
/* 
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"Err.h"
#include"ObjectMesh.h"
#include"Base.h"
#include"MemoryDebug.h"
#include"CarveHelper.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"ObjectCGO.h"
#include "Feedback.h"

static 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(static_cast<int>(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->G, I->Field.get()));
  } else {
    PyList_SetItem(result, 16, PConvAutoNone(NULL));
  }
  return (PConvAutoNone(result));
}

static int ObjectMeshStateMapExists(ObjectMesh *I, ObjectMeshState *ms){
  return ExecutiveFindObjectMapByName(I->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 {
      *I = ObjectMeshState(G);
      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 = PConvFromPyListItem(G, 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 {
          I->Field.reset(IsosurfNewFromPyList(G, tmp));
          ok = I->Field != nullptr;
        }
	CPythonVal_Free(tmp);
      }
    }
  }
  return (ok);
}

static int ObjectMeshAllStatesFromPyList(ObjectMesh * I, PyObject * list)
{

  int ok = true;
  int a;
  VecCheckEmplace(I->State, I->NState, I->G);
  if(ok)
    ok = PyList_Check(list);
  if(ok) {
    for(a = 0; a < I->NState; a++) {
      auto *el = PyList_GetItem(list, a);
      ok = ObjectMeshStateFromPyList(I->G, &I->State[a], el);
      if(!ok)
        break;
    }
  }
  return (ok);
}

int ObjectMeshNewFromPyList(PyMOLGlobals * G, PyObject * list, ObjectMesh ** result)
{
  int ok = true;
  ObjectMesh *I = NULL;
  (*result) = NULL;

  if(ok)
    ok = (list != NULL);
  if(ok)
    ok = PyList_Check(list);
  /* TO SUPPORT BACKWARDS COMPATIBILITY...
     Always check ll when adding new PyList_GetItem's */

  I = new ObjectMesh(G);
  CHECKOK(ok, I);

  if(ok)
    ok = ObjectFromPyList(G, PyList_GetItem(list, 0), I);
  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 {
    DeleteP(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));
    PyList_SetItem(result, 1, PyInt_FromLong(I->NState));
    PyList_SetItem(result, 2, ObjectMeshAllStatesAsPyList(I));
  } else {
    /* save ObjectMesh as ObjectCGO */
    ObjectCGO *retObjectCGO = new ObjectCGO(I->G);
    ObjectCopyHeader(retObjectCGO, I);
    retObjectCGO->type = cObjectCGO;

    int a;
    PRINTFB(I->G, FB_ObjectMesh, FB_Errors)
      "ObjectMesh-Warning: map has been deleted, saving as CGO.\n"
      ENDFB(I->G);
    for(a = 0; a < I->NState; a++) {
      CGO *cgo = ObjectMeshRenderImpl(I, 0, 1, a);
      retObjectCGO = ObjectCGOFromCGO(I->G, retObjectCGO, cgo, a);
      
    }
    ObjectSetRepVisMask(retObjectCGO, cRepCGOBit, cVis_AS);
    result = ObjectCGOAsPyList(retObjectCGO);
    DeleteP(retObjectCGO);
  }
  return (PConvAutoNone(result));
}

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);
        I->invalidate(cRepAll, cRepInvAll, a);
        result = true;
      }
    }
  }
  return result;
}

void ObjectMeshDump(ObjectMesh * I, const char *fname, int state, int quiet)
{
  float *v;
  int *n;
  int c;
  FILE *f;
  f = fopen(fname, "wb");
  if(!f) {
    ErrMessage(I->G, "ObjectMeshDump", "can't open file for writing");
  }
  else {
    if(state < I->NState) {
      n = I->State[state].N.data();
      v = I->State[state].V.data();
      if(n && v)
        while(*n) {
          c = *(n++);
          if(I->State[state].MeshMode == cIsomeshMode::isomesh) {
            fprintf(f, "\n");
          }
          while(c--) {
            fprintf(f, "%10.4f%10.4f%10.4f\n", v[0], v[1], v[2]);
            v += 3;
          }
        }
    }
    fclose(f);
    if (!quiet) {
      PRINTFB(I->G, FB_ObjectMesh, FB_Actions)
        " ObjectMeshDump: %s written to %s\n", I->Name, fname ENDFB(I->G);
    }
  }
}

void ObjectMesh::invalidate(cRep_t rep, cRepInv_t level, int state)
{
  auto I = this;
  if(level >= cRepInvExtents) {
    I->ExtentFlag = false;
  }
  if((rep == cRepMesh) || (rep == cRepAll) || (rep == cRepCell)) {

    for(StateIterator iter(I->G, NULL, state, I->NState); iter.next();) {
      ObjectMeshState *ms = &I->State[iter.state];

      ms->shaderCGO.reset();
      ms->shaderUnitCellCGO.reset();

      ms->RefreshFlag = true;
      if(level >= cRepInvAll) {
        ms->ResurfaceFlag = true;
        SceneChanged(I->G);
      } else if(level >= cRepInvColor) {
        ms->RecolorFlag = true;
        SceneChanged(I->G);
      } else {
        SceneInvalidate(I->G);
      }
    }
  }
}

pymol::Result<float> ObjectMeshGetLevel(ObjectMesh * I, int state)
{
  if(state >= I->NState) {
    return pymol::make_error("Invalid Mesh state");
  } else {
    if(state < 0) {
      state = 0;
    }
    auto ms = &I->State[state];
    if(ms->Active) {
      return ms->Level;
    } else {
      return pymol::make_error("Invalid Mesh state");
    }
  }
}

int ObjectMeshSetLevel(ObjectMesh * I, float level, int state, int quiet)
{
  int ok = true;
  if(state >= I->NState) {
    ok = false;
  } else {
    for(StateIterator iter(I->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 == cIsomeshMode::isomesh) {
    cur_color = SettingGet_color(I->G, I->Setting.get(), NULL, cSetting_mesh_color);
  } else if(ms->MeshMode == cIsomeshMode::isodot) {
    cur_color = SettingGet_color(I->G, I->Setting.get(), NULL, cSetting_dot_color);
  }

  if(cur_color == -1)
    cur_color = I->Color;

  if(ColorCheckRamped(I->G, cur_color))
    one_color_flag = false;

  ms->OneColor = cur_color;
  if(ms->V) {
    int ramped_flag = false;
    float *v = ms->V.data();
    float *vc;
    int *rc;
    int a;
    int state = ms - I->State.data();
    int n_vert = VLAGetSize(ms->V) / 3;
    int base_n_vert = ms->base_n_V / 3;

    if(!ms->VC.empty() && (ms->VCsize < n_vert)) {
      ms->VC.clear();
      ms->RC.clear();
    }

    if(ms->VC.empty()) {
      ms->VCsize = n_vert;
      ms->VC = std::vector<float>(n_vert * 3);
    }
    if(ms->RC.empty()) {
      ms->RC = std::vector<int>(n_vert);
    }
    rc = ms->RC.data();
    vc = ms->VC.data();
    if(vc) {
      for(a = 0; a < n_vert; a++) {
        if(a == base_n_vert) {
          int new_color = SettingGet_color(I->G, I->Setting.get(),
                                           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->G, cur_color)) {
          ColorGetRamped(I->G, cur_color, v, vc, state);
          *rc = cur_color;
          ramped_flag = true;
        } else {
          const float *col = ColorGet(I->G, cur_color);
          copy3f(col, vc);
        }
        rc++;
        vc += 3;
        v += 3;
      }
    }

    if(one_color_flag && (!ramped_flag)) {
      ms->VC.clear();
      ms->RC.clear();
    } else if((!ramped_flag)
              ||
              (!SettingGet_b(I->G, NULL, I->Setting.get(), cSetting_ray_color_ramps))) {
      ms->RC.clear();
    }
  }
}

void ObjectMesh::update()
{
  auto I = this;
  int a;
  int c;
  ObjectMeshState *ms;
  ObjectMapState *oms = NULL;
  ObjectMap *map = NULL;

  int *n;
  float *v;
  int n_cur;
  int n_seg;
  int n_line;
  int flag;
  int last_flag = 0;
  int mesh_skip = SettingGet_i(G, I->Setting.get(), NULL, cSetting_mesh_skip);

  for(a = 0; a < I->NState; a++) {
    ms = &I->State[a];
    if(ms->Active) {

      map = ExecutiveFindObjectMapByName(I->G, ms->MapName);
      if(!map) {
        PRINTFB(I->G, FB_ObjectMesh, FB_Errors)
          "ObjectMeshUpdate-Error: map '%s' has been deleted.\n", ms->MapName
          ENDFB(I->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->visRep & cRepCellBit)) {
            ms->UnitCellCGO.reset(CrystalGetUnitCellCGO(&ms->Crystal));
          }

          if(!oms->Matrix.empty()) {
            ObjectStateSetMatrix(ms, oms->Matrix.data());
          } else if(!ms->Matrix.empty()) {
            ObjectStateResetMatrix(ms);
          }
          ms->RefreshFlag = false;
        }
      }

      if(map && oms && ms->N && ms->V && (I->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->Name ENDFB(G);
          }
          if(ms->Field) {
            field = ms->Field.get();
          } else if(oms->Field) {
            field = oms->Field.get();
          }

          if(field) {
            {
              float *min_ext, *max_ext;
              float tmp_min[3], tmp_max[3];
              if(MatrixInvTransformExtentsR44d3f(ms->Matrix.data(),
                                                 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->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->G, I->Setting.get(), NULL,
                          field,
                          ms->Level,
                          ms->N, ms->V,
                          ms->Range, ms->MeshMode, mesh_skip, ms->AltLevel);

            if(!SettingGet_b
               (I->G, I->Setting.get(), NULL, cSetting_mesh_negative_visible)) {
              ms->base_n_V = VLAGetSize(ms->V);
            } else if(ms->MeshMode != cIsomeshMode::gradient) {
              /* do we want the negative surface too? */

              pymol::vla<int> N2(10000);
              pymol::vla<float> V2(10000);

              IsosurfVolume(I->G, I->Setting.get(), 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.data()) + (sizeof(float) * base_n_V),
                       V2, sizeof(float) * addl_n_V);

                /* copy strip counts */

                memcpy(((char *) ms->N.data()) + (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->Matrix.empty() && VLAGetSize(ms->N) && VLAGetSize(ms->V)) {
              int count;
              /* take map coordinates back to view coordinates if necessary */
              v = ms->V.data();
              count = VLAGetSize(ms->V) / 3;
              while(count--) {
                transform44d3f(ms->Matrix.data(), v, v);
                v += 3;
              }
            }

          }
          if(ms->CarveFlag && ms->AtomVertex && VLAGetSize(ms->N) && VLAGetSize(ms->V)) {
            /* cull my friend, cull */
            auto carvehelper = CarveHelper(G, ms->CarveBuffer, ms->AtomVertex,
                VLAGetSize(ms->AtomVertex) / 3);
            {
              pymol::vla<int> old_n = std::move(ms->N);
              pymol::vla<float> old_v = std::move(ms->V);
              ms->N = pymol::vla<int>(old_n.size());
              ms->V = pymol::vla<float>(old_v.size());

              n = old_n.data();
              v = old_v.data();
              n_cur = 0;
              n_seg = 0;
              n_line = 0;
              while(*n) {
                last_flag = false;
                c = *(n++);
                while(c--) {
                  flag = !carvehelper.is_excluded(v);
                  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 (v - old_v.data() == ms->base_n_V) {
                    ms->base_n_V = n_line * 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;
            }
          }
        }
        if(ms->RecolorFlag) {
          ObjectMeshStateUpdateColors(I, ms);
          ms->RecolorFlag = false;
        }
      }

      ms->shaderCGO.reset();
      ms->shaderUnitCellCGO.reset();
    }
    SceneInvalidate(I->G);
  }
  if(!I->ExtentFlag) {
    ObjectMeshRecomputeExtent(I);
    if(I->ExtentFlag)
      SceneInvalidate(I->G);
  }
}


void ObjectMesh::render(RenderInfo * info)
{
  ObjectMeshRenderImpl(this, info, false, 0);
}

static short ObjectMeshStateRenderShader(ObjectMeshState *ms, ObjectMesh *I,
    RenderInfo *info, short mesh_as_cylinders, float mesh_width)
{
  PyMOLGlobals *G = I->G;
  CShaderPrg *shaderPrg = nullptr;

  if (!mesh_as_cylinders) {
    shaderPrg = G->ShaderMgr->Enable_DefaultShader(info->pass);
    shaderPrg->SetLightingEnabled(0);
    shaderPrg->Set1i("two_sided_lighting_enabled",
		     SceneGetTwoSidedLighting(G));
  }

  CGORender(ms->shaderCGO.get(), NULL, NULL, NULL, info, NULL);

  if (shaderPrg) {
    shaderPrg->Disable();
  }

  if (ms->shaderUnitCellCGO){
    shaderPrg = G->ShaderMgr->Enable_DefaultShader(info->pass);
    shaderPrg->SetLightingEnabled(0);
    CGORender(ms->shaderUnitCellCGO.get(), NULL, NULL, NULL, info, NULL);
    shaderPrg->Disable();
  }

  return true;
}

static CGO *ObjectMeshRenderImpl(ObjectMesh * I, RenderInfo * info, int returnCGO, int stateArg)
{
  PyMOLGlobals *G = I->G;
  float *v = NULL;
  float *vc;
  int *rc;
  float radius;
  int state = 0;
  CRay *ray = 0;
  bool pick = false;
  RenderPass pass = RenderPass::Antialias;
  int *n = NULL;
  int c;
  float line_width, mesh_width = SettingGet_f(I->G, I->Setting.get(), 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, info);

  for(StateIterator iter(I->G, I->Setting.get(), state, I->NState); iter.next();) {
    ms = &I->State[iter.state];

    if(!ms->Active || !ms->V || !ms->N)
      continue;

    auto transparency =
        SettingGet<float>(G, I->Setting.get(), nullptr, cSetting_transparency);

    {
        v = ms->V.data();
        n = ms->N.data();
        if(ok && ray) {
          if(ms->UnitCellCGO && (I->visRep & cRepCellBit)){
            ok &= CGORenderRay(ms->UnitCellCGO.get(), ray, info, ColorGet(I->G, I->Color),
			       NULL, I->Setting.get(), NULL);
	    if (!ok){
	      ms->UnitCellCGO.reset();
	      break;
	    }
	  }
          if(ms->MeshMode != cIsomeshMode::isodot) {
            radius = SettingGet_f(I->G, I->Setting.get(), NULL, cSetting_mesh_radius);

            if(radius == 0.0F) {
              radius = ray->PixelRadius * line_width / 2.0F;
            }
          } else {
            radius = SettingGet_f(I->G, I->Setting.get(), NULL, cSetting_dot_radius);
            if(radius == 0.0F) {
              radius =
                ray->PixelRadius * SettingGet_f(I->G, I->Setting.get(), NULL,
                                                cSetting_dot_width) / 1.4142F;
            }
          }

          if(ok && n && v && (I->visRep & cRepMeshBit)) {
            float cc[3];
            float colA[3], colB[3];
            ColorGetEncoded(G, ms->OneColor, cc);
            vc = ms->VC.data();
            rc = ms->RC.data();

            ray->transparentf(transparency);

            if(ms->MeshMode == cIsomeshMode::isodot) {
              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 == RenderPass::Antialias) {
	      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 != cIsomeshMode::isodot;

	      if (ms->shaderCGO && (!use_shader || (mesh_as_cylinders ^ ms->shaderCGO->has_draw_cylinder_buffers))){
            ms->shaderCGO.reset();
            ms->shaderUnitCellCGO.reset();
	      }

	      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;
                CGOAlpha(shaderCGO, 1.f - transparency);
	      }

	      if(ms->UnitCellCGO && (I->visRep & cRepCellBit)) {
		const float *color = ColorGet(I->G, I->Color);
		if (!use_shader) {
		  CGORender(ms->UnitCellCGO.get(), color, I->Setting.get(), NULL, info, NULL);
		} else if(!ms->shaderUnitCellCGO) {
		  CGO *newUnitCellCGO = CGONewSized(G, 0);
		  CGOColorv(newUnitCellCGO, color);
		  CGOAppend(newUnitCellCGO, ms->UnitCellCGO.get());
                  ms->shaderUnitCellCGO.reset(
                      CGOOptimizeToVBONotIndexedNoShader(newUnitCellCGO));
                  CGOFree(newUnitCellCGO);
		  ms->shaderUnitCellCGO->use_shader = true;
		}
	      }

	      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, true);
	      } else {
		SceneResetNormal(I->G, false);
	      }
	      if(n && v && (I->visRep & cRepMeshBit)) {
		if(use_shader) {
		  vc = ms->VC.data();

		  if(!vc)
		    ok &= CGOColorv(shaderCGO, ColorGet(I->G, ms->OneColor));

		  if (!mesh_as_cylinders){
		    if(ms->MeshMode == cIsomeshMode::isodot){
		      ok &= CGODotwidth(shaderCGO, SettingGet_f
				  (I->G, I->Setting.get(), NULL, cSetting_dot_width));
		    } else {
		      ok &= CGOSpecial(shaderCGO, LINEWIDTH_DYNAMIC_MESH); 
		    }
		  } 

		  if(!ok) break;

		  if (mesh_as_cylinders){
		    if(returnCGO) {
		      ok &= CGOSpecial(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 &= (bool)shaderCGO->add<cgo::draw::shadercylinder2ndcolor>(shaderCGO, v, axis, 1.f, 15, vc);
                        } else {
                          ok &= (bool)shaderCGO->add<cgo::draw::shadercylinder>(v, axis, 1.f, 15);
                        }
                      }
		    }
		  } else {
		    while(ok && *n) {
		      c = *(n++);
		      if(ms->MeshMode == cIsomeshMode::isodot)
			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 {
#ifndef PURE_OPENGL_ES_2
		  vc = ms->VC.data();

		  if(!vc)
		    glColor3fv(ColorGet(I->G, ms->OneColor));
		  if(ms->MeshMode == cIsomeshMode::isodot){
		    glPointSize(SettingGet_f
				(I->G, I->Setting.get(), NULL, cSetting_dot_width));
		  } else {
		    glLineWidth(line_width);
		  }
		  while(*n) {
		    c = *(n++);
		    if(ms->MeshMode == cIsomeshMode::isodot)
		      glBegin(GL_POINTS);
		    else
		      glBegin(GL_LINE_STRIP);
		    while(c--) {
		      if(vc) {
			glColor3fv(vc);
			vc += 3;
		      }
		      glVertex3fv(v);
		      v += 3;
		    }
		    glEnd();
		  }
#endif
		}
	      }
	      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.reset(shaderCGO);
		  }
		  if (ok){
		    if (mesh_as_cylinders){
                      CGO *tmpCGO = CGONew(G);
                      ok &= CGOEnable(tmpCGO, GL_CYLINDER_SHADER);
                      if (ok) ok &= CGOSpecial(tmpCGO, MESH_WIDTH_FOR_SURFACES);
                      convertcgo = CGOConvertShaderCylindersToCylinderShader(ms->shaderCGO.get(), tmpCGO);
                      if (ok) ok &= CGOAppendNoStop(tmpCGO, convertcgo);
                      if (ok) ok &= CGODisable(tmpCGO, GL_CYLINDER_SHADER);
                      if (ok) ok &= CGOStop(tmpCGO);
                      CGOFreeWithoutVBOs(convertcgo);
                      convertcgo = tmpCGO;
                      convertcgo->use_shader = convertcgo->has_draw_cylinder_buffers = true;
		    } else {
		      convertcgo = CGOOptimizeToVBONotIndexedWithReturnedData(ms->shaderCGO.get(), 0, false, NULL);
		    }
		    CHECKOK(ok, convertcgo);
		  }
		  if (convertcgo){
		    ms->shaderCGO.reset(convertcgo);
		  }
		}
		
		if(!ok) break;

                ok &= ObjectMeshStateRenderShader(ms, I, info, mesh_as_cylinders, mesh_width);
	      }
	  }
	}
    }
  }
  if (!ok){
    I->invalidate(cRepMesh, cRepInvPurge, -1);
    I->invalidate(cRepCGO, cRepInvPurge, -1);
    ObjectSetRepVisMask(I, 0, cVis_AS);
  }

  return NULL;
}


/*========================================================================*/

int ObjectMesh::getNFrame() const
{
  return NState;
}


/*========================================================================*/
ObjectMesh::ObjectMesh(PyMOLGlobals * G) : pymol::CObject(G)
{
  auto I = this;
  I->type = cObjectMesh;
}


/*========================================================================*/
ObjectMeshState::ObjectMeshState(PyMOLGlobals* G)
    : CObjectState(G)
    , Crystal(G)
{
  V = pymol::vla<float>(10000);
  N = pymol::vla<int>(10000);
}

/*========================================================================*/
ObjectMesh *ObjectMeshFromXtalSym(PyMOLGlobals * G, ObjectMesh * obj, ObjectMap * map,
                                  CSymmetry * sym,
                                  int map_state,
                                  int state, float *mn, float *mx,
                                  float level, cIsomeshMode 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 = new ObjectMesh(G);
  } else {
    I = obj;
  }
  CHECKOK(ok, I);

  if (ok){
    if(state < 0)
      state = I->NState;
    if(I->NState <= state) {
      VecCheckEmplace(I->State, state, G);
      if (ok)
	I->NState = state + 1;
    }
  }

  if (ok){
    ms = &I->State[state];
    *ms = ObjectMeshState(G);
  }

  if (ok){
    strcpy(ms->MapName, map->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 == cIsomeshMode::gradient) && (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->Matrix.empty()) {
      ok &= ObjectStateSetMatrix(ms, oms->Matrix.data());
    } else if(!ms->Matrix.empty()) {
      ObjectStateResetMatrix(ms);
    }

    if (ok) {
      float *min_ext, *max_ext;
      float tmp_min[3], tmp_max[3];
      if(MatrixInvTransformExtentsR44d3f(ms->Matrix.data(),
                                         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.get(), &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 = pymol::make_copyable<Isofield>(I->G, fdim);

          expand_result =
            IsosurfExpand(oms->Field.get(), ms->Field.get(), &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.get(), &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 = pymol::vla_take_ownership(vert_vla);
    }
    if(I) {
      ObjectMeshRecomputeExtent(I);
    }
    I->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) {
    DeleteP(I);
  }
  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, cIsomeshMode 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->ExtentMax);
          copy3f(ms->ExtentMin, I->ExtentMin);
        } else {
          max3f(ms->ExtentMax, I->ExtentMax, I->ExtentMax);
          min3f(ms->ExtentMin, I->ExtentMin, I->ExtentMin);
        }
      }
    }
  }

  I->ExtentFlag = extent_flag;

  if(I->TTTFlag && I->ExtentFlag) {
    const float *ttt;
    double tttd[16];
    if(ObjectGetTTT(I, &ttt, -1)) {
      convertTTTfR44d(ttt, tttd);
      MatrixTransformExtentsR44d3f(tttd,
                                   I->ExtentMin, I->ExtentMax,
                                   I->ExtentMin, I->ExtentMax);
    }
  }
}

pymol::CObject* ObjectMesh::clone() const
{
  return new ObjectMesh(*this);
}

