diff --git a/Code/GraphMol/FileParsers/ProximityBonds.cpp b/Code/GraphMol/FileParsers/ProximityBonds.cpp
index 6f3b1b2c9..e4e70f339 100644
--- a/Code/GraphMol/FileParsers/ProximityBonds.cpp
+++ b/Code/GraphMol/FileParsers/ProximityBonds.cpp
@@ -1,393 +1,393 @@
-//
-//  Copyright (C) 2013-2017 Greg Landrum and NextMove Software
-//
-//   @@ All Rights Reserved @@
-//  This file is part of the RDKit.
-//  The contents are covered by the terms of the BSD license
-//  which is included in the file license.txt, found at the root
-//  of the RDKit source tree.
-//
-#include "ProximityBonds.h"
-#include <algorithm>
-#include <GraphMol/RDKitBase.h>
-#include <GraphMol/RWMol.h>
-#include <GraphMol/MonomerInfo.h>
-
-namespace RDKit {
-
-static const double EXTDIST = 0.45;
-// static const double MAXRAD   = 2.50;
-// static const double MINDIST  = 0.40;
-static const double MAXDIST = 5.45;      // 2*MAXRAD + EXTDIST
-static const double MINDIST2 = 0.16;     // MINDIST*MINDIST
-static const double MAXDIST2 = 29.7025;  // MAXDIST*MAXDIST
-
-struct ProximityEntry {
-  float x, y, z, r;
-  int atm, hash, next, elem;
-
-  bool operator<(const ProximityEntry &p) const { return x < p.x; }
-};
-
-static bool IsBonded(ProximityEntry *p, ProximityEntry *q, unsigned int flags) {
-  if (flags & ctdIGNORE_H_H_CONTACTS && p->elem == 1 && q->elem == 1)
-    return false;
-  double dx = (double)p->x - (double)q->x;
-  double dist2 = dx * dx;
-  if (dist2 > MAXDIST2) return false;
-  double dy = (double)p->y - (double)q->y;
-  dist2 += dy * dy;
-  if (dist2 > MAXDIST2) return false;
-  double dz = (double)p->z - (double)q->z;
-  dist2 += dz * dz;
-
-  if (dist2 > MAXDIST2 || dist2 < MINDIST2) return false;
-
-  double radius = (double)p->r + (double)q->r + EXTDIST;
-  return dist2 <= radius * radius;
-}
-
-bool SamePDBResidue(AtomPDBResidueInfo *p, AtomPDBResidueInfo *q) {
-  return p->getResidueNumber() == q->getResidueNumber() &&
-         p->getResidueName() == q->getResidueName() &&
-         p->getChainId() == q->getChainId() &&
-         p->getInsertionCode() == q->getInsertionCode();
-}
-
-static bool IsBlacklistedAtom(Atom *atom) {
-  // blacklist metals, noble gasses and halogens
-  int elem = atom->getAtomicNum();
-  // make an inverse query (non-metals and metaloids)
-  if ((5 <= elem && elem <= 8) || (14 <= elem && elem <= 16) ||
-      (32 <= elem && elem <= 34) || (51 <= elem && elem <= 52))
-    return false;
-  else
-    return true;
-}
-
-bool IsBlacklistedPair(Atom *beg_atom, Atom *end_atom) {
-  PRECONDITION(beg_atom, "empty atom");
-  PRECONDITION(end_atom, "empty atom");
-
-  AtomPDBResidueInfo *beg_info =
-      (AtomPDBResidueInfo *)beg_atom->getMonomerInfo();
-  AtomPDBResidueInfo *end_info =
-      (AtomPDBResidueInfo *)end_atom->getMonomerInfo();
-  if (!beg_info || beg_info->getMonomerType() != AtomMonomerInfo::PDBRESIDUE)
-    return false;
-  if (!end_info || end_info->getMonomerType() != AtomMonomerInfo::PDBRESIDUE)
-    return false;
-
-  if (!SamePDBResidue(beg_info, end_info)) {
-    if (IsBlacklistedAtom(beg_atom) || IsBlacklistedAtom(end_atom)) return true;
-    // Dont make bonds to waters
-    if (beg_info->getResidueName() == "HOH" ||
-        end_info->getResidueName() == "HOH")
-      return true;
-  }
-  return false;
-}
-
-/*
-static void ConnectTheDots_Small(RWMol *mol)
-{
-unsigned int count = mol->getNumAtoms();
-ProximityEntry *tmp = (ProximityEntry*)malloc(count*sizeof(ProximityEntry));
-PeriodicTable *table = PeriodicTable::getTable();
-Conformer *conf = &mol->getConformer();
-for (unsigned int i=0; i<count; i++) {
-  Atom *atom = mol->getAtomWithIdx(i);
-  unsigned int elem = atom->getAtomicNum();
-  RDGeom::Point3D p = conf->getAtomPos(i);
-  ProximityEntry *tmpi = tmp+i;
-  tmpi->x = (float)p.x;
-  tmpi->y = (float)p.y;
-  tmpi->z = (float)p.z;
-  tmpi->r = (float)table->getRcovalent(elem);
-  for (unsigned int j=0; j<i; j++) {
-    ProximityEntry *tmpj = tmp+j;
-    if (IsBonded(tmpi,tmpj) && !mol->getBondBetweenAtoms(i,j))
-      mol->addBond(i,j,Bond::SINGLE);
-  }
-}
-free(tmp);
-}
-
-
-static void ConnectTheDots_Medium(RWMol *mol)
-{
-int count = mol->getNumAtoms();
-std::vector<ProximityEntry> tmp(count);
-PeriodicTable *table = PeriodicTable::getTable();
-Conformer *conf = &mol->getConformer();
-for (int i=0; i<count; i++) {
-  Atom *atom = mol->getAtomWithIdx(i);
-  unsigned int elem = atom->getAtomicNum();
-  RDGeom::Point3D p = conf->getAtomPos(i);
-  ProximityEntry *tmpi = &tmp[i];
-  tmpi->x = (float)p.x;
-  tmpi->y = (float)p.y;
-  tmpi->z = (float)p.z;
-  tmpi->r = (float)table->getRcovalent(elem);
-  tmpi->atm = i;
-}
-
-std::stable_sort(tmp.begin(),tmp.end());
-
-for (int j=0; j<count; j++) {
-  ProximityEntry *tmpj = &tmp[j];
-  double limit = tmpj->x - MAXDIST;
-  for (int k=j-1; k>=0; k--) {
-    ProximityEntry *tmpk = &tmp[k];
-    if (tmpk->x < limit)
-      break;
-    if (IsBonded(tmpj,tmpk) &&
-        !mol->getBondBetweenAtoms(tmpj->atm,tmpk->atm))
-      mol->addBond(tmpj->atm,tmpk->atm,Bond::SINGLE);
-  }
-}
-}
-*/
-
-#define HASHSIZE 1024
-#define HASHMASK 1023
-#define HASHX 571
-#define HASHY 127
-#define HASHZ 3
-
-static void ConnectTheDots_Large(RWMol *mol, unsigned int flags) {
-  int HashTable[HASHSIZE];
-  memset(HashTable, -1, sizeof(HashTable));
-
-  unsigned int count = mol->getNumAtoms();
-  ProximityEntry *tmp =
-      (ProximityEntry *)malloc(count * sizeof(ProximityEntry));
-      CHECK_INVARIANT(tmp,"bad allocation");
-  PeriodicTable *table = PeriodicTable::getTable();
-  Conformer *conf = &mol->getConformer();
-
-  for (unsigned int i = 0; i < count; i++) {
-    Atom *atom = mol->getAtomWithIdx(i);
-    unsigned int elem = atom->getAtomicNum();
-    RDGeom::Point3D p = conf->getAtomPos(i);
-    ProximityEntry *tmpi = tmp + i;
-    tmpi->x = (float)p.x;
-    tmpi->y = (float)p.y;
-    tmpi->z = (float)p.z;
-    tmpi->r = (float)table->getRcovalent(elem);
-    tmpi->atm = i;
-    tmpi->elem = elem;
-
-    int hash = HASHX * (int)(p.x / MAXDIST) + HASHY * (int)(p.y / MAXDIST) +
-               HASHZ * (int)(p.z / MAXDIST);
-
-    for (int dx = -HASHX; dx <= HASHX; dx += HASHX)
-      for (int dy = -HASHY; dy <= HASHY; dy += HASHY)
-        for (int dz = -HASHZ; dz <= HASHZ; dz += HASHZ) {
-          int probe = hash + dx + dy + dz;
-          int list = HashTable[probe & HASHMASK];
-          while (list != -1) {
-            ProximityEntry *tmpj = &tmp[list];
-            if (tmpj->hash == probe && IsBonded(tmpi, tmpj, flags) &&
-                !mol->getBondBetweenAtoms(tmpi->atm, tmpj->atm) &&
-                !IsBlacklistedPair(atom, mol->getAtomWithIdx(tmpj->atm)))
-              mol->addBond(tmpi->atm, tmpj->atm, Bond::SINGLE);
-            list = tmpj->next;
-          }
-        }
-    int list = hash & HASHMASK;
-    tmpi->next = HashTable[list];
-    HashTable[list] = i;
-    tmpi->hash = hash;
-  }
-  // Cleanup pass
-  for (unsigned int i = 0; i < count; i++) {
-    Atom *atom = mol->getAtomWithIdx(i);
-    unsigned int elem = atom->getAtomicNum();
-    // detect multivalent Hs, which could happen with ConnectTheDots
-    if (elem == 1 && atom->getDegree() > 1) {
-      AtomPDBResidueInfo *atom_info =
-          (AtomPDBResidueInfo *)(atom->getMonomerInfo());
-      // cut all but shortest Bond
-      RDGeom::Point3D p = conf->getAtomPos(i);
-      RDKit::RWMol::ADJ_ITER nbr, end_nbr;
-      boost::tie(nbr, end_nbr) = mol->getAtomNeighbors(atom);
-      float best = 10000;
-      unsigned int best_idx = mol->getNumAtoms() + 1;
-      while (nbr != end_nbr) {
-        RDGeom::Point3D pn = conf->getAtomPos(*nbr);
-        float d = (p - pn).length();
-        AtomPDBResidueInfo *n_info =
-            (AtomPDBResidueInfo *)(mol->getAtomWithIdx(*nbr)->getMonomerInfo());
-        if (d < best &&
-            atom_info->getResidueNumber() == n_info->getResidueNumber()) {
-          best = d;
-          best_idx = *nbr;
-        }
-        ++nbr;
-      }
-      // iterate again and remove all but closest
-      boost::tie(nbr, end_nbr) = mol->getAtomNeighbors(atom);
-      while (nbr != end_nbr) {
-        if (*nbr == best_idx) {
-          Bond *bond = mol->getBondBetweenAtoms(i, *nbr);
-          bond->setBondType(Bond::SINGLE);  // make sure this one is single
-        } else {
-          mol->removeBond(i, *nbr);
-        }
-        ++nbr;
-      }
-    }
-  }
-  free(tmp);
-}
-
-void ConnectTheDots(RWMol *mol, unsigned int flags) {
-  if (!mol || !mol->getNumConformers()) return;
-  // Determine optimal algorithm to use by getNumAtoms()?
-  ConnectTheDots_Large(mol, flags);
-}
-
-// These are macros to allow their use in C++ constants
-#define BCNAM(A, B, C) (((A) << 16) | ((B) << 8) | (C))
-#define BCATM(A, B, C, D) (((A) << 24) | ((B) << 16) | ((C) << 8) | (D))
-
-static bool StandardPDBDoubleBond(unsigned int rescode, unsigned int atm1,
-                                  unsigned int atm2) {
-  if (atm1 > atm2) {
-    unsigned int tmp = atm1;
-    atm1 = atm2;
-    atm2 = tmp;
-  }
-
-  switch (rescode) {
-    case BCNAM('A', 'L', 'A'):
-    case BCNAM('C', 'Y', 'S'):
-    case BCNAM('G', 'L', 'Y'):
-    case BCNAM('I', 'L', 'E'):
-    case BCNAM('L', 'E', 'U'):
-    case BCNAM('L', 'Y', 'S'):
-    case BCNAM('M', 'E', 'T'):
-    case BCNAM('P', 'R', 'O'):
-    case BCNAM('S', 'E', 'R'):
-    case BCNAM('T', 'H', 'R'):
-    case BCNAM('V', 'A', 'L'):
-      if (atm1 == BCATM(' ', 'C', ' ', ' ') &&
-          atm2 == BCATM(' ', 'O', ' ', ' '))
-        return true;
-      break;
-    case BCNAM('A', 'R', 'G'):
-      if (atm1 == BCATM(' ', 'C', ' ', ' ') &&
-          atm2 == BCATM(' ', 'O', ' ', ' '))
-        return true;
-      if (atm1 == BCATM(' ', 'C', 'Z', ' ') &&
-          atm2 == BCATM(' ', 'N', 'H', '2'))
-        return true;
-      break;
-    case BCNAM('A', 'S', 'N'):
-    case BCNAM('A', 'S', 'P'):
-      if (atm1 == BCATM(' ', 'C', ' ', ' ') &&
-          atm2 == BCATM(' ', 'O', ' ', ' '))
-        return true;
-      if (atm1 == BCATM(' ', 'C', 'G', ' ') &&
-          atm2 == BCATM(' ', 'O', 'D', '1'))
-        return true;
-      break;
-    case BCNAM('G', 'L', 'N'):
-    case BCNAM('G', 'L', 'U'):
-      if (atm1 == BCATM(' ', 'C', ' ', ' ') &&
-          atm2 == BCATM(' ', 'O', ' ', ' '))
-        return true;
-      if (atm1 == BCATM(' ', 'C', 'D', ' ') &&
-          atm2 == BCATM(' ', 'O', 'E', '1'))
-        return true;
-      break;
-    case BCNAM('H', 'I', 'S'):
-      if (atm1 == BCATM(' ', 'C', ' ', ' ') &&
-          atm2 == BCATM(' ', 'O', ' ', ' '))
-        return true;
-      if (atm1 == BCATM(' ', 'C', 'D', '2') &&
-          atm2 == BCATM(' ', 'C', 'G', ' '))
-        return true;
-      if (atm1 == BCATM(' ', 'C', 'E', '1') &&
-          atm2 == BCATM(' ', 'N', 'D', '1'))
-        return true;
-      break;
-    case BCNAM('P', 'H', 'E'):
-    case BCNAM('T', 'Y', 'R'):
-      if (atm1 == BCATM(' ', 'C', ' ', ' ') &&
-          atm2 == BCATM(' ', 'O', ' ', ' '))
-        return true;
-      if (atm1 == BCATM(' ', 'C', 'D', '1') &&
-          atm2 == BCATM(' ', 'C', 'G', ' '))
-        return true;
-      if (atm1 == BCATM(' ', 'C', 'D', '2') &&
-          atm2 == BCATM(' ', 'C', 'E', '2'))
-        return true;
-      if (atm1 == BCATM(' ', 'C', 'E', '1') &&
-          atm2 == BCATM(' ', 'C', 'Z', ' '))
-        return true;
-      break;
-    case BCNAM('T', 'R', 'P'):
-      if (atm1 == BCATM(' ', 'C', ' ', ' ') &&
-          atm2 == BCATM(' ', 'O', ' ', ' '))
-        return true;
-      if (atm1 == BCATM(' ', 'C', 'D', '1') &&
-          atm2 == BCATM(' ', 'C', 'G', ' '))
-        return true;
-      if (atm1 == BCATM(' ', 'C', 'D', '2') &&
-          atm2 == BCATM(' ', 'C', 'E', '2'))
-        return true;
-      if (atm1 == BCATM(' ', 'C', 'E', '3') &&
-          atm2 == BCATM(' ', 'C', 'Z', '3'))
-        return true;
-      if (atm1 == BCATM(' ', 'C', 'H', '2') &&
-          atm2 == BCATM(' ', 'C', 'Z', '2'))
-        return true;
-      break;
-  }
-  return false;
-}
-
-static bool StandardPDBDoubleBond(RWMol *mol, Atom *beg, Atom *end) {
-  AtomPDBResidueInfo *bInfo = (AtomPDBResidueInfo *)beg->getMonomerInfo();
-  if (!bInfo || bInfo->getMonomerType() != AtomMonomerInfo::PDBRESIDUE)
-    return false;
-  AtomPDBResidueInfo *eInfo = (AtomPDBResidueInfo *)end->getMonomerInfo();
-  if (!eInfo || eInfo->getMonomerType() != AtomMonomerInfo::PDBRESIDUE)
-    return false;
-  if (!SamePDBResidue(bInfo, eInfo)) return false;
-  if (bInfo->getIsHeteroAtom() || eInfo->getIsHeteroAtom()) return false;
-
-  const char *ptr = bInfo->getResidueName().c_str();
-  unsigned int rescode = BCNAM(ptr[0], ptr[1], ptr[2]);
-  ptr = bInfo->getName().c_str();
-  unsigned int atm1 = BCATM(ptr[0], ptr[1], ptr[2], ptr[3]);
-  ptr = eInfo->getName().c_str();
-  unsigned int atm2 = BCATM(ptr[0], ptr[1], ptr[2], ptr[3]);
-
-  if (!StandardPDBDoubleBond(rescode, atm1, atm2)) return false;
-
-  // Check that neither end already has a double bond
-  ROMol::OBOND_ITER_PAIR bp;
-  for (bp = mol->getAtomBonds(beg); bp.first != bp.second; ++bp.first)
-    if ((*mol)[*bp.first]->getBondType() == Bond::DOUBLE) return false;
-  for (bp = mol->getAtomBonds(end); bp.first != bp.second; ++bp.first)
-    if ((*mol)[*bp.first]->getBondType() == Bond::DOUBLE) return false;
-
-  return true;
-}
-
-void StandardPDBResidueBondOrders(RWMol *mol) {
-  RWMol::BondIterator bondIt;
-  for (bondIt = mol->beginBonds(); bondIt != mol->endBonds(); ++bondIt) {
-    Bond *bond = *bondIt;
-    if (bond->getBondType() == Bond::SINGLE) {
-      Atom *beg = bond->getBeginAtom();
-      Atom *end = bond->getEndAtom();
-      if (StandardPDBDoubleBond(mol, beg, end)) bond->setBondType(Bond::DOUBLE);
-    }
-  }
-}
-
-}  // namespace RDKit
+//
+//  Copyright (C) 2013-2017 Greg Landrum and NextMove Software
+//
+//   @@ All Rights Reserved @@
+//  This file is part of the RDKit.
+//  The contents are covered by the terms of the BSD license
+//  which is included in the file license.txt, found at the root
+//  of the RDKit source tree.
+//
+#include "ProximityBonds.h"
+#include <algorithm>
+#include <GraphMol/RDKitBase.h>
+#include <GraphMol/RWMol.h>
+#include <GraphMol/MonomerInfo.h>
+
+namespace RDKit {
+
+static const double EXTDIST = 0.45;
+// static const double MAXRAD   = 2.50;
+// static const double MINDIST  = 0.40;
+static const double MAXDIST = 5.45;      // 2*MAXRAD + EXTDIST
+static const double MINDIST2 = 0.16;     // MINDIST*MINDIST
+static const double MAXDIST2 = 29.7025;  // MAXDIST*MAXDIST
+
+struct ProximityEntry {
+  float x, y, z, r;
+  int atm, hash, next, elem;
+
+  bool operator<(const ProximityEntry &p) const { return x < p.x; }
+};
+
+static bool IsBonded(ProximityEntry *p, ProximityEntry *q, unsigned int flags) {
+  if (flags & ctdIGNORE_H_H_CONTACTS && p->elem == 1 && q->elem == 1)
+    return false;
+  double dx = (double)p->x - (double)q->x;
+  double dist2 = dx * dx;
+  if (dist2 > MAXDIST2) return false;
+  double dy = (double)p->y - (double)q->y;
+  dist2 += dy * dy;
+  if (dist2 > MAXDIST2) return false;
+  double dz = (double)p->z - (double)q->z;
+  dist2 += dz * dz;
+
+  if (dist2 > MAXDIST2 || dist2 < MINDIST2) return false;
+
+  double radius = (double)p->r + (double)q->r + EXTDIST;
+  return dist2 <= radius * radius;
+}
+
+bool SamePDBResidue(AtomPDBResidueInfo *p, AtomPDBResidueInfo *q) {
+  return p->getResidueNumber() == q->getResidueNumber() &&
+         p->getResidueName() == q->getResidueName() &&
+         p->getChainId() == q->getChainId() &&
+         p->getInsertionCode() == q->getInsertionCode();
+}
+
+static bool IsBlacklistedAtom(Atom *atom) {
+  // blacklist metals, noble gasses and halogens
+  int elem = atom->getAtomicNum();
+  // make an inverse query (non-metals and metaloids)
+  if ((5 <= elem && elem <= 8) || (14 <= elem && elem <= 16) ||
+      (32 <= elem && elem <= 34) || (51 <= elem && elem <= 52))
+    return false;
+  else
+    return true;
+}
+
+bool IsBlacklistedPair(Atom *beg_atom, Atom *end_atom) {
+  PRECONDITION(beg_atom, "empty atom");
+  PRECONDITION(end_atom, "empty atom");
+
+  AtomPDBResidueInfo *beg_info =
+      (AtomPDBResidueInfo *)beg_atom->getMonomerInfo();
+  AtomPDBResidueInfo *end_info =
+      (AtomPDBResidueInfo *)end_atom->getMonomerInfo();
+  if (!beg_info || beg_info->getMonomerType() != AtomMonomerInfo::PDBRESIDUE)
+    return false;
+  if (!end_info || end_info->getMonomerType() != AtomMonomerInfo::PDBRESIDUE)
+    return false;
+
+  if (!SamePDBResidue(beg_info, end_info)) {
+    if (IsBlacklistedAtom(beg_atom) || IsBlacklistedAtom(end_atom)) return true;
+    // Dont make bonds to waters
+    if (beg_info->getResidueName() == "HOH" ||
+        end_info->getResidueName() == "HOH")
+      return true;
+  }
+  return false;
+}
+
+/*
+static void ConnectTheDots_Small(RWMol *mol)
+{
+unsigned int count = mol->getNumAtoms();
+ProximityEntry *tmp = (ProximityEntry*)malloc(count*sizeof(ProximityEntry));
+PeriodicTable *table = PeriodicTable::getTable();
+Conformer *conf = &mol->getConformer();
+for (unsigned int i=0; i<count; i++) {
+  Atom *atom = mol->getAtomWithIdx(i);
+  unsigned int elem = atom->getAtomicNum();
+  RDGeom::Point3D p = conf->getAtomPos(i);
+  ProximityEntry *tmpi = tmp+i;
+  tmpi->x = (float)p.x;
+  tmpi->y = (float)p.y;
+  tmpi->z = (float)p.z;
+  tmpi->r = (float)table->getRcovalent(elem);
+  for (unsigned int j=0; j<i; j++) {
+    ProximityEntry *tmpj = tmp+j;
+    if (IsBonded(tmpi,tmpj) && !mol->getBondBetweenAtoms(i,j))
+      mol->addBond(i,j,Bond::SINGLE);
+  }
+}
+free(tmp);
+}
+
+
+static void ConnectTheDots_Medium(RWMol *mol)
+{
+int count = mol->getNumAtoms();
+std::vector<ProximityEntry> tmp(count);
+PeriodicTable *table = PeriodicTable::getTable();
+Conformer *conf = &mol->getConformer();
+for (int i=0; i<count; i++) {
+  Atom *atom = mol->getAtomWithIdx(i);
+  unsigned int elem = atom->getAtomicNum();
+  RDGeom::Point3D p = conf->getAtomPos(i);
+  ProximityEntry *tmpi = &tmp[i];
+  tmpi->x = (float)p.x;
+  tmpi->y = (float)p.y;
+  tmpi->z = (float)p.z;
+  tmpi->r = (float)table->getRcovalent(elem);
+  tmpi->atm = i;
+}
+
+std::stable_sort(tmp.begin(),tmp.end());
+
+for (int j=0; j<count; j++) {
+  ProximityEntry *tmpj = &tmp[j];
+  double limit = tmpj->x - MAXDIST;
+  for (int k=j-1; k>=0; k--) {
+    ProximityEntry *tmpk = &tmp[k];
+    if (tmpk->x < limit)
+      break;
+    if (IsBonded(tmpj,tmpk) &&
+        !mol->getBondBetweenAtoms(tmpj->atm,tmpk->atm))
+      mol->addBond(tmpj->atm,tmpk->atm,Bond::SINGLE);
+  }
+}
+}
+*/
+
+#define HASHSIZE 1024
+#define HASHMASK 1023
+#define HASHX 571
+#define HASHY 127
+#define HASHZ 3
+
+static void ConnectTheDots_Large(RWMol *mol, unsigned int flags) {
+  int HashTable[HASHSIZE];
+  memset(HashTable, -1, sizeof(HashTable));
+
+  unsigned int count = mol->getNumAtoms();
+  ProximityEntry *tmp =
+      (ProximityEntry *)malloc(count * sizeof(ProximityEntry));
+      CHECK_INVARIANT(tmp,"bad allocation");
+  PeriodicTable *table = PeriodicTable::getTable();
+  Conformer *conf = &mol->getConformer();
+
+  for (unsigned int i = 0; i < count; i++) {
+    Atom *atom = mol->getAtomWithIdx(i);
+    unsigned int elem = atom->getAtomicNum();
+    RDGeom::Point3D p = conf->getAtomPos(i);
+    ProximityEntry *tmpi = tmp + i;
+    tmpi->x = (float)p.x;
+    tmpi->y = (float)p.y;
+    tmpi->z = (float)p.z;
+    tmpi->r = (float)table->getRcovalent(elem);
+    tmpi->atm = i;
+    tmpi->elem = elem;
+
+    int hash = HASHX * (int)(p.x / MAXDIST) + HASHY * (int)(p.y / MAXDIST) +
+               HASHZ * (int)(p.z / MAXDIST);
+
+    for (int dx = -HASHX; dx <= HASHX; dx += HASHX)
+      for (int dy = -HASHY; dy <= HASHY; dy += HASHY)
+        for (int dz = -HASHZ; dz <= HASHZ; dz += HASHZ) {
+          int probe = hash + dx + dy + dz;
+          int list = HashTable[probe & HASHMASK];
+          while (list != -1) {
+            ProximityEntry *tmpj = &tmp[list];
+            if (tmpj->hash == probe && IsBonded(tmpi, tmpj, flags) &&
+                !mol->getBondBetweenAtoms(tmpi->atm, tmpj->atm) &&
+                !IsBlacklistedPair(atom, mol->getAtomWithIdx(tmpj->atm)))
+              mol->addBond(tmpi->atm, tmpj->atm, Bond::SINGLE);
+            list = tmpj->next;
+          }
+        }
+    int list = hash & HASHMASK;
+    tmpi->next = HashTable[list];
+    HashTable[list] = i;
+    tmpi->hash = hash;
+  }
+  // Cleanup pass
+  for (unsigned int i = 0; i < count; i++) {
+    Atom *atom = mol->getAtomWithIdx(i);
+    unsigned int elem = atom->getAtomicNum();
+    // detect multivalent Hs, which could happen with ConnectTheDots
+    if (elem == 1 && atom->getDegree() > 1) {
+      AtomPDBResidueInfo *atom_info =
+          (AtomPDBResidueInfo *)(atom->getMonomerInfo());
+      // cut all but shortest Bond
+      RDGeom::Point3D p = conf->getAtomPos(i);
+      RDKit::RWMol::ADJ_ITER nbr, end_nbr;
+      boost::tie(nbr, end_nbr) = mol->getAtomNeighbors(atom);
+      float best = 10000;
+      unsigned int best_idx = mol->getNumAtoms() + 1;
+      while (nbr != end_nbr) {
+        RDGeom::Point3D pn = conf->getAtomPos(*nbr);
+        float d = (p - pn).length();
+        AtomPDBResidueInfo *n_info =
+            (AtomPDBResidueInfo *)(mol->getAtomWithIdx(*nbr)->getMonomerInfo());
+        if (d < best &&
+            atom_info->getResidueNumber() == n_info->getResidueNumber()) {
+          best = d;
+          best_idx = *nbr;
+        }
+        ++nbr;
+      }
+      // iterate again and remove all but closest
+      boost::tie(nbr, end_nbr) = mol->getAtomNeighbors(atom);
+      while (nbr != end_nbr) {
+        if (*nbr == best_idx) {
+          Bond *bond = mol->getBondBetweenAtoms(i, *nbr);
+          bond->setBondType(Bond::SINGLE);  // make sure this one is single
+        } else {
+          mol->removeBond(i, *nbr);
+        }
+        ++nbr;
+      }
+    }
+  }
+  free(tmp);
+}
+
+void ConnectTheDots(RWMol *mol, unsigned int flags) {
+  if (!mol || !mol->getNumConformers()) return;
+  // Determine optimal algorithm to use by getNumAtoms()?
+  ConnectTheDots_Large(mol, flags);
+}
+
+// These are macros to allow their use in C++ constants
+#define BCNAM(A, B, C) (((A) << 16) | ((B) << 8) | (C))
+#define BCATM(A, B, C, D) (((A) << 24) | ((B) << 16) | ((C) << 8) | (D))
+
+static bool StandardPDBDoubleBond(unsigned int rescode, unsigned int atm1,
+                                  unsigned int atm2) {
+  if (atm1 > atm2) {
+    unsigned int tmp = atm1;
+    atm1 = atm2;
+    atm2 = tmp;
+  }
+
+  switch (rescode) {
+    case BCNAM('A', 'L', 'A'):
+    case BCNAM('C', 'Y', 'S'):
+    case BCNAM('G', 'L', 'Y'):
+    case BCNAM('I', 'L', 'E'):
+    case BCNAM('L', 'E', 'U'):
+    case BCNAM('L', 'Y', 'S'):
+    case BCNAM('M', 'E', 'T'):
+    case BCNAM('P', 'R', 'O'):
+    case BCNAM('S', 'E', 'R'):
+    case BCNAM('T', 'H', 'R'):
+    case BCNAM('V', 'A', 'L'):
+      if (atm1 == BCATM(' ', 'C', ' ', ' ') &&
+          atm2 == BCATM(' ', 'O', ' ', ' '))
+        return true;
+      break;
+    case BCNAM('A', 'R', 'G'):
+      if (atm1 == BCATM(' ', 'C', ' ', ' ') &&
+          atm2 == BCATM(' ', 'O', ' ', ' '))
+        return true;
+      if (atm1 == BCATM(' ', 'C', 'Z', ' ') &&
+          atm2 == BCATM(' ', 'N', 'H', '2'))
+        return true;
+      break;
+    case BCNAM('A', 'S', 'N'):
+    case BCNAM('A', 'S', 'P'):
+      if (atm1 == BCATM(' ', 'C', ' ', ' ') &&
+          atm2 == BCATM(' ', 'O', ' ', ' '))
+        return true;
+      if (atm1 == BCATM(' ', 'C', 'G', ' ') &&
+          atm2 == BCATM(' ', 'O', 'D', '1'))
+        return true;
+      break;
+    case BCNAM('G', 'L', 'N'):
+    case BCNAM('G', 'L', 'U'):
+      if (atm1 == BCATM(' ', 'C', ' ', ' ') &&
+          atm2 == BCATM(' ', 'O', ' ', ' '))
+        return true;
+      if (atm1 == BCATM(' ', 'C', 'D', ' ') &&
+          atm2 == BCATM(' ', 'O', 'E', '1'))
+        return true;
+      break;
+    case BCNAM('H', 'I', 'S'):
+      if (atm1 == BCATM(' ', 'C', ' ', ' ') &&
+          atm2 == BCATM(' ', 'O', ' ', ' '))
+        return true;
+      if (atm1 == BCATM(' ', 'C', 'D', '2') &&
+          atm2 == BCATM(' ', 'C', 'G', ' '))
+        return true;
+      if (atm1 == BCATM(' ', 'C', 'E', '1') &&
+          atm2 == BCATM(' ', 'N', 'D', '1'))
+        return true;
+      break;
+    case BCNAM('P', 'H', 'E'):
+    case BCNAM('T', 'Y', 'R'):
+      if (atm1 == BCATM(' ', 'C', ' ', ' ') &&
+          atm2 == BCATM(' ', 'O', ' ', ' '))
+        return true;
+      if (atm1 == BCATM(' ', 'C', 'D', '1') &&
+          atm2 == BCATM(' ', 'C', 'G', ' '))
+        return true;
+      if (atm1 == BCATM(' ', 'C', 'D', '2') &&
+          atm2 == BCATM(' ', 'C', 'E', '2'))
+        return true;
+      if (atm1 == BCATM(' ', 'C', 'E', '1') &&
+          atm2 == BCATM(' ', 'C', 'Z', ' '))
+        return true;
+      break;
+    case BCNAM('T', 'R', 'P'):
+      if (atm1 == BCATM(' ', 'C', ' ', ' ') &&
+          atm2 == BCATM(' ', 'O', ' ', ' '))
+        return true;
+      if (atm1 == BCATM(' ', 'C', 'D', '1') &&
+          atm2 == BCATM(' ', 'C', 'G', ' '))
+        return true;
+      if (atm1 == BCATM(' ', 'C', 'D', '2') &&
+          atm2 == BCATM(' ', 'C', 'E', '2'))
+        return true;
+      if (atm1 == BCATM(' ', 'C', 'E', '3') &&
+          atm2 == BCATM(' ', 'C', 'Z', '3'))
+        return true;
+      if (atm1 == BCATM(' ', 'C', 'H', '2') &&
+          atm2 == BCATM(' ', 'C', 'Z', '2'))
+        return true;
+      break;
+  }
+  return false;
+}
+
+static bool StandardPDBDoubleBond(RWMol *mol, Atom *beg, Atom *end) {
+  AtomPDBResidueInfo *bInfo = (AtomPDBResidueInfo *)beg->getMonomerInfo();
+  if (!bInfo || bInfo->getMonomerType() != AtomMonomerInfo::PDBRESIDUE)
+    return false;
+  AtomPDBResidueInfo *eInfo = (AtomPDBResidueInfo *)end->getMonomerInfo();
+  if (!eInfo || eInfo->getMonomerType() != AtomMonomerInfo::PDBRESIDUE)
+    return false;
+  if (!SamePDBResidue(bInfo, eInfo)) return false;
+  if (bInfo->getIsHeteroAtom() || eInfo->getIsHeteroAtom()) return false;
+
+  const char *ptr = bInfo->getResidueName().c_str();
+  unsigned int rescode = BCNAM(ptr[0], ptr[1], ptr[2]);
+  ptr = bInfo->getName().c_str();
+  unsigned int atm1 = BCATM(ptr[0], ptr[1], ptr[2], ptr[3]);
+  ptr = eInfo->getName().c_str();
+  unsigned int atm2 = BCATM(ptr[0], ptr[1], ptr[2], ptr[3]);
+
+  if (!StandardPDBDoubleBond(rescode, atm1, atm2)) return false;
+
+  // Check that neither end already has a double bond
+  ROMol::OBOND_ITER_PAIR bp;
+  for (bp = mol->getAtomBonds(beg); bp.first != bp.second; ++bp.first)
+    if ((*mol)[*bp.first]->getBondType() == Bond::DOUBLE) return false;
+  for (bp = mol->getAtomBonds(end); bp.first != bp.second; ++bp.first)
+    if ((*mol)[*bp.first]->getBondType() == Bond::DOUBLE) return false;
+
+  return true;
+}
+
+void StandardPDBResidueBondOrders(RWMol *mol) {
+  RWMol::BondIterator bondIt;
+  for (bondIt = mol->beginBonds(); bondIt != mol->endBonds(); ++bondIt) {
+    Bond *bond = *bondIt;
+    if (bond->getBondType() == Bond::SINGLE) {
+      Atom *beg = bond->getBeginAtom();
+      Atom *end = bond->getEndAtom();
+      if (StandardPDBDoubleBond(mol, beg, end)) bond->setBondType(Bond::DOUBLE);
+    }
+  }
+}
+
+}  // namespace RDKit
diff --git a/Code/GraphMol/ForceFieldHelpers/FFConvenience.h b/Code/GraphMol/ForceFieldHelpers/FFConvenience.h
index db04b84ba..b06b4f199 100644
--- a/Code/GraphMol/ForceFieldHelpers/FFConvenience.h
+++ b/Code/GraphMol/ForceFieldHelpers/FFConvenience.h
@@ -1,122 +1,122 @@
-//
-//  Copyright (C) 2019 Paolo Tosco
-//
-//   @@ All Rights Reserved @@
-//  This file is part of the RDKit.
-//  The contents are covered by the terms of the BSD license
-//  which is included in the file license.txt, found at the root
-//  of the RDKit source tree.
-//
-#include <RDGeneral/export.h>
-#ifndef RD_FFCONVENIENCE_H
-#define RD_FFCONVENIENCE_H
-#include <ForceField/ForceField.h>
-#include <RDGeneral/RDThreads.h>
-
-namespace RDKit {
-class ROMol;
-namespace ForceFieldsHelper {
-namespace detail {
-#ifdef RDK_THREADSAFE_SSS
-void OptimizeMoleculeConfsHelper_(ForceFields::ForceField ff, ROMol *mol,
-                                      std::vector<std::pair<int, double>> *res,
-                                      unsigned int threadIdx,
-                                      unsigned int numThreads, int maxIters) {
-  PRECONDITION(mol, "mol must not be nullptr");
-  PRECONDITION(res, "res must not be nullptr");
-  PRECONDITION(res->size() >= mol->getNumConformers(), "res->size() must be >= mol->getNumConformers()");
-  unsigned int i = 0;
-  ff.positions().resize(mol->getNumAtoms());
-  for (ROMol::ConformerIterator cit = mol->beginConformers();
-       cit != mol->endConformers(); ++cit, ++i) {
-    if (i % numThreads != threadIdx) continue;
-    for (unsigned int aidx = 0; aidx < mol->getNumAtoms(); ++aidx) {
-      ff.positions()[aidx] = &(*cit)->getAtomPos(aidx);
-    }
-    ff.initialize();
-    int needsMore = ff.minimize(maxIters);
-    double e = ff.calcEnergy();
-    (*res)[i] = std::make_pair(needsMore, e);
-  }
-}
-
-void OptimizeMoleculeConfsMT(ROMol &mol, const ForceFields::ForceField &ff,
-                               std::vector<std::pair<int, double>> &res,
-                               int numThreads, int maxIters) {
-  std::vector<std::thread> tg;
-  for (int ti = 0; ti < numThreads; ++ti) {
-    tg.emplace_back(std::thread(detail::OptimizeMoleculeConfsHelper_,
-                                ff, &mol, &res, ti, numThreads, maxIters));
-  }
-  for (auto &thread : tg) {
-    if (thread.joinable()) thread.join();
-  }
-}
-#endif
-
-void OptimizeMoleculeConfsST(ROMol &mol, ForceFields::ForceField &ff,
-                               std::vector<std::pair<int, double>> &res,
-                               int maxIters) {
-  PRECONDITION(res.size() >= mol.getNumConformers(), "res.size() must be >= mol.getNumConformers()");
-  unsigned int i = 0;
-  for (ROMol::ConformerIterator cit = mol.beginConformers();
-       cit != mol.endConformers(); ++cit, ++i) {
-    for (unsigned int aidx = 0; aidx < mol.getNumAtoms(); ++aidx) {
-      ff.positions()[aidx] = &(*cit)->getAtomPos(aidx);
-    }
-    ff.initialize();
-    int needsMore = ff.minimize(maxIters);
-    double e = ff.calcEnergy();
-    res[i] = std::make_pair(needsMore, e);
-  }
-}
-}  // end of detail namespace
-
-//! Convenience function for optimizing a molecule using a pre-generated force-field
-/*
-  \param ff         the force-field
-  \param res        vector of (needsMore,energy) pairs
-  \param maxIters   the maximum number of force-field iterations
-
-  \return a pair with:
-     first: -1 if parameters were missing, 0 if the optimization converged, 1 if
-  more iterations are required.
-     second: the energy
-*/
-std::pair<int, double> OptimizeMolecule(ForceFields::ForceField &ff, int maxIters = 1000) {
-  ff.initialize();
-  int res = ff.minimize(maxIters);
-  double e = ff.calcEnergy();
-  return std::make_pair(res, e);
-}
-
-//! Convenience function for optimizing all of a molecule's conformations using
-// a pre-generated force-field
-/*
-  \param mol        the molecule to use
-  \param ff         the force-field
-  \param res        vector of (needsMore,energy) pairs
-  \param numThreads the number of simultaneous threads to use (only has an
-                    effect if the RDKit is compiled with thread support).
-                    If set to zero, the max supported by the system will be
-  used.
-  \param maxIters   the maximum number of force-field iterations
-
-*/
-void OptimizeMoleculeConfs(ROMol &mol, ForceFields::ForceField &ff,
-                             std::vector<std::pair<int, double>> &res,
-                             int numThreads = 1, int maxIters = 1000) {
-  res.resize(mol.getNumConformers());
-  numThreads = getNumThreadsToUse(numThreads);
-  if (numThreads == 1) {
-    detail::OptimizeMoleculeConfsST(mol, ff, res, maxIters);
-  }
-#ifdef RDK_THREADSAFE_SSS
-  else {
-    detail::OptimizeMoleculeConfsMT(mol, ff, res, numThreads, maxIters);
-  }
-#endif
-}
-}  // end of namespace ForceFieldsHelper
-}  // end of namespace RDKit
-#endif
+//
+//  Copyright (C) 2019 Paolo Tosco
+//
+//   @@ All Rights Reserved @@
+//  This file is part of the RDKit.
+//  The contents are covered by the terms of the BSD license
+//  which is included in the file license.txt, found at the root
+//  of the RDKit source tree.
+//
+#include <RDGeneral/export.h>
+#ifndef RD_FFCONVENIENCE_H
+#define RD_FFCONVENIENCE_H
+#include <ForceField/ForceField.h>
+#include <RDGeneral/RDThreads.h>
+
+namespace RDKit {
+class ROMol;
+namespace ForceFieldsHelper {
+namespace detail {
+#ifdef RDK_THREADSAFE_SSS
+void OptimizeMoleculeConfsHelper_(ForceFields::ForceField ff, ROMol *mol,
+                                      std::vector<std::pair<int, double>> *res,
+                                      unsigned int threadIdx,
+                                      unsigned int numThreads, int maxIters) {
+  PRECONDITION(mol, "mol must not be nullptr");
+  PRECONDITION(res, "res must not be nullptr");
+  PRECONDITION(res->size() >= mol->getNumConformers(), "res->size() must be >= mol->getNumConformers()");
+  unsigned int i = 0;
+  ff.positions().resize(mol->getNumAtoms());
+  for (ROMol::ConformerIterator cit = mol->beginConformers();
+       cit != mol->endConformers(); ++cit, ++i) {
+    if (i % numThreads != threadIdx) continue;
+    for (unsigned int aidx = 0; aidx < mol->getNumAtoms(); ++aidx) {
+      ff.positions()[aidx] = &(*cit)->getAtomPos(aidx);
+    }
+    ff.initialize();
+    int needsMore = ff.minimize(maxIters);
+    double e = ff.calcEnergy();
+    (*res)[i] = std::make_pair(needsMore, e);
+  }
+}
+
+void OptimizeMoleculeConfsMT(ROMol &mol, const ForceFields::ForceField &ff,
+                               std::vector<std::pair<int, double>> &res,
+                               int numThreads, int maxIters) {
+  std::vector<std::thread> tg;
+  for (int ti = 0; ti < numThreads; ++ti) {
+    tg.emplace_back(std::thread(detail::OptimizeMoleculeConfsHelper_,
+                                ff, &mol, &res, ti, numThreads, maxIters));
+  }
+  for (auto &thread : tg) {
+    if (thread.joinable()) thread.join();
+  }
+}
+#endif
+
+void OptimizeMoleculeConfsST(ROMol &mol, ForceFields::ForceField &ff,
+                               std::vector<std::pair<int, double>> &res,
+                               int maxIters) {
+  PRECONDITION(res.size() >= mol.getNumConformers(), "res.size() must be >= mol.getNumConformers()");
+  unsigned int i = 0;
+  for (ROMol::ConformerIterator cit = mol.beginConformers();
+       cit != mol.endConformers(); ++cit, ++i) {
+    for (unsigned int aidx = 0; aidx < mol.getNumAtoms(); ++aidx) {
+      ff.positions()[aidx] = &(*cit)->getAtomPos(aidx);
+    }
+    ff.initialize();
+    int needsMore = ff.minimize(maxIters);
+    double e = ff.calcEnergy();
+    res[i] = std::make_pair(needsMore, e);
+  }
+}
+}  // end of detail namespace
+
+//! Convenience function for optimizing a molecule using a pre-generated force-field
+/*
+  \param ff         the force-field
+  \param res        vector of (needsMore,energy) pairs
+  \param maxIters   the maximum number of force-field iterations
+
+  \return a pair with:
+     first: -1 if parameters were missing, 0 if the optimization converged, 1 if
+  more iterations are required.
+     second: the energy
+*/
+std::pair<int, double> OptimizeMolecule(ForceFields::ForceField &ff, int maxIters = 1000) {
+  ff.initialize();
+  int res = ff.minimize(maxIters);
+  double e = ff.calcEnergy();
+  return std::make_pair(res, e);
+}
+
+//! Convenience function for optimizing all of a molecule's conformations using
+// a pre-generated force-field
+/*
+  \param mol        the molecule to use
+  \param ff         the force-field
+  \param res        vector of (needsMore,energy) pairs
+  \param numThreads the number of simultaneous threads to use (only has an
+                    effect if the RDKit is compiled with thread support).
+                    If set to zero, the max supported by the system will be
+  used.
+  \param maxIters   the maximum number of force-field iterations
+
+*/
+void OptimizeMoleculeConfs(ROMol &mol, ForceFields::ForceField &ff,
+                             std::vector<std::pair<int, double>> &res,
+                             int numThreads = 1, int maxIters = 1000) {
+  res.resize(mol.getNumConformers());
+  numThreads = getNumThreadsToUse(numThreads);
+  if (numThreads == 1) {
+    detail::OptimizeMoleculeConfsST(mol, ff, res, maxIters);
+  }
+#ifdef RDK_THREADSAFE_SSS
+  else {
+    detail::OptimizeMoleculeConfsMT(mol, ff, res, numThreads, maxIters);
+  }
+#endif
+}
+}  // end of namespace ForceFieldsHelper
+}  // end of namespace RDKit
+#endif
diff --git a/Code/GraphMol/Wrap/SubstanceGroup.cpp b/Code/GraphMol/Wrap/SubstanceGroup.cpp
index b7ffafc55..a72f18bfb 100644
--- a/Code/GraphMol/Wrap/SubstanceGroup.cpp
+++ b/Code/GraphMol/Wrap/SubstanceGroup.cpp
@@ -1,117 +1,117 @@
-//
-//  Copyright (C) 2019 Greg Landrum
-//
-//   @@ All Rights Reserved @@
-//  This file is part of the RDKit.
-//  The contents are covered by the terms of the BSD license
-//  which is included in the file license.txt, found at the root
-//  of the RDKit source tree.
-//
-
-#define NO_IMPORT_ARRAY
-#include <boost/python.hpp>
-#include <boost/python/suite/indexing/vector_indexing_suite.hpp>
-#include <string>
-
-// ours
-#include <GraphMol/RDKitBase.h>
-#include <GraphMol/SubstanceGroup.h>
-#include "props.hpp"
-
-namespace python = boost::python;
-
-namespace RDKit {
-
-namespace {
-std::vector<SubstanceGroup> getMolSubstanceGroups(ROMol &mol) {
-  return getSubstanceGroups(mol);
-}
-void clearMolSubstanceGroups(ROMol &mol) {
-  std::vector<SubstanceGroup> &sgs = getSubstanceGroups(mol);
-  sgs.clear();
-}
-}  // namespace
-
-std::string sGroupClassDoc =
-    "A collection of atoms and bonds with associated properties\n";
-
-struct sgroup_wrap {
-  static void wrap() {
-    // register the vector_indexing_suite for SubstanceGroups
-    // if it hasn't already been done.
-    // logic from https://stackoverflow.com/a/13017303
-    boost::python::type_info info =
-        boost::python::type_id<std::vector<RDKit::SubstanceGroup>>();
-    const boost::python::converter::registration *reg =
-        boost::python::converter::registry::query(info);
-    if (reg == NULL || (*reg).m_to_python == NULL) {
-      python::class_<std::vector<RDKit::SubstanceGroup>>("SubstanceGroup_VECT")
-          .def(python::vector_indexing_suite<
-               std::vector<RDKit::SubstanceGroup>>());
-    }
-
-    python::class_<SubstanceGroup, boost::shared_ptr<SubstanceGroup>>(
-        "SubstanceGroup", sGroupClassDoc.c_str(), python::no_init)
-        .def("GetOwningMol", &SubstanceGroup::getOwningMol,
-             "returns the molecule owning this SubstanceGroup",
-             python::return_internal_reference<>())
-        .def("GetIndexInMol", &SubstanceGroup::getIndexInMol,
-             "returns the index of this SubstanceGroup in the owning "
-             "molecule's list.")
-        .def(
-            "GetAtoms", &SubstanceGroup::getAtoms,
-            "returns a list of the indices of the atoms in this SubstanceGroup",
-            python::return_value_policy<python::copy_const_reference>())
-        .def("GetParentAtoms", &SubstanceGroup::getParentAtoms,
-             "returns a list of the indices of the parent atoms in this "
-             "SubstanceGroup",
-             python::return_value_policy<python::copy_const_reference>())
-        .def(
-            "GetBonds", &SubstanceGroup::getBonds,
-            "returns a list of the indices of the bonds in this SubstanceGroup",
-            python::return_value_policy<python::copy_const_reference>())
-        .def("HasProp",
-             (bool (RDProps::*)(const std::string &) const) &
-                 SubstanceGroup::hasProp,
-             "returns whether or not a particular property exists")
-        .def("GetProp",
-             (std::string(RDProps::*)(const std::string &) const) &
-                 SubstanceGroup::getProp<std::string>,
-             "returns the value of a particular property")
-        .def("GetIntProp",
-             (int (RDProps::*)(const std::string &) const) &
-                 SubstanceGroup::getProp<int>,
-             "returns the value of a particular property")
-        .def("GetUnsignedProp",
-             (unsigned int (RDProps::*)(const std::string &) const) &
-                 SubstanceGroup::getProp<unsigned int>,
-             "returns the value of a particular property")
-        .def("GetDoubleProp",
-             (double (RDProps::*)(const std::string &) const) &
-                 SubstanceGroup::getProp<double>,
-             "returns the value of a particular property")
-        .def("GetBoolProp",
-             (bool (RDProps::*)(const std::string &) const) &
-                 SubstanceGroup::getProp<bool>,
-             "returns the value of a particular property")
-        .def("GetPropNames", &SubstanceGroup::getPropList,
-             (python::arg("self"), python::arg("includePrivate") = false,
-              python::arg("includeComputed") = false),
-             "Returns a list of the properties set on the SubstanceGroup.\n\n")
-        .def("GetPropsAsDict", GetPropsAsDict<SubstanceGroup>,
-             (python::arg("self"), python::arg("includePrivate") = true,
-              python::arg("includeComputed") = true),
-             "Returns a dictionary of the properties set on the "
-             "SubstanceGroup.\n"
-             " n.b. some properties cannot be converted to python types.\n");
-    python::def("GetMolSubstanceGroups", &getMolSubstanceGroups,
-                "returns the SubstanceGroups for a molecule (if any)",
-                python::with_custodian_and_ward_postcall<0, 1>());
-    python::def("ClearMolSubstanceGroups", &clearMolSubstanceGroups,
-                "removes all SubstanceGroups from a molecule (if any)");
-    // FIX: needs something tying the lifetime to the mol
-  }
-};
-}  // namespace RDKit
-
-void wrap_sgroup() { RDKit::sgroup_wrap::wrap(); }
+//
+//  Copyright (C) 2019 Greg Landrum
+//
+//   @@ All Rights Reserved @@
+//  This file is part of the RDKit.
+//  The contents are covered by the terms of the BSD license
+//  which is included in the file license.txt, found at the root
+//  of the RDKit source tree.
+//
+
+#define NO_IMPORT_ARRAY
+#include <boost/python.hpp>
+#include <boost/python/suite/indexing/vector_indexing_suite.hpp>
+#include <string>
+
+// ours
+#include <GraphMol/RDKitBase.h>
+#include <GraphMol/SubstanceGroup.h>
+#include "props.hpp"
+
+namespace python = boost::python;
+
+namespace RDKit {
+
+namespace {
+std::vector<SubstanceGroup> getMolSubstanceGroups(ROMol &mol) {
+  return getSubstanceGroups(mol);
+}
+void clearMolSubstanceGroups(ROMol &mol) {
+  std::vector<SubstanceGroup> &sgs = getSubstanceGroups(mol);
+  sgs.clear();
+}
+}  // namespace
+
+std::string sGroupClassDoc =
+    "A collection of atoms and bonds with associated properties\n";
+
+struct sgroup_wrap {
+  static void wrap() {
+    // register the vector_indexing_suite for SubstanceGroups
+    // if it hasn't already been done.
+    // logic from https://stackoverflow.com/a/13017303
+    boost::python::type_info info =
+        boost::python::type_id<std::vector<RDKit::SubstanceGroup>>();
+    const boost::python::converter::registration *reg =
+        boost::python::converter::registry::query(info);
+    if (reg == NULL || (*reg).m_to_python == NULL) {
+      python::class_<std::vector<RDKit::SubstanceGroup>>("SubstanceGroup_VECT")
+          .def(python::vector_indexing_suite<
+               std::vector<RDKit::SubstanceGroup>>());
+    }
+
+    python::class_<SubstanceGroup, boost::shared_ptr<SubstanceGroup>>(
+        "SubstanceGroup", sGroupClassDoc.c_str(), python::no_init)
+        .def("GetOwningMol", &SubstanceGroup::getOwningMol,
+             "returns the molecule owning this SubstanceGroup",
+             python::return_internal_reference<>())
+        .def("GetIndexInMol", &SubstanceGroup::getIndexInMol,
+             "returns the index of this SubstanceGroup in the owning "
+             "molecule's list.")
+        .def(
+            "GetAtoms", &SubstanceGroup::getAtoms,
+            "returns a list of the indices of the atoms in this SubstanceGroup",
+            python::return_value_policy<python::copy_const_reference>())
+        .def("GetParentAtoms", &SubstanceGroup::getParentAtoms,
+             "returns a list of the indices of the parent atoms in this "
+             "SubstanceGroup",
+             python::return_value_policy<python::copy_const_reference>())
+        .def(
+            "GetBonds", &SubstanceGroup::getBonds,
+            "returns a list of the indices of the bonds in this SubstanceGroup",
+            python::return_value_policy<python::copy_const_reference>())
+        .def("HasProp",
+             (bool (RDProps::*)(const std::string &) const) &
+                 SubstanceGroup::hasProp,
+             "returns whether or not a particular property exists")
+        .def("GetProp",
+             (std::string(RDProps::*)(const std::string &) const) &
+                 SubstanceGroup::getProp<std::string>,
+             "returns the value of a particular property")
+        .def("GetIntProp",
+             (int (RDProps::*)(const std::string &) const) &
+                 SubstanceGroup::getProp<int>,
+             "returns the value of a particular property")
+        .def("GetUnsignedProp",
+             (unsigned int (RDProps::*)(const std::string &) const) &
+                 SubstanceGroup::getProp<unsigned int>,
+             "returns the value of a particular property")
+        .def("GetDoubleProp",
+             (double (RDProps::*)(const std::string &) const) &
+                 SubstanceGroup::getProp<double>,
+             "returns the value of a particular property")
+        .def("GetBoolProp",
+             (bool (RDProps::*)(const std::string &) const) &
+                 SubstanceGroup::getProp<bool>,
+             "returns the value of a particular property")
+        .def("GetPropNames", &SubstanceGroup::getPropList,
+             (python::arg("self"), python::arg("includePrivate") = false,
+              python::arg("includeComputed") = false),
+             "Returns a list of the properties set on the SubstanceGroup.\n\n")
+        .def("GetPropsAsDict", GetPropsAsDict<SubstanceGroup>,
+             (python::arg("self"), python::arg("includePrivate") = true,
+              python::arg("includeComputed") = true),
+             "Returns a dictionary of the properties set on the "
+             "SubstanceGroup.\n"
+             " n.b. some properties cannot be converted to python types.\n");
+    python::def("GetMolSubstanceGroups", &getMolSubstanceGroups,
+                "returns the SubstanceGroups for a molecule (if any)",
+                python::with_custodian_and_ward_postcall<0, 1>());
+    python::def("ClearMolSubstanceGroups", &clearMolSubstanceGroups,
+                "removes all SubstanceGroups from a molecule (if any)");
+    // FIX: needs something tying the lifetime to the mol
+  }
+};
+}  // namespace RDKit
+
+void wrap_sgroup() { RDKit::sgroup_wrap::wrap(); }
diff --git a/Contrib/PBF/PBFRDKit.cpp b/Contrib/PBF/PBFRDKit.cpp
index b9a7fab7a..7e2965740 100644
--- a/Contrib/PBF/PBFRDKit.cpp
+++ b/Contrib/PBF/PBFRDKit.cpp
@@ -1,156 +1,156 @@
-//
-//  Copyright (c) 2012, Institue of Cancer Research.
-//  All rights reserved.
-//
-// Redistribution and use in source and binary forms, with or without
-//modification, are permitted provided that the following conditions are
-// met:
-//
-//     * Redistributions of source code must retain the above copyright
-//       notice, this list of conditions and the following disclaimer.
-//     * Redistributions in binary form must reproduce the above
-//       copyright notice, this list of conditions and the following
-//       disclaimer in the documentation and/or other materials provided
-//       with the distribution.
-//     * Neither the name of Institue of Cancer Research.
-//       nor the names of its contributors may be used to endorse or promote
-//       products derived from this software without specific prior written permission.
-//
-// THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS
-// "AS IS" AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT
-// LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR
-// A PARTICULAR PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT
-// OWNER OR CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL,
-// SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT
-// LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE,
-// DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY
-// THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT
-// (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE
-// OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
-//
-// For more information on the Plane of Best Fit please see http://pubs.acs.org/doi/abs/10.1021/ci300293f
-//
-//  If this code has been useful to you, please include the reference
-//  in any work which has made use of it:
-
-//  Plane of Best Fit: A Novel Method to Characterize the Three-Dimensionality of Molecules, Nicholas C. Firth, Nathan Brown, and Julian Blagg, Journal of Chemical Information and Modeling 2012 52 (10), 2516-2525
-
-//
-//
-// Created by Nicholas Firth, November 2011
-// Modified by Greg Landrum for inclusion in the RDKit distribution November 2012
-//
-
-#include "PBFRDKit.h"
-#include <Numerics/Matrix.h>
-#include <Numerics/SquareMatrix.h>
-#include <Numerics/SymmMatrix.h>
-#include <boost/foreach.hpp>
-
-#include <Eigen/Dense>
-using namespace RDKit;
-
-void getSmallestEigenVector(double fSumXX,double fSumXY,double fSumXZ,
-                            double fSumYY,double fSumYZ,double fSumZZ,
-                            double &x,double &y, double &z);
-
-double distanceFromAPlane(const RDGeom::Point3D &pt,const std::vector<double> &plane, double denom){
-  double numer=0.0;
-  numer = std::fabs(pt.x*plane[0]+pt.y*plane[1]+pt.z*plane[2]+plane[3]);
-
-  return numer/denom;
-}
-
-bool getBestFitPlane(const std::vector<RDGeom::Point3D> &points,
-                     std::vector<double> &plane,
-                     const std::vector<double> *weights) {
-  PRECONDITION((!weights || weights->size()>=points.size()),"bad weights vector");
-  RDGeom::Point3D origin(0,0,0);
-  double wSum=0.0;
-
-  for(unsigned int i=0;i<points.size();++i){
-    if(weights){
-      double w=(*weights)[i];
-      wSum+=w;
-      origin+=points[i]*w;
-    } else {
-      wSum+=1;
-      origin+=points[i];
-    }
-  }
-  origin /= wSum;
-
-  double sumXX=0,sumXY=0,sumXZ=0,sumYY=0,sumYZ=0,sumZZ=0;
-  for(unsigned int i=0;i<points.size();++i){
-    RDGeom::Point3D delta=points[i]-origin;
-    if(weights){
-      double w=(*weights)[i];
-      delta *= w;
-    }
-    sumXX += delta.x*delta.x;
-    sumXY += delta.x*delta.y;
-    sumXZ += delta.x*delta.z;
-    sumYY += delta.y*delta.y;
-    sumYZ += delta.y*delta.z;
-    sumZZ += delta.z*delta.z;
-  }
-  sumXX/=wSum;
-  sumXY/=wSum;
-  sumXZ/=wSum;
-  sumYY/=wSum;
-  sumYZ/=wSum;
-  sumZZ/=wSum;
-
-  Eigen::Matrix3d mat;
-  mat << sumXX, sumXY, sumXZ,
-    sumXY, sumYY, sumYZ,
-    sumXZ, sumYZ, sumZZ;
-  Eigen::SelfAdjointEigenSolver<Eigen::Matrix3d> eigensolver(mat);
-  if(eigensolver.info()!=Eigen::Success){
-    BOOST_LOG(rdErrorLog)<<"eigenvalue calculation did not converge"<<std::endl;
-    return 0.0;
-  }
-  RDGeom::Point3D normal;
-  normal.x=eigensolver.eigenvectors()(0,0);
-  normal.y=eigensolver.eigenvectors()(1,0);
-  normal.z=eigensolver.eigenvectors()(2,0);
-
-  plane[0] = normal.x;
-  plane[1] = normal.y;
-  plane[2] = normal.z;
-  plane[3] = -1*normal.dotProduct(origin);
-  
-}
-
-double PBFRD(ROMol& mol,int confId){
-  PRECONDITION(mol.getNumConformers()>=1,"molecule has no conformers")
-  int numAtoms = mol.getNumAtoms();
-  if(numAtoms<4) return 0;
-
-  const Conformer &conf = mol.getConformer(confId);
-  if(!conf.is3D()) return 0 ;
-
-  std::vector<RDGeom::Point3D> points;
-  points.reserve(numAtoms);
-  for(unsigned int i=0; i<numAtoms; ++i){
-    points.push_back(conf.getAtomPos(i));
-  } 
-    
-  std::vector<double> plane(4);
-  getBestFitPlane(points,plane,0);
-
-  double denom=0.0;
-  for(unsigned int i=0; i<3; ++i){
-    denom += plane[i]*plane[i];
-  }
-  denom = pow(denom,0.5);
-    
-  double res=0.0;
-  for(unsigned int i=0; i<numAtoms; ++i){
-    res+= distanceFromAPlane(points[i], plane, denom);
-  }
-  res /= numAtoms;
-
-  return res;
-}
-
+//
+//  Copyright (c) 2012, Institue of Cancer Research.
+//  All rights reserved.
+//
+// Redistribution and use in source and binary forms, with or without
+//modification, are permitted provided that the following conditions are
+// met:
+//
+//     * Redistributions of source code must retain the above copyright
+//       notice, this list of conditions and the following disclaimer.
+//     * Redistributions in binary form must reproduce the above
+//       copyright notice, this list of conditions and the following
+//       disclaimer in the documentation and/or other materials provided
+//       with the distribution.
+//     * Neither the name of Institue of Cancer Research.
+//       nor the names of its contributors may be used to endorse or promote
+//       products derived from this software without specific prior written permission.
+//
+// THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS
+// "AS IS" AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT
+// LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR
+// A PARTICULAR PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT
+// OWNER OR CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL,
+// SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT
+// LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE,
+// DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY
+// THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT
+// (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE
+// OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
+//
+// For more information on the Plane of Best Fit please see http://pubs.acs.org/doi/abs/10.1021/ci300293f
+//
+//  If this code has been useful to you, please include the reference
+//  in any work which has made use of it:
+
+//  Plane of Best Fit: A Novel Method to Characterize the Three-Dimensionality of Molecules, Nicholas C. Firth, Nathan Brown, and Julian Blagg, Journal of Chemical Information and Modeling 2012 52 (10), 2516-2525
+
+//
+//
+// Created by Nicholas Firth, November 2011
+// Modified by Greg Landrum for inclusion in the RDKit distribution November 2012
+//
+
+#include "PBFRDKit.h"
+#include <Numerics/Matrix.h>
+#include <Numerics/SquareMatrix.h>
+#include <Numerics/SymmMatrix.h>
+#include <boost/foreach.hpp>
+
+#include <Eigen/Dense>
+using namespace RDKit;
+
+void getSmallestEigenVector(double fSumXX,double fSumXY,double fSumXZ,
+                            double fSumYY,double fSumYZ,double fSumZZ,
+                            double &x,double &y, double &z);
+
+double distanceFromAPlane(const RDGeom::Point3D &pt,const std::vector<double> &plane, double denom){
+  double numer=0.0;
+  numer = std::fabs(pt.x*plane[0]+pt.y*plane[1]+pt.z*plane[2]+plane[3]);
+
+  return numer/denom;
+}
+
+bool getBestFitPlane(const std::vector<RDGeom::Point3D> &points,
+                     std::vector<double> &plane,
+                     const std::vector<double> *weights) {
+  PRECONDITION((!weights || weights->size()>=points.size()),"bad weights vector");
+  RDGeom::Point3D origin(0,0,0);
+  double wSum=0.0;
+
+  for(unsigned int i=0;i<points.size();++i){
+    if(weights){
+      double w=(*weights)[i];
+      wSum+=w;
+      origin+=points[i]*w;
+    } else {
+      wSum+=1;
+      origin+=points[i];
+    }
+  }
+  origin /= wSum;
+
+  double sumXX=0,sumXY=0,sumXZ=0,sumYY=0,sumYZ=0,sumZZ=0;
+  for(unsigned int i=0;i<points.size();++i){
+    RDGeom::Point3D delta=points[i]-origin;
+    if(weights){
+      double w=(*weights)[i];
+      delta *= w;
+    }
+    sumXX += delta.x*delta.x;
+    sumXY += delta.x*delta.y;
+    sumXZ += delta.x*delta.z;
+    sumYY += delta.y*delta.y;
+    sumYZ += delta.y*delta.z;
+    sumZZ += delta.z*delta.z;
+  }
+  sumXX/=wSum;
+  sumXY/=wSum;
+  sumXZ/=wSum;
+  sumYY/=wSum;
+  sumYZ/=wSum;
+  sumZZ/=wSum;
+
+  Eigen::Matrix3d mat;
+  mat << sumXX, sumXY, sumXZ,
+    sumXY, sumYY, sumYZ,
+    sumXZ, sumYZ, sumZZ;
+  Eigen::SelfAdjointEigenSolver<Eigen::Matrix3d> eigensolver(mat);
+  if(eigensolver.info()!=Eigen::Success){
+    BOOST_LOG(rdErrorLog)<<"eigenvalue calculation did not converge"<<std::endl;
+    return 0.0;
+  }
+  RDGeom::Point3D normal;
+  normal.x=eigensolver.eigenvectors()(0,0);
+  normal.y=eigensolver.eigenvectors()(1,0);
+  normal.z=eigensolver.eigenvectors()(2,0);
+
+  plane[0] = normal.x;
+  plane[1] = normal.y;
+  plane[2] = normal.z;
+  plane[3] = -1*normal.dotProduct(origin);
+  
+}
+
+double PBFRD(ROMol& mol,int confId){
+  PRECONDITION(mol.getNumConformers()>=1,"molecule has no conformers")
+  int numAtoms = mol.getNumAtoms();
+  if(numAtoms<4) return 0;
+
+  const Conformer &conf = mol.getConformer(confId);
+  if(!conf.is3D()) return 0 ;
+
+  std::vector<RDGeom::Point3D> points;
+  points.reserve(numAtoms);
+  for(unsigned int i=0; i<numAtoms; ++i){
+    points.push_back(conf.getAtomPos(i));
+  } 
+    
+  std::vector<double> plane(4);
+  getBestFitPlane(points,plane,0);
+
+  double denom=0.0;
+  for(unsigned int i=0; i<3; ++i){
+    denom += plane[i]*plane[i];
+  }
+  denom = pow(denom,0.5);
+    
+  double res=0.0;
+  for(unsigned int i=0; i<numAtoms; ++i){
+    res+= distanceFromAPlane(points[i], plane, denom);
+  }
+  res /= numAtoms;
+
+  return res;
+}
+
diff --git a/Contrib/PBF/PBFRDKit.h b/Contrib/PBF/PBFRDKit.h
index e49a3abc6..ab0a36e75 100644
--- a/Contrib/PBF/PBFRDKit.h
+++ b/Contrib/PBF/PBFRDKit.h
@@ -1,59 +1,59 @@
-//
-//  Copyright (c) 2012, Institue of Cancer Research.
-//  All rights reserved.
-//
-// Redistribution and use in source and binary forms, with or without
-//modification, are permitted provided that the following conditions are
-// met:
-//
-//     * Redistributions of source code must retain the above copyright
-//       notice, this list of conditions and the following disclaimer.
-//     * Redistributions in binary form must reproduce the above
-//       copyright notice, this list of conditions and the following
-//       disclaimer in the documentation and/or other materials provided
-//       with the distribution.
-//     * Neither the name of Institue of Cancer Research.
-//       nor the names of its contributors may be used to endorse or promote
-//       products derived from this software without specific prior written permission.
-//
-// THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS
-// "AS IS" AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT
-// LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR
-// A PARTICULAR PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT
-// OWNER OR CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL,
-// SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT
-// LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE,
-// DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY
-// THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT
-// (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE
-// OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
-//
-// For more information on the Plane of Best Fit please see http://pubs.acs.org/doi/abs/10.1021/ci300293f
-//
-//  If this code has been useful to you, please include the reference
-//  in any work which has made use of it:
-
-//  Plane of Best Fit: A Novel Method to Characterize the Three-Dimensionality of Molecules, Nicholas C. Firth, Nathan Brown, and Julian Blagg, Journal of Chemical Information and Modeling 2012 52 (10), 2516-2525
-
-//
-//
-// Created by Nicholas Firth, November 2011
-
-
-
-#ifndef _PBFRDKit_h
-#define _PBFRDKit_h
-
-
-#include <iostream>
-
-#include <GraphMol/RDKitBase.h>
-#include <GraphMol/MolOps.h>
-#include <GraphMol/Conformer.h>
-#include <math.h>
-
-using namespace RDKit;
-
-double PBFRD(ROMol&,int confId=-1);
-
-#endif
+//
+//  Copyright (c) 2012, Institue of Cancer Research.
+//  All rights reserved.
+//
+// Redistribution and use in source and binary forms, with or without
+//modification, are permitted provided that the following conditions are
+// met:
+//
+//     * Redistributions of source code must retain the above copyright
+//       notice, this list of conditions and the following disclaimer.
+//     * Redistributions in binary form must reproduce the above
+//       copyright notice, this list of conditions and the following
+//       disclaimer in the documentation and/or other materials provided
+//       with the distribution.
+//     * Neither the name of Institue of Cancer Research.
+//       nor the names of its contributors may be used to endorse or promote
+//       products derived from this software without specific prior written permission.
+//
+// THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS
+// "AS IS" AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT
+// LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR
+// A PARTICULAR PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT
+// OWNER OR CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL,
+// SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT
+// LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE,
+// DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY
+// THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT
+// (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE
+// OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
+//
+// For more information on the Plane of Best Fit please see http://pubs.acs.org/doi/abs/10.1021/ci300293f
+//
+//  If this code has been useful to you, please include the reference
+//  in any work which has made use of it:
+
+//  Plane of Best Fit: A Novel Method to Characterize the Three-Dimensionality of Molecules, Nicholas C. Firth, Nathan Brown, and Julian Blagg, Journal of Chemical Information and Modeling 2012 52 (10), 2516-2525
+
+//
+//
+// Created by Nicholas Firth, November 2011
+
+
+
+#ifndef _PBFRDKit_h
+#define _PBFRDKit_h
+
+
+#include <iostream>
+
+#include <GraphMol/RDKitBase.h>
+#include <GraphMol/MolOps.h>
+#include <GraphMol/Conformer.h>
+#include <math.h>
+
+using namespace RDKit;
+
+double PBFRD(ROMol&,int confId=-1);
+
+#endif
diff --git a/build_support/pkg_version.py b/build_support/pkg_version.py
index b3906030c..121ee7eaf 100644
--- a/build_support/pkg_version.py
+++ b/build_support/pkg_version.py
@@ -1,72 +1,72 @@
-from __future__ import print_function
-import os
-import re
-from datetime import datetime
-from setuptools import setup
-
-pkg_version = ''
-src_dir = os.path.realpath(__file__)
-have_src_dir = os.path.isfile(src_dir)
-i = 0
-while (i < 2 and have_src_dir):
-  i += 1
-  src_dir = os.path.dirname(src_dir)
-  have_src_dir = os.path.isdir(src_dir)
-if (not have_src_dir):
-  raise OSError('Could not find SRC_DIR, got: ' + str(src_dir))
-# parse root CMakeLists.txt and Code/cmake/Modules/RDKitUtils.cmake
-root_cmakelists_path = os.path.join(src_dir, 'CMakeLists.txt')
-rdkitutils_path = os.path.join(src_dir, 'Code', 'cmake',
-  'Modules', 'RDKitUtils.cmake')
-
-var_dict = {}
-for file in (root_cmakelists_path, rdkitutils_path):
-  with open(file, 'rt') as hnd:
-    # vars we want to read
-    var_set = set(['RDKit_Year', 'RDKit_Month', 'RDKit_Revision',
-      'RDKit_ABI', 'RDKit_RELEASENAME'])
-    line = hnd.readline()
-    while (line):
-      # is this an uncommented set command?
-      m = re.match('^\s*set\s*\((\w+)\s*\"(.*)\"\s*\)',
-        line, re.IGNORECASE)
-      # if it is
-      if (m is not None):
-        # extract the var name
-        var_name = m.group(1)
-        if (var_name in var_set):
-          # if the var name is in the vars we want to read
-          var_value = m.group(2)
-          keepLooping = True
-          while (keepLooping):
-            # recursively replace variables we already found
-            m = re.match('^.*\${(\w+)}', var_value)
-            keepLooping = (m is not None)
-            if (keepLooping):
-              v = var_dict.get(m.group(1))
-              # if the variable is not defined, remove
-              # the preceding dot
-              eat_dot = 0
-              if (v is None):
-                v = ''
-                eat_dot = 1
-              # replace variable name with its value
-              s = m.start(1) - (2 + eat_dot)
-              e = m.end(1) + 1
-              var_value = var_value[:s] + v + var_value[e:]
-          # assign variable value and keep parsing
-          var_dict[var_name] = var_value
-      line = hnd.readline()
-d = datetime.today().strftime('%Y%m%d')
-rdkitVersion = var_dict.get('RDKit_RELEASENAME')
-if (rdkitVersion is not None):
-  if rdkitVersion.endswith('.dev1'):
-    pkg_version = rdkitVersion[:-1] + d
-  else:
-    pkg_version = rdkitVersion
-else:
-  # if extracting rdkitVersion somehow failed, use the date
-    pkg_version = d
-
-print('rdkitVersion:', pkg_version)
-setup(rdkitVersion = pkg_version)
+from __future__ import print_function
+import os
+import re
+from datetime import datetime
+from setuptools import setup
+
+pkg_version = ''
+src_dir = os.path.realpath(__file__)
+have_src_dir = os.path.isfile(src_dir)
+i = 0
+while (i < 2 and have_src_dir):
+  i += 1
+  src_dir = os.path.dirname(src_dir)
+  have_src_dir = os.path.isdir(src_dir)
+if (not have_src_dir):
+  raise OSError('Could not find SRC_DIR, got: ' + str(src_dir))
+# parse root CMakeLists.txt and Code/cmake/Modules/RDKitUtils.cmake
+root_cmakelists_path = os.path.join(src_dir, 'CMakeLists.txt')
+rdkitutils_path = os.path.join(src_dir, 'Code', 'cmake',
+  'Modules', 'RDKitUtils.cmake')
+
+var_dict = {}
+for file in (root_cmakelists_path, rdkitutils_path):
+  with open(file, 'rt') as hnd:
+    # vars we want to read
+    var_set = set(['RDKit_Year', 'RDKit_Month', 'RDKit_Revision',
+      'RDKit_ABI', 'RDKit_RELEASENAME'])
+    line = hnd.readline()
+    while (line):
+      # is this an uncommented set command?
+      m = re.match('^\s*set\s*\((\w+)\s*\"(.*)\"\s*\)',
+        line, re.IGNORECASE)
+      # if it is
+      if (m is not None):
+        # extract the var name
+        var_name = m.group(1)
+        if (var_name in var_set):
+          # if the var name is in the vars we want to read
+          var_value = m.group(2)
+          keepLooping = True
+          while (keepLooping):
+            # recursively replace variables we already found
+            m = re.match('^.*\${(\w+)}', var_value)
+            keepLooping = (m is not None)
+            if (keepLooping):
+              v = var_dict.get(m.group(1))
+              # if the variable is not defined, remove
+              # the preceding dot
+              eat_dot = 0
+              if (v is None):
+                v = ''
+                eat_dot = 1
+              # replace variable name with its value
+              s = m.start(1) - (2 + eat_dot)
+              e = m.end(1) + 1
+              var_value = var_value[:s] + v + var_value[e:]
+          # assign variable value and keep parsing
+          var_dict[var_name] = var_value
+      line = hnd.readline()
+d = datetime.today().strftime('%Y%m%d')
+rdkitVersion = var_dict.get('RDKit_RELEASENAME')
+if (rdkitVersion is not None):
+  if rdkitVersion.endswith('.dev1'):
+    pkg_version = rdkitVersion[:-1] + d
+  else:
+    pkg_version = rdkitVersion
+else:
+  # if extracting rdkitVersion somehow failed, use the date
+    pkg_version = d
+
+print('rdkitVersion:', pkg_version)
+setup(rdkitVersion = pkg_version)