Crystal = *(oms->Symmetry->Crystal);
fdim[0] = eff_range[3] - eff_range[0];
fdim[1] = eff_range[4] - eff_range[1];
fdim[2] = eff_range[5] - eff_range[2];
ms->Field = IsosurfFieldAlloc(I->Obj.G, fdim);
expand_result =
IsosurfExpand(oms->Field, ms->Field, oms->Symmetry->Crystal, sym, eff_range);
if(expand_result == 0) {
ok = false;
if(!quiet) {
PRINTFB(G, FB_ObjectMesh, FB_Warnings)
" ObjectMesh-Warning: no symmetry expanded map points found.\n" ENDFB(G);
}
} else {
if(!quiet) {
PRINTFB(G, FB_ObjectMesh, FB_Warnings)
" ObjectMesh-Warning: not all symmetry expanded points covered by map.\n"
ENDFB(G);
}
}
ms->Range[0] = 0;
ms->Range[1] = 0;
ms->Range[2] = 0;
ms->Range[3] = fdim[0];
ms->Range[4] = fdim[1];
ms->Range[5] = fdim[2];
} else {
/* mesh entirely contained within bounds of current map */
int a;
for(a = 0; a < 6; a++) {
ms->Range[a] = eff_range[a];
}
}
} else {
IsosurfGetRange(G, oms->Field, oms->Symmetry->Crystal, min_ext, max_ext, ms->Range, true);
}
}
ms->ExtentFlag = true;
}
if(ok) {
if(carve != 0.0) {
ms->CarveFlag = true;
ms->CarveBuffer = carve;
ms->AtomVertex = vert_vla;
}
if(I) {
ObjectMeshRecomputeExtent(I);
}
I->Obj.ExtentFlag = true;
/* printf("Brick %d %d %d %d %d %d\n",I->Range[0],I->Range[1],I->Range[2],I->Range[3],I->Range[4],I->Range[5]); */
}
if(!ok && created) {
ObjectMeshFree(I);
I = NULL;
}
SceneChanged(G);
SceneCountFrames(G);
return (I);
}
/*========================================================================*/
ObjectMesh *ObjectMeshFromBox(PyMOLGlobals * G, ObjectMesh * obj, ObjectMap * map,
int map_state,
int state, float *mn, float *mx,
float level, int meshMode,
float carve, float *vert_vla, float alt_level, int quiet)
{
return ObjectMeshFromXtalSym(G, obj, map, NULL, map_state, state, mn, mx,
level, meshMode, carve, vert_vla, alt_level, quiet);
}
/*========================================================================*/
void ObjectMeshRecomputeExtent(ObjectMesh * I)
{
int extent_flag = false;
int a;
ObjectMeshState *ms;
for(a = 0; a < I->NState; a++) {
ms = I->State + a;
if(ms->Active) {
if(ms->ExtentFlag) {
if(!extent_flag) {
extent_flag = true;
copy3f(ms->ExtentMax, I->Obj.ExtentMax);
copy3f(ms->ExtentMin, I->Obj.ExtentMin);
} else {
max3f(ms->ExtentMax, I->Obj.ExtentMax, I->Obj.ExtentMax);
min3f(ms->ExtentMin, I->Obj.ExtentMin, I->Obj.ExtentMin);
}
}
}
}
I->Obj.ExtentFlag = extent_flag;
if(I->Obj.TTTFlag && I->Obj.ExtentFlag) {
const float *ttt;
double tttd[16];
if(ObjectGetTTT(&I->Obj, &ttt, -1)) {
convertTTTfR44d(ttt, tttd);
MatrixTransformExtentsR44d3f(tttd,
I->Obj.ExtentMin, I->Obj.ExtentMax,
I->Obj.ExtentMin, I->Obj.ExtentMax);
}
}
}
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