@@ -267,10 +267,10 @@ void contourAndDrawGaussians(MolDraw2D &drawer,
       maxP.y = std::max(loc.y, maxP.y);
     }
     Point2D dims = maxP - minP;
-    minP.x -= drawer.drawOptions().padding * dims.x;
-    minP.y -= drawer.drawOptions().padding * dims.y;
-    maxP.x += drawer.drawOptions().padding * dims.x;
-    maxP.y += drawer.drawOptions().padding * dims.y;
+    minP.x -= fabs(drawer.drawOptions().padding) * dims.x;
+    minP.y -= fabs(drawer.drawOptions().padding) * dims.y;
+    maxP.x += fabs(drawer.drawOptions().padding) * dims.x;
+    maxP.y += fabs(drawer.drawOptions().padding) * dims.y;
 
     if (params.extraGridPadding > 0) {
       Point2D p1(0, 0), p2(params.extraGridPadding, 0);
//
//  Copyright (C) 2016-2019 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.
//
#include <GraphMol/MolDraw2D/MolDraw2D.h>
#include <GraphMol/MolDraw2D/MolDraw2DUtils.h>

#include <GraphMol/RWMol.h>
#include <GraphMol/MolOps.h>
#include <GraphMol/Depictor/RDDepictor.h>
#include <GraphMol/FileParsers/MolFileStereochem.h>

#include <RDGeneral/BoostStartInclude.h>
#include <boost/foreach.hpp>
#include <boost/lexical_cast.hpp>
#include <boost/property_tree/ptree.hpp>
#include <boost/property_tree/json_parser.hpp>
#include <RDGeneral/BoostEndInclude.h>
#include <limits>
#include <cmath>
#include <Numerics/Conrec.h>

namespace RDKit {
namespace MolDraw2DUtils {

namespace {
bool isAtomCandForChiralH(const RWMol &mol, const Atom *atom) {
  // conditions for needing a chiral H:
  //   - stereochem specified
  //   - in at least two rings
  if ((!mol.getRingInfo()->isInitialized() ||
       mol.getRingInfo()->numAtomRings(atom->getIdx()) > 1) &&
      (atom->getChiralTag() == Atom::CHI_TETRAHEDRAL_CCW ||
       atom->getChiralTag() == Atom::CHI_TETRAHEDRAL_CW)) {
    return true;
  }
  return false;
}
}  // end of anonymous namespace

void prepareMolForDrawing(RWMol &mol, bool kekulize, bool addChiralHs,
                          bool wedgeBonds, bool forceCoords) {
  if (kekulize) {
    MolOps::Kekulize(mol, false);  // kekulize, but keep the aromatic flags!
  }
  if (addChiralHs) {
    std::vector<unsigned int> chiralAts;
    for (RWMol::AtomIterator atIt = mol.beginAtoms(); atIt != mol.endAtoms();
         ++atIt) {
      if (isAtomCandForChiralH(mol, *atIt)) {
        chiralAts.push_back((*atIt)->getIdx());
      }
    }
    if (chiralAts.size()) {
      bool addCoords = false;
      if (!forceCoords && mol.getNumConformers()) addCoords = true;
      MolOps::addHs(mol, false, addCoords, &chiralAts);
    }
  }
  if (forceCoords || !mol.getNumConformers()) {
    // compute 2D coordinates in a standard orientation:
    const bool canonOrient = true;
    RDDepict::compute2DCoords(mol, nullptr, canonOrient);
  }
  if (wedgeBonds) {
    WedgeMolBonds(mol, &mol.getConformer());
  }
}

void prepareAndDrawMolecule(MolDraw2D &drawer, const ROMol &mol,
                            const std::string &legend,
                            const std::vector<int> *highlight_atoms,
                            const std::vector<int> *highlight_bonds,
                            const std::map<int, DrawColour> *highlight_atom_map,
                            const std::map<int, DrawColour> *highlight_bond_map,
                            const std::map<int, double> *highlight_radii,
                            int confId) {
  RWMol cpy(mol);
  prepareMolForDrawing(cpy);
  drawer.drawMolecule(cpy, legend, highlight_atoms, highlight_bonds,
                      highlight_atom_map, highlight_bond_map, highlight_radii,
                      confId);
}

void updateDrawerParamsFromJSON(MolDraw2D &drawer, const char *json) {
  PRECONDITION(json, "no parameter string");
  updateDrawerParamsFromJSON(drawer, std::string(json));
};
#define PT_OPT_GET(opt) opts.opt = pt.get(#opt, opts.opt)

void get_colour_option(boost::property_tree::ptree *pt, const char *pnm,
                       DrawColour &colour) {
  PRECONDITION(pnm && strlen(pnm), "bad property name");
  if (pt->find(pnm) == pt->not_found()) return;

  boost::property_tree::ptree::const_iterator itm = pt->get_child(pnm).begin();
  colour.r = itm->second.get_value<float>();
  ++itm;
  colour.g = itm->second.get_value<float>();
  ++itm;
  colour.b = itm->second.get_value<float>();
  ++itm;
}

void updateDrawerParamsFromJSON(MolDraw2D &drawer, const std::string &json) {
  if (json == "") return;
  std::istringstream ss;
  ss.str(json);
  MolDrawOptions &opts = drawer.drawOptions();
  boost::property_tree::ptree pt;
  boost::property_tree::read_json(ss, pt);
  PT_OPT_GET(atomLabelDeuteriumTritium);
  PT_OPT_GET(dummiesAreAttachments);
  PT_OPT_GET(circleAtoms);
  PT_OPT_GET(continuousHighlight);
  PT_OPT_GET(flagCloseContactsDist);
  PT_OPT_GET(includeAtomTags);
  PT_OPT_GET(clearBackground);
  PT_OPT_GET(legendFontSize);
  PT_OPT_GET(multipleBondOffset);
  PT_OPT_GET(padding);
  PT_OPT_GET(additionalAtomLabelPadding);
  get_colour_option(&pt, "highlightColour", opts.highlightColour);
  get_colour_option(&pt, "backgroundColour", opts.backgroundColour);
  get_colour_option(&pt, "legendColour", opts.legendColour);
  if (pt.find("atomLabels") != pt.not_found()) {
    BOOST_FOREACH (boost::property_tree::ptree::value_type const &item,
                   pt.get_child("atomLabels")) {
      opts.atomLabels[boost::lexical_cast<int>(item.first)] =
          item.second.get_value<std::string>();
    }
  }
}

void contourAndDrawGrid(MolDraw2D &drawer, const double *grid,
                        const std::vector<double> &xcoords,
                        const std::vector<double> &ycoords, size_t nContours,
                        std::vector<double> &levels,
                        const ContourParams &params) {
  PRECONDITION(grid, "no data");
  PRECONDITION(params.colourMap.size() > 1,
               "colourMap must have at least two entries");

  if (params.setScale) {
    Point2D minP = {xcoords[0], ycoords[0]};
    Point2D maxP = {xcoords.back(), ycoords.back()};
    drawer.setScale(drawer.width(), drawer.height(), minP, maxP);
  }

  size_t nX = xcoords.size();
  size_t nY = ycoords.size();
  double minV = std::numeric_limits<double>::max();
  double maxV = -std::numeric_limits<double>::max();
  if (!levels.size() || params.fillGrid) {
    for (size_t i = 0; i < nX; ++i) {
      for (size_t j = 0; j < nY; ++j) {
        minV = std::min(minV, grid[i * nY + j]);
        maxV = std::max(maxV, grid[i * nY + j]);
      }
    }
    if (!levels.size()) {
      levels.resize(nContours);
      for (size_t i = 0; i < nContours; ++i) {
        levels[i] = minV + i * (maxV - minV) / (nContours - 1);
      }
    }
  }
  if (maxV <= minV) return;

  const auto olw = drawer.lineWidth();
  const auto odash = drawer.dash();
  const auto ocolor = drawer.colour();
  const auto ofill = drawer.fillPolys();
  const auto owidth = drawer.lineWidth();
  if (params.fillGrid) {
    drawer.setFillPolys(true);
    drawer.setLineWidth(1);
    auto delta = (maxV - minV);
    if (params.colourMap.size() > 2) {
      // need to find how fractionally far we are from zero, not the min
      if (-minV > maxV)
        delta = -minV;
      else
        delta = maxV;
    }
    for (size_t i = 0; i < nX - 1; ++i) {
      for (size_t j = 0; j < nY - 1; ++j) {
        auto gridV = grid[i * nY + j];
        auto fracV = (gridV - minV) / delta;
        if (params.colourMap.size() > 2) {
          // need to find how fractionally far we are from zero, not the min
          fracV = gridV / delta;
          if (fracV < 0) fracV *= -1;
        }
        DrawColour fillColour;
        auto c1 = (gridV < 0 || params.colourMap.size() == 2)
                      ? params.colourMap[1]
                      : params.colourMap[1];
        auto c2 = (gridV < 0 || params.colourMap.size() == 2)
                      ? params.colourMap[0]
                      : params.colourMap[2];
        auto c = c1 + (c2 - c1) * fracV;
        // don't bother drawing boxes that are the same as the background color:
        double tol = 0.01;
        if (c.feq(drawer.drawOptions().backgroundColour, tol)) {
          continue;
        }
        drawer.setColour(c);
        Point2D p1 = {xcoords[i], ycoords[j]};
        Point2D p2 = {xcoords[i + 1], ycoords[j + 1]};
        drawer.drawRect(p1, p2);
      }
    }
  }

  if (nContours) {
    if(nContours > levels.size()){
      throw ValueErrorException("nContours larger than the size of the level list");
    }
    std::vector<conrec::ConrecSegment> segs;
    conrec::Contour(grid, 0, nX - 1, 0, nY - 1, xcoords.data(), ycoords.data(),
                    nContours, levels.data(), segs);
    static DashPattern negDash = {2, 6};
    static DashPattern posDash;
    drawer.setColour(params.contourColour);
    drawer.setLineWidth(params.contourWidth);
    for (const auto &seg : segs) {
      if (params.dashNegative && seg.isoVal < 0) {
        drawer.setDash(negDash);
      } else {
        drawer.setDash(posDash);
      }
      drawer.drawLine(seg.p1, seg.p2);
    }
  }

  drawer.setDash(odash);
  drawer.setLineWidth(olw);
  drawer.setColour(ocolor);
  drawer.setFillPolys(ofill);
  drawer.setLineWidth(owidth);
};

void contourAndDrawGaussians(MolDraw2D &drawer,
                             const std::vector<Point2D> &locs,
                             const std::vector<double> &weights,
                             const std::vector<double> &widths,
                             size_t nContours, std::vector<double> &levels,
                             const ContourParams &params) {
  PRECONDITION(locs.size() == weights.size(), "size mismatch");
  PRECONDITION(locs.size() == widths.size(), "size mismatch");

  // start by setting up the grid
  if (params.setScale) {
    Point2D minP, maxP;
    minP.x = minP.y = std::numeric_limits<double>::max();
    maxP.x = maxP.y = -std::numeric_limits<double>::max();
    for (const auto &loc : locs) {
      minP.x = std::min(loc.x, minP.x);
      minP.y = std::min(loc.y, minP.y);
      maxP.x = std::max(loc.x, maxP.x);
      maxP.y = std::max(loc.y, maxP.y);
    }
    Point2D dims = maxP - minP;
    minP.x -= drawer.drawOptions().padding * dims.x;
    minP.y -= drawer.drawOptions().padding * dims.y;
    maxP.x += drawer.drawOptions().padding * dims.x;
    maxP.y += drawer.drawOptions().padding * dims.y;

    if (params.extraGridPadding > 0) {
      Point2D p1(0, 0), p2(params.extraGridPadding, 0);
      double pad =
          fabs(drawer.getDrawCoords(p2).x - drawer.getDrawCoords(p1).x);
      minP.x -= pad;
      minP.y -= pad;
      maxP.x += pad;
      maxP.y += pad;
    }

    drawer.setScale(drawer.width(), drawer.height(), minP, maxP);
  }

  size_t nx = (size_t)ceil(drawer.range().x / params.gridResolution) + 1;
  size_t ny = (size_t)ceil(drawer.range().y / params.gridResolution) + 1;
  std::vector<double> xcoords(nx);
  for (size_t i = 0; i < nx; ++i) {
    xcoords[i] = drawer.minPt().x + i * params.gridResolution;
  }
  std::vector<double> ycoords(ny);
  for (size_t i = 0; i < ny; ++i) {
    ycoords[i] = drawer.minPt().y + i * params.gridResolution;
  }
  std::unique_ptr<double[]> grid(new double[nx * ny]);

  // populate the grid from the gaussians:
  for (size_t ix = 0; ix < nx; ++ix) {
    auto px = drawer.minPt().x + ix * params.gridResolution;
    for (size_t iy = 0; iy < ny; ++iy) {
      auto py = drawer.minPt().y + iy * params.gridResolution;
      Point2D pt(px, py);
      double accum = 0.0;
      for (size_t ig = 0; ig < locs.size(); ++ig) {
        auto d2 = (pt - locs[ig]).lengthSq();
        auto contrib = weights[ig] / widths[ig] *
                       exp(-0.5 * d2 / (widths[ig] * widths[ig]));
        accum += contrib;
      }
      grid[ix * ny + iy] = accum / (2 * M_PI);
    }
  }

  // and render it:
  ContourParams paramsCopy = params;
  paramsCopy.setScale = false;  // if scaling was needed, we did it already
  contourAndDrawGrid(drawer, grid.get(), xcoords, ycoords, nContours, levels,
                     paramsCopy);
};
}  // namespace MolDraw2DUtils
}  // namespace RDKit

Are these changes connected to the bug? It's not clear to me that they are correct. It seems to me that if the padding is negative (for some reason), it should have the corresponding effect.