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RepSurface.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"RepSurface.h"
#include"Map.h"
#include"Scene.h"
#include"Sphere.h"
#include"Setting.h"
#include"Color.h"
#include"ObjectMolecule.h"
#include"Triangle.h"
#include"Vector.h"
#include"Feedback.h"
#include"main.h"
#include"Util.h"
#include"CGO.h"
#include"P.h"
#include"PConv.h"
#include"Selector.h"

#ifdef NT
#undef NT
#endif

00046 typedef struct RepSurface {
  Rep R;
  int N;
  int NT;
  int proximity;
  float *V, *VN, *VC, *VA;
  int *RC;
  int *Vis;
  int *T, *S;                   /* S=strips */
  int solidFlag;
  int oneColorFlag, oneColor;
  int allVisibleFlag;
  int *LastVisib;
  int *LastColor;
  int Type;
  float max_vdw;
  CGO *debug;
} RepSurface;

void RepSurfaceFree(RepSurface * I);
int RepSurfaceSameVis(RepSurface * I, CoordSet * cs);

void RepSurfaceColor(RepSurface * I, CoordSet * cs);

void RepSurfaceFree(RepSurface * I)
{
  VLAFreeP(I->V);
  VLAFreeP(I->VN);
  FreeP(I->VC);
  FreeP(I->VA);
  FreeP(I->RC);
  FreeP(I->Vis);
  FreeP(I->LastColor);
  FreeP(I->LastVisib);
  CGOFree(I->debug);
  VLAFreeP(I->T);
  VLAFreeP(I->S);
  RepPurge(&I->R);              /* unnecessary, but a good idea */
  OOFreeP(I);
}

00087 typedef struct {
  int nDot;
  float *dot;
  float *dotNormal;
  int *dotCode;
} SolventDot;

00094 typedef struct {
  float vdw;
  int flags;
} SurfaceJobAtomInfo;

static SolventDot *SolventDotNew(PyMOLGlobals * G,
                                 float *coord,
                                 SurfaceJobAtomInfo * atom_info,
                                 float probe_radius, SphereRec * sp,
                                 int *present,
                                 int circumscribe, int surface_mode,
                                 int surface_solvent, int cavity_cull,
                                 int all_visible_flag, float max_vdw,
                                 int cavity_mode, float cavity_radius, 
                                 float cavity_cutoff);

static void SolventDotFree(SolventDot * I)
{
  if(I) {
    VLAFreeP(I->dot);
    VLAFreeP(I->dotNormal);
    VLAFreeP(I->dotCode);
  }
  OOFreeP(I);
}

#if 0
static int ZOrderFn(float *array, int l, int r)
{
  return (array[l] <= array[r]);
}

static int ZRevOrderFn(float *array, int l, int r)
{
  return (array[l] >= array[r]);
}
#endif

static int check_and_add(int *cache, int spacing, int t0, int t1)
{
  int *rec;
  int cnt;
  t0++;
  t1++;

  rec = cache + spacing * t0;
  cnt = spacing;
  while(cnt > 0) {
    if(*rec == t1)
      return 1;
    if(!*rec) {
      *rec = t1;
      break;
    }
    rec++;
    cnt--;
  }
  rec = cache + spacing * t1;
  cnt = spacing;
  while(cnt > 0) {
    if(*rec == t0)
      return 1;
    if(!*rec) {
      *rec = t0;
      break;
    }
    rec++;
    cnt--;
  }
  return 0;
}

static void RepSurfaceRender(RepSurface * I, RenderInfo * info)
{
  CRay *ray = info->ray;
  Picking **pick = info->pick;
  PyMOLGlobals *G = I->R.G;
  float *v = I->V;
  float *vn = I->VN;
  float *vc = I->VC;
  float *va = I->VA;
  int *rc = I->RC;
  int *t = I->T;
  int *s = I->S;
  int c = I->N;
  int *vi = I->Vis;
  float alpha;
  int t_mode;

  if((I->Type != 1) && (!s)) {
    return;
  }

  alpha = SettingGet_f(G, I->R.cs->Setting, I->R.obj->Setting, cSetting_transparency);
  alpha = 1.0F - alpha;
  if(fabs(alpha - 1.0) < R_SMALL4)
    alpha = 1.0F;
  if(ray) {
    ray->fTransparentf(ray, 1.0F - alpha);
    if(I->Type == 1) {
      /* dot surface */

      float radius;

      radius = SettingGet_f(G, I->R.cs->Setting, I->R.obj->Setting, cSetting_dot_radius);

      if(radius == 0.0F) {
        radius = ray->PixelRadius * SettingGet_f(G, I->R.cs->Setting,
                                                 I->R.obj->Setting,
                                                 cSetting_dot_width) / 1.4142F;
      }

      if(I->oneColorFlag) {
        float col[3];
        ColorGetEncoded(G, I->oneColor, col);
        ray->fColor3fv(ray, col);
      }

      if(c)
        while(c--) {
          if(*vi) {
            if(!I->oneColorFlag) {
              ray->fColor3fv(ray, vc);
            }
            ray->fSphere3fv(ray, v, radius);
          }
          vi++;
          vc += 3;
          v += 3;
        }
    } else if((I->Type == 0) || (I->Type == 3) || (I->Type == 4) || (I->Type == 5)) {   /* solid surface */
      c = I->NT;

      if(I->oneColorFlag) {
        float col[3];
        ColorGetEncoded(G, I->oneColor, col);
        while(c--) {
          if((I->proximity
              && ((*(vi + (*t))) || (*(vi + (*(t + 1)))) || (*(vi + (*(t + 2))))))
             || ((*(vi + (*t))) && (*(vi + (*(t + 1)))) && (*(vi + (*(t + 2))))))
            ray->fTriangle3fv(ray, v + (*t) * 3, v + (*(t + 1)) * 3, v + (*(t + 2)) * 3,
                              vn + (*t) * 3, vn + (*(t + 1)) * 3, vn + (*(t + 2)) * 3,
                              col, col, col);
          t += 3;
        }
      } else {
        float colA[3], colB[3], colC[3];
        while(c--) {
          register int ttA = *t, ttB = *(t + 1), ttC = *(t + 2);
          if((I->proximity && ((*(vi + ttA)) || (*(vi + ttB)) || (*(vi + ttC)))) ||
             ((*(vi + ttA)) && (*(vi + ttB)) && (*(vi + ttC)))) {
            register int ttA3 = ttA * 3, ttB3 = ttB * 3, ttC3 = ttC * 3;
            register float *cA = vc + ttA3, *cB = vc + ttB3, *cC = vc + ttC3;
            if(rc) {
              if(rc[ttA] < -1)
                ColorGetEncoded(G, rc[ttA], (cA = colA));
              if(rc[ttB] < -1)
                ColorGetEncoded(G, rc[ttB], (cB = colB));
              if(rc[ttC] < -1)
                ColorGetEncoded(G, rc[ttC], (cC = colC));
            }
            if((*(vi + ttA)) || (*(vi + ttB)) || (*(vi + ttC))) {
              if(va) {
                ray->fTriangleTrans3fv(ray, v + ttA3, v + ttB3, v + ttC3,
                                       vn + ttA3, vn + ttB3, vn + ttC3,
                                       cA, cB, cC,
                                       1.0F - va[ttA], 1.0F - va[ttB], 1.0F - va[ttC]);
              } else {
                ray->fTriangle3fv(ray, v + ttA3, v + ttB3, v + ttC3,
                                  vn + ttA3, vn + ttB3, vn + ttC3, cA, cB, cC);
              }
            }
          }
          t += 3;
        }
      }
    } else if(I->Type == 2) {   /* triangle mesh surface */

      float radius;
      int t0, t1, t2;
      int spacing = 10;
      int *cache = Calloc(int, spacing * (I->N + 1));

      radius = SettingGet_f(G, I->R.cs->Setting, I->R.obj->Setting, cSetting_mesh_radius);

      if(radius == 0.0F) {
        float line_width =
          SettingGet_f(G, I->R.cs->Setting, I->R.obj->Setting, cSetting_mesh_width);
        line_width = SceneGetDynamicLineWidth(info, line_width);

        radius = ray->PixelRadius * line_width / 2.0F;
      }

      c = I->NT;
      if(I->oneColorFlag) {
        float col[3];
        ColorGetEncoded(G, I->oneColor, col);
        while(c--) {
          t0 = (*t);
          t1 = (*(t + 1));
          t2 = (*(t + 2));
          if((I->proximity && ((*(vi + t0)) || (*(vi + t1)) || (*(vi + t2)))) ||
             ((*(vi + t0)) && (*(vi + t1)) && (*(vi + t2)))) {
            if(!check_and_add(cache, spacing, t0, t1))
              ray->fSausage3fv(ray, v + t0 * 3, v + t1 * 3, radius, col, col);
            if(!check_and_add(cache, spacing, t1, t2))
              ray->fSausage3fv(ray, v + t1 * 3, v + t2 * 3, radius, col, col);
            if(!check_and_add(cache, spacing, t2, t0))
              ray->fSausage3fv(ray, v + t2 * 3, v + t0 * 3, radius, col, col);
          }
          t += 3;
        }
      } else {
        while(c--) {
          t0 = (*t);
          t1 = (*(t + 1));
          t2 = (*(t + 2));

          if((I->proximity && ((*(vi + t0)) || (*(vi + t1)) || (*(vi + t2)))) ||
             ((*(vi + t0)) && (*(vi + t1)) && (*(vi + t2))))
            if((*(vi + t0)) || (*(vi + t1)) || (*(vi + t2))) {
              if(!check_and_add(cache, spacing, t0, t1))
                ray->fSausage3fv(ray, v + t0 * 3, v + t1 * 3, radius, vc + t0 * 3,
                                 vc + t1 * 3);
              if(!check_and_add(cache, spacing, t1, t2))
                ray->fSausage3fv(ray, v + t1 * 3, v + t2 * 3, radius, vc + t1 * 3,
                                 vc + t2 * 3);
              if(!check_and_add(cache, spacing, t2, t0))
                ray->fSausage3fv(ray, v + t2 * 3, v + t0 * 3, radius, vc + t2 * 3,
                                 vc + t0 * 3);
            }
          t += 3;
        }
      }
      FreeP(cache);
    }
    ray->fTransparentf(ray, 0.0);
  } else if(G->HaveGUI && G->ValidContext) {
    if(pick) {
    } else {
      if(I->debug)
        CGORenderGL(I->debug, NULL, NULL, NULL, info);
      if(I->Type == 1) {

        /* no triangle information, so we're rendering dots only */

        int normals =
          SettingGet_i(G, I->R.cs->Setting, I->R.obj->Setting, cSetting_dot_normals);
        int lighting =
          SettingGet_i(G, I->R.cs->Setting, I->R.obj->Setting, cSetting_dot_lighting);
        int use_dlst;
        if(!normals)
          SceneResetNormal(G, true);
        if(!lighting)
          if(!info->line_lighting)
            glDisable(GL_LIGHTING);

        use_dlst = (int) SettingGet(G, cSetting_use_display_lists);
        if(use_dlst && I->R.displayList) {
          glCallList(I->R.displayList);
        } else {

          if(use_dlst) {
            if(!I->R.displayList) {
              I->R.displayList = glGenLists(1);
              if(I->R.displayList) {
                glNewList(I->R.displayList, GL_COMPILE_AND_EXECUTE);
              }
            }
          }
          glPointSize(SettingGet_f
                      (G, I->R.cs->Setting, I->R.obj->Setting, cSetting_dot_width));

          if(c) {
            glColor3f(1.0, 0.0, 0.0);
            glBegin(GL_POINTS);
            if(I->oneColorFlag) {
              glColor3fv(ColorGet(G, I->oneColor));
            }

            while(c--) {
              if(*vi) {
                if(!I->oneColorFlag) {
                  glColor3fv(vc);
                }
                if(normals)
                  glNormal3fv(vn);
                glVertex3fv(v);
              }
              vi++;
              vc += 3;
              vn += 3;
              v += 3;
            }
            glEnd();
          }

          if(use_dlst && I->R.displayList) {
            glEndList();
          }
        }
        if(!lighting)
          glEnable(GL_LIGHTING);
      } else if(I->Type == 2) { /* rendering triangle mesh */

        int normals =
          SettingGet_i(G, I->R.cs->Setting, I->R.obj->Setting, cSetting_mesh_normals);
        int lighting =
          SettingGet_i(G, I->R.cs->Setting, I->R.obj->Setting, cSetting_mesh_lighting);
        int use_dlst;
        if(!normals)
          SceneResetNormal(G, true);
        if(!lighting)
          if(!info->line_lighting)
            glDisable(GL_LIGHTING);

        use_dlst = (int) SettingGet(G, cSetting_use_display_lists);
        if(use_dlst && I->R.displayList) {
          glCallList(I->R.displayList);
        } else {

          float line_width =
            SettingGet_f(G, I->R.cs->Setting, I->R.obj->Setting, cSetting_mesh_width);
          line_width = SceneGetDynamicLineWidth(info, line_width);

          glLineWidth(line_width);

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

          c = I->NT;
          if(c) {
            if(I->oneColorFlag) {
              glColor3fv(ColorGet(G, I->oneColor));
              while(c--) {
                if((I->proximity
                    && ((*(vi + (*t))) || (*(vi + (*(t + 1)))) || (*(vi + (*(t + 2))))))
                   || ((*(vi + (*t))) && (*(vi + (*(t + 1)))) && (*(vi + (*(t + 2)))))) {
                  if(normals) {

                    glBegin(GL_LINE_STRIP);

                    glNormal3fv(vn + (*(t + 2)) * 3);
                    glVertex3fv(v + (*(t + 2)) * 3);

                    glNormal3fv(vn + (*t) * 3);
                    glVertex3fv(v + (*t) * 3);
                    t++;
                    glNormal3fv(vn + (*t) * 3);
                    glVertex3fv(v + (*t) * 3);
                    t++;
                    glNormal3fv(vn + (*t) * 3);
                    glVertex3fv(v + (*t) * 3);
                    t++;
                    glEnd();
                  } else {
                    glBegin(GL_LINE_STRIP);

                    glVertex3fv(v + (*(t + 2)) * 3);
                    glVertex3fv(v + (*t) * 3);
                    t++;
                    glVertex3fv(v + (*t) * 3);
                    t++;
                    glVertex3fv(v + (*t) * 3);
                    t++;
                    glEnd();
                  }
                } else
                  t += 3;
              }
            } else {
              while(c--) {
                if((I->proximity
                    && ((*(vi + (*t))) || (*(vi + (*(t + 1)))) || (*(vi + (*(t + 2))))))
                   || ((*(vi + (*t))) && (*(vi + (*(t + 1)))) && (*(vi + (*(t + 2)))))) {
                  if(normals) {

                    glBegin(GL_LINE_STRIP);

                    glColor3fv(vc + (*(t + 2)) * 3);
                    glNormal3fv(vn + (*(t + 2)) * 3);
                    glVertex3fv(v + (*(t + 2)) * 3);

                    glColor3fv(vc + (*t) * 3);
                    glNormal3fv(vn + (*t) * 3);
                    glVertex3fv(v + (*t) * 3);
                    t++;
                    glColor3fv(vc + (*t) * 3);
                    glNormal3fv(vn + (*t) * 3);
                    glVertex3fv(v + (*t) * 3);
                    t++;
                    glColor3fv(vc + (*t) * 3);
                    glNormal3fv(vn + (*t) * 3);
                    glVertex3fv(v + (*t) * 3);
                    t++;
                    glEnd();
                  } else {
                    glBegin(GL_LINE_STRIP);

                    glColor3fv(vc + (*(t + 2)) * 3);
                    glVertex3fv(v + (*(t + 2)) * 3);

                    glColor3fv(vc + (*t) * 3);
                    glVertex3fv(v + (*t) * 3);
                    t++;
                    glColor3fv(vc + (*t) * 3);
                    glVertex3fv(v + (*t) * 3);
                    t++;
                    glColor3fv(vc + (*t) * 3);
                    glVertex3fv(v + (*t) * 3);
                    t++;
                    glEnd();

                  }
                } else
                  t += 3;
              }
            }
          }
          if(use_dlst && I->R.displayList) {
            glEndList();
          }
        }
        if(!lighting)
          glEnable(GL_LIGHTING);
      } else {
        /* we're rendering triangles */

        if((alpha != 1.0) || va) {

          t_mode =
            SettingGet_i(G, I->R.cs->Setting, I->R.obj->Setting,
                         cSetting_transparency_mode);

          if(info && info->alpha_cgo) {
            t_mode = 0;
          }

          if(t_mode) {

            float **t_buf = NULL, **tb;
            float *z_value = NULL, *zv;
            int *ix = NULL;
            int n_tri = 0;
            float sum[3];
            float matrix[16];

            glGetFloatv(GL_MODELVIEW_MATRIX, matrix);

            if(I->oneColorFlag) {
              t_buf = Alloc(float *, I->NT * 6);
            } else {
              t_buf = Alloc(float *, I->NT * 12);
            }

            z_value = Alloc(float, I->NT);
            ix = Alloc(int, I->NT);

            zv = z_value;
            tb = t_buf;
            c = I->NT;
            if(I->oneColorFlag) {
              while(c--) {
                if((I->proximity
                    && ((*(vi + (*t))) || (*(vi + (*(t + 1)))) || (*(vi + (*(t + 2))))))
                   || ((*(vi + (*t))) && (*(vi + (*(t + 1)))) && (*(vi + (*(t + 2)))))) {

                  *(tb++) = vn + (*t) * 3;
                  *(tb++) = v + (*t) * 3;
                  *(tb++) = vn + (*(t + 1)) * 3;
                  *(tb++) = v + (*(t + 1)) * 3;
                  *(tb++) = vn + (*(t + 2)) * 3;
                  *(tb++) = v + (*(t + 2)) * 3;

                  add3f(tb[-1], tb[-3], sum);
                  add3f(sum, tb[-5], sum);

                  *(zv++) = matrix[2] * sum[0] + matrix[6] * sum[1] + matrix[10] * sum[2];
                  n_tri++;
                }
                t += 3;
              }
            } else {
              while(c--) {
                if((I->proximity
                    && ((*(vi + (*t))) || (*(vi + (*(t + 1)))) || (*(vi + (*(t + 2))))))
                   || ((*(vi + (*t))) && (*(vi + (*(t + 1)))) && (*(vi + (*(t + 2))))))
                  if((*(vi + (*t))) || (*(vi + (*(t + 1)))) || (*(vi + (*(t + 2))))) {

                    if(va)
                      *(tb++) = va + (*t);
                    else
                      *(tb++) = &alpha;
                    *(tb++) = vc + (*t) * 3;
                    *(tb++) = vn + (*t) * 3;
                    *(tb++) = v + (*t) * 3;

                    if(va)
                      *(tb++) = va + (*(t + 1));
                    else
                      *(tb++) = &alpha;
                    *(tb++) = vc + (*(t + 1)) * 3;
                    *(tb++) = vn + (*(t + 1)) * 3;
                    *(tb++) = v + (*(t + 1)) * 3;

                    if(va)
                      *(tb++) = va + (*(t + 2));
                    else
                      *(tb++) = &alpha;
                    *(tb++) = vc + (*(t + 2)) * 3;
                    *(tb++) = vn + (*(t + 2)) * 3;
                    *(tb++) = v + (*(t + 2)) * 3;

                    add3f(tb[-1], tb[-5], sum);
                    add3f(sum, tb[-9], sum);

                    *(zv++) =
                      matrix[2] * sum[0] + matrix[6] * sum[1] + matrix[10] * sum[2];
                    n_tri++;
                  }
                t += 3;
              }
            }

            switch (t_mode) {
            case 1:
              UtilSemiSortFloatIndex(n_tri, z_value, ix, true);
              /* UtilSortIndex(n_tri,z_value,ix,(UtilOrderFn*)ZOrderFn); */
              break;
            default:
              UtilSemiSortFloatIndex(n_tri, z_value, ix, false);
              /* UtilSortIndex(n_tri,z_value,ix,(UtilOrderFn*)ZRevOrderFn); */
              break;
            }

            c = n_tri;
            if(I->oneColorFlag) {
              float col[3];
              ColorGetEncoded(G, I->oneColor, col);
              glColor4f(col[0], col[1], col[2], alpha);
              glBegin(GL_TRIANGLES);
              for(c = 0; c < n_tri; c++) {

                tb = t_buf + 6 * ix[c];

                glNormal3fv(*(tb++));
                glVertex3fv(*(tb++));
                glNormal3fv(*(tb++));
                glVertex3fv(*(tb++));
                glNormal3fv(*(tb++));
                glVertex3fv(*(tb++));
              }
              glEnd();
            } else {
              glBegin(GL_TRIANGLES);
              for(c = 0; c < n_tri; c++) {
                float *vv, *v_alpha;

                tb = t_buf + 12 * ix[c];

                v_alpha = *(tb++);
                vv = *(tb++);
                glColor4f(vv[0], vv[1], vv[2], *v_alpha);
                glNormal3fv(*(tb++));
                glVertex3fv(*(tb++));

                v_alpha = *(tb++);
                vv = *(tb++);
                glColor4f(vv[0], vv[1], vv[2], *v_alpha);
                glNormal3fv(*(tb++));
                glVertex3fv(*(tb++));

                v_alpha = *(tb++);
                vv = *(tb++);
                glColor4f(vv[0], vv[1], vv[2], *v_alpha);
                glNormal3fv(*(tb++));
                glVertex3fv(*(tb++));

              }
              glEnd();
            }

            FreeP(ix);
            FreeP(z_value);
            FreeP(t_buf);
          } else {
            if(info->alpha_cgo) {       /* global transparency sort */

              if(I->allVisibleFlag) {
                if(I->oneColorFlag) {
                  float col[3];
                  ColorGetEncoded(G, I->oneColor, col);

                  glColor4f(col[0], col[1], col[2], alpha);
                  c = *(s++);
                  while(c) {
                    int parity = 0;
                    s += 2;
                    while(c--) {
                      CGOAlphaTriangle(info->alpha_cgo,
                                       v + s[-2] * 3, v + s[-1] * 3, v + (*s) * 3,
                                       vn + s[-2] * 3, vn + s[-1] * 3, vn + (*s) * 3,
                                       col, col, col, alpha, alpha, alpha, parity);

                      s++;
                      parity = !parity;
                    }
                    c = *(s++);
                  }
                } else {
                  c = *(s++);
                  while(c) {
                    float *col0, *col1, *col2;
                    int parity = 0;
                    float alpha0, alpha1, alpha2;
                    col0 = vc + (*s) * 3;
                    if(va) {
                      alpha0 = va[(*s)];
                    } else {
                      alpha0 = alpha;
                    }
                    s++;
                    col1 = vc + (*s) * 3;
                    if(va) {
                      alpha1 = va[(*s)];
                    } else {
                      alpha1 = alpha;
                    }
                    s++;
                    while(c--) {
                      col2 = vc + (*s) * 3;
                      if(va) {
                        alpha2 = va[(*s)];
                      } else {
                        alpha2 = alpha;
                      }
                      CGOAlphaTriangle(info->alpha_cgo,
                                       v + s[-2] * 3, v + s[-1] * 3, v + (*s) * 3,
                                       vn + s[-2] * 3, vn + s[-1] * 3, vn + (*s) * 3,
                                       col0, col1, col2, alpha0, alpha1, alpha2, parity);
                      alpha0 = alpha1;
                      alpha1 = alpha2;
                      col0 = col1;
                      col1 = col2;
                      s++;
                      parity = !parity;
                    }
                    c = *(s++);
                  }
                }
              } else {          /* subset s */
                c = I->NT;
                if(c) {
                  if(I->oneColorFlag) {
                    float color[3];
                    ColorGetEncoded(G, I->oneColor, color);
                    while(c--) {
                      if((I->proximity && ((*(vi + (*t))) || (*(vi + (*(t + 1))))
                                           || (*(vi + (*(t + 2)))))) || ((*(vi + (*t)))
                                                                         &&
                                                                         (*
                                                                          (vi +
                                                                           (*(t + 1))))
                                                                         &&
                                                                         (*
                                                                          (vi +
                                                                           (*(t + 2))))))
                      {

                        CGOAlphaTriangle(info->alpha_cgo,
                                         v + t[0] * 3, v + t[1] * 3, v + t[2] * 3,
                                         vn + t[0] * 3, vn + t[1] * 3, vn + t[2] * 3,
                                         color, color, color, alpha, alpha, alpha, 0);
                      }
                      t += 3;
                    }
                  } else {
                    while(c--) {
                      if((I->proximity && ((*(vi + (*t))) || (*(vi + (*(t + 1))))
                                           || (*(vi + (*(t + 2)))))) || ((*(vi + (*t)))
                                                                         &&
                                                                         (*
                                                                          (vi +
                                                                           (*(t + 1))))
                                                                         &&
                                                                         (*
                                                                          (vi +
                                                                           (*(t + 2))))))
                      {

                        if(va) {
                          CGOAlphaTriangle(info->alpha_cgo,
                                           v + t[0] * 3, v + t[1] * 3, v + t[2] * 3,
                                           vn + t[0] * 3, vn + t[1] * 3, vn + t[2] * 3,
                                           vc + t[0] * 3, vc + t[1] * 3, vc + t[2] * 3,
                                           va[t[0]], va[t[1]], va[t[2]], 0);
                        } else {
                          CGOAlphaTriangle(info->alpha_cgo,
                                           v + t[0] * 3, v + t[1] * 3, v + t[2] * 3,
                                           vn + t[0] * 3, vn + t[1] * 3, vn + t[2] * 3,
                                           vc + t[0] * 3, vc + t[1] * 3, vc + t[2] * 3,
                                           alpha, alpha, alpha, 0);
                        }
                      }
                      t += 3;
                    }
                  }
                  glEnd();
                }
              }
            } else {

              /* fast and ugly */
              /*          glCullFace(GL_BACK);
                 glEnable(GL_CULL_FACE);
                 glDepthMask(GL_FALSE); */
              if(I->allVisibleFlag) {
                if(I->oneColorFlag) {
                  float col[3];
                  ColorGetEncoded(G, I->oneColor, col);

                  glColor4f(col[0], col[1], col[2], alpha);
                  c = *(s++);
                  while(c) {
                    glBegin(GL_TRIANGLE_STRIP);
                    glNormal3fv(vn + (*s) * 3);
                    glVertex3fv(v + (*s) * 3);
                    s++;
                    glNormal3fv(vn + (*s) * 3);
                    glVertex3fv(v + (*s) * 3);
                    s++;
                    while(c--) {
                      glNormal3fv(vn + (*s) * 3);
                      glVertex3fv(v + (*s) * 3);
                      s++;
                    }
                    glEnd();
                    c = *(s++);
                  }
                } else {
                  c = *(s++);
                  while(c) {
                    float *col;

                    glBegin(GL_TRIANGLE_STRIP);
                    col = vc + (*s) * 3;
                    if(va) {
                      glColor4f(col[0], col[1], col[2], va[(*s)]);
                    } else {
                      glColor4f(col[0], col[1], col[2], alpha);
                    }
                    glNormal3fv(vn + (*s) * 3);
                    glVertex3fv(v + (*s) * 3);
                    s++;
                    col = vc + (*s) * 3;
                    if(va) {
                      glColor4f(col[0], col[1], col[2], va[(*s)]);
                    } else {
                      glColor4f(col[0], col[1], col[2], alpha);
                    }
                    glNormal3fv(vn + (*s) * 3);
                    glVertex3fv(v + (*s) * 3);
                    s++;
                    while(c--) {
                      col = vc + (*s) * 3;
                      if(va) {
                        glColor4f(col[0], col[1], col[2], va[(*s)]);
                      } else {
                        glColor4f(col[0], col[1], col[2], alpha);
                      }
                      glNormal3fv(vn + (*s) * 3);
                      glVertex3fv(v + (*s) * 3);
                      s++;
                    }
                    glEnd();
                    c = *(s++);
                  }
                }

              } else {          /* subset s */
                c = I->NT;
                if(c) {
                  glBegin(GL_TRIANGLES);

                  if(I->oneColorFlag) {
                    float color[3];
                    float *col;
                    ColorGetEncoded(G, I->oneColor, color);

                    glColor4f(color[0], color[1], color[2], alpha);
                    while(c--) {
                      if((I->proximity && ((*(vi + (*t))) || (*(vi + (*(t + 1))))
                                           || (*(vi + (*(t + 2)))))) || ((*(vi + (*t)))
                                                                         &&
                                                                         (*
                                                                          (vi +
                                                                           (*(t + 1))))
                                                                         &&
                                                                         (*
                                                                          (vi +
                                                                           (*(t + 2))))))
                      {

                        col = vc + (*t) * 3;
                        glNormal3fv(vn + (*t) * 3);
                        glVertex3fv(v + (*t) * 3);
                        t++;
                        col = vc + (*t) * 3;
                        glNormal3fv(vn + (*t) * 3);
                        glVertex3fv(v + (*t) * 3);
                        t++;
                        col = vc + (*t) * 3;
                        glNormal3fv(vn + (*t) * 3);
                        glVertex3fv(v + (*t) * 3);
                        t++;
                      } else
                        t += 3;
                    }
                  } else {
                    float *col;
                    while(c--) {
                      if((I->proximity && ((*(vi + (*t))) || (*(vi + (*(t + 1))))
                                           || (*(vi + (*(t + 2)))))) || ((*(vi + (*t)))
                                                                         &&
                                                                         (*
                                                                          (vi +
                                                                           (*(t + 1))))
                                                                         &&
                                                                         (*
                                                                          (vi +
                                                                           (*(t + 2))))))
                      {

                        col = vc + (*t) * 3;
                        if(va) {
                          glColor4f(col[0], col[1], col[2], va[(*t)]);
                        } else {
                          glColor4f(col[0], col[1], col[2], alpha);
                        }
                        glNormal3fv(vn + (*t) * 3);
                        glVertex3fv(v + (*t) * 3);
                        t++;
                        col = vc + (*t) * 3;
                        if(va) {
                          glColor4f(col[0], col[1], col[2], va[(*t)]);
                        } else {
                          glColor4f(col[0], col[1], col[2], alpha);
                        }
                        glNormal3fv(vn + (*t) * 3);
                        glVertex3fv(v + (*t) * 3);
                        t++;
                        col = vc + (*t) * 3;
                        if(va) {
                          glColor4f(col[0], col[1], col[2], va[(*t)]);
                        } else {
                          glColor4f(col[0], col[1], col[2], alpha);
                        }
                        glNormal3fv(vn + (*t) * 3);
                        glVertex3fv(v + (*t) * 3);
                        t++;
                      } else
                        t += 3;
                    }
                  }
                  glEnd();
                }
              }
            }
            /*          glDisable(GL_CULL_FACE);
               glDepthMask(GL_TRUE); */
          }
        } else {                /* opaque */

          int use_dlst, simplify = 0;
          use_dlst = (int) SettingGet(G, cSetting_use_display_lists);
          simplify = (int) SettingGet(G, cSetting_simplify_display_lists);
          if(use_dlst && I->R.displayList) {
            glCallList(I->R.displayList);
          } else {

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

            if(I->allVisibleFlag) {
              if(I->oneColorFlag) {
                if(use_dlst && simplify) {      /* simplify: try to help display list optimizer */
                  glColor3fv(ColorGet(G, I->oneColor));
                  c = *(s++);
                  while(c) {
                    glBegin(GL_TRIANGLES);
                    s += 2;
                    while(c--) {
                      s -= 2;
                      glNormal3fv(vn + (*s) * 3);
                      glVertex3fv(v + (*s) * 3);
                      s++;
                      glNormal3fv(vn + (*s) * 3);
                      glVertex3fv(v + (*s) * 3);
                      s++;
                      glNormal3fv(vn + (*s) * 3);
                      glVertex3fv(v + (*s) * 3);
                      s++;
                    }
                    glEnd();
                    c = *(s++);
                  }
                } else {
                  glColor3fv(ColorGet(G, I->oneColor));
                  c = *(s++);
                  while(c) {
                    glBegin(GL_TRIANGLE_STRIP);
                    glNormal3fv(vn + (*s) * 3);
                    glVertex3fv(v + (*s) * 3);
                    s++;
                    glNormal3fv(vn + (*s) * 3);
                    glVertex3fv(v + (*s) * 3);
                    s++;
                    while(c--) {
                      glNormal3fv(vn + (*s) * 3);
                      glVertex3fv(v + (*s) * 3);
                      s++;
                    }
                    glEnd();
                    c = *(s++);
                  }
                }               /* use_dlst&&simplify */
              } else {          /* not one color */
                if(use_dlst && simplify) {      /* simplify: try to help display list optimizer */
                  c = *(s++);
                  while(c) {
                    glBegin(GL_TRIANGLES);
                    s += 2;
                    while(c--) {
                      s -= 2;
                      glColor3fv(vc + (*s) * 3);
                      glNormal3fv(vn + (*s) * 3);
                      glVertex3fv(v + (*s) * 3);
                      s++;
                      glColor3fv(vc + (*s) * 3);
                      glNormal3fv(vn + (*s) * 3);
                      glVertex3fv(v + (*s) * 3);
                      s++;
                      glColor3fv(vc + (*s) * 3);
                      glNormal3fv(vn + (*s) * 3);
                      glVertex3fv(v + (*s) * 3);
                      s++;
                    }
                    glEnd();
                    c = *(s++);
                  }
                } else {
                  c = *(s++);
                  while(c) {
                    glBegin(GL_TRIANGLE_STRIP);
                    glColor3fv(vc + (*s) * 3);
                    glNormal3fv(vn + (*s) * 3);
                    glVertex3fv(v + (*s) * 3);
                    s++;
                    glColor3fv(vc + (*s) * 3);
                    glNormal3fv(vn + (*s) * 3);
                    glVertex3fv(v + (*s) * 3);
                    s++;
                    while(c--) {
                      glColor3fv(vc + (*s) * 3);
                      glNormal3fv(vn + (*s) * 3);
                      glVertex3fv(v + (*s) * 3);
                      s++;
                    }
                    glEnd();
                    c = *(s++);
                  }
                }
              }                 /* one color */
            } else {            /* subsets */
              c = I->NT;
              if(c) {
                glBegin(GL_TRIANGLES);
                if(I->oneColorFlag) {
                  glColor3fv(ColorGet(G, I->oneColor));
                  while(c--) {
                    if((I->proximity && ((*(vi + (*t))) || (*(vi + (*(t + 1))))
                                         || (*(vi + (*(t + 2)))))) || ((*(vi + (*t)))
                                                                       &&
                                                                       (*
                                                                        (vi + (*(t + 1))))
                                                                       &&
                                                                       (*
                                                                        (vi +
                                                                         (*(t + 2)))))) {

                      glNormal3fv(vn + (*t) * 3);
                      glVertex3fv(v + (*t) * 3);
                      t++;
                      glNormal3fv(vn + (*t) * 3);
                      glVertex3fv(v + (*t) * 3);
                      t++;
                      glNormal3fv(vn + (*t) * 3);
                      glVertex3fv(v + (*t) * 3);
                      t++;
                    } else
                      t += 3;
                  }
                } else {
                  while(c--) {
                    if((I->proximity && ((*(vi + (*t))) || (*(vi + (*(t + 1))))
                                         || (*(vi + (*(t + 2)))))) || ((*(vi + (*t)))
                                                                       &&
                                                                       (*
                                                                        (vi + (*(t + 1))))
                                                                       &&
                                                                       (*
                                                                        (vi +
                                                                         (*(t + 2)))))) {

                      glColor3fv(vc + (*t) * 3);
                      glNormal3fv(vn + (*t) * 3);
                      glVertex3fv(v + (*t) * 3);
                      t++;
                      glColor3fv(vc + (*t) * 3);
                      glNormal3fv(vn + (*t) * 3);
                      glVertex3fv(v + (*t) * 3);
                      t++;
                      glColor3fv(vc + (*t) * 3);
                      glNormal3fv(vn + (*t) * 3);
                      glVertex3fv(v + (*t) * 3);
                      t++;
                    } else
                      t += 3;
                  }
                }
                glEnd();
              }
            }
            if(use_dlst && I->R.displayList) {
              glEndList();
            }
          }
        }
      }
      if(SettingGet(G, cSetting_surface_debug)) {
        t = I->T;
        c = I->NT;
        if(c) {
          glBegin(GL_TRIANGLES);
          while(c--) {

            if(I->allVisibleFlag
               ||
               ((I->proximity
                 && ((*(vi + (*t))) || (*(vi + (*(t + 1)))) || (*(vi + (*(t + 2))))))
                || ((*(vi + (*t))) && (*(vi + (*(t + 1)))) && (*(vi + (*(t + 2))))))) {

              glNormal3fv(vn + (*t) * 3);
              glVertex3fv(v + (*t) * 3);
              t++;
              glNormal3fv(vn + (*t) * 3);
              glVertex3fv(v + (*t) * 3);
              t++;
              glNormal3fv(vn + (*t) * 3);
              glVertex3fv(v + (*t) * 3);
              t++;
            } else {
              t += 3;
            }
          }
          glEnd();
        }

        t = I->T;
        c = I->NT;
        if(c) {
          glColor3f(0.0, 1.0, 0.0);
          glLineWidth(1.0F);
          while(c--) {
            glBegin(GL_LINE_STRIP);

            if(I->allVisibleFlag
               ||
               ((I->proximity
                 && ((*(vi + (*t))) || (*(vi + (*(t + 1)))) || (*(vi + (*(t + 2))))))
                || ((*(vi + (*t))) && (*(vi + (*(t + 1)))) && (*(vi + (*(t + 2))))))) {

              glNormal3fv(vn + (*t) * 3);
              glVertex3fv(v + (*t) * 3);
              t++;
              glNormal3fv(vn + (*t) * 3);
              glVertex3fv(v + (*t) * 3);
              t++;
              glNormal3fv(vn + (*t) * 3);
              glVertex3fv(v + (*t) * 3);
              t++;
            } else {
              t += 3;
            }
            glEnd();
          }
        }
        c = I->N;
        if(c) {
          glColor3f(1.0, 0.0, 0.0);
          glBegin(GL_LINES);
          SceneResetNormal(G, true);
          while(c--) {
            glVertex3fv(v);
            glVertex3f(v[0] + vn[0] / 2, v[1] + vn[1] / 2, v[2] + vn[2] / 2);
            v += 3;
            vn += 3;
          }
          glEnd();
        }
      }
    }
  }
}

int RepSurfaceSameVis(RepSurface * 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[cRepSurface]) {
      same = false;
      break;
    }
    if(*(lc++) != *(cc++)) {
      same = false;
      break;
    }
  }
  return (same);
}

void RepSurfaceColor(RepSurface * I, CoordSet * cs)
{
  PyMOLGlobals *G = cs->State.G;
  MapType *map;
  int a, i0, i, j, c1;
  float *v0, *vc, *c0, *va;
  float *n0;
  int *vi, *lv, *lc, *cc;
  int first_color;
  float *v_pos, v_above[3];
  int ramp_above;
  ObjectMolecule *obj;
  float probe_radius;
  float dist;
  float cutoff;
  int inclH;
  int inclInvis;
  int cullByFlag = false;
  int surface_mode;
  int surface_color;
  int *present = NULL;
  int *rc;
  int ramped_flag = false;

  int carve_state = 0;
  int carve_flag = false;
  float carve_cutoff;
  float carve_normal_cutoff;
  int carve_normal_flag;
  char *carve_selection = NULL;
  float *carve_vla = NULL;
  MapType *carve_map = NULL;

  int clear_state = 0;
  int clear_flag = false;
  float clear_cutoff;
  char *clear_selection = NULL;
  float *clear_vla = NULL;
  int state = I->R.context.state;
  float transp;
  int variable_alpha = false;

  MapType *clear_map = NULL;

  AtomInfoType *ai2 = NULL, *ai1;

  obj = cs->Obj;
  surface_mode = SettingGet_i(G, cs->Setting, obj->Obj.Setting, cSetting_surface_mode);
  ramp_above =
    SettingGet_i(G, cs->Setting, obj->Obj.Setting, cSetting_surface_ramp_above_mode);
  surface_color =
    SettingGet_color(G, cs->Setting, obj->Obj.Setting, cSetting_surface_color);
  cullByFlag = (surface_mode == cRepSurface_by_flags);
  inclH = !((surface_mode == cRepSurface_heavy_atoms)
            || (surface_mode == cRepSurface_vis_heavy_only));
  inclInvis = !((surface_mode == cRepSurface_vis_only)
                || (surface_mode == cRepSurface_vis_heavy_only));
  probe_radius = SettingGet_f(G, cs->Setting, obj->Obj.Setting, cSetting_solvent_radius);
  I->proximity =
    SettingGet_b(G, cs->Setting, obj->Obj.Setting, cSetting_surface_proximity);
  carve_cutoff =
    SettingGet_f(G, cs->Setting, obj->Obj.Setting, cSetting_surface_carve_cutoff);
  clear_cutoff =
    SettingGet_f(G, cs->Setting, obj->Obj.Setting, cSetting_surface_clear_cutoff);
  transp = SettingGet_f(G, cs->Setting, obj->Obj.Setting, cSetting_transparency);
  carve_normal_cutoff =
    SettingGet_f(G, cs->Setting, obj->Obj.Setting, cSetting_surface_carve_normal_cutoff);
  carve_normal_flag = carve_normal_cutoff > (-1.0F);

  cutoff = I->max_vdw + 2 * probe_radius;

  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[cRepSurface];
    *(lc++) = *(cc++);
  }

  if(I->N) {
    if(carve_cutoff > 0.0F) {
      carve_state =
        SettingGet_i(G, cs->Setting, obj->Obj.Setting, cSetting_surface_carve_state) - 1;
      carve_selection =
        SettingGet_s(G, cs->Setting, obj->Obj.Setting, cSetting_surface_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_surface_clear_state) - 1;
      clear_selection =
        SettingGet_s(G, cs->Setting, obj->Obj.Setting, cSetting_surface_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;
    }

    if(!I->VC)
      I->VC = Alloc(float, 3 * I->N);
    vc = I->VC;
    if(!I->VA)
      I->VA = Alloc(float, I->N);
    va = I->VA;
    if(!I->RC)
      I->RC = Alloc(int, I->N);
    rc = I->RC;
    if(!I->Vis)
      I->Vis = Alloc(int, I->N);
    vi = I->Vis;
    if(ColorCheckRamped(G, surface_color)) {
      I->oneColorFlag = false;
    } else {
      I->oneColorFlag = true;
    }
    first_color = -1;

    present = Alloc(int, cs->NIndex);
    {
      int *ap = present;
      for(a = 0; a < cs->NIndex; a++) {
        ai1 = obj->AtomInfo + cs->IdxToAtm[a];
        if(ai1->visRep[cRepSurface] &&
           (inclH || (!ai1->hydrogen)) &&
           ((!cullByFlag) || (!(ai1->flags & (cAtomFlag_ignore | cAtomFlag_exfoliate)))))
          *ap = 2;
        else
          *ap = 0;
        ap++;
      }
    }

    map =
      MapNewFlagged(G, 2 * I->max_vdw + probe_radius, cs->Coord, cs->NIndex, NULL,
                    present);
    MapSetupExpress(map);

    if(inclInvis) {
      /* add in nearby invisibles */
      float probe_radiusX2 = probe_radius * 2;
      for(a = 0; a < cs->NIndex; a++)
        if(!present[a]) {
          ai1 = obj->AtomInfo + cs->IdxToAtm[a];
          if((!cullByFlag) || !(ai1->flags & cAtomFlag_ignore)) {
            v0 = cs->Coord + 3 * a;
            i = *(MapLocusEStart(map, v0));
            if(i) {
              j = map->EList[i++];
              while(j >= 0) {
                if(present[j] > 1) {
                  ai2 = obj->AtomInfo + cs->IdxToAtm[j];
                  if(within3f
                     (cs->Coord + 3 * j, v0, ai1->vdw + ai2->vdw + probe_radiusX2)) {
                    present[a] = 1;
                    break;
                  }
                }
                j = map->EList[i++];
              }
            }
          }
        }
    }
    MapFree(map);
    map = NULL;

    /* now, assign colors to each point */
    map = MapNewFlagged(G, cutoff, cs->Coord, cs->NIndex, NULL, present);
    if(map) {
      MapSetupExpress(map);
      for(a = 0; a < I->N; a++) {
        float at_transp = transp;

        AtomInfoType *ai0 = NULL;
        float minDist = MAXFLOAT;
        c1 = 1;
        i0 = -1;
        v0 = I->V + 3 * a;
        n0 = I->VN + 3 * a;
        vi = I->Vis + a;
        /* colors */
        i = *(MapLocusEStart(map, v0));
        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_surface_color;
          transp = SettingGet_f(G, cs->Setting, obj->Obj.Setting, cSetting_transparency);

          AtomInfoGetSetting_f(G, ai0, cSetting_transparency, transp, &at_transp);

          AtomInfoGetSetting_color(G, ai0, cSetting_surface_color,
                                   surface_color, &at_surface_color);

          if(at_surface_color != -1) {
            c1 = at_surface_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(I->allVisibleFlag)
            *vi = 1;
          else {
            ai2 = obj->AtomInfo + cs->IdxToAtm[i0];
            if(ai2->visRep[cRepSurface] &&
               (inclH || (!ai2->hydrogen)) &&
               ((!cullByFlag) || (!(ai2->flags &
                                    (cAtomFlag_ignore | cAtomFlag_exfoliate)))))
              *vi = 1;
            else
              *vi = 0;
          }
        } else {
          *vi = 0;
        }
        if(carve_flag && (*vi)) {       /* is point visible, and are we carving? */
          *vi = 0;

          if(carve_map) {

            i = *(MapLocusEStart(carve_map, v0));
            if(i) {
              j = carve_map->EList[i++];
              while(j >= 0) {
                register float *v_targ = carve_vla + 3 * j;
                if(within3f(v_targ, v0, carve_cutoff)) {
                  if(!carve_normal_flag) {
                    *vi = 1;
                    break;
                  } else {
                    float v_to[3];
                    subtract3f(v_targ, v0, v_to);
                    if(dot_product3f(v_to, n0) >= carve_normal_cutoff) {
                      *vi = 1;
                      break;
                    }
                  }
                }
                j = carve_map->EList[i++];
              }
            }
          }
        }
        if(clear_flag && (*vi)) {       /* is point visible, and are we clearing? */
          if(clear_map) {
            i = *(MapLocusEStart(clear_map, v0));
            if(i) {
              j = clear_map->EList[i++];
              while(j >= 0) {
                if(within3f(clear_vla + 3 * j, v0, clear_cutoff)) {
                  *vi = 0;
                  break;
                }
                j = clear_map->EList[i++];
              }
            }
          }
        }
        /*
           if(ColorCheckRamped(G,surface_color)) {
           c1 = surface_color;
           }
         */

        if(ColorCheckRamped(G, c1)) {
          I->oneColorFlag = false;
          switch (ramp_above) {
          case 1:
            copy3f(n0, v_above);
            scale3f(v_above, probe_radius, v_above);
            add3f(v0, v_above, v_above);
            v_pos = v_above;
            rc[0] = -1;
            break;
          default:
            v_pos = v0;
            rc[0] = c1;
            ramped_flag = true;
            break;
          }
          ColorGetRamped(G, c1, v_pos, vc, state);
          vc += 3;
          rc++;
        } else {
          c0 = ColorGet(G, c1);
          *(rc++) = c1;
          *(vc++) = *(c0++);
          *(vc++) = *(c0++);
          *(vc++) = *(c0++);
        }
        if(at_transp != transp)
          variable_alpha = true;
        *(va++) = 1.0F - at_transp;

        if(!*vi)
          I->allVisibleFlag = false;
        vi++;
      }
      MapFree(map);
    }
    if(variable_alpha)
      I->oneColorFlag = false;

    if(I->oneColorFlag) {
      I->oneColor = first_color;
    }
  }
  /*
     if(surface_color>=0) {
     I->oneColorFlag=true;
     I->oneColor=surface_color;
     }
   */

  if(G->HaveGUI) {
    if(I->R.displayList) {
      if(PIsGlutThread()) {
        if(G->ValidContext) {
          glDeleteLists(I->R.displayList, 1);
          I->R.displayList = 0;
        }
      } else {
        char buffer[255];       /* pass this off to the main thread */
        sprintf(buffer, "_cmd.gl_delete_lists(cmd._COb,%d,%d)\n", I->R.displayList, 1);
        PParse(G, buffer);
        I->R.displayList = 0;
      }
    }
  }

  if(I->VA && (!variable_alpha)) {
    FreeP(I->VA);
    I->VA = NULL;
  }

  if(carve_map)
    MapFree(carve_map);
  VLAFreeP(carve_vla);
  if(clear_map)
    MapFree(clear_map);
  VLAFreeP(clear_vla);
  if((!ramped_flag)
     || (!SettingGet_b(G, cs->Setting, obj->Obj.Setting, cSetting_ray_color_ramps)))
    FreeP(I->RC);
  FreeP(present);
}

01632 typedef struct {
  /* input */
  float *coord;
  SurfaceJobAtomInfo *atomInfo;

  float maxVdw;
  int allVisibleFlag;

  int nPresent;
  int *presentVla;

  int solventSphereIndex, sphereIndex;

  int surfaceType;
  int circumscribe;
  float probeRadius;
  float carveCutoff;
  float *carveVla;

  int surfaceMode;
  int surfaceSolvent;
  int cavityCull;
  float pointSep;
  float trimCutoff;
  float trimFactor;

  int cavityMode;
  float cavityRadius;
  float cavityCutoff;

  /* results */
  float *V, *VN;
  int N, *T, *S, NT;

} SurfaceJob;

static void SurfaceJobPurgeResult(PyMOLGlobals * G, SurfaceJob * I)
{
  I->N = 0;
  I->NT = 0;
  VLAFreeP(I->V);
  I->V = NULL;
  VLAFreeP(I->VN);
  I->VN = NULL;
  VLAFreeP(I->T);
  I->T = NULL;
  VLAFreeP(I->S);
  I->S = NULL;
}

#ifndef _PYMOL_NOPY
OV_INLINE_STATIC PyObject *SurfaceJobAtomInfoAsPyTuple(SurfaceJobAtomInfo * atom_info)
{
  PyObject *result = NULL;
  if(atom_info) {
    ov_size size = 2 * VLAGetSize(atom_info) + 1;
    result = PyTuple_New(size);
    if(result) {
      ov_size i;
      PyTuple_SetItem(result, 0, PyInt_FromLong(2));    /* width of array */
      for(i = 1; i < size; i += 2) {
        PyTuple_SetItem(result, i, PyFloat_FromDouble(atom_info->vdw));
        PyTuple_SetItem(result, i + 1, PyInt_FromLong(atom_info->flags));
        atom_info++;
      }
    }
  }
  return (PConvAutoNone(result));
}

OV_INLINE_STATIC SurfaceJobAtomInfo *SurfaceJobAtomInfoVLAFromPyTuple(PyObject * tuple)
{
  SurfaceJobAtomInfo *result = NULL;
  if(tuple && PyTuple_Check(tuple)) {
    ov_size size = PyTuple_Size(tuple);
    if(size) {
      ov_size width = PyInt_AsLong(PyTuple_GetItem(tuple, 0));
      if(width == 2) {
        ov_size vla_size = (size - 1) / 2;
        result = VLAlloc(SurfaceJobAtomInfo, vla_size);
        if(result) {
          SurfaceJobAtomInfo *atom_info = result;
          ov_size i;
          for(i = 1; i < size; i += 2) {
            atom_info->vdw = (float) PyFloat_AsDouble(PyTuple_GetItem(tuple, i));
            atom_info->flags = PyInt_AsLong(PyTuple_GetItem(tuple, i + 1));
            atom_info++;
          }
        }
      }
    }
  }
  return (result);
}

OV_INLINE_STATIC PyObject *SurfaceJobInputAsTuple(PyMOLGlobals * G, SurfaceJob * I)
{
  PyObject *result = PyTuple_New(21);
  if(result) {
    PyTuple_SetItem(result, 0, PyString_FromString("SurfaceJob"));
    PyTuple_SetItem(result, 1, PyInt_FromLong(1));      /* version */
    PyTuple_SetItem(result, 2, PConvFloatVLAToPyTuple(I->coord));
    PyTuple_SetItem(result, 3, SurfaceJobAtomInfoAsPyTuple(I->atomInfo));
    PyTuple_SetItem(result, 4, PyFloat_FromDouble(I->maxVdw));
    PyTuple_SetItem(result, 5, PyInt_FromLong(I->allVisibleFlag));
    PyTuple_SetItem(result, 6, PyInt_FromLong(I->nPresent));
    PyTuple_SetItem(result, 7, PConvIntVLAToPyTuple(I->presentVla));
    PyTuple_SetItem(result, 8, PyInt_FromLong(I->solventSphereIndex));
    PyTuple_SetItem(result, 9, PyInt_FromLong(I->sphereIndex));
    PyTuple_SetItem(result, 10, PyInt_FromLong(I->surfaceType));
    PyTuple_SetItem(result, 11, PyInt_FromLong(I->circumscribe));
    PyTuple_SetItem(result, 12, PyFloat_FromDouble(I->probeRadius));
    PyTuple_SetItem(result, 13, PyFloat_FromDouble(I->carveCutoff));
    PyTuple_SetItem(result, 14, PConvFloatVLAToPyTuple(I->carveVla));
    PyTuple_SetItem(result, 15, PyInt_FromLong(I->surfaceMode));
    PyTuple_SetItem(result, 16, PyInt_FromLong(I->surfaceSolvent));
    PyTuple_SetItem(result, 17, PyInt_FromLong(I->cavityCull));
    PyTuple_SetItem(result, 18, PyFloat_FromDouble(I->pointSep));
    PyTuple_SetItem(result, 19, PyFloat_FromDouble(I->trimCutoff));
    PyTuple_SetItem(result, 20, PyFloat_FromDouble(I->trimFactor));

    PyTuple_SetItem(result, 21, PyInt_FromLong(I->cavityMode));
    PyTuple_SetItem(result, 22, PyFloat_FromDouble(I->cavityRadius));
    PyTuple_SetItem(result, 23, PyFloat_FromDouble(I->cavityCutoff));
    
  }
  return result;
}

OV_INLINE_STATIC PyObject *SurfaceJobResultAsTuple(PyMOLGlobals * G, SurfaceJob * I)
{
  PyObject *result = PyTuple_New(6);
  if(result) {
    PyTuple_SetItem(result, 0, PyInt_FromLong(I->N));
    PyTuple_SetItem(result, 1, PConvFloatVLAToPyTuple(I->V));
    PyTuple_SetItem(result, 2, PConvFloatVLAToPyTuple(I->VN));
    PyTuple_SetItem(result, 3, PyInt_FromLong(I->NT));
    PyTuple_SetItem(result, 4, PConvIntVLAToPyTuple(I->T));
    PyTuple_SetItem(result, 5, PConvIntVLAToPyTuple(I->S));
  }
  return result;
}

OV_INLINE_STATIC ov_status SurfaceJobResultFromTuple(PyMOLGlobals * G,
                                                     SurfaceJob * I, PyObject * tuple)
{
  ov_status status = OV_STATUS_FAILURE;
  SurfaceJobPurgeResult(G, I);
  if(tuple && PyTuple_Check(tuple)) {
    ov_size size = PyTuple_Size(tuple);
    if(size >= 6) {
      status = OV_STATUS_SUCCESS;

      I->N = PyInt_AsLong(PyTuple_GetItem(tuple, 0));
      if(OV_OK(status))
        status = PConvPyTupleToFloatVLA(&I->V, PyTuple_GetItem(tuple, 1));
      if(OV_OK(status))
        status = PConvPyTupleToFloatVLA(&I->VN, PyTuple_GetItem(tuple, 2));
      I->NT = PyInt_AsLong(PyTuple_GetItem(tuple, 3));
      if(OV_OK(status))
        status = PConvPyTupleToIntVLA(&I->T, PyTuple_GetItem(tuple, 4));
      if(OV_OK(status))
        status = PConvPyTupleToIntVLA(&I->S, PyTuple_GetItem(tuple, 5));
    }
    if(OV_ERR(status))
      SurfaceJobPurgeResult(G, I);
  }
  return status;
}
#endif

static SurfaceJob *SurfaceJobNew(PyMOLGlobals * G)
{
  OOCalloc(G, SurfaceJob);
  return I;
}

static void SurfaceJobFree(PyMOLGlobals * G, SurfaceJob * I)
{
  SurfaceJobPurgeResult(G, I);
  VLAFreeP(I->coord);
  VLAFreeP(I->presentVla);
  VLAFreeP(I->atomInfo);
  VLAFreeP(I->carveVla);
  OOFreeP(I);
}

static int SurfaceJobRun(PyMOLGlobals * G, SurfaceJob * I)
{
  int ok = true;
  int MaxN;
  int n_index = VLAGetSize(I->atomInfo);
  int n_present = I->nPresent;
  SphereRec *sp = G->Sphere->Sphere[I->sphereIndex];
  SphereRec *ssp = G->Sphere->Sphere[I->solventSphereIndex];

  SurfaceJobPurgeResult(G, I);

  {
    /* compute limiting storage requirements */
    int tmp = n_present;
    if(tmp < 1)
      tmp = 1;
    if(sp->nDot < ssp->nDot)
      MaxN = tmp * ssp->nDot;
    else
      MaxN = tmp * sp->nDot;
  }

  I->V = VLAlloc(float, (MaxN + 1) * 3);
  I->VN = VLAlloc(float, (MaxN + 1) * 3);

  if(G->Interrupt)
    ok = false;

  if(!(I->V && I->VN) || (!ok)) {       /* bail out point -- try to reduce crashes */
    PRINTFB(G, FB_RepSurface, FB_Errors)
      "Error-RepSurface: insufficient memory to calculate surface at this quality.\n"
      ENDFB(G);
    VLAFreeP(I->V);
    I->V = NULL;
    VLAFreeP(I->VN);
    I->VN = NULL;
    ok = false;
  } else {
    SolventDot *sol_dot = NULL;
    float *v = I->V;
    float *vn = I->VN;
    MapType *carve_map = NULL;
    float probe_radius = I->probeRadius;
    int circumscribe = I->circumscribe;
    int surface_type = I->surfaceType;
    float point_sep = I->pointSep;
    float *I_coord = I->coord;
    int *present_vla = I->presentVla;
    SurfaceJobAtomInfo *I_atom_info = I->atomInfo;

    I->N = 0;

    sol_dot = SolventDotNew(G, I->coord, I->atomInfo, probe_radius,
                            ssp, present_vla,
                            circumscribe, I->surfaceMode, I->surfaceSolvent,
                            I->cavityCull, I->allVisibleFlag, I->maxVdw,
                            I->cavityMode, I->cavityRadius, I->cavityCutoff);

    if((!sol_dot) || (G->Interrupt))
      ok = false;

    if(ok && sol_dot) {
      if(!I->surfaceSolvent) {

        float solv_tole = point_sep * 0.04F;
        float probe_rad_more;
        float probe_rad_less;
        float probe_rad_less2;

        if(probe_radius < (2.5F * point_sep)) { /* minimum probe radius allowed */
          probe_radius = 2.5F * point_sep;
        }

        probe_rad_more = probe_radius * (1.0F + solv_tole);

        switch (surface_type) {
        case 0:                /* solid */
        case 3:
        case 4:
        case 5:
        case 6:
          probe_rad_less = probe_radius;
          break;
        default:
          probe_rad_less = probe_radius * (1.0F - solv_tole);
          break;
        }
        probe_rad_less2 = probe_rad_less * probe_rad_less;

        if(surface_type >= 5) { /* effectively double-weights atom points */
          if(sol_dot->nDot) {
            int a;
            float *v0 = sol_dot->dot;
            float *n0 = sol_dot->dotNormal;
            for(a = 0; a < sol_dot->nDot; a++) {
              scale3f(n0, -probe_radius, v);
              add3f(v0, v, v);
              copy3f(n0, vn);
              v += 3;
              vn += 3;
              n0 += 3;
              v0 += 3;
              I->N++;
            }
          }
        }
        if(G->Interrupt)
          ok = false;
        if(ok) {
          MapType *map, *solv_map;
          map = MapNewFlagged(G, I->maxVdw + probe_rad_more,
                              I->coord, VLAGetSize(I->coord) / 3, NULL, NULL);

          solv_map = MapNew(G, probe_rad_less, sol_dot->dot, sol_dot->nDot, NULL);
          if(map && solv_map) {

            MapSetupExpress(solv_map);
            MapSetupExpress(map);

            if(sol_dot->nDot) {
              int *dc = sol_dot->dotCode;
              Vector3f *dot = Alloc(Vector3f, sp->nDot);
              float *v0, *n0;

              {
                int b;
                for(b = 0; b < sp->nDot; b++) {
                  scale3f(sp->dot[b], probe_radius, dot[b]);
                }
              }
              v0 = sol_dot->dot;
              n0 = sol_dot->dotNormal;
              {
                int a, b;
                float dist2 = probe_rad_less2;
                int sp_nDot = sp->nDot;
                for(a = 0; a < sol_dot->nDot; a++) {
                  if(dc[a] || (surface_type < 6)) {     /* surface type 6 is completely scribed */
                    OrthoBusyFast(G, a + sol_dot->nDot * 2, sol_dot->nDot * 5); /* 2/5 to 3/5 */
                    for(b = 0; b < sp_nDot; b++) {
                      float *dot_b = dot[b];
                      v[0] = v0[0] + dot_b[0];
                      v[1] = v0[1] + dot_b[1];
                      v[2] = v0[2] + dot_b[2];
                      {
                        int flag = true;
                        int ii;
                        if((ii = *(MapLocusEStart(solv_map, v)))) {
                          register float *i_dot = sol_dot->dot;
                          register float dist = probe_rad_less;
                          register int *elist_ii = solv_map->EList + ii;
                          register float v_0 = v[0];
                          register int jj_next, jj = *(elist_ii++);
                          register float v_1 = v[1];
                          register float *v1 = i_dot + 3 * jj;
                          register float v_2 = v[2];
                          while(jj >= 0) {
                            /* huge bottleneck -- optimized for superscaler processors */
                            register float dx = v1[0], dy, dz;
                            jj_next = *(elist_ii++);
                            dx -= v_0;
                            if(jj != a) {
                              dx = (dx < 0.0F) ? -dx : dx;
                              dy = v1[1] - v_1;
                              if(!(dx > dist)) {
                                dy = (dy < 0.0F) ? -dy : dy;
                                dz = v1[2] - v_2;
                                if(!(dy > dist)) {
                                  dx = dx * dx;
                                  dz = (dz < 0.0F) ? -dz : dz;
                                  dy = dy * dy;
                                  if(!(dz > dist)) {
                                    dx = dx + dy;
                                    dz = dz * dz;
                                    if(!(dx > dist2))
                                      if((dx + dz) <= dist2) {
                                        flag = false;
                                        break;
                                      }
                                  }
                                }
                              }
                            }
                            v1 = i_dot + 3 * jj_next;
                            jj = jj_next;
                          }
                        }

                        /* at this point, we have points on the interior of the solvent surface,
                           so now we need to further trim that surface to cover atoms that are present */

                        if(flag) {
                          register int i = *(MapLocusEStart(map, v));
                          if(i) {
                            register int j = map->EList[i++];
                            while(j >= 0) {
                              SurfaceJobAtomInfo *atom_info = I_atom_info + j;
                              if((!present_vla) || present_vla[j]) {
                                if(within3f
                                   (I_coord + 3 * j, v,
                                    atom_info->vdw + probe_rad_more)) {
                                  flag = false;
                                  break;
                                }
                              }
                              j = map->EList[i++];
                            }
                          }
                          if(!flag) {   /* compute the normals */
                            vn[0] = -sp->dot[b][0];
                            vn[1] = -sp->dot[b][1];
                            vn[2] = -sp->dot[b][2];
                            if(I->N < MaxN) {
                              I->N++;
                              v += 3;
                              vn += 3;
                            } else {
                              int v_offset = v - I->V;
                              int vn_offset = vn - I->VN;
                              MaxN = MaxN * 2;
                              VLASize(I->V, float, (MaxN + 1) * 3);
                              VLASize(I->VN, float, (MaxN + 1) * 3);
                              v = I->V + v_offset;
                              vn = I->VN + vn_offset;
                            }
                          }
                        }
                      }
                    }
                  }
                  v0 += 3;
                  n0 += 3;
                  if(G->Interrupt) {
                    ok = false;
                    break;
                  }
                }
              }
              FreeP(dot);
            }
          }
          MapFree(solv_map);
          MapFree(map);
        }
      } else {
        float *v0 = sol_dot->dot;
        float *n0 = sol_dot->dotNormal;
        int a;
        circumscribe = 0;
        if(sol_dot->nDot) {
          for(a = 0; a < sol_dot->nDot; a++) {
            *(v++) = *(v0++);
            *(vn++) = *(n0++);
            *(v++) = *(v0++);
            *(vn++) = *(n0++);
            *(v++) = *(v0++);
            *(vn++) = *(n0++);
            I->N++;
          }
        }
      }
    }
    SolventDotFree(sol_dot);
    sol_dot = NULL;
    if(G->Interrupt)
      ok = false;
    if(ok) {
      int refine, ref_count = 1;

      if((surface_type == 0) && (circumscribe)) {
        ref_count = 2;          /* these constants need more tuning... */
      }

      for(refine = 0; refine < ref_count; refine++) {

        /* add new vertices in regions where curvature is very high
           or where there are gaps with no points */

        if(ok && I->N && (surface_type == 0) && (circumscribe)) {
          int n_new = 0;

          float neighborhood = 2.6 * point_sep; /* these constants need more tuning... */
          float dot_cutoff = 0.666;
          float insert_cutoff = 1.1 * point_sep;

          float map_cutoff = neighborhood;
          float *new_dot = VLAlloc(float, 1000);

          if(map_cutoff < (2.9 * point_sep)) {  /* these constants need more tuning... */
            map_cutoff = 2.9 * point_sep;
          }

          {
            MapType *map = NULL;
            int a;
            map = MapNew(G, map_cutoff, I->V, I->N, NULL);
            MapSetupExpress(map);
            v = I->V;
            vn = I->VN;
            for(a = 0; a < I->N; a++) {
              register int i = *(MapLocusEStart(map, v));
              if(i) {
                register int j = map->EList[i++];
                while(j >= 0) {
                  if(j > a) {
                    float *v0 = I->V + 3 * j;
                    if(within3f(v0, v, map_cutoff)) {
                      int add_new = false;
                      float *n0 = I->VN + 3 * j;
                      VLACheck(new_dot, float, n_new * 6 + 5);
                      {
                        float *v1 = new_dot + n_new * 6;
                        average3f(v, v0, v1);
                        if((dot_product3f(n0, vn) < dot_cutoff)
                           && (within3f(v0, v, neighborhood)))
                          add_new = true;
                        else {
                          /* if points are too far apart, insert a new one */
                          register int ii = *(MapLocusEStart(map, v1));
                          if(ii) {
                            int found = false;
                            register int jj = map->EList[ii++];
                            while(jj >= 0) {
                              if(jj != j) {
                                float *vv0 = I->V + 3 * jj;
                                if(within3f(vv0, v1, insert_cutoff)) {
                                  found = true;
                                  break;
                                }
                              }
                              jj = map->EList[ii++];
                            }
                            if(!found)
                              add_new = true;
                          }
                        }
                        if(add_new) {
                          /* highly divergent */
                          float *n1 = v1 + 3;
                          n_new++;
                          average3f(vn, n0, n1);
                          normalize3f(n1);
                        }
                      }
                    }
                  }
                  j = map->EList[i++];
                }
              }
              v += 3;
              vn += 3;
            }
            MapFree(map);
          }
          if(n_new) {
            float *n1 = new_dot + 3;
            float *v1 = new_dot;
            VLASize(I->V, float, 3 * (I->N + n_new));
            VLASize(I->VN, float, 3 * (I->N + n_new));
            v = I->V + 3 * I->N;
            vn = I->VN + 3 * I->N;
            I->N += n_new;
            while(n_new--) {
              copy3f(v1, v);
              copy3f(n1, vn);
              v += 3;
              vn += 3;
              v1 += 6;
              n1 += 6;
            }
          }
          VLAFreeP(new_dot);
        }

        if(ok && I->N && (surface_type == 0) && (circumscribe)) {

          float cutoff = 0.5 * probe_radius;

          /* combine scribing with an atom proximity cleanup pass */

          int *dot_flag = Calloc(int, I->N);
          MapType *map =
            MapNewFlagged(G, I->maxVdw + probe_radius, I_coord, n_index, NULL,
                          present_vla);
          int a;
          MapSetupExpress(map);
          v = I->V;
          for(a = 0; a < I->N; a++) {
            register int i = *(MapLocusEStart(map, v));
            if(i) {
              register int j = map->EList[i++];
              while(j >= 0) {
                SurfaceJobAtomInfo *atom_info = I_atom_info + j;
                if((!present_vla) || present_vla[j]) {
                  if(within3f(I_coord + 3 * j, v, atom_info->vdw + cutoff)) {
                    dot_flag[a] = true;
                  }
                }
                j = map->EList[i++];
              }
            }
            v += 3;
            if(G->Interrupt) {
              ok = false;
              break;
            }
          }

          MapFree(map);
          map = NULL;

          if(ok) {
            /* purge unused dots */

            float *v0 = I->V;
            float *vn0 = I->VN;
            int *p = dot_flag;
            int c = I->N;
            int a;
            v = I->V;
            vn = I->VN;
            I->N = 0;
            for(a = 0; a < c; a++) {
              if(*(p++)) {
                *(v0++) = *(v++);
                *(v0++) = *(v++);
                *(v0++) = *(v++);
                *(vn0++) = *(vn++);
                *(vn0++) = *(vn++);
                *(vn0++) = *(vn++);
                I->N++;
              } else {
                v += 3;
                vn += 3;
              }
            }
          }
          FreeP(dot_flag);
        }

        /* now, eliminate dots that are too close to each other */

        /*    CGOColor(I->debug,0.0,1.0,0.0);
           CGOBegin(I->debug,GL_POINTS);
           for(a=0;a<I->N;a++)
           CGOVertexv(I->debug,I->V+3*a);
           CGOEnd(I->debug);
         */

        if(ok && I->N) {
          int repeat_flag = true;
          float min_dot = 0.1F;
          int *dot_flag = Alloc(int, I->N);
          while(repeat_flag) {
            repeat_flag = false;

            if(surface_type >= 3) {
              register int jj;
              float dist;
              register float nearest;
              register float min_sep2 = point_sep * point_sep;
              float diff[3];
              {
                int a;
                for(a = 0; a < I->N; a++)
                  dot_flag[a] = 1;
              }
              {
                MapType *map = MapNew(G, point_sep + 0.05F, I->V, I->N, NULL);
                int a;
                MapSetupExpress(map);
                v = I->V;
                vn = I->VN;
                for(a = 0; a < I->N; a++) {
                  if(dot_flag[a]) {
                    register int i = *(MapLocusEStart(map, v));
                    if(i) {
                      register int j = map->EList[i++];
                      jj = I->N;
                      nearest = point_sep + 1.0F;
                      while(j >= 0) {
                        if(j > a) {
                          if(dot_flag[j]) {
                            if(dot_product3f(I->VN + (3 * j), vn) > min_dot) {
                              if(within3fret
                                 (I->V + (3 * j), v, point_sep, min_sep2, diff, &dist)) {
                                repeat_flag = true;
                                if(dist < nearest) {
                                  /* try to be as determinstic as possible
                                     in terms of how we collapse points */
                                  jj = j;
                                  nearest = dist;
                                } else if((j < jj) && (fabs(dist - nearest) < R_SMALL4)) {
                                  jj = j;
                                  nearest = dist;
                                }
                              }
                            }
                          }
                        }
                        j = map->EList[i++];
                      }

                      if(jj < I->N) {
                        dot_flag[jj] = 0;
                        add3f(vn, I->VN + (3 * jj), vn);
                        average3f(I->V + (3 * jj), v, v);
                        repeat_flag = true;
                      }
                    }
                  }
                  v += 3;
                  vn += 3;
                  if(G->Interrupt) {
                    ok = false;
                    break;
                  }
                }
                MapFree(map);
              }
            } else {            /* surface types < 3 */
              int a;
              MapType *map = MapNew(G, -point_sep, I->V, I->N, NULL);
              for(a = 0; a < I->N; a++)
                dot_flag[a] = 1;
              MapSetupExpress(map);
              v = I->V;
              vn = I->VN;
              for(a = 0; a < I->N; a++) {
                if(dot_flag[a]) {
                  register int i = *(MapLocusEStart(map, v));
                  if(i) {
                    register int j = map->EList[i++];
                    while(j >= 0) {
                      if(j != a) {
                        if(dot_flag[j]) {
                          if(within3f(I->V + (3 * j), v, point_sep)) {
                            dot_flag[j] = 0;
                            add3f(vn, I->VN + (3 * j), vn);
                            average3f(I->V + (3 * j), v, v);
                            repeat_flag = true;
                          }
                        }
                      }
                      j = map->EList[i++];
                    }
                  }
                }
                v += 3;
                vn += 3;
                if(G->Interrupt) {
                  ok = false;
                  break;
                }
              }
              MapFree(map);
            }

            if(ok) {
              float *v0 = I->V;
              float *vn0 = I->VN;
              int *p = dot_flag;
              int c = I->N;
              int a;
              v = I->V;
              vn = I->VN;
              I->N = 0;
              for(a = 0; a < c; a++) {
                if(*(p++)) {
                  *(v0++) = *(v++);
                  *(v0++) = *(v++);
                  *(v0++) = *(v++);
                  normalize3f(vn);
                  *(vn0++) = *(vn++);
                  *(vn0++) = *(vn++);
                  *(vn0++) = *(vn++);
                  I->N++;
                } else {
                  v += 3;
                  vn += 3;
                }
              }
            }
            if(G->Interrupt) {
              ok = false;
              break;
            }
          }
          FreeP(dot_flag);
        }

        /* now eliminate troublesome vertices in regions of extremely high curvature */

        if(ok && (surface_type != 3) &&
           I->N && (I->trimCutoff > 0.0F) && (I->trimFactor > 0.0F)) {
          float trim_cutoff = I->trimCutoff;
          float trim_factor = I->trimFactor;
          int repeat_flag = true;
          float neighborhood = trim_factor * point_sep;
          float dot_sum;
          int n_nbr;
          int *dot_flag = Alloc(int, I->N);
          if(surface_type == 6) {       /* emprical tweaks */
            trim_factor *= 2.5;
            trim_cutoff *= 1.5;
          }
          while(repeat_flag) {
            int a;
            MapType *map = MapNew(G, neighborhood, I->V, I->N, NULL);
            repeat_flag = false;

            for(a = 0; a < I->N; a++)
              dot_flag[a] = 1;
            MapSetupExpress(map);
            v = I->V;
            vn = I->VN;
            for(a = 0; a < I->N; a++) {
              if(dot_flag[a]) {
                register int i = *(MapLocusEStart(map, v));
                if(i) {
                  register int j = map->EList[i++];
                  n_nbr = 0;
                  dot_sum = 0.0F;
                  while(j >= 0) {
                    if(j != a) {
                      if(dot_flag[j]) {
                        float *v0 = I->V + 3 * j;
                        if(within3f(v0, v, neighborhood)) {
                          float *n0 = I->VN + 3 * j;
                          dot_sum += dot_product3f(n0, vn);
                          n_nbr++;
                        }
                      }
                    }
                    j = map->EList[i++];
                  }

                  if(n_nbr) {
                    dot_sum /= n_nbr;
                    if(dot_sum < trim_cutoff) {
                      dot_flag[a] = false;
                      repeat_flag = true;
                    }
                  }
                }
              }
              v += 3;
              vn += 3;
              if(G->Interrupt) {
                ok = false;
                break;
              }
            }

            if(ok) {
              float *v0 = I->V;
              float *vn0 = I->VN;
              int *p = dot_flag;
              int c = I->N;
              v = I->V;
              vn = I->VN;
              I->N = 0;
              for(a = 0; a < c; a++) {
                if(*(p++)) {
                  *(v0++) = *(v++);
                  *(v0++) = *(v++);
                  *(v0++) = *(v++);
                  normalize3f(vn);
                  *(vn0++) = *(vn++);
                  *(vn0++) = *(vn++);
                  *(vn0++) = *(vn++);
                  I->N++;
                } else {
                  v += 3;
                  vn += 3;
                }
              }
            }
            MapFree(map);
            if(G->Interrupt) {
              ok = false;
              break;
            }
          }
          FreeP(dot_flag);
        }
        if(G->Interrupt) {
          ok = false;
          break;
        }
      }
    }

    if(I->N && I->V && I->VN) {
      VLASizeForSure(I->V, float, 3 * I->N);
      VLASizeForSure(I->VN, float, 3 * I->N);
    }

    PRINTFB(G, FB_RepSurface, FB_Blather)
      " RepSurface: %i surface points.\n", I->N ENDFB(G);

    if(G->Interrupt)
      ok = false;

    OrthoBusyFast(G, 3, 5);
    if(ok && I->N) {
      if(surface_type != 1) {   /* not a dot surface... */
        float cutoff = point_sep * 5.0F;
        if((cutoff > probe_radius) && (!I->surfaceSolvent))
          cutoff = probe_radius;
        I->T = TrianglePointsToSurface(G, I->V, I->VN, I->N, cutoff, &I->NT, &I->S, NULL, 
                                       I->cavityMode);
        PRINTFB(G, FB_RepSurface, FB_Blather)
          " RepSurface: %i triangles.\n", I->NT ENDFB(G);
      }
    } else {
      VLASizeForSure(I->V, float, 1);
      VLASizeForSure(I->VN, float, 1);
    }
    if(carve_map)
      MapFree(carve_map);
  }
  return ok;
}

Rep *RepSurfaceNew(CoordSet * cs, int state)
{
  int ok = true;
  PyMOLGlobals *G = cs->State.G;
  ObjectMolecule *obj = cs->Obj;
  OOCalloc(G, RepSurface);

  {
    int surface_mode =
      SettingGet_i(G, cs->Setting, obj->Obj.Setting, cSetting_surface_mode);
    int cullByFlag = (surface_mode == cRepSurface_by_flags);
    int inclH = !((surface_mode == cRepSurface_heavy_atoms)
                  || (surface_mode == cRepSurface_vis_heavy_only));
    int inclInvis = !((surface_mode == cRepSurface_vis_only)
                      || (surface_mode == cRepSurface_vis_heavy_only));
    int visFlag = false;

    if(obj->RepVisCache[cRepSurface]) {
      register int *idx_to_atm = cs->IdxToAtm;
      register AtomInfoType *obj_AtomInfo = obj->AtomInfo;
      register int a, cs_NIndex = cs->NIndex;
      for(a = 0; a < cs_NIndex; a++) {
        register AtomInfoType *ai1 = obj_AtomInfo + *(idx_to_atm++);
        if(ai1->visRep[cRepSurface] &&
           (inclH || (!ai1->hydrogen)) &&
           ((!cullByFlag) || (!(ai1->flags &
                                (cAtomFlag_exfoliate | cAtomFlag_ignore))))) {
          visFlag = true;
          break;
        }
      }
    }
    if(!visFlag) {
      OOFreeP(I);
      return (NULL);            /* skip if no thing visible */
    }

    {
      int surface_flag = false;

      int surface_type =
        SettingGet_i(G, cs->Setting, obj->Obj.Setting, cSetting_surface_type);
      int surface_solvent =
        SettingGet_b(G, cs->Setting, obj->Obj.Setting, cSetting_surface_solvent);
      int surface_quality =
        SettingGet_i(G, cs->Setting, obj->Obj.Setting, cSetting_surface_quality);
      float probe_radius =
        SettingGet_f(G, cs->Setting, obj->Obj.Setting, cSetting_solvent_radius);
      int optimize =
        SettingGet_i(G, cs->Setting, obj->Obj.Setting, cSetting_surface_optimize_subsets);

      int circumscribe =
        SettingGet_i(G, cs->Setting, obj->Obj.Setting, cSetting_surface_circumscribe);
      float trim_cutoff =
        SettingGet_f(G, cs->Setting, obj->Obj.Setting, cSetting_surface_trim_cutoff);

      float trim_factor =
        SettingGet_f(G, cs->Setting, obj->Obj.Setting, cSetting_surface_trim_factor);
      int sphere_idx = 0, solv_sph_idx = 0;
      MapType *map = NULL;
      float point_sep;
      int *present_vla = NULL;
      int n_present = 0;
      int carve_state = 0;
      int carve_flag = false;
      float carve_cutoff;
      char *carve_selection = NULL;
      float *carve_vla = NULL;
      MapType *carve_map = NULL;

      int cavity_mode = SettingGet_i(G, cs->Setting, obj->Obj.Setting, cSetting_surface_cavity_mode);
      float cavity_radius = SettingGet_f(G, cs->Setting, obj->Obj.Setting, cSetting_surface_cavity_radius);
      float cavity_cutoff = SettingGet_f(G, cs->Setting, obj->Obj.Setting, cSetting_surface_cavity_cutoff);

      I->Type = surface_type;

      I->max_vdw = ObjectMoleculeGetMaxVDW(obj);

      if(surface_quality >= 4) {        /* totally impractical */
        point_sep =
          SettingGet_f(G, cs->Setting, obj->Obj.Setting, cSetting_surface_best) / 4;
        sphere_idx = 4;
        solv_sph_idx = 4;
        if(circumscribe < 0)
          circumscribe = 91;
      } else {
        switch (surface_quality) {
        case 3:                /* nearly impractical */
          point_sep =
            SettingGet_f(G, cs->Setting, obj->Obj.Setting, cSetting_surface_best) / 3;
          sphere_idx = 4;
          solv_sph_idx = 3;
          if(circumscribe < 0)
            circumscribe = 71;
          break;
        case 2:
          /* nearly perfect */
          point_sep =
            SettingGet_f(G, cs->Setting, obj->Obj.Setting, cSetting_surface_best) / 2;
          sphere_idx = 3;
          solv_sph_idx = 3;
          if(circumscribe < 0)
            circumscribe = 41;
          break;
        case 1:
          /* good */
          point_sep =
            SettingGet_f(G, cs->Setting, obj->Obj.Setting, cSetting_surface_best);
          sphere_idx = 2;
          solv_sph_idx = 3;
          if((circumscribe < 0) && (surface_type == 6))
            circumscribe = 40;
          break;
        case 0:
          /* 0 - normal */
          point_sep =
            SettingGet_f(G, cs->Setting, obj->Obj.Setting, cSetting_surface_normal);
          sphere_idx = 1;
          solv_sph_idx = 2;
          if((circumscribe < 0) && (surface_type == 6))
            circumscribe = 30;
          break;
        case -1:
          /* -1 */
          point_sep =
            SettingGet_f(G, cs->Setting, obj->Obj.Setting, cSetting_surface_poor);
          sphere_idx = 1;
          solv_sph_idx = 2;
          if((circumscribe < 0) && (surface_type == 6))
            circumscribe = 10;
          break;
        case -2:
          /* -2 god awful */
          point_sep =
            SettingGet_f(G, cs->Setting, obj->Obj.Setting, cSetting_surface_poor) * 1.5F;
          sphere_idx = 1;
          solv_sph_idx = 1;
          break;
        case -3:
          /* -3 miserable */
          point_sep =
            SettingGet_f(G, cs->Setting, obj->Obj.Setting, cSetting_surface_miserable);
          sphere_idx = 1;
          solv_sph_idx = 1;
          break;
        default:
          point_sep =
            SettingGet_f(G, cs->Setting, obj->Obj.Setting,
                         cSetting_surface_miserable) * 1.18F;
          sphere_idx = 0;
          solv_sph_idx = 1;
        }
      }

      if((circumscribe < 0) || (!surface_solvent))
        circumscribe = 0;

      RepInit(G, &I->R);
      I->R.context.object = (void *) obj;
      I->R.context.state = state;
      I->R.fRender = (void (*)(struct Rep *, RenderInfo * info)) RepSurfaceRender;
      I->R.fFree = (void (*)(struct Rep *)) RepSurfaceFree;
      I->R.fRecolor = (void (*)(struct Rep *, struct CoordSet *)) RepSurfaceColor;
      I->R.fSameVis = (int (*)(struct Rep *, struct CoordSet *)) RepSurfaceSameVis;
      I->R.obj = (CObject *) (cs->Obj);
      I->R.cs = cs;
      I->allVisibleFlag = true;
      obj = cs->Obj;

      /* don't waist time computing a Surface unless we need it!! */
      {
        register int *idx_to_atm = cs->IdxToAtm;
        register AtomInfoType *obj_AtomInfo = obj->AtomInfo;
        register int a, cs_NIndex = cs->NIndex;
        for(a = 0; a < cs_NIndex; a++) {
          register AtomInfoType *ai1 = obj_AtomInfo + *(idx_to_atm++);
          if(ai1->visRep[cRepSurface] &&
             (inclH || (!ai1->hydrogen)) &&
             ((!cullByFlag) || (!(ai1->flags &
                                  (cAtomFlag_exfoliate | cAtomFlag_ignore)))))
            surface_flag = true;
          else {
            I->allVisibleFlag = false;
            if(surface_flag)
              break;
          }
        }
      }
      if(surface_flag) {
        SurfaceJobAtomInfo *atom_info = VLACalloc(SurfaceJobAtomInfo, cs->NIndex);
        if(atom_info) {
          AtomInfoType *i_ai, *obj_atom_info = obj->AtomInfo;
          int *idx_to_atm = cs->IdxToAtm;
          int n_index = cs->NIndex;
          SurfaceJobAtomInfo *i_atom_info = atom_info;
          int i;
          for(i = 0; i < n_index; i++) {
            i_ai = obj_atom_info + idx_to_atm[i];
            /* just surfacing flags */
            i_atom_info->flags = i_ai->flags & (cAtomFlag_ignore | cAtomFlag_exfoliate);
            i_atom_info->vdw = i_ai->vdw;
            i_atom_info++;
          }
        }

        OrthoBusyFast(G, 0, 1);

        n_present = cs->NIndex;

        carve_selection =
          SettingGet_s(G, cs->Setting, obj->Obj.Setting,
                       cSetting_surface_carve_selection);
        carve_cutoff =
          SettingGet_f(G, cs->Setting, obj->Obj.Setting, cSetting_surface_carve_cutoff);
        if((!carve_selection) || (!carve_selection[0]))
          carve_cutoff = 0.0F;
        if(carve_cutoff > 0.0F) {
          carve_state =
            SettingGet_i(G, cs->Setting, obj->Obj.Setting,
                         cSetting_surface_carve_state) - 1;
          carve_cutoff += 2 * I->max_vdw + probe_radius;

          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;
          I->allVisibleFlag = false;
        }
        if(!I->allVisibleFlag) {
          /* optimize the space over which we calculate a surface */

          /* first find out which atoms are actually to be surfaced */

          present_vla = VLAlloc(int, cs->NIndex);
          {
            register int *ap = present_vla;
            register int *idx_to_atm = cs->IdxToAtm;
            register AtomInfoType *obj_AtomInfo = obj->AtomInfo;
            register int a, cs_NIndex = cs->NIndex;
            for(a = 0; a < cs_NIndex; a++) {
              register AtomInfoType *ai1 = obj_AtomInfo + *(idx_to_atm++);
              if(ai1->visRep[cRepSurface] &&
                 (inclH || (!ai1->hydrogen)) &&
                 ((!cullByFlag) || (!(ai1->flags &
                                      (cAtomFlag_ignore | cAtomFlag_exfoliate)))))
                *ap = 2;
              else
                *ap = 0;
              ap++;
            }
          }

          map =
            MapNewFlagged(G, 2 * I->max_vdw + probe_radius, cs->Coord, cs->NIndex, NULL,
                          present_vla);
          MapSetupExpress(map);

          if(inclInvis) {
            /* then add in the nearby atoms which are not surfaced and not ignored */
            float probe_radiusX2 = probe_radius * 2;
            int a;
            for(a = 0; a < cs->NIndex; a++)
              if(!present_vla[a]) {
                AtomInfoType *ai1 = obj->AtomInfo + cs->IdxToAtm[a];
                if((inclH || (!ai1->hydrogen)) &&
                   ((!cullByFlag) || 
                    !(ai1->flags & cAtomFlag_ignore))) {
                  float *v0 = cs->Coord + 3 * a;
                  int i = *(MapLocusEStart(map, v0));
                  if(optimize) {
                    if(i) {
                      int j = map->EList[i++];
                      while(j >= 0) {
                        if(present_vla[j] > 1) {
                          AtomInfoType *ai2 = obj->AtomInfo + cs->IdxToAtm[j];
                          if(within3f
                             (cs->Coord + 3 * j, v0,
                              ai1->vdw + ai2->vdw + probe_radiusX2)) {
                            present_vla[a] = 1;
                            break;
                          }
                        }
                        j = map->EList[i++];
                      }
                    }
                  } else
                    present_vla[a] = 1;
                }
              }
          }

          if(carve_flag && (!optimize)) {
            /* and optimize for carved region */
            int a;
            for(a = 0; a < cs->NIndex; a++) {
              int include_flag = false;
              if(carve_map) {
                float *v0 = cs->Coord + 3 * a;
                int i = *(MapLocusEStart(carve_map, v0));
                if(i) {
                  int j = carve_map->EList[i++];
                  while(j >= 0) {
                    if(within3f(carve_vla + 3 * j, v0, carve_cutoff)) {
                      include_flag = true;
                      break;
                    }
                    j = carve_map->EList[i++];
                  }
                }
              }
              if(!include_flag)
                present_vla[a] = 0;
            }
          }
          MapFree(map);
          map = NULL;

          /* now count how many atoms we actually need to think about */

          n_present = 0;
          {
            int a;
            for(a = 0; a < cs->NIndex; a++) {
              if(present_vla[a]) {
                n_present++;
              }
            }
          }
        }

        {
          SurfaceJob *surf_job = SurfaceJobNew(G);

          if(surf_job) {

            surf_job->maxVdw = I->max_vdw;
            surf_job->allVisibleFlag = I->allVisibleFlag;

            surf_job->atomInfo = atom_info;
            atom_info = NULL;

            surf_job->nPresent = n_present;
            if(present_vla && optimize) {
              /* implies that n_present < cs->NIndex, so eliminate
                 irrelevant atoms & coordinates if we are optimizing subsets */
              surf_job->coord = VLAlloc(float, n_present * 3);
              {
                int *p = present_vla;
                SurfaceJobAtomInfo *ai_src = surf_job->atomInfo;
                SurfaceJobAtomInfo *ai_dst = surf_job->atomInfo;
                float *v_src = cs->Coord;
                float *v_dst = surf_job->coord;
                int a;

                for(a = 0; a < cs->NIndex; a++) {
                  if(*(p++)) {
                    copy3f(v_src, v_dst);
                    v_dst += 3;
                    if(ai_dst != ai_src)
                      *ai_dst = *ai_src;
                    ai_dst++;
                  }
                  v_src += 3;
                  ai_src++;
                }
              }
              VLASize(surf_job->atomInfo, SurfaceJobAtomInfo, n_present);
            } else {
              surf_job->presentVla = present_vla;
              present_vla = NULL;
              surf_job->coord = VLAlloc(float, cs->NIndex * 3);
              if(surf_job->coord)
                UtilCopyMem(surf_job->coord, cs->Coord, sizeof(float) * 3 * cs->NIndex);
            }

            surf_job->sphereIndex = sphere_idx;
            surf_job->solventSphereIndex = solv_sph_idx;

            surf_job->surfaceType = surface_type;
            surf_job->circumscribe = circumscribe;
            surf_job->probeRadius = probe_radius;
            surf_job->pointSep = point_sep;

            surf_job->trimCutoff = trim_cutoff;
            surf_job->trimFactor = trim_factor;

            surf_job->cavityMode = cavity_mode;
            surf_job->cavityRadius = cavity_radius;
            surf_job->cavityCutoff = cavity_cutoff;

            if(carve_vla)
              surf_job->carveVla = VLACopy(carve_vla, float);
            surf_job->carveCutoff = carve_cutoff;

            surf_job->surfaceMode = surface_mode;
            surf_job->surfaceSolvent = surface_solvent;

            surf_job->cavityCull = SettingGet_i(G, cs->Setting,
                                                obj->Obj.Setting, cSetting_cavity_cull);
          }

          if(G->Interrupt)
            ok = false;

          if(ok) {
            int found = false;
#ifndef _PYMOL_NOPY
            PyObject *entry = NULL;
            PyObject *output = NULL;
            PyObject *input = NULL;
            int cache_mode =
              SettingGet_i(G, cs->Setting, obj->Obj.Setting, cSetting_cache_mode);

            if(cache_mode > 0) {
              int blocked = PAutoBlock(G);
              input = SurfaceJobInputAsTuple(G, surf_job);

              if(PCacheGet(G, &output, &entry, input) == OV_STATUS_YES) {
                if(OV_OK(SurfaceJobResultFromTuple(G, surf_job, output))) {
                  found = true;
                  PXDecRef(input);
                  input = NULL;
                  PXDecRef(entry);
                  entry = NULL;
                }
                PXDecRef(output);
                output = NULL;
              }
              if(PyErr_Occurred())
                PyErr_Print();

              PAutoUnblock(G, blocked);
            }
#endif
            if(!found) {

              SurfaceJobRun(G, surf_job);

#ifndef _PYMOL_NOPY
              if(cache_mode > 1) {
                int blocked = PAutoBlock(G);
                output = SurfaceJobResultAsTuple(G, surf_job);
                PCacheSet(G, entry, output);
                PXDecRef(entry);
                entry = NULL;
                PXDecRef(output);
                output = NULL;
                PXDecRef(input);
                input = NULL;
                PAutoUnblock(G, blocked);
              }
#endif
            }
#ifndef _PYMOL_NOPY
            if(entry || input || output) {
              int blocked = PAutoBlock(G);
              PXDecRef(entry);
              PXDecRef(input);
              PXDecRef(output);
              PAutoUnblock(G, blocked);
            }
#endif
          }
          /* surf_job must be valid at this point */

          I->N = surf_job->N;
          surf_job->N = 0;
          I->V = surf_job->V;
          surf_job->V = NULL;
          I->VN = surf_job->VN;
          surf_job->VN = NULL;
          I->NT = surf_job->NT;
          surf_job->NT = 0;
          I->T = surf_job->T;
          surf_job->T = NULL;
          I->S = surf_job->S;
          surf_job->S = NULL;

          SurfaceJobPurgeResult(G, surf_job);
          SurfaceJobFree(G, surf_job);

        }
        VLAFreeP(atom_info);

        if(G->Interrupt)
          ok = false;

        if(ok)
          RepSurfaceColor(I, cs);
      }
      if(carve_map)
        MapFree(carve_map);
      VLAFreeP(carve_vla);
      VLAFreeP(present_vla);
      if(I->debug)
        CGOStop(I->debug);
      OrthoBusyFast(G, 4, 4);
      if(!ok) {
        RepSurfaceFree(I);
        I = NULL;
      }
      return ((void *) (struct Rep *) I);
    }
  }
}

static SolventDot *SolventDotNew(PyMOLGlobals * G,
                                 float *coord,
                                 SurfaceJobAtomInfo * atom_info,
                                 float probe_radius, SphereRec * sp,
                                 int *present,
                                 int circumscribe, int surface_mode,
                                 int surface_solvent, int cavity_cull,
                                 int all_visible_flag, float max_vdw,
                                 int cavity_mode, float cavity_radius, 
                                 float cavity_cutoff)
{
  int ok = true;
  int b;
  float vdw;
  float probe_radius_plus;
  int maxDot = 0;
  int stopDot;
  int n_coord = VLAGetSize(atom_info);
  Vector3f *sp_dot = sp->dot;
  OOCalloc(G, SolventDot);

  /*  printf("%p %p %p %f %p %p %p %d %d %d %d %d %f\n",
     G,
     coord,
     atom_info,
     probe_radius,sp,
     extent,present,
     circumscribe,  surface_mode, 
     surface_solvent,  cavity_cull,
     all_visible_flag, max_vdw);
   */

  stopDot = n_coord * sp->nDot + 2 * circumscribe;
  I->dot = VLAlloc(float, (stopDot + 1) * 3);
  I->dotNormal = VLAlloc(float, (stopDot + 1) * 3);
  I->dotCode = VLACalloc(int, stopDot + 1);

  probe_radius_plus = probe_radius * 1.5F;

  I->nDot = 0;
  {
    int dotCnt = 0;
    MapType *map =
      MapNewFlagged(G, max_vdw + probe_radius, coord, n_coord, NULL, present);
    if(G->Interrupt)
      ok = false;
    if(map && ok) {
      float *v = I->dot;
      float *n = I->dotNormal;
      int *dc = I->dotCode;
      int maxCnt = 0;

      MapSetupExpress(map);
      {
        int a;
        int skip_flag;

        SurfaceJobAtomInfo *a_atom_info = atom_info;
        for(a = 0; a < n_coord; a++) {
          OrthoBusyFast(G, a, n_coord * 5);
          if((!present) || (present[a])) {
            register int i;
            float *v0 = coord + 3 * a;
            vdw = a_atom_info->vdw + probe_radius;

            skip_flag = false;

            i = *(MapLocusEStart(map, v0));
            if(i) {
              register int j = map->EList[i++];
              while(j >= 0) {
                SurfaceJobAtomInfo *j_atom_info = atom_info + j;
                if(j > a)       /* only check if this is atom trails */
                  if((!present) || present[j]) {
                    if((j_atom_info->vdw == a_atom_info->vdw)) {        /* handle singularities */
                      float *v1 = coord + 3 * j;
                      if((v0[0] == v1[0]) && (v0[1] == v1[1]) && (v0[2] == v1[2]))
                        skip_flag = true;
                    }
                  }
                j = map->EList[i++];
              }
            }
            if(!skip_flag) {
              for(b = 0; b < sp->nDot; b++) {
                float *sp_dot_b = (float*)(sp_dot + b);
                register int i;
                int flag = true;
                v[0] = v0[0] + vdw * (n[0] = sp_dot_b[0]);
                v[1] = v0[1] + vdw * (n[1] = sp_dot_b[1]);
                v[2] = v0[2] + vdw * (n[2] = sp_dot_b[2]);
                i = *(MapLocusEStart(map, v));
                if(i) {
                  register int j = map->EList[i++];
                  while(j >= 0) {
                    SurfaceJobAtomInfo *j_atom_info = atom_info + j;
                    if((!present) || present[j]) {
                      if(j != a) {
                        skip_flag = false;
                        if(j_atom_info->vdw == a_atom_info->vdw) {      /* handle singularities */
                          float *v1 = coord + 3 * j;
                          if((v0[0] == v1[0]) && (v0[1] == v1[1]) && (v0[2] == v1[2]))
                            skip_flag = true;
                        }
                        if(!skip_flag)
                          if(within3f(coord + 3 * j, v, j_atom_info->vdw + probe_radius)) {
                            flag = false;
                            break;
                          }
                      }
                    }
                    j = map->EList[i++];
                  }
                }
                if(flag && (dotCnt < stopDot)) {
                  dotCnt++;
                  v += 3;
                  n += 3;
                  dc++;
                  I->nDot++;
                }
              }
            }
            if(dotCnt > maxCnt) {
              maxCnt = dotCnt;
              maxDot = I->nDot - 1;
            }
          }
          a_atom_info++;
        }
      }

      /* for each pair of proximal atoms, circumscribe a circle for their intersection */

      /*    CGOReset(G->DebugCGO); */

      {
        MapType *map2 = NULL;
        if(circumscribe && (!surface_solvent))
          map2 =
            MapNewFlagged(G, 2 * (max_vdw + probe_radius), coord, n_coord, NULL, present);

        if(G->Interrupt)
          ok = false;
        if(map2 && ok) {
          /*        CGOBegin(G->DebugCGO,GL_LINES); */
          int a;
          int skip_flag;

          SurfaceJobAtomInfo *a_atom_info = atom_info;
          MapSetupExpress(map2);
          for(a = 0; a < n_coord; a++) {
            if((!present) || present[a]) {
              register int i;
              float vdw2;
              float *v0 = coord + 3 * a;
              vdw = a_atom_info->vdw + probe_radius;
              vdw2 = vdw * vdw;

              skip_flag = false;

              i = *(MapLocusEStart(map2, v0));
              if(i) {
                register int j = map2->EList[i++];
                while(j >= 0) {
                  SurfaceJobAtomInfo *j_atom_info = atom_info + j;
                  if(j > a)     /* only check if this is atom trails */
                    if((!present) || present[j]) {
                      if((j_atom_info->vdw == a_atom_info->vdw)) {      /* handle singularities */
                        float *v2 = coord + 3 * j;
                        if((v0[0] == v2[0]) && (v0[1] == v2[1]) && (v0[2] == v2[2]))
                          skip_flag = true;
                      }
                    }
                  j = map2->EList[i++];
                }
              }

              if(!skip_flag) {
                register int ii = *(MapLocusEStart(map2, v0));
                if(ii) {
                  register int jj = map2->EList[ii++];
                  while(jj >= 0) {
                    SurfaceJobAtomInfo *jj_atom_info = atom_info + jj;
                    float dist;
                    if(jj > a)  /* only check if this is atom trails */
                      if((!present) || present[jj]) {
                        float vdw3 = jj_atom_info->vdw + probe_radius;

                        float *v2 = coord + 3 * jj;
                        dist = (float) diff3f(v0, v2);
                        if((dist > R_SMALL4) && (dist < (vdw + vdw3))) {
                          float vz[3], vx[3], vy[3], vp[3];
                          float tri_a = vdw, tri_b = vdw3, tri_c = dist;
                          float tri_s = (tri_a + tri_b + tri_c) * 0.5F;
                          float area = (float) sqrt1f(tri_s * (tri_s - tri_a) *
                                                      (tri_s - tri_b) * (tri_s - tri_c));
                          float radius = (2 * area) / dist;
                          float adj = (float) sqrt1f(vdw2 - radius * radius);

                          subtract3f(v2, v0, vz);
                          get_system1f3f(vz, vx, vy);

                          copy3f(vz, vp);
                          scale3f(vp, adj, vp);
                          add3f(v0, vp, vp);

                          for(b = 0; b <= circumscribe; b++) {
                            float xcos = (float) cos((b * 2 * cPI) / circumscribe);
                            float ysin = (float) sin((b * 2 * cPI) / circumscribe);
                            float xcosr = xcos * radius;
                            float ysinr = ysin * radius;
                            int flag = true;
                            v[0] = vp[0] + vx[0] * xcosr + vy[0] * ysinr;
                            v[1] = vp[1] + vx[1] * xcosr + vy[1] * ysinr;
                            v[2] = vp[2] + vx[2] * xcosr + vy[2] * ysinr;

                            i = *(MapLocusEStart(map, v));
                            if(i) {
                              register int j = map->EList[i++];
                              while(j >= 0) {
                                SurfaceJobAtomInfo *j_atom_info = atom_info + j;
                                if((!present) || present[j])
                                  if((j != a) && (j != jj)) {
                                    skip_flag = false;
                                    if(a_atom_info->vdw == j_atom_info->vdw) {  /* handle singularities */
                                      float *v1 = coord + 3 * j;
                                      if((v0[0] == v1[0]) &&
                                         (v0[1] == v1[1]) && (v0[2] == v1[2]))
                                        skip_flag = true;
                                    }
                                    if(jj_atom_info->vdw == j_atom_info->vdw) { /* handle singularities */
                                      float *v1 = coord + 3 * j;
                                      if((v2[0] == v1[0]) &&
                                         (v2[1] == v1[1]) && (v2[2] == v1[2]))
                                        skip_flag = true;
                                    }
                                    if(!skip_flag)
                                      if(within3f
                                         (coord + 3 * j, v,
                                          j_atom_info->vdw + probe_radius)) {
                                        flag = false;
                                        break;
                                      }
                                  }
                                j = map->EList[i++];
                              }
                            }
                            if(flag && (dotCnt < stopDot)) {
                              float vt0[3], vt2[3];
                              subtract3f(v0, v, vt0);
                              subtract3f(v2, v, vt2);
                              normalize3f(vt0);
                              normalize3f(vt2);
                              add3f(vt0, vt2, n);
                              invert3f(n);
                              normalize3f(n);
                              /*
                                 n[0] = vx[0] * xcos + vy[0] * ysin;
                                 n[1] = vx[1] * xcos + vy[1] * ysin;
                                 n[2] = vx[2] * xcos + vy[2] * ysin;
                               */

#if 0
                              {
                                float sum[3];
                                scale3f(n, 0.2, sum);
                                add3f(v, sum, sum);
                                CGOVertexv(G->DebugCGO, v);
                                CGOVertexv(G->DebugCGO, sum);
                              }
#endif

                              *dc = 1;  /* mark as exempt */

                              dotCnt++;
                              v += 3;
                              n += 3;
                              dc++;
                              I->nDot++;
                            }
                          }
                        }
                      }
                    jj = map2->EList[ii++];
                  }
                }
              }
            }
            a_atom_info++;
            if(G->Interrupt) {
              ok = false;
              break;
            }
          }
        }
        MapFree(map2);
      }
    }
    MapFree(map);
    /*    CGOEnd(G->DebugCGO); */
  }

  if(cavity_mode) {
    float *cavityDot = VLAlloc(float, (stopDot + 1) * 3);
    int nCavityDot = 0;
    int dotCnt = 0;
    if(cavity_radius<0.0F) {
      cavity_radius = - probe_radius * cavity_radius;
    }
    if(cavity_cutoff<0.0F) {
      cavity_cutoff = cavity_radius - cavity_cutoff * probe_radius;
    }
    {
      MapType *map =
        MapNewFlagged(G, max_vdw + cavity_radius, coord, n_coord, NULL, present);
      if(G->Interrupt)
        ok = false;
      if(map && ok) {
        float *v = cavityDot;
        MapSetupExpress(map);
        {
          int a;
          int skip_flag;
          SurfaceJobAtomInfo *a_atom_info = atom_info;
          for(a = 0; a < n_coord; a++) {
            if((!present) || (present[a])) {
              register int i;
              float *v0 = coord + 3 * a;
              vdw = a_atom_info->vdw + cavity_radius;
              skip_flag = false;
              i = *(MapLocusEStart(map, v0));
              if(i) {
                register int j = map->EList[i++];
                while(j >= 0) {
                  SurfaceJobAtomInfo *j_atom_info = atom_info + j;
                  if(j > a)       /* only check if this is atom trails */
                    if((!present) || present[j]) {
                      if((j_atom_info->vdw == a_atom_info->vdw)) {        /* handle singularities */
                        float *v1 = coord + 3 * j;
                        if((v0[0] == v1[0]) && (v0[1] == v1[1]) && (v0[2] == v1[2]))
                          skip_flag = true;
                      }
                    }
                  j = map->EList[i++];
                }
              }
              if(!skip_flag) {
                for(b = 0; b < sp->nDot; b++) {
                  float *sp_dot_b = (float*)(sp_dot + b);
                  register int i;
                  int flag = true;
                  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]);
                  i = *(MapLocusEStart(map, v));
                  if(i) {
                    register int j = map->EList[i++];
                    while(j >= 0) {
                      SurfaceJobAtomInfo *j_atom_info = atom_info + j;
                      if((!present) || present[j]) {
                        if(j != a) {
                          skip_flag = false;
                          if(j_atom_info->vdw == a_atom_info->vdw) {
                            /* handle singularities */
                            float *v1 = coord + 3 * j;
                            if((v0[0] == v1[0]) && (v0[1] == v1[1]) && (v0[2] == v1[2]))
                              skip_flag = true;
                          }
                          if(!skip_flag) {
                            if(within3f(coord + 3 * j, v, j_atom_info->vdw + cavity_radius)) {
                              flag = false;
                              break;
                            }
                          }
                        }
                      }
                      j = map->EList[i++];
                    }
                  }
                  if(flag && (dotCnt < stopDot)) {
                    v += 3;
                    nCavityDot++;
                    dotCnt++;
                  }
                }
              }
            }
            a_atom_info++;
          }
        }
      }
      MapFree(map);
    }
    {
      int *dot_flag = Calloc(int, I->nDot);
      ErrChkPtr(G, dot_flag);
      {
        MapType *map = MapNew(G, cavity_cutoff, cavityDot, nCavityDot, NULL);
        if(map) {
          MapSetupExpress(map);
          {
            int *p = dot_flag;
            float *v = I->dot;
            int a;
            for(a = 0; a < I->nDot; a++) {
              register int i = *(MapLocusEStart(map, v));
              if(i) {
                register int j = map->EList[i++];
                while(j >= 0) {
                  if(within3f(cavityDot + (3 * j), v, cavity_cutoff)) {
                    *p = true;
                    break;
                  }
                  j = map->EList[i++];
                }
              }
              v += 3;
              p++;
              if(G->Interrupt) {
                ok = false;
                break;
              }
            }
          }
        }
        MapFree(map);
      }
      
      {
        float *v0 = I->dot;
        float *n0 = I->dotNormal;
        int *dc0 = I->dotCode;
        int *p = dot_flag;
        int c = I->nDot;
        float *n = n0;
        float *v = v0;
        int *dc = dc0;
        int a;
        I->nDot = 0;
        for(a = 0; a < c; a++) {
          if(!*(p++)) {
            *(v0++) = *(v++);
            *(n0++) = *(n++);
            *(v0++) = *(v++);
            *(n0++) = *(n++);
            *(v0++) = *(v++);
            *(n0++) = *(n++);
            *(dc0++) = *(dc++);
            I->nDot++;
          } else {
            v += 3;
            n += 3;
          }
        }
        PRINTFD(G, FB_RepSurface)
          " SolventDotNew-DEBUG: %d->%d\n", c, I->nDot ENDFD;
      }
      FreeP(dot_flag);
    }
    VLAFreeP(cavityDot);

  } 
  if(ok && (cavity_mode != 1) && (cavity_cull > 0) && 
     (probe_radius > 0.75F) && (!surface_solvent)) {
    int *dot_flag = Calloc(int, I->nDot);
    ErrChkPtr(G, dot_flag);

#if 0
    dot_flag[maxDot] = 1;       /* this guarantees that we have a valid dot */
#endif

    {
      MapType *map = MapNew(G, probe_radius_plus, I->dot, I->nDot, NULL);
      if(map) {
        int flag = true;
        MapSetupExpress(map);
        while(flag) {
          int *p = dot_flag;
          float *v = I->dot;
          int a;
          flag = false;
          for(a = 0; a < I->nDot; a++) {
            if(!dot_flag[a]) {
              register int i = *(MapLocusEStart(map, v));
              int cnt = 0;

              if(i) {
                register int 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);
    }

    {
      float *v0 = I->dot;
      float *n0 = I->dotNormal;
      int *dc0 = I->dotCode;
      int *p = dot_flag;
      int c = I->nDot;
      float *n = n0;
      float *v = v0;
      int *dc = dc0;
      int a;
      I->nDot = 0;
      for(a = 0; a < c; a++) {
        if(*(p++)) {
          *(v0++) = *(v++);
          *(n0++) = *(n++);
          *(v0++) = *(v++);
          *(n0++) = *(n++);
          *(v0++) = *(v++);
          *(n0++) = *(n++);
          *(dc0++) = *(dc++);
          I->nDot++;
        } else {
          v += 3;
          n += 3;
        }
      }
      PRINTFD(G, FB_RepSurface)
        " SolventDotNew-DEBUG: %d->%d\n", c, I->nDot ENDFD;
    }

    FreeP(dot_flag);
  }
#if 0
  {
    CGOReset(G->DebugCGO);
    CGOBegin(G->DebugCGO, GL_LINES);
    c = I->nDot;
    v = (v0 = I->dot);
    n = (n0 = I->dotNormal);
    for(a = 0; a < c; a++) {
      float sum[3];
      add3f(v, n, sum);
      CGOVertexv(G->DebugCGO, v);
      CGOVertexv(G->DebugCGO, sum);
      v += 3;
      n += 3;
    }
    CGOEnd(G->DebugCGO);
  }
#endif
  if(!ok) {
    SolventDotFree(I);
    I = NULL;
  }
  return I;
}

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