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RepMesh.c

/* 
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_predef.h"
#include"os_std.h"
#include"os_gl.h"

#include"Base.h"
#include"MemoryDebug.h"
#include"OOMac.h"
#include"RepMesh.h"
#include"Map.h"
#include"Isosurf.h"
#include"Scene.h"
#include"Sphere.h"
#include"Setting.h"
#include"Color.h"
#include"main.h"
#include"PyMOLGlobals.h"
#include"Selector.h"

typedef struct RepMesh {
  Rep R;
  int *N;
  int NTot;
  float *V, *VC;
  int NDot;
  float *Dot;
  float Radius, Width;
  int oneColorFlag;
  int oneColor;
  int *LastVisib;
  int *LastColor;
  float max_vdw;
  int mesh_type;
} RepMesh;

#include"ObjectMolecule.h"

void RepMeshFree(RepMesh * I);
void RepMeshColor(RepMesh * I, CoordSet * cs);
int RepMeshSameVis(RepMesh * I, CoordSet * cs);

void RepMeshInit(void)
{
}

void RepMeshFree(RepMesh * I)
{
  FreeP(I->VC);
  VLAFreeP(I->V);
  VLAFreeP(I->N);
  FreeP(I->LastColor);
  FreeP(I->LastVisib);
  OOFreeP(I);
}

int RepMeshGetSolventDots(RepMesh * I, CoordSet * cs, float *min, float *max,
                          float probe_radius);

static void RepMeshRender(RepMesh * I, RenderInfo * info)
{
  CRay *ray = info->ray;
  Picking **pick = info->pick;
  PyMOLGlobals *G = I->R.G;
  float *v = I->V;
  float *vc = I->VC;
  int *n = I->N;
  int c;
  float *col = NULL;
  float line_width = SceneGetDynamicLineWidth(info, I->Width);

  if(ray) {
    if(n) {
      float radius;

      if(I->Radius <= 0.0F) {
        radius = ray->PixelRadius * line_width / 2.0F;
      } else {
        radius = I->Radius;
      }
      /* looks like were missing some code here --

         what about mesh_type?

       */

      if(I->oneColorFlag)
        col = ColorGet(G, I->oneColor);
      ray->fColor3fv(ray, ColorGet(G, I->R.obj->Color));
      switch (I->mesh_type) {
      case 0:
        while(*n) {
          c = *(n++);
          if(c--) {
            vc += 3;
            v += 3;
            if(I->oneColorFlag) {
              while(c--) {
                ray->fSausage3fv(ray, v - 3, v, radius, col, col);
                v += 3;
                vc += 3;
              }
            } else {
              while(c--) {
                ray->fSausage3fv(ray, v - 3, v, radius, vc - 3, vc);
                v += 3;
                vc += 3;
              }
            }
          }
        }
      case 1:
        while(*n) {
          c = *(n++);
          if(I->oneColorFlag) {
            ray->fColor3fv(ray, col);
            while(c--) {
              ray->fSphere3fv(ray, v, radius);
              v += 3;
              vc += 3;
            }
          } else {
            while(c--) {
              ray->fColor3fv(ray, vc);
              ray->fSphere3fv(ray, v, radius);
              v += 3;
              vc += 3;
            }
          }
        }
        break;
      }
    }
  } else if(G->HaveGUI && G->ValidContext) {
    if(pick) {
    } else {
      int use_dlst;
      int lighting =
        SettingGet_i(G, I->R.cs->Setting, I->R.obj->Setting, cSetting_mesh_lighting);

      SceneResetNormal(G, true);
      if(!lighting) {
        if(!info->line_lighting)
          glDisable(GL_LIGHTING);
      }
      switch (I->mesh_type) {
      case 0:
        if(info->width_scale_flag)
          glLineWidth(line_width * info->width_scale);
        else
          glLineWidth(line_width);
        break;
      case 1:
        if(info->width_scale_flag)
          glPointSize(SettingGet_f
                      (G, I->R.cs->Setting, I->R.obj->Setting,
                       cSetting_dot_width) * info->width_scale);
        else
          glPointSize(SettingGet_f
                      (G, I->R.cs->Setting, I->R.obj->Setting, cSetting_dot_width));
        break;
      }
      use_dlst = (int) SettingGet(G, cSetting_use_display_lists);

      if(use_dlst && I->R.displayList && I->R.displayListInvalid) {
        glDeleteLists(I->R.displayList, 1);
        I->R.displayList = 0;
        I->R.displayListInvalid = false;
      }

      if(use_dlst && I->R.displayList) {
        glCallList(I->R.displayList);
      } else {
        SceneResetNormal(G, false);

        if(use_dlst) {
          if(!I->R.displayList) {
            I->R.displayList = glGenLists(1);
            if(I->R.displayList) {
              glNewList(I->R.displayList, GL_COMPILE_AND_EXECUTE);
            }
          }
        }

        switch (I->mesh_type) {
        case 0:
          if(n) {
            if(I->oneColorFlag) {
              while(*n) {
                glColor3fv(ColorGet(G, I->oneColor));
                c = *(n++);
                glBegin(GL_LINE_STRIP);
                while(c--) {
                  glVertex3fv(v);
                  v += 3;
                }
                glEnd();
              }
            } else {
              while(*n) {
                c = *(n++);
                glBegin(GL_LINE_STRIP);
                while(c--) {
                  glColor3fv(vc);
                  vc += 3;
                  glVertex3fv(v);
                  v += 3;
                }
                glEnd();
              }
            }
          }
          break;
        case 1:
          glPointSize(SettingGet_f
                      (G, I->R.cs->Setting, I->R.obj->Setting, cSetting_dot_width));
          if(n) {
            if(I->oneColorFlag) {
              while(*n) {
                glColor3fv(ColorGet(G, I->oneColor));
                c = *(n++);
                glBegin(GL_POINTS);
                while(c--) {
                  glVertex3fv(v);
                  v += 3;
                }
                glEnd();
              }
            } else {
              while(*n) {
                c = *(n++);
                glBegin(GL_POINTS);
                while(c--) {
                  glColor3fv(vc);
                  vc += 3;
                  glVertex3fv(v);
                  v += 3;
                }
                glEnd();
              }
            }
          }
          break;
        }
        if(use_dlst && I->R.displayList) {
          glEndList();
        }
      }
      if(!lighting)
        glEnable(GL_LIGHTING);
    }
  }
}

int RepMeshSameVis(RepMesh * I, CoordSet * cs)
{
  int same = true;
  int *lv, *lc, *cc;
  int a;
  AtomInfoType *ai;

  ai = cs->Obj->AtomInfo;
  lv = I->LastVisib;
  lc = I->LastColor;
  cc = cs->Color;

  for(a = 0; a < cs->NIndex; a++) {
    if(*(lv++) != (ai + cs->IdxToAtm[a])->visRep[cRepMesh]) {
      same = false;
      break;
    }
    if(*(lc++) != *(cc++)) {
      same = false;
      break;
    }
  }
  return (same);
}

void RepMeshColor(RepMesh * I, CoordSet * cs)
{
  PyMOLGlobals *G = cs->State.G;
  MapType *map;
  int a, i0, i, j, h, k, l, c1;
  float *v0, *vc, *c0;
  int *lv, *lc, *cc;
  int first_color;
  ObjectMolecule *obj;
  float probe_radius;
  float dist, minDist;
  int inclH;
  int cullByFlag = false;
  int mesh_mode;
  int mesh_color;
  AtomInfoType *ai2;
  int state = I->R.context.state;

  obj = cs->Obj;

  probe_radius = SettingGet_f(G, cs->Setting, obj->Obj.Setting, cSetting_solvent_radius);
  mesh_color = SettingGet_color(G, cs->Setting, obj->Obj.Setting, cSetting_mesh_color);
  mesh_mode = SettingGet_i(G, cs->Setting, obj->Obj.Setting, cSetting_mesh_mode);
  cullByFlag = (mesh_mode == cRepMesh_by_flags);
  inclH = !(mesh_mode == cRepMesh_heavy_atoms);

  if(!I->LastVisib)
    I->LastVisib = Alloc(int, cs->NIndex);
  if(!I->LastColor)
    I->LastColor = Alloc(int, cs->NIndex);
  lv = I->LastVisib;
  lc = I->LastColor;
  cc = cs->Color;
  ai2 = obj->AtomInfo;
  for(a = 0; a < cs->NIndex; a++) {
    *(lv++) = (ai2 + cs->IdxToAtm[a])->visRep[cRepMesh];
    *(lc++) = *(cc++);
  }

  if(I->mesh_type != 1) {
    I->Width = SettingGet_f(G, cs->Setting, obj->Obj.Setting, cSetting_mesh_width);
    I->Radius = SettingGet_f(G, cs->Setting, obj->Obj.Setting, cSetting_mesh_radius);
  } else {
    I->Width = SettingGet_f(G, cs->Setting, obj->Obj.Setting, cSetting_dot_width);
    I->Radius = SettingGet_f(G, cs->Setting, obj->Obj.Setting, cSetting_dot_radius);
  }
  I->R.displayListInvalid = true;

  if(I->NTot) {
    obj = cs->Obj;
    if(ColorCheckRamped(G, mesh_color)) {
      I->oneColorFlag = false;
    } else {
      I->oneColorFlag = true;
    }
    first_color = -1;
    if(!I->VC)
      I->VC = Alloc(float, 3 * I->NTot);
    vc = I->VC;
    /* now, assign colors to each point */
    map = MapNew(G, I->max_vdw + probe_radius, cs->Coord, cs->NIndex, NULL);
    if(map) {
      MapSetupExpress(map);
      for(a = 0; a < I->NTot; a++) {
        AtomInfoType *ai0 = NULL;
        c1 = 1;
        minDist = MAXFLOAT;
        i0 = -1;
        v0 = I->V + 3 * a;
        MapLocus(map, v0, &h, &k, &l);

        i = *(MapEStart(map, h, k, l));
        if(i) {
          j = map->EList[i++];
          while(j >= 0) {
            ai2 = obj->AtomInfo + cs->IdxToAtm[j];
            if((inclH || (!ai2->hydrogen)) &&
               ((!cullByFlag) || (!(ai2->flags & cAtomFlag_ignore)))) {
              dist = (float) diff3f(v0, cs->Coord + j * 3) - ai2->vdw;
              if(dist < minDist) {
                i0 = j;
                ai0 = ai2;
                minDist = dist;
              }
            }
            j = map->EList[i++];
          }
        }

        if(i0 >= 0) {
          int at_mesh_color;

          AtomInfoGetSetting_color(G, ai0, cSetting_mesh_color,
                                   mesh_color, &at_mesh_color);

          if(at_mesh_color != -1) {
            c1 = at_mesh_color;
          } else {
            c1 = *(cs->Color + i0);
          }
          if(I->oneColorFlag) {
            if(first_color >= 0) {
              if(first_color != c1)
                I->oneColorFlag = false;
            } else
              first_color = c1;
          }
        }
        /*
           if(ColorCheckRamped(G,mesh_color)) {
           c1 = mesh_color;
           }
         */

        if(ColorCheckRamped(G, c1)) {
          I->oneColorFlag = false;
          ColorGetRamped(G, c1, v0, vc, state);
          vc += 3;
        } else {
          c0 = ColorGet(G, c1);
          *(vc++) = *(c0++);
          *(vc++) = *(c0++);
          *(vc++) = *(c0++);
        }
      }
      MapFree(map);
    }
    if(I->oneColorFlag) {
      I->oneColor = first_color;
    }
  }
  /*
     if(mesh_color>=0) {
     I->oneColorFlag=1;
     I->oneColor=mesh_color;
     }
   */

}

Rep *RepMeshNew(CoordSet * cs, int state)
{
  PyMOLGlobals *G = cs->State.G;
  ObjectMolecule *obj;
  CoordSet *ccs;
  int a, b, c, d, h, k, l, *n;
  MapType *map = NULL, *smap = NULL;
  /* grid */
  Vector3f minE, maxE, sizeE;
  float size;
  int dims[3];
  float gridSize;
  Isofield *field;
  Vector3f point;
  float vLen, pVal, vdw;
  int aNear;
  float aLen;
  int cur;
  int meshFlag = false;
  int inSolvFlag;
  float probe_radius, probe_radius2;
  float min_spacing;
  int visFlag;
  int mesh_mode;
  int cullByFlag;
  int inclH;
  int solv_acc;
  int mesh_type;
  int mesh_skip;
  int ok = true;

  AtomInfoType *ai1;

  OOAlloc(G, RepMesh);

  PRINTFD(G, FB_RepMesh)
  " RepMeshNew-DEBUG: entered with coord-set %p\n", (void *) cs ENDFD;
  obj = cs->Obj;
  I->R.context.object = (void *) obj;
  I->R.context.state = state;

  probe_radius = SettingGet_f(G, cs->Setting, obj->Obj.Setting, cSetting_solvent_radius);
  probe_radius2 = probe_radius * probe_radius;
  solv_acc = (SettingGet_i(G, cs->Setting, obj->Obj.Setting, cSetting_mesh_solvent));
  mesh_type = SettingGet_i(G, cs->Setting, obj->Obj.Setting, cSetting_mesh_type);
  mesh_skip = SettingGet_i(G, cs->Setting, obj->Obj.Setting, cSetting_mesh_skip);

  mesh_mode = SettingGet_i(G, cs->Setting, obj->Obj.Setting, cSetting_mesh_mode);
  cullByFlag = (mesh_mode == cRepMesh_by_flags);
  inclH = !(mesh_mode == cRepMesh_heavy_atoms);
  visFlag = false;
  if(obj->RepVisCache[cRepMesh])
    for(a = 0; a < cs->NIndex; a++) {
      ai1 = obj->AtomInfo + cs->IdxToAtm[a];
      if(ai1->visRep[cRepMesh] &&
         (inclH || (!ai1->hydrogen)) &&
         ((!cullByFlag) || (!(ai1->flags & (cAtomFlag_exfoliate | cAtomFlag_ignore))))) {
        visFlag = true;
        break;
      }
    }
  if(!visFlag) {
    OOFreeP(I);
    return (NULL);              /* skip if no dots are visible */
  }

  I->max_vdw = ObjectMoleculeGetMaxVDW(obj) + solv_acc * probe_radius;

  RepInit(G, &I->R);

  min_spacing = SettingGet_f(G, cs->Setting, obj->Obj.Setting, cSetting_min_mesh_spacing);

  I->N = NULL;
  I->NTot = 0;
  I->V = NULL;
  I->VC = NULL;
  I->NDot = 0;
  I->Dot = NULL;
  I->R.fRender = (void (*)(struct Rep *, RenderInfo *)) RepMeshRender;
  I->R.fFree = (void (*)(struct Rep *)) RepMeshFree;
  I->R.obj = (CObject *) cs->Obj;
  I->R.cs = cs;
  I->R.fRecolor = (void (*)(struct Rep *, struct CoordSet *)) RepMeshColor;
  I->R.fSameVis = (int (*)(struct Rep *, struct CoordSet *)) RepMeshSameVis;
  I->LastVisib = NULL;
  I->LastColor = NULL;
  I->mesh_type = mesh_type;
  I->Radius = SettingGet_f(G, cs->Setting, obj->Obj.Setting, cSetting_mesh_radius);

  meshFlag = true;

  if(meshFlag) {
    float trim_cutoff =
      SettingGet_f(G, cs->Setting, obj->Obj.Setting, cSetting_mesh_cutoff);
    int trim_flag = false;
    float *trim_vla = NULL;
    MapType *trim_map = NULL;

    int carve_state = 0;
    int carve_flag = false;
    float carve_cutoff =
      SettingGet_f(G, cs->Setting, obj->Obj.Setting, cSetting_mesh_carve_cutoff);
    char *carve_selection = NULL;
    float *carve_vla = NULL;
    MapType *carve_map = NULL;

    int clear_state = 0;
    int clear_flag = false;
    float clear_cutoff =
      SettingGet_f(G, cs->Setting, obj->Obj.Setting, cSetting_mesh_clear_cutoff);
    char *clear_selection = NULL;
    float *clear_vla = NULL;
    MapType *clear_map = NULL;

    int mesh_max = SettingGet_i(G, cs->Setting, obj->Obj.Setting, cSetting_mesh_grid_max);
    if(mesh_max < 1)
      mesh_max = 1;

    if(trim_cutoff < 0.0F) {
      trim_cutoff = I->max_vdw + probe_radius;
    }

    if(trim_cutoff > 0.0F) {
      int nc = 0;
      trim_vla = VLAlloc(float, cs->NIndex * 3);
      for(c = 0; c < cs->NIndex; c++) {
        ai1 = obj->AtomInfo + cs->IdxToAtm[c];
        if(ai1->visRep[cRepMesh] &&
           (inclH || (!ai1->hydrogen)) &&
           ((!cullByFlag) ||
            (!(ai1->flags & (cAtomFlag_ignore | cAtomFlag_exfoliate))))) {
          VLACheck(trim_vla, float, nc * 3 + 2);
          {
            float *src = cs->Coord + 3 * c;
            float *dst = trim_vla + 3 * nc;
            *(dst++) = *(src++);
            *(dst++) = *(src++);
            *(dst++) = *(src++);
            nc++;
          }
        }
      }
      if(nc) {
        trim_map = MapNew(G, trim_cutoff, trim_vla, nc, NULL);
        if(trim_map) {
          MapSetupExpress(trim_map);
          trim_flag = true;
        }
      }
    }

    if(carve_cutoff > 0.0F) {
      carve_state =
        SettingGet_i(G, cs->Setting, obj->Obj.Setting, cSetting_mesh_carve_state) - 1;
      carve_selection =
        SettingGet_s(G, cs->Setting, obj->Obj.Setting, cSetting_mesh_carve_selection);
      if(carve_selection)
        carve_map = SelectorGetSpacialMapFromSeleCoord(G,
                                                       SelectorIndexByName(G,
                                                                           carve_selection),
                                                       carve_state, carve_cutoff,
                                                       &carve_vla);
      if(carve_map) {
        MapSetupExpress(carve_map);
        carve_flag = true;
      }
    }
    if(clear_cutoff > 0.0F) {
      clear_state =
        SettingGet_i(G, cs->Setting, obj->Obj.Setting, cSetting_mesh_clear_state) - 1;
      clear_selection =
        SettingGet_s(G, cs->Setting, obj->Obj.Setting, cSetting_mesh_clear_selection);
      if(clear_selection)
        clear_map = SelectorGetSpacialMapFromSeleCoord(G,
                                                       SelectorIndexByName(G,
                                                                           clear_selection),
                                                       clear_state, clear_cutoff,
                                                       &clear_vla);
      if(clear_map) {
        MapSetupExpress(clear_map);
        clear_flag = true;
      }
    }

    I->V = VLAMalloc(1000, sizeof(float), 9, false);
    I->N = VLAMalloc(100, sizeof(int), 9, false);

    I->N[0] = 0;

    for(c = 0; c < 3; c++) {
      /*                  minE[c]=(cs->Obj->Obj.extent[2*c]-MAX_VDW)-0.25;
         maxE[c]=(cs->Obj->Obj.extent[2*c+1]+MAX_VDW)+0.25;
       */
      minE[c] = MAXFLOAT;
      maxE[c] = -(MAXFLOAT);
    }

    for(b = 0; b < obj->NCSet; b++) {
      ccs = obj->CSet[b];
      if(ccs) {
        for(c = 0; c < ccs->NIndex; c++) {
          ai1 = obj->AtomInfo + ccs->IdxToAtm[c];       /* WLD fixed 011218 */
          if(ai1->visRep[cRepMesh] &&
             (inclH || (!ai1->hydrogen)) &&
             ((!cullByFlag) ||
              (!(ai1->flags & (cAtomFlag_ignore | cAtomFlag_exfoliate))))) {
            for(d = 0; d < 3; d++) {
              if(minE[d] > ccs->Coord[(3 * c) + d])
                minE[d] = ccs->Coord[(3 * c) + d];
              if(maxE[d] < ccs->Coord[(3 * c) + d])
                maxE[d] = ccs->Coord[(3 * c) + d];
            }
          }
        }
      }
    }

    for(c = 0; c < 3; c++) {
      minE[c] -= (float) (I->max_vdw + 0.25F);
      maxE[c] += (float) (I->max_vdw + 0.25F);
    }

    subtract3f(maxE, minE, sizeE);

    size = sizeE[0];
    if(sizeE[1] > size)
      size = sizeE[1];
    if(sizeE[2] > size)
      size = sizeE[2];

    gridSize = size / mesh_max; /* grid size is the largest axis divided by 25 */

    if(gridSize < min_spacing)
      gridSize = min_spacing;

    for(c = 0; c < 3; c++)
      dims[c] = (int) ((sizeE[c] / gridSize) + 1.5F);

    field = IsosurfFieldAlloc(G, dims);

    for(a = 0; a < dims[0]; a++)
      for(b = 0; b < dims[1]; b++)
        for(c = 0; c < dims[2]; c++)
          F3(field->data, a, b, c) = 2.0;

    OrthoBusyFast(G, 0, 1);
    if(!solv_acc)
      ok = RepMeshGetSolventDots(I, cs, minE, maxE, probe_radius);
    if(ok) {
      smap = MapNew(G, probe_radius, I->Dot, I->NDot, NULL);
      map = MapNew(G, I->max_vdw + probe_radius, cs->Coord, cs->NIndex, NULL);
    }
    if(ok && map && smap) {
      MapSetupExpress(smap);
      MapSetupExpress(map);
      for(a = 0; a < dims[0]; a++) {
        OrthoBusyFast(G, dims[0] + a, dims[0] * 3);
        point[0] = minE[0] + a * gridSize;
        for(b = 0; b < dims[1]; b++) {
          point[1] = minE[1] + b * gridSize;
          for(c = 0; c < dims[2]; c++) {
            float bestDist;
            float dist2vdw;
            float vdw_add = solv_acc * probe_radius;
            point[2] = minE[2] + c * gridSize;
            copy3f(point, F3Ptr(field->points, a, b, c));
            aNear = -1;
            bestDist = MAXFLOAT;
            aLen = MAXFLOAT;
            MapLocus(map, point, &h, &k, &l);
            d = *(MapEStart(map, h, k, l));
            if(d) {
              cur = map->EList[d++];
              while(cur >= 0) {
                ai1 = obj->AtomInfo + cs->IdxToAtm[cur];
                if((inclH || (!ai1->hydrogen)) &&
                   ((!cullByFlag) || (!(ai1->flags & cAtomFlag_ignore)))) {
                  vLen = (float) diff3f(point, cs->Coord + (cur * 3));
                  dist2vdw = vLen - (ai1->vdw + vdw_add);
                  if(dist2vdw < bestDist) {
                    bestDist = dist2vdw;
                    aLen = vLen;
                    aNear = cur;
                  }
                }
                cur = map->EList[d++];
              }
            }
            if(aNear >= 0) {    /* near an atom... */
              pVal = aLen;      /* pVal is the distance from atom center */
              vdw = cs->Obj->AtomInfo[cs->IdxToAtm[aNear]].vdw + solv_acc * probe_radius;
              if((!solv_acc) && (pVal > vdw) && (pVal < (vdw + probe_radius))) {        /* point outside an atom */
                inSolvFlag = false;
                /* this point lies within a water radius of the atom, so
                   lets see if it is actually near a water */
                aLen = MAXFLOAT;

                MapLocus(smap, point, &h, &k, &l);
                d = *(MapEStart(smap, h, k, l));
                if(d) {
                  cur = smap->EList[d++];
                  while(cur >= 0) {
                    vLen = diffsq3f(point, I->Dot + (cur * 3));
                    if(vLen < probe_radius2) {  /* within a water radius */
                      inSolvFlag = true;
                      break;
                    } else if(vLen < aLen) {    /* not within water radius */
                      aLen = vLen;      /* but nearest distance anyway */
                    }
                    cur = smap->EList[d++];
                  }
                }
                aLen = (float) sqrt1f(aLen);
                if(inSolvFlag) {        /* point is inside a water, so a linear crossing point works fine */
                  pVal = pVal / vdw;
                } else {        /* point is not inside a water, so we need to guestimate a value depending
                                 * on where the point is */
                  if(aLen < (2 * probe_radius)) {
                    pVal = 1.05F * (2 * probe_radius - aLen) / probe_radius;
                    /* within a radius, so assign based on water surface, but error on the side of exclusion */

                  } else {
                    pVal = 0.0; /* further than one water away... */
                  }
                }
              } else {          /* either within atom or outside solvent shell */
                pVal = pVal / vdw;
              }
              if(pVal < F3(field->data, a, b, c))
                F3(field->data, a, b, c) = pVal;
            }
          }
        }
        if(G->Interrupt) {
          ok = false;
          break;
        }
      }
    }
    MapFree(smap);
    MapFree(map);
    FreeP(I->Dot);
    OrthoBusyFast(G, 2, 3);
    if(ok) {
      IsosurfVolume(G, NULL, NULL, field, 1.0, &I->N, &I->V, NULL, mesh_type, mesh_skip,
                    1.0F);
    }
    IsosurfFieldFree(G, field);
    if(I->N && I->V && (carve_flag || clear_flag || trim_flag)) {
      int cur_size = VLAGetSize(I->N);
      if((mesh_type == 0) && cur_size) {
        int *n = I->N;
        int *new_n = VLACalloc(int, cur_size);
        int new_size = 0;
        float *new_v = I->V;
        float *v = I->V;
        while((c = *(n++))) {
          int new_c = 0;
          float *last_v = NULL;
          while(c--) {
            int a_keeper = false;
            if(trim_map) {
              register int i = *(MapLocusEStart(trim_map, v));
              if(i) {
                register int j = trim_map->EList[i++];
                while(j >= 0) {
                  register float *v_targ = trim_vla + 3 * j;
                  if(within3f(v_targ, v, trim_cutoff)) {
                    a_keeper = true;
                    break;
                  }
                  j = trim_map->EList[i++];
                }
              }
            } else {
              a_keeper = true;
            }

            if(a_keeper && carve_map) {
              register int i = *(MapLocusEStart(carve_map, v));
              a_keeper = false;
              if(i) {
                register int j = carve_map->EList[i++];
                while(j >= 0) {
                  register float *v_targ = carve_vla + 3 * j;
                  if(within3f(v_targ, v, carve_cutoff)) {
                    a_keeper = true;
                    break;
                  }
                  j = carve_map->EList[i++];
                }
              }
            }

            if(clear_map) {
              register int i = *(MapLocusEStart(clear_map, v));
              if(i) {
                register int j = clear_map->EList[i++];
                while(j >= 0) {
                  if(within3f(clear_vla + 3 * j, v, clear_cutoff)) {
                    a_keeper = false;
                    break;
                  }
                  j = clear_map->EList[i++];
                }
              }
            }
            if(a_keeper) {
              if(new_c) {
                new_c++;
                *(new_v++) = *(v++);
                *(new_v++) = *(v++);
                *(new_v++) = *(v++);
              } else {
                if(last_v) {
                  new_c += 2;
                  *(new_v++) = *(last_v++);
                  *(new_v++) = *(last_v++);
                  *(new_v++) = *(last_v++);
                  *(new_v++) = *(v++);
                  *(new_v++) = *(v++);
                  *(new_v++) = *(v++);
                  last_v = NULL;
                } else {
                  last_v = v;
                  v += 3;
                }
              }
            } else {
              last_v = NULL;
              v += 3;
              if(new_c) {
                VLACheck(new_n, int, new_size + 1);     /* extends the zero count sentinel */
                new_n[new_size] = new_c;
                new_size++;
                new_c = 0;
              }
            }
          }
          if(new_c) {
            VLACheck(new_n, int, new_size + 1); /* extends the zero count sentinel */
            new_n[new_size] = new_c;
            new_size++;
            new_c = 0;
          }
        }
        VLAFreeP(I->N);
        I->N = new_n;
      }
    }
    MapFree(trim_map);
    MapFree(carve_map);
    MapFree(clear_map);
    VLAFreeP(trim_vla);
    VLAFreeP(carve_vla);
    VLAFreeP(clear_vla);
    n = I->N;
    I->NTot = 0;
    while(*n)
      I->NTot += *(n++);
    RepMeshColor(I, cs);
    OrthoBusyFast(G, 3, 4);
  }
  OrthoBusyFast(G, 4, 4);
  return ((void *) (struct Rep *) I);
}

int RepMeshGetSolventDots(RepMesh * I, CoordSet * cs, float *min, float *max,
                          float probe_radius)
{
  PyMOLGlobals *G = cs->State.G;
  ObjectMolecule *obj = cs->Obj;
  int a, b, c, a1, a2, flag, i, h, k, l, j;
  int ok = true;
  float *v, *v0, vdw;
  MapType *map;
  int inFlag, *p, *dot_flag;
  SphereRec *sp = G->Sphere->Sphere[0];
  int cavity_cull;
  float probe_radius_plus;
  int dotCnt, maxCnt, maxDot = 0;
  int cnt;
  int inclH, mesh_mode, cullByFlag;
  AtomInfoType *ai1, *ai2;
  int ds = SettingGet_i(G, cs->Setting, obj->Obj.Setting, cSetting_mesh_quality);

  if(ds < 0)
    ds = 0;
  if(ds > 4)
    ds = 4;
  sp = G->Sphere->Sphere[ds];

  cavity_cull = SettingGet_i(G, cs->Setting, obj->Obj.Setting, cSetting_cavity_cull);

  mesh_mode = SettingGet_i(G, cs->Setting, obj->Obj.Setting, cSetting_mesh_mode);
  cullByFlag = (mesh_mode == cRepMesh_by_flags);
  inclH = !(mesh_mode == cRepMesh_heavy_atoms);

  I->Dot = (float *) mmalloc(sizeof(float) * cs->NIndex * 3 * sp->nDot);
  ErrChkPtr(G, I->Dot);

  probe_radius_plus = probe_radius * 1.5F;

  I->NDot = 0;
  map = MapNew(G, I->max_vdw + probe_radius, cs->Coord, cs->NIndex, NULL);
  if(map) {
    MapSetupExpress(map);
    maxCnt = 0;
    v = I->Dot;
    for(a = 0; a < cs->NIndex; a++) {

      ai1 = obj->AtomInfo + cs->IdxToAtm[a];
      if((inclH || (!ai1->hydrogen)) &&
         ((!cullByFlag) || (!(ai1->flags & (cAtomFlag_ignore))))) {
        OrthoBusyFast(G, a, cs->NIndex * 3);
        dotCnt = 0;
        a1 = cs->IdxToAtm[a];
        v0 = cs->Coord + 3 * a;
        vdw = cs->Obj->AtomInfo[a1].vdw + probe_radius;
        inFlag = true;
        for(c = 0; c < 3; c++) {
          if((min[c] - v0[c]) > vdw) {
            inFlag = false;
            break;
          };
          if((v0[c] - max[c]) > vdw) {
            inFlag = false;
            break;
          };
        }
        if(inFlag)
          for(b = 0; b < sp->nDot; b++) {
            v[0] = v0[0] + vdw * sp->dot[b][0];
            v[1] = v0[1] + vdw * sp->dot[b][1];
            v[2] = v0[2] + vdw * sp->dot[b][2];
            MapLocus(map, v, &h, &k, &l);
            flag = true;
            i = *(MapEStart(map, h, k, l));
            if(i) {
              j = map->EList[i++];
              while(j >= 0) {

                ai2 = obj->AtomInfo + cs->IdxToAtm[j];
                if((inclH || (!ai2->hydrogen)) &&
                   ((!cullByFlag) || (!(ai2->flags & cAtomFlag_ignore))))
                  if(j != a) {
                    a2 = cs->IdxToAtm[j];
                    if(within3f
                       (cs->Coord + 3 * j, v, cs->Obj->AtomInfo[a2].vdw + probe_radius)) {
                      flag = false;
                      break;
                    }
                  }
                j = map->EList[i++];
              }
            }
            if(flag) {
              dotCnt++;
              v += 3;
              I->NDot++;
            }
          }
        if(dotCnt > maxCnt) {
          maxCnt = dotCnt;
          maxDot = I->NDot - 1;
        }
      }
      if(G->Interrupt) {
        ok = false;
        break;
      }
    }
    MapFree(map);
  }

  if(ok && (cavity_cull > 0)) {
    dot_flag = Alloc(int, I->NDot);
    ErrChkPtr(G, dot_flag);
    for(a = 0; a < I->NDot; a++) {
      dot_flag[a] = 0;
    }
    dot_flag[maxDot] = 1;       /* this guarantees that we have a valid dot */

    map = MapNew(G, probe_radius_plus, I->Dot, I->NDot, NULL);
    if(map) {
      MapSetupExpress(map);

      flag = true;
      while(flag) {
        p = dot_flag;
        v = I->Dot;

        flag = false;
        for(a = 0; a < I->NDot; a++) {
          if(!dot_flag[a]) {
            cnt = 0;
            MapLocus(map, v, &h, &k, &l);
            i = *(MapEStart(map, h, k, l));
            if(i) {
              j = map->EList[i++];
              while(j >= 0) {
                if(j != a) {
                  if(within3f(I->Dot + (3 * j), v, probe_radius_plus)) {
                    if(dot_flag[j]) {
                      *p = true;
                      flag = true;
                      break;
                    }
                    cnt++;
                    if(cnt > cavity_cull) {
                      *p = true;
                      flag = true;
                      break;
                    }
                  }
                }
                j = map->EList[i++];
              }
            }
          }
          v += 3;
          p++;
        }
        if(G->Interrupt) {
          ok = false;
          break;
        }
      }
      MapFree(map);
    }
    v0 = I->Dot;
    v = I->Dot;
    p = dot_flag;
    c = I->NDot;
    I->NDot = 0;
    for(a = 0; a < c; a++) {
      if(*(p++)) {
        *(v0++) = *(v++);
        *(v0++) = *(v++);
        *(v0++) = *(v++);
        I->NDot++;
      } else {
        v += 3;
      }
    }
    FreeP(dot_flag);
  }
  if(!ok) {
    FreeP(I->Dot);
    I->NDot = 0;
  }
  return ok;
}

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