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rdkit/Code/GraphMol/MolDraw2D/catch_tests.cpp
Paolo Tosco 50aea5cf62 Fix issues arising from useMolBlockWedging and the new atropisomer kekulization code (#7540) 
* - When depictions are made using the useMolBlockWedging flag, make sure that kekulization is done after original wedging has been applied to reduce the odds that bond wedges are placed on double bonds
- Refactored MinimalLib code to avoid code duplication
- get_molblock() should reapplyMolBlockWedging on a copy of the passed molecule rather than on the original
- Added unit tests

* Update Code/MinimalLib/jswrapper.cpp

Co-authored-by: Greg Landrum <greg.landrum@gmail.com>

---------

Co-authored-by: ptosco <paolo.tosco@novartis.com>
Co-authored-by: Greg Landrum <greg.landrum@gmail.com>
2024-06-20 19:32:41 +02:00

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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},
{"testWedgingShouldBeOnSingleBond.svg", 1002741488U},
};
// 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");
}
}
SECTION(
"basics 3: make sure reapplyMolBlockWedging is called before prepareMolForDrawing") {
auto m = R"CTAB(
Mrv2311 05242408162D
0 0 0 0 0 999 V3000
M V30 BEGIN CTAB
M V30 COUNTS 14 15 0 0 0
M V30 BEGIN ATOM
M V30 1 C 2.0006 -1.54 0 0
M V30 2 N 2.0006 -3.08 0 0
M V30 3 C 0.6669 -3.85 0 0
M V30 4 C -0.6668 -3.08 0 0
M V30 5 C -0.6668 -1.54 0 0
M V30 6 C -2.0006 -0.77 0 0
M V30 7 C 0.6669 -0.77 0 0
M V30 8 C 0.6669 0.77 0 0
M V30 9 C -0.6668 1.54 0 0
M V30 10 C -2.0006 0.77 0 0
M V30 11 C -0.6668 3.08 0 0
M V30 12 C 0.6669 3.85 0 0
M V30 13 C 2.0006 3.08 0 0
M V30 14 C 2.0006 1.54 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 1 7 5 CFG=3
M V30 7 2 7 1
M V30 8 1 7 8
M V30 9 2 8 9
M V30 10 1 9 10
M V30 11 1 9 11
M V30 12 2 11 12
M V30 13 1 12 13
M V30 14 2 13 14
M V30 15 1 8 14
M V30 END BOND
M V30 END CTAB
M END
)CTAB"_ctab;
REQUIRE(m);
int panelHeight = -1;
int panelWidth = -1;
bool noFreeType = true;
MolDraw2DSVG drawer(350, 300, panelWidth, panelHeight, noFreeType);
drawer.drawOptions().useMolBlockWedging = true;
drawer.drawMolecule(*m);
drawer.finishDrawing();
auto text = drawer.getDrawingText();
std::ofstream outs("testWedgingShouldBeOnSingleBond.svg");
outs << text;
outs.close();
check_file_hash("testWedgingShouldBeOnSingleBond.svg");
std::regex regex1(
"<path class='bond-5 atom-6 atom-4'.*style='fill:none;fill-rule:evenodd;stroke:#000000;stroke-width:1\\.0px;stroke-linecap:butt;stroke-linejoin:miter;stroke-opacity:1' />");
std::regex regex2(
"<path class='bond-5 atom-6 atom-4'.*style='fill:none;fill-rule:evenodd;stroke:#000000;stroke-width:2\\.0px;stroke-linecap:butt;stroke-linejoin:miter;stroke-opacity:1' />");
size_t nRegex1Matches = std::distance(
std::sregex_token_iterator(text.begin(), text.end(), regex1),
std::sregex_token_iterator());
CHECK(nRegex1Matches > 6); // check the bond is hashed
auto dat2 = *std::sregex_iterator(text.begin(), text.end(), regex2);
CHECK(dat2.empty()); // check the bond is single
}
}
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