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CGO.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"Feedback.h"
#include"CGO.h"
#include"Base.h"
#include"OOMac.h"
#include"Setting.h"
#include"Sphere.h"
#include"PConv.h"
#include"GadgetSet.h"
#include"VFont.h"
#include"P.h"
#include"PyMOLGlobals.h"
#include"Ray.h"
#include"Util.h"
#include"Scene.h"
#include"Matrix.h"

#define CGO_read_int(p) (*((int*)(p++)))
#define CGO_get_int(p) (*((int*)(p)))
#define CGO_write_int(p,i) ((*((int*)(p++)))=(i))
#define CGO_put_int(p,i) ((*((int*)(p)))=(i))

00043 struct _CCGORenderer {
  PyMOLGlobals *G;
  float alpha;
};

int CGORendererInit(PyMOLGlobals * G)
{
  register CCGORenderer *I = NULL;

  I = (G->CGORenderer = Calloc(CCGORenderer, 1));
  if(I) {
    I->G = G;
    I->alpha = 1.0F;
    return 1;
  } else
    return 0;
}

void CGORendererFree(PyMOLGlobals * G)
{
  FreeP(G->CGORenderer);
}

int CGO_sz[] = {
  CGO_NULL_SZ,
  CGO_NULL_SZ,
  CGO_BEGIN_SZ,
  CGO_END_SZ,

  CGO_VERTEX_SZ,
  CGO_NORMAL_SZ,
  CGO_COLOR_SZ,
  CGO_SPHERE_SZ,

  CGO_TRIANGLE_SZ,
  CGO_CYLINDER_SZ,
  CGO_LINEWIDTH_SZ,
  CGO_WIDTHSCALE_SZ,

  CGO_ENABLE_SZ,
  CGO_DISABLE_SZ,
  CGO_SAUSAGE_SZ,
  CGO_CUSTOM_CYLINDER_SZ,

  CGO_DOTWIDTH_SZ,
  CGO_ALPHA_TRIANGLE_SZ,
  CGO_ELLIPSOID_SZ,
  CGO_FONT_SZ,

  CGO_FONT_SCALE_SZ,
  CGO_FONT_VERTEX_SZ,
  CGO_FONT_AXES_SZ,
  CGO_CHAR_SZ,

  CGO_INDENT_SZ,
  CGO_ALPHA_SZ,
  CGO_QUADRIC_SZ,
  CGO_CONE_SZ,

  CGO_NULL_SZ,
  CGO_NULL_SZ,
  CGO_RESET_NORMAL_SZ,
  CGO_PICK_COLOR_SZ,
};

typedef void CGO_op(CCGORenderer * I, float *);
typedef CGO_op *CGO_op_fn;

static float *CGO_add(CGO * I, int c);
static float *CGO_size(CGO * I, int sz);
static void subdivide(int n, float *x, float *y);
static void CGOSimpleCylinder(CGO * I, float *v1, float *v2, float tube_size, float *c1,
                              float *c2, int cap1, int cap2);
static void CGOSimpleEllipsoid(CGO * I, float *v, float vdw, float *n0, float *n1,
                               float *n2);
static void CGOSimpleQuadric(CGO * I, float *v, float vdw, float *q);
static void CGOSimpleSphere(CGO * I, float *v, float vdw);
static void CGOSimpleCone(CGO * I, float *v1, float *v2, float r1, float r2, float *c1,
                          float *c2, int cap1, int cap2);

CGO *CGOProcessShape(CGO * I, struct GadgetSet *gs, CGO * result)
{
  register float *p, *pc = I->op;
  register float *n, *nc;
  register int op;
  int sz;

  if(!result)
    result = CGONew(I->G);
  CGOReset(result);
  VLACheck(result->op, float, I->c + 32);

  while((op = (CGO_MASK & CGO_read_int(pc)))) {
    sz = CGO_sz[op];
    nc = CGO_add(result, sz + 1);
    *(nc++) = *(pc - 1);
    switch (op) {
    case CGO_NORMAL:
      GadgetSetFetchNormal(gs, pc, nc);
      break;
    case CGO_COLOR:
      GadgetSetFetchColor(gs, pc, nc);
      break;
    case CGO_VERTEX:
      GadgetSetFetch(gs, pc, nc);
      break;
    case CGO_FONT_VERTEX:
      GadgetSetFetch(gs, pc, nc);
      break;
    case CGO_SPHERE:
      GadgetSetFetch(gs, pc, nc);
      *(nc + 3) = *(pc + 3);
      break;
    case CGO_CUSTOM_CYLINDER:
      GadgetSetFetch(gs, pc, nc);
      GadgetSetFetch(gs, pc + 3, nc + 3);
      GadgetSetFetchColor(gs, pc + 7, nc + 7);
      GadgetSetFetchColor(gs, pc + 10, nc + 10);
      *(nc + 6) = *(pc + 6);
      *(nc + 13) = *(pc + 13);
      *(nc + 14) = *(pc + 14);
      break;
    case CGO_CYLINDER:
      GadgetSetFetch(gs, pc, nc);
      GadgetSetFetch(gs, pc + 3, nc + 3);
      GadgetSetFetchColor(gs, pc + 7, nc + 7);
      GadgetSetFetchColor(gs, pc + 10, nc + 10);
      *(nc + 6) = *(pc + 6);
      break;
    case CGO_SAUSAGE:
      GadgetSetFetch(gs, pc, nc);
      GadgetSetFetch(gs, pc + 3, nc + 3);
      GadgetSetFetchColor(gs, pc + 7, nc + 7);
      GadgetSetFetchColor(gs, pc + 10, nc + 10);
      *(nc + 6) = *(pc + 6);
      break;
    case CGO_TRIANGLE:
      GadgetSetFetch(gs, pc, nc);
      GadgetSetFetch(gs, pc + 3, nc + 3);
      GadgetSetFetch(gs, pc + 6, nc + 6);
      GadgetSetFetchNormal(gs, pc + 9, nc + 9);
      GadgetSetFetchNormal(gs, pc + 12, nc + 12);
      GadgetSetFetchNormal(gs, pc + 15, nc + 15);
      GadgetSetFetchColor(gs, pc + 18, nc + 18);
      GadgetSetFetchColor(gs, pc + 21, nc + 21);
      GadgetSetFetchColor(gs, pc + 24, nc + 24);
      break;
    default:
      p = pc;
      n = nc;
      while(sz--)
        *(n++) = *(p++);
      break;
    }
    pc += CGO_sz[op];
    nc += CGO_sz[op];
  }
  CGOStop(result);
  return (result);
}

#ifndef _PYMOL_NOPY

static PyObject *CGOArrayAsPyList(CGO * I)
{

  register float *pc = I->op;
  register int op;
  int i;
  int cc;
  PyObject *result = NULL;

  result = PyList_New(I->c);

  i = 0;
  if(I->c) {
    while((op = (CGO_MASK & CGO_read_int(pc)))) {
      PyList_SetItem(result, i++, PyFloat_FromDouble((float) op));
      cc = CGO_sz[op];
      switch (op) {             /* now convert any instructions with int arguments */
      case CGO_BEGIN:
      case CGO_ENABLE:
      case CGO_DISABLE:
        PyList_SetItem(result, i++, PyFloat_FromDouble((float) CGO_read_int(pc)));
        cc--;
        break;
      }
      if(cc > 0)
        while(cc--) {
          PyList_SetItem(result, i++, PyFloat_FromDouble(*(pc++)));
        }
    }
  }
  while(i < I->c) {
    PyList_SetItem(result, i++, PyFloat_FromDouble((float) CGO_STOP));
  }
  return (result);
}
#endif

#ifndef _PYMOL_NOPY

static int CGOArrayFromPyListInPlace(PyObject * list, CGO * I)
{
  int a;
  int c = I->c;
  int cc = 0;
  int ok = true;
  float *pc;
  int sz, op;
  int l;
  if(!list) {
    ok = false;
  } else if(!PyList_Check(list)) {
    ok = false;
  } else {
    l = PyList_Size(list);
    if(l != I->c)
      ok = false;
  }
  if(ok) {
    pc = I->op;

    while(c > 0) {
      op = (int) PyFloat_AsDouble(PyList_GetItem(list, cc++));
      op = op & CGO_MASK;
      c--;
      sz = CGO_sz[op];
      CGO_write_int(pc, op);
      ok = true;

      switch (op) {             /* now convert any instructions with int arguments */
      case CGO_BEGIN:
      case CGO_ENABLE:
      case CGO_DISABLE:
        CGO_write_int(pc, (int) PyFloat_AsDouble(PyList_GetItem(list, cc++)));
        c--;
        sz--;
        break;
      }

      for(a = 0; a < sz; a++) {
        *(pc++) = (float) PyFloat_AsDouble(PyList_GetItem(list, cc++));
        c--;
      }
    }
  }
  return (ok);
}
#endif

PyObject *CGOAsPyList(CGO * I)
{
#ifdef _PYMOL_NOPY
  return NULL;
#else
  PyObject *result;
  result = PyList_New(2);
  PyList_SetItem(result, 0, PyInt_FromLong(I->c));
  PyList_SetItem(result, 1, CGOArrayAsPyList(I));
  return (result);
#endif
}

CGO *CGONewFromPyList(PyMOLGlobals * G, PyObject * list, int version)
{
#ifdef _PYMOL_NOPY
  return NULL;
#else
  int ok = true;
  int ll;
  OOCalloc(G, CGO);
  I->G = G;
  I->op = NULL;

  if(ok)
    ok = (list != NULL);
  if(ok)
    ok = PyList_Check(list);
  if(ok)
    ll = PyList_Size(list);
  /* TO ENABLE BACKWARDS COMPATIBILITY...
     Always check ll when adding new PyList_GetItem's */
  if(ok)
    ok = PConvPyIntToInt(PyList_GetItem(list, 0), &I->c);
  if(ok)
    ok = ((I->op = VLAlloc(float, I->c + 1)) != NULL);
  if((version > 0) && (version <= 86)) {
    if(ok)
      ok = PConvPyListToFloatArrayInPlace(PyList_GetItem(list, 1), I->op, I->c);
  } else {
    if(ok)
      ok = CGOArrayFromPyListInPlace(PyList_GetItem(list, 1), I);
  }

  if(!ok) {
    CGOFree(I);
    I = NULL;
  }
  return (I);
#endif
}

CGO *CGONew(PyMOLGlobals * G)
{
  OOCalloc(G, CGO);
  I->G = G;
  I->op = VLAlloc(float, 33);
  return (I);
}

CGO *CGONewSized(PyMOLGlobals * G, int size)
{
  OOCalloc(G, CGO);
  I->G = G;
  I->op = VLAlloc(float, size + 32);
  return (I);
}

void CGOReset(CGO * I)
{
  I->c = 0;
  I->z_flag = false;
}

void CGOFree(CGO * I)
{
  if(I) {
    if(I->i_start) {
      FreeP(I->i_start);
    }
    VLAFreeP(I->op);
  }
  OOFreeP(I);
}

static float *CGO_add(CGO * I, int c)
{
  float *at;
  VLACheck(I->op, float, I->c + c);
  at = I->op + I->c;
  I->c += c;
  return (at);
}

static float *CGO_size(CGO * I, int sz)
{
  float *at;
  VLASize(I->op, float, sz);
  at = I->op + I->c;
  I->c = sz;
  return (at);
}


/*===== Object Creation Routines =======*/

int CGOFromFloatArray(CGO * I, float *src, int len)
{
  int op, iarg;
  int c;
  int ok;
  int all_ok = true;
  int bad_entry = 0;
  int sz;
  int a;
  int cc = 0;
  float val;
  float *pc, *save_pc, *tf;
  VLACheck(I->op, float, I->c + len + 32);
  save_pc = I->op + I->c;
  while(len-- > 0) {
    cc++;
    c = 1;
    op = CGO_MASK & ((int) (*(src++)));
    sz = CGO_sz[op];
    if(len < sz)
      break;                    /* discard short instruction */
    len -= sz;
    pc = save_pc;
    CGO_write_int(pc, op);
    ok = true;
    for(a = 0; a < sz; a++) {
      cc++;
      val = *(src++);
      if((FLT_MAX - val) > 0.0F) {      /* make sure we have a real float */
        *(pc++) = val;
      } else {
        *(pc++) = 0.0;
        ok = false;
      }
    }
    if(ok) {
      switch (op) {             /* now convert any instructions with int arguments */
      case CGO_BEGIN:
      case CGO_ENABLE:
      case CGO_DISABLE:
        tf = save_pc + 1;
        iarg = (int) *(tf);
        CGO_write_int(tf, iarg);
        break;
      }
      save_pc = pc;
      I->c += sz + 1;
    } else {                    /* discard illegal instructions */
      if(all_ok)
        bad_entry = cc;
      all_ok = false;
    }
  }
  return (bad_entry);
}

void CGOBegin(CGO * I, int mode)
{
  float *pc = CGO_add(I, 2);
  CGO_write_int(pc, CGO_BEGIN);
  CGO_write_int(pc, mode);
}

void CGOEnable(CGO * I, int mode)
{
  float *pc = CGO_add(I, 2);
  CGO_write_int(pc, CGO_ENABLE);
  CGO_write_int(pc, mode);
}

void CGODisable(CGO * I, int mode)
{
  float *pc = CGO_add(I, 2);
  CGO_write_int(pc, CGO_DISABLE);
  CGO_write_int(pc, mode);
}

void CGOLinewidth(CGO * I, float v)
{
  float *pc = CGO_add(I, 2);
  CGO_write_int(pc, CGO_LINEWIDTH);
  *(pc++) = v;
}

void CGODotwidth(CGO * I, float v)
{
  float *pc = CGO_add(I, 2);
  CGO_write_int(pc, CGO_DOTWIDTH);
  *(pc++) = v;
}

void CGOCylinderv(CGO * I, float *p1, float *p2, float r, float *c1, float *c2)
{
  float *pc = CGO_add(I, 14);
  CGO_write_int(pc, CGO_CYLINDER);
  *(pc++) = *(p1++);
  *(pc++) = *(p1++);
  *(pc++) = *(p1++);
  *(pc++) = *(p2++);
  *(pc++) = *(p2++);
  *(pc++) = *(p2++);
  *(pc++) = r;
  *(pc++) = *(c1++);
  *(pc++) = *(c1++);
  *(pc++) = *(c1++);
  *(pc++) = *(c2++);
  *(pc++) = *(c2++);
  *(pc++) = *(c2++);
}

void CGOCustomCylinderv(CGO * I, float *p1, float *p2, float r, float *c1, float *c2,
                        float cap1, float cap2)
{
  float *pc = CGO_add(I, 16);
  CGO_write_int(pc, CGO_CUSTOM_CYLINDER);
  *(pc++) = *(p1++);
  *(pc++) = *(p1++);
  *(pc++) = *(p1++);
  *(pc++) = *(p2++);
  *(pc++) = *(p2++);
  *(pc++) = *(p2++);
  *(pc++) = r;
  *(pc++) = *(c1++);
  *(pc++) = *(c1++);
  *(pc++) = *(c1++);
  *(pc++) = *(c2++);
  *(pc++) = *(c2++);
  *(pc++) = *(c2++);
  *(pc++) = cap1;
  *(pc++) = cap2;
}

void CGOConev(CGO * I, float *p1, float *p2, float r1, float r2, float *c1, float *c2,
              float cap1, float cap2)
{
  float *pc = CGO_add(I, 17);
  CGO_write_int(pc, CGO_CONE);
  *(pc++) = *(p1++);
  *(pc++) = *(p1++);
  *(pc++) = *(p1++);
  *(pc++) = *(p2++);
  *(pc++) = *(p2++);
  *(pc++) = *(p2++);
  *(pc++) = r1;
  *(pc++) = r2;
  *(pc++) = *(c1++);
  *(pc++) = *(c1++);
  *(pc++) = *(c1++);
  *(pc++) = *(c2++);
  *(pc++) = *(c2++);
  *(pc++) = *(c2++);
  *(pc++) = cap1;
  *(pc++) = cap2;
}

void CGOPickColor(CGO * I, int index, int bond)
{
  float *pc = CGO_add(I, 3);
  CGO_write_int(pc, CGO_PICK_COLOR);
  *(pc++) = (float) index;
  *(pc++) = (float) bond;
}

void CGOAlpha(CGO * I, float alpha)
{
  float *pc = CGO_add(I, 2);
  CGO_write_int(pc, CGO_ALPHA);
  *(pc++) = alpha;
}

void CGOSphere(CGO * I, float *v1, float r)
{
  float *pc = CGO_add(I, 5);
  CGO_write_int(pc, CGO_SPHERE);
  *(pc++) = *(v1++);
  *(pc++) = *(v1++);
  *(pc++) = *(v1++);
  *(pc++) = r;
}

void CGOEllipsoid(CGO * I, float *v1, float r, float *n1, float *n2, float *n3)
{
  float *pc = CGO_add(I, 14);
  CGO_write_int(pc, CGO_ELLIPSOID);

  *(pc++) = *(v1++);
  *(pc++) = *(v1++);
  *(pc++) = *(v1++);
  *(pc++) = r;
  *(pc++) = *(n1++);
  *(pc++) = *(n1++);
  *(pc++) = *(n1++);
  *(pc++) = *(n2++);
  *(pc++) = *(n2++);
  *(pc++) = *(n2++);
  *(pc++) = *(n3++);
  *(pc++) = *(n3++);
  *(pc++) = *(n3++);
}

void CGOQuadric(CGO * I, float *v, float r, float *q)
{
  float *pc = CGO_add(I, 15);
  CGO_write_int(pc, CGO_QUADRIC);

  *(pc++) = *(v++);
  *(pc++) = *(v++);
  *(pc++) = *(v++);
  *(pc++) = r;

  *(pc++) = *(q++);
  *(pc++) = *(q++);
  *(pc++) = *(q++);
  *(pc++) = *(q++);
  *(pc++) = *(q++);

  *(pc++) = *(q++);
  *(pc++) = *(q++);
  *(pc++) = *(q++);
  *(pc++) = *(q++);
  *(pc++) = *(q++);

}

void CGOSausage(CGO * I, float *v1, float *v2, float r, float *c1, float *c2)
{
  float *pc = CGO_add(I, 14);
  CGO_write_int(pc, CGO_SAUSAGE);
  *(pc++) = *(v1++);
  *(pc++) = *(v1++);
  *(pc++) = *(v1++);
  *(pc++) = *(v2++);
  *(pc++) = *(v2++);
  *(pc++) = *(v2++);
  *(pc++) = r;
  *(pc++) = *(c1++);
  *(pc++) = *(c1++);
  *(pc++) = *(c1++);
  *(pc++) = *(c2++);
  *(pc++) = *(c2++);
  *(pc++) = *(c2++);
}

void CGOSetZVector(CGO * I, float z0, float z1, float z2)
{
  I->z_flag = true;
  I->z_vector[0] = z0;
  I->z_vector[1] = z1;
  I->z_vector[2] = z2;
  I->z_min = FLT_MAX;
  I->z_max = -FLT_MAX;
}

const static float one_third = 1.0F / 3.0F;
const static float _0 = 0.0F;

void CGOAlphaTriangle(CGO * I,
                      float *v1, float *v2, float *v3,
                      float *n1, float *n2, float *n3,
                      float *c1, float *c2, float *c3,
                      float a1, float a2, float a3, int reverse)
{
  if(v1 && v2 && v3) {
    float *pc = CGO_add(I, CGO_ALPHA_TRIANGLE_SZ + 1);
    register float z = _0;

    CGO_write_int(pc, CGO_ALPHA_TRIANGLE);
    CGO_write_int(pc, 0);
    *(pc++) = (v1[0] + v2[0] + v3[0]) * one_third;
    *(pc++) = (v1[1] + v2[1] + v3[1]) * one_third;
    *(pc++) = (v1[2] + v2[2] + v3[2]) * one_third;
    if(I->z_flag) {
      register float *zv = I->z_vector;
      z = pc[-3] * zv[0] + pc[-2] * zv[1] + pc[-1] * zv[2];
      if(z > I->z_max)
        I->z_max = z;
      if(z < I->z_min)
        I->z_min = z;
    }
    *(pc++) = z;

    if(reverse) {
      *(pc++) = *(v2++);        /* vertices @ +5 */
      *(pc++) = *(v2++);
      *(pc++) = *(v2++);
      *(pc++) = *(v1++);
      *(pc++) = *(v1++);
      *(pc++) = *(v1++);
    } else {
      *(pc++) = *(v1++);        /* vertices @ +5 */
      *(pc++) = *(v1++);
      *(pc++) = *(v1++);
      *(pc++) = *(v2++);
      *(pc++) = *(v2++);
      *(pc++) = *(v2++);
    }

    *(pc++) = *(v3++);
    *(pc++) = *(v3++);
    *(pc++) = *(v3++);

    if(reverse) {
      *(pc++) = *(n2++);        /* normals @ +14 */
      *(pc++) = *(n2++);
      *(pc++) = *(n2++);
      *(pc++) = *(n1++);
      *(pc++) = *(n1++);
      *(pc++) = *(n1++);
    } else {
      *(pc++) = *(n1++);        /* normals @ +14 */
      *(pc++) = *(n1++);
      *(pc++) = *(n1++);
      *(pc++) = *(n2++);
      *(pc++) = *(n2++);
      *(pc++) = *(n2++);
    }
    *(pc++) = *(n3++);
    *(pc++) = *(n3++);
    *(pc++) = *(n3++);

    if(reverse) {
      *(pc++) = *(c2++);        /* colors @ +23 */
      *(pc++) = *(c2++);
      *(pc++) = *(c2++);
      *(pc++) = a2;
      *(pc++) = *(c1++);
      *(pc++) = *(c1++);
      *(pc++) = *(c1++);
      *(pc++) = a1;
    } else {
      *(pc++) = *(c1++);        /* colors @ +23 */
      *(pc++) = *(c1++);
      *(pc++) = *(c1++);
      *(pc++) = a1;
      *(pc++) = *(c2++);
      *(pc++) = *(c2++);
      *(pc++) = *(c2++);
      *(pc++) = a2;
    }
    *(pc++) = *(c3++);
    *(pc++) = *(c3++);
    *(pc++) = *(c3++);
    *(pc++) = a3;
  }
}

void CGOVertex(CGO * I, float v1, float v2, float v3)
{
  float *pc = CGO_add(I, 4);
  CGO_write_int(pc, CGO_VERTEX);
  *(pc++) = v1;
  *(pc++) = v2;
  *(pc++) = v3;
}

void CGOVertexv(CGO * I, float *v)
{
  float *pc = CGO_add(I, 4);
  CGO_write_int(pc, CGO_VERTEX);
  *(pc++) = *(v++);
  *(pc++) = *(v++);
  *(pc++) = *(v++);
}

void CGOColor(CGO * I, float v1, float v2, float v3)
{
  float *pc = CGO_add(I, 4);
  CGO_write_int(pc, CGO_COLOR);
  *(pc++) = v1;
  *(pc++) = v2;
  *(pc++) = v3;
}

void CGOColorv(CGO * I, float *v)
{
  float *pc = CGO_add(I, 4);
  CGO_write_int(pc, CGO_COLOR);
  *(pc++) = *(v++);
  *(pc++) = *(v++);
  *(pc++) = *(v++);
}

void CGONormal(CGO * I, float v1, float v2, float v3)
{
  float *pc = CGO_add(I, 4);
  CGO_write_int(pc, CGO_NORMAL);
  *(pc++) = v1;
  *(pc++) = v2;
  *(pc++) = v3;
}

void CGOResetNormal(CGO * I, int mode)
{
  float *pc = CGO_add(I, 2);
  CGO_write_int(pc, CGO_RESET_NORMAL);
  CGO_write_int(pc, mode);
}

void CGOFontVertexv(CGO * I, float *v)
{
  float *pc = CGO_add(I, 4);
  CGO_write_int(pc, CGO_FONT_VERTEX);
  *(pc++) = *(v++);
  *(pc++) = *(v++);
  *(pc++) = *(v++);
}

void CGOFontVertex(CGO * I, float x, float y, float z)
{
  float *pc = CGO_add(I, 4);
  CGO_write_int(pc, CGO_FONT_VERTEX);
  *(pc++) = x;
  *(pc++) = y;
  *(pc++) = z;
}

void CGOFontScale(CGO * I, float v1, float v2)
{
  float *pc = CGO_add(I, 3);
  CGO_write_int(pc, CGO_FONT_SCALE);
  *(pc++) = v1;
  *(pc++) = v2;
}

void CGOChar(CGO * I, char c)
{
  float *pc = CGO_add(I, 2);
  CGO_write_int(pc, CGO_CHAR);
  *(pc++) = (float) c;
}

void CGOIndent(CGO * I, char c, float dir)
{
  float *pc = CGO_add(I, 3);
  CGO_write_int(pc, CGO_INDENT);
  *(pc++) = (float) c;
  *(pc++) = dir;
}

void CGOWrite(CGO * I, char *str)
{
  float *pc;

  while(*str) {
    pc = CGO_add(I, 2);
    CGO_write_int(pc, CGO_CHAR);
    *(pc++) = (float) *(str++);
  }
}

void CGOWriteLeft(CGO * I, char *str)
{
  float *pc;
  char *s;
  s = str;
  while(*s) {
    pc = CGO_add(I, 3);
    CGO_write_int(pc, CGO_INDENT);
    *(pc++) = (float) *(s++);
    *(pc++) = -1.0F;
  }
  s = str;
  while(*s) {
    pc = CGO_add(I, 2);
    CGO_write_int(pc, CGO_CHAR);
    *(pc++) = (float) *(s++);
  }
}

void CGOWriteIndent(CGO * I, char *str, float indent)
{
  float *pc;
  char *s;
  s = str;
  while(*s) {
    pc = CGO_add(I, 3);
    CGO_write_int(pc, CGO_INDENT);
    *(pc++) = (float) *(s++);
    *(pc++) = indent;
  }
  s = str;
  while(*s) {
    pc = CGO_add(I, 2);
    CGO_write_int(pc, CGO_CHAR);
    *(pc++) = (float) *(s++);
  }
}

void CGONormalv(CGO * I, float *v)
{
  float *pc = CGO_add(I, 4);
  CGO_write_int(pc, CGO_NORMAL);
  *(pc++) = *(v++);
  *(pc++) = *(v++);
  *(pc++) = *(v++);
}

void CGOEnd(CGO * I)
{
  float *pc = CGO_add(I, 1);
  CGO_write_int(pc, CGO_END);
}

void CGOStop(CGO * I)
{
  /* add enough zeros to prevent overrun in the event of corruption
   * (include more zeros than the longest instruction in the compiler 

   * although this is wasteful, it does prevent crashes...
   */

#define CGO_STOP_ZEROS 16

  float *pc = CGO_size(I, I->c + CGO_STOP_ZEROS);

  UtilZeroMem(pc, sizeof(float) * CGO_STOP_ZEROS);
}

int CGOCheckComplex(CGO * I)
{
  register float *pc = I->op;
  int fc = 0;
  int nEdge;
  int op;
  SphereRec *sp;

  sp = I->G->Sphere->Sphere[1];

  nEdge = (int) SettingGet(I->G, cSetting_stick_quality);

  while((op = (CGO_MASK & CGO_read_int(pc)))) {
    switch (op) {
    case CGO_CYLINDER:
    case CGO_CONE:
    case CGO_SAUSAGE:
    case CGO_CUSTOM_CYLINDER:
      fc += 3 * (3 + (nEdge + 1) * 9) + 9;
      break;
    case CGO_ELLIPSOID:
    case CGO_QUADRIC:
    case CGO_SPHERE:
      fc += (sp->NVertTot * 6) + (sp->NStrip * 3) + 3;
      break;
    }
    pc += CGO_sz[op];
  }
  return (fc);
}

int CGOPreloadFonts(CGO * I)
{
  int ok = true;
  register float *pc = I->op;
  int op;
  int font_seen = false;
  int font_id;
  int blocked = false;

  blocked = PAutoBlock(I->G);
  while((op = (CGO_MASK & CGO_read_int(pc)))) {
    switch (op) {
    case CGO_FONT:
      ok = ok && (VFontLoad(I->G, 1.0, 1, 1, true));
      font_seen = true;
      break;
    case CGO_CHAR:
      if(!font_seen) {
        font_id = VFontLoad(I->G, 1.0, 1, 1, true);
        ok = ok && font_id;
        font_seen = true;
      }
      break;
    }
    pc += CGO_sz[op];
  }
  if(blocked)
    PUnblock(I->G);

  return (ok);
}

int CGOCheckForText(CGO * I)
{
  register float *pc = I->op;
  int fc = 0;
  int op;

  while((op = (CGO_MASK & CGO_read_int(pc)))) {
    switch (op) {
    case CGO_FONT:
    case CGO_FONT_AXES:
    case CGO_FONT_SCALE:
      fc++;
      break;
    case CGO_INDENT:
    case CGO_FONT_VERTEX:
      fc++;
      break;
    case CGO_CHAR:
      fc += 3 + 2 * 3 * 10;     /* est 10 lines per char */
      break;
    }
    pc += CGO_sz[op];
  }
  PRINTFD(I->G, FB_CGO)
    " CGOCheckForText-Debug: %d\n", fc ENDFD;

  return (fc);
}

CGO *CGODrawText(CGO * I, int est, float *camera)
{                               /* assumes blocked intepreter */
  CGO *cgo;

  register float *pc = I->op;
  register float *nc;
  register int op;
  float *save_pc;
  int sz;
  int font_id = 0;
  char text[2] = " ";
  float pos[] = { 0.0F, 0.0F, 0.0F };
  float axes[] = { 1.0F, 0.0F, 0.0F,
    0.0F, 1.0F, 0.0F,
    0.0F, 0.0F, 1.0F
  };
  float scale[2] = { 1.0, 1.0 };

  cgo = CGONewSized(I->G, I->c + est);

  while((op = (CGO_MASK & CGO_read_int(pc)))) {
    save_pc = pc;
    switch (op) {
    case CGO_FONT:
      break;
    case CGO_FONT_AXES:
      break;
    case CGO_FONT_SCALE:
      scale[0] = pc[0];
      scale[1] = pc[1];
      break;
    case CGO_FONT_VERTEX:
      copy3f(pc, pos);
      break;
    case CGO_INDENT:
      text[0] = (unsigned char) *pc;
      VFontIndent(I->G, font_id, text, pos, scale, axes, pc[1]);
      break;
    case CGO_CHAR:
      if(!font_id) {
        font_id = VFontLoad(I->G, 1.0, 1, 1, false);
      }
      text[0] = (unsigned char) *pc;
      VFontWriteToCGO(I->G, font_id, cgo, text, pos, scale, axes);
      break;
    default:
      sz = CGO_sz[op];
      nc = CGO_add(cgo, sz + 1);
      *(nc++) = *(pc - 1);
      while(sz--)
        *(nc++) = *(pc++);
    }
    pc = save_pc;
    pc += CGO_sz[op];
  }
  CGOStop(cgo);
  return (cgo);
}

CGO *CGOSimplify(CGO * I, int est)
{
  CGO *cgo;

  register float *pc = I->op;
  register float *nc;
  register int op;
  float *save_pc;
  int sz;

  cgo = CGONewSized(I->G, I->c + est);

  while((op = (CGO_MASK & CGO_read_int(pc)))) {
    save_pc = pc;
    switch (op) {
    case CGO_CYLINDER:
      CGOSimpleCylinder(cgo, pc, pc + 3, *(pc + 6), pc + 7, pc + 10, 1, 1);
      break;
    case CGO_CONE:
      CGOSimpleCone(cgo, pc, pc + 3, *(pc + 6), *(pc + 7), pc + 8, pc + 11,
                    (int) *(pc + 14), (int) *(pc + 15));
      break;
    case CGO_SAUSAGE:
      CGOSimpleCylinder(cgo, pc, pc + 3, *(pc + 6), pc + 7, pc + 10, 2, 2);
      break;
    case CGO_CUSTOM_CYLINDER:
      CGOSimpleCylinder(cgo, pc, pc + 3, *(pc + 6), pc + 7, pc + 10, (int) *(pc + 13),
                        (int) *(pc + 14));
      break;
    case CGO_SPHERE:
      CGOSimpleSphere(cgo, pc, *(pc + 3));
      break;
    case CGO_ELLIPSOID:
      CGOSimpleEllipsoid(cgo, pc, *(pc + 3), pc + 4, pc + 7, pc + 10);
      break;
    case CGO_QUADRIC:
      CGOSimpleQuadric(cgo, pc, *(pc + 3), pc + 4);
      break;
    default:
      sz = CGO_sz[op];
      nc = CGO_add(cgo, sz + 1);
      *(nc++) = *(pc - 1);
      while(sz--)
        *(nc++) = *(pc++);
    }
    pc = save_pc;
    pc += CGO_sz[op];
  }
  CGOStop(cgo);
  return (cgo);
}


/* ======== Raytrace Renderer ======== */

int CGOGetExtent(CGO * I, float *mn, float *mx)
{
  register float *pc = I->op;
  register int op;
  int result = false;

#define check_extent(v,r) {\
    if(!result) {\
      mn[0]=((*(v  ))-r); \
      mx[0]=((*(v  ))+r);  \
      mn[1]=((*(v+1))-r); \
      mx[1]=((*(v+1))+r); \
      mn[2]=((*(v+2))-r); \
      mx[2]=((*(v+2))+r); \
      result=true; \
  } else {\
       if(mn[0]>((*(v    ))-r)) mn[0]=((*(v    ))-r); \
       if(mx[0]<((*(v    ))+r)) mx[0]=((*(v    ))+r); \
       if(mn[1]>((*((v)+1))-r)) mn[1]=((*((v)+1))-r); \
       if(mx[1]<((*((v)+1))+r)) mx[1]=((*((v)+1))+r); \
       if(mn[2]>((*((v)+2))-r)) mn[2]=((*((v)+2))-r); \
       if(mx[2]<((*((v)+2))+r)) mx[2]=((*((v)+2))+r); }}

  while((op = (CGO_MASK & CGO_read_int(pc)))) {
    switch (op) {
    case CGO_VERTEX:
      check_extent(pc, 0);
      break;
    case CGO_SPHERE:
    case CGO_ELLIPSOID:
      check_extent(pc, *(pc + 3));
      break;
    case CGO_CYLINDER:
    case CGO_CONE:
    case CGO_SAUSAGE:
    case CGO_CUSTOM_CYLINDER:
      check_extent(pc, *(pc + 6));
      check_extent(pc + 3, *(pc + 6));
      break;
    case CGO_TRIANGLE:
      check_extent(pc, 0);
      check_extent(pc + 3, 0);
      check_extent(pc + 6, 0);
      break;
    }
    pc += CGO_sz[op];
  }
  return (result);
}

static int CGOQuadricToEllipsoid(float *v, float r, float *q,
                                 float *r_el, float *n0, float *n1, float *n2)
{
  int ok = false;
  double inp_matrix[16];
  double e_val[4];
  double e_vec[16];
  double inverse[16];

  inp_matrix[0] = q[0];
  inp_matrix[1] = q[3];
  inp_matrix[2] = q[5];
  inp_matrix[3] = q[6];
  inp_matrix[4] = q[3];
  inp_matrix[5] = q[1];
  inp_matrix[6] = q[4];
  inp_matrix[7] = q[7];
  inp_matrix[8] = q[5];
  inp_matrix[9] = q[4];
  inp_matrix[10] = q[2];
  inp_matrix[11] = q[8];
  inp_matrix[12] = q[6];
  inp_matrix[13] = q[7];
  inp_matrix[14] = q[8];
  inp_matrix[15] = q[9];

  if(xx_matrix_invert(inverse, inp_matrix, 4)) {

    /* inverse now contains Uij coefficients */
    float pradius = sqrt1f(-1 / inverse[15]);
    int n_rot;

    if(xx_matrix_jacobi_solve(e_vec, e_val, &n_rot, inverse, 4)) {
      float mag[3];
      float scale[3];
      float mx;
      n0[0] = e_vec[0];
      n0[1] = e_vec[4];
      n0[2] = e_vec[8];
      n1[0] = e_vec[1];
      n1[1] = e_vec[5];
      n1[2] = e_vec[9];
      n2[0] = e_vec[2];
      n2[1] = e_vec[6];
      n2[2] = e_vec[10];

      normalize3f(n0);
      normalize3f(n1);
      normalize3f(n2);
      mag[0] = sqrt1f(e_val[0]);
      mag[1] = sqrt1f(e_val[1]);
      mag[2] = sqrt1f(e_val[2]);

      mx = mag[0];
      if(mx < mag[1])
        mx = mag[1];
      if(mx < mag[2])
        mx = mag[2];

      scale[0] = mag[0] / mx;
      scale[1] = mag[1] / mx;
      scale[2] = mag[2] / mx;

      scale3f(n0, scale[0], n0);
      scale3f(n1, scale[1], n1);
      scale3f(n2, scale[2], n2);

      *r_el = mx * pradius;
      ok = true;
    }
  }
  return ok;
}

static void CGORenderQuadricRay(CRay * ray, float *v, float r, float *q)
{
  float r_el, n0[3], n1[3], n2[3];
  if(CGOQuadricToEllipsoid(v, r, q, &r_el, n0, n1, n2))
    ray->fEllipsoid3fv(ray, v, r_el, n0, n1, n2);

}


/* ======== Raytrace Renderer ======== */

void CGORenderRay(CGO * I, CRay * ray, float *color, CSetting * set1, CSetting * set2)
{
  register float *pc;
  register int op;
  int vc = 0;
  float linewidth = 1.0F;
  float widthscale = 0.15F;
  float lineradius, dotradius, dotwidth;
  float white[] = { 1.0, 1.0, 1.0 };
  float zee[] = { 0.0, 0.0, 1.0 };
  
  float *n0 = NULL, *n1 = NULL, *n2 = NULL, *v0 = NULL, *v1 = NULL, *v2 = NULL, *c0 =
    NULL, *c1 = NULL, *c2 = NULL;
  int mode = -1;

  /* workaround; multi-state ray-trace bug */
  if (I)
    pc = I->op;
  else return;

  I->G->CGORenderer->alpha =
    1.0F - SettingGet_f(I->G, set1, set2, cSetting_cgo_transparency);

  widthscale = SettingGet_f(I->G, set1, set2, cSetting_cgo_ray_width_scale);

  /*  printf("debug %8.9f\n",SceneGetScreenVertexScale(I->G,zee)); */
  linewidth = SettingGet_f(I->G, set1, set2, cSetting_cgo_line_width);
  if(linewidth < 0.0F)
    linewidth = 1.0F;
  lineradius = SettingGet_f(I->G, set1, set2, cSetting_cgo_line_radius);
  dotwidth = SettingGet_f(I->G, set1, set2, cSetting_cgo_dot_width);
  dotradius = SettingGet_f(I->G, set1, set2, cSetting_cgo_dot_radius);
  if(lineradius < 0.0F)
    lineradius = linewidth * ray->PixelRadius / 2.0F;
  if(dotradius < 0.0F)
    dotradius = dotwidth * ray->PixelRadius / 2.0F;
  if(widthscale < 0.0F)
    widthscale = ray->PixelRadius / 2.0F;

  if(color)
    c0 = color;
  else
    c0 = white;
  ray->fTransparentf(ray, 1.0F - I->G->CGORenderer->alpha);

  while((op = (CGO_MASK & CGO_read_int(pc)))) {
    switch (op) {
    case CGO_BEGIN:
      mode = CGO_get_int(pc);
      vc = 0;
      n0 = zee;
      break;
    case CGO_END:
      switch (mode) {
      case GL_LINE_LOOP:
        if(vc > 1)
          ray->fSausage3fv(ray, v0, v2, lineradius, c0, c2);
        break;
      }
      mode = -1;
      break;
    case CGO_WIDTHSCALE:
      widthscale = *pc;
      lineradius = widthscale * linewidth;
      dotradius = widthscale * dotwidth;
      break;
    case CGO_DOTWIDTH:
      dotwidth = *pc;
      dotradius = widthscale * dotwidth;
      break;
    case CGO_LINEWIDTH:
      linewidth = *pc;
      lineradius = widthscale * linewidth;
      break;
    case CGO_NORMAL:
      n0 = pc;
      break;
    case CGO_COLOR:
      c0 = pc;
      ray->fColor3fv(ray, c0);
      break;
    case CGO_ALPHA:
      I->G->CGORenderer->alpha = *pc;
      ray->fTransparentf(ray, 1.0F - *pc);
      break;
    case CGO_VERTEX:
      v0 = pc;
      switch (mode) {
      case GL_POINTS:
        ray->fSphere3fv(ray, v0, dotradius);
        break;
      case GL_LINES:
        if(vc & 0x1)
          ray->fSausage3fv(ray, v0, v1, lineradius, c0, c1);
        v1 = v0;
        c1 = c0;
        break;
      case GL_LINE_STRIP:
        if(vc)
          ray->fSausage3fv(ray, v0, v1, lineradius, c0, c1);
        v1 = v0;
        c1 = c0;
        break;
      case GL_LINE_LOOP:
        if(vc)
          ray->fSausage3fv(ray, v0, v1, lineradius, c0, c1);
        else {
          v2 = v0;
          c2 = c0;
        }
        v1 = v0;
        c1 = c0;
        break;
      case GL_TRIANGLES:
        if(3 * ((vc + 1) / 3) == vc + 1)
          ray->fTriangle3fv(ray, v0, v1, v2, n0, n1, n2, c0, c1, c2);
        v2 = v1;
        c2 = c1;
        n2 = n1;
        v1 = v0;
        c1 = c0;
        n1 = n0;
        break;
      case GL_TRIANGLE_STRIP:
        if(vc > 1)
          ray->fTriangle3fv(ray, v0, v1, v2, n0, n1, n2, c0, c1, c2);
        v2 = v1;
        c2 = c1;
        n2 = n1;
        v1 = v0;
        c1 = c0;
        n1 = n0;
        break;
      case GL_TRIANGLE_FAN:
        if(vc > 1)
          ray->fTriangle3fv(ray, v0, v1, v2, n0, n1, n2, c0, c1, c2);
        else if(!vc) {
          n2 = n0;
          v2 = v0;
          c2 = c0;
        }
        v1 = v0;
        c1 = c0;
        n1 = n0;
        break;
      }
      vc++;
      break;
    case CGO_SPHERE:
      ray->fColor3fv(ray, c0);
      ray->fSphere3fv(ray, pc, *(pc + 3));
      break;
    case CGO_ELLIPSOID:
      ray->fColor3fv(ray, c0);
      ray->fEllipsoid3fv(ray, pc, *(pc + 3), pc + 4, pc + 7, pc + 10);
      break;
    case CGO_QUADRIC:
      ray->fColor3fv(ray, c0);
      CGORenderQuadricRay(ray, pc, *(pc + 3), pc + 4);
      break;
    case CGO_CONE:
      ray->fCone3fv(ray, pc, pc + 3, *(pc + 6), *(pc + 7), pc + 8, pc + 11,
                    (int) *(pc + 14), (int) *(pc + 15));
      break;
    case CGO_CUSTOM_CYLINDER:
      ray->fCustomCylinder3fv(ray, pc, pc + 3, *(pc + 6), pc + 7, pc + 10,
                              (int) *(pc + 13), (int) *(pc + 14));
      break;
    case CGO_CYLINDER:
      ray->fCylinder3fv(ray, pc, pc + 3, *(pc + 6), pc + 7, pc + 10);
      break;
    case CGO_SAUSAGE:
      ray->fSausage3fv(ray, pc, pc + 3, *(pc + 6), pc + 7, pc + 10);
      break;
    case CGO_TRIANGLE:
      ray->fTriangle3fv(ray, pc, pc + 3, pc + 6, pc + 9, pc + 12, pc + 15, pc + 18,
                        pc + 21, pc + 24);
      break;
    default:
      break;
    }
    pc += CGO_sz[op];
  }

  ray->fTransparentf(ray, 0.0F);
}


/* ======== GL Rendering ======== */

static void CGO_gl_begin(CCGORenderer * I, float *pc)
{
  glBegin(CGO_read_int(pc));
}

static void CGO_gl_end(CCGORenderer * I, float *pc)
{
  glEnd();
}

static void CGO_gl_linewidth(CCGORenderer * I, float *pc)
{
  glLineWidth(*pc);
}

static void CGO_gl_dotwidth(CCGORenderer * I, float *pc)
{
  glPointSize(*pc);
}

static void CGO_gl_enable(CCGORenderer * I, float *pc)
{
  glEnable(CGO_read_int(pc));
}

static void CGO_gl_disable(CCGORenderer * I, float *pc)
{
  glDisable(CGO_read_int(pc));
}

static void CGO_gl_alpha(CCGORenderer * I, float *pc)
{
  I->alpha = *pc;
}

static void CGO_gl_reset_normal(CCGORenderer * I, float *pc)
{
  SceneResetNormal(I->G, CGO_read_int(pc));
}

static void CGO_gl_null(CCGORenderer * I, float *pc)
{
}

static void CGO_gl_vertex(CCGORenderer * I, float *v)
{
  glVertex3fv(v);
}

static void CGO_gl_normal(CCGORenderer * I, float *v)
{
  glNormal3fv(v);
}

static void CGO_gl_color(CCGORenderer * I, float *v)
{
  glColor4f(v[0], v[1], v[2], I->alpha);
}


/* dispatch table for OpenGL */

CGO_op_fn CGO_gl[] = {
  CGO_gl_null,                  /* 0x00 */
  CGO_gl_null,                  /* 0x01 */
  CGO_gl_begin,                 /* 0x02 */
  CGO_gl_end,                   /* 0x03 */
  CGO_gl_vertex,                /* 0x04 */
  CGO_gl_normal,                /* 0x05 */
  CGO_gl_color,                 /* 0x06 */
  CGO_gl_null,                  /* 0x07 */
  CGO_gl_null,                  /* 0x08 */
  CGO_gl_null,                  /* 0x09 */

  CGO_gl_linewidth,             /* 0x0A */
  CGO_gl_null,                  /* 0x0B */
  CGO_gl_enable,                /* 0x0C */
  CGO_gl_disable,               /* 0x0D */
  CGO_gl_null,                  /* 0x0E */
  CGO_gl_null,                  /* 0x0F */

  CGO_gl_dotwidth,              /* 0X10 */
  CGO_gl_null,                  /* 0x11 */
  CGO_gl_null,                  /* 0x12 */
  CGO_gl_null,                  /* 0X13 */

  CGO_gl_null,                  /* 0X14 */
  CGO_gl_null,                  /* 0x15 */
  CGO_gl_null,                  /* 0x16 */
  CGO_gl_null,                  /* 0X17 */

  CGO_gl_null,                  /* 0X18 */
  CGO_gl_alpha,                 /* 0x19 */
  CGO_gl_null,                  /* 0x1A */
  CGO_gl_null,                  /* 0X1B */

  CGO_gl_null,                  /* 0X1C */
  CGO_gl_null,                  /* 0x1D */
  CGO_gl_reset_normal,          /* 0x1E */
  CGO_gl_null,                  /* pick color  0X1F */
};

void CGORenderGLPicking(CGO * I, Picking ** pick, PickContext * context, CSetting * set1,
                        CSetting * set2)
{
  register PyMOLGlobals *G = I->G;
  if(G->ValidContext) {
    register float *pc = I->op;
    register int op;
    register CCGORenderer *R = G->CGORenderer;
    int i, j;
    Picking *p;

    if(I->c) {
      i = (*pick)->src.index;

      glLineWidth(SettingGet_f(G, set1, set2, cSetting_cgo_line_width));

      while((op = (CGO_MASK & CGO_read_int(pc)))) {
        if(op != CGO_PICK_COLOR) {
          if(op != CGO_COLOR) {
            CGO_gl[op] (R, pc); /* ignore color changes */
          }
        } else {
          i++;
          if(!(*pick)[0].src.bond) {
            /* pass 1 - low order bits */

            glColor3ub((uchar) ((i & 0xF) << 4), (uchar) ((i & 0xF0) | 0x8), (uchar) ((i & 0xF00) >> 4));       /* we're encoding the index into the color */
            VLACheck((*pick), Picking, i);
            p = (*pick) + i;
            p->context = (*context);
            p->src.index = (int) *pc;
            p->src.bond = (int) *(pc + 1);      /* actually holds state information */
          } else {
            /* pass 2 - high order bits */

            j = i >> 12;

            glColor3ub((uchar) ((j & 0xF) << 4), (uchar) ((j & 0xF0) | 0x8),
                       (uchar) ((j & 0xF00) >> 4));

          }

        }
        pc += CGO_sz[op];
      }
      (*pick)[0].src.index = i; /* pass the count */

    }
  }
}

void CGORenderGL(CGO * I, float *color, CSetting * set1, CSetting * set2,
                 RenderInfo * info)

/* this should be as fast as you can make it...

 * the ASM loop is about 2X long as raw looped GL calls,

 * but hopefully superscaler processors won't care */
{
  register PyMOLGlobals *G = I->G;
  if(G->ValidContext) {
    register float *pc = I->op;
    register int op;
    register CCGORenderer *R = G->CGORenderer;
    register float _1 = 1.0F;

    SceneResetNormal(I->G, true);
    if(I->c) {
      R->alpha = 1.0F - SettingGet_f(I->G, set1, set2, cSetting_cgo_transparency);
      if(color)
        glColor4f(color[0], color[1], color[2], R->alpha);
      else
        glColor4f(1.0, 1.0, 1.0, R->alpha);
      if(info && info->width_scale_flag) {
        glLineWidth(SettingGet_f(I->G, set1, set2, cSetting_cgo_line_width) *
                    info->width_scale);
        glPointSize(SettingGet_f(I->G, set1, set2, cSetting_cgo_dot_width) *
                    info->width_scale);

      } else {
        glLineWidth(SettingGet_f(I->G, set1, set2, cSetting_cgo_line_width));
        glPointSize(SettingGet_f(I->G, set1, set2, cSetting_cgo_dot_width));
      }

      if(info->alpha_cgo) {     /* we're sorting transparent triangles globally */
        register int mode = -1;
        float *n0 = NULL, *n1 = NULL, *n2 = NULL, *v0 = NULL, *v1 = NULL, *v2 =
          NULL, *c0 = NULL, *c1 = NULL, *c2 = NULL;
        float zee[] = { 0.0, 0.0, 1.0 };
        int vc = 0;
        while((op = (CGO_MASK & CGO_read_int(pc)))) {
          if((R->alpha != _1)) {
            switch (op) {       /* transpareny */
            case CGO_BEGIN:
              mode = CGO_get_int(pc);
              CGO_gl_begin(R, pc);
              vc = 0;
              n0 = zee;
              break;
            case CGO_END:
              CGO_gl_end(R, pc);
              mode = -1;
              break;
            case CGO_NORMAL:
              switch (mode) {
              case GL_TRIANGLES:
              case GL_TRIANGLE_STRIP:
              case GL_TRIANGLE_FAN:
                n0 = pc;
                break;
              default:
                CGO_gl_normal(R, pc);
              }
              break;
            case CGO_COLOR:
              c0 = pc;
              CGO_gl_color(R, pc);
              break;
            case CGO_TRIANGLE:
              CGOAlphaTriangle(info->alpha_cgo,
                               pc, pc + 3, pc + 6, pc + 9, pc + 12, pc + 15, pc + 18,
                               pc + 21, pc + 24, R->alpha, R->alpha, R->alpha, false);
              break;
            case CGO_VERTEX:
              v0 = pc;
              switch (mode) {
              case GL_TRIANGLES:
                if(3 * ((vc + 1) / 3) == vc + 1) {
                  CGOAlphaTriangle(info->alpha_cgo,
                                   v0, v1, v2, n0, n1, n2, c0, c1, c2,
                                   R->alpha, R->alpha, R->alpha, true);
                }
                v2 = v1;
                c2 = c1;
                n2 = n1;
                v1 = v0;
                c1 = c0;
                n1 = n0;
                vc++;
                break;
              case GL_TRIANGLE_STRIP:
                if(vc > 1) {
                  CGOAlphaTriangle(info->alpha_cgo,
                                   v0, v1, v2, n0, n1, n2, c0, c1, c2,
                                   R->alpha, R->alpha, R->alpha, !(vc & 0x1));
                }
                v2 = v1;
                c2 = c1;
                n2 = n1;
                v1 = v0;
                c1 = c0;
                n1 = n0;
                vc++;
                break;
              case GL_TRIANGLE_FAN:
                if(vc > 1) {
                  CGOAlphaTriangle(info->alpha_cgo,
                                   v0, v1, v2, n0, n1, n2, c0, c1, c2,
                                   R->alpha, R->alpha, R->alpha, false);
                } else if(!vc) {
                  n2 = n0;
                  v2 = v0;
                  c2 = c0;
                }
                v1 = v0;
                c1 = c0;
                n1 = n0;
                vc++;
                break;
              default:
                CGO_gl_vertex(R, pc);
                break;
              }
              break;
            default:
              CGO_gl[op] (R, pc);
              break;
            }
          } else {              /* opaque */
            CGO_gl[op] (R, pc);
          }
          pc += CGO_sz[op];
        }
      } else {
        while((op = (CGO_MASK & CGO_read_int(pc)))) {
          CGO_gl[op] (R, pc);
          pc += CGO_sz[op];
        }
      }
    }
  }
}

void CGORenderGLAlpha(CGO * I, RenderInfo * info)
{
  register PyMOLGlobals *G = I->G;
  if(G->ValidContext && I->c) {

    /* 1. transform and measure range (if not already known) 
       2. bin into linked lists based on Z-centers
       3. render by layer */

    if(I->z_flag) {
      if(!I->i_start) {
        I->i_size = 256;
        I->i_start = Calloc(int, I->i_size);
      } else {
        UtilZeroMem(I->i_start, sizeof(int) * I->i_size);
      }
      {
        register float z_min = I->z_min;
        register int i_size = I->i_size;
        register float range_factor = (0.9999F * i_size) / (I->z_max - z_min);
        register float *base = I->op;
        register float *pc = base;
        register int op, i, ii;
        register int *start = I->i_start;
        register int delta = 1;
        /* bin the triangles */

        while((op = (CGO_MASK & CGO_read_int(pc)))) {
          switch (op) {
          case CGO_ALPHA_TRIANGLE:
            i = (int) ((pc[4] - z_min) * range_factor);
            if(i < 0)
              i = 0;
            if(i >= i_size)
              i = i_size;
            CGO_put_int(pc, start[i]);
            start[i] = (pc - base);     /* NOTE: will always be > 0 since we have CGO_read_int'd */
            break;
          }
          pc += CGO_sz[op];
        }

        if(SettingGetGlobal_i(G, cSetting_transparency_mode) == 2) {
          delta = -1;
          start += (i_size - 1);
        }

        /* now render by bin */

        glBegin(GL_TRIANGLES);
        for(i = 0; i < i_size; i++) {
          ii = *start;
          start += delta;
          while(ii) {
            pc = base + ii;

            glColor4fv(pc + 23);
            glNormal3fv(pc + 14);
            glVertex3fv(pc + 5);
            glColor4fv(pc + 27);
            glNormal3fv(pc + 17);
            glVertex3fv(pc + 8);
            glColor4fv(pc + 31);
            glNormal3fv(pc + 20);
            glVertex3fv(pc + 11);

            ii = CGO_get_int(pc);
          }
        }
        glEnd();
      }
    } else {
      register float *pc = I->op;
      register int op;
      glBegin(GL_TRIANGLES);
      while((op = (CGO_MASK & CGO_read_int(pc)))) {
        switch (op) {
        case CGO_ALPHA_TRIANGLE:
          glColor4fv(pc + 23);
          glNormal3fv(pc + 14);
          glVertex3fv(pc + 5);
          glColor4fv(pc + 27);
          glNormal3fv(pc + 17);
          glVertex3fv(pc + 8);
          glColor4fv(pc + 31);
          glNormal3fv(pc + 20);
          glVertex3fv(pc + 11);
          break;
        }
        pc += CGO_sz[op];
      }
      glEnd();
    }
  }
}


/* translation function which turns cylinders and spheres into triangles */

static void CGOSimpleSphere(CGO * I, float *v, float vdw)
{
  SphereRec *sp;
  int *q, *s;
  int b, c;
  int ds;

  ds = SettingGet_i(I->G, NULL, NULL, cSetting_cgo_sphere_quality);
  if(ds < 0)
    ds = 0;
  if(ds > 3)
    ds = 3;
  sp = I->G->Sphere->Sphere[ds];

  q = sp->Sequence;
  s = sp->StripLen;

  for(b = 0; b < sp->NStrip; b++) {
    CGOBegin(I, GL_TRIANGLE_STRIP);
    for(c = 0; c < (*s); c++) {
      CGONormalv(I, sp->dot[*q]);
      CGOVertex(I, v[0] + vdw * sp->dot[*q][0],
                v[1] + vdw * sp->dot[*q][1], v[2] + vdw * sp->dot[*q][2]);
      q++;
    }
    CGOEnd(I);
    s++;
  }
}

static void CGOSimpleQuadric(CGO * I, float *v, float r, float *q)
{
  float r_el, n0[3], n1[3], n2[3];
  if(CGOQuadricToEllipsoid(v, r, q, &r_el, n0, n1, n2))
    CGOSimpleEllipsoid(I, v, r_el, n0, n1, n2);
}

static void CGOSimpleEllipsoid(CGO * I, float *v, float vdw, float *n0, float *n1,
                               float *n2)
{
  SphereRec *sp;
  int *q, *s;
  int b, c;
  int ds;
  float nn0[3], nn1[3], nn2[3];
  float scale[3], scale_sq[3];

  normalize23f(n0, nn0);
  normalize23f(n1, nn1);
  normalize23f(n2, nn2);

  scale[0] = (float) length3f(n0);
  scale[1] = (float) length3f(n1);
  scale[2] = (float) length3f(n2);

  scale_sq[0] = scale[0] * scale[0];
  scale_sq[1] = scale[1] * scale[1];
  scale_sq[2] = scale[2] * scale[2];

  ds = SettingGet_i(I->G, NULL, NULL, cSetting_cgo_ellipsoid_quality);
  if(ds < 0)
    ds = SettingGet_i(I->G, NULL, NULL, cSetting_ellipsoid_quality);
  if(ds < 0)
    ds = 0;
  if(ds > 3)
    ds = 3;
  sp = I->G->Sphere->Sphere[ds];

  q = sp->Sequence;
  s = sp->StripLen;

  for(b = 0; b < sp->NStrip; b++) {
    CGOBegin(I, GL_TRIANGLE_STRIP);
    for(c = 0; c < (*s); c++) {
      float *sp_dot_q = sp->dot[*q];
      float s0 = vdw * sp_dot_q[0];
      float s1 = vdw * sp_dot_q[1];
      float s2 = vdw * sp_dot_q[2];
      float d0[3], d1[3], d2[3], vv[3], direction[3];
      float dd0, dd1, dd2, ss0, ss1, ss2;
      float comp0[3], comp1[3], comp2[3];
      float surfnormal[3];
      int i;

      scale3f(n0, s0, d0);
      scale3f(n1, s1, d1);
      scale3f(n2, s2, d2);

      for(i = 0; i < 3; i++) {
        vv[i] = d0[i] + d1[i] + d2[i];
      }
      normalize23f(vv, direction);
      add3f(v, vv, vv);

      dd0 = dot_product3f(direction, nn0);
      dd1 = dot_product3f(direction, nn1);
      dd2 = dot_product3f(direction, nn2);

      if(scale[0] > R_SMALL8) {
        ss0 = dd0 / scale_sq[0];
      } else {
        ss0 = 0.0F;
      }
      if(scale[1] > R_SMALL8) {
        ss1 = dd1 / scale_sq[1];
      } else {
        ss1 = 0.0F;
      }

      if(scale[2] > R_SMALL8) {
        ss2 = dd2 / scale_sq[2];
      } else {
        ss2 = 0.0F;
      }

      scale3f(nn0, ss0, comp0);
      scale3f(nn1, ss1, comp1);
      scale3f(nn2, ss2, comp2);

      for(i = 0; i < 3; i++) {
        surfnormal[i] = comp0[i] + comp1[i] + comp2[i];
      }
      normalize3f(surfnormal);

      CGONormalv(I, surfnormal);
      CGOVertexv(I, vv);
      q++;
    }
    CGOEnd(I);
    s++;
  }
}

static void subdivide(int n, float *x, float *y)
{
  int a;
  if(n < 3) {
    n = 3;
  }
  for(a = 0; a <= n; a++) {
    x[a] = (float) cos(a * 2 * PI / n);
    y[a] = (float) sin(a * 2 * PI / n);
  }
}

static void CGOSimpleCylinder(CGO * I, float *v1, float *v2, float tube_size, float *c1,
                              float *c2, int cap1, int cap2)
{

#define MAX_EDGE 50

  float d[3], t[3], p0[3], p1[3], p2[3], vv1[3], vv2[3], v_buf[9], *v;
  float x[MAX_EDGE + 1], y[MAX_EDGE + 1];
  float overlap;
  float nub;
  int colorFlag;
  int nEdge;
  int c;

  v = v_buf;
  nEdge = (int) SettingGet(I->G, cSetting_stick_quality);
  overlap = tube_size * SettingGet(I->G, cSetting_stick_overlap);
  nub = tube_size * SettingGet(I->G, cSetting_stick_nub);

  if(nEdge > MAX_EDGE)
    nEdge = MAX_EDGE;
  subdivide(nEdge, x, y);

  colorFlag = (c1 != c2) && c2;

  CGOColorv(I, c1);

  /* direction vector */

  p0[0] = (v2[0] - v1[0]);
  p0[1] = (v2[1] - v1[1]);
  p0[2] = (v2[2] - v1[2]);

  normalize3f(p0);

  if(cap1 == cCylCapRound) {
    vv1[0] = v1[0] - p0[0] * overlap;
    vv1[1] = v1[1] - p0[1] * overlap;
    vv1[2] = v1[2] - p0[2] * overlap;
  } else {
    vv1[0] = v1[0];
    vv1[1] = v1[1];
    vv1[2] = v1[2];
  }
  if(cap2 == cCylCapRound) {
    vv2[0] = v2[0] + p0[0] * overlap;
    vv2[1] = v2[1] + p0[1] * overlap;
    vv2[2] = v2[2] + p0[2] * overlap;
  } else {
    vv2[0] = v2[0];
    vv2[1] = v2[1];
    vv2[2] = v2[2];
  }

  d[0] = (vv2[0] - vv1[0]);
  d[1] = (vv2[1] - vv1[1]);
  d[2] = (vv2[2] - vv1[2]);

  get_divergent3f(d, t);

  cross_product3f(d, t, p1);

  normalize3f(p1);

  cross_product3f(d, p1, p2);

  normalize3f(p2);

  /* now we have a coordinate system */

  CGOBegin(I, GL_TRIANGLE_STRIP);
  for(c = nEdge; c >= 0; c--) {
    v[0] = p1[0] * x[c] + p2[0] * y[c];
    v[1] = p1[1] * x[c] + p2[1] * y[c];
    v[2] = p1[2] * x[c] + p2[2] * y[c];

    v[3] = vv1[0] + v[0] * tube_size;
    v[4] = vv1[1] + v[1] * tube_size;
    v[5] = vv1[2] + v[2] * tube_size;

    v[6] = v[3] + d[0];
    v[7] = v[4] + d[1];
    v[8] = v[5] + d[2];

    CGONormalv(I, v);
    if(colorFlag)
      CGOColorv(I, c1);
    CGOVertexv(I, v + 3);
    if(colorFlag)
      CGOColorv(I, c2);
    CGOVertexv(I, v + 6);
  }
  CGOEnd(I);

  if(cap1) {
    v[0] = -p0[0];
    v[1] = -p0[1];
    v[2] = -p0[2];

    if(cap1 == cCylCapRound) {
      v[3] = vv1[0] - p0[0] * nub;
      v[4] = vv1[1] - p0[1] * nub;
      v[5] = vv1[2] - p0[2] * nub;
    } else {
      v[3] = vv1[0];
      v[4] = vv1[1];
      v[5] = vv1[2];
    }

    if(colorFlag)
      CGOColorv(I, c1);
    CGOBegin(I, GL_TRIANGLE_FAN);
    CGONormalv(I, v);
    CGOVertexv(I, v + 3);

    for(c = nEdge; c >= 0; c--) {
      v[0] = p1[0] * x[c] + p2[0] * y[c];
      v[1] = p1[1] * x[c] + p2[1] * y[c];
      v[2] = p1[2] * x[c] + p2[2] * y[c];

      v[3] = vv1[0] + v[0] * tube_size;
      v[4] = vv1[1] + v[1] * tube_size;
      v[5] = vv1[2] + v[2] * tube_size;

      if(cap1 == cCylCapRound)
        CGONormalv(I, v);
      CGOVertexv(I, v + 3);
    }
    CGOEnd(I);
  }

  if(cap2) {

    v[0] = p0[0];
    v[1] = p0[1];
    v[2] = p0[2];

    if(cap2 == cCylCapRound) {
      v[3] = vv2[0] + p0[0] * nub;
      v[4] = vv2[1] + p0[1] * nub;
      v[5] = vv2[2] + p0[2] * nub;
    } else {
      v[3] = vv2[0];
      v[4] = vv2[1];
      v[5] = vv2[2];
    }

    if(colorFlag)
      CGOColorv(I, c2);
    CGOBegin(I, GL_TRIANGLE_FAN);
    CGONormalv(I, v);
    CGOVertexv(I, v + 3);

    for(c = 0; c <= nEdge; c++) {
      v[0] = p1[0] * x[c] + p2[0] * y[c];
      v[1] = p1[1] * x[c] + p2[1] * y[c];
      v[2] = p1[2] * x[c] + p2[2] * y[c];

      v[3] = vv2[0] + v[0] * tube_size;
      v[4] = vv2[1] + v[1] * tube_size;
      v[5] = vv2[2] + v[2] * tube_size;

      if(cap2 == cCylCapRound)
        CGONormalv(I, v);
      CGOVertexv(I, v + 3);
    }
    CGOEnd(I);
  }
}

static void CGOSimpleCone(CGO * I, float *v1, float *v2, float r1, float r2,
                          float *c1, float *c2, int cap1, int cap2)
{

#define MAX_EDGE 50

  float d[3], t[3], p0[3], p1[3], p2[3], vv1[3], vv2[3], v_buf[9], *v;
  float x[MAX_EDGE + 1], y[MAX_EDGE + 1], edge_normal[3 * (MAX_EDGE + 1)];
#if 0
  float overlap1, overlap2;
#endif
  float nub1, nub2;
  int colorFlag;
  int nEdge;
  int c;

  v = v_buf;
  nEdge = (int) SettingGet(I->G, cSetting_cone_quality);
#if 0
  overlap1 = r1 * SettingGet(I->G, cSetting_stick_overlap);
  overlap2 = r2 * SettingGet(I->G, cSetting_stick_overlap);
#endif

  nub1 = r1 * SettingGet(I->G, cSetting_stick_nub);
  nub2 = r2 * SettingGet(I->G, cSetting_stick_nub);

  if(nEdge > MAX_EDGE)
    nEdge = MAX_EDGE;
  subdivide(nEdge, x, y);

  colorFlag = (c1 != c2) && c2;

  CGOColorv(I, c1);

  /* direction vector */

  p0[0] = (v2[0] - v1[0]);
  p0[1] = (v2[1] - v1[1]);
  p0[2] = (v2[2] - v1[2]);

  normalize3f(p0);

#if 0
  if(cap1 == cCylCapRound)
    ) {
    vv1[0] = v1[0] - p0[0] * overlap1;
    vv1[1] = v1[1] - p0[1] * overlap1;
    vv1[2] = v1[2] - p0[2] * overlap1;
  } else
#endif

  {
    vv1[0] = v1[0];
    vv1[1] = v1[1];
    vv1[2] = v1[2];
  }

#if 0
  if(cap2 == cCylCapRound) {
    vv2[0] = v2[0] + p0[0] * overlap2;
    vv2[1] = v2[1] + p0[1] * overlap2;
    vv2[2] = v2[2] + p0[2] * overlap2;
  } else
#endif

  {
    vv2[0] = v2[0];
    vv2[1] = v2[1];
    vv2[2] = v2[2];
  }

  d[0] = (vv2[0] - vv1[0]);
  d[1] = (vv2[1] - vv1[1]);
  d[2] = (vv2[2] - vv1[2]);

  get_divergent3f(d, t);

  cross_product3f(d, t, p1);

  normalize3f(p1);

  cross_product3f(d, p1, p2);

  normalize3f(p2);

  /* now we have a coordinate system */

  {
    float len = diff3f(v1, v2);
    float vt[3], nt[3];
    float slope = 0.0F;

    if(len) {
      slope = (r1 - r2) / len;
    }
    for(c = nEdge; c >= 0; c--) {
      vt[0] = p1[0] * x[c] + p2[0] * y[c];
      vt[1] = p1[1] * x[c] + p2[1] * y[c];
      vt[2] = p1[2] * x[c] + p2[2] * y[c];

      scale3f(p0, slope, nt);
      add3f(nt, vt, vt);
      normalize3f(vt);
      copy3f(vt, edge_normal + 3 * c);
    }
  }

  /* now we have normals */

  CGOBegin(I, GL_TRIANGLE_STRIP);
  for(c = nEdge; c >= 0; c--) {
    v[0] = p1[0] * x[c] + p2[0] * y[c];
    v[1] = p1[1] * x[c] + p2[1] * y[c];
    v[2] = p1[2] * x[c] + p2[2] * y[c];

    v[3] = vv1[0] + v[0] * r1;
    v[4] = vv1[1] + v[1] * r1;
    v[5] = vv1[2] + v[2] * r1;

    v[6] = vv1[0] + v[0] * r2 + d[0];
    v[7] = vv1[1] + v[1] * r2 + d[1];
    v[8] = vv1[2] + v[2] * r2 + d[2];

    CGONormalv(I, edge_normal + 3 * c);
    if(colorFlag)
      CGOColorv(I, c1);
    CGOVertexv(I, v + 3);
    if(colorFlag)
      CGOColorv(I, c2);
    CGOVertexv(I, v + 6);
  }
  CGOEnd(I);

  if(cap1) {
    v[0] = -p0[0];
    v[1] = -p0[1];
    v[2] = -p0[2];

#if 0
    if(cap1 == cCylCapRound) {
      v[3] = vv1[0] - p0[0] * nub1;
      v[4] = vv1[1] - p0[1] * nub1;
      v[5] = vv1[2] - p0[2] * nub1;
    } else
#endif
    {
      v[3] = vv1[0];
      v[4] = vv1[1];
      v[5] = vv1[2];
    }

    if(colorFlag)
      CGOColorv(I, c1);
    CGOBegin(I, GL_TRIANGLE_FAN);
    CGONormalv(I, v);
    CGOVertexv(I, v + 3);

    for(c = nEdge; c >= 0; c--) {
      v[0] = p1[0] * x[c] + p2[0] * y[c];
      v[1] = p1[1] * x[c] + p2[1] * y[c];
      v[2] = p1[2] * x[c] + p2[2] * y[c];

      v[3] = vv1[0] + v[0] * r1;
      v[4] = vv1[1] + v[1] * r1;
      v[5] = vv1[2] + v[2] * r1;

      if(cap1 == cCylCapRound)
        CGONormalv(I, v);
      CGOVertexv(I, v + 3);
    }
    CGOEnd(I);
  }

  if(cap2) {

    v[0] = p0[0];
    v[1] = p0[1];
    v[2] = p0[2];

#if 0
    if(cap2 == cCylCapRound) {
      v[3] = vv2[0] + p0[0] * nub2;
      v[4] = vv2[1] + p0[1] * nub2;
      v[5] = vv2[2] + p0[2] * nub2;
    } else
#endif
    {
      v[3] = vv2[0];
      v[4] = vv2[1];
      v[5] = vv2[2];
    }

    if(colorFlag)
      CGOColorv(I, c2);
    CGOBegin(I, GL_TRIANGLE_FAN);
    CGONormalv(I, v);
    CGOVertexv(I, v + 3);

    for(c = 0; c <= nEdge; c++) {
      v[0] = p1[0] * x[c] + p2[0] * y[c];
      v[1] = p1[1] * x[c] + p2[1] * y[c];
      v[2] = p1[2] * x[c] + p2[2] * y[c];

      v[3] = vv2[0] + v[0] * r2;
      v[4] = vv2[1] + v[1] * r2;
      v[5] = vv2[2] + v[2] * r2;

      if(cap2 == cCylCapRound)
        CGONormalv(I, v);
      CGOVertexv(I, v + 3);
    }
    CGOEnd(I);
  }
}

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