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rdkit/Code/GraphMol/MolDraw2D/test1.cpp
Greg Landrum b29f463298 A variety of drawing-related changes (#986) 
* Fixes #982
also changes bond-wedging algorithm to favor lighter non-ring bonds

* prefer wedging bonds to lower-degree atoms

* Fixes #983

* small fixes
- Fix a problem where a chiral atom is selected to draw a wedge to instead of a ring atom
- Fix a problem where two calls to PrepareMolForDrawing() led to two wedged bonds from an atom.

* Fixes #985

This isn't the most satisfying solution (the wedged bonds are sometimes a bit too large), but it gives reasonable results on the test cases I've tried.
2016-08-18 11:39:27 +02:00

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//
// Copyright (C) 2015 Greg Landrum
//
// @@ All Rights Reserved @@
// This file is part of the RDKit.
// The contents are covered by the terms of the BSD license
// which is included in the file license.txt, found at the root
// of the RDKit source tree.
//
#include <RDGeneral/utils.h>
#include <RDGeneral/Invariant.h>
#include <RDGeneral/RDLog.h>
#include <GraphMol/RDKitBase.h>
#include <GraphMol/SmilesParse/SmilesParse.h>
#include <GraphMol/FileParsers/MolSupplier.h>
#include <GraphMol/FileParsers/FileParsers.h>
#include <GraphMol/Depictor/RDDepictor.h>
#include <GraphMol/FileParsers/MolFileStereochem.h>
#include <GraphMol/MolDraw2D/MolDraw2D.h>
#include <GraphMol/MolDraw2D/MolDraw2DSVG.h>
#include <GraphMol/MolDraw2D/MolDraw2DUtils.h>
#include <iostream>
#include <fstream>
#include <sstream>
using namespace RDKit;
void test1() {
std::cout << " ----------------- Test 1" << std::endl;
{
std::string smiles = "CO[C@@H](O)C1=C(O[C@H](F)Cl)C(C#N)=C1ONNC[NH3+]";
ROMol *m = SmilesToMol(smiles);
TEST_ASSERT(m);
RDDepict::compute2DCoords(*m);
WedgeMolBonds(*m, &(m->getConformer()));
std::ofstream outs("test1_1.svg");
MolDraw2DSVG drawer(300, 300, outs);
drawer.drawMolecule(*m);
drawer.finishDrawing();
outs.flush();
delete m;
}
{
// make sure this works with the stringstream too:
std::string smiles = "CO[C@@H](O)C1=C(O[C@H](F)Cl)C=C1ONNC[NH3+]";
ROMol *m = SmilesToMol(smiles);
TEST_ASSERT(m);
RDDepict::compute2DCoords(*m);
WedgeMolBonds(*m, &(m->getConformer()));
MolDraw2DSVG drawer(300, 300);
drawer.drawMolecule(*m);
drawer.finishDrawing();
std::string text = drawer.getDrawingText();
TEST_ASSERT(text.find("<svg:svg") != std::string::npos);
TEST_ASSERT(text.find("</svg:svg>") != std::string::npos);
delete m;
}
{
std::string smiles = "Cc1c(C(=O)NCCO)[n+](=O)c2ccccc2n1[O-]";
ROMol *m = SmilesToMol(smiles);
TEST_ASSERT(m);
RDDepict::compute2DCoords(*m);
WedgeMolBonds(*m, &(m->getConformer()));
std::ofstream outs("test1_2.svg");
MolDraw2DSVG drawer(300, 300, outs);
drawer.drawMolecule(*m);
drawer.finishDrawing();
outs.flush();
delete m;
}
{
std::string smiles = "Cc1c(C(=O)NCCO)[n+](=O)c2ccccc2n1[O-]";
ROMol *m = SmilesToMol(smiles);
TEST_ASSERT(m);
RDDepict::compute2DCoords(*m);
WedgeMolBonds(*m, &(m->getConformer()));
std::ofstream outs("test1_3.svg");
MolDraw2DSVG drawer(300, 300, outs);
std::vector<int> highlights;
highlights.push_back(0);
highlights.push_back(4);
highlights.push_back(5);
drawer.drawMolecule(*m, &highlights);
drawer.finishDrawing();
outs.flush();
delete m;
}
std::cout << " Done" << std::endl;
}
#ifdef RDK_CAIRO_BUILD
#include <cairo.h>
#include "MolDraw2DCairo.h"
void test2() {
std::cout << " ----------------- Test 2" << std::endl;
{
std::string smiles = "CO[C@@H](O)C1=C(O[C@H](F)Cl)C(C#N)=C1ONNC[NH3+]";
ROMol *m = SmilesToMol(smiles);
TEST_ASSERT(m);
RDDepict::compute2DCoords(*m);
WedgeMolBonds(*m, &(m->getConformer()));
MolDraw2DCairo drawer(300, 300);
drawer.drawMolecule(*m);
drawer.finishDrawing();
drawer.writeDrawingText("test2_1.png");
delete m;
}
{
std::string smiles = "Cc1c(C(=O)NCCO)[n+](=O)c2ccccc2n1[O-]";
ROMol *m = SmilesToMol(smiles);
TEST_ASSERT(m);
RDDepict::compute2DCoords(*m);
WedgeMolBonds(*m, &(m->getConformer()));
MolDraw2DCairo drawer(300, 300);
drawer.drawMolecule(*m);
drawer.finishDrawing();
std::string drawing = drawer.getDrawingText();
std::ofstream ofs("test2_2.png");
ofs.write(drawing.c_str(), drawing.size());
delete m;
}
{
// ensure we still work with a client-provided drawing context
std::string smiles = "Cc1c(C(=O)NCCO)[n+](=O)c2ccccc2n1[O-]";
ROMol *m = SmilesToMol(smiles);
TEST_ASSERT(m);
RDDepict::compute2DCoords(*m);
WedgeMolBonds(*m, &(m->getConformer()));
cairo_surface_t *surface =
cairo_image_surface_create(CAIRO_FORMAT_ARGB32, 300, 300);
cairo_t *cr = cairo_create(surface);
MolDraw2DCairo drawer(300, 300, cr);
std::vector<int> highlights;
highlights.push_back(0);
highlights.push_back(4);
highlights.push_back(5);
drawer.drawMolecule(*m, &highlights);
drawer.finishDrawing();
cairo_destroy(cr);
cairo_surface_write_to_png(surface, "test2_3.png");
cairo_surface_destroy(surface);
delete m;
}
std::cout << " Done" << std::endl;
}
#else // RDK_CAIRO_BUILD
void test2() {}
#endif
void test3() {
std::cout << " ----------------- Test 3" << std::endl;
{
std::string smiles = "C1CC1CC1ON1";
std::string nameBase = "test3_1";
ROMol *m = SmilesToMol(smiles);
TEST_ASSERT(m);
RDDepict::compute2DCoords(*m);
WedgeMolBonds(*m, &(m->getConformer()));
static const int ha[] = {0, 3, 4, 5};
std::vector<int> highlight_atoms(ha, ha + sizeof(ha) / sizeof(int));
std::map<int, std::string> atomLabels;
atomLabels[2] = "C1";
atomLabels[1] = "a<sub>3</sub><sup>4</sup>";
atomLabels[0] = "[CH2;X2:4]";
atomLabels[6] = "[NH2+:7]";
#ifdef RDK_CAIRO_BUILD
{
MolDraw2DCairo drawer(300, 300);
drawer.drawOptions().atomLabels = atomLabels;
drawer.drawMolecule(*m, &highlight_atoms);
drawer.finishDrawing();
drawer.writeDrawingText(nameBase + ".png");
}
#endif
{
std::ofstream outs((nameBase + ".svg").c_str());
MolDraw2DSVG drawer(300, 300, outs);
drawer.drawOptions().atomLabels = atomLabels;
drawer.drawMolecule(*m, &highlight_atoms);
drawer.finishDrawing();
outs.flush();
}
delete m;
}
{
std::string smiles = "C1CC1CC1ON1";
std::string nameBase = "test3_2";
ROMol *m = SmilesToMol(smiles);
TEST_ASSERT(m);
RDDepict::compute2DCoords(*m);
WedgeMolBonds(*m, &(m->getConformer()));
static const int ha[] = {0, 3, 4, 5};
std::vector<int> highlight_atoms(ha, ha + sizeof(ha) / sizeof(int));
#ifdef RDK_CAIRO_BUILD
{
MolDraw2DCairo drawer(300, 300);
drawer.drawOptions().circleAtoms = false;
drawer.drawMolecule(*m, &highlight_atoms);
drawer.finishDrawing();
drawer.writeDrawingText(nameBase + ".png");
}
#endif
{
std::ofstream outs((nameBase + ".svg").c_str());
MolDraw2DSVG drawer(300, 300, outs);
drawer.drawOptions().circleAtoms = false;
drawer.drawMolecule(*m, &highlight_atoms);
drawer.finishDrawing();
outs.flush();
}
delete m;
}
{
std::string smiles = "Cc1c(C(=O)NCCO)[n+](=O)c2ccccc2n1[O-]";
std::string nameBase = "test3_3";
ROMol *m = SmilesToMol(smiles);
TEST_ASSERT(m);
RDDepict::compute2DCoords(*m);
WedgeMolBonds(*m, &(m->getConformer()));
static const int ha[] = {11, 12, 13, 14, 15, 16};
std::vector<int> highlight_atoms(ha, ha + sizeof(ha) / sizeof(int));
std::map<int, DrawColour> highlight_colors;
highlight_colors[12] = DrawColour(0, 0, 1);
highlight_colors[13] = DrawColour(0, 1, 0);
#ifdef RDK_CAIRO_BUILD
{
MolDraw2DCairo drawer(300, 300);
drawer.drawOptions().circleAtoms = true;
drawer.drawMolecule(*m, &highlight_atoms, &highlight_colors);
drawer.finishDrawing();
drawer.writeDrawingText(nameBase + ".png");
}
#endif
{
std::ofstream outs((nameBase + ".svg").c_str());
MolDraw2DSVG drawer(300, 300, outs);
drawer.drawOptions().circleAtoms = true;
drawer.drawMolecule(*m, &highlight_atoms, &highlight_colors);
drawer.finishDrawing();
outs.flush();
}
delete m;
}
{
std::string smiles = "Cc1c(C(=O)NCCO)[n+](=O)c2ccccc2n1[O-]";
std::string nameBase = "test3_4";
ROMol *m = SmilesToMol(smiles);
TEST_ASSERT(m);
RDDepict::compute2DCoords(*m);
WedgeMolBonds(*m, &(m->getConformer()));
static const int ha[] = {11, 12, 13, 14, 15, 16, 3};
std::vector<int> highlight_atoms(ha, ha + sizeof(ha) / sizeof(int));
std::map<int, DrawColour> highlight_colors;
highlight_colors[12] = DrawColour(.5, .5, 1);
highlight_colors[13] = DrawColour(.5, 1, .5);
MolDrawOptions options;
options.circleAtoms = true;
options.highlightColour = DrawColour(1, .5, .5);
options.continuousHighlight = true;
#ifdef RDK_CAIRO_BUILD
{
MolDraw2DCairo drawer(300, 300);
drawer.drawOptions() = options;
drawer.drawMolecule(*m, &highlight_atoms, &highlight_colors);
drawer.finishDrawing();
drawer.writeDrawingText(nameBase + ".png");
}
#endif
{
std::ofstream outs((nameBase + ".svg").c_str());
MolDraw2DSVG drawer(300, 300, outs);
drawer.drawOptions() = options;
drawer.drawMolecule(*m, &highlight_atoms, &highlight_colors);
drawer.finishDrawing();
outs.flush();
}
delete m;
}
{
std::string smiles =
"CCOC(=O)Nc1ccc(SCC2COC(Cn3ccnc3)(c3ccc(Cl)cc3Cl)O2)cc1";
std::string nameBase = "test3_5";
ROMol *m = SmilesToMol(smiles);
TEST_ASSERT(m);
RDDepict::compute2DCoords(*m);
WedgeMolBonds(*m, &(m->getConformer()));
static const int ha[] = {17, 18, 19, 20, 21, 6, 7, 8, 9, 31, 32};
std::vector<int> highlight_atoms(ha, ha + sizeof(ha) / sizeof(int));
std::map<int, DrawColour> highlight_colors;
MolDrawOptions options;
options.circleAtoms = true;
options.highlightColour = DrawColour(1, .5, .5);
options.continuousHighlight = true;
#ifdef RDK_CAIRO_BUILD
{
MolDraw2DCairo drawer(200, 200);
drawer.drawOptions() = options;
drawer.drawMolecule(*m, &highlight_atoms, &highlight_colors);
drawer.finishDrawing();
drawer.writeDrawingText(nameBase + ".png");
}
#endif
{
std::ofstream outs((nameBase + ".svg").c_str());
MolDraw2DSVG drawer(200, 200, outs);
drawer.drawOptions() = options;
drawer.drawMolecule(*m, &highlight_atoms, &highlight_colors);
drawer.finishDrawing();
outs.flush();
}
delete m;
}
{
std::string smiles =
"CCOC(=O)Nc1ccc(SCC2COC(Cn3ccnc3)(c3ccc(Cl)cc3Cl)O2)cc1";
std::string nameBase = "test3_6";
ROMol *m = SmilesToMol(smiles);
TEST_ASSERT(m);
RDDepict::compute2DCoords(*m);
WedgeMolBonds(*m, &(m->getConformer()));
MolDrawOptions options;
static const int ha1[] = {17, 18, 19, 20, 21};
std::vector<int> highlight_atoms1(ha1, ha1 + sizeof(ha1) / sizeof(int));
options.atomRegions.push_back(highlight_atoms1);
static const int ha2[] = {6, 7, 8, 9, 31, 32};
std::vector<int> highlight_atoms2(ha2, ha2 + sizeof(ha2) / sizeof(int));
options.atomRegions.push_back(highlight_atoms2);
options.includeAtomTags = true;
#ifdef RDK_CAIRO_BUILD
{
MolDraw2DCairo drawer(300, 300);
drawer.drawOptions() = options;
drawer.drawMolecule(*m);
drawer.finishDrawing();
drawer.writeDrawingText(nameBase + ".png");
}
#endif
{
std::ofstream outs((nameBase + ".svg").c_str());
MolDraw2DSVG drawer(300, 300, outs);
drawer.drawOptions() = options;
drawer.drawMolecule(*m);
drawer.finishDrawing();
outs.flush();
}
delete m;
}
{
std::string smiles =
"CCOC(=O)Nc1ccc(SCC2COC(Cn3ccnc3)(c3ccc(Cl)cc3Cl)O2)cc1";
std::string nameBase = "test3_7";
ROMol *m = SmilesToMol(smiles);
TEST_ASSERT(m);
RDDepict::compute2DCoords(*m);
WedgeMolBonds(*m, &(m->getConformer()));
MolDrawOptions options;
options.continuousHighlight = true;
static const int ha[] = {17, 20, 25};
std::vector<int> highlight_atoms(ha, ha + sizeof(ha) / sizeof(int));
std::map<int, double> highlight_radii;
highlight_radii[17] = 0.5;
highlight_radii[20] = 1.0;
std::map<int, DrawColour> highlight_colors;
highlight_colors[17] = DrawColour(.5, .5, 1.);
#ifdef RDK_CAIRO_BUILD
{
MolDraw2DCairo drawer(300, 300);
drawer.drawOptions() = options;
drawer.drawMolecule(*m, &highlight_atoms, &highlight_colors,
&highlight_radii);
drawer.finishDrawing();
drawer.writeDrawingText(nameBase + ".png");
}
#endif
{
std::ofstream outs((nameBase + ".svg").c_str());
MolDraw2DSVG drawer(300, 300, outs);
drawer.drawOptions() = options;
drawer.drawMolecule(*m, &highlight_atoms, &highlight_colors,
&highlight_radii);
drawer.finishDrawing();
outs.flush();
}
delete m;
}
std::cout << " Done" << std::endl;
}
void test4() {
std::cout << " ----------------- Test 4" << std::endl;
{
std::string fName = getenv("RDBASE");
fName += "/Code/GraphMol/MolDraw2D/test_dir";
fName += "/clash.mol";
ROMol *m = MolFileToMol(fName);
std::string nameBase = "test4_1";
TEST_ASSERT(m);
#ifdef RDK_CAIRO_BUILD
{
MolDraw2DCairo drawer(300, 300);
drawer.drawMolecule(*m);
drawer.finishDrawing();
drawer.writeDrawingText(nameBase + ".png");
}
#endif
{
std::ofstream outs((nameBase + ".svg").c_str());
MolDraw2DSVG drawer(300, 300, outs);
drawer.drawMolecule(*m);
drawer.finishDrawing();
outs.flush();
}
delete m;
}
std::cout << " Done" << std::endl;
}
void test5() {
std::cout << " ----------------- Test 5" << std::endl;
{
std::string smiles = "*c1cc(*)cc(*)c1";
std::string nameBase = "test5_1";
ROMol *m = SmilesToMol(smiles);
TEST_ASSERT(m);
RDDepict::compute2DCoords(*m);
WedgeMolBonds(*m, &(m->getConformer()));
MolDrawOptions options;
options.dummiesAreAttachments = true;
options.atomLabels[0] = "R1";
#ifdef RDK_CAIRO_BUILD
{
MolDraw2DCairo drawer(300, 300);
drawer.drawOptions() = options;
drawer.drawMolecule(*m);
drawer.finishDrawing();
drawer.writeDrawingText(nameBase + ".png");
}
#endif
{
std::ofstream outs((nameBase + ".svg").c_str());
MolDraw2DSVG drawer(300, 300, outs);
drawer.drawOptions() = options;
drawer.drawMolecule(*m);
drawer.finishDrawing();
outs.flush();
}
delete m;
}
std::cout << " Done" << std::endl;
}
#ifdef RDK_TEST_MULTITHREADED
#include <RDGeneral/BoostStartInclude.h>
#include <boost/thread.hpp>
#include <RDGeneral/BoostEndInclude.h>
namespace {
void runblock(const std::vector<ROMol *> &mols,
const std::vector<std::string> &refData, unsigned int count,
unsigned int idx) {
for (unsigned int j = 0; j < 200; j++) {
for (unsigned int i = 0; i < mols.size(); ++i) {
if (i % count != idx) continue;
ROMol *mol = mols[i];
MolDraw2DSVG drawer(300, 300);
drawer.drawMolecule(*mol);
drawer.finishDrawing();
std::string text = drawer.getDrawingText();
TEST_ASSERT(text == refData[i]);
}
}
}
}
void testMultiThreaded() {
std::cout << " ----------------- Test multi-threaded drawing" << std::endl;
std::string fName = getenv("RDBASE");
fName += "/Data/NCI/first_200.props.sdf";
RDKit::SDMolSupplier suppl(fName);
std::cerr << "reading molecules" << std::endl;
std::vector<ROMol *> mols;
while (!suppl.atEnd() && mols.size() < 100) {
ROMol *mol = 0;
try {
mol = suppl.next();
} catch (...) {
continue;
}
if (!mol) continue;
mols.push_back(mol);
}
std::cerr << "generating reference drawings" << std::endl;
std::vector<std::string> refData(mols.size());
for (unsigned int i = 0; i < mols.size(); ++i) {
MolDraw2DSVG drawer(300, 300);
drawer.drawMolecule(*(mols[i]));
drawer.finishDrawing();
refData[i] = drawer.getDrawingText();
TEST_ASSERT(refData[i].find("<svg:svg") != std::string::npos);
TEST_ASSERT(refData[i].find("</svg:svg>") != std::string::npos);
}
boost::thread_group tg;
unsigned int count = 4;
std::cerr << "processing" << std::endl;
for (unsigned int i = 0; i < count; ++i) {
std::cerr << " launch :" << i << std::endl;
std::cerr.flush();
tg.add_thread(new boost::thread(runblock, mols, refData, count, i));
}
tg.join_all();
std::cerr << " Done" << std::endl;
}
#else
void testMultiThreaded() {}
#endif
void test6() {
std::cout << " ----------------- Test 6 (atom labels)" << std::endl;
{
std::string smiles = "CC[13CH2][CH2:7][CH-]C[15NH2+]C";
std::string nameBase = "test5_1";
ROMol *m = SmilesToMol(smiles);
TEST_ASSERT(m);
RDDepict::compute2DCoords(*m);
WedgeMolBonds(*m, &(m->getConformer()));
MolDraw2DSVG drawer(300, 300);
drawer.drawMolecule(*m);
drawer.finishDrawing();
std::string txt = drawer.getDrawingText();
std::ofstream outs("test6_1.svg");
outs << txt;
// TEST_ASSERT(txt.find("<svg:svg")!=std::string::npos);
}
std::cerr << " Done" << std::endl;
}
void test7() {
std::cout << " ----------------- Test 7 (backgrounds)" << std::endl;
std::string smiles = "CCC";
ROMol *m = SmilesToMol(smiles);
TEST_ASSERT(m);
RDDepict::compute2DCoords(*m);
{
std::string nameBase = "test7_1";
MolDraw2DSVG drawer(300, 300);
drawer.drawOptions().clearBackground = false;
drawer.drawMolecule(*m);
drawer.finishDrawing();
std::string txt = drawer.getDrawingText();
std::ofstream outs((nameBase + ".svg").c_str());
outs << txt;
TEST_ASSERT(txt.find("<svg:svg") != std::string::npos);
TEST_ASSERT(txt.find("<svg:rect") == std::string::npos);
}
#ifdef RDK_CAIRO_BUILD
{
std::string nameBase = "test7_1";
MolDraw2DCairo drawer(300, 300);
drawer.drawOptions().clearBackground = false;
drawer.drawMolecule(*m);
drawer.finishDrawing();
drawer.writeDrawingText(nameBase + ".png");
}
#endif
{
std::string nameBase = "test7_2";
MolDraw2DSVG drawer(300, 300);
drawer.drawOptions().backgroundColour = DrawColour(.8, .8, .8);
drawer.drawMolecule(*m);
drawer.finishDrawing();
std::string txt = drawer.getDrawingText();
std::ofstream outs((nameBase + ".svg").c_str());
outs << txt;
TEST_ASSERT(txt.find("<svg:svg") != std::string::npos);
TEST_ASSERT(txt.find("<svg:rect") != std::string::npos);
TEST_ASSERT(txt.find("fill:#CCCCCC") != std::string::npos);
}
#ifdef RDK_CAIRO_BUILD
{
std::string nameBase = "test7_2";
MolDraw2DCairo drawer(300, 300);
drawer.drawOptions().backgroundColour = DrawColour(.8, .8, .8);
drawer.drawMolecule(*m);
drawer.finishDrawing();
drawer.writeDrawingText(nameBase + ".png");
}
#endif
std::cerr << " Done" << std::endl;
}
void test8PrepareMolForDrawing() {
std::cout << " ----------------- Test8: PrepareMolDrawing" << std::endl;
{
std::string smiles = "c1ccccc1[C@H](F)Cl";
ROMol *m = SmilesToMol(smiles);
TEST_ASSERT(m);
{
RWMol nm(*m);
TEST_ASSERT(nm.getNumAtoms() == 9)
MolDraw2DUtils::prepareMolForDrawing(nm);
TEST_ASSERT(nm.getNumAtoms() == 9); // this is a test for github #982
TEST_ASSERT(nm.getNumConformers() == 1);
TEST_ASSERT(!nm.getConformer().is3D());
TEST_ASSERT(nm.getBondBetweenAtoms(0, 1)->getBondType() !=
Bond::AROMATIC);
TEST_ASSERT(nm.getBondBetweenAtoms(0, 1)->getIsAromatic());
TEST_ASSERT(nm.getBondBetweenAtoms(6, 7)->getBondType() == Bond::SINGLE);
TEST_ASSERT(nm.getBondBetweenAtoms(6, 7)->getBondDir() ==
Bond::BEGINWEDGE);
// make sure we can do it again:
MolDraw2DUtils::prepareMolForDrawing(nm);
TEST_ASSERT(nm.getNumAtoms() == 9);
TEST_ASSERT(nm.getNumConformers() == 1);
TEST_ASSERT(nm.getBondBetweenAtoms(0, 1)->getBondType() !=
Bond::AROMATIC);
TEST_ASSERT(nm.getBondBetweenAtoms(0, 1)->getIsAromatic());
}
{
RWMol nm(*m);
TEST_ASSERT(nm.getNumAtoms() == 9)
MolDraw2DUtils::prepareMolForDrawing(nm, false);
TEST_ASSERT(nm.getNumAtoms() == 9);
TEST_ASSERT(nm.getNumConformers() == 1);
TEST_ASSERT(nm.getBondBetweenAtoms(0, 1)->getBondType() ==
Bond::AROMATIC);
TEST_ASSERT(nm.getBondBetweenAtoms(0, 1)->getIsAromatic());
}
{
RWMol nm(*m);
TEST_ASSERT(nm.getNumAtoms() == 9)
MolDraw2DUtils::prepareMolForDrawing(nm, false, false);
TEST_ASSERT(nm.getNumAtoms() == 9);
TEST_ASSERT(nm.getNumConformers() == 1);
TEST_ASSERT(nm.getBondBetweenAtoms(0, 1)->getBondType() ==
Bond::AROMATIC);
TEST_ASSERT(nm.getBondBetweenAtoms(0, 1)->getIsAromatic());
}
{
RWMol nm(*m);
TEST_ASSERT(nm.getNumAtoms() == 9)
MolDraw2DUtils::prepareMolForDrawing(nm, false, true);
TEST_ASSERT(nm.getNumAtoms() == 9);
TEST_ASSERT(nm.getNumConformers() == 1);
TEST_ASSERT(nm.getBondBetweenAtoms(0, 1)->getBondType() ==
Bond::AROMATIC);
TEST_ASSERT(nm.getBondBetweenAtoms(0, 1)->getIsAromatic());
}
{
RWMol nm(*m);
TEST_ASSERT(nm.getNumAtoms() == 9)
MolDraw2DUtils::prepareMolForDrawing(nm, true, true, false);
TEST_ASSERT(nm.getNumAtoms() == 9);
TEST_ASSERT(nm.getNumConformers() == 1);
TEST_ASSERT(nm.getBondBetweenAtoms(0, 1)->getBondType() !=
Bond::AROMATIC);
TEST_ASSERT(nm.getBondBetweenAtoms(0, 1)->getIsAromatic());
TEST_ASSERT(nm.getBondBetweenAtoms(6, 7)->getBondType() == Bond::SINGLE);
TEST_ASSERT(nm.getBondBetweenAtoms(6, 7)->getBondDir() == Bond::NONE);
}
{
// by default we don't force conformer generation
RWMol nm(*m);
RDDepict::compute2DCoords(nm);
nm.getConformer().set3D(true); // it's not really, we're cheating
TEST_ASSERT(nm.getNumAtoms() == 9)
MolDraw2DUtils::prepareMolForDrawing(nm);
TEST_ASSERT(nm.getNumAtoms() == 9);
TEST_ASSERT(nm.getNumConformers() == 1); // we have a conformer anyway
TEST_ASSERT(nm.getConformer().is3D());
// but if we do force, it blows out that conformer:
MolDraw2DUtils::prepareMolForDrawing(nm, true, true, true, true);
TEST_ASSERT(!nm.getConformer().is3D());
}
delete m;
}
{
std::string smiles = "C1CC[C@H]2NCCCC2C1";
ROMol *m = SmilesToMol(smiles);
TEST_ASSERT(m);
{
RWMol nm(*m);
TEST_ASSERT(nm.getNumAtoms() == 10)
MolDraw2DUtils::prepareMolForDrawing(nm);
TEST_ASSERT(nm.getNumAtoms() == 11);
TEST_ASSERT(nm.getNumConformers() == 1);
TEST_ASSERT(!nm.getConformer().is3D());
TEST_ASSERT(nm.getBondBetweenAtoms(3, 10)->getBondType() == Bond::SINGLE);
TEST_ASSERT(nm.getBondBetweenAtoms(3, 10)->getBondDir() ==
Bond::BEGINDASH);
// make sure we can do it again:
MolDraw2DUtils::prepareMolForDrawing(nm);
TEST_ASSERT(nm.getNumAtoms() == 11);
TEST_ASSERT(nm.getNumConformers() == 1);
TEST_ASSERT(nm.getBondBetweenAtoms(3, 10)->getBondType() == Bond::SINGLE);
TEST_ASSERT(nm.getBondBetweenAtoms(3, 10)->getBondDir() ==
Bond::BEGINDASH);
}
{
RWMol nm(*m);
TEST_ASSERT(nm.getNumAtoms() == 10)
MolDraw2DUtils::prepareMolForDrawing(nm, false, false);
TEST_ASSERT(nm.getNumAtoms() == 10);
TEST_ASSERT(nm.getNumConformers() == 1);
TEST_ASSERT(nm.getBondBetweenAtoms(3, 2)->getBondType() == Bond::SINGLE);
TEST_ASSERT(nm.getBondBetweenAtoms(3, 2)->getBondDir() ==
Bond::BEGINWEDGE);
}
delete m;
}
std::cerr << " Done" << std::endl;
}
void testGithub781() {
std::cout
<< " ----------------- Test Github #781: Rendering single-atom molecules"
<< std::endl;
{
std::string smiles = "C";
ROMol *m = SmilesToMol(smiles);
TEST_ASSERT(m);
RDDepict::compute2DCoords(*m);
MolDraw2DSVG drawer(300, 300);
drawer.drawMolecule(*m);
drawer.finishDrawing();
std::string txt = drawer.getDrawingText();
TEST_ASSERT(txt.find("<svg:svg") != std::string::npos);
TEST_ASSERT(txt.find("<svg:tspan>CH</svg:tspan>") != std::string::npos);
delete m;
}
{
std::string smiles = "[C]";
ROMol *m = SmilesToMol(smiles);
TEST_ASSERT(m);
RDDepict::compute2DCoords(*m);
MolDraw2DSVG drawer(300, 300);
drawer.drawMolecule(*m);
drawer.finishDrawing();
std::string txt = drawer.getDrawingText();
TEST_ASSERT(txt.find("<svg:svg") != std::string::npos);
TEST_ASSERT(txt.find("<svg:tspan>C</svg:tspan>") != std::string::npos);
delete m;
}
{
std::string smiles = "C.CC.[Cl-]";
ROMol *m = SmilesToMol(smiles);
TEST_ASSERT(m);
RDDepict::compute2DCoords(*m);
MolDraw2DSVG drawer(300, 300);
drawer.drawMolecule(*m);
drawer.finishDrawing();
std::string txt = drawer.getDrawingText();
TEST_ASSERT(txt.find("<svg:svg") != std::string::npos);
TEST_ASSERT(txt.find("<svg:tspan>CH</svg:tspan>") != std::string::npos);
TEST_ASSERT(txt.find("<svg:tspan>Cl</svg:tspan>") != std::string::npos);
delete m;
}
{ // empty molecule
ROMol *m = new ROMol();
TEST_ASSERT(m);
RDDepict::compute2DCoords(*m);
MolDraw2DSVG drawer(300, 300);
drawer.drawMolecule(*m);
drawer.finishDrawing();
std::string txt = drawer.getDrawingText();
TEST_ASSERT(txt.find("<svg:svg") != std::string::npos);
TEST_ASSERT(txt.find("<svg:tspan>") == std::string::npos);
delete m;
}
std::cerr << " Done" << std::endl;
}
void testGithub774() {
std::cout << " ----------------- Test Github774" << std::endl;
{
std::string smiles =
"Cc1c(C(=O)NCC[NH3+])[n+](=O)c2cc(CC[C@](F)(Cl)Br)ccc2n1[O-]";
std::string nameBase = "test774_1";
RWMol *m = SmilesToMol(smiles);
TEST_ASSERT(m);
RDDepict::compute2DCoords(*m);
WedgeMolBonds(*m, &(m->getConformer()));
MolOps::Kekulize(*m);
#ifdef RDK_CAIRO_BUILD
{
MolDraw2DCairo drawer(300, 300);
drawer.drawMolecule(*m);
drawer.finishDrawing();
drawer.writeDrawingText(nameBase + ".png");
}
#endif
{
std::ofstream outs((nameBase + ".svg").c_str());
MolDraw2DSVG drawer(300, 300, outs);
drawer.drawMolecule(*m);
drawer.finishDrawing();
outs.flush();
Point2D ocoords(1.0, 2.0);
Point2D dcoords =
drawer.getAtomCoords(std::make_pair(ocoords.x, ocoords.y));
Point2D acoords = drawer.getDrawCoords(dcoords);
TEST_ASSERT(feq(acoords.x, 1.0));
TEST_ASSERT(feq(acoords.y, 2.0));
}
// m->setProp("_Name","mol");
// std::cerr<<MolToMolBlock(*m)<<std::endl;
delete m;
}
{
std::string smiles =
"CC(=O)\\C=C\\CC1[C@H]2N([C@@H](C(=O)O)C(C)(C)S2(=O)=O)C1=O";
std::string nameBase = "test774_2";
RWMol *m = SmilesToMol(smiles);
TEST_ASSERT(m);
RDDepict::compute2DCoords(*m);
WedgeMolBonds(*m, &(m->getConformer()));
MolOps::Kekulize(*m);
#ifdef RDK_CAIRO_BUILD
{
MolDraw2DCairo drawer(300, 300);
drawer.drawMolecule(*m);
drawer.finishDrawing();
drawer.writeDrawingText(nameBase + ".png");
}
#endif
{
std::ofstream outs((nameBase + ".svg").c_str());
MolDraw2DSVG drawer(300, 300, outs);
drawer.drawMolecule(*m);
drawer.finishDrawing();
outs.flush();
}
// m->setProp("_Name","mol");
// std::cerr<<MolToMolBlock(*m)<<std::endl;
delete m;
}
std::cerr << " Done" << std::endl;
}
void test9MolLegends() {
std::cout << " ----------------- Test 9 (molecule legends)" << std::endl;
{
std::string smiles = "CC[13CH2][CH2:7][CH-]C[15NH2+]C";
std::string nameBase = "test5_1";
ROMol *m = SmilesToMol(smiles);
TEST_ASSERT(m);
RDDepict::compute2DCoords(*m);
WedgeMolBonds(*m, &(m->getConformer()));
MolDraw2DSVG drawer(300, 300);
drawer.drawMolecule(*m, "mol legend");
drawer.finishDrawing();
std::string txt = drawer.getDrawingText();
std::ofstream outs("test9_1.svg");
outs << txt;
// TEST_ASSERT(txt.find("<svg:svg")!=std::string::npos);
}
std::cerr << " Done" << std::endl;
}
void testGithub852() {
std::cout << " ----------------- Test Github852: Lines used to wedge bonds "
"are too thick"
<< std::endl;
{
std::string smiles =
"COc1cccc(NC(=O)[C@H](Cl)Sc2nc(ns2)c3ccccc3Cl)c1"; // made up
std::string nameBase = "test852_1";
RWMol *m = SmilesToMol(smiles);
TEST_ASSERT(m);
MolDraw2DUtils::prepareMolForDrawing(*m);
#ifdef RDK_CAIRO_BUILD
{
MolDraw2DCairo drawer(300, 300);
drawer.drawMolecule(*m);
drawer.finishDrawing();
drawer.writeDrawingText(nameBase + ".png");
}
#endif
{
std::ofstream outs((nameBase + ".svg").c_str());
MolDraw2DSVG drawer(300, 300, outs);
drawer.drawMolecule(*m);
drawer.finishDrawing();
outs.flush();
}
delete m;
}
{
std::string smiles =
"C[C@]12CC[C@@H]3c4ccc(cc4CC[C@H]3[C@@H]1CC[C@@H]2O)O"; // estradiol
std::string nameBase = "test852_2";
RWMol *m = SmilesToMol(smiles);
TEST_ASSERT(m);
MolDraw2DUtils::prepareMolForDrawing(*m);
#ifdef RDK_CAIRO_BUILD
{
MolDraw2DCairo drawer(300, 300);
drawer.drawMolecule(*m);
drawer.finishDrawing();
drawer.writeDrawingText(nameBase + ".png");
}
#endif
{
std::ofstream outs((nameBase + ".svg").c_str());
MolDraw2DSVG drawer(300, 300, outs);
drawer.drawMolecule(*m);
drawer.finishDrawing();
outs.flush();
}
delete m;
}
std::cerr << " Done" << std::endl;
}
void testGithub860() {
std::cout << " ----------------- Test Github860: Atom symbols in wrong order "
"if bond comes from right"
<< std::endl;
{
std::string smiles = "[15NH3+:1]-C#C-[15NH3+:2]";
std::string nameBase = "test860_1";
RWMol *m = SmilesToMol(smiles);
TEST_ASSERT(m);
MolDraw2DUtils::prepareMolForDrawing(*m);
#ifdef RDK_CAIRO_BUILD
{
MolDraw2DCairo drawer(300, 300);
drawer.drawMolecule(*m);
drawer.finishDrawing();
drawer.writeDrawingText(nameBase + ".png");
}
#endif
{
std::ofstream outs((nameBase + ".svg").c_str());
MolDraw2DSVG drawer(300, 300, outs);
drawer.drawMolecule(*m);
drawer.finishDrawing();
outs.flush();
}
}
{
std::string smiles =
"[15NH3+:1]-C#C-C([15NH3+:2])([15NH3+:3])-C#C-[15NH3+:4]";
std::string nameBase = "test860_2";
RWMol *m = SmilesToMol(smiles);
TEST_ASSERT(m);
MolDraw2DUtils::prepareMolForDrawing(*m);
#ifdef RDK_CAIRO_BUILD
{
MolDraw2DCairo drawer(300, 300);
drawer.drawMolecule(*m);
drawer.finishDrawing();
drawer.writeDrawingText(nameBase + ".png");
}
#endif
{
std::ofstream outs((nameBase + ".svg").c_str());
MolDraw2DSVG drawer(300, 300, outs);
drawer.drawMolecule(*m);
drawer.finishDrawing();
outs.flush();
}
}
{
std::string smiles = "[15NH3+:1]-CCCCCCCC-[15NH3+:4]";
std::string nameBase = "test860_3";
RWMol *m = SmilesToMol(smiles);
TEST_ASSERT(m);
MolDraw2DUtils::prepareMolForDrawing(*m);
#ifdef RDK_CAIRO_BUILD
{
MolDraw2DCairo drawer(300, 300);
drawer.drawMolecule(*m);
drawer.finishDrawing();
drawer.writeDrawingText(nameBase + ".png");
}
#endif
{
std::ofstream outs((nameBase + ".svg").c_str());
MolDraw2DSVG drawer(300, 300, outs);
drawer.drawMolecule(*m);
drawer.finishDrawing();
outs.flush();
}
}
std::cerr << " Done" << std::endl;
}
void testGithub910() {
std::cout << " ----------------- Test Github #910: ugly coordinates "
"generated for peptide chains"
<< std::endl;
// this really isn't much of a test, but it does help visually confirm that
// things are actually ok
{
// this is a ChEMBL molecule
std::string smiles =
"CSCC[C@H](NC(=O)[C@@H](CCC(N)=O)NC(=O)[C@@H](N)Cc1c[nH]c2ccccc12)C(=O)"
"NCC(=O)N[C@@H](Cc1c[nH]cn1)C(=O)N[C@@H](CO)C(=O)O";
ROMol *m = SmilesToMol(smiles);
TEST_ASSERT(m);
RDDepict::compute2DCoords(*m);
WedgeMolBonds(*m, &(m->getConformer()));
std::ofstream outs("test910_1.svg");
MolDraw2DSVG drawer(600, 300, outs);
drawer.drawMolecule(*m);
drawer.finishDrawing();
outs.flush();
delete m;
}
{ // now with Hs
// this is a ChEMBL molecule
std::string smiles =
"CSCC[C@H](NC(=O)[C@@H](CCC(N)=O)NC(=O)[C@@H](N)Cc1c[nH]c2ccccc12)C(=O)"
"NCC(=O)N[C@@H](Cc1c[nH]cn1)C(=O)N[C@@H](CO)C(=O)O";
RWMol *m = SmilesToMol(smiles);
TEST_ASSERT(m);
MolDraw2DUtils::prepareMolForDrawing(*m);
std::ofstream outs("test910_2.svg");
MolDraw2DSVG drawer(600, 300, outs);
drawer.drawMolecule(*m);
drawer.finishDrawing();
outs.flush();
delete m;
}
std::cerr << " Done" << std::endl;
}
void testGithub932() {
std::cout
<< " ----------------- Test Github #932: mistake in SVG for wedged bonds"
<< std::endl;
{
std::string smiles = "CC[C@](F)(Cl)Br";
RWMol *m = SmilesToMol(smiles);
TEST_ASSERT(m);
MolDraw2DUtils::prepareMolForDrawing(*m);
MolDraw2DSVG drawer(200, 200);
drawer.drawMolecule(*m);
drawer.finishDrawing();
std::string text = drawer.getDrawingText();
TEST_ASSERT(text.find("evenoddstroke") == std::string::npos);
delete m;
}
std::cerr << " Done" << std::endl;
}
void testGithub953() {
std::cout
<< " ----------------- Test Github #953: default color should not be cyan"
<< std::endl;
{
std::string smiles = "[Nb]";
RWMol *m = SmilesToMol(smiles);
TEST_ASSERT(m);
MolDraw2DUtils::prepareMolForDrawing(*m);
MolDraw2DSVG drawer(200, 200);
drawer.drawMolecule(*m);
drawer.finishDrawing();
std::string text = drawer.getDrawingText();
TEST_ASSERT(text.find("#00FFFF") == std::string::npos);
delete m;
}
std::cerr << " Done" << std::endl;
}
void testGithub983() {
std::cout << " ----------------- Test Github #983: wedged bonds between "
"chiral centers drawn improperly"
<< std::endl;
{
// this has an ugly drawing (wedged bond between chiral centers) but we
// force it to be drawn that way just to check.
std::string mb =
"\n\
Mrv1561 07241608122D\n\
\n\
6 5 0 0 0 0 999 V2000\n\
8.6830 -9.5982 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0\n\
9.3975 -9.1857 0.0000 C 0 0 2 0 0 0 0 0 0 0 0 0\n\
10.1120 -9.5982 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0\n\
9.3975 -8.3607 0.0000 Cl 0 0 0 0 0 0 0 0 0 0 0 0\n\
10.8264 -9.1857 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0\n\
10.1120 -10.4232 0.0000 F 0 0 0 0 0 0 0 0 0 0 0 0\n\
1 2 1 0 0 0 0\n\
3 5 1 0 0 0 0\n\
3 2 1 1 0 0 0\n\
2 4 1 1 0 0 0\n\
3 6 1 0 0 0 0\n\
M END";
RWMol *m = MolBlockToMol(mb, false, false);
TEST_ASSERT(m);
MolOps::sanitizeMol(*m);
MolDraw2DUtils::prepareMolForDrawing(*m);
MolDraw2DSVG drawer(200, 200);
drawer.drawMolecule(*m);
drawer.finishDrawing();
std::string text = drawer.getDrawingText();
std::ofstream outs("test983_1.svg");
outs << text;
outs.flush();
TEST_ASSERT(text.find("<svg:path d='M 130.309,117.496 73.5169,75.8928 "
"65.8827,89.1161 130.309,117.496' "
"style='fill:#000000") != std::string::npos);
delete m;
}
{
std::string mb =
"\n\
Mrv1561 07241616282D\n\
\n\
12 12 0 0 1 0 999 V2000\n\
10.4656 -7.9623 0.0000 F 0 0 0 0 0 0 0 0 0 0 0 0\n\
9.7496 -8.3748 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0\n\
8.9075 -9.4746 0.0000 C 0 0 2 0 0 0 0 0 0 0 0 0\n\
7.5671 -9.4746 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0\n\
8.2373 -8.9934 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0\n\
8.6497 -10.2651 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0\n\
9.0392 -7.9623 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0\n\
7.8249 -10.2651 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0\n\
7.1547 -10.1792 0.0000 F 0 0 0 0 0 0 0 0 0 0 0 0\n\
6.8567 -9.0622 0.0000 F 0 0 0 0 0 0 0 0 0 0 0 0\n\
10.3338 -8.9591 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0\n\
8.6841 -8.6669 0.0000 H 0 0 0 0 0 0 0 0 0 0 0 0\n\
2 1 1 0 0 0 0\n\
3 2 1 0 0 0 0\n\
4 5 1 0 0 0 0\n\
5 3 1 0 0 0 0\n\
6 3 1 0 0 0 0\n\
7 2 1 0 0 0 0\n\
8 6 1 0 0 0 0\n\
9 4 1 0 0 0 0\n\
10 4 1 0 0 0 0\n\
2 11 1 6 0 0 0\n\
3 12 1 6 0 0 0\n\
8 4 1 0 0 0 0\n\
M END";
RWMol *m = MolBlockToMol(mb);
TEST_ASSERT(m);
MolDraw2DUtils::prepareMolForDrawing(*m);
TEST_ASSERT(m->getBondBetweenAtoms(2, 1)->getBondType() == Bond::SINGLE);
TEST_ASSERT(m->getBondBetweenAtoms(2, 1)->getBondDir() == Bond::NONE);
TEST_ASSERT(m->getBondBetweenAtoms(2, 4)->getBondType() == Bond::SINGLE);
TEST_ASSERT(m->getBondBetweenAtoms(2, 4)->getBondDir() == Bond::BEGINWEDGE);
MolDraw2DSVG drawer(200, 200);
drawer.drawMolecule(*m);
drawer.finishDrawing();
std::string text = drawer.getDrawingText();
std::ofstream outs("test983_2.svg");
outs << text;
outs.flush();
TEST_ASSERT(text.find("<svg:path d='M 107.911,115.963 80.5887,91.4454 "
"75.9452,97.9126 107.911,115.963' "
"style='fill:#000000;") != std::string::npos);
MolDraw2DUtils::prepareMolForDrawing(*m);
TEST_ASSERT(m->getBondBetweenAtoms(2, 1)->getBondType() == Bond::SINGLE);
TEST_ASSERT(m->getBondBetweenAtoms(2, 1)->getBondDir() == Bond::NONE);
TEST_ASSERT(m->getBondBetweenAtoms(2, 4)->getBondType() == Bond::SINGLE);
TEST_ASSERT(m->getBondBetweenAtoms(2, 4)->getBondDir() == Bond::BEGINWEDGE);
RWMol nm(*m);
MolDraw2DUtils::prepareMolForDrawing(nm);
TEST_ASSERT(nm.getBondBetweenAtoms(2, 1)->getBondType() == Bond::SINGLE);
TEST_ASSERT(nm.getBondBetweenAtoms(2, 1)->getBondDir() == Bond::NONE);
TEST_ASSERT(nm.getBondBetweenAtoms(2, 4)->getBondType() == Bond::SINGLE);
TEST_ASSERT(nm.getBondBetweenAtoms(2, 4)->getBondDir() == Bond::BEGINWEDGE);
delete m;
}
std::cerr << " Done" << std::endl;
}
int main() {
RDLog::InitLogs();
#if 1
test1();
test2();
test4();
test5();
test6();
test7();
test8PrepareMolForDrawing();
testMultiThreaded();
testGithub781();
test3();
testGithub774();
test9MolLegends();
testGithub852();
testGithub860();
#endif
testGithub910();
testGithub932();
testGithub953();
testGithub983();
}
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