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e32292802814e4a93df3d54d409395186647cecb
rdkit/Code/GraphMol/MolDraw2D/MolDraw2D.cpp
Greg Landrum e322928028 swap boost::tuple to std::tuple (#5851)
2022-12-16 16:01:19 +01:00

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//
// Copyright (C) 2014-2022 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/AtomSymbol.h>
#include <GraphMol/MolDraw2D/DrawMol.h>
#include <GraphMol/MolDraw2D/DrawText.h>
#include <GraphMol/MolDraw2D/DrawMol.h>
#include <GraphMol/MolDraw2D/DrawMolMCH.h>
#include <GraphMol/MolDraw2D/MolDraw2D.h>
#include <GraphMol/MolDraw2D/MolDraw2DHelpers.h>
#include <GraphMol/MolDraw2D/MolDraw2DDetails.h>
#include <GraphMol/MolDraw2D/MolDraw2DUtils.h>
#include <GraphMol/ChemReactions/ReactionParser.h>
#include <GraphMol/FileParsers/MolSGroupParsing.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 <GraphMol/FileParsers/FileParserUtils.h>
#include <GraphMol/MolEnumerator/LinkNode.h>
#include <Geometry/Transform3D.h>
#include <algorithm>
#include <cstdlib>
#include <cmath>
#include <limits>
#include <memory>
#include <boost/lexical_cast.hpp>
#include <boost/assign/list_of.hpp>
#include <boost/format.hpp>
using namespace boost;
using namespace std;
namespace RDKit {
// ****************************************************************************
MolDraw2D::MolDraw2D(int width, int height, int panelWidth, int panelHeight)
: width_(width),
height_(height),
panel_width_(panelWidth > 0 ? panelWidth : width),
panel_height_(panelHeight > 0 ? panelHeight : height),
legend_height_(0),
scale_(1.0),
fontScale_(1.0),
x_offset_(0),
y_offset_(0),
fill_polys_(true),
activeMolIdx_(-1),
activeAtmIdx1_(-1),
activeAtmIdx2_(-1),
activeBndIdx_(-1) {}
// ****************************************************************************
MolDraw2D::~MolDraw2D() {}
// ****************************************************************************
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) {
setupTextDrawer();
drawMols_.emplace_back(new MolDraw2D_detail::DrawMol(
mol, legend, panelWidth(), panelHeight(), drawOptions(), *text_drawer_,
highlight_atoms, highlight_bonds, highlight_atom_map, highlight_bond_map,
nullptr, highlight_radii, supportsAnnotations(), confId));
drawMols_.back()->setOffsets(x_offset_, y_offset_);
drawMols_.back()->createDrawObjects();
fixVariableDimensions(*drawMols_.back());
++activeMolIdx_;
startDrawing();
drawTheMolecule(*drawMols_.back());
}
// ****************************************************************************
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) {
MolDraw2D_detail::getBondHighlightsForAtoms(mol, *highlight_atoms,
highlight_bonds);
}
drawMolecule(mol, legend, highlight_atoms, &highlight_bonds,
highlight_atom_map, nullptr, highlight_radii, confId);
}
// ****************************************************************************
// keeping this one to preserve the public API, although it is no longer
// very useful.
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) {
drawMolecule(mol, "", highlight_atoms, highlight_bonds, highlight_atom_map,
highlight_bond_map, highlight_radii, confId);
}
// ****************************************************************************
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) {
setupTextDrawer();
MolDraw2D_detail::DrawMol *dm = new MolDraw2D_detail::DrawMolMCH(
mol, legend, panelWidth(), panelHeight(), drawOptions(), *text_drawer_,
highlight_atom_map, highlight_bond_map, highlight_radii,
highlight_linewidth_multipliers, confId);
drawMols_.emplace_back(dm);
drawMols_.back()->createDrawObjects();
fixVariableDimensions(*drawMols_.back());
++activeMolIdx_;
startDrawing();
drawTheMolecule((*drawMols_.back()));
return;
}
// ****************************************************************************
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");
PRECONDITION(width_ > 0 && height_ > 0,
"drawMolecules() needs a fixed canvas size");
if (mols.empty()) {
return;
}
setupTextDrawer();
int minScaleMol = 0;
int minFontScaleMol = 0;
int nCols = width() / panelWidth();
int nRows = height() / panelHeight();
for (size_t i = 0; i < mols.size(); ++i) {
if (!mols[i]) {
continue;
}
std::string legend = legends ? (*legends)[i] : "";
const std::vector<int> *ha =
highlight_atoms ? &(*highlight_atoms)[i] : nullptr;
const std::map<int, DrawColour> *ham =
highlight_atom_maps ? &(*highlight_atom_maps)[i] : nullptr;
const std::map<int, DrawColour> *hbm =
highlight_bond_maps ? &(*highlight_bond_maps)[i] : nullptr;
int confId = confIds ? (*confIds)[i] : -1;
const std::map<int, double> *hr =
highlight_radii ? &(*highlight_radii)[i] : nullptr;
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>());
MolDraw2D_detail::getBondHighlightsForAtoms(
*mols[i], (*highlight_atoms)[i], *lhighlight_bonds);
};
auto prevSize = drawMols_.size();
drawMols_.emplace_back(new MolDraw2D_detail::DrawMol(
*mols[i], legend, panelWidth(), panelHeight(), drawOptions(),
*text_drawer_, ha, lhighlight_bonds.get(), ham, hbm, nullptr, hr,
supportsAnnotations(), confId));
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;
}
drawMols_.back()->setOffsets(col * panelWidth(), row * panelHeight());
drawMols_.back()->createDrawObjects();
if (drawMols_.back()->getScale() < drawMols_[minScaleMol]->getScale()) {
minScaleMol = prevSize;
}
if (drawMols_.back()->getFontScale() <
drawMols_[minFontScaleMol]->getFontScale()) {
minFontScaleMol = prevSize;
}
}
for (auto &drawMol : drawMols_) {
if (drawOptions().drawMolsSameScale) {
drawMol->setScale(drawMols_[minScaleMol]->getScale(),
drawMols_[minFontScaleMol]->getFontScale(), true);
}
drawMol->tagAtomsWithCoords();
}
if (!drawMols_.empty()) {
activeMolIdx_ = 0;
startDrawing();
for (size_t i = 0; i < drawMols_.size(); ++i) {
activeMolIdx_ = i;
drawTheMolecule((*drawMols_[i]));
}
} else {
activeMolIdx_ = -1;
}
}
// ****************************************************************************
void MolDraw2D::drawReaction(
const ChemicalReaction &rxn, bool highlightByReactant,
const std::vector<DrawColour> *highlightColorsReactants,
const std::vector<int> *confIds) {
std::vector<std::shared_ptr<MolDraw2D_detail::DrawMol>> reagents;
std::vector<std::shared_ptr<MolDraw2D_detail::DrawMol>> products;
std::vector<std::shared_ptr<MolDraw2D_detail::DrawMol>> agents;
// Copy the reaction because processing for drawing alters it.
ChemicalReaction nrxn(rxn);
// I think a larger minimum font size than the default works better for this
int mfs = drawOptions().minFontSize > 12 ? drawOptions().minFontSize : 12;
text_drawer_->setMinFontSize(mfs);
int plusWidth;
getReactionDrawMols(nrxn, highlightByReactant, highlightColorsReactants,
confIds, reagents, products, agents, plusWidth);
if (height_ == -1) {
for (auto &dm : drawMols_) {
height_ = std::max(height_, dm->height_);
}
}
std::vector<Point2D> offsets;
Point2D arrowBeg, arrowEnd;
calcReactionOffsets(reagents, products, agents, plusWidth, offsets, arrowBeg,
arrowEnd);
activeMolIdx_ = -1;
startDrawing();
int xOffset = 0;
xOffset = drawReactionPart(reagents, plusWidth, xOffset, offsets);
// make sure the arrowhead is big enough
double frac = 0.05;
double delta = (arrowEnd - arrowBeg).length() * frac;
// an arbitrary 5 pixel minimum
if (delta < 5) {
frac *= 5 / delta;
}
xOffset = drawReactionPart(agents, 0, xOffset, offsets);
xOffset = drawReactionPart(products, plusWidth, xOffset, offsets);
auto osbw = drawOptions().scaleBondWidth;
if (reagents.empty() && products.empty() && agents.empty()) {
// if it's an empty reaction, we won't have a DrawMol with a scale,
// so we won't be able to do a scaled bond width
drawOptions().scaleBondWidth = false;
}
drawArrow(arrowBeg, arrowEnd, false, frac, M_PI / 6,
drawOptions().symbolColour, true);
drawOptions().scaleBondWidth = osbw;
if (drawOptions().includeMetadata) {
this->updateMetadata(rxn);
}
}
// ****************************************************************************
void MolDraw2D::drawLine(const Point2D &cds1, const Point2D &cds2,
const DrawColour &col1, const DrawColour &col2,
bool rawCoords) {
if (drawOptions().comicMode) {
// if rawCoords, we need a much bigger deviation.
auto dev = rawCoords ? 0.5 : 0.03;
auto scl = rawCoords ? 1.0 : scale_;
setFillPolys(false);
if (col1 == col2) {
setColour(col1);
auto pts =
MolDraw2D_detail::handdrawnLine(cds1, cds2, scl, true, true, 4, dev);
drawPolygon(pts, rawCoords);
} else {
auto mid = (cds1 + cds2) * 0.5;
setColour(col1);
auto pts =
MolDraw2D_detail::handdrawnLine(cds1, mid, scl, true, false, 4, dev);
drawPolygon(pts);
setColour(col2);
auto pts2 =
MolDraw2D_detail::handdrawnLine(mid, cds2, scl, false, true, 4, dev);
drawPolygon(pts2, rawCoords);
}
} else {
if (col1 == col2) {
setColour(col1);
drawLine(cds1, cds2, rawCoords);
} else {
auto mid = (cds1 + cds2) * 0.5;
setColour(col1);
drawLine(cds1, mid, rawCoords);
setColour(col2);
drawLine(mid, cds2, rawCoords);
}
}
}
// ****************************************************************************
void MolDraw2D::drawTriangle(const Point2D &cds1, const Point2D &cds2,
const Point2D &cds3, bool rawCoords) {
std::vector<Point2D> pts;
if (!drawOptions().comicMode) {
pts = {cds1, cds2, cds3};
} else {
double dev = rawCoords ? 0.5 : 0.03;
double scl = rawCoords ? 1.0 : scale_;
auto lpts =
MolDraw2D_detail::handdrawnLine(cds1, cds2, scl, false, false, 4, dev);
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, rawCoords);
};
// ****************************************************************************
void MolDraw2D::drawEllipse(const Point2D &cds1, const Point2D &cds2,
bool rawCoords) {
std::vector<Point2D> pts;
MolDraw2D_detail::arcPoints(cds1, cds2, pts, 0, 360);
drawPolygon(pts, rawCoords);
}
// ****************************************************************************
void MolDraw2D::drawArc(const Point2D &centre, double radius, double ang1,
double ang2, bool rawCoords) {
drawArc(centre, radius, radius, ang1, ang2, rawCoords);
}
// ****************************************************************************
void MolDraw2D::drawArc(const Point2D &centre, double xradius, double yradius,
double ang1, double ang2, bool rawCoords) {
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 = ang1 * 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(x, y);
}
if (fillPolys()) {
// otherwise it draws an arc back to the pts.front() rather than filling
// in the sector.
pts.push_back(centre);
}
drawPolygon(pts, rawCoords);
}
// ****************************************************************************
void MolDraw2D::drawRect(const Point2D &cds1, const Point2D &cds2,
bool rawCoords) {
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.push_back(cds1);
}
drawPolygon(pts, rawCoords);
}
// ****************************************************************************
// 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, bool rawCoords) {
auto perp = MolDraw2D_detail::calcPerpendicular(cds1, cds2);
auto p1 = Point2D(cds2.x - perp.x * len / 2, cds2.y - perp.y * len / 2);
auto p2 = Point2D(cds2.x + perp.x * len / 2, cds2.y + perp.y * len / 2);
drawWavyLine(p1, p2, col, col, nSegments, rawCoords);
}
// ****************************************************************************
void MolDraw2D::drawWavyLine(const Point2D &cds1, const Point2D &cds2,
const DrawColour &col1, const DrawColour &col2,
unsigned int, double, bool rawCoords) {
drawLine(cds1, cds2, col1, col2, rawCoords);
}
// ****************************************************************************
void MolDraw2D::drawArrow(const Point2D &arrowBegin, const Point2D &arrowEnd,
bool asPolygon, double frac, double angle,
const DrawColour &col, bool rawCoords) {
auto delta = arrowBegin - arrowEnd;
double cos_angle = std::cos(angle), sin_angle = std::sin(angle);
auto p1 = arrowEnd;
p1.x += frac * (delta.x * cos_angle + delta.y * sin_angle);
p1.y += frac * (delta.y * cos_angle - delta.x * sin_angle);
auto 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, col, col, rawCoords);
if (!asPolygon) {
drawLine(arrowEnd, p1, col, col, rawCoords);
drawLine(arrowEnd, p2, col, col, rawCoords);
} else {
std::vector<Point2D> pts = {p1, arrowEnd, p2};
bool fps = fillPolys();
auto dc = colour();
setFillPolys(true);
setColour(col);
drawPolygon(pts, rawCoords);
setFillPolys(fps);
setColour(dc);
}
}
// ****************************************************************************
void MolDraw2D::drawPlus(const Point2D &plusPos, int plusWidth,
const DrawColour &col, bool rawCoords) {
Point2D end1(plusPos.x, plusPos.y - plusWidth);
Point2D end2(plusPos.x, plusPos.y + plusWidth);
drawLine(end1, end2, col, col, rawCoords);
end1 = Point2D(plusPos.x - plusWidth, plusPos.y);
end2 = Point2D(plusPos.x + plusWidth, plusPos.y);
drawLine(end1, end2, col, col, rawCoords);
}
// ****************************************************************************
// draws the string centred on cds
void MolDraw2D::drawString(const string &str, const Point2D &cds,
bool rawCoords) {
auto draw_cds = rawCoords ? cds : getDrawCoords(cds);
text_drawer_->drawString(str, draw_cds, MolDraw2D_detail::OrientType::N);
// int olw = lineWidth();
// setLineWidth(0);
// text_drawer_->drawStringRects(str, OrientType::N, TextAlignType::MIDDLE,
// draw_cds, *this, rawCoords);
// setLineWidth(olw);
}
// ****************************************************************************
void MolDraw2D::drawString(const std::string &str, const Point2D &cds,
MolDraw2D_detail::TextAlignType talign,
bool rawCoords) {
auto draw_cds = rawCoords ? cds : getDrawCoords(cds);
text_drawer_->drawString(str, draw_cds, talign);
}
// ****************************************************************************
// transform a set of coords in the molecule's coordinate system
// to drawing system coordinates. Prefers globalDrawTrans_ if it exists.
Point2D MolDraw2D::getDrawCoords(const Point2D &mol_cds) const {
PRECONDITION(globalDrawTrans_ || !drawMols_.empty(), "no scaling info");
if (globalDrawTrans_) {
return globalDrawTrans_->getDrawCoords(mol_cds);
} else {
return drawMols_[activeMolIdx_]->getDrawCoords(mol_cds);
}
}
// ****************************************************************************
Point2D MolDraw2D::getDrawCoords(int at_num) const {
// this one can't use globalDrawTrans_, obviously.
PRECONDITION(activeMolIdx_ >= 0 &&
static_cast<size_t>(activeMolIdx_) <= drawMols_.size(),
"bad active mol index");
PRECONDITION(!drawMols_.empty(), "no draw mols");
PRECONDITION(
static_cast<size_t>(at_num) < drawMols_[activeMolIdx_]->atCds_.size(),
"bad atom number");
return drawMols_[activeMolIdx_]->getDrawCoords(at_num);
}
// ****************************************************************************
Point2D MolDraw2D::getAtomCoords(const pair<int, int> &screen_cds) const {
// Prefers globalDrawTrans_ if it exists.
PRECONDITION(globalDrawTrans_ || !drawMols_.empty(), "no scaling info");
return getAtomCoords(
make_pair(double(screen_cds.first), double(screen_cds.second)));
}
// ****************************************************************************
// Prefers globalDrawTrans_ if it exists.
Point2D MolDraw2D::getAtomCoords(const pair<double, double> &screen_cds) const {
// Prefers globalDrawTrans_ if it exists.
PRECONDITION(globalDrawTrans_ || !drawMols_.empty(), "no scaling info");
if (globalDrawTrans_) {
return globalDrawTrans_->getAtomCoords(
Point2D(screen_cds.first, screen_cds.second));
} else {
return drawMols_[activeMolIdx_]->getAtomCoords(
Point2D(screen_cds.first, screen_cds.second));
}
}
// ****************************************************************************
Point2D MolDraw2D::getAtomCoords(int at_num) const {
PRECONDITION(!drawMols_.empty() && activeMolIdx_ >= 0 &&
static_cast<size_t>(activeMolIdx_) <= drawMols_.size(),
"bad active mol index");
return drawMols_[activeMolIdx_]->getAtomCoords(at_num);
}
// ****************************************************************************
const std::vector<Point2D> &MolDraw2D::atomCoords() const {
PRECONDITION(activeMolIdx_ >= 0, "no index");
return drawMols_[activeMolIdx_]->atCds_;
}
// ****************************************************************************
const std::vector<std::pair<std::string, MolDraw2D_detail::OrientType>>
&MolDraw2D::atomSyms() const {
PRECONDITION(activeMolIdx_ >= 0, "no index");
return drawMols_[activeMolIdx_]->atomSyms_;
}
// ****************************************************************************
double MolDraw2D::getDrawLineWidth() const {
double width = lineWidth();
if (drawOptions().scaleBondWidth) {
// lineWidthScaleFactor is defined in MolDraw2DHelpers.h
width *= scale() * lineWidthScaleFactor;
if (width < 0.0) {
width = 0.0;
}
}
return width;
}
// ****************************************************************************
Point2D MolDraw2D::minPt() const {
// Prefers globalDrawTrans_ if it exists.
PRECONDITION(globalDrawTrans_ || activeMolIdx_ >= 0, "bad active mol");
// the ys are inverted in the DrawMol.
if (globalDrawTrans_) {
return Point2D(globalDrawTrans_->xMin_, -globalDrawTrans_->yMax_);
} else {
return Point2D(drawMols_[activeMolIdx_]->xMin_,
-drawMols_[activeMolIdx_]->yMax_);
}
}
// ****************************************************************************
Point2D MolDraw2D::range() const {
// Prefers globalDrawTrans_ if it exists.
PRECONDITION(globalDrawTrans_ || activeMolIdx_ >= 0, "bad active mol");
if (globalDrawTrans_) {
return Point2D(globalDrawTrans_->xRange_, globalDrawTrans_->yRange_);
} else {
return Point2D(drawMols_[activeMolIdx_]->xRange_,
drawMols_[activeMolIdx_]->yRange_);
}
}
// ****************************************************************************
double MolDraw2D::scale() const {
PRECONDITION(activeMolIdx_ >= 0 &&
static_cast<size_t>(activeMolIdx_) <= drawMols_.size(),
"bad active mol index");
return drawMols_[activeMolIdx_]->getScale();
}
// ****************************************************************************
double MolDraw2D::fontSize() const { return text_drawer_->fontSize(); }
// ****************************************************************************
void MolDraw2D::setFontSize(double new_size) {
text_drawer_->setFontSize(new_size);
}
// ****************************************************************************
void MolDraw2D::setScale(double newScale) { scale_ = newScale; }
// ****************************************************************************
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_min, x_max, x_range, y_min, y_max, y_range;
bool setFontScale = false;
if (mol) {
setupTextDrawer();
std::shared_ptr<MolDraw2D_detail::DrawMol> drawMol(
new MolDraw2D_detail::DrawMol(*mol, "", panelWidth(), panelHeight(),
drawOptions(), *text_drawer_));
drawMol->createDrawObjects();
// in the DrawMol, the ys are all inverted.
x_min = min(minv.x, drawMol->xMin_);
y_min = min(minv.y, -drawMol->yMax_);
x_max = max(maxv.x, drawMol->xMax_);
y_max = max(maxv.y, -drawMol->yMin_);
fontScale_ = drawMol->getFontScale();
setFontScale = true;
} 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;
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;
x_max = x_min + x_range;
y_min -= drawOptions().padding * y_range;
y_range *= 1 + 2 * drawOptions().padding;
y_max = y_min + y_range;
scale_ = std::min(double(width) / x_range, double(height) / y_range);
// Absent any other information, we'll have to go with fontScale_ the
// same as scale_.
if (!setFontScale) {
// get the text drawer to decide on a suitable fontScale.
double ofs = text_drawer_->fontScale();
text_drawer_->setFontScale(scale_);
fontScale_ = text_drawer_->fontScale();
text_drawer_->setFontScale(ofs, true);
} else {
fontScale_ *= scale_ / fontScale_;
}
forceScale_ = true;
MolDraw2D_detail::DrawMol *drawMol = new MolDraw2D_detail::DrawMol(
panelWidth(), panelHeight(), drawOptions(), *text_drawer_, x_min, x_max,
y_min, y_max, scale_, fontScale_);
Point2D trans, scale, toCentre;
drawMol->getDrawTransformers(trans, scale, toCentre);
globalDrawTrans_.reset(drawMol);
}
// ****************************************************************************
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,
MolDraw2D_detail::OrientType orient,
double &label_width, double &label_height) const {
if (orient == MolDraw2D_detail::OrientType::N ||
orient == MolDraw2D_detail::OrientType::S) {
label_height = 0.0;
label_width = 0.0;
vector<string> sym_bits =
MolDraw2D_detail::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,
MolDraw2D_detail::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);
auto draw_cds = getDrawCoords(cds);
x_min += draw_cds.x;
x_max += draw_cds.x;
y_min += draw_cds.y;
y_max += draw_cds.y;
auto new_mins = getAtomCoords(make_pair(x_min, y_min));
auto 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);
}
}
// ****************************************************************************
void MolDraw2D::setActiveMolIdx(int newIdx) {
PRECONDITION(newIdx >= -1 && newIdx < static_cast<int>(drawMols_.size()),
"bad new activeMolIdx_");
activeMolIdx_ = newIdx;
}
// ****************************************************************************
void MolDraw2D::setActiveAtmIdx(int at_idx1, int at_idx2) {
at_idx1 = (at_idx1 < 0 ? -1 : at_idx1);
at_idx2 = (at_idx2 < 0 ? -1 : at_idx2);
if (at_idx2 >= 0 && at_idx1 < 0) {
std::swap(at_idx1, at_idx2);
}
activeAtmIdx1_ = at_idx1;
activeAtmIdx2_ = at_idx2;
}
// ****************************************************************************
void MolDraw2D::fixVariableDimensions(
const MolDraw2D_detail::DrawMol &drawMol) {
if (panel_width_ == -1) {
width_ = panel_width_ = drawMol.width_;
}
if (panel_height_ == -1) {
height_ = panel_height_ = drawMol.height_;
}
}
// ****************************************************************************
void MolDraw2D::getReactionDrawMols(
const ChemicalReaction &rxn, bool highlightByReactant,
const std::vector<DrawColour> *highlightColorsReactants,
const std::vector<int> *confIds,
std::vector<std::shared_ptr<MolDraw2D_detail::DrawMol>> &reagents,
std::vector<std::shared_ptr<MolDraw2D_detail::DrawMol>> &products,
std::vector<std::shared_ptr<MolDraw2D_detail::DrawMol>> &agents,
int &plusWidth) {
ChemicalReaction nrxn(rxn);
const double agentFrac = 0.4;
double minScale = std::numeric_limits<double>::max(), minFontScale;
std::map<int, DrawColour> atomColours;
findReactionHighlights(rxn, highlightByReactant, highlightColorsReactants,
atomColours);
// reactants & products
makeReactionComponents(rxn.getReactants(), confIds, height(), atomColours,
reagents, minScale, minFontScale);
makeReactionComponents(rxn.getProducts(), confIds, height(), atomColours,
products, minScale, minFontScale);
for (auto &reagent : reagents) {
reagent->setScale(minScale, minFontScale);
reagent->shrinkToFit(false);
}
for (auto &product : products) {
product->setScale(minScale, minFontScale);
product->shrinkToFit(false);
}
// set the spacing for the plus signs to be 0.5 Angstrom.
plusWidth = minScale;
// agents
int agentHeight = int(agentFrac * height_);
minScale = std::numeric_limits<double>::max();
makeReactionComponents(rxn.getAgents(), confIds, agentHeight, atomColours,
agents, minScale, minFontScale);
for (auto &agent : agents) {
agent->setScale(minScale, minFontScale);
agent->shrinkToFit(false);
}
// set the active atom/bond indices so they run in series for all pieces.
// DrawMols start each new set at 0 by default. The original code had
// reagents, products then agents, so do the same here.
int atomIdxOffset = 0, bondIdxOffset = 0;
for (auto &dm : drawMols_) {
dm->activeAtmIdxOffset_ = atomIdxOffset;
dm->activeBndIdxOffset_ = bondIdxOffset;
atomIdxOffset += dm->drawMol_->getNumAtoms();
bondIdxOffset += dm->drawMol_->getNumBonds();
}
}
// ****************************************************************************
void MolDraw2D::makeReactionComponents(
const std::vector<RDKit::ROMOL_SPTR> &bits, const std::vector<int> *confIds,
int heightToUse, std::map<int, DrawColour> &atomColours,
std::vector<std::shared_ptr<MolDraw2D_detail::DrawMol>> &dms,
double &minScale, double &minFontScale) {
for (size_t midx = 0; midx < bits.size(); ++midx) {
std::vector<int> highlightAtoms, highlightBonds;
std::map<int, DrawColour> highlightAtomMap, highlightBondMap;
int cid = -1;
if (confIds) {
cid = (*confIds)[midx];
}
auto fragMol = bits[midx].get();
for (auto atom : fragMol->atoms()) {
auto ai = atomColours.find(atom->getAtomMapNum());
for (auto bond : fragMol->bonds()) {
auto beg = bond->getBeginAtom();
auto begi = atomColours.find(beg->getAtomMapNum());
if (begi != atomColours.end()) {
auto end = bond->getEndAtom();
auto endi = atomColours.find(end->getAtomMapNum());
if (endi != atomColours.end() && begi->second == endi->second) {
highlightBonds.push_back(bond->getIdx());
highlightBondMap.insert(
std::make_pair(bond->getIdx(), begi->second));
}
}
}
if (ai != atomColours.end()) {
highlightAtoms.push_back(atom->getIdx());
highlightAtomMap.insert(std::make_pair(atom->getIdx(), ai->second));
atom->setAtomMapNum(0);
}
}
makeReactionDrawMol(*(RWMol *)bits[midx].get(), cid, heightToUse,
highlightAtoms, highlightBonds, highlightAtomMap,
highlightBondMap, dms);
if (dms.back()->getScale() < minScale) {
minScale = dms.back()->getScale();
minFontScale = dms.back()->getFontScale();
}
}
}
// ****************************************************************************
void MolDraw2D::makeReactionDrawMol(
RWMol &mol, int confId, int molHeight,
const std::vector<int> &highlightAtoms,
const std::vector<int> &highlightBonds,
const std::map<int, DrawColour> &highlightAtomMap,
const std::map<int, DrawColour> &highlightBondMap,
std::vector<std::shared_ptr<MolDraw2D_detail::DrawMol>> &mols) {
mol.updatePropertyCache(false);
if (drawOptions().prepareMolsBeforeDrawing) {
try {
RDLog::LogStateSetter blocker;
MolOps::Kekulize(mol, false); // kekulize, but keep the aromatic flags!
} catch (const MolSanitizeException &) {
// don't need to do anything
}
MolOps::setHybridization(mol);
}
if (!mol.getNumConformers()) {
const bool canonOrient = true;
RDDepict::compute2DCoords(mol, nullptr, canonOrient);
} else {
// we need to center the molecule
MolDraw2D_detail::centerMolForDrawing(mol, confId);
}
// when preparing a reaction component to be drawn we should neither kekulize
// (we did that above if required) nor add chiralHs
const bool kekulize = false;
const bool addChiralHs = false;
MolDraw2DUtils::prepareMolForDrawing(mol, kekulize, addChiralHs);
// the height is fixed, but the width is allowed to be as large as the
// height and molecule dimensions dictate.
mols.emplace_back(new MolDraw2D_detail::DrawMol(
mol, "", -1, molHeight, drawOptions(), *text_drawer_, &highlightAtoms,
&highlightBonds, &highlightAtomMap, &highlightBondMap, nullptr, nullptr,
supportsAnnotations(), confId, true));
mols.back()->createDrawObjects();
drawMols_.push_back(mols.back());
++activeMolIdx_;
}
// ****************************************************************************
void MolDraw2D::calcReactionOffsets(
std::vector<std::shared_ptr<MolDraw2D_detail::DrawMol>> &reagents,
std::vector<std::shared_ptr<MolDraw2D_detail::DrawMol>> &products,
std::vector<std::shared_ptr<MolDraw2D_detail::DrawMol>> &agents,
int &plusWidth, std::vector<Point2D> &offsets, Point2D &arrowBeg,
Point2D &arrowEnd) {
// calculate the total width of the drawing - it may need re-scaling if
// it's too wide for the panel.
const int arrowMult = 2; // number of plusWidths for an empty arrow.
auto reactionWidth = [&](int gapWidth) -> int {
int totWidth = 0;
if (!reagents.empty()) {
for (auto &dm : reagents) {
totWidth += dm->width_;
}
totWidth += gapWidth * (reagents.size() - 1);
}
if (agents.empty()) {
totWidth += arrowMult * gapWidth;
} else {
// the agent doesn't start at front of arrow
for (auto &dm : agents) {
totWidth += dm->width_ + gapWidth;
}
totWidth += gapWidth * (agents.size() - 1) / 2;
}
totWidth += gapWidth; // either side of arrow
if (!products.empty()) {
for (auto &dm : products) {
totWidth += dm->width_;
}
// we don't want a plus after the last product
totWidth += gapWidth * (products.size() - 1);
}
return totWidth;
};
auto scaleDrawMols =
[&](std::vector<std::shared_ptr<MolDraw2D_detail::DrawMol>> &dms,
double stretch) {
for (auto &dm : dms) {
dm->setScale(stretch * dm->getScale(), stretch * dm->getFontScale(),
false);
dm->shrinkToFit(false);
}
};
if (width_ == -1) {
width_ = reactionWidth(plusWidth);
}
// The DrawMols are sized/scaled according to the height() which is all
// there is to go on initially, so they may be wider than the width() in
// total. If so, shrink them to fit. Because the shrinkng imposes min and max
// font sizes, we may not get the smaller size we want first go, so iterate
// until we do or we give up.
int totWidth = reactionWidth(plusWidth);
for (int i = 0; i < 5; ++i) {
auto maxWidthIt =
std::max_element(drawMols_.begin(), drawMols_.end(),
[&](std::shared_ptr<MolDraw2D_detail::DrawMol> &lhs,
std::shared_ptr<MolDraw2D_detail::DrawMol> &rhs) {
return lhs->width_ < rhs->width_;
});
plusWidth = (*maxWidthIt)->width_ / 4;
plusWidth = plusWidth > width() / 20 ? width() / 20 : plusWidth;
auto oldTotWidth = totWidth;
auto stretch = double(width_ * (1 - drawOptions().padding)) / totWidth;
// If stretch < 1, we need to shrink the DrawMols to fit. This isn't
// necessary if we're just stretching them along the panel as they already
// fit for height.
if (stretch < 1.0) {
scaleDrawMols(reagents, stretch);
scaleDrawMols(agents, stretch);
scaleDrawMols(products, stretch);
} else {
break;
}
totWidth = reactionWidth(plusWidth);
if (fabs(totWidth - oldTotWidth) < 0.01 * width()) {
break;
}
}
// make sure plusWidth remains 1A, in pixels.
if (!reagents.empty()) {
plusWidth = reagents.front()->scale_;
} else if (!products.empty()) {
plusWidth = products.front()->scale_;
}
// if there's space, we can afford make the extras a bit bigger.
int numGaps = reagents.empty() ? 0 : reagents.size() - 1;
numGaps += products.empty() ? 0 : products.size() - 1;
numGaps += 1; // for either side of the arrow
numGaps += agents.empty() ? 2 : agents.size() - 1;
if (width() - totWidth > numGaps * 5) {
plusWidth += 5;
}
totWidth = reactionWidth(plusWidth);
// And finally work out where to put all the pieces, centring them.
int xOffset = (width() - totWidth) / 2;
for (size_t i = 0; i < reagents.size(); ++i) {
offsets.emplace_back(xOffset, (height() - reagents[i]->height_) / 2);
xOffset += reagents[i]->width_ + plusWidth;
}
if (reagents.empty()) {
xOffset += plusWidth / 2;
} else {
// only half a plusWidth to the arrow
xOffset -= plusWidth / 2;
}
arrowBeg.y = height() / 2;
arrowBeg.x = xOffset;
if (agents.empty()) {
arrowEnd = Point2D(arrowBeg.x + arrowMult * plusWidth, height() / 2);
} else {
xOffset += plusWidth / 2;
for (size_t i = 0; i < agents.size(); ++i) {
offsets.emplace_back(xOffset, 0.45 * height() - agents[i]->height_);
xOffset += agents[i]->width_ + plusWidth / 2;
}
// the overlap at the end of the arrow has already been added in the loop
arrowEnd = Point2D(xOffset, height() / 2);
}
xOffset = arrowEnd.x + plusWidth / 2;
for (size_t i = 0; i < products.size(); ++i) {
offsets.emplace_back(xOffset, (height() - products[i]->height_) / 2);
xOffset += products[i]->width_ + plusWidth;
}
}
// ****************************************************************************
int MolDraw2D::drawReactionPart(
std::vector<std::shared_ptr<MolDraw2D_detail::DrawMol>> &reactBit,
int plusWidth, int initOffset, const std::vector<Point2D> &offsets) {
if (reactBit.empty()) {
return initOffset;
}
Point2D plusPos(0.0, height() / 2);
for (size_t i = 0; i < reactBit.size(); ++i) {
++activeMolIdx_;
reactBit[i]->setOffsets(offsets[initOffset].x, offsets[initOffset].y);
reactBit[i]->draw(*this);
#if 0
// this is convenient for debugging
setColour(DrawColour(0, 1.0, 1.0));
drawLine(Point2D(offsets[initOffset].x + reactBit[i]->width_, 0),
Point2D(offsets[initOffset].x + reactBit[i]->width_, height_),
true);
drawLine(Point2D(offsets[initOffset].x, 0),
Point2D(offsets[initOffset].x, height_), true);
setColour(DrawColour(1.0, 0, 1.0));
drawLine(Point2D(offsets[initOffset].x, offsets[initOffset].y),
Point2D(offsets[initOffset].x + reactBit[i]->width_,
offsets[initOffset].y),
true);
drawLine(Point2D(offsets[initOffset].x,
offsets[initOffset].y + reactBit[i]->height_),
Point2D(offsets[initOffset].x + reactBit[i]->width_,
offsets[initOffset].y + reactBit[i]->height_),
true);
#endif
if (plusWidth && i < reactBit.size() - 1) {
plusPos.x = (offsets[initOffset].x + reactBit[i]->width_ +
offsets[initOffset + 1].x) /
2;
int plusStroke = plusWidth > 30 ? 10 : plusWidth / 3;
drawPlus(plusPos, plusStroke, drawOptions().symbolColour, true);
}
++initOffset;
}
return initOffset;
}
// ****************************************************************************
void MolDraw2D::findReactionHighlights(
const ChemicalReaction &rxn, bool highlightByReactant,
const std::vector<DrawColour> *highlightColorsReactants,
std::map<int, DrawColour> &atomColours) const {
std::unique_ptr<ROMol> tmol(ChemicalReactionToRxnMol(rxn));
if (highlightByReactant) {
const auto *colors = &drawOptions().highlightColourPalette;
if (highlightColorsReactants) {
colors = highlightColorsReactants;
}
for (size_t midx = 0; midx < rxn.getReactants().size(); ++midx) {
auto fragMol = rxn.getReactants()[midx].get();
for (auto &atom : fragMol->atoms()) {
int atomRole = -1;
if (atom->getPropIfPresent("molRxnRole", atomRole) && atomRole == 1 &&
atom->getAtomMapNum()) {
atomColours.insert(std::make_pair(atom->getAtomMapNum(),
(*colors)[midx % colors->size()]));
}
}
}
}
}
// ****************************************************************************
void MolDraw2D::startDrawing() {
if (needs_init_) {
initDrawing();
needs_init_ = false;
}
if (activeMolIdx_ <= 0 && drawOptions().clearBackground) {
clearDrawing();
}
}
// ****************************************************************************
void MolDraw2D::drawTheMolecule(MolDraw2D_detail::DrawMol &drawMol) {
if (globalDrawTrans_) {
drawMol.setTransformation(*globalDrawTrans_);
} else if (forceScale_) {
drawMol.setScale(scale_, fontScale_);
}
drawMol.draw(*this);
if (drawOptions().includeMetadata) {
this->updateMetadata(*drawMol.drawMol_, drawMol.confId_);
}
}
// ****************************************************************************
void MolDraw2D::setupTextDrawer() {
text_drawer_->setMaxFontSize(drawOptions().maxFontSize);
text_drawer_->setMinFontSize(drawOptions().minFontSize);
if (drawOptions().baseFontSize > 0.0) {
text_drawer_->setBaseFontSize(drawOptions().baseFontSize);
}
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;
}
}
} // namespace RDKit
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