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rdkit/Code/GraphMol/MolDraw2D/catch_tests.cpp
Greg Landrum 8c27805fa3 Allow wedged double and aromatic bonds (#7495) 
* support wedging in double and aromatic bonds

This is a first pass and the testing isn't really there.

* add expected test results (from windows...)
switch to not using freetype for the tests

* response to review
2024-06-07 05:09:33 +02:00

9693 lines
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//
// Copyright (C) 2019-2023 Greg Landrum and other RDKit contributors
//
// @@ 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 <catch2/catch_all.hpp>
#include <numeric>
#include <random>
#include <GraphMol/RDKitBase.h>
#include <RDGeneral/hash/hash.hpp>
#include <GraphMol/Chirality.h>
#include <GraphMol/SmilesParse/SmilesParse.h>
#include <GraphMol/MolDraw2D/MolDraw2D.h>
#include <GraphMol/MolDraw2D/MolDraw2DSVG.h>
#include <GraphMol/MolDraw2D/MolDraw2DUtils.h>
#include <GraphMol/MolDraw2D/MolDraw2DDetails.h>
#include <GraphMol/MolDraw2D/DrawMol.h>
#include <GraphMol/FileParsers/FileParsers.h>
#include <GraphMol/FileParsers/PNGParser.h>
#include <boost/algorithm/string/split.hpp>
#include <GraphMol/ChemReactions/Reaction.h>
#include <GraphMol/ChemReactions/ReactionParser.h>
#include <GraphMol/CIPLabeler/CIPLabeler.h>
#include <GraphMol/Depictor/RDDepictor.h>
#include <Geometry/point.h>
#include <regex>
#ifdef RDK_BUILD_CAIRO_SUPPORT
#include <cairo.h>
#include "MolDraw2DCairo.h"
#endif
// a lot of the tests check <text> flags in the SVG. That doesn't
// happen with the Freetype versions
static const bool NO_FREETYPE = true;
namespace {
// if the generated SVG hashes to the value we're expecting, delete
// the file. That way, only the files that need inspection will be
// left at the end of the run.
// The hand-drawn pictures will fail this frequently due to the use
// of random numbers to draw the lines. As well as all the testHandDrawn
// files, this includes testBrackets-5a.svg and testPositionVariation-1b.svg
const bool DELETE_WITH_GOOD_HASH = true;
// The expected hash code for a file may be included in these maps, or
// provided in the call to check_file_hash().
// These values are for a build with FreeType, so expect them all to be
// wrong when building without.
const std::map<std::string, std::hash_result_t> SVG_HASHES = {
{"testAtomTags_1.svg", 3187798125U},
{"testAtomTags_2.svg", 822910240U},
{"testAtomTags_3.svg", 2244078420U},
{"contourMol_1.svg", 2604538953U},
{"contourMol_2.svg", 572669511U},
{"contourMol_3.svg", 936771429U},
{"contourMol_4.svg", 3302971362U},
{"contourMol_5.svg", 2230414999U},
{"testDativeBonds_1.svg", 3550231997U},
{"testDativeBonds_2.svg", 2510476717U},
{"testDativeBonds_3.svg", 1742381275U},
{"testDativeBonds_2a.svg", 3936523099U},
{"testDativeBonds_2b.svg", 1652957675U},
{"testDativeBonds_2c.svg", 630355005U},
{"testDativeBonds_2d.svg", 2346072497U},
{"testZeroOrderBonds_1.svg", 3733430366U},
{"testFoundations_1.svg", 2350247048U},
{"testFoundations_2.svg", 15997352U},
{"testTest_1.svg", 15997352U},
{"testKekulizationProblems_1.svg", 3009056821U},
{"testAtomBondIndices_1.svg", 2702803018U},
{"testAtomBondIndices_2.svg", 1564350363U},
{"testAtomBondIndices_3.svg", 2316486733U},
{"testAtomBondIndices_4.svg", 1200363593U},
{"testAtomBondIndices_5.svg", 1502163147U},
{"testAtomBondIndices_6.svg", 1659568104U},
{"testGithub3226_1.svg", 831257877U},
{"testGithub3226_2.svg", 3517325227U},
{"testGithub3226_3.svg", 3609721552U},
{"testGithub3369_1.svg", 2194263901U},
{"testIncludeRadicals_1a.svg", 1829641340U},
{"testIncludeRadicals_1b.svg", 4184066907U},
{"testLegendsAndDrawing-1.svg", 3563802758U},
{"testGithub3577-1.svg", 1294276543U},
{"testHandDrawn-1.svg", 2253418236U},
{"testHandDrawn-2.svg", 4132716144U},
{"testHandDrawn-3.svg", 4199337510U},
{"testHandDrawn-4.svg", 4197407865U},
{"testHandDrawn-5a.svg", 3628607349U},
{"testHandDrawn-5b.svg", 2522138089U},
{"testBrackets-1a.svg", 4189399574U},
{"testBrackets-1b.svg", 3773894816U},
{"testBrackets-1c.svg", 4189399574U},
{"testBrackets-1d.svg", 3773894816U},
{"testBrackets-1e.svg", 2492125470U},
{"testBrackets-2a.svg", 1050851904U},
{"testBrackets-2b.svg", 776446765U},
{"testBrackets-2c.svg", 1050851904U},
{"testBrackets-2d.svg", 776446765U},
{"testBrackets-3a.svg", 1374944956U},
{"testBrackets-4a.svg", 3837821771U},
{"testBrackets-4b.svg", 1477006167U},
{"testBrackets-5a.svg", 3061667963U},
{"testBrackets-5768.svg", 2559120196U},
{"testSGroupData-1a.svg", 426096222U},
{"testSGroupData-1b.svg", 1688385103U},
{"testSGroupData-2a.svg", 195363059U},
{"testSGroupData-2b.svg", 942041938U},
{"testSGroupData-3a.svg", 2405789536U},
{"testPositionVariation-1.svg", 1347003808U},
{"testPositionVariation-1b.svg", 174339626U},
{"testPositionVariation-2.svg", 473948585U},
{"testPositionVariation-3.svg", 4039188982U},
{"testPositionVariation-4.svg", 3407574474U},
{"testNoAtomLabels-1.svg", 4255907058U},
{"testNoAtomLabels-2.svg", 3643749531U},
{"testQueryBonds-1a.svg", 1525751327U},
{"testQueryBonds-1b.svg", 3339941561U},
{"testQueryBonds-1c.svg", 375371096U},
{"testQueryBonds-2.svg", 3399320861U},
{"testLinkNodes-2-0.svg", 145749789U},
{"testLinkNodes-2-30.svg", 3203923109U},
{"testLinkNodes-2-60.svg", 2004079267U},
{"testLinkNodes-2-90.svg", 171994932U},
{"testLinkNodes-2-120.svg", 673333745U},
{"testLinkNodes-2-150.svg", 51965551U},
{"testLinkNodes-2-180.svg", 433020402U},
{"testMolAnnotations-1.svg", 1638024035U},
{"testMolAnnotations-2a.svg", 3029896996U},
{"testMolAnnotations-2b.svg", 3110016833U},
{"testMolAnnotations-2c.svg", 611992302U},
{"testMolAnnotations-3a.svg", 55379064U},
{"testMolAnnotations-3b.svg", 936144383U},
{"testMolAnnotations-3c.svg", 3983292921U},
{"testMolAnnotations-3d.svg", 748075045U},
{"testMolAnnotations-4a.svg", 3474490519U},
{"testLinkNodes-1-0.svg", 3845035394U},
{"testLinkNodes-1-30.svg", 3207457801U},
{"testLinkNodes-1-60.svg", 2620138210U},
{"testLinkNodes-1-90.svg", 1457485851U},
{"testLinkNodes-1-120.svg", 4267267665U},
{"testLinkNodes-1-150.svg", 574622776U},
{"testLinkNodes-1-180.svg", 2541146503U},
{"testGithub3744.svg", 387800653U},
{"testAtomLists-1.svg", 1887579391U},
{"testAtomLists-2.svg", 555139782U},
{"testIsoDummyIso.svg", 2405371137U},
{"testNoIsoDummyIso.svg", 748558214U},
{"testIsoNoDummyIso.svg", 3054263824U},
{"testNoIsoNoDummyIso.svg", 1185561148U},
{"testDeuteriumTritium.svg", 1867318569U},
{"testHydrogenBonds1.svg", 2605974904U},
{"testHydrogenBonds2.svg", 645414593U},
{"testGithub3912.1.svg", 2513727029U},
{"testGithub3912.2.svg", 3814673891U},
{"testGithub2976.svg", 2669316911U},
{"testReactionCoords.svg", 402445764U},
{"testAnnotationColors.svg", 2216313312U},
{"testGithub4323_1.svg", 2536621192U},
{"testGithub4323_2.svg", 2120846759U},
{"testGithub4323_3.svg", 4156867630U},
{"testGithub4323_4.svg", 3824125601U},
{"testGithub4238_1.svg", 2621118499U},
{"testGithub4508_1.svg", 2047652713U},
{"testGithub4508_1b.svg", 2681019776U},
{"testGithub4508_2.svg", 1382076550U},
{"testGithub4508_2b.svg", 4005636724U},
{"testGithub4538.svg", 2797362550U},
{"testDarkMode.1.svg", 4157562958U},
{"testMonochrome.1.svg", 482290994U},
{"testMonochrome.2.svg", 2128285153U},
{"testAvalon.1.svg", 477303888U},
{"testCDK.1.svg", 1764612361U},
{"testGithub4519_1.svg", 736612670U},
{"testGithub4519_2.svg", 171503813U},
{"testGithub4519_3.svg", 3396792960U},
{"testGithub4519_4.svg", 3924693257U},
{"testBaseFontSize.1a.svg", 1295117205U},
{"testBaseFontSize.1b.svg", 3595811515U},
{"testBaseFontSize.2a.svg", 2958687877U},
{"testBaseFontSize.2b.svg", 1786972332U},
{"testFlexiCanvas.1a.svg", 2633733362U},
{"testFlexiCanvas.1b.svg", 1541095928U},
{"testFlexiCanvas.1c.svg", 3204351481U},
{"testFlexiCanvas.1d.svg", 1753089731U},
{"testFlexiCanvas.2.svg", 665664909U},
{"testSemiFlexiCanvas.1a.svg", 1541095928U},
{"testSemiFlexiCanvas.1b.svg", 3020732451U},
{"testSemiFlexiCanvas.1c.svg", 4178696811U},
{"testFlexiCanvas.3.svg", 2819587550U},
{"testFlexiCanvas.4a.svg", 1486952473U},
{"testFlexiCanvas.4b.svg", 1957607740U},
{"testFlexiCanvas.4c.svg", 3955371857U},
{"testFlexiCanvas.4d.svg", 1137945621U},
{"testFlexiCanvas.5a.svg", 3968863584U},
{"testFlexiCanvas.5b.svg", 649567318U},
{"testFlexiCanvas.5c.svg", 1826396133U},
{"testFlexiCanvas.5d.svg", 1730603480U},
{"testFlexiCanvas.6a.svg", 3085867303U},
{"testFlexiCanvas.6b.svg", 2819164642U},
{"testFlexiCanvas.6c.svg", 3085867303U},
{"testFlexiCanvas.6d.svg", 3085867303U},
{"testFlexiCanvas.7a.svg", 514767495U},
{"testFlexiCanvas.7b.svg", 4275125955U},
{"testFlexiCanvas.7c.svg", 514767495U},
{"testFlexiCanvas.7d.svg", 514767495U},
{"testGithub4764.sz1.svg", 3611125861U},
{"testGithub4764.sz2.svg", 1936114454U},
{"testGithub4764.sz3.svg", 2712214121U},
{"testDrawArc1.svg", 3279637525U},
{"testMetalWedges.svg", 2896721486U},
{"testVariableLegend_1.svg", 1817838365U},
{"testVariableLegend_2.svg", 1038247753U},
{"testVariableLegend_3.svg", 2073034956U},
{"testGithub_5061.svg", 83338095U},
{"testGithub_5185.svg", 3800073130U},
{"testGithub_5269_1.svg", 3886922298U},
{"testGithub_5269_2.svg", 2890052584U},
{"test_classes_wavy_bonds.svg", 1694809514U},
{"testGithub_5383_1.svg", 1391972140U},
{"github5156_1.svg", 2145907703U},
{"github5156_2.svg", 4184795863U},
{"github5156_3.svg", 420595965U},
{"test_molblock_wedges.svg", 1106580037U},
{"github5383_1.svg", 3666750661U},
{"acs1996_1.svg", 1111630317U},
{"acs1996_2.svg", 1521279517U},
{"acs1996_3.svg", 879041204U},
{"acs1996_4.svg", 1550424006U},
{"acs1996_5.svg", 1680320774U},
{"acs1996_6.svg", 3810124161U},
{"acs1996_7.svg", 1113821459U},
{"acs1996_8.svg", 2477908768U},
{"acs1996_9.svg", 3747924004U},
{"acs1996_10.svg", 2229333301U},
{"acs1996_11.svg", 4107969968U},
{"acs1996_12.svg", 2930884583U},
{"test_unspec_stereo.svg", 3923423666U},
{"light_blue_h_no_label_1.svg", 1615074554U},
{"test_github_5534.svg", 4139208597U},
{"bond_highlights_1.svg", 3940401825U},
{"bond_highlights_2.svg", 4196744632U},
{"bond_highlights_3.svg", 851066096U},
{"bond_highlights_4.svg", 851066096U},
{"bond_highlights_5.svg", 2352169547U},
{"bond_highlights_6.svg", 4191585723U},
{"bond_highlights_7.svg", 2160801877U},
{"bond_highlights_8.svg", 2956924065U},
{"bond_highlights_9.svg", 3999278931U},
{"testGithub5486_1.svg", 3146085634U},
{"testGithub5511_1.svg", 3975118836U},
{"testGithub5511_2.svg", 1730094503U},
{"test_github5767.svg", 3943519724U},
{"test_github5704_1.svg", 1676917819U},
{"test_github5704_2.svg", 2959183882U},
{"test_github5704_3.svg", 1303839406U},
{"test_github5704_4.svg", 578468407U},
{"test_github5943.svg", 1113511714U},
{"test_github5947.svg", 337972125U},
{"test_github5767.svg", 3943519724U},
{"test_github5949.svg", 420848566U},
{"test_github5974.svg", 1522014196U},
{"test_github5963.svg", 3467316956U},
{"test_github6025.svg", 2316385019U},
{"test_github5963.svg", 3467316956U},
{"test_github6027_1.svg", 1504848694U},
{"test_github6027_2.svg", 765638922U},
{"test_complex_query_atoms_1.svg", 1058348348U},
{"test_complex_query_atoms_2.svg", 3820627663U},
{"test_complex_query_atoms_3.svg", 2574610745U},
{"test_complex_query_atoms_4.svg", 2574610745U},
{"test_complex_query_atoms_5.svg", 2239402605U},
{"test_complex_query_atoms_6.svg", 2784917732U},
{"test_complex_query_atoms_7.svg", 4016570948U},
{"test_complex_query_atoms_8.svg", 1215989604U},
{"test_complex_query_atoms_9.svg", 774489308U},
{"test_complex_query_atoms_10.svg", 1888858967U},
{"test_complex_query_atoms_11.svg", 2202417832U},
{"test_complex_query_atoms_12.svg", 4094464645U},
{"test_complex_query_atoms_13.svg", 2082462146U},
{"test_complex_query_atoms_14.svg", 3306293765U},
{"test_complex_query_atoms_15.svg", 422354297U},
{"test_complex_query_atoms_16.svg", 1559600050U},
{"test_github6041b.svg", 444537337U},
{"test_github6111_1.svg", 57798875U},
{"test_github6112.svg", 3278777629U},
{"test_github6160_1.svg", 518073509U},
{"test_github6160_2.svg", 2491651948U},
{"test_github6160_3.svg", 2709442517U},
{"test_github6170.svg", 1561786551U},
{"test_getMolSize.svg", 1258513283U},
{"test_github6200_1.svg", 1044179149U},
{"test_github6200_2.svg", 2658818798U},
{"test_queryColour_1.svg", 778322651U},
{"test_queryColour_2.svg", 45913095U},
{"github6336_1.svg", 612606818U},
{"github6416.svg", 3814405016U},
{"test_github6397_1.svg", 4203615821U},
{"test_github6397_2.svg", 3422233570U},
{"test_github6397_3.svg", 3320683230U},
{"test_github6397_4.svg", 2960192928U},
{"test_github6397_5.svg", 1245534660U},
{"test_github6400_1.svg", 2792561051U},
{"github6504_1.svg", 1429448598U},
{"github6504_2.svg", 2871662880U},
{"github6569_1.svg", 116573839U},
{"github6569_2.svg", 2367779037U},
{"lasso_highlights_1.svg", 3709434534U},
{"lasso_highlights_2.svg", 757121560U},
{"lasso_highlights_3.svg", 556406365U},
{"lasso_highlights_4.svg", 4148844874U},
{"lasso_highlights_5.svg", 1281259383U},
{"lasso_highlights_6.svg", 2113147733U},
{"lasso_highlights_7.svg", 514868036U},
{"lasso_highlights_8.svg", 3231367552U},
{"testGithub6685_1.svg", 1835717197U},
{"testGithub6685_2.svg", 116380465U},
{"testGithub6685_3.svg", 409385402U},
{"testGithub6685_4.svg", 1239628830U},
{"bad_lasso_1.svg", 726527516U},
{"AtropCanon1.svg", 1587179714U},
{"AtropManyChiralsEnhanced.svg", 3871032500U},
{"testGithub6968.svg", 1554428830U},
{"testGithub7036.svg", 2355702607U},
{"testWedgeNonSingleBonds-1.svg", 865601717U},
{"testWedgeNonSingleBonds-2.svg", 2960559495U},
{"testWedgeNonSingleBonds-3.svg", 1428196589U},
{"testWedgeNonSingleBonds-4.svg", 3897680387U},
{"testWedgeNonSingleBonds-5.svg", 2183530217U},
{"testWedgeNonSingleBonds-6.svg", 238313010U},
{"testWedgeNonSingleBonds-7.svg", 3641456570U},
{"testWedgeNonSingleBonds-8.svg", 3209701539U},
};
// These PNG hashes aren't completely reliable due to floating point cruft,
// but they can still reduce the number of drawings that need visual
// inspection. At present, the files
// testPNGMetadata_2.png
// give different results on my MBP and Ubuntu 20.04 VM. The SVGs work
// better because the floats are all output to only 1 decimal place so there
// is a much smaller chance of different systems producing different files.
const std::map<std::string, std::hash_result_t> PNG_HASHES = {
{"testGithub3226_1.png", 2350054896U},
{"testGithub3226_2.png", 606206725U},
{"testGithub3226_3.png", 2282880418U},
{"testPNGMetadata_1.png", 2423299691U},
{"testPNGMetadata_2.png", 2803353117U},
{"testHandDrawn-1.png", 698316547U},
{"testHandDrawn-2.png", 1605553248U},
{"testHandDrawn-3.png", 2881952238U},
{"testHandDrawn-4.png", 3431655453U},
{"testHandDrawn-5.png", 3439548169U},
{"testGithub4323_1.png", 3723958844U},
{"testGithub4323_3.png", 2185913679U},
{"testFlexiCanvas.2a.png", 3217758043U},
{"testFlexiCanvas.2b.png", 4070063910U},
{"testGithub4764.sz1.png", 98827714U},
{"testGithub4764.sz2.png", 89252465U},
{"testGithub4764.sz3.png", 148503574U},
{"testGithub4238_1.png", 3410617836U},
{"github5383_1.png", 992803933U},
{"acs1996_1.png", 2957839025U},
{"acs1996_2.png", 2664798808U},
{"github6336_1.png", 2958833204U}};
std::hash_result_t hash_file(const std::string &filename) {
std::ifstream ifs(filename, std::ios_base::binary);
std::string file_contents(std::istreambuf_iterator<char>{ifs}, {});
if (filename.substr(filename.length() - 4) == ".svg") {
// deal with MSDOS newlines.
file_contents.erase(
remove(file_contents.begin(), file_contents.end(), '\r'),
file_contents.end());
}
return gboost::hash_range(file_contents.begin(), file_contents.end());
}
void check_file_hash(const std::string &filename,
std::hash_result_t exp_hash = 0U) {
// std::cout << filename << " : " << hash_file(filename) << "U" <<
// std::endl;
std::map<std::string, std::hash_result_t>::const_iterator it;
if (filename.substr(filename.length() - 4) == ".svg") {
it = SVG_HASHES.find(filename);
} else {
it = PNG_HASHES.find(filename);
}
std::hash_result_t file_hash = hash_file(filename);
if (exp_hash == 0U) {
exp_hash = it == SVG_HASHES.end() ? 0U : it->second;
}
if (it != SVG_HASHES.end() && file_hash == exp_hash) {
if (DELETE_WITH_GOOD_HASH) {
std::remove(filename.c_str());
}
} else {
std::cout << "file " << filename << " gave hash " << file_hash
<< "U not the expected " << exp_hash << "U" << std::endl;
}
}
} // namespace
using namespace RDKit;
TEST_CASE("prepareAndDrawMolecule", "[drawing]") {
SECTION("basics") {
auto m1 = "C1N[C@@H]2OCC12"_smiles;
REQUIRE(m1);
// we will be able to recognize that the prep worked because there
// will be an H in the output:
MolDraw2DSVG drawer(200, 200, -1, -1, NO_FREETYPE);
MolDraw2DUtils::prepareAndDrawMolecule(drawer, *m1);
drawer.finishDrawing();
std::string text = drawer.getDrawingText();
CHECK(text.find(">H</text>") != std::string::npos);
}
SECTION("kekulize") {
auto m1 = "c1ccccc1"_smiles;
REQUIRE(m1);
{
MolDraw2DSVG drawer(200, 200, -1, -1, NO_FREETYPE);
MolDraw2DUtils::prepareAndDrawMolecule(drawer, *m1);
drawer.finishDrawing();
std::string text = drawer.getDrawingText();
CHECK(text.find("stroke-dasharray") == std::string::npos);
}
{
MolDraw2DSVG drawer(200, 200, -1, -1, NO_FREETYPE);
MolDraw2DUtils::prepareAndDrawMolecule(drawer, *m1, "", nullptr, nullptr,
nullptr, nullptr, nullptr, -1,
false);
drawer.finishDrawing();
std::string text = drawer.getDrawingText();
CHECK(text.find("stroke-dasharray") != std::string::npos);
}
}
}
TEST_CASE("tag atoms in SVG", "[drawing][SVG]") {
SECTION("basics") {
auto m1 = "C1N[C@@H]2OCC12"_smiles;
REQUIRE(m1);
MolDraw2DSVG drawer(200, 200, -1, -1, NO_FREETYPE);
MolDraw2DUtils::prepareMolForDrawing(*m1);
drawer.drawMolecule(*m1);
std::map<std::string, std::string> actions;
actions["onclick"] = "alert";
double radius = 0.2;
drawer.tagAtoms(*m1, radius, actions);
drawer.finishDrawing();
std::string text = drawer.getDrawingText();
std::ofstream outs("testAtomTags_1.svg");
outs << text;
outs.close();
check_file_hash("testAtomTags_1.svg");
CHECK(text.find("<circle") != std::string::npos);
CHECK(text.find("<circle") != std::string::npos);
CHECK(text.find("atom-selector") != std::string::npos);
CHECK(text.find("bond-selector") != std::string::npos);
}
SECTION("inject prop to class") {
auto m1 = "C1N[C@@H]2OCC12"_smiles;
REQUIRE(m1);
for (auto atom : m1->atoms()) {
auto prop = boost::format("__prop_class_atom_%d") % atom->getIdx();
atom->setProp("_tagClass", prop.str());
}
for (auto bond : m1->bonds()) {
auto prop = boost::format("__prop_class_bond_%d") % bond->getIdx();
bond->setProp("_tagClass", prop.str());
}
MolDraw2DSVG drawer(200, 200, -1, -1, NO_FREETYPE);
MolDraw2DUtils::prepareMolForDrawing(*m1);
drawer.drawMolecule(*m1);
drawer.tagAtoms(*m1);
drawer.finishDrawing();
std::string text = drawer.getDrawingText();
std::ofstream outs("testAtomTags_2.svg");
outs << text;
outs.close();
check_file_hash("testAtomTags_2.svg");
size_t i = 0;
size_t c = 0;
while (true) {
auto i2 = text.find("__prop_class_atom_", i);
if (i2 == std::string::npos) {
break;
}
i = i2 + 1;
c++;
}
CHECK(c == 6);
i = 0;
c = 0;
while (true) {
auto i2 = text.find("__prop_class_bond_", i);
if (i2 == std::string::npos) {
break;
}
i = i2 + 1;
c++;
}
CHECK(c == 7);
}
}
TEST_CASE("metadata in SVG", "[drawing][SVG]") {
SECTION("inject prop to metada") {
auto m1 = "C1N[C@@H]2OCC12"_smiles;
REQUIRE(m1);
for (auto atom : m1->atoms()) {
auto prop = boost::format("__prop_metadata_atom_%d") % atom->getIdx();
atom->setProp("_metaData-atom-inject-prop", prop.str());
}
for (auto bond : m1->bonds()) {
auto prop = boost::format("__prop_metadata_bond_%d") % bond->getIdx();
bond->setProp("_metaData-bond-inject-prop", prop.str());
}
MolDraw2DSVG drawer(200, 200, -1, -1, NO_FREETYPE);
MolDraw2DUtils::prepareMolForDrawing(*m1);
drawer.drawMolecule(*m1);
drawer.addMoleculeMetadata(*m1);
drawer.finishDrawing();
std::string text = drawer.getDrawingText();
std::ofstream outs("testAtomTags_3.svg");
outs << text;
outs.close();
check_file_hash("testAtomTags_3.svg");
size_t i = 0;
size_t c = 0;
while (true) {
auto i2 = text.find("atom-inject-prop=\"__prop_metadata_atom_", i);
if (i2 == std::string::npos) {
break;
}
i = i2 + 1;
c++;
}
CHECK(c == 6);
i = 0;
c = 0;
while (true) {
auto i2 = text.find("bond-inject-prop=\"__prop_metadata_bond_", i);
if (i2 == std::string::npos) {
break;
}
i = i2 + 1;
c++;
}
CHECK(c == 7);
}
}
TEST_CASE("contour data", "[drawing][conrec]") {
auto m1 = "C1N[C@@H]2OCC12"_smiles;
REQUIRE(m1);
SECTION("grid basics") {
MolDraw2DSVG drawer(250, 250, -1, -1, NO_FREETYPE);
MolDraw2DUtils::prepareMolForDrawing(*m1);
const size_t gridSz = 100;
auto grid = std::make_unique<double[]>(gridSz * gridSz);
std::vector<double> xps(gridSz);
std::vector<double> yps(gridSz);
double minX = 1000, minY = 1000, maxX = -1000, maxY = -1000;
const auto conf = m1->getConformer();
for (size_t i = 0; i < conf.getNumAtoms(); ++i) {
minX = std::min(minX, conf.getAtomPos(i).x);
minY = std::min(minY, conf.getAtomPos(i).y);
maxX = std::max(maxX, conf.getAtomPos(i).x);
maxY = std::max(maxY, conf.getAtomPos(i).y);
}
double x1 = minX - 0.5, y1 = minY - 0.5, x2 = maxX + 0.5, y2 = maxY + 0.5;
double dx = (x2 - x1) / gridSz, dy = (y2 - y1) / gridSz;
double maxV = 0.0;
for (size_t ix = 0; ix < gridSz; ++ix) {
auto px = x1 + ix * dx;
xps[ix] = px;
for (size_t iy = 0; iy < gridSz; ++iy) {
auto py = y1 + iy * dy;
if (ix == 0) {
yps[iy] = py;
}
RDGeom::Point2D loc(px, py);
double val = 0.0;
for (size_t ia = 0; ia < conf.getNumAtoms(); ++ia) {
auto dv = loc - RDGeom::Point2D(conf.getAtomPos(ia).x,
conf.getAtomPos(ia).y);
auto r = dv.length();
if (r > 0.1) {
val += 1 / r;
}
}
maxV = std::max(val, maxV);
grid[ix * gridSz + iy] = val;
}
}
std::vector<double> levels;
drawer.clearDrawing();
MolDraw2DUtils::contourAndDrawGrid(drawer, grid.get(), xps, yps, 10, levels,
MolDraw2DUtils::ContourParams(),
m1.get());
drawer.drawOptions().clearBackground = false;
drawer.drawMolecule(*m1);
drawer.finishDrawing();
std::string text = drawer.getDrawingText();
std::ofstream outs("contourMol_1.svg");
outs << text;
outs.close();
check_file_hash("contourMol_1.svg");
}
SECTION("gaussian basics") {
MolDraw2DSVG drawer(250, 250, -1, -1, NO_FREETYPE);
MolDraw2DUtils::prepareMolForDrawing(*m1);
drawer.drawOptions().padding = 0.1;
const auto conf = m1->getConformer();
std::vector<Point2D> cents(conf.getNumAtoms());
std::vector<double> weights(conf.getNumAtoms());
std::vector<double> widths(conf.getNumAtoms());
for (size_t i = 0; i < conf.getNumAtoms(); ++i) {
cents[i] = Point2D(conf.getAtomPos(i).x, conf.getAtomPos(i).y);
weights[i] = 1;
widths[i] = 0.4 * PeriodicTable::getTable()->getRcovalent(
m1->getAtomWithIdx(i)->getAtomicNum());
}
std::vector<double> levels;
drawer.clearDrawing();
MolDraw2DUtils::contourAndDrawGaussians(
drawer, cents, weights, widths, 10, levels,
MolDraw2DUtils::ContourParams(), m1.get());
drawer.drawOptions().clearBackground = false;
drawer.drawMolecule(*m1);
drawer.finishDrawing();
std::string text = drawer.getDrawingText();
std::ofstream outs("contourMol_2.svg");
outs << text;
outs.close();
check_file_hash("contourMol_2.svg");
}
SECTION("gaussian fill") {
MolDraw2DSVG drawer(250, 250, -1, -1, NO_FREETYPE);
MolDraw2DUtils::prepareMolForDrawing(*m1);
drawer.drawOptions().padding = 0.1;
const auto conf = m1->getConformer();
std::vector<Point2D> cents(conf.getNumAtoms());
std::vector<double> weights(conf.getNumAtoms());
std::vector<double> widths(conf.getNumAtoms());
for (size_t i = 0; i < conf.getNumAtoms(); ++i) {
cents[i] = Point2D(conf.getAtomPos(i).x, conf.getAtomPos(i).y);
weights[i] = i % 2 ? -.5 : 1;
widths[i] = 0.4 * PeriodicTable::getTable()->getRcovalent(
m1->getAtomWithIdx(i)->getAtomicNum());
}
std::vector<double> levels;
MolDraw2DUtils::ContourParams cps;
cps.fillGrid = true;
drawer.clearDrawing();
MolDraw2DUtils::contourAndDrawGaussians(drawer, cents, weights, widths, 10,
levels, cps, m1.get());
drawer.drawOptions().clearBackground = false;
drawer.drawMolecule(*m1);
drawer.finishDrawing();
std::string text = drawer.getDrawingText();
std::ofstream outs("contourMol_3.svg");
outs << text;
outs.close();
check_file_hash("contourMol_3.svg");
}
SECTION("gaussian fill 2") {
auto m2 = "C1N[C@@H]2OCC12C=CC"_smiles;
REQUIRE(m2);
MolDraw2DSVG drawer(450, 250, -1, -1, NO_FREETYPE);
MolDraw2DUtils::prepareMolForDrawing(*m2);
drawer.drawOptions().padding = 0.1;
const auto conf = m2->getConformer();
std::vector<Point2D> cents(conf.getNumAtoms());
std::vector<double> weights(conf.getNumAtoms());
std::vector<double> widths(conf.getNumAtoms());
for (size_t i = 0; i < conf.getNumAtoms(); ++i) {
cents[i] = Point2D(conf.getAtomPos(i).x, conf.getAtomPos(i).y);
weights[i] = i % 2 ? -0.5 : 1;
widths[i] = 0.3 * PeriodicTable::getTable()->getRcovalent(
m2->getAtomWithIdx(i)->getAtomicNum());
}
std::vector<double> levels;
MolDraw2DUtils::ContourParams cps;
cps.fillGrid = true;
cps.gridResolution = 0.5;
drawer.clearDrawing();
MolDraw2DUtils::contourAndDrawGaussians(drawer, cents, weights, widths, 10,
levels, cps, m2.get());
drawer.drawOptions().clearBackground = false;
drawer.drawMolecule(*m2);
drawer.finishDrawing();
std::string text = drawer.getDrawingText();
std::ofstream outs("contourMol_4.svg");
outs << text;
outs.close();
check_file_hash("contourMol_4.svg");
}
SECTION("gaussian no fill") {
MolDraw2DSVG drawer(250, 250, -1, -1, NO_FREETYPE);
MolDraw2DUtils::prepareMolForDrawing(*m1);
drawer.drawOptions().padding = 0.1;
const auto conf = m1->getConformer();
std::vector<Point2D> cents(conf.getNumAtoms());
std::vector<double> weights(conf.getNumAtoms());
std::vector<double> widths(conf.getNumAtoms());
for (size_t i = 0; i < conf.getNumAtoms(); ++i) {
cents[i] = Point2D(conf.getAtomPos(i).x, conf.getAtomPos(i).y);
weights[i] = i % 2 ? -1 : 1;
widths[i] = 0.4 * PeriodicTable::getTable()->getRcovalent(
m1->getAtomWithIdx(i)->getAtomicNum());
}
std::vector<double> levels;
MolDraw2DUtils::ContourParams cps;
cps.contourColour = DrawColour(.2, .2, .2);
drawer.clearDrawing();
MolDraw2DUtils::contourAndDrawGaussians(drawer, cents, weights, widths, 10,
levels, cps, m1.get());
drawer.drawOptions().clearBackground = false;
drawer.drawMolecule(*m1);
drawer.finishDrawing();
std::string text = drawer.getDrawingText();
std::ofstream outs("contourMol_5.svg");
outs << text;
outs.close();
check_file_hash("contourMol_5.svg");
}
}
TEST_CASE("dative bonds", "[drawing][organometallics]") {
SECTION("basics") {
auto m1 = "N->[Pt]"_smiles;
REQUIRE(m1);
MolDraw2DSVG drawer(200, 200, -1, -1, NO_FREETYPE);
MolDraw2DUtils::prepareMolForDrawing(*m1);
drawer.drawMolecule(*m1);
drawer.finishDrawing();
std::string text = drawer.getDrawingText();
std::ofstream outs("testDativeBonds_1.svg");
outs << text;
outs.close();
check_file_hash("testDativeBonds_1.svg");
std::regex d1(
"<path class='bond-0 atom-0 atom-1' d='M (\\d+\\.\\d+),(\\d+\\.\\d+) L (\\d+\\.\\d+),(\\d+\\.\\d+)' style='fill:none;fill-rule:evenodd;stroke:#0000FF");
auto dat1 = *std::sregex_iterator(text.begin(), text.end(), d1);
CHECK_THAT(stod(dat1[1]), Catch::Matchers::WithinAbs(78.2, 0.1));
CHECK_THAT(stod(dat1[2]), Catch::Matchers::WithinAbs(88.0, 0.1));
CHECK_THAT(stod(dat1[3]), Catch::Matchers::WithinAbs(113.4, 0.1));
CHECK_THAT(stod(dat1[4]), Catch::Matchers::WithinAbs(88.0, 0.1));
}
SECTION("more complex") {
auto m1 = "N->1[C@@H]2CCCC[C@H]2N->[Pt]11OC(=O)C(=O)O1"_smiles;
REQUIRE(m1);
MolDraw2DSVG drawer(200, 200, -1, -1, NO_FREETYPE);
MolDraw2DUtils::prepareMolForDrawing(*m1);
drawer.drawMolecule(*m1);
drawer.finishDrawing();
std::string text = drawer.getDrawingText();
std::ofstream outs("testDativeBonds_2.svg");
outs << text;
outs.close();
check_file_hash("testDativeBonds_2.svg");
std::regex d1(
"<path class='bond-7 atom-7 atom-8' d='M (\\d+\\.\\d+),(\\d+\\.\\d+) L (\\d+\\.\\d+),(\\d+\\.\\d+)' style='fill:none;fill-rule:evenodd;stroke:#0000FF");
auto dat1 = *std::sregex_iterator(text.begin(), text.end(), d1);
CHECK_THAT(stod(dat1[1]), Catch::Matchers::WithinAbs(100.9, 0.1));
CHECK_THAT(stod(dat1[2]), Catch::Matchers::WithinAbs(77.5, 0.1));
CHECK_THAT(stod(dat1[3]), Catch::Matchers::WithinAbs(95.8, 0.1));
CHECK_THAT(stod(dat1[4]), Catch::Matchers::WithinAbs(84.7, 0.1));
}
SECTION("test colours") {
// the dative bonds point the wrong way, but the point is to test
// if the tip of the arrow is blue.
auto m1 = "[Cu++]->1->2.N1CCN2"_smiles;
REQUIRE(m1);
MolDraw2DSVG drawer(200, 200, -1, -1, NO_FREETYPE);
MolDraw2DUtils::prepareMolForDrawing(*m1);
drawer.drawMolecule(*m1);
drawer.finishDrawing();
std::string text = drawer.getDrawingText();
std::ofstream outs("testDativeBonds_3.svg");
outs << text;
outs.close();
check_file_hash("testDativeBonds_3.svg");
std::regex d1(
"<path class='bond-2 atom-3 atom-4' d='M (\\d+\\.\\d+),(\\d+\\.\\d+) L (\\d+\\.\\d+),(\\d+\\.\\d+)' style='fill:none;fill-rule:evenodd;stroke:#0000FF");
auto dat1 = *std::sregex_iterator(text.begin(), text.end(), d1);
CHECK_THAT(stod(dat1[1]), Catch::Matchers::WithinAbs(53.5, 0.1));
CHECK_THAT(stod(dat1[2]), Catch::Matchers::WithinAbs(140.2, 0.1));
CHECK_THAT(stod(dat1[3]), Catch::Matchers::WithinAbs(80.7, 0.1));
CHECK_THAT(stod(dat1[4]), Catch::Matchers::WithinAbs(149.0, 0.1));
}
SECTION("dative series") {
auto m1 = "N->1[C@@H]2CCCC[C@H]2N->[Pt]11OC(=O)C(=O)O1"_smiles;
REQUIRE(m1);
{
MolDraw2DSVG drawer(150, 150, -1, -1, NO_FREETYPE);
MolDraw2DUtils::prepareMolForDrawing(*m1);
drawer.drawMolecule(*m1);
drawer.finishDrawing();
std::string text = drawer.getDrawingText();
std::ofstream outs("testDativeBonds_2a.svg");
outs << text;
outs.close();
check_file_hash("testDativeBonds_2a.svg");
}
{
MolDraw2DSVG drawer(250, 250, -1, -1, NO_FREETYPE);
MolDraw2DUtils::prepareMolForDrawing(*m1);
drawer.drawMolecule(*m1);
drawer.finishDrawing();
std::string text = drawer.getDrawingText();
std::ofstream outs("testDativeBonds_2b.svg");
outs << text;
outs.close();
check_file_hash("testDativeBonds_2b.svg");
}
{
MolDraw2DSVG drawer(350, 350, -1, -1, NO_FREETYPE);
MolDraw2DUtils::prepareMolForDrawing(*m1);
drawer.drawMolecule(*m1);
drawer.finishDrawing();
std::string text = drawer.getDrawingText();
std::ofstream outs("testDativeBonds_2c.svg");
outs << text;
outs.close();
check_file_hash("testDativeBonds_2c.svg");
}
{
MolDraw2DSVG drawer(450, 450, -1, -1, NO_FREETYPE);
MolDraw2DUtils::prepareMolForDrawing(*m1);
drawer.drawMolecule(*m1);
drawer.finishDrawing();
std::string text = drawer.getDrawingText();
std::ofstream outs("testDativeBonds_2d.svg");
outs << text;
outs.close();
check_file_hash("testDativeBonds_2d.svg");
}
}
}
TEST_CASE("zero-order bonds", "[drawing][organometallics]") {
SECTION("basics") {
auto m1 = "N-[Pt]"_smiles;
REQUIRE(m1);
m1->getBondWithIdx(0)->setBondType(Bond::ZERO);
MolDraw2DSVG drawer(200, 200, -1, -1, NO_FREETYPE);
MolDraw2DUtils::prepareMolForDrawing(*m1);
drawer.drawMolecule(*m1);
drawer.finishDrawing();
std::string text = drawer.getDrawingText();
std::ofstream outs("testZeroOrderBonds_1.svg");
outs << text;
outs.close();
check_file_hash("testZeroOrderBonds_1.svg");
CHECK(text.find("stroke-dasharray:2,2") != std::string::npos);
}
}
TEST_CASE("copying drawing options", "[drawing]") {
auto m1 = "C1N[C@@H]2OCC12"_smiles;
REQUIRE(m1);
SECTION("foundations") {
{
MolDraw2DSVG drawer(200, 200, -1, -1, NO_FREETYPE);
MolDraw2DUtils::prepareAndDrawMolecule(drawer, *m1);
drawer.finishDrawing();
std::string text = drawer.getDrawingText();
std::ofstream outs("testFoundations_1.svg");
outs << text;
outs.close();
check_file_hash("testFoundations_1.svg");
CHECK(text.find("fill:#0000FF' >N</text>") != std::string::npos);
}
{
MolDraw2DSVG drawer(200, 200, -1, -1, NO_FREETYPE);
assignBWPalette(drawer.drawOptions().atomColourPalette);
MolDraw2DUtils::prepareAndDrawMolecule(drawer, *m1);
drawer.finishDrawing();
std::string text = drawer.getDrawingText();
std::ofstream outs("testFoundations_2.svg");
outs << text;
outs.close();
check_file_hash("testFoundations_2.svg");
CHECK(text.find("fill:#0000FF' >N</text>") == std::string::npos);
CHECK(text.find("fill:#000000' >N</text>") != std::string::npos);
}
}
SECTION("test") {
{
MolDraw2DSVG drawer(200, 200, -1, -1, NO_FREETYPE);
MolDrawOptions options = drawer.drawOptions();
assignBWPalette(options.atomColourPalette);
drawer.drawOptions() = options;
MolDraw2DUtils::prepareAndDrawMolecule(drawer, *m1);
drawer.finishDrawing();
std::string text = drawer.getDrawingText();
std::ofstream outs("testTest_1.svg");
outs << text;
outs.close();
check_file_hash("testTest_1.svg");
CHECK(text.find("fill:#0000FF' >N</text>") == std::string::npos);
CHECK(text.find("fill:#000000' >N</text>") != std::string::npos);
}
}
}
TEST_CASE("bad DrawMolecules() when molecules are not kekulized",
"[drawing][bug]") {
auto m1 = "CCN(CC)CCn1nc2c3ccccc3sc3c(CNS(C)(=O)=O)ccc1c32"_smiles;
REQUIRE(m1);
SECTION("foundations") {
MolDraw2DSVG drawer(500, 200, 250, 200, NO_FREETYPE);
drawer.drawOptions().prepareMolsBeforeDrawing = false;
RWMol dm1(*m1);
RWMol dm2(*m1);
bool kekulize = false;
MolDraw2DUtils::prepareMolForDrawing(dm1, kekulize);
kekulize = true;
MolDraw2DUtils::prepareMolForDrawing(dm2, kekulize);
MOL_PTR_VECT ms{&dm1, &dm2};
drawer.drawMolecule(dm1);
drawer.finishDrawing();
std::string text = drawer.getDrawingText();
std::ofstream outs("testKekulizationProblems_1.svg");
outs << text;
outs.close();
check_file_hash("testKekulizationProblems_1.svg");
// this is a very crude test - really we just need to look at the SVG - but
// it's better than nothing.
CHECK(text.find(
"<path class='bond-18' d='M 169.076,79.056 L 191.285,69.2653' "
"style='fill:none;fill-rule:evenodd;stroke:#000000;stroke-width:"
"2px;stroke-linecap:butt;stroke-linejoin:miter;stroke-opacity:1;"
"stroke-dasharray:6,6' />") == std::string::npos);
}
}
TEST_CASE("draw atom/bond indices", "[drawing]") {
auto m1 = "C[C@H](F)N"_smiles;
auto m2 = "C[C@@H](F)N"_smiles;
REQUIRE(m1);
REQUIRE(m2);
SECTION("foundations") {
{
MolDraw2DSVG drawer(250, 200, -1, -1, NO_FREETYPE);
drawer.drawMolecule(*m1);
drawer.finishDrawing();
std::string text = drawer.getDrawingText();
std::ofstream outs("testAtomBondIndices_1.svg");
outs << text;
outs.close();
check_file_hash("testAtomBondIndices_1.svg");
CHECK(text.find(">1</text>") == std::string::npos);
CHECK(text.find(">(</text>") == std::string::npos);
CHECK(text.find(">S</text>") == std::string::npos);
CHECK(text.find(">)</text>") == std::string::npos);
}
{
MolDraw2DSVG drawer(250, 200, -1, -1, NO_FREETYPE);
drawer.drawOptions().addAtomIndices = true;
drawer.drawMolecule(*m1);
drawer.finishDrawing();
std::string text = drawer.getDrawingText();
std::ofstream outs("testAtomBondIndices_2.svg");
outs << text;
outs.close();
check_file_hash("testAtomBondIndices_2.svg");
CHECK(text.find(">1</text>") != std::string::npos);
// it only appears once though:
CHECK(text.find(">1</text>", text.find(">1</text>") + 1) ==
std::string::npos);
CHECK(text.find("1,(S)") == std::string::npos);
}
{
MolDraw2DSVG drawer(250, 200, -1, -1, NO_FREETYPE);
drawer.drawOptions().addBondIndices = true;
drawer.drawMolecule(*m1);
drawer.finishDrawing();
std::string text = drawer.getDrawingText();
std::ofstream outs("testAtomBondIndices_3.svg");
outs << text;
outs.close();
check_file_hash("testAtomBondIndices_3.svg");
CHECK(text.find(">1</text>") != std::string::npos);
// it only appears once though:
CHECK(text.find(">1</text>", text.find(">1</text>") + 1) ==
std::string::npos);
}
{
MolDraw2DSVG drawer(250, 200, -1, -1, NO_FREETYPE);
drawer.drawOptions().addAtomIndices = true;
drawer.drawOptions().addBondIndices = true;
drawer.drawMolecule(*m1);
drawer.finishDrawing();
std::string text = drawer.getDrawingText();
std::ofstream outs("testAtomBondIndices_4.svg");
outs << text;
outs.close();
check_file_hash("testAtomBondIndices_4.svg");
CHECK(text.find(">1</text>") != std::string::npos);
// it appears twice:
CHECK(text.find(">1</text>", text.find(">1</text>") + 1) !=
std::string::npos);
}
{
MolDraw2DSVG drawer(250, 200, -1, -1, NO_FREETYPE);
m1->getAtomWithIdx(2)->setProp(common_properties::atomNote, "foo");
drawer.drawOptions().addAtomIndices = true;
drawer.drawOptions().addStereoAnnotation = true;
drawer.drawMolecule(*m1);
m1->getAtomWithIdx(2)->clearProp(common_properties::atomNote);
drawer.finishDrawing();
std::string text = drawer.getDrawingText();
std::ofstream outs("testAtomBondIndices_5.svg");
outs << text;
outs.close();
check_file_hash("testAtomBondIndices_5.svg");
CHECK(text.find(">1</text>") != std::string::npos);
CHECK(text.find(">,</text>") != std::string::npos);
CHECK(text.find(">(</text>") != std::string::npos);
CHECK(text.find(">S</text>") != std::string::npos);
CHECK(text.find(")</text>") != std::string::npos);
CHECK(text.find(">2</text>") != std::string::npos);
CHECK(text.find(">f</text>") != std::string::npos);
CHECK(text.find(">o</text>") != std::string::npos);
}
{
// Make sure it works for solid wedges as well.
MolDraw2DSVG drawer(250, 200, -1, -1, NO_FREETYPE);
drawer.drawOptions().addAtomIndices = true;
drawer.drawMolecule(*m2);
drawer.finishDrawing();
std::string text = drawer.getDrawingText();
std::ofstream outs("testAtomBondIndices_6.svg");
outs << text;
outs.close();
check_file_hash("testAtomBondIndices_6.svg");
CHECK(text.find(">1</text>") != std::string::npos);
// it only appears once though:
CHECK(text.find(">1</text>", text.find(">1</text>") + 1) ==
std::string::npos);
CHECK(text.find("1,(S)") == std::string::npos);
}
}
}
TEST_CASE("Github #3226: Lines in wedge bonds being drawn too closely together",
"[drawing]") {
auto m1 =
"C[C@H](C1=C(C=CC(=C1Cl)F)Cl)OC2=C(N=CC(=C2)C3=CN(N=C3)C4CCNCC4)N"_smiles;
REQUIRE(m1);
SECTION("larger SVG") {
{
MolDraw2DSVG drawer(450, 400);
drawer.drawMolecule(*m1);
drawer.finishDrawing();
std::string text = drawer.getDrawingText();
std::ofstream outs("testGithub3226_1.svg");
outs << text;
outs.close();
check_file_hash("testGithub3226_1.svg");
std::vector<std::string> tkns;
boost::algorithm::find_all(tkns, text, "bond-0");
CHECK(tkns.size() == 10);
}
}
#ifdef RDK_BUILD_CAIRO_SUPPORT
SECTION("larger PNG") {
{
MolDraw2DCairo drawer(450, 400);
drawer.drawMolecule(*m1);
drawer.finishDrawing();
drawer.writeDrawingText("testGithub3226_1.png");
check_file_hash("testGithub3226_1.png");
}
}
#endif
SECTION("smaller SVG") {
{
MolDraw2DSVG drawer(200, 150);
drawer.drawMolecule(*m1);
drawer.finishDrawing();
std::string text = drawer.getDrawingText();
std::ofstream outs("testGithub3226_2.svg");
outs << text;
outs.close();
check_file_hash("testGithub3226_2.svg");
std::vector<std::string> tkns;
boost::algorithm::find_all(tkns, text, "bond-0");
CHECK(tkns.size() == 4);
}
}
#ifdef RDK_BUILD_CAIRO_SUPPORT
SECTION("smaller PNG") {
{
MolDraw2DCairo drawer(200, 150);
drawer.drawMolecule(*m1);
drawer.finishDrawing();
drawer.writeDrawingText("testGithub3226_2.png");
check_file_hash("testGithub3226_2.png");
}
}
#endif
SECTION("middle SVG") {
{
MolDraw2DSVG drawer(300, 200);
drawer.drawMolecule(*m1);
drawer.finishDrawing();
std::string text = drawer.getDrawingText();
std::ofstream outs("testGithub3226_3.svg");
outs << text;
outs.close();
check_file_hash("testGithub3226_3.svg");
std::vector<std::string> tkns;
boost::algorithm::find_all(tkns, text, "bond-0");
CHECK(tkns.size() == 7);
}
}
#ifdef RDK_BUILD_CAIRO_SUPPORT
SECTION("middle PNG") {
{
MolDraw2DCairo drawer(250, 200);
drawer.drawMolecule(*m1);
drawer.finishDrawing();
drawer.writeDrawingText("testGithub3226_3.png");
check_file_hash("testGithub3226_3.png");
}
}
#endif
}
TEST_CASE("github #3258: ", "[drawing][bug]") {
auto m1 = "CCN"_smiles;
REQUIRE(m1);
SECTION("foundations") {
MolDraw2DSVG drawer(500, 200, 250, 200, NO_FREETYPE);
drawer.drawOptions().addAtomIndices = true;
drawer.drawOptions().addBondIndices = true;
RWMol dm1(*m1);
RWMol dm2(*m1);
MOL_PTR_VECT ms{&dm1, &dm2};
drawer.drawMolecules(ms);
drawer.finishDrawing();
std::string text = drawer.getDrawingText();
CHECK(text.find(">,</text>") == std::string::npos);
CHECK(!dm1.hasProp("_atomIndicesAdded"));
CHECK(!dm1.hasProp("_bondIndicesAdded"));
}
}
#ifdef RDK_BUILD_CAIRO_SUPPORT
TEST_CASE("adding png metadata", "[drawing][png]") {
SECTION("molecule") {
auto m1 = R"CTAB(
Mrv2014 08172015242D
0 0 0 0 0 999 V3000
M V30 BEGIN CTAB
M V30 COUNTS 3 2 0 0 0
M V30 BEGIN ATOM
M V30 1 C 2.31 -1.3337 0 0
M V30 2 C 3.6437 -2.1037 0 0
M V30 3 O 4.9774 -1.3337 0 0
M V30 END ATOM
M V30 BEGIN BOND
M V30 1 1 1 2
M V30 2 1 2 3
M V30 END BOND
M V30 END CTAB
M END
)CTAB"_ctab;
REQUIRE(m1);
{
MolDraw2DCairo drawer(250, 200);
drawer.drawMolecule(*m1);
drawer.finishDrawing();
auto png = drawer.getDrawingText();
drawer.writeDrawingText("testPNGMetadata_1.png");
check_file_hash("testPNGMetadata_1.png");
CHECK(png.find(PNGData::smilesTag) != std::string::npos);
CHECK(png.find(PNGData::molTag) != std::string::npos);
CHECK(png.find(PNGData::pklTag) != std::string::npos);
std::unique_ptr<ROMol> newmol(PNGStringToMol(png));
REQUIRE(newmol);
CHECK(MolToCXSmiles(*m1) == MolToCXSmiles(*newmol));
}
{ // disable metadata output
MolDraw2DCairo drawer(250, 200);
drawer.drawOptions().includeMetadata = false;
drawer.drawMolecule(*m1);
drawer.finishDrawing();
auto png = drawer.getDrawingText();
CHECK(png.find(PNGData::smilesTag) == std::string::npos);
CHECK(png.find(PNGData::molTag) == std::string::npos);
CHECK(png.find(PNGData::pklTag) == std::string::npos);
}
{ // draw multiple molecules
MolDraw2DCairo drawer(250, 200);
drawer.drawMolecule(*m1);
drawer.drawMolecule(*m1);
drawer.finishDrawing();
auto png = drawer.getDrawingText();
CHECK(png.find(PNGData::smilesTag) != std::string::npos);
CHECK(png.find(PNGData::molTag) != std::string::npos);
CHECK(png.find(PNGData::pklTag) != std::string::npos);
CHECK(png.find(PNGData::smilesTag + "1") != std::string::npos);
CHECK(png.find(PNGData::molTag + "1") != std::string::npos);
CHECK(png.find(PNGData::pklTag + "1") != std::string::npos);
}
}
SECTION("reaction") {
std::unique_ptr<ChemicalReaction> rxn(RxnSmartsToChemicalReaction(
"[N:1][C:2][C:3](=[O:4])[O:5].[N:6][C:7][C:8](=[O:9])[O:10]>>[N:1]1[C:"
"2][C:3](=[O:4])[N:6][C:7][C:8]1=[O:9].[O:5][O:10]"));
REQUIRE(rxn);
{
MolDraw2DCairo drawer(600, 200);
drawer.drawReaction(*rxn);
drawer.finishDrawing();
auto png = drawer.getDrawingText();
drawer.writeDrawingText("testPNGMetadata_2.png");
check_file_hash("testPNGMetadata_2.png");
CHECK(png.find(PNGData::smilesTag) == std::string::npos);
CHECK(png.find(PNGData::molTag) == std::string::npos);
CHECK(png.find(PNGData::pklTag) == std::string::npos);
CHECK(png.find(PNGData::rxnPklTag) != std::string::npos);
CHECK(png.find(PNGData::rxnSmartsTag) != std::string::npos);
std::unique_ptr<ChemicalReaction> rxn2(PNGStringToChemicalReaction(png));
REQUIRE(rxn2);
CHECK(ChemicalReactionToRxnSmarts(*rxn) ==
ChemicalReactionToRxnSmarts(*rxn2));
}
{ // disable metadata
MolDraw2DCairo drawer(600, 200);
drawer.drawOptions().includeMetadata = false;
drawer.drawReaction(*rxn);
drawer.finishDrawing();
auto png = drawer.getDrawingText();
CHECK(png.find(PNGData::smilesTag) == std::string::npos);
CHECK(png.find(PNGData::molTag) == std::string::npos);
CHECK(png.find(PNGData::pklTag) == std::string::npos);
CHECK(png.find(PNGData::rxnPklTag) == std::string::npos);
CHECK(png.find(PNGData::rxnSmartsTag) == std::string::npos);
}
}
}
#endif
TEST_CASE(
"github #3392: prepareMolForDrawing() incorrectly adds chiral Hs if no "
"ring info is present",
"[bug]") {
SECTION("foundations") {
SmilesParserParams ps;
ps.sanitize = false;
ps.removeHs = false;
std::unique_ptr<RWMol> m1(SmilesToMol("C[C@H](F)Cl", ps));
REQUIRE(m1);
m1->updatePropertyCache();
CHECK(m1->getNumAtoms() == 4);
const bool kekulize = false;
const bool addChiralHs = true;
MolDraw2DUtils::prepareMolForDrawing(*m1, kekulize, addChiralHs);
CHECK(m1->getNumAtoms() == 4);
}
}
TEST_CASE(
"github #3369: support new CIP code and StereoGroups in addStereoAnnotations()") {
auto m1 =
"C[C@@H]1N[C@H](C)[C@@H]([C@H](C)[C@@H]1C)C1[C@@H](C)O[C@@H](C)[C@@H](C)[C@H]1C/C=C/C |a:5,o1:1,8,o2:14,16,&1:11,18,&2:3,6,r|"_smiles;
REQUIRE(m1);
SECTION("works with the drawing code") {
MolDraw2DSVG drawer(300, 250);
RWMol dm1(*m1);
Chirality::addStereoAnnotations(dm1);
drawer.drawMolecule(dm1);
drawer.finishDrawing();
std::string text = drawer.getDrawingText();
std::ofstream outs("testGithub3369_1.svg");
outs << text;
outs.close();
check_file_hash("testGithub3369_1.svg");
}
}
TEST_CASE("includeRadicals", "[options]") {
SECTION("basics") {
auto m = "[O][C]"_smiles;
REQUIRE(m);
int panelHeight = -1;
int panelWidth = -1;
bool noFreeType = true;
{
MolDraw2DSVG drawer(250, 200, panelWidth, panelHeight, noFreeType);
drawer.drawMolecule(*m);
drawer.finishDrawing();
auto text = drawer.getDrawingText();
std::ofstream outs("testIncludeRadicals_1a.svg");
outs << text;
outs.close();
check_file_hash("testIncludeRadicals_1a.svg");
CHECK(text.find("<path class='atom-0' d='M") != std::string::npos);
}
{
MolDraw2DSVG drawer(250, 200, panelWidth, panelHeight, noFreeType);
drawer.drawOptions().includeRadicals = false;
drawer.drawMolecule(*m);
drawer.finishDrawing();
auto text = drawer.getDrawingText();
std::ofstream outs("testIncludeRadicals_1b.svg");
outs << text;
outs.close();
check_file_hash("testIncludeRadicals_1b.svg");
CHECK(text.find("<path class='atom-0' d='M") == std::string::npos);
}
}
}
TEST_CASE("including legend in drawing results in offset drawing later",
"[bug]") {
SECTION("basics") {
auto m = "c1ccccc1"_smiles;
REQUIRE(m);
MolDraw2DUtils::prepareMolForDrawing(*m);
auto &conf = m->getConformer();
std::vector<Point2D> polyg;
for (const auto &pt : conf.getPositions()) {
polyg.emplace_back(pt);
}
MolDraw2DSVG drawer(350, 300);
drawer.drawMolecule(*m, "molecule legend");
drawer.setFillPolys(true);
drawer.setColour(DrawColour(1.0, 0.3, 1.0));
drawer.drawPolygon(polyg);
drawer.finishDrawing();
auto text = drawer.getDrawingText();
std::ofstream outs("testLegendsAndDrawing-1.svg");
outs << text;
outs.close();
outs.close();
check_file_hash("testLegendsAndDrawing-1.svg");
// make sure the polygon starts at a bond
CHECK(text.find("<path class='bond-0 atom-0 atom-1' d='M 315.3,136.5") !=
std::string::npos);
CHECK(text.find("<path d='M 311.8,142.6") != std::string::npos);
}
}
TEST_CASE("Github #3577", "[bug]") {
SECTION("basics") {
auto m = "CCC"_smiles;
REQUIRE(m);
MolDraw2DUtils::prepareMolForDrawing(*m);
m->getAtomWithIdx(1)->setProp("atomNote", "CCC");
m->getAtomWithIdx(2)->setProp("atomNote", "ccc");
m->getBondWithIdx(0)->setProp("bondNote", "CCC");
MolDraw2DSVG drawer(350, 300);
drawer.drawMolecule(*m);
drawer.finishDrawing();
auto text = drawer.getDrawingText();
std::ofstream outs("testGithub3577-1.svg");
outs << text;
outs.close();
check_file_hash("testGithub3577-1.svg");
}
}
TEST_CASE("hand drawn", "[play]") {
SECTION("basics") {
auto m =
"CC[CH](C)[CH]1NC(=O)[CH](Cc2ccc(O)cc2)NC(=O)[CH](N)CSSC[CH](C(=O)N2CCC[CH]2C(=O)N[CH](CC(C)C)C(=O)NCC(N)=O)NC(=O)[CH](CC(N)=O)NC(=O)[CH](CCC(N)=O)NC1=O"_smiles;
REQUIRE(m);
RDDepict::preferCoordGen = true;
MolDraw2DUtils::prepareMolForDrawing(*m);
std::string fName = getenv("RDBASE");
fName += "/Data/Fonts/ComicNeue-Regular.ttf";
{
MolDraw2DSVG drawer(450, 400);
drawer.drawOptions().fontFile = fName;
drawer.drawOptions().comicMode = true;
drawer.drawMolecule(*m, "Oxytocin (flat)");
drawer.finishDrawing();
auto text = drawer.getDrawingText();
std::ofstream outs("testHandDrawn-1.svg");
outs << text;
outs.close();
check_file_hash("testHandDrawn-1.svg");
}
#ifdef RDK_BUILD_CAIRO_SUPPORT
{
MolDraw2DCairo drawer(450, 400);
drawer.drawOptions().fontFile = fName;
drawer.drawOptions().comicMode = true;
drawer.drawMolecule(*m, "Oxytocin (flat)");
drawer.finishDrawing();
drawer.writeDrawingText("testHandDrawn-1.png");
check_file_hash("testHandDrawn-1.png");
}
#endif
}
SECTION("with chirality") {
auto m =
"CC[C@H](C)[C@@H]1NC(=O)[C@H](Cc2ccc(O)cc2)NC(=O)[C@@H](N)CSSC[C@@H](C(=O)N2CCC[C@H]2C(=O)N[C@@H](CC(C)C)C(=O)NCC(N)=O)NC(=O)[C@H](CC(N)=O)NC(=O)[C@H](CCC(N)=O)NC1=O"_smiles;
REQUIRE(m);
RDDepict::preferCoordGen = true;
MolDraw2DUtils::prepareMolForDrawing(*m);
std::string fName = getenv("RDBASE");
fName += "/Data/Fonts/ComicNeue-Regular.ttf";
{
MolDraw2DSVG drawer(450, 400);
drawer.drawOptions().fontFile = fName;
drawer.drawOptions().comicMode = true;
drawer.drawMolecule(*m, "Oxytocin");
drawer.finishDrawing();
auto text = drawer.getDrawingText();
std::ofstream outs("testHandDrawn-2.svg");
outs << text;
outs.close();
check_file_hash("testHandDrawn-2.svg");
}
#ifdef RDK_BUILD_CAIRO_SUPPORT
{
MolDraw2DCairo drawer(450, 400);
drawer.drawOptions().fontFile = fName;
drawer.drawOptions().comicMode = true;
drawer.drawMolecule(*m, "Oxytocin");
drawer.finishDrawing();
drawer.writeDrawingText("testHandDrawn-2.png");
check_file_hash("testHandDrawn-2.png");
}
#endif
}
SECTION("smaller") {
auto m = "N=c1nc([C@H]2NCCCC2)cc(N)n1O"_smiles;
REQUIRE(m);
RDDepict::preferCoordGen = true;
MolDraw2DUtils::prepareMolForDrawing(*m);
std::string fName = getenv("RDBASE");
fName += "/Data/Fonts/ComicNeue-Regular.ttf";
{
MolDraw2DSVG drawer(350, 300);
drawer.drawOptions().fontFile = fName;
drawer.drawOptions().comicMode = true;
drawer.drawMolecule(*m);
drawer.finishDrawing();
auto text = drawer.getDrawingText();
std::ofstream outs("testHandDrawn-3.svg");
outs << text;
outs.close();
check_file_hash("testHandDrawn-3.svg");
}
#ifdef RDK_BUILD_CAIRO_SUPPORT
{
MolDraw2DCairo drawer(350, 300);
drawer.drawOptions().fontFile = fName;
drawer.drawOptions().comicMode = true;
drawer.drawMolecule(*m);
drawer.finishDrawing();
drawer.writeDrawingText("testHandDrawn-3.png");
check_file_hash("testHandDrawn-3.png");
}
#endif
}
SECTION("another one") {
auto m =
"CCCc1nn(C)c2c(=O)nc(-c3cc(S(=O)(=O)N4CCN(C)CC4)ccc3OCC)[nH]c12"_smiles;
REQUIRE(m);
RDDepict::preferCoordGen = true;
MolDraw2DUtils::prepareMolForDrawing(*m);
std::string fName = getenv("RDBASE");
fName += "/Data/Fonts/ComicNeue-Regular.ttf";
{
MolDraw2DSVG drawer(350, 300);
drawer.drawOptions().fontFile = fName;
drawer.drawOptions().comicMode = true;
drawer.drawMolecule(*m);
drawer.finishDrawing();
auto text = drawer.getDrawingText();
std::ofstream outs("testHandDrawn-4.svg");
outs << text;
outs.close();
check_file_hash("testHandDrawn-4.svg");
}
#ifdef RDK_BUILD_CAIRO_SUPPORT
{
MolDraw2DCairo drawer(350, 300);
drawer.drawOptions().fontFile = fName;
drawer.drawOptions().comicMode = true;
drawer.drawMolecule(*m);
drawer.finishDrawing();
drawer.writeDrawingText("testHandDrawn-4.png");
check_file_hash("testHandDrawn-4.png");
}
#endif
}
SECTION("large") {
auto m =
"CC[C@H](C)[C@@H](C(=O)N[C@@H]([C@@H](C)CC)C(=O)N[C@@H](CCCCN)C(=O)N[C@@H](CC(=O)N)C(=O)N[C@@H](C)C(=O)N[C@@H](Cc1ccc(cc1)O)C(=O)N[C@@H](CCCCN)C(=O)N[C@@H](CCCCN)C(=O)NCC(=O)N[C@@H](CCC(=O)N)C(=O)O)NC(=O)[C@H](C)NC(=O)[C@H](CC(=O)N)NC(=O)[C@H](CCCCN)NC(=O)[C@H](Cc2ccccc2)NC(=O)[C@H](CC(C)C)NC(=O)[C@H]([C@@H](C)O)NC(=O)[C@H](C(C)C)NC(=O)[C@H](CC(C)C)NC(=O)[C@@H]3CCCN3C(=O)[C@H]([C@@H](C)O)NC(=O)[C@H](CCC(=O)N)NC(=O)[C@H](CO)NC(=O)[C@H](CCCCN)NC(=O)[C@H](CCC(=O)N)NC(=O)[C@H](CO)NC(=O)[C@H]([C@@H](C)O)NC(=O)[C@H](CCSC)NC(=O)[C@H](Cc4ccccc4)NC(=O)CNC(=O)CNC(=O)[C@H](Cc5ccc(cc5)O)N"_smiles;
REQUIRE(m);
RDDepict::preferCoordGen = true;
MolDraw2DUtils::prepareMolForDrawing(*m);
std::string fName = getenv("RDBASE");
fName += "/Data/Fonts/ComicNeue-Regular.ttf";
{
MolDraw2DSVG drawer(900, 450);
drawer.drawMolecule(*m);
drawer.finishDrawing();
auto text = drawer.getDrawingText();
std::ofstream outs("testHandDrawn-5a.svg");
outs << text;
outs.close();
check_file_hash("testHandDrawn-5a.svg");
}
{
MolDraw2DSVG drawer(900, 450);
drawer.drawOptions().fontFile = fName;
drawer.drawOptions().comicMode = true;
drawer.drawMolecule(*m);
drawer.finishDrawing();
auto text = drawer.getDrawingText();
std::ofstream outs("testHandDrawn-5b.svg");
outs << text;
outs.close();
check_file_hash("testHandDrawn-5b.svg");
}
#ifdef RDK_BUILD_CAIRO_SUPPORT
{
MolDraw2DCairo drawer(900, 450);
drawer.drawOptions().fontFile = fName;
drawer.drawOptions().comicMode = true;
drawer.drawMolecule(*m);
drawer.finishDrawing();
drawer.writeDrawingText("testHandDrawn-5.png");
check_file_hash("testHandDrawn-5.png");
}
#endif
}
}
TEST_CASE("drawMoleculeBrackets", "[extras]") {
SECTION("basics") {
auto m = R"CTAB(
ACCLDraw11042015112D
0 0 0 0 0 999 V3000
M V30 BEGIN CTAB
M V30 COUNTS 5 4 1 0 0
M V30 BEGIN ATOM
M V30 1 C 7 -6.7813 0 0
M V30 2 C 8.0229 -6.1907 0 0 CFG=3
M V30 3 C 8.0229 -5.0092 0 0
M V30 4 C 9.046 -6.7814 0 0
M V30 5 C 10.0692 -6.1907 0 0
M V30 END ATOM
M V30 BEGIN BOND
M V30 1 1 1 2
M V30 2 1 2 3
M V30 3 1 2 4
M V30 4 1 4 5
M V30 END BOND
M V30 BEGIN SGROUP
M V30 1 SRU 1 ATOMS=(3 3 2 4) XBONDS=(2 1 4) BRKXYZ=(9 7.51 -7.08 0 7.51 -
M V30 -5.9 0 0 0 0) BRKXYZ=(9 9.56 -5.9 0 9.56 -7.08 0 0 0 0) -
M V30 CONNECT=HT LABEL=n
M V30 END SGROUP
M V30 END CTAB
M END
)CTAB"_ctab;
REQUIRE(m);
{
MolDraw2DSVG drawer(350, 300);
drawer.drawMolecule(*m);
drawer.finishDrawing();
auto text = drawer.getDrawingText();
std::ofstream outs("testBrackets-1a.svg");
outs << text;
outs.close();
check_file_hash("testBrackets-1a.svg");
}
{ // rotation
MolDraw2DSVG drawer(350, 300);
drawer.drawOptions().rotate = 90;
drawer.drawMolecule(*m);
drawer.finishDrawing();
auto text = drawer.getDrawingText();
std::ofstream outs("testBrackets-1b.svg");
outs << text;
outs.close();
check_file_hash("testBrackets-1b.svg");
}
{ // centering
MolDraw2DSVG drawer(350, 300);
drawer.drawOptions().centreMoleculesBeforeDrawing = true;
drawer.drawMolecule(*m);
drawer.finishDrawing();
auto text = drawer.getDrawingText();
std::ofstream outs("testBrackets-1c.svg");
outs << text;
outs.close();
check_file_hash("testBrackets-1c.svg");
}
{ // rotation + centering
MolDraw2DSVG drawer(350, 300);
drawer.drawOptions().centreMoleculesBeforeDrawing = true;
drawer.drawOptions().rotate = 90;
drawer.drawMolecule(*m);
drawer.finishDrawing();
auto text = drawer.getDrawingText();
std::ofstream outs("testBrackets-1d.svg");
outs << text;
outs.close();
check_file_hash("testBrackets-1d.svg");
}
{ // rotation
MolDraw2DSVG drawer(350, 300);
drawer.drawOptions().rotate = 180;
drawer.drawMolecule(*m);
drawer.finishDrawing();
auto text = drawer.getDrawingText();
std::ofstream outs("testBrackets-1e.svg");
outs << text;
outs.close();
check_file_hash("testBrackets-1e.svg");
}
}
SECTION("three brackets") {
auto m = R"CTAB(three brackets
Mrv2014 11052006542D
0 0 0 0 0 999 V3000
M V30 BEGIN CTAB
M V30 COUNTS 6 5 1 0 0
M V30 BEGIN ATOM
M V30 1 * -1.375 3.1667 0 0
M V30 2 C -0.0413 3.9367 0 0
M V30 3 C 1.2924 3.1667 0 0
M V30 4 * 2.626 3.9367 0 0
M V30 5 C 0.0003 5.6017 0 0
M V30 6 * 1.334 6.3717 0 0
M V30 END ATOM
M V30 BEGIN BOND
M V30 1 1 1 2
M V30 2 1 2 3
M V30 3 1 3 4
M V30 4 1 2 5
M V30 5 1 5 6
M V30 END BOND
M V30 BEGIN SGROUP
M V30 1 SRU 0 ATOMS=(3 2 3 5) XBONDS=(3 1 3 5) BRKXYZ=(9 0.0875 6.7189 0 -
M V30 1.0115 5.1185 0 0 0 0) BRKXYZ=(9 1.3795 4.2839 0 2.3035 2.6835 0 0 0 -
M V30 0) BRKXYZ=(9 -0.1285 2.8194 0 -1.0525 4.4198 0 0 0 0) CONNECT=HT -
M V30 LABEL=n
M V30 END SGROUP
M V30 END CTAB
M END)CTAB"_ctab;
REQUIRE(m);
{
MolDraw2DSVG drawer(350, 300);
drawer.drawMolecule(*m);
drawer.finishDrawing();
auto text = drawer.getDrawingText();
std::ofstream outs("testBrackets-2a.svg");
outs << text;
outs.close();
check_file_hash("testBrackets-2a.svg");
}
{ // rotation
MolDraw2DSVG drawer(350, 300);
drawer.drawOptions().rotate = 90;
drawer.drawMolecule(*m);
drawer.finishDrawing();
auto text = drawer.getDrawingText();
std::ofstream outs("testBrackets-2b.svg");
outs << text;
outs.close();
check_file_hash("testBrackets-2b.svg");
}
{ // centering
MolDraw2DSVG drawer(350, 300);
drawer.drawOptions().centreMoleculesBeforeDrawing = true;
drawer.drawMolecule(*m);
drawer.finishDrawing();
auto text = drawer.getDrawingText();
std::ofstream outs("testBrackets-2c.svg");
outs << text;
outs.close();
check_file_hash("testBrackets-2c.svg");
}
{ // rotation + centering
MolDraw2DSVG drawer(350, 300);
drawer.drawOptions().centreMoleculesBeforeDrawing = true;
drawer.drawOptions().rotate = 90;
drawer.drawMolecule(*m);
drawer.finishDrawing();
auto text = drawer.getDrawingText();
std::ofstream outs("testBrackets-2d.svg");
outs << text;
outs.close();
check_file_hash("testBrackets-2d.svg");
}
}
SECTION("ChEBI 59342") {
// thanks to John Mayfield for pointing out the example
auto m = R"CTAB(ChEBI59342
Marvin 05041012302D
29 30 0 0 1 0 999 V2000
10.1615 -7.7974 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0
8.7305 -6.9763 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0
8.7309 -7.8004 0.0000 C 0 0 2 0 0 0 0 0 0 0 0 0
9.4464 -8.2109 0.0000 C 0 0 2 0 0 0 0 0 0 0 0 0
8.0153 -8.2225 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0
9.4464 -9.0437 0.0000 C 0 0 2 0 0 0 0 0 0 0 0 0
8.0138 -9.0500 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0
8.7293 -9.4606 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0
10.1669 -9.4529 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0
7.3058 -9.4590 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
8.7368 -10.2801 0.0000 N 0 0 0 0 0 0 0 0 0 0 0 0
8.0263 -10.6992 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
8.0339 -11.5241 0.0000 H 0 0 0 0 0 0 0 0 0 0 0 0
7.3081 -10.2933 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0
8.7305 -5.3264 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0
8.0159 -5.7369 0.0000 C 0 0 2 0 0 0 0 0 0 0 0 0
8.0159 -6.5618 0.0000 C 0 0 2 0 0 0 0 0 0 0 0 0
7.2936 -5.3263 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0
7.2936 -6.9762 0.0000 C 0 0 2 0 0 0 0 0 0 0 0 0
6.5751 -5.7368 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0
6.5751 -6.5618 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0
7.2973 -7.8049 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0
5.8681 -5.3263 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
5.8680 -6.9762 0.0000 N 0 0 0 0 0 0 0 0 0 0 0 0
5.1510 -6.5684 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
4.4392 -6.9856 0.0000 H 0 0 0 0 0 0 0 0 0 0 0 0
5.1455 -5.7435 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0
10.4142 -5.3560 0.0000 * 0 0 0 0 0 0 0 0 0 0 0 0
11.5590 -7.8297 0.0000 * 0 0 0 0 0 0 0 0 0 0 0 0
3 2 1 6 0 0 0
3 4 1 0 0 0 0
3 5 1 0 0 0 0
4 6 1 0 0 0 0
4 1 1 1 0 0 0
5 7 1 0 0 0 0
6 8 1 0 0 0 0
6 9 1 1 0 0 0
7 10 1 1 0 0 0
8 11 1 6 0 0 0
7 8 1 0 0 0 0
13 12 1 0 0 0 0
14 12 2 0 0 0 0
11 12 1 0 0 0 0
16 15 1 6 0 0 0
16 17 1 0 0 0 0
16 18 1 0 0 0 0
17 19 1 0 0 0 0
17 2 1 1 0 0 0
18 20 1 0 0 0 0
19 21 1 0 0 0 0
19 22 1 1 0 0 0
20 23 1 1 0 0 0
21 24 1 6 0 0 0
20 21 1 0 0 0 0
26 25 1 0 0 0 0
27 25 2 0 0 0 0
24 25 1 0 0 0 0
15 28 1 0 0 0 0
1 29 1 0 0 0 0
M STY 1 1 SRU
M SCN 1 1 HT
M SAL 1 15 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15
M SAL 1 12 16 17 18 19 20 21 22 23 24 25 26 27
M SDI 1 4 9.4310 -4.9261 9.4165 -5.7510
M SDI 1 4 10.7464 -7.3983 10.7274 -8.2231
M SBL 1 2 30 29
M SMT 1 n
M END)CTAB"_ctab;
REQUIRE(m);
{
MolDraw2DSVG drawer(350, 300);
drawer.drawMolecule(*m);
drawer.finishDrawing();
auto text = drawer.getDrawingText();
std::ofstream outs("testBrackets-3a.svg");
outs << text;
outs.close();
check_file_hash("testBrackets-3a.svg");
}
}
SECTION("pathological bracket orientation") {
{ // including the bonds
auto m = R"CTAB(bogus
Mrv2014 11202009512D
0 0 0 0 0 999 V3000
M V30 BEGIN CTAB
M V30 COUNTS 9 8 1 0 1
M V30 BEGIN ATOM
M V30 1 C 23.5462 -14.464 0 0
M V30 2 C 20.8231 -13.0254 0 0
M V30 3 C 20.8776 -14.5628 0 0
M V30 4 C 22.2391 -15.2819 0 0
M V30 5 C 16.2969 -9.9426 0 0
M V30 6 C 14.963 -10.7089 0 0
M V30 7 C 19.463 -12.2987 0 0
M V30 8 * 19.4398 -9.9979 0 0
M V30 9 * 26.1554 -14.4332 0 0
M V30 END ATOM
M V30 BEGIN BOND
M V30 1 1 3 4
M V30 2 1 6 7
M V30 3 1 5 8
M V30 4 1 1 9
M V30 5 1 7 2
M V30 6 1 6 5
M V30 7 1 4 1
M V30 8 1 3 2
M V30 END BOND
M V30 BEGIN SGROUP
M V30 1 SRU 0 ATOMS=(7 4 3 7 6 5 2 1) XBONDS=(2 3 4) BRKXYZ=(9 17.6045 -
M V30 -9.1954 0 17.5775 -10.7352 0 0 0 0) BRKXYZ=(9 24.6113 -13.6813 0 -
M V30 24.6296 -15.2213 0 0 0 0) CONNECT=HT LABEL=n
M V30 END SGROUP
M V30 END CTAB
M END
)CTAB"_ctab;
REQUIRE(m);
MolDraw2DSVG drawer(350, 300);
drawer.drawMolecule(*m);
drawer.finishDrawing();
auto text = drawer.getDrawingText();
std::ofstream outs("testBrackets-4a.svg");
outs << text;
outs.close();
check_file_hash("testBrackets-4a.svg");
}
{ // no bonds in the sgroup, the bracket should point the other way
// (towards the majority of the atoms in the sgroup)
auto m = R"CTAB(bogus
Mrv2014 11202009512D
0 0 0 0 0 999 V3000
M V30 BEGIN CTAB
M V30 COUNTS 9 8 1 0 1
M V30 BEGIN ATOM
M V30 1 C 23.5462 -14.464 0 0
M V30 2 C 20.8231 -13.0254 0 0
M V30 3 C 20.8776 -14.5628 0 0
M V30 4 C 22.2391 -15.2819 0 0
M V30 5 C 16.2969 -9.9426 0 0
M V30 6 C 14.963 -10.7089 0 0
M V30 7 C 19.463 -12.2987 0 0
M V30 8 * 19.4398 -9.9979 0 0
M V30 9 * 26.1554 -14.4332 0 0
M V30 END ATOM
M V30 BEGIN BOND
M V30 1 1 3 4
M V30 2 1 6 7
M V30 3 1 5 8
M V30 4 1 1 9
M V30 5 1 7 2
M V30 6 1 6 5
M V30 7 1 4 1
M V30 8 1 3 2
M V30 END BOND
M V30 BEGIN SGROUP
M V30 1 SRU 0 ATOMS=(7 4 3 7 6 5 2 1) BRKXYZ=(9 17.6045 -
M V30 -9.1954 0 17.5775 -10.7352 0 0 0 0) BRKXYZ=(9 24.6113 -13.6813 0 -
M V30 24.6296 -15.2213 0 0 0 0) CONNECT=HT LABEL=n
M V30 END SGROUP
M V30 END CTAB
M END
)CTAB"_ctab;
REQUIRE(m);
MolDraw2DSVG drawer(350, 300);
drawer.drawMolecule(*m);
drawer.finishDrawing();
auto text = drawer.getDrawingText();
std::ofstream outs("testBrackets-4b.svg");
outs << text;
outs.close();
check_file_hash("testBrackets-4b.svg");
}
}
SECTION("comic brackets (no font though)") {
auto m = R"CTAB(
ACCLDraw11042015112D
0 0 0 0 0 999 V3000
M V30 BEGIN CTAB
M V30 COUNTS 5 4 1 0 0
M V30 BEGIN ATOM
M V30 1 C 7 -6.7813 0 0
M V30 2 C 8.0229 -6.1907 0 0 CFG=3
M V30 3 C 8.0229 -5.0092 0 0
M V30 4 C 9.046 -6.7814 0 0
M V30 5 C 10.0692 -6.1907 0 0
M V30 END ATOM
M V30 BEGIN BOND
M V30 1 1 1 2
M V30 2 1 2 3
M V30 3 1 2 4
M V30 4 1 4 5
M V30 END BOND
M V30 BEGIN SGROUP
M V30 1 SRU 1 ATOMS=(3 3 2 4) XBONDS=(2 1 4) BRKXYZ=(9 7.51 -7.08 0 7.51 -
M V30 -5.9 0 0 0 0) BRKXYZ=(9 9.56 -5.9 0 9.56 -7.08 0 0 0 0) -
M V30 CONNECT=HT LABEL=n
M V30 END SGROUP
M V30 END CTAB
M END
)CTAB"_ctab;
REQUIRE(m);
{
MolDraw2DSVG drawer(350, 300);
drawer.drawOptions().comicMode = true;
drawer.drawMolecule(*m);
drawer.finishDrawing();
auto text = drawer.getDrawingText();
std::ofstream outs("testBrackets-5a.svg");
outs << text;
outs.close();
check_file_hash("testBrackets-5a.svg");
}
}
SECTION("Github5768 - rightmost bracket wrong way round.)") {
auto m = R"CTAB(
Marvin 10140911012D
19 18 0 0 0 0 999 V2000
-2.0296 1.6372 0.0000 Si 0 0 0 0 0 0 0 0 0 0 0 0
-2.0296 2.4622 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
-2.0296 0.8122 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
-2.8546 1.6372 0.0000 * 0 0 0 0 0 0 0 0 0 0 0 0
-1.2046 1.6372 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0
-0.3796 1.6372 0.0000 Si 0 0 0 0 0 0 0 0 0 0 0 0
0.4454 1.6372 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0
-0.3796 0.8122 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
-0.3796 2.4622 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
0.3349 0.3997 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
1.0494 0.8122 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
1.7638 0.3997 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0
1.2704 1.6372 0.0000 * 0 0 0 0 0 0 0 0 0 0 0 0
2.4783 0.8122 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
3.1928 0.3996 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
3.9072 0.8121 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0
4.6217 0.3996 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
5.3362 0.8120 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
6.0506 0.3995 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0
1 2 1 0 0 0 0
1 3 1 0 0 0 0
1 4 1 0 0 0 0
1 5 1 0 0 0 0
5 6 1 0 0 0 0
6 7 1 0 0 0 0
6 8 1 0 0 0 0
6 9 1 0 0 0 0
8 10 1 0 0 0 0
10 11 1 0 0 0 0
7 13 1 0 0 0 0
11 12 1 0 0 0 0
12 14 1 0 0 0 0
14 15 1 0 0 0 0
15 16 1 0 0 0 0
16 17 1 0 0 0 0
17 18 1 0 0 0 0
18 19 1 0 0 0 0
M STY 2 1 SRU 2 SRU
M SCN 1 1 HT
M SAL 1 4 1 2 3 5
M SDI 1 4 -0.8649 2.0497 -0.8649 1.2247
M SDI 1 4 -2.3693 1.2247 -2.3693 2.0497
M SBL 1 2 3 5
M SMT 1 n
M SCN 1 2 HT
M SAL 2 13 6 7 8 9 10 11 12 14 15 16 17 18 19
M SDI 2 4 0.7851 2.0497 0.7851 1.2247
M SDI 2 4 -0.7193 1.2247 -0.7193 2.0497
M SBL 2 2 5 11
M SMT 2 m
M END
)CTAB"_ctab;
REQUIRE(m);
{
MolDraw2DSVG drawer(350, 300);
drawer.drawOptions().addAtomIndices = true;
drawer.drawMolecule(*m);
drawer.finishDrawing();
auto text = drawer.getDrawingText();
std::ofstream outs("testBrackets-5768.svg");
outs << text;
outs.close();
check_file_hash("testBrackets-5768.svg");
}
}
}
#ifdef RDK_BUILD_CAIRO_SUPPORT
TEST_CASE("github #3543: Error adding PNG metadata when kekulize=False",
"[bug][metadata][png]") {
SECTION("basics") {
auto m = "n1cccc1"_smarts;
m->updatePropertyCache(false);
MolDraw2DCairo drawer(350, 300);
bool kekulize = false;
MolDraw2DUtils::prepareMolForDrawing(*m, kekulize);
drawer.drawOptions().prepareMolsBeforeDrawing = false;
drawer.drawMolecule(*m);
drawer.finishDrawing();
auto png = drawer.getDrawingText();
}
SECTION("as reported") {
auto m = "n1cnc2c(n)ncnc12"_smarts;
m->updatePropertyCache(false);
MolDraw2DCairo drawer(350, 300);
bool kekulize = false;
MolDraw2DUtils::prepareMolForDrawing(*m, kekulize);
drawer.drawOptions().prepareMolsBeforeDrawing = false;
drawer.drawMolecule(*m);
drawer.finishDrawing();
auto png = drawer.getDrawingText();
}
}
#endif
TEST_CASE("SGroup Data") {
SECTION("ABS") {
auto m = R"CTAB(
Mrv2014 12072015352D
0 0 0 0 0 999 V3000
M V30 BEGIN CTAB
M V30 COUNTS 9 9 1 0 0
M V30 BEGIN ATOM
M V30 1 C -6.5833 4.3317 0 0
M V30 2 C -7.917 3.5617 0 0
M V30 3 C -7.917 2.0216 0 0
M V30 4 C -6.5833 1.2516 0 0
M V30 5 C -5.2497 2.0216 0 0
M V30 6 C -5.2497 3.5617 0 0
M V30 7 C -3.916 4.3317 0 0
M V30 8 O -3.916 5.8717 0 0
M V30 9 O -2.5823 3.5617 0 0
M V30 END ATOM
M V30 BEGIN BOND
M V30 1 1 1 2
M V30 2 2 2 3
M V30 3 1 3 4
M V30 4 2 4 5
M V30 5 1 5 6
M V30 6 2 1 6
M V30 7 1 6 7
M V30 8 2 7 8
M V30 9 1 7 9
M V30 END BOND
M V30 BEGIN SGROUP
M V30 1 DAT 0 ATOMS=(1 9) FIELDNAME=pKa -
M V30 FIELDDISP=" -2.2073 2.3950 DAU ALL 0 0" -
M V30 MRV_FIELDDISP=0 FIELDDATA=4.2
M V30 END SGROUP
M V30 END CTAB
M END
)CTAB"_ctab;
REQUIRE(m);
{
MolDraw2DSVG drawer(350, 300);
drawer.drawMolecule(*m, "abs");
drawer.finishDrawing();
auto text = drawer.getDrawingText();
std::ofstream outs("testSGroupData-1a.svg");
outs << text;
outs.close();
check_file_hash("testSGroupData-1a.svg");
}
{
MolDraw2DSVG drawer(350, 300);
drawer.drawOptions().centreMoleculesBeforeDrawing = true;
drawer.drawOptions().rotate = 90;
drawer.drawMolecule(*m, "centered, rotated");
drawer.finishDrawing();
auto text = drawer.getDrawingText();
std::ofstream outs("testSGroupData-1b.svg");
outs << text;
outs.close();
check_file_hash("testSGroupData-1b.svg");
}
}
SECTION("REL") {
auto m = R"CTAB(
Mrv2014 12072015352D
0 0 0 0 0 999 V3000
M V30 BEGIN CTAB
M V30 COUNTS 9 9 1 0 0
M V30 BEGIN ATOM
M V30 1 C -6.5833 4.3317 0 0
M V30 2 C -7.917 3.5617 0 0
M V30 3 C -7.917 2.0216 0 0
M V30 4 C -6.5833 1.2516 0 0
M V30 5 C -5.2497 2.0216 0 0
M V30 6 C -5.2497 3.5617 0 0
M V30 7 C -3.916 4.3317 0 0
M V30 8 O -3.916 5.8717 0 0
M V30 9 O -2.5823 3.5617 0 0
M V30 END ATOM
M V30 BEGIN BOND
M V30 1 1 1 2
M V30 2 2 2 3
M V30 3 1 3 4
M V30 4 2 4 5
M V30 5 1 5 6
M V30 6 2 1 6
M V30 7 1 6 7
M V30 8 2 7 8
M V30 9 1 7 9
M V30 END BOND
M V30 BEGIN SGROUP
M V30 1 DAT 0 ATOMS=(1 9) FIELDNAME=pKa -
M V30 FIELDDISP=" 0.2000 0.2000 DRU ALL 0 0" -
M V30 MRV_FIELDDISP=0 FIELDDATA=4.2
M V30 END SGROUP
M V30 END CTAB
M END
)CTAB"_ctab;
REQUIRE(m);
{
MolDraw2DSVG drawer(350, 300);
drawer.drawMolecule(*m, "rel");
drawer.finishDrawing();
auto text = drawer.getDrawingText();
std::ofstream outs("testSGroupData-2a.svg");
outs << text;
outs.close();
check_file_hash("testSGroupData-2a.svg");
}
{
MolDraw2DSVG drawer(350, 300);
drawer.drawOptions().centreMoleculesBeforeDrawing = true;
drawer.drawOptions().rotate = 90;
drawer.drawMolecule(*m, "rel, centered, rotated");
drawer.finishDrawing();
auto text = drawer.getDrawingText();
std::ofstream outs("testSGroupData-2b.svg");
outs << text;
outs.close();
check_file_hash("testSGroupData-2b.svg");
}
}
{
auto m = R"CTAB(random example found on internet
JSDraw204221719232D
20 21 0 0 0 0 0 V2000
10.1710 -5.6553 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
10.9428 -4.2996 0.0000 N 0 0 0 0 0 0 0 0 0 0 0 0
8.6110 -5.6647 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0
10.9591 -7.0015 0.0000 N 0 0 0 0 0 0 0 0 0 0 0 0
12.5190 -6.9921 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
13.3072 -8.3384 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0
13.2909 -5.6364 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
12.5028 -4.2902 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
13.2746 -2.9345 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0
14.8508 -5.6270 0.0000 N 0 0 0 0 0 0 0 0 0 0 0 0
15.6226 -4.2713 0.0000 N 0 0 0 0 0 0 0 0 0 0 0 0
20.3026 -4.2431 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
19.5307 -5.5987 0.0000 N 0 0 0 0 0 0 0 0 0 0 0 0
21.8625 -4.2336 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0
19.5144 -2.8968 0.0000 N 0 0 0 0 0 0 0 0 0 0 0 0
17.9544 -2.9062 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
17.1663 -1.5600 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0
17.1826 -4.2619 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
17.9708 -5.6082 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
17.1989 -6.9638 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0
1 2 1 0 0 0 0
1 3 2 0 0 0 0
1 4 1 0 0 0 0
4 5 2 0 0 0 0
5 6 1 0 0 0 0
5 7 1 0 0 0 0
7 8 1 0 0 0 0
8 9 2 0 0 0 0
8 2 1 0 0 0 0
7 10 1 0 0 0 0
10 11 2 0 0 0 0
12 13 1 0 0 0 0
12 14 2 0 0 0 0
12 15 1 0 0 0 0
15 16 1 0 0 0 0
16 17 2 0 0 0 0
16 18 1 0 0 0 0
18 19 1 0 0 0 0
19 20 1 0 0 0 0
19 13 2 0 0 0 0
11 18 1 0 0 0 0
M STY 1 1 DAT
M SDT 1 UNKNOWN F
M SDD 1 16.0856 -8.1573 DA ALL 1 5
M SED 1 Ni-complex
M END)CTAB"_ctab;
{
MolDraw2DSVG drawer(350, 300);
drawer.drawMolecule(*m);
drawer.finishDrawing();
auto text = drawer.getDrawingText();
std::ofstream outs("testSGroupData-3a.svg");
outs << text;
outs.close();
check_file_hash("testSGroupData-3a.svg");
}
}
}
TEST_CASE("position variation bonds", "[extras]") {
SECTION("simple") {
auto m = R"CTAB(
Mrv2014 12092006072D
0 0 0 0 0 999 V3000
M V30 BEGIN CTAB
M V30 COUNTS 9 8 0 0 0
M V30 BEGIN ATOM
M V30 1 C -4.7083 4.915 0 0
M V30 2 C -6.042 4.145 0 0
M V30 3 C -6.042 2.605 0 0
M V30 4 C -4.7083 1.835 0 0
M V30 5 C -3.3747 2.605 0 0
M V30 6 C -3.3747 4.145 0 0
M V30 7 * -3.8192 3.8883 0 0
M V30 8 O -3.8192 6.1983 0 0
M V30 9 C -2.4855 6.9683 0 0
M V30 END ATOM
M V30 BEGIN BOND
M V30 1 1 1 2
M V30 2 2 2 3
M V30 3 1 3 4
M V30 4 2 4 5
M V30 5 1 5 6
M V30 6 2 1 6
M V30 7 1 7 8 ENDPTS=(3 1 6 5) ATTACH=ANY
M V30 8 1 8 9
M V30 END BOND
M V30 END CTAB
M END
)CTAB"_ctab;
REQUIRE(m);
{
MolDraw2DSVG drawer(350, 300);
drawer.drawMolecule(*m, "variations");
drawer.finishDrawing();
auto text = drawer.getDrawingText();
std::ofstream outs("testPositionVariation-1.svg");
outs << text;
outs.close();
check_file_hash("testPositionVariation-1.svg");
}
{ // make sure comic mode doesn't screw this up
MolDraw2DSVG drawer(350, 300);
drawer.drawOptions().comicMode = true;
drawer.drawMolecule(*m, "comic variations");
drawer.finishDrawing();
auto text = drawer.getDrawingText();
std::ofstream outs("testPositionVariation-1b.svg");
outs << text;
outs.close();
check_file_hash("testPositionVariation-1b.svg");
}
}
SECTION("multiple") {
auto m = R"CTAB(
Mrv2014 12092006082D
0 0 0 0 0 999 V3000
M V30 BEGIN CTAB
M V30 COUNTS 15 14 0 0 0
M V30 BEGIN ATOM
M V30 1 C -4.7083 4.915 0 0
M V30 2 C -6.042 4.145 0 0
M V30 3 C -6.042 2.605 0 0
M V30 4 C -4.7083 1.835 0 0
M V30 5 C -3.3747 2.605 0 0
M V30 6 C -3.3747 4.145 0 0
M V30 7 * -3.8192 3.8883 0 0
M V30 8 O -3.8192 6.1983 0 0
M V30 9 C -2.4855 6.9683 0 0
M V30 10 C -7.3757 4.915 0 0
M V30 11 C -8.7093 4.145 0 0
M V30 12 C -8.7093 2.605 0 0
M V30 13 C -7.3757 1.835 0 0
M V30 14 * -8.7093 3.375 0 0
M V30 15 O -10.2922 3.375 0 0
M V30 END ATOM
M V30 BEGIN BOND
M V30 1 1 1 2
M V30 2 1 2 3
M V30 3 1 3 4
M V30 4 2 4 5
M V30 5 1 5 6
M V30 6 2 1 6
M V30 7 1 7 8 ENDPTS=(3 1 6 5) ATTACH=ANY
M V30 8 1 8 9
M V30 9 1 10 11
M V30 10 2 11 12
M V30 11 1 12 13
M V30 12 2 10 2
M V30 13 2 13 3
M V30 14 1 14 15 ENDPTS=(2 11 12) ATTACH=ANY
M V30 END BOND
M V30 END CTAB
M END
)CTAB"_ctab;
REQUIRE(m);
{
MolDraw2DSVG drawer(350, 300);
drawer.drawMolecule(*m, "multiple variations");
drawer.finishDrawing();
auto text = drawer.getDrawingText();
std::ofstream outs("testPositionVariation-2.svg");
outs << text;
outs.close();
check_file_hash("testPositionVariation-2.svg");
}
}
SECTION("non-contiguous") {
auto m = R"CTAB(
Mrv2014 12092006102D
0 0 0 0 0 999 V3000
M V30 BEGIN CTAB
M V30 COUNTS 9 8 0 0 0
M V30 BEGIN ATOM
M V30 1 C -0.875 8.7484 0 0
M V30 2 C -2.2087 7.9784 0 0
M V30 3 C -2.2087 6.4383 0 0
M V30 4 C -0.875 5.6683 0 0
M V30 5 C 0.4587 6.4383 0 0
M V30 6 C 0.4587 7.9784 0 0
M V30 7 * -0.4304 6.9517 0 0
M V30 8 O -0.4304 4.6417 0 0
M V30 9 C -1.7641 3.8717 0 0
M V30 END ATOM
M V30 BEGIN BOND
M V30 1 1 1 2
M V30 2 2 2 3
M V30 3 1 3 4
M V30 4 2 4 5
M V30 5 1 5 6
M V30 6 2 1 6
M V30 7 1 7 8 ENDPTS=(3 1 5 4) ATTACH=ANY
M V30 8 1 8 9
M V30 END BOND
M V30 END CTAB
M END
)CTAB"_ctab;
REQUIRE(m);
{
MolDraw2DSVG drawer(350, 300);
drawer.drawMolecule(*m, "non-contiguous atoms");
drawer.finishDrawing();
auto text = drawer.getDrawingText();
std::ofstream outs("testPositionVariation-3.svg");
outs << text;
outs.close();
check_file_hash("testPositionVariation-3.svg");
}
}
SECTION("larger mol") {
auto m = R"CTAB(
Mrv2014 12092009152D
0 0 0 0 0 999 V3000
M V30 BEGIN CTAB
M V30 COUNTS 23 24 0 0 0
M V30 BEGIN ATOM
M V30 1 C -0.875 8.7484 0 0
M V30 2 C -2.2087 7.9784 0 0
M V30 3 C -2.2087 6.4383 0 0
M V30 4 C -0.875 5.6683 0 0
M V30 5 N 0.4587 6.4383 0 0
M V30 6 C 0.4587 7.9784 0 0
M V30 7 * -0.4304 6.9517 0 0
M V30 8 O -0.4304 4.6417 0 0
M V30 9 C -1.7641 3.8717 0 0
M V30 10 C -3.5423 8.7484 0 0
M V30 11 C -4.876 7.9784 0 0
M V30 12 C -4.876 6.4383 0 0
M V30 13 C -3.5423 5.6683 0 0
M V30 14 C -4.876 11.0584 0 0
M V30 15 C -6.2097 10.2884 0 0
M V30 16 C -6.2097 8.7484 0 0
M V30 17 C -3.5423 10.2884 0 0
M V30 18 C -6.2097 13.3685 0 0
M V30 19 C -7.5433 12.5985 0 0
M V30 20 C -7.5433 11.0584 0 0
M V30 21 C -4.876 12.5985 0 0
M V30 22 * -5.5428 9.1334 0 0
M V30 23 C -7.3712 7.7304 0 0
M V30 END ATOM
M V30 BEGIN BOND
M V30 1 1 1 2
M V30 2 2 2 3
M V30 3 1 3 4
M V30 4 2 4 5
M V30 5 1 5 6
M V30 6 2 1 6
M V30 7 1 7 8 ENDPTS=(3 1 4 5) ATTACH=ANY
M V30 8 1 8 9
M V30 9 2 10 11
M V30 10 1 11 12
M V30 11 2 12 13
M V30 12 1 10 2
M V30 13 1 13 3
M V30 14 1 14 15
M V30 15 2 15 16
M V30 16 2 14 17
M V30 17 1 10 17
M V30 18 1 16 11
M V30 19 1 18 19
M V30 20 2 19 20
M V30 21 2 18 21
M V30 22 1 14 21
M V30 23 1 20 15
M V30 24 1 22 23 ENDPTS=(2 15 11) ATTACH=ANY
M V30 END BOND
M V30 END CTAB
M END
)CTAB"_ctab;
REQUIRE(m);
{
MolDraw2DSVG drawer(250, 200);
drawer.drawMolecule(*m, "smaller");
drawer.finishDrawing();
auto text = drawer.getDrawingText();
std::ofstream outs("testPositionVariation-4.svg");
outs << text;
outs.close();
check_file_hash("testPositionVariation-4.svg");
}
}
}
TEST_CASE("disable atom labels", "[feature]") {
SECTION("basics") {
{
auto m = "NCC(=O)O"_smiles;
MolDraw2DSVG drawer(350, 300);
MolDraw2DUtils::prepareMolForDrawing(*m);
drawer.drawOptions().noAtomLabels = true;
drawer.drawMolecule(*m);
drawer.finishDrawing();
auto text = drawer.getDrawingText();
std::ofstream outs("testNoAtomLabels-1.svg");
outs << text;
outs.close();
check_file_hash("testNoAtomLabels-1.svg");
CHECK(text.find("class='atom-0") == std::string::npos);
CHECK(text.find("class='atom-3") == std::string::npos);
}
{
auto m = "F[C@H](O)C[C@@H](Cl)I"_smiles;
MolDraw2DSVG drawer(350, 300);
MolDraw2DUtils::prepareMolForDrawing(*m);
drawer.drawOptions().noAtomLabels = true;
drawer.drawMolecule(*m);
drawer.finishDrawing();
auto text = drawer.getDrawingText();
std::ofstream outs("testNoAtomLabels-2.svg");
outs << text;
outs.close();
check_file_hash("testNoAtomLabels-2.svg");
}
}
}
TEST_CASE("drawing query bonds", "[queries]") {
SECTION("basics") {
auto m = R"CTAB(
Mrv2014 12072005332D
0 0 0 0 0 999 V3000
M V30 BEGIN CTAB
M V30 COUNTS 14 14 0 0 0
M V30 BEGIN ATOM
M V30 1 C 3.7917 -2.96 0 0
M V30 2 C 2.458 -3.73 0 0
M V30 3 C 2.458 -5.27 0 0
M V30 4 C 3.7917 -6.04 0 0
M V30 5 C 5.1253 -5.27 0 0
M V30 6 C 5.1253 -3.73 0 0
M V30 7 C 6.459 -2.96 0 0
M V30 8 C 3.7917 -7.58 0 0
M V30 9 C 4.8806 -8.669 0 0
M V30 10 C 4.482 -10.1565 0 0
M V30 11 C 6.459 -6.04 0 0
M V30 12 C 7.7927 -5.27 0 0
M V30 13 C 9.1263 -6.0399 0 0
M V30 14 C 9.1263 -7.5799 0 0
M V30 END ATOM
M V30 BEGIN BOND
M V30 1 1 2 3
M V30 2 1 4 5
M V30 3 1 1 6
M V30 4 5 1 2
M V30 5 6 5 6
M V30 6 7 3 4
M V30 7 8 6 7
M V30 8 1 4 8
M V30 9 1 8 9 TOPO=1
M V30 10 1 9 10 TOPO=2
M V30 11 1 5 11
M V30 12 1 12 13
M V30 13 2 11 12 TOPO=1
M V30 14 2 13 14 TOPO=2
M V30 END BOND
M V30 END CTAB
M END
)CTAB"_ctab;
REQUIRE(m);
{
MolDraw2DSVG drawer(350, 300);
drawer.drawMolecule(*m);
drawer.finishDrawing();
auto text = drawer.getDrawingText();
std::ofstream outs("testQueryBonds-1a.svg");
outs << text;
outs.close();
check_file_hash("testQueryBonds-1a.svg");
}
{
MolDraw2DSVG drawer(350, 300);
m->getBondWithIdx(3)->setProp("bondNote", "S/D");
m->getBondWithIdx(4)->setProp("bondNote", "S/A");
m->getBondWithIdx(5)->setProp("bondNote", "D/A");
m->getBondWithIdx(6)->setProp("bondNote", "Any");
drawer.drawMolecule(*m);
drawer.finishDrawing();
auto text = drawer.getDrawingText();
std::ofstream outs("testQueryBonds-1b.svg");
outs << text;
outs.close();
check_file_hash("testQueryBonds-1b.svg");
}
{
MolDraw2DSVG drawer(350, 300);
std::vector<int> highlightAtoms = {0, 1, 2, 3, 4, 5, 7, 8, 9};
std::vector<int> highlightBonds = {0, 3, 2, 4, 1, 5, 8, 9};
drawer.drawMolecule(*m, "", &highlightAtoms, &highlightBonds);
drawer.finishDrawing();
auto text = drawer.getDrawingText();
std::ofstream outs("testQueryBonds-1c.svg");
outs << text;
outs.close();
check_file_hash("testQueryBonds-1c.svg");
}
}
SECTION("smaller drawing") {
auto m = R"CTAB(
Mrv2014 12012004302D
0 0 0 0 0 999 V3000
M V30 BEGIN CTAB
M V30 COUNTS 26 29 0 0 0
M V30 BEGIN ATOM
M V30 1 O 3.7917 -2.96 0 0
M V30 2 C 2.458 -3.73 0 0
M V30 3 C 2.458 -5.27 0 0
M V30 4 N 3.7917 -6.04 0 0
M V30 5 N 5.1253 -5.27 0 0
M V30 6 C 5.1253 -3.73 0 0
M V30 7 C 6.459 -2.96 0 0
M V30 8 C 3.7917 -7.58 0 0
M V30 9 C 4.8806 -8.669 0 0
M V30 10 C 4.482 -10.1565 0 0
M V30 11 C 1.1243 -2.9599 0 0
M V30 12 C -0.2093 -3.73 0 0
M V30 13 C -0.2093 -5.27 0 0
M V30 14 C 1.1243 -6.04 0 0
M V30 15 C -0.2093 -0.6499 0 0
M V30 16 C -1.543 -1.4199 0 0
M V30 17 C -1.543 -2.9599 0 0
M V30 18 C 1.1243 -1.4199 0 0
M V30 19 C -2.8767 -0.6499 0 0
M V30 20 C -4.2103 -1.4199 0 0
M V30 21 C -4.2103 -2.9599 0 0
M V30 22 C -2.8767 -3.73 0 0
M V30 23 C -5.544 -3.7299 0 0
M V30 24 C -6.8777 -2.9599 0 0
M V30 25 C -8.2114 -3.7299 0 0
M V30 26 C -9.5451 -2.9599 0 0
M V30 END ATOM
M V30 BEGIN BOND
M V30 1 1 2 3
M V30 2 1 4 5
M V30 3 1 1 6
M V30 4 5 1 2
M V30 5 6 5 6
M V30 6 7 3 4
M V30 7 8 6 7
M V30 8 1 4 8
M V30 9 1 8 9 TOPO=1
M V30 10 1 9 10 TOPO=2
M V30 11 1 12 13
M V30 12 1 13 14
M V30 13 1 14 3
M V30 14 1 11 2
M V30 15 1 15 16
M V30 16 1 16 17
M V30 17 2 15 18
M V30 18 1 11 18
M V30 19 1 17 12
M V30 20 2 12 11
M V30 21 1 19 20
M V30 22 2 20 21
M V30 23 1 21 22
M V30 24 2 19 16
M V30 25 2 22 17
M V30 26 1 21 23
M V30 27 1 23 24
M V30 28 1 24 25
M V30 29 1 25 26
M V30 END BOND
M V30 END CTAB
M END
)CTAB"_ctab;
REQUIRE(m);
{
MolDraw2DSVG drawer(250, 200);
drawer.drawMolecule(*m);
drawer.finishDrawing();
auto text = drawer.getDrawingText();
std::ofstream outs("testQueryBonds-2.svg");
outs << text;
outs.close();
check_file_hash("testQueryBonds-2.svg");
}
}
SECTION("two linknodes") {
auto m = R"CTAB(two linknodes
Mrv2014 07072016412D
0 0 0 0 0 999 V3000
M V30 BEGIN CTAB
M V30 COUNTS 7 7 0 0 0
M V30 BEGIN ATOM
M V30 1 C 8.25 12.1847 0 0
M V30 2 C 6.9164 12.9547 0 0
M V30 3 C 7.2366 14.4611 0 0
M V30 4 C 8.7681 14.622 0 0
M V30 5 C 9.3945 13.2151 0 0
M V30 6 O 8.25 10.6447 0 0
M V30 7 F 9.5382 15.9557 0 0
M V30 END ATOM
M V30 BEGIN BOND
M V30 1 1 1 2
M V30 2 1 2 3
M V30 3 1 4 5
M V30 4 1 1 5
M V30 5 1 3 4
M V30 6 1 1 6
M V30 7 1 4 7
M V30 END BOND
M V30 LINKNODE 1 3 2 1 2 1 5
M V30 LINKNODE 1 4 2 4 3 4 5
M V30 END CTAB
M END)CTAB"_ctab;
std::vector<int> rotns = {0, 30, 60, 90, 120, 150, 180};
for (auto rotn : rotns) {
MolDraw2DSVG drawer(350, 300);
drawer.drawOptions().rotate = (double)rotn;
drawer.drawMolecule(*m);
drawer.finishDrawing();
auto text = drawer.getDrawingText();
std::string filename(
(boost::format("testLinkNodes-2-%d.svg") % rotn).str());
std::ofstream outs(filename);
outs << text;
outs.close();
check_file_hash(filename);
}
}
}
TEST_CASE("molecule annotations", "[extra]") {
int panelHeight = -1;
int panelWidth = -1;
bool noFreeType = false;
SECTION("basics") {
auto m = "NCC(=O)O"_smiles;
MolDraw2DSVG drawer(350, 300, panelWidth, panelHeight, noFreeType);
MolDraw2DUtils::prepareMolForDrawing(*m);
m->setProp(common_properties::molNote, "molecule note");
drawer.drawMolecule(*m, "with note");
drawer.finishDrawing();
auto text = drawer.getDrawingText();
std::ofstream outs("testMolAnnotations-1.svg");
outs << text;
outs.close();
check_file_hash("testMolAnnotations-1.svg");
CHECK(text.find("class='note'") != std::string::npos);
}
SECTION("chiral flag") {
auto m = R"CTAB(
Mrv2014 12152012512D
0 0 0 0 0 999 V3000
M V30 BEGIN CTAB
M V30 COUNTS 8 8 0 0 1
M V30 BEGIN ATOM
M V30 1 C -0.6317 0.6787 0 0 CFG=2
M V30 2 C -1.7207 1.7677 0 0
M V30 3 C 0.4571 1.7677 0 0
M V30 4 C -0.6317 2.8566 0 0 CFG=1
M V30 5 C 0.1729 4.1698 0 0
M V30 6 N -0.5619 5.5231 0 0
M V30 7 C -1.4364 4.1698 0 0
M V30 8 C -0.6316 -0.8613 0 0
M V30 END ATOM
M V30 BEGIN BOND
M V30 1 1 1 2 CFG=3
M V30 2 1 1 3
M V30 3 1 4 3
M V30 4 1 4 2
M V30 5 1 4 5
M V30 6 1 5 6
M V30 7 1 4 7 CFG=1
M V30 8 1 1 8
M V30 END BOND
M V30 END CTAB
M END
)CTAB"_ctab;
{
MolDraw2DSVG drawer(350, 300, panelWidth, panelHeight, noFreeType);
drawer.drawMolecule(*m, "chiral flag set, option disabled");
drawer.finishDrawing();
auto text = drawer.getDrawingText();
std::ofstream outs("testMolAnnotations-2a.svg");
outs << text;
outs.close();
check_file_hash("testMolAnnotations-2a.svg");
CHECK(text.find("class='note'") == std::string::npos);
}
{
MolDraw2DSVG drawer(350, 300, panelWidth, panelHeight, noFreeType);
drawer.drawOptions().includeChiralFlagLabel = true;
drawer.drawMolecule(*m, "chiral flag set, option enabled");
drawer.finishDrawing();
auto text = drawer.getDrawingText();
std::ofstream outs("testMolAnnotations-2b.svg");
outs << text;
outs.close();
check_file_hash("testMolAnnotations-2b.svg");
CHECK(text.find("class='note'") != std::string::npos);
}
{
MolDraw2DSVG drawer(350, 300, panelWidth, panelHeight, noFreeType);
drawer.drawOptions().includeChiralFlagLabel = true;
m->clearProp(common_properties::_MolFileChiralFlag);
drawer.drawMolecule(*m, "chiral flag not set, option enabled");
drawer.finishDrawing();
auto text = drawer.getDrawingText();
std::ofstream outs("testMolAnnotations-2c.svg");
outs << text;
outs.close();
check_file_hash("testMolAnnotations-2c.svg");
CHECK(text.find("class='note'") == std::string::npos);
}
}
SECTION("simplified stereo 1") {
{
auto m = "C[C@H](F)[C@@H](F)[C@@H](C)Cl |o1:3,5,1|"_smiles;
MolDraw2DSVG drawer(350, 300, panelWidth, panelHeight, noFreeType);
MolDraw2DUtils::prepareMolForDrawing(*m);
drawer.drawOptions().addStereoAnnotation = true;
drawer.drawMolecule(*m, "enhanced no flag");
drawer.finishDrawing();
auto text = drawer.getDrawingText();
std::ofstream outs("testMolAnnotations-3a.svg");
outs << text;
outs.close();
check_file_hash("testMolAnnotations-3a.svg");
}
{
auto m = "C[C@H](F)[C@@H](F)[C@@H](C)Cl |o1:3,5,1|"_smiles;
MolDraw2DSVG drawer(350, 300, panelWidth, panelHeight, noFreeType);
MolDraw2DUtils::prepareMolForDrawing(*m);
drawer.drawOptions().addStereoAnnotation = true;
drawer.drawOptions().simplifiedStereoGroupLabel = true;
drawer.drawMolecule(*m, "enhanced with flag");
drawer.finishDrawing();
auto text = drawer.getDrawingText();
std::ofstream outs("testMolAnnotations-3b.svg");
outs << text;
outs.close();
check_file_hash("testMolAnnotations-3b.svg");
}
{
auto m = "C[C@H](F)[C@@H](F)[C@@H](C)Cl |&1:3,5,1|"_smiles;
MolDraw2DSVG drawer(350, 300, panelWidth, panelHeight, noFreeType);
MolDraw2DUtils::prepareMolForDrawing(*m);
drawer.drawOptions().addStereoAnnotation = true;
drawer.drawOptions().simplifiedStereoGroupLabel = true;
drawer.drawMolecule(*m, "enhanced & with flag");
drawer.finishDrawing();
auto text = drawer.getDrawingText();
std::ofstream outs("testMolAnnotations-3c.svg");
outs << text;
outs.close();
check_file_hash("testMolAnnotations-3c.svg");
}
}
SECTION("simplified stereo 2") {
auto m = "C[C@H](F)[C@@H](F)[C@@H](C)Cl |o1:3,5,o2:1|"_smiles;
MolDraw2DSVG drawer(350, 300, panelWidth, panelHeight, noFreeType);
drawer.drawOptions().addStereoAnnotation = true;
drawer.drawOptions().simplifiedStereoGroupLabel = true;
MolDraw2DUtils::prepareMolForDrawing(*m);
drawer.drawMolecule(*m, "multi-groups");
drawer.finishDrawing();
auto text = drawer.getDrawingText();
std::ofstream outs("testMolAnnotations-3d.svg");
outs << text;
outs.close();
check_file_hash("testMolAnnotations-3d.svg");
}
SECTION("label placement") {
auto m = R"CTAB(
Mrv2014 12162004412D
0 0 0 0 0 999 V3000
M V30 BEGIN CTAB
M V30 COUNTS 16 15 0 0 0
M V30 BEGIN ATOM
M V30 1 C -9.2917 3.5833 0 0
M V30 2 C -7.958 4.3533 0 0 CFG=2
M V30 3 C -6.6243 3.5833 0 0 CFG=1
M V30 4 C -5.2906 4.3533 0 0 CFG=2
M V30 5 Cl -7.958 5.8933 0 0
M V30 6 F -6.6243 2.0433 0 0
M V30 7 F -3.957 3.5833 0 0
M V30 8 C -5.2906 5.8933 0 0
M V30 9 C -3.957 6.6633 0 0
M V30 10 C -3.957 8.2033 0 0
M V30 11 C -2.6233 8.9733 0 0
M V30 12 C -2.6233 5.8933 0 0
M V30 13 C -5.2906 8.9733 0 0
M V30 14 C -2.6233 10.5133 0 0
M V30 15 C -1.2896 8.2033 0 0
M V30 16 C -1.2896 6.6633 0 0
M V30 END ATOM
M V30 BEGIN BOND
M V30 1 1 1 2
M V30 2 1 2 3
M V30 3 1 3 4
M V30 4 1 2 5 CFG=1
M V30 5 1 3 6 CFG=1
M V30 6 1 4 7 CFG=1
M V30 7 1 4 8
M V30 8 1 8 9
M V30 9 1 9 10
M V30 10 1 10 11
M V30 11 1 9 12
M V30 12 1 10 13
M V30 13 1 11 14
M V30 14 1 11 15
M V30 15 1 12 16
M V30 END BOND
M V30 BEGIN COLLECTION
M V30 MDLV30/STEREL1 ATOMS=(3 2 3 4)
M V30 END COLLECTION
M V30 END CTAB
M END
)CTAB"_ctab;
MolDraw2DSVG drawer(350, 300, panelWidth, panelHeight, noFreeType);
drawer.drawOptions().addStereoAnnotation = true;
drawer.drawOptions().simplifiedStereoGroupLabel = true;
drawer.drawMolecule(*m, "label crowding");
drawer.finishDrawing();
auto text = drawer.getDrawingText();
std::ofstream outs("testMolAnnotations-4a.svg");
outs << text;
outs.close();
check_file_hash("testMolAnnotations-4a.svg");
}
}
TEST_CASE("draw link nodes", "[extras]") {
SECTION("one linknode") {
auto m = R"CTAB(one linknode
Mrv2007 06222005102D
0 0 0 0 0 999 V3000
M V30 BEGIN CTAB
M V30 COUNTS 6 6 0 0 0
M V30 BEGIN ATOM
M V30 1 C 8.25 12.1847 0 0
M V30 2 C 6.9164 12.9547 0 0
M V30 3 C 6.9164 14.4947 0 0
M V30 4 C 9.5836 14.4947 0 0
M V30 5 C 9.5836 12.9547 0 0
M V30 6 O 8.25 10.6447 0 0
M V30 END ATOM
M V30 BEGIN BOND
M V30 1 1 1 2
M V30 2 1 2 3
M V30 3 1 4 5
M V30 4 1 1 5
M V30 5 1 3 4
M V30 6 1 1 6
M V30 END BOND
M V30 LINKNODE 1 4 2 1 2 1 5
M V30 END CTAB
M END)CTAB"_ctab;
std::vector<int> rotns = {0, 30, 60, 90, 120, 150, 180};
for (auto rotn : rotns) {
MolDraw2DSVG drawer(350, 300);
drawer.drawOptions().rotate = (double)rotn;
drawer.drawMolecule(*m);
drawer.finishDrawing();
auto text = drawer.getDrawingText();
std::ofstream outs(
(boost::format("testLinkNodes-1-%d.svg") % rotn).str());
outs << text;
outs.close();
check_file_hash((boost::format("testLinkNodes-1-%d.svg") % rotn).str());
}
}
}
TEST_CASE("Github #3744: Double bonds incorrectly drawn outside the ring",
"[drawing]") {
SECTION("SVG") {
ROMOL_SPTR m1(MolBlockToMol(R"CTAB(
RDKit 2D
6 6 0 0 0 0 0 0 0 0999 V2000
0.0684 -1.2135 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
1.4949 -0.7500 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
1.4949 0.7500 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
0.0684 1.2135 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
-0.8133 0.0000 0.0000 N 0 0 0 0 0 0 0 0 0 0 0 0
-2.3133 -0.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
1 2 2 0
2 3 1 0
3 4 2 0
4 5 1 0
5 6 1 0
5 1 1 0
M END)CTAB"));
REQUIRE(m1);
MolDraw2DSVG drawer(400, 300);
drawer.drawMolecule(*m1);
drawer.finishDrawing();
std::string text = drawer.getDrawingText();
std::ofstream outs("testGithub3744.svg");
outs << text;
outs.close();
check_file_hash("testGithub3744.svg");
std::vector<std::string> bond0;
std::vector<std::string> bond2;
std::istringstream ss(text);
std::string line;
while (std::getline(ss, line)) {
if (line.find("bond-0") != std::string::npos) {
bond0.push_back(line);
} else if (line.find("bond-2") != std::string::npos) {
bond2.push_back(line);
}
}
CHECK(bond0.size() == 2);
CHECK(bond2.size() == 2);
std::regex regex(
"^.*d='M\\s+(\\d+\\.\\d+),(\\d+\\.\\d+)\\s+L\\s+(\\d+\\.\\d+),(\\d+\\."
"\\d+)'.*$");
std::smatch bond0OuterMatch;
CHECK(std::regex_match(bond0[0], bond0OuterMatch, regex));
CHECK(bond0OuterMatch.size() == 5);
std::smatch bond0InnerMatch;
CHECK(std::regex_match(bond0[1], bond0InnerMatch, regex));
CHECK(bond0InnerMatch.size() == 5);
std::smatch bond2OuterMatch;
CHECK(std::regex_match(bond2[0], bond2OuterMatch, regex));
CHECK(bond2OuterMatch.size() == 5);
std::smatch bond2InnerMatch;
CHECK(std::regex_match(bond2[1], bond2InnerMatch, regex));
CHECK(bond2InnerMatch.size() == 5);
RDGeom::Point2D bond0InnerCtd(
RDGeom::Point2D(std::stof(bond0InnerMatch[1]),
std::stof(bond0InnerMatch[2])) +
RDGeom::Point2D(std::stof(bond0InnerMatch[3]),
std::stof(bond0InnerMatch[4])) /
2.0);
RDGeom::Point2D bond0OuterCtd(
RDGeom::Point2D(std::stof(bond0OuterMatch[1]),
std::stof(bond0OuterMatch[2])) +
RDGeom::Point2D(std::stof(bond0OuterMatch[3]),
std::stof(bond0OuterMatch[4])) /
2.0);
RDGeom::Point2D bond2InnerCtd(
RDGeom::Point2D(std::stof(bond2InnerMatch[1]),
std::stof(bond2InnerMatch[2])) +
RDGeom::Point2D(std::stof(bond2InnerMatch[3]),
std::stof(bond2InnerMatch[4])) /
2.0);
RDGeom::Point2D bond2OuterCtd(
RDGeom::Point2D(std::stof(bond2OuterMatch[1]),
std::stof(bond2OuterMatch[2])) +
RDGeom::Point2D(std::stof(bond2OuterMatch[3]),
std::stof(bond2OuterMatch[4])) /
2.0);
// we look at the two double bonds of pyrrole
// we check that the ratio between the distance of the centroids of the
// outer bonds and the distance of the centroids of the inner bonds is at
// least 1.275, otherwise the inner bonds are not actually inside the ring.
float outerBondsDistance = (bond0OuterCtd - bond2OuterCtd).length();
float innerBondsDistance = (bond0InnerCtd - bond2InnerCtd).length();
CHECK(outerBondsDistance / innerBondsDistance > 1.275f);
}
}
TEST_CASE("draw atom list queries", "[extras]") {
SECTION("atom list") {
auto m = R"CTAB(
Mrv2102 02112115002D
0 0 0 0 0 999 V3000
M V30 BEGIN CTAB
M V30 COUNTS 3 3 0 0 0
M V30 BEGIN ATOM
M V30 1 [N,O,S] 9.2083 12.8058 0 0
M V30 2 C 8.4383 11.4721 0 0
M V30 3 C 9.9783 11.4721 0 0
M V30 END ATOM
M V30 BEGIN BOND
M V30 1 1 1 2
M V30 2 1 3 1
M V30 3 1 2 3
M V30 END BOND
M V30 END CTAB
M END
)CTAB"_ctab;
REQUIRE(m);
MolDraw2DSVG drawer(350, 300);
drawer.drawMolecule(*m, "atom list");
drawer.finishDrawing();
auto text = drawer.getDrawingText();
std::ofstream outs("testAtomLists-1.svg");
outs << text;
outs.close();
check_file_hash("testAtomLists-1.svg");
}
SECTION("NOT atom list") {
auto m = R"CTAB(
Mrv2102 02112115032D
0 0 0 0 0 999 V3000
M V30 BEGIN CTAB
M V30 COUNTS 3 3 0 0 0
M V30 BEGIN ATOM
M V30 1 "NOT [N,O,S]" 9.2083 12.8058 0 0
M V30 2 C 8.4383 11.4721 0 0
M V30 3 C 9.9783 11.4721 0 0
M V30 END ATOM
M V30 BEGIN BOND
M V30 1 1 1 2
M V30 2 1 3 1
M V30 3 1 2 3
M V30 END BOND
M V30 END CTAB
M END
)CTAB"_ctab;
REQUIRE(m);
MolDraw2DSVG drawer(350, 300);
drawer.drawMolecule(*m, "NOT atom list");
drawer.finishDrawing();
auto text = drawer.getDrawingText();
std::ofstream outs("testAtomLists-2.svg");
outs << text;
outs.close();
check_file_hash("testAtomLists-2.svg");
}
}
TEST_CASE("test the options that toggle isotope labels", "[drawing]") {
SECTION("test all permutations") {
auto m = "[1*]c1cc([2*])c([3*])c[14c]1"_smiles;
REQUIRE(m);
std::regex regex(R"regex(<text\s+.*>\d</text>)regex");
std::smatch match;
std::string line;
{
MolDraw2DSVG drawer(300, 300, -1, -1, true);
drawer.drawMolecule(*m);
drawer.finishDrawing();
std::string textIsoDummyIso = drawer.getDrawingText();
std::ofstream outs("testIsoDummyIso.svg");
outs << textIsoDummyIso;
outs.close();
check_file_hash("testIsoDummyIso.svg");
size_t nIsoDummyIso = std::distance(
std::sregex_token_iterator(textIsoDummyIso.begin(),
textIsoDummyIso.end(), regex),
std::sregex_token_iterator());
CHECK(nIsoDummyIso == 5);
}
{
MolDraw2DSVG drawer(300, 300, -1, -1, true);
drawer.drawOptions().isotopeLabels = false;
drawer.drawMolecule(*m);
drawer.finishDrawing();
std::string textNoIsoDummyIso = drawer.getDrawingText();
std::ofstream outs("testNoIsoDummyIso.svg");
outs << textNoIsoDummyIso;
outs.close();
check_file_hash("testNoIsoDummyIso.svg");
size_t nNoIsoDummyIso = std::distance(
std::sregex_token_iterator(textNoIsoDummyIso.begin(),
textNoIsoDummyIso.end(), regex, 1),
std::sregex_token_iterator());
CHECK(nNoIsoDummyIso == 3);
}
{
MolDraw2DSVG drawer(300, 300, -1, -1, true);
drawer.drawOptions().dummyIsotopeLabels = false;
drawer.drawMolecule(*m);
drawer.finishDrawing();
std::string textIsoNoDummyIso = drawer.getDrawingText();
std::ofstream outs("testIsoNoDummyIso.svg");
outs << textIsoNoDummyIso;
outs.close();
check_file_hash("testIsoNoDummyIso.svg");
size_t nIsoNoDummyIso = std::distance(
std::sregex_token_iterator(textIsoNoDummyIso.begin(),
textIsoNoDummyIso.end(), regex, 1),
std::sregex_token_iterator());
CHECK(nIsoNoDummyIso == 2);
}
{
MolDraw2DSVG drawer(300, 300, -1, -1, true);
drawer.drawOptions().isotopeLabels = false;
drawer.drawOptions().dummyIsotopeLabels = false;
drawer.drawMolecule(*m);
drawer.finishDrawing();
std::string textNoIsoNoDummyIso = drawer.getDrawingText();
std::ofstream outs("testNoIsoNoDummyIso.svg");
outs << textNoIsoNoDummyIso;
outs.close();
check_file_hash("testNoIsoNoDummyIso.svg");
size_t nNoIsoNoDummyIso = std::distance(
std::sregex_token_iterator(textNoIsoNoDummyIso.begin(),
textNoIsoNoDummyIso.end(), regex, 1),
std::sregex_token_iterator());
CHECK(nNoIsoNoDummyIso == 0);
}
}
SECTION("test that D/T show up even if isotope labels are hidden") {
auto m = "C([1H])([2H])([3H])[H]"_smiles;
std::regex regex(R"regex(<text\s+.*>[DT]</text>)regex");
std::smatch match;
REQUIRE(m);
std::string line;
MolDraw2DSVG drawer(300, 300, -1, -1, true);
drawer.drawOptions().isotopeLabels = false;
drawer.drawOptions().dummyIsotopeLabels = false;
drawer.drawOptions().atomLabelDeuteriumTritium = true;
drawer.drawMolecule(*m);
drawer.finishDrawing();
std::string textDeuteriumTritium = drawer.getDrawingText();
std::ofstream outs("testDeuteriumTritium.svg");
outs << textDeuteriumTritium;
outs.close();
check_file_hash("testDeuteriumTritium.svg");
size_t nDeuteriumTritium = std::distance(
std::sregex_token_iterator(textDeuteriumTritium.begin(),
textDeuteriumTritium.end(), regex, 1),
std::sregex_token_iterator());
CHECK(nDeuteriumTritium == 2);
}
}
TEST_CASE("draw hydrogen bonds", "[drawing]") {
SECTION("basics") {
auto m = R"CTAB(
Mrv2014 03022114422D
0 0 0 0 0 999 V3000
M V30 BEGIN CTAB
M V30 COUNTS 8 8 0 0 0
M V30 BEGIN ATOM
M V30 1 C -5.4583 -0.125 0 0
M V30 2 C -4.1247 0.645 0 0
M V30 3 C -2.791 -0.125 0 0
M V30 4 C -1.4573 0.645 0 0
M V30 5 O -2.791 -1.665 0 0
M V30 6 C -6.792 0.645 0 0
M V30 7 O -5.4583 -1.665 0 0
M V30 8 H -4.1247 -2.435 0 0
M V30 END ATOM
M V30 BEGIN BOND
M V30 1 1 1 2
M V30 2 1 2 3
M V30 3 1 3 4
M V30 4 2 3 5
M V30 5 1 1 6
M V30 6 1 1 7
M V30 7 1 7 8
M V30 8 10 5 8
M V30 END BOND
M V30 END CTAB
M END
)CTAB"_ctab;
REQUIRE(m);
MolDraw2DSVG drawer(300, 300);
drawer.drawMolecule(*m);
drawer.finishDrawing();
std::ofstream outs("testHydrogenBonds1.svg");
outs << drawer.getDrawingText();
outs.close();
check_file_hash("testHydrogenBonds1.svg");
}
SECTION("from CXSMILES") {
auto m = "CC1O[H]O=C(C)C1 |H:4.3|"_smiles;
REQUIRE(m);
MolDraw2DSVG drawer(300, 300);
drawer.drawMolecule(*m);
drawer.finishDrawing();
std::ofstream outs("testHydrogenBonds2.svg");
outs << drawer.getDrawingText();
outs.close();
check_file_hash("testHydrogenBonds2.svg");
}
}
TEST_CASE("github #3912: cannot draw atom lists from SMARTS", "[query][bug]") {
SECTION("original") {
auto m = "C-[N,O]"_smarts;
REQUIRE(m);
int panelWidth = -1;
int panelHeight = -1;
bool noFreeType = true;
MolDraw2DSVG drawer(300, 300, panelWidth, panelHeight, noFreeType);
drawer.drawMolecule(*m);
drawer.finishDrawing();
std::ofstream outs("testGithub3912.1.svg");
auto txt = drawer.getDrawingText();
outs << txt;
outs.close();
check_file_hash("testGithub3912.1.svg");
CHECK(txt.find(">N<") != std::string::npos);
CHECK(txt.find(">O<") != std::string::npos);
CHECK(txt.find(">!<") == std::string::npos);
}
SECTION("negated") {
auto m = "C-[N,O]"_smarts;
REQUIRE(m);
REQUIRE(m->getAtomWithIdx(1)->hasQuery());
m->getAtomWithIdx(1)->getQuery()->setNegation(true);
int panelWidth = -1;
int panelHeight = -1;
bool noFreeType = true;
MolDraw2DSVG drawer(300, 300, panelWidth, panelHeight, noFreeType);
drawer.drawMolecule(*m);
drawer.finishDrawing();
std::ofstream outs("testGithub3912.2.svg");
auto txt = drawer.getDrawingText();
outs << txt;
outs.close();
check_file_hash("testGithub3912.2.svg");
CHECK(txt.find(">N<") != std::string::npos);
CHECK(txt.find(">O<") != std::string::npos);
CHECK(txt.find(">!<") != std::string::npos);
}
}
TEST_CASE("github #2976: kekulizing reactions when drawing", "[reactions]") {
SECTION("basics") {
bool asSmiles = true;
std::unique_ptr<ChemicalReaction> rxn{
RxnSmartsToChemicalReaction("c1ccccc1>>c1ncccc1", nullptr, asSmiles)};
MolDraw2DSVG drawer(450, 200);
drawer.drawReaction(*rxn);
drawer.finishDrawing();
std::ofstream outs("testGithub2976.svg");
auto txt = drawer.getDrawingText();
outs << txt;
outs.close();
check_file_hash("testGithub2976.svg");
}
}
TEST_CASE("preserve Reaction coordinates", "[reactions]") {
SECTION("basics") {
std::string data = R"RXN($RXN
Mrv16822 031301211645
2 2 1
$MOL
Mrv1682203132116452D
3 2 0 0 0 0 999 V2000
-4.3304 2.5893 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0
-4.3304 1.7643 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
-3.5054 1.7643 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
1 2 1 0 0 0 0
2 3 1 0 0 0 0
M END
$MOL
Mrv1682203132116452D
2 1 0 0 0 0 999 V2000
-2.1652 2.6339 0.0000 N 0 0 0 0 0 0 0 0 0 0 0 0
-2.1652 1.8089 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
1 2 1 0 0 0 0
M END
$MOL
Mrv1682203132116452D
3 2 0 0 0 0 999 V2000
3.6109 1.9512 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
2.7859 1.9512 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
2.7859 2.7762 0.0000 N 0 0 0 0 0 0 0 0 0 0 0 0
2 1 1 0 0 0 0
3 2 1 0 0 0 0
M END
$MOL
Mrv1682203132116452D
2 1 0 0 0 0 999 V2000
4.9511 1.9959 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
4.9511 2.8209 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0
2 1 1 0 0 0 0
M END
$MOL
Mrv1682203132116452D
2 1 0 0 0 0 999 V2000
-0.3571 2.7232 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
-0.4003 3.5471 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0
1 2 1 0 0 0 0
M END
)RXN";
std::unique_ptr<ChemicalReaction> rxn{RxnBlockToChemicalReaction(data)};
MolDraw2DSVG drawer(450, 200);
drawer.drawReaction(*rxn);
drawer.finishDrawing();
std::ofstream outs("testReactionCoords.svg");
auto txt = drawer.getDrawingText();
outs << txt;
outs.close();
check_file_hash("testReactionCoords.svg");
// the reaction is drawn with some bonds vertical, make sure they remain
// vertical
{
std::regex regex("class='bond-0.*? d='M (\\d+\\.\\d+).* L (\\d+\\.\\d+)");
std::smatch bondMatch;
CHECK(std::regex_search(txt, bondMatch, regex));
CHECK(bondMatch.size() == 3); // match both halves of the bond
CHECK(bondMatch[1].str() == bondMatch[2].str());
}
{
std::regex regex("class='bond-2.*? d='M (\\d+\\.\\d+).* L (\\d+\\.\\d+)");
std::smatch bondMatch;
CHECK(std::regex_search(txt, bondMatch, regex));
CHECK(bondMatch.size() == 3); // match both halves of the bond
CHECK(bondMatch[1].str() == bondMatch[2].str());
}
{
std::regex regex("class='bond-4.*? d='M (\\d+\\.\\d+).* L (\\d+\\.\\d+)");
std::smatch bondMatch;
CHECK(std::regex_search(txt, bondMatch, regex));
CHECK(bondMatch.size() == 3); // match both halves of the bond
CHECK(bondMatch[1].str() == bondMatch[2].str());
}
}
}
TEST_CASE("support annotation colors", "[drawing]") {
SECTION("basics") {
auto m = "CCCO"_smiles;
REQUIRE(m);
int panelWidth = -1;
int panelHeight = -1;
bool noFreeType = true;
MolDraw2DSVG drawer(300, 300, panelWidth, panelHeight, noFreeType);
drawer.drawOptions().annotationColour = DrawColour{0, 0, 1, 1};
drawer.drawOptions().addAtomIndices = true;
drawer.drawMolecule(*m, "blue annotations");
drawer.finishDrawing();
std::ofstream outs("testAnnotationColors.svg");
auto txt = drawer.getDrawingText();
outs << txt;
outs.close();
check_file_hash("testAnnotationColors.svg");
CHECK(txt.find("fill:#0000FF' >2<") != std::string::npos);
}
}
TEST_CASE("Github #4238: prepareMolForDrawing and wavy bonds") {
{
auto mol = "CC=CC"_smiles;
REQUIRE(mol);
mol->getBondWithIdx(1)->setStereoAtoms(0, 3);
mol->getBondWithIdx(1)->setStereo(Bond::BondStereo::STEREOANY);
bool kekulize = true;
bool addChiralHs = true;
bool wedgeBonds = true;
bool forceCoords = true;
bool wavyBonds = false;
MolDraw2DUtils::prepareMolForDrawing(*mol, kekulize, addChiralHs,
wedgeBonds, forceCoords, wavyBonds);
CHECK(mol->getBondWithIdx(0)->getBondDir() == Bond::BondDir::NONE);
CHECK(mol->getBondWithIdx(1)->getStereo() == Bond::BondStereo::STEREOANY);
RWMol mol2(*mol);
wavyBonds = true;
MolDraw2DUtils::prepareMolForDrawing(mol2, kekulize, addChiralHs,
wedgeBonds, forceCoords, wavyBonds);
CHECK(mol2.getBondWithIdx(0)->getBondDir() == Bond::BondDir::UNKNOWN);
CHECK(mol2.getBondWithIdx(1)->getStereo() == Bond::BondStereo::STEREONONE);
MOL_PTR_VECT ms{mol.get(), &mol2};
{
MolDraw2DSVG drawer(500, 200, 250, 200);
// drawer.drawOptions().prepareMolsBeforeDrawing = false;
std::vector<std::string> legends = {"before", "after"};
drawer.drawMolecules(ms, &legends);
drawer.finishDrawing();
std::string text = drawer.getDrawingText();
std::ofstream outs("testGithub4238_1.svg");
outs << text;
outs.flush();
check_file_hash("testGithub4238_1.svg");
}
#ifdef RDK_BUILD_CAIRO_SUPPORT
{
MolDraw2DCairo drawer(500, 200, 250, 200);
std::vector<std::string> legends = {"before", "after"};
drawer.drawMolecules(ms, &legends);
drawer.finishDrawing();
drawer.writeDrawingText("testGithub4238_1.png");
check_file_hash("testGithub4238_1.png");
}
#endif
}
}
TEST_CASE("Github #4323: support providing RGBA colors") {
auto mol = "CCCO"_smiles;
REQUIRE(mol);
#ifdef RDK_BUILD_FREETYPE_SUPPORT
SECTION("with alpha") {
MolDraw2DSVG drawer(200, 150);
drawer.drawOptions().legendColour = DrawColour(1, 0, 1, 0.3);
drawer.drawOptions().backgroundColour = DrawColour(0.5, 0.5, 0.5, 0.3);
drawer.drawMolecule(*mol, "partially transparent legend/background");
drawer.finishDrawing();
std::string text = drawer.getDrawingText();
std::ofstream outs("testGithub4323_1.svg");
outs << text;
outs.flush();
// background
CHECK(text.find("fill:#7F7F7F4C;") != std::string::npos);
CHECK(text.find("fill:#7F7F7F;") == std::string::npos);
// legend
CHECK(text.find("fill='#FF00FF4C'") != std::string::npos);
CHECK(text.find("fill='#FF00FF'") == std::string::npos);
check_file_hash("testGithub4323_1.svg");
}
SECTION("without alpha") {
MolDraw2DSVG drawer(200, 150);
drawer.drawOptions().legendColour = DrawColour(1, 0, 1);
drawer.drawOptions().backgroundColour = DrawColour(0.5, 0.5, 0.5);
drawer.drawMolecule(*mol, "no transparency");
drawer.finishDrawing();
std::string text = drawer.getDrawingText();
std::ofstream outs("testGithub4323_2.svg");
outs << text;
outs.flush();
// background
CHECK(text.find("fill:#7F7F7F4C;") == std::string::npos);
CHECK(text.find("fill:#7F7F7F;") != std::string::npos);
// legend
CHECK(text.find("fill='#FF00FF4C'") == std::string::npos);
CHECK(text.find("fill='#FF00FF'") != std::string::npos);
check_file_hash("testGithub4323_2.svg");
}
#endif
SECTION("no FT with alpha") {
MolDraw2DSVG drawer(200, 150, -1, -1, NO_FREETYPE);
drawer.drawOptions().legendColour = DrawColour(1, 0, 1, 0.3);
drawer.drawOptions().backgroundColour = DrawColour(0.5, 0.5, 0.5, 0.3);
drawer.drawMolecule(*mol, "partially transparent legend/background");
drawer.finishDrawing();
std::string text = drawer.getDrawingText();
std::ofstream outs("testGithub4323_3.svg");
outs << text;
outs.flush();
// background
CHECK(text.find("fill:#7F7F7F4C;") != std::string::npos);
CHECK(text.find("fill:#7F7F7F;") == std::string::npos);
// legend
CHECK(text.find("fill:#FF00FF4C'") != std::string::npos);
CHECK(text.find("fill:#FF00FF'") == std::string::npos);
check_file_hash("testGithub4323_3.svg");
}
SECTION("no FT without alpha") {
MolDraw2DSVG drawer(200, 150, -1, -1, NO_FREETYPE);
drawer.drawOptions().legendColour = DrawColour(1, 0, 1);
drawer.drawOptions().backgroundColour = DrawColour(0.5, 0.5, 0.5);
drawer.drawMolecule(*mol, "no transparency");
drawer.finishDrawing();
std::string text = drawer.getDrawingText();
std::ofstream outs("testGithub4323_4.svg");
outs << text;
outs.flush();
// background
CHECK(text.find("fill:#7F7F7F4C;") == std::string::npos);
CHECK(text.find("fill:#7F7F7F;") != std::string::npos);
// legend
CHECK(text.find("fill:#FF00FF4C'") == std::string::npos);
CHECK(text.find("fill:#FF00FF'") != std::string::npos);
check_file_hash("testGithub4323_4.svg");
}
#ifdef RDK_BUILD_CAIRO_SUPPORT
#ifdef RDK_BUILD_FREETYPE_SUPPORT
SECTION("Cairo with alpha") {
MolDraw2DCairo drawer(200, 150);
drawer.drawOptions().legendColour = DrawColour(1, 0, 1, 0.3);
drawer.drawOptions().backgroundColour = DrawColour(0.5, 0.5, 0.5, 0.3);
drawer.drawMolecule(*mol, "partially transparent legend/background");
drawer.finishDrawing();
drawer.writeDrawingText("testGithub4323_1.png");
check_file_hash("testGithub4323_1.png");
}
#endif
SECTION("No FT Cairo with alpha") {
MolDraw2DCairo drawer(200, 150, -1, -1, NO_FREETYPE);
drawer.drawOptions().legendColour = DrawColour(1, 0, 1, 0.3);
drawer.drawOptions().backgroundColour = DrawColour(0.5, 0.5, 0.5, 0.3);
drawer.drawMolecule(*mol, "partially transparent legend/background");
drawer.finishDrawing();
drawer.writeDrawingText("testGithub4323_3.png");
check_file_hash("testGithub4323_3.png");
}
#endif
}
TEST_CASE(
"Github #4508: SubstanceGroup labels sometimes overlap with atoms in image "
"generation") {
SECTION("Basics") {
auto mol = R"CTAB(
Mrv2114 09132120172D
0 0 0 0 0 999 V3000
M V30 BEGIN CTAB
M V30 COUNTS 8 8 1 0 1
M V30 BEGIN ATOM
M V30 1 C -0.5878 0.8085 0 0
M V30 2 C -1.9434 0.078 0 0
M V30 3 C -1.9884 -1.4614 0 0
M V30 4 C -0.6778 -2.2702 0 0
M V30 5 C 0.6778 -1.5394 0 0
M V30 6 C 0.7228 -0.0001 0 0
M V30 7 N -0.5428 2.3478 0 0
M V30 8 O 1.9884 -2.3479 0 0
M V30 END ATOM
M V30 BEGIN BOND
M V30 1 2 1 2
M V30 2 1 2 3
M V30 3 2 3 4
M V30 4 1 4 5
M V30 5 2 5 6
M V30 6 1 6 1
M V30 7 1 1 7
M V30 8 1 5 8
M V30 END BOND
M V30 BEGIN SGROUP
M V30 1 DAT 0 ATOMS=(1 7) FIELDNAME=UV FIELDINFO=nm -
M V30 FIELDDISP=" 0.0000 0.0000 DRU ALL 0 0" -
M V30 MRV_FIELDDISP=0 FIELDDATA=340
M V30 END SGROUP
M V30 END CTAB
M END)CTAB"_ctab;
REQUIRE(mol);
{
MolDraw2DSVG drawer(300, 250);
drawer.drawMolecule(*mol, "data label with DRU");
drawer.finishDrawing();
std::string text = drawer.getDrawingText();
std::ofstream outs("testGithub4508_1.svg");
outs << text;
outs.flush();
check_file_hash("testGithub4508_1.svg");
}
// remove the sgroup-atom atom... the SGroup will not be drawn
auto &sgs = getSubstanceGroups(*mol);
CHECK(sgs.size() == 1);
sgs[0].setAtoms(std::vector<unsigned int>());
{
MolDraw2DSVG drawer(300, 250);
drawer.drawMolecule(*mol, "no data label drawn");
drawer.finishDrawing();
std::string text = drawer.getDrawingText();
std::ofstream outs("testGithub4508_1b.svg");
outs << text;
outs.flush();
check_file_hash("testGithub4508_1b.svg");
}
}
SECTION("Absolute") {
auto mol = R"CTAB(
Mrv2114 09132120172D
0 0 0 0 0 999 V3000
M V30 BEGIN CTAB
M V30 COUNTS 8 8 1 0 1
M V30 BEGIN ATOM
M V30 1 C -0.5878 0.8085 0 0
M V30 2 C -1.9434 0.078 0 0
M V30 3 C -1.9884 -1.4614 0 0
M V30 4 C -0.6778 -2.2702 0 0
M V30 5 C 0.6778 -1.5394 0 0
M V30 6 C 0.7228 -0.0001 0 0
M V30 7 N -0.5428 2.3478 0 0
M V30 8 O 1.9884 -2.3479 0 0
M V30 END ATOM
M V30 BEGIN BOND
M V30 1 2 1 2
M V30 2 1 2 3
M V30 3 2 3 4
M V30 4 1 4 5
M V30 5 2 5 6
M V30 6 1 6 1
M V30 7 1 1 7
M V30 8 1 5 8
M V30 END BOND
M V30 BEGIN SGROUP
M V30 1 DAT 0 ATOMS=(1 7) FIELDNAME=UV FIELDINFO=nm -
M V30 FIELDDISP=" 0.0000 0.0000 DAU ALL 0 0" -
M V30 MRV_FIELDDISP=0 FIELDDATA=340
M V30 END SGROUP
M V30 END CTAB
M END)CTAB"_ctab;
REQUIRE(mol);
{
MolDraw2DSVG drawer(300, 250);
drawer.drawMolecule(*mol, "data label with DAU\n(expect odd placement)");
drawer.finishDrawing();
std::string text = drawer.getDrawingText();
std::ofstream outs("testGithub4508_2.svg");
outs << text;
outs.flush();
check_file_hash("testGithub4508_2.svg");
}
// remove the sgroup-atom atom... the SGroup will still be drawn
auto &sgs = getSubstanceGroups(*mol);
CHECK(sgs.size() == 1);
sgs[0].setAtoms(std::vector<unsigned int>());
{
MolDraw2DSVG drawer(300, 250);
drawer.drawMolecule(*mol,
"DAU, no associated atom\n(expect odd placement)");
drawer.finishDrawing();
std::string text = drawer.getDrawingText();
std::ofstream outs("testGithub4508_2b.svg");
outs << text;
outs.flush();
check_file_hash("testGithub4508_2b.svg");
}
}
}
TEST_CASE("Github #4538 drawMolecules crash") {
auto m = "CCc1ccccc1"_smiles;
REQUIRE(m);
RDDepict::compute2DCoords(*m);
ROMol m1(*m);
ROMol m2(*m);
std::vector<ROMol *> mols{&m1, &m2};
SECTION("basics") {
MolDraw2DSVG drawer(500, 200, 250, 200);
drawer.drawOptions().prepareMolsBeforeDrawing = false;
drawer.drawMolecules(mols);
drawer.finishDrawing();
auto text = drawer.getDrawingText();
std::ofstream outs("testGithub4538.svg");
outs << text;
outs.flush();
check_file_hash("testGithub4538.svg");
}
}
TEST_CASE("dark mode mol drawing") {
SECTION("Basics") {
auto m =
"CS(=O)(=O)COC(=N)c1cc(Cl)cnc1[NH3+] |SgD:7:note:some extra text:=:::|"_smiles;
REQUIRE(m);
MolDraw2DSVG drawer(350, 300);
setDarkMode(drawer);
drawer.drawMolecule(*m, "dark mode!");
drawer.finishDrawing();
auto text = drawer.getDrawingText();
std::ofstream outs("testDarkMode.1.svg");
outs << text;
outs.flush();
check_file_hash("testDarkMode.1.svg");
}
}
TEST_CASE("monochrome mol drawing") {
SECTION("Basics") {
auto m =
"CS(=O)(=O)COC(=N)c1cc(Cl)cnc1[NH3+] |SgD:7:note:some extra text:=:::|"_smiles;
REQUIRE(m);
MolDraw2DSVG drawer(350, 300);
setMonochromeMode(drawer, DrawColour{0.1, 0.1, 0.6},
DrawColour{0.75, 0.75, 0.75});
drawer.drawMolecule(*m, "monochrome");
drawer.finishDrawing();
auto text = drawer.getDrawingText();
std::ofstream outs("testMonochrome.1.svg");
outs << text;
outs.flush();
check_file_hash("testMonochrome.1.svg");
}
SECTION("Basics inverted") {
auto m =
"CS(=O)(=O)COC(=N)c1cc(Cl)cnc1[NH3+] |SgD:7:note:some extra text:=:::|"_smiles;
REQUIRE(m);
MolDraw2DSVG drawer(350, 300);
setMonochromeMode(drawer, DrawColour{0.75, 0.75, 0.75},
DrawColour{0.1, 0.1, 0.6});
drawer.drawMolecule(*m, "monochrome");
drawer.finishDrawing();
auto text = drawer.getDrawingText();
std::ofstream outs("testMonochrome.2.svg");
outs << text;
outs.flush();
check_file_hash("testMonochrome.2.svg");
}
}
TEST_CASE("other palettes") {
auto m =
"CS(=O)(=O)COC(=N)c1c(I)c(Cl)c(Br)nc1[NH2+]CP(=O) |SgD:7:note:some extra text:=:::|"_smiles;
REQUIRE(m);
SECTION("Avalon") {
MolDraw2DSVG drawer(350, 300);
assignAvalonPalette(drawer.drawOptions().atomColourPalette);
drawer.drawMolecule(*m, "Avalon");
drawer.finishDrawing();
auto text = drawer.getDrawingText();
std::ofstream outs("testAvalon.1.svg");
outs << text;
outs.flush();
check_file_hash("testAvalon.1.svg");
}
SECTION("CDK") {
MolDraw2DSVG drawer(350, 300);
assignCDKPalette(drawer.drawOptions().atomColourPalette);
drawer.drawMolecule(*m, "CDK");
drawer.finishDrawing();
auto text = drawer.getDrawingText();
std::ofstream outs("testCDK.1.svg");
outs << text;
outs.flush();
check_file_hash("testCDK.1.svg");
}
}
TEST_CASE("SDD record parsing") {
auto mol = R"CTAB(
Mrv2008 11122110292D
6 6 0 0 0 0 999 V2000
9.3527 2.5661 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
8.6382 2.1536 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
8.6382 1.3286 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
9.3527 0.9161 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
10.0671 1.3286 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
10.0671 2.1536 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
1 2 1 0 0 0 0
2 3 2 0 0 0 0
3 4 1 0 0 0 0
4 5 2 0 0 0 0
5 6 1 0 0 0 0
1 6 2 0 0 0 0
M STY 1 1 DAT
M SLB 1 1 1
M SAL 1 1 1
M SDT 1 NAME
M SDD 1 -2345.1234-2345.1234 DR ALL 1 0
M SED 1 Hello World
M END
)CTAB"_ctab;
// SDD record has format
// M SDD sss xxxxx.xxxxyyyyy.yyyy eeefgh i jjjkkk ll m noo
MolDraw2DSVG drawer(350, 300, -1, -1, 1);
drawer.drawMolecule(*mol);
drawer.finishDrawing();
auto text = drawer.getDrawingText();
std::string name("Hello World");
for (auto &c : name) {
std::stringstream ss;
ss << " >" << c << "</text>";
auto pos = text.find(ss.str());
CHECK(pos != std::string::npos);
}
}
TEST_CASE("Github #4519 bad placement of datafield labels") {
auto mol1 = R"CTAB(
RDKit 2D
0 0 0 0 0 0 0 0 0 0999 V3000
M V30 BEGIN CTAB
M V30 COUNTS 5 4 1 0 0
M V30 BEGIN ATOM
M V30 1 C 0.000000 0.000000 0.000000 0
M V30 2 C 1.299038 0.750000 0.000000 0
M V30 3 C 2.598076 -0.000000 0.000000 0
M V30 4 C 1.299038 2.250000 0.000000 0
M V30 5 C 2.598076 3.000000 0.000000 0
M V30 END ATOM
M V30 BEGIN BOND
M V30 1 1 1 2
M V30 2 2 2 3
M V30 3 1 2 4
M V30 4 2 4 5
M V30 END BOND
M V30 BEGIN SGROUP
M V30 1 DAT 0 ATOMS=(5 2 4 5 3 1) FIELDNAME="Lambda Max" FIELDINFO=nm -
M V30 FIELDDATA="2222"
M V30 END SGROUP
M V30 END CTAB
M END)CTAB"_ctab;
REQUIRE(mol1);
auto mol2 = R"CTAB(
RDKit 2D
0 0 0 0 0 0 0 0 0 0999 V3000
M V30 BEGIN CTAB
M V30 COUNTS 8 8 1 0 0
M V30 BEGIN ATOM
M V30 1 N 3.000000 0.000000 0.000000 0
M V30 2 C 1.500000 0.000000 0.000000 0
M V30 3 C 0.750000 -1.299038 0.000000 0
M V30 4 C -0.750000 -1.299038 0.000000 0
M V30 5 C -1.500000 0.000000 0.000000 0
M V30 6 C -0.750000 1.299038 0.000000 0
M V30 7 O -1.500000 2.598076 0.000000 0
M V30 8 C 0.750000 1.299038 0.000000 0
M V30 END ATOM
M V30 BEGIN BOND
M V30 1 1 1 2
M V30 2 2 2 3
M V30 3 1 3 4
M V30 4 2 4 5
M V30 5 1 5 6
M V30 6 1 6 7
M V30 7 2 6 8
M V30 8 1 8 2
M V30 END BOND
M V30 BEGIN SGROUP
M V30 1 DAT 0 ATOMS=(1 1) FIELDNAME=UV FIELDINFO=nm -
M V30 FIELDDISP=" 0.0000 0.0000 DR ALL 0 0" -
M V30 FIELDDATA="340"
M V30 END SGROUP
M V30 END CTAB
M END)CTAB"_ctab;
REQUIRE(mol2);
auto mol3 = R"CTAB(
RDKit 2D
0 0 0 0 0 0 0 0 0 0999 V3000
M V30 BEGIN CTAB
M V30 COUNTS 4 3 1 0 0
M V30 BEGIN ATOM
M V30 1 C -0.750000 -1.299038 0.000000 0
M V30 2 C 0.000000 0.000000 0.000000 0
M V30 3 C 1.500000 0.000000 0.000000 0
M V30 4 C 2.250000 1.299038 0.000000 0
M V30 END ATOM
M V30 BEGIN BOND
M V30 1 1 1 2
M V30 2 2 2 3
M V30 3 1 3 4
M V30 END BOND
M V30 BEGIN SGROUP
M V30 1 DAT 0 ATOMS=(1 3) FIELDNAME=Stereo -
M V30 FIELDDATA="Cis"
M V30 END SGROUP
M V30 END CTAB
M END)CTAB"_ctab;
REQUIRE(mol3);
std::vector<std::string> legends = {
"datafield label bad placement1", "datafield label bad placement2",
"datafield label bad placement3"}; // std::vector<std::string> legends =
// {"datafield label bad
// placement2"};
{
MolDraw2DSVG drawer(300, 250);
drawer.drawMolecule(*mol1, legends[0]);
drawer.finishDrawing();
std::string text = drawer.getDrawingText();
std::ofstream outs("testGithub4519_1.svg");
outs << text;
outs.flush();
check_file_hash("testGithub4519_1.svg");
}
{
MolDraw2DSVG drawer(300, 250);
drawer.drawMolecule(*mol2, legends[1]);
drawer.finishDrawing();
std::string text = drawer.getDrawingText();
std::ofstream outs("testGithub4519_2.svg");
outs << text;
outs.flush();
check_file_hash("testGithub4519_2.svg");
}
{
MolDraw2DSVG drawer(300, 250);
drawer.drawMolecule(*mol3, legends[2]);
drawer.finishDrawing();
std::string text = drawer.getDrawingText();
std::ofstream outs("testGithub4519_3.svg");
outs << text;
outs.flush();
check_file_hash("testGithub4519_3.svg");
}
{
std::vector<ROMol *> mols;
mols.push_back(mol1.get());
mols.push_back(mol2.get());
mols.push_back(mol3.get());
MolDraw2DSVG drawer(900, 250, 300, 250);
drawer.drawMolecules(mols, &legends);
drawer.finishDrawing();
std::string text = drawer.getDrawingText();
std::ofstream outs("testGithub4519_4.svg");
outs << text;
outs.flush();
outs.close();
check_file_hash("testGithub4519_4.svg");
}
}
TEST_CASE("changing baseFontSize") {
RDDepict::preferCoordGen = false;
auto mol1 =
"CC(C)C[C@H](NC(=O)[C@H](CCCCN)NC(=O)[C@H](CS)NC(=O)CNC(=O)[C@H](C)NC(=O)[C@H](CCCCN)NC(=O)[C@H](CC(C)C)NC(=O)CNC(=O)[C@H](C)NC(=O)[C@H](CS)NC(=O)[C@H](CCCCN)NC(=O)[C@H](C)NC(=O)[C@@H](NC(=O)[C@H](CS)NC(=O)CNC(=O)[C@H](C)NC(=O)[C@H](CCCCN)NC(=O)CNC(=O)[C@H](C)NC(=O)[C@H](CCCCN)NC(=O)[C@H](C)N)[C@@H](C)O)C(=O)O"_smiles;
REQUIRE(mol1);
MolDraw2DUtils::prepareMolForDrawing(*mol1);
auto mol2 = "C[C@H](N)C(=O)N[C@@H](CCCCN)C(=O)N[C@@H](C)C(=O)NCC(=O)O"_smiles;
REQUIRE(mol2);
MolDraw2DUtils::prepareMolForDrawing(*mol2);
SECTION("basics-large") {
MolDraw2DSVG drawer(350, 300, -1, -1, 1);
drawer.drawMolecule(*mol1);
drawer.finishDrawing();
CHECK(drawer.fontSize() == Catch::Approx(6.0).margin(0.1));
auto text = drawer.getDrawingText();
std::ofstream outs("testBaseFontSize.1a.svg");
outs << text;
outs.flush();
check_file_hash("testBaseFontSize.1a.svg");
}
SECTION("increase size - large") {
// here we change the base font size, but it doesn't matter since the
// structure is big enough we end up stuck with the minimum font size.
MolDraw2DSVG drawer(350, 300, -1, -1, 1);
drawer.drawOptions().baseFontSize = 0.9;
drawer.drawMolecule(*mol1);
drawer.finishDrawing();
CHECK(drawer.fontSize() == Catch::Approx(5.5).margin(.1));
auto text = drawer.getDrawingText();
std::ofstream outs("testBaseFontSize.1b.svg");
outs << text;
outs.flush();
check_file_hash("testBaseFontSize.1b.svg");
}
SECTION("basics-small") {
MolDraw2DSVG drawer(350, 300, -1, -1, 1);
drawer.drawMolecule(*mol2);
drawer.finishDrawing();
CHECK(drawer.fontSize() == Catch::Approx(14.0).margin(0.1));
auto text = drawer.getDrawingText();
std::ofstream outs("testBaseFontSize.2a.svg");
outs << text;
outs.flush();
check_file_hash("testBaseFontSize.2a.svg");
}
SECTION("increase size - smaller") {
MolDraw2DSVG drawer(350, 300, -1, -1, 1);
drawer.drawOptions().baseFontSize = 0.9;
drawer.drawMolecule(*mol2);
drawer.finishDrawing();
CHECK(drawer.fontSize() == Catch::Approx(20.25).margin(0.1));
auto text = drawer.getDrawingText();
std::ofstream outs("testBaseFontSize.2b.svg");
outs << text;
outs.flush();
check_file_hash("testBaseFontSize.2b.svg");
}
}
TEST_CASE("flexicanvas: set canvas size automatically") {
// note that these examples use Freetype if it's available.
auto mol1 = "CCN(CC)CCn1nc2c3ccccc3sc3c(CNS(C)(=O)=O)ccc1c32"_smiles;
REQUIRE(mol1);
MolDraw2DUtils::prepareMolForDrawing(*mol1);
auto mol2 = R"CTAB(
Mrv2108 11192104292D
0 0 0 0 0 999 V3000
M V30 BEGIN CTAB
M V30 COUNTS 5 5 0 0 0
M V30 BEGIN ATOM
M V30 1 C -5.2 -1.4 0 0
M V30 2 O -5.2 -2.8 0 0
M V30 3 C -3.7 -1.4 0 0
M V30 4 C -3.7 -2.8 0 0 CFG=1
M V30 5 N -2.5994 -3.9839 0 0
M V30 END ATOM
M V30 BEGIN BOND
M V30 1 1 1 2
M V30 2 1 1 3
M V30 3 1 2 4
M V30 4 1 3 4
M V30 5 1 4 5 CFG=1
M V30 END BOND
M V30 END CTAB
M END
)CTAB"_ctab;
REQUIRE(mol2);
MolDraw2DUtils::prepareMolForDrawing(*mol2);
SECTION("fixed canvas") {
MolDraw2DSVG drawer(308, 223, -1, -1);
drawer.drawMolecule(*mol1);
drawer.finishDrawing();
auto text = drawer.getDrawingText();
std::ofstream outs("testFlexiCanvas.1a.svg");
outs << text;
outs.flush();
check_file_hash("testFlexiCanvas.1a.svg");
}
SECTION("flexicanvas1") {
MolDraw2DSVG drawer(-1, -1, -1, -1);
drawer.drawMolecule(*mol1);
drawer.finishDrawing();
auto text = drawer.getDrawingText();
std::ofstream outs("testFlexiCanvas.1b.svg");
outs << text;
outs.flush();
check_file_hash("testFlexiCanvas.1b.svg");
}
SECTION("flexicanvas1") {
MolDraw2DSVG drawer(-1, -1, -1, -1);
drawer.drawOptions().scalingFactor = 30;
drawer.drawOptions().baseFontSize = 0.6;
drawer.drawMolecule(*mol1);
drawer.finishDrawing();
auto text = drawer.getDrawingText();
std::ofstream outs("testFlexiCanvas.1c.svg");
outs << text;
outs.flush();
check_file_hash("testFlexiCanvas.1c.svg");
}
SECTION("flexicanvas1") {
MolDraw2DSVG drawer(-1, -1, -1, -1);
drawer.drawOptions().scalingFactor = 30;
drawer.drawOptions().fixedFontSize = 32;
drawer.drawMolecule(*mol1);
drawer.finishDrawing();
CHECK(drawer.fontSize() == Catch::Approx(32).margin(0.1));
auto text = drawer.getDrawingText();
std::ofstream outs("testFlexiCanvas.1d.svg");
outs << text;
outs.flush();
check_file_hash("testFlexiCanvas.1d.svg");
}
SECTION("square") {
MolDraw2DSVG drawer(-1, -1, -1, -1);
drawer.drawOptions().baseFontSize = 0.8;
drawer.drawMolecule(*mol2);
drawer.finishDrawing();
auto text = drawer.getDrawingText();
std::ofstream outs("testFlexiCanvas.2.svg");
outs << text;
outs.flush();
check_file_hash("testFlexiCanvas.2.svg");
}
#ifdef RDK_BUILD_CAIRO_SUPPORT
SECTION("square PNG no freetype") {
MolDraw2DCairo drawer(-1, -1, -1, -1, true);
drawer.drawOptions().baseFontSize = 0.8;
drawer.drawMolecule(*mol2);
drawer.finishDrawing();
auto text = drawer.getDrawingText();
std::ofstream outs("testFlexiCanvas.2a.png");
outs << text;
outs.flush();
check_file_hash("testFlexiCanvas.2a.png");
}
SECTION("square PNG with freetype") {
MolDraw2DCairo drawer(-1, -1, -1, -1, false);
drawer.drawOptions().baseFontSize = 0.8;
drawer.drawMolecule(*mol2);
drawer.finishDrawing();
auto text = drawer.getDrawingText();
std::ofstream outs("testFlexiCanvas.2b.png");
outs << text;
outs.flush();
check_file_hash("testFlexiCanvas.2b.png");
}
#endif
// semiflexicanvas - with freetype
SECTION("semiflexicanvas1") {
MolDraw2DSVG drawer(308, -1, -1, -1, false);
drawer.drawOptions().scalingFactor = 30;
drawer.drawOptions().baseFontSize = 0.6;
drawer.drawMolecule(*mol1);
drawer.finishDrawing();
auto text = drawer.getDrawingText();
std::ofstream outs("testSemiFlexiCanvas.1a.svg");
outs << text;
outs.flush();
check_file_hash("testSemiFlexiCanvas.1a.svg");
}
SECTION("semiflexicanvas2") {
MolDraw2DSVG drawer(-1, 223, -1, -1, false);
drawer.drawOptions().scalingFactor = 30;
drawer.drawOptions().baseFontSize = 0.6;
drawer.drawMolecule(*mol1);
drawer.finishDrawing();
auto text = drawer.getDrawingText();
std::ofstream outs("testSemiFlexiCanvas.1b.svg");
outs << text;
outs.flush();
check_file_hash("testSemiFlexiCanvas.1b.svg");
}
SECTION("semiflexicanvas3") {
auto mol3 = "ON"_smiles;
REQUIRE(mol3);
MolDraw2DSVG drawer(-1, 150, -1, -1, false);
drawer.drawOptions().scalingFactor = 30;
drawer.drawOptions().baseFontSize = 0.6;
drawer.drawMolecule(*mol3);
drawer.finishDrawing();
auto text = drawer.getDrawingText();
std::ofstream outs("testSemiFlexiCanvas.1c.svg");
outs << text;
outs.flush();
check_file_hash("testSemiFlexiCanvas.1c.svg");
}
SECTION("reaction") {
std::unique_ptr<ChemicalReaction> rxn(RxnSmartsToChemicalReaction(
"[N:1]-[C:2]-[C:3](=[O:4])-[O:5].[N:6]-[C:7]-[C:8](=[O:9])-[O:10]>>[N:"
"1]1-[C:2]-[C:3](=[O:4])-[N:6]-[C:7]-[C:8]-1=[O:9].[O:5]=[O:10]"));
MolDraw2DSVG drawer(-1, -1, -1, -1, true);
drawer.drawReaction(*rxn);
drawer.finishDrawing();
auto text = drawer.getDrawingText();
std::ofstream outs("testFlexiCanvas.3.svg");
outs << text;
outs.flush();
check_file_hash("testFlexiCanvas.3.svg");
}
SECTION("data labels") {
auto mol1 = R"CTAB(
RDKit 2D
0 0 0 0 0 0 0 0 0 0999 V3000
M V30 BEGIN CTAB
M V30 COUNTS 5 4 1 0 0
M V30 BEGIN ATOM
M V30 1 C 0.000000 0.000000 0.000000 0
M V30 2 C 1.299038 0.750000 0.000000 0
M V30 3 C 2.598076 -0.000000 0.000000 0
M V30 4 C 1.299038 2.250000 0.000000 0
M V30 5 C 2.598076 3.000000 0.000000 0
M V30 END ATOM
M V30 BEGIN BOND
M V30 1 1 1 2
M V30 2 2 2 3
M V30 3 1 2 4
M V30 4 2 4 5
M V30 END BOND
M V30 BEGIN SGROUP
M V30 1 DAT 0 ATOMS=(5 2 4 5 3 1) FIELDNAME="Lambda Max" FIELDINFO=nm -
M V30 FIELDDATA="2222"
M V30 END SGROUP
M V30 END CTAB
M END)CTAB"_ctab;
REQUIRE(mol1);
{
MolDraw2DSVG drawer(-1, -1);
drawer.drawMolecule(*mol1);
drawer.finishDrawing();
auto text = drawer.getDrawingText();
std::ofstream outs("testFlexiCanvas.4a.svg");
outs << text;
outs.flush();
check_file_hash("testFlexiCanvas.4a.svg");
}
{
MolDraw2DSVG drawer(-1, -1);
drawer.drawMolecule(*mol1, "legendary");
drawer.finishDrawing();
auto text = drawer.getDrawingText();
std::ofstream outs("testFlexiCanvas.4b.svg");
outs << text;
outs.flush();
check_file_hash("testFlexiCanvas.4b.svg");
}
{
MolDraw2DSVG drawer(-1, -1);
drawer.drawMolecule(*mol1, "doubly\nlegendary");
drawer.finishDrawing();
auto text = drawer.getDrawingText();
std::ofstream outs("testFlexiCanvas.4c.svg");
outs << text;
outs.flush();
check_file_hash("testFlexiCanvas.4c.svg");
}
{
MolDraw2DSVG drawer(-1, -1);
drawer.drawOptions().legendFraction = 0.25;
drawer.drawOptions().legendFontSize = 32;
drawer.drawMolecule(*mol1, "Hugely\nLegendary");
drawer.finishDrawing();
auto text = drawer.getDrawingText();
std::ofstream outs("testFlexiCanvas.4d.svg");
outs << text;
outs.flush();
check_file_hash("testFlexiCanvas.4d.svg");
}
}
SECTION("including legends") {
// add an atomNote so that we can compare font sizes
mol1->getAtomWithIdx(0)->setProp(common_properties::atomNote, "n1");
{
MolDraw2DSVG drawer(-1, -1);
drawer.drawMolecule(*mol1, "legend");
drawer.finishDrawing();
auto text = drawer.getDrawingText();
std::ofstream outs("testFlexiCanvas.5a.svg");
outs << text;
outs.flush();
check_file_hash("testFlexiCanvas.5a.svg");
}
{
MolDraw2DSVG drawer(-1, -1);
drawer.drawMolecule(*mol1, "legend\nwith two lines");
drawer.finishDrawing();
auto text = drawer.getDrawingText();
std::ofstream outs("testFlexiCanvas.5b.svg");
outs << text;
outs.flush();
check_file_hash("testFlexiCanvas.5b.svg");
}
{
MolDraw2DSVG drawer(-1, -1);
drawer.drawOptions().scalingFactor = 45;
drawer.drawMolecule(*mol1, "legend");
drawer.finishDrawing();
auto text = drawer.getDrawingText();
std::ofstream outs("testFlexiCanvas.5c.svg");
outs << text;
outs.flush();
check_file_hash("testFlexiCanvas.5c.svg");
}
{
MolDraw2DSVG drawer(-1, -1);
drawer.drawOptions().scalingFactor = 10;
drawer.drawMolecule(*mol1, "legend");
drawer.finishDrawing();
auto text = drawer.getDrawingText();
std::ofstream outs("testFlexiCanvas.5d.svg");
outs << text;
outs.flush();
check_file_hash("testFlexiCanvas.5d.svg");
}
}
SECTION("partially flexicanvas (height) + legends") {
// add an atomNote so that we can compare font sizes
mol1->getAtomWithIdx(0)->setProp(common_properties::atomNote, "n1");
{
MolDraw2DSVG drawer(-1, 200);
drawer.drawMolecule(*mol1, "legend");
drawer.finishDrawing();
auto text = drawer.getDrawingText();
std::ofstream outs("testFlexiCanvas.6a.svg");
outs << text;
outs.flush();
check_file_hash("testFlexiCanvas.6a.svg");
}
{
MolDraw2DSVG drawer(-1, 200);
drawer.drawMolecule(*mol1, "legend\nwith two lines");
drawer.finishDrawing();
auto text = drawer.getDrawingText();
std::ofstream outs("testFlexiCanvas.6b.svg");
outs << text;
outs.flush();
check_file_hash("testFlexiCanvas.6b.svg");
}
{
MolDraw2DSVG drawer(-1, 200);
drawer.drawOptions().scalingFactor = 45;
drawer.drawMolecule(*mol1, "legend");
drawer.finishDrawing();
auto text = drawer.getDrawingText();
std::ofstream outs("testFlexiCanvas.6c.svg");
outs << text;
outs.flush();
check_file_hash("testFlexiCanvas.6c.svg");
}
{
MolDraw2DSVG drawer(-1, 200);
drawer.drawOptions().scalingFactor = 10;
drawer.drawMolecule(*mol1, "legend");
drawer.finishDrawing();
auto text = drawer.getDrawingText();
std::ofstream outs("testFlexiCanvas.6d.svg");
outs << text;
outs.flush();
check_file_hash("testFlexiCanvas.6d.svg");
}
}
SECTION("partially flexicanvas (width) + legends") {
// add an atomNote so that we can compare font sizes
mol1->getAtomWithIdx(0)->setProp(common_properties::atomNote, "n1");
{
MolDraw2DSVG drawer(300, -1);
drawer.drawMolecule(*mol1, "legend");
drawer.finishDrawing();
auto text = drawer.getDrawingText();
std::ofstream outs("testFlexiCanvas.7a.svg");
outs << text;
outs.flush();
check_file_hash("testFlexiCanvas.7a.svg");
}
{
MolDraw2DSVG drawer(300, -1);
drawer.drawMolecule(*mol1, "legend\nwith two lines");
drawer.finishDrawing();
auto text = drawer.getDrawingText();
std::ofstream outs("testFlexiCanvas.7b.svg");
outs << text;
outs.flush();
check_file_hash("testFlexiCanvas.7b.svg");
}
{
MolDraw2DSVG drawer(300, -1);
drawer.drawOptions().scalingFactor = 45;
drawer.drawMolecule(*mol1, "legend");
drawer.finishDrawing();
auto text = drawer.getDrawingText();
std::ofstream outs("testFlexiCanvas.7c.svg");
outs << text;
outs.flush();
check_file_hash("testFlexiCanvas.7c.svg");
}
{
MolDraw2DSVG drawer(300, -1);
drawer.drawOptions().scalingFactor = 10;
drawer.drawMolecule(*mol1, "legend");
drawer.finishDrawing();
auto text = drawer.getDrawingText();
std::ofstream outs("testFlexiCanvas.7d.svg");
outs << text;
outs.flush();
check_file_hash("testFlexiCanvas.7d.svg");
}
}
}
TEST_CASE("Github #4764") {
SECTION("basics") {
auto mol = "c1ccccc1-C1CCCCC1"_smiles;
REQUIRE(mol);
std::vector<int> highlights{6, 7, 8, 9, 10, 11};
{
MolDraw2DSVG drawer(200, 150);
drawer.drawMolecule(*mol, "highlight", &highlights);
drawer.finishDrawing();
auto text = drawer.getDrawingText();
std::ofstream outs("testGithub4764.sz1.svg");
outs << text;
outs.flush();
check_file_hash("testGithub4764.sz1.svg");
}
{
MolDraw2DSVG drawer(400, 350);
drawer.drawMolecule(*mol, "highlight", &highlights);
drawer.finishDrawing();
auto text = drawer.getDrawingText();
std::ofstream outs("testGithub4764.sz2.svg");
outs << text;
outs.flush();
check_file_hash("testGithub4764.sz2.svg");
}
{
MolDraw2DSVG drawer(800, 700);
drawer.drawMolecule(*mol, "highlight", &highlights);
drawer.finishDrawing();
auto text = drawer.getDrawingText();
std::ofstream outs("testGithub4764.sz3.svg");
outs << text;
outs.flush();
check_file_hash("testGithub4764.sz3.svg");
}
#ifdef RDK_BUILD_CAIRO_SUPPORT
{
MolDraw2DCairo drawer(200, 150);
drawer.drawMolecule(*mol, "highlight", &highlights);
drawer.finishDrawing();
drawer.writeDrawingText("testGithub4764.sz1.png");
check_file_hash("testGithub4764.sz1.png");
}
{
MolDraw2DCairo drawer(400, 350);
drawer.drawMolecule(*mol, "highlight", &highlights);
drawer.finishDrawing();
drawer.writeDrawingText("testGithub4764.sz2.png");
check_file_hash("testGithub4764.sz2.png");
}
{
MolDraw2DCairo drawer(800, 700);
drawer.drawMolecule(*mol, "highlight", &highlights);
drawer.finishDrawing();
drawer.writeDrawingText("testGithub4764.sz3.png");
check_file_hash("testGithub4764.sz3.png");
}
#endif
// check_file_hash("testGithub4538.svg");
}
}
TEST_CASE("drawArc starting from wrong angle") {
SECTION("basics") {
auto mol = R"CTAB(
RDKit 2D
9 9 0 0 0 0 0 0 0 0999 V2000
-1.2135 -0.7027 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
-0.0000 -1.5844 0.0000 N 0 0 0 0 0 0 0 0 0 0 0 0
1.2135 -0.7027 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
0.7500 0.7238 0.0000 N 0 0 0 0 0 0 0 0 0 0 0 0
-0.7500 0.7238 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
-1.6317 1.9374 0.0000 F 0 0 0 0 0 0 0 0 0 0 0 0
-2.6401 -1.1663 0.0000 F 0 0 0 0 0 0 0 0 0 0 0 0
2.6401 -1.1663 0.0000 F 0 0 0 0 0 0 0 0 0 0 0 0
1.6317 1.9374 0.0000 F 0 0 0 0 0 0 0 0 0 0 0 0
1 2 1 0
2 3 2 0
3 4 1 0
4 5 1 0
5 6 1 0
5 1 2 0
1 7 1 0
3 8 1 0
4 9 1 0
M END)CTAB"_ctab;
REQUIRE(mol);
{
MolDraw2DSVG drawer(400, 350);
drawer.drawOptions().noAtomLabels = true;
drawer.drawMolecule(*mol, "drawArc");
drawer.setFillPolys(false);
drawer.setColour({1, 0, 0});
drawer.drawArc(mol->getConformer().getAtomPos(3), 0.3, -72, 54);
drawer.drawArc(mol->getConformer().getAtomPos(0), 0.3, -162, -36);
drawer.drawArc(mol->getConformer().getAtomPos(4), 0.3, 126, 252);
drawer.drawArc(mol->getConformer().getAtomPos(2), 0.3, -18, 108);
drawer.finishDrawing();
auto text = drawer.getDrawingText();
std::ofstream outs("testDrawArc1.svg");
outs << text;
outs.flush();
check_file_hash("testDrawArc1.svg");
}
}
}
TEST_CASE("wedged bonds to metals drawn in the wrong direction") {
SECTION("basics") {
auto m = R"CTAB(
Mrv2108 01092205442D
0 0 0 0 0 999 V3000
M V30 BEGIN CTAB
M V30 COUNTS 5 4 0 0 0
M V30 BEGIN ATOM
M V30 1 F 10.6667 -0.75 0 0
M V30 2 Pt 10.6667 -2.29 0 0 CFG=1
M V30 3 Cl 12.2067 -2.29 0 0
M V30 4 C 10.6667 -3.83 0 0
M V30 5 O 9.1267 -2.29 0 0
M V30 END ATOM
M V30 BEGIN BOND
M V30 1 1 1 2
M V30 2 1 2 3
M V30 3 1 2 4 CFG=1
M V30 4 1 2 5 CFG=3
M V30 END BOND
M V30 END CTAB
M END)CTAB"_ctab;
m->getBondWithIdx(2)->setBondDir(Bond::BondDir::BEGINWEDGE);
m->getBondWithIdx(3)->setBondDir(Bond::BondDir::BEGINDASH);
MolDraw2DSVG drawer(250, 200);
assignBWPalette(drawer.drawOptions().atomColourPalette);
drawer.drawMolecule(*m, "check wedges");
drawer.finishDrawing();
auto text = drawer.getDrawingText();
std::ofstream outs("testMetalWedges.svg");
outs << text;
outs.flush();
check_file_hash("testMetalWedges.svg");
}
}
TEST_CASE("vary proportion of panel for legend", "[drawing]") {
SECTION("basics") {
auto m1 = "C1N[C@@H]2OCC12"_smiles;
REQUIRE(m1);
// These look a bit pants with NO_FREETYPE=true, but much better with
// Freetype.
{
// default legend
MolDraw2DSVG drawer(200, 200, -1, -1, NO_FREETYPE);
MolDraw2DUtils::prepareAndDrawMolecule(drawer, *m1, "default legend");
drawer.finishDrawing();
auto text = drawer.getDrawingText();
std::ofstream outs("testVariableLegend_1.svg");
outs << text;
outs.flush();
CHECK(text.find("<text x='34.5' y='190.0' class='legend' "
"style='font-size:16px;") != std::string::npos);
check_file_hash("testVariableLegend_1.svg");
}
{
// 1/4 of panel
MolDraw2DSVG drawer(200, 200, -1, -1, NO_FREETYPE);
drawer.drawOptions().legendFraction = 0.25;
drawer.drawOptions().legendFontSize = 32;
MolDraw2DUtils::prepareAndDrawMolecule(drawer, *m1, "massive legend");
drawer.finishDrawing();
auto text = drawer.getDrawingText();
std::ofstream outs("testVariableLegend_2.svg");
outs << text;
outs.flush();
CHECK(text.find("<text x='2.8' y='190.0' class='legend' "
"style='font-size:31px;") != std::string::npos);
check_file_hash("testVariableLegend_2.svg");
}
{
// tiny
MolDraw2DSVG drawer(200, 200, -1, -1, NO_FREETYPE);
drawer.drawOptions().legendFraction = 0.05;
MolDraw2DUtils::prepareAndDrawMolecule(drawer, *m1, "small legend");
drawer.finishDrawing();
auto text = drawer.getDrawingText();
std::ofstream outs("testVariableLegend_3.svg");
outs << text;
outs.flush();
CHECK(text.find("<text x='72.4' y='190.0' class='legend' "
"style='font-size:11px;") != std::string::npos);
check_file_hash("testVariableLegend_3.svg");
}
}
}
TEST_CASE(
"Github 5061 - draw reaction with no reagents and scaleBondWidth true") {
SECTION("basics") {
std::string data = R"RXN($RXN
Mrv16425 091201171606
0 1
$MOL
Mrv1642509121716062D
2 1 0 0 0 0 999 V2000
3.5357 0.0000 0.0000 R# 0 0 0 0 0 0 0 0 0 0 0 0
2.7107 0.0000 0.0000 R# 0 0 0 0 0 0 0 0 0 0 0 0
1 2 1 0 0 0 0
M RGP 2 1 1 2 2
M END)RXN";
{
std::unique_ptr<ChemicalReaction> rxn{RxnBlockToChemicalReaction(data)};
MolDraw2DSVG drawer(450, 200);
drawer.drawOptions().scaleBondWidth = true;
drawer.drawReaction(*rxn);
drawer.finishDrawing();
auto text = drawer.getDrawingText();
std::ofstream outs("testGithub_5061.svg");
outs << text;
outs.flush();
check_file_hash("testGithub_5061.svg");
}
}
}
TEST_CASE("Github 5185 - don't draw atom indices between double bond") {
SECTION("basics") {
auto m1 = "OC(=O)CCCC(=O)O"_smiles;
REQUIRE(m1);
{
// default legend
MolDraw2DSVG drawer(400, 200, -1, -1);
drawer.drawOptions().addAtomIndices = true;
MolDraw2DUtils::prepareAndDrawMolecule(drawer, *m1);
drawer.finishDrawing();
auto text = drawer.getDrawingText();
std::ofstream outs("testGithub_5185.svg");
outs << text;
outs.flush();
#ifdef RDK_BUILD_FREETYPE_SUPPORT
// the 2nd note
CHECK(text.find("<path class='note' d='M 94.4 129.6") !=
std::string::npos);
check_file_hash("testGithub_5185.svg");
#else
CHECK(text.find("<text x='91.5' y='130.0' class='note' ") !=
std::string::npos);
#endif
}
}
}
TEST_CASE(
"Github 5259 - drawReaction should not fail when prepareMolsBeforeDrawing "
"is false") {
SECTION("basics") {
auto rxn = "[CH3:1][OH:2]>>[CH2:1]=[OH0:2]"_rxnsmarts;
REQUIRE(rxn);
MolDraw2DSVG drawer(400, 200, -1, -1);
drawer.drawOptions().prepareMolsBeforeDrawing = false;
REQUIRE_NOTHROW(drawer.drawReaction(*rxn));
}
}
TEST_CASE("Github 5269 - bad index positions with highlights") {
SECTION("basics") {
auto m1 = "CC(=O)Oc1c(C(=O)O)cccc1"_smiles;
auto q1 = "CC(=O)Oc1c(C(=O)O)cccc1"_smarts;
REQUIRE(m1);
REQUIRE(q1);
{
std::vector<int> hit_atoms;
std::vector<MatchVectType> hits_vect;
SubstructMatch(*m1, *q1, hits_vect);
for (size_t i = 0; i < hits_vect.size(); ++i) {
for (size_t j = 0; j < hits_vect[i].size(); ++j) {
hit_atoms.push_back(hits_vect[i][j].second);
}
}
std::vector<int> hit_bonds;
for (int i : hit_atoms) {
for (int j : hit_atoms) {
if (i > j) {
Bond *bnd = m1->getBondBetweenAtoms(i, j);
if (bnd) {
hit_bonds.push_back(bnd->getIdx());
}
}
}
}
{
MolDraw2DSVG drawer(400, 400, -1, -1);
drawer.drawOptions().addAtomIndices = true;
drawer.drawMolecule(*m1, &hit_atoms, &hit_bonds);
drawer.finishDrawing();
auto text = drawer.getDrawingText();
std::ofstream outs("testGithub_5269_1.svg");
outs << text;
outs.flush();
#ifdef RDK_BUILD_FREETYPE_SUPPORT
check_file_hash("testGithub_5269_1.svg");
#endif
}
}
}
{
auto m2 = "CN(C)C(C)C=O"_smiles;
REQUIRE(m2);
std::vector<int> hit_atoms{0, 1, 2};
auto atom = m2->getAtomWithIdx(0);
atom->setProp(common_properties::atomNote, "0.91");
atom = m2->getAtomWithIdx(1);
atom->setProp(common_properties::atomNote, "1.03");
atom = m2->getAtomWithIdx(2);
atom->setProp(common_properties::atomNote, "0.74");
MolDraw2DSVG drawer(400, 400, -1, -1);
drawer.drawMolecule(*m2, &hit_atoms);
drawer.finishDrawing();
auto text = drawer.getDrawingText();
std::ofstream outs("testGithub_5269_2.svg");
outs << text;
outs.flush();
#ifdef RDK_BUILD_FREETYPE_SUPPORT
check_file_hash("testGithub_5269_2.svg");
#endif
}
}
#ifdef RDK_BUILD_CAIRO_SUPPORT
TEST_CASE("drawing doesn't destroy reaction properties", "[drawing]") {
auto rxn = "[CH3:1][OH:2]>>[CH2:1]=[OH0:2]"_rxnsmarts;
REQUIRE(rxn);
MolDraw2DCairo drawer(400, 200);
bool highlightByReactant = true;
drawer.drawReaction(*rxn, highlightByReactant);
drawer.finishDrawing();
auto png = drawer.getDrawingText();
std::unique_ptr<ChemicalReaction> rxn2{PNGStringToChemicalReaction(png)};
REQUIRE(rxn2);
CHECK(rxn->getReactants()[0]->getAtomWithIdx(0)->getAtomMapNum() == 1);
CHECK(rxn->getReactants()[0]->getAtomWithIdx(1)->getAtomMapNum() == 2);
CHECK(rxn2->getReactants()[0]->getAtomWithIdx(0)->getAtomMapNum() == 1);
CHECK(rxn2->getReactants()[0]->getAtomWithIdx(1)->getAtomMapNum() == 2);
}
#endif
TEST_CASE("Class values in SVG for wavy bonds.") {
SECTION("basics") {
auto m1 = R"CTAB(mol1
ChemDraw05162216032D
11 11 0 0 0 0 0 0 0 0999 V2000
1.1514 0.9038 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
1.1514 0.0788 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
1.9360 -0.1762 0.0000 N 0 0 0 0 0 0 0 0 0 0 0 0
2.4209 0.4913 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
1.9360 1.1587 0.0000 N 0 0 0 0 0 0 0 0 0 0 0 0
0.4369 -0.3337 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
-0.2775 0.0788 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
-0.9920 -0.3337 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
-1.7065 0.0788 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
-2.4209 -0.3337 0.0000 N 0 0 0 0 0 0 0 0 0 0 0 0
0.4369 -1.1587 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
1 2 2 0
2 3 1 0
3 4 2 0
4 5 1 0
5 1 1 0
2 6 1 0
6 7 1 0
7 8 2 3
8 9 1 0
9 10 3 0
6 11 1 4
M END)CTAB"_ctab;
REQUIRE(m1);
auto b10 = m1->getBondWithIdx(10);
b10->setBondDir(Bond::UNKNOWN);
MolDraw2DSVG drawer(400, 400, -1, -1);
drawer.drawMolecule(*m1);
drawer.finishDrawing();
auto text = drawer.getDrawingText();
CHECK(text.find("<path class='bond-10 atom-5 atom-10'") !=
std::string::npos);
std::ofstream outs("test_classes_wavy_bonds.svg");
outs << text;
outs.flush();
#ifdef RDK_BUILD_FREETYPE_SUPPORT
check_file_hash("test_classes_wavy_bonds.svg");
#endif
}
}
TEST_CASE("GitHub #5383: cairo error when using similarity maps", "") {
auto m1 = "C1N[C@@H]2OCC12"_smiles;
REQUIRE(m1);
MolDraw2DUtils::prepareMolForDrawing(*m1);
const auto conf = m1->getConformer();
std::vector<Point2D> cents(conf.getNumAtoms());
std::vector<double> weights(conf.getNumAtoms());
std::vector<double> widths(conf.getNumAtoms());
for (size_t i = 0; i < conf.getNumAtoms(); ++i) {
cents[i] = Point2D(conf.getAtomPos(i).x, conf.getAtomPos(i).y);
weights[i] = 1;
widths[i] = 0.4 * PeriodicTable::getTable()->getRcovalent(
m1->getAtomWithIdx(i)->getAtomicNum());
}
SECTION("svg basics") {
MolDraw2DSVG drawer(250, 250, -1, -1, NO_FREETYPE);
drawer.drawOptions().padding = 0.1;
drawer.clearDrawing();
std::vector<double> levels;
MolDraw2DUtils::contourAndDrawGaussians(
drawer, cents, weights, widths, 10, levels,
MolDraw2DUtils::ContourParams(), m1.get());
drawer.drawOptions().clearBackground = false;
drawer.drawMolecule(*m1);
drawer.finishDrawing();
auto text = drawer.getDrawingText();
CHECK(text.find("width='250px' height='250px' viewBox='0 0 250 250'>") !=
std::string::npos);
std::ofstream outs("github5383_1.svg");
outs << text;
outs.flush();
check_file_hash("github5383_1.svg");
}
SECTION("svg basics") {
MolDraw2DSVG drawer(250, 250, -1, -1, NO_FREETYPE);
drawer.drawOptions().padding = 0.0;
drawer.clearDrawing();
std::vector<double> levels;
MolDraw2DUtils::contourAndDrawGaussians(
drawer, cents, weights, widths, 10, levels,
MolDraw2DUtils::ContourParams(), m1.get());
drawer.drawOptions().clearBackground = false;
drawer.drawMolecule(*m1);
drawer.finishDrawing();
auto text = drawer.getDrawingText();
CHECK(text.find("width='250px' height='250px' viewBox='0 0 250 250'>") !=
std::string::npos);
std::ofstream outs("github5383_2.svg");
outs << text;
outs.flush();
check_file_hash("github5383_2.svg");
}
#ifdef RDK_BUILD_CAIRO_SUPPORT
SECTION("cairo basics") {
MolDraw2DCairo drawer(250, 250, -1, -1, NO_FREETYPE);
drawer.drawOptions().padding = 0.1;
drawer.clearDrawing();
std::vector<double> levels;
MolDraw2DUtils::contourAndDrawGaussians(
drawer, cents, weights, widths, 10, levels,
MolDraw2DUtils::ContourParams(), m1.get());
drawer.drawOptions().clearBackground = false;
drawer.drawMolecule(*m1);
drawer.finishDrawing();
drawer.writeDrawingText("github5383_1.png");
check_file_hash("github5383_1.png");
}
#endif
}
TEST_CASE("github #5156") {
SECTION("basics") {
SmilesParserParams ps;
ps.sanitize = false;
std::unique_ptr<RWMol> m{SmilesToMol("c1ccnc1", ps)};
REQUIRE(m);
unsigned int failed;
MolOps::sanitizeMol(*m, failed,
MolOps::SANITIZE_ALL ^ MolOps::SANITIZE_KEKULIZE);
MolDraw2DSVG d2d(200, 200);
d2d.drawOptions().prepareMolsBeforeDrawing = false;
d2d.drawMolecule(*m);
d2d.finishDrawing();
auto text = d2d.getDrawingText();
// CHECK(text.find("width='250px' height='250px' viewBox='0 0 250 250'>") !=
// std::string::npos);
std::ofstream outs("github5156_1.svg");
outs << text;
outs.flush();
check_file_hash("github5156_1.svg");
}
SECTION("as reported") {
auto m =
"[#6](:,-[#6]-,:[#7]-,:[#6]1:[#6]:[#6]:[#6]:[#6]:[#6]:1):,-[#6]:,-[#7]:,-[#6]"_smarts;
REQUIRE(m);
MolDraw2DSVG d2d(200, 200);
d2d.drawOptions().prepareMolsBeforeDrawing = false;
d2d.drawMolecule(*m);
d2d.finishDrawing();
auto text = d2d.getDrawingText();
// CHECK(text.find("width='250px' height='250px' viewBox='0 0 250 250'>") !=
// std::string::npos);
std::ofstream outs("github5156_2.svg");
outs << text;
outs.flush();
check_file_hash("github5156_2.svg");
}
SECTION("check no wedging") {
// if we aren't preparing molecules, we won't end up with wedging in this
// case
auto m = "C[C@H](F)Cl"_smiles;
REQUIRE(m);
MolDraw2DSVG d2d(200, 200);
d2d.drawOptions().prepareMolsBeforeDrawing = false;
d2d.drawMolecule(*m);
d2d.finishDrawing();
auto text = d2d.getDrawingText();
CHECK(text.find(" Z' style='fill=#000000") == std::string::npos);
std::ofstream outs("github5156_3.svg");
outs << text;
outs.flush();
check_file_hash("github5156_3.svg");
}
}
TEST_CASE("ACS 1996 mode") {
SECTION("basics") {
std::string nameBase = "acs1996_";
{
auto m = R"CTAB(mol1
ChemDraw05162216032D
11 11 0 0 0 0 0 0 0 0999 V2000
1.1514 0.9038 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
1.1514 0.0788 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
1.9360 -0.1762 0.0000 N 0 0 0 0 0 0 0 0 0 0 0 0
2.4209 0.4913 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
1.9360 1.1587 0.0000 N 0 0 0 0 0 0 0 0 0 0 0 0
0.4369 -0.3337 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
-0.2775 0.0788 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
-0.9920 -0.3337 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
-1.7065 0.0788 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
-2.4209 -0.3337 0.0000 N 0 0 0 0 0 0 0 0 0 0 0 0
0.4369 -1.1587 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
1 2 2 0
2 3 1 0
3 4 2 0
4 5 1 0
5 1 1 0
2 6 1 0
6 7 1 0
7 8 2 3
8 9 1 0
9 10 3 0
6 11 1 4
M END)CTAB"_ctab;
REQUIRE(m);
{
MolDraw2DSVG drawer(-1, -1);
MolDraw2DUtils::drawMolACS1996(drawer, *m, "Mol 1", nullptr, nullptr);
drawer.finishDrawing();
std::string text = drawer.getDrawingText();
std::ofstream outs(nameBase + "1.svg");
outs << text;
outs.flush();
outs.close();
check_file_hash(nameBase + "1.svg");
}
#ifdef RDK_BUILD_CAIRO_SUPPORT
{
MolDraw2DCairo drawer(-1, -1);
MolDraw2DUtils::drawMolACS1996(drawer, *m, "Mol 1", nullptr, nullptr);
drawer.finishDrawing();
drawer.writeDrawingText(nameBase + "1.png");
check_file_hash(nameBase + "1.png");
}
#endif
}
{
auto m = R"CTAB(mol2
ChemDraw06062216302D
0 0 0 0 0 0 V3000
M V30 BEGIN CTAB
M V30 COUNTS 11 11 0 0 1
M V30 BEGIN ATOM
M V30 1 C 1.151400 0.903800 0.000000 0
M V30 2 C 1.151400 0.078800 0.000000 0
M V30 3 N 1.935999 -0.176199 0.000000 0
M V30 4 C 2.420899 0.491300 0.000000 0
M V30 5 N 1.935999 1.158700 0.000000 0
M V30 6 C 0.436900 -0.333700 0.000000 0
M V30 7 C -0.277500 0.078800 0.000000 0
M V30 8 C -0.992000 -0.333700 0.000000 0
M V30 9 C -1.706500 0.078800 0.000000 0
M V30 10 N -2.420899 -0.333700 0.000000 0
M V30 11 C 0.436900 -1.158700 0.000000 0
M V30 END ATOM
M V30 BEGIN BOND
M V30 1 2 1 2
M V30 2 1 2 3
M V30 3 2 3 4
M V30 4 1 4 5
M V30 5 1 5 1
M V30 6 1 2 6
M V30 7 1 6 7
M V30 8 2 7 8 CFG=2
M V30 9 1 8 9
M V30 10 3 9 10
M V30 11 1 6 11 CFG=3
M V30 END BOND
M V30 BEGIN COLLECTION
M V30 MDLV30/STEABS ATOMS=(1 6)
M V30 END COLLECTION
M V30 END CTAB
M END
)CTAB"_ctab;
REQUIRE(m);
MolDraw2DSVG drawer(-1, -1);
MolDraw2DUtils::drawMolACS1996(drawer, *m, "Mol 2", nullptr, nullptr);
drawer.finishDrawing();
std::string text = drawer.getDrawingText();
std::ofstream outs(nameBase + "2.svg");
outs << text;
outs.flush();
outs.close();
check_file_hash(nameBase + "2.svg");
#ifdef RDK_BUILD_CAIRO_SUPPORT
{
MolDraw2DCairo drawer(-1, -1);
MolDraw2DUtils::drawMolACS1996(drawer, *m, "Mol 2", nullptr, nullptr);
drawer.finishDrawing();
drawer.writeDrawingText(nameBase + "2.png");
check_file_hash(nameBase + "2.png");
}
#endif
}
{
auto m = "C[C@H](I)CC(Cl)C[C@@H](F)C"_smiles;
m->setProp<std::string>("_Name", "mol3");
REQUIRE(m);
MolDraw2DUtils::prepareMolForDrawing(*m);
MolDraw2DSVG drawer(-1, -1);
MolDraw2DUtils::drawMolACS1996(drawer, *m, "Mol 3", nullptr, nullptr);
drawer.finishDrawing();
std::string text = drawer.getDrawingText();
std::ofstream outs(nameBase + "3.svg");
outs << text;
outs.flush();
outs.close();
check_file_hash(nameBase + "3.svg");
}
{
auto m = "CC(I)CC(Cl)CC(F)C"_smiles;
m->setProp<std::string>("_Name", "mol4");
REQUIRE(m);
MolDraw2DUtils::prepareMolForDrawing(*m);
MolDraw2DSVG drawer(-1, -1);
drawer.drawOptions().unspecifiedStereoIsUnknown = true;
MolDraw2DUtils::drawMolACS1996(drawer, *m, "Mol 4", nullptr, nullptr);
drawer.finishDrawing();
std::string text = drawer.getDrawingText();
std::ofstream outs(nameBase + "4.svg");
outs << text;
outs.flush();
outs.close();
check_file_hash(nameBase + "4.svg");
}
{
auto m = R"CTAB(mol5
ChemDraw06112209342D
0 0 0 0 0 0 V3000
M V30 BEGIN CTAB
M V30 COUNTS 30 33 0 0 1
M V30 BEGIN ATOM
M V30 1 C -2.240810 -1.031250 0.000000 0
M V30 2 C -2.240810 -0.206250 0.000000 0
M V30 3 C -2.955281 0.206250 0.000000 0
M V30 4 C -2.955281 1.031250 0.000000 0
M V30 5 C -3.669752 1.443750 0.000000 0
M V30 6 C -4.384224 1.031250 0.000000 0
M V30 7 C -4.384224 0.206250 0.000000 0
M V30 8 C -3.669752 -0.206250 0.000000 0
M V30 9 Cl -3.669752 -1.031250 0.000000 0
M V30 10 F -5.098694 -0.206250 0.000000 0
M V30 11 Cl -2.240810 1.443750 0.000000 0
M V30 12 O -1.526340 0.206250 0.000000 0
M V30 13 C -0.811869 -0.206250 0.000000 0
M V30 14 C -0.811869 -1.031250 0.000000 0
M V30 15 N -0.097397 -1.443750 0.000000 0
M V30 16 C 0.617074 -1.031250 0.000000 0
M V30 17 C 0.617074 -0.206250 0.000000 0
M V30 18 C -0.097397 0.206250 0.000000 0
M V30 19 C 1.331544 0.206250 0.000000 0
M V30 20 C 2.085220 -0.129308 0.000000 0
M V30 21 N 2.637252 0.483787 0.000000 0
M V30 22 N 2.224752 1.198258 0.000000 0
M V30 23 C 1.417781 1.026730 0.000000 0
M V30 24 C 3.457733 0.397551 0.000000 0
M V30 25 C 3.942655 1.064990 0.000000 0
M V30 26 C 4.763136 0.978754 0.000000 0
M V30 27 N 5.098694 0.225079 0.000000 0
M V30 28 C 4.613771 -0.442361 0.000000 0
M V30 29 C 3.793290 -0.356124 0.000000 0
M V30 30 N -1.526340 -1.443750 0.000000 0
M V30 END ATOM
M V30 BEGIN BOND
M V30 1 1 2 1 CFG=3
M V30 2 1 2 3
M V30 3 2 3 4
M V30 4 1 4 5
M V30 5 2 5 6
M V30 6 1 6 7
M V30 7 2 7 8
M V30 8 1 3 8
M V30 9 1 8 9
M V30 10 1 7 10
M V30 11 1 4 11
M V30 12 1 2 12
M V30 13 1 12 13
M V30 14 2 13 14
M V30 15 1 14 15
M V30 16 2 15 16
M V30 17 1 16 17
M V30 18 2 17 18
M V30 19 1 13 18
M V30 20 1 17 19
M V30 21 2 19 20
M V30 22 1 20 21
M V30 23 1 21 22
M V30 24 2 22 23
M V30 25 1 19 23
M V30 26 1 21 24
M V30 27 1 24 25
M V30 28 1 25 26
M V30 29 1 26 27
M V30 30 1 27 28
M V30 31 1 28 29
M V30 32 1 24 29
M V30 33 1 14 30
M V30 END BOND
M V30 BEGIN COLLECTION
M V30 MDLV30/STEABS ATOMS=(1 2)
M V30 END COLLECTION
M V30 END CTAB
M END
)CTAB"_ctab;
MolDraw2DSVG drawer(-1, -1);
MolDraw2DUtils::drawMolACS1996(drawer, *m, "Mol 5", nullptr, nullptr);
drawer.finishDrawing();
std::string text = drawer.getDrawingText();
std::ofstream outs(nameBase + "5.svg");
outs << text;
outs.flush();
outs.close();
check_file_hash(nameBase + "5.svg");
}
{
auto m = R"CTAB(mol6
ChemDraw06132212082D
0 0 0 0 0 0 V3000
M V30 BEGIN CTAB
M V30 COUNTS 16 15 0 0 0
M V30 BEGIN ATOM
M V30 1 C -1.427702 0.413216 0.000000 0
M V30 2 C -0.715712 0.824284 0.000000 0
M V30 3 C -2.139692 0.824284 0.000000 0
M V30 4 C -0.003721 0.413216 0.000000 0
M V30 5 C 0.708270 0.824284 0.000000 0
M V30 6 C 1.420260 0.413216 0.000000 0
M V30 7 C 0.708270 1.646420 0.000000 0
M V30 8 C -1.427702 -0.408920 0.000000 0
M V30 9 C -0.715712 -0.819988 0.000000 0
M V30 10 C -2.139692 -0.819988 0.000000 0
M V30 11 C -0.003721 -0.408920 0.000000 0
M V30 12 C 2.134731 0.825716 0.000000 0
M V30 13 C 0.710751 -0.821420 0.000000 0
M V30 14 C 1.425221 -0.408920 0.000000 0
M V30 15 C 2.139692 -0.821420 0.000000 0
M V30 16 C 2.139692 -1.646420 0.000000 0
M V30 END ATOM
M V30 BEGIN BOND
M V30 1 1 1 2
M V30 2 2 1 3
M V30 3 1 2 4
M V30 4 2 4 5
M V30 5 1 5 6
M V30 6 1 5 7
M V30 7 1 1 8
M V30 8 2 8 9 CFG=2
M V30 9 1 8 10
M V30 10 1 9 11
M V30 11 2 6 12
M V30 12 2 11 13
M V30 13 1 13 14
M V30 14 2 14 15
M V30 15 1 15 16
M V30 END BOND
M V30 END CTAB
M END
)CTAB"_ctab;
REQUIRE(m);
MolDraw2DSVG drawer(-1, -1);
MolDraw2DUtils::drawMolACS1996(drawer, *m, "Mol 6", nullptr, nullptr);
drawer.finishDrawing();
std::string text = drawer.getDrawingText();
std::ofstream outs(nameBase + "6.svg");
outs << text;
outs.flush();
outs.close();
check_file_hash(nameBase + "6.svg");
}
{
auto m = R"CTAB(mol7
ChemDraw06192209312D
0 0 0 0 0 0 V3000
M V30 BEGIN CTAB
M V30 COUNTS 18 17 0 0 0
M V30 BEGIN ATOM
M V30 1 C -2.147146 0.827156 0.000000 0
M V30 2 C -1.432676 1.239655 0.000000 0
M V30 3 O -2.861616 1.239655 0.000000 0
M V30 4 C -0.718205 0.827156 0.000000 0
M V30 5 C -0.003735 1.239655 0.000000 0
M V30 6 C 0.710736 0.827156 0.000000 0
M V30 7 C -0.003735 2.064654 0.000000 0
M V30 8 C -2.147146 0.002156 0.000000 0
M V30 9 C -1.432676 -0.410344 0.000000 0
M V30 10 C -2.861616 -0.410344 0.000000 0
M V30 11 C -0.718205 0.002156 0.000000 0
M V30 12 S 1.427695 1.241093 0.000000 0
M V30 13 C -0.001244 -0.411781 0.000000 0
M V30 14 C 0.715714 0.002156 0.000000 0
M V30 15 C 1.432674 -0.411781 0.000000 0
M V30 16 C 1.432674 -1.239654 0.000000 0
M V30 17 C 2.147145 -1.652154 0.000000 0
M V30 18 C 2.861616 -2.064654 0.000000 0
M V30 END ATOM
M V30 BEGIN BOND
M V30 1 1 1 2
M V30 2 2 1 3
M V30 3 1 2 4
M V30 4 2 4 5
M V30 5 1 5 6
M V30 6 1 5 7
M V30 7 1 1 8
M V30 8 2 8 9 CFG=2
M V30 9 1 8 10
M V30 10 1 9 11
M V30 11 2 6 12
M V30 12 2 11 13
M V30 13 1 13 14
M V30 14 2 14 15
M V30 15 1 15 16
M V30 16 2 16 17
M V30 17 2 17 18
M V30 END BOND
M V30 END CTAB
M END
)CTAB"_ctab;
REQUIRE(m);
MolDraw2DSVG drawer(-1, -1);
MolDraw2DUtils::drawMolACS1996(drawer, *m, "Mol 7", nullptr, nullptr);
drawer.finishDrawing();
std::string text = drawer.getDrawingText();
std::ofstream outs(nameBase + "7.svg");
outs << text;
outs.flush();
outs.close();
check_file_hash(nameBase + "7.svg");
}
{
auto m = R"CTAB(mol8
ChemDraw07042207302D
0 0 0 0 0 0 V3000
M V30 BEGIN CTAB
M V30 COUNTS 18 17 0 0 1
M V30 BEGIN ATOM
M V30 1 C -2.500648 -0.206250 0.000000 0
M V30 2 C -1.786177 0.206250 0.000000 0
M V30 3 C -1.071707 -0.206250 0.000000 0
M V30 4 C -0.357237 0.206250 0.000000 0
M V30 5 C 0.357236 -0.206250 0.000000 0
M V30 6 C 1.071707 0.206250 0.000000 0
M V30 7 C 1.786177 -0.206250 0.000000 0
M V30 8 C 2.500648 0.206250 0.000000 0
M V30 9 C -1.786177 1.031251 0.000000 0
M V30 10 C -2.500648 1.443750 0.000000 0
M V30 11 C -0.357237 1.031251 0.000000 0
M V30 12 C -1.071707 1.443750 0.000000 0
M V30 13 C 0.357236 1.443750 0.000000 0
M V30 14 C 1.786177 -1.031250 0.000000 0
M V30 15 C 2.500648 -1.443750 0.000000 0
M V30 16 Cl 0.357236 -1.031250 0.000000 0
M V30 17 C -1.071707 -1.031250 0.000000 0
M V30 18 C 1.071707 1.031250 0.000000 0
M V30 END ATOM
M V30 BEGIN BOND
M V30 1 1 1 2
M V30 2 1 2 3
M V30 3 1 3 4
M V30 4 1 4 5
M V30 5 1 5 6
M V30 6 1 6 7
M V30 7 1 7 8
M V30 8 1 2 9 CFG=3
M V30 9 1 9 10
M V30 10 1 4 11 CFG=3
M V30 11 1 11 12
M V30 12 1 11 13
M V30 13 1 7 14 CFG=3
M V30 14 2 14 15
M V30 15 1 5 16 CFG=3
M V30 16 1 3 17
M V30 17 1 6 18 CFG=3
M V30 END BOND
M V30 BEGIN COLLECTION
M V30 MDLV30/STEABS ATOMS=(5 2 4 5 6 7)
M V30 END COLLECTION
M V30 END CTAB
M END
)CTAB"_ctab;
REQUIRE(m);
MolDraw2DSVG drawer(-1, -1);
MolDraw2DUtils::drawMolACS1996(drawer, *m, "Mol 8", nullptr, nullptr);
drawer.finishDrawing();
std::string text = drawer.getDrawingText();
std::ofstream outs(nameBase + "8.svg");
outs << text;
outs.flush();
outs.close();
check_file_hash(nameBase + "8.svg");
}
{
auto m = R"CTAB(mol9
ChemDraw06302215142D
0 0 0 0 0 0 V3000
M V30 BEGIN CTAB
M V30 COUNTS 22 21 0 0 1
M V30 BEGIN ATOM
M V30 1 C -2.857884 -0.412500 0.000000 0
M V30 2 C -2.143413 0.000000 0.000000 0
M V30 3 C -1.428942 -0.412500 0.000000 0
M V30 4 C -0.714471 0.000000 0.000000 0
M V30 5 C 0.000000 -0.412500 0.000000 0
M V30 6 C 0.714471 0.000000 0.000000 0
M V30 7 C 1.428941 -0.412500 0.000000 0
M V30 8 C 2.143413 0.000000 0.000000 0
M V30 9 C -2.143413 0.825000 0.000000 0
M V30 10 C -2.857884 1.237500 0.000000 0
M V30 11 C -0.714471 0.825000 0.000000 0
M V30 12 C -1.428942 1.237500 0.000000 0
M V30 13 C 0.000000 1.237500 0.000000 0
M V30 14 C 1.428941 -1.237500 0.000000 0
M V30 15 C 2.143413 -1.650000 0.000000 0
M V30 16 Cl 0.000000 -1.237500 0.000000 0
M V30 17 C -1.428942 -1.237500 0.000000 0
M V30 18 C 2.857884 -0.412500 0.000000 0
M V30 19 C 2.143413 0.825000 0.000000 0
M V30 20 C 1.428941 1.237500 0.000000 0
M V30 21 C 2.857884 1.237500 0.000000 0
M V30 22 C 2.143413 1.650000 0.000000 0
M V30 END ATOM
M V30 BEGIN BOND
M V30 1 1 1 2
M V30 2 1 2 3
M V30 3 1 3 4
M V30 4 1 4 5
M V30 5 1 5 6
M V30 6 1 6 7
M V30 7 1 7 8
M V30 8 1 2 9 CFG=1
M V30 9 1 9 10
M V30 10 1 4 11 CFG=1
M V30 11 1 11 12
M V30 12 1 11 13
M V30 13 1 7 14 CFG=1
M V30 14 2 14 15
M V30 15 1 5 16 CFG=1
M V30 16 1 3 17
M V30 17 1 8 18
M V30 18 1 8 19 CFG=1
M V30 19 1 19 20
M V30 20 1 19 21
M V30 21 1 19 22
M V30 END BOND
M V30 BEGIN COLLECTION
M V30 MDLV30/STEABS ATOMS=(5 2 4 5 7 8)
M V30 END COLLECTION
M V30 END CTAB
M END
)CTAB"_ctab;
REQUIRE(m);
MolDraw2DSVG drawer(-1, -1);
drawer.drawOptions().useMolBlockWedging = true;
MolDraw2DUtils::drawMolACS1996(drawer, *m, "Mol 9", nullptr, nullptr);
drawer.finishDrawing();
std::string text = drawer.getDrawingText();
std::ofstream outs(nameBase + "9.svg");
outs << text;
outs.flush();
outs.close();
check_file_hash(nameBase + "9.svg");
}
{
auto m = R"CTAB(mol10
ChemDraw07062213362D
0 0 0 0 0 0 V3000
M V30 BEGIN CTAB
M V30 COUNTS 8 7 0 0 0
M V30 BEGIN ATOM
M V30 1 C -0.357235 -1.031250 0.000000 0
M V30 2 C -0.357235 -0.206250 0.000000 0
M V30 3 N -1.071706 0.206250 0.000000 0
M V30 4 O -1.786177 -0.206250 0.000000 0
M V30 5 C 0.357236 0.206250 0.000000 0
M V30 6 N 1.071706 -0.206250 0.000000 0
M V30 7 O 1.786177 0.206250 0.000000 0
M V30 8 C 0.357236 1.031250 0.000000 0
M V30 END ATOM
M V30 BEGIN BOND
M V30 1 1 1 2
M V30 2 2 2 3 CFG=2
M V30 3 1 3 4
M V30 4 1 2 5
M V30 5 2 5 6 CFG=2
M V30 6 1 6 7
M V30 7 1 5 8
M V30 END BOND
M V30 END CTAB
M END
)CTAB"_ctab;
REQUIRE(m);
MolDraw2DSVG drawer(-1, -1);
MolDraw2DUtils::drawMolACS1996(drawer, *m, "Mol 10", nullptr, nullptr);
drawer.finishDrawing();
std::string text = drawer.getDrawingText();
std::ofstream outs(nameBase + "10.svg");
outs << text;
outs.flush();
outs.close();
check_file_hash(nameBase + "10.svg");
}
{
auto m = "CCOC(=O)Nc1ccc(SCC2COC(Cn3ccnc3)(c3ccc(Cl)cc3Cl)O2)cc1"_smiles;
REQUIRE(m);
MolDraw2DUtils::prepareMolForDrawing(*m);
std::vector<int> highlight_atoms{17, 18, 19, 20, 21, 6, 7, 8, 9, 31, 32};
std::map<int, DrawColour> atom_highlight_colors;
atom_highlight_colors[8] = DrawColour(1.0, 1.0, 0.0);
atom_highlight_colors[31] = DrawColour(0.0, 1.0, 1.0);
std::vector<int> highlight_bonds{0, 1, 2, 11, 15, 19};
std::map<int, DrawColour> bond_highlight_colors;
bond_highlight_colors[0] = DrawColour(1.0, 1.0, 0.0);
bond_highlight_colors[11] = DrawColour(0.0, 1.0, 1.0);
MolDrawOptions options;
options.circleAtoms = true;
options.highlightColour = DrawColour(1, .5, .5);
options.continuousHighlight = true;
MolDraw2DSVG drawer(-1, -1);
drawer.drawOptions() = options;
MolDraw2DUtils::drawMolACS1996(drawer, *m, "Mol 11", &highlight_atoms,
&highlight_bonds, &atom_highlight_colors,
&bond_highlight_colors);
drawer.finishDrawing();
std::string text = drawer.getDrawingText();
std::ofstream outs(nameBase + "11.svg");
outs << text;
outs.flush();
outs.close();
check_file_hash(nameBase + "11.svg");
}
auto drawnBondLength = [&](const std::string &r1,
const std::string &t) -> double {
std::regex regex1(r1);
auto match_begin = std::sregex_iterator(t.begin(), t.end(), regex1);
auto match_end = std::sregex_iterator();
std::vector<Point2D> ends;
for (std::sregex_iterator i = match_begin; i != match_end; ++i) {
std::smatch match = *i;
ends.push_back(Point2D(std::stod(match[1]), std::stod(match[2])));
ends.push_back(Point2D(std::stod(match[3]), std::stod(match[4])));
}
return (ends[0] - ends[1]).length();
};
{
// make sure it also works with an arbitrarily sized drawer.
auto m = "c1ccccc1"_smiles;
REQUIRE(m);
MolDraw2DUtils::prepareMolForDrawing(*m);
MolDraw2DSVG drawer(500, 500);
MolDraw2DUtils::drawMolACS1996(drawer, *m, "Mol 12", nullptr, nullptr);
drawer.finishDrawing();
std::string text = drawer.getDrawingText();
std::ofstream outs(nameBase + "12.svg");
outs << text;
outs.flush();
outs.close();
std::string regex =
R"(class='bond-0 atom-0 atom-1' d='M ([\d.]*),([\d.]*) L ([\d.]*),([\d.]*)')";
double dbl = drawnBondLength(regex, text);
// the bonds should all be 14.4 long, but the SVG is only written
// to 1 decimal place, so rounding errors are largish.
CHECK(dbl == Catch::Approx(14.4253));
regex =
R"(class='bond-1 atom-1 atom-2' d='M ([\d.]*),([\d.]*) L ([\d.]*),([\d.]*)')";
dbl = drawnBondLength(regex, text);
CHECK(dbl == Catch::Approx(14.4));
check_file_hash(nameBase + "12.svg");
}
}
}
TEST_CASE("Unspecified stereochemistry means unknown.", "") {
auto m1 = "ClC(I)(F)C=CC"_smiles;
REQUIRE(m1);
MolDraw2DUtils::prepareMolForDrawing(*m1);
MolDraw2DSVG drawer(250, 250, -1, -1, NO_FREETYPE);
drawer.drawOptions().unspecifiedStereoIsUnknown = true;
drawer.drawMolecule(*m1);
drawer.finishDrawing();
auto text = drawer.getDrawingText();
std::ofstream outs("test_unspec_stereo.svg");
outs << text;
outs.flush();
std::regex regex1("class='bond-2 atom-1 atom-3' .*M.*C");
std::smatch wavyMatch;
CHECK(std::regex_search(text, wavyMatch, regex1));
CHECK(wavyMatch.size() == 1);
std::regex regex2(
"class='bond-4 atom-4 atom-5' d='M (\\d+\\.\\d+),(\\d+\\.\\d+) L "
"(\\d+\\.\\d+),(\\d+\\.\\d+)'");
std::ptrdiff_t const match_count(
std::distance(std::sregex_iterator(text.begin(), text.end(), regex2),
std::sregex_iterator()));
CHECK(match_count == 2);
// Check that the 2 bonds aren't parallel
auto cross1Match = std::sregex_iterator(text.begin(), text.end(), regex2);
Point2D point1{stod((*cross1Match)[1]), stod((*cross1Match)[2])};
Point2D point2{stod((*cross1Match)[3]), stod((*cross1Match)[4])};
auto vec1 = point1.directionVector(point2);
++cross1Match;
Point2D point3{stod((*cross1Match)[1]), stod((*cross1Match)[2])};
Point2D point4{stod((*cross1Match)[3]), stod((*cross1Match)[4])};
auto vec2 = point3.directionVector(point4);
CHECK(vec1.dotProduct(vec2) != Catch::Approx(1.0).margin(1.0e-4));
check_file_hash("test_unspec_stereo.svg");
}
TEST_CASE("Colour H light blue with no atom labels", "") {
auto m1 = "C[C@]12CCCC[C@H]1OCCC2"_smiles;
MolDraw2DUtils::prepareMolForDrawing(*m1);
MolDraw2DSVG drawer(250, 250, -1, -1, NO_FREETYPE);
drawer.drawOptions().noAtomLabels = true;
drawer.drawMolecule(*m1);
drawer.finishDrawing();
auto text = drawer.getDrawingText();
std::ofstream outs("light_blue_h_no_label_1.svg");
outs << text;
outs.flush();
std::regex regex1(R"(class='bond-12 atom-6 atom-11'.*fill:#ADD8E5)");
std::smatch regex1Match;
CHECK(std::regex_search(text, regex1Match, regex1));
CHECK(regex1Match.size() == 1);
check_file_hash("light_blue_h_no_label_1.svg");
}
TEST_CASE("Bond Highlights", "") {
auto m1 = "c1c(OCC)cncc1CCCC=O"_smiles;
REQUIRE(m1);
MolDraw2DUtils::prepareMolForDrawing(*m1);
{
// only bonds highlighted, continuous highlighting, highlights
// joining neatly.
MolDraw2DSVG drawer(250, 250, -1, -1, NO_FREETYPE);
drawer.drawOptions().addBondIndices = true;
std::vector<int> highAts{};
std::vector<int> highBnds{0, 1, 4, 5, 6, 7, 13};
// std::vector<int> highBnds{0, 1, 4};
drawer.drawMolecule(*m1, &highAts, &highBnds);
drawer.finishDrawing();
auto text = drawer.getDrawingText();
std::ofstream outs("bond_highlights_1.svg");
outs << text;
outs.flush();
check_file_hash("bond_highlights_1.svg");
}
{
// same as 1, but with highlighting as coloured bonds. The O for
// atom 2 is red because it is not highlighted, though bond 1 from
// the pyridyl is.
MolDraw2DSVG drawer(250, 250, -1, -1, NO_FREETYPE);
std::vector<int> highAts{};
std::vector<int> highBnds{0, 1, 4, 5, 6, 7, 13};
drawer.drawOptions().continuousHighlight = false;
drawer.drawOptions().circleAtoms = false;
drawer.drawOptions().addAtomIndices = true;
drawer.drawMolecule(*m1, &highAts, &highBnds);
drawer.finishDrawing();
auto text = drawer.getDrawingText();
std::ofstream outs("bond_highlights_2.svg");
outs << text;
outs.flush();
check_file_hash("bond_highlights_2.svg");
}
{
// same bonds highlighted, but some atoms highlighted with
// different colours. Where an atom and a bond off it are
// highlighted in different colours, the bond colour takes
// precedence and the atom highlight is lost unless it has
// an atom symbol drawn or there's a non-highlighted bond
// off it. Thus half of bond 8 should be green, as is
// the N of atom 6 and the two half bonds off atom 10.
MolDraw2DSVG drawer(250, 250, -1, -1, NO_FREETYPE);
std::vector<int> highAts{0, 1, 5, 6, 7, 8, 10};
std::vector<int> highBnds{0, 1, 4, 5, 6, 7, 13};
std::map<int, DrawColour> atom_highlight_colors;
atom_highlight_colors[0] = DrawColour(0.0, 1.0, 0.0);
atom_highlight_colors[5] = DrawColour(0.0, 1.0, 0.0);
atom_highlight_colors[6] = DrawColour(0.0, 1.0, 0.0);
atom_highlight_colors[7] = DrawColour(0.0, 1.0, 0.0);
atom_highlight_colors[8] = DrawColour(0.0, 1.0, 0.0);
atom_highlight_colors[10] = DrawColour(0.0, 1.0, 0.0);
drawer.drawOptions().addAtomIndices = true;
drawer.drawOptions().addBondIndices = true;
drawer.drawOptions().continuousHighlight = false;
drawer.drawOptions().circleAtoms = false;
drawer.drawMolecule(*m1, &highAts, &highBnds, &atom_highlight_colors);
drawer.finishDrawing();
auto text = drawer.getDrawingText();
std::ofstream outs("bond_highlights_3.svg");
outs << text;
outs.flush();
check_file_hash("bond_highlights_3.svg");
}
{
// same as 3, except that the N on atom 6 isn't highlighted,
// but both bonds off it are, so it gets the highlight colour.
MolDraw2DSVG drawer(250, 250, -1, -1, NO_FREETYPE);
std::vector<int> highAts{0, 1, 5, 7, 8, 10};
std::vector<int> highBnds{0, 1, 4, 5, 6, 7, 13};
std::map<int, DrawColour> atom_highlight_colors;
atom_highlight_colors[0] = DrawColour(0.0, 1.0, 0.0);
atom_highlight_colors[5] = DrawColour(0.0, 1.0, 0.0);
atom_highlight_colors[7] = DrawColour(0.0, 1.0, 0.0);
atom_highlight_colors[8] = DrawColour(0.0, 1.0, 0.0);
atom_highlight_colors[10] = DrawColour(0.0, 1.0, 0.0);
drawer.drawOptions().addAtomIndices = true;
drawer.drawOptions().addBondIndices = true;
drawer.drawOptions().continuousHighlight = false;
drawer.drawOptions().circleAtoms = false;
drawer.drawMolecule(*m1, &highAts, &highBnds, &atom_highlight_colors);
drawer.finishDrawing();
auto text = drawer.getDrawingText();
std::ofstream outs("bond_highlights_4.svg");
outs << text;
outs.flush();
check_file_hash("bond_highlights_4.svg");
}
{
// same as 4, except that atom 6 has a highlight colour assigned
// in the map, but isn't highlighted. It just happens that it's
// the default highlight colour.
MolDraw2DSVG drawer(250, 250, -1, -1, NO_FREETYPE);
std::vector<int> highAts{0, 1, 5, 7, 8, 10};
std::vector<int> highBnds{0, 1, 4, 5, 6, 7, 13};
std::map<int, DrawColour> atom_highlight_colors;
atom_highlight_colors[0] = DrawColour(0.0, 1.0, 0.0);
atom_highlight_colors[5] = DrawColour(0.0, 1.0, 0.0);
atom_highlight_colors[6] = drawer.drawOptions().highlightColour;
atom_highlight_colors[7] = DrawColour(0.0, 1.0, 0.0);
atom_highlight_colors[8] = DrawColour(0.0, 1.0, 0.0);
atom_highlight_colors[10] = DrawColour(0.0, 1.0, 0.0);
drawer.drawOptions().addAtomIndices = true;
drawer.drawOptions().addBondIndices = true;
drawer.drawOptions().continuousHighlight = false;
drawer.drawOptions().circleAtoms = false;
drawer.drawMolecule(*m1, &highAts, &highBnds, &atom_highlight_colors);
drawer.finishDrawing();
auto text = drawer.getDrawingText();
std::ofstream outs("bond_highlights_5.svg");
outs << text;
outs.flush();
check_file_hash("bond_highlights_5.svg");
}
{
// same as 3, but showing that atom circles can be used
// to rescue the missing atom highlights.
MolDraw2DSVG drawer(250, 250, -1, -1, NO_FREETYPE);
std::vector<int> highAts{0, 1, 5, 6, 7, 8, 10};
std::vector<int> highBnds{0, 1, 4, 5, 6, 7, 13};
std::map<int, DrawColour> atom_highlight_colors;
atom_highlight_colors[0] = DrawColour(0.0, 1.0, 0.0);
atom_highlight_colors[5] = DrawColour(0.0, 1.0, 0.0);
atom_highlight_colors[6] = DrawColour(0.0, 1.0, 0.0);
atom_highlight_colors[7] = DrawColour(0.0, 1.0, 0.0);
atom_highlight_colors[8] = DrawColour(0.0, 1.0, 0.0);
atom_highlight_colors[10] = DrawColour(0.0, 1.0, 0.0);
drawer.drawOptions().addAtomIndices = true;
drawer.drawOptions().addBondIndices = true;
drawer.drawOptions().continuousHighlight = false;
drawer.drawOptions().circleAtoms = true;
drawer.drawMolecule(*m1, &highAts, &highBnds, &atom_highlight_colors);
drawer.finishDrawing();
auto text = drawer.getDrawingText();
std::ofstream outs("bond_highlights_6.svg");
outs << text;
outs.flush();
check_file_hash("bond_highlights_6.svg");
}
{
// same as 1, but in ACS1996 mode.
MolDraw2DSVG drawer(-1, -1, -1, -1, NO_FREETYPE);
std::vector<int> highAts{};
std::vector<int> highBnds{0, 1, 4, 5, 6, 7, 13};
drawer.drawOptions().continuousHighlight = false;
drawer.drawOptions().circleAtoms = false;
MolDraw2DUtils::drawMolACS1996(drawer, *m1, "", &highAts, &highBnds);
drawer.drawMolecule(*m1, &highAts, &highBnds);
drawer.finishDrawing();
auto text = drawer.getDrawingText();
std::ofstream outs("bond_highlights_7.svg");
outs << text;
outs.flush();
check_file_hash("bond_highlights_7.svg");
}
{
// check 3- and 4-way intersections of continuous highlights are ok
auto m = "c1c(C(C)(C)C)cccc1"_smiles;
REQUIRE(m);
MolDraw2DUtils::prepareMolForDrawing(*m);
MolDraw2DSVG drawer(250, 250, -1, -1, NO_FREETYPE);
drawer.drawOptions().continuousHighlight = true;
drawer.drawOptions().addBondIndices = true;
std::vector<int> highBnds{0, 1, 2, 3, 4, 5, 6};
std::map<int, DrawColour> bond_highlight_colors;
bond_highlight_colors[0] = DrawColour(1.0, 0.0, 0.0);
bond_highlight_colors[1] = DrawColour(0.0, 1.0, 0.0);
bond_highlight_colors[3] = DrawColour(1.0, 0.0, 0.0);
bond_highlight_colors[4] = DrawColour(0.0, 1.0, 0.0);
bond_highlight_colors[5] = DrawColour(0.0, 0.0, 1.0);
drawer.drawMolecule(*m, nullptr, &highBnds, nullptr,
&bond_highlight_colors);
drawer.finishDrawing();
auto text = drawer.getDrawingText();
std::ofstream outs("bond_highlights_8.svg");
outs << text;
outs.flush();
check_file_hash("bond_highlights_8.svg");
}
{
// cyclopropane (Github5592)
auto m = "CC1CC1"_smiles;
REQUIRE(m);
MolDraw2DUtils::prepareMolForDrawing(*m);
std::vector<int> highBnds{1, 2, 3};
std::map<int, DrawColour> bond_highlight_colors;
bond_highlight_colors[1] = DrawColour(1.0, 0.0, 0.0);
bond_highlight_colors[2] = DrawColour(0.0, 1.0, 0.0);
bond_highlight_colors[3] = DrawColour(0.0, 0.0, 1.0);
MolDraw2DSVG drawer(250, 250, -1, -1, NO_FREETYPE);
drawer.drawOptions().continuousHighlight = true;
drawer.drawMolecule(*m, nullptr, &highBnds, nullptr,
&bond_highlight_colors);
drawer.finishDrawing();
auto text = drawer.getDrawingText();
std::ofstream outs("bond_highlights_9.svg");
outs << text;
std::regex regex1(
R"(class='bond-[\d*] atom-[\d] atom-[\d]' d='M ([\d.]*),([\d.]*) L ([\d.]*),([\d.]*) L ([\d.]*),([\d.]*) L ([\d.]*),([\d.]*) Z')");
auto match_begin = std::sregex_iterator(text.begin(), text.end(), regex1);
auto match_end = std::sregex_iterator();
std::vector<Point2D> ends;
for (std::sregex_iterator i = match_begin; i != match_end; ++i) {
// with this result, match[0] is the whole string that matched,
// match[1] is the 1st float (the x coord of the M), match[2]
// is the 2nd float, etc.
std::smatch match = *i;
ends.push_back(Point2D(std::stod(match[1]), std::stod(match[2])));
ends.push_back(Point2D(std::stod(match[3]), std::stod(match[4])));
ends.push_back(Point2D(std::stod(match[5]), std::stod(match[6])));
ends.push_back(Point2D(std::stod(match[7]), std::stod(match[8])));
}
CHECK(ends.size() == 12);
// When this had a bug in it, it drew a butterfly-type motif, because
// ends 2 and 3 were the wrong way round.
for (int i = 0; i < 12; i += 4) {
CHECK(!MolDraw2D_detail::doLinesIntersect(
ends[i], ends[i + 3], ends[i + 1], ends[i + 2], nullptr));
}
outs.flush();
check_file_hash("bond_highlights_9.svg");
}
}
TEST_CASE("drawMolecules should not crash on null molecules",
"[drawing][bug]") {
auto m1 = "c1ccccc1"_smiles;
auto m2 = "c1ccncc1"_smiles;
REQUIRE(m1);
REQUIRE(m2);
MolDraw2DSVG drawer(1000, 200, 100, 100, NO_FREETYPE);
RWMol dm1(*m1);
RWMol dm2(*m2);
MOL_PTR_VECT ms{&dm1, nullptr, nullptr, nullptr, nullptr, nullptr,
nullptr, nullptr, nullptr, nullptr, &dm2};
drawer.drawMolecules(ms);
drawer.finishDrawing();
auto text = drawer.getDrawingText();
std::regex regex1("<path d=");
auto nMatches =
std::distance(std::sregex_iterator(text.begin(), text.end(), regex1),
std::sregex_iterator());
CHECK(nMatches == 11);
}
TEST_CASE("Crossed bonds in transdecene") {
SECTION("basics") {
std::string nameBase = "testGithub5486_";
{
auto m = R"CTAB(
ChemDraw08042214332D
10 10 0 0 0 0 0 0 0 0999 V2000
-1.4289 0.4125 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
-1.4289 -0.4125 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
-0.7145 -0.8250 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
0.0000 -0.4125 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
0.0000 0.4125 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
-0.7145 0.8250 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
0.7145 -0.8250 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
1.4289 -0.4125 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
1.4289 0.4125 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
0.7145 0.8250 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
1 2 1 0
2 3 1 0
3 4 1 0
5 6 2 0
6 1 1 0
4 7 1 0
7 8 1 0
8 9 1 0
9 10 1 0
10 5 1 0
M END)CTAB"_ctab;
REQUIRE(m);
{
MolDraw2DSVG drawer(300, 300);
drawer.drawMolecule(*m);
drawer.finishDrawing();
std::string text = drawer.getDrawingText();
std::ofstream outs(nameBase + "1.svg");
outs << text;
outs.flush();
outs.close();
std::regex regex1(
R"(class='bond-3 atom-4 atom-5' d='M ([\d.]*),([\d.]*) L ([\d.]*),([\d.]*)')");
auto match_begin =
std::sregex_iterator(text.begin(), text.end(), regex1);
auto match_end = std::sregex_iterator();
std::vector<Point2D> ends;
for (std::sregex_iterator i = match_begin; i != match_end; ++i) {
std::smatch match = *i;
ends.push_back(Point2D(std::stod(match[1]), std::stod(match[2])));
ends.push_back(Point2D(std::stod(match[3]), std::stod(match[4])));
}
CHECK(ends.size() == 4);
CHECK(!MolDraw2D_detail::doLinesIntersect(ends[0], ends[1], ends[2],
ends[3], nullptr));
check_file_hash(nameBase + "1.svg");
}
}
}
}
TEST_CASE("Bad O position in aldehydes", "") {
std::string nameBase("testGithub5511_");
{
auto m1 = "O=Cc1cccc(C=O)c1"_smiles;
REQUIRE(m1);
MolDraw2DUtils::prepareMolForDrawing(*m1);
MolDraw2DSVG drawer(250, 250, -1, -1, NO_FREETYPE);
drawer.drawOptions().addAtomIndices = true;
drawer.drawMolecule(*m1);
drawer.finishDrawing();
auto text = drawer.getDrawingText();
std::string filename = nameBase + "1.svg";
std::ofstream outs(filename);
outs << text;
outs.flush();
check_file_hash(filename);
}
{
auto m = R"CTAB(
RDKit 2D
11 11 0 0 0 0 0 0 0 0999 V2000
-4.2885 0.5445 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
-2.9895 1.2945 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0
-1.6818 0.5394 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
-0.3738 1.2945 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
0.9342 0.5394 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
2.2422 1.2945 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
2.2422 2.7945 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0
0.9342 -0.9708 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
-0.3738 -1.7262 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
-1.6818 -0.9708 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
-2.9895 -1.7262 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0
1 2 1 0
2 3 1 0
3 4 2 0
4 5 1 0
5 6 1 0
6 7 2 0
5 8 2 0
8 9 1 0
9 10 2 0
10 11 1 0
10 3 1 0
M END
)CTAB"_ctab;
REQUIRE(m);
MolDraw2DSVG drawer(250, 250, -1, -1);
drawer.drawOptions().addAtomIndices = true;
drawer.drawMolecule(*m);
drawer.finishDrawing();
std::string text = drawer.getDrawingText();
std::string filename = nameBase + "2.svg";
std::ofstream outs(filename);
outs << text;
outs.flush();
check_file_hash(filename);
}
}
TEST_CASE("Github5534") {
std::string nameBase = "test_github_5534";
{
auto m = R"CTAB(
INFOCHEM 2D 1 1.00000 0.00000 0
45 45 0 0 0 0 0 0 0 0999 V2000
-1.3388 1.6804 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
-1.0303 1.6804 0.0000 Si 0 0 0 0 0 0 0 0 0 0 0 0
-1.0303 1.9890 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
-1.0303 1.3609 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
-0.0496 -0.6997 0.0000 F 0 0 0 0 0 0 0 0 0 0 0 0
-0.0496 -0.3581 0.0000 F 0 0 0 0 0 0 0 0 0 0 0 0
-0.0496 -0.0386 0.0000 F 0 0 0 0 0 0 0 0 0 0 0 0
-0.0496 0.2810 0.0000 F 0 0 0 0 0 0 0 0 0 0 0 0
-0.0496 0.6116 0.0000 F 0 0 0 0 0 0 0 0 0 0 0 0
-0.0826 0.9532 0.0000 F 0 0 0 0 0 0 0 0 0 0 0 0
-0.0496 -1.0193 0.0000 F 0 0 0 0 0 0 0 0 0 0 0 0
-0.0496 -1.3499 0.0000 F 0 0 0 0 0 0 0 0 0 0 0 0
-0.0496 -1.6694 0.0000 F 0 0 0 0 0 0 0 0 0 0 0 0
0.6116 -0.6997 0.0000 F 0 0 0 0 0 0 0 0 0 0 0 0
0.6116 -0.3581 0.0000 F 0 0 0 0 0 0 0 0 0 0 0 0
0.6116 -0.0386 0.0000 F 0 0 0 0 0 0 0 0 0 0 0 0
0.6116 0.2810 0.0000 F 0 0 0 0 0 0 0 0 0 0 0 0
0.6116 0.6116 0.0000 F 0 0 0 0 0 0 0 0 0 0 0 0
0.6116 0.9532 0.0000 F 0 0 0 0 0 0 0 0 0 0 0 0
0.6116 -1.0193 0.0000 F 0 0 0 0 0 0 0 0 0 0 0 0
0.6116 -1.3499 0.0000 F 0 0 0 0 0 0 0 0 0 0 0 0
0.6116 -1.6694 0.0000 F 0 0 0 0 0 0 0 0 0 0 0 0
1.0303 1.6804 0.0000 Si 0 0 0 0 0 0 0 0 0 0 0 0
1.0303 2.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
1.0303 1.3609 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
1.3388 1.6804 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
0.2810 -0.6997 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
0.2810 -0.3581 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
0.2810 -0.0386 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
0.2810 0.2810 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
0.2810 0.6116 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
0.2810 0.9532 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
0.3361 1.2948 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
0.1708 1.4601 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
0.3581 1.6804 0.0000 Si 0 0 0 0 0 0 0 0 0 0 0 0
0.0275 1.6804 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0
0.3581 1.9890 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
0.2810 -1.0193 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
0.2810 -1.3499 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
0.2810 -1.6694 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
0.2810 -2.0000 0.0000 F 0 0 0 0 0 0 0 0 0 0 0 0
-0.6997 1.6804 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0
-0.3691 1.6804 0.0000 Si 0 0 0 0 0 0 0 0 0 0 0 0
-0.3691 1.9890 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
-0.3691 1.3609 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
1 2 1 0 0 0 0
1 23 1 0 0 0 0
1 35 1 0 0 0 0
2 3 1 0 0 0 0
2 4 1 0 0 0 0
2 42 1 0 0 0 0
5 27 1 0 0 0 0
6 28 1 0 0 0 0
7 29 1 0 0 0 0
8 30 1 0 0 0 0
9 31 1 0 0 0 0
10 32 1 0 0 0 0
11 38 1 0 0 0 0
12 39 1 0 0 0 0
13 40 1 0 0 0 0
14 27 1 0 0 0 0
15 28 1 0 0 0 0
16 29 1 0 0 0 0
17 30 1 0 0 0 0
18 31 1 0 0 0 0
19 32 1 0 0 0 0
20 38 1 0 0 0 0
21 39 1 0 0 0 0
22 40 1 0 0 0 0
23 24 1 0 0 0 0
23 25 1 0 0 0 0
23 26 1 0 0 0 0
27 28 1 0 0 0 0
27 38 1 0 0 0 0
28 29 1 0 0 0 0
29 30 1 0 0 0 0
30 31 1 0 0 0 0
31 32 1 0 0 0 0
32 33 1 0 0 0 0
33 34 1 0 0 0 0
34 35 1 0 0 0 0
35 36 1 0 0 0 0
35 37 1 0 0 0 0
36 43 1 0 0 0 0
38 39 1 0 0 0 0
39 40 1 0 0 0 0
40 41 1 0 0 0 0
42 43 1 0 0 0 0
43 44 1 0 0 0 0
43 45 1 0 0 0 0
M STY 2 1 GEN 2 GEN
M SAL 1 15 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41
M SBL 1 15 7 16 8 17 9 18 10 19 11 20 12 21 3 39 13
M SBL 1 5 22 14 23 15 24
M SDI 1 4 -0.0386 2.0661 -0.0386 1.1846
M SDI 1 4 0.4683 2.0661 0.4683 1.1846
M SAL 2 4 42 43 44 45
M SBL 2 2 6 39
M SDI 2 4 -0.7658 2.0661 -0.7658 1.1846
M SDI 2 4 -0.2149 2.0661 -0.2149 1.1846
M END
)CTAB"_ctab;
REQUIRE(m);
{
MolDraw2DSVG drawer(300, 300, 300, 300, NO_FREETYPE);
drawer.drawMolecule(*m);
drawer.finishDrawing();
std::string text = drawer.getDrawingText();
std::ofstream outs(nameBase + ".svg");
outs << text;
outs.flush();
outs.close();
check_file_hash(nameBase + ".svg");
}
}
}
TEST_CASE(
"Github5704: set bond highlight color when atom highlight color changes") {
std::string nameBase = "test_github5704";
auto m =
"CCCO |(-1.97961,-0.1365,;-0.599379,0.450827,;0.599379,-0.450827,;1.97961,0.1365,)|"_smiles;
REQUIRE(m);
std::regex redline(R"RE(<path .*fill:#FF7F7F)RE");
std::regex blueline(R"RE(<path .*fill:#4C4CFF)RE");
SECTION("no atom colors specified, default behavior") {
MolDraw2DSVG drawer(300, 300, 300, 300, NO_FREETYPE);
std::vector<int> aids{0, 1, 2};
drawer.drawMolecule(*m, "red bond highlight", &aids);
drawer.finishDrawing();
std::string text = drawer.getDrawingText();
std::smatch rematch;
CHECK(std::regex_search(text, rematch, redline));
CHECK(!std::regex_search(text, rematch, blueline));
std::ofstream outs(nameBase + "_1.svg");
outs << text;
outs.flush();
outs.close();
check_file_hash(nameBase + "_1.svg");
}
SECTION("both ends specified") {
MolDraw2DSVG drawer(300, 300, 300, 300, NO_FREETYPE);
std::vector<int> aids{0, 1, 2};
std::map<int, DrawColour> acolors{
{0, {.3, .3, 1}}, {1, {.3, .3, 1}}, {2, {.3, .3, 1}}};
drawer.drawMolecule(*m, "blue bond highlight", &aids, &acolors);
drawer.finishDrawing();
std::string text = drawer.getDrawingText();
std::smatch rematch;
CHECK(!std::regex_search(text, rematch, redline));
CHECK(std::regex_search(text, rematch, blueline));
std::ofstream outs(nameBase + "_2.svg");
outs << text;
outs.flush();
outs.close();
check_file_hash(nameBase + "_2.svg");
}
SECTION("color just on begin") {
MolDraw2DSVG drawer(300, 300, 300, 300, NO_FREETYPE);
std::vector<int> aids{0, 1};
std::map<int, DrawColour> acolors{{0, {.3, .3, 1}}};
drawer.drawMolecule(*m, "blue bond highlight", &aids, &acolors);
drawer.finishDrawing();
std::string text = drawer.getDrawingText();
std::smatch rematch;
CHECK(!std::regex_search(text, rematch, redline));
CHECK(std::regex_search(text, rematch, blueline));
std::ofstream outs(nameBase + "_3.svg");
outs << text;
outs.flush();
outs.close();
check_file_hash(nameBase + "_3.svg");
}
SECTION("color just on end") {
MolDraw2DSVG drawer(300, 300, 300, 300, NO_FREETYPE);
std::vector<int> aids{0, 1};
std::map<int, DrawColour> acolors{{1, {.3, .3, 1}}};
drawer.drawMolecule(*m, "blue bond highlight", &aids, &acolors);
drawer.finishDrawing();
std::string text = drawer.getDrawingText();
std::smatch rematch;
CHECK(!std::regex_search(text, rematch, redline));
CHECK(std::regex_search(text, rematch, blueline));
std::ofstream outs(nameBase + "_4.svg");
outs << text;
outs.flush();
outs.close();
check_file_hash(nameBase + "_4.svg");
}
}
TEST_CASE("Github5767: monomer label missing for MON SGroups ") {
std::string nameBase = "test_github5767";
auto m = R"CTAB(
Marvin 06091012252D
13 11 0 0 0 0 999 V2000
-3.5063 2.1509 0.0000 N 0 0 0 0 0 0 0 0 0 0 0 0
-2.7918 2.5634 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
-2.0773 2.1509 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
-1.3628 2.5634 0.0000 N 0 0 0 0 0 0 0 0 0 0 0 0
-0.6484 2.1509 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
0.0661 2.5634 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
0.7806 2.1509 0.0000 N 0 0 0 0 0 0 0 0 0 0 0 0
-2.9984 -0.4714 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
-2.2839 -0.0589 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
-1.5695 -0.4714 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
-0.8550 -0.0589 0.0000 Cl 0 0 0 0 0 0 0 0 0 0 0 0
-2.9984 0.3536 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0
0.6777 -0.1775 0.0000 Cl 0 0 0 0 0 0 0 0 0 0 0 0
1 2 1 0 0 0 0
2 3 1 0 0 0 0
3 4 1 0 0 0 0
4 5 1 0 0 0 0
5 6 1 0 0 0 0
6 7 1 0 0 0 0
8 9 1 0 0 0 0
9 10 1 0 0 0 0
10 11 1 0 0 0 0
9 12 1 0 0 0 0
12 8 1 0 0 0 0
M STY 2 1 MON 2 MON
M SAL 1 7 1 2 3 4 5 6 7
M SDI 1 4 -3.9263 1.7309 -3.9263 2.9834
M SDI 1 4 1.2006 2.9834 1.2006 1.7309
M SAL 2 5 8 9 10 11 12
M SDI 2 4 -3.4184 -0.8914 -3.4184 0.7736
M SDI 2 4 -0.4350 0.7736 -0.4350 -0.8914
M END
)CTAB"_ctab;
REQUIRE(m);
{
MolDraw2DSVG drawer(300, 300, 300, 300, true);
drawer.drawMolecule(*m);
drawer.finishDrawing();
std::string text = drawer.getDrawingText();
std::ofstream outs(nameBase + ".svg");
outs << text;
outs.flush();
outs.close();
// there should be 2 each of " >[mon]</text>"
std::vector<std::string> needed{" >m</text>", " >o</text>", " >n</text>"};
for (const auto &n : needed) {
std::regex rn(n);
std::ptrdiff_t const match_count(
std::distance(std::sregex_iterator(text.begin(), text.end(), rn),
std::sregex_iterator()));
CHECK(match_count == 2);
}
check_file_hash(nameBase + ".svg");
}
}
TEST_CASE("Github5947: Ellipse extremes not calculated correctly.") {
std::string nameBase = "test_github5947";
auto m = "c1ccccn1"_smiles;
TEST_ASSERT(m);
RDDepict::compute2DCoords(*m);
std::vector<int> highlight_atoms{0, 1, 2, 3, 4, 5};
MolDraw2DSVG drawer(400, 400);
drawer.drawOptions().highlightRadius = 1.0;
drawer.drawMolecule(*m, &highlight_atoms);
drawer.finishDrawing();
std::string text = drawer.getDrawingText();
std::ofstream outs(nameBase + ".svg");
outs << text;
outs.flush();
outs.close();
std::regex r1("<ellipse cx=.*rx='(\\d+\\.\\d+)' ry='(\\d+\\.\\d+)'");
std::ptrdiff_t const match_count(
std::distance(std::sregex_iterator(text.begin(), text.end(), r1),
std::sregex_iterator()));
CHECK(match_count == 6);
// all the ellipses should have a radius of roughly 72.0
auto match_begin = std::sregex_iterator(text.begin(), text.end(), r1);
auto match_end = std::sregex_iterator();
for (std::sregex_iterator i = match_begin; i != match_end; ++i) {
std::smatch match = *i;
CHECK_THAT(stod(match[1]), Catch::Matchers::WithinAbs(72.0, 0.1));
CHECK_THAT(stod(match[2]), Catch::Matchers::WithinAbs(72.0, 0.1));
}
// check that the first ellipse is in the right place
std::regex r2("<ellipse cx='(\\d+\\.\\d+)' cy='(\\d+\\.\\d+)'");
auto ell1 = *std::sregex_iterator(text.begin(), text.end(), r2);
CHECK_THAT(stod(ell1[1]), Catch::Matchers::WithinAbs(308.0, 0.1));
CHECK_THAT(stod(ell1[2]), Catch::Matchers::WithinAbs(200.0, 0.1));
check_file_hash(nameBase + ".svg");
}
TEST_CASE("Github5943: bad ellipses for atom end points") {
std::string nameBase = "test_github5943";
auto m = R"CTAB(ferrocene
RDKit 2D
0 0 0 0 0 0 0 0 0 0999 V3000
M V30 BEGIN CTAB
M V30 COUNTS 15 14 0 0 0
M V30 BEGIN ATOM
M V30 1 C 0.619616 1.206807 0.000000 0 CHG=-1
M V30 2 C 0.211483 1.768553 0.000000 0
M V30 3 C -1.283936 1.861329 0.000000 0
M V30 4 C -1.796429 1.358429 0.000000 0
M V30 5 C -0.634726 0.966480 0.000000 0
M V30 6 C 0.654379 -1.415344 0.000000 0 CHG=-1
M V30 7 C 0.249886 -0.858607 0.000000 0
M V30 8 C -1.232145 -0.766661 0.000000 0
M V30 9 C -1.740121 -1.265073 0.000000 0
M V30 10 C -0.580425 -1.662922 0.000000 0
M V30 11 C 1.759743 0.755930 0.000000 0
M V30 12 C 1.796429 -1.861329 0.000000 0
M V30 13 Fe -0.554442 0.032137 0.000000 0 VAL=2
M V30 14 * -0.601210 1.478619 0.000000 0
M V30 15 * -0.537835 -1.172363 0.000000 0
M V30 END ATOM
M V30 BEGIN BOND
M V30 1 1 1 5
M V30 2 2 4 5
M V30 3 1 4 3
M V30 4 2 2 3
M V30 5 1 1 2
M V30 6 1 6 10
M V30 7 2 9 10
M V30 8 1 9 8
M V30 9 2 7 8
M V30 10 1 6 7
M V30 11 1 1 11
M V30 12 1 6 12
M V30 13 9 14 13 ENDPTS=(5 1 2 3 4 5) ATTACH=ANY
M V30 14 9 15 13 ENDPTS=(5 9 10 7 8 6) ATTACH=ANY
M V30 END BOND
M V30 END CTAB
M END
)CTAB"_ctab;
REQUIRE(m);
{
MolDraw2DSVG drawer(300, 300, 300, 300, true);
drawer.drawMolecule(*m);
drawer.finishDrawing();
std::string text = drawer.getDrawingText();
std::ofstream outs(nameBase + ".svg");
outs << text;
outs.flush();
outs.close();
std::regex r("<ellipse cx=.*rx='(\\d+\\.\\d+)' ry='(\\d+\\.\\d+)'");
std::ptrdiff_t const match_count(
std::distance(std::sregex_iterator(text.begin(), text.end(), r),
std::sregex_iterator()));
CHECK(match_count == 10);
// all the ellipses should have a radius of roughly 25.2.
auto match_begin = std::sregex_iterator(text.begin(), text.end(), r);
auto match_end = std::sregex_iterator();
for (std::sregex_iterator i = match_begin; i != match_end; ++i) {
std::smatch match = *i;
CHECK_THAT(stod(match[1]), Catch::Matchers::WithinAbs(25.0, 0.1));
CHECK_THAT(stod(match[2]), Catch::Matchers::WithinAbs(25.0, 0.1));
}
check_file_hash(nameBase + ".svg");
}
}
TEST_CASE("Github5949: fixed size for dative arrow heads") {
std::string nameBase = "test_github5949";
auto m = R"CTAB(ferrocene
RDKit 2D
0 0 0 0 0 0 0 0 0 0999 V3000
M V30 BEGIN CTAB
M V30 COUNTS 15 14 0 0 0
M V30 BEGIN ATOM
M V30 1 C 0.619616 1.206807 0.000000 0 CHG=-1
M V30 2 C 0.211483 1.768553 0.000000 0
M V30 3 C -1.283936 1.861329 0.000000 0
M V30 4 C -1.796429 1.358429 0.000000 0
M V30 5 C -0.634726 0.966480 0.000000 0
M V30 6 C 0.654379 -1.415344 0.000000 0 CHG=-1
M V30 7 C 0.249886 -0.858607 0.000000 0
M V30 8 C -1.232145 -0.766661 0.000000 0
M V30 9 C -1.740121 -1.265073 0.000000 0
M V30 10 C -0.580425 -1.662922 0.000000 0
M V30 11 C 1.759743 0.755930 0.000000 0
M V30 12 C 1.796429 -1.861329 0.000000 0
M V30 13 Fe -0.554442 0.032137 0.000000 0 VAL=2
M V30 14 * -0.601210 1.478619 0.000000 0
M V30 15 * -0.537835 -1.172363 0.000000 0
M V30 END ATOM
M V30 BEGIN BOND
M V30 1 1 1 5
M V30 2 2 4 5
M V30 3 1 4 3
M V30 4 2 2 3
M V30 5 1 1 2
M V30 6 1 6 10
M V30 7 2 9 10
M V30 8 1 9 8
M V30 9 2 7 8
M V30 10 1 6 7
M V30 11 1 1 11
M V30 12 1 6 12
M V30 13 9 14 13 ENDPTS=(5 1 2 3 4 5) ATTACH=ANY
M V30 14 9 15 13 ENDPTS=(5 9 10 7 8 6) ATTACH=ANY
M V30 END BOND
M V30 END CTAB
M END
)CTAB"_ctab;
REQUIRE(m);
{
MolDraw2DSVG drawer(300, 300, 300, 300, false);
drawer.drawOptions().addAtomIndices = true;
drawer.drawMolecule(*m);
drawer.finishDrawing();
std::string text = drawer.getDrawingText();
std::ofstream outs(nameBase + ".svg");
outs << text;
outs.flush();
outs.close();
auto extract_ends = [](const std::string &text, const std::regex &r,
std::vector<Point2D> &ends) -> void {
auto match_begin = std::sregex_iterator(text.begin(), text.end(), r);
auto match_end = std::sregex_iterator();
for (std::sregex_iterator i = match_begin; i != match_end; ++i) {
std::smatch match = *i;
ends.push_back(Point2D(std::stod(match[1]), std::stod(match[2])));
ends.push_back(Point2D(std::stod(match[3]), std::stod(match[4])));
ends.push_back(Point2D(std::stod(match[5]), std::stod(match[6])));
}
};
std::regex head1(
"atom-13 atom-12' d='M\\s+(\\d+\\.\\d+),(\\d+\\.\\d+)"
" L\\s+(\\d+\\.\\d+),(\\d+\\.\\d+) L\\s+(\\d+\\.\\d+),(\\d+\\.\\d+) Z'");
std::vector<Point2D> ends1;
extract_ends(text, head1, ends1);
CHECK(ends1.size() == 3);
std::regex head2(
"atom-14 atom-12' d='M\\s+(\\d+\\.\\d+),(\\d+\\.\\d+)"
" L\\s+(\\d+\\.\\d+),(\\d+\\.\\d+) L\\s+(\\d+\\.\\d+),(\\d+\\.\\d+) Z'");
std::vector<Point2D> ends2;
extract_ends(text, head2, ends2);
CHECK(ends2.size() == 3);
auto h1s1 = (ends1[0] - ends1[1]).length();
auto h2s1 = (ends2[0] - ends2[1]).length();
// there's still a small difference in size of arrow head because the
// allowance for mitring is done as a fraction of the overall arrow
// length.
CHECK_THAT(h1s1, Catch::Matchers::WithinAbs(h2s1, 0.1));
auto h1s2 = (ends1[0] - ends1[2]).length();
auto h2s2 = (ends2[0] - ends2[2]).length();
CHECK_THAT(h1s2, Catch::Matchers::WithinAbs(h2s2, 0.1));
check_file_hash(nameBase + ".svg");
}
}
TEST_CASE("Github5974: drawing code should not generate kekulization errors") {
SECTION("basics") {
SmilesParserParams ps;
ps.sanitize = false;
std::unique_ptr<RWMol> mol(SmilesToMol("c1nccc1", ps));
REQUIRE(mol);
mol->updatePropertyCache();
MolDraw2DSVG drawer(300, 300, -1, -1, false);
// the test here is really just that calling drawMolecule() doesn't throw an
// exception
drawer.drawMolecule(*mol);
drawer.finishDrawing();
std::string text = drawer.getDrawingText();
std::ofstream outs("test_github5974.svg");
outs << text;
outs.flush();
outs.close();
check_file_hash("test_github5974.svg");
}
}
TEST_CASE("Github5963: bond end wrong on wedge") {
std::string nameBase = "test_github5963";
{
auto m = "COc1ccc([S@@](=O)Cc2ccccc2)cc1"_smiles;
MolDraw2DSVG drawer(300, 300, 300, 300, true);
RDDepict::compute2DCoords(*m);
drawer.drawOptions().addBondIndices = true;
drawer.drawMolecule(*m);
drawer.finishDrawing();
std::string text = drawer.getDrawingText();
std::ofstream outs(nameBase + ".svg");
outs << text;
outs.flush();
outs.close();
std::regex bond7(
"'bond-7 atom-6 atom-8' d='M\\s+(\\d+\\.\\d+),(\\d+\\.\\d+)"
" L\\s+(\\d+\\.\\d+),(\\d+\\.\\d+) L\\s+(\\d+\\.\\d+),(\\d+\\.\\d+) Z'");
// there should be 3 matches for bond7, of which we are interested in the
// 2nd
std::ptrdiff_t const match_count(
std::distance(std::sregex_iterator(text.begin(), text.end(), bond7),
std::sregex_iterator()));
CHECK(match_count == 3);
auto bond7_match = std::sregex_iterator(text.begin(), text.end(), bond7);
++bond7_match;
std::smatch match7 = *bond7_match;
std::regex bond8(
"'bond-8 atom-8 atom-9' d='M\\s+(\\d+\\.\\d+),(\\d+\\.\\d+)"
" L\\s+(\\d+\\.\\d+),(\\d+\\.\\d+)'");
// only 1 bond8 match
auto bond8_match = std::sregex_iterator(text.begin(), text.end(), bond8);
std::smatch match8 = *bond8_match;
// the middle point of the triangle should be the same as the start of the
// line
Point2D midtri(std::stod(match7[3]), std::stod(match7[4]));
Point2D startline(std::stod(match8[1]), std::stod(match8[2]));
CHECK_THAT((midtri - startline).length(),
Catch::Matchers::WithinAbs(0.0, 0.1));
check_file_hash(nameBase + ".svg");
}
}
TEST_CASE("Github6025: bad bonds on tiny canvas") {
std::string nameBase = "test_github6025";
auto m1 = R"CTAB(
-ISIS- 02031614092D
35 39 0 0 0 0 0 0 0 0999 V2000
9.1292 9.8417 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
10.6292 9.8417 0.0000 N 0 0 3 0 0 0 0 0 0 0 0 0
8.3792 8.5417 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
10.6292 4.6417 0.0000 N 0 0 0 0 0 0 0 0 0 0 0 0
11.3792 3.3583 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
11.3792 5.9417 0.0000 N 0 0 0 0 0 0 0 0 0 0 0 0
10.6292 2.0500 0.0000 N 0 0 3 0 0 0 0 0 0 0 0 0
6.8792 8.5417 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
6.1292 7.2417 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
11.3792 8.5417 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
8.3792 5.9417 0.0000 N 0 0 0 0 0 0 0 0 0 0 0 0
4.6292 7.2417 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
8.3792 11.1417 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0
2.3792 8.5417 0.0000 N 0 0 0 0 0 0 0 0 0 0 0 0
2.3792 5.9417 0.0000 N 0 0 0 0 0 0 0 0 0 0 0 0
9.1292 2.0500 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
12.8792 3.3583 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
1.6292 7.2417 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
12.8792 5.9417 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
9.1292 7.2417 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
12.8792 8.5417 0.0000 C 0 0 3 0 0 0 0 0 0 0 0 0
13.6292 7.2417 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
11.3792 11.1417 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
6.8792 5.9417 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
13.6292 4.6417 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
3.8792 8.5417 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
3.8792 5.9417 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
11.3792 0.7500 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
12.8792 11.1417 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
13.6292 9.8417 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
8.3792 0.7500 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
8.3792 3.3583 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
6.8792 3.3583 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
6.8792 0.7500 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
6.1292 2.0500 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
2 1 1 0 0 0 0
3 1 1 0 0 0 0
4 6 1 0 0 0 0
5 17 1 0 0 0 0
6 19 2 0 0 0 0
7 5 1 0 0 0 0
8 3 1 0 0 0 0
9 8 2 0 0 0 0
10 2 1 0 0 0 0
11 20 1 0 0 0 0
12 9 1 0 0 0 0
13 1 2 0 0 0 0
14 26 2 0 0 0 0
15 27 1 0 0 0 0
16 7 1 0 0 0 0
17 25 2 0 0 0 0
18 15 2 0 0 0 0
19 22 1 0 0 0 0
20 3 2 0 0 0 0
21 10 1 0 0 0 0
22 21 1 0 0 0 0
23 2 1 0 0 0 0
24 11 2 0 0 0 0
25 19 1 0 0 0 0
26 12 1 0 0 0 0
27 12 2 0 0 0 0
28 7 1 0 0 0 0
29 23 1 0 0 0 0
30 29 1 0 0 0 0
31 16 2 0 0 0 0
32 16 1 0 0 0 0
33 32 2 0 0 0 0
34 31 1 0 0 0 0
35 33 1 0 0 0 0
24 9 1 0 0 0 0
30 21 1 0 0 0 0
18 14 1 0 0 0 0
5 4 2 0 0 0 0
34 35 2 0 0 0 0
M END
)CTAB"_ctab;
REQUIRE(m1);
{
MolDraw2DSVG drawer(25, 25, 25, 25, false);
drawer.drawOptions().addAtomIndices = true;
drawer.drawMolecule(*m1);
drawer.finishDrawing();
std::string text = drawer.getDrawingText();
std::ofstream outs(nameBase + ".svg");
outs << text;
outs.flush();
outs.close();
auto check_bond = [](const std::string &text, const std::regex &r) {
// there should be 4 matches for each regex, and all the x coords should
// be > 0.0. The bug manifested itself by some of them being < 0.0 and
// thus off the side of the picture.
std::ptrdiff_t const match_count(
std::distance(std::sregex_iterator(text.begin(), text.end(), r),
std::sregex_iterator()));
CHECK(match_count == 4);
auto match_begin = std::sregex_iterator(text.begin(), text.end(), r);
auto match_end = std::sregex_iterator();
for (std::sregex_iterator i = match_begin; i != match_end; ++i) {
std::smatch match = *i;
CHECK(stod(match[1]) > 0.0);
CHECK(stod(match[3]) > 0.0);
}
};
std::regex bond9(
"'bond-9 atom-10 atom-19' d='M\\s+(\\d+\\.\\d+),(\\d+\\.\\d+)"
" L\\s+(\\d+\\.\\d+),(\\d+\\.\\d+)");
std::regex bond16(
"'bond-16 atom-17 atom-14' d='M\\s+(\\d+\\.\\d+),(\\d+\\.\\d+)"
" L\\s+(\\d+\\.\\d+),(\\d+\\.\\d+)");
check_bond(text, bond9);
check_bond(text, bond16);
check_file_hash(nameBase + ".svg");
}
}
TEST_CASE("Github6027: bad bonds with co-linear double bond") {
std::string nameBase = "test_github6027";
auto m1 = R"CTAB(
MJ201100
15 16 0 0 0 0 0 0 0 0999 V2000
-2.6052 -0.0931 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
-2.6052 0.7318 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
-3.3197 1.1444 0.0000 N 0 0 0 0 0 0 0 0 0 0 0 0
-4.0346 0.7318 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
-4.0347 -0.0931 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
-3.3197 -0.5055 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
-3.3197 1.9693 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
-3.3197 2.7943 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
-1.8908 -0.5055 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
-1.1764 0.7318 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
-1.1764 -0.0931 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
-0.4620 -0.5055 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
0.2523 -0.0931 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
0.2524 0.7318 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
-0.4620 1.1444 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
1 2 1 0 0 0 0
2 3 1 0 0 0 0
5 6 1 0 0 0 0
6 1 1 0 0 0 0
3 7 1 0 0 0 0
7 8 2 0 0 0 0
13 14 1 0 0 0 0
14 15 1 0 0 0 0
10 11 1 0 0 0 0
15 10 1 0 0 0 0
11 12 1 0 0 0 0
12 13 1 0 0 0 0
3 4 1 0 0 0 0
4 5 1 0 0 0 0
9 1 1 0 0 0 0
11 9 1 0 0 0 0
M END
)CTAB"_ctab;
REQUIRE(m1);
{
MolDraw2DSVG drawer(250, 250, 250, 250, false);
drawer.drawOptions().addAtomIndices = true;
drawer.drawMolecule(*m1);
drawer.finishDrawing();
std::string text = drawer.getDrawingText();
std::ofstream outs(nameBase + "_1.svg");
outs << text;
outs.flush();
outs.close();
std::regex bond5(
"'bond-5 atom-6 atom-7' d='M\\s+(\\d+\\.\\d+),(\\d+\\.\\d+)"
" L\\s+(\\d+\\.\\d+),(\\d+\\.\\d+)");
// There are 2 bonds, and the x coords of their 2 ends should be
// the same, because the offending bond is exactly vertical, and their
// corresponding y coords should be the same. The bug
// manifested itself by giving the 2nd line coords
// M 210.3,169.3 L 63.6,41.0.
std::ptrdiff_t const match_count(
std::distance(std::sregex_iterator(text.begin(), text.end(), bond5),
std::sregex_iterator()));
CHECK(match_count == 2);
auto match_begin = std::sregex_iterator(text.begin(), text.end(), bond5);
auto match_end = std::sregex_iterator();
std::vector<float> ys;
for (std::sregex_iterator i = match_begin; i != match_end; ++i) {
std::smatch match = *i;
ys.push_back(stod(match[2]));
ys.push_back(stod(match[4]));
CHECK(match[1] == match[3]);
}
CHECK(ys[0] == ys[2]);
CHECK(ys[1] == ys[3]);
check_file_hash(nameBase + "_1.svg");
}
{
// make sure the double bond lines are still parallel when rotated
// (they weren't, the first time.)
MolDraw2DSVG drawer(250, 250, 250, 250, false);
drawer.drawOptions().addAtomIndices = true;
drawer.drawOptions().rotate = 120;
drawer.drawMolecule(*m1);
drawer.finishDrawing();
std::string text = drawer.getDrawingText();
std::ofstream outs(nameBase + "_2.svg");
outs << text;
outs.flush();
outs.close();
// check that the two lines are parallel.
std::regex bond5(
"'bond-5 atom-6 atom-7' d='M\\s+(\\d+\\.\\d+),(\\d+\\.\\d+)"
" L\\s+(\\d+\\.\\d+),(\\d+\\.\\d+)");
std::ptrdiff_t const match_count(
std::distance(std::sregex_iterator(text.begin(), text.end(), bond5),
std::sregex_iterator()));
CHECK(match_count == 2);
auto match_begin = std::sregex_iterator(text.begin(), text.end(), bond5);
auto match_end = std::sregex_iterator();
std::vector<Point2D> points;
for (std::sregex_iterator i = match_begin; i != match_end; ++i) {
std::smatch match = *i;
points.push_back(Point2D(stod(match[4]), stod(match[2])));
points.push_back(Point2D(stod(match[3]), stod(match[4])));
}
auto vec1 = points[0].directionVector(points[1]);
auto vec2 = points[2].directionVector(points[3]);
CHECK_THAT(vec1.dotProduct(vec2), Catch::Matchers::WithinAbs(1.0, 2.0e-4));
check_file_hash(nameBase + "_2.svg");
}
}
TEST_CASE("Down/dashed wedge not visible on small canvas..") {
std::string nameBase = "test_github6041b";
auto m =
"CC(C)(F)c1noc(N2CCCN([C@H]3CC[C@H](COc4ccc(S(C)(=O)=O)cc4F)CC3)CC2)n1"_smiles;
MolDraw2DSVG drawer(125, 125);
RDDepict::compute2DCoords(*m);
MolDraw2DUtils::setACS1996Options(drawer.drawOptions(), 1.5);
drawer.drawOptions().fixedFontSize = -1;
drawer.drawMolecule(*m);
drawer.finishDrawing();
std::string text = drawer.getDrawingText();
std::ofstream outs(nameBase + ".svg");
outs << text;
outs.flush();
outs.close();
std::regex bond12(
"'bond-12 atom-13 atom-12' d='M\\s+(\\d+\\.\\d+),(\\d+\\.\\d+)"
" L\\s+(\\d+\\.\\d+),(\\d+\\.\\d+)");
std::ptrdiff_t const match_count(
std::distance(std::sregex_iterator(text.begin(), text.end(), bond12),
std::sregex_iterator()));
CHECK(match_count == 3);
check_file_hash(nameBase + ".svg");
}
TEST_CASE("Github6054: MDL query atoms should not trigger an exception") {
SECTION("any heavy") {
auto a = R"CTAB(
MJ201100
6 6 0 0 0 0 0 0 0 0999 V2000
-1.7633 0.8919 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
-2.4778 0.4794 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
-2.4778 -0.3456 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
-1.7633 -0.7580 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
-1.0488 -0.3456 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
-1.0488 0.4794 0.0000 A 0 0 0 0 0 0 0 0 0 0 0 0
1 2 1 0 0 0 0
2 3 1 0 0 0 0
3 4 1 0 0 0 0
4 5 1 0 0 0 0
1 6 1 0 0 0 0
5 6 1 0 0 0 0
M END
)CTAB"_ctab;
REQUIRE(a);
{
MolDraw2DSVG drawer(250, 250, -1, -1, NO_FREETYPE);
REQUIRE_NOTHROW(drawer.drawMolecule(*a));
}
}
}
TEST_CASE("Optionally depict complex query atoms in a more compact form") {
std::string nameBase = "test_complex_query_atoms";
auto extractQueryAtomSymbol = [](const std::string &text) {
std::istringstream ss(text);
std::string line;
std::regex regex("^<text[^>]*>([^<])*</text>");
std::smatch match;
std::string res;
while (std::getline(ss, line)) {
if (std::regex_match(line, match, regex)) {
CHECK(match.size() == 2);
res += match[1];
}
}
return res;
};
SECTION("any heavy") {
auto a = R"CTAB(
MJ201100
6 6 0 0 0 0 0 0 0 0999 V2000
-1.7633 0.8919 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
-2.4778 0.4794 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
-2.4778 -0.3456 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
-1.7633 -0.7580 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
-1.0488 -0.3456 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
-1.0488 0.4794 0.0000 A 0 0 0 0 0 0 0 0 0 0 0 0
1 2 1 0 0 0 0
2 3 1 0 0 0 0
3 4 1 0 0 0 0
4 5 1 0 0 0 0
1 6 1 0 0 0 0
5 6 1 0 0 0 0
M END
)CTAB"_ctab;
REQUIRE(a);
{
MolDraw2DSVG drawer(250, 250, -1, -1, NO_FREETYPE);
drawer.drawOptions().useComplexQueryAtomSymbols = false;
REQUIRE_NOTHROW(drawer.drawMolecule(*a));
drawer.finishDrawing();
std::string text = drawer.getDrawingText();
std::ofstream outs(nameBase + "_1.svg");
outs << text;
outs.flush();
outs.close();
CHECK(extractQueryAtomSymbol(text) == "![H]");
check_file_hash(nameBase + "_1.svg");
}
{
MolDraw2DSVG drawer(250, 250, -1, -1, NO_FREETYPE);
REQUIRE_NOTHROW(drawer.drawMolecule(*a));
drawer.finishDrawing();
std::string text = drawer.getDrawingText();
std::ofstream outs(nameBase + "_2.svg");
outs << text;
outs.flush();
outs.close();
CHECK(a->getAtomWithIdx(a->getNumAtoms() - 1)->getQueryType() == "A");
CHECK(extractQueryAtomSymbol(text) == "A");
check_file_hash(nameBase + "_2.svg");
}
}
SECTION("any atom") {
auto ah = R"CTAB(
MJ201100
6 6 0 0 0 0 0 0 0 0999 V2000
-1.7633 0.8919 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
-2.4778 0.4794 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
-2.4778 -0.3456 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
-1.7633 -0.7580 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
-1.0488 -0.3456 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
-1.0488 0.4794 0.0000 AH 0 0 0 0 0 0 0 0 0 0 0 0
1 2 1 0 0 0 0
2 3 1 0 0 0 0
3 4 1 0 0 0 0
4 5 1 0 0 0 0
1 6 1 0 0 0 0
5 6 1 0 0 0 0
M END
)CTAB"_ctab;
REQUIRE(ah);
{
MolDraw2DSVG drawer(250, 250, -1, -1, NO_FREETYPE);
drawer.drawOptions().useComplexQueryAtomSymbols = false;
REQUIRE_NOTHROW(drawer.drawMolecule(*ah));
drawer.finishDrawing();
std::string text = drawer.getDrawingText();
std::ofstream outs(nameBase + "_3.svg");
outs << text;
outs.flush();
outs.close();
CHECK(extractQueryAtomSymbol(text) == "*");
check_file_hash(nameBase + "_3.svg");
}
{
MolDraw2DSVG drawer(250, 250, -1, -1, NO_FREETYPE);
REQUIRE_NOTHROW(drawer.drawMolecule(*ah));
drawer.finishDrawing();
std::string text = drawer.getDrawingText();
std::ofstream outs(nameBase + "_4.svg");
outs << text;
outs.flush();
outs.close();
CHECK(ah->getAtomWithIdx(ah->getNumAtoms() - 1)->getQueryType() == "AH");
CHECK(extractQueryAtomSymbol(text) == "*");
check_file_hash(nameBase + "_4.svg");
}
}
SECTION("any hetero") {
auto q = R"CTAB(
MJ201100
6 6 0 0 0 0 0 0 0 0999 V2000
-1.7633 0.8919 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
-2.4778 0.4794 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
-2.4778 -0.3456 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
-1.7633 -0.7580 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
-1.0488 -0.3456 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
-1.0488 0.4794 0.0000 Q 0 0 0 0 0 0 0 0 0 0 0 0
1 2 1 0 0 0 0
2 3 1 0 0 0 0
3 4 1 0 0 0 0
4 5 1 0 0 0 0
1 6 1 0 0 0 0
5 6 1 0 0 0 0
M END
)CTAB"_ctab;
REQUIRE(q);
{
MolDraw2DSVG drawer(250, 250, -1, -1, NO_FREETYPE);
drawer.drawOptions().useComplexQueryAtomSymbols = false;
REQUIRE_NOTHROW(drawer.drawMolecule(*q));
drawer.finishDrawing();
std::string text = drawer.getDrawingText();
std::ofstream outs(nameBase + "_5.svg");
outs << text;
outs.flush();
outs.close();
CHECK(extractQueryAtomSymbol(text) == "![C,H]");
check_file_hash(nameBase + "_5.svg");
}
{
MolDraw2DSVG drawer(250, 250, -1, -1, NO_FREETYPE);
REQUIRE_NOTHROW(drawer.drawMolecule(*q));
drawer.finishDrawing();
std::string text = drawer.getDrawingText();
std::ofstream outs(nameBase + "_6.svg");
outs << text;
outs.flush();
outs.close();
CHECK(q->getAtomWithIdx(q->getNumAtoms() - 1)->getQueryType() == "Q");
CHECK(extractQueryAtomSymbol(text) == "Q");
check_file_hash(nameBase + "_6.svg");
}
}
SECTION("any hetero or hydrogen") {
auto qh = R"CTAB(
MJ201100
6 6 0 0 0 0 0 0 0 0999 V2000
-1.7633 0.8919 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
-2.4778 0.4794 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
-2.4778 -0.3456 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
-1.7633 -0.7580 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
-1.0488 -0.3456 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
-1.0488 0.4794 0.0000 QH 0 0 0 0 0 0 0 0 0 0 0 0
1 2 1 0 0 0 0
2 3 1 0 0 0 0
3 4 1 0 0 0 0
4 5 1 0 0 0 0
1 6 1 0 0 0 0
5 6 1 0 0 0 0
M END
)CTAB"_ctab;
REQUIRE(qh);
{
MolDraw2DSVG drawer(250, 250, -1, -1, NO_FREETYPE);
drawer.drawOptions().useComplexQueryAtomSymbols = false;
REQUIRE_NOTHROW(drawer.drawMolecule(*qh));
drawer.finishDrawing();
std::string text = drawer.getDrawingText();
std::ofstream outs(nameBase + "_7.svg");
outs << text;
outs.flush();
outs.close();
CHECK(extractQueryAtomSymbol(text) == "![C]");
check_file_hash(nameBase + "_7.svg");
}
{
MolDraw2DSVG drawer(250, 250, -1, -1, NO_FREETYPE);
REQUIRE_NOTHROW(drawer.drawMolecule(*qh));
drawer.finishDrawing();
std::string text = drawer.getDrawingText();
std::ofstream outs(nameBase + "_8.svg");
outs << text;
outs.flush();
outs.close();
CHECK(qh->getAtomWithIdx(qh->getNumAtoms() - 1)->getQueryType() == "QH");
CHECK(extractQueryAtomSymbol(text) == "QH");
check_file_hash(nameBase + "_8.svg");
}
}
SECTION("any halo") {
auto x = R"CTAB(
MJ201100
7 7 0 0 0 0 0 0 0 0999 V2000
-1.7633 0.8919 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
-2.4778 0.4794 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
-2.4778 -0.3456 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
-1.7633 -0.7580 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
-1.0488 -0.3456 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
-1.0488 0.4794 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
-0.3344 0.8919 0.0000 X 0 0 0 0 0 0 0 0 0 0 0 0
1 2 1 0 0 0 0
2 3 1 0 0 0 0
3 4 1 0 0 0 0
4 5 1 0 0 0 0
1 6 1 0 0 0 0
5 6 1 0 0 0 0
6 7 1 0 0 0 0
M END
)CTAB"_ctab;
REQUIRE(x);
{
MolDraw2DSVG drawer(250, 250, -1, -1, NO_FREETYPE);
drawer.drawOptions().useComplexQueryAtomSymbols = false;
REQUIRE_NOTHROW(drawer.drawMolecule(*x));
drawer.finishDrawing();
std::string text = drawer.getDrawingText();
std::ofstream outs(nameBase + "_9.svg");
outs << text;
outs.flush();
outs.close();
CHECK(extractQueryAtomSymbol(text) == "[F,Cl,Br,I,At]");
check_file_hash(nameBase + "_9.svg");
}
{
MolDraw2DSVG drawer(250, 250, -1, -1, NO_FREETYPE);
REQUIRE_NOTHROW(drawer.drawMolecule(*x));
drawer.finishDrawing();
std::string text = drawer.getDrawingText();
std::ofstream outs(nameBase + "_10.svg");
outs << text;
outs.flush();
outs.close();
CHECK(x->getAtomWithIdx(x->getNumAtoms() - 1)->getQueryType() == "X");
CHECK(extractQueryAtomSymbol(text) == "X");
check_file_hash(nameBase + "_10.svg");
}
}
SECTION("any halo or hydrogen") {
auto xh = R"CTAB(
MJ201100
7 7 0 0 0 0 0 0 0 0999 V2000
-1.7633 0.8919 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
-2.4778 0.4794 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
-2.4778 -0.3456 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
-1.7633 -0.7580 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
-1.0488 -0.3456 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
-1.0488 0.4794 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
-0.3344 0.8919 0.0000 XH 0 0 0 0 0 0 0 0 0 0 0 0
1 2 1 0 0 0 0
2 3 1 0 0 0 0
3 4 1 0 0 0 0
4 5 1 0 0 0 0
1 6 1 0 0 0 0
5 6 1 0 0 0 0
6 7 1 0 0 0 0
M END
)CTAB"_ctab;
REQUIRE(xh);
{
MolDraw2DSVG drawer(250, 250, -1, -1, NO_FREETYPE);
drawer.drawOptions().useComplexQueryAtomSymbols = false;
REQUIRE_NOTHROW(drawer.drawMolecule(*xh));
drawer.finishDrawing();
std::string text = drawer.getDrawingText();
std::ofstream outs(nameBase + "_11.svg");
outs << text;
outs.flush();
outs.close();
CHECK(extractQueryAtomSymbol(text) == "[F,Cl,Br,I,At,H]");
check_file_hash(nameBase + "_11.svg");
}
{
MolDraw2DSVG drawer(250, 250, -1, -1, NO_FREETYPE);
REQUIRE_NOTHROW(drawer.drawMolecule(*xh));
drawer.finishDrawing();
std::string text = drawer.getDrawingText();
std::ofstream outs(nameBase + "_12.svg");
outs << text;
outs.flush();
outs.close();
CHECK(xh->getAtomWithIdx(xh->getNumAtoms() - 1)->getQueryType() == "XH");
CHECK(extractQueryAtomSymbol(text) == "XH");
check_file_hash(nameBase + "_12.svg");
}
}
SECTION("any metal") {
auto m = R"CTAB(
MJ201100
7 7 0 0 0 0 0 0 0 0999 V2000
-1.7633 0.8919 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
-2.4778 0.4794 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
-2.4778 -0.3456 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
-1.7633 -0.7580 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
-1.0488 -0.3456 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
-1.0488 0.4794 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
-0.3344 0.8919 0.0000 M 0 0 0 0 0 0 0 0 0 0 0 0
1 2 1 0 0 0 0
2 3 1 0 0 0 0
3 4 1 0 0 0 0
4 5 1 0 0 0 0
1 6 1 0 0 0 0
5 6 1 0 0 0 0
6 7 1 0 0 0 0
M END
)CTAB"_ctab;
REQUIRE(m);
{
MolDraw2DSVG drawer(250, 250, -1, -1, NO_FREETYPE);
drawer.drawOptions().useComplexQueryAtomSymbols = false;
REQUIRE_NOTHROW(drawer.drawMolecule(*m));
drawer.finishDrawing();
std::string text = drawer.getDrawingText();
std::ofstream outs(nameBase + "_13.svg");
outs << text;
outs.flush();
outs.close();
CHECK(extractQueryAtomSymbol(text) ==
"![*,He,B,C,N,O,F,Ne,Si,P,S,Cl,Ar,As,Se,Br,Kr,Te,I,Xe,At,Rn,H]");
check_file_hash(nameBase + "_13.svg");
}
{
MolDraw2DSVG drawer(250, 250, -1, -1, NO_FREETYPE);
REQUIRE_NOTHROW(drawer.drawMolecule(*m));
drawer.finishDrawing();
std::string text = drawer.getDrawingText();
std::ofstream outs(nameBase + "_14.svg");
outs << text;
outs.flush();
outs.close();
CHECK(m->getAtomWithIdx(m->getNumAtoms() - 1)->getQueryType() == "M");
CHECK(extractQueryAtomSymbol(text) == "M");
check_file_hash(nameBase + "_14.svg");
}
}
SECTION("any metal or hydrogen") {
auto mh = R"CTAB(
MJ201100
7 7 0 0 0 0 0 0 0 0999 V2000
-1.7633 0.8919 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
-2.4778 0.4794 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
-2.4778 -0.3456 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
-1.7633 -0.7580 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
-1.0488 -0.3456 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
-1.0488 0.4794 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
-0.3344 0.8919 0.0000 MH 0 0 0 0 0 0 0 0 0 0 0 0
1 2 1 0 0 0 0
2 3 1 0 0 0 0
3 4 1 0 0 0 0
4 5 1 0 0 0 0
1 6 1 0 0 0 0
5 6 1 0 0 0 0
6 7 1 0 0 0 0
M END
)CTAB"_ctab;
REQUIRE(mh);
{
MolDraw2DSVG drawer(250, 250, -1, -1, NO_FREETYPE);
drawer.drawOptions().useComplexQueryAtomSymbols = false;
REQUIRE_NOTHROW(drawer.drawMolecule(*mh));
drawer.finishDrawing();
std::string text = drawer.getDrawingText();
std::ofstream outs(nameBase + "_15.svg");
outs << text;
outs.flush();
outs.close();
CHECK(extractQueryAtomSymbol(text) ==
"![*,He,B,C,N,O,F,Ne,Si,P,S,Cl,Ar,As,Se,Br,Kr,Te,I,Xe,At,Rn]");
check_file_hash(nameBase + "_15.svg");
}
{
MolDraw2DSVG drawer(250, 250, -1, -1, NO_FREETYPE);
REQUIRE_NOTHROW(drawer.drawMolecule(*mh));
drawer.finishDrawing();
std::string text = drawer.getDrawingText();
std::ofstream outs(nameBase + "_16.svg");
outs << text;
outs.flush();
outs.close();
CHECK(mh->getAtomWithIdx(mh->getNumAtoms() - 1)->getQueryType() == "MH");
CHECK(extractQueryAtomSymbol(text) == "MH");
check_file_hash(nameBase + "_16.svg");
}
}
}
TEST_CASE("ACS1996 mode crops small molecules - Github 6111") {
std::string nameBase = "test_github6111";
{
auto m = "[*:1]N[*:2]"_smiles;
RDDepict::compute2DCoords(*m);
m->setProp<std::string>("_Name", "mol1");
REQUIRE(m);
MolDraw2DSVG drawer(-1, -1);
MolDraw2DUtils::drawMolACS1996(drawer, *m, "", nullptr, nullptr);
drawer.finishDrawing();
std::string text = drawer.getDrawingText();
std::ofstream outs(nameBase + "_1.svg");
outs << text;
outs.flush();
outs.close();
// check that selected y coords don't go outside of the viewBox.
std::regex vbox(R"(viewBox='(\d+)\s+(\d+)\s+(\d+)\s+(\d+)'>)");
auto match1_begin = std::sregex_iterator(text.begin(), text.end(), vbox);
std::smatch match = *match1_begin;
auto ymin = std::stod(match[2]);
auto ymax = std::stod(match[4]);
std::regex atom0(R"(class='atom-\d+' d='M\s+(\d+\.\d+)\s+(\d+\.\d+))");
auto match2_begin = std::sregex_iterator(text.begin(), text.end(), atom0);
auto match2_end = std::sregex_iterator();
for (std::sregex_iterator i = match2_begin; i != match2_end; ++i) {
std::smatch match = *i;
auto y = std::stod(match[2]);
CHECK((y >= ymin && y <= ymax));
}
check_file_hash(nameBase + "_1.svg");
}
}
TEST_CASE("ACS1996 should not throw exception with no coords - Github 6112") {
std::string nameBase = "test_github6112";
auto m = "C[C@H](I)CC(Cl)C[C@@H](F)C"_smiles;
m->setProp<std::string>("_Name", "mol1");
REQUIRE(m);
MolDraw2DSVG drawer(-1, -1);
MolDraw2DUtils::drawMolACS1996(drawer, *m, "Mol 1", nullptr, nullptr);
drawer.finishDrawing();
std::string text = drawer.getDrawingText();
std::ofstream outs(nameBase + ".svg");
outs << text;
outs.flush();
outs.close();
check_file_hash(nameBase + ".svg");
}
TEST_CASE("Bad double bond - Github 6160") {
std::string nameBase = "test_github6160";
std::vector<std::string> smiles{"c1ccccc1NC=NCCS(=O)(=NC)N",
"c1ccccc1NC=NCCS(=O)(=NCC(Cl)(F)C)N",
"c1ccccc1NC=NCCS(=O)(=CCC(Cl)(F)C)N"};
for (auto i = 0u; i < smiles.size(); ++i) {
std::unique_ptr<ROMol> m(SmilesToMol(smiles[i]));
m->setProp<std::string>("_Name", "mol" + std::to_string(i + 1));
REQUIRE(m);
MolDraw2DSVG drawer(300, 300, -1, -1, NO_FREETYPE);
// it's a bit easier to deal with in BW.
assignBWPalette(drawer.drawOptions().atomColourPalette);
drawer.drawOptions().addBondIndices = true;
drawer.drawOptions().addAtomIndices = true;
MolDraw2DUtils::prepareAndDrawMolecule(drawer, *m);
drawer.finishDrawing();
std::string text = drawer.getDrawingText();
std::string svgName = nameBase + "_" + std::to_string(i + 1) + ".svg";
std::ofstream outs(svgName);
outs << text;
outs.flush();
outs.close();
// check that the two lines for bond atom-11 atom-13 are parallel.
std::regex bond5(
"'bond-12 atom-11 atom-13' d='M\\s+(\\d+\\.\\d+),(\\d+\\.\\d+)"
" L\\s+(\\d+\\.\\d+),(\\d+\\.\\d+)");
std::ptrdiff_t const match_count(
std::distance(std::sregex_iterator(text.begin(), text.end(), bond5),
std::sregex_iterator()));
CHECK(match_count == 2);
auto match_begin = std::sregex_iterator(text.begin(), text.end(), bond5);
auto match_end = std::sregex_iterator();
std::vector<Point2D> points;
for (std::sregex_iterator i = match_begin; i != match_end; ++i) {
std::smatch match = *i;
points.push_back(Point2D(stod(match[1]), stod(match[2])));
points.push_back(Point2D(stod(match[3]), stod(match[4])));
}
auto vec1 = points[0].directionVector(points[1]);
auto vec2 = points[2].directionVector(points[3]);
CHECK(vec1.dotProduct(vec2) == Catch::Approx(1.0).margin(1.0e-4));
check_file_hash(svgName);
}
}
TEST_CASE("No crossing for oddly drawn double bond - Github 6170") {
std::string nameBase = "test_github6170";
auto m = R"CTAB(
RDKit 2D
8 7 0 0 0 0 0 0 0 0999 V2000
3.0428 -1.6819 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
3.0022 1.7243 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
1.8934 -1.6549 0.0000 N 0 0 0 0 0 0 0 0 0 0 0 0
4.1949 -2.8653 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
1.9237 1.6929 0.0000 N 0 0 0 0 0 0 0 0 0 0 0 0
4.1521 2.9055 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
0.6779 -1.6657 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
0.6267 1.6960 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
1 2 1 0
1 3 2 3
1 4 1 0
2 5 2 3
2 6 1 0
3 7 1 0
5 8 1 0
M END
)CTAB"_ctab;
auto doBondsIntersect = [](const std::string &text,
const std::regex &bond) -> void {
std::ptrdiff_t const match_count(
std::distance(std::sregex_iterator(text.begin(), text.end(), bond),
std::sregex_iterator()));
CHECK(match_count == 2);
auto match_begin = std::sregex_iterator(text.begin(), text.end(), bond);
auto match_end = std::sregex_iterator();
std::vector<Point2D> points;
for (std::sregex_iterator i = match_begin; i != match_end; ++i) {
std::smatch match = *i;
points.push_back(Point2D(stod(match[1]), stod(match[2])));
points.push_back(Point2D(stod(match[3]), stod(match[4])));
}
CHECK(MolDraw2D_detail::doLinesIntersect(points[0], points[1], points[2],
points[3], nullptr));
};
REQUIRE(m);
{
MolDraw2DSVG drawer(250, 250, -1, -1, NO_FREETYPE);
// it's a bit easier to deal with in BW.
assignBWPalette(drawer.drawOptions().atomColourPalette);
drawer.drawOptions().addAtomIndices = true;
REQUIRE_NOTHROW(drawer.drawMolecule(*m));
drawer.finishDrawing();
std::string text = drawer.getDrawingText();
std::ofstream outs(nameBase + ".svg");
outs << text;
outs.flush();
outs.close();
// check that the two lines for both double bonds intersect.
std::regex bond1(
"'bond-1 atom-0 atom-2' d='M\\s+(\\d+\\.\\d+),(\\d+\\.\\d+)"
" L\\s+(\\d+\\.\\d+),(\\d+\\.\\d+)");
doBondsIntersect(text, bond1);
std::regex bond3(
"'bond-3 atom-1 atom-4' d='M\\s+(\\d+\\.\\d+),(\\d+\\.\\d+)"
" L\\s+(\\d+\\.\\d+),(\\d+\\.\\d+)");
doBondsIntersect(text, bond3);
check_file_hash(nameBase + ".svg");
}
}
TEST_CASE("getMolSize()") {
std::string nameBase = "test_getMolSize";
auto mol = "Oc1ccc(C(=O)O)cc1"_smiles;
REQUIRE(mol);
SECTION("basics") {
MolDraw2DSVG drawer(-1, -1);
drawer.drawMolecule(*mol);
auto dims = std::make_pair(drawer.width(), drawer.height());
CHECK(dims == drawer.getMolSize(*mol));
}
SECTION("calculate size pre-drawing") {
MolDraw2DSVG drawer(-1, -1);
auto sz = drawer.getMolSize(*mol);
drawer.drawMolecule(*mol);
auto dims = std::make_pair(drawer.width(), drawer.height());
CHECK(dims == sz);
CHECK(dims == drawer.getMolSize(*mol));
}
SECTION("drawing with it") {
MolDraw2DSVG drawer(1000, 1000, -1, -1, true);
drawer.setFlexiMode(true);
drawer.clearDrawing();
drawer.drawOptions().clearBackground = false;
auto dims = drawer.getMolSize(*mol, "m1");
drawer.setOffset(500 - dims.first / 2, 500 - dims.second / 2);
drawer.drawMolecule(*mol, "m1");
auto dims2 = drawer.getMolSize(*mol, "m2");
CHECK(dims == dims2);
drawer.setOffset(500 - dims2.first / 2 + 100, 300 + dims2.second);
drawer.drawMolecule(*mol, "m2");
drawer.setOffset(500 - dims2.first / 2 - 200, 700 + dims2.second);
drawer.drawMolecule(*mol, "m3");
drawer.setOffset(500 - dims2.first / 2 - 400, 500 + dims2.second / 2);
drawer.drawMolecule(*mol, "m4");
drawer.finishDrawing();
std::string text = drawer.getDrawingText();
std::ofstream outs(nameBase + ".svg");
outs << text;
outs.flush();
outs.close();
check_file_hash(nameBase + ".svg");
}
}
TEST_CASE(
"Filled circles in multi-coloured highlights with very large circles - Github 6200") {
std::string nameBase = "test_github6200";
auto testArcs = [](const std::string &text, const std::regex &atomLine,
int numArcs, double arcLength) -> void {
std::ptrdiff_t const match_count(
std::distance(std::sregex_iterator(text.begin(), text.end(), atomLine),
std::sregex_iterator()));
CHECK(match_count == numArcs);
auto match_begin = std::sregex_iterator(text.begin(), text.end(), atomLine);
auto match_end = std::sregex_iterator();
// Check that the lengths of the lines in the arc are the correct size.
for (std::sregex_iterator i = match_begin; i != match_end; ++i) {
std::smatch match = *i;
auto p1 = Point2D(stod(match[1]), stod(match[2]));
auto p2 = Point2D(stod(match[3]), stod(match[4]));
auto p3 = Point2D(stod(match[5]), stod(match[6]));
CHECK_THAT((p1 - p2).length(),
Catch::Matchers::WithinAbs(arcLength, 0.1));
CHECK_THAT((p2 - p3).length(),
Catch::Matchers::WithinAbs(arcLength, 0.1));
}
};
{
auto m = "N#CC(C#N)=C1C(=O)c2cccc3cccc1c23"_smiles;
REQUIRE(m);
std::vector<DrawColour> colours = {
DrawColour(0.8, 0.0, 0.8), DrawColour(0.8, 0.8, 0.0),
DrawColour(0.0, 0.8, 0.8), DrawColour(0.0, 0.0, 0.8)};
auto rings = m->getRingInfo();
auto &atomRings = rings->atomRings();
std::map<int, std::vector<DrawColour>> atomCols;
std::map<int, double> atomRads;
for (auto i = 0u; i < atomRings.size(); ++i) {
for (auto j = 0u; j < atomRings[i].size(); ++j) {
auto ex = atomCols.find(atomRings[i][j]);
if (ex == atomCols.end()) {
std::vector<DrawColour> cvec(1, colours[i]);
atomCols.insert(std::make_pair(atomRings[i][j], cvec));
} else {
if (ex->second.end() ==
find(ex->second.begin(), ex->second.end(), colours[i])) {
ex->second.push_back(colours[i]);
}
}
atomRads[atomRings[i][j]] = 0.35;
}
}
auto &bondRings = rings->bondRings();
std::map<int, int> bondMults;
std::map<int, std::vector<DrawColour>> bondCols;
for (auto i = 0u; i < bondRings.size(); ++i) {
for (auto j = 0u; j < bondRings[i].size(); ++j) {
auto ex = bondCols.find(bondRings[i][j]);
if (ex == bondCols.end()) {
std::vector<DrawColour> cvec(1, colours[i]);
bondCols.insert(std::make_pair(bondRings[i][j], cvec));
} else {
if (ex->second.end() ==
find(ex->second.begin(), ex->second.end(), colours[i])) {
ex->second.push_back(colours[i]);
}
}
}
}
{
MolDraw2DSVG drawer(300, 300, -1, -1, NO_FREETYPE);
drawer.drawOptions().fillHighlights = true;
drawer.drawMoleculeWithHighlights(*m, "Test 1", atomCols, bondCols,
atomRads, bondMults);
drawer.finishDrawing();
std::string text = drawer.getDrawingText();
std::string svgName = nameBase + "_1.svg";
std::ofstream outs(svgName);
outs << text;
outs.flush();
outs.close();
std::regex atom17(
"class='atom-17' d='M\\s+(\\d+\\.\\d+),(\\d+\\.\\d+)"
" L\\s+(\\d+\\.\\d+),(\\d+\\.\\d+) L\\s+(\\d+\\.\\d+),(\\d+\\.\\d+)");
// there are 3 arcs on atom-17, for a 3 colour highlight.
testArcs(text, atom17, 3, 0.85);
}
check_file_hash(nameBase + "_1.svg");
}
{
// Check that #6194 is the same issue and also fixed.
auto m = "CCC"_smiles;
REQUIRE(m);
std::vector<DrawColour> colours = {DrawColour(0.8, 0.0, 0.8),
DrawColour(0.8, 0.8, 0.0)};
std::map<int, std::vector<DrawColour>> atomCols;
atomCols.insert(std::make_pair(0, std::vector<DrawColour>{colours[0]}));
atomCols.insert(std::make_pair(1, std::vector<DrawColour>{colours[0]}));
atomCols.insert(
std::make_pair(2, std::vector<DrawColour>{colours[0], colours[1]}));
std::map<int, double> atomRads;
std::map<int, int> bondMults;
std::map<int, std::vector<DrawColour>> bondCols;
MolDraw2DSVG drawer(300, 300, -1, -1, NO_FREETYPE);
drawer.drawOptions().fillHighlights = true;
drawer.drawMoleculeWithHighlights(*m, "Test 1", atomCols, bondCols,
atomRads, bondMults);
drawer.finishDrawing();
std::string text = drawer.getDrawingText();
std::string svgName = nameBase + "_2.svg";
std::ofstream outs(svgName);
outs << text;
outs.flush();
outs.close();
std::regex atom2(
"class='atom-2' d='M\\s+(\\d+\\.\\d+),(\\d+\\.\\d+)"
" L\\s+(\\d+\\.\\d+),(\\d+\\.\\d+) L\\s+(\\d+\\.\\d+),(\\d+\\.\\d+)");
// there are 2 arcs on atom-2, for a 2 colour highlight.
testArcs(text, atom2, 2, 2.15);
check_file_hash(nameBase + "_2.svg");
}
}
TEST_CASE("queryColour can be set to a non-default value") {
std::string nameBase = "test_queryColour";
auto m = "c1ccc2nc([*:1])nc([*:2])c2c1"_smarts;
REQUIRE(m);
{
// Check that default queryColour is #7F7F7F.
MolDraw2DSVG drawer(300, 300, -1, -1, NO_FREETYPE);
drawer.drawMolecule(*m);
drawer.finishDrawing();
std::string text = drawer.getDrawingText();
std::string svgName = nameBase + "_1.svg";
std::ofstream outs(svgName);
outs << text;
outs.flush();
outs.close();
CHECK(text.find("#7F7F7F") != std::string::npos);
check_file_hash(nameBase + "_1.svg");
}
{
// Check that queryColour can be set to black.
DrawColour queryColour(0.0, 0.0, 0.0);
MolDraw2DSVG drawer(300, 300, -1, -1, NO_FREETYPE);
drawer.drawOptions().queryColour = queryColour;
drawer.drawMolecule(*m);
drawer.finishDrawing();
std::string text = drawer.getDrawingText();
std::string svgName = nameBase + "_2.svg";
std::ofstream outs(svgName);
outs << text;
outs.flush();
outs.close();
CHECK(text.find("#7F7F7F") == std::string::npos);
check_file_hash(nameBase + "_2.svg");
}
}
TEST_CASE(
"Github #6336: calling drawing commands before drawing a molecule with MolDraw2DCairo") {
std::string nameBase = "github6336";
#ifdef RDK_BUILD_CAIRO_SUPPORT
SECTION("cairo") {
MolDraw2DCairo drawer(300, 300, -1, -1, NO_FREETYPE);
drawer.setColour(DrawColour(1, 0, 1));
drawer.drawRect(Point2D(10, 10), Point2D(150, 150), true);
drawer.setColour(DrawColour(0, 1, 1));
drawer.drawLine(Point2D(150, 150), Point2D(250, 299), true);
drawer.finishDrawing();
drawer.writeDrawingText(nameBase + "_1.png");
check_file_hash(nameBase + "_1.png");
}
#endif
SECTION("SVG") {
MolDraw2DSVG drawer(300, 300, -1, -1, NO_FREETYPE);
drawer.setColour(DrawColour(1, 0, 1));
drawer.drawRect(Point2D(10, 10), Point2D(150, 150), true);
drawer.setColour(DrawColour(0, 1, 1));
drawer.drawLine(Point2D(150, 150), Point2D(250, 299), true);
drawer.finishDrawing();
std::ofstream outs(nameBase + "_1.svg");
outs << drawer.getDrawingText();
outs.flush();
outs.close();
check_file_hash(nameBase + "_1.svg");
}
}
TEST_CASE("Github #6416: crash with colinear atoms") {
std::string name = "github6416.svg";
auto m = R"CTAB(168010013
RDKit 2D
0 0 0 0 0 0 0 0 0 0999 V3000
M V30 BEGIN CTAB
M V30 COUNTS 35 36 0 0 1
M V30 BEGIN ATOM
M V30 1 F 11.000000 -1.318000 0.000000 0
M V30 2 F 12.000000 -2.318000 0.000000 0
M V30 3 F 11.000000 -3.318000 0.000000 0
M V30 4 O 6.207100 2.719200 0.000000 0
M V30 5 O 6.500000 0.280000 0.000000 0
M V30 6 O 6.500000 -1.452000 0.000000 0
M V30 7 N 8.000000 -0.586000 0.000000 0
M V30 8 C 3.500000 2.012100 0.000000 0
M V30 9 C 4.000000 1.146000 0.000000 0
M V30 10 C 2.500000 2.012100 0.000000 0
M V30 11 C 5.500000 2.012100 0.000000 0
M V30 12 C 4.000000 2.878100 0.000000 0
M V30 13 C 2.000000 1.146000 0.000000 0
M V30 14 C 5.000000 1.146000 0.000000 0
M V30 15 C 5.000000 2.878100 0.000000 0
M V30 16 C 4.500000 2.012100 0.000000 0
M V30 17 C 3.000000 1.146000 0.000000 0
M V30 18 C 5.500000 0.280000 0.000000 0
M V30 19 C 2.500000 0.280000 0.000000 0
M V30 20 C 6.465900 1.753200 0.000000 0
M V30 21 C 5.000000 -0.586000 0.000000 0
M V30 22 C 2.500000 -1.452000 0.000000 0
M V30 23 C 3.500000 -1.452000 0.000000 0
M V30 24 C 2.000000 -0.586000 0.000000 0
M V30 25 C 4.000000 -0.586000 0.000000 0
M V30 26 C 3.500000 0.280000 0.000000 0
M V30 27 C 3.000000 -0.586000 0.000000 0
M V30 28 C 7.000000 -0.586000 0.000000 0
M V30 29 C 8.500000 -1.452000 0.000000 0
M V30 30 C 9.500000 -1.452000 0.000000 0
M V30 31 C 8.000000 -2.318000 0.000000 0
M V30 32 C 10.000000 -2.318000 0.000000 0
M V30 33 C 8.500000 -3.184100 0.000000 0
M V30 34 C 9.500000 -3.184100 0.000000 0
M V30 35 C 11.000000 -2.318000 0.000000 0
M V30 END ATOM
M V30 BEGIN BOND
M V30 1 1 1 35
M V30 2 1 2 35
M V30 3 1 3 35
M V30 4 1 4 11
M V30 5 1 5 18
M V30 6 1 5 28
M V30 7 2 6 28
M V30 8 1 7 28
M V30 9 1 7 29
M V30 10 1 8 9
M V30 11 1 8 10
M V30 12 1 8 12
M V30 13 1 9 16
M V30 14 1 9 17
M V30 15 1 10 13
M V30 16 1 11 14
M V30 17 1 11 15
M V30 18 1 11 20
M V30 19 2 12 15 CFG=2
M V30 20 1 13 19
M V30 21 1 14 18
M V30 22 1 18 21
M V30 23 2 19 24 CFG=2
M V30 24 1 19 26
M V30 25 2 21 25 CFG=2
M V30 26 1 22 23
M V30 27 1 22 24
M V30 28 1 23 25
M V30 29 1 25 27
M V30 30 2 29 30
M V30 31 1 29 31
M V30 32 1 30 32
M V30 33 2 31 33
M V30 34 2 32 34
M V30 35 1 32 35
M V30 36 1 33 34
M V30 END BOND
M V30 END CTAB
M END
)CTAB"_ctab;
REQUIRE(m);
MolDraw2DSVG drawer(300, 300, -1, -1);
drawer.drawMolecule(*m);
drawer.finishDrawing();
std::ofstream outs(name);
outs << drawer.getDrawingText();
outs.flush();
outs.close();
check_file_hash(name);
}
TEST_CASE("Github 6397 - chiral tag overlapping atom label") {
const static std::regex absA(
"<text x='(\\d+\\.\\d+)' y='(\\d+\\.\\d+)' class='note'.*>A</text>");
auto checkABS = [](const std::string &text, int expCount, double expX,
double expY) {
std::ptrdiff_t const match_count(
std::distance(std::sregex_iterator(text.begin(), text.end(), absA),
std::sregex_iterator()));
CHECK(match_count == expCount);
auto match_begin = std::sregex_iterator(text.begin(), text.end(), absA);
std::smatch match = *match_begin;
double x = stod(match[1]);
CHECK_THAT(x, Catch::Matchers::WithinAbs(expX, 0.1));
double y = stod(match[2]);
CHECK_THAT(y, Catch::Matchers::WithinAbs(expY, 0.1));
};
std::string nameBase = "test_github6397";
auto m1 = R"CTAB(
RDKit 2D
9 9 0 0 1 0 0 0 0 0999 V2000
2.3094 -1.6667 0.0000 F 0 0 0 0 0 0 0 0 0 0 0 0
1.0104 -0.9167 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
-0.2887 -1.6667 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
-1.5877 -0.9167 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
-1.5877 0.5833 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
-2.8868 1.3333 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0
-0.2887 1.3333 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
1.0104 0.5833 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
2.3094 1.3333 0.0000 Cl 0 0 0 0 0 0 0 0 0 0 0 0
1 2 1 0
2 3 1 0
3 4 1 0
4 5 1 0
5 6 1 1
5 7 1 0
7 8 1 0
8 9 1 6
8 2 1 0
M END)CTAB"_ctab;
REQUIRE(m1);
{
MolDraw2DSVG drawer(300, 300, -1, -1, NO_FREETYPE);
drawer.drawOptions().includeChiralFlagLabel = true;
drawer.drawMolecule(*m1);
drawer.finishDrawing();
std::string text = drawer.getDrawingText();
std::string svgName = nameBase + "_1.svg";
std::ofstream outs(svgName);
outs << text;
outs.flush();
outs.close();
checkABS(text, 1, 239.5, 34.5);
check_file_hash(svgName);
}
auto m2 = R"CTAB(ACS Document 1996
ChemDraw06062309122D
0 0 0 0 0 0 V3000
M V30 BEGIN CTAB
M V30 COUNTS 10 10 0 0 1
M V30 BEGIN ATOM
M V30 1 C -0.714471 0.000000 0.000000 0
M V30 2 C -0.714471 -0.825000 0.000000 0
M V30 3 C 0.000000 -1.237500 0.000000 0
M V30 4 C 0.714472 -0.825000 0.000000 0
M V30 5 C 0.714472 0.000000 0.000000 0
M V30 6 C 0.000000 0.412500 0.000000 0
M V30 7 C 1.428942 0.412500 0.000000 0
M V30 8 Cl 1.428942 1.237500 0.000000 0
M V30 9 O -1.428942 0.412500 0.000000 0
M V30 10 F -1.428942 -1.237500 0.000000 0
M V30 END ATOM
M V30 BEGIN BOND
M V30 1 1 1 2
M V30 2 1 2 3
M V30 3 1 3 4
M V30 4 1 4 5
M V30 5 1 5 6
M V30 6 1 6 1
M V30 7 1 5 7 CFG=1
M V30 8 1 7 8
M V30 9 1 1 9 CFG=1
M V30 10 1 2 10 CFG=1
M V30 END BOND
M V30 BEGIN COLLECTION
M V30 MDLV30/STEABS ATOMS=(3 1 2 5)
M V30 END COLLECTION
M V30 END CTAB
M END)CTAB"_ctab;
REQUIRE(m2);
{
MolDraw2DSVG drawer(300, 300, -1, -1, NO_FREETYPE);
drawer.drawOptions().includeChiralFlagLabel = true;
drawer.drawMolecule(*m2, "Important legend");
drawer.finishDrawing();
std::string text = drawer.getDrawingText();
std::string svgName = nameBase + "_2.svg";
std::ofstream outs(svgName);
outs << text;
outs.flush();
outs.close();
checkABS(text, 1, 0.0, 52.0);
check_file_hash(svgName);
}
auto m3 = R"CTAB(ACS Document 1996
ChemDraw06062312152D
0 0 0 0 0 0 V3000
M V30 BEGIN CTAB
M V30 COUNTS 12 12 0 0 1
M V30 BEGIN ATOM
M V30 1 C -0.714471 0.412500 0.000000 0
M V30 2 C -0.714471 -0.412500 0.000000 0
M V30 3 C 0.000000 -0.825000 0.000000 0
M V30 4 C 0.714472 -0.412500 0.000000 0
M V30 5 C 0.714472 0.412500 0.000000 0
M V30 6 C 0.000000 0.825000 0.000000 0
M V30 7 C 1.428942 0.825000 0.000000 0
M V30 8 C -1.428942 0.825000 0.000000 0
M V30 9 C 1.428942 -0.825000 0.000000 0
M V30 10 C 1.428942 1.650000 0.000000 0
M V30 11 O -1.428942 1.650000 0.000000 0
M V30 12 I 1.428942 -1.650000 0.000000 0
M V30 END ATOM
M V30 BEGIN BOND
M V30 1 1 1 2
M V30 2 1 2 3
M V30 3 1 3 4
M V30 4 1 4 5
M V30 5 1 5 6
M V30 6 1 6 1
M V30 7 1 5 7 CFG=1
M V30 8 1 1 8 CFG=1
M V30 9 1 4 9 CFG=1
M V30 10 1 7 10
M V30 11 1 8 11
M V30 12 1 9 12
M V30 END BOND
M V30 BEGIN COLLECTION
M V30 MDLV30/STEABS ATOMS=(3 1 4 5)
M V30 END COLLECTION
M V30 END CTAB
M END)CTAB"_ctab;
REQUIRE(m3);
{
MolDraw2DSVG drawer(300, 300, -1, -1, NO_FREETYPE);
drawer.drawOptions().includeChiralFlagLabel = true;
drawer.drawMolecule(*m3, "Important legend");
drawer.finishDrawing();
std::string text = drawer.getDrawingText();
std::string svgName = nameBase + "_3.svg";
std::ofstream outs(svgName);
outs << text;
outs.flush();
outs.close();
checkABS(text, 1, 0.0, 258.3);
check_file_hash(svgName);
}
{
// make sure the ABS follows the molecule.
MolDraw2DSVG drawer(500, 400, 250, 200, NO_FREETYPE);
drawer.drawOptions().includeChiralFlagLabel = true;
drawer.drawMolecule(*m1, "m1");
drawer.setOffset(250, 0);
drawer.drawMolecule(*m2, "m2");
drawer.setOffset(0, 200);
drawer.drawMolecule(*m3, "m3");
drawer.setOffset(250, 200);
drawer.finishDrawing();
std::string text = drawer.getDrawingText();
std::string svgName = nameBase + "_4.svg";
std::ofstream outs(svgName);
outs << text;
outs.flush();
outs.close();
checkABS(text, 3, 0.0, 173.3);
text = std::regex_replace(text, absA, "",
std::regex_constants::format_first_only);
checkABS(text, 2, 250.0, 42.8);
text = std::regex_replace(text, absA, "",
std::regex_constants::format_first_only);
checkABS(text, 1, 191.4, 233.4);
check_file_hash(svgName);
}
{
// Visual check to make sure it works in Freetype mode as well.
MolDraw2DSVG drawer(500, 400, 250, 200);
drawer.drawOptions().includeChiralFlagLabel = true;
drawer.drawMolecule(*m1, "m1");
drawer.setOffset(250, 0);
drawer.drawMolecule(*m2, "m2");
drawer.setOffset(0, 200);
drawer.drawMolecule(*m3, "m3");
drawer.setOffset(250, 200);
drawer.finishDrawing();
std::string text = drawer.getDrawingText();
std::string svgName = nameBase + "_5.svg";
std::ofstream outs(svgName);
outs << text;
outs.flush();
outs.close();
check_file_hash(svgName);
}
}
TEST_CASE("Github #6400: extra padding, no legend apparent") {
std::string nameBase = "test_github6400";
auto m = "CCCOC"_smiles;
REQUIRE(m);
MolDraw2DSVG drawer(300, 300, -1, -1, NO_FREETYPE);
drawer.drawOptions().padding = 0.2;
drawer.drawMolecule(*m, "Legendary Big Padding");
drawer.finishDrawing();
std::ofstream outs(nameBase + "_1.svg");
auto text = drawer.getDrawingText();
// The original bug manifested itself with a font size of 0 for the
// legend. Fixed, it comes out at 16.
CHECK(text.find("font-size:0px") == std::string::npos);
REQUIRE(text.find("font-size:16px") != std::string::npos);
outs << text;
outs.flush();
outs.close();
check_file_hash(nameBase + "_1.svg");
}
TEST_CASE("Github #6504: double bonds not drawn correctly for sulfoximines") {
std::string baseName = "github6504";
auto m1 = R"CTAB(
RDKit 2D
7 6 0 0 0 0 0 0 0 0999 V2000
-3.3489 -2.7067 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
-2.0093 -3.4808 0.0000 N 0 0 0 0 0 0 0 0 0 0 0 0
-0.6698 -2.7067 0.0000 S 0 0 0 0 0 0 0 0 0 0 0 0
0.6696 -3.4792 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0
-0.6698 -1.1601 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
0.6696 -0.3864 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
-0.6698 -4.2536 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
1 2 1 0
2 3 2 0
3 4 2 0
3 5 1 0
5 6 1 0
3 7 1 1
M END
)CTAB"_ctab;
// The bug report showed different manifestations of the problem
// using the given coords and those generated from scratch.
REQUIRE(m1);
std::unique_ptr<RDKit::ROMol> m2(new RDKit::ROMol(*m1));
RDDepict::compute2DCoords(*m2);
// The test, in both cases, is that the 2 ends of the lines
// making bond 1 are separated by a small distance. It's a two
// colour line, so the relevant points are 0,4 and 3,7.
auto checkEndSep = [](const std::string &text) {
std::regex bond5(
"'bond-1 atom-1 atom-2' d='M\\s+(\\d+\\.\\d+),(\\d+\\.\\d+)"
" L\\s+(\\d+\\.\\d+),(\\d+\\.\\d+)");
std::ptrdiff_t const match_count(
std::distance(std::sregex_iterator(text.begin(), text.end(), bond5),
std::sregex_iterator()));
CHECK(match_count == 4);
auto match_begin = std::sregex_iterator(text.begin(), text.end(), bond5);
auto match_end = std::sregex_iterator();
std::vector<Point2D> points;
for (std::sregex_iterator i = match_begin; i != match_end; ++i) {
std::smatch match = *i;
points.push_back(Point2D(stod(match[1]), stod(match[2])));
points.push_back(Point2D(stod(match[3]), stod(match[4])));
}
auto d1 = (points[0] - points[4]).length();
auto d2 = (points[3] - points[7]).length();
// the distances should be > 10 and roughly equal. They are
// 12 and 14 pixels apart in the two molecules.
CHECK(d1 > 10.0);
CHECK(d2 > 10.0);
CHECK_THAT(fabs(d1 - d2), Catch::Matchers::WithinAbs(0.0, 0.1));
};
{
MolDraw2DSVG drawer(300, 300, -1, -1);
drawer.drawOptions().addAtomIndices = true;
drawer.drawMolecule(*m1);
drawer.finishDrawing();
std::ofstream outs(baseName + "_1.svg");
std::string text = drawer.getDrawingText();
outs << text;
outs.flush();
outs.close();
checkEndSep(text);
check_file_hash(baseName + "_1.svg");
}
{
MolDraw2DSVG drawer(300, 300, -1, -1);
drawer.drawOptions().addAtomIndices = true;
drawer.drawMolecule(*m2);
drawer.finishDrawing();
std::ofstream outs(baseName + "_2.svg");
std::string text = drawer.getDrawingText();
outs << text;
outs.flush();
outs.close();
checkEndSep(text);
check_file_hash(baseName + "_2.svg");
}
}
TEST_CASE("Github #6569: placement of bond labels bad when atoms overlap") {
std::string baseName = "github6569";
auto m = R"CTAB(CHEMBL3612237
RDKit 2D
14 15 0 0 0 0 0 0 0 0999 V2000
-0.6828 -1.6239 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
-0.6828 0.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
0.6090 0.5905 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
1.9007 0.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
1.9007 -1.6239 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
0.6090 -2.3805 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
1.9007 1.3471 0.0000 N 0 0 0 0 0 0 0 0 0 0 0 0
-0.6828 1.3471 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
0.6090 2.0668 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
-0.6319 1.4849 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
-0.5072 2.6784 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0
-1.7280 0.9964 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0
-0.6828 0.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
1.9007 0.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
1 2 1 0
1 6 1 0
2 3 1 0
3 4 1 0
4 5 1 0
5 6 1 0
4 7 1 0
2 8 1 0
8 9 1 0
7 9 1 0
3 10 1 1
10 11 1 0
10 12 2 0
2 13 1 1
4 14 1 1
M END
)CTAB"_ctab;
REQUIRE(m);
{
MolDraw2DSVG drawer(300, 300, -1, -1);
drawer.drawOptions().addAtomIndices = true;
drawer.drawMolecule(*m);
drawer.finishDrawing();
std::ofstream outs(baseName + "_1.svg");
std::string text = drawer.getDrawingText();
outs << text;
outs.flush();
outs.close();
// All the coords came out as nan in the buggy version
CHECK(text.find("nan") == std::string::npos);
check_file_hash(baseName + "_1.svg");
}
{
MolDraw2DSVG drawer(300, 300, -1, -1);
drawer.drawOptions().addBondIndices = true;
drawer.drawMolecule(*m);
drawer.finishDrawing();
std::ofstream outs(baseName + "_2.svg");
std::string text = drawer.getDrawingText();
outs << text;
outs.flush();
outs.close();
// All the coords came out as nan in the buggy version
CHECK(text.find("nan") == std::string::npos);
check_file_hash(baseName + "_2.svg");
}
}
TEST_CASE("Lasso highlights") {
std::string baseName = "lasso_highlights_";
auto get_all_hit_atoms = [](ROMol &mol,
const std::string &smt) -> std::vector<int> {
std::vector<int> hit_atoms;
RWMol *query = SmartsToMol(smt);
std::vector<MatchVectType> hits_vect;
SubstructMatch(mol, *query, hits_vect);
for (size_t i = 0; i < hits_vect.size(); ++i) {
for (size_t j = 0; j < hits_vect[i].size(); ++j) {
hit_atoms.push_back(hits_vect[i][j].second);
}
}
delete query;
return hit_atoms;
};
auto update_colour_map = [](const std::vector<int> &ats, DrawColour col,
std::map<int, std::vector<DrawColour>> &ha_map) {
for (auto h : ats) {
auto ex = ha_map.find(h);
if (ex == ha_map.end()) {
std::vector<DrawColour> cvec(1, col);
ha_map.insert(make_pair(h, cvec));
} else {
if (ex->second.end() ==
find(ex->second.begin(), ex->second.end(), col)) {
ex->second.push_back(col);
}
}
}
};
std::map<int, double> h_rads;
std::map<int, int> h_lw_mult;
{
std::string smiles = "CO[C@@H](O)C1=C(O[C@H](F)Cl)C(C#N)=C1ONNC[NH3+]";
std::unique_ptr<ROMol> m(SmilesToMol(smiles));
RDDepict::compute2DCoords(*m);
std::vector<std::string> smarts = {"CONN", "N#CC~CO", "C=CON", "CONNCN"};
std::vector<DrawColour> colours = {
DrawColour(1.0, 0.0, 0.0), DrawColour(0.0, 1.0, 0.0),
DrawColour(0.0, 0.0, 1.0), DrawColour(1.0, 0.55, 0.0)};
std::map<int, std::vector<DrawColour>> ha_map;
std::map<int, std::vector<DrawColour>> hb_map;
for (size_t i = 0; i < smarts.size(); ++i) {
std::vector<int> hit_atoms = get_all_hit_atoms(*m, smarts[i]);
update_colour_map(hit_atoms, colours[i], ha_map);
}
MolDraw2DSVG drawer(500, 500);
drawer.drawOptions().multiColourHighlightStyle =
RDKit::MultiColourHighlightStyle::LASSO;
drawer.drawOptions().addAtomIndices = true;
drawer.drawMoleculeWithHighlights(*m, "Lasso 1", ha_map, hb_map, h_rads,
h_lw_mult);
drawer.finishDrawing();
std::string text = drawer.getDrawingText();
std::ofstream outs(baseName + "1.svg");
outs << text;
outs.flush();
outs.close();
// atom 16 should have 1 red arc
std::regex a16(
"<path class='atom-16' d='M (\\d+\\.\\d+),(\\d+\\.\\d+) L (\\d+\\.\\d+),(\\d+\\.\\d+).*stroke:#FF0000;");
std::ptrdiff_t const match_count(
std::distance(std::sregex_iterator(text.begin(), text.end(), a16),
std::sregex_iterator()));
CHECK(match_count == 1);
auto a16reg = std::sregex_iterator(text.begin(), text.end(), a16);
auto dat1 = *a16reg;
#ifdef RDK_BUILD_FREETYPE_SUPPORT
CHECK_THAT(stod(dat1[1]), Catch::Matchers::WithinAbs(273.1, 0.1));
CHECK_THAT(stod(dat1[2]), Catch::Matchers::WithinAbs(131.2, 0.1));
CHECK_THAT(stod(dat1[3]), Catch::Matchers::WithinAbs(272.1, 0.1));
CHECK_THAT(stod(dat1[4]), Catch::Matchers::WithinAbs(130.0, 0.1));
check_file_hash(baseName + "1.svg");
#else
CHECK_THAT(stod(dat1[1]), Catch::Matchers::WithinAbs(274.9, 0.1));
CHECK_THAT(stod(dat1[2]), Catch::Matchers::WithinAbs(130.9, 0.1));
CHECK_THAT(stod(dat1[3]), Catch::Matchers::WithinAbs(273.9, 0.1));
CHECK_THAT(stod(dat1[4]), Catch::Matchers::WithinAbs(129.7, 0.1));
#endif
}
{
// The non-overlapping atom sets should have radii the same size.
std::string smiles = "CO[C@@H](O)C1=C(O[C@H](F)Cl)C(C#N)=C1ONNC[NH3+]";
std::unique_ptr<ROMol> m(SmilesToMol(smiles));
RDDepict::compute2DCoords(*m);
std::vector<std::string> smarts = {"CONN", "COC[OH]", "N#CC~CO"};
std::vector<DrawColour> colours = {DrawColour(1.0, 0.0, 0.0),
DrawColour(0.0, 1.0, 0.0),
DrawColour(0.0, 0.0, 1.0)};
std::map<int, std::vector<DrawColour>> ha_map;
std::map<int, std::vector<DrawColour>> hb_map;
for (size_t i = 0; i < smarts.size(); ++i) {
std::vector<int> hit_atoms = get_all_hit_atoms(*m, smarts[i]);
update_colour_map(hit_atoms, colours[i], ha_map);
}
std::map<int, double> h_rads;
std::map<int, int> h_lw_mult;
MolDraw2DSVG drawer(500, 500);
drawer.drawOptions().multiColourHighlightStyle =
RDKit::MultiColourHighlightStyle::LASSO;
drawer.drawMoleculeWithHighlights(*m, "Lasso 2", ha_map, hb_map, h_rads,
h_lw_mult);
drawer.finishDrawing();
std::string text = drawer.getDrawingText();
std::ofstream outs(baseName + "2.svg");
outs << text;
outs.flush();
outs.close();
#ifdef RDK_BUILD_FREETYPE_SUPPORT
// atom 0 should have 1 green arc
std::regex a0(
"<path class='atom-0' d='M (\\d+\\.\\d+),(\\d+\\.\\d+) L (\\d+\\.\\d+),(\\d+\\.\\d+).*stroke:#00FF00;");
std::ptrdiff_t const match_count(
std::distance(std::sregex_iterator(text.begin(), text.end(), a0),
std::sregex_iterator()));
CHECK(match_count == 1);
auto a0reg = std::sregex_iterator(text.begin(), text.end(), a0);
auto dat1 = *a0reg;
CHECK_THAT(stod(dat1[1]), Catch::Matchers::WithinAbs(389.5, 0.1));
CHECK_THAT(stod(dat1[2]), Catch::Matchers::WithinAbs(214.4, 0.1));
CHECK_THAT(stod(dat1[3]), Catch::Matchers::WithinAbs(390.2, 0.1));
CHECK_THAT(stod(dat1[4]), Catch::Matchers::WithinAbs(213.9, 0.1));
check_file_hash(baseName + "2.svg");
#endif
}
{
// Another example.
std::string smiles = "c1ccncc1c1ccc(C2CCC2)cc1";
std::unique_ptr<ROMol> m(SmilesToMol(smiles));
RDDepict::compute2DCoords(*m);
std::vector<std::string> smarts = {"a1aaaaa1a1aaaaa1", "c1ccccn1",
"c1ccccc1", "C1CCC1"};
std::vector<DrawColour> colours = {
DrawColour(1.0, 0.0, 0.0), DrawColour(0.0, 1.0, 0.0),
DrawColour(0.0, 0.0, 1.0), DrawColour(1.0, 0.55, 0.0)};
std::map<int, std::vector<DrawColour>> ha_map;
std::map<int, std::vector<DrawColour>> hb_map;
for (size_t i = 0; i < smarts.size(); ++i) {
std::vector<int> hit_atoms = get_all_hit_atoms(*m, smarts[i]);
update_colour_map(hit_atoms, colours[i], ha_map);
}
std::map<int, double> h_rads;
std::map<int, int> h_lw_mult;
MolDraw2DSVG drawer(500, 500);
drawer.drawOptions().multiColourHighlightStyle =
RDKit::MultiColourHighlightStyle::LASSO;
drawer.drawOptions().addAtomIndices = true;
drawer.drawMoleculeWithHighlights(*m, "Lasso 3", ha_map, hb_map, h_rads,
h_lw_mult);
drawer.finishDrawing();
std::string text = drawer.getDrawingText();
std::ofstream outs(baseName + "3.svg");
outs << text;
outs.flush();
outs.close();
#ifdef RDK_BUILD_FREETYPE_SUPPORT
// atom 0 should have 4 arcs
std::regex a0(
"<path class='atom-0' d='M (\\d+\\.\\d+),(\\d+\\.\\d+) L (\\d+\\.\\d+),(\\d+\\.\\d+)");
std::ptrdiff_t const match_count(
std::distance(std::sregex_iterator(text.begin(), text.end(), a0),
std::sregex_iterator()));
CHECK(match_count == 4);
auto a0reg = std::sregex_iterator(text.begin(), text.end(), a0);
auto dat1 = *a0reg;
CHECK_THAT(stod(dat1[1]), Catch::Matchers::WithinAbs(229.1, 0.1));
CHECK_THAT(stod(dat1[2]), Catch::Matchers::WithinAbs(365.1, 0.1));
CHECK_THAT(stod(dat1[3]), Catch::Matchers::WithinAbs(228.9, 0.1));
CHECK_THAT(stod(dat1[4]), Catch::Matchers::WithinAbs(364.2, 0.1));
a0reg++;
dat1 = *a0reg;
CHECK_THAT(stod(dat1[1]), Catch::Matchers::WithinAbs(244.3, 0.1));
CHECK_THAT(stod(dat1[2]), Catch::Matchers::WithinAbs(351.7, 0.1));
CHECK_THAT(stod(dat1[3]), Catch::Matchers::WithinAbs(245.2, 0.1));
CHECK_THAT(stod(dat1[4]), Catch::Matchers::WithinAbs(352.0, 0.1));
check_file_hash(baseName + "3.svg");
#endif
}
{
// Showing use of highlight_bond_map to control which bonds are drawn.
// Bond highlight colours are ignored.
std::string smiles = "c1ccccc1c1ccccc1";
std::unique_ptr<ROMol> m(SmilesToMol(smiles));
RDDepict::compute2DCoords(*m);
std::map<int, std::vector<DrawColour>> ha_map;
for (int i = 0; i < 12; ++i) {
ha_map.insert(
std::pair{i, std::vector<DrawColour>(1, DrawColour(1.0, 0.0, 0.0))});
}
std::map<int, std::vector<DrawColour>> hb_map;
{
MolDraw2DSVG drawer(500, 500);
drawer.drawOptions().multiColourHighlightStyle =
RDKit::MultiColourHighlightStyle::LASSO;
drawer.drawOptions().addAtomIndices = true;
drawer.drawMoleculeWithHighlights(*m, "Lasso 4", ha_map, hb_map, h_rads,
h_lw_mult);
drawer.finishDrawing();
std::string text = drawer.getDrawingText();
std::ofstream outs(baseName + "4.svg");
outs << text;
outs.flush();
outs.close();
#ifdef RDK_BUILD_FREETYPE_SUPPORT
// All the atoms should have 2 arcs except 5 and 6. Check those for
// atom 5.
std::regex a5(
"<path class='atom-5' d='M (\\d+\\.\\d+),(\\d+\\.\\d+) L (\\d+\\.\\d+),(\\d+\\.\\d+)");
std::ptrdiff_t const match_count(
std::distance(std::sregex_iterator(text.begin(), text.end(), a5),
std::sregex_iterator()));
CHECK(match_count == 3);
auto a5reg = std::sregex_iterator(text.begin(), text.end(), a5);
auto dat1 = *a5reg;
CHECK_THAT(stod(dat1[1]), Catch::Matchers::WithinAbs(223.2, 0.1));
CHECK_THAT(stod(dat1[2]), Catch::Matchers::WithinAbs(280.4, 0.1));
CHECK_THAT(stod(dat1[3]), Catch::Matchers::WithinAbs(221.9, 0.1));
CHECK_THAT(stod(dat1[4]), Catch::Matchers::WithinAbs(280.0, 0.1));
a5reg++;
dat1 = *a5reg;
CHECK_THAT(stod(dat1[1]), Catch::Matchers::WithinAbs(217.4, 0.1));
CHECK_THAT(stod(dat1[2]), Catch::Matchers::WithinAbs(251.6, 0.1));
CHECK_THAT(stod(dat1[3]), Catch::Matchers::WithinAbs(218.4, 0.1));
CHECK_THAT(stod(dat1[4]), Catch::Matchers::WithinAbs(250.7, 0.1));
a5reg++;
dat1 = *a5reg;
CHECK_THAT(stod(dat1[1]), Catch::Matchers::WithinAbs(245.3, 0.1));
CHECK_THAT(stod(dat1[2]), Catch::Matchers::WithinAbs(261.0, 0.1));
CHECK_THAT(stod(dat1[3]), Catch::Matchers::WithinAbs(245.5, 0.1));
CHECK_THAT(stod(dat1[4]), Catch::Matchers::WithinAbs(262.3, 0.1));
// There should be 2 lines in red, the lasso along the bi-phenyl
// bond.
std::regex bond5("<path class='bond-5 atom-5 atom-6.*stroke:#FF0000;");
std::ptrdiff_t const match_count1(
std::distance(std::sregex_iterator(text.begin(), text.end(), bond5),
std::sregex_iterator()));
CHECK(match_count1 == 2);
check_file_hash(baseName + "4.svg");
#endif
}
// Set up the bond highlights for everything but the bi-phenyl bond,
// colouring the bonds green although the colour will be ignored.
for (int i = 0; i < 13; ++i) {
if (i != 5) {
hb_map.insert(std::pair{
i, std::vector<DrawColour>(1, DrawColour(0.0, 1.0, 0.0))});
}
}
{
MolDraw2DSVG drawer(500, 500);
drawer.drawOptions().multiColourHighlightStyle =
RDKit::MultiColourHighlightStyle::LASSO;
drawer.drawOptions().addAtomIndices = true;
drawer.drawOptions().addBondIndices = true;
drawer.drawMoleculeWithHighlights(*m, "Lasso 5", ha_map, hb_map, h_rads,
h_lw_mult);
drawer.finishDrawing();
std::string text = drawer.getDrawingText();
std::ofstream outs(baseName + "5.svg");
outs << text;
outs.flush();
outs.close();
#ifdef RDK_BUILD_FREETYPE_SUPPORT
// All the atoms should have 2 arcs except 5 and 6. Check those for
// atom 11.
std::regex a11(
"<path class='atom-11' d='M (\\d+\\.\\d+),(\\d+\\.\\d+) L (\\d+\\.\\d+),(\\d+\\.\\d+)");
std::ptrdiff_t const match_count(
std::distance(std::sregex_iterator(text.begin(), text.end(), a11),
std::sregex_iterator()));
CHECK(match_count == 2);
auto a11reg = std::sregex_iterator(text.begin(), text.end(), a11);
auto dat1 = *a11reg;
CHECK_THAT(stod(dat1[1]), Catch::Matchers::WithinAbs(223.2, 0.1));
CHECK_THAT(stod(dat1[2]), Catch::Matchers::WithinAbs(133.1, 0.1));
CHECK_THAT(stod(dat1[3]), Catch::Matchers::WithinAbs(221.8, 0.1));
CHECK_THAT(stod(dat1[4]), Catch::Matchers::WithinAbs(132.6, 0.1));
a11reg++;
dat1 = *a11reg;
CHECK_THAT(stod(dat1[1]), Catch::Matchers::WithinAbs(245.3, 0.1));
CHECK_THAT(stod(dat1[2]), Catch::Matchers::WithinAbs(113.7, 0.1));
CHECK_THAT(stod(dat1[3]), Catch::Matchers::WithinAbs(245.5, 0.1));
CHECK_THAT(stod(dat1[4]), Catch::Matchers::WithinAbs(115.0, 0.1));
// There should not be any red lines for bond 5.
std::regex bond5("<path class='bond-5 atom-5 atom-6.*stroke:#FF0000;");
std::ptrdiff_t const match_count1(
std::distance(std::sregex_iterator(text.begin(), text.end(), bond5),
std::sregex_iterator()));
CHECK(match_count1 == 0);
check_file_hash(baseName + "5.svg");
#endif
}
}
{
// Bug with large radii lassos.
auto m = R"CTAB(
RDKit 2D
0 0 0 0 0 0 0 0 0 0999 V3000
M V30 BEGIN CTAB
M V30 COUNTS 19 19 0 0 0
M V30 BEGIN ATOM
M V30 1 C 2.745421 0.232979 0.000000 0
M V30 2 O 1.879821 -0.268021 0.000000 0
M V30 3 C 1.013221 0.231179 0.000000 0
M V30 4 O 1.012421 1.231179 0.000000 0
M V30 5 C 0.147621 -0.269821 0.000000 0
M V30 6 C -0.110179 -1.236021 0.000000 0
M V30 7 O 0.390821 -2.101621 0.000000 0
M V30 8 C 1.390821 -2.100621 0.000000 0
M V30 9 F 1.889821 -1.234221 0.000000 0
M V30 10 Cl 1.891621 -2.966221 0.000000 0
M V30 11 C -1.076379 -0.978021 0.000000 0
M V30 12 C -1.941979 -1.479021 0.000000 0
M V30 13 N -2.807579 -1.980021 0.000000 0
M V30 14 C -0.818579 -0.011821 0.000000 0
M V30 15 O -1.319379 0.853779 0.000000 0
M V30 16 N -0.820379 1.720379 0.000000 0
M V30 17 N -1.321379 2.585779 0.000000 0
M V30 18 C -0.822379 3.452379 0.000000 0
M V30 19 N -1.323379 4.317779 0.000000 0 CHG=1 VAL=4
M V30 END ATOM
M V30 BEGIN BOND
M V30 1 1 1 2
M V30 2 1 2 3
M V30 3 1 3 4 CFG=3
M V30 4 1 3 5
M V30 5 2 5 6
M V30 6 1 6 7
M V30 7 1 7 8
M V30 8 1 8 9 CFG=3
M V30 9 1 8 10
M V30 10 1 6 11
M V30 11 1 11 12
M V30 12 3 12 13
M V30 13 2 11 14
M V30 14 1 14 15
M V30 15 1 15 16
M V30 16 1 16 17
M V30 17 1 17 18
M V30 18 1 18 19
M V30 19 1 14 5
M V30 END BOND
M V30 END CTAB
M END)CTAB"_ctab;
REQUIRE(m);
std::vector<std::string> smarts = {"CONN", "N#CC~CO", "C=CON", "CONNCN"};
std::vector<DrawColour> colours = {
DrawColour(1.0, 0.0, 0.0), DrawColour(0.0, 1.0, 0.0),
DrawColour(0.0, 0.0, 1.0), DrawColour(1.0, 0.55, 0.0)};
std::map<int, std::vector<DrawColour>> ha_map;
std::map<int, std::vector<DrawColour>> hb_map;
for (size_t i = 0; i < smarts.size(); ++i) {
std::vector<int> hit_atoms = get_all_hit_atoms(*m, smarts[i]);
update_colour_map(hit_atoms, colours[i], ha_map);
}
std::map<int, double> h_rads;
for (auto [idx, val] : ha_map) {
h_rads[idx] = 0.4;
}
MolDraw2DSVG drawer(500, 500);
drawer.drawOptions().fillHighlights = false;
drawer.drawOptions().addAtomIndices = true;
drawer.drawOptions().multiColourHighlightStyle =
RDKit::MultiColourHighlightStyle::LASSO;
drawer.drawMoleculeWithHighlights(*m, "Lasso 6", ha_map, hb_map, h_rads,
h_lw_mult);
drawer.finishDrawing();
std::string text = drawer.getDrawingText();
std::ofstream outs(baseName + "6.svg");
outs << text;
outs.flush();
outs.close();
#ifdef RDK_BUILD_FREETYPE_SUPPORT
// The arcs on 13 have been a hassle in the past. There should be 6 of them
std::regex a13(
"<path class='atom-13' d='M (\\d+\\.\\d+),(\\d+\\.\\d+) L (\\d+\\.\\d+),(\\d+\\.\\d+)");
std::ptrdiff_t const match_count(
std::distance(std::sregex_iterator(text.begin(), text.end(), a13),
std::sregex_iterator()));
CHECK(match_count == 6);
// Check the penultimate one is in the right place
auto a13reg = std::sregex_iterator(text.begin(), text.end(), a13);
// you can't add 4, apparently.
a13reg++;
a13reg++;
a13reg++;
a13reg++;
auto dat1 = *a13reg;
CHECK_THAT(stod(dat1[1]), Catch::Matchers::WithinAbs(236.1, 0.1));
CHECK_THAT(stod(dat1[2]), Catch::Matchers::WithinAbs(238.2, 0.1));
CHECK_THAT(stod(dat1[3]), Catch::Matchers::WithinAbs(238.9, 0.1));
CHECK_THAT(stod(dat1[4]), Catch::Matchers::WithinAbs(239.4, 0.1));
check_file_hash(baseName + "6.svg");
#endif
}
{
// Bug with different radii in lassos.
auto m = R"CTAB(
RDKit 2D
0 0 0 0 0 0 0 0 0 0999 V3000
M V30 BEGIN CTAB
M V30 COUNTS 19 19 0 0 0
M V30 BEGIN ATOM
M V30 1 C 2.745421 0.232979 0.000000 0
M V30 2 O 1.879821 -0.268021 0.000000 0
M V30 3 C 1.013221 0.231179 0.000000 0
M V30 4 O 1.012421 1.231179 0.000000 0
M V30 5 C 0.147621 -0.269821 0.000000 0
M V30 6 C -0.110179 -1.236021 0.000000 0
M V30 7 O 0.390821 -2.101621 0.000000 0
M V30 8 C 1.390821 -2.100621 0.000000 0
M V30 9 F 1.889821 -1.234221 0.000000 0
M V30 10 Cl 1.891621 -2.966221 0.000000 0
M V30 11 C -1.076379 -0.978021 0.000000 0
M V30 12 C -1.941979 -1.479021 0.000000 0
M V30 13 N -2.807579 -1.980021 0.000000 0
M V30 14 C -0.818579 -0.011821 0.000000 0
M V30 15 O -1.319379 0.853779 0.000000 0
M V30 16 N -0.820379 1.720379 0.000000 0
M V30 17 N -1.321379 2.585779 0.000000 0
M V30 18 C -0.822379 3.452379 0.000000 0
M V30 19 N -1.323379 4.317779 0.000000 0 CHG=1 VAL=4
M V30 END ATOM
M V30 BEGIN BOND
M V30 1 1 1 2
M V30 2 1 2 3
M V30 3 1 3 4 CFG=3
M V30 4 1 3 5
M V30 5 2 5 6
M V30 6 1 6 7
M V30 7 1 7 8
M V30 8 1 8 9 CFG=3
M V30 9 1 8 10
M V30 10 1 6 11
M V30 11 1 11 12
M V30 12 3 12 13
M V30 13 2 11 14
M V30 14 1 14 15
M V30 15 1 15 16
M V30 16 1 16 17
M V30 17 1 17 18
M V30 18 1 18 19
M V30 19 1 14 5
M V30 END BOND
M V30 END CTAB
M END)CTAB"_ctab;
REQUIRE(m);
std::vector<std::string> smarts = {"CONN", "N#CC~CO", "C=CON", "CONNCN"};
std::vector<DrawColour> colours = {
DrawColour(1.0, 0.0, 0.0), DrawColour(0.0, 1.0, 0.0),
DrawColour(0.0, 0.0, 1.0), DrawColour(1.0, 0.55, 0.0)};
std::map<int, std::vector<DrawColour>> ha_map;
std::map<int, std::vector<DrawColour>> hb_map;
for (size_t i = 0; i < smarts.size(); ++i) {
std::vector<int> hit_atoms = get_all_hit_atoms(*m, smarts[i]);
update_colour_map(hit_atoms, colours[i], ha_map);
}
std::map<int, double> h_rads;
for (auto [idx, val] : ha_map) {
h_rads[idx] = 0.3;
}
h_rads[13] = 0.4;
MolDraw2DSVG drawer(500, 500);
drawer.drawOptions().fillHighlights = false;
drawer.drawOptions().addAtomIndices = true;
drawer.drawOptions().multiColourHighlightStyle =
RDKit::MultiColourHighlightStyle::LASSO;
drawer.drawMoleculeWithHighlights(*m, "Lasso 7", ha_map, hb_map, h_rads,
h_lw_mult);
drawer.finishDrawing();
std::string text = drawer.getDrawingText();
std::ofstream outs(baseName + "7.svg");
outs << text;
outs.flush();
outs.close();
#ifdef RDK_BUILD_FREETYPE_SUPPORT
// The arcs on 13 have been a hassle in the past. There should be 6 of them
std::regex a13(
"<path class='atom-13' d='M (\\d+\\.\\d+),(\\d+\\.\\d+) L (\\d+\\.\\d+),(\\d+\\.\\d+)");
std::ptrdiff_t const match_count(
std::distance(std::sregex_iterator(text.begin(), text.end(), a13),
std::sregex_iterator()));
CHECK(match_count == 6);
// Check the last one is in the right place
auto a13reg = std::sregex_iterator(text.begin(), text.end(), a13);
// you can't add 5, apparently.
a13reg++;
a13reg++;
a13reg++;
a13reg++;
a13reg++;
auto dat1 = *a13reg;
CHECK_THAT(stod(dat1[1]), Catch::Matchers::WithinAbs(244.1, 0.1));
CHECK_THAT(stod(dat1[2]), Catch::Matchers::WithinAbs(218.7, 0.1));
CHECK_THAT(stod(dat1[3]), Catch::Matchers::WithinAbs(248.2, 0.1));
CHECK_THAT(stod(dat1[4]), Catch::Matchers::WithinAbs(220.8, 0.1));
check_file_hash(baseName + "7.svg");
#endif
}
{
// Simple 4-connected and 0-connected atoms test.
auto m = R"CTAB(
RDKit 2D
6 4 0 0 0 0 0 0 0 0999 V2000
-1.2990 -0.7500 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
0.0000 -0.0000 0.0000 S 0 0 0 0 0 0 0 0 0 0 0 0
0.7500 -1.2990 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0
-0.7500 1.2990 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0
1.2990 0.7500 0.0000 N 0 0 0 0 0 4 0 0 0 0 0 0
2.2990 0.0000 0.0000 Cl 0 0 0 0 0 15 0 0 0 0 0 0
1 2 1 0
2 3 2 0
2 4 2 0
2 5 1 0
M CHG 2 5 1 6 -1
M END)CTAB"_ctab;
REQUIRE(m);
MolDraw2DSVG drawer(500, 500);
drawer.drawOptions().fillHighlights = false;
drawer.drawOptions().addAtomIndices = true;
drawer.drawOptions().multiColourHighlightStyle =
RDKit::MultiColourHighlightStyle::LASSO;
std::map<int, std::vector<DrawColour>> ha_map;
std::map<int, std::vector<DrawColour>> hb_map;
std::vector<DrawColour> colours = {
DrawColour(1.0, 0.0, 0.0), DrawColour(0.0, 1.0, 0.0),
DrawColour(0.0, 0.0, 1.0), DrawColour(1.0, 0.55, 0.0)};
std::vector<DrawColour> cvec(1, colours[0]);
for (unsigned int i = 0; i < m->getNumAtoms(); ++i) {
ha_map.insert(std::make_pair(i, cvec));
}
std::map<int, double> h_rads;
std::map<int, int> h_lw_mult;
drawer.drawMoleculeWithHighlights(*m, "Lasso 8", ha_map, hb_map, h_rads,
h_lw_mult);
drawer.finishDrawing();
std::string text = drawer.getDrawingText();
std::ofstream outs(baseName + "8.svg");
outs << text;
outs.flush();
outs.close();
#ifdef RDK_BUILD_FREETYPE_SUPPORT
// Check one of the arcs starts in the right place. There was a time
// when they didn't on Windows machines.
std::regex a0(
"<path class='atom-0' d='M (\\d+\\.\\d+),(\\d+\\.\\d+) L (\\d+\\.\\d+),(\\d+\\.\\d+)");
auto dat1 = *std::sregex_iterator(text.begin(), text.end(), a0);
CHECK_THAT(stod(dat1[1]), Catch::Matchers::WithinAbs(87.6, 0.1));
CHECK_THAT(stod(dat1[2]), Catch::Matchers::WithinAbs(318.1, 0.1));
CHECK_THAT(stod(dat1[3]), Catch::Matchers::WithinAbs(86.6, 0.1));
CHECK_THAT(stod(dat1[4]), Catch::Matchers::WithinAbs(320.7, 0.1));
// There should be no arc for atom 1.
std::regex a1(
"<path class='atom-1' d='M (\\d+\\.\\d+),(\\d+\\.\\d+) L (\\d+\\.\\d+),(\\d+\\.\\d+)");
std::ptrdiff_t const match_count(
std::distance(std::sregex_iterator(text.begin(), text.end(), a1),
std::sregex_iterator()));
CHECK(match_count == 0);
check_file_hash(baseName + "8.svg");
#endif
}
}
TEST_CASE("Github 6683 - SVGs with ridiculous width and/or height") {
std::string baseName = "testGithub6683_";
{
const char *rxnBlock = R"RXN($RXN
Mrv1920 090120231611
3 1
$MOL
Mrv1920 09012316112D
1 0 0 0 0 0 999 V2000
-12.3227 -0.2785 0.0000 Cl 0 0 0 0 0 0 0 0 0 0 0 0
M END
$MOL
Mrv1920 09012316112D
11 11 0 0 0 0 999 V2000
-6.0796 -0.5503 0.0000 Cl 0 0 0 0 0 0 0 0 0 0 0 0
-6.7352 -0.0493 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
-6.6291 0.7688 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0
-7.4967 -0.3666 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0
-8.1522 0.1344 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
-8.9137 -0.1829 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
-9.5692 0.3181 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
-10.3307 0.0008 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
-10.4370 -0.8173 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
-9.7813 -1.3182 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
-9.0199 -1.0009 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
1 2 1 0 0 0 0
2 3 2 0 0 0 0
2 4 1 0 0 0 0
4 5 1 0 0 0 0
5 6 1 0 0 0 0
6 7 4 0 0 0 0
7 8 4 0 0 0 0
8 9 4 0 0 0 0
9 10 4 0 0 0 0
10 11 4 0 0 0 0
11 6 4 0 0 0 0
M END
$MOL
Mrv1920 09012316112D
10 10 0 0 0 0 999 V2000
-3.2982 1.9786 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
-3.4043 1.1605 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0
-2.7488 0.6596 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
-1.9872 0.9767 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0
-2.8547 -0.1585 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
-2.1992 -0.6594 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
-2.3055 -1.4777 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
-3.0669 -1.7949 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
-3.7225 -1.2939 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
-3.6163 -0.4759 0.0000 N 0 0 0 0 0 0 0 0 0 0 0 0
1 2 1 0 0 0 0
2 3 1 0 0 0 0
3 4 2 0 0 0 0
3 5 1 0 0 0 0
5 6 1 0 0 0 0
6 7 1 0 0 0 0
7 8 1 0 0 0 0
8 9 1 0 0 0 0
9 10 1 0 0 0 0
10 5 1 0 0 0 0
M END
$MOL
Mrv1920 09012316112D
20 21 0 0 0 0 999 V2000
7.3862 1.9786 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
7.2800 1.1605 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0
7.9356 0.6596 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
8.6971 0.9768 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0
7.8294 -0.1586 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
8.4850 -0.6595 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
8.3789 -1.4777 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
7.6173 -1.7950 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
6.9619 -1.2939 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
7.0679 -0.4758 0.0000 N 0 0 0 0 0 0 0 0 0 0 0 0
6.4124 0.0252 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
6.5186 0.8432 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0
5.6509 -0.2920 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0
4.9954 0.2089 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
4.2337 -0.1084 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
3.5784 0.3926 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
2.8166 0.0753 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
2.7107 -0.7427 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
3.3661 -1.2438 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
4.1276 -0.9266 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
1 2 1 0 0 0 0
2 3 1 0 0 0 0
3 4 2 0 0 0 0
3 5 1 0 0 0 0
5 6 1 0 0 0 0
6 7 1 0 0 0 0
7 8 1 0 0 0 0
8 9 1 0 0 0 0
9 10 1 0 0 0 0
10 11 1 0 0 0 0
11 12 2 0 0 0 0
11 13 1 0 0 0 0
13 14 1 0 0 0 0
14 15 1 0 0 0 0
15 16 4 0 0 0 0
16 17 4 0 0 0 0
17 18 4 0 0 0 0
18 19 4 0 0 0 0
19 20 4 0 0 0 0
10 5 1 0 0 0 0
20 15 4 0 0 0 0
M END)RXN";
std::unique_ptr<ChemicalReaction> rxn(RxnBlockToChemicalReaction(rxnBlock));
MolDraw2DSVG drawer(-1, -1);
auto reactIter = rxn->beginReactantTemplates();
CHECK_THROWS_AS(MolDraw2DUtils::setACS1996Options(
drawer.drawOptions(),
MolDraw2DUtils::meanBondLength(*(*reactIter)) * 0.7),
ValueErrorException);
}
}
TEST_CASE("Github 6685 - flexicanvas cuts off bottom of reaction") {
std::string baseName = "testGithub6685_";
auto checkImage = [](const std::string &text) {
// extract the dimensions of the image
std::regex getDims("width='(\\d+)px' height='(\\d+)px' viewBox=");
auto match_begin = std::sregex_iterator(text.begin(), text.end(), getDims);
auto width = stod((*match_begin)[1]);
auto height = stod((*match_begin)[2]);
std::regex bond(
"<path class='bond-\\d+ atom-\\d+ atom-\\d+' d='M (-?\\d+.\\d+),(-?\\d+.\\d+) L (-?\\d+.\\d+),(-?\\d+.\\d+)' style=");
std::regex character(
"Q (-?\\d+.\\d+) (-?\\d+.\\d+), (-?\\d+.\\d+) (-?\\d+.\\d+)");
for (const auto &reg : {bond, character}) {
match_begin = std::sregex_iterator(text.begin(), text.end(), reg);
auto match_end = std::sregex_iterator();
for (std::sregex_iterator i = match_begin; i != match_end; ++i) {
std::smatch match = *i;
auto x1 = stod(match[1]);
auto y1 = stod(match[2]);
auto x2 = stod(match[3]);
auto y2 = stod(match[4]);
CHECK(x1 >= 0);
CHECK(x1 <= width);
CHECK((y1 >= 0 && y1 <= height));
CHECK(y1 <= height);
CHECK(x2 >= 0);
CHECK(x2 <= width);
CHECK(y2 >= 0);
CHECK(y2 <= height);
}
}
};
{
const char *rxnBlock = R"RXN($RXN
Mrv1920 090120231611
3 1
$MOL
Mrv1920 09012316112D
1 0 0 0 0 0 999 V2000
-12.3227 -0.2785 0.0000 Cl 0 0 0 0 0 0 0 0 0 0 0 0
M END
$MOL
Mrv1920 09012316112D
11 11 0 0 0 0 999 V2000
-6.0796 -0.5503 0.0000 Cl 0 0 0 0 0 0 0 0 0 0 0 0
-6.7352 -0.0493 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
-6.6291 0.7688 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0
-7.4967 -0.3666 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0
-8.1522 0.1344 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
-8.9137 -0.1829 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
-9.5692 0.3181 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
-10.3307 0.0008 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
-10.4370 -0.8173 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
-9.7813 -1.3182 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
-9.0199 -1.0009 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
1 2 1 0 0 0 0
2 3 2 0 0 0 0
2 4 1 0 0 0 0
4 5 1 0 0 0 0
5 6 1 0 0 0 0
6 7 4 0 0 0 0
7 8 4 0 0 0 0
8 9 4 0 0 0 0
9 10 4 0 0 0 0
10 11 4 0 0 0 0
11 6 4 0 0 0 0
M END
$MOL
Mrv1920 09012316112D
10 10 0 0 0 0 999 V2000
-3.2982 1.9786 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
-3.4043 1.1605 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0
-2.7488 0.6596 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
-1.9872 0.9767 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0
-2.8547 -0.1585 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
-2.1992 -0.6594 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
-2.3055 -1.4777 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
-3.0669 -1.7949 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
-3.7225 -1.2939 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
-3.6163 -0.4759 0.0000 N 0 0 0 0 0 0 0 0 0 0 0 0
1 2 1 0 0 0 0
2 3 1 0 0 0 0
3 4 2 0 0 0 0
3 5 1 0 0 0 0
5 6 1 0 0 0 0
6 7 1 0 0 0 0
7 8 1 0 0 0 0
8 9 1 0 0 0 0
9 10 1 0 0 0 0
10 5 1 0 0 0 0
M END
$MOL
Mrv1920 09012316112D
20 21 0 0 0 0 999 V2000
7.3862 1.9786 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
7.2800 1.1605 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0
7.9356 0.6596 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
8.6971 0.9768 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0
7.8294 -0.1586 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
8.4850 -0.6595 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
8.3789 -1.4777 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
7.6173 -1.7950 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
6.9619 -1.2939 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
7.0679 -0.4758 0.0000 N 0 0 0 0 0 0 0 0 0 0 0 0
6.4124 0.0252 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
6.5186 0.8432 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0
5.6509 -0.2920 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0
4.9954 0.2089 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
4.2337 -0.1084 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
3.5784 0.3926 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
2.8166 0.0753 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
2.7107 -0.7427 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
3.3661 -1.2438 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
4.1276 -0.9266 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
1 2 1 0 0 0 0
2 3 1 0 0 0 0
3 4 2 0 0 0 0
3 5 1 0 0 0 0
5 6 1 0 0 0 0
6 7 1 0 0 0 0
7 8 1 0 0 0 0
8 9 1 0 0 0 0
9 10 1 0 0 0 0
10 11 1 0 0 0 0
11 12 2 0 0 0 0
11 13 1 0 0 0 0
13 14 1 0 0 0 0
14 15 1 0 0 0 0
15 16 4 0 0 0 0
16 17 4 0 0 0 0
17 18 4 0 0 0 0
18 19 4 0 0 0 0
19 20 4 0 0 0 0
10 5 1 0 0 0 0
20 15 4 0 0 0 0
M END)RXN";
std::unique_ptr<ChemicalReaction> rxn(RxnBlockToChemicalReaction(rxnBlock));
MolDraw2DSVG drawer(-1, -1);
drawer.drawReaction(*rxn);
drawer.finishDrawing();
std::string text = drawer.getDrawingText();
std::ofstream outs((baseName + "1.svg").c_str());
outs << text;
outs.close();
checkImage(text);
check_file_hash(baseName + "1.svg");
}
{
const char *rxnBlock = R"RXN($RXN
Mrv1920 090220231847
2 1
$MOL
Mrv1920 09022318472D
2 1 0 0 0 0 999 V2000
-7.4817 -0.2130 0.0000 N 0 0 0 0 0 0 0 0 0 0 0 0
-6.6567 -0.2130 0.0000 N 0 0 0 0 0 0 0 0 0 0 0 0
1 2 1 0 0 0 0
M END
$MOL
Mrv1920 09022318472D
9 8 0 0 0 0 999 V2000
-3.3781 2.1354 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
-3.5235 1.3233 0.0000 N 0 0 0 0 0 0 0 0 0 0 0 0
-4.2996 1.0435 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
-2.8932 0.7914 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
-3.0387 -0.0206 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
-3.7812 -0.3803 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
-2.8567 -1.3430 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
-2.4672 -0.6157 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
-1.6500 -0.5031 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0
1 2 1 0 0 0 0
2 3 1 0 0 0 0
2 4 1 0 0 0 0
4 5 2 0 0 0 0
5 6 1 0 0 0 0
7 8 1 0 0 0 0
8 9 2 0 0 0 0
8 5 1 0 0 0 0
M END
$MOL
Mrv1920 09022318472D
8 8 0 0 0 0 999 V2000
5.5359 -0.2650 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
5.3537 1.0574 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
4.6115 0.6978 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
3.7993 0.8433 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
3.4102 0.1159 0.0000 N 0 0 0 0 0 0 0 0 0 0 0 0
3.9815 -0.4790 0.0000 N 0 0 0 0 0 0 0 0 0 0 0 0
4.7240 -0.1195 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
2.5929 0.0033 0.0000 H 0 0 0 0 0 0 0 0 0 0 0 0
2 3 1 0 0 0 0
3 4 4 0 0 0 0
4 5 4 0 0 0 0
5 6 4 0 0 0 0
6 7 4 0 0 0 0
7 1 1 0 0 0 0
7 3 4 0 0 0 0
5 8 1 0 0 0 0
M END)RXN";
std::unique_ptr<ChemicalReaction> rxn(RxnBlockToChemicalReaction(rxnBlock));
MolDraw2DSVG drawer(-1, -1);
drawer.drawReaction(*rxn);
drawer.finishDrawing();
std::string text = drawer.getDrawingText();
std::ofstream outs((baseName + "2.svg").c_str());
outs << text;
outs.close();
checkImage(text);
check_file_hash(baseName + "2.svg");
}
{
const char *rxnBlock = R"RXN($RXN
Mrv1920 090220231850
1 2
$MOL
Mrv1920 09022318502D
20 22 0 0 0 0 999 V2000
-2.4533 -0.5079 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
-3.0179 0.0939 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
-3.8212 -0.0941 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
-4.0600 -0.8837 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
-4.8633 -1.0715 0.0000 N 0 0 0 0 0 0 0 0 0 0 0 0
-5.4277 -0.4698 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
-6.2311 -0.6577 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
-6.7954 -0.0558 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
-7.5987 -0.2436 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
-7.8377 -1.0333 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
-7.2734 -1.6351 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
-6.4701 -1.4473 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
-5.1888 0.3199 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
-4.3855 0.5077 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
-4.1465 1.2974 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
-4.7110 1.8993 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
-5.5142 1.7114 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
-5.7532 0.9218 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
-3.4957 -1.4854 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
-2.6923 -1.2975 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
1 2 4 0 0 0 0
2 3 4 0 0 0 0
3 4 4 0 0 0 0
4 5 1 0 0 0 0
5 6 2 3 0 0 0
6 7 1 0 0 0 0
7 8 4 0 0 0 0
8 9 4 0 0 0 0
9 10 4 0 0 0 0
10 11 4 0 0 0 0
11 12 4 0 0 0 0
6 13 1 0 0 0 0
13 14 4 0 0 0 0
14 15 4 0 0 0 0
15 16 4 0 0 0 0
16 17 4 0 0 0 0
17 18 4 0 0 0 0
4 19 4 0 0 0 0
19 20 4 0 0 0 0
20 1 4 0 0 0 0
12 7 4 0 0 0 0
18 13 4 0 0 0 0
M END
$MOL
Mrv1920 09022318502D
7 7 0 0 0 0 999 V2000
5.5920 0.3948 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
5.0277 0.9966 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
4.2244 0.8087 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
3.9855 0.0191 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
3.1821 -0.1689 0.0000 N 0 0 0 0 0 0 0 0 0 0 0 0
4.5499 -0.5827 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
5.3531 -0.3949 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
1 2 4 0 0 0 0
2 3 4 0 0 0 0
3 4 4 0 0 0 0
4 5 1 0 0 0 0
4 6 4 0 0 0 0
6 7 4 0 0 0 0
7 1 4 0 0 0 0
M END
$MOL
Mrv1920 09022318502D
1 0 0 0 0 0 999 V2000
8.3990 0.0732 0.0000 Cl 0 0 0 0 0 0 0 0 0 0 0 0
M END
)RXN";
std::unique_ptr<ChemicalReaction> rxn(RxnBlockToChemicalReaction(rxnBlock));
MolDraw2DSVG drawer(-1, -1);
drawer.drawReaction(*rxn);
drawer.finishDrawing();
std::string text = drawer.getDrawingText();
std::ofstream outs((baseName + "3.svg").c_str());
outs << text;
outs.close();
checkImage(text);
check_file_hash(baseName + "3.svg");
}
{
// This one was clipped on the right hand side at one point.
std::string smarts(
"[cH:1]1[cH:2][cH:3][c:4][cH:5][cH:6]1>>[cH:3]1[cH:2][c:1]([cH:6][cH:5][c:4]1)Cl");
bool useSmiles = true;
std::unique_ptr<ChemicalReaction> rxn(
RxnSmartsToChemicalReaction(smarts, nullptr, useSmiles));
MolDraw2DSVG drawer(600, 150);
drawer.drawOptions().padding = 0.0;
drawer.drawReaction(*rxn);
drawer.finishDrawing();
std::string text = drawer.getDrawingText();
std::ofstream outs((baseName + "4.svg").c_str());
outs << text;
outs.close();
checkImage(text);
check_file_hash(baseName + "4.svg");
}
}
TEST_CASE("Github 6749 : various bad things in the lasso highlighting") {
std::string baseName = "bad_lasso_";
auto mol =
"CCCS(=O)(=O)Nc1ccc(F)c(c1F)C(=O)c2c[nH]c3c2cc(cn3)c4ccc(Cl)cc4"_smiles;
REQUIRE(mol);
auto update_colour_map =
[](const std::vector<int> &ats, DrawColour col,
std::map<int, std::vector<DrawColour>> &ha_map) -> void {
for (auto h : ats) {
auto ex = ha_map.find(h);
if (ex == ha_map.end()) {
std::vector<DrawColour> cvec(1, col);
ha_map.insert(make_pair(h, cvec));
} else {
if (ex->second.end() ==
find(ex->second.begin(), ex->second.end(), col)) {
ex->second.push_back(col);
}
}
}
};
auto update_bond_map =
[](const std::vector<int> &ats, DrawColour col, const ROMol &mol,
std::map<int, std::vector<DrawColour>> &hb_map) -> void {
for (auto at1 : ats) {
for (auto at2 : ats) {
if (at1 > at2) {
auto b = mol.getBondBetweenAtoms(at1, at2);
if (b) {
auto ex = hb_map.find(b->getIdx());
if (ex == hb_map.end()) {
std::vector<DrawColour> cvec(1, col);
hb_map.insert(make_pair(b->getIdx(), cvec));
} else {
ex->second.push_back(col);
}
}
}
}
}
};
std::vector<DrawColour> colours = {
DrawColour(1.0, 0.2, 1.0), DrawColour(0.2, 1.0, 1.0),
DrawColour(0.8, 0.8, 0.2), DrawColour(0.4, 0.4, 0.2)};
std::map<int, std::vector<DrawColour>> ha_map;
std::map<int, std::vector<DrawColour>> hb_map;
update_colour_map({6, 19, 25}, colours[0], ha_map);
update_bond_map({6, 19, 25}, colours[0], *mol, hb_map);
update_colour_map({25, 4, 5, 11, 14, 16}, colours[1], ha_map);
update_bond_map({25, 4, 5, 11, 14, 16}, colours[1], *mol, hb_map);
update_colour_map({19, 25, 17, 18, 20, 21, 7, 8, 9, 10, 12,
13, 22, 23, 24, 26, 27, 28, 29, 31, 32},
colours[2], ha_map);
update_bond_map({19, 25, 17, 18, 20, 21, 7, 8, 9, 10, 12,
13, 22, 23, 24, 26, 27, 28, 29, 31, 32},
colours[2], *mol, hb_map);
// If there are duplicate colours in the list, there was a bug where
// arcs weren't removed correctly (Github 6749)
ha_map[20].push_back(colours[2]);
ha_map[21].push_back(colours[2]);
update_colour_map({7, 8, 9, 10, 12, 13, 26, 27, 28, 29, 31, 32}, colours[3],
ha_map);
update_bond_map({7, 8, 9, 10, 12, 13, 26, 27, 28, 29, 31, 32}, colours[3],
*mol, hb_map);
std::map<int, double> h_rads;
std::map<int, int> h_lw_mult;
MolDraw2DSVG drawer(600, 400);
drawer.drawOptions().multiColourHighlightStyle =
RDKit::MultiColourHighlightStyle::LASSO;
drawer.drawOptions().fillHighlights = false;
drawer.drawOptions().addAtomIndices = true;
drawer.drawMoleculeWithHighlights(*mol, "Bad Lasso", ha_map, hb_map, h_rads,
h_lw_mult);
drawer.finishDrawing();
std::string text = drawer.getDrawingText();
std::ofstream outs(baseName + "1.svg");
outs << text;
outs.flush();
outs.close();
std::regex atom20("<path class='atom-20'");
// there should be 3 matches for "class='atom-20'" - the buggy version gave 5
std::ptrdiff_t const match_count(
std::distance(std::sregex_iterator(text.begin(), text.end(), atom20),
std::sregex_iterator()));
CHECK(match_count == 3);
check_file_hash(baseName + "1.svg");
}
TEST_CASE("atropisomers") {
{
auto mol =
"CC1=CC=C(Cl)C(C)=C1N1C=CC=C1Cl |(-0.7234,-1.1614,;-0.6697,0.3775,;0.69,1.1007,;0.7439,2.6396,;-0.5622,3.4557,;-0.5085,4.9947,;-1.9218,2.7328,;-3.2279,3.5487,;-1.9757,1.1937,;-3.3354,0.4706,;-3.8113,-0.994,;-5.3513,-0.994,;-5.8272,0.4706,;-4.5813,1.3758,;-4.5813,2.9158,),wD:8.8|"_smiles;
REQUIRE(mol);
bool kekulize = true;
bool addChiralHs = true;
bool wedgeBonds = true;
bool forceCoords = true;
bool wavyBonds = true;
MolDraw2DUtils::prepareMolForDrawing(*mol, kekulize, addChiralHs,
wedgeBonds, forceCoords, wavyBonds);
CHECK(mol->getBondWithIdx(8)->getBondDir() == Bond::BondDir::NONE);
CHECK(mol->getBondWithIdx(8)->getStereo() ==
Bond::BondStereo::STEREOATROPCW);
MOL_PTR_VECT ms{mol.get()};
{
MolDraw2DSVG drawer(500, 200, 250, 200);
// drawer.drawOptions().prepareMolsBeforeDrawing = false;
std::vector<std::string> legends = {"AtropCanon1"};
drawer.drawMolecules(ms, &legends);
drawer.finishDrawing();
std::string text = drawer.getDrawingText();
std::ofstream outs("AtropCanon1.svg");
outs << text;
outs.flush();
check_file_hash("AtropCanon1.svg");
}
}
{
auto mol =
"O=C1C=CNC(=O)N1C(=C)[C@]([C@H](C)Br)([C@@H](F)C)[C@H](Cl)C |(2.8625,1.0561,;2.2921,-0.5174,;3.4688,-1.0018,;3.6019,-2.4682,;2.3988,-3.3169,;1.0621,-2.6992,;0.1062,-3.9298,;0.9288,-1.2328,;-0.5563,-0.6124,;-1.5367,-1.8,;-0.8947,0.9647,;-0.8778,2.5678,;-0.1398,3.9298,;-1.9563,3.6407,;0.5974,1.3136,;1.1268,-0.0778,;1.9954,1.9251,;-2.4534,0.7177,;-3.6019,1.737,;-3.4495,-0.4655,),wD:14.15,wU:7.7,11.13,10.14,17.18,o1:7,10,14,&1:11,17|"_smiles;
REQUIRE(mol);
bool kekulize = true;
bool addChiralHs = true;
bool wedgeBonds = true;
bool forceCoords = true;
bool wavyBonds = true;
MolDraw2DUtils::prepareMolForDrawing(*mol, kekulize, addChiralHs,
wedgeBonds, forceCoords, wavyBonds);
CHECK(mol->getBondWithIdx(7)->getBondDir() == Bond::BondDir::NONE);
CHECK(mol->getBondWithIdx(7)->getStereo() ==
Bond::BondStereo::STEREOATROPCCW);
MOL_PTR_VECT ms{mol.get()};
{
MolDraw2DSVG drawer(500, 200, 250, 200);
// drawer.drawOptions().prepareMolsBeforeDrawing = false;
std::vector<std::string> legends = {"AtropManyChiralsEnhanced"};
drawer.drawMolecules(ms, &legends);
drawer.finishDrawing();
std::string text = drawer.getDrawingText();
std::ofstream outs("AtropManyChiralsEnhanced.svg");
outs << text;
outs.flush();
check_file_hash("AtropManyChiralsEnhanced.svg");
}
}
}
TEST_CASE("Github6968 - bad bond highlights with triple bonds") {
// The issue is that in the linear highlight across the triple bond,
// some of the highlights didn't appear, and others were
// triangular - the corners of the rectangle weren't all distinct.
auto m = "ClCC#CCOC(=O)Nc1cccc(c1)Cl"_smiles;
std::vector<unsigned int> atOrder(m->getNumAtoms(), 0);
std::iota(atOrder.begin(), atOrder.end(), 0);
REQUIRE(m);
{
// Because I worried about the atom order giving a non-general
// result, repeat it 10 times with atoms in random order.
for (int testNum = 0; testNum < 10; ++testNum) {
std::unique_ptr<ROMol> mol(MolOps::renumberAtoms(*m, atOrder));
MolDraw2DSVG drawer(350, 300);
std::vector<int> highlightAtoms = {};
// Helpfully, the atoms are scrambled but not the bonds.
std::vector<int> highlightBonds = {1, 2, 3};
drawer.drawOptions().addAtomIndices = true;
drawer.drawOptions().addBondIndices = true;
drawer.drawMolecule(*mol, "", &highlightAtoms, &highlightBonds);
drawer.finishDrawing();
auto text = drawer.getDrawingText();
std::regex bond(
"<path class='bond-(\\d+) atom-(\\d+) atom-(\\d+)' d='M (-?\\d+.\\d+),"
"(-?\\d+.\\d+) L (-?\\d+.\\d+),(-?\\d+.\\d+) L (-?\\d+.\\d+),"
"(-?\\d+.\\d+) L (-?\\d+.\\d+),(-?\\d+.\\d+) Z' style=");
auto match_begin = std::sregex_iterator(text.begin(), text.end(), bond);
auto match_end = std::sregex_iterator();
for (std::sregex_iterator i = match_begin; i != match_end; ++i) {
std::smatch match = *i;
std::vector<Point2D> pts;
for (int j = 4; j < 12; j += 2) {
pts.push_back(Point2D(stod(match[j]), stod(match[j + 1])));
}
// None of the points should be on top of each other
for (size_t j = 0; j < 3; ++j) {
for (size_t k = j + 1; k < 4; ++k) {
CHECK((pts[j] - pts[k]).lengthSq() > 1.0e-4);
}
}
}
if (testNum == 0) {
std::ofstream outs("testGithub6968.svg");
outs << text;
outs.close();
check_file_hash("testGithub6968.svg");
}
std::shuffle(atOrder.begin(), atOrder.end(),
std::mt19937{std::random_device{}()});
}
}
}
TEST_CASE("Github7036 - triple bond to wedge not right") {
// The issue is that the middle line of a triple bond
// ends in the wrong place when the incident bond is
// a wedge. Wedge to single bond included for visual
// check that that isn't broken in the fix.
auto m = "C1[C@@H](CN)CCN[C@H]1C#N"_smiles;
REQUIRE(m);
{
MolDraw2DSVG drawer(350, 300);
drawer.drawOptions().addAtomIndices = true;
drawer.drawOptions().addBondIndices = true;
drawer.drawMolecule(*m);
drawer.finishDrawing();
auto text = drawer.getDrawingText();
std::ofstream outs("testGithub7036.svg");
outs << text;
outs.close();
std::regex bond(
"<path class='bond-8 atom-8 atom-9' d='M (-?\\d+.\\d+),(-?\\d+.\\d+)"
" L (-?\\d+.\\d+),(-?\\d+.\\d+)' style=");
// The problem is the first line in the bond, which comes in 2 parts
// that should be co-linear.
auto match_begin = std::sregex_iterator(text.begin(), text.end(), bond);
std::smatch match = *match_begin;
std::vector<Point2D> pts;
pts.push_back(Point2D(stod(match[1]), stod(match[2])));
pts.push_back(Point2D(stod(match[3]), stod(match[4])));
++match_begin;
match = *match_begin;
pts.push_back(Point2D(stod(match[1]), stod(match[2])));
pts.push_back(Point2D(stod(match[3]), stod(match[4])));
double dot = pts[0].directionVector(pts[1]).dotProduct(
pts[2].directionVector(pts[3]));
CHECK_THAT(fabs(dot), Catch::Matchers::WithinAbs(1.0, 0.001));
check_file_hash("testGithub7036.svg");
}
}
TEST_CASE("Github7317 - very long bond not drawn to both atoms") {
auto m1 = R"CTAB(2244
RDKit 2D
0 0 0 0 0 0 0 0 0 0999 V3000
M V30 BEGIN CTAB
M V30 COUNTS 13 13 0 0 0
M V30 BEGIN ATOM
M V30 1 O 2.598085 -1.499986 0.000000 0
M V30 2 O -1.299010 -3.749995 0.000000 0
M V30 3 O 9.923686 -6.081460 0.000000 0
M V30 4 O 3.897122 0.750042 0.000000 0
M V30 5 C 1.299042 -0.749993 0.000000 0
M V30 6 C 0.000027 -1.499967 0.000000 0
M V30 7 C 1.299015 0.749974 0.000000 0
M V30 8 C -1.299015 -0.749974 0.000000 0
M V30 9 C -0.000027 1.499967 0.000000 0
M V30 10 C -1.299042 0.749993 0.000000 0
M V30 11 C 0.000005 -3.000021 0.000000 0
M V30 12 C 3.897099 -0.750011 0.000000 0
M V30 13 C 5.196142 -1.500004 0.000000 0
M V30 END ATOM
M V30 BEGIN BOND
M V30 1 1 1 5
M V30 2 1 1 12
M V30 3 1 2 11
M V30 4 2 3 11
M V30 5 2 4 12
M V30 6 2 5 6
M V30 7 1 5 7
M V30 8 1 6 8
M V30 9 1 6 11
M V30 10 2 7 9
M V30 11 2 8 10
M V30 12 1 9 10
M V30 13 1 12 13
M V30 END BOND
M V30 END CTAB
M END)CTAB"_ctab;
REQUIRE(m1);
MolDraw2DSVG drawer(350, 300);
drawer.drawOptions().addAtomIndices = true;
drawer.drawOptions().addBondIndices = true;
drawer.drawMolecule(*m1);
drawer.finishDrawing();
auto text = drawer.getDrawingText();
std::regex bond3(
"<path class='bond-3 atom-2 atom-10' d='M (-?\\d+.\\d+),(-?\\d+.\\d+)"
" L (-?\\d+.\\d+),(-?\\d+.\\d+)' style=");
auto match3_begin = std::sregex_iterator(text.begin(), text.end(), bond3);
auto match3_end = std::sregex_iterator();
std::vector<Point2D> pts3;
for (std::sregex_iterator i = match3_begin; i != match3_end; ++i) {
std::smatch match = *i;
pts3.push_back(Point2D(stod(match[1]), stod(match[2])));
pts3.push_back(Point2D(stod(match[3]), stod(match[4])));
}
std::regex bond8(
"<path class='bond-8 atom-5 atom-10' d='M (-?\\d+.\\d+),(-?\\d+.\\d+)"
" L (-?\\d+.\\d+),(-?\\d+.\\d+)' style=");
auto match_begin8 = std::sregex_iterator(text.begin(), text.end(), bond8);
std::smatch match8 = *match_begin8;
std::vector<Point2D> pts8;
pts8.push_back(Point2D(stod(match8[1]), stod(match8[2])));
pts8.push_back(Point2D(stod(match8[3]), stod(match8[4])));
// pts3[3] and pts3[7] are the atom 10 ends of bond3, pts8[1] is
// the atom 10 end of bond 8. They should be close to each other.
CHECK((pts8[1] - pts3[3]).length() < 10.0);
CHECK((pts8[1] - pts3[7]).length() < 10.0);
if ((pts8[1] - pts3[3]).length() >= 10.0 ||
(pts8[1] - pts3[7]).length() >= 10.0) {
// Someone will want to have a look at it.
std::ofstream outs("testGithub7317.svg");
outs << text;
outs.close();
}
}
#ifdef RDK_BUILD_CAIRO_SUPPORT
TEST_CASE(
"github #7409: drawing mol with a non zero confID results in bad confID error") {
SECTION("basics") {
auto m = "CC |(-0.75,0,;0.75,0,)|"_smiles;
REQUIRE(m);
CHECK(m->getNumConformers() == 1);
m->getConformer().setId(5);
MolDraw2DCairo drawer(350, 300);
// it's enough to test that this doesn't throw
drawer.drawMolecule(*m);
}
}
#endif
TEST_CASE("wedge non-single bonds") {
int panelHeight = -1;
int panelWidth = -1;
bool noFreeType = false;
MolDraw2DSVG drawer(350, 300, panelWidth, panelHeight, noFreeType);
drawer.drawOptions().prepareMolsBeforeDrawing = false;
SECTION("basics 1: aromatic bonds") {
auto m =
"CC(=O)C1=CC=CC=C1C |wU:1.0, (-0.954,-1.74918,;-0.9532,-0.74918,;-1.8188,-0.24858,;-0.0868,-0.24998,;0.7788,-0.75058,;1.6452,-0.25138,;1.646,0.74862,;0.7804,1.24942,;-0.086,0.75002,;-0.9516,1.25082,)|"_smiles;
REQUIRE(m);
m->getBondBetweenAtoms(3, 4)->setBondDir(Bond::BondDir::BEGINWEDGE);
{
int panelHeight = -1;
int panelWidth = -1;
bool noFreeType = false;
MolDraw2DSVG drawer(350, 300, panelWidth, panelHeight, noFreeType);
drawer.drawOptions().prepareMolsBeforeDrawing = false;
drawer.drawMolecule(*m);
drawer.finishDrawing();
auto text = drawer.getDrawingText();
std::ofstream outs("testWedgeNonSingleBonds-1.svg");
outs << text;
outs.close();
check_file_hash("testWedgeNonSingleBonds-1.svg");
}
m->getBondBetweenAtoms(3, 4)->setBondDir(Bond::BondDir::BEGINDASH);
{
int panelHeight = -1;
int panelWidth = -1;
bool noFreeType = false;
MolDraw2DSVG drawer(350, 300, panelWidth, panelHeight, noFreeType);
drawer.drawOptions().prepareMolsBeforeDrawing = false;
drawer.drawMolecule(*m);
drawer.finishDrawing();
auto text = drawer.getDrawingText();
std::ofstream outs("testWedgeNonSingleBonds-2.svg");
outs << text;
outs.close();
check_file_hash("testWedgeNonSingleBonds-2.svg");
}
}
SECTION("basics 2 : aromatic bonds, draw to a heteroatom") {
auto m =
"CC(=O)C1=NC=CC=C1C |wU:1.0, (-0.954,-1.74918,;-0.9532,-0.74918,;-1.8188,-0.24858,;-0.0868,-0.24998,;0.7788,-0.75058,;1.6452,-0.25138,;1.646,0.74862,;0.7804,1.24942,;-0.086,0.75002,;-0.9516,1.25082,)|"_smiles;
REQUIRE(m);
m->getBondBetweenAtoms(3, 4)->setBondDir(Bond::BondDir::BEGINWEDGE);
{
int panelHeight = -1;
int panelWidth = -1;
bool noFreeType = false;
MolDraw2DSVG drawer(350, 300, panelWidth, panelHeight, noFreeType);
drawer.drawOptions().prepareMolsBeforeDrawing = false;
drawer.drawMolecule(*m);
drawer.finishDrawing();
auto text = drawer.getDrawingText();
std::ofstream outs("testWedgeNonSingleBonds-3.svg");
outs << text;
outs.close();
check_file_hash("testWedgeNonSingleBonds-3.svg");
}
m->getBondBetweenAtoms(3, 4)->setBondDir(Bond::BondDir::BEGINDASH);
{
int panelHeight = -1;
int panelWidth = -1;
bool noFreeType = false;
MolDraw2DSVG drawer(350, 300, panelWidth, panelHeight, noFreeType);
drawer.drawOptions().prepareMolsBeforeDrawing = false;
drawer.drawMolecule(*m);
drawer.finishDrawing();
auto text = drawer.getDrawingText();
std::ofstream outs("testWedgeNonSingleBonds-4.svg");
outs << text;
outs.close();
check_file_hash("testWedgeNonSingleBonds-4.svg");
}
}
SECTION("basics 3: double bonds") {
auto m =
"CC(=O)C1=CC=CC=C1C |wU:1.0, (-0.954,-1.74918,;-0.9532,-0.74918,;-1.8188,-0.24858,;-0.0868,-0.24998,;0.7788,-0.75058,;1.6452,-0.25138,;1.646,0.74862,;0.7804,1.24942,;-0.086,0.75002,;-0.9516,1.25082,)|"_smiles;
REQUIRE(m);
MolOps::Kekulize(*m);
CHECK(m->getBondBetweenAtoms(3, 4)->getBondType() ==
Bond::BondType::DOUBLE);
m->getBondBetweenAtoms(3, 4)->setBondDir(Bond::BondDir::BEGINWEDGE);
{
int panelHeight = -1;
int panelWidth = -1;
bool noFreeType = false;
MolDraw2DSVG drawer(350, 300, panelWidth, panelHeight, noFreeType);
drawer.drawOptions().prepareMolsBeforeDrawing = false;
drawer.drawMolecule(*m);
drawer.finishDrawing();
auto text = drawer.getDrawingText();
std::ofstream outs("testWedgeNonSingleBonds-5.svg");
outs << text;
outs.close();
check_file_hash("testWedgeNonSingleBonds-5.svg");
}
m->getBondBetweenAtoms(3, 4)->setBondDir(Bond::BondDir::BEGINDASH);
{
int panelHeight = -1;
int panelWidth = -1;
bool noFreeType = false;
MolDraw2DSVG drawer(350, 300, panelWidth, panelHeight, noFreeType);
drawer.drawOptions().prepareMolsBeforeDrawing = false;
drawer.drawMolecule(*m);
drawer.finishDrawing();
auto text = drawer.getDrawingText();
std::ofstream outs("testWedgeNonSingleBonds-6.svg");
outs << text;
outs.close();
check_file_hash("testWedgeNonSingleBonds-6.svg");
}
}
SECTION("basics 3: double bonds, draw to a heteroatom") {
auto m =
"CC(=O)C1=NC=CC=C1C |wU:1.0, (-0.954,-1.74918,;-0.9532,-0.74918,;-1.8188,-0.24858,;-0.0868,-0.24998,;0.7788,-0.75058,;1.6452,-0.25138,;1.646,0.74862,;0.7804,1.24942,;-0.086,0.75002,;-0.9516,1.25082,)|"_smiles;
REQUIRE(m);
MolOps::Kekulize(*m);
CHECK(m->getBondBetweenAtoms(3, 4)->getBondType() ==
Bond::BondType::DOUBLE);
m->getBondBetweenAtoms(3, 4)->setBondDir(Bond::BondDir::BEGINWEDGE);
{
int panelHeight = -1;
int panelWidth = -1;
bool noFreeType = false;
MolDraw2DSVG drawer(350, 300, panelWidth, panelHeight, noFreeType);
drawer.drawOptions().prepareMolsBeforeDrawing = false;
drawer.drawMolecule(*m);
drawer.finishDrawing();
auto text = drawer.getDrawingText();
std::ofstream outs("testWedgeNonSingleBonds-7.svg");
outs << text;
outs.close();
check_file_hash("testWedgeNonSingleBonds-7.svg");
}
m->getBondBetweenAtoms(3, 4)->setBondDir(Bond::BondDir::BEGINDASH);
{
int panelHeight = -1;
int panelWidth = -1;
bool noFreeType = false;
MolDraw2DSVG drawer(350, 300, panelWidth, panelHeight, noFreeType);
drawer.drawOptions().prepareMolsBeforeDrawing = false;
drawer.drawMolecule(*m);
drawer.finishDrawing();
auto text = drawer.getDrawingText();
std::ofstream outs("testWedgeNonSingleBonds-8.svg");
outs << text;
outs.close();
check_file_hash("testWedgeNonSingleBonds-8.svg");
}
}
}
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