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rdkit/Code/GraphMol/MolDraw2D/MolDraw2D.cpp
Greg Landrum bed5b95ae4 Fixes #3543 (#3615) 
* does not work

* Fixes #3543

* remove debug printing
2020-12-08 08:45:46 -05:00

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//
// Copyright (C) 2014-2020 David Cosgrove and 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.
//
// Original author: David Cosgrove (AstraZeneca)
// 27th May 2014
//
// Extensively modified by Greg Landrum
//
#include <GraphMol/QueryOps.h>
#include <GraphMol/MolDraw2D/DrawText.h>
#include <GraphMol/MolDraw2D/MolDraw2D.h>
#include <GraphMol/MolDraw2D/MolDraw2DDetails.h>
#include <GraphMol/MolDraw2D/MolDraw2DUtils.h>
#include <GraphMol/ChemReactions/ReactionParser.h>
#include <GraphMol/Depictor/RDDepictor.h>
#include <Geometry/point.h>
#include <Geometry/Transform2D.h>
#include <Numerics/SquareMatrix.h>
#include <Numerics/Matrix.h>
#include <GraphMol/MolTransforms/MolTransforms.h>
#include <Geometry/Transform3D.h>
#include <algorithm>
#include <cstdlib>
#include <cmath>
#include <limits>
#include <memory>
#include <boost/lexical_cast.hpp>
#include <boost/tuple/tuple_comparison.hpp>
#include <boost/assign/list_of.hpp>
#include <boost/format.hpp>
using namespace boost;
using namespace std;
namespace RDKit {
namespace {
void getBondHighlightsForAtoms(const ROMol &mol,
const vector<int> &highlight_atoms,
vector<int> &highlight_bonds) {
highlight_bonds.clear();
for (auto ai = highlight_atoms.begin(); ai != highlight_atoms.end(); ++ai) {
for (auto aj = ai + 1; aj != highlight_atoms.end(); ++aj) {
const Bond *bnd = mol.getBondBetweenAtoms(*ai, *aj);
if (bnd) {
highlight_bonds.push_back(bnd->getIdx());
}
}
}
}
} // namespace
// ****************************************************************************
MolDraw2D::MolDraw2D(int width, int height, int panelWidth, int panelHeight)
: needs_scale_(true),
width_(width),
height_(height),
panel_width_(panelWidth > 0 ? panelWidth : width),
panel_height_(panelHeight > 0 ? panelHeight : height),
legend_height_(0),
scale_(1.0),
x_min_(0.0),
y_min_(0.0),
x_range_(0.0),
y_range_(0.0),
x_trans_(0.0),
y_trans_(0.0),
x_offset_(0),
y_offset_(0),
fill_polys_(true),
activeMolIdx_(-1) {}
// ****************************************************************************
MolDraw2D::~MolDraw2D() {}
// ****************************************************************************
void MolDraw2D::drawMolecule(const ROMol &mol,
const vector<int> *highlight_atoms,
const map<int, DrawColour> *highlight_atom_map,
const std::map<int, double> *highlight_radii,
int confId) {
drawMolecule(mol, "", highlight_atoms, highlight_atom_map, highlight_radii,
confId);
}
// ****************************************************************************
void MolDraw2D::drawMolecule(const ROMol &mol, const std::string &legend,
const vector<int> *highlight_atoms,
const map<int, DrawColour> *highlight_atom_map,
const std::map<int, double> *highlight_radii,
int confId) {
vector<int> highlight_bonds;
if (highlight_atoms) {
getBondHighlightsForAtoms(mol, *highlight_atoms, highlight_bonds);
}
drawMolecule(mol, legend, highlight_atoms, &highlight_bonds,
highlight_atom_map, nullptr, highlight_radii, confId);
}
// ****************************************************************************
void MolDraw2D::doContinuousHighlighting(
const ROMol &mol, const vector<int> *highlight_atoms,
const vector<int> *highlight_bonds,
const map<int, DrawColour> *highlight_atom_map,
const map<int, DrawColour> *highlight_bond_map,
const std::map<int, double> *highlight_radii) {
PRECONDITION(activeMolIdx_ >= 0, "bad active mol");
int orig_lw = lineWidth();
int tgt_lw = getHighlightBondWidth(-1, nullptr);
if (tgt_lw < 2) {
tgt_lw = 2;
}
bool orig_fp = fillPolys();
if (highlight_bonds) {
for (auto this_at : mol.atoms()) {
int this_idx = this_at->getIdx();
for (const auto &nbri : make_iterator_range(mol.getAtomBonds(this_at))) {
const Bond *bond = mol[nbri];
int nbr_idx = bond->getOtherAtomIdx(this_idx);
if (nbr_idx < static_cast<int>(at_cds_[activeMolIdx_].size()) &&
nbr_idx > this_idx) {
if (std::find(highlight_bonds->begin(), highlight_bonds->end(),
bond->getIdx()) != highlight_bonds->end()) {
DrawColour col = drawOptions().highlightColour;
if (highlight_bond_map &&
highlight_bond_map->find(bond->getIdx()) !=
highlight_bond_map->end()) {
col = highlight_bond_map->find(bond->getIdx())->second;
}
setLineWidth(tgt_lw);
Point2D at1_cds = at_cds_[activeMolIdx_][this_idx];
Point2D at2_cds = at_cds_[activeMolIdx_][nbr_idx];
bool orig_slw = drawOptions().scaleBondWidth;
drawOptions().scaleBondWidth =
drawOptions().scaleHighlightBondWidth;
drawLine(at1_cds, at2_cds, col, col);
drawOptions().scaleBondWidth = orig_slw;
}
}
}
}
}
if (highlight_atoms) {
if (!drawOptions().fillHighlights) {
// we need a narrower circle
setLineWidth(tgt_lw / 2);
}
for (auto this_at : mol.atoms()) {
int this_idx = this_at->getIdx();
if (std::find(highlight_atoms->begin(), highlight_atoms->end(),
this_idx) != highlight_atoms->end()) {
DrawColour col = drawOptions().highlightColour;
if (highlight_atom_map &&
highlight_atom_map->find(this_idx) != highlight_atom_map->end()) {
col = highlight_atom_map->find(this_idx)->second;
}
vector<DrawColour> cols(1, col);
drawHighlightedAtom(this_idx, cols, highlight_radii);
}
}
}
setLineWidth(orig_lw);
setFillPolys(orig_fp);
}
// ****************************************************************************
void MolDraw2D::drawMolecule(const ROMol &mol,
const vector<int> *highlight_atoms,
const vector<int> *highlight_bonds,
const map<int, DrawColour> *highlight_atom_map,
const map<int, DrawColour> *highlight_bond_map,
const std::map<int, double> *highlight_radii,
int confId) {
int origWidth = lineWidth();
pushDrawDetails();
setupTextDrawer();
unique_ptr<RWMol> rwmol =
setupMoleculeDraw(mol, highlight_atoms, highlight_radii, confId);
ROMol const &draw_mol = rwmol ? *(rwmol) : mol;
if (!draw_mol.getNumConformers()) {
// clearly, the molecule is in a sorry state.
return;
}
if (drawOptions().continuousHighlight) {
// if we're doing continuous highlighting, start by drawing the highlights
doContinuousHighlighting(draw_mol, highlight_atoms, highlight_bonds,
highlight_atom_map, highlight_bond_map,
highlight_radii);
// at this point we shouldn't be doing any more highlighting, so blow out
// those variables. This alters the behaviour of drawBonds below.
highlight_bonds = nullptr;
highlight_atoms = nullptr;
} else if (drawOptions().circleAtoms && highlight_atoms) {
setFillPolys(drawOptions().fillHighlights);
for (auto this_at : draw_mol.atoms()) {
int this_idx = this_at->getIdx();
if (std::find(highlight_atoms->begin(), highlight_atoms->end(),
this_idx) != highlight_atoms->end()) {
if (highlight_atom_map &&
highlight_atom_map->find(this_idx) != highlight_atom_map->end()) {
setColour(highlight_atom_map->find(this_idx)->second);
} else {
setColour(drawOptions().highlightColour);
}
Point2D p1 = at_cds_[activeMolIdx_][this_idx];
Point2D p2 = at_cds_[activeMolIdx_][this_idx];
double radius = drawOptions().highlightRadius;
if (highlight_radii &&
highlight_radii->find(this_idx) != highlight_radii->end()) {
radius = highlight_radii->find(this_idx)->second;
}
Point2D offset(radius, radius);
p1 -= offset;
p2 += offset;
drawEllipse(p1, p2);
}
}
setFillPolys(true);
}
drawBonds(draw_mol, highlight_atoms, highlight_atom_map, highlight_bonds,
highlight_bond_map);
vector<DrawColour> atom_colours;
for (auto this_at : draw_mol.atoms()) {
atom_colours.emplace_back(
getColour(this_at->getIdx(), highlight_atoms, highlight_atom_map));
}
finishMoleculeDraw(draw_mol, atom_colours);
// popDrawDetails();
setLineWidth(origWidth);
if (drawOptions().includeMetadata) {
this->updateMetadata(draw_mol, confId);
}
// {
// Point2D p1(x_min_, y_min_), p2(x_min_ + x_range_, y_min_ + y_range_);
// setColour(DrawColour(0, 0, 0));
// setFillPolys(false);
// drawRect(p1, p2);
// }
}
// ****************************************************************************
void MolDraw2D::drawMolecule(const ROMol &mol, const std::string &legend,
const vector<int> *highlight_atoms,
const vector<int> *highlight_bonds,
const map<int, DrawColour> *highlight_atom_map,
const map<int, DrawColour> *highlight_bond_map,
const std::map<int, double> *highlight_radii,
int confId) {
if (!legend.empty()) {
legend_height_ = int(0.05 * double(panelHeight()));
if (legend_height_ < 20) {
legend_height_ = 20;
}
} else {
legend_height_ = 0;
}
drawMolecule(mol, highlight_atoms, highlight_bonds, highlight_atom_map,
highlight_bond_map, highlight_radii, confId);
drawLegend(legend);
}
// ****************************************************************************
void MolDraw2D::drawMoleculeWithHighlights(
const ROMol &mol, const string &legend,
const map<int, vector<DrawColour>> &highlight_atom_map,
const map<int, vector<DrawColour>> &highlight_bond_map,
const map<int, double> &highlight_radii,
const map<int, int> &highlight_linewidth_multipliers, int confId) {
int origWidth = lineWidth();
vector<int> highlight_atoms;
for (auto ha : highlight_atom_map) {
highlight_atoms.emplace_back(ha.first);
}
if (!legend.empty()) {
legend_height_ = int(0.05 * double(panelHeight()));
} else {
legend_height_ = 0;
}
pushDrawDetails();
unique_ptr<RWMol> rwmol =
setupMoleculeDraw(mol, &highlight_atoms, &highlight_radii, confId);
ROMol const &draw_mol = rwmol ? *(rwmol) : mol;
if (!draw_mol.getNumConformers()) {
// clearly, the molecule is in a sorry state.
return;
}
bool orig_fp = fillPolys();
setFillPolys(drawOptions().fillHighlights);
// draw the highlighted bonds first, so the atoms hide the ragged
// ends. This only works with filled highlighting, obs. If not, we need
// the highlight radii to work out the intersection of the bond highlight
// with the atom highlight.
drawHighlightedBonds(draw_mol, highlight_bond_map,
highlight_linewidth_multipliers, &highlight_radii);
for (auto ha : highlight_atom_map) {
// cout << "highlighting atom " << ha.first << " with " << ha.second.size()
// << " colours" << endl;
drawHighlightedAtom(ha.first, ha.second, &highlight_radii);
}
setFillPolys(orig_fp);
// draw plain bonds on top of highlights. Use black if either highlight
// colour is the same as the colour it would have been.
vector<pair<DrawColour, DrawColour>> bond_colours;
for (auto bond : draw_mol.bonds()) {
int beg_at = bond->getBeginAtomIdx();
DrawColour col1 = getColour(beg_at);
int end_at = bond->getEndAtomIdx();
DrawColour col2 = getColour(end_at);
auto hb = highlight_bond_map.find(bond->getIdx());
if (hb != highlight_bond_map.end()) {
const vector<DrawColour> &cols = hb->second;
if (find(cols.begin(), cols.end(), col1) == cols.end() ||
find(cols.begin(), cols.end(), col2) == cols.end()) {
col1 = DrawColour(0.0, 0.0, 0.0);
col2 = col1;
}
}
bond_colours.emplace_back(make_pair(col1, col2));
}
drawBonds(draw_mol, nullptr, nullptr, nullptr, nullptr, &bond_colours);
vector<DrawColour> atom_colours;
for (auto this_at : draw_mol.atoms()) {
// Get colours together for the atom labels.
// Passing nullptr means that we'll get a colour based on atomic number
// only.
atom_colours.emplace_back(getColour(this_at->getIdx(), nullptr, nullptr));
// if the chosen colour is a highlight colour for this atom, choose black
// instead so it is still visible.
auto ha = highlight_atom_map.find(this_at->getIdx());
if (ha != highlight_atom_map.end()) {
if (find(ha->second.begin(), ha->second.end(), atom_colours.back()) !=
ha->second.end()) {
atom_colours.back() = DrawColour(0.0, 0.0, 0.0);
}
}
}
// this puts on atom labels and such
finishMoleculeDraw(draw_mol, atom_colours);
setLineWidth(origWidth);
drawLegend(legend);
popDrawDetails();
}
// ****************************************************************************
void MolDraw2D::get2DCoordsMol(RWMol &mol, double &offset, double spacing,
double &maxY, double &minY, int confId,
bool shiftAgents, double coordScale) {
try {
RDLog::BlockLogs blocker;
MolOps::sanitizeMol(mol);
} catch (const MolSanitizeException &) {
mol.updatePropertyCache(false);
try {
RDLog::BlockLogs blocker;
MolOps::Kekulize(mol, false); // kekulize, but keep the aromatic flags!
} catch (const MolSanitizeException &) {
// don't need to do anything
}
MolOps::setHybridization(mol);
}
const bool canonOrient = true;
const bool kekulize = false; // don't kekulize, we just did that
RDDepict::compute2DCoords(mol, nullptr, canonOrient);
MolDraw2DUtils::prepareMolForDrawing(mol, kekulize);
double minX = 1e8;
double maxX = -1e8;
double vShift = 0;
if (shiftAgents) {
vShift = 1.1 * maxY / 2;
}
pushDrawDetails();
extractAtomCoords(mol, confId, false);
extractAtomSymbols(mol);
for (unsigned int i = 0; i < mol.getNumAtoms(); ++i) {
RDGeom::Point2D p = at_cds_[activeMolIdx_][i];
Atom *at = mol.getAtomWithIdx(i);
// allow for the width of the atom label.
auto at_lab = getAtomSymbolAndOrientation(*at);
double width = 0.0, height = 0.0;
if (!at_lab.first.empty()) {
getLabelSize(at_lab.first, at_lab.second, width, height);
}
if (at_lab.second == OrientType::W) {
p.x -= width;
} else {
p.x -= width / 2;
}
p *= coordScale;
minX = std::min(minX, p.x);
}
offset += fabs(minX);
Conformer &conf = mol.getConformer(confId);
for (unsigned int i = 0; i < mol.getNumAtoms(); ++i) {
RDGeom::Point2D p = at_cds_[activeMolIdx_][i];
p.y = p.y * coordScale + vShift;
Atom *at = mol.getAtomWithIdx(i);
// allow for the width of the atom label.
auto at_lab = getAtomSymbolAndOrientation(*at);
double width = 0.0, height = 0.0;
if (!at_lab.first.empty()) {
getLabelSize(at_lab.first, at_lab.second, width, height);
}
height /= 2.0;
if (at_lab.second != OrientType::E) {
width /= 2.0;
}
if (!shiftAgents) {
maxY = std::max(p.y + height, maxY);
minY = std::min(p.y - height, minY);
}
p.x = p.x * coordScale + offset;
maxX = std::max(p.x + width, maxX);
// now copy the transformed coords back to the actual
// molecules. The initial calculations were done on the
// copies taken by extractAtomCoords, and that was so
// we could re-use existing code for scaling the picture
// including labels.
RDGeom::Point3D &at_cds = conf.getAtomPos(i);
at_cds.x = p.x;
at_cds.y = p.y;
}
offset = maxX + spacing;
popDrawDetails();
}
// ****************************************************************************
void MolDraw2D::get2DCoordsForReaction(ChemicalReaction &rxn,
Point2D &arrowBegin, Point2D &arrowEnd,
std::vector<double> &plusLocs,
double spacing,
const std::vector<int> *confIds) {
plusLocs.resize(0);
double maxY = -1e8, minY = 1e8;
double offset = 0.0;
// reactants
for (unsigned int midx = 0; midx < rxn.getNumReactantTemplates(); ++midx) {
// add space for the "+" if required
if (midx > 0) {
plusLocs.push_back(offset);
offset += spacing;
}
ROMOL_SPTR reactant = rxn.getReactants()[midx];
int cid = -1;
if (confIds) {
cid = (*confIds)[midx];
}
get2DCoordsMol(*(RWMol *)reactant.get(), offset, spacing, maxY, minY, cid,
false, 1.0);
}
arrowBegin.x = offset;
offset += spacing;
double begAgentOffset = offset;
// we need to do the products now so that we know the full y range.
// these will have the wrong X coordinates, but we'll fix that later.
offset = 0;
for (unsigned int midx = 0; midx < rxn.getNumProductTemplates(); ++midx) {
// add space for the "+" if required
if (midx > 0) {
plusLocs.push_back(offset);
offset += spacing;
}
ROMOL_SPTR product = rxn.getProducts()[midx];
int cid = -1;
if (confIds) {
cid = (*confIds)[rxn.getNumReactantTemplates() +
rxn.getNumAgentTemplates() + midx];
}
get2DCoordsMol(*(RWMol *)product.get(), offset, spacing, maxY, minY, cid,
false, 1.0);
}
offset = begAgentOffset;
// agents
for (unsigned int midx = 0; midx < rxn.getNumAgentTemplates(); ++midx) {
ROMOL_SPTR agent = rxn.getAgents()[midx];
int cid = -1;
if (confIds) {
cid = (*confIds)[rxn.getNumReactantTemplates() + midx];
}
get2DCoordsMol(*(RWMol *)agent.get(), offset, spacing, maxY, minY, cid,
true, 0.45);
}
if (rxn.getNumAgentTemplates()) {
arrowEnd.x = offset; //- spacing;
} else {
arrowEnd.x = offset + 3 * spacing;
}
offset = arrowEnd.x + 1.5 * spacing;
// now translate the products over
for (unsigned int midx = 0; midx < rxn.getNumProductTemplates(); ++midx) {
ROMOL_SPTR product = rxn.getProducts()[midx];
int cid = -1;
if (confIds) {
cid = (*confIds)[rxn.getNumReactantTemplates() +
rxn.getNumAgentTemplates() + midx];
}
Conformer &conf = product->getConformer(cid);
for (unsigned int aidx = 0; aidx < product->getNumAtoms(); ++aidx) {
conf.getAtomPos(aidx).x += offset;
}
}
// fix the plus signs too
unsigned int startP = 0;
if (rxn.getNumReactantTemplates() > 1) {
startP = rxn.getNumReactantTemplates() - 1;
}
for (unsigned int pidx = startP; pidx < plusLocs.size(); ++pidx) {
plusLocs[pidx] += offset;
}
arrowBegin.y = arrowEnd.y = minY + (maxY - minY) / 2;
}
// ****************************************************************************
void MolDraw2D::drawReaction(
const ChemicalReaction &rxn, bool highlightByReactant,
const std::vector<DrawColour> *highlightColorsReactants,
const std::vector<int> *confIds) {
ChemicalReaction nrxn(rxn);
double spacing = 1.0;
Point2D arrowBegin, arrowEnd;
std::vector<double> plusLocs;
get2DCoordsForReaction(nrxn, arrowBegin, arrowEnd, plusLocs, spacing,
confIds);
MolDrawOptions origDrawOptions = drawOptions();
drawOptions().prepareMolsBeforeDrawing = false;
drawOptions().includeMetadata = false;
ROMol *tmol = ChemicalReactionToRxnMol(nrxn);
MolOps::findSSSR(*tmol);
if (needs_scale_ &&
(!nrxn.getNumReactantTemplates() || !nrxn.getNumProductTemplates())) {
// drawMolecule() will figure out the scaling so that the molecule
// fits the drawing pane. In order to ensure that we have space for the
// arrow, we need to figure out the scaling on our own.
RWMol tmol2;
tmol2.addAtom(new Atom(0), true, true);
tmol2.addAtom(new Atom(0), true, true);
tmol2.addConformer(new Conformer(2), true);
tmol2.getConformer().getAtomPos(0) =
RDGeom::Point3D(arrowBegin.x, arrowBegin.y, 0);
tmol2.getConformer().getAtomPos(1) =
RDGeom::Point3D(arrowEnd.x, arrowEnd.y, 0);
for (auto atom : tmol2.atoms()) {
atom->calcImplicitValence();
}
tmol2.insertMol(*tmol);
pushDrawDetails();
extractAtomCoords(tmol2, 0, true);
extractAtomSymbols(tmol2);
calculateScale(panelWidth(), drawHeight(), tmol2);
needs_scale_ = false;
popDrawDetails();
}
std::vector<int> *atom_highlights = nullptr;
std::map<int, DrawColour> *atom_highlight_colors = nullptr;
std::vector<int> *bond_highlights = nullptr;
std::map<int, DrawColour> *bond_highlight_colors = nullptr;
if (highlightByReactant) {
const std::vector<DrawColour> *colors =
&drawOptions().highlightColourPalette;
if (highlightColorsReactants) {
colors = highlightColorsReactants;
}
std::vector<int> atomfragmap;
MolOps::getMolFrags(*tmol, atomfragmap);
atom_highlights = new std::vector<int>();
atom_highlight_colors = new std::map<int, DrawColour>();
bond_highlights = new std::vector<int>();
bond_highlight_colors = new std::map<int, DrawColour>();
std::map<int, int> atommap_fragmap;
for (unsigned int aidx = 0; aidx < tmol->getNumAtoms(); ++aidx) {
int atomRole = -1;
Atom *atom = tmol->getAtomWithIdx(aidx);
if (atom->getPropIfPresent("molRxnRole", atomRole) && atomRole == 1 &&
atom->getAtomMapNum()) {
atommap_fragmap[atom->getAtomMapNum()] = atomfragmap[aidx];
atom_highlights->push_back(aidx);
(*atom_highlight_colors)[aidx] =
(*colors)[atomfragmap[aidx] % colors->size()];
atom->setAtomMapNum(0);
// add highlighted bonds to lower-numbered
// (and thus already covered) neighbors
for (const auto &nbri :
make_iterator_range(tmol->getAtomNeighbors(atom))) {
const Atom *nbr = (*tmol)[nbri];
if (nbr->getIdx() < aidx &&
atomfragmap[nbr->getIdx()] == atomfragmap[aidx]) {
int bondIdx =
tmol->getBondBetweenAtoms(aidx, nbr->getIdx())->getIdx();
bond_highlights->push_back(bondIdx);
(*bond_highlight_colors)[bondIdx] = (*atom_highlight_colors)[aidx];
}
}
}
}
for (unsigned int aidx = 0; aidx < tmol->getNumAtoms(); ++aidx) {
int atomRole = -1;
Atom *atom = tmol->getAtomWithIdx(aidx);
if (atom->getPropIfPresent("molRxnRole", atomRole) && atomRole == 2 &&
atom->getAtomMapNum() &&
atommap_fragmap.find(atom->getAtomMapNum()) !=
atommap_fragmap.end()) {
atom_highlights->push_back(aidx);
(*atom_highlight_colors)[aidx] =
(*colors)[atommap_fragmap[atom->getAtomMapNum()] % colors->size()];
atom->setAtomMapNum(0);
// add highlighted bonds to lower-numbered
// (and thus already covered) neighbors
for (const auto &nbri :
make_iterator_range(tmol->getAtomNeighbors(atom))) {
const Atom *nbr = (*tmol)[nbri];
if (nbr->getIdx() < aidx && (*atom_highlight_colors)[nbr->getIdx()] ==
(*atom_highlight_colors)[aidx]) {
int bondIdx =
tmol->getBondBetweenAtoms(aidx, nbr->getIdx())->getIdx();
bond_highlights->push_back(bondIdx);
(*bond_highlight_colors)[bondIdx] = (*atom_highlight_colors)[aidx];
}
}
}
}
}
drawMolecule(*tmol, "", atom_highlights, bond_highlights,
atom_highlight_colors, bond_highlight_colors);
delete tmol;
delete atom_highlights;
delete atom_highlight_colors;
delete bond_highlights;
delete bond_highlight_colors;
double o_font_scale = text_drawer_->fontScale();
double fsize = text_drawer_->fontSize();
double new_font_scale =
2.0 * o_font_scale * drawOptions().legendFontSize / fsize;
text_drawer_->setFontScale(new_font_scale);
DrawColour odc = colour();
setColour(options_.symbolColour);
// now add the symbols
for (auto plusLoc : plusLocs) {
Point2D loc(plusLoc, arrowBegin.y);
drawString("+", loc);
}
// The arrow:
drawArrow(arrowBegin, arrowEnd);
if (origDrawOptions.includeMetadata) {
this->updateMetadata(nrxn);
}
setColour(odc);
text_drawer_->setFontScale(o_font_scale);
drawOptions() = origDrawOptions;
}
// ****************************************************************************
void MolDraw2D::drawMolecules(
const std::vector<ROMol *> &mols, const std::vector<std::string> *legends,
const std::vector<std::vector<int>> *highlight_atoms,
const std::vector<std::vector<int>> *highlight_bonds,
const std::vector<std::map<int, DrawColour>> *highlight_atom_maps,
const std::vector<std::map<int, DrawColour>> *highlight_bond_maps,
const std::vector<std::map<int, double>> *highlight_radii,
const std::vector<int> *confIds) {
PRECONDITION(!legends || legends->size() == mols.size(), "bad size");
PRECONDITION(!highlight_atoms || highlight_atoms->size() == mols.size(),
"bad size");
PRECONDITION(!highlight_bonds || highlight_bonds->size() == mols.size(),
"bad size");
PRECONDITION(
!highlight_atom_maps || highlight_atom_maps->size() == mols.size(),
"bad size");
PRECONDITION(
!highlight_bond_maps || highlight_bond_maps->size() == mols.size(),
"bad size");
PRECONDITION(!highlight_radii || highlight_radii->size() == mols.size(),
"bad size");
PRECONDITION(!confIds || confIds->size() == mols.size(), "bad size");
PRECONDITION(panel_width_ != 0, "panel width cannot be zero");
PRECONDITION(panel_height_ != 0, "panel height cannot be zero");
if (!mols.size()) {
return;
}
setupTextDrawer();
vector<unique_ptr<RWMol>> tmols;
calculateScale(panelWidth(), drawHeight(), mols, highlight_atoms,
highlight_radii, confIds, tmols);
// so drawMolecule doesn't recalculate the scale each time, and
// undo all the good work.
needs_scale_ = false;
int nCols = width() / panelWidth();
int nRows = height() / panelHeight();
for (unsigned int i = 0; i < mols.size(); ++i) {
if (!mols[i]) {
continue;
}
int row = 0;
// note that this also works when no panel size is specified since
// the panel dimensions defaults to -1
if (nRows > 1) {
row = i / nCols;
}
int col = 0;
if (nCols > 1) {
col = i % nCols;
}
setOffset(col * panelWidth(), row * panelHeight());
ROMol *draw_mol = tmols[i] ? tmols[i].get() : mols[i];
unique_ptr<vector<int>> lhighlight_bonds;
if (highlight_bonds) {
lhighlight_bonds.reset(new std::vector<int>((*highlight_bonds)[i]));
} else if (drawOptions().continuousHighlight && highlight_atoms) {
lhighlight_bonds.reset(new vector<int>());
getBondHighlightsForAtoms(*draw_mol, (*highlight_atoms)[i],
*lhighlight_bonds);
};
drawMolecule(*draw_mol, legends ? (*legends)[i] : "",
highlight_atoms ? &(*highlight_atoms)[i] : nullptr,
lhighlight_bonds.get(),
highlight_atom_maps ? &(*highlight_atom_maps)[i] : nullptr,
highlight_bond_maps ? &(*highlight_bond_maps)[i] : nullptr,
highlight_radii ? &(*highlight_radii)[i] : nullptr,
confIds ? (*confIds)[i] : -1);
// save the drawn positions of the atoms on the molecule. This is the only
// way that we can later add metadata
auto tag = boost::str(boost::format("_atomdrawpos_%d") %
(confIds ? (*confIds)[i] : -1));
for (unsigned int j = 0; j < mols[i]->getNumAtoms(); ++j) {
auto pt = getDrawCoords(j);
mols[i]->getAtomWithIdx(j)->setProp(tag, pt, true);
}
}
}
// ****************************************************************************
void MolDraw2D::highlightCloseContacts() {
if (drawOptions().flagCloseContactsDist < 0) {
return;
}
int tol =
drawOptions().flagCloseContactsDist * drawOptions().flagCloseContactsDist;
boost::dynamic_bitset<> flagged(at_cds_[activeMolIdx_].size());
for (unsigned int i = 0; i < at_cds_[activeMolIdx_].size(); ++i) {
if (flagged[i]) {
continue;
}
Point2D ci = getDrawCoords(at_cds_[activeMolIdx_][i]);
for (unsigned int j = i + 1; j < at_cds_[activeMolIdx_].size(); ++j) {
if (flagged[j]) {
continue;
}
Point2D cj = getDrawCoords(at_cds_[activeMolIdx_][j]);
double d = (cj - ci).lengthSq();
if (d <= tol) {
flagged.set(i);
flagged.set(j);
break;
}
}
if (flagged[i]) {
Point2D p1 = at_cds_[activeMolIdx_][i];
Point2D p2 = p1;
Point2D offset(0.1, 0.1);
p1 -= offset;
p2 += offset;
bool ofp = fillPolys();
setFillPolys(false);
DrawColour odc = colour();
setColour(DrawColour(1, 0, 0));
drawRect(p1, p2);
setColour(odc);
setFillPolys(ofp);
}
}
}
// ****************************************************************************
// transform a set of coords in the molecule's coordinate system
// to drawing system coordinates
Point2D MolDraw2D::getDrawCoords(const Point2D &mol_cds) const {
double x = scale_ * (mol_cds.x - x_min_ + x_trans_);
double y = scale_ * (mol_cds.y - y_min_ + y_trans_);
// y is now the distance from the top of the image, we need to
// invert that:
x += x_offset_;
y -= y_offset_;
y = panelHeight() - legend_height_ - y;
return Point2D(x, y);
}
// ****************************************************************************
Point2D MolDraw2D::getDrawCoords(int at_num) const {
PRECONDITION(activeMolIdx_ >= 0, "bad mol idx");
return getDrawCoords(at_cds_[activeMolIdx_][at_num]);
}
// ****************************************************************************
Point2D MolDraw2D::getAtomCoords(const pair<int, int> &screen_cds) const {
return getAtomCoords(
make_pair(double(screen_cds.first), double(screen_cds.second)));
}
Point2D MolDraw2D::getAtomCoords(const pair<double, double> &screen_cds) const {
double screen_x = screen_cds.first - x_offset_;
double screen_y = screen_cds.second - y_offset_;
auto x = double(screen_x / scale_ + x_min_ - x_trans_);
auto y = double(y_min_ - y_trans_ -
(screen_y - panelHeight() + legend_height_) / scale_);
return Point2D(x, y);
}
// ****************************************************************************
Point2D MolDraw2D::getAtomCoords(int at_num) const {
PRECONDITION(activeMolIdx_ >= 0, "bad active mol");
return at_cds_[activeMolIdx_][at_num];
}
// ****************************************************************************
double MolDraw2D::fontSize() const { return text_drawer_->fontSize(); }
// ****************************************************************************
void MolDraw2D::setFontSize(double new_size) {
text_drawer_->setFontSize(new_size);
}
// ****************************************************************************
void MolDraw2D::setScale(int width, int height, const Point2D &minv,
const Point2D &maxv, const ROMol *mol) {
PRECONDITION(width > 0, "bad width");
PRECONDITION(height > 0, "bad height");
double x_max, y_max;
if (mol) {
pushDrawDetails();
unique_ptr<RWMol> tmol =
setupDrawMolecule(*mol, nullptr, nullptr, -1, width, height);
calculateScale(height, width, *tmol);
popDrawDetails();
x_min_ = min(minv.x, x_min_);
y_min_ = min(minv.y, y_min_);
x_max = max(maxv.x, x_range_ + x_min_);
y_max = max(maxv.y, y_range_ + y_min_);
} else {
x_min_ = minv.x;
y_min_ = minv.y;
x_max = maxv.x;
y_max = maxv.y;
}
x_range_ = x_max - x_min_;
y_range_ = y_max - y_min_;
needs_scale_ = false;
if (x_range_ < 1.0e-4) {
x_range_ = 1.0;
x_min_ = -0.5;
}
if (y_range_ < 1.0e-4) {
y_range_ = 1.0;
y_min_ = -0.5;
}
// put a buffer round the drawing and calculate a final scale
x_min_ -= drawOptions().padding * x_range_;
x_range_ *= 1 + 2 * drawOptions().padding;
y_min_ -= drawOptions().padding * y_range_;
y_range_ *= 1 + 2 * drawOptions().padding;
scale_ = std::min(double(width) / x_range_, double(height) / y_range_);
text_drawer_->setFontScale(scale_);
double y_mid = y_min_ + 0.5 * y_range_;
double x_mid = x_min_ + 0.5 * x_range_;
x_trans_ = y_trans_ = 0.0; // getDrawCoords uses [xy_]trans_
Point2D mid = getDrawCoords(Point2D(x_mid, y_mid));
// that used the offset, we need to remove that:
mid.x -= x_offset_;
mid.y += y_offset_;
x_trans_ = (width / 2 - mid.x) / scale_;
y_trans_ = (mid.y - height / 2) / scale_;
}
// ****************************************************************************
void MolDraw2D::calculateScale(int width, int height, const ROMol &mol,
const std::vector<int> *highlight_atoms,
const std::map<int, double> *highlight_radii) {
PRECONDITION(width > 0, "bad width");
PRECONDITION(height > 0, "bad height");
PRECONDITION(activeMolIdx_ >= 0, "bad active mol");
// cout << "calculateScale width = " << width << " height = " << height
// << endl;
x_min_ = y_min_ = numeric_limits<double>::max();
double x_max(-x_min_), y_max(-y_min_);
// first find the bounding box defined by the atoms
for (const auto &pt : at_cds_[activeMolIdx_]) {
x_min_ = std::min(pt.x, x_min_);
y_min_ = std::min(pt.y, y_min_);
x_max = std::max(pt.x, x_max);
y_max = std::max(pt.y, y_max);
}
// adjust based on the shapes (if any)
for (const auto &shp : shapes_[activeMolIdx_]) {
for (const auto &pt : shp.points) {
x_min_ = std::min(pt.x, x_min_);
y_min_ = std::min(pt.y, y_min_);
x_max = std::max(pt.x, x_max);
y_max = std::max(pt.y, y_max);
}
}
// calculate the x and y spans
x_range_ = x_max - x_min_;
y_range_ = y_max - y_min_;
if (x_range_ < 1e-4) {
x_range_ = 2.0;
x_min_ -= 1.0;
x_max += 1.0;
}
if (y_range_ < 1e-4) {
y_range_ = 2.0;
y_min_ -= 1.0;
y_max += 1.0;
}
scale_ = std::min(double(width) / x_range_, double(height) / y_range_);
// we may need to adjust the scale if there are atom symbols that go off
// the edges, and we probably need to do it iteratively because
// get_string_size uses the current value of scale_.
// We also need to adjust for highlighted atoms if there are any.
// And now we need to take account of strings with N/S orientation
// as well.
while (scale_ > 1e-4) {
text_drawer_->setFontScale(scale_);
adjustScaleForAtomLabels(highlight_atoms, highlight_radii);
adjustScaleForRadicals(mol);
if (supportsAnnotations() && !annotations_.empty() &&
!annotations_[activeMolIdx_].empty()) {
adjustScaleForAnnotation(annotations_[activeMolIdx_]);
}
double old_scale = scale_;
scale_ = std::min(double(width) / x_range_, double(height) / y_range_);
if (fabs(scale_ - old_scale) < 0.1) {
break;
}
}
// put a 5% buffer round the drawing and calculate a final scale
x_min_ -= drawOptions().padding * x_range_;
x_range_ *= 1 + 2 * drawOptions().padding;
y_min_ -= drawOptions().padding * y_range_;
y_range_ *= 1 + 2 * drawOptions().padding;
if (x_range_ > 1e-4 || y_range_ > 1e-4) {
scale_ = std::min(double(width) / x_range_, double(height) / y_range_);
double fix_scale = scale_;
// after all that, use the fixed scale unless it's too big, in which case
// scale the drawing down to fit.
// fixedScale takes precedence if both it and fixedBondLength are given.
if (drawOptions().fixedBondLength > 0.0) {
fix_scale = drawOptions().fixedBondLength;
}
if (drawOptions().fixedScale > 0.0) {
fix_scale = double(width) * drawOptions().fixedScale;
}
if (scale_ > fix_scale) {
scale_ = fix_scale;
}
centrePicture(width, height);
} else {
scale_ = 1;
x_trans_ = 0.;
y_trans_ = 0.;
}
text_drawer_->setFontScale(scale_);
// cout << "leaving calculateScale" << endl;
// cout << "final scale : " << scale_ << endl;
}
// ****************************************************************************
void MolDraw2D::calculateScale(int width, int height,
const vector<ROMol *> &mols,
const vector<vector<int>> *highlight_atoms,
const vector<map<int, double>> *highlight_radii,
const vector<int> *confIds,
vector<unique_ptr<RWMol>> &tmols) {
double global_x_min, global_x_max, global_y_min, global_y_max;
global_x_min = global_y_min = numeric_limits<double>::max();
global_x_max = global_y_max = -numeric_limits<double>::max();
for (size_t i = 0; i < mols.size(); ++i) {
tabulaRasa();
if (!mols[i]) {
tmols.emplace_back(unique_ptr<RWMol>(new RWMol));
continue;
}
const vector<int> *ha = highlight_atoms ? &(*highlight_atoms)[i] : nullptr;
const map<int, double> *hr =
highlight_radii ? &(*highlight_radii)[i] : nullptr;
int id = confIds ? (*confIds)[i] : -1;
pushDrawDetails();
needs_scale_ = true;
unique_ptr<RWMol> rwmol =
setupDrawMolecule(*mols[i], ha, hr, id, width, height);
double x_max = x_min_ + x_range_;
double y_max = y_min_ + y_range_;
global_x_min = min(x_min_, global_x_min);
global_x_max = max(x_max, global_x_max);
global_y_min = min(y_min_, global_y_min);
global_y_max = max(y_max, global_y_max);
tmols.emplace_back(std::move(rwmol));
popDrawDetails();
}
x_min_ = global_x_min;
y_min_ = global_y_min;
x_range_ = global_x_max - global_x_min;
y_range_ = global_y_max - global_y_min;
scale_ = std::min(double(width) / x_range_, double(height) / y_range_);
text_drawer_->setFontScale(scale_);
centrePicture(width, height);
}
// ****************************************************************************
void MolDraw2D::centrePicture(int width, int height) {
double y_mid = y_min_ + 0.5 * y_range_;
double x_mid = x_min_ + 0.5 * x_range_;
Point2D mid;
// this is getDrawCoords() but using height rather than height()
// to turn round the y coord and not using x_trans_ and y_trans_
// which we are trying to calculate at this point.
mid.x = scale_ * (x_mid - x_min_);
mid.y = scale_ * (y_mid - y_min_);
// y is now the distance from the top of the image, we need to
// invert that:
mid.x += x_offset_;
mid.y -= y_offset_;
mid.y = height - mid.y;
// that used the offset, we need to remove that:
mid.x -= x_offset_;
mid.y += y_offset_;
x_trans_ = (width / 2 - mid.x) / scale_;
y_trans_ = (mid.y - height / 2) / scale_;
};
namespace {} // namespace
// ****************************************************************************
void MolDraw2D::drawLine(const Point2D &cds1, const Point2D &cds2,
const DrawColour &col1, const DrawColour &col2) {
if (drawOptions().comicMode) {
setFillPolys(false);
if (col1 == col2) {
setColour(col1);
auto pts =
MolDraw2D_detail::handdrawnLine(cds1, cds2, scale_, true, true);
drawPolygon(pts);
} else {
Point2D mid = (cds1 + cds2) * 0.5;
setColour(col1);
auto pts =
MolDraw2D_detail::handdrawnLine(cds1, mid, scale_, true, false);
drawPolygon(pts);
setColour(col2);
auto pts2 =
MolDraw2D_detail::handdrawnLine(mid, cds2, scale_, false, true);
drawPolygon(pts2);
}
} else {
if (col1 == col2) {
setColour(col1);
drawLine(cds1, cds2);
} else {
Point2D mid = (cds1 + cds2) * 0.5;
setColour(col1);
drawLine(cds1, mid);
setColour(col2);
drawLine(mid, cds2);
}
}
}
// ****************************************************************************
void MolDraw2D::getStringSize(const std::string &label, double &label_width,
double &label_height) const {
text_drawer_->getStringSize(label, label_width, label_height);
label_width /= scale();
label_height /= scale();
// cout << label << " : " << label_width << " by " << label_height
// << " : " << scale() << endl;
}
// ****************************************************************************
void MolDraw2D::getLabelSize(const string &label, OrientType orient,
double &label_width, double &label_height) const {
if (orient == OrientType::N || orient == OrientType::S) {
label_height = 0.0;
label_width = 0.0;
vector<string> sym_bits = atomLabelToPieces(label, orient);
double height, width;
for (auto bit : sym_bits) {
getStringSize(bit, width, height);
if (width > label_width) {
label_width = width;
}
label_height += height;
}
} else {
getStringSize(label, label_width, label_height);
}
}
// ****************************************************************************
void MolDraw2D::getStringExtremes(const string &label, OrientType orient,
const Point2D &cds, double &x_min,
double &y_min, double &x_max,
double &y_max) const {
text_drawer_->getStringExtremes(label, orient, x_min, y_min, x_max, y_max);
Point2D draw_cds = getDrawCoords(cds);
x_min += draw_cds.x;
x_max += draw_cds.x;
y_min += draw_cds.y;
y_max += draw_cds.y;
Point2D new_mins = getAtomCoords(make_pair(x_min, y_min));
Point2D new_maxs = getAtomCoords(make_pair(x_max, y_max));
x_min = new_mins.x;
y_min = new_mins.y;
x_max = new_maxs.x;
y_max = new_maxs.y;
// draw coords to atom coords reverses y
if (y_min > y_max) {
swap(y_min, y_max);
}
}
// ****************************************************************************
// draws the string centred on cds
void MolDraw2D::drawString(const string &str, const Point2D &cds) {
Point2D draw_cds = getDrawCoords(cds);
text_drawer_->drawString(str, draw_cds, OrientType::N);
// int olw = lineWidth();
// setLineWidth(0);
// text_drawer_->drawStringRects(str, OrientType::N, draw_cds, *this);
// setLineWidth(olw);
}
// ****************************************************************************
void MolDraw2D::drawString(const std::string &str, const Point2D &cds,
TextAlignType talign) {
Point2D draw_cds = getDrawCoords(cds);
text_drawer_->drawString(str, draw_cds, talign);
}
// ****************************************************************************
DrawColour MolDraw2D::getColour(
int atom_idx, const std::vector<int> *highlight_atoms,
const std::map<int, DrawColour> *highlight_map) {
PRECONDITION(activeMolIdx_ >= 0, "bad mol idx");
PRECONDITION(atom_idx >= 0, "bad atom_idx");
PRECONDITION(rdcast<int>(atomic_nums_[activeMolIdx_].size()) > atom_idx,
"bad atom_idx");
DrawColour retval =
getColourByAtomicNum(atomic_nums_[activeMolIdx_][atom_idx]);
// set contents of highlight_atoms to red
if (!drawOptions().circleAtoms && !drawOptions().continuousHighlight) {
if (highlight_atoms &&
highlight_atoms->end() !=
find(highlight_atoms->begin(), highlight_atoms->end(), atom_idx)) {
retval = drawOptions().highlightColour;
}
// over-ride with explicit colour from highlight_map if there is one
if (highlight_map) {
auto p = highlight_map->find(atom_idx);
if (p != highlight_map->end()) {
retval = p->second;
}
}
}
return retval;
}
// ****************************************************************************
DrawColour MolDraw2D::getColourByAtomicNum(int atomic_num) {
DrawColour res;
if (drawOptions().atomColourPalette.find(atomic_num) !=
drawOptions().atomColourPalette.end()) {
res = drawOptions().atomColourPalette[atomic_num];
} else if (atomic_num != -1 && drawOptions().atomColourPalette.find(-1) !=
drawOptions().atomColourPalette.end()) {
// if -1 is in the palette, we use that for undefined colors
res = drawOptions().atomColourPalette[-1];
} else {
// if all else fails, default to black:
res = DrawColour(0, 0, 0);
}
return res;
}
// ****************************************************************************
unique_ptr<RWMol> MolDraw2D::setupDrawMolecule(
const ROMol &mol, const vector<int> *highlight_atoms,
const map<int, double> *highlight_radii, int confId, int width,
int height) {
// prepareMolForDrawing needs a RWMol but don't copy the original mol
// if we don't need to
unique_ptr<RWMol> rwmol;
if (drawOptions().prepareMolsBeforeDrawing || !mol.getNumConformers()) {
rwmol.reset(new RWMol(mol));
MolDraw2DUtils::prepareMolForDrawing(*rwmol);
}
if (drawOptions().centreMoleculesBeforeDrawing) {
if (!rwmol) rwmol.reset(new RWMol(mol));
if (rwmol->getNumConformers()) {
auto &conf = rwmol->getConformer(confId);
RDGeom::Transform3D tf;
auto centroid = MolTransforms::computeCentroid(conf);
centroid *= -1;
tf.SetTranslation(centroid);
MolTransforms::transformConformer(conf, tf);
MolTransforms::transformMolSubstanceGroups(*rwmol, tf);
}
}
ROMol const &draw_mol = rwmol ? *(rwmol) : mol;
if (!draw_mol.getNumConformers()) {
// clearly, the molecule is in a sorry state.
return rwmol;
}
if (drawOptions().addStereoAnnotation) {
MolDraw2D_detail::addStereoAnnotation(draw_mol);
}
if (drawOptions().addAtomIndices) {
MolDraw2D_detail::addAtomIndices(draw_mol);
}
if (drawOptions().addBondIndices) {
MolDraw2D_detail::addBondIndices(draw_mol);
}
if (!activeMolIdx_) {
if (drawOptions().clearBackground) {
clearDrawing();
}
}
bool updateBBox = !activeMolIdx_;
extractAtomCoords(draw_mol, confId, updateBBox);
extractAtomSymbols(draw_mol);
extractAtomNotes(draw_mol);
extractBondNotes(draw_mol);
extractRadicals(draw_mol);
extractBrackets(draw_mol);
if (!activeMolIdx_ && needs_scale_) {
calculateScale(width, height, draw_mol, highlight_atoms, highlight_radii);
needs_scale_ = false;
}
return rwmol;
}
// ****************************************************************************
void MolDraw2D::pushDrawDetails() {
at_cds_.push_back(std::vector<Point2D>());
atomic_nums_.push_back(std::vector<int>());
atom_syms_.push_back(std::vector<std::pair<std::string, OrientType>>());
annotations_.push_back(std::vector<AnnotationType>());
shapes_.push_back(std::vector<MolDrawShape>());
radicals_.push_back(
std::vector<std::pair<std::shared_ptr<StringRect>, OrientType>>());
activeMolIdx_++;
}
// ****************************************************************************
void MolDraw2D::popDrawDetails() {
activeMolIdx_--;
annotations_.pop_back();
shapes_.pop_back();
atom_syms_.pop_back();
atomic_nums_.pop_back();
radicals_.pop_back();
at_cds_.pop_back();
}
// ****************************************************************************
unique_ptr<RWMol> MolDraw2D::setupMoleculeDraw(
const ROMol &mol, const vector<int> *highlight_atoms,
const map<int, double> *highlight_radii, int confId) {
unique_ptr<RWMol> rwmol =
setupDrawMolecule(mol, highlight_atoms, highlight_radii, confId,
panelWidth(), drawHeight());
ROMol const &draw_mol = rwmol ? *(rwmol) : mol;
if (drawOptions().includeAtomTags) {
tagAtoms(draw_mol);
}
if (drawOptions().atomRegions.size()) {
for (const std::vector<int> &region : drawOptions().atomRegions) {
if (region.size() > 1) {
Point2D minv = at_cds_[activeMolIdx_][region[0]];
Point2D maxv = at_cds_[activeMolIdx_][region[0]];
for (int idx : region) {
const Point2D &pt = at_cds_[activeMolIdx_][idx];
minv.x = std::min(minv.x, pt.x);
minv.y = std::min(minv.y, pt.y);
maxv.x = std::max(maxv.x, pt.x);
maxv.y = std::max(maxv.y, pt.y);
}
Point2D center = (maxv + minv) / 2;
Point2D size = (maxv - minv);
size *= 0.2;
minv -= size / 2;
maxv += size / 2;
setColour(DrawColour(.8, .8, .8));
// drawEllipse(minv,maxv);
drawRect(minv, maxv);
}
}
}
return rwmol;
}
// ****************************************************************************
void MolDraw2D::setupTextDrawer() {
text_drawer_->setMaxFontSize(drawOptions().maxFontSize);
text_drawer_->setMinFontSize(drawOptions().minFontSize);
try {
text_drawer_->setFontFile(drawOptions().fontFile);
} catch (std::runtime_error &e) {
BOOST_LOG(rdWarningLog) << e.what() << std::endl;
text_drawer_->setFontFile("");
BOOST_LOG(rdWarningLog) << "Falling back to original font file "
<< text_drawer_->getFontFile() << "." << std::endl;
}
}
// ****************************************************************************
void MolDraw2D::drawBonds(
const ROMol &draw_mol, const vector<int> *highlight_atoms,
const map<int, DrawColour> *highlight_atom_map,
const vector<int> *highlight_bonds,
const map<int, DrawColour> *highlight_bond_map,
const std::vector<std::pair<DrawColour, DrawColour>> *bond_colours) {
for (auto this_at : draw_mol.atoms()) {
int this_idx = this_at->getIdx();
for (const auto &nbri :
make_iterator_range(draw_mol.getAtomBonds(this_at))) {
const Bond *bond = draw_mol[nbri];
int nbr_idx = bond->getOtherAtomIdx(this_idx);
if (nbr_idx < static_cast<int>(at_cds_[activeMolIdx_].size()) &&
nbr_idx > this_idx) {
drawBond(draw_mol, bond, this_idx, nbr_idx, highlight_atoms,
highlight_atom_map, highlight_bonds, highlight_bond_map,
bond_colours);
}
}
}
}
// ****************************************************************************
void MolDraw2D::finishMoleculeDraw(const RDKit::ROMol &draw_mol,
const vector<DrawColour> &atom_colours) {
if (drawOptions().dummiesAreAttachments) {
for (auto at1 : draw_mol.atoms()) {
if (at1->hasProp(common_properties::atomLabel) ||
drawOptions().atomLabels.find(at1->getIdx()) !=
drawOptions().atomLabels.end()) {
// skip dummies that explicitly have a label provided
continue;
}
if (at1->getAtomicNum() == 0 && at1->getDegree() == 1) {
Point2D &at1_cds = at_cds_[activeMolIdx_][at1->getIdx()];
const auto &iter_pair = draw_mol.getAtomNeighbors(at1);
const Atom *at2 = draw_mol[*iter_pair.first];
Point2D &at2_cds = at_cds_[activeMolIdx_][at2->getIdx()];
drawAttachmentLine(at2_cds, at1_cds, DrawColour(.5, .5, .5));
}
}
}
for (int i = 0, is = atom_syms_[activeMolIdx_].size(); i < is; ++i) {
if (!atom_syms_[activeMolIdx_][i].first.empty()) {
drawAtomLabel(i, atom_colours[i]);
}
}
text_drawer_->setColour(DrawColour(0.0, 0.0, 0.0));
if (!supportsAnnotations() && !annotations_.empty()) {
BOOST_LOG(rdWarningLog) << "annotations not currently supported for this "
"MolDraw2D class, they will be ignored."
<< std::endl;
} else {
for (const auto &annotation : annotations_[activeMolIdx_]) {
drawAnnotation(annotation);
}
}
if (drawOptions().includeRadicals) {
drawRadicals(draw_mol);
}
if (!shapes_[activeMolIdx_].empty()) {
MolDraw2D_detail::drawShapes(*this, shapes_[activeMolIdx_]);
}
if (drawOptions().flagCloseContactsDist >= 0) {
highlightCloseContacts();
}
}
// ****************************************************************************
void MolDraw2D::drawLegend(const string &legend) {
int olh = legend_height_;
legend_height_ = 0; // so we use the whole panel
auto calc_legend_height = [&](const std::vector<std::string> &legend_bits,
double &total_width, double &total_height) {
total_width = total_height = 0;
for (auto bit : legend_bits) {
double x_min, y_min, x_max, y_max;
text_drawer_->getStringExtremes(bit, OrientType::N, x_min, y_min, x_max,
y_max, true);
total_height += y_max - y_min;
total_width = std::max(total_width, x_max - x_min);
}
};
if (!legend.empty()) {
std::vector<std::string> legend_bits;
// split any strings on newlines
string next_piece;
for (auto c : legend) {
if (c == '\n') {
if (!next_piece.empty()) {
legend_bits.push_back(next_piece);
}
next_piece = "";
} else {
next_piece += c;
}
}
if (!next_piece.empty()) {
legend_bits.push_back(next_piece);
}
double ominfs = text_drawer_->minFontSize();
text_drawer_->setMinFontSize(-1);
double o_font_scale = text_drawer_->fontScale();
double fsize = text_drawer_->fontSize();
double new_font_scale = o_font_scale * drawOptions().legendFontSize / fsize;
text_drawer_->setFontScale(new_font_scale);
double total_width, total_height;
calc_legend_height(legend_bits, total_width, total_height);
if (total_height > olh) {
new_font_scale *= double(olh) / total_height;
text_drawer_->setFontScale(new_font_scale);
calc_legend_height(legend_bits, total_width, total_height);
}
if (total_width > panelWidth()) {
new_font_scale *= double(panelWidth()) / total_width;
text_drawer_->setFontScale(new_font_scale);
calc_legend_height(legend_bits, total_width, total_height);
}
text_drawer_->setColour(drawOptions().legendColour);
Point2D loc(x_offset_ + panelWidth() / 2,
y_offset_ + panelHeight() - total_height);
for (auto bit : legend_bits) {
text_drawer_->drawString(bit, loc, TextAlignType::MIDDLE);
double x_min, y_min, x_max, y_max;
text_drawer_->getStringExtremes(bit, OrientType::N, x_min, y_min, x_max,
y_max, true);
loc.y += y_max - y_min;
}
text_drawer_->setMinFontSize(ominfs);
text_drawer_->setFontScale(o_font_scale);
}
legend_height_ = olh;
}
// ****************************************************************************
void MolDraw2D::drawHighlightedAtom(int atom_idx,
const vector<DrawColour> &colours,
const map<int, double> *highlight_radii) {
double xradius, yradius;
Point2D centre;
calcLabelEllipse(atom_idx, highlight_radii, centre, xradius, yradius);
int orig_lw = lineWidth();
bool orig_fp = fillPolys();
if (!drawOptions().fillHighlights) {
setLineWidth(getHighlightBondWidth(-1, nullptr));
setFillPolys(false);
} else {
setFillPolys(true);
}
if (colours.size() == 1) {
setColour(colours.front());
Point2D offset(xradius, yradius);
Point2D p1 = centre - offset;
Point2D p2 = centre + offset;
if (fillPolys()) {
setLineWidth(1);
}
drawEllipse(p1, p2);
// drawArc(centre, xradius, yradius, 0.0, 360.0);
} else {
double arc_size = 360.0 / double(colours.size());
double arc_start = -90.0;
for (size_t i = 0; i < colours.size(); ++i) {
setColour(colours[i]);
drawArc(centre, xradius, yradius, arc_start, arc_start + arc_size);
arc_start += arc_size;
}
}
setFillPolys(orig_fp);
setLineWidth(orig_lw);
}
// ****************************************************************************
void MolDraw2D::calcLabelEllipse(int atom_idx,
const map<int, double> *highlight_radii,
Point2D &centre, double &xradius,
double &yradius) const {
centre = at_cds_[activeMolIdx_][atom_idx];
xradius = drawOptions().highlightRadius;
yradius = xradius;
if (highlight_radii &&
highlight_radii->find(atom_idx) != highlight_radii->end()) {
xradius = highlight_radii->find(atom_idx)->second;
yradius = xradius;
}
if (drawOptions().atomHighlightsAreCircles ||
atom_syms_[activeMolIdx_][atom_idx].first.empty()) {
return;
}
string atsym = atom_syms_[activeMolIdx_][atom_idx].first;
OrientType orient = atom_syms_[activeMolIdx_][atom_idx].second;
double x_min, y_min, x_max, y_max;
getStringExtremes(atsym, orient, centre, x_min, y_min, x_max, y_max);
static const double root_2 = sqrt(2.0);
xradius = max(xradius, root_2 * 0.5 * (x_max - x_min));
yradius = max(yradius, root_2 * 0.5 * (y_max - y_min));
centre.x = 0.5 * (x_max + x_min);
centre.y = 0.5 * (y_max + y_min);
}
// ****************************************************************************
StringRect MolDraw2D::calcAnnotationPosition(const ROMol &mol,
const Atom *atom) {
StringRect note_rect;
string note = atom->getProp<string>(common_properties::atomNote);
if (note.empty()) {
note_rect.width_ = -1.0; // so we know it's not valid.
return note_rect;
}
Point2D const &at_cds = at_cds_[activeMolIdx_][atom->getIdx()];
note_rect.trans_.x = at_cds.x;
note_rect.trans_.y = at_cds.y;
double start_ang = getNoteStartAngle(mol, atom);
calcAtomAnnotationPosition(mol, atom, start_ang, note_rect);
return note_rect;
}
// ****************************************************************************
StringRect MolDraw2D::calcAnnotationPosition(const ROMol &mol,
const Bond *bond) {
StringRect note_rect;
string note = bond->getProp<string>(common_properties::bondNote);
if (note.empty()) {
note_rect.width_ = -1.0; // so we know it's not valid.
return note_rect;
}
vector<std::shared_ptr<StringRect>> rects;
vector<TextDrawType> draw_modes;
vector<char> draw_chars;
// at this point, the scale() should still be 1, so min and max font sizes
// don't make sense, as we're effectively operating on atom coords rather
// than draw.
double full_font_scale = text_drawer_->fontScale();
double min_fs = text_drawer_->minFontSize();
text_drawer_->setMinFontSize(-1);
double max_fs = text_drawer_->maxFontSize();
text_drawer_->setMaxFontSize(-1);
text_drawer_->setFontScale(drawOptions().annotationFontScale *
full_font_scale);
text_drawer_->getStringRects(note, OrientType::N, rects, draw_modes,
draw_chars);
text_drawer_->setFontScale(full_font_scale);
text_drawer_->setMinFontSize(min_fs);
text_drawer_->setMaxFontSize(max_fs);
Point2D const &at1_cds = at_cds_[activeMolIdx_][bond->getBeginAtomIdx()];
Point2D const &at2_cds = at_cds_[activeMolIdx_][bond->getEndAtomIdx()];
Point2D perp = calcPerpendicular(at1_cds, at2_cds);
Point2D bond_vec = at1_cds.directionVector(at2_cds);
double bond_len = (at1_cds - at2_cds).length();
vector<double> mid_offsets{0.5, 0.33, 0.66, 0.25, 0.75};
double offset_step = drawOptions().multipleBondOffset;
StringRect least_worst_rect = StringRect();
least_worst_rect.clash_score_ = 100;
for (auto mo : mid_offsets) {
Point2D mid = at1_cds + bond_vec * bond_len * mo;
for (int j = 1; j < 6; ++j) {
if (j == 1 && bond->getBondType() > 1) {
continue; // multiple bonds will need a bigger offset.
}
double offset = j * offset_step;
note_rect.trans_ = mid + perp * offset;
StringRect tr(note_rect);
tr.trans_ =
getAtomCoords(make_pair(note_rect.trans_.x, note_rect.trans_.y));
tr.width_ *= scale();
tr.height_ *= scale();
if (!doesBondNoteClash(tr, rects, mol, bond)) {
return note_rect;
}
if (note_rect.clash_score_ < least_worst_rect.clash_score_) {
least_worst_rect = note_rect;
}
note_rect.trans_ = mid - perp * offset;
tr.trans_ =
getAtomCoords(make_pair(note_rect.trans_.x, note_rect.trans_.y));
if (!doesBondNoteClash(tr, rects, mol, bond)) {
return note_rect;
}
if (note_rect.clash_score_ < least_worst_rect.clash_score_) {
least_worst_rect = note_rect;
}
}
}
return least_worst_rect;
}
// ****************************************************************************
void MolDraw2D::calcAtomAnnotationPosition(const ROMol &mol, const Atom *atom,
double start_ang, StringRect &rect) {
Point2D const &at_cds = at_cds_[activeMolIdx_][atom->getIdx()];
auto const &atsym = atom_syms_[activeMolIdx_][atom->getIdx()];
string note = atom->getProp<string>(common_properties::atomNote);
vector<std::shared_ptr<StringRect>> rects;
vector<TextDrawType> draw_modes;
vector<char> draw_chars;
// at this point, the scale() should still be 1, so min and max font sizes
// don't make sense, as we're effectively operating on atom coords rather
// than draw.
double full_font_scale = text_drawer_->fontScale();
double min_fs = text_drawer_->minFontSize();
text_drawer_->setMinFontSize(-1);
double max_fs = text_drawer_->maxFontSize();
text_drawer_->setMaxFontSize(-1);
text_drawer_->setFontScale(drawOptions().annotationFontScale *
full_font_scale);
text_drawer_->getStringRects(note, OrientType::N, rects, draw_modes,
draw_chars);
text_drawer_->setFontScale(full_font_scale);
text_drawer_->setMinFontSize(min_fs);
text_drawer_->setMaxFontSize(max_fs);
double rad_step = 0.25;
StringRect least_worst_rect = StringRect();
least_worst_rect.clash_score_ = 100;
for (int j = 1; j < 4; ++j) {
double note_rad = j * rad_step;
// experience suggests if there's an atom symbol, the close in
// radius won't work.
if (j == 1 && !atsym.first.empty()) {
continue;
}
// scan at 30 degree intervals around the atom looking for somewhere
// clear for the annotation.
for (int i = 0; i < 12; ++i) {
double ang = start_ang + i * 30.0 * M_PI / 180.0;
rect.trans_.x = at_cds.x + cos(ang) * note_rad;
rect.trans_.y = at_cds.y + sin(ang) * note_rad;
// doesAtomNoteClash expects the rect to be in draw coords
StringRect tr(rect);
tr.trans_ = getAtomCoords(make_pair(rect.trans_.x, rect.trans_.y));
tr.width_ *= scale();
tr.height_ *= scale();
if (!doesAtomNoteClash(tr, rects, mol, atom->getIdx())) {
return;
} else {
if (rect.clash_score_ < least_worst_rect.clash_score_) {
least_worst_rect = rect;
}
}
}
}
rect = least_worst_rect;
}
// ****************************************************************************
void MolDraw2D::drawHighlightedBonds(
const RDKit::ROMol &mol,
const map<int, vector<DrawColour>> &highlight_bond_map,
const map<int, int> &highlight_linewidth_multipliers,
const map<int, double> *highlight_radii) {
int orig_lw = lineWidth();
for (auto hb : highlight_bond_map) {
int bond_idx = hb.first;
if (!drawOptions().fillHighlights) {
setLineWidth(
getHighlightBondWidth(bond_idx, &highlight_linewidth_multipliers));
}
auto bond = mol.getBondWithIdx(bond_idx);
int at1_idx = bond->getBeginAtomIdx();
int at2_idx = bond->getEndAtomIdx();
Point2D at1_cds = at_cds_[activeMolIdx_][at1_idx];
Point2D at2_cds = at_cds_[activeMolIdx_][at2_idx];
Point2D perp = calcPerpendicular(at1_cds, at2_cds);
double rad = 0.7 * drawOptions().highlightRadius;
auto draw_adjusted_line = [&](Point2D p1, Point2D p2) {
adjustLineEndForHighlight(at1_idx, highlight_radii, p2, p1);
adjustLineEndForHighlight(at2_idx, highlight_radii, p1, p2);
bool orig_lws = drawOptions().scaleBondWidth;
drawOptions().scaleBondWidth = drawOptions().scaleHighlightBondWidth;
drawLine(p1, p2);
drawOptions().scaleBondWidth = orig_lws;
};
if (hb.second.size() < 2) {
DrawColour col;
if (hb.second.empty()) {
col = drawOptions().highlightColour;
} else {
col = hb.second.front();
}
setColour(col);
if (drawOptions().fillHighlights) {
vector<Point2D> line_pts;
line_pts.emplace_back(at1_cds + perp * rad);
line_pts.emplace_back(at2_cds + perp * rad);
line_pts.emplace_back(at2_cds - perp * rad);
line_pts.emplace_back(at1_cds - perp * rad);
drawPolygon(line_pts);
} else {
draw_adjusted_line(at1_cds + perp * rad, at2_cds + perp * rad);
draw_adjusted_line(at1_cds - perp * rad, at2_cds - perp * rad);
}
} else {
double col_rad = 2.0 * rad / hb.second.size();
if (drawOptions().fillHighlights) {
Point2D p1 = at1_cds - perp * rad;
Point2D p2 = at2_cds - perp * rad;
vector<Point2D> line_pts;
for (size_t i = 0; i < hb.second.size(); ++i) {
setColour(hb.second[i]);
line_pts.clear();
line_pts.emplace_back(p1);
line_pts.emplace_back(p1 + perp * col_rad);
line_pts.emplace_back(p2 + perp * col_rad);
line_pts.emplace_back(p2);
drawPolygon(line_pts);
p1 += perp * col_rad;
p2 += perp * col_rad;
}
} else {
int step = 0;
for (size_t i = 0; i < hb.second.size(); ++i) {
setColour(hb.second[i]);
// draw even numbers from the bottom, odd from the top
Point2D offset = perp * (rad - step * col_rad);
if (!(i % 2)) {
draw_adjusted_line(at1_cds - offset, at2_cds - offset);
} else {
draw_adjusted_line(at1_cds + offset, at2_cds + offset);
step++;
}
}
}
}
setLineWidth(orig_lw);
}
}
// ****************************************************************************
int MolDraw2D::getHighlightBondWidth(
int bond_idx, const map<int, int> *highlight_linewidth_multipliers) const {
int bwm = drawOptions().highlightBondWidthMultiplier;
// if we're not doing filled highlights, the lines need to be narrower
if (!drawOptions().fillHighlights) {
bwm /= 2;
if (bwm < 1) {
bwm = 1;
}
}
if (highlight_linewidth_multipliers &&
!highlight_linewidth_multipliers->empty()) {
auto it = highlight_linewidth_multipliers->find(bond_idx);
if (it != highlight_linewidth_multipliers->end()) {
bwm = it->second;
}
}
int tgt_lw = lineWidth() * bwm;
return tgt_lw;
}
// ****************************************************************************
void MolDraw2D::adjustLineEndForHighlight(
int at_idx, const map<int, double> *highlight_radii, Point2D p1,
Point2D &p2) const {
// this code is transliterated from
// http://csharphelper.com/blog/2017/08/calculate-where-a-line-segment-and-an-ellipse-intersect-in-c/
// which has it in C#
double xradius, yradius;
Point2D centre;
calcLabelEllipse(at_idx, highlight_radii, centre, xradius, yradius);
// cout << "ellipse is : " << centre.x << ", " << centre.y << " rads " <<
// xradius << " and " << yradius << endl; cout << "p1 = " << p1.x << ", " <<
// p1.y << endl << "p2 = " << p2.x << ", " << p2.y << endl;
if (xradius < 1.0e-6 || yradius < 1.0e-6) {
return;
}
// move everything so the ellipse is centred on the origin.
p1 -= centre;
p2 -= centre;
double a2 = xradius * xradius;
double b2 = yradius * yradius;
double A =
(p2.x - p1.x) * (p2.x - p1.x) / a2 + (p2.y - p1.y) * (p2.y - p1.y) / b2;
double B = 2.0 * p1.x * (p2.x - p1.x) / a2 + 2.0 * p1.y * (p2.y - p1.y) / b2;
double C = p1.x * p1.x / a2 + p1.y * p1.y / b2 - 1.0;
auto t_to_point = [&](double t) -> Point2D {
Point2D ret_val;
ret_val.x = p1.x + (p2.x - p1.x) * t + centre.x;
ret_val.y = p1.y + (p2.y - p1.y) * t + centre.y;
return ret_val;
};
double disc = B * B - 4.0 * A * C;
if (disc < 0.0) {
// no solutions, leave things as they are. Bit crap, though.
return;
} else if (fabs(disc) < 1.0e-6) {
// 1 solution
double t = -B / (2.0 * A);
// cout << "t = " << t << endl;
p2 = t_to_point(t);
} else {
// 2 solutions - take the one nearest p1.
double disc_rt = sqrt(disc);
double t1 = (-B + disc_rt) / (2.0 * A);
double t2 = (-B - disc_rt) / (2.0 * A);
// cout << "t1 = " << t1 << " t2 = " << t2 << endl;
double t;
// prefer the t between 0 and 1, as that must be between the original
// points. If both are, prefer the lower, as that will be nearest p1,
// so on the bit of the ellipse the line comes to first.
bool t1_ok = (t1 >= 0.0 && t1 <= 1.0);
bool t2_ok = (t2 >= 0.0 && t2 <= 1.0);
if (t1_ok && !t2_ok) {
t = t1;
} else if (t2_ok && !t1_ok) {
t = t2;
} else if (t1_ok && t2_ok) {
t = min(t1, t2);
} else {
// the intersections are both outside the line between p1 and p2
// so don't do anything.
return;
}
// cout << "using t = " << t << endl;
p2 = t_to_point(t);
}
// cout << "p2 = " << p2.x << ", " << p2.y << endl;
}
// ****************************************************************************
void MolDraw2D::extractAtomCoords(const ROMol &mol, int confId,
bool updateBBox) {
PRECONDITION(activeMolIdx_ >= 0, "no mol id");
PRECONDITION(static_cast<int>(at_cds_.size()) > activeMolIdx_, "no space");
PRECONDITION(static_cast<int>(atomic_nums_.size()) > activeMolIdx_,
"no space");
PRECONDITION(static_cast<int>(mol.getNumConformers()) > 0, "no coords");
if (updateBBox) {
bbox_[0].x = bbox_[0].y = numeric_limits<double>::max();
bbox_[1].x = bbox_[1].y = -1 * numeric_limits<double>::max();
}
const RDGeom::POINT3D_VECT &locs = mol.getConformer(confId).getPositions();
// the transformation rotates anti-clockwise, as is conventional, but
// probably not what our user expects.
double rot = -drawOptions().rotate * M_PI / 180.0;
// assuming that if drawOptions().rotate is set to 0.0, rot will be
// exactly 0.0 without worrying about floating point number dust. Does
// anyone know if this is true? It's not the end of the world if not,
// as it's just an extra largely pointless rotation.
// Floating point numbers are like piles of sand; every time you move
// them around, you lose a little sand and pick up a little dirt.
// — Brian Kernighan and P.J. Plauger
// Nothing brings fear to my heart more than a floating point number.
// — Gerald Jay Sussman
// Some developers, when encountering a problem, say: “I know, I’ll
// use floating-point numbers!” Now, they have 1.9999999997 problems.
// — unknown
RDGeom::Transform2D trans;
trans.SetTransform(Point2D(0.0, 0.0), rot);
at_cds_[activeMolIdx_].clear();
for (auto this_at : mol.atoms()) {
int this_idx = this_at->getIdx();
Point2D pt(locs[this_idx].x, locs[this_idx].y);
if (rot != 0.0) {
trans.TransformPoint(pt);
}
at_cds_[activeMolIdx_].emplace_back(pt);
if (updateBBox) {
bbox_[0].x = std::min(bbox_[0].x, pt.x);
bbox_[0].y = std::min(bbox_[0].y, pt.y);
bbox_[1].x = std::max(bbox_[1].x, pt.x);
bbox_[1].y = std::max(bbox_[1].y, pt.y);
}
}
}
// ****************************************************************************
void MolDraw2D::extractAtomSymbols(const ROMol &mol) {
PRECONDITION(activeMolIdx_ >= 0, "no mol id");
PRECONDITION(static_cast<int>(atom_syms_.size()) > activeMolIdx_, "no space");
PRECONDITION(static_cast<int>(atomic_nums_.size()) > activeMolIdx_,
"no space");
atomic_nums_[activeMolIdx_].clear();
for (auto at1 : mol.atoms()) {
atom_syms_[activeMolIdx_].emplace_back(getAtomSymbolAndOrientation(*at1));
atomic_nums_[activeMolIdx_].emplace_back(at1->getAtomicNum());
}
}
// ****************************************************************************
void MolDraw2D::extractAtomNotes(const ROMol &mol) {
PRECONDITION(activeMolIdx_ >= 0, "no mol id");
PRECONDITION(static_cast<int>(annotations_.size()) > activeMolIdx_,
"no space");
for (auto atom : mol.atoms()) {
std::string note;
if (atom->getPropIfPresent(common_properties::atomNote, note)) {
if (!note.empty()) {
auto note_rect = calcAnnotationPosition(mol, atom);
if (note_rect.width_ < 0.0) {
cerr << "Couldn't find good place for note " << note << " for atom "
<< atom->getIdx() << endl;
} else {
AnnotationType annot;
annot.text_ = note;
annot.rect_ = note_rect;
annotations_[activeMolIdx_].push_back(annot);
}
}
}
}
}
// ****************************************************************************
void MolDraw2D::extractBondNotes(const ROMol &mol) {
PRECONDITION(activeMolIdx_ >= 0, "no mol id");
PRECONDITION(static_cast<int>(annotations_.size()) > activeMolIdx_,
"no space");
for (auto bond : mol.bonds()) {
std::string note;
if (bond->getPropIfPresent(common_properties::bondNote, note)) {
if (!note.empty()) {
auto note_rect = calcAnnotationPosition(mol, bond);
if (note_rect.width_ < 0.0) {
cerr << "Couldn't find good place for note " << note << " for bond "
<< bond->getIdx() << endl;
} else {
AnnotationType annot;
annot.text_ = note;
annot.rect_ = note_rect;
annotations_[activeMolIdx_].push_back(annot);
}
}
}
}
}
// ****************************************************************************
void MolDraw2D::extractRadicals(const ROMol &mol) {
PRECONDITION(activeMolIdx_ >= 0, "no mol id");
PRECONDITION(static_cast<int>(radicals_.size()) > activeMolIdx_, "no space");
for (auto atom : mol.atoms()) {
if (!atom->getNumRadicalElectrons()) {
continue;
}
std::shared_ptr<StringRect> rad_rect(new StringRect);
OrientType orient = calcRadicalRect(mol, atom, *rad_rect);
radicals_[activeMolIdx_].push_back(make_pair(rad_rect, orient));
}
}
// ****************************************************************************
void MolDraw2D::extractBrackets(const ROMol &mol) {
PRECONDITION(activeMolIdx_ >= 0, "no mol id");
PRECONDITION(static_cast<int>(shapes_.size()) > activeMolIdx_, "no space");
PRECONDITION(static_cast<int>(annotations_.size()) > activeMolIdx_,
"no space");
shapes_[activeMolIdx_].clear();
auto &sgs = getSubstanceGroups(mol);
if (sgs.empty()) {
return;
}
// details of this transformation are in extractAtomCoords
double rot = -drawOptions().rotate * M_PI / 180.0;
RDGeom::Transform2D trans;
trans.SetTransform(Point2D(0.0, 0.0), rot);
for (auto &sg : sgs) {
if (sg.getBrackets().empty()) {
continue;
}
// figure out the location of the reference point we'll use to figure out
// which direction the bracket points
// Thanks to John Mayfield for the thoughts on the best way to do this:
// http://efficientbits.blogspot.com/2015/11/bringing-molfile-sgroups-to-cdk.html
Point2D refPt{0., 0.};
if (!sg.getAtoms().empty()) {
// use the average position of the atoms in the sgroup
for (auto aidx : sg.getAtoms()) {
refPt += at_cds_[activeMolIdx_][aidx];
}
refPt /= sg.getAtoms().size();
}
std::vector<std::pair<Point2D, Point2D>> sgBondSegments;
for (auto bndIdx : sg.getBonds()) {
const auto bnd = mol.getBondWithIdx(bndIdx);
if (std::find(sg.getAtoms().begin(), sg.getAtoms().end(),
bnd->getBeginAtomIdx()) != sg.getAtoms().end()) {
sgBondSegments.push_back(
std::make_pair(at_cds_[activeMolIdx_][bnd->getBeginAtomIdx()],
at_cds_[activeMolIdx_][bnd->getEndAtomIdx()]));
} else if (std::find(sg.getAtoms().begin(), sg.getAtoms().end(),
bnd->getEndAtomIdx()) != sg.getAtoms().end()) {
sgBondSegments.push_back(
std::make_pair(at_cds_[activeMolIdx_][bnd->getEndAtomIdx()],
at_cds_[activeMolIdx_][bnd->getBeginAtomIdx()]));
}
}
for (const auto &brk : sg.getBrackets()) {
Point2D p1{brk[0]};
Point2D p2{brk[1]};
trans.TransformPoint(p1);
trans.TransformPoint(p2);
MolDrawShape shp;
shp.points =
MolDraw2D_detail::getBracketPoints(p1, p2, refPt, sgBondSegments);
shp.shapeType = MolDrawShapeType::Polyline;
shapes_[activeMolIdx_].emplace_back(std::move(shp));
}
if (supportsAnnotations()) {
// FIX: we could imagine changing this to always show the annotations on
// the right-most (or bottom-most) bracket
std::string connect;
if (sg.getPropIfPresent("CONNECT", connect)) {
// annotations go on the last bracket of an sgroup
const auto &brkShp = shapes_[activeMolIdx_].back();
StringRect rect;
// CONNECT goes at the top
auto topPt = brkShp.points[1];
auto brkPt = brkShp.points[0];
if (brkShp.points[2].y > topPt.y) {
topPt = brkShp.points[2];
brkPt = brkShp.points[3];
}
rect.trans_ = topPt + (topPt - brkPt);
AnnotationType annot;
annot.text_ = connect;
annot.rect_ = rect;
// if we're to the right of the bracket, we need to left justify,
// otherwise things seem to work as is
if (brkPt.x < topPt.x) {
annot.align_ = TextAlignType::START;
}
annotations_[activeMolIdx_].push_back(annot);
}
std::string label;
if (sg.getPropIfPresent("LABEL", label)) {
// annotations go on the last bracket of an sgroup
const auto &brkShp = shapes_[activeMolIdx_].back();
StringRect rect;
// LABEL goes at the bottom
auto botPt = brkShp.points[2];
auto brkPt = brkShp.points[3];
if (brkShp.points[1].y < botPt.y) {
botPt = brkShp.points[1];
brkPt = brkShp.points[0];
}
rect.trans_ = botPt + (botPt - brkPt);
AnnotationType annot;
annot.text_ = label;
annot.rect_ = rect;
annotations_[activeMolIdx_].push_back(annot);
}
}
}
} // namespace RDKit
// ****************************************************************************
void MolDraw2D::drawBond(
const ROMol &mol, const Bond *bond, int at1_idx, int at2_idx,
const vector<int> *highlight_atoms,
const map<int, DrawColour> *highlight_atom_map,
const vector<int> *highlight_bonds,
const map<int, DrawColour> *highlight_bond_map,
const std::vector<std::pair<DrawColour, DrawColour>> *bond_colours) {
PRECONDITION(bond, "no bond");
PRECONDITION(activeMolIdx_ >= 0, "bad mol idx");
RDUNUSED_PARAM(highlight_atoms);
RDUNUSED_PARAM(highlight_atom_map);
static const DashPattern noDash;
static const DashPattern dots = assign::list_of(2)(6);
static const DashPattern dashes = assign::list_of(6)(6);
static const DashPattern shortDashes = assign::list_of(2)(2);
const Atom *at1 = mol.getAtomWithIdx(at1_idx);
const Atom *at2 = mol.getAtomWithIdx(at2_idx);
Point2D at1_cds = at_cds_[activeMolIdx_][at1_idx];
Point2D at2_cds = at_cds_[activeMolIdx_][at2_idx];
double double_bond_offset = options_.multipleBondOffset;
// mol files from, for example, Marvin use a bond length of 1 for just about
// everything. When this is the case, the default multipleBondOffset is just
// too much, so scale it back.
if ((at1_cds - at2_cds).lengthSq() < 1.4) {
double_bond_offset *= 0.6;
}
adjustBondEndForLabel(at1_idx, at2_cds, at1_cds);
adjustBondEndForLabel(at2_idx, at1_cds, at2_cds);
bool highlight_bond = false;
if (highlight_bonds &&
std::find(highlight_bonds->begin(), highlight_bonds->end(),
bond->getIdx()) != highlight_bonds->end()) {
highlight_bond = true;
}
DrawColour col1, col2;
int orig_lw = lineWidth();
if (bond_colours) {
col1 = (*bond_colours)[bond->getIdx()].first;
col2 = (*bond_colours)[bond->getIdx()].second;
} else {
if (!highlight_bond) {
col1 = getColour(at1_idx);
col2 = getColour(at2_idx);
} else {
if (highlight_bond_map && highlight_bond_map->find(bond->getIdx()) !=
highlight_bond_map->end()) {
col1 = col2 = highlight_bond_map->find(bond->getIdx())->second;
} else {
col1 = col2 = drawOptions().highlightColour;
}
if (drawOptions().continuousHighlight) {
setLineWidth(getHighlightBondWidth(bond->getIdx(), nullptr));
} else {
setLineWidth(getHighlightBondWidth(bond->getIdx(), nullptr) / 4);
}
}
}
Bond::BondType bt = bond->getBondType();
bool isComplex = false;
if (bond->hasQuery()) {
std::string descr = bond->getQuery()->getDescription();
if (bond->getQuery()->getNegation() || descr != "BondOrder") {
isComplex = true;
}
if (isComplex) {
setDash(dots);
bool orig_slw = drawOptions().scaleBondWidth;
if (highlight_bond) {
drawOptions().scaleBondWidth = drawOptions().scaleHighlightBondWidth;
}
drawLine(at1_cds, at2_cds, col1, col2);
drawOptions().scaleBondWidth = orig_slw;
setDash(noDash);
} else {
bt = static_cast<Bond::BondType>(
static_cast<BOND_EQUALS_QUERY *>(bond->getQuery())->getVal());
}
}
if (!isComplex) {
// it's a double bond and one end is 1-connected, do two lines parallel
// to the atom-atom line.
if (bt == Bond::DOUBLE || bt == Bond::AROMATIC) {
Point2D l1s, l1f, l2s, l2f;
calcDoubleBondLines(mol, double_bond_offset, bond, at1_cds, at2_cds, l1s,
l1f, l2s, l2f);
bool orig_slw = drawOptions().scaleBondWidth;
if (highlight_bond) {
drawOptions().scaleBondWidth = drawOptions().scaleHighlightBondWidth;
}
drawLine(l1s, l1f, col1, col2);
if (bt == Bond::AROMATIC) {
setDash(dashes);
}
drawLine(l2s, l2f, col1, col2);
if (bt == Bond::AROMATIC) {
setDash(noDash);
}
drawOptions().scaleBondWidth = orig_slw;
} else if (Bond::SINGLE == bt && (Bond::BEGINWEDGE == bond->getBondDir() ||
Bond::BEGINDASH == bond->getBondDir())) {
// std::cerr << "WEDGE: from " << at1->getIdx() << " | "
// << bond->getBeginAtomIdx() << "-" << bond->getEndAtomIdx()
// << std::endl;
// swap the direction if at1 has does not have stereochem set
// or if at2 does have stereochem set and the bond starts there
if ((at1->getChiralTag() != Atom::CHI_TETRAHEDRAL_CW &&
at1->getChiralTag() != Atom::CHI_TETRAHEDRAL_CCW) ||
(at1->getIdx() != bond->getBeginAtomIdx() &&
(at2->getChiralTag() == Atom::CHI_TETRAHEDRAL_CW ||
at2->getChiralTag() == Atom::CHI_TETRAHEDRAL_CCW))) {
// std::cerr << " swap" << std::endl;
swap(at1_cds, at2_cds);
swap(col1, col2);
}
// deliberately not scaling highlighted bond width
if (Bond::BEGINWEDGE == bond->getBondDir()) {
drawWedgedBond(at1_cds, at2_cds, false, col1, col2);
} else {
drawWedgedBond(at1_cds, at2_cds, true, col1, col2);
}
} else if (Bond::SINGLE == bt && Bond::UNKNOWN == bond->getBondDir()) {
// unspecified stereo
// deliberately not scaling highlighted bond width
drawWavyLine(at1_cds, at2_cds, col1, col2);
} else if (Bond::DATIVE == bt || Bond::DATIVEL == bt ||
Bond::DATIVER == bt) {
// deliberately not scaling highlighted bond width as I think
// the arrowhead will look ugly.
if (static_cast<unsigned int>(at1_idx) == bond->getBeginAtomIdx()) {
drawDativeBond(at1_cds, at2_cds, col1, col2);
} else {
drawDativeBond(at2_cds, at1_cds, col2, col1);
}
} else if (Bond::ZERO == bt) {
setDash(shortDashes);
bool orig_slw = drawOptions().scaleBondWidth;
if (highlight_bond) {
drawOptions().scaleBondWidth = drawOptions().scaleHighlightBondWidth;
}
drawLine(at1_cds, at2_cds, col1, col2);
drawOptions().scaleBondWidth = orig_slw;
setDash(noDash);
} else {
// in all other cases, we will definitely want to draw a line between
// the two atoms
bool orig_slw = drawOptions().scaleBondWidth;
if (highlight_bond) {
drawOptions().scaleBondWidth = drawOptions().scaleHighlightBondWidth;
}
drawLine(at1_cds, at2_cds, col1, col2);
if (Bond::TRIPLE == bt) {
Point2D l1s, l1f, l2s, l2f;
calcTripleBondLines(double_bond_offset, bond, at1_cds, at2_cds, l1s,
l1f, l2s, l2f);
drawLine(l1s, l1f, col1, col2);
drawLine(l2s, l2f, col1, col2);
}
drawOptions().scaleBondWidth = orig_slw;
}
}
if (highlight_bond) {
setLineWidth(orig_lw);
}
}
// ****************************************************************************
void MolDraw2D::drawWedgedBond(const Point2D &cds1, const Point2D &cds2,
bool draw_dashed, const DrawColour &col1,
const DrawColour &col2) {
Point2D perp = calcPerpendicular(cds1, cds2);
Point2D disp = perp * 0.15;
// make sure the displacement isn't too large using the current scale factor
// (part of github #985)
// the constants are empirical to make sure that the wedge is visible, but
// not absurdly large.
if (scale_ > 40) {
disp *= .6;
}
Point2D end1 = cds2 + disp;
Point2D end2 = cds2 - disp;
setColour(col1);
if (draw_dashed) {
setFillPolys(false);
unsigned int nDashes;
// empirical cutoff to make sure we don't have too many dashes in the
// wedge:
auto factor = scale_ * (cds1 - cds2).lengthSq();
if (factor < 20) {
nDashes = 3;
} else if (factor < 30) {
nDashes = 4;
} else if (factor < 45) {
nDashes = 5;
} else {
nDashes = 6;
}
int orig_lw = lineWidth();
int tgt_lw = 1; // use the minimum line width
setLineWidth(tgt_lw);
Point2D e1 = end1 - cds1;
Point2D e2 = end2 - cds1;
for (unsigned int i = 1; i < nDashes + 1; ++i) {
if ((nDashes / 2 + 1) == i) {
setColour(col2);
}
Point2D e11 = cds1 + e1 * (rdcast<double>(i) / nDashes);
Point2D e22 = cds1 + e2 * (rdcast<double>(i) / nDashes);
if (drawOptions().comicMode) {
auto pts = MolDraw2D_detail::handdrawnLine(e11, e22, scale_);
drawPolygon(pts);
} else {
drawLine(e11, e22);
}
}
setLineWidth(orig_lw);
} else {
setFillPolys(true);
if (col1 == col2) {
drawTriangle(cds1, end1, end2);
} else {
Point2D e1 = end1 - cds1;
Point2D e2 = end2 - cds1;
Point2D mid1 = cds1 + e1 * 0.5;
Point2D mid2 = cds1 + e2 * 0.5;
drawTriangle(cds1, mid1, mid2);
setColour(col2);
drawTriangle(mid1, end2, end1);
drawTriangle(mid1, mid2, end2);
}
}
} // namespace RDKit
// ****************************************************************************
void MolDraw2D::drawDativeBond(const Point2D &cds1, const Point2D &cds2,
const DrawColour &col1, const DrawColour &col2) {
Point2D mid = (cds1 + cds2) * 0.5;
drawLine(cds1, mid, col1, col1);
setColour(col2);
bool asPolygon = true;
double frac = 0.2;
double angle = M_PI / 6;
// the polygon triangle at the end extends past cds2, so step back a bit
// so as not to trample on anything else.
Point2D delta = mid - cds2;
Point2D end = cds2 + delta * frac;
drawArrow(mid, end, asPolygon, frac, angle);
}
// ****************************************************************************
void MolDraw2D::drawAtomLabel(int atom_num,
const std::vector<int> *highlight_atoms,
const std::map<int, DrawColour> *highlight_map) {
drawAtomLabel(atom_num, getColour(atom_num, highlight_atoms, highlight_map));
}
// ****************************************************************************
void MolDraw2D::drawAtomLabel(int atom_num, const DrawColour &draw_colour) {
text_drawer_->setColour(draw_colour);
Point2D draw_cds = getDrawCoords(atom_num);
text_drawer_->drawString(atom_syms_[activeMolIdx_][atom_num].first, draw_cds,
atom_syms_[activeMolIdx_][atom_num].second);
// this is useful for debugging the drawings.
// int olw = lineWidth();
// setLineWidth(1);
// text_drawer_->drawStringRects(atom_syms_[activeMolIdx_][atom_num].first,
// atom_syms_[activeMolIdx_][atom_num].second,
// draw_cds, *this);
// setLineWidth(olw);
}
// ****************************************************************************
void MolDraw2D::drawAnnotation(const AnnotationType &annot) {
double full_font_scale = text_drawer_->fontScale();
// turn off minFontSize for the annotation, as we do want it to be smaller
// than the letters, even if that makes it tiny. The annotation positions
// have been calculated on the assumption that this is the case, and if
// minFontSize is applied, they may well clash with the atom symbols.
double omfs = text_drawer_->minFontSize();
text_drawer_->setMinFontSize(-1);
text_drawer_->setFontScale(drawOptions().annotationFontScale *
full_font_scale);
Point2D draw_cds = getDrawCoords(annot.rect_.trans_);
text_drawer_->drawString(annot.text_, draw_cds, annot.align_);
text_drawer_->setMinFontSize(omfs);
text_drawer_->setFontScale(full_font_scale);
}
// ****************************************************************************
OrientType MolDraw2D::calcRadicalRect(const ROMol &mol, const Atom *atom,
StringRect &rad_rect) {
int num_rade = atom->getNumRadicalElectrons();
double spot_rad = 0.2 * drawOptions().multipleBondOffset;
Point2D const &at_cds = at_cds_[activeMolIdx_][atom->getIdx()];
string const &at_sym = atom_syms_[activeMolIdx_][atom->getIdx()].first;
OrientType orient = atom_syms_[activeMolIdx_][atom->getIdx()].second;
double rad_size = (3 * num_rade - 1) * spot_rad;
rad_size = (4 * num_rade - 2) * spot_rad;
double x_min, y_min, x_max, y_max;
Point2D at_draw_cds = getDrawCoords(at_cds);
if (!at_sym.empty()) {
text_drawer_->getStringExtremes(at_sym, orient, x_min, y_min, x_max, y_max);
x_min += at_draw_cds.x;
x_max += at_draw_cds.x;
y_min += at_draw_cds.y;
y_max += at_draw_cds.y;
} else {
x_min = at_draw_cds.x - 3 * spot_rad * text_drawer_->fontScale();
x_max = at_draw_cds.x + 3 * spot_rad * text_drawer_->fontScale();
y_min = at_draw_cds.y - 3 * spot_rad * text_drawer_->fontScale();
y_max = at_draw_cds.y + 3 * spot_rad * text_drawer_->fontScale();
}
auto rect_to_atom_coords = [&](StringRect &rect) {
rect.width_ /= text_drawer_->fontScale();
rect.height_ /= text_drawer_->fontScale();
rect.trans_ = getAtomCoords(make_pair(rect.trans_.x, rect.trans_.y));
};
auto try_all = [&](OrientType ornt) -> bool {
vector<std::shared_ptr<StringRect>> rad_rects(
1, std::shared_ptr<StringRect>(new StringRect(rad_rect)));
if (!text_drawer_->doesRectIntersect(at_sym, ornt, at_cds, rad_rect) &&
!doesAtomNoteClash(rad_rect, rad_rects, mol, atom->getIdx())) {
rect_to_atom_coords(rad_rect);
return true;
} else {
return false;
}
};
auto try_north = [&]() -> bool {
rad_rect.width_ = rad_size * text_drawer_->fontScale();
rad_rect.height_ = spot_rad * 3.0 * text_drawer_->fontScale();
rad_rect.trans_.x = at_draw_cds.x;
rad_rect.trans_.y = y_max + 0.5 * rad_rect.height_;
return try_all(OrientType::N);
};
auto try_south = [&]() -> bool {
rad_rect.width_ = rad_size * text_drawer_->fontScale();
rad_rect.height_ = spot_rad * 3.0 * text_drawer_->fontScale();
rad_rect.trans_.x = at_draw_cds.x;
rad_rect.trans_.y = y_min - 0.5 * rad_rect.height_;
return try_all(OrientType::S);
};
auto try_east = [&]() -> bool {
rad_rect.trans_.x = x_max + 3.0 * spot_rad * text_drawer_->fontScale();
rad_rect.trans_.y = at_draw_cds.y;
rad_rect.width_ = spot_rad * 1.5 * text_drawer_->fontScale();
rad_rect.height_ = rad_size * text_drawer_->fontScale();
return try_all(OrientType::E);
};
auto try_west = [&]() -> bool {
rad_rect.trans_.x = x_min - 3.0 * spot_rad * text_drawer_->fontScale();
rad_rect.trans_.y = at_draw_cds.y;
rad_rect.width_ = spot_rad * 1.5 * text_drawer_->fontScale();
rad_rect.height_ = rad_size * text_drawer_->fontScale();
return try_all(OrientType::W);
};
auto try_rads = [&](OrientType ornt) -> bool {
switch (ornt) {
case OrientType::N:
case OrientType::C:
return try_north();
case OrientType::E:
return try_east();
case OrientType::S:
return try_south();
case OrientType::W:
return try_west();
}
return false;
};
if (try_rads(orient)) {
return orient;
}
OrientType all_ors[4] = {OrientType::N, OrientType::E, OrientType::S,
OrientType::W};
for (int io = 0; io < 4; ++io) {
if (orient != all_ors[io]) {
if (try_rads(all_ors[io])) {
return all_ors[io];
}
}
}
// stick them N irrespective of a clash whilst muttering "sod it"
// under our breath.
try_north();
return OrientType::N;
}
namespace {} // namespace
// ****************************************************************************
void MolDraw2D::drawRadicals(const ROMol &mol) {
// take account of differing font scale and main scale if we've hit
// max or min font size.
double f_scale = text_drawer_->fontScale() / scale();
double spot_rad = 0.2 * drawOptions().multipleBondOffset * f_scale;
setColour(DrawColour(0.0, 0.0, 0.0));
// Point2D should be in atom coords
auto draw_spot = [&](const Point2D &cds) {
bool ofp = fillPolys();
setFillPolys(true);
int olw = lineWidth();
setLineWidth(0);
drawArc(cds, spot_rad, 0, 360);
setLineWidth(olw);
setFillPolys(ofp);
};
// cds in draw coords
auto draw_spots = [&](const Point2D &cds, int num_spots, double width,
int dir = 0) {
Point2D ncds = cds;
switch (num_spots) {
case 3:
draw_spot(ncds);
if (dir) {
ncds.y = cds.y - 0.5 * width + spot_rad;
} else {
ncds.x = cds.x - 0.5 * width + spot_rad;
}
draw_spot(ncds);
if (dir) {
ncds.y = cds.y + 0.5 * width - spot_rad;
} else {
ncds.x = cds.x + 0.5 * width - spot_rad;
}
draw_spot(ncds);
/* fallthrough */
case 1:
draw_spot(cds);
break;
case 4:
if (dir) {
ncds.y = cds.y + 6.0 * spot_rad;
} else {
ncds.x = cds.x + 6.0 * spot_rad;
}
draw_spot(ncds);
if (dir) {
ncds.y = cds.y - 6.0 * spot_rad;
} else {
ncds.x = cds.x - 6.0 * spot_rad;
}
draw_spot(ncds);
/* fallthrough */
case 2:
if (dir) {
ncds.y = cds.y + 2.0 * spot_rad;
} else {
ncds.x = cds.x + 2.0 * spot_rad;
}
draw_spot(ncds);
if (dir) {
ncds.y = cds.y - 2.0 * spot_rad;
} else {
ncds.x = cds.x - 2.0 * spot_rad;
}
draw_spot(ncds);
break;
}
};
size_t rad_num = 0;
for (auto atom : mol.atoms()) {
int num_rade = atom->getNumRadicalElectrons();
if (!num_rade) {
continue;
}
auto rad_rect = radicals_[activeMolIdx_][rad_num].first;
OrientType draw_or = radicals_[activeMolIdx_][rad_num].second;
if (draw_or == OrientType::N || draw_or == OrientType::S ||
draw_or == OrientType::C) {
draw_spots(rad_rect->trans_, num_rade, rad_rect->width_, 0);
} else {
draw_spots(rad_rect->trans_, num_rade, rad_rect->height_, 1);
}
++rad_num;
}
}
// ****************************************************************************
double MolDraw2D::getNoteStartAngle(const ROMol &mol, const Atom *atom) const {
if (atom->getDegree() == 0) {
return M_PI / 2.0;
}
Point2D at_cds = at_cds_[activeMolIdx_][atom->getIdx()];
vector<Point2D> bond_vecs;
for (const auto &nbr : make_iterator_range(mol.getAtomNeighbors(atom))) {
Point2D bond_vec = at_cds.directionVector(at_cds_[activeMolIdx_][nbr]);
bond_vec.normalize();
bond_vecs.emplace_back(bond_vec);
}
Point2D ret_vec;
if (bond_vecs.size() == 1) {
if (atom_syms_[activeMolIdx_][atom->getIdx()].first.empty()) {
// go with perpendicular to bond. This is mostly to avoid getting
// a zero at the end of a bond to carbon, which looks like a black
// oxygen atom in the default font in SVG and PNG.
ret_vec.x = bond_vecs[0].y;
ret_vec.y = -bond_vecs[0].x;
} else {
// go opposite end
ret_vec = -bond_vecs[0];
}
} else if (bond_vecs.size() == 2) {
ret_vec = bond_vecs[0] + bond_vecs[1];
if (ret_vec.lengthSq() > 1.0e-6) {
if (!atom->getNumImplicitHs() || atom->getAtomicNum() == 6) {
// prefer outside the angle, unless there are Hs that will be in
// the way, probably.
ret_vec *= -1.0;
}
} else {
// it must be a -# or == or some such. Take perpendicular to
// one of them
ret_vec.x = -bond_vecs.front().y;
ret_vec.y = bond_vecs.front().x;
ret_vec.normalize();
}
} else {
// just take 2 that are probably adjacent
double discrim = 4.0 * M_PI / bond_vecs.size();
for (size_t i = 0; i < bond_vecs.size() - 1; ++i) {
for (size_t j = i + 1; j < bond_vecs.size(); ++j) {
double ang = acos(bond_vecs[i].dotProduct(bond_vecs[j]));
if (ang < discrim) {
ret_vec = bond_vecs[i] + bond_vecs[j];
ret_vec.normalize();
discrim = -1.0;
break;
}
}
}
if (discrim > 0.0) {
ret_vec = bond_vecs[0] + bond_vecs[1];
ret_vec *= -1.0;
}
}
// start angle is the angle between ret_vec and the x axis
return atan2(ret_vec.y, ret_vec.x);
}
// ****************************************************************************
bool MolDraw2D::doesAtomNoteClash(
StringRect &note_rect, const vector<std::shared_ptr<StringRect>> &rects,
const ROMol &mol, unsigned int atom_idx) {
auto atom = mol.getAtomWithIdx(atom_idx);
note_rect.clash_score_ = 0;
if (doesNoteClashNbourBonds(note_rect, rects, mol, atom)) {
return true;
}
note_rect.clash_score_ = 1;
if (doesNoteClashAtomLabels(note_rect, rects, mol, atom_idx)) {
return true;
}
note_rect.clash_score_ = 2;
if (doesNoteClashOtherNotes(note_rect, rects)) {
return true;
}
note_rect.clash_score_ = 3;
return false;
}
// ****************************************************************************
bool MolDraw2D::doesBondNoteClash(
StringRect &note_rect, const vector<std::shared_ptr<StringRect>> &rects,
const ROMol &mol, const Bond *bond) {
note_rect.clash_score_ = 0;
string note = bond->getProp<string>(common_properties::bondNote);
if (doesNoteClashNbourBonds(note_rect, rects, mol, bond->getBeginAtom())) {
return true;
}
note_rect.clash_score_ = 1;
unsigned int atom_idx = bond->getBeginAtomIdx();
if (doesNoteClashAtomLabels(note_rect, rects, mol, atom_idx)) {
return true;
}
note_rect.clash_score_ = 2;
if (doesNoteClashOtherNotes(note_rect, rects)) {
return true;
}
note_rect.clash_score_ = 3;
return false;
}
// ****************************************************************************
bool MolDraw2D::doesNoteClashNbourBonds(
const StringRect &note_rect,
const vector<std::shared_ptr<StringRect>> &rects, const ROMol &mol,
const Atom *atom) const {
double double_bond_offset = -1.0;
Point2D const &at2_dcds =
getDrawCoords(at_cds_[activeMolIdx_][atom->getIdx()]);
double line_width = lineWidth() * scale() * 0.02;
for (const auto &nbr : make_iterator_range(mol.getAtomNeighbors(atom))) {
Point2D const &at1_dcds = getDrawCoords(at_cds_[activeMolIdx_][nbr]);
if (text_drawer_->doesLineIntersect(rects, note_rect.trans_, at1_dcds,
at2_dcds, line_width)) {
return true;
}
// now see about clashing with other lines if not single
auto bond = mol.getBondBetweenAtoms(atom->getIdx(), nbr);
Bond::BondType bt = bond->getBondType();
if (bt == Bond::SINGLE) {
continue;
}
if (double_bond_offset < 0.0) {
double_bond_offset = options_.multipleBondOffset;
// mol files from, for example, Marvin use a bond length of 1 for just
// about everything. When this is the case, the default multipleBondOffset
// is just too much, so scale it back.
if ((at1_dcds - at2_dcds).lengthSq() < 1.4 * scale()) {
double_bond_offset *= 0.6;
}
}
if (bt == Bond::DOUBLE || bt == Bond::AROMATIC || bt == Bond::TRIPLE) {
Point2D l1s, l1f, l2s, l2f;
if (bt == Bond::DOUBLE || bt == Bond::AROMATIC) {
// use the atom coords for this ot make sure the perp goes the
// correct way (y coordinate issue).
calcDoubleBondLines(
mol, double_bond_offset, bond, at_cds_[activeMolIdx_][nbr],
at_cds_[activeMolIdx_][atom->getIdx()], l1s, l1f, l2s, l2f);
} else {
calcTripleBondLines(
double_bond_offset, bond, at_cds_[activeMolIdx_][nbr],
at_cds_[activeMolIdx_][atom->getIdx()], l1s, l1f, l2s, l2f);
}
l1s = getDrawCoords(l1s);
l1f = getDrawCoords(l1f);
l2s = getDrawCoords(l2s);
l2f = getDrawCoords(l2f);
if (text_drawer_->doesLineIntersect(rects, note_rect.trans_, l1s, l1f,
line_width) ||
text_drawer_->doesLineIntersect(rects, note_rect.trans_, l2s, l2f,
line_width)) {
return true;
}
}
}
return false;
}
// ****************************************************************************
bool MolDraw2D::doesNoteClashAtomLabels(
const StringRect &note_rect,
const vector<std::shared_ptr<StringRect>> &rects, const ROMol &mol,
unsigned int atom_idx) const {
// try the atom_idx first as it's the most likely clash
Point2D draw_cds = getDrawCoords(atom_idx);
if (text_drawer_->doesStringIntersect(
rects, note_rect.trans_, atom_syms_[activeMolIdx_][atom_idx].first,
atom_syms_[activeMolIdx_][atom_idx].second, draw_cds)) {
return true;
}
// if it's cluttered, it might clash with other labels.
for (auto atom : mol.atoms()) {
if (atom_idx == atom->getIdx()) {
continue;
}
const auto &atsym = atom_syms_[activeMolIdx_][atom->getIdx()];
if (atsym.first.empty()) {
continue;
}
draw_cds = getDrawCoords(atom->getIdx());
if (text_drawer_->doesStringIntersect(rects, note_rect.trans_, atsym.first,
atsym.second, draw_cds)) {
return true;
}
}
return false;
}
// ****************************************************************************
bool MolDraw2D::doesNoteClashOtherNotes(
const StringRect &note_rect,
const vector<std::shared_ptr<StringRect>> &rects) const {
for (auto const &annot : annotations_[activeMolIdx_]) {
if (text_drawer_->doesRectIntersect(rects, note_rect.trans_, annot.rect_)) {
return true;
}
}
return false;
}
// ****************************************************************************
// calculate normalised perpendicular to vector between two coords
Point2D MolDraw2D::calcPerpendicular(const Point2D &cds1,
const Point2D &cds2) const {
double bv[2] = {cds1.x - cds2.x, cds1.y - cds2.y};
double perp[2] = {-bv[1], bv[0]};
double perp_len = sqrt(perp[0] * perp[0] + perp[1] * perp[1]);
perp[0] /= perp_len;
perp[1] /= perp_len;
return Point2D(perp[0], perp[1]);
}
// ****************************************************************************
void MolDraw2D::calcDoubleBondLines(const ROMol &mol, double offset,
const Bond *bond, const Point2D &at1_cds,
const Point2D &at2_cds, Point2D &l1s,
Point2D &l1f, Point2D &l2s,
Point2D &l2f) const {
// the percent shorter that the extra bonds in a double bond are
const double multipleBondTruncation = 0.15;
Atom *at1 = bond->getBeginAtom();
Atom *at2 = bond->getEndAtom();
Point2D perp;
if (1 == at1->getDegree() || 1 == at2->getDegree() || isLinearAtom(*at1) ||
isLinearAtom(*at2)) {
perp = calcPerpendicular(at1_cds, at2_cds) * offset;
l1s = at1_cds + perp;
l1f = at2_cds + perp;
l2s = at1_cds - perp;
l2f = at2_cds - perp;
} else if ((Bond::EITHERDOUBLE == bond->getBondDir()) ||
(Bond::STEREOANY == bond->getStereo())) {
// crossed bond
perp = calcPerpendicular(at1_cds, at2_cds) * offset;
l1s = at1_cds + perp;
l1f = at2_cds - perp;
l2s = at1_cds - perp;
l2f = at2_cds + perp;
} else {
l1s = at1_cds;
l1f = at2_cds;
offset *= 2.0;
if (mol.getRingInfo()->numBondRings(bond->getIdx())) {
// in a ring, we need to draw the bond inside the ring
perp = bondInsideRing(mol, bond, at1_cds, at2_cds);
} else {
perp = bondInsideDoubleBond(mol, bond);
}
Point2D bv = at1_cds - at2_cds;
l2s = at1_cds - bv * multipleBondTruncation + perp * offset;
l2f = at2_cds + bv * multipleBondTruncation + perp * offset;
}
}
// ****************************************************************************
bool MolDraw2D::isLinearAtom(const Atom &atom) const {
if (atom.getDegree() == 2) {
Point2D bond_vecs[2];
Bond::BondType bts[2];
Point2D const &at_cds = at_cds_[activeMolIdx_][atom.getIdx()];
ROMol const &mol = atom.getOwningMol();
int i = 0;
for (const auto &nbr : make_iterator_range(mol.getAtomNeighbors(&atom))) {
Point2D bond_vec = at_cds.directionVector(at_cds_[activeMolIdx_][nbr]);
bond_vec.normalize();
bond_vecs[i] = bond_vec;
bts[i] = mol.getBondBetweenAtoms(atom.getIdx(), nbr)->getBondType();
++i;
}
return (bts[0] == bts[1] && bond_vecs[0].dotProduct(bond_vecs[1]) < -0.95);
}
return false;
}
// ****************************************************************************
void MolDraw2D::calcTripleBondLines(double offset, const Bond *bond,
const Point2D &at1_cds,
const Point2D &at2_cds, Point2D &l1s,
Point2D &l1f, Point2D &l2s,
Point2D &l2f) const {
// the percent shorter that the extra bonds in a double bond are
const double multipleBondTruncation = 0.15;
Atom *at1 = bond->getBeginAtom();
Atom *at2 = bond->getEndAtom();
// 2 lines, a bit shorter and offset on the perpendicular
double dbo = 2.0 * offset;
Point2D perp = calcPerpendicular(at1_cds, at2_cds);
double end1_trunc = 1 == at1->getDegree() ? 0.0 : multipleBondTruncation;
double end2_trunc = 1 == at2->getDegree() ? 0.0 : multipleBondTruncation;
Point2D bv = at1_cds - at2_cds;
l1s = at1_cds - (bv * end1_trunc) + perp * dbo;
l1f = at2_cds + (bv * end2_trunc) + perp * dbo;
l2s = at1_cds - (bv * end1_trunc) - perp * dbo;
l2f = at2_cds + (bv * end2_trunc) - perp * dbo;
}
// ****************************************************************************
double MolDraw2D::getDrawLineWidth() const {
double width = lineWidth();
// This works fairly well for SVG and Cairo. 0.02 is picked by eye
if (drawOptions().scaleBondWidth) {
width *= scale() * 0.02;
if (width < 0.0) {
width = 0.0;
}
}
return width;
}
// ****************************************************************************
// cds1 and cds2 are 2 atoms in a ring. Returns the perpendicular pointing
// into the ring
Point2D MolDraw2D::bondInsideRing(const ROMol &mol, const Bond *bond,
const Point2D &cds1,
const Point2D &cds2) const {
vector<size_t> bond_in_rings;
auto bond_rings = mol.getRingInfo()->bondRings();
for (size_t i = 0; i < bond_rings.size(); ++i) {
if (find(bond_rings[i].begin(), bond_rings[i].end(), bond->getIdx()) !=
bond_rings[i].end()) {
bond_in_rings.push_back(i);
}
}
// find another bond in the ring connected to bond, use the
// other end of it as the 3rd atom.
auto calc_perp = [&](const Bond *bond, const INT_VECT &ring) -> Point2D * {
Atom *bgn_atom = bond->getBeginAtom();
for (const auto &nbri2 : make_iterator_range(mol.getAtomBonds(bgn_atom))) {
const Bond *bond2 = mol[nbri2];
if (bond2 == bond) {
continue;
}
if (find(ring.begin(), ring.end(), bond2->getIdx()) != ring.end()) {
int atom3 = bond2->getOtherAtomIdx(bond->getBeginAtomIdx());
Point2D *ret = new Point2D;
*ret =
calcInnerPerpendicular(cds1, cds2, at_cds_[activeMolIdx_][atom3]);
return ret;
}
}
return nullptr;
};
if (bond_in_rings.size() > 1) {
// bond is in more than 1 ring. Choose one that is the same aromaticity
// as the bond, so that if bond is aromatic, the double bond is inside
// the aromatic ring. This is important for morphine, for example,
// where there are fused aromatic and aliphatic rings.
// morphine: CN1CC[C@]23c4c5ccc(O)c4O[C@H]2[C@@H](O)C=C[C@H]3[C@H]1C5
for (size_t i = 0; i < bond_in_rings.size(); ++i) {
auto ring = bond_rings[bond_in_rings[i]];
bool ring_ok = true;
for (auto bond_idx : ring) {
const Bond *bond2 = mol.getBondWithIdx(bond_idx);
if (bond->getIsAromatic() != bond2->getIsAromatic()) {
ring_ok = false;
break;
}
}
if (!ring_ok) {
continue;
}
Point2D *ret = calc_perp(bond, ring);
if (ret) {
Point2D real_ret(*ret);
delete ret;
return real_ret;
}
}
}
// either bond is in 1 ring, or we couldn't decide above, so just use the
// first one
auto ring = bond_rings[bond_in_rings.front()];
Point2D *ret = calc_perp(bond, ring);
if (ret) {
Point2D real_ret(*ret);
delete ret;
return real_ret;
}
// failsafe that it will hopefully never see.
return calcPerpendicular(cds1, cds2);
}
// ****************************************************************************
// cds1 and cds2 are 2 atoms in a chain double bond. Returns the
// perpendicular pointing into the inside of the bond
Point2D MolDraw2D::bondInsideDoubleBond(const ROMol &mol,
const Bond *bond) const {
// a chain double bond, where it looks nicer IMO if the 2nd line is inside
// the angle of outgoing bond. Unless it's an allene, where nothing
// looks great.
const Atom *at1 = bond->getBeginAtom();
const Atom *at2 = bond->getEndAtom();
const Atom *bond_atom, *end_atom;
if (at1->getDegree() > 1) {
bond_atom = at1;
end_atom = at2;
} else {
bond_atom = at2;
end_atom = at1;
}
int at3 = -1; // to stop the compiler whinging.
for (const auto &nbri2 : make_iterator_range(mol.getAtomBonds(bond_atom))) {
const Bond *bond2 = mol[nbri2];
if (bond != bond2) {
at3 = bond2->getOtherAtomIdx(bond_atom->getIdx());
break;
}
}
return calcInnerPerpendicular(at_cds_[activeMolIdx_][end_atom->getIdx()],
at_cds_[activeMolIdx_][bond_atom->getIdx()],
at_cds_[activeMolIdx_][at3]);
}
// ****************************************************************************
// calculate normalised perpendicular to vector between two coords, such that
// it's inside the angle made between (1 and 2) and (2 and 3).
Point2D MolDraw2D::calcInnerPerpendicular(const Point2D &cds1,
const Point2D &cds2,
const Point2D &cds3) const {
Point2D perp = calcPerpendicular(cds1, cds2);
double v1[2] = {cds1.x - cds2.x, cds1.y - cds2.y};
double v2[2] = {cds2.x - cds3.x, cds2.y - cds3.y};
double obv[2] = {v1[0] - v2[0], v1[1] - v2[1]};
// if dot product of centre_dir and perp < 0.0, they're pointing in opposite
// directions, so reverse perp
if (obv[0] * perp.x + obv[1] * perp.y < 0.0) {
perp.x *= -1.0;
perp.y *= -1.0;
}
return perp;
}
// ****************************************************************************
// take the coords for atnum, with neighbour nbr_cds, and move cds out to
// accommodate the label associated with it.
void MolDraw2D::adjustBondEndForLabel(int atnum, const Point2D &nbr_cds,
Point2D &cds) const {
if (atom_syms_[activeMolIdx_][atnum].first.empty()) {
return;
}
Point2D draw_cds = getDrawCoords(cds);
Point2D nbr_draw_cds = getDrawCoords(nbr_cds);
text_drawer_->adjustLineForString(atom_syms_[activeMolIdx_][atnum].first,
atom_syms_[activeMolIdx_][atnum].second,
nbr_draw_cds, draw_cds);
cds = getAtomCoords(make_pair(draw_cds.x, draw_cds.y));
if (drawOptions().additionalAtomLabelPadding > 0.0) {
// directionVector is normalised.
Point2D bond =
cds.directionVector(nbr_cds) * drawOptions().additionalAtomLabelPadding;
cds += bond;
}
}
// ****************************************************************************
pair<string, OrientType> MolDraw2D::getAtomSymbolAndOrientation(
const Atom &atom) const {
OrientType orient = getAtomOrientation(atom);
string symbol = getAtomSymbol(atom, orient);
return std::make_pair(symbol, orient);
}
// ****************************************************************************
string MolDraw2D::getAtomSymbol(const RDKit::Atom &atom,
OrientType orientation) const {
// adds XML-like annotation for super- and sub-script, in the same manner
// as MolDrawing.py. My first thought was for a LaTeX-like system,
// obviously...
string symbol;
bool literal_symbol = true;
unsigned int iso = atom.getIsotope();
if (drawOptions().atomLabels.find(atom.getIdx()) !=
drawOptions().atomLabels.end()) {
// specified labels are trump: no matter what else happens we will show
// them.
symbol = drawOptions().atomLabels.find(atom.getIdx())->second;
} else if (atom.hasProp(common_properties::_displayLabel) ||
atom.hasProp(common_properties::_displayLabelW)) {
// logic here: if either _displayLabel or _displayLabelW is set, we will
// definitely use one of those. if only one is set, we'll use that one if
// both are set and the orientation is W then we'll use _displayLabelW,
// otherwise _displayLabel
std::string lbl;
std::string lblw;
atom.getPropIfPresent(common_properties::_displayLabel, lbl);
atom.getPropIfPresent(common_properties::_displayLabelW, lblw);
if (lbl.empty()) {
lbl = lblw;
}
if (orientation == OrientType::W && !lblw.empty()) {
symbol = lblw;
} else {
symbol = lbl;
}
} else if (atom.hasProp(common_properties::atomLabel)) {
symbol = atom.getProp<std::string>(common_properties::atomLabel);
} else if (drawOptions().dummiesAreAttachments && atom.getAtomicNum() == 0 &&
atom.getDegree() == 1) {
symbol = "";
literal_symbol = false;
} else if (isComplexQuery(&atom)) {
symbol = "?";
} else if (drawOptions().atomLabelDeuteriumTritium &&
atom.getAtomicNum() == 1 && (iso == 2 || iso == 3)) {
symbol = ((iso == 2) ? "D" : "T");
iso = 0;
} else {
literal_symbol = false;
std::vector<std::string> preText, postText;
// first thing after the symbol is the atom map
if (atom.hasProp("molAtomMapNumber")) {
string map_num = "";
atom.getProp("molAtomMapNumber", map_num);
postText.push_back(std::string(":") + map_num);
}
if (0 != atom.getFormalCharge()) {
// charge always comes post the symbol
int ichg = atom.getFormalCharge();
string sgn = ichg > 0 ? string("+") : string("-");
ichg = abs(ichg);
if (ichg > 1) {
sgn = std::to_string(ichg) + sgn;
}
// put the charge as a superscript
postText.push_back(string("<sup>") + sgn + string("</sup>"));
}
int num_h = (atom.getAtomicNum() == 6 && atom.getDegree() > 0)
? 0
: atom.getTotalNumHs(); // FIX: still not quite right
if (drawOptions().explicitMethyl && atom.getAtomicNum() == 6 &&
atom.getDegree() == 1) {
symbol += atom.getSymbol();
num_h = atom.getTotalNumHs();
}
if (num_h > 0 && !atom.hasQuery()) {
// the H text comes after the atomic symbol
std::string h = "H";
if (num_h > 1) {
// put the number as a subscript
h += string("<sub>") + std::to_string(num_h) + string("</sub>");
}
postText.push_back(h);
}
if (0 != iso) {
// isotope always comes before the symbol
preText.push_back(std::string("<sup>") + std::to_string(iso) +
std::string("</sup>"));
}
symbol = "";
for (const std::string &se : preText) {
symbol += se;
}
// allenes need a C, but extend to any atom with degree 2 and both
// bonds in a line.
if (isLinearAtom(atom) ||
(atom.getAtomicNum() != 6 || atom.getDegree() == 0 || preText.size() ||
postText.size())) {
symbol += atom.getSymbol();
}
for (const std::string &se : postText) {
symbol += se;
}
}
if (literal_symbol && !symbol.empty()) {
symbol = "<lit>" + symbol + "</lit>";
}
// cout << "Atom symbol " << atom.getIdx() << " : " << symbol << endl;
return symbol;
} // namespace RDKit
// ****************************************************************************
OrientType MolDraw2D::getAtomOrientation(const RDKit::Atom &atom) const {
// cout << "Atomic " << atom.getAtomicNum() << " degree : "
// << atom.getDegree() << " : " << atom.getTotalNumHs() << endl;
// anything with a slope of more than 70 degrees is vertical. This way,
// the NH in an indole is vertical as RDKit lays it out normally (72ish
// degrees) but the 2 amino groups of c1ccccc1C1CCC(N)(N)CC1 are E and W
// when they are drawn at the bottom of the molecule.
static const double VERT_SLOPE = tan(70.0 * M_PI / 180.0);
auto mol = atom.getOwningMol();
const Point2D &at1_cds = at_cds_[activeMolIdx_][atom.getIdx()];
Point2D nbr_sum(0.0, 0.0);
// cout << "Nbours for atom : " << at1->getIdx() << endl;
for (const auto &nbri : make_iterator_range(mol.getAtomBonds(&atom))) {
const Bond *bond = mol[nbri];
const Point2D &at2_cds =
at_cds_[activeMolIdx_][bond->getOtherAtomIdx(atom.getIdx())];
nbr_sum += at2_cds - at1_cds;
}
OrientType orient = OrientType::C;
if (atom.getDegree()) {
double islope = 1000.0;
if (fabs(nbr_sum.x) > 1.0e-4) {
islope = nbr_sum.y / nbr_sum.x;
}
if (fabs(islope) <= VERT_SLOPE) {
if (nbr_sum.x > 0.0) {
orient = OrientType::W;
} else {
orient = OrientType::E;
}
} else {
if (nbr_sum.y > 0.0) {
orient = OrientType::N;
} else {
orient = OrientType::S;
}
}
// atoms of single degree should always be either W or E, never N or S. If
// either of the latter, make it E if the slope is close to vertical,
// otherwise have it either as required.
if (orient == OrientType::N || orient == OrientType::S) {
if (atom.getDegree() == 1) {
if (fabs(islope) > VERT_SLOPE) {
orient = OrientType::E;
} else {
if (nbr_sum.x > 0.0) {
orient = OrientType::W;
} else {
orient = OrientType::E;
}
}
} else if (atom.getDegree() == 3) {
// Atoms of degree 3 can sometimes have a bond pointing down with S
// orientation or up with N orientation, which puts the H on the bond.
auto mol = atom.getOwningMol();
const Point2D &at1_cds = at_cds_[activeMolIdx_][atom.getIdx()];
for (const auto &nbri : make_iterator_range(mol.getAtomBonds(&atom))) {
const Bond *bond = mol[nbri];
const Point2D &at2_cds =
at_cds_[activeMolIdx_][bond->getOtherAtomIdx(atom.getIdx())];
Point2D bond_vec = at2_cds - at1_cds;
double ang = atan(bond_vec.y / bond_vec.x) * 180.0 / M_PI;
if (ang > 80.0 && ang < 100.0 && orient == OrientType::S) {
orient = OrientType::N;
break;
} else if (ang < -80.0 && ang > -100.0 && orient == OrientType::N) {
orient = OrientType::S;
break;
}
}
}
}
} else {
// last check: degree zero atoms from the last three periods should have
// the Hs first
static int HsListedFirstSrc[] = {8, 9, 16, 17, 34, 35, 52, 53, 84, 85};
std::vector<int> HsListedFirst(
HsListedFirstSrc,
HsListedFirstSrc + sizeof(HsListedFirstSrc) / sizeof(int));
if (std::find(HsListedFirst.begin(), HsListedFirst.end(),
atom.getAtomicNum()) != HsListedFirst.end()) {
orient = OrientType::W;
} else {
orient = OrientType::E;
}
}
return orient;
}
// ****************************************************************************
void MolDraw2D::adjustScaleForAtomLabels(
const std::vector<int> *highlight_atoms,
const map<int, double> *highlight_radii) {
double x_max(x_min_ + x_range_), y_max(y_min_ + y_range_);
for (size_t i = 0; i < atom_syms_[activeMolIdx_].size(); ++i) {
if (!atom_syms_[activeMolIdx_][i].first.empty()) {
double this_x_min, this_y_min, this_x_max, this_y_max;
getStringExtremes(atom_syms_[activeMolIdx_][i].first,
atom_syms_[activeMolIdx_][i].second,
at_cds_[activeMolIdx_][i], this_x_min, this_y_min,
this_x_max, this_y_max);
x_max = std::max(x_max, this_x_max);
x_min_ = std::min(x_min_, this_x_min);
y_max = std::max(y_max, this_y_max);
y_min_ = std::min(y_min_, this_y_min);
}
if (highlight_atoms &&
highlight_atoms->end() !=
find(highlight_atoms->begin(), highlight_atoms->end(), i)) {
Point2D centre;
double xradius, yradius;
// this involves a 2nd call to text_drawer_->getStringRect, but never mind
calcLabelEllipse(i, highlight_radii, centre, xradius, yradius);
double this_x_min = centre.x - xradius;
double this_x_max = centre.x + xradius;
double this_y_min = centre.y - yradius;
double this_y_max = centre.y + yradius;
x_max = std::max(x_max, this_x_max);
x_min_ = std::min(x_min_, this_x_min);
y_max = std::max(y_max, this_y_max);
y_min_ = std::min(y_min_, this_y_min);
}
}
x_range_ = max(x_max - x_min_, x_range_);
y_range_ = max(y_max - y_min_, y_range_);
}
// ****************************************************************************
void MolDraw2D::adjustScaleForRadicals(const ROMol &mol) {
if (scale() != text_drawer_->fontScale()) {
// we've hit max or min font size, so re-compute radical rectangles as
// they'll be too far from the character.
radicals_[activeMolIdx_].clear();
extractRadicals(mol);
}
double x_max(x_min_ + x_range_), y_max(y_min_ + y_range_);
for (auto rad_pair : radicals_[activeMolIdx_]) {
auto rad_rect = rad_pair.first;
x_max = max(x_max, rad_rect->trans_.x + rad_rect->width_ / 2.0);
y_max = max(y_max, rad_rect->trans_.y + rad_rect->height_ / 2.0);
x_min_ = min(x_min_, rad_rect->trans_.x - rad_rect->width_ / 2.0);
y_min_ = min(y_min_, rad_rect->trans_.y - rad_rect->height_ / 2.0);
}
x_range_ = max(x_max - x_min_, x_range_);
y_range_ = max(y_max - y_min_, y_range_);
}
// ****************************************************************************
void MolDraw2D::adjustScaleForAnnotation(const vector<AnnotationType> &notes) {
double x_max(x_min_ + x_range_), y_max(y_min_ + y_range_);
for (auto const &pr : notes) {
const auto &note_rect = pr.rect_;
double this_x_max = note_rect.trans_.x + note_rect.width_ / 2.0;
double this_x_min = note_rect.trans_.x - note_rect.width_ / 2.0;
double this_y_max = note_rect.trans_.y + note_rect.height_ / 2.0;
double this_y_min = note_rect.trans_.y - note_rect.height_ / 2.0;
x_max = std::max(x_max, this_x_max);
x_min_ = std::min(x_min_, this_x_min);
y_max = std::max(y_max, this_y_max);
y_min_ = std::min(y_min_, this_y_min);
}
x_range_ = max(x_max - x_min_, x_range_);
y_range_ = max(y_max - y_min_, y_range_);
}
// ****************************************************************************
void MolDraw2D::drawTriangle(const Point2D &cds1, const Point2D &cds2,
const Point2D &cds3) {
std::vector<Point2D> pts;
if (!drawOptions().comicMode) {
pts = {cds1, cds2, cds3};
} else {
auto lpts = MolDraw2D_detail::handdrawnLine(cds1, cds2, scale_);
std::move(lpts.begin(), lpts.end(), std::back_inserter(pts));
lpts = MolDraw2D_detail::handdrawnLine(cds2, cds3, scale_);
std::move(lpts.begin(), lpts.end(), std::back_inserter(pts));
lpts = MolDraw2D_detail::handdrawnLine(cds3, cds1, scale_);
std::move(lpts.begin(), lpts.end(), std::back_inserter(pts));
}
drawPolygon(pts);
};
// ****************************************************************************
void MolDraw2D::drawArrow(const Point2D &arrowBegin, const Point2D &arrowEnd,
bool asPolygon, double frac, double angle) {
Point2D delta = arrowBegin - arrowEnd;
double cos_angle = std::cos(angle), sin_angle = std::sin(angle);
Point2D p1 = arrowEnd;
p1.x += frac * (delta.x * cos_angle + delta.y * sin_angle);
p1.y += frac * (delta.y * cos_angle - delta.x * sin_angle);
Point2D p2 = arrowEnd;
p2.x += frac * (delta.x * cos_angle - delta.y * sin_angle);
p2.y += frac * (delta.y * cos_angle + delta.x * sin_angle);
drawLine(arrowBegin, arrowEnd);
if (!asPolygon) {
drawLine(arrowEnd, p1);
drawLine(arrowEnd, p2);
} else {
std::vector<Point2D> pts = {p1, arrowEnd, p2};
bool fps = fillPolys();
setFillPolys(true);
drawPolygon(pts);
setFillPolys(fps);
}
}
// ****************************************************************************
void MolDraw2D::tabulaRasa() {
scale_ = 1.0;
x_trans_ = y_trans_ = 0.0;
x_offset_ = y_offset_ = 0;
d_metadata.clear();
d_numMetadataEntries = 0;
}
// ****************************************************************************
void MolDraw2D::drawEllipse(const Point2D &cds1, const Point2D &cds2) {
std::vector<Point2D> pts;
MolDraw2D_detail::arcPoints(cds1, cds2, pts, 0, 360);
drawPolygon(pts);
}
// ****************************************************************************
void MolDraw2D::drawArc(const Point2D &centre, double radius, double ang1,
double ang2) {
drawArc(centre, radius, radius, ang1, ang2);
}
// ****************************************************************************
void MolDraw2D::drawArc(const Point2D &centre, double xradius, double yradius,
double ang1, double ang2) {
std::vector<Point2D> pts;
// 5 degree increments should be plenty, as the circles are probably
// going to be small.
int num_steps = 1 + int((ang2 - ang1) / 5.0);
double ang_incr = double((ang2 - ang1) / num_steps) * M_PI / 180.0;
double start_ang_rads = ang2 * M_PI / 180.0;
for (int i = 0; i <= num_steps; ++i) {
double ang = start_ang_rads + double(i) * ang_incr;
double x = centre.x + xradius * cos(ang);
double y = centre.y + yradius * sin(ang);
pts.emplace_back(Point2D(x, y));
}
if (fillPolys()) {
// otherwise it draws an arc back to the pts.front() rather than filling
// in the sector.
pts.emplace_back(centre);
}
drawPolygon(pts);
}
// ****************************************************************************
void MolDraw2D::drawRect(const Point2D &cds1, const Point2D &cds2) {
std::vector<Point2D> pts(4);
pts[0] = cds1;
pts[1] = Point2D(cds1.x, cds2.y);
pts[2] = cds2;
pts[3] = Point2D(cds2.x, cds1.y);
// if fillPolys() is false, it doesn't close the polygon because of
// its use for drawing filled or open ellipse segments.
if (!fillPolys()) {
pts.emplace_back(cds1);
}
drawPolygon(pts);
}
void MolDraw2D::drawWavyLine(const Point2D &cds1, const Point2D &cds2,
const DrawColour &col1, const DrawColour &col2,
unsigned int nSegments, double vertOffset) {
RDUNUSED_PARAM(nSegments);
RDUNUSED_PARAM(vertOffset);
drawLine(cds1, cds2, col1, col2);
}
// ****************************************************************************
// we draw the line at cds2, perpendicular to the line cds1-cds2
void MolDraw2D::drawAttachmentLine(const Point2D &cds1, const Point2D &cds2,
const DrawColour &col, double len,
unsigned int nSegments) {
Point2D perp = calcPerpendicular(cds1, cds2);
Point2D p1 = Point2D(cds2.x - perp.x * len / 2, cds2.y - perp.y * len / 2);
Point2D p2 = Point2D(cds2.x + perp.x * len / 2, cds2.y + perp.y * len / 2);
drawWavyLine(p1, p2, col, col, nSegments);
}
// ****************************************************************************
bool doLinesIntersect(const Point2D &l1s, const Point2D &l1f,
const Point2D &l2s, const Point2D &l2f, Point2D *ip) {
// using spell from answer 2 of
// https://stackoverflow.com/questions/563198/how-do-you-detect-where-two-line-segments-intersect
double s1_x = l1f.x - l1s.x;
double s1_y = l1f.y - l1s.y;
double s2_x = l2f.x - l2s.x;
double s2_y = l2f.y - l2s.y;
double d = (-s2_x * s1_y + s1_x * s2_y);
if (d == 0.0) {
// parallel lines.
return false;
}
double s, t;
s = (-s1_y * (l1s.x - l2s.x) + s1_x * (l1s.y - l2s.y)) / d;
t = (s2_x * (l1s.y - l2s.y) - s2_y * (l1s.x - l2s.x)) / d;
if (s >= 0 && s <= 1 && t >= 0 && t <= 1) {
if (ip) {
ip->x = l1s.x + t * s1_x;
ip->y = l1s.y + t * s1_y;
}
return true;
}
return false;
}
// ****************************************************************************
bool doesLineIntersectLabel(const Point2D &ls, const Point2D &lf,
const StringRect &lab_rect, double padding) {
Point2D tl, tr, br, bl;
lab_rect.calcCorners(tl, tr, br, bl, padding);
// first check if line is completely inside label. Unlikely, but who
// knows?
if (ls.x >= tl.x && ls.x <= br.x && lf.x >= tl.x && lf.x <= br.x &&
ls.y <= tl.y && ls.y >= br.y && lf.y <= tl.y && lf.y >= br.y) {
return true;
}
if (doLinesIntersect(ls, lf, tl, tr) || doLinesIntersect(ls, lf, tr, br) ||
doLinesIntersect(ls, lf, br, bl) || doLinesIntersect(ls, lf, bl, tl)) {
return true;
}
return false;
}
} // namespace RDKit
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