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ObjectMolecule2.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"Debug.h"
#include"Parse.h"
#include"OOMac.h"
#include"Vector.h"
#include"PConv.h"
#include"ObjectMolecule.h"
#include"Feedback.h"
#include"Util.h"
#include"AtomInfo.h"
#include"Selector.h"
#include"ObjectDist.h"
#include"Executive.h"
#include"P.h"
#include"ObjectCGO.h"
#include"Scene.h"

#define ntrim ParseNTrim
#define nextline ParseNextLine
#define ncopy ParseNCopy
#define nskip ParseNSkip

#define cResvMask 0x7FFF

#define cMaxOther 6

00048 typedef struct {
  int n_cyclic_arom, cyclic_arom[cMaxOther];
  int n_arom, arom[cMaxOther];
  int n_high_val, high_val[cMaxOther];
  int n_cyclic, cyclic[cMaxOther];
  int n_planer, planer[cMaxOther];
  int n_rest, rest[cMaxOther];
  int score;
} OtherRec;

static int populate_other(OtherRec * other, int at, AtomInfoType * ai, BondType * bd,
                          int *neighbor)
{
  int five_cycle = false;
  int six_cycle = false;

  {
    int mem[9], nbr[7];
    const int ESCAPE_MAX = 500;
    register int escape_count;

    escape_count = ESCAPE_MAX;  /* don't get bogged down with structures 
                                   that have unreasonable connectivity */
    mem[0] = bd->index[0];
    mem[1] = bd->index[1];
    nbr[1] = neighbor[mem[1]] + 1;
    while(((mem[2] = neighbor[nbr[1]]) >= 0)) {
      if(mem[2] != mem[0]) {
        nbr[2] = neighbor[mem[2]] + 1;
        while(((mem[3] = neighbor[nbr[2]]) >= 0)) {
          if(mem[3] != mem[1]) {
            nbr[3] = neighbor[mem[3]] + 1;
            while(((mem[4] = neighbor[nbr[3]]) >= 0)) {
              if((mem[4] != mem[2]) && (mem[4] != mem[1]) && (mem[4] != mem[0])) {
                nbr[4] = neighbor[mem[4]] + 1;
                while(((mem[5] = neighbor[nbr[4]]) >= 0)) {
                  if(!(escape_count--))
                    goto escape;
                  if((mem[5] != mem[3]) && (mem[5] != mem[2]) && (mem[5] != mem[1])) {
                    if(mem[5] == mem[0]) {      /* five-cycle */
                      five_cycle = true;
                    }
                    nbr[5] = neighbor[mem[5]] + 1;
                    while(((mem[6] = neighbor[nbr[5]]) >= 0)) {
                      if((mem[6] != mem[4]) && (mem[6] != mem[3]) && (mem[6] != mem[2])
                         && (mem[6] != mem[1])) {
                        if(mem[6] == mem[0]) {  /* six-cycle */
                          six_cycle = true;
                        }
                      }
                      nbr[5] += 2;
                    }
                  }
                  nbr[4] += 2;
                }
              }
              nbr[3] += 2;
            }
          }
          nbr[2] += 2;
        }
      }
      nbr[1] += 2;
    }
  }
escape:

  if(bd->order == 4) {          /* aromatic */
    if((five_cycle || six_cycle) && (other->n_cyclic_arom < cMaxOther)) {
      other->cyclic_arom[other->n_cyclic_arom++] = at;
      if(five_cycle && six_cycle)
        other->score += 34;
      else if(five_cycle)
        other->score += 33;
      else
        other->score += 32;
      return 1;
    } else if(other->n_arom < cMaxOther) {
      other->arom[other->n_arom++] = at;
      other->score += 64;
      return 1;
    }
  }
  if(bd->order > 1) {
    if(other->n_high_val < cMaxOther) {
      other->high_val[other->n_high_val++] = at;
      other->score += 16;
      return 1;
    }
  }
  if(five_cycle || six_cycle) {
    if(other->n_cyclic < cMaxOther) {
      other->cyclic[other->n_cyclic++] = at;
      other->score += 8;
      return 1;
    }
  }
  if(ai->geom == cAtomInfoPlanar) {
    if(other->n_planer < cMaxOther) {
      other->planer[other->n_planer++] = at;
      other->score += 4;
      return 1;
    }
  }
  if(other->n_rest < cMaxOther) {
    other->rest[other->n_rest++] = at;
    other->score += 1;
    return 1;
  }
  return 0;
}

static int append_index(int *result, int offset, int a1, int a2, int score, int ar_count)
{
  int c;
  c = result[a1];
  while(c < offset) {
    if(result[c] == a2) {       /* already entered */
      if(result[c + 1] < score) {
        result[c + 1] = score;
        result[c + 2] = ar_count;
      }
      return offset;
    }
    c += 3;
  }
  result[offset++] = a2;
  result[offset++] = score;
  result[offset++] = ar_count;
  return offset;
}

int ObjectMoleculeAddPseudoatom(ObjectMolecule * I, int sele_index, char *name,
                                char *resn, char *resi, char *chain,
                                char *segi, char *elem, float vdw,
                                int hetatm, float b, float q, char *label,
                                float *pos, int color, int state, int mode, int quiet)
{
  PyMOLGlobals *G = I->Obj.G;
  int start_state = 0, stop_state = 0;
  int nAtom = 1;
  int extant_only = false;
  int ai_merged = false;
  float pos_array[3] = { 0.0F, 0.0F, 0.0F };
  int ok = true;

  AtomInfoType *atInfo = VLACalloc(AtomInfoType, 1);

  if(state >= 0) {              /* specific state */
    start_state = state;
    stop_state = state + 1;
  } else if(state == -1) {      /* current state */
    start_state = ObjectGetCurrentState(&I->Obj, true);
    stop_state = start_state + 1;
  } else {                      /* all states */
    if(sele_index >= 0) {
      start_state = 0;
      stop_state = SelectorCountStates(G, sele_index);
      if(state == -3)
        extant_only = true;
    } else {
      start_state = 0;
      stop_state = ExecutiveCountStates(G, cKeywordAll);
      if(stop_state < 1)
        stop_state = 1;
    }
  }
  {
    /* match existing properties of the old atom */
    int auto_show_lines = (int) SettingGet(G, cSetting_auto_show_lines);
    int auto_show_spheres = (int) SettingGet(G, cSetting_auto_show_spheres);
    int auto_show_nonbonded = (int) SettingGet(G, cSetting_auto_show_nonbonded);
    AtomInfoType *ai = atInfo;
    ai->resv = AtomResvFromResi(resi);
    ai->hetatm = hetatm;
    ai->geom = cAtomInfoNone;
    ai->q = q;
    ai->b = b;
    strcpy(ai->chain, chain);
    strcpy(ai->resi, resi);
    strcpy(ai->segi, segi);
    strcpy(ai->resn, resn);
    strcpy(ai->name, name);
    strcpy(ai->elem, elem);
    ai->visRep[cRepLine] = auto_show_lines;
    ai->visRep[cRepNonbonded] = auto_show_nonbonded;
    ai->visRep[cRepSphere] = auto_show_spheres;
    ai->id = -1;
    ai->rank = -1;
    if(vdw >= 0.0F)
      ai->vdw = vdw;
    else
      ai->vdw = 1.0F;
    if(label[0]) {
      OVreturn_word ret = OVLexicon_GetFromCString(G->Lexicon, label);
      if(OVreturn_IS_OK(ret)) {
        ai->label = ret.word;
        ai->visRep[cRepLabel] = true;
        ai->visRep[cRepLine] = false;
        ai->visRep[cRepNonbonded] = false;
        ai->visRep[cRepSphere] = false;
      }
    }
    if(color < 0) {
      AtomInfoAssignColors(I->Obj.G, ai);
      if((ai->elem[0] == 'C') && (ai->elem[1] == 0))
        /* carbons are always colored according to the object color */
        ai->color = I->Obj.Color;
    } else {
      ai->color = color;
    }
    AtomInfoAssignParameters(I->Obj.G, ai);
    AtomInfoUniquefyNames(I->Obj.G, I->AtomInfo, I->NAtom, ai, NULL, 1);
    if(!quiet) {
      PRINTFB(G, FB_ObjectMolecule, FB_Actions)
        " ObjMol: created %s/%s/%s/%s`%s/%s\n",
        I->Obj.Name, ai->segi, ai->chain, ai->resn, ai->resi, ai->name ENDFB(G);
    }
  }

  for(state = start_state; state < stop_state; state++) {

    CoordSet *cset = NULL;

    if((extant_only && (state < I->NCSet) && I->CSet[state]) || !extant_only) {

      if(sele_index >= 0) {
        ObjectMoleculeOpRec op;
        ObjectMoleculeOpRecInit(&op);
        op.code = OMOP_CSetSumVertices;
        op.cs1 = state;

        ExecutiveObjMolSeleOp(I->Obj.G, sele_index, &op);

        if(op.i1) {
          float factor = 1.0F / op.i1;
          scale3f(op.v1, factor, pos_array);
          pos = pos_array;

          if(vdw < 0.0F) {
            switch (mode) {
            case 1:
              ObjectMoleculeOpRecInit(&op);
              op.code = OMOP_CSetMaxDistToPt;
              copy3f(pos_array, op.v1);
              op.cs1 = state;
              ExecutiveObjMolSeleOp(I->Obj.G, sele_index, &op);
              vdw = op.f1;
              break;
            case 2:
              ObjectMoleculeOpRecInit(&op);
              op.code = OMOP_CSetSumSqDistToPt;
              copy3f(pos_array, op.v1);
              op.cs1 = state;
              ExecutiveObjMolSeleOp(I->Obj.G, sele_index, &op);
              vdw = sqrt1f(op.d1 / op.i1);
              break;
            case 0:
            default:
              vdw = 0.5F;
              break;
            }
            if(vdw >= 0.0F)
              atInfo->vdw = vdw;        /* NOTE: only uses vdw from first state selection... */
          }
        } else {
          pos = NULL;           /* skip this state */
        }
      } else if(!pos) {
        pos = pos_array;
        SceneGetPos(I->Obj.G, pos);
      }

      if(pos) {                 /* only add coordinate to state if we have position for it */

        float *coord = VLAlloc(float, 3 * nAtom);

        copy3f(pos, coord);

        cset = CoordSetNew(I->Obj.G);
        cset->NIndex = nAtom;
        cset->Coord = coord;
        cset->TmpBond = NULL;
        cset->NTmpBond = 0;

        cset->Obj = I;
        if(cset->fEnumIndices)
          cset->fEnumIndices(cset);
        if(!ai_merged) {
          ObjectMoleculeMerge(I, atInfo, cset, false, cAIC_AllMask, true);      /* NOTE: will release atInfo */
          ObjectMoleculeExtendIndices(I, -1);
          ObjectMoleculeUpdateNeighbors(I);
          ai_merged = true;
        }
        if(state >= I->NCSet) {
          VLACheck(I->CSet, CoordSet *, state);
          I->NCSet = state + 1;
        }
        if(!I->CSet[state]) {
          /* new coordinate set */
          I->CSet[state] = cset;
          cset = NULL;
        } else {
          /* merge coordinate set */
          CoordSetMerge(I->CSet[state], cset);
          if(cset->fFree) {
            cset->fFree(cset);
            cset = NULL;
          }
        }
      }
    }
  }
  if(ai_merged) {
    ObjectMoleculeSort(I);
    ObjectMoleculeUpdateIDNumbers(I);
    ObjectMoleculeUpdateNonbonded(I);
    ObjectMoleculeInvalidate(I, cRepAll, cRepInvAtoms, -1);
  } else {
    VLAFreeP(atInfo);
  }
  return (ok);
}

int *ObjectMoleculeGetPrioritizedOtherIndexList(ObjectMolecule * I, CoordSet * cs)
{
  int a, b;
  int b1, b2, a1, a2, a3;
  OtherRec *o;
  OtherRec *other = Calloc(OtherRec, cs->NIndex);
  int *result = NULL;
  int offset;
  int n_alloc = 0;
  BondType *bd;

  ObjectMoleculeUpdateNeighbors(I);
  bd = I->Bond;
  for(a = 0; a < I->NBond; a++) {
    b1 = bd->index[0];
    b2 = bd->index[1];
    if(I->DiscreteFlag) {
      if((cs == I->DiscreteCSet[b1]) && (cs == I->DiscreteCSet[b2])) {
        a1 = I->DiscreteAtmToIdx[b1];
        a2 = I->DiscreteAtmToIdx[b2];
      } else {
        a1 = -1;
        a2 = -1;
      }
    } else {
      a1 = cs->AtmToIdx[b1];
      a2 = cs->AtmToIdx[b2];
    }
    if((a1 >= 0) && (a2 >= 0)) {
      n_alloc += populate_other(other + a1, a2, I->AtomInfo + b2, bd, I->Neighbor);
      n_alloc += populate_other(other + a2, a1, I->AtomInfo + b1, bd, I->Neighbor);
    }
    bd++;
  }

  n_alloc = 3 * (n_alloc + cs->NIndex);
  o = other;
  result = Alloc(int, n_alloc);
  for(a = 0; a < cs->NIndex; a++) {
    result[a] = -1;
  }
  offset = cs->NIndex;
  bd = I->Bond;
  for(a = 0; a < I->NBond; a++) {
    b1 = bd->index[0];
    b2 = bd->index[1];
    if(I->DiscreteFlag) {
      if((cs == I->DiscreteCSet[b1]) && (cs == I->DiscreteCSet[b2])) {
        a1 = I->DiscreteAtmToIdx[b1];
        a2 = I->DiscreteAtmToIdx[b2];
      } else {
        a1 = -1;
        a2 = -1;
      }
    } else {
      a1 = cs->AtmToIdx[b1];
      a2 = cs->AtmToIdx[b2];
    }
    if((a1 >= 0) && (a2 >= 0)) {
      if(result[a1] < 0) {
        o = other + a1;
        result[a1] = offset;
        for(b = 0; b < o->n_cyclic_arom; b++) {
          a3 = o->cyclic_arom[b];
          offset = append_index(result, offset, a1, a3, 128 + other[a3].score, 1);
        }
        for(b = 0; b < o->n_arom; b++) {
          a3 = o->arom[b];
          offset = append_index(result, offset, a1, a3, 64 + other[a3].score, 1);
        }
        for(b = 0; b < o->n_high_val; b++) {
          a3 = o->high_val[b];
          offset = append_index(result, offset, a1, a3, 16 + other[a3].score, 0);
        }
        for(b = 0; b < o->n_cyclic; b++) {
          a3 = o->cyclic[b];
          offset = append_index(result, offset, a1, a3, 8 + other[a3].score, 0);
        }
        for(b = 0; b < o->n_planer; b++) {
          a3 = o->planer[b];
          offset = append_index(result, offset, a1, a3, 2 + other[a3].score, 0);
        }
        for(b = 0; b < o->n_rest; b++) {
          a3 = o->rest[b];
          offset = append_index(result, offset, a1, a3, 1 + other[a3].score, 0);
        }
        result[offset++] = -1;
      }

      if(result[a2] < 0) {
        o = other + a2;
        result[a2] = offset;
        for(b = 0; b < o->n_cyclic_arom; b++) {
          a3 = o->cyclic_arom[b];
          offset = append_index(result, offset, a2, a3, 128 + other[a3].score, 1);
        }
        for(b = 0; b < o->n_arom; b++) {
          a3 = o->arom[b];
          offset = append_index(result, offset, a2, a3, 64 + other[a3].score, 1);
        }
        for(b = 0; b < o->n_high_val; b++) {
          a3 = o->high_val[b];
          offset = append_index(result, offset, a2, a3, 16 + other[a3].score, 0);
        }
        for(b = 0; b < o->n_cyclic; b++) {
          a3 = o->cyclic[b];
          offset = append_index(result, offset, a2, a3, 8 + other[a3].score, 0);
        }
        for(b = 0; b < o->n_planer; b++) {
          a3 = o->planer[b];
          offset = append_index(result, offset, a2, a3, 2 + other[a3].score, 0);
        }
        for(b = 0; b < o->n_rest; b++) {
          a3 = o->rest[b];
          offset = append_index(result, offset, a2, a3, 1 + other[a3].score, 0);
        }
        result[offset++] = -1;
      }

    }
    bd++;
  }
  FreeP(other);
  return result;
}

int ObjectMoleculeGetNearestBlendedColor(ObjectMolecule * I, float *point,
                                         float cutoff, int state, float *dist,
                                         float *color, int sub_vdw)
{
  int result = -1;
  float tot_weight = 0.0F;
  float cutoff2 = cutoff * cutoff;
  register float nearest = -1.0F;

  color[0] = 0.0F;
  color[1] = 0.0F;
  color[2] = 0.0F;

  if(state < 0)
    state = ObjectGetCurrentState(&I->Obj, true);

  if((state >= 0) && (state < I->NCSet)) {
    CoordSet *cs = I->CSet[state];
    if(cs) {
      MapType *map;
      CoordSetUpdateCoord2IdxMap(cs, cutoff);
      if(sub_vdw) {
        cutoff -= MAX_VDW;
        cutoff2 = cutoff * cutoff;
      }
      nearest = cutoff2;
      if((map = cs->Coord2Idx)) {
        int a, b, c, d, e, f, j;
        register float test;
        register float *v;
        MapLocus(map, point, &a, &b, &c);
        for(d = a - 1; d <= a + 1; d++)
          for(e = b - 1; e <= b + 1; e++)
            for(f = c - 1; f <= c + 1; f++) {
              j = *(MapFirst(map, d, e, f));
              while(j >= 0) {
                v = cs->Coord + (3 * j);
                test = diffsq3f(v, point);
                if(sub_vdw) {
                  test = sqrt1f(test);
                  test -= I->AtomInfo[cs->IdxToAtm[j]].vdw;
                  if(test < 0.0F)
                    test = 0.0F;
                  test = test * test;
                }
                if(test < cutoff2) {
                  float weight = cutoff - sqrt1f(test);
                  float *at_col = ColorGet(I->Obj.G, I->AtomInfo[cs->IdxToAtm[j]].color);
                  color[0] += at_col[0] * weight;
                  color[1] += at_col[1] * weight;
                  color[2] += at_col[2] * weight;
                  tot_weight += weight;
                }
                if(test <= nearest) {
                  result = j;
                  nearest = test;
                }
                j = MapNext(map, j);
              }
            }
      } else {
        register int j;
        register float test, *v = cs->Coord;
        for(j = 0; j < cs->NIndex; j++) {
          test = diffsq3f(v, point);
          if(sub_vdw) {
            test = sqrt1f(test);
            test -= I->AtomInfo[cs->IdxToAtm[j]].vdw;
            if(test < 0.0F)
              test = 0.0F;
            test = test * test;
          }
          if(test < cutoff2) {
            float weight = cutoff - sqrt1f(test);
            float *color = ColorGet(I->Obj.G, I->AtomInfo[cs->IdxToAtm[j]].color);
            color[0] += color[0] * weight;
            color[1] += color[1] * weight;
            color[2] += color[2] * weight;
            tot_weight += weight;
          }
          if(test <= nearest) {
            result = j;
            nearest = test;
          }
          v += 3;
        }
      }
      if(result >= 0)
        result = cs->IdxToAtm[result];
    }
  }
  if(dist) {
    if(result >= 0) {
      *dist = sqrt1f(nearest);
      if(tot_weight > 0.0F) {
        color[0] /= tot_weight;
        color[1] /= tot_weight;
        color[2] /= tot_weight;
      }
    } else {
      *dist = -1.0F;
    }
  }
  return result;
}

int ObjectMoleculeGetNearestAtomIndex(ObjectMolecule * I, float *point, float cutoff,
                                      int state, float *dist)
{
  int result = -1;
  register float nearest = -1.0F;
  if(state < 0)
    state = ObjectGetCurrentState(&I->Obj, true);
  if((state >= 0) && (state < I->NCSet)) {
    CoordSet *cs = I->CSet[state];
    if(cs) {
      MapType *map;
      CoordSetUpdateCoord2IdxMap(cs, cutoff);
      nearest = cutoff * cutoff;
      if((map = cs->Coord2Idx)) {
        int a, b, c, d, e, f, j;
        register float test;
        register float *v;
        MapLocus(map, point, &a, &b, &c);
        for(d = a - 1; d <= a + 1; d++)
          for(e = b - 1; e <= b + 1; e++)
            for(f = c - 1; f <= c + 1; f++) {
              j = *(MapFirst(map, d, e, f));
              while(j >= 0) {
                v = cs->Coord + (3 * j);
                test = diffsq3f(v, point);
                if(test <= nearest) {
                  result = j;
                  nearest = test;
                }
                j = MapNext(map, j);
              }
            }
      } else {
        register int j;
        register float test, *v = cs->Coord;
        for(j = 0; j < cs->NIndex; j++) {
          test = diffsq3f(v, point);
          if(test <= nearest) {
            result = j;
            nearest = test;
          }
          v += 3;
        }
      }
      if(result >= 0)
        result = cs->IdxToAtm[result];
    }
  }
  if(dist) {
    if(result >= 0) {
      *dist = sqrt1f(nearest);
    } else {
      *dist = -1.0F;
    }
  }
  return result;
}

int ObjectMoleculeGetPrioritizedOther(int *other, int a1, int a2, int *double_sided)
{
  int a3 = -1;
  int lvl = -1, ck, ck_lvl;
  int offset;
  int ar_count = 0;

  a3 = -1;
  lvl = -1;
  if(a1 >= 0) {
    offset = other[a1];
    if(offset >= 0) {
      while(1) {
        ck = other[offset];
        if(ck != a2) {
          if(ck >= 0) {
            ck_lvl = other[offset + 1];
            if(ck_lvl > lvl) {
              a3 = ck;
              lvl = ck_lvl;
            }
            ar_count += other[offset + 2];
          } else
            break;
        }
        offset += 3;
      }
    }
  }
  if(a2 >= 0) {
    offset = other[a2];
    if(offset >= 0) {
      while(1) {
        ck = other[offset];
        if(ck != a1) {
          if(ck >= 0) {
            ck_lvl = other[offset + 1];
            if(ck_lvl > lvl) {
              a3 = ck;
              lvl = ck_lvl;
            }
            ar_count += other[offset + 2];
          } else
            break;
        }
        offset += 3;
      }
    }
  }

  if(double_sided) {
    if(ar_count == 4)
      *double_sided = true;
    else
      *double_sided = false;
  }
  return a3;
}

int ObjectMoleculeIsAtomBondedToName(ObjectMolecule * obj, int a0, char *name)
{
  int a2, s;
  int bonded = false;

  if(a0 >= 0) {
    s = obj->Neighbor[a0];
    s++;                        /* skip count */
    while(1) {
      a2 = obj->Neighbor[s];
      if(a2 < 0)
        break;
      if(WordMatch(obj->Obj.G, obj->AtomInfo[a2].name, name, true) < 0)
        bonded = true;
      break;
      s += 2;
    }
  }
  return bonded;
}

int ObjectMoleculeAreAtomsBonded2(ObjectMolecule * obj0, int a0, ObjectMolecule * obj1,
                                  int a1)
{
  /* assumes neighbor list is current */

  if(obj0 != obj1)
    return false;
  else {
    int a2, s;

    if(a0 >= 0) {
      s = obj0->Neighbor[a0];
      s++;                      /* skip count */
      while(1) {
        a2 = obj0->Neighbor[s];
        if(a2 < 0)
          break;
        if(a1 == a2)
          return true;
        s += 2;
      }
    }
  }
  return false;
}

int ObjectMoleculeDoesAtomNeighborSele(ObjectMolecule * I, int index, int sele)
{
  int result = false;
  ObjectMoleculeUpdateNeighbors(I);
  if(index < I->NAtom) {
    int a1;
    int n;
    AtomInfoType *ai;

    n = I->Neighbor[index] + 1;
    while(1) {                  /* look for an attached non-hydrogen as a base */
      a1 = I->Neighbor[n];
      n += 2;
      if(a1 < 0)
        break;
      ai = I->AtomInfo + a1;
      if(SelectorIsMember(I->Obj.G, ai->selEntry, sele)) {
        result = true;
        break;
      }
    }
  }
  return result;
}

static void assign_pdb_known_residue(PyMOLGlobals * G, AtomInfoType * ai1,
                                     AtomInfoType * ai2, int *bond_order)
{
  int order = *(bond_order);
  char *name1 = ai1->name;
  char *name2 = ai2->name;
  char *resn1 = ai1->resn;

  /* nasty high-speed hack to get bond valences and formal charges 
     for standard residues */
  if(((!name1[1]) && (!name2[1])) &&
     (((name1[0] == 'C') && (name2[0] == 'O')) ||
      ((name1[0] == 'O') && (name2[0] == 'C')))) {
    order = 2;
  } else if((!name2[1]) && (name2[0] == 'C') && (!strcmp(name1, "OXT"))) {
    ai1->formalCharge = -1;
    ai1->chemFlag = false;
  } else if((!name1[1]) && (name1[0] == 'C') && (!strcmp(name2, "OXT"))) {
    ai2->formalCharge = -1;
    ai2->chemFlag = false;
  } else {
    switch (resn1[0]) {
    case 'A':
      switch (resn1[1]) {
      case 'R':
        switch (resn1[2]) {
        case 'G':              /* ARG... */
          switch (resn1[3]) {
          case 0:
          case 'P':            /*  ARG, ARGP */
            if(!strcmp(name1, "NH1")) {
              ai1->formalCharge = 1;
              ai1->chemFlag = false;
            } else if(!strcmp(name2, "NH1")) {
              ai2->formalCharge = 1;
              ai2->chemFlag = false;
            }
            break;
          }
          if(((!strcmp(name1, "CZ")) && (!strcmp(name2, "NH1"))) ||
             ((!strcmp(name2, "CZ")) && (!strcmp(name1, "NH1"))))
            order = 2;
          break;
        }
        break;
      case 'S':
        switch (resn1[2]) {
        case 'P':              /* ASP... */
          switch (resn1[3]) {
          case 0:
          case 'M':            /* ASP, ASPM minus assumption */
            if(!strcmp(name1, "OD2")) {
              ai1->formalCharge = -1;
              ai1->chemFlag = false;
            } else if(!strcmp(name2, "OD2")) {
              ai2->formalCharge = -1;
              ai2->chemFlag = false;
            }
            break;
          }
          if(((!strcmp(name1, "CG")) && (!strcmp(name2, "OD1"))) ||
             ((!strcmp(name2, "CG")) && (!strcmp(name1, "OD1"))))
            order = 2;
          break;
        case 'N':              /* ASN  */
          if(((!strcmp(name1, "CG")) && (!strcmp(name2, "OD1"))) ||
             ((!strcmp(name2, "CG")) && (!strcmp(name1, "OD1"))))
            order = 2;
          break;
        }
        break;
      case 0:
        if(((!strcmp(name1, "O2P")) || (!strcmp(name1, "OP2")))) {
          ai1->formalCharge = -1;
          ai1->chemFlag = false;
        } else if(((!strcmp(name2, "O2P")) || (!strcmp(name2, "OP2")))) {
          ai2->formalCharge = -1;
          ai2->chemFlag = false;
        }
        if(((!strcmp(name1, "C8")) && (!strcmp(name2, "N7"))) ||
           ((!strcmp(name2, "C8")) && (!strcmp(name1, "N7"))))
          order = 2;
        else if(((!strcmp(name1, "C4")) && (!strcmp(name2, "C5"))) ||
                ((!strcmp(name2, "C4")) && (!strcmp(name1, "C5"))))
          order = 2;

        else if(((!strcmp(name1, "C6")) && (!strcmp(name2, "N1"))) ||
                ((!strcmp(name2, "C6")) && (!strcmp(name1, "N1"))))
          order = 2;
        else if(((!strcmp(name1, "C2")) && (!strcmp(name2, "N3"))) ||
                ((!strcmp(name2, "C2")) && (!strcmp(name1, "N3"))))
          order = 2;
        else
          if(((!strcmp(name1, "P"))
              && (((!strcmp(name2, "O1P")) || (!strcmp(name2, "OP1")))))
             || ((!strcmp(name2, "P"))
                 && (((!strcmp(name1, "O1P")) || (!strcmp(name1, "OP1"))))))
          order = 2;
        break;
      }
      break;
    case 'C':
      if(resn1[1] == 0) {
        if(((!strcmp(name1, "O2P")) || (!strcmp(name1, "OP2")))) {
          ai1->formalCharge = -1;
          ai1->chemFlag = false;
        } else if(((!strcmp(name2, "O2P")) || (!strcmp(name2, "OP2")))) {
          ai2->formalCharge = -1;
          ai2->chemFlag = false;
        }
        if(((!strcmp(name1, "C2")) && (!strcmp(name2, "O2"))) ||
           ((!strcmp(name2, "C2")) && (!strcmp(name1, "O2"))))
          order = 2;
        else if(((!strcmp(name1, "C4")) && (!strcmp(name2, "N3"))) ||
                ((!strcmp(name2, "C4")) && (!strcmp(name1, "N3"))))
          order = 2;

        else if(((!strcmp(name1, "C5")) && (!strcmp(name2, "C6"))) ||
                ((!strcmp(name2, "C5")) && (!strcmp(name1, "C6"))))
          order = 2;
        else
          if(((!strcmp(name1, "P"))
              && (((!strcmp(name2, "O1P")) || (!strcmp(name2, "OP1")))))
             || ((!strcmp(name2, "P"))
                 && (((!strcmp(name1, "O1P")) || (!strcmp(name1, "OP1"))))))
          order = 2;
      }
      break;
    case 'D':                  /* deoxy nucleic acids */
      switch (resn1[1]) {
      case 'A':
        if(resn1[2] == 0) {
          if(((!strcmp(name1, "O2P")) || (!strcmp(name1, "OP2")))) {
            ai1->formalCharge = -1;
            ai1->chemFlag = false;
          } else if(((!strcmp(name2, "O2P")) || (!strcmp(name2, "OP2")))) {
            ai2->formalCharge = -1;
            ai2->chemFlag = false;
          }
          if(((!strcmp(name1, "C8")) && (!strcmp(name2, "N7"))) ||
             ((!strcmp(name2, "C8")) && (!strcmp(name1, "N7"))))
            order = 2;
          else if(((!strcmp(name1, "C4")) && (!strcmp(name2, "C5"))) ||
                  ((!strcmp(name2, "C4")) && (!strcmp(name1, "C5"))))
            order = 2;

          else if(((!strcmp(name1, "C6")) && (!strcmp(name2, "N1"))) ||
                  ((!strcmp(name2, "C6")) && (!strcmp(name1, "N1"))))
            order = 2;
          else if(((!strcmp(name1, "C2")) && (!strcmp(name2, "N3"))) ||
                  ((!strcmp(name2, "C2")) && (!strcmp(name1, "N3"))))
            order = 2;
          else
            if(((!strcmp(name1, "P"))
                && (((!strcmp(name2, "O1P")) || (!strcmp(name2, "OP1")))))
               || ((!strcmp(name2, "P"))
                   && (((!strcmp(name1, "O1P")) || (!strcmp(name1, "OP1"))))))
            order = 2;
        }
        break;
      case 'C':
        if(resn1[2] == 0) {
          if(((!strcmp(name1, "O2P")) || (!strcmp(name1, "OP2")))) {
            ai1->formalCharge = -1;
            ai1->chemFlag = false;
          } else if(((!strcmp(name2, "O2P")) || (!strcmp(name2, "OP2")))) {
            ai2->formalCharge = -1;
            ai2->chemFlag = false;
          }
          if(((!strcmp(name1, "C2")) && (!strcmp(name2, "O2"))) ||
             ((!strcmp(name2, "C2")) && (!strcmp(name1, "O2"))))
            order = 2;
          else if(((!strcmp(name1, "C4")) && (!strcmp(name2, "N3"))) ||
                  ((!strcmp(name2, "C4")) && (!strcmp(name1, "N3"))))
            order = 2;

          else if(((!strcmp(name1, "C5")) && (!strcmp(name2, "C6"))) ||
                  ((!strcmp(name2, "C5")) && (!strcmp(name1, "C6"))))
            order = 2;
          else
            if(((!strcmp(name1, "P"))
                && (((!strcmp(name2, "O1P")) || (!strcmp(name2, "OP1")))))
               || ((!strcmp(name2, "P"))
                   && (((!strcmp(name1, "O1P")) || (!strcmp(name1, "OP1"))))))
            order = 2;
        }
        break;
      case 'T':
        if(resn1[2] == 0) {
          if(((!strcmp(name1, "O2P")) || (!strcmp(name1, "OP2"))))
            ai1->formalCharge = -1;
          else if(((!strcmp(name2, "O2P")) || (!strcmp(name2, "OP2"))))
            ai2->formalCharge = -1;

          if(((!strcmp(name1, "C2")) && (!strcmp(name2, "O2"))) ||
             ((!strcmp(name2, "C2")) && (!strcmp(name1, "O2"))))
            order = 2;
          else if(((!strcmp(name1, "C4")) && (!strcmp(name2, "O4"))) ||
                  ((!strcmp(name2, "C4")) && (!strcmp(name1, "O4"))))
            order = 2;

          else if(((!strcmp(name1, "C5")) && (!strcmp(name2, "C6"))) ||
                  ((!strcmp(name2, "C5")) && (!strcmp(name1, "C6"))))
            order = 2;
          else
            if(((!strcmp(name1, "P"))
                && (((!strcmp(name2, "O1P")) || (!strcmp(name2, "OP1")))))
               || ((!strcmp(name2, "P"))
                   && (((!strcmp(name1, "O1P")) || (!strcmp(name1, "OP1"))))))
            order = 2;
        }
        break;
      case 'G':
        if(resn1[2] == 0) {
          if(((!strcmp(name1, "O2P")) || (!strcmp(name1, "OP2")))) {
            ai1->formalCharge = -1;
            ai1->chemFlag = false;
          } else if(((!strcmp(name2, "O2P")) || (!strcmp(name2, "OP2")))) {
            ai2->formalCharge = -1;
            ai2->chemFlag = false;
          }
          if(((!strcmp(name1, "C6")) && (!strcmp(name2, "O6"))) ||
             ((!strcmp(name2, "C6")) && (!strcmp(name1, "O6"))))
            order = 2;
          else if(((!strcmp(name1, "C2")) && (!strcmp(name2, "N3"))) ||
                  ((!strcmp(name2, "C2")) && (!strcmp(name1, "N3"))))
            order = 2;
          else if(((!strcmp(name1, "C8")) && (!strcmp(name2, "N7"))) ||
                  ((!strcmp(name2, "C8")) && (!strcmp(name1, "N7"))))
            order = 2;
          else if(((!strcmp(name1, "C4")) && (!strcmp(name2, "C5"))) ||
                  ((!strcmp(name2, "C4")) && (!strcmp(name1, "C5"))))
            order = 2;
          else
            if(((!strcmp(name1, "P"))
                && (((!strcmp(name2, "O1P")) || (!strcmp(name2, "OP1")))))
               || ((!strcmp(name2, "P"))
                   && (((!strcmp(name1, "O1P")) || (!strcmp(name1, "OP1"))))))
            order = 2;
        }
        break;
      case 'U':
        if(resn1[2] == 0) {
          if(((!strcmp(name1, "O2P")) || (!strcmp(name1, "OP2")))) {
            ai1->formalCharge = -1;
            ai1->chemFlag = false;
          } else if(((!strcmp(name2, "O2P")) || (!strcmp(name2, "OP2")))) {
            ai2->formalCharge = -1;
            ai2->chemFlag = false;
          }

          if(((!strcmp(name1, "C2")) && (!strcmp(name2, "O2"))) ||
             ((!strcmp(name2, "C2")) && (!strcmp(name1, "O2"))))
            order = 2;
          else if(((!strcmp(name1, "C4")) && (!strcmp(name2, "O4"))) ||
                  ((!strcmp(name2, "C4")) && (!strcmp(name1, "O4"))))
            order = 2;

          else if(((!strcmp(name1, "C5")) && (!strcmp(name2, "C6"))) ||
                  ((!strcmp(name2, "C5")) && (!strcmp(name1, "C6"))))
            order = 2;
          else
            if(((!strcmp(name1, "P"))
                && (((!strcmp(name2, "O1P")) || (!strcmp(name2, "OP1")))))
               || ((!strcmp(name2, "P"))
                   && (((!strcmp(name1, "O1P")) || (!strcmp(name1, "OP1"))))))
            order = 2;
        }
        break;
      }
      break;
    case 'G':
      switch (resn1[1]) {
      case 'L':
        switch (resn1[2]) {
        case 'U':              /* GLU missing GLUN, GLUH, GLH handling */
          switch (resn1[3]) {
          case 0:
          case 'M':            /* minus */
            if(!strcmp(name1, "OE2")) {
              ai1->formalCharge = -1;
              ai1->chemFlag = false;
            } else if(!strcmp(name2, "OE2")) {
              ai2->formalCharge = -1;
              ai2->chemFlag = false;
            }
            break;
          }
          if(((!strcmp(name1, "CD")) && (!strcmp(name2, "OE1"))) ||
             ((!strcmp(name2, "CD")) && (!strcmp(name1, "OE1"))))
            order = 2;
          break;
        case 'N':              /* GLN or GLU */
          if(((!strcmp(name1, "CD")) && (!strcmp(name2, "OE1"))) ||
             ((!strcmp(name2, "CD")) && (!strcmp(name1, "OE1"))))
            order = 2;
          break;
        }
        break;
      case 0:
        if(((!strcmp(name1, "O2P")) || (!strcmp(name1, "OP2")))) {
          ai1->formalCharge = -1;
          ai1->chemFlag = false;
        } else if(((!strcmp(name2, "O2P")) || (!strcmp(name2, "OP2")))) {
          ai2->formalCharge = -1;
          ai2->chemFlag = false;
        }

        if(((!strcmp(name1, "C6")) && (!strcmp(name2, "O6"))) ||
           ((!strcmp(name2, "C6")) && (!strcmp(name1, "O6"))))
          order = 2;
        else if(((!strcmp(name1, "C2")) && (!strcmp(name2, "N3"))) ||
                ((!strcmp(name2, "C2")) && (!strcmp(name1, "N3"))))
          order = 2;
        else if(((!strcmp(name1, "C8")) && (!strcmp(name2, "N7"))) ||
                ((!strcmp(name2, "C8")) && (!strcmp(name1, "N7"))))
          order = 2;
        else if(((!strcmp(name1, "C4")) && (!strcmp(name2, "C5"))) ||
                ((!strcmp(name2, "C4")) && (!strcmp(name1, "C5"))))
          order = 2;
        else
          if(((!strcmp(name1, "P"))
              && (((!strcmp(name2, "O1P")) || (!strcmp(name2, "OP1")))))
             || ((!strcmp(name2, "P"))
                 && (((!strcmp(name1, "O1P")) || (!strcmp(name1, "OP1"))))))
          order = 2;
        break;
      }
      break;
    case 'H':
      switch (resn1[1]) {
      case 'I':
        switch (resn1[2]) {
        case 'P':
          if(!strcmp(name1, "ND1")) {
            ai1->formalCharge = 1;
            ai1->chemFlag = false;
          } else if(!strcmp(name2, "ND1")) {
            ai2->formalCharge = 1;
            ai2->chemFlag = false;
          }
          if(((!strcmp(name1, "CG")) && (!strcmp(name2, "CD2"))) ||
             ((!strcmp(name2, "CG")) && (!strcmp(name1, "CD2"))))
            order = 2;
          else if(((!strcmp(name1, "CE1")) && (!strcmp(name2, "ND1"))) ||
                  ((!strcmp(name2, "CE1")) && (!strcmp(name1, "ND1"))))
            order = 2;
          break;
        case 'S':
          switch (resn1[3]) {
          case 'A':            /* HISA Gromacs */
          case 'D':            /* HISD Quanta */
            if(((!strcmp(name1, "CG")) && (!strcmp(name2, "CD2"))) ||
               ((!strcmp(name2, "CG")) && (!strcmp(name1, "CD2"))))
              order = 2;
            else if(((!strcmp(name1, "CE1")) && (!strcmp(name2, "NE2"))) ||
                    ((!strcmp(name2, "CE1")) && (!strcmp(name1, "NE2"))))
              order = 2;
            break;
          case 0:              /* plain HIS */
          case 'B':            /* HISB Gromacs */
          case 'E':            /* HISE Quanta */
            if(((!strcmp(name1, "CG")) && (!strcmp(name2, "CD2"))) ||
               ((!strcmp(name2, "CG")) && (!strcmp(name1, "CD2"))))
              order = 2;
            else if(((!strcmp(name1, "CE1")) && (!strcmp(name2, "ND1"))) ||
                    ((!strcmp(name2, "CE1")) && (!strcmp(name1, "ND1"))))
              order = 2;
            break;
          case 'H':            /* HISH Gromacs */
          case 'P':            /* HISP Quanta */
            if(!strcmp(name1, "ND1")) {
              ai1->formalCharge = 1;
              ai1->chemFlag = false;
            } else if(!strcmp(name2, "ND1")) {
              ai2->formalCharge = 1;
              ai2->chemFlag = false;
            }
            if(((!strcmp(name1, "CG")) && (!strcmp(name2, "CD2"))) ||
               ((!strcmp(name2, "CG")) && (!strcmp(name1, "CD2"))))
              order = 2;
            else if(((!strcmp(name1, "CE1")) && (!strcmp(name2, "ND1"))) ||
                    ((!strcmp(name2, "CE1")) && (!strcmp(name1, "ND1"))))
              order = 2;
            break;
          }
          break;
        case 'E':              /* HIE */
          if(((!strcmp(name1, "CG")) && (!strcmp(name2, "CD2"))) ||
             ((!strcmp(name2, "CG")) && (!strcmp(name1, "CD2"))))
            order = 2;
          else if(((!strcmp(name1, "CE1")) && (!strcmp(name2, "ND1"))) ||
                  ((!strcmp(name2, "CE1")) && (!strcmp(name1, "ND1"))))
            order = 2;
          break;
        case 'D':              /* HID */
          if(((!strcmp(name1, "CG")) && (!strcmp(name2, "CD2"))) ||
             ((!strcmp(name2, "CG")) && (!strcmp(name1, "CD2"))))
            order = 2;
          else if(((!strcmp(name1, "CE1")) && (!strcmp(name2, "NE2"))) ||
                  ((!strcmp(name2, "CE1")) && (!strcmp(name1, "NE2"))))
            order = 2;
          break;
        }
        break;
      }
      break;
    case 'I':
      if(resn1[1] == 0) {
        if(((!strcmp(name1, "O2P")) || (!strcmp(name1, "OP2")))) {
          ai1->formalCharge = -1;
          ai1->chemFlag = false;
        } else if(((!strcmp(name2, "O2P")) || (!strcmp(name2, "OP2")))) {
          ai2->formalCharge = -1;
          ai2->chemFlag = false;
        }
        if(((!strcmp(name1, "C8")) && (!strcmp(name2, "N7"))) ||
           ((!strcmp(name2, "C8")) && (!strcmp(name1, "N7"))))
          order = 2;
        else if(((!strcmp(name1, "C4")) && (!strcmp(name2, "C5"))) ||
                ((!strcmp(name2, "C4")) && (!strcmp(name1, "C5"))))
          order = 2;

        else if(((!strcmp(name1, "C6")) && (!strcmp(name2, "N1"))) ||
                ((!strcmp(name2, "C6")) && (!strcmp(name1, "N1"))))
          order = 2;
        else if(((!strcmp(name1, "C2")) && (!strcmp(name2, "N3"))) ||
                ((!strcmp(name2, "C2")) && (!strcmp(name1, "N3"))))
          order = 2;
        else
          if(((!strcmp(name1, "P"))
              && (((!strcmp(name2, "O1P")) || (!strcmp(name2, "OP1")))))
             || ((!strcmp(name2, "P"))
                 && (((!strcmp(name1, "O1P")) || (!strcmp(name1, "OP1"))))))
          order = 2;
      }
      break;
    case 'P':
      switch (resn1[1]) {
      case 'H':                /* PHE */
        if(resn1[2] == 'E') {
          if(((!strcmp(name1, "CG")) && (!strcmp(name2, "CD1"))) ||
             ((!strcmp(name2, "CG")) && (!strcmp(name1, "CD1"))))
            order = 2;
          else if(((!strcmp(name1, "CZ")) && (!strcmp(name2, "CE1"))) ||
                  ((!strcmp(name2, "CZ")) && (!strcmp(name1, "CE1"))))
            order = 2;

          else if(((!strcmp(name1, "CE2")) && (!strcmp(name2, "CD2"))) ||
                  ((!strcmp(name2, "CE2")) && (!strcmp(name1, "CD2"))))
            order = 2;
          break;
        }
      }
      break;
    case 'L':
      switch (resn1[1]) {
      case 'Y':
        switch (resn1[2]) {
        case 'S':              /* LYS. */
          switch (resn1[3]) {
          case 0:
          case 'P':            /* LYS, LYSP */
            if(!strcmp(name1, "NZ")) {
              ai1->formalCharge = 1;
              ai1->chemFlag = false;
            } else if(!strcmp(name2, "NZ")) {
              ai2->formalCharge = 1;
              ai2->chemFlag = false;
            }
            break;
          }
          break;
        }
        break;
      }
      break;
    case 'T':
      switch (resn1[1]) {
      case 'Y':                /* TYR */
        if(resn1[2] == 'R') {
          if(((!strcmp(name1, "CG")) && (!strcmp(name2, "CD1"))) ||
             ((!strcmp(name2, "CG")) && (!strcmp(name1, "CD1"))))
            order = 2;
          else if(((!strcmp(name1, "CZ")) && (!strcmp(name2, "CE1"))) ||
                  ((!strcmp(name2, "CZ")) && (!strcmp(name1, "CE1"))))
            order = 2;

          else if(((!strcmp(name1, "CE2")) && (!strcmp(name2, "CD2"))) ||
                  ((!strcmp(name2, "CE2")) && (!strcmp(name1, "CD2"))))
            order = 2;
          break;
        }
        break;
      case 'R':
        if(resn1[2] == 'P') {
          if(((!strcmp(name1, "CG")) && (!strcmp(name2, "CD1"))) ||
             ((!strcmp(name2, "CG")) && (!strcmp(name1, "CD1"))))
            order = 2;
          else if(((!strcmp(name1, "CZ3")) && (!strcmp(name2, "CE3"))) ||
                  ((!strcmp(name2, "CZ3")) && (!strcmp(name1, "CE3"))))
            order = 2;
          else if(((!strcmp(name1, "CZ2")) && (!strcmp(name2, "CH2"))) ||
                  ((!strcmp(name2, "CZ2")) && (!strcmp(name1, "CH2"))))
            order = 2;
          else if(((!strcmp(name1, "CE2")) && (!strcmp(name2, "CD2"))) ||
                  ((!strcmp(name2, "CE2")) && (!strcmp(name1, "CD2"))))
            order = 2;
          break;
        }
        break;
      case 0:
        if(((!strcmp(name1, "O2P")) || (!strcmp(name1, "OP2")))) {
          ai1->formalCharge = -1;
          ai1->chemFlag = false;
        } else if(((!strcmp(name2, "O2P")) || (!strcmp(name2, "OP2")))) {
          ai2->formalCharge = -1;
          ai2->chemFlag = false;
        }

        if(((!strcmp(name1, "C2")) && (!strcmp(name2, "O2"))) ||
           ((!strcmp(name2, "C2")) && (!strcmp(name1, "O2"))))
          order = 2;
        else if(((!strcmp(name1, "C4")) && (!strcmp(name2, "O4"))) ||
                ((!strcmp(name2, "C4")) && (!strcmp(name1, "O4"))))
          order = 2;

        else if(((!strcmp(name1, "C5")) && (!strcmp(name2, "C6"))) ||
                ((!strcmp(name2, "C5")) && (!strcmp(name1, "C6"))))
          order = 2;
        else
          if(((!strcmp(name1, "P"))
              && (((!strcmp(name2, "O1P")) || (!strcmp(name2, "OP1")))))
             || ((!strcmp(name2, "P"))
                 && (((!strcmp(name1, "O1P")) || (!strcmp(name1, "OP1"))))))
          order = 2;
        break;
      }
      break;
    case 'U':
      if(resn1[1] == 0) {
        if(((!strcmp(name1, "O2P")) || (!strcmp(name1, "OP2")))) {
          ai1->formalCharge = -1;
          ai1->chemFlag = false;
        } else if(((!strcmp(name2, "O2P")) || (!strcmp(name2, "OP2")))) {
          ai2->formalCharge = -1;
          ai2->chemFlag = false;
        }
        if(((!strcmp(name1, "C2")) && (!strcmp(name2, "O2"))) ||
           ((!strcmp(name2, "C2")) && (!strcmp(name1, "O2"))))
          order = 2;
        else if(((!strcmp(name1, "C4")) && (!strcmp(name2, "O4"))) ||
                ((!strcmp(name2, "C4")) && (!strcmp(name1, "O4"))))
          order = 2;

        else if(((!strcmp(name1, "C5")) && (!strcmp(name2, "C6"))) ||
                ((!strcmp(name2, "C5")) && (!strcmp(name1, "C6"))))
          order = 2;
        else
          if(((!strcmp(name1, "P"))
              && (((!strcmp(name2, "O1P")) || (!strcmp(name2, "OP1")))))
             || ((!strcmp(name2, "P"))
                 && (((!strcmp(name1, "O1P")) || (!strcmp(name1, "OP1"))))))
          order = 2;
      }
      break;
    }
  }
  *(bond_order) = order;
}

void ObjectMoleculeFixChemistry(ObjectMolecule * I, int sele1, int sele2, int invalidate)
{
  int b;
  int flag = false;
  int s1, s2;
  AtomInfoType *ai1, *ai2;
  int order;
  BondType *bond;
  bond = I->Bond;
  for(b = 0; b < I->NBond; b++) {
    flag = false;
    ai1 = I->AtomInfo + bond->index[0];
    ai2 = I->AtomInfo + bond->index[1];
    s1 = ai1->selEntry;
    s2 = ai2->selEntry;

    if((SelectorIsMember(I->Obj.G, s1, sele1) &&
        SelectorIsMember(I->Obj.G, s2, sele2)) ||
       (SelectorIsMember(I->Obj.G, s2, sele1) && SelectorIsMember(I->Obj.G, s1, sele2))) {
      order = -1;
      if(!ai1->resn[3]) {       /* Standard disconnected PDB residue */
        if(AtomInfoSameResidue(I->Obj.G, ai1, ai2)) {
          assign_pdb_known_residue(I->Obj.G, ai1, ai2, &order);
        }
      }
      if(order > 0) {
        bond->order = order;
        ai1->chemFlag = false;
        ai2->chemFlag = false;
        flag = true;
      } else if(invalidate) {
        ai1->chemFlag = false;
        ai2->chemFlag = false;
        flag = true;
      }
    }
    bond++;
  }
  if(flag) {
    ObjectMoleculeInvalidate(I, cRepAll, cRepInvAll, -1);
    SceneChanged(I->Obj.G);
  }
}

void ObjMolPairwiseInit(ObjMolPairwise * pairwise)
{
  UtilZeroMem((char *) pairwise, sizeof(ObjMolPairwise));
  pairwise->trg_vla = VLAlloc(int, 10);
  pairwise->mbl_vla = VLAlloc(int, 10);
}

void ObjMolPairwisePurge(ObjMolPairwise * pairwise)
{
  VLAFreeP(pairwise->trg_vla);
  VLAFreeP(pairwise->mbl_vla);
}

int ObjectMoleculeConvertIDsToIndices(ObjectMolecule * I, int *id, int n_id)
{
  /* return true if all IDs are unique, false if otherwise */

  int min_id, max_id, range, *lookup = NULL;
  int unique = true;

  /* this routine only works if IDs cover a reasonable range --
     should rewrite using a hash table */

  if(I->NAtom) {

    /* determine range */

    {
      int a, cur_id;
      cur_id = I->AtomInfo[0].id;
      min_id = cur_id;
      max_id = cur_id;
      for(a = 1; a < I->NAtom; a++) {
        cur_id = I->AtomInfo[a].id;
        if(min_id > cur_id)
          min_id = cur_id;
        if(max_id < cur_id)
          max_id = cur_id;
      }
    }

    /* create cross-reference table */

    {
      int a, offset;

      range = max_id - min_id + 1;
      lookup = Calloc(int, range);
      for(a = 0; a < I->NAtom; a++) {
        offset = I->AtomInfo[a].id - min_id;
        if(!lookup[offset])
          lookup[offset] = a + 1;
        else
          unique = false;
      }
    }

    /* iterate through IDs and replace with indices or -1 */

    {
      int i, offset, lkup;

      for(i = 0; i < n_id; i++) {
        offset = id[i] - min_id;
        if((offset >= 0) && (offset < range)) {
          lkup = lookup[offset];
          if(lkup > 0) {
            id[i] = lkup - 1;
          } else {
            id[i] = -1;         /* negative means no match */
          }
        } else
          id[i] = -1;
      }
    }
  }

  FreeP(lookup);
  return unique;

}

static char *check_next_pdb_object(char *p, int skip_to_next)
{
  char *start = p;
  char *line_start;
  char cc[MAXLINELEN];
  while(*p) {
    line_start = p;
    p = ncopy(cc, p, 6);
    if((cc[0] == 'H') &&
       (cc[1] == 'E') &&
       (cc[2] == 'A') && (cc[3] == 'D') && (cc[4] == 'E') && (cc[5] == 'R')) {
      if(skip_to_next)
        return line_start;
      else
        return start;
    } else if(((cc[0] == 'A') &&        /* ATOM */
               (cc[1] == 'T') && (cc[2] == 'O') && (cc[3] == 'M') && (cc[4] == ' ') && (cc[5] == ' ')) || ((cc[0] == 'H') &&    /* HETATM */
                                                                                                           (cc[1] == 'E') && (cc[2] == 'T') && (cc[3] == 'A') && (cc[4] == 'T') && (cc[5] == 'M'))) {
      p = nskip(p, 5);
      ParseNTrim(cc, p, 14);
      /* this is a special workaround for the bogus HETATM entry in PDB 4ZN2:
         HETATM20829              0       0.000   0.000   0.000  1.00  0.00      4ZN20773
         which screws up our PDB test case */
      if(cc[0]) {
        return start;
      }
    } else if(((cc[0] == 'E') &&        /* if we pass over the END of the current PDB file, then reset start */
               (cc[1] == 'N') && (cc[2] == 'D'))) {
      if(strcmp("END", cc) == 0) {      /* END */
        if(skip_to_next) {
          start = line_start;
        }
      }
    }
    p = nextline(p);
  }
  return NULL;
}

static int get_multi_object_status(char *p)
{                               /* expensive -- only call
                                   this if there is no
                                   other way to determine
                                   this information */
  int seen_header = 0;
  char cc[MAXLINELEN];
  while(*p) {
    p = ncopy(cc, p, 6);
    if((cc[0] == 'H') &&
       (cc[1] == 'E') &&
       (cc[2] == 'A') && (cc[3] == 'D') && (cc[4] == 'E') && (cc[5] == 'R')) {
      if(seen_header) {
        return 1;
      } else {
        seen_header = true;
      }
    }
    p = nextline(p);
  }
  return -1;
}

int ObjectMoleculeAutoDisableAtomNameWildcard(ObjectMolecule * I)
{
  PyMOLGlobals *G = I->Obj.G;
  char wildcard = 0;
  int found_wildcard = false;

  {
    char *tmp = SettingGet_s(G, NULL, I->Obj.Setting, cSetting_atom_name_wildcard);
    if(tmp && tmp[0]) {
      wildcard = *tmp;
    } else {
      tmp = SettingGet_s(G, NULL, I->Obj.Setting, cSetting_wildcard);
      if(tmp) {
        wildcard = *tmp;
      }
    }
    if(wildcard == 32)
      wildcard = 0;

  }

  if(wildcard) {
    register int a;
    register char *p, ch;
    register AtomInfoType *ai = I->AtomInfo;

    for(a = 0; a < I->NAtom; a++) {
      p = ai->name;
      while((ch = *(p++))) {
        if(ch == wildcard) {
          found_wildcard = true;
          break;
        }
      }
      ai++;
    }
    if(found_wildcard) {
      ExecutiveSetObjSettingFromString(G, cSetting_atom_name_wildcard, " ",
                                       &I->Obj, -1, true, true);
    }
  }
  return found_wildcard;
}


/*========================================================================*/
#define PDB_MAX_TAGS 64

CoordSet *ObjectMoleculePDBStr2CoordSet(PyMOLGlobals * G,
                                        char *buffer,
                                        AtomInfoType ** atInfoPtr,
                                        char **restart_model,
                                        char *segi_override,
                                        M4XAnnoType * m4x,
                                        char *pdb_name,
                                        char **next_pdb,
                                        PDBInfoRec * info, int quiet, int *model_number)
{

  register char *p;
  int nAtom;
  int a, b, c;
  float *coord = NULL;
  CoordSet *cset = NULL;
  AtomInfoType *atInfo = NULL, *ai;
  int AFlag;
  char SSCode;
  int atomCount;
  int bondFlag = false;
  BondType *bond = NULL, *ii1, *ii2;
  int *idx;
  int nBond = 0;
  int b1, b2, nReal, maxAt;
  CSymmetry *symmetry = NULL;
  int auto_show_lines = (int) SettingGet(G, cSetting_auto_show_lines);
  int auto_show_nonbonded = (int) SettingGet(G, cSetting_auto_show_nonbonded);
  int auto_show_spheres = (int) SettingGet(G, cSetting_auto_show_spheres);
  int reformat_names = (int) SettingGet(G, cSetting_pdb_reformat_names_mode);
  int truncate_resn = SettingGetGlobal_b(G, cSetting_pdb_truncate_residue_name);
  char *tags_in = SettingGetGlobal_s(G, cSetting_pdb_echo_tags), *tag_start[PDB_MAX_TAGS];
  int n_tags = 0;
  int foundNextModelFlag = false;
  int ssFlag = false;
  int ss_resv1 = 0, ss_resv2 = 0;
  ResIdent ss_resi1 = "", ss_resi2 = "";
  unsigned char ss_chain1 = 0, ss_chain2 = 0;
  SSEntry *ss_list = NULL;
  int n_ss = 1;
  int *(ss[256]);               /* one array for each chain identifier */

  char cc[MAXLINELEN], tags[MAXLINELEN];
  char cc_saved, ctmp;
  int index;
  int ignore_pdb_segi = 0;
  int ss_valid, ss_found = false;
  SSEntry *sst;
  int ssi = 0;
  int only_read_one_model = false;
  int ignore_conect = SettingGetGlobal_b(G, cSetting_pdb_ignore_conect);
  int have_bond_order = false;
  int seen_model, in_model = false;
  int seen_conect = false;
  int have_conect = false;
  int is_end_of_object = false;
  int literal_names = SettingGetGlobal_b(G, cSetting_pdb_literal_names);
  int bogus_name_alignment = true;
  AtomName literal_name = "";

  if(tags_in && (!quiet) && (!*restart_model)) {
    char *p = tags;
    strcpy(tags, tags_in);

    while(*p) {
      while(*p == ' ')          /* skip spaces */
        p++;
      if(*p) {
        tag_start[n_tags] = p;
        n_tags++;
        while(*p) {
          if(*p != ',') {
            if(*p == ' ')
              *p = 0;
            p++;
          } else
            break;
        }
        if(*p) {                /* terminate tag */
          *p = 0;
          p++;
        }
      }
    }
  }

  if(literal_names)
    reformat_names = 0;

  ignore_pdb_segi = (int) SettingGet(G, cSetting_ignore_pdb_segi);

  p = buffer;
  nAtom = 0;
  if(atInfoPtr)
    atInfo = *atInfoPtr;

  if(!atInfo)
    ErrFatal(G, "PDBStr2CoordSet", "need atom information record!");    /* failsafe for old version.. */

  if(buffer == *restart_model)
    only_read_one_model = true;
  else if(info && (info->multiplex > 0)) {
    only_read_one_model = true;
    if(!info->multi_object_status) {    /* figure out if this is a multi-object (multi-HEADER) pdb file */
      info->multi_object_status = get_multi_object_status(p);
    }
  }
  /* PASS 1 */
  {
    int seen_end_of_atoms = false;

    *restart_model = NULL;
    while(*p) {
      if(n_tags && !quiet) {
        int skip = false;

        if((p[0] == 'H') &&
           (p[1] == 'E') &&
           (p[2] == 'A') && (p[3] == 'D') && (p[4] == 'E') && (p[5] == 'R')) {
          if(nAtom > 0) {
            /* don't print HEADER until next time */
            skip = true;
          }
        }
        if(!skip) {
          /* fast unrolled string match */
          register int tc = 0;
          register char *q;
          register int same;
          while(tc < n_tags) {
            same = true;
            q = tag_start[tc];
            if(p[0] != q[0])
              same = false;
            else if(p[0] && q[0]) {
              if((p[1] != q[1]) && !((p[1] == ' ') && !q[1]))
                same = false;
              else if(p[1] && q[1]) {
                if((p[2] != q[2]) && !((p[2] == ' ') && !q[2]))
                  same = false;
                else if(p[3] && q[3]) {
                  if((p[3] != q[3]) && !((p[3] == ' ') && !q[3]))
                    same = false;
                  else if(p[4] && q[4]) {
                    if((p[4] != q[4]) && !((p[4] == ' ') && !q[4]))
                      same = false;
                    else if(p[5] && q[5]) {
                      if((p[5] != q[5]) && !((p[5] == ' ') && !q[5]))
                        same = false;
                    }
                  }
                }
              }
            }
            if(same) {
              ParseNTrimRight(cc, p, MAXLINELEN - 1);
              /*              OrthoAddOutput(G," PDB: "); */
              OrthoAddOutput(G, cc);
              OrthoNewLine(G, NULL, true);
            }
            tc++;
          }
        }
      }
      if(((p[0] == 'A') && (p[1] == 'T') && (p[2] == 'O') && (p[3] == 'M')) ||  /* ATOM */
         ((p[0] == 'H') && (p[1] == 'E') && (p[2] == 'T') &&    /* HETATM */
          (p[3] == 'A') && (p[4] == 'T') && (p[5] == 'M') && (!*restart_model))) {
        if(!seen_end_of_atoms)
          nAtom++;
        if(bogus_name_alignment) {
          ncopy(cc, nskip(p, 12), 4);   /* copy the atom field */
          if((cc[0] == 32) && (cc[1] != 32)) {  /* check to see if indentation was followed correctly */
            bogus_name_alignment = false;
          }
        }
      } else if((p[0] == 'H') && (p[1] == 'E') && (p[2] == 'L') && (p[3] == 'I') && (p[4] == 'X'))      /* HELIX */
        ssFlag = true;
      else if((p[0] == 'S') && (p[1] == 'H') && (p[2] == 'E') && (p[3] == 'E') && (p[4] == 'T'))        /* SHEET */
        ssFlag = true;
      else if((p[0] == 'H') &&  /* HEADER */
              (p[1] == 'E') &&
              (p[2] == 'A') && (p[3] == 'D') && (p[4] == 'E') && (p[5] == 'R')) {
        if(nAtom > 0) {         /* if we've already found atom records, then this must be a new pdb */
          (*next_pdb) = p;
          break;
        }
      } else if((p[0] == 'R') && (p[1] == 'E') && (p[2] == 'M') &&      /* REMARK */
                (p[3] == 'A') && (p[4] == 'R') && (p[5] == 'K')) {
        ntrim(cc, p, 30);
        if(strcmp("REMARK    GENERATED BY TRJCONV", cc) == 0)
          if(info)
            info->ignore_header_names = true;
      } else if((p[0] == 'E') && (p[1] == 'N') && (p[2] == 'D') &&      /* ENDMDL */
                (p[3] == 'M') && (p[4] == 'D') && (p[5] == 'L') && (!*restart_model)) {
        *restart_model = nextline(p);
        seen_end_of_atoms = true;
        if(only_read_one_model)
          break;
      } else if((p[0] == 'E') && (p[1] == 'N') && (p[2] == 'D')) {      /* stop parsing after END */
        ntrim(cc, p, 6);
        if(strcmp("END", cc) == 0) {    /* END */
          seen_end_of_atoms = true;
          if(next_pdb) {
            p = nextline(p);
            ncopy(cc, p, 6);
            if(strcmp("HEADER", cc) == 0) {
              (*next_pdb) = p;  /* found another PDB file after this one... */
            } else if(strcmp("ENDMDL", cc) == 0) {
              seen_end_of_atoms = false;
            }
          }
          break;
        }
      } else if((p[0] == 'C') && (p[1] == 'O') && (p[2] == 'N') && (p[3] == 'E') && (p[4] == 'C') && (p[5] == 'T')) {   /* CONECT */
        have_conect = true;
        if(!ignore_conect) 
          bondFlag = true;
      } else if((p[0] == 'U') && (p[1] == 'S') && (p[2] == 'E') &&
                (p[3] == 'R') && (!*restart_model)) {

        /* Metaphorics key now 'USER M4X ', changed from 'USER    ' */
        if((p[4] == ' ') && (p[5] == 'M') && (p[6] == '4') &&
           (p[7] == 'X') && (p[8] == ' ') && m4x) {
          p = nskip(p, 10);
          p = ntrim(cc, p, 6);
          m4x->annotated_flag = true;
          switch (cc[0]) {
          case 'H':
            if(WordMatchExact(G, "HINT", cc, true)) {
              p = nskip(p, 1);
              p = ntrim(cc, p, 6);      /* get context name */
              if(WordMatchExact(G, "ALIGN", cc, true)) {        /* ALIGN is special */
                if(!m4x->align) {
                  m4x->align = Calloc(M4XAlignType, 1);
                  M4XAlignInit(m4x->align);
                  p = nskip(p, 8);
                  p = ntrim(cc, p, 6);  /* get visibility of this structure */
                }
              } else if(WordMatchExact(G, "HIDE", cc, true)) {
                m4x->invisible = 1;
              } else {
                if(!m4x->context) {
                  m4x->context = VLACalloc(M4XContextType, 10);
                }
                if(m4x->context) {
                  int cn;
                  int found = false;

                  /* does context already exist ? */
                  for(cn = 0; cn < m4x->n_context; cn++) {
                    if(WordMatchExact(G, m4x->context[cn].name, cc, true)) {
                      found = true;
                      break;
                    }
                  }

                  /* if not, then create it */
                  if(!found) {
                    cn = m4x->n_context++;
                    VLACheck(m4x->context, M4XContextType, cn);
                    UtilNCopy(m4x->context[cn].name, cc, sizeof(WordType));
                  }

                  while(*cc) {
                    p = nskip(p, 1);
                    p = ntrim(cc, p, 6);
                    switch (cc[0]) {
                    case 'B':
                      if(WordMatchExact(G, "BORDER", cc, true)) {
                        /* ignore PDB CONECT if BORDER present */
                        ignore_conect = true;
                        have_bond_order = true;
                        bondFlag = true;
                      }
                      break;
                    case 'S':
                      if(WordMatchExact(G, "SITE", cc, true)) {
                        if(!m4x->context[cn].site) {
                          m4x->context[cn].site = VLAlloc(int, 50);
                        }
                      }
                      break;
                    case 'L':
                      if(WordMatchExact(G, "LIGAND", cc, true)) {
                        if(!m4x->context[cn].ligand) {
                          m4x->context[cn].ligand = VLAlloc(int, 50);
                        }
                      }
                      break;
                    case 'W':
                      if(WordMatchExact(G, "WATER", cc, true)) {
                        if(!m4x->context[cn].water) {
                          m4x->context[cn].water = VLAlloc(int, 50);
                        }
                      }
                      break;
                    case 'H':
                      if(WordMatchExact(G, "HBOND", cc, true)) {
                        if(!m4x->context[cn].hbond) {
                          m4x->context[cn].hbond = VLAlloc(M4XBondType, 50);
                        }
                      }
                      break;
                    case 'N':
                      if(WordMatchExact(G, "NBOND", cc, true)) {
                        if(!m4x->context[cn].nbond) {
                          m4x->context[cn].nbond = VLAlloc(M4XBondType, 50);
                        }
                      }
                      break;
                    }
                  }
                }
              }
            }
          }
        }
      }
      p = nextline(p);
    }
  }

  *restart_model = NULL;
  coord = VLAlloc(float, 3 * nAtom);

  if(atInfo)
    VLACheck(atInfo, AtomInfoType, nAtom);

  if(bondFlag) {
    nBond = 0;
    bond = VLACalloc(BondType, 6 * nAtom);
  }
  p = buffer;
  PRINTFB(G, FB_ObjectMolecule, FB_Blather)
    " ObjectMoleculeReadPDB: Found %i atoms...\n", nAtom ENDFB(G);

  if(ssFlag) {
    for(a = 0; a <= 255; a++) {
      ss[a] = 0;
    }
    ss_list = VLAlloc(SSEntry, 50);
  }

  a = 0;                        /* WATCHOUT */
  atomCount = 0;

  /* PASS 2 */
  seen_model = false;

  while(*p) {
    /*      printf("%c%c%c%c%c%c\n",p[0],p[1],p[2],p[3],p[4],p[5]); */
    AFlag = false;
    SSCode = 0;
    if((p[0] == 'A') &&         /* ATOM */
       (p[1] == 'T') && (p[2] == 'O') && (p[3] == 'M'))
      AFlag = 1;
    else if((p[0] == 'H') &&    /* HETATM */
            (p[1] == 'E') &&
            (p[2] == 'T') && (p[3] == 'A') && (p[4] == 'T') && (p[5] == 'M'))
      AFlag = 2;
    else if((p[0] == 'H') &&    /* HEADER */
            (p[1] == 'E') &&
            (p[2] == 'A') && (p[3] == 'D') && (p[4] == 'E') && (p[5] == 'R')) {

      if(pdb_name) {
        if(atomCount > 0) {
          /* have we already read atoms?  then this is probably a new PDB file */
          (*next_pdb) = p;      /* found another PDB file after this one... */
          break;
        } else if((!info) || (!info->ignore_header_names)) {
          /* if this isn't an MD trajectory... */
          char *pp;
          pp = nskip(p, 62);    /* is there a four-letter PDB code? */
          pp = ntrim(pdb_name, pp, 4);
          if(pdb_name[0] == 0) {        /* if not, is there a plain name (for MERCK!) */
            p = nskip(p, 6);
            p = ntrim(cc, p, 44);
            UtilNCopy(pdb_name, cc, WordLength);
          } else {
            p = pp;
          }
        }
      }
    } else if((p[0] == 'M') &&  /* MODEL */
              (p[1] == 'O') && (p[2] == 'D') && (p[3] == 'E') && (p[4] == 'L')) {
      if(model_number) {
        int tmp;
        p = nskip(p, 10);
        p = ncopy(cc, p, 5);
        if(sscanf(cc, "%d", &tmp) == 1)
          *model_number = tmp;
      }
      seen_model = true;
      in_model = true;
    } else if((p[0] == 'H') &&  /* HELIX */
              (p[1] == 'E') && (p[2] == 'L') && (p[3] == 'I') && (p[4] == 'X')) {
      ss_valid = true;

      p = nskip(p, 19);
      ss_chain1 = (*p);
      p = nskip(p, 2);
      p = ncopy(cc, p, 4);
      if(!sscanf(cc, "%s", ss_resi1))
        ss_valid = false;
      if(!sscanf(cc, "%d", &ss_resv1))
        ss_valid = false;

      p = nskip(p, 6);
      ss_chain2 = (*p);
      p = nskip(p, 2);
      p = ncopy(cc, p, 4);

      if(!sscanf(cc, "%s", ss_resi2))
        ss_valid = false;
      if(!sscanf(cc, "%d", &ss_resv2))
        ss_valid = false;

      if(ss_valid) {
        PRINTFB(G, FB_ObjectMolecule, FB_Blather)
          " ObjectMolecule: read HELIX %c %s %c %s\n",
          ss_chain1, ss_resi1, ss_chain2, ss_resi2 ENDFB(G);
        SSCode = 'H';
      }

      if(ss_chain1 == ' ')
        ss_chain1 = 0;
      if(ss_chain2 == ' ')
        ss_chain2 = 0;

    } else if((p[0] == 'S') &&  /* SHEET */
              (p[1] == 'H') && (p[2] == 'E') && (p[3] == 'E') && (p[4] == 'T')) {
      ss_valid = true;
      p = nskip(p, 21);
      ss_chain1 = (*p);
      p = nskip(p, 1);
      p = ncopy(cc, p, 4);
      if(!sscanf(cc, "%s", ss_resi1))
        ss_valid = false;
      if(!sscanf(cc, "%d", &ss_resv1))
        ss_valid = false;
      p = nskip(p, 6);
      ss_chain2 = (*p);
      p = nskip(p, 1);
      p = ncopy(cc, p, 4);
      if(!sscanf(cc, "%s", ss_resi2))
        ss_valid = false;
      if(!sscanf(cc, "%d", &ss_resv2))
        ss_valid = false;

      if(ss_valid) {
        PRINTFB(G, FB_ObjectMolecule, FB_Blather)
          " ObjectMolecule: read SHEET %c %s %c %s\n",
          ss_chain1, ss_resi1, ss_chain2, ss_resi2 ENDFB(G);
        SSCode = 'S';
      }

      if(ss_chain1 == ' ')
        ss_chain1 = 0;
      if(ss_chain2 == ' ')
        ss_chain2 = 0;

    } else if((p[0] == 'E') &&  /* ENDMDL */
              (p[1] == 'N') &&
              (p[2] == 'D') && (p[3] == 'M') && (p[4] == 'D') && (p[5] == 'L')) {
      if(*restart_model)
        in_model = false;
      else {
        *restart_model = nextline(p);
        in_model = false;
        if(only_read_one_model) {
          char *pp;
          pp = nextline(p);
          if((pp[0] == 'E') &&  /* END we're going to be starting a new object... */
             (pp[1] == 'N') && (pp[2] == 'D')) {
            (*next_pdb) = check_next_pdb_object(nextline(pp), true);
            if(info && (info->multiplex == 0)) {
              /* multiplex == 0:  FORCED multimodel behavior with concatenated PDB files */
              (*restart_model) = (*next_pdb);
              (*next_pdb) = NULL;
              foundNextModelFlag = true;
              info->multi_object_status = -1;
            } else {
              is_end_of_object = true;
            }
          } else if((pp[0] == 'M') &&   /* not a new object...just a new state (model) */
                    (pp[1] == 'O') && (pp[2] == 'D') && (pp[3] == 'E') && (pp[4] == 'L')) {
            if(info && (info->multiplex > 0)) { /* end object if we're multiplexing */
              (*next_pdb) = check_next_pdb_object(pp, true);
              (*restart_model) = NULL;
            } else
              is_end_of_object = false;
          } else {
            if(pp[0] > 32)      /* more content follows... */
              (*next_pdb) = check_next_pdb_object(pp, true);
            else
              (*next_pdb) = NULL;       /* at end of file */
          }
          break;
        }
      }
    } else if((p[0] == 'E') &&  /* END */
              (p[1] == 'N') && (p[2] == 'D')) {
      ntrim(cc, p, 6);
      if((strcmp("END", cc) == 0) && (!in_model)) {     /* stop parsing here... */
        char *pp;
        pp = nextline(p);       /* ...unless we're in MODEL or next line is itself ENDMDL */
        p = ncopy(cc, p, 6);
        if(!((cc[0] == 'E') && (cc[1] == 'N') && (cc[2] == 'D') && (cc[3] == 'M') && (cc[4] == 'D') && (cc[5] == 'L'))) {       /* NOTE: this test seems unnecessary given strcmp above... */
          if(!*next_pdb) {
            (*next_pdb) = check_next_pdb_object(pp, false);
          }
          if((*next_pdb) && info && (!info->multiplex) && !(*restart_model)) {
            /* multiplex == 0:  FORCED multimodel behavior with concatenated PDB files */
            (*restart_model) = (*next_pdb);
            (*next_pdb) = NULL;
            foundNextModelFlag = true;
            info->multi_object_status = -1;
            is_end_of_object = false;
            break;
          }
          if(*next_pdb) {       /* we've found another object... */
            if(*restart_model)
              is_end_of_object = false; /* however, if we're parsing multi-models, then we're not yet at the end */
            else
              is_end_of_object = true;
            break;
          } else if(!seen_model)
            break;
        }
      }
    } else if((p[0] == 'C') &&  /* CRYST1 */
              (p[1] == 'R') &&
              (p[2] == 'Y') &&
              (p[3] == 'S') && (p[4] == 'T') && (p[5] == '1') && (!*restart_model)) {
      if(!symmetry)
        symmetry = SymmetryNew(G);
      if(symmetry) {
        int symFlag = true;
        PRINTFB(G, FB_ObjectMolecule, FB_Blather)
          " PDBStrToCoordSet: Attempting to read symmetry information\n" ENDFB(G);
        p = nskip(p, 6);
        symFlag = true;
        p = ncopy(cc, p, 9);
        if(sscanf(cc, "%f", &symmetry->Crystal->Dim[0]) != 1)
          symFlag = false;
        p = ncopy(cc, p, 9);
        if(sscanf(cc, "%f", &symmetry->Crystal->Dim[1]) != 1)
          symFlag = false;
        p = ncopy(cc, p, 9);
        if(sscanf(cc, "%f", &symmetry->Crystal->Dim[2]) != 1)
          symFlag = false;
        p = ncopy(cc, p, 7);
        if(sscanf(cc, "%f", &symmetry->Crystal->Angle[0]) != 1)
          symFlag = false;
        p = ncopy(cc, p, 7);
        if(sscanf(cc, "%f", &symmetry->Crystal->Angle[1]) != 1)
          symFlag = false;
        p = ncopy(cc, p, 7);
        if(sscanf(cc, "%f", &symmetry->Crystal->Angle[2]) != 1)
          symFlag = false;
        p = nskip(p, 1);
        p = ncopy(symmetry->SpaceGroup, p, 11);
        UtilCleanStr(symmetry->SpaceGroup);
        p = ncopy(cc, p, 3);
        if(sscanf(cc, "%d", &symmetry->PDBZValue) != 1)
          symmetry->PDBZValue = 1;
        if(!symFlag) {
          ErrMessage(G, "PDBStrToCoordSet", "Error reading CRYST1 record\n");
          SymmetryFree(symmetry);
          symmetry = NULL;
        }
      }
    } else if((p[0] == 'S') &&  /* SCALEn */
              (p[1] == 'C') &&
              (p[2] == 'A') &&
              (p[3] == 'L') && (p[4] == 'E') && (!*restart_model) && info) {
      switch (p[5]) {
      case '1':
      case '2':
      case '3':
        {
          int flag = (p[5] - '1');
          int offset = flag * 4;
          int scale_flag = true;
          p = nskip(p, 10);
          p = ncopy(cc, p, 10);
          if(sscanf(cc, "%f", &info->scale.matrix[offset]) != 1)
            scale_flag = false;
          p = ncopy(cc, p, 10);
          if(sscanf(cc, "%f", &info->scale.matrix[offset + 1]) != 1)
            scale_flag = false;
          p = ncopy(cc, p, 10);
          if(sscanf(cc, "%f", &info->scale.matrix[offset + 2]) != 1)
            scale_flag = false;
          p = nskip(p, 5);
          p = ncopy(cc, p, 10);
          if(sscanf(cc, "%f", &info->scale.matrix[offset + 3]) != 1)
            scale_flag = false;
          if(scale_flag)
            info->scale.flag[flag] = true;
          PRINTFB(G, FB_ObjectMolecule, FB_Blather)
            " PDBStrToCoordSet: SCALE%d %8.4f %8.4f %8.4f %8.4f\n", flag + 1,
            info->scale.matrix[offset],
            info->scale.matrix[offset + 1],
            info->scale.matrix[offset + 2], info->scale.matrix[offset + 3]
            ENDFB(G);
        }
        break;
      }
    } else if((p[0] == 'C') &&  /* CONECT */
              (p[1] == 'O') &&
              (p[2] == 'N') &&
              (p[3] == 'E') &&
              (p[4] == 'C') &&
              (p[5] == 'T') &&
              bondFlag && (!ignore_conect) && ((!*restart_model) || (!in_model))) {
      seen_conect = true;
      p = nskip(p, 6);
      p = ncopy(cc, p, 5);
      if(sscanf(cc, "%d", &b1) == 1)
        while(1) {
          p = ncopy(cc, p, 5);
          if(sscanf(cc, "%d", &b2) != 1)
            break;
          else {
            if((b1 >= 0) && (b2 >= 0) && (b1 != b2)) {  /* IDs must be positive and distinct */
              VLACheck(bond, BondType, nBond);
              if(b1 <= b2) {
                bond[nBond].index[0] = b1;      /* temporarily store the atom indexes */
                bond[nBond].index[1] = b2;
                bond[nBond].order = 1;
                bond[nBond].stereo = 0;
              } else {
                bond[nBond].index[0] = b2;
                bond[nBond].index[1] = b1;
                bond[nBond].order = 1;
                bond[nBond].stereo = 0;
              }
              nBond++;
            }
          }
        }
    } else if((p[0] == 'U') &&  /* USER */
              (p[1] == 'S') && (p[2] == 'E') && (p[3] == 'R') && (!*restart_model)) {
      /* Metaphorics key 'USER M4X ' was 'USER     ' */
      if((p[4] == ' ') &&
         (p[5] == 'M') && (p[6] == '4') && (p[7] == 'X') && (p[8] == ' ') && m4x) {

        int parsed_flag = false;

        p = nskip(p, 10);
        p = ntrim(cc, p, 6);

        /* is this a context name or a USER record? */
        switch (cc[0]) {
        case 'X':
          if(WordMatchExact(G, "XNAME", cc, true)) {    /* object name */
            p = nskip(p, 1);
            p = ntrim(m4x->xname, p, 10);
            if(m4x->xname[0]) {
              m4x->xname_flag = true;
              parsed_flag = true;
            }
          }
          break;
        case 'A':              /* alignment information */
          if(WordMatchExact(G, "ALIGN", cc, true)) {
            if(m4x->align && m4x->align->id_at_point) {
              M4XAlignType *align = m4x->align;
              char target[11];
              int atom_id, point_id;
              float fitness;
              p = nskip(p, 1);
              p = ncopy(cc, p, 6);
              if(sscanf(cc, "%d", &atom_id) == 1) {
                p = nskip(p, 1);
                p = ntrim(target, p, 10);
                if(target[0]) {
                  if(!align->target[0])
                    UtilNCopy(align->target, target, WordLength);
                  if(WordMatchExact(G, align->target, target, true)) {  /* must match the one target allowed */
                    p = nskip(p, 1);
                    p = ncopy(cc, p, 6);
                    if(sscanf(cc, "%d", &point_id) == 1) {
                      p = nskip(p, 1);
                      p = ncopy(cc, p, 6);
                      if(sscanf(cc, "%f", &fitness) == 1) {
                        VLACheck(align->id_at_point, int, point_id);
                        VLACheck(align->fitness, float, point_id);
                        if(point_id >= align->n_point)
                          align->n_point = point_id + 1;
                        align->id_at_point[point_id] = atom_id;
                        align->fitness[point_id] = fitness;
                        /*                        printf("read alignment atom %d to target %s point %d fitness %8.3f\n",
                           atom_id,target,point_id,fitness); */
                      }
                    }
                  }
                }
              }
            }
            parsed_flag = true;
          }
          break;
        }

        if((!parsed_flag) && m4x->context) {    /* named context of some sort... */
          int cn;
          int found = false;

          /* does context already exist ? */
          for(cn = 0; cn < m4x->n_context; cn++) {
            if(WordMatchExact(G, m4x->context[cn].name, cc, true)) {
              found = true;
              break;
            }
          }

          if(found) {

            M4XContextType *cont = m4x->context + cn;

            p = nskip(p, 1);
            p = ntrim(cc, p, 6);
            switch (cc[0]) {
            case 'B':
              if(WordMatchExact(G, "BORDER", cc, true) && bondFlag) {
                int order;

                p = nskip(p, 1);
                p = ncopy(cc, p, 6);
                if(sscanf(cc, "%d", &b1) == 1) {
                  p = nskip(p, 1);
                  p = ncopy(cc, p, 6);
                  if(sscanf(cc, "%d", &b2) == 1) {
                    p = nskip(p, 1);
                    p = ncopy(cc, p, 6);
                    if(sscanf(cc, "%d", &order) == 1) {
                      if((b1 >= 0) && (b2 >= 0)) {      /* IDs must be positive */
                        VLACheck(bond, BondType, nBond);
                        if(b1 <= b2) {
                          bond[nBond].index[0] = b1;    /* temporarily store the atom indexes */
                          bond[nBond].index[1] = b2;
                          bond[nBond].order = order;
                          bond[nBond].stereo = 0;

                        } else {
                          bond[nBond].index[0] = b2;
                          bond[nBond].index[1] = b1;
                          bond[nBond].order = order;
                          bond[nBond].stereo = 0;
                        }
                        nBond++;
                      }
                    }
                  }
                }
              }
              break;
            case 'S':
              if(WordMatchExact(G, "SITE", cc, true)) {
                if(cont->site) {
                  int id;
                  while(*cc) {
                    p = nskip(p, 1);
                    p = ncopy(cc, p, 6);
                    if(sscanf(cc, "%d", &id) == 1) {
                      VLACheck(cont->site, int, cont->n_site);
                      cont->site[cont->n_site++] = id;
                    }
                  }
                }
              }
              break;
            case 'L':
              if(WordMatchExact(G, "LIGAND", cc, true)) {
                if(cont->ligand) {
                  int id;
                  while(*cc) {
                    p = nskip(p, 1);
                    p = ncopy(cc, p, 6);
                    if(sscanf(cc, "%d", &id) == 1) {
                      VLACheck(cont->ligand, int, cont->n_ligand);
                      cont->ligand[cont->n_ligand++] = id;
                    }
                  }
                }
              }
              break;
            case 'W':
              if(WordMatchExact(G, "WATER", cc, true)) {
                if(cont->water) {
                  int id;
                  while(*cc) {
                    p = nskip(p, 1);
                    p = ncopy(cc, p, 6);
                    if(sscanf(cc, "%d", &id) == 1) {
                      VLACheck(cont->water, int, cont->n_water);
                      cont->water[cont->n_water++] = id;
                    }
                  }
                }
              }
              break;
            case 'H':
              if(WordMatchExact(G, "HBOND", cc, true)) {
                if(cont->hbond) {
                  int id1, id2;
                  float strength;
                  p = nskip(p, 1);
                  p = ncopy(cc, p, 6);
                  if(sscanf(cc, "%d", &id1) == 1) {
                    p = nskip(p, 1);
                    p = ncopy(cc, p, 6);
                    if(sscanf(cc, "%d", &id2) == 1) {
                      p = nskip(p, 1);
                      p = ncopy(cc, p, 6);
                      if(sscanf(cc, "%f", &strength) == 1) {
                        VLACheck(cont->hbond, M4XBondType, cont->n_hbond);
                        cont->hbond[cont->n_hbond].atom1 = id1;
                        cont->hbond[cont->n_hbond].atom2 = id2;
                        cont->hbond[cont->n_hbond].strength = strength;
                        cont->n_hbond++;
                      }
                    }
                  }
                }
              }
              break;
            case 'N':
              if(WordMatchExact(G, "NBOND", cc, true)) {
                if(cont->nbond) {
                  int id1, id2;
                  float strength;
                  p = nskip(p, 1);
                  p = ncopy(cc, p, 6);
                  if(sscanf(cc, "%d", &id1) == 1) {
                    p = nskip(p, 1);
                    p = ncopy(cc, p, 6);
                    if(sscanf(cc, "%d", &id2) == 1) {
                      p = nskip(p, 1);
                      p = ncopy(cc, p, 6);
                      if(sscanf(cc, "%f", &strength) == 1) {
                        VLACheck(cont->nbond, M4XBondType, cont->n_nbond);
                        cont->nbond[cont->n_nbond].atom1 = id1;
                        cont->nbond[cont->n_nbond].atom2 = id2;
                        cont->nbond[cont->n_nbond].strength = strength;
                        cont->n_nbond++;
                      }
                    }
                  }
                }
              }
              break;
            }
          }
        }
      }
    } else if((p[0] == 'A') &&  /* ANISOU */
              (p[1] == 'N') &&
              (p[2] == 'I') &&
              (p[3] == 'S') &&
              (p[4] == 'O') && (p[5] == 'U') && (!*restart_model) && (atomCount)) {
      ai = atInfo + atomCount - 1;

      /* TODO: check atom identifier match */

      {
        int dummy;
        p = nskip(p, 6);
        p = ncopy(cc, p, 5);
        if(!sscanf(cc, "%d", &dummy))
          dummy = 0;
        if(dummy == ai->id) {   /* ATOM ID must match */
          p = nskip(p, 17);
          {
            int dummy;
            p = ncopy(cc, p, 7);
            if(sscanf(cc, "%d", &dummy))
              ai->U11 = dummy / 10000.0F;
            p = ncopy(cc, p, 7);
            if(sscanf(cc, "%d", &dummy))
              ai->U22 = dummy / 10000.0F;
            p = ncopy(cc, p, 7);
            if(sscanf(cc, "%d", &dummy))
              ai->U33 = dummy / 10000.0F;
            p = ncopy(cc, p, 7);
            if(sscanf(cc, "%d", &dummy))
              ai->U12 = dummy / 10000.0F;
            p = ncopy(cc, p, 7);
            if(sscanf(cc, "%d", &dummy))
              ai->U13 = dummy / 10000.0F;
            p = ncopy(cc, p, 7);
            if(sscanf(cc, "%d", &dummy))
              ai->U23 = dummy / 10000.0F;
          }
        }
      }
    }

    /* END KEYWORDS */

    /* Secondary structure records */

    if(SSCode) {

      /* pretty confusing how this works... the following efficient (i.e. array-based)
         secondary structure lookup even when there are multiple insertion codes
         and where there may be multiple SS records for the residue using different 
         insertion codes */

      if(!ss[ss_chain1]) {      /* allocate new array for chain if necc. */
        ss[ss_chain1] = Calloc(int, cResvMask + 1);
      }

      sst = NULL;
      for(b = ss_resv1; b <= ss_resv2; b++) {   /* iterate over all residues indicated */
        index = b & cResvMask;
        if(ss[ss_chain1][index])
          sst = NULL;           /* make a unique copy in the event of multiple entries for one resv */
        if(!sst) {
          VLACheck(ss_list, SSEntry, n_ss);
          ssi = n_ss++;
          sst = ss_list + ssi;
          sst->resv1 = ss_resv1;
          sst->resv2 = ss_resv2;
          sst->chain1 = ss_chain1;
          sst->chain2 = ss_chain2;
          sst->type = SSCode;
          strcpy(sst->resi1, ss_resi1);
          strcpy(sst->resi2, ss_resi2);
          ss_found = true;
        }
        sst->next = ss[ss_chain1][index];
        ss[ss_chain1][index] = ssi;
        if(sst->next)
          sst = NULL;           /* force another unique copy */
      }

      if(ss_chain2 != ss_chain1) {      /* handle case where chains are not the same (undefined in PDB spec?) */
        if(!ss[ss_chain2]) {
          ss[ss_chain2] = Calloc(int, cResvMask + 1);
        }
        sst = NULL;
        for(b = ss_resv1; b <= ss_resv2; b++) { /* iterate over all residues indicated */
          index = b & cResvMask;
          if(ss[ss_chain2][index])
            sst = NULL;         /* make a unique copy in the event of multiple entries for one resv */
          if(!sst) {
            VLACheck(ss_list, SSEntry, n_ss);
            ssi = n_ss++;
            sst = ss_list + ssi;
            sst->resv1 = ss_resv1;
            sst->resv2 = ss_resv2;
            sst->chain1 = ss_chain1;
            sst->chain2 = ss_chain2;
            sst->type = SSCode;
            strcpy(sst->resi1, ss_resi1);
            strcpy(sst->resi2, ss_resi2);
          }
          sst->next = ss[ss_chain2][index];
          ss[ss_chain2][index] = ssi;
          if(sst->next)
            sst = NULL;         /* force another unique copy */
        }
      }
    }
    /* Atom records */

    if(AFlag && (!*restart_model)) {
      ai = atInfo + atomCount;
      p = nskip(p, 6);
      p = ncopy(cc, p, 5);
      if(!sscanf(cc, "%d", &ai->id))
        ai->id = 0;
      ai->rank = atomCount;

      p = nskip(p, 1);          /* to 12 */
      p = ncopy(literal_name, p, 4);
      if(literal_names) {
        strcpy(ai->name, literal_name);
      } else {
        ParseNTrim(ai->name, literal_name, 4);
      }

      p = ncopy(cc, p, 1);
      if(*cc == 32)
        ai->alt[0] = 0;
      else {
        ai->alt[0] = *cc;
        ai->alt[1] = 0;
      }

      p = ncopy(cc, p, 4);      /* now allowing for 4-letter residues */
      if(!sscanf(cc, "%s", ai->resn))
        ai->resn[0] = 0;
      else if(truncate_resn)    /* unless specifically disabled */
        ai->resn[3] = 0;

      if(ai->name[0]) {
        int name_len = strlen(ai->name);
        char name[4];
        switch (reformat_names) {
        case 1:                /* pdb compliant: HH12 becomes 2HH1, etc. */
          if(name_len > 3) {
            if((ai->name[0] >= 'A') && ((ai->name[0] <= 'Z')) &&
               (ai->name[3] >= '0') && (ai->name[3] <= '9')) {
              if(!(((ai->name[1] >= 'a') && (ai->name[1] <= 'z')) || ((ai->name[0] == 'C') && (ai->name[1] == 'L')) ||  /* try to be smart about */
                   ((ai->name[0] == 'B') && (ai->name[1] == 'R')) ||    /* distinguishing common atoms */
                   ((ai->name[0] == 'C') && (ai->name[1] == 'A')) ||    /* in all-caps from typical */
                   ((ai->name[0] == 'F') && (ai->name[1] == 'E')) ||    /* nonatomic abbreviations */
                   ((ai->name[0] == 'C') && (ai->name[1] == 'U')) ||
                   ((ai->name[0] == 'N') && (ai->name[1] == 'A')) ||
                   ((ai->name[0] == 'N') && (ai->name[1] == 'I')) ||
                   ((ai->name[0] == 'M') && (ai->name[1] == 'G')) ||
                   ((ai->name[0] == 'M') && (ai->name[1] == 'N')) ||
                   ((ai->name[0] == 'H') && (ai->name[1] == 'G')) ||
                   ((ai->name[0] == 'S') && (ai->name[1] == 'E')) ||
                   ((ai->name[0] == 'S') && (ai->name[1] == 'I')) ||
                   ((ai->name[0] == 'Z') && (ai->name[1] == 'N'))
                 )) {
                ctmp = ai->name[3];
                ai->name[3] = ai->name[2];
                ai->name[2] = ai->name[1];
                ai->name[1] = ai->name[0];
                ai->name[0] = ctmp;
              }
            }
          } else if(name_len == 3) {
            if((ai->name[0] == 'H') &&
               (ai->name[1] >= 'A') && ((ai->name[1] <= 'Z')) &&
               (ai->name[2] >= '0') && (ai->name[2] <= '9')) {
              AtomInfoGetPDB3LetHydroName(G, ai->resn, ai->name, name);
              if(name[0] == ' ')
                strcpy(ai->name, name + 1);
              else
                strcpy(ai->name, name);
            }
          }
          break;
        case 2:                /* amber compliant: 2HH1 becomes HH12 */
        case 3:                /* pdb compliant, but use IUPAC within PyMOL */
          if(ai->name[0]) {
            if((ai->name[0] >= '0') && (ai->name[0] <= '9') &&
               (!((ai->name[1] >= '0') && (ai->name[1] <= '9'))) && (ai->name[1] != 0)) {
              switch (strlen(ai->name)) {
              default:
                break;
              case 2:
                ctmp = ai->name[0];
                ai->name[0] = ai->name[1];
                ai->name[1] = ctmp;
                break;
              case 3:
                ctmp = ai->name[0];
                ai->name[0] = ai->name[1];
                ai->name[1] = ai->name[2];
                ai->name[2] = ctmp;
                break;
              case 4:
                ctmp = ai->name[0];
                ai->name[0] = ai->name[1];
                ai->name[1] = ai->name[2];
                ai->name[2] = ai->name[3];
                ai->name[3] = ctmp;
                break;
              }
              break;
        default:               /* AS IS */
              break;
            }
          }
          break;
        case 4:                /* simply read trim and write back out with 3-letter names starting from the
                                   second column, and four-letter names starting in the first */
          ncopy(cc, ai->name, 44);
          ParseNTrim(ai->name, cc, 4);
          break;
        }
      }

      p = ncopy(cc, p, 1);
      if(*cc == ' ')
        ai->chain[0] = 0;
      else {
        ai->chain[0] = *cc;
        ai->chain[1] = 0;
      }

      p = ncopy(cc, p, 5);      /* we treat insertion records as part of the residue identifier */
      if(!sscanf(cc, "%s", ai->resi))
        ai->resi[0] = 0;
      ai->resv = AtomResvFromResi(ai->resi);

      if(ssFlag) {              /* get secondary structure information (if avail) */

        ss_chain1 = ai->chain[0];
        index = ai->resv & cResvMask;
        if(ss[ss_chain1]) {
          ssi = ss[ss_chain1][index];
          while(ssi) {
            sst = ss_list + ssi;        /* contains shared entry, or unique linked list for each residue */
            /*                printf("%d<=%d<=%d, %s<=%s<=%s ", 
               sst->resv1,ai->resv,sst->resv2,
               sst->resi1,ai->resi,sst->resi2); */
            if(ai->resv >= sst->resv1)
              if(ai->resv <= sst->resv2)
                if((ai->resv != sst->resv1)
                   || (WordCompare(G, ai->resi, sst->resi1, true) >= 0))
                  if((ai->resv != sst->resv2)
                     || (WordCompare(G, ai->resi, sst->resi2, true) <= 0)) {
                    ai->ssType[0] = sst->type;
                    /*                          printf(" Y\n"); */
                    break;
                  }
            /*                printf(" N\n"); */
            ssi = sst->next;
          }
        }

      } else {
        ai->cartoon = cCartoon_tube;
      }
      if((!info) || (!info->is_pqr_file)) {     /* standard PDB file */

        p = nskip(p, 3);
        p = ncopy(cc, p, 8);
        sscanf(cc, "%f", coord + a);
        p = ncopy(cc, p, 8);
        sscanf(cc, "%f", coord + (a + 1));
        p = ncopy(cc, p, 8);
        sscanf(cc, "%f", coord + (a + 2));

        p = ncopy(cc, p, 6);
        if(!sscanf(cc, "%f", &ai->q))
          ai->q = 1.0;

        p = ncopy(cc, p, 6);
        if(!sscanf(cc, "%f", &ai->b))
          ai->b = 0.0;

        p = nskip(p, 6);
        p = ncopy(cc, p, 4);
        if(!ignore_pdb_segi) {
          if(!segi_override[0]) {
            if(!sscanf(cc, "%s", ai->segi))
              ai->segi[0] = 0;
            else {
              cc_saved = cc[3];
              ncopy(cc, p, 4);
              if((cc_saved == '1') &&   /* atom ID overflow? (nonstandard use...)... */
                 (cc[0] == '0') &&
                 (cc[1] == '0') && (cc[2] == '0') && (cc[3] == '0') && atomCount) {
                strcpy(segi_override, (ai - 1)->segi);
                strcpy(ai->segi, (ai - 1)->segi);
              }
            }
          } else {
            strcpy(ai->segi, segi_override);
          }
        } else {
          ai->segi[0] = 0;
        }

        p = ncopy(cc, p, 2);
        if(!sscanf(cc, "%s", ai->elem))
          ai->elem[0] = 0;
        else if(!((((ai->elem[0] >= 'a') && (ai->elem[0] <= 'z')) ||    /* don't get confused by PDB misuse */
                   ((ai->elem[0] >= 'A') && (ai->elem[0] <= 'Z'))) &&
                  (((ai->elem[1] == 0) ||
                    ((ai->elem[1] >= 'a') && (ai->elem[1] <= 'z')) ||
                    ((ai->elem[1] >= 'A') && (ai->elem[1] <= 'Z'))))))
          ai->elem[0] = 0;

        if(!ai->elem[0]) {
          if(((literal_name[0] == ' ') || ((literal_name[0] >= '0') && (literal_name[0] <= '9'))) && (literal_name[1] >= 'A') && (literal_name[1] <= 'Z')) {    /* infer element from name column */
            ai->elem[0] = literal_name[1];
            ai->elem[1] = 0;
          } else if(((literal_name[0] >= 'A') && (literal_name[0] <= 'Z')) && (((literal_name[1] >= 'A') && (literal_name[1] <= 'Z')) || ((literal_name[1] >= 'a') && (literal_name[1] <= 'z')))) {     /* infer element from name column */
            ai->elem[0] = literal_name[0];
            ai->elem[2] = 0;
            if((literal_name[1] >= 'A') && (literal_name[1] <= 'Z')) {  /* second letter is capitalized */
              if(bogus_name_alignment) {
                /* if other atom names aren't properly aligned */
                ai->elem[1] = 0;        /* kill 2nd letter */
              } else if(literal_name[0] == 'H') {
                /* or if this is an ultra-bogus PDB with inconsistent 
                   indendentation, and this is likely a hydrogen */
                ai->elem[1] = 0;        /* kill 2nd letter */
              } else {
                ai->elem[1] = tolower(literal_name[1]);
              }
            } else
              ai->elem[1] = literal_name[1];
          }
        }

        p = ncopy(cc, p, 2);
        if((cc[1] == '-') || (cc[1] == '+')) {
          /* only read formal charge when sign is present */
          char ctmp = cc[0];
          cc[0] = cc[1];
          cc[1] = ctmp;
          if(!sscanf(cc, "%d", &ai->formalCharge))
            ai->formalCharge = 0;
        }

        for(c = 0; c < cRepCnt; c++) {
          ai->visRep[c] = false;
        }

        /* end normal PDB */
      } else if(info && info->is_pqr_file) {
        /* PQR file format...not well defined, but basically PDB
           with charge and radius instead of B and Q.  Right now,
           we insist on PDB column format through the chain ID,
           and then switch over to whitespace delimited parsing 
           for the coordinates, charge, and radius */

        p = ParseWordNumberCopy(cc, p, MAXLINELEN - 1);
        sscanf(cc, "%f", coord + a);
        p = ParseWordNumberCopy(cc, p, MAXLINELEN - 1);
        sscanf(cc, "%f", coord + (a + 1));
        p = ParseWordNumberCopy(cc, p, MAXLINELEN - 1);
        sscanf(cc, "%f", coord + (a + 2));

        p = ParseWordNumberCopy(cc, p, MAXLINELEN - 1);
        if(!sscanf(cc, "%f", &ai->partialCharge))
          ai->partialCharge = 0.0F;

        p = ParseWordNumberCopy(cc, p, MAXLINELEN - 1);
        if(sscanf(cc, "%f", &ai->elec_radius) != 1)
          ai->elec_radius = 0.0F;
      }

      ai->visRep[cRepLine] = auto_show_lines;   /* show lines by default */
      ai->visRep[cRepNonbonded] = auto_show_nonbonded;  /* show lines by default */
      ai->visRep[cRepSphere] = auto_show_spheres;

      if(AFlag == 1)
        ai->hetatm = 0;
      else {
        ai->hetatm = 1;
        ai->flags = cAtomFlag_ignore;
      }

      AtomInfoAssignParameters(G, ai);
      AtomInfoAssignColors(G, ai);

      PRINTFD(G, FB_ObjectMolecule)
        "%s %s %s %s %8.3f %8.3f %8.3f %6.2f %6.2f %s\n",
        ai->name, ai->resn, ai->resi, ai->chain,
        *(coord + a), *(coord + a + 1), *(coord + a + 2), ai->b, ai->q, ai->segi ENDFD;

      if(atomCount < (nAtom - 1)) {     /* safety */
        a += 3;
        atomCount++;
      }
    }
    p = nextline(p);
  }

  /* END PASS 2 */

  if(bondFlag) {
    UtilSortInPlace(G, bond, nBond, sizeof(BondType), (UtilOrderFn *) BondInOrder);
    if(nBond) {
      if(!have_bond_order) {    /* handle PDB bond-order kludge */
        ii1 = bond;
        ii2 = bond + 1;
        nReal = 1;
        ii1->order = 1;
        a = nBond - 1;
        while(a) {
          if((ii1->index[0] == ii2->index[0]) && (ii1->index[1] == ii2->index[1])) {
            ii1->order++;       /* count dup */
          } else {
            ii1++;              /* non-dup, make copy */
            ii1->index[0] = ii2->index[0];
            ii1->index[1] = ii2->index[1];
            ii1->order = ii2->order;
            ii1->stereo = ii2->stereo;
            nReal++;
          }
          ii2++;
          a--;
        }
        nBond = nReal;
      }
      /* now, find atoms we're looking for */

      /* determine ranges */
      maxAt = nAtom;
      ii1 = bond;
      for(a = 0; a < nBond; a++) {
        if(ii1->index[0] > maxAt)
          maxAt = ii1->index[0];
        if(ii1->index[1] > maxAt)
          maxAt = ii1->index[1];
        ii1++;
      }
      for(a = 0; a < nAtom; a++)
        if(maxAt < atInfo[a].id)
          maxAt = atInfo[a].id;
      /* build index */
      maxAt++;
      idx = Alloc(int, maxAt + 1);
      for(a = 0; a < maxAt; a++) {
        idx[a] = -1;
      }
      for(a = 0; a < nAtom; a++)
        idx[atInfo[a].id] = a;
      /* convert indices to bonds */
      ii1 = bond;
      ii2 = bond;
      nReal = 0;
      {
        int unbond_cations = SettingGetGlobal_i(G, cSetting_pdb_unbond_cations);
        int flag;

        for(a = 0; a < nBond; a++) {

          if((ii1->index[0] >= 0) && ((ii1->index[1]) >= 0)) {
            if((idx[ii1->index[0]] >= 0) && (idx[ii1->index[1]] >= 0)) {        /* in case PDB file has bad bonds */
              ii2->index[0] = idx[ii1->index[0]];
              ii2->index[1] = idx[ii1->index[1]];
              ii2->order = ii1->order;
              if((ii2->index[0] >= 0) && (ii2->index[1] >= 0)) {

                if(!have_bond_order) {  /* handle PDB bond order kludge */
                  if(ii1->order <= 2)
                    ii2->order = 1;
                  else if(ii1->order <= 4)
                    ii2->order = 2;
                  else if(ii1->order <= 6)
                    ii2->order = 3;
                  else
                    ii2->order = 4;
                }
                flag = true;
                if(unbond_cations) {
                  if(AtomInfoIsFreeCation(G, atInfo + ii2->index[0]))
                    flag = false;
                  else if(AtomInfoIsFreeCation(G, atInfo + ii2->index[1]))
                    flag = false;
                }
                if(flag) {
                  atInfo[ii2->index[0]].bonded = true;
                  atInfo[ii2->index[1]].bonded = true;
                  nReal++;
                  ii2++;
                }
              }
            }
          }
          ii1++;
        }
      }
      nBond = nReal;
      FreeP(idx);
    }
  }
  if(ss_found && !quiet) {
    PRINTFB(G, FB_ObjectMolecule, FB_Details)
      " ObjectMolecule: Read secondary structure assignments.\n" ENDFB(G);
  }
  if(symmetry && !quiet && (!only_read_one_model)) {
    PRINTFB(G, FB_ObjectMolecule, FB_Details)
      " ObjectMolecule: Read crystal symmetry information.\n" ENDFB(G);
  }
  PRINTFB(G, FB_ObjectMolecule, FB_Blather)
    " PDBStr2CoordSet: Read %d bonds from CONECT records (%p).\n", nBond,
    (void *) bond ENDFB(G);
  cset = CoordSetNew(G);
  cset->NIndex = nAtom;
  cset->Coord = coord;
  cset->TmpBond = bond;
  cset->NTmpBond = nBond;
  if(symmetry)
    cset->Symmetry = symmetry;
  if(atInfoPtr)
    *atInfoPtr = atInfo;

  if((*restart_model) && (!foundNextModelFlag)) {
    /* if plan on need to reading another model into this object, 
       make sure there is another model to read... */
    p = *restart_model;
    while(*p) {
      if((p[0] == 'H') && (p[1] == 'E') && (p[2] == 'A') &&
         (p[3] == 'D') && (p[4] == 'E') && (p[5] == 'R')) {
        /* seeing HEADER means we're off the end of the existing file */
        break;
      }
      if((p[0] == 'M') && (p[1] == 'O') && (p[2] == 'D') &&
         (p[3] == 'E') && (p[4] == 'L') && (p[5] == ' ')) {
        foundNextModelFlag = true;
        break;
      }
      if((p[0] == 'E') && (p[1] == 'N') && (p[2] == 'D') &&
         (p[3] == 'M') && (p[4] == 'D') && (p[5] == 'L')) {
        foundNextModelFlag = true;
        break;
      }
      p = nextline(p);
    }
    if(!foundNextModelFlag) {
      *restart_model = NULL;
    }
  }

  if(ssFlag) {
    for(a = 0; a <= 255; a++) {
      FreeP(ss[a]);
    }
    VLAFreeP(ss_list);
  }

  if(!seen_model)
    *model_number = 1;

  if((*restart_model) && (*next_pdb)) { /* if we're mixing multistate objects and
                                           trajectories, then enforce sanity by 
                                           reading the models first... */
    if(is_end_of_object)
      (*restart_model) = NULL;
    else if((*next_pdb) < (*restart_model))
      (*next_pdb) = NULL;
  }
  return (cset);
}


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

void ObjectMoleculeM4XAnnotate(ObjectMolecule * I, M4XAnnoType * m4x, char *script_file,
                               int match_colors, int nbr_sele)
{
  int a;
  WordType name;
  M4XContextType *cont;

  if(m4x) {
    for(a = 0; a < m4x->n_context; a++) {
      cont = m4x->context + a;

      if(cont->site) {
        UtilNCopy(name, I->Obj.Name, sizeof(WordType));
        UtilNConcat(name, "_", sizeof(WordType));
        UtilNConcat(name, cont->name, sizeof(WordType));
        UtilNConcat(name, "_site", sizeof(WordType));
        SelectorSelectByID(I->Obj.G, name, I, cont->site, cont->n_site);
      }
      if(cont->ligand) {
        UtilNCopy(name, I->Obj.Name, sizeof(WordType));
        UtilNConcat(name, "_", sizeof(WordType));
        UtilNConcat(name, cont->name, sizeof(WordType));
        UtilNConcat(name, "_ligand", sizeof(WordType));
        SelectorSelectByID(I->Obj.G, name, I, cont->ligand, cont->n_ligand);
      }
      if(cont->water) {
        UtilNCopy(name, I->Obj.Name, sizeof(WordType));
        UtilNConcat(name, "_", sizeof(WordType));
        UtilNConcat(name, cont->name, sizeof(WordType));
        UtilNConcat(name, "_water", sizeof(WordType));
        SelectorSelectByID(I->Obj.G, name, I, cont->water, cont->n_water);
      }
      if(cont->hbond) {
        ObjectDist *distObj;
        UtilNCopy(name, I->Obj.Name, sizeof(WordType));
        UtilNConcat(name, "_", sizeof(WordType));
        UtilNConcat(name, cont->name, sizeof(WordType));
        UtilNConcat(name, "_hbond", sizeof(WordType));
        ExecutiveDelete(I->Obj.G, name);
        distObj = ObjectDistNewFromM4XBond(I->Obj.G, NULL,
                                           I, cont->hbond, cont->n_hbond, nbr_sele);
        if(match_colors)
          distObj->Obj.Color = I->Obj.Color;
        else
          distObj->Obj.Color = ColorGetIndex(I->Obj.G, "yellow");
        ObjectSetName((CObject *) distObj, name);
        if(distObj)
          ExecutiveManageObject(I->Obj.G, (CObject *) distObj, false, true);
      }

      if(cont->nbond && 0) {
        /*        ObjectDist *distObj; */
        UtilNCopy(name, I->Obj.Name, sizeof(WordType));
        UtilNConcat(name, "_", sizeof(WordType));
        UtilNConcat(name, cont->name, sizeof(WordType));
        UtilNConcat(name, "_nbond", sizeof(WordType));
        ExecutiveDelete(I->Obj.G, name);
        /*        distObj = ObjectDistNewFromM4XBond(I->Obj.G,NULL,
           I,
           cont->nbond,
           cont->n_nbond);
           if(distObj)
           ExecutiveManageObject(I->Obj.G,(CObject*)distObj,false,true); */

        {
          CGO *cgo = NULL;
          ObjectCGO *ocgo;

          cgo = CGONew(I->Obj.G);
          /*
             CGOBegin(cgo,GL_LINES);
             for(a=0;a<op1.nvv1;a++) {
             CGOVertexv(cgo,op2.vv1+(a*3));
             MatrixApplyTTTfn3f(1,v1,op2.ttt,op1.vv1+(a*3));
             CGOVertexv(cgo,v1);
           */
          CGOEnd(cgo);
          CGOStop(cgo);
          ocgo = ObjectCGOFromCGO(I->Obj.G, NULL, cgo, 0);
          if(match_colors)
            ocgo->Obj.Color = I->Obj.Color;
          else
            ocgo->Obj.Color = ColorGetIndex(I->Obj.G, "yellow");
          ObjectSetName((CObject *) ocgo, name);
          ExecutiveDelete(I->Obj.G, name);

          ExecutiveManageObject(I->Obj.G, (CObject *) ocgo, false, true);

          SceneInvalidate(I->Obj.G);
        }

      }

    }
    if(script_file)
      PParse(I->Obj.G, script_file);
  }
}

void ObjectMoleculeInitHBondCriteria(PyMOLGlobals * G, HBondCriteria * hbc)
{
  hbc->maxAngle = SettingGet_f(G, NULL, NULL, cSetting_h_bond_max_angle);
  hbc->maxDistAtMaxAngle = SettingGet_f(G, NULL, NULL, cSetting_h_bond_cutoff_edge);
  hbc->maxDistAtZero = SettingGet_f(G, NULL, NULL, cSetting_h_bond_cutoff_center);
  hbc->power_a = SettingGet_f(G, NULL, NULL, cSetting_h_bond_power_a);
  hbc->power_b = SettingGet_f(G, NULL, NULL, cSetting_h_bond_power_b);
  hbc->cone_dangle =
    (float) cos(PI * 0.5 * SettingGet_f(G, NULL, NULL, cSetting_h_bond_cone) / 180.0F);
  if(hbc->maxDistAtMaxAngle != 0.0F) {
    hbc->factor_a = (float) (0.5 / pow(hbc->maxAngle, hbc->power_a));
    hbc->factor_b = (float) (0.5 / pow(hbc->maxAngle, hbc->power_b));
  }
}

static int ObjectMoleculeTestHBond(float *donToAcc, float *donToH, float *hToAcc,
                                   float *accPlane, HBondCriteria * hbc)
{
  float nDonToAcc[3], nDonToH[3], nAccPlane[3], nHToAcc[3];
  double angle;
  double cutoff;
  double curve;
  double dist;
  float dangle;

/* A ~~ H - D */

  normalize23f(donToAcc, nDonToAcc);
  normalize23f(hToAcc, nHToAcc);
  if(accPlane) {                /* remember, plane need not exist if it's water... */
    normalize23f(accPlane, nAccPlane);
#if 0
    if(dot_product3f(nDonToAcc, nAccPlane) > (-hbc->cone_dangle))       /* don't allow D behind Acceptor plan */
      return 0;
#endif
    if(dot_product3f(nHToAcc, nAccPlane) > (-hbc->cone_dangle)) /* don't allow H behind Acceptor plane */
      return 0;
  }

  normalize23f(donToH, nDonToH);
  normalize23f(donToAcc, nDonToAcc);

  dangle = dot_product3f(nDonToH, nDonToAcc);
  if((dangle < 1.0F) && (dangle > 0.0F))
    angle = 180.0 * acos((double) dangle) / PI;
  else if(dangle > 0.0F)
    angle = 0.0;
  else
    angle = 90.0;

  if(angle > hbc->maxAngle)
    return 0;

  /* interpolate cutoff based on ADH angle */

  if(hbc->maxDistAtMaxAngle != 0.0F) {
    curve = (pow(angle, hbc->power_a) * hbc->factor_a +
             pow(angle, hbc->power_b) * hbc->factor_b);

    cutoff = (hbc->maxDistAtMaxAngle * curve) + (hbc->maxDistAtZero * (1.0 - curve));
  } else {
    cutoff = hbc->maxDistAtZero;
  }

  /*
     printf("angle %8.3f curve %8.3f %8.3f %8.3f %8.3f\n",angle,
     curve,cutoff,hbc->maxDistAtMaxAngle,hbc->maxDistAtZero);
   */

  dist = length3f(donToAcc);

  if(dist > cutoff)
    return 0;
  else
    return 1;

}


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

static int ObjectMoleculeFindBestDonorH(ObjectMolecule * I,
                                        int atom,
                                        int state, float *dir, float *best, int *is_real)
{
  int result = 0;
  CoordSet *cs;
  int n, nn;
  int idx;
  int a1;
  float cand[3], cand_dir[3];
  float best_dot = 0.0F, cand_dot;
  float *orig;

  ObjectMoleculeUpdateNeighbors(I);

  if((state >= 0) && (state < I->NCSet) && (cs = I->CSet[state]) && (atom < I->NAtom)) {

    if(I->DiscreteFlag) {
      if(cs == I->DiscreteCSet[atom]) {
        idx = I->DiscreteAtmToIdx[atom];
      } else {
        idx = -1;
      }
    } else {
      idx = cs->AtmToIdx[atom];
    }

    if(idx >= 0) {

      orig = cs->Coord + 3 * idx;

      /*  do we need to add any new hydrogens? */

      n = I->Neighbor[atom];
      nn = I->Neighbor[n++];

      /*      printf("nn %d valence %d %s\n",nn,
         I->AtomInfo[atom].valence,I->AtomInfo[atom].name);
         {
         int i;
         for(i=0;i<nn;i++) {
         printf("%d \n",I->Neighbor[n+2*i]);
         }
         }
       */

      if((nn < I->AtomInfo[atom].valence) || I->AtomInfo[atom].hb_donor) {      /* is there an implicit hydrogen? */
        if(ObjectMoleculeFindOpenValenceVector(I, state, atom, best, dir, -1)) {
          result = true;
          best_dot = dot_product3f(best, dir);
          add3f(orig, best, best);
          if(is_real)
            *is_real = false;
        }
      }
      /* iterate through real hydrogens looking for best match
         with desired direction */

      while(1) {                /* look for an attached non-hydrogen as a base */
        a1 = I->Neighbor[n];
        n += 2;
        if(a1 < 0)
          break;
        if(I->AtomInfo[a1].protons == 1) {      /* hydrogen */
          if(ObjectMoleculeGetAtomVertex(I, state, a1, cand)) { /* present */

            subtract3f(cand, orig, cand_dir);
            normalize3f(cand_dir);
            cand_dot = dot_product3f(cand_dir, dir);
            if(result) {        /* improved */
              if((best_dot < cand_dot) || ((is_real) && (!*is_real))) {
                best_dot = cand_dot;
                copy3f(cand, best);
                if(is_real)
                  *is_real = true;
              }
            } else {            /* first */
              result = true;
              copy3f(cand, best);
              best_dot = cand_dot;
              if(is_real)
                *is_real = true;
            }
          }
        }
      }
    }
  }
  return result;
}


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

int ObjectMoleculeGetCheckHBond(int *h_is_real,
                                float *h_crd_ret,
                                ObjectMolecule * don_obj,
                                int don_atom,
                                int don_state,
                                ObjectMolecule * acc_obj,
                                int acc_atom, int acc_state, HBondCriteria * hbc)
{
  int result = 0;
  CoordSet *csD, *csA;
  int idxD, idxA;
  float *vAcc, *vDon;
  float donToAcc[3];
  float donToH[3];
  float bestH[3];
  float hToAcc[3];
  float accPlane[3], *vAccPlane = NULL;

  /* first, check for existence of coordinate sets */

  if((don_state >= 0) &&
     (don_state < don_obj->NCSet) &&
     (csD = don_obj->CSet[don_state]) &&
     (acc_state >= 0) &&
     (acc_state < acc_obj->NCSet) &&
     (csA = acc_obj->CSet[acc_state]) &&
     (don_atom < don_obj->NAtom) && (acc_atom < acc_obj->NAtom)) {

    /* now check for coordinates of these actual atoms */

    if(don_obj->DiscreteFlag) {
      if(csD == don_obj->DiscreteCSet[don_atom]) {
        idxD = don_obj->DiscreteAtmToIdx[don_atom];
      } else {
        idxD = -1;
      }
    } else {
      idxD = csD->AtmToIdx[don_atom];
    }

    if(acc_obj->DiscreteFlag) {
      if(csA == acc_obj->DiscreteCSet[acc_atom]) {
        idxA = acc_obj->DiscreteAtmToIdx[acc_atom];
      } else {
        idxA = -1;
      }
    } else {
      idxA = csA->AtmToIdx[acc_atom];
    }

    if((idxA >= 0) && (idxD >= 0)) {

      /* now get local geometries, including 
         real or virtual hydrogen atom positions */

      vDon = csD->Coord + 3 * idxD;
      vAcc = csA->Coord + 3 * idxA;

      subtract3f(vAcc, vDon, donToAcc);

      if(ObjectMoleculeFindBestDonorH(don_obj,
                                      don_atom, don_state, donToAcc, bestH, h_is_real)) {

        subtract3f(bestH, vDon, donToH);
        subtract3f(vAcc, bestH, hToAcc);

        if(ObjectMoleculeGetAvgHBondVector(acc_obj, acc_atom,
                                           acc_state, accPlane, hToAcc) > 0.1) {
          vAccPlane = &accPlane[0];
        }
#if 0
        {
          float tmp[3];
          CGOLinewidth(DebugCGO, 4.0F);
          CGOBegin(DebugCGO, GL_LINES);

          CGOColor(DebugCGO, 0.0F, 1.0F, 0.0F); /* green */
          CGOVertexv(DebugCGO, vDon);
          normalize23f(donToAcc, tmp);
          add3f(vDon, tmp, tmp);
          CGOVertexv(DebugCGO, tmp);

          CGOColor(DebugCGO, 1.0F, 0.0F, 0.0F); /* red */
          CGOVertexv(DebugCGO, bestH);
          normalize23f(hToAcc, tmp);
          add3f(bestH, tmp, tmp);
          CGOVertexv(DebugCGO, tmp);

          CGOColor(DebugCGO, 0.0F, 1.0F, 1.0F); /* cyan */
          CGOVertexv(DebugCGO, vDon);
          normalize23f(donToH, tmp);
          add3f(vDon, tmp, tmp);
          CGOVertexv(DebugCGO, tmp);

          if(vAccPlane) {
            CGOColor(DebugCGO, 1.0F, 1.0F, 0.0F);       /* yellow */
            CGOVertexv(DebugCGO, vAcc);
            normalize23f(vAccPlane, tmp);
            add3f(vAcc, tmp, tmp);
            CGOVertexv(DebugCGO, tmp);
          }

          CGOEnd(DebugCGO);

        }
#endif
        result = ObjectMoleculeTestHBond(donToAcc, donToH, hToAcc, vAccPlane, hbc);
        if(result && h_crd_ret && h_is_real && *h_is_real)
          copy3f(bestH, h_crd_ret);
      }
    }
  }

  return (result);
}


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

float ObjectMoleculeGetMaxVDW(ObjectMolecule * I)
{
  float max_vdw = 0.0F;
  int a;
  AtomInfoType *ai;
  if(I->NAtom) {
    ai = I->AtomInfo;
    for(a = 0; a < I->NAtom; a++) {
      if(max_vdw < ai->vdw)
        max_vdw = ai->vdw;
      ai++;
    }
  }
  return (max_vdw);
}


/*========================================================================*/
#ifndef _PYMOL_NOPY
static PyObject *ObjectMoleculeCSetAsPyList(ObjectMolecule * I)
{
  PyObject *result = NULL;
  int a;
  result = PyList_New(I->NCSet);
  for(a = 0; a < I->NCSet; a++) {
    if(I->CSet[a]) {
      PyList_SetItem(result, a, CoordSetAsPyList(I->CSet[a]));
    } else {
      PyList_SetItem(result, a, PConvAutoNone(Py_None));
    }
  }
  return (PConvAutoNone(result));
}
#endif


/*static PyObject *ObjectMoleculeDiscreteCSetAsPyList(ObjectMolecule *I)
  {
  PyObject *result = NULL;
  return(PConvAutoNone(result));
  }*/

#ifndef _PYMOL_NOPY
static int ObjectMoleculeCSetFromPyList(ObjectMolecule * I, PyObject * list)
{
  int ok = true;
  int a;
  if(ok)
    ok = PyList_Check(list);
  if(ok) {
    VLACheck(I->CSet, CoordSet *, I->NCSet);
    for(a = 0; a < I->NCSet; a++) {
      if(ok)
        ok = CoordSetFromPyList(I->Obj.G, PyList_GetItem(list, a), &I->CSet[a]);
      PRINTFB(I->Obj.G, FB_ObjectMolecule, FB_Debugging)
        " ObjectMoleculeCSetFromPyList: ok %d after CoordSet %d\n", ok, a ENDFB(I->Obj.G);

      if(ok)
        if(I->CSet[a])          /* WLD 030205 */
          I->CSet[a]->Obj = I;
    }
  }
  return (ok);
}
#endif

#ifndef _PYMOL_NOPY
static PyObject *ObjectMoleculeBondAsPyList(ObjectMolecule * I)
{
  PyObject *result = NULL;
  PyObject *bond_list;
  BondType *bond;
  int a;

  result = PyList_New(I->NBond);
  bond = I->Bond;
  for(a = 0; a < I->NBond; a++) {
    bond_list = PyList_New(7);
    PyList_SetItem(bond_list, 0, PyInt_FromLong(bond->index[0]));
    PyList_SetItem(bond_list, 1, PyInt_FromLong(bond->index[1]));
    PyList_SetItem(bond_list, 2, PyInt_FromLong(bond->order));
    PyList_SetItem(bond_list, 3, PyInt_FromLong(bond->id));
    PyList_SetItem(bond_list, 4, PyInt_FromLong(bond->stereo));
    PyList_SetItem(bond_list, 5, PyInt_FromLong(bond->unique_id));
    PyList_SetItem(bond_list, 6, PyInt_FromLong(bond->has_setting));
    PyList_SetItem(result, a, bond_list);
    bond++;
  }

  return (PConvAutoNone(result));
}
#endif

#ifndef _PYMOL_NOPY
static int ObjectMoleculeBondFromPyList(ObjectMolecule * I, PyObject * list)
{
  int ok = true;
  int a;
  int stereo, ll = 0;
  PyObject *bond_list = NULL;
  BondType *bond;
  if(ok)
    ok = PyList_Check(list);
  if(ok)
    ok = ((I->Bond = VLAlloc(BondType, I->NBond)) != NULL);
  bond = I->Bond;
  for(a = 0; a < I->NBond; a++) {
    if(ok)
      bond_list = PyList_GetItem(list, a);
    if(ok)
      ok = PyList_Check(bond_list);
    if(ok)
      ll = PyList_Size(bond_list);
    if(ok)
      ok = PConvPyIntToInt(PyList_GetItem(bond_list, 0), &bond->index[0]);
    if(ok)
      ok = PConvPyIntToInt(PyList_GetItem(bond_list, 1), &bond->index[1]);
    if(ok)
      ok = PConvPyIntToInt(PyList_GetItem(bond_list, 2), &bond->order);
    if(ok)
      ok = PConvPyIntToInt(PyList_GetItem(bond_list, 3), &bond->id);
    if(ok)
      ok = PConvPyIntToInt(PyList_GetItem(bond_list, 4), &stereo);
    if(ok)
      bond->stereo = (short int) stereo;
    if(ok && (ll > 5)) {
      int has_setting;
      if(ok)
        ok = PConvPyIntToInt(PyList_GetItem(bond_list, 5), &bond->unique_id);
      if(ok)
        ok = PConvPyIntToInt(PyList_GetItem(bond_list, 6), &has_setting);
      if(ok)
        bond->has_setting = (short int) has_setting;
      if(ok && bond->unique_id) {       /* reserve existing IDs */
        bond->unique_id = SettingUniqueConvertOldSessionID(I->Obj.G, bond->unique_id);
        AtomInfoReserveUniqueID(I->Obj.G, bond->unique_id);
      }
    }
    bond++;
  }
  PRINTFB(I->Obj.G, FB_ObjectMolecule, FB_Debugging)
    " ObjectMoleculeBondFromPyList: ok %d after restore\n", ok ENDFB(I->Obj.G);

  return (ok);
}
#endif

#ifndef _PYMOL_NOPY
static PyObject *ObjectMoleculeAtomAsPyList(ObjectMolecule * I)
{
  PyObject *result = NULL;
  AtomInfoType *ai;
  int a;

  result = PyList_New(I->NAtom);
  ai = I->AtomInfo;
  for(a = 0; a < I->NAtom; a++) {
    PyList_SetItem(result, a, AtomInfoAsPyList(I->Obj.G, ai));
    ai++;
  }
  return (PConvAutoNone(result));
}
#endif

#ifndef _PYMOL_NOPY
static int ObjectMoleculeAtomFromPyList(ObjectMolecule * I, PyObject * list)
{
  int ok = true;
  int a;
  AtomInfoType *ai;
  if(ok)
    ok = PyList_Check(list);
  VLACheck(I->AtomInfo, AtomInfoType, I->NAtom + 1);
  ai = I->AtomInfo;
  for(a = 0; a < I->NAtom; a++) {
    if(ok)
      ok = AtomInfoFromPyList(I->Obj.G, ai, PyList_GetItem(list, a));
    ai++;
  }
  PRINTFB(I->Obj.G, FB_ObjectMolecule, FB_Debugging)
    " ObjectMoleculeAtomFromPyList: ok %d \n", ok ENDFB(I->Obj.G);
  return (ok);
}
#endif

int ObjectMoleculeNewFromPyList(PyMOLGlobals * G, PyObject * list,
                                ObjectMolecule ** result)
{
#ifdef _PYMOL_NOPY
  return 0;
#else
  int ok = true;
  ObjectMolecule *I = NULL;
  int discrete_flag;
  int ll;
  (*result) = NULL;

  if(ok)
    ok = PyList_Check(list);
  if(ok)
    ll = PyList_Size(list);
  /* TO SUPPORT BACKWARDS COMPATIBILITY...
     Always check ll when adding new PyList_GetItem's */
  if(ok)
    ok = PConvPyIntToInt(PyList_GetItem(list, 8), &discrete_flag);

  I = ObjectMoleculeNew(G, discrete_flag);
  if(ok)
    ok = (I != NULL);

  if(ok)
    ok = ObjectFromPyList(G, PyList_GetItem(list, 0), &I->Obj);
  if(ok)
    ok = PConvPyIntToInt(PyList_GetItem(list, 1), &I->NCSet);
  if(ok)
    ok = PConvPyIntToInt(PyList_GetItem(list, 2), &I->NBond);
  if(ok)
    ok = PConvPyIntToInt(PyList_GetItem(list, 3), &I->NAtom);
  if(ok)
    ok = ObjectMoleculeCSetFromPyList(I, PyList_GetItem(list, 4));
  if(ok)
    ok = CoordSetFromPyList(G, PyList_GetItem(list, 5), &I->CSTmpl);
  if(ok)
    ok = ObjectMoleculeBondFromPyList(I, PyList_GetItem(list, 6));
  if(ok)
    ok = ObjectMoleculeAtomFromPyList(I, PyList_GetItem(list, 7));
  if(ok)
    ok = PConvPyIntToInt(PyList_GetItem(list, 8), &I->DiscreteFlag);
  if(ok)
    ok = PConvPyIntToInt(PyList_GetItem(list, 9), &I->NDiscrete);
  if(ok)
    I->Symmetry = SymmetryNewFromPyList(G, PyList_GetItem(list, 10));
  if(ok)
    ok = PConvPyIntToInt(PyList_GetItem(list, 11), &I->CurCSet);
  if(ok)
    ok = PConvPyIntToInt(PyList_GetItem(list, 12), &I->BondCounter);
  if(ok)
    ok = PConvPyIntToInt(PyList_GetItem(list, 13), &I->AtomCounter);
  if(ok && I->DiscreteFlag) {
    int *dcs = NULL;
    int a, i;
    CoordSet *cs;
    VLACheck(I->DiscreteAtmToIdx, int, I->NDiscrete);
    VLACheck(I->DiscreteCSet, CoordSet *, I->NDiscrete);
    if(ok)
      ok =
        PConvPyListToIntArrayInPlace(PyList_GetItem(list, 14), I->DiscreteAtmToIdx,
                                     I->NDiscrete);
    if(ok)
      ok = PConvPyListToIntArray(PyList_GetItem(list, 15), &dcs);
    if(ok) {

      for(a = 0; a < I->NDiscrete; a++) {
        i = dcs[a];
        I->DiscreteCSet[a] = NULL;
        if(i >= 0) {
          if(i < I->NCSet) {
            cs = I->CSet[i];
            if(cs) {
              I->DiscreteCSet[a] = cs;
            }
          }
        }
      }
    }
    FreeP(dcs);
  }

  ObjectMoleculeInvalidate(I, cRepAll, cRepInvAll, -1);
  if(ok)
    (*result) = I;
  else {
    /* cleanup? */
  }

  return (ok);
#endif
}


/*========================================================================*/
PyObject *ObjectMoleculeAsPyList(ObjectMolecule * I)
{
#ifdef _PYMOL_NOPY
  return NULL;
#else
  PyObject *result = NULL;

  /* first, dump the atoms */

  result = PyList_New(16);
  PyList_SetItem(result, 0, ObjectAsPyList(&I->Obj));
  PyList_SetItem(result, 1, PyInt_FromLong(I->NCSet));
  PyList_SetItem(result, 2, PyInt_FromLong(I->NBond));
  PyList_SetItem(result, 3, PyInt_FromLong(I->NAtom));
  PyList_SetItem(result, 4, ObjectMoleculeCSetAsPyList(I));
  PyList_SetItem(result, 5, CoordSetAsPyList(I->CSTmpl));
  PyList_SetItem(result, 6, ObjectMoleculeBondAsPyList(I));
  PyList_SetItem(result, 7, ObjectMoleculeAtomAsPyList(I));
  PyList_SetItem(result, 8, PyInt_FromLong(I->DiscreteFlag));
  PyList_SetItem(result, 9, PyInt_FromLong(I->NDiscrete));
  PyList_SetItem(result, 10, SymmetryAsPyList(I->Symmetry));
  PyList_SetItem(result, 11, PyInt_FromLong(I->CurCSet));
  PyList_SetItem(result, 12, PyInt_FromLong(I->BondCounter));
  PyList_SetItem(result, 13, PyInt_FromLong(I->AtomCounter));

  if(I->DiscreteFlag) {
    int *dcs;
    int a;
    CoordSet *cs;

    /* get coordinate set indices */

    for(a = 0; a < I->NCSet; a++) {
      cs = I->CSet[a];
      if(cs) {
        cs->tmp_index = a;
      }
    }

    dcs = Alloc(int, I->NDiscrete);

    for(a = 0; a < I->NDiscrete; a++) {
      cs = I->DiscreteCSet[a];
      if(cs)
        dcs[a] = cs->tmp_index;
      else
        dcs[a] = -1;
    }

    PyList_SetItem(result, 14, PConvIntArrayToPyList(I->DiscreteAtmToIdx, I->NDiscrete));
    PyList_SetItem(result, 15, PConvIntArrayToPyList(dcs, I->NDiscrete));
    FreeP(dcs);
  } else {
    PyList_SetItem(result, 14, PConvAutoNone(NULL));
    PyList_SetItem(result, 15, PConvAutoNone(NULL));
  }

#if 0
  CObject Obj;
  struct CoordSet **CSet;
  int NCSet;
  struct CoordSet *CSTmpl;      /* template for trajectories, etc. */
  BondType *Bond;
  AtomInfoType *AtomInfo;
  int NAtom;
  int NBond;
  int DiscreteFlag, NDiscrete;
  int *DiscreteAtmToIdx;
  struct CoordSet **DiscreteCSet;
  int CurCSet;
  int SeleBase;                 /* for internal usage by  selector & only valid during selection process */
  CSymmetry *Symmetry;
  int *Neighbor;
  float *UndoCoord[cUndoMask + 1];
  int UndoState[cUndoMask + 1];
  int UndoNIndex[cUndoMask + 1];
  int UndoIter;
  CGO *UnitCellCGO;
  int BondCounter;
  int AtomCounter;
  struct CSculpt *Sculpt;
#endif

  return (PConvAutoNone(result));
#endif
}


/*========================================================================*/
int ObjectMoleculeConnect(ObjectMolecule * I, BondType ** bond, AtomInfoType * ai,
                          struct CoordSet *cs, int bondSearchMode,
                          int connectModeOverride)
{
#define cMULT 1
  PyMOLGlobals *G = I->Obj.G;
  int a, b, c, d, e, f, i, j;
  int a1, a2;
  float *v1, *v2, dst;
  int maxBond;
  MapType *map;
  int nBond;
  BondType *ii1, *ii2;
  int flag;
  int order;
  AtomInfoType *ai1, *ai2;
  /* Sulfur cutoff */
  float cutoff_s;
  /* Hydrogen cutoff */
  float cutoff_h;
  float cutoff_v;
  float cutoff;
  float max_cutoff;
  int water_flag;
  int repeat = true;
  int discrete_chains = SettingGetGlobal_i(G, cSetting_pdb_discrete_chains);
  int connect_bonded = SettingGetGlobal_b(G, cSetting_connect_bonded);
  int connect_mode = SettingGetGlobal_i(G, cSetting_connect_mode);
  int unbond_cations = SettingGetGlobal_i(G, cSetting_pdb_unbond_cations);
  cutoff_v = SettingGet(G, cSetting_connect_cutoff);
  cutoff_s = cutoff_v + 0.2F;
  cutoff_h = cutoff_v - 0.2F;
  max_cutoff = cutoff_s;

  if(connectModeOverride >= 0)
    connect_mode = connectModeOverride;

  if(connect_mode == 2) {       /* force use of distance-based connectivity,
                                   ignoring that provided with file */
    bondSearchMode = true;      /* if connect_mode==2 and loading a MOL2, crash! */
    cs->NTmpBond = 0;
    if (cs->TmpBond)
      FreeP(cs->TmpBond);
  }

  /*  FeedbackMask[FB_ObjectMolecule]=0xFF; */
  nBond = 0;
  maxBond = cs->NIndex * 8;
  (*bond) = VLACalloc(BondType, maxBond);
  while(repeat) {
    repeat = false;

    /* 
     * BOND SEARCH MODE
     */
    if(cs->NIndex && bondSearchMode) {  /* &&(!I->DiscreteFlag) WLD 010527 */
      /* if there are atoms, and we need to search for bonds, instead of using
       * (possibly) supplied CONECT records... */

      PRINTFB(G, FB_ObjectMolecule, FB_Blather)
        " ObjectMoleculeConnect: Searching for bonds amongst %d coordinates.\n",
        cs->NIndex ENDFB(G);
      if(Feedback(G, FB_ObjectMolecule, FB_Debugging)) {
        for(a = 0; a < cs->NIndex; a++)
          printf(" ObjectMoleculeConnect: coord %d %8.3f %8.3f %8.3f\n",
                 a, cs->Coord[a * 3], cs->Coord[a * 3 + 1], cs->Coord[a * 3 + 2]);
      }

      switch (connect_mode) {
      /* DISTANCE BASED CONNECTIONS */
      case 0:                  /* distance-based and explicit (not HETATM to HETATM) */
      case 3:                  /* distance-based and explicit (even HETATM to HETATM) */
      case 2:                  /* distance-based only */  {
          /* distance-based bond location  */
          int violations = 0;
          int *cnt = Alloc(int, cs->NIndex);
          int valcnt;

        /* initialize each atom's (max) expected valence */
          for(i = 0; i < cs->NIndex; i++) {
            valcnt = AtomInfoGetExpectedValence(G, ai + cs->IdxToAtm[i]);
            if(valcnt < 0)
              valcnt = 6;
            cnt[i] = valcnt;
          }

        /* make a map of the local neighborhood in space */
          map = MapNew(G, max_cutoff + MAX_VDW, cs->Coord, cs->NIndex, NULL);
          if(map) {
            int dim12 = map->D1D2;
            int dim2 = map->Dim[2];

            for(i = 0; i < cs->NIndex; i++) {
              if(nBond > maxBond)
                break;
            /* atom i's position in space */
              v1 = cs->Coord + (3 * i);

              a1 = cs->IdxToAtm[i];
              ai1 = ai + a1;

              MapLocus(map, v1, &a, &b, &c);
            /* d = [a-1, a, a+1] */
              for(d = a - 1; d <= a + 1; d++) {
                int *j_ptr1 = map->Head + d * dim12 + (b - 1) * dim2;
            /* e = [b-1, b, b+1] */
                for(e = b - 1; e <= b + 1; e++) {
                  int *j_ptr2 = j_ptr1 + c - 1;
                  j_ptr1 += dim2;
              /* f = [c-1, c, c+1] */
                  for(f = c - 1; f <= c + 1; f++) {
                    j = *(j_ptr2++);    /*  *MapFirst(map,d,e,f)); */
                    while(j >= 0) {

                      if(i < j) {
                  /* position in space for atom 2 */
                        v2 = cs->Coord + (3 * j);
                        dst = (float) diff3f(v1, v2);

                        a2 = cs->IdxToAtm[j];
                        ai2 = ai + a2;

                        dst -= ((ai1->vdw + ai2->vdw) / 2);

                        /* quick hack for water detection.  
                           they don't usually don't have CONECT records 
                           and may not be HETATMs though they are supposed to be... 

                     This checks whether either atom in the bond
                     is a known wter.
                  */

                        water_flag = false;
                        if(AtomInfoKnownWaterResName(G, ai1->resn))
                          water_flag = true;
                        else if(AtomInfoKnownWaterResName(G, ai2->resn))
                          water_flag = true;

                        /* workaround for hydrogens and sulfurs... */

                        if(ai1->hydrogen || ai2->hydrogen)
                          cutoff = cutoff_h;
                        else if(((ai1->elem[0] == 'S') && (!ai1->elem[1])) ||
                                ((ai2->elem[0] == 'S') && (!ai2->elem[1])))
                          cutoff = cutoff_s;
                        else
                          cutoff = cutoff_v;

                  /* here's our complex atomic connectivity allow / disallow */

                        if((dst <= cutoff) && /* too close to be non-covalent, AND*/ 
                    
                           (!(ai1->hydrogen && ai2->hydrogen)) && /* not both hydrogen (what about H2?), AND */

                           (water_flag ||  /* known to be a water */
                            (!cs->TmpBond) || /* or no connectivity information present in file */
                            ((!(ai1->hetatm && ai2->hetatm) || /* or not both PDB HETATMS */
                              (connect_mode == 3))) || 

                            ((ai1->hetatm && ai2->hetatm) && /* both hetatms, and both recognized polymer residue? */
                             AtomInfoKnownPolymerResName(ai1->resn) && /* (new PDB rule allows these to be HETATMs */
                             AtomInfoKnownPolymerResName(ai2->resn))

                            ) && /* or we're no excluding HETATM -> HETATM bonds, AND*/
                           
                           
                           ((discrete_chains < 1) || /* we allow intra-chain bonds */
                            (ai1->chain[0] == ai2->chain[0])) && /* or atoms are in the same chain, AND */
                           
                           (connect_bonded || /* we're allowing explicitly bonded atoms to be auto-connected */
                            (!(ai1->bonded && ai2->bonded))) /* or neither atom was previously bonded */
                           
                           ) {
                          
                    /* WE THINK WE HAVE A BOND */
                          flag = true;

                    /* unbond edge cases */

                    /* atoms in same water molecule or different? */
                          if(water_flag)
                            if(!AtomInfoSameResidue(G, ai1, ai2)) /* don't connect water atoms in different residues */
                              flag = false;

                    /* atoms have same alt. conformations? from same molecule? */
                          if(flag) {
                            if(ai1->alt[0] != ai2->alt[0]) {    /* handle alternate conformers */
                              if(ai1->alt[0] && ai2->alt[0])
                                flag = false;   /* don't connect atoms with different, non-NULL
                                                   alternate conformations */
                            } else if(ai1->alt[0] && ai2->alt[0])
                              if(!AtomInfoSameResidue(G, ai1, ai2))
                                if(ai1->alt[0] != ai2->alt[0])
                                  flag = false; /* don't connect different, non-NULL 
                                                   alt conformations in 
                                                   different residues */
                          }
                    
                    /* do not bond different water molecules, even if their alt. confs. match */
                          if(flag) {
                            if(ai1->alt[0] || ai2->alt[0])
                              if(water_flag)    /* hack to clean up water bonds */
                                if(!AtomInfoSameResidue(G, ai1, ai2))
                                  flag = false;
                          }

                    /* if either is a cation, unbond is user wants */
                          if(flag && unbond_cations) {
                            if(AtomInfoIsFreeCation(G, ai1))
                              flag = false;
                            else if(AtomInfoIsFreeCation(G, ai2))
                              flag = false;
                          }

                    /* we have a bond, now process it */
                          if(flag) {
                            VLACheck((*bond), BondType, nBond);
                            (*bond)[nBond].index[0] = a1;
                            (*bond)[nBond].index[1] = a2;
                            (*bond)[nBond].stereo = 0;
                            order = 1;
                      /* if we allow bonds between chains and it screws up the
                       * bonding, disallow inter-chain bonds */
                            if(discrete_chains < 0) {   /* if we're allowing bonds between chains,
                                                           then make sure things don't get out of hand */
                              if(cnt[i] == -1)
                                violations++;
                              if(cnt[j] == -1)
                                violations++;
                        /* decrement free valences, since we have a bond */
                              cnt[i]--;
                              cnt[j]--;
                              if(violations > (cs->NIndex >> 3)) {
                                /* if more than 12% of the structure has excessive #'s of bonds... */
                                PRINTFB(G, FB_ObjectMolecule, FB_Blather)
                                  " ObjectMoleculeConnect: Assuming chains are discrete...\n"
                                  ENDFB(G);
                                discrete_chains = 1;
                                repeat = true;
                                goto do_it_again;
                              }
                            }
                      /* selenomethionine; double-bond the carbonyl if present */
                            if(ai1->hetatm && (!ai1->resn[3])) {        /* common HETATMs we should know about... */
                              switch (ai1->resn[0]) {
                              case 'M':
                                switch (ai1->resn[1]) {
                                case 'S':
                                  switch (ai1->resn[2]) {
                                  case 'E':
                            /* if carbonyl in same residue, double bond it */
                                    if(((!ai1->name[1]) && (!ai2->name[1])) &&
                                       (((ai1->name[0] == 'C') && (ai2->name[0] == 'O'))
                                        || ((ai1->name[0] == 'O')
                                            && (ai2->name[0] == 'C')))) {
                                      if(AtomInfoSameResidue(G, ai1, ai2)) {
                                        order = 2;
                                      }
                                    }
                                    break;
                                  }
                                  break;
                                }
                                break;
                              }
                            } else if((!ai1->hetatm)) {
                              if(AtomInfoSameResidue(I->Obj.G, ai1, ai2)) {
                                /* hookup standard disconnected PDB residue */
                                assign_pdb_known_residue(G, ai1, ai2, &order);
                              }
                            }
                            (*bond)[nBond].order = -order;      /* store tentative valence as negative */
                            nBond++;
                          }
                        }
                      }
                      j = MapNext(map, j);
                    }
                  }
                }
              }
            }
          do_it_again:
            MapFree(map);
            FreeP(cnt);
          }
        }
      case 1:                  /* only use explicit connectivity from file (don't do anything) */
        break;
      case 4:                  /* dictionary-based connectivity */
        /* TODO */
        break;
      }
      PRINTFB(G, FB_ObjectMolecule, FB_Blather)
        " ObjectMoleculeConnect: Found %d bonds.\n", nBond ENDFB(G);
      if(Feedback(G, FB_ObjectMolecule, FB_Debugging)) {
        for(a = 0; a < nBond; a++)
          printf(" ObjectMoleculeConnect: bond %d ind0 %d ind1 %d\n",
                 a, (*bond)[a].index[0], (*bond)[a].index[1]);
      }
    }
    if(repeat) {
      nBond = 0;
    }
  }
  /* if we have explicit connectivity, determine if we need to set check_conect_all */
  if(cs->NTmpBond && cs->TmpBond) {
    int check_conect_all = false;
    int pdb_conect_all = false;
    PRINTFB(G, FB_ObjectMolecule, FB_Blather)
      " ObjectMoleculeConnect: incorporating explicit bonds. %d %d\n",
      nBond, cs->NTmpBond ENDFB(G);
    if((nBond == 0) && (cs->NTmpBond > 0) &&
       bondSearchMode && (connect_mode == 0) && cs->NIndex) {
      /* if no bonds were found, and we have explicit connectivity,
       * try to determine if we need to set pdb_conect_mode */
      for(i = 0; i < cs->NIndex; i++) {
        a1 = cs->IdxToAtm[i];
        ai1 = ai + a1;
        if(ai1->bonded && (!ai1->hetatm)) {
          /* apparent PDB ATOM record with explicit bonding... */
          check_conect_all = true;
          break;
        }
      }
    }

    VLACheck((*bond), BondType, (nBond + cs->NTmpBond));
    ii1 = (*bond) + nBond;
    ii2 = cs->TmpBond;
    {
      register int n_atom = I->NAtom;
      for(a = 0; a < cs->NTmpBond; a++) {
        a1 = cs->IdxToAtm[ii2->index[0]];       /* convert bonds from index space */
        a2 = cs->IdxToAtm[ii2->index[1]];       /* to atom space */
        if((a1 >= 0) && (a2 >= 0) && (a1 < n_atom) && (a2 < n_atom)) {
          if(check_conect_all) {
            if((!ai[a1].hetatm) && (!ai[a2].hetatm)) {
              /* found bond between non-HETATMs -- so tell PyMOL to CONECT all ATOMs
               * when writing out a PDB file */
              pdb_conect_all = true;
            }
          }
          ai[a1].bonded = true;
          ai[a2].bonded = true;
          (*ii1) = (*ii2);      /* note this copies owned ids and thus settings etc. */
          ii1->index[0] = a1;
          ii1->index[1] = a2;
          ii1++;
          ii2++;

        }
      }
    }

    nBond = nBond + cs->NTmpBond;
    VLAFreeP(cs->TmpBond);
    cs->NTmpBond = 0;

    if(pdb_conect_all) {
      int dummy;
      if(!SettingGetIfDefined_b(G, I->Obj.Setting, cSetting_pdb_conect_all, &dummy)) {
        CSetting **handle = NULL;
        if(I->Obj.fGetSettingHandle) {
          handle = I->Obj.fGetSettingHandle(&I->Obj, -1);
          if(handle) {
            SettingCheckHandle(G, handle);
            SettingSet_b(*handle, cSetting_pdb_conect_all, true);
          }
        }
      }
    }
  }
  
  /* Link b/t ligand and residue? */
  if(cs->NTmpLinkBond && cs->TmpLinkBond) {
    PRINTFB(G, FB_ObjectMolecule, FB_Blather)
      "ObjectMoleculeConnect: incorporating linkage bonds. %d %d\n",
      nBond, cs->NTmpLinkBond ENDFB(G);
    VLACheck((*bond), BondType, (nBond + cs->NTmpLinkBond));
    ii1 = (*bond) + nBond;
    ii2 = cs->TmpLinkBond;
    for(a = 0; a < cs->NTmpLinkBond; a++) {
      a1 = ii2->index[0];       /* first atom is in object */
      a2 = cs->IdxToAtm[ii2->index[1]]; /* second is in the cset */
      ai[a1].bonded = true;
      ai[a2].bonded = true;
      (*ii1) = (*ii2);          /* note this copies owned ids and thus settings etc. */
      ii1->index[0] = a1;
      ii1->index[1] = a2;
      ii1++;
      ii2++;
    }
    nBond = nBond + cs->NTmpLinkBond;
    VLAFreeP(cs->TmpLinkBond);
    cs->NTmpLinkBond = 0;
  }

  PRINTFD(G, FB_ObjectMolecule)
    " ObjectMoleculeConnect: elminating duplicates with %d bonds...\n", nBond ENDFD;

  if(!I->DiscreteFlag) {
    UtilSortInPlace(G, (*bond), nBond, sizeof(BondType), (UtilOrderFn *) BondInOrder);
    if(nBond) {                 /* eliminate duplicates */
      ii1 = (*bond) + 1;
      ii2 = (*bond) + 1;
      a = nBond - 1;
      nBond = 1;
      if(a > 0)
        while(a--) {
          if((ii2->index[0] != (ii1 - 1)->index[0]) ||
             (ii2->index[1] != (ii1 - 1)->index[1])) {
            *(ii1++) = *(ii2++);        /* copy bond */
            nBond++;
          } else {
            if((ii2->order > 0) && ((ii1 - 1)->order < 0))
              (ii1 - 1)->order = ii2->order;    /* use most certain valence */
            ii2++;              /* skip bond */
          }
        }
      VLASize((*bond), BondType, nBond);
    }
  }
  /* restore bond oder positivity */

  ii1 = *bond;
  for(a = 0; a < nBond; a++) {
    if(ii1->order < 0)
      ii1->order = -ii1->order;
    ii1++;
  }

  PRINTFD(G, FB_ObjectMolecule)
    " ObjectMoleculeConnect: leaving with %d bonds...\n", nBond ENDFD;
  return (nBond);
}


/*========================================================================*/
void ObjectMoleculeSort(ObjectMolecule * I)
{                               /* sorts atoms and bonds */
  int *index;
  int *outdex = NULL;
  register int a, b;
  CoordSet *cs, **dcs;
  AtomInfoType *atInfo;
  int *dAtmToIdx;
  if(!I->DiscreteFlag) {        /* currently, discrete objects are never sorted */
    int n_bytes = sizeof(int) * I->NAtom;
    int already_in_order = true;
    int i_NAtom = I->NAtom;
    index = AtomInfoGetSortedIndex(I->Obj.G, &I->Obj, I->AtomInfo, i_NAtom, &outdex);
    for(a = 0; a < i_NAtom; a++) {
      if(index[a] != a) {
        already_in_order = false;
        break;
      }
    }
    if(!already_in_order) {     /* if we aren't already in perfect order */

      for(a = 0; a < I->NBond; a++) {   /* bonds */
        I->Bond[a].index[0] = outdex[I->Bond[a].index[0]];
        I->Bond[a].index[1] = outdex[I->Bond[a].index[1]];
      }

      for(a = -1; a < I->NCSet; a++) {  /* coordinate set mapping */
        if(a < 0) {
          cs = I->CSTmpl;
        } else {
          cs = I->CSet[a];
        }

        if(cs) {
          register int cs_NIndex = cs->NIndex;
          register int *cs_IdxToAtm = cs->IdxToAtm;
          register int *cs_AtmToIdx = cs->AtmToIdx;
          for(b = 0; b < cs_NIndex; b++)
            cs_IdxToAtm[b] = outdex[cs_IdxToAtm[b]];
          if(cs_AtmToIdx) {
            memset(cs_AtmToIdx, -1, n_bytes);
            /*          for(b=0;b<i_NAtom;b++)
               cs_AtmToIdx[b]=-1; */
            for(b = 0; b < cs_NIndex; b++) {
              cs_AtmToIdx[cs_IdxToAtm[b]] = b;
            }
          }
        }
      }

      atInfo = (AtomInfoType *) VLAMalloc(i_NAtom, sizeof(AtomInfoType), 5, true);
      /* autozero here is important */
      for(a = 0; a < i_NAtom; a++)
        atInfo[a] = I->AtomInfo[index[a]];
      VLAFreeP(I->AtomInfo);
      I->AtomInfo = atInfo;

      if(I->DiscreteFlag) {
        dcs = VLAlloc(CoordSet *, i_NAtom);
        dAtmToIdx = VLAlloc(int, i_NAtom);
        for(a = 0; a < i_NAtom; a++) {
          b = index[a];
          dcs[a] = I->DiscreteCSet[b];
          dAtmToIdx[a] = I->DiscreteAtmToIdx[b];
        }
        VLAFreeP(I->DiscreteCSet);
        VLAFreeP(I->DiscreteAtmToIdx);
        I->DiscreteCSet = dcs;
        I->DiscreteAtmToIdx = dAtmToIdx;
      }
    }
    AtomInfoFreeSortedIndexes(I->Obj.G, index, outdex);

    UtilSortInPlace(I->Obj.G, I->Bond, I->NBond, sizeof(BondType),
                    (UtilOrderFn *) BondInOrder);
    /* sort...important! */
    ObjectMoleculeInvalidate(I, cRepAll, cRepInvAtoms, -1);     /* important */

  }
}

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