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rdkit/Code/GraphMol/MolDraw2D/test1.cpp
Ricardo Rodriguez 7b7a8a4e17 Refactor iostreams includes (#8846) 
* refactor iostreams includes

* restore ostream to MonomerInfo.cpp
2025-10-08 16:08:01 +02:00

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//
// Copyright (C) 2015-2021 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 <RDGeneral/test.h>
#include <RDGeneral/utils.h>
#include <RDGeneral/Invariant.h>
#include <RDGeneral/RDLog.h>
#include <RDGeneral/hash/hash.hpp>
#include <GraphMol/RDKitBase.h>
#include <GraphMol/MolOps.h>
#include <GraphMol/SmilesParse/SmilesParse.h>
#include <GraphMol/FileParsers/MolSupplier.h>
#include <GraphMol/FileParsers/FileParsers.h>
#include <GraphMol/Depictor/RDDepictor.h>
#include <GraphMol/FileParsers/MolFileStereochem.h>
#include <GraphMol/MolTransforms/MolTransforms.h>
#include <GraphMol/MolDraw2D/MolDraw2D.h>
#include <GraphMol/MolDraw2D/MolDraw2DSVG.h>
#include <GraphMol/MolDraw2D/MolDraw2DUtils.h>
#include <GraphMol/test_fixtures.h>
#include <algorithm>
#include <cstdio>
#include <iosfwd>
#include <iterator>
#include <map>
#include <fstream>
#include <sstream>
#include <regex>
// if 0, turns off a lot of the FREETYPE TEST_ASSERT checks
// because sometimes you want to look at all the pictures first.
#define DO_TEST_ASSERT 1
#ifdef RDK_BUILD_FREETYPE_SUPPORT
static const std::map<std::string, std::hash_result_t> SVG_HASHES = {
{"test1_1.svg", 1617157703U},
{"test1_2.svg", 1799670018U},
{"test1_3.svg", 2382509631U},
{"test1_4.svg", 4252277495U},
{"test1_5.svg", 2811480876U},
{"test1_6.svg", 2635907956U},
{"test1_7.svg", 3677608850U},
{"test4_1.svg", 4157966746U},
{"test5_1.svg", 4074479420U},
{"test5_2.svg", 1125439478U},
{"test5_3.svg", 3322548698U},
{"test6_1.svg", 3623418420U},
{"test6_2.svg", 3885689795U},
{"test6_3.svg", 2753286335U},
{"test7_1.svg", 1967202587U},
{"test7_2.svg", 4217504234U},
{"testGithub781_1.svg", 45764976U},
{"testGithub781_2.svg", 964035371U},
{"testGithub781_3.svg", 1463918610U},
{"testGithub781_4.svg", 112971309U},
{"testGithub781_5.svg", 2840696942U},
{"testGithub781_6.svg", 1059414825U},
{"test3_1.svg", 586189704U},
{"test3_2.svg", 1700916148U},
{"test3_3.svg", 1375178959U},
{"test3_4.svg", 187720898U},
{"test3_5.svg", 300865579U},
{"test3_6.svg", 729637096U},
{"test3_7.svg", 2700118064U},
{"test774_1.svg", 1108618931U},
{"test774_2.svg", 577567569U},
{"test9_1.svg", 1484349178U},
{"test852_1.svg", 2306783336U},
{"test852_2.svg", 936665195U},
{"test852_2a.svg", 3499587182U},
{"test852_2b.svg", 2141021605U},
{"test852_2c.svg", 465009830U},
{"test852_2d.svg", 714117851U},
{"test860_1.svg", 4071399203U},
{"test860_2.svg", 3926063275U},
{"test860_3.svg", 2583192182U},
{"test910_1.svg", 2101353772U},
{"test910_2.svg", 3090433026U},
{"test983_1.svg", 2373378601U},
{"test983_2.svg", 2571223561U},
{"testNoDeuterium.svg", 1852412299U},
{"testNoTritium.svg", 3648261446U},
{"testDeuterium.svg", 1732266714U},
{"testTritium.svg", 761248656U},
{"crossed_bonds.svg", 3239666213U},
{"test10_1.svg", 502155973U},
{"test10_2.svg", 3289667916U},
{"test10_3.svg", 2681596657U},
{"test10_4.svg", 2620790292U},
{"test10_5.svg", 2715569518U},
{"test10_6.svg", 2984792612U},
{"test11_1.svg", 568621130U},
{"test11_2.svg", 1278518938U},
{"test12_1.svg", 826649652U},
{"test12_5.svg", 3309074342U},
{"test12_3.svg", 3930752601U},
{"test12_4.svg", 3930752601U},
{"test12_2.svg", 3096703157U},
{"test13_1.svg", 3606927863U},
{"testGithub1090_1.svg", 874921274U},
{"test1271_1.svg", 1756490064U},
{"test1271_2.svg", 3464983192U},
{"test1271_3.svg", 244396434U},
{"test1271_4.svg", 244396434U},
{"test1271_5.svg", 1050442325U},
{"test1322_1.svg", 843693353U},
{"test1322_2.svg", 2204609576U},
{"test14_1.svg", 3999745197U},
{"test14_2.svg", 1367250174U},
{"test15_1.svg", 2704862730U},
{"test15_2.svg", 659023204U},
{"test17_1.svg", 75329691U},
{"test17_2.svg", 2699803606U},
{"test17_3.svg", 2996396838U},
{"test17_4.svg", 2390212603U},
{"test18_1.svg", 1704156856U},
{"test18_2.svg", 597526679U},
{"test18_3.svg", 3425044116U},
{"test18_4.svg", 1519252882U},
{"test18_5.svg", 486224214U},
{"test18_6.svg", 3016814772U},
{"test18_7.svg", 926168958U},
{"test19_1.svg", 4060393720U},
{"test19_2.svg", 4171949096U},
{"test16_1.svg", 62134348U},
{"test16_2.svg", 3050459518U},
{"testGithub2063_1.svg", 1908318348U},
{"testGithub2063_2.svg", 1908318348U},
{"testGithub2151_1.svg", 4119581143U},
{"testGithub2151_2.svg", 425960913U},
{"testGithub2762.svg", 6657792U},
{"testGithub2931_1.svg", 3635831631U},
{"testGithub2931_2.svg", 2281185190U},
{"testGithub2931_3.svg", 2885834646U},
{"testGithub2931_4.svg", 709559976U},
{"test20_1.svg", 4276517022U},
{"test20_2.svg", 2037634551U},
{"test20_3.svg", 2689385188U},
{"test20_4.svg", 4113839132U},
{"test21_1.svg", 390968884U},
{"test21_2.svg", 3050176664U},
{"test22_1.svg", 3688394300U},
{"test22_2.svg", 1963311622U},
{"testGithub3112_1.svg", 75452578U},
{"testGithub3112_2.svg", 2379426157U},
{"testGithub3112_3.svg", 102822156U},
{"testGithub3112_4.svg", 497518508U},
{"testGithub3305_1.svg", 3688394300U},
{"testGithub3305_2.svg", 3172298658U},
{"testGithub3305_3.svg", 30441258U},
{"testGithub3305_4.svg", 300865579U},
{"testGithub3305_5.svg", 1335449325U},
{"testGithub3305_6.svg", 4242832627U},
{"testGithub3305_7.svg", 1080046861U},
{"testGithub3391_1.svg", 1082073469U},
{"testGithub3391_2.svg", 1941002529U},
{"testGithub3391_3.svg", 2929587661U},
{"testGithub3391_4.svg", 3877564580U},
{"testGithub4156_1.svg", 3897707793U},
{"testGithub4156_2.svg", 2067399849U},
{"test23_1.svg", 244577595U},
{"testGithub4496_1.svg", 148519702U},
{"testGithub5006_1.svg", 484020409U},
};
#else
static const std::map<std::string, std::hash_result_t> SVG_HASHES = {
{"test1_1.svg", 550835844U},
{"test1_2.svg", 1800381435U},
{"test1_3.svg", 2440830147U},
{"test1_4.svg", 3696344414U},
{"test1_5.svg", 762580538U},
{"test1_6.svg", 3976836415U},
{"test1_7.svg", 2322019586U},
{"test4_1.svg", 3904017932U},
{"test5_1.svg", 795947420U},
{"test5_2.svg", 1125439478U},
{"test5_3.svg", 1972076988U},
{"test6_1.svg", 975295027U},
{"test6_2.svg", 3885689795U},
{"test6_3.svg", 1462323670U},
{"test7_1.svg", 1967202587U},
{"test7_2.svg", 4217504234U},
{"testGithub781_1.svg", 3207306052U},
{"testGithub781_2.svg", 654027269U},
{"testGithub781_3.svg", 1406186712U},
{"testGithub781_4.svg", 617169423U},
{"testGithub781_5.svg", 2840696942U},
{"testGithub781_6.svg", 2700448827U},
{"test3_1.svg", 1864668966U},
{"test3_2.svg", 1703099924U},
{"test3_3.svg", 2859175047U},
{"test3_4.svg", 2538983199U},
{"test3_5.svg", 268764605U},
{"test3_6.svg", 106421589U},
{"test3_7.svg", 182072330U},
{"test774_1.svg", 1806511429U},
{"test774_2.svg", 3280904264U},
{"test9_1.svg", 1559079325U},
{"test852_1.svg", 2633683070U},
{"test852_2.svg", 3178235826U},
{"test852_2a.svg", 2448053459U},
{"test852_2b.svg", 2800824989U},
{"test852_2c.svg", 2229152216U},
{"test852_2d.svg", 3728986844U},
{"test860_1.svg", 1181005139U},
{"test860_2.svg", 1117691346U},
{"test860_3.svg", 3748952980U},
{"test910_1.svg", 3289686668U},
{"test910_2.svg", 1990959135U},
{"test983_1.svg", 2394066032U},
{"test983_2.svg", 2793911073U},
{"testNoDeuterium.svg", 3284355480U},
{"testNoTritium.svg", 3671254335U},
{"testDeuterium.svg", 1588045678U},
{"testTritium.svg", 983784078U},
{"crossed_bonds.svg", 3239666213U},
{"test10_1.svg", 3091851118U},
{"test10_2.svg", 1982678359U},
{"test10_3.svg", 1939909196U},
{"test10_4.svg", 3561706426U},
{"test10_5.svg", 1816138269U},
{"test10_6.svg", 1980002010U},
{"test11_1.svg", 657855104U},
{"test11_2.svg", 919842717U},
{"test12_1.svg", 38483069U},
{"test12_5.svg", 3783985534U},
{"test12_3.svg", 965019070U},
{"test12_4.svg", 965019070U},
{"test12_2.svg", 1072849234U},
{"test13_1.svg", 140141460U},
{"testGithub1090_1.svg", 394634505U},
{"test1271_1.svg", 1756490064U},
{"test1271_2.svg", 3464983192U},
{"test1271_3.svg", 1332755355U},
{"test1271_4.svg", 1332755355U},
{"test1271_5.svg", 3119394798U},
{"test1322_1.svg", 1119342286U},
{"test1322_2.svg", 1418822069U},
{"test14_1.svg", 2006572335U},
{"test14_2.svg", 4239272366U},
{"test15_1.svg", 4015937389U},
{"test15_2.svg", 749782288U},
{"test17_1.svg", 2496201320U},
{"test17_2.svg", 1781539117U},
{"test17_3.svg", 1326675939U},
{"test17_4.svg", 3705607024U},
{"test18_1.svg", 2903860946U},
{"test18_2.svg", 2863786258U},
{"test18_3.svg", 1289123656U},
{"test18_4.svg", 3866177118U},
{"test18_5.svg", 510653044U},
{"test18_6.svg", 3900355221U},
{"test18_7.svg", 1968448844U},
{"test19_1.svg", 3910758575U},
{"test19_2.svg", 3794790265U},
{"test16_1.svg", 42583033U},
{"test16_2.svg", 2168187083U},
{"testGithub2063_1.svg", 1848845541U},
{"testGithub2063_2.svg", 1848845541U},
{"testGithub2151_1.svg", 3170136101U},
{"testGithub2151_2.svg", 2589699046U},
{"testGithub2762.svg", 3010512419U},
{"testGithub2931_1.svg", 718635370U},
{"testGithub2931_2.svg", 621846436U},
{"testGithub2931_3.svg", 1320211947U},
{"testGithub2931_4.svg", 3936209277U},
{"test20_1.svg", 3782184906U},
{"test20_2.svg", 3219585663U},
{"test20_3.svg", 4137362554U},
{"test20_4.svg", 666420033U},
{"test22_1.svg", 3688394300U},
{"test22_2.svg", 3625077986U},
{"testGithub3112_1.svg", 59370110U},
{"testGithub3112_2.svg", 2675400755U},
{"testGithub3112_3.svg", 2363092454U},
{"testGithub3112_4.svg", 358998579U},
{"testGithub3305_1.svg", 3688394300U},
{"testGithub3305_2.svg", 3172298658U},
{"testGithub3305_3.svg", 30441258U},
{"testGithub3305_4.svg", 268764605U},
{"testGithub3305_5.svg", 889227771U},
{"testGithub3305_6.svg", 661247164U},
{"testGithub3305_7.svg", 1237001849U},
{"testGithub3391_1.svg", 3583014215U},
{"testGithub3391_2.svg", 1768103867U},
{"testGithub3391_3.svg", 2986477009U},
{"testGithub3391_4.svg", 4156829873U},
{"test23_1.svg", 3718784337U},
{"testGithub4496_1.svg", 832097418U},
{"testGithub5006_1.svg", 1549575149U},
};
#endif
// 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
// test20_2.png test3_5.png test3_7.png test774_2.png testGithub3305_5.png
// testGithub3305_7.png test2_2.png test3_6.png test5_1.png
// testGithub3305_4.png testGithub3305_6.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.
static const std::map<std::string, std::hash_result_t> PNG_HASHES = {
{"test2_1.png", 638584804U},
{"test2_2.png", 610424244U},
{"test2_3.png", 2179746375U},
{"test4_1.png", 3993974247U},
{"test5_1.png", 571291290U},
{"test5_2.png", 97265124U},
{"test5_3.png", 606188176U},
{"test7_1.png", 1322246680U},
{"test7_2.png", 1499012715U},
{"test3_1.png", 675908852U},
{"test3_2.png", 2452584093U},
{"test3_3.png", 1907006999U},
{"test3_4.png", 2305641511U},
{"test3_5.png", 3842605920U},
{"test3_6.png", 662622011U},
{"test3_7.png", 469729412U},
{"test774_1.png", 428322245U},
{"test774_2.png", 4095288521U},
{"test852_1.png", 271517011U},
{"test852_2.png", 967452082U},
{"test860_1.png", 2835587240U},
{"test860_2.png", 1116015475U},
{"test860_3.png", 1872467868U},
{"test20_1.png", 200877868U},
{"test20_2.png", 1651164846U},
{"test20_3.png", 1463603076U},
{"test20_4.png", 1714613205U},
{"testGithub3305_1.png", 3303791649U},
{"testGithub3305_2.png", 4003267433U},
{"testGithub3305_3.png", 273338209U},
{"testGithub3305_4.png", 3842605920U},
{"testGithub3305_5.png", 151279576U},
{"testGithub3305_6.png", 613418460U},
{"testGithub3305_7.png", 2835747678U},
};
using namespace RDKit;
// 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.
static const bool DELETE_WITH_GOOD_HASH = true;
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;
}
}
void test1() {
std::cout << " ----------------- Test 1" << std::endl;
{
auto m = "CO[C@@H](O)C1=C(O[C@H](F)Cl)C(C#N)=C1ONNC[NH3+]"_smiles;
TEST_ASSERT(m);
RDDepict::compute2DCoords(*m);
Chirality::wedgeMolBonds(*m, &(m->getConformer()));
std::ofstream outs("test1_1.svg");
MolDraw2DSVG drawer(300, 300, outs);
drawer.drawMolecule(*m);
drawer.finishDrawing();
outs.flush();
outs.close();
check_file_hash("test1_1.svg");
}
{
// make sure this works with the stringstream too:
std::string smiles = "CO[C@@H](O)C1=C(O[C@H](F)Cl)C=C1ONNC[NH3+]";
ROMol *m = SmilesToMol(smiles);
TEST_ASSERT(m);
RDDepict::compute2DCoords(*m);
Chirality::wedgeMolBonds(*m, &(m->getConformer()));
MolDraw2DSVG drawer(300, 300);
drawer.drawMolecule(*m);
drawer.finishDrawing();
std::string text = drawer.getDrawingText();
TEST_ASSERT(text.find("<svg") != std::string::npos);
TEST_ASSERT(text.find("</svg>") != std::string::npos);
delete m;
}
{
std::string smiles = "Cc1c(C(=O)NCCO)[n+](=O)c2ccccc2n1[O-]";
ROMol *m = SmilesToMol(smiles);
TEST_ASSERT(m);
RDDepict::compute2DCoords(*m);
Chirality::wedgeMolBonds(*m, &(m->getConformer()));
std::ofstream outs("test1_2.svg");
MolDraw2DSVG drawer(300, 300, outs);
drawer.drawMolecule(*m);
drawer.finishDrawing();
outs.flush();
outs.close();
check_file_hash("test1_2.svg");
delete m;
}
{
std::string smiles = "Cc1c(C(=O)NCCO)[n+](=O)c2ccccc2n1[O-]";
ROMol *m = SmilesToMol(smiles);
TEST_ASSERT(m);
RDDepict::compute2DCoords(*m);
Chirality::wedgeMolBonds(*m, &(m->getConformer()));
std::ofstream outs("test1_3.svg");
MolDraw2DSVG drawer(300, 300, outs);
std::vector<int> highlights;
highlights.push_back(0);
highlights.push_back(4);
highlights.push_back(5);
drawer.drawMolecule(*m, &highlights);
drawer.finishDrawing();
outs.flush();
outs.close();
check_file_hash("test1_3.svg");
delete m;
}
{
std::string smiles = "CO[C@@H](O)C1=C(O[C@H](F)Cl)C(C#N)=C1ONNC[NH3+]";
ROMol *m = SmilesToMol(smiles);
TEST_ASSERT(m);
RDDepict::compute2DCoords(*m);
Chirality::wedgeMolBonds(*m, &(m->getConformer()));
std::ofstream outs("test1_4.svg");
MolDraw2DSVG drawer(300, 300, outs);
drawer.drawOptions().additionalAtomLabelPadding = 0.25;
drawer.drawMolecule(*m);
drawer.finishDrawing();
outs.flush();
outs.close();
check_file_hash("test1_4.svg");
delete m;
}
{
// in this one, all three double bonds in the phenyl ring need to be inside
// the aromatic ring. There was a time when one of them strayed into the
// aliphatic ring.
std::string smiles =
"CN1CC[C@]23c4c5ccc(O)c4O[C@H]2[C@@H](O)C=C[C@H]3[C@H]1C5";
ROMol *m = SmilesToMol(smiles);
TEST_ASSERT(m);
std::unique_ptr<ROMol> romol(MolOps::removeAllHs(*m));
RDDepict::compute2DCoords(*romol);
Chirality::wedgeMolBonds(*romol, &(romol->getConformer()));
std::ofstream outs("test1_5.svg");
MolDraw2DSVG drawer(300, 300, outs);
drawer.drawMolecule(*romol);
drawer.finishDrawing();
outs.flush();
outs.close();
// note that this hash check is likely to fail at the moment, due
// to issue #4205.
check_file_hash("test1_5.svg");
delete m;
}
{
// Here, the H should be between the two bonds off the N, not
// on top of the vertical one.
std::string smiles = "C[NH+](C)CCC";
std::string nameBase = "test1_6";
ROMol *m = SmilesToMol(smiles);
TEST_ASSERT(m);
RDDepict::compute2DCoords(*m);
Chirality::wedgeMolBonds(*m, &(m->getConformer()));
MolDraw2DSVG drawer(300, 300);
drawer.drawMolecule(*m);
drawer.finishDrawing();
std::string txt = drawer.getDrawingText();
std::ofstream outs("test1_6.svg");
outs << txt;
outs.flush();
outs.close();
check_file_hash("test1_6.svg");
delete m;
}
{
// check that splitBonds is working
auto m = "c1ccncc1COC"_smiles;
TEST_ASSERT(m);
RDDepict::compute2DCoords(*m);
Chirality::wedgeMolBonds(*m, &(m->getConformer()));
std::ofstream outs("test1_7.svg");
MolDraw2DSVG drawer(300, 300);
drawer.drawOptions().splitBonds = true;
drawer.drawMolecule(*m);
drawer.finishDrawing();
std::string txt = drawer.getDrawingText();
outs << txt;
outs.flush();
outs.close();
// returns count of non-overlapping occurrences of 'sub' in 'str'
// from
// https://stackoverflow.com/questions/22489073/counting-the-number-of-occurrences-of-a-string-within-a-string
auto countSubstring = [](const std::string &str,
const std::string &sub) -> int {
if (sub.length() == 0) {
return 0;
}
int count = 0;
for (size_t offset = str.find(sub); offset != std::string::npos;
offset = str.find(sub, offset + sub.length())) {
++count;
}
return count;
};
// this is a double bond
TEST_ASSERT(countSubstring(txt, "class='bond-0 atom-0'") == 2);
TEST_ASSERT(countSubstring(txt, "class='bond-0 atom-1'") == 2);
// this is how it would be if splitBonds wasn't working.
TEST_ASSERT(countSubstring(txt, "class='bond-0 atom-0 atom-1'") == 0);
check_file_hash("test1_7.svg");
}
std::cout << " Done" << std::endl;
}
#ifdef RDK_BUILD_CAIRO_SUPPORT
#include <cairo.h>
#include "MolDraw2DCairo.h"
void test2() {
std::cout << " ----------------- Test 2" << std::endl;
{
std::string smiles = "CO[C@@H](O)C1=C(O[C@H](F)Cl)C(C#N)=C1ONNC[NH3+]";
ROMol *m = SmilesToMol(smiles);
TEST_ASSERT(m);
RDDepict::compute2DCoords(*m);
WedgeMolBonds(*m, &(m->getConformer()));
MolDraw2DCairo drawer(300, 300);
drawer.drawMolecule(*m);
drawer.finishDrawing();
drawer.writeDrawingText("test2_1.png");
check_file_hash("test2_1.png");
delete m;
}
{
std::string smiles = "Cc1c(C(=O)NCCO)[n+](=O)c2ccccc2n1[O-]";
ROMol *m = SmilesToMol(smiles);
TEST_ASSERT(m);
RDDepict::compute2DCoords(*m);
WedgeMolBonds(*m, &(m->getConformer()));
MolDraw2DCairo drawer(300, 300);
drawer.drawMolecule(*m);
drawer.finishDrawing();
std::string drawing = drawer.getDrawingText();
TEST_ASSERT(drawing.size() > 0);
std::ofstream ofs("test2_2.png");
ofs.write(drawing.c_str(), drawing.size());
check_file_hash("test2_2.png");
delete m;
}
{
// ensure we still work with a client-provided drawing context
std::string smiles = "Cc1c(C(=O)NCCO)[n+](=O)c2ccccc2n1[O-]";
ROMol *m = SmilesToMol(smiles);
TEST_ASSERT(m);
RDDepict::compute2DCoords(*m);
WedgeMolBonds(*m, &(m->getConformer()));
cairo_surface_t *surface =
cairo_image_surface_create(CAIRO_FORMAT_ARGB32, 300, 300);
cairo_t *cr = cairo_create(surface);
MolDraw2DCairo drawer(300, 300, cr);
std::vector<int> highlights;
highlights.push_back(0);
highlights.push_back(4);
highlights.push_back(5);
drawer.drawMolecule(*m, &highlights);
drawer.finishDrawing();
cairo_destroy(cr);
cairo_surface_write_to_png(surface, "test2_3.png");
cairo_surface_destroy(surface);
check_file_hash("test2_3.png");
delete m;
}
std::cout << " Done" << std::endl;
}
#else // RDK_BUILD_CAIRO_SUPPORT
void test2() {}
#endif
void test3() {
std::cout << " ----------------- Test 3" << std::endl;
{
std::string smiles = "C1CC1CC1ON1";
std::string nameBase = "test3_1";
ROMol *m = SmilesToMol(smiles);
TEST_ASSERT(m);
RDDepict::compute2DCoords(*m);
Chirality::wedgeMolBonds(*m, &(m->getConformer()));
static const int ha[] = {0, 3, 4, 5};
std::vector<int> highlight_atoms(ha, ha + sizeof(ha) / sizeof(int));
std::map<int, std::string> atomLabels;
atomLabels[2] = "C1";
atomLabels[1] = "a<sub>3</sub><sup>4</sup>";
atomLabels[0] = "[CH2;X2:4]";
atomLabels[6] = "[NH2+:7]";
#ifdef RDK_BUILD_CAIRO_SUPPORT
{
MolDraw2DCairo drawer(300, 300);
drawer.drawOptions().atomLabels = atomLabels;
drawer.drawMolecule(*m, &highlight_atoms);
drawer.finishDrawing();
drawer.writeDrawingText(nameBase + ".png");
check_file_hash(nameBase + ".png");
}
#endif
{
std::ofstream outs((nameBase + ".svg").c_str());
MolDraw2DSVG drawer(300, 300, outs);
drawer.drawOptions().atomLabels = atomLabels;
drawer.drawMolecule(*m, &highlight_atoms);
drawer.finishDrawing();
outs.flush();
outs.close();
check_file_hash(nameBase + ".svg");
}
delete m;
}
{
std::string smiles = "C1CC1CC1ON1";
std::string nameBase = "test3_2";
ROMol *m = SmilesToMol(smiles);
TEST_ASSERT(m);
RDDepict::compute2DCoords(*m);
Chirality::wedgeMolBonds(*m, &(m->getConformer()));
static const int ha[] = {0, 3, 4, 5};
std::vector<int> highlight_atoms(ha, ha + sizeof(ha) / sizeof(int));
#ifdef RDK_BUILD_CAIRO_SUPPORT
{
MolDraw2DCairo drawer(300, 300);
drawer.drawOptions().circleAtoms = false;
drawer.drawMolecule(*m, &highlight_atoms);
drawer.finishDrawing();
drawer.writeDrawingText(nameBase + ".png");
check_file_hash(nameBase + ".png");
}
#endif
{
std::ofstream outs((nameBase + ".svg").c_str());
MolDraw2DSVG drawer(300, 300, outs);
drawer.drawOptions().circleAtoms = false;
drawer.drawMolecule(*m, &highlight_atoms);
drawer.finishDrawing();
outs.flush();
outs.close();
check_file_hash(nameBase + ".svg");
}
delete m;
}
{
std::string smiles = "Cc1c(C(=O)NCCO)[n+](=O)c2ccccc2n1[O-]";
std::string nameBase = "test3_3";
ROMol *m = SmilesToMol(smiles);
TEST_ASSERT(m);
RDDepict::compute2DCoords(*m);
Chirality::wedgeMolBonds(*m, &(m->getConformer()));
static const int ha[] = {11, 12, 13, 14, 15, 16};
std::vector<int> highlight_atoms(ha, ha + sizeof(ha) / sizeof(int));
std::map<int, DrawColour> highlight_colors;
highlight_colors[12] = DrawColour(0, 0, 1);
highlight_colors[13] = DrawColour(0, 1, 0);
#ifdef RDK_BUILD_CAIRO_SUPPORT
{
MolDraw2DCairo drawer(300, 300);
drawer.drawOptions().circleAtoms = true;
drawer.drawMolecule(*m, &highlight_atoms, &highlight_colors);
drawer.finishDrawing();
drawer.writeDrawingText(nameBase + ".png");
check_file_hash(nameBase + ".png");
}
#endif
{
std::ofstream outs((nameBase + ".svg").c_str());
MolDraw2DSVG drawer(300, 300, outs);
drawer.drawOptions().circleAtoms = true;
drawer.drawMolecule(*m, &highlight_atoms, &highlight_colors);
drawer.finishDrawing();
outs.flush();
outs.close();
check_file_hash(nameBase + ".svg");
}
delete m;
}
{
std::string smiles = "Cc1c(C(=O)NCCO)[n+](=O)c2ccccc2n1[O-]";
std::string nameBase = "test3_4";
ROMol *m = SmilesToMol(smiles);
TEST_ASSERT(m);
RDDepict::compute2DCoords(*m);
Chirality::wedgeMolBonds(*m, &(m->getConformer()));
static const int ha[] = {11, 12, 13, 14, 15, 16, 3};
std::vector<int> highlight_atoms(ha, ha + sizeof(ha) / sizeof(int));
std::map<int, DrawColour> highlight_colors;
highlight_colors[12] = DrawColour(.5, .5, 1);
highlight_colors[13] = DrawColour(.5, 1, .5);
MolDrawOptions options;
options.circleAtoms = true;
options.highlightColour = DrawColour(1, .5, .5);
options.continuousHighlight = true;
#ifdef RDK_BUILD_CAIRO_SUPPORT
{
MolDraw2DCairo drawer(300, 300);
drawer.drawOptions() = options;
drawer.drawMolecule(*m, &highlight_atoms, &highlight_colors);
drawer.finishDrawing();
drawer.writeDrawingText(nameBase + ".png");
check_file_hash(nameBase + ".png");
}
#endif
{
std::ofstream outs((nameBase + ".svg").c_str());
MolDraw2DSVG drawer(300, 300, outs);
drawer.drawOptions() = options;
drawer.drawMolecule(*m, &highlight_atoms, &highlight_colors);
drawer.finishDrawing();
outs.flush();
outs.close();
check_file_hash(nameBase + ".svg");
}
delete m;
}
{
std::string smiles =
"CCOC(=O)Nc1ccc(SCC2COC(Cn3ccnc3)(c3ccc(Cl)cc3Cl)O2)cc1";
std::string nameBase = "test3_5";
ROMol *m = SmilesToMol(smiles);
TEST_ASSERT(m);
RDDepict::compute2DCoords(*m);
Chirality::wedgeMolBonds(*m, &(m->getConformer()));
static const int ha[] = {17, 18, 19, 20, 21, 6, 7, 8, 9, 31, 32};
std::vector<int> highlight_atoms(ha, ha + sizeof(ha) / sizeof(int));
std::map<int, DrawColour> highlight_colors;
MolDrawOptions options;
options.circleAtoms = true;
options.highlightColour = DrawColour(1, .5, .5);
options.continuousHighlight = true;
#ifdef RDK_BUILD_CAIRO_SUPPORT
{
MolDraw2DCairo drawer(200, 200);
drawer.drawOptions() = options;
drawer.drawMolecule(*m, &highlight_atoms, &highlight_colors);
drawer.finishDrawing();
drawer.writeDrawingText(nameBase + ".png");
check_file_hash(nameBase + ".png");
}
#endif
{
std::ofstream outs((nameBase + ".svg").c_str());
MolDraw2DSVG drawer(200, 200, outs);
drawer.drawOptions() = options;
drawer.drawMolecule(*m, &highlight_atoms, &highlight_colors);
drawer.finishDrawing();
outs.flush();
outs.close();
check_file_hash(nameBase + ".svg");
}
delete m;
}
{
std::string smiles =
"CCOC(=O)Nc1ccc(SCC2COC(Cn3ccnc3)(c3ccc(Cl)cc3Cl)O2)cc1";
std::string nameBase = "test3_6";
ROMol *m = SmilesToMol(smiles);
TEST_ASSERT(m);
RDDepict::compute2DCoords(*m);
Chirality::wedgeMolBonds(*m, &(m->getConformer()));
MolDrawOptions options;
static const int ha1[] = {17, 18, 19, 20, 21};
std::vector<int> highlight_atoms1(ha1, ha1 + sizeof(ha1) / sizeof(int));
options.atomRegions.push_back(highlight_atoms1);
static const int ha2[] = {6, 7, 8, 9, 31, 32};
std::vector<int> highlight_atoms2(ha2, ha2 + sizeof(ha2) / sizeof(int));
options.atomRegions.push_back(highlight_atoms2);
options.includeAtomTags = true;
#ifdef RDK_BUILD_CAIRO_SUPPORT
{
MolDraw2DCairo drawer(300, 300);
drawer.drawOptions() = options;
drawer.drawMolecule(*m);
drawer.finishDrawing();
drawer.writeDrawingText(nameBase + ".png");
check_file_hash(nameBase + ".png");
}
#endif
{
std::ofstream outs((nameBase + ".svg").c_str());
MolDraw2DSVG drawer(300, 300, outs);
drawer.drawOptions() = options;
drawer.drawMolecule(*m);
drawer.finishDrawing();
outs.flush();
outs.close();
check_file_hash(nameBase + ".svg");
}
delete m;
}
{
std::string smiles =
"CCOC(=O)Nc1ccc(SCC2COC(Cn3ccnc3)(c3ccc(Cl)cc3Cl)O2)cc1";
std::string nameBase = "test3_7";
ROMol *m = SmilesToMol(smiles);
TEST_ASSERT(m);
RDDepict::compute2DCoords(*m);
Chirality::wedgeMolBonds(*m, &(m->getConformer()));
MolDrawOptions options;
options.continuousHighlight = true;
static const int ha[] = {17, 20, 25};
std::vector<int> highlight_atoms(ha, ha + sizeof(ha) / sizeof(int));
std::map<int, double> highlight_radii;
highlight_radii[17] = 0.5;
highlight_radii[20] = 1.0;
std::map<int, DrawColour> highlight_colors;
highlight_colors[17] = DrawColour(.5, .5, 1.);
#ifdef RDK_BUILD_CAIRO_SUPPORT
{
MolDraw2DCairo drawer(300, 300);
drawer.drawOptions() = options;
drawer.drawMolecule(*m, &highlight_atoms, &highlight_colors,
&highlight_radii);
drawer.finishDrawing();
drawer.writeDrawingText(nameBase + ".png");
check_file_hash(nameBase + ".png");
}
#endif
{
std::ofstream outs((nameBase + ".svg").c_str());
MolDraw2DSVG drawer(300, 300, outs);
drawer.drawOptions() = options;
drawer.drawMolecule(*m, &highlight_atoms, &highlight_colors,
&highlight_radii);
drawer.finishDrawing();
outs.flush();
outs.close();
check_file_hash(nameBase + ".svg");
}
delete m;
}
std::cout << " Done" << std::endl;
}
void test4() {
std::cout << " ----------------- Test 4" << std::endl;
{
std::string fName = getenv("RDBASE");
fName += "/Code/GraphMol/MolDraw2D/test_dir";
fName += "/clash.mol";
ROMol *m = MolFileToMol(fName);
std::string nameBase = "test4_1";
TEST_ASSERT(m);
#ifdef RDK_BUILD_CAIRO_SUPPORT
{
MolDraw2DCairo drawer(300, 300);
drawer.drawMolecule(*m);
drawer.finishDrawing();
drawer.writeDrawingText(nameBase + ".png");
check_file_hash(nameBase + ".png");
}
#endif
{
std::ofstream outs((nameBase + ".svg").c_str());
MolDraw2DSVG drawer(300, 300, outs);
drawer.drawMolecule(*m);
drawer.finishDrawing();
outs.flush();
outs.close();
check_file_hash(nameBase + ".svg");
}
delete m;
}
std::cout << " Done" << std::endl;
}
void test5() {
std::cout << " ----------------- Test 5" << std::endl;
{
std::string smiles = "*c1cc(*)cc(*)c1";
std::string nameBase = "test5_1";
ROMol *m = SmilesToMol(smiles);
TEST_ASSERT(m);
RDDepict::compute2DCoords(*m);
Chirality::wedgeMolBonds(*m, &(m->getConformer()));
MolDrawOptions options;
options.dummiesAreAttachments = true;
options.atomLabels[0] = "R1";
#ifdef RDK_BUILD_CAIRO_SUPPORT
{
MolDraw2DCairo drawer(300, 300);
drawer.drawOptions() = options;
drawer.drawMolecule(*m);
drawer.finishDrawing();
drawer.writeDrawingText(nameBase + ".png");
check_file_hash(nameBase + ".png");
}
#endif
{
std::ofstream outs((nameBase + ".svg").c_str());
MolDraw2DSVG drawer(300, 300, outs);
drawer.drawOptions() = options;
drawer.drawMolecule(*m);
drawer.finishDrawing();
outs.flush();
outs.close();
check_file_hash(nameBase + ".svg");
}
delete m;
}
{
std::string smiles = "*C";
std::string nameBase = "test5_2";
ROMol *m = SmilesToMol(smiles);
TEST_ASSERT(m);
RDDepict::compute2DCoords(*m, nullptr, true);
Chirality::wedgeMolBonds(*m, &(m->getConformer()));
MolDrawOptions options;
options.dummiesAreAttachments = true;
#ifdef RDK_BUILD_CAIRO_SUPPORT
{
MolDraw2DCairo drawer(300, 300);
drawer.drawOptions() = options;
drawer.drawMolecule(*m);
drawer.finishDrawing();
drawer.writeDrawingText(nameBase + ".png");
check_file_hash(nameBase + ".png");
}
#endif
{
std::ofstream outs((nameBase + ".svg").c_str());
MolDraw2DSVG drawer(300, 300, outs);
drawer.drawOptions() = options;
drawer.drawMolecule(*m);
drawer.finishDrawing();
outs.flush();
outs.close();
check_file_hash(nameBase + ".svg");
}
delete m;
}
{
std::string smiles = "CC(F)(Cl)Br";
std::string nameBase = "test5_3";
ROMol *m = SmilesToMol(smiles);
TEST_ASSERT(m);
m->getBondBetweenAtoms(1, 2)->setBondDir(Bond::UNKNOWN);
RDDepict::compute2DCoords(*m, nullptr, true);
Chirality::wedgeMolBonds(*m, &(m->getConformer()));
MolDrawOptions options;
options.dummiesAreAttachments = true;
#ifdef RDK_BUILD_CAIRO_SUPPORT
{
MolDraw2DCairo drawer(300, 300);
drawer.drawOptions() = options;
drawer.drawMolecule(*m);
drawer.finishDrawing();
drawer.writeDrawingText(nameBase + ".png");
check_file_hash(nameBase + ".png");
}
#endif
{
std::ofstream outs((nameBase + ".svg").c_str());
MolDraw2DSVG drawer(300, 300, outs);
drawer.drawOptions() = options;
drawer.drawMolecule(*m);
drawer.finishDrawing();
outs.flush();
outs.close();
check_file_hash(nameBase + ".svg");
}
delete m;
}
std::cout << " Done" << std::endl;
}
#ifdef RDK_TEST_MULTITHREADED
#include <thread>
#include <future>
namespace {
void runblock(const std::vector<ROMol *> &mols,
const std::vector<std::string> &refData, unsigned int count,
unsigned int idx) {
for (unsigned int j = 0; j < 200; j++) {
for (unsigned int i = 0; i < mols.size(); ++i) {
if (i % count != idx) {
continue;
}
ROMol *mol = mols[i];
MolDraw2DSVG drawer(300, 300);
drawer.drawMolecule(*mol);
drawer.finishDrawing();
std::string text = drawer.getDrawingText();
TEST_ASSERT(text == refData[i]);
}
}
}
} // namespace
void testMultiThreaded() {
std::cout << " ----------------- Test multi-threaded drawing" << std::endl;
std::string fName = getenv("RDBASE");
fName += "/Data/NCI/first_200.props.sdf";
RDKit::SDMolSupplier suppl(fName);
std::cerr << "reading molecules" << std::endl;
std::vector<ROMol *> mols;
while (!suppl.atEnd() && mols.size() < 100) {
ROMol *mol = nullptr;
try {
mol = suppl.next();
} catch (...) {
continue;
}
if (!mol) {
continue;
}
mols.push_back(mol);
}
std::cerr << "generating reference drawings" << std::endl;
std::vector<std::string> refData(mols.size());
for (unsigned int i = 0; i < mols.size(); ++i) {
MolDraw2DSVG drawer(300, 300);
drawer.drawMolecule(*(mols[i]));
drawer.finishDrawing();
refData[i] = drawer.getDrawingText();
TEST_ASSERT(refData[i].find("<svg") != std::string::npos);
TEST_ASSERT(refData[i].find("</svg>") != std::string::npos);
}
std::vector<std::future<void>> tg;
unsigned int count = 4;
std::cerr << "processing" << std::endl;
for (unsigned int i = 0; i < count; ++i) {
std::cerr << " launch :" << i << std::endl;
std::cerr.flush();
tg.emplace_back(
std::async(std::launch::async, runblock, mols, refData, count, i));
}
for (auto &fut : tg) {
fut.get();
}
for (auto &&mol : mols) {
delete mol;
}
std::cerr << " Done" << std::endl;
}
#else
void testMultiThreaded() {}
#endif
void test6() {
std::cout << " ----------------- Test 6 (atom labels)" << std::endl;
{
std::string smiles = "CC[13CH2][CH2:7][CH-]C[15NH2+]C";
std::string nameBase = "test6_1";
ROMol *m = SmilesToMol(smiles);
TEST_ASSERT(m);
RDDepict::compute2DCoords(*m);
Chirality::wedgeMolBonds(*m, &(m->getConformer()));
MolDraw2DSVG drawer(300, 300);
drawer.drawMolecule(*m);
drawer.finishDrawing();
std::string txt = drawer.getDrawingText();
std::ofstream outs(nameBase + ".svg");
outs << txt;
// TEST_ASSERT(txt.find("<svg")!=std::string::npos);
outs.flush();
outs.close();
outs.close();
check_file_hash(nameBase + ".svg");
delete m;
}
{
auto m = "[C]1[C][C][CH][CH][CH]1"_smiles;
std::string nameBase = "test6_2";
TEST_ASSERT(m);
RDDepict::compute2DCoords(*m);
MolDraw2DSVG drawer(300, 300);
drawer.drawMolecule(*m);
drawer.finishDrawing();
std::string txt = drawer.getDrawingText();
TEST_ASSERT(txt.find("<svg") != std::string::npos);
std::ofstream outs(nameBase + ".svg");
outs << txt;
outs.close();
// start of bond-0
#if DO_TEST_ASSERT
TEST_ASSERT(
txt.find("<path class='bond-0 atom-0 atom-1' d='M 268.9,148.0") !=
std::string::npos);
// start of first radical spot
TEST_ASSERT(
txt.find("<path class='atom-0' d='M 282.9,152.0 L 282.9,152.2") !=
std::string::npos);
#endif
check_file_hash(nameBase + ".svg");
}
{
auto m = "N[C]"_smiles;
std::string nameBase = "test6_3";
TEST_ASSERT(m);
RDDepict::compute2DCoords(*m);
MolDraw2DSVG drawer(300, 300);
drawer.drawMolecule(*m);
drawer.finishDrawing();
std::string txt = drawer.getDrawingText();
TEST_ASSERT(txt.find("<svg") != std::string::npos);
std::ofstream outs(nameBase + ".svg");
outs << txt;
outs.close();
// start of bond-0
#if DO_TEST_ASSERT
#ifdef RDK_BUILD_FREETYPE_SUPPORT
TEST_ASSERT(
txt.find("<path class='bond-0 atom-0 atom-1' d='M 186.8,118.4") !=
std::string::npos);
// start of first radical spot
TEST_ASSERT(txt.find("<path class='atom-1' d='M 43.8,190.3 L 43.8,190.4") !=
std::string::npos);
#else
TEST_ASSERT(
txt.find("<path class='bond-0 atom-0 atom-1' d='M 186.5,117.8") !=
std::string::npos);
// start of first radical spot
#endif
#endif
check_file_hash(nameBase + ".svg");
}
std::cerr << " Done" << std::endl;
}
void test7() {
std::cout << " ----------------- Test 7 (backgrounds)" << std::endl;
std::string smiles = "CCC";
ROMol *m = SmilesToMol(smiles);
TEST_ASSERT(m);
RDDepict::compute2DCoords(*m);
{
std::string nameBase = "test7_1";
MolDraw2DSVG drawer(300, 300);
drawer.drawOptions().clearBackground = false;
drawer.drawMolecule(*m);
drawer.finishDrawing();
std::string txt = drawer.getDrawingText();
std::ofstream outs((nameBase + ".svg").c_str());
outs << txt;
outs.flush();
outs.close();
check_file_hash(nameBase + ".svg");
TEST_ASSERT(txt.find("<svg") != std::string::npos);
TEST_ASSERT(txt.find("<rect") == std::string::npos);
}
#ifdef RDK_BUILD_CAIRO_SUPPORT
{
std::string nameBase = "test7_1";
MolDraw2DCairo drawer(300, 300);
drawer.drawOptions().clearBackground = false;
drawer.drawMolecule(*m);
drawer.finishDrawing();
drawer.writeDrawingText(nameBase + ".png");
check_file_hash(nameBase + ".png");
}
#endif
{
std::string nameBase = "test7_2";
MolDraw2DSVG drawer(300, 300);
drawer.drawOptions().backgroundColour = DrawColour(.8, .8, .8);
drawer.drawMolecule(*m);
drawer.finishDrawing();
std::string txt = drawer.getDrawingText();
std::ofstream outs((nameBase + ".svg").c_str());
outs << txt;
outs.flush();
outs.close();
check_file_hash(nameBase + ".svg");
TEST_ASSERT(txt.find("<svg") != std::string::npos);
TEST_ASSERT(txt.find("<rect") != std::string::npos);
TEST_ASSERT(txt.find("fill:#CCCCCC") != std::string::npos);
}
#ifdef RDK_BUILD_CAIRO_SUPPORT
{
std::string nameBase = "test7_2";
MolDraw2DCairo drawer(300, 300);
drawer.drawOptions().backgroundColour = DrawColour(.8, .8, .8);
drawer.drawMolecule(*m);
drawer.finishDrawing();
drawer.writeDrawingText(nameBase + ".png");
check_file_hash(nameBase + ".png");
}
#endif
delete m;
std::cerr << " Done" << std::endl;
}
void test8PrepareMolForDrawing() {
std::cout << " ----------------- Test8: PrepareMolDrawing" << std::endl;
{
std::string smiles = "c1ccccc1[C@H](F)Cl";
ROMol *m = SmilesToMol(smiles);
TEST_ASSERT(m);
{
RWMol nm(*m);
TEST_ASSERT(nm.getNumAtoms() == 9)
MolDraw2DUtils::prepareMolForDrawing(nm);
TEST_ASSERT(nm.getNumAtoms() == 9); // this is a test for github #982
TEST_ASSERT(nm.getNumConformers() == 1);
TEST_ASSERT(!nm.getConformer().is3D());
TEST_ASSERT(nm.getBondBetweenAtoms(0, 1)->getBondType() !=
Bond::AROMATIC);
TEST_ASSERT(nm.getBondBetweenAtoms(0, 1)->getIsAromatic());
TEST_ASSERT(nm.getBondBetweenAtoms(6, 7)->getBondType() == Bond::SINGLE);
TEST_ASSERT(nm.getBondBetweenAtoms(6, 7)->getBondDir() ==
Bond::BEGINWEDGE);
// make sure we can do it again:
MolDraw2DUtils::prepareMolForDrawing(nm);
TEST_ASSERT(nm.getNumAtoms() == 9);
TEST_ASSERT(nm.getNumConformers() == 1);
TEST_ASSERT(nm.getBondBetweenAtoms(0, 1)->getBondType() !=
Bond::AROMATIC);
TEST_ASSERT(nm.getBondBetweenAtoms(0, 1)->getIsAromatic());
}
{
RWMol nm(*m);
TEST_ASSERT(nm.getNumAtoms() == 9)
MolDraw2DUtils::prepareMolForDrawing(nm, false);
TEST_ASSERT(nm.getNumAtoms() == 9);
TEST_ASSERT(nm.getNumConformers() == 1);
TEST_ASSERT(nm.getBondBetweenAtoms(0, 1)->getBondType() ==
Bond::AROMATIC);
TEST_ASSERT(nm.getBondBetweenAtoms(0, 1)->getIsAromatic());
}
{
RWMol nm(*m);
TEST_ASSERT(nm.getNumAtoms() == 9)
MolDraw2DUtils::prepareMolForDrawing(nm, false, false);
TEST_ASSERT(nm.getNumAtoms() == 9);
TEST_ASSERT(nm.getNumConformers() == 1);
TEST_ASSERT(nm.getBondBetweenAtoms(0, 1)->getBondType() ==
Bond::AROMATIC);
TEST_ASSERT(nm.getBondBetweenAtoms(0, 1)->getIsAromatic());
}
{
RWMol nm(*m);
TEST_ASSERT(nm.getNumAtoms() == 9)
MolDraw2DUtils::prepareMolForDrawing(nm, false, true);
TEST_ASSERT(nm.getNumAtoms() == 9);
TEST_ASSERT(nm.getNumConformers() == 1);
TEST_ASSERT(nm.getBondBetweenAtoms(0, 1)->getBondType() ==
Bond::AROMATIC);
TEST_ASSERT(nm.getBondBetweenAtoms(0, 1)->getIsAromatic());
}
{
RWMol nm(*m);
TEST_ASSERT(nm.getNumAtoms() == 9)
MolDraw2DUtils::prepareMolForDrawing(nm, true, true, false);
TEST_ASSERT(nm.getNumAtoms() == 9);
TEST_ASSERT(nm.getNumConformers() == 1);
TEST_ASSERT(nm.getBondBetweenAtoms(0, 1)->getBondType() !=
Bond::AROMATIC);
TEST_ASSERT(nm.getBondBetweenAtoms(0, 1)->getIsAromatic());
TEST_ASSERT(nm.getBondBetweenAtoms(6, 7)->getBondType() == Bond::SINGLE);
TEST_ASSERT(nm.getBondBetweenAtoms(6, 7)->getBondDir() == Bond::NONE);
}
{
// by default we don't force conformer generation
RWMol nm(*m);
RDDepict::compute2DCoords(nm);
nm.getConformer().set3D(true); // it's not really, we're cheating
TEST_ASSERT(nm.getNumAtoms() == 9)
MolDraw2DUtils::prepareMolForDrawing(nm);
TEST_ASSERT(nm.getNumAtoms() == 9);
TEST_ASSERT(nm.getNumConformers() == 1); // we have a conformer anyway
TEST_ASSERT(nm.getConformer().is3D());
// but if we do force, it blows out that conformer:
MolDraw2DUtils::prepareMolForDrawing(nm, true, true, true, true);
TEST_ASSERT(!nm.getConformer().is3D());
}
delete m;
}
{
std::string smiles = "C1CC[C@H]2NCCCC2C1";
ROMol *m = SmilesToMol(smiles);
TEST_ASSERT(m);
{
RWMol nm(*m);
TEST_ASSERT(nm.getNumAtoms() == 10)
MolDraw2DUtils::prepareMolForDrawing(nm);
TEST_ASSERT(nm.getNumAtoms() == 11);
TEST_ASSERT(nm.getNumConformers() == 1);
TEST_ASSERT(!nm.getConformer().is3D());
TEST_ASSERT(nm.getBondBetweenAtoms(3, 10)->getBondType() == Bond::SINGLE);
TEST_ASSERT(nm.getBondBetweenAtoms(3, 10)->getBondDir() ==
Bond::BEGINDASH);
// make sure we can do it again:
MolDraw2DUtils::prepareMolForDrawing(nm);
TEST_ASSERT(nm.getNumAtoms() == 11);
TEST_ASSERT(nm.getNumConformers() == 1);
TEST_ASSERT(nm.getBondBetweenAtoms(3, 10)->getBondType() == Bond::SINGLE);
TEST_ASSERT(nm.getBondBetweenAtoms(3, 10)->getBondDir() ==
Bond::BEGINDASH);
}
{
RWMol nm(*m);
TEST_ASSERT(nm.getNumAtoms() == 10)
MolDraw2DUtils::prepareMolForDrawing(nm, false, false);
TEST_ASSERT(nm.getNumAtoms() == 10);
TEST_ASSERT(nm.getNumConformers() == 1);
TEST_ASSERT(nm.getBondBetweenAtoms(3, 2)->getBondType() == Bond::SINGLE);
TEST_ASSERT(nm.getBondBetweenAtoms(3, 2)->getBondDir() ==
Bond::BEGINWEDGE);
}
delete m;
}
std::cerr << " Done" << std::endl;
}
void testGithub781() {
std::cout << " ----------------- Test Github #781: Rendering single-atom "
"molecules"
<< std::endl;
{
auto m = "C"_smiles;
TEST_ASSERT(m);
RDDepict::compute2DCoords(*m);
MolDraw2DSVG drawer(300, 300);
drawer.drawMolecule(*m);
drawer.finishDrawing();
std::string txt = drawer.getDrawingText();
TEST_ASSERT(txt.find("<svg") != std::string::npos);
// write the file so we can update the coords below more easily
// if the font changes, for example.
std::ofstream outs("testGithub781_1.svg");
outs << txt;
outs.close();
#ifdef RDK_BUILD_FREETYPE_SUPPORT
#if DO_TEST_ASSERT
// the start of the C
TEST_ASSERT(txt.find("<path class='atom-0' d='M 116.1 143.0") !=
std::string::npos)
// the start of the H
TEST_ASSERT(txt.find("<path class='atom-0' d='M 141.7 128.9") !=
std::string::npos)
#endif
#else
TEST_ASSERT(txt.find(">C</text>") != std::string::npos);
TEST_ASSERT(txt.find(">H</text>") != std::string::npos);
TEST_ASSERT(txt.find(">4</text>") != std::string::npos);
TEST_ASSERT(txt.find("font-size:40px") != std::string::npos);
TEST_ASSERT(txt.find("font-size:26px") != std::string::npos);
#endif
check_file_hash("testGithub781_1.svg");
}
{
auto m = "O"_smiles;
TEST_ASSERT(m);
RDDepict::compute2DCoords(*m);
MolDraw2DSVG drawer(300, 300);
drawer.drawMolecule(*m);
drawer.finishDrawing();
std::string txt = drawer.getDrawingText();
TEST_ASSERT(txt.find("<svg") != std::string::npos);
std::ofstream outs("testGithub781_2.svg");
outs << txt;
outs.close();
#ifdef RDK_BUILD_FREETYPE_SUPPORT
#if DO_TEST_ASSERT
// start of the H
TEST_ASSERT(txt.find("<path class='atom-0' d='M 114.9 128.9") !=
std::string::npos);
// start of the O
TEST_ASSERT(txt.find("<path class='atom-0' d='M 142.7 156.2") !=
std::string::npos);
#endif
#else
TEST_ASSERT(txt.find("<tspan>OH</tspan>") == std::string::npos);
#endif
check_file_hash("testGithub781_2.svg");
}
{
auto m = "[C]"_smiles;
TEST_ASSERT(m);
RDDepict::compute2DCoords(*m);
MolDraw2DSVG drawer(600, 600);
drawer.drawMolecule(*m);
drawer.finishDrawing();
std::string txt = drawer.getDrawingText();
TEST_ASSERT(txt.find("<svg") != std::string::npos);
std::ofstream outs("testGithub781_3.svg");
outs << txt;
outs.close();
#ifdef RDK_BUILD_FREETYPE_SUPPORT
#if DO_TEST_ASSERT
// The C
TEST_ASSERT(txt.find("<path class='atom-0' d='M 285.3 299.9") !=
std::string::npos);
// the first radical marker
TEST_ASSERT(
txt.find("<path class='atom-0' d='M 315.2,311.8 L 315.2,312.0") !=
std::string::npos);
#endif
#else
TEST_ASSERT(txt.find(">C</text>") != std::string::npos);
// the first radical marker
TEST_ASSERT(
txt.find("<path class='atom-0' d='M 316.2,309.0 L 316.2,309.2") !=
std::string::npos);
#endif
check_file_hash("testGithub781_3.svg");
}
{
auto m = "C.CC.[Cl-]"_smiles;
TEST_ASSERT(m);
RDDepict::compute2DCoords(*m);
MolDraw2DSVG drawer(300, 300);
drawer.drawMolecule(*m);
drawer.finishDrawing();
std::string txt = drawer.getDrawingText();
TEST_ASSERT(txt.find("<svg") != std::string::npos);
std::ofstream outs("testGithub781_4.svg");
outs << txt;
outs.close();
#ifdef RDK_BUILD_FREETYPE_SUPPORT
#if DO_TEST_ASSERT
// start of C
TEST_ASSERT(txt.find("<path class='atom-0' d='M 37.4 193.5") !=
std::string::npos);
// start of l
TEST_ASSERT(txt.find("<path class='atom-3' d='M 46.4 78.1") !=
std::string::npos);
#endif
#else
TEST_ASSERT(txt.find(">C</text>") != std::string::npos);
TEST_ASSERT(txt.find(">H</text>") != std::string::npos);
TEST_ASSERT(txt.find(">l</text>") != std::string::npos);
#endif
check_file_hash("testGithub781_4.svg");
}
{ // empty molecule
auto *m = new ROMol();
TEST_ASSERT(m);
RDDepict::compute2DCoords(*m);
MolDraw2DSVG drawer(300, 300);
drawer.drawMolecule(*m);
drawer.finishDrawing();
std::string txt = drawer.getDrawingText();
TEST_ASSERT(txt.find("<svg") != std::string::npos);
// the Freetype version just draws the white canvas.
std::ofstream outs("testGithub781_5.svg");
outs << txt;
outs.close();
#ifdef RDK_BUILD_FREETYPE_SUPPORT
#else
TEST_ASSERT(txt.find("<tspan>") == std::string::npos);
#endif
check_file_hash("testGithub781_5.svg");
delete m;
}
{
// Make sure it also centres correctly with a maxFontSize, which it
// didn't always do.
auto m = "C"_smiles;
TEST_ASSERT(m);
RDDepict::compute2DCoords(*m);
MolDraw2DSVG drawer(200, 200);
drawer.drawOptions().maxFontSize = 14;
drawer.drawMolecule(*m);
drawer.finishDrawing();
std::string txt = drawer.getDrawingText();
TEST_ASSERT(txt.find("<svg") != std::string::npos);
// write the file so we can update the coords below more easily
// if the font changes, for example.
std::ofstream outs("testGithub781_6.svg");
outs << txt;
outs.close();
#ifdef RDK_BUILD_FREETYPE_SUPPORT
#if DO_TEST_ASSERT
// the start of the C
TEST_ASSERT(txt.find("<path class='atom-0' d='M 88.1 97.6") !=
std::string::npos)
// the start of the H
TEST_ASSERT(txt.find("<path class='atom-0' d='M 97.1 92.6") !=
std::string::npos)
#endif
#else
TEST_ASSERT(txt.find(">C</text>") != std::string::npos);
TEST_ASSERT(txt.find(">H</text>") != std::string::npos);
TEST_ASSERT(txt.find(">4</text>") != std::string::npos);
TEST_ASSERT(txt.find("font-size:14px") != std::string::npos);
TEST_ASSERT(txt.find("font-size:9px") != std::string::npos);
#endif
check_file_hash("testGithub781_6.svg");
}
std::cerr << " Done" << std::endl;
}
void testGithub774() {
std::cout << " ----------------- Test Github774: upside-down drawings"
<< std::endl;
{
std::string smiles =
"Cc1c(C(=O)NCC[NH3+])[n+](=O)c2cc(CC[C@](F)(Cl)Br)ccc2n1[O-]";
std::string nameBase = "test774_1";
RWMol *m = SmilesToMol(smiles);
TEST_ASSERT(m);
RDDepict::compute2DCoords(*m);
Chirality::wedgeMolBonds(*m, &(m->getConformer()));
MolOps::Kekulize(*m);
#ifdef RDK_BUILD_CAIRO_SUPPORT
{
MolDraw2DCairo drawer(300, 300);
drawer.drawMolecule(*m);
drawer.finishDrawing();
drawer.writeDrawingText(nameBase + ".png");
check_file_hash(nameBase + ".png");
}
#endif
{
std::ofstream outs((nameBase + ".svg").c_str());
MolDraw2DSVG drawer(300, 300, outs);
drawer.drawMolecule(*m);
drawer.finishDrawing();
outs.flush();
outs.close();
Point2D ocoords(1.0, 2.0);
Point2D dcoords =
drawer.getAtomCoords(std::make_pair(ocoords.x, ocoords.y));
Point2D acoords = drawer.getDrawCoords(dcoords);
TEST_ASSERT(feq(acoords.x, 1.0));
TEST_ASSERT(feq(acoords.y, 2.0));
check_file_hash(nameBase + ".svg");
}
// m->setProp("_Name","mol");
// std::cerr<<MolToMolBlock(*m)<<std::endl;
delete m;
}
{
std::string smiles =
"CC(=O)\\C=C\\CC1[C@H]2N([C@@H](C(=O)O)C(C)(C)S2(=O)=O)C1=O";
std::string nameBase = "test774_2";
RWMol *m = SmilesToMol(smiles);
TEST_ASSERT(m);
RDDepict::compute2DCoords(*m);
Chirality::wedgeMolBonds(*m, &(m->getConformer()));
MolOps::Kekulize(*m);
#ifdef RDK_BUILD_CAIRO_SUPPORT
{
MolDraw2DCairo drawer(300, 300);
drawer.drawMolecule(*m);
drawer.finishDrawing();
drawer.writeDrawingText(nameBase + ".png");
check_file_hash(nameBase + ".png");
}
#endif
{
std::ofstream outs((nameBase + ".svg").c_str());
MolDraw2DSVG drawer(300, 300, outs);
drawer.drawMolecule(*m);
drawer.finishDrawing();
outs.flush();
outs.close();
check_file_hash(nameBase + ".svg");
}
// m->setProp("_Name","mol");\home\tad\cdd\cdd_rdkit\pr_atropisomers2\rdkit\Code\GraphMol\MolDraw2D\test1.cppChirality::
// std::cerr<<MolToMolBlock(*m)<<std::endl;
delete m;
}
std::cerr << " Done" << std::endl;
}
void test9MolLegends() {
std::cout << " ----------------- Test 9 (molecule legends)" << std::endl;
{
auto m = "CC[13CH2][CH2:7][CH-]C[15NH2+]C"_smiles;
TEST_ASSERT(m);
RDDepict::compute2DCoords(*m);
Chirality::wedgeMolBonds(*m, &(m->getConformer()));
MolDraw2DSVG drawer(300, 300);
drawer.drawMolecule(*m, "mol legend");
drawer.finishDrawing();
std::string txt = drawer.getDrawingText();
std::ofstream outs("test9_1.svg");
outs << txt;
// There's a bizarre thing whereby this file comes up as identical on my
// MBP and Ubuntu 20.04 systems, but the hash codes are different.
check_file_hash("test9_1.svg");
}
std::cerr << " Done" << std::endl;
}
void testGithub852() {
std::cout << " ----------------- Test Github852: Lines used to wedge bonds "
"are too thick"
<< std::endl;
{
std::string smiles =
"COc1cccc(NC(=O)[C@H](Cl)Sc2nc(ns2)c3ccccc3Cl)c1"; // made up
std::string nameBase = "test852_1";
RWMol *m = SmilesToMol(smiles);
TEST_ASSERT(m);
MolDraw2DUtils::prepareMolForDrawing(*m);
#ifdef RDK_BUILD_CAIRO_SUPPORT
{
MolDraw2DCairo drawer(300, 300);
drawer.drawMolecule(*m);
drawer.finishDrawing();
drawer.writeDrawingText(nameBase + ".png");
check_file_hash(nameBase + ".png");
}
#endif
{
std::ofstream outs((nameBase + ".svg").c_str());
MolDraw2DSVG drawer(300, 300, outs);
drawer.drawMolecule(*m);
drawer.finishDrawing();
outs.flush();
outs.close();
check_file_hash(nameBase + ".svg");
}
delete m;
}
{
std::string smiles =
"C[C@]12CC[C@@H]3c4ccc(cc4CC[C@H]3[C@@H]1CC[C@@H]2O)O"; // estradiol
std::string nameBase = "test852_2";
RWMol *m = SmilesToMol(smiles);
TEST_ASSERT(m);
MolDraw2DUtils::prepareMolForDrawing(*m);
#ifdef RDK_BUILD_CAIRO_SUPPORT
{
MolDraw2DCairo drawer(300, 300);
drawer.drawMolecule(*m);
drawer.finishDrawing();
drawer.writeDrawingText(nameBase + ".png");
check_file_hash(nameBase + ".png");
}
#endif
{
std::ofstream outs((nameBase + ".svg").c_str());
MolDraw2DSVG drawer(300, 300, outs);
drawer.drawMolecule(*m);
drawer.finishDrawing();
outs.flush();
outs.close();
check_file_hash(nameBase + ".svg");
}
delete m;
}
{
std::string smiles =
"C[C@]12CC[C@@H]3c4ccc(cc4CC[C@H]3[C@@H]1CC[C@@H]2O)O"; // estradiol
RWMol *m = SmilesToMol(smiles);
TEST_ASSERT(m);
MolDraw2DUtils::prepareMolForDrawing(*m);
{
std::cerr << "----------------" << std::endl;
std::string nameBase = "test852_2a";
std::ofstream outs((nameBase + ".svg").c_str());
MolDraw2DSVG drawer(200, 200, outs);
drawer.drawMolecule(*m);
drawer.finishDrawing();
outs.flush();
outs.close();
check_file_hash(nameBase + ".svg");
}
{
std::cerr << "----------------" << std::endl;
std::string nameBase = "test852_2b";
std::ofstream outs((nameBase + ".svg").c_str());
MolDraw2DSVG drawer(250, 250, outs);
drawer.drawMolecule(*m);
drawer.finishDrawing();
outs.flush();
outs.close();
check_file_hash(nameBase + ".svg");
}
{
std::cerr << "----------------" << std::endl;
std::string nameBase = "test852_2c";
std::ofstream outs((nameBase + ".svg").c_str());
MolDraw2DSVG drawer(400, 400, outs);
drawer.drawMolecule(*m);
drawer.finishDrawing();
outs.flush();
outs.close();
check_file_hash(nameBase + ".svg");
}
{
std::cerr << "----------------" << std::endl;
std::string nameBase = "test852_2d";
std::ofstream outs((nameBase + ".svg").c_str());
MolDraw2DSVG drawer(500, 500, outs);
drawer.drawMolecule(*m);
drawer.finishDrawing();
outs.flush();
outs.close();
check_file_hash(nameBase + ".svg");
}
delete m;
}
std::cerr << " Done" << std::endl;
}
void testGithub860() {
std::cout << " ----------------- Test Github860: Atom symbols in wrong order "
"if bond comes from right"
<< std::endl;
{
auto m = "[15NH3+:1]-C#C-[15NH3+:2]"_smiles;
std::string nameBase = "test860_1";
TEST_ASSERT(m);
MolDraw2DUtils::prepareMolForDrawing(*m);
#ifdef RDK_BUILD_CAIRO_SUPPORT
{
MolDraw2DCairo drawer(300, 300);
drawer.drawMolecule(*m);
drawer.finishDrawing();
drawer.writeDrawingText(nameBase + ".png");
check_file_hash(nameBase + ".png");
}
#endif
{
std::ofstream outs((nameBase + ".svg").c_str());
MolDraw2DSVG drawer(300, 300, outs);
drawer.drawMolecule(*m);
drawer.finishDrawing();
outs.flush();
outs.close();
check_file_hash(nameBase + ".svg");
}
}
{
auto m = "[15NH3+:1]-C#C-C([15NH3+:2])([15NH3+:3])-C#C-[15NH3+:4]"_smiles;
std::string nameBase = "test860_2";
TEST_ASSERT(m);
MolDraw2DUtils::prepareMolForDrawing(*m);
#ifdef RDK_BUILD_CAIRO_SUPPORT
{
MolDraw2DCairo drawer(300, 300);
drawer.drawMolecule(*m);
drawer.finishDrawing();
drawer.writeDrawingText(nameBase + ".png");
check_file_hash(nameBase + ".png");
}
#endif
{
std::ofstream outs((nameBase + ".svg").c_str());
MolDraw2DSVG drawer(300, 300, outs);
drawer.drawMolecule(*m);
drawer.finishDrawing();
outs.flush();
outs.close();
check_file_hash(nameBase + ".svg");
}
}
{
auto m = "[15NH3+:1]-CCCCCCCC-[15NH3+:4]"_smiles;
std::string nameBase = "test860_3";
TEST_ASSERT(m);
MolDraw2DUtils::prepareMolForDrawing(*m);
#ifdef RDK_BUILD_CAIRO_SUPPORT
{
MolDraw2DCairo drawer(300, 300);
drawer.drawMolecule(*m);
drawer.finishDrawing();
drawer.writeDrawingText(nameBase + ".png");
check_file_hash(nameBase + ".png");
}
#endif
{
std::ofstream outs((nameBase + ".svg").c_str());
MolDraw2DSVG drawer(300, 300, outs);
drawer.drawMolecule(*m);
drawer.finishDrawing();
outs.flush();
outs.close();
check_file_hash(nameBase + ".svg");
}
}
std::cerr << " Done" << std::endl;
}
void testGithub910() {
std::cout << " ----------------- Test Github #910: ugly coordinates "
"generated for peptide chains"
<< std::endl;
// this really isn't much of a test, but it does help visually confirm that
// things are actually ok
{
// this is a ChEMBL molecule
std::string smiles =
"CSCC[C@H](NC(=O)[C@@H](CCC(N)=O)NC(=O)[C@@H](N)Cc1c[nH]c2ccccc12)C(="
"O)"
"NCC(=O)N[C@@H](Cc1c[nH]cn1)C(=O)N[C@@H](CO)C(=O)O";
ROMol *m = SmilesToMol(smiles);
TEST_ASSERT(m);
RDDepict::compute2DCoords(*m);
Chirality::wedgeMolBonds(*m, &(m->getConformer()));
std::ofstream outs("test910_1.svg");
MolDraw2DSVG drawer(600, 300, outs);
drawer.drawMolecule(*m);
drawer.finishDrawing();
outs.flush();
outs.close();
check_file_hash("test910_1.svg");
delete m;
}
{ // now with Hs
// this is a ChEMBL molecule
std::string smiles =
"CSCC[C@H](NC(=O)[C@@H](CCC(N)=O)NC(=O)[C@@H](N)Cc1c[nH]c2ccccc12)C(="
"O)"
"NCC(=O)N[C@@H](Cc1c[nH]cn1)C(=O)N[C@@H](CO)C(=O)O";
RWMol *m = SmilesToMol(smiles);
TEST_ASSERT(m);
MolDraw2DUtils::prepareMolForDrawing(*m);
std::ofstream outs("test910_2.svg");
MolDraw2DSVG drawer(600, 300, outs);
drawer.drawMolecule(*m);
drawer.finishDrawing();
outs.flush();
outs.close();
check_file_hash("test910_2.svg");
delete m;
}
std::cerr << " Done" << std::endl;
}
void testGithub932() {
std::cout << " ----------------- Test Github #932: mistake in SVG for "
"wedged bonds"
<< std::endl;
{
std::string smiles = "CC[C@](F)(Cl)Br";
RWMol *m = SmilesToMol(smiles);
TEST_ASSERT(m);
MolDraw2DUtils::prepareMolForDrawing(*m);
MolDraw2DSVG drawer(200, 200);
drawer.drawMolecule(*m);
drawer.finishDrawing();
std::string text = drawer.getDrawingText();
TEST_ASSERT(text.find("evenoddstroke") == std::string::npos);
delete m;
}
std::cerr << " Done" << std::endl;
}
void testGithub953() {
std::cout << " ----------------- Test Github #953: default color should "
"not be cyan"
<< std::endl;
{
std::string smiles = "[Nb]";
RWMol *m = SmilesToMol(smiles);
TEST_ASSERT(m);
MolDraw2DUtils::prepareMolForDrawing(*m);
MolDraw2DSVG drawer(200, 200);
drawer.drawMolecule(*m);
drawer.finishDrawing();
std::string text = drawer.getDrawingText();
TEST_ASSERT(text.find("#00FFFF") == std::string::npos);
delete m;
}
std::cerr << " Done" << std::endl;
}
void testGithub983() {
std::cout << " ----------------- Test Github #983: wedged bonds between "
"chiral centers drawn improperly"
<< std::endl;
{
// this has an ugly drawing (wedged bond between chiral centers) but we
// force it to be drawn that way just to check.
std::string mb =
"\n\
Mrv1561 07241608122D\n\
\n\
6 5 0 0 0 0 999 V2000\n\
8.6830 -9.5982 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0\n\
9.3975 -9.1857 0.0000 C 0 0 2 0 0 0 0 0 0 0 0 0\n\
10.1120 -9.5982 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0\n\
9.3975 -8.3607 0.0000 Cl 0 0 0 0 0 0 0 0 0 0 0 0\n\
10.8264 -9.1857 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0\n\
10.1120 -10.4232 0.0000 F 0 0 0 0 0 0 0 0 0 0 0 0\n\
1 2 1 0 0 0 0\n\
3 5 1 0 0 0 0\n\
3 2 1 1 0 0 0\n\
2 4 1 1 0 0 0\n\
3 6 1 0 0 0 0\n\
M END";
RWMol *m = MolBlockToMol(mb, false, false);
TEST_ASSERT(m);
MolOps::sanitizeMol(*m);
MolDraw2DUtils::prepareMolForDrawing(*m);
MolDraw2DSVG drawer(200, 200);
drawer.drawMolecule(*m);
drawer.finishDrawing();
std::string text = drawer.getDrawingText();
std::ofstream outs("test983_1.svg");
outs << text;
outs.flush();
outs.close();
#ifdef RDK_BUILD_FREETYPE_SUPPORT
#if DO_TEST_ASSERT
TEST_ASSERT(
text.find(
"<path class='bond-0 atom-1 atom-0' d='M 74.3,85.7 L 25.1,119.2 "
"L 20.7,111.5 Z' style='fill:#000000;") != std::string::npos);
#endif
#else
TEST_ASSERT(text.find("<path class='bond-1 atom-2 atom-4' d='M 125.3,110.6 "
"L 173.7,77.6 L 178.1,85.2 Z' style='fill:#000000") !=
std::string::npos);
#endif
check_file_hash("test983_1.svg");
delete m;
}
{
std::string mb =
"\n\
Mrv1561 07241616282D\n\
\n\
12 12 0 0 1 0 999 V2000\n\
10.4656 -7.9623 0.0000 F 0 0 0 0 0 0 0 0 0 0 0 0\n\
9.7496 -8.3748 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0\n\
8.9075 -9.4746 0.0000 C 0 0 2 0 0 0 0 0 0 0 0 0\n\
7.5671 -9.4746 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0\n\
8.2373 -8.9934 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0\n\
8.6497 -10.2651 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0\n\
9.0392 -7.9623 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0\n\
7.8249 -10.2651 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0\n\
7.1547 -10.1792 0.0000 F 0 0 0 0 0 0 0 0 0 0 0 0\n\
6.8567 -9.0622 0.0000 F 0 0 0 0 0 0 0 0 0 0 0 0\n\
10.3338 -8.9591 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0\n\
8.6841 -8.6669 0.0000 H 0 0 0 0 0 0 0 0 0 0 0 0\n\
2 1 1 0 0 0 0\n\
3 2 1 0 0 0 0\n\
4 5 1 0 0 0 0\n\
5 3 1 0 0 0 0\n\
6 3 1 0 0 0 0\n\
7 2 1 0 0 0 0\n\
8 6 1 0 0 0 0\n\
9 4 1 0 0 0 0\n\
10 4 1 0 0 0 0\n\
2 11 1 6 0 0 0\n\
3 12 1 6 0 0 0\n\
8 4 1 0 0 0 0\n\
M END";
RWMol *m = MolBlockToMol(mb);
TEST_ASSERT(m);
MolDraw2DUtils::prepareMolForDrawing(*m);
TEST_ASSERT(m->getBondBetweenAtoms(2, 1)->getBondType() == Bond::SINGLE);
TEST_ASSERT(m->getBondBetweenAtoms(2, 1)->getBondDir() == Bond::NONE);
TEST_ASSERT(m->getBondBetweenAtoms(2, 4)->getBondType() == Bond::SINGLE);
TEST_ASSERT(m->getBondBetweenAtoms(2, 4)->getBondDir() == Bond::BEGINWEDGE);
MolDraw2DSVG drawer(200, 200);
drawer.drawMolecule(*m);
drawer.finishDrawing();
std::string text = drawer.getDrawingText();
std::ofstream outs("test983_2.svg");
outs << text;
outs.flush();
outs.close();
#ifdef RDK_BUILD_FREETYPE_SUPPORT
#if DO_TEST_ASSERT
TEST_ASSERT(text.find("<path class='bond-3 atom-2 atom-4' d='M 103.4,117.3"
" L 72.1,98.5 L 77.0,95.0 Z' style='fill:#000000;") !=
std::string::npos);
#endif
#else
TEST_ASSERT(text.find("<path class='bond-3 atom-2 atom-4' d='M 105.0,114.6 "
"L 74.0,95.9 L 78.8,92.5 Z' style='fill:#000000;") !=
std::string::npos);
#endif
check_file_hash("test983_2.svg");
MolDraw2DUtils::prepareMolForDrawing(*m);
TEST_ASSERT(m->getBondBetweenAtoms(2, 1)->getBondType() == Bond::SINGLE);
TEST_ASSERT(m->getBondBetweenAtoms(2, 1)->getBondDir() == Bond::NONE);
TEST_ASSERT(m->getBondBetweenAtoms(2, 4)->getBondType() == Bond::SINGLE);
TEST_ASSERT(m->getBondBetweenAtoms(2, 4)->getBondDir() == Bond::BEGINWEDGE);
RWMol nm(*m);
MolDraw2DUtils::prepareMolForDrawing(nm);
TEST_ASSERT(nm.getBondBetweenAtoms(2, 1)->getBondType() == Bond::SINGLE);
TEST_ASSERT(nm.getBondBetweenAtoms(2, 1)->getBondDir() == Bond::NONE);
TEST_ASSERT(nm.getBondBetweenAtoms(2, 4)->getBondType() == Bond::SINGLE);
TEST_ASSERT(nm.getBondBetweenAtoms(2, 4)->getBondDir() == Bond::BEGINWEDGE);
delete m;
}
std::cerr << " Done" << std::endl;
}
void testDeuteriumTritium() {
std::cout << " ----------------- Test Deuterium, Tritium" << std::endl;
{
auto m = "C([2H])([2H])([2H])[2H]"_smiles;
RDDepict::compute2DCoords(*m);
std::string nameBase = "testNoDeuterium";
std::ofstream outs((nameBase + ".svg").c_str());
MolDraw2DSVG drawer(300, 300, outs);
drawer.drawOptions().atomLabelDeuteriumTritium = false;
drawer.drawMolecule(*m);
drawer.finishDrawing();
outs.close();
std::ifstream ins((nameBase + ".svg").c_str());
bool ok = true;
unsigned int count = 0;
while (ok) {
std::string line;
std::getline(ins, line);
ok = (ins.good() && !ins.eof());
if (!ok) {
continue;
}
#ifdef RDK_BUILD_FREETYPE_SUPPORT
#if DO_TEST_ASSERT
// there are no characters to look for, but each atom should
// be made of 2 glyphs, the superscript 2 and the H.
if ((line.find("atom-") != std::string::npos)) {
if ((line.find("bond-") == std::string::npos)) {
++count;
}
}
#endif
#else
// a bit kludgy, but...
if (line.find("<text x='245.5' y='152.6' class='atom-1' "
"style='font-size:26px;font-style:normal;font-weight:"
"normal;fill-opacity:1;stroke:none;font-family:sans-serif;"
"text-anchor:start;fill:#000000' >2</text>") !=
std::string::npos) {
++count;
}
#endif
}
#ifdef RDK_BUILD_FREETYPE_SUPPORT
#if DO_TEST_ASSERT
TEST_ASSERT(count == 8);
#endif
#else
// the first superscript 2
TEST_ASSERT(count == 1);
#endif
check_file_hash(nameBase + ".svg");
}
{
auto m = "C([3H])([3H])([3H])[3H]"_smiles;
RDDepict::compute2DCoords(*m);
std::string nameBase = "testNoTritium";
std::ofstream outs((nameBase + ".svg").c_str());
MolDraw2DSVG drawer(300, 300, outs);
drawer.drawOptions().atomLabelDeuteriumTritium = false;
drawer.drawMolecule(*m);
drawer.finishDrawing();
outs.close();
std::ifstream ins((nameBase + ".svg").c_str());
bool ok = true;
unsigned int count = 0;
while (ok) {
std::string line;
std::getline(ins, line);
ok = (ins.good() && !ins.eof());
if (!ok) {
continue;
}
#ifdef RDK_BUILD_FREETYPE_SUPPORT
#if DO_TEST_ASSERT
// there are no characters to look for, but each atom should
// be made of 2 glyphs, the superscript 3 and the H.
if ((line.find("atom-") != std::string::npos)) {
if ((line.find("bond-") == std::string::npos)) {
++count;
}
}
#endif
#else
if (line.find("<text x='245.5' y='152.6' class='atom-1' "
"style='font-size:26px;font-style:normal;font-weight:"
"normal;fill-opacity:1;stroke:none;font-family:sans-serif;"
"text-anchor:start;fill:#000000' >3</text>") !=
std::string::npos) {
++count;
}
#endif
}
#ifdef RDK_BUILD_FREETYPE_SUPPORT
#if DO_TEST_ASSERT
TEST_ASSERT(count == 8);
#endif
#else
TEST_ASSERT(count == 1);
#endif
check_file_hash(nameBase + ".svg");
}
{
auto m = "C([2H])([2H])([2H])[2H]"_smiles;
RDDepict::compute2DCoords(*m);
std::string nameBase = "testDeuterium";
std::ofstream outs((nameBase + ".svg").c_str());
MolDraw2DSVG drawer(300, 300, outs);
drawer.drawOptions().atomLabelDeuteriumTritium = true;
drawer.drawMolecule(*m);
drawer.finishDrawing();
outs.close();
std::ifstream ins((nameBase + ".svg").c_str());
bool ok = true;
unsigned int count = 0;
while (ok) {
std::string line;
std::getline(ins, line);
ok = (ins.good() && !ins.eof());
if (!ok) {
continue;
}
#ifdef RDK_BUILD_FREETYPE_SUPPORT
// there should be just 1 glyph per atom - a D
if ((line.find("atom-") != std::string::npos)) {
if ((line.find("bond-") == std::string::npos)) {
++count;
}
}
#else
if ((line.find("baseline-shift:super") == std::string::npos) &&
(line.find(">2<") == std::string::npos) &&
(line.find(">D<") != std::string::npos)) {
++count;
}
#endif
}
#if DO_TEST_ASSERT
TEST_ASSERT(count == 4);
#endif
check_file_hash(nameBase + ".svg");
}
{
auto m = "C([3H])([3H])([3H])[3H]"_smiles;
RDDepict::compute2DCoords(*m);
std::string nameBase = "testTritium";
std::ofstream outs((nameBase + ".svg").c_str());
MolDraw2DSVG drawer(300, 300, outs);
drawer.drawOptions().atomLabelDeuteriumTritium = true;
drawer.drawMolecule(*m);
drawer.finishDrawing();
outs.close();
std::ifstream ins((nameBase + ".svg").c_str());
bool ok = true;
unsigned int count = 0;
while (ok) {
std::string line;
std::getline(ins, line);
ok = (ins.good() && !ins.eof());
if (!ok) {
continue;
}
#ifdef RDK_BUILD_FREETYPE_SUPPORT
// there should be just 1 glyph per atom - a T
if ((line.find("atom-") != std::string::npos)) {
if ((line.find("bond-") == std::string::npos)) {
++count;
}
}
#else
if ((line.find("baseline-shift:super") == std::string::npos) &&
(line.find(">3<") == std::string::npos) &&
(line.find(">T<") != std::string::npos)) {
++count;
}
#endif
}
#if DO_TEST_ASSERT
TEST_ASSERT(count == 4);
#endif
check_file_hash(nameBase + ".svg");
}
std::cerr << " Done" << std::endl;
}
void testCrossedBonds() {
std::cerr << " ----------------- Test crossed bonds" << std::endl;
{
std::string smiles = "CC=CC";
RWMol *m = SmilesToMol(smiles);
TEST_ASSERT(m);
m->getBondWithIdx(1)->setBondDir(Bond::EITHERDOUBLE);
MolDraw2DUtils::prepareMolForDrawing(*m);
std::string nameBase = "crossed_bonds";
std::ofstream outs((nameBase + ".svg").c_str());
MolDraw2DSVG drawer(300, 300, outs);
drawer.drawMolecule(*m);
drawer.finishDrawing();
outs.close();
check_file_hash(nameBase + ".svg");
delete m;
}
std::cerr << " Done" << std::endl;
}
void test10DrawSecondMol() {
std::cout << " ----------------- Testing drawing a second molecule"
<< std::endl;
std::string mb1 =
"\n\
Mrv1561 08301611102D\n\
\n\
3 2 0 0 0 0 999 V2000\n\
-2.5670 1.3616 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0\n\
-1.8525 1.7741 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0\n\
-1.1380 1.3616 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0\n\
1 2 1 0 0 0 0\n\
2 3 1 0 0 0 0\n\
M END";
RWMol *m1 = MolBlockToMol(mb1);
TEST_ASSERT(m1);
MolOps::sanitizeMol(*m1);
MolDraw2DUtils::prepareMolForDrawing(*m1);
RDGeom::Point3D c1 = MolTransforms::computeCentroid(m1->getConformer());
for (unsigned int i = 0; i < m1->getNumAtoms(); ++i) {
RDGeom::Point3D &p = m1->getConformer().getAtomPos(i);
p -= c1;
}
std::string mb2 =
"\n\
Mrv1561 08301611122D\n\
\n\
3 2 0 0 0 0 999 V2000\n\
-1.9900 2.2136 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0\n\
-1.5775 1.4991 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0\n\
-1.9900 0.7846 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0\n\
1 2 1 0 0 0 0\n\
2 3 1 0 0 0 0\n\
M END";
RWMol *m2 = MolBlockToMol(mb2);
TEST_ASSERT(m2);
MolOps::sanitizeMol(*m2);
MolDraw2DUtils::prepareMolForDrawing(*m2);
RDGeom::Point3D c2 = MolTransforms::computeCentroid(m2->getConformer());
for (unsigned int i = 0; i < m2->getNumAtoms(); ++i) {
RDGeom::Point3D &p = m2->getConformer().getAtomPos(i);
p -= c2;
}
{
MolDraw2DSVG drawer(200, 200);
drawer.drawOptions().padding = 0.2;
drawer.drawMolecule(*m1);
drawer.drawMolecule(*m2);
drawer.finishDrawing();
std::string text = drawer.getDrawingText();
std::ofstream outs("test10_1.svg");
outs << text;
outs.flush();
outs.close();
check_file_hash("test10_1.svg");
}
{
MolDraw2DSVG drawer(200, 200);
drawer.drawOptions().padding = 0.2;
drawer.drawMolecule(*m2);
drawer.drawMolecule(*m1);
drawer.finishDrawing();
std::string text = drawer.getDrawingText();
std::ofstream outs("test10_2.svg");
outs << text;
outs.flush();
outs.close();
check_file_hash("test10_2.svg");
}
{
MolDraw2DSVG drawer(400, 200, 200, 200);
drawer.drawOptions().padding = 0.2;
drawer.drawMolecule(*m1);
drawer.setOffset(200, 0);
drawer.drawMolecule(*m2);
drawer.finishDrawing();
std::string text = drawer.getDrawingText();
std::ofstream outs("test10_3.svg");
outs << text;
outs.flush();
outs.close();
check_file_hash("test10_3.svg");
}
{
MolDraw2DSVG drawer(200, 400, 200, 200);
drawer.drawOptions().padding = 0.2;
drawer.drawMolecule(*m1);
drawer.setOffset(0, 200);
drawer.drawMolecule(*m2);
drawer.finishDrawing();
std::string text = drawer.getDrawingText();
std::ofstream outs("test10_4.svg");
outs << text;
outs.flush();
outs.close();
check_file_hash("test10_4.svg");
}
{
MolDraw2DSVG drawer(200, 400, 200, 200);
Point2D minv(1000, 1000);
Point2D maxv(-1000, -1000);
for (unsigned int i = 0; i < m1->getNumAtoms(); ++i) {
const RDGeom::Point3D &pti = m1->getConformer().getAtomPos(i);
minv.x = std::min(minv.x, pti.x);
minv.y = std::min(minv.y, pti.y);
maxv.x = std::max(maxv.x, pti.x);
maxv.y = std::max(maxv.y, pti.y);
}
drawer.setScale(200, 200, minv, maxv);
drawer.drawMolecule(*m1);
drawer.setOffset(0, 200);
drawer.drawMolecule(*m2);
drawer.finishDrawing();
std::string text = drawer.getDrawingText();
std::ofstream outs("test10_5.svg");
outs << text;
outs.flush();
outs.close();
check_file_hash("test10_5.svg");
}
{
MolDraw2DSVG drawer(200, 400, 200, 200);
Point2D minv(1000, 1000);
Point2D maxv(-1000, -1000);
for (unsigned int i = 0; i < m1->getNumAtoms(); ++i) {
const RDGeom::Point3D &pti = m1->getConformer().getAtomPos(i);
minv.x = std::min(minv.x, pti.x);
minv.y = std::min(minv.y, pti.y);
maxv.x = std::max(maxv.x, pti.x);
maxv.y = std::max(maxv.y, pti.y);
}
drawer.drawOptions().padding = 0.2;
drawer.setScale(200, 200, minv, maxv);
drawer.drawMolecule(*m1);
drawer.setOffset(0, 200);
drawer.drawMolecule(*m2);
drawer.finishDrawing();
std::string text = drawer.getDrawingText();
std::ofstream outs("test10_6.svg");
outs << text;
outs.flush();
outs.close();
check_file_hash("test10_6.svg");
}
delete m1;
delete m2;
std::cerr << " Done" << std::endl;
}
void test11DrawMolGrid() {
std::cout << " ----------------- Testing drawing a grid of molecules"
<< std::endl;
auto m1 = "COc1cccc(NC(=O)[C@H](Cl)Sc2nc(ns2)c3ccccc3Cl)c1"_smiles;
TEST_ASSERT(m1);
MolDraw2DUtils::prepareMolForDrawing(*m1);
RDGeom::Point3D c1 = MolTransforms::computeCentroid(m1->getConformer());
for (unsigned int i = 0; i < m1->getNumAtoms(); ++i) {
RDGeom::Point3D &p = m1->getConformer().getAtomPos(i);
p -= c1;
}
auto m2 = "NC(=O)[C@H](Cl)Sc1ncns1"_smiles;
TEST_ASSERT(m2);
MolDraw2DUtils::prepareMolForDrawing(*m2);
RDGeom::Point3D c2 = MolTransforms::computeCentroid(m2->getConformer());
for (unsigned int i = 0; i < m2->getNumAtoms(); ++i) {
RDGeom::Point3D &p = m2->getConformer().getAtomPos(i);
p -= c2;
}
auto m3 = "BrCNC(=O)[C@H](Cl)Sc1ncns1"_smiles;
TEST_ASSERT(m3);
MolDraw2DUtils::prepareMolForDrawing(*m3);
RDGeom::Point3D c3 = MolTransforms::computeCentroid(m3->getConformer());
for (unsigned int i = 0; i < m3->getNumAtoms(); ++i) {
RDGeom::Point3D &p = m3->getConformer().getAtomPos(i);
p -= c3;
}
{
MolDraw2DSVG drawer(500, 400, 250, 200);
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.drawMolecule(*m1, "m4");
drawer.finishDrawing();
std::string text = drawer.getDrawingText();
std::ofstream outs("test11_1.svg");
outs << text;
outs.flush();
outs.close();
check_file_hash("test11_1.svg");
}
{
// drawing "out of order" - really this time, calling DrawMolecule
// in a different order. Previously, they were put in the grid
// with different offsets but still in the order m1, m2, m1, m2
// which hid a bug where calculateScale was only called for the first
// molecule. This didn't show because m1 gets a smaller scale than
// m2. It was a real mess if calculateScale was called for m2 first.
// With the new DrawMol code, each molecule gets its own scale.
MolDraw2DSVG drawer(500, 400, 250, 200);
drawer.setOffset(0, 0);
drawer.drawMolecule(*m2, "m2");
drawer.setOffset(250, 0);
drawer.drawMolecule(*m1, "m1");
drawer.setOffset(0, 200);
drawer.drawMolecule(*m1, "m3");
drawer.setOffset(250, 200);
drawer.drawMolecule(*m2, "m4");
drawer.finishDrawing();
std::string text = drawer.getDrawingText();
std::ofstream outs("test11_2.svg");
outs << text;
outs.flush();
outs.close();
check_file_hash("test11_2.svg");
}
std::cerr << " Done" << std::endl;
}
void test12DrawMols() {
std::cout << " ----------------- Testing drawMolecules" << std::endl;
auto setup_mol = [](const std::string &smi, const std::string leg,
std::vector<ROMol *> &mols,
std::vector<std::string> &legends) {
mols.push_back(SmilesToMol(smi));
TEST_ASSERT(mols.back());
legends.push_back(leg);
};
std::vector<ROMol *> mols;
std::unique_ptr<std::vector<std::string>> legends(
new std::vector<std::string>());
// made up SMILES, each with sequence F, Cl, Br so we can see which
// ones are drawn, which ones are missing.
setup_mol("COc1cccc(NC(=O)[C@H](F)Sc2nc(ns2)c3ccccc3F)c1", "m1", mols,
*legends);
setup_mol("NC(=O)[C@H](F)Sc1ncns1", "m2", mols, *legends);
setup_mol("COc1cccc(NC(=O)[C@H](Cl)Sc2nc(ns2)c3ccccc3F)c1", "m3", mols,
*legends);
setup_mol("NC(=O)[C@H](Cl)Sc1ncns1", "m4", mols, *legends);
setup_mol("COc1cccc(NC(=O)[C@H](Br)Sc2nc(ns2)c3ccccc3F)c1", "m5", mols,
*legends);
setup_mol("NC(=O)[C@H](Br)Sc1ncns1", "m6", mols, *legends);
{
MolDraw2DSVG drawer(750, 400, 250, 200);
drawer.drawMolecules(mols, legends.get());
drawer.finishDrawing();
std::string text = drawer.getDrawingText();
std::ofstream outs("test12_1.svg");
outs << text;
outs.flush();
outs.close();
check_file_hash("test12_1.svg");
}
{
MolDraw2DSVG drawer(750, 400, 250, 200);
drawer.drawOptions().drawMolsSameScale = false;
drawer.drawMolecules(mols, legends.get());
drawer.finishDrawing();
std::string text = drawer.getDrawingText();
std::ofstream outs("test12_5.svg");
outs << text;
outs.flush();
outs.close();
check_file_hash("test12_5.svg");
}
{ // github #1325: multiple molecules in one pane
MolDraw2DSVG drawer(300, 300, 300, 300);
drawer.drawMolecules(mols);
drawer.finishDrawing();
std::string text = drawer.getDrawingText();
std::ofstream outs("test12_3.svg");
outs << text;
outs.flush();
outs.close();
check_file_hash("test12_3.svg");
}
{ // github #1325: multiple molecules in one pane
MolDraw2DSVG drawer(300, 300);
drawer.drawMolecules(mols);
drawer.finishDrawing();
std::string text = drawer.getDrawingText();
std::ofstream outs("test12_4.svg");
outs << text;
outs.flush();
outs.close();
check_file_hash("test12_4.svg");
}
{
delete mols[2];
delete mols[4];
mols[2] = nullptr;
mols[4] = nullptr;
MolDraw2DSVG drawer(750, 400, 250, 200);
drawer.drawMolecules(mols);
drawer.finishDrawing();
std::string text = drawer.getDrawingText();
std::ofstream outs("test12_2.svg");
outs << text;
outs.flush();
outs.close();
check_file_hash("test12_2.svg");
}
for (auto m : mols) {
delete m;
}
std::cerr << " Done" << std::endl;
}
void test13JSONConfig() {
std::cerr << " ----------------- Test JSON Configuration" << std::endl;
auto m = "CCO"_smiles;
TEST_ASSERT(m);
const char *json =
"{\"legendColour\":[1.0,0.5,1.0], \"rotate\": 90, "
"\"bondLineWidth\": 5}";
MolDraw2DUtils::prepareMolForDrawing(*m);
{
MolDraw2DSVG drawer(250, 200);
MolDraw2DUtils::updateDrawerParamsFromJSON(drawer, json);
drawer.drawMolecule(*m, "foo");
drawer.finishDrawing();
std::string text = drawer.getDrawingText();
std::ofstream outs("test13_1.svg");
outs << text;
outs.close();
#ifdef RDK_BUILD_FREETYPE_SUPPORT
#if DO_TEST_ASSERT
// we'll just have to assume that this pink is for the legend
TEST_ASSERT(text.find("' fill='#FF7FFF") != std::string::npos);
TEST_ASSERT(text.find("<path class='bond-0 atom-0 atom-1' d='M 121.1,10.0"
" L 164.2,84.6'") != std::string::npos);
#endif
#else
TEST_ASSERT(text.find("sans-serif;text-anchor:start;fill:#FF7FFF") !=
std::string::npos);
TEST_ASSERT(text.find("<path class='bond-0 atom-0 atom-1' d='M 119.8,10.0"
" L 161.7,82.6'") != std::string::npos);
#endif
// these days the bond line width scales with the rest of the
// drawing, and at this size this comes out as 5px.
TEST_ASSERT(text.find("stroke-width:5.0px") != std::string::npos);
check_file_hash("test13_1.svg");
}
{
MolDraw2DSVG drawer(250, 200);
MolDrawOptions opts;
MolDraw2DUtils::updateMolDrawOptionsFromJSON(opts, json);
drawer.drawOptions() = opts;
drawer.drawMolecule(*m, "foo");
drawer.finishDrawing();
std::string text = drawer.getDrawingText();
#ifdef RDK_BUILD_FREETYPE_SUPPORT
#if DO_TEST_ASSERT
// we'll just have to assume that this pink is for the legend
TEST_ASSERT(text.find("' fill='#FF7FFF") != std::string::npos);
TEST_ASSERT(text.find("<path class='bond-0 atom-0 atom-1' d='M 121.1,10.0"
" L 164.2,84.6'") != std::string::npos);
#endif
#else
TEST_ASSERT(text.find("sans-serif;text-anchor:start;fill:#FF7FFF") !=
std::string::npos);
TEST_ASSERT(
text.find(
"<path class='bond-0 atom-0 atom-1' d='M 119.8,10.0 L 161.7,82.6'") !=
std::string::npos);
#endif
// these days the bond line width scales with the rest of the
// drawing, and at this size this comes out as 5px.
TEST_ASSERT(text.find("stroke-width:5.0px") != std::string::npos);
}
std::cerr << " Done" << std::endl;
}
void testGithub1090() {
std::cout << " ----------------- Testing github 1090: escape html characters "
"in SVG output"
<< std::endl;
std::string smiles = "CCOC"; // made up
RWMol *m1 = SmilesToMol(smiles);
TEST_ASSERT(m1);
MolDraw2DUtils::prepareMolForDrawing(*m1);
{
ROMol lm(*m1);
MolDraw2DSVG drawer(250, 200);
drawer.drawOptions().atomLabels[0] = "C&1";
drawer.drawOptions().atomLabels[1] = "[CH2<1]";
drawer.drawOptions().atomLabels[3] = "[C>1H3]";
drawer.drawMolecule(lm, "legend&legend>1");
drawer.finishDrawing();
std::string text = drawer.getDrawingText();
std::ofstream outs("testGithub1090_1.svg");
outs << text;
outs.flush();
outs.close();
check_file_hash("testGithub1090_1.svg");
TEST_ASSERT(text.find("C&1") == std::string::npos);
TEST_ASSERT(text.find("<<") == std::string::npos);
TEST_ASSERT(text.find(">>") == std::string::npos);
TEST_ASSERT(text.find("d&l") == std::string::npos);
}
delete m1;
std::cerr << " Done" << std::endl;
}
void testGithub1035() {
std::cout << " ----------------- Testing github 1035: overflow bug in SVG "
"color generation"
<< std::endl;
std::string smiles = "CCOC"; // made up
RWMol *m1 = SmilesToMol(smiles);
TEST_ASSERT(m1);
MolDraw2DUtils::prepareMolForDrawing(*m1);
std::vector<int> highlights;
highlights.push_back(0);
highlights.push_back(1);
{
MolDraw2DSVG drawer(250, 200);
drawer.drawOptions().highlightColour = DrawColour(1.1, .5, .5);
bool ok = false;
try {
drawer.drawMolecule(*m1, &highlights);
} catch (const ValueErrorException &) {
ok = true;
}
TEST_ASSERT(ok);
}
{
MolDraw2DSVG drawer(250, 200);
drawer.drawOptions().highlightColour = DrawColour(.1, -.5, .5);
bool ok = false;
try {
drawer.drawMolecule(*m1, &highlights);
} catch (const ValueErrorException &) {
ok = true;
}
TEST_ASSERT(ok);
}
{
MolDraw2DSVG drawer(250, 200);
drawer.drawOptions().highlightColour = DrawColour(1., .5, 1.5);
bool ok = false;
try {
drawer.drawMolecule(*m1, &highlights);
} catch (const ValueErrorException &) {
ok = true;
}
TEST_ASSERT(ok);
}
delete m1;
std::cerr << " Done" << std::endl;
}
void testGithub1271() {
std::cout << " ----------------- Testing github 1271: MolDraw2D not drawing "
"anything for molecules aligned with the X or Y axes"
<< std::endl;
{
std::string mb =
"ethane\n\
RDKit 2D\n\
\n\
2 1 0 0 0 0 0 0 0 0999 V2000\n\
-0.7500 0.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0\n\
0.7500 -0.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0\n\
1 2 1 0\n\
M END";
RWMol *m = MolBlockToMol(mb);
TEST_ASSERT(m);
MolDraw2DUtils::prepareMolForDrawing(*m);
MolDraw2DSVG drawer(200, 200);
drawer.drawMolecule(*m);
drawer.finishDrawing();
std::string text = drawer.getDrawingText();
std::ofstream outs("test1271_1.svg");
outs << text;
outs.flush();
outs.close();
check_file_hash("test1271_1.svg");
TEST_ASSERT(text.find("d='M 0,200 0,200") == std::string::npos);
delete m;
}
{
std::string mb =
"ethane\n\
RDKit 2D\n\
\n\
2 1 0 0 0 0 0 0 0 0999 V2000\n\
-0.0000 0.5000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0\n\
0.0000 -0.5000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0\n\
1 2 1 0\n\
M END";
RWMol *m = MolBlockToMol(mb);
TEST_ASSERT(m);
MolDraw2DUtils::prepareMolForDrawing(*m);
MolDraw2DSVG drawer(200, 200);
drawer.drawMolecule(*m);
drawer.finishDrawing();
std::string text = drawer.getDrawingText();
std::ofstream outs("test1271_2.svg");
outs << text;
outs.flush();
outs.close();
check_file_hash("test1271_2.svg");
TEST_ASSERT(text.find("d='M 0,200 0,200") == std::string::npos);
delete m;
}
{
std::string mb =
"water\n\
RDKit 2D\n\
\n\
1 0 0 0 0 0 0 0 0 0999 V2000\n\
-0.0000 0.0000 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0\n\
M END";
RWMol *m = MolBlockToMol(mb);
TEST_ASSERT(m);
MolDraw2DUtils::prepareMolForDrawing(*m);
MolDraw2DSVG drawer(200, 200);
drawer.drawMolecule(*m);
drawer.finishDrawing();
std::string text = drawer.getDrawingText();
std::ofstream outs("test1271_3.svg");
outs << text;
outs.flush();
outs.close();
check_file_hash("test1271_3.svg");
TEST_ASSERT(text.find("d='M 0,200 0,200") == std::string::npos);
delete m;
}
{
std::string mb =
"water\n\
RDKit 2D\n\
\n\
1 0 0 0 0 0 0 0 0 0999 V2000\n\
-0.0000 0.5000 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0\n\
M END";
RWMol *m = MolBlockToMol(mb);
TEST_ASSERT(m);
MolDraw2DUtils::prepareMolForDrawing(*m);
MolDraw2DSVG drawer(200, 200);
drawer.drawMolecule(*m);
drawer.finishDrawing();
std::string text = drawer.getDrawingText();
std::ofstream outs("test1271_4.svg");
outs << text;
outs.flush();
outs.close();
check_file_hash("test1271_4.svg");
TEST_ASSERT(text.find("d='M 0,200 0,200") == std::string::npos);
delete m;
}
{
std::string smiles = "C=C(O)C(O)"; // made up
RWMol *m1 = SmilesToMol(smiles);
TEST_ASSERT(m1);
MolDraw2DUtils::prepareMolForDrawing(*m1);
smiles = "O";
RWMol *m2 = SmilesToMol(smiles);
TEST_ASSERT(m2);
MolDraw2DUtils::prepareMolForDrawing(*m2);
MolDraw2DSVG drawer(500, 200, 250, 200);
drawer.drawMolecule(*m1, "m1");
drawer.setOffset(250, 0);
drawer.drawMolecule(*m2, "m2");
drawer.finishDrawing();
std::string text = drawer.getDrawingText();
std::ofstream outs("test1271_5.svg");
outs << text;
outs.flush();
outs.close();
check_file_hash("test1271_5.svg");
delete m1;
delete m2;
}
std::cerr << " Done" << std::endl;
}
void testGithub1322() {
std::cout << " ----------------- Testing github 1322: add custom atom labels"
<< std::endl;
{
auto m1 = "CCC[Se]"_smiles; // made up
TEST_ASSERT(m1);
MolDraw2DUtils::prepareMolForDrawing(*m1);
{
MolDraw2DSVG drawer(500, 200, 250, 200);
drawer.drawMolecule(*m1, "m1");
drawer.finishDrawing();
std::string text = drawer.getDrawingText();
std::ofstream outs("test1322_1.svg");
outs << text;
outs.flush();
outs.close();
check_file_hash("test1322_1.svg");
#ifdef RDK_BUILD_FREETYPE_SUPPORT
#if DO_TEST_ASSERT
// there should be 2 paths of class atom-3, one for the S,
// one for the e, one for the radical and one bond = 4.
size_t start_pos = 0;
int count = 0;
while (true) {
start_pos = text.find("atom-3", start_pos);
if (start_pos == std::string::npos) {
break;
}
++count;
++start_pos;
}
TEST_ASSERT(count == 4);
#endif
#else
TEST_ASSERT(text.find(">S</text>") != std::string::npos);
TEST_ASSERT(text.find(">e</text>") != std::string::npos);
#endif
}
{
m1->getAtomWithIdx(3)->setProp(common_properties::atomLabel,
"customlabel");
MolDraw2DSVG drawer(500, 200, 250, 200);
drawer.drawMolecule(*m1, "m1");
drawer.finishDrawing();
std::string text = drawer.getDrawingText();
std::ofstream outs("test1322_2.svg");
outs << text;
outs.flush();
outs.close();
check_file_hash("test1322_2.svg");
#ifdef RDK_BUILD_FREETYPE_SUPPORT
#if DO_TEST_ASSERT
// there should be 11 paths of class atom-3, one for each letter
// of customlabel, one for the radical and one bond = 13.
size_t start_pos = 0;
int count = 0;
while (true) {
start_pos = text.find("atom-3", start_pos);
if (start_pos == std::string::npos) {
break;
}
++count;
++start_pos;
}
TEST_ASSERT(count == 13);
#endif
#else
TEST_ASSERT(text.find(">S</text>") == std::string::npos);
TEST_ASSERT(text.find(">s</text>") != std::string::npos);
TEST_ASSERT(text.find(">b</text>") != std::string::npos);
#endif
}
}
std::cerr << " Done" << std::endl;
}
void test14BWPalette() {
std::cout << " ----------------- Testing use of a black & white palette"
<< std::endl;
{
std::string smiles = "CNC(Cl)C(=O)O";
RWMol *m1 = SmilesToMol(smiles);
TEST_ASSERT(m1);
MolDraw2DUtils::prepareMolForDrawing(*m1);
{ // start with color
MolDraw2DSVG drawer(200, 200);
drawer.drawMolecule(*m1, "m1");
drawer.finishDrawing();
std::string text = drawer.getDrawingText();
TEST_ASSERT(text.find("stroke:#00CC00") != std::string::npos);
std::ofstream outs("test14_1.svg");
outs << text;
outs.flush();
outs.close();
check_file_hash("test14_1.svg");
}
{ // now B&W
MolDraw2DSVG drawer(200, 200);
assignBWPalette(drawer.drawOptions().atomColourPalette);
drawer.drawMolecule(*m1, "m1");
drawer.finishDrawing();
std::string text = drawer.getDrawingText();
TEST_ASSERT(text.find("stroke:#00CC00") == std::string::npos);
std::ofstream outs("test14_2.svg");
outs << text;
outs.flush();
outs.close();
check_file_hash("test14_2.svg");
}
delete m1;
}
std::cerr << " Done" << std::endl;
}
void test15ContinuousHighlightingWithGrid() {
std::cerr << " ----------------- Testing use of continuous highlighting with "
"drawMolecules"
<< std::endl;
{
std::string smiles =
"COc1cccc(NC(=O)[C@H](Cl)Sc2nc(ns2)c3ccccc3Cl)c1"; // made up
RWMol *m1 = SmilesToMol(smiles);
TEST_ASSERT(m1);
smiles = "NC(=O)[C@H](Cl)Sc1ncns1"; // made up
RWMol *m2 = SmilesToMol(smiles);
TEST_ASSERT(m2);
std::vector<ROMol *> mols;
mols.push_back(m1);
mols.push_back(m2);
std::vector<std::vector<int>> atHighlights(2);
atHighlights[0].push_back(0);
atHighlights[0].push_back(1);
atHighlights[0].push_back(2);
atHighlights[0].push_back(6);
atHighlights[1].push_back(0);
atHighlights[1].push_back(1);
atHighlights[1].push_back(2);
atHighlights[1].push_back(6);
{
MolDraw2DSVG drawer(500, 200, 250, 200);
drawer.drawOptions().continuousHighlight = false;
drawer.drawMolecules(mols, nullptr, &atHighlights);
drawer.finishDrawing();
std::string text = drawer.getDrawingText();
std::ofstream outs("test15_1.svg");
outs << text;
outs.flush();
outs.close();
check_file_hash("test15_1.svg");
#if DO_TEST_ASSERT
TEST_ASSERT(text.find("stroke:#FF7F7F;stroke-width:0.0px;") ==
std::string::npos);
#endif
}
{
MolDraw2DSVG drawer(500, 200, 250, 200);
drawer.drawOptions().continuousHighlight = true;
drawer.drawOptions().splitBonds = true;
drawer.drawMolecules(mols, nullptr, &atHighlights);
drawer.finishDrawing();
std::string text = drawer.getDrawingText();
std::ofstream outs("test15_2.svg");
outs << text;
outs.flush();
outs.close();
check_file_hash("test15_2.svg");
#if DO_TEST_ASSERT
TEST_ASSERT(text.find("stroke:#FF7F7F;stroke-width:0.0px") !=
std::string::npos);
#endif
}
for (auto &&mol : mols) {
delete mol;
}
}
std::cerr << " Done" << std::endl;
}
void testGithub1829() {
std::cerr << " ----------------- Testing github 1829: crash when "
"drawMolecules() is called with an empty list"
<< std::endl;
{
std::vector<ROMol *> mols;
MolDraw2DSVG drawer(750, 400, 250, 200);
// this should run quietly without complaining
drawer.drawMolecules(mols);
drawer.finishDrawing();
std::string text = drawer.getDrawingText();
}
std::cerr << " Done" << std::endl;
}
void test16MoleculeMetadata() {
std::cout << " ----------------- Testing inclusion of molecule metadata"
<< std::endl;
{
std::string smiles = "CN[C@H](Cl)C(=O)O";
std::unique_ptr<RWMol> m1(SmilesToMol(smiles));
TEST_ASSERT(m1);
MolDraw2DUtils::prepareMolForDrawing(*m1);
{ // one molecule
MolDraw2DSVG drawer(200, 200);
drawer.drawMolecule(*m1, "m1");
drawer.addMoleculeMetadata(*m1);
drawer.finishDrawing();
std::string text = drawer.getDrawingText();
std::ofstream outs("test16_1.svg");
outs << text;
outs.flush();
outs.close();
#if DO_TEST_ASSERT
TEST_ASSERT(text.find("idx=\"2\" atom-smiles=\"[NH]\" drawing-x=\"55.") !=
std::string::npos);
TEST_ASSERT(text.find("idx=\"2\" begin-atom-idx=\"2\" end-atom-idx=\"3\" "
"bond-smiles=\"-\"") != std::string::npos);
#endif
check_file_hash("test16_1.svg");
}
{ // multiple molecules
MolDraw2DSVG drawer(400, 400, 200, 200);
auto *rom = rdcast<ROMol *>(m1.get());
std::vector<ROMol *> ms = {new ROMol(*rom), new ROMol(*rom),
new ROMol(*rom), new ROMol(*rom)};
drawer.drawMolecules(ms);
drawer.addMoleculeMetadata(ms);
drawer.finishDrawing();
std::string text = drawer.getDrawingText();
std::ofstream outs("test16_2.svg");
outs << text;
outs.flush();
outs.close();
#if DO_TEST_ASSERT
TEST_ASSERT(text.find("idx=\"2\" atom-smiles=\"[NH]\" drawing-x=\"55.") !=
std::string::npos);
TEST_ASSERT(
text.find("idx=\"2\" atom-smiles=\"[NH]\" drawing-x=\"255.") !=
std::string::npos);
#endif
check_file_hash("test16_2.svg");
for (auto ptr : ms) {
delete ptr;
}
}
}
std::cerr << " Done" << std::endl;
}
void test17MaxMinFontSize() {
std::cout << " ----------------- Test 17 - Testing maximum font size"
<< std::endl;
{
auto m = R"CTAB(
Mrv2014 03142110062D
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 -4.4137 4.3863 0 0
M V30 2 C -5.7475 3.6163 0 0
M V30 3 C -5.7475 2.0763 0 0
M V30 4 C -4.4137 1.3063 0 0
M V30 5 N -3.08 2.0763 0 0
M V30 6 C -3.0801 3.6163 0 0
M V30 END ATOM
M V30 BEGIN BOND
M V30 1 1 1 2
M V30 2 2 1 6
M V30 3 2 2 3
M V30 4 1 3 4
M V30 5 2 4 5
M V30 6 1 5 6
M V30 END BOND
M V30 END CTAB
M END
)CTAB"_ctab;
TEST_ASSERT(m);
std::string nameBase = "test17_";
#if 1
{
std::ofstream outs((nameBase + "1.svg").c_str());
MolDraw2DSVG drawer(300, 300);
drawer.drawMolecule(*m);
drawer.finishDrawing();
std::string text = drawer.getDrawingText();
outs << text;
outs.flush();
outs.close();
#ifdef RDK_BUILD_FREETYPE_SUPPORT
#if DO_TEST_ASSERT
// where it starts drawing the N is a poor surrogate for checking
// the font size, but all we have.
TEST_ASSERT(text.find("<path class='atom-4' d='M 255.3 203.3") !=
std::string::npos);
#endif
#else
TEST_ASSERT(text.find("font-size:40px") != std::string::npos);
#endif
check_file_hash(nameBase + "1.svg");
}
{
std::ofstream outs((nameBase + "2.svg").c_str());
MolDraw2DSVG drawer(300, 300);
drawer.drawOptions().maxFontSize = -1;
drawer.drawMolecule(*m);
drawer.finishDrawing();
std::string text = drawer.getDrawingText();
outs << text;
outs.flush();
outs.close();
#ifdef RDK_BUILD_FREETYPE_SUPPORT
#if DO_TEST_ASSERT
// where it starts drawing the N
TEST_ASSERT(text.find("<path class='atom-4' d='M 251.6 198.9") !=
std::string::npos);
#endif
#else
TEST_ASSERT(text.find("font-size:52px") != std::string::npos);
#endif
check_file_hash(nameBase + "2.svg");
}
#endif
{
std::ofstream outs((nameBase + "3.svg").c_str());
MolDraw2DSVG drawer(300, 300);
drawer.drawOptions().maxFontSize = 20;
drawer.drawMolecule(*m);
drawer.finishDrawing();
std::string text = drawer.getDrawingText();
outs << text;
outs.flush();
outs.close();
#ifdef RDK_BUILD_FREETYPE_SUPPORT
#if DO_TEST_ASSERT
// where it starts drawing the N
TEST_ASSERT(text.find("<path class='atom-4' d='M 261.1 210.4") !=
std::string::npos);
#endif
#else
TEST_ASSERT(text.find("font-size:20px") != std::string::npos);
#endif
check_file_hash(nameBase + "3.svg");
}
{
auto m1 =
"C[C@H](C1=C(C=CC(=C1Cl)F)Cl)OC2=C(N=CC(=C2)C3"
"=CN(N=C3)C4CCNCC4)N"_smiles;
std::ofstream outs((nameBase + "4.svg").c_str());
MolDraw2DSVG drawer(200, 200);
// this is currently the default min font size. Repeated for
// documentation of test.
// TODO : check - default is currently 6
drawer.drawOptions().minFontSize = 12;
drawer.drawMolecule(*m1);
drawer.finishDrawing();
std::string text = drawer.getDrawingText();
outs << text;
outs.flush();
outs.close();
#ifdef RDK_BUILD_FREETYPE_SUPPORT
#if DO_TEST_ASSERT
TEST_ASSERT(text.find("<path class='atom-8' d='M 166.1 92.7") !=
std::string::npos);
#endif
#else
TEST_ASSERT(text.find("font-size:12px") != std::string::npos);
#endif
check_file_hash(nameBase + "4.svg");
}
}
std::cerr << " Done" << std::endl;
}
void test18FixedScales() {
std::cout << " ----------------- Testing use of fixed scales for drawing."
<< std::endl;
UseLegacyStereoPerceptionFixture fx(true);
std::string nameBase = "test18_";
{
auto m = "Clc1ccccc1"_smiles;
TEST_ASSERT(m);
{
MolDraw2DSVG drawer(300, 300);
drawer.drawMolecule(*m, "default");
drawer.finishDrawing();
std::string text = drawer.getDrawingText();
std::ofstream outs((nameBase + "1.svg").c_str());
outs << text;
outs.flush();
outs.close();
#ifdef RDK_BUILD_FREETYPE_SUPPORT
#if DO_TEST_ASSERT
// where it starts drawing the l is a poor surrogate for checking
// the font size, but all we have.
TEST_ASSERT(text.find("<path class='atom-0' d='M 260.9 137.3") !=
std::string::npos);
#endif
#else
TEST_ASSERT(text.find("font-size:33px") != std::string::npos);
#endif
check_file_hash(nameBase + "1.svg");
}
{
MolDraw2DSVG drawer(300, 300);
// fix scale so bond is 5% of window width.
drawer.drawOptions().fixedScale = 0.05;
drawer.drawMolecule(*m, "fixedScale 0.05");
drawer.finishDrawing();
std::string text = drawer.getDrawingText();
std::ofstream outs((nameBase + "2.svg").c_str());
outs << text;
outs.flush();
outs.close();
#ifdef RDK_BUILD_FREETYPE_SUPPORT
#if DO_TEST_ASSERT
// where it starts drawing the l.
TEST_ASSERT(text.find("<path class='atom-0' d='M 176.4 136.7") !=
std::string::npos);
#endif
#else
TEST_ASSERT(text.find("font-size:8px") != std::string::npos);
#endif
check_file_hash(nameBase + "2.svg");
}
}
{
std::string smi =
"C[C@@H](N[C@@H]1CC[C@@H](C(=O)N2CCC(C(=O)N3CCCC3)"
"(c3ccccc3)CC2)C(C)(C)C1)c1ccc(Cl)cc1";
std::unique_ptr<ROMol> m(SmilesToMol(smi));
TEST_ASSERT(m);
{
MolDraw2DSVG drawer(300, 300);
drawer.drawMolecule(*m, "default");
drawer.finishDrawing();
std::string text = drawer.getDrawingText();
std::ofstream outs((nameBase + "3.svg").c_str());
outs << text;
outs.flush();
outs.close();
#ifdef RDK_BUILD_FREETYPE_SUPPORT
#if DO_TEST_ASSERT
TEST_ASSERT(text.find("<path class='atom-2' d='M 74.1 170.0") !=
std::string::npos);
#endif
#else
TEST_ASSERT(text.find("font-size:9px") != std::string::npos);
#endif
check_file_hash(nameBase + "3.svg");
}
{
// fix bond length to 10 pixels.
MolDraw2DSVG drawer(300, 300);
drawer.drawOptions().fixedBondLength = 10;
drawer.drawMolecule(*m, "fixedBondLength 10");
drawer.finishDrawing();
std::string text = drawer.getDrawingText();
std::ofstream outs((nameBase + "4.svg").c_str());
outs << text;
outs.flush();
outs.close();
#ifdef RDK_BUILD_FREETYPE_SUPPORT
#if DO_TEST_ASSERT
TEST_ASSERT(text.find("<path class='atom-2' d='M 104.0 156.8") !=
std::string::npos);
#endif
#else
TEST_ASSERT(text.find("font-size:6px") != std::string::npos);
#endif
check_file_hash(nameBase + "4.svg");
}
{
MolDraw2DSVG drawer(300, 300);
drawer.drawOptions().fixedBondLength = 30;
drawer.drawMolecule(*m, "fixedBondLength 30");
drawer.finishDrawing();
std::string text = drawer.getDrawingText();
std::ofstream outs((nameBase + "5.svg").c_str());
outs << text;
outs.flush();
outs.close();
#ifdef RDK_BUILD_FREETYPE_SUPPORT
#if DO_TEST_ASSERT
TEST_ASSERT(text.find("<path class='atom-2' d='M 74.1 170.0") !=
std::string::npos);
#endif
#else
TEST_ASSERT(text.find("font-size:9px") != std::string::npos);
#endif
check_file_hash(nameBase + "5.svg");
}
{
// this one fixes font size ot 24.
MolDraw2DSVG drawer(300, 300);
drawer.drawOptions().fixedFontSize = 24;
// to make sure it over-rides maxFontSize
drawer.drawOptions().maxFontSize = 20;
drawer.drawMolecule(*m, "fontSize 24");
drawer.finishDrawing();
TEST_ASSERT(drawer.fontSize() == 24);
std::string text = drawer.getDrawingText();
std::ofstream outs((nameBase + "6.svg").c_str());
outs << text;
outs.flush();
outs.close();
#ifdef RDK_BUILD_FREETYPE_SUPPORT
#if DO_TEST_ASSERT
TEST_ASSERT(text.find("<path class='atom-2' d='M 71.9 167.7") !=
std::string::npos);
#endif
#else
TEST_ASSERT(text.find("font-size:24px") != std::string::npos);
#endif
check_file_hash(nameBase + "6.svg");
}
{
// this one fixes font size ot 4. Default minFontSize is 6.
MolDraw2DSVG drawer(300, 300);
drawer.drawOptions().fixedFontSize = 4;
drawer.drawMolecule(*m, "fontSize 4");
drawer.finishDrawing();
TEST_ASSERT(drawer.fontSize() == 4);
std::string text = drawer.getDrawingText();
std::ofstream outs((nameBase + "7.svg").c_str());
outs << text;
outs.flush();
outs.close();
#ifdef RDK_BUILD_FREETYPE_SUPPORT
#if DO_TEST_ASSERT
TEST_ASSERT(text.find("<path class='atom-2' d='M 75.0 171.0") !=
std::string::npos);
#endif
#else
TEST_ASSERT(text.find("font-size:4px") != std::string::npos);
#endif
check_file_hash(nameBase + "7.svg");
}
}
std::cerr << " Done" << std::endl;
}
void test19RotateDrawing() {
std::cout << " ----------------- Testing rotation of 2D drawing."
<< std::endl;
std::string nameBase = "test19_";
{
std::string smi = "Clc1ccccc1";
std::unique_ptr<ROMol> m(SmilesToMol(smi));
TEST_ASSERT(m);
{
MolDraw2DSVG drawer(300, 300);
drawer.drawMolecule(*m);
drawer.finishDrawing();
std::string text = drawer.getDrawingText();
std::ofstream outs((nameBase + "1.svg").c_str());
outs << text;
outs.flush();
outs.close();
#ifdef RDK_BUILD_FREETYPE_SUPPORT
#if DO_TEST_ASSERT
TEST_ASSERT(text.find("<path class='atom-0' d='M 260.9 150.8") !=
std::string::npos);
#endif
#else
TEST_ASSERT(text.find("<text x='255.8' y='166.7' class='atom-0'") !=
std::string::npos);
#endif
check_file_hash(nameBase + "1.svg");
}
{
MolDraw2DSVG drawer(300, 300);
drawer.drawOptions().rotate = 90.0;
drawer.drawMolecule(*m);
drawer.finishDrawing();
std::string text = drawer.getDrawingText();
std::ofstream outs((nameBase + "2.svg").c_str());
outs << text;
outs.flush();
outs.close();
#ifdef RDK_BUILD_FREETYPE_SUPPORT
#if DO_TEST_ASSERT
TEST_ASSERT(text.find("<path class='atom-0' d='M 140.7 272.5") !=
std::string::npos);
#endif
#else
TEST_ASSERT(text.find("<text x='139.9' y='285.0' class='atom-0'") !=
std::string::npos);
#endif
check_file_hash(nameBase + "2.svg");
}
}
std::cerr << " Done" << std::endl;
}
void testGithub2063() {
std::cout << " ----------------- Testing Github2063: Drawing racemic bond "
"stereo as crossed bonds should be the default"
<< std::endl;
{
std::string molb = R"molb(squiggle bond
Mrv1810 09301816112D
4 3 0 0 0 0 999 V2000
0.5804 -0.3125 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
1.2948 0.1000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
-0.1341 0.1000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
2.0093 -0.3125 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
1 2 2 0 0 0 0
1 3 1 0 0 0 0
2 4 1 4 0 0 0
M END)molb";
std::unique_ptr<RWMol> m1(MolBlockToMol(molb));
TEST_ASSERT(m1);
MolDraw2DUtils::prepareMolForDrawing(*m1);
MolDraw2DSVG drawer(200, 200);
drawer.drawMolecule(*m1, "m1");
drawer.addMoleculeMetadata(*m1);
drawer.finishDrawing();
std::string text = drawer.getDrawingText();
std::ofstream outs("testGithub2063_1.svg");
outs << text;
outs.flush();
outs.close();
#if DO_TEST_ASSERT
TEST_ASSERT(text.find("<path class='bond-0 atom-0 atom-1' d='M 70.0,100.8 L"
" 130.0,78.2'") != std::string::npos);
TEST_ASSERT(text.find("<path class='bond-1 atom-0 atom-2' d='M 70.0,112.8"
" L 10.0,78.2'") != std::string::npos);
#endif
check_file_hash("testGithub2063_1.svg");
}
{
std::string molb = R"molb(crossed bond
Mrv1810 09301816112D
4 3 0 0 0 0 999 V2000
0.5804 -0.3125 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
1.2948 0.1000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
-0.1341 0.1000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
2.0093 -0.3125 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
1 2 2 3 0 0 0
1 3 1 0 0 0 0
2 4 1 0 0 0 0
M END)molb";
std::unique_ptr<RWMol> m1(MolBlockToMol(molb));
TEST_ASSERT(m1);
MolDraw2DUtils::prepareMolForDrawing(*m1);
MolDraw2DSVG drawer(200, 200);
drawer.drawMolecule(*m1, "m1");
drawer.addMoleculeMetadata(*m1);
drawer.finishDrawing();
std::string text = drawer.getDrawingText();
std::ofstream outs("testGithub2063_2.svg");
outs << text;
outs.flush();
outs.close();
#if DO_TEST_ASSERT
TEST_ASSERT(text.find("<path class='bond-0 atom-0 atom-1' d='M 70.0,100.8"
" L 130.0,78.2'") != std::string::npos);
TEST_ASSERT(text.find("<path class='bond-1 atom-0 atom-2' d='M 70.0,112.8 "
"L 10.0,78.2'") != std::string::npos);
#endif
check_file_hash("testGithub2063_2.svg");
}
std::cerr << " Done" << std::endl;
}
void testGithub2151() {
std::cout << " ----------------- Testing Github2151: MolDraw2D: line width "
"should be controlled by MolDrawOptions"
<< std::endl;
{
auto m1 = "C[C@H](F)c1ccc(C#N)cc1"_smiles;
TEST_ASSERT(m1);
MolDraw2DUtils::prepareMolForDrawing(*m1);
{
MolDraw2DSVG drawer(200, 200);
drawer.drawMolecule(*m1);
drawer.addMoleculeMetadata(*m1);
drawer.finishDrawing();
std::string text = drawer.getDrawingText();
std::ofstream outs("testGithub2151_1.svg");
outs << text;
outs.flush();
outs.close();
#if DO_TEST_ASSERT
TEST_ASSERT(text.find("stroke-width:2.0px") != std::string::npos);
TEST_ASSERT(text.find("stroke-width:3.0px") == std::string::npos);
#endif
check_file_hash("testGithub2151_1.svg");
}
{
MolDraw2DSVG drawer(200, 200);
drawer.drawOptions().bondLineWidth = 8;
drawer.drawMolecule(*m1);
drawer.addMoleculeMetadata(*m1);
drawer.finishDrawing();
std::string text = drawer.getDrawingText();
std::ofstream outs("testGithub2151_2.svg");
outs << text;
outs.flush();
outs.close();
#if DO_TEST_ASSERT
TEST_ASSERT(text.find("stroke-width:8.0px") != std::string::npos);
#endif
check_file_hash("testGithub2151_2.svg");
}
}
std::cerr << " Done" << std::endl;
}
void testGithub2762() {
std::cout << " ----------------- Testing testGithub2762: MolDraw2D: HCl "
"and ethane should be drawn"
<< std::endl;
{
auto m1 = "Cl"_smiles;
TEST_ASSERT(m1);
auto m2 = "CC"_smiles;
TEST_ASSERT(m2);
MolDraw2DUtils::prepareMolForDrawing(*m1);
MolDraw2DUtils::prepareMolForDrawing(*m2);
std::vector<ROMol *> mols;
mols.push_back(m1.get());
mols.push_back(m2.get());
MolDraw2DSVG drawer(500, 250, 250, 250);
drawer.drawMolecules(mols);
drawer.finishDrawing();
std::string text = drawer.getDrawingText();
std::ofstream outs("testGithub2762.svg");
outs << text;
outs.flush();
outs.close();
#if DO_TEST_ASSERT
TEST_ASSERT(text.find("font-size:0px") == std::string::npos);
TEST_ASSERT(text.find("'bond-0' d='M 0.0,200.0 L 0.0,200.0'") ==
std::string::npos);
#endif
check_file_hash("testGithub2762.svg");
}
std::cerr << " Done" << std::endl;
}
void testGithub2931() {
std::cout << " ----------------- Testing testGithub2931: multi-coloured"
" molecule highlights."
<< std::endl;
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 get_all_hit_bonds =
[](ROMol &mol, const std::vector<int> &hit_atoms) -> std::vector<int> {
std::vector<int> hit_bonds;
for (int i : hit_atoms) {
for (int j : hit_atoms) {
if (i > j) {
Bond *bnd = mol.getBondBetweenAtoms(i, j);
if (bnd) {
hit_bonds.push_back(bnd->getIdx());
}
}
}
}
return hit_bonds;
};
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::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);
Chirality::wedgeMolBonds(*m, &(m->getConformer()));
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]);
std::vector<int> hit_bonds = get_all_hit_bonds(*m, hit_atoms);
update_colour_map(hit_atoms, colours[i], ha_map);
update_colour_map(hit_bonds, colours[i], hb_map);
}
std::map<int, double> h_rads;
std::map<int, int> h_lw_mult;
{
MolDraw2DSVG drawer(500, 500);
drawer.drawOptions().fillHighlights = false;
drawer.drawOptions().continuousHighlight = true;
drawer.drawMoleculeWithHighlights(*m, "Test 1", ha_map, hb_map, h_rads,
h_lw_mult);
drawer.finishDrawing();
std::string text = drawer.getDrawingText();
std::ofstream outs("testGithub2931_1.svg");
outs << text;
outs.flush();
outs.close();
std::regex r1(
"<ellipse cx='(\\d+\\.\\d+)' cy='(\\d+\\.\\d+)'"
" rx='(\\d+\\.\\d+)' ry='(\\d+\\.\\d+)' class='atom-6'");
std::smatch match = *std::sregex_iterator(text.begin(), text.end(), r1);
#ifdef RDK_BUILD_FREETYPE_SUPPORT
#if DO_TEST_ASSERT
TEST_ASSERT(text.find("stroke:#FF8C00;stroke-width:8.0px") !=
std::string::npos);
// it's an ellipse, so different radii
TEST_ASSERT(fabs(stod(match[1]) - 243) <
1); // significant variability with freetype version here
TEST_ASSERT(fabs(stod(match[2]) - 350.2) < 1.0);
TEST_ASSERT(fabs(stod(match[3]) - 12.0) < 0.2);
TEST_ASSERT(fabs(stod(match[4]) - 12.4) < 0.2);
#endif
#else
TEST_ASSERT(text.find("stroke:#FF8C00;stroke-width:8.0px") !=
std::string::npos);
TEST_ASSERT(fabs(stod(match[1]) - 243.4) < 0.1);
TEST_ASSERT(fabs(stod(match[2]) - 349.3) < 0.1);
TEST_ASSERT(fabs(stod(match[3]) - 9.7) < 0.1);
TEST_ASSERT(fabs(stod(match[4]) - 11.0) < 0.1);
#endif
check_file_hash("testGithub2931_1.svg");
}
{
MolDraw2DSVG drawer(500, 500);
drawer.drawOptions().fillHighlights = false;
drawer.drawOptions().continuousHighlight = true;
drawer.drawOptions().atomHighlightsAreCircles = true;
drawer.drawMoleculeWithHighlights(*m, "Test 2", ha_map, hb_map, h_rads,
h_lw_mult);
drawer.finishDrawing();
std::string text = drawer.getDrawingText();
std::ofstream outs("testGithub2931_2.svg");
outs << text;
outs.flush();
outs.close();
std::regex r1(
"<ellipse cx='(\\d+\\.\\d+)' cy='(\\d+\\.\\d+)'"
" rx='(\\d+\\.\\d+)' ry='(\\d+\\.\\d+)' class='atom-6'");
std::smatch match = *std::sregex_iterator(text.begin(), text.end(), r1);
#ifdef RDK_BUILD_FREETYPE_SUPPORT
#if DO_TEST_ASSERT
TEST_ASSERT(text.find("stroke:#FF8C00;stroke-width:8.0px") !=
std::string::npos);
// it's a circle
TEST_ASSERT(fabs(stod(match[1]) - 243.9) < 0.1);
TEST_ASSERT(fabs(stod(match[2]) - 350.0) < 0.1);
TEST_ASSERT(fabs(stod(match[3]) - 12.2) < 0.1);
TEST_ASSERT(fabs(stod(match[4]) - 12.2) < 0.1);
#endif
#else
TEST_ASSERT(text.find("stroke:#FF8C00;stroke-width:8.0px") !=
std::string::npos);
TEST_ASSERT(fabs(stod(match[1]) - 243.9) < 0.1);
TEST_ASSERT(fabs(stod(match[2]) - 347.7) < 0.1);
TEST_ASSERT(fabs(stod(match[3]) - 12.1) < 0.1);
TEST_ASSERT(fabs(stod(match[4]) - 12.1) < 0.1);
#endif
check_file_hash("testGithub2931_2.svg");
}
{
MolDraw2DSVG drawer(500, 500);
drawer.drawOptions().fillHighlights = false;
std::map<int, int> hb_lw_mult;
for (auto &hbi : hb_map) {
hb_lw_mult[hbi.first] = 20;
}
drawer.drawMoleculeWithHighlights(*m, "Test3", ha_map, hb_map, h_rads,
hb_lw_mult);
drawer.finishDrawing();
std::string text = drawer.getDrawingText();
std::ofstream outs("testGithub2931_3.svg");
outs << text;
outs.flush();
outs.close();
#ifdef RDK_BUILD_FREETYPE_SUPPORT
#if DO_TEST_ASSERT
TEST_ASSERT(text.find("stroke:#FF8C00;stroke-width:40.0px") !=
std::string::npos);
#endif
#else
TEST_ASSERT(text.find("stroke:#FF8C00;stroke-width:40.0px") !=
std::string::npos);
#endif
check_file_hash("testGithub2931_3.svg");
}
{
MolDraw2DSVG drawer(500, 500);
drawer.drawOptions().fillHighlights = false;
drawer.drawOptions().continuousHighlight = true;
drawer.drawOptions().fixedFontSize = 10;
drawer.drawOptions().addAtomIndices = true;
drawer.drawOptions().addBondIndices = true;
drawer.drawMoleculeWithHighlights(*m, "Test 4", ha_map, hb_map, h_rads,
h_lw_mult);
drawer.finishDrawing();
std::string text = drawer.getDrawingText();
std::ofstream outs("testGithub2931_4.svg");
outs << text;
outs.flush();
outs.close();
#ifdef RDK_BUILD_FREETYPE_SUPPORT
#if DO_TEST_ASSERT
TEST_ASSERT(text.find("stroke:#FF8C00;stroke-width:8.0px") !=
std::string::npos);
TEST_ASSERT(
text.find("<ellipse cx='246.7' cy='341.6' rx='11.6' ry='11.6'"
" class='atom-6' style='fill:none;stroke:#00FF00;") !=
std::string::npos);
#endif
#else
TEST_ASSERT(text.find("stroke:#FF8C00;stroke-width:8.0px") !=
std::string::npos);
TEST_ASSERT(
text.find("<ellipse cx='247.8' cy='294.5' rx='11.6' ry='11.6' "
"class='atom-5' style='fill:none;stroke:#00FF00") !=
std::string::npos);
#endif
check_file_hash("testGithub2931_4.svg");
}
}
std::cerr << " Done" << std::endl;
}
void testGithub3112() {
std::cout << " ----------------- Testing drawing of legends." << std::endl;
{
auto m = "CCCC"_smiles;
TEST_ASSERT(m);
MolDraw2DUtils::prepareMolForDrawing(*m);
MolDraw2DSVG drawer(250, 200);
drawer.drawMolecule(*m, "foobar");
drawer.finishDrawing();
std::string text = drawer.getDrawingText();
std::ofstream outs("testGithub3112_1.svg");
outs << text;
outs.close();
#ifdef RDK_BUILD_FREETYPE_SUPPORT
#if DO_TEST_ASSERT
// this is the b (4th character)
TEST_ASSERT(text.find("<path class='legend' d='M 134.6 185.3") !=
std::string::npos);
#endif
#else
TEST_ASSERT(text.find("<text x='120.5' y='190.0' class='legend' "
"style='font-size:16px;font-style:normal;font-weight:"
"normal;fill-opacity:1;stroke:none;font-family:sans-"
"serif;text-anchor:start;fill:#000000' >b</text>") !=
std::string::npos);
#endif
check_file_hash("testGithub3112_1.svg");
}
{
auto m = "CCCC"_smiles;
TEST_ASSERT(m);
MolDraw2DUtils::prepareMolForDrawing(*m);
MolDraw2DSVG drawer(250, 200);
drawer.drawMolecule(*m, "foo\nbar");
drawer.finishDrawing();
std::string text = drawer.getDrawingText();
std::ofstream outs("testGithub3112_2.svg");
outs << text;
outs.close();
#ifdef RDK_BUILD_FREETYPE_SUPPORT
#if DO_TEST_ASSERT
// this is the b on the 2nd line.
TEST_ASSERT(text.find("<path class='legend' d='M 119.7 184.3") !=
std::string::npos);
#endif
#else
TEST_ASSERT(text.find("<text x='111.1' y='190.0' class='legend' "
"style='font-size:11px;font-style:normal;font-weight:"
"normal;fill-opacity:1;stroke:none;font-family:sans-"
"serif;text-anchor:start;fill:#000000' >b</text>") !=
std::string::npos);
#endif
check_file_hash("testGithub3112_2.svg");
}
{
auto m = "CCCC"_smiles;
TEST_ASSERT(m);
MolDraw2DUtils::prepareMolForDrawing(*m);
MolDraw2DSVG drawer(250, 200);
drawer.drawMolecule(
*m,
"No one in their right mind would have a legend this long, surely.");
drawer.finishDrawing();
std::string text = drawer.getDrawingText();
std::ofstream outs("testGithub3112_3.svg");
outs << text;
outs.close();
#ifdef RDK_BUILD_FREETYPE_SUPPORT
#if DO_TEST_ASSERT
// The first letter, N.
TEST_ASSERT(text.find("<path class='legend' d='M 12.9 182.6") !=
std::string::npos);
#endif
#else
TEST_ASSERT(text.find("<text x='9.7' y='190.0' class='legend' "
"style='font-size:9px;font-style:normal;font-weight:"
"normal;fill-opacity:1;stroke:none;font-family:sans-"
"serif;text-anchor:start;fill:#000000' >N</text>") !=
std::string::npos);
#endif
check_file_hash("testGithub3112_3.svg");
}
{
auto m = "CCCC"_smiles;
TEST_ASSERT(m);
MolDraw2DUtils::prepareMolForDrawing(*m);
MolDraw2DSVG drawer(250, 200);
drawer.drawMolecule(
*m,
"No one in their right mind would\nhave a legend this long, surely.");
drawer.finishDrawing();
std::string text = drawer.getDrawingText();
std::ofstream outs("testGithub3112_4.svg");
outs << text;
outs.close();
#ifdef RDK_BUILD_FREETYPE_SUPPORT
#if DO_TEST_ASSERT
// The first letter, N
TEST_ASSERT(text.find("<path class='legend' d='M 59.9 172.5") !=
std::string::npos);
#endif
#else
TEST_ASSERT(text.find("<text x='57.2' y='181.0' class='legend' "
"style='font-size:11px;font-style:normal;font-weight:"
"normal;fill-opacity:1;stroke:none;font-family:sans-"
"serif;text-anchor:start;fill:#000000' >N</text>") !=
std::string::npos);
#endif
check_file_hash("testGithub3112_4.svg");
}
std::cerr << " Done" << std::endl;
}
void test20Annotate() {
std::cout << " ----------------- Testing annotation of 2D Drawing."
<< std::endl;
// add serial numbers to the atoms in the molecule.
// There's an option for this, but for debugging it's sometimes
// useful to be able to put notes on just a few atoms.
auto addAtomSerialNumbers = [](ROMol &mol) {
for (auto atom : mol.atoms()) {
atom->setProp(common_properties::atomNote, atom->getIdx());
}
};
auto addBondSerialNumbers = [](ROMol &mol) {
for (auto bond : mol.bonds()) {
bond->setProp(common_properties::bondNote, bond->getIdx());
}
};
{
auto m1 = "S=C1N=C(NC(CC#N)(C)C=C=C)NC2=NNN=C21"_smiles;
addAtomSerialNumbers(*m1);
addBondSerialNumbers(*m1);
#ifdef RDK_BUILD_CAIRO_SUPPORT
{
MolDraw2DCairo drawer(500, 500);
drawer.drawMolecule(*m1);
drawer.finishDrawing();
drawer.writeDrawingText("test20_1.png");
check_file_hash("test20_1.png");
}
#endif
MolDraw2DSVG drawer(500, 500);
drawer.drawMolecule(*m1);
drawer.finishDrawing();
std::string text = drawer.getDrawingText();
std::ofstream outs("test20_1.svg");
outs << text;
outs.flush();
outs.close();
#ifdef RDK_BUILD_FREETYPE_SUPPORT
#if DO_TEST_ASSERT
// first note (atom 0)
TEST_ASSERT(text.find("<path class='note' d='M 51.9 122.3") !=
std::string::npos);
#endif
#else
// first one of atom note 11
TEST_ASSERT(text.find("<text x='392.8' y='215.5' class='note' "
"style='font-size:11px;font-style:normal;font-weight:"
"normal;fill-opacity:1;stroke:none;font-family:sans-"
"serif;text-anchor:start;fill:#000000' >1</text>") !=
std::string::npos);
#endif
check_file_hash("test20_1.svg");
}
{
auto m1 = "C[C@@H](F)/C=C/[C@H](O)C"_smiles;
#ifdef RDK_BUILD_CAIRO_SUPPORT
{
MolDraw2DCairo drawer(300, 300);
drawer.drawOptions().addStereoAnnotation = true;
drawer.drawMolecule(*m1);
drawer.finishDrawing();
drawer.writeDrawingText("test20_2.png");
check_file_hash("test20_2.png");
}
#endif
MolDraw2DSVG drawer(500, 500);
drawer.drawOptions().addStereoAnnotation = true;
drawer.drawMolecule(*m1);
drawer.finishDrawing();
std::string text = drawer.getDrawingText();
std::ofstream outs("test20_2.svg");
outs << text;
outs.flush();
outs.close();
#ifdef RDK_BUILD_FREETYPE_SUPPORT
#if DO_TEST_ASSERT
// last note
TEST_ASSERT(text.find("<path class='CIP_Code' d='M 273.9 236.3") !=
std::string::npos);
#endif
#else
// this is the (E)
TEST_ASSERT(text.find("<text x='260.3' y='232.0' class='CIP_Code' "
"style='font-size:20px;font-style:normal;font-weight:"
"normal;fill-opacity:1;stroke:none;font-family:sans-"
"serif;text-anchor:start;fill:#7F7FFF' >E</text>") !=
std::string::npos);
#endif
check_file_hash("test20_2.svg");
}
{
auto m1 = "S=C1N=C(NC(CC#N)(C)C=C=C)NC2=NNN=C21"_smiles;
auto atom = m1->getAtomWithIdx(3);
atom->setProp("atomNote", "foolish annotation");
auto bond = m1->getBondWithIdx(5);
bond->setProp("bondNote", "way too long to be useful");
#ifdef RDK_BUILD_CAIRO_SUPPORT
{
MolDraw2DCairo drawer(300, 300);
drawer.drawOptions().addStereoAnnotation = true;
drawer.drawMolecule(*m1);
drawer.finishDrawing();
drawer.writeDrawingText("test20_3.png");
check_file_hash("test20_3.png");
}
#endif
MolDraw2DSVG drawer(500, 500);
drawer.drawOptions().addStereoAnnotation = true;
drawer.drawMolecule(*m1);
drawer.finishDrawing();
std::string text = drawer.getDrawingText();
std::ofstream outs("test20_3.svg");
outs << text;
outs.flush();
outs.close();
#ifdef RDK_BUILD_FREETYPE_SUPPORT
#if DO_TEST_ASSERT
// first note
TEST_ASSERT(text.find("<path class='note' d='M 157.4 177.9") !=
std::string::npos);
#endif
#else
// f of foolish
TEST_ASSERT(text.find("<text x='146.4' y='182.4' class='note' "
"style='font-size:12px;font-style:normal;font-weight:"
"normal;fill-opacity:1;stroke:none;font-family:sans-"
"serif;text-anchor:start;fill:#000000' >f</text>") !=
std::string::npos);
#endif
check_file_hash("test20_3.svg");
}
{
auto m1 = "S=C1N=C(NC(CC#N)(C)C=C=C)NC2=NNN=C21"_smiles;
#ifdef RDK_BUILD_CAIRO_SUPPORT
{
MolDraw2DCairo drawer(200, 200);
drawer.drawOptions().addAtomIndices = true;
drawer.drawMolecule(*m1);
drawer.finishDrawing();
drawer.writeDrawingText("test20_4.png");
check_file_hash("test20_4.png");
}
#endif
MolDraw2DSVG drawer(200, 200);
drawer.drawOptions().addAtomIndices = true;
drawer.drawMolecule(*m1);
drawer.finishDrawing();
std::string text = drawer.getDrawingText();
std::ofstream outs("test20_4.svg");
outs << text;
outs.flush();
outs.close();
#ifdef RDK_BUILD_FREETYPE_SUPPORT
#if DO_TEST_ASSERT
// first note (atom 0)
TEST_ASSERT(text.find("<path class='note' d='M 20.7 48.9") !=
std::string::npos);
#endif
#else
// first one of atom note 11
TEST_ASSERT(text.find("<text x='157.1' y='86.2' class='note' "
"style='font-size:4px;font-style:normal;font-weight:"
"normal;fill-opacity:1;stroke:none;font-family:sans-"
"serif;text-anchor:start;fill:#000000' >1</text>") !=
std::string::npos);
#endif
check_file_hash("test20_4.svg");
}
std::cerr << " Done" << std::endl;
}
void test21FontFile() {
#ifdef RDK_BUILD_FREETYPE_SUPPORT
std::cout << " ----------------- Test 21 - different font" << std::endl;
// You have to look at this one, there's no algorithmic check.
{
auto m = "CO[C@@H](O)C1=C(O[C@H](F)Cl)C(C#N)=C1ONNC[NH3+]"_smiles;
TEST_ASSERT(m);
RDDepict::compute2DCoords(*m);
Chirality::wedgeMolBonds(*m, &(m->getConformer()));
std::ofstream outs("test21_1.svg");
MolDraw2DSVG drawer(500, 500, outs);
std::string fName = getenv("RDBASE");
fName += "/Data/Fonts/Amadeus.ttf";
drawer.drawOptions().fontFile = fName;
drawer.drawMolecule(*m);
drawer.finishDrawing();
outs.flush();
outs.close();
check_file_hash("test21_1.svg");
}
{
auto m = "CO[C@@H](O)C1=C(O[C@H](F)Cl)C(C#N)=C1ONNC[NH3+]"_smiles;
TEST_ASSERT(m);
RDDepict::compute2DCoords(*m);
Chirality::wedgeMolBonds(*m, &(m->getConformer()));
std::ofstream outs("test21_2.svg");
MolDraw2DSVG drawer(500, 500, outs);
std::string fName = getenv("RDBASE");
fName += "/Data/Fonts/No_Such_Font_File.ttf";
drawer.drawOptions().fontFile = fName;
drawer.drawMolecule(*m);
drawer.finishDrawing();
outs.flush();
outs.close();
check_file_hash("test21_2.svg");
}
std::cerr << "Done" << std::endl;
#endif
}
void test22ExplicitMethyl() {
std::cout << " ----------------- Test 22 - draw explicit methyls."
<< std::endl;
auto m = "CCC(C#C)C=C"_smiles;
TEST_ASSERT(m);
RDDepict::compute2DCoords(*m);
{
MolDraw2DSVG drawer(300, 300);
drawer.drawMolecule(*m);
drawer.finishDrawing();
std::string text = drawer.getDrawingText();
std::ofstream outs("test22_1.svg");
outs << text;
outs.flush();
outs.close();
TEST_ASSERT(text.find("class='atom-") == std::string::npos);
check_file_hash("test22_1.svg");
}
{
MolDraw2DSVG drawer(300, 300);
drawer.drawOptions().explicitMethyl = true;
drawer.drawMolecule(*m);
drawer.finishDrawing();
std::string text = drawer.getDrawingText();
std::ofstream outs("test22_2.svg");
outs << text;
outs.flush();
outs.close();
TEST_ASSERT(text.find("class='atom-") != std::string::npos);
check_file_hash("test22_2.svg");
}
std::cerr << "Done" << std::endl;
}
void testGithub3305() {
std::cout
<< " ----------------- Test Github 3305 - change and scale line widths."
<< std::endl;
auto m = "CCC(C#C)C=C"_smiles;
TEST_ASSERT(m);
RDDepict::compute2DCoords(*m);
std::string nameBase = "testGithub3305_";
{
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();
TEST_ASSERT(text.find("stroke-width:2.0px") != std::string::npos);
check_file_hash(nameBase + "1.svg");
}
{
MolDraw2DSVG drawer(600, 600);
drawer.drawOptions().bondLineWidth = 2;
drawer.drawMolecule(*m);
drawer.finishDrawing();
std::string text = drawer.getDrawingText();
std::ofstream outs(nameBase + "2.svg");
outs << text;
outs.flush();
outs.close();
TEST_ASSERT(text.find("stroke-width:2.0px") != std::string::npos);
check_file_hash(nameBase + "2.svg");
}
{
MolDraw2DSVG drawer(600, 600);
drawer.drawOptions().bondLineWidth = 2;
drawer.drawOptions().scaleBondWidth = true;
drawer.drawMolecule(*m);
drawer.finishDrawing();
std::string text = drawer.getDrawingText();
std::ofstream outs(nameBase + "3.svg");
outs << text;
outs.flush();
outs.close();
#if DO_TEST_ASSERT
TEST_ASSERT(text.find("stroke-width:4.2px") != std::string::npos);
#endif
check_file_hash(nameBase + "3.svg");
}
#ifdef RDK_BUILD_CAIRO_SUPPORT
{
MolDraw2DCairo drawer(300, 300);
drawer.drawMolecule(*m);
drawer.finishDrawing();
drawer.writeDrawingText(nameBase + "1.png");
check_file_hash(nameBase + "1.png");
}
{
MolDraw2DCairo drawer(600, 600);
drawer.drawOptions().bondLineWidth = 2;
drawer.drawMolecule(*m);
drawer.finishDrawing();
drawer.writeDrawingText(nameBase + "2.png");
check_file_hash(nameBase + "2.png");
}
{
MolDraw2DCairo drawer(600, 600);
drawer.drawOptions().bondLineWidth = 2;
drawer.drawOptions().scaleBondWidth = true;
drawer.drawMolecule(*m);
drawer.finishDrawing();
drawer.writeDrawingText(nameBase + "3.png");
check_file_hash(nameBase + "3.png");
}
#endif
{
auto m = "CCOC(=O)Nc1ccc(SCC2COC(Cn3ccnc3)(c3ccc(Cl)cc3Cl)O2)cc1"_smiles;
TEST_ASSERT(m);
RDDepict::compute2DCoords(*m);
Chirality::wedgeMolBonds(*m, &(m->getConformer()));
static const int ha[] = {17, 18, 19, 20, 21, 6, 7, 8, 9, 31, 32};
std::vector<int> highlight_atoms(ha, ha + sizeof(ha) / sizeof(int));
std::map<int, DrawColour> highlight_colors;
MolDrawOptions options;
options.circleAtoms = true;
options.highlightColour = DrawColour(1, .5, .5);
options.continuousHighlight = true;
#ifdef RDK_BUILD_CAIRO_SUPPORT
{
MolDraw2DCairo drawer(200, 200);
options.scaleHighlightBondWidth = true;
drawer.drawOptions() = options;
drawer.drawMolecule(*m, &highlight_atoms, &highlight_colors);
drawer.finishDrawing();
drawer.writeDrawingText(nameBase + "4.png");
check_file_hash(nameBase + "4.png");
}
#endif
// check that the regex digs out a rectangle with the expected corners,
// within a tolerance. Used by the next 2 tests.
auto check_corners = [](const std::string &text, std::regex &regex,
const std::vector<Point2D> &expected) -> void {
auto match_begin = std::sregex_iterator(text.begin(), text.end(), regex);
std::vector<Point2D> actual;
std::smatch match = *match_begin;
actual.push_back(Point2D(std::stod(match[1]), std::stod(match[2])));
actual.push_back(Point2D(std::stod(match[3]), std::stod(match[4])));
actual.push_back(Point2D(std::stod(match[5]), std::stod(match[6])));
actual.push_back(Point2D(std::stod(match[7]), std::stod(match[8])));
int num_matched = 0;
for (const auto &e : expected) {
for (const auto &a : actual) {
if ((e - a).lengthSq() <= 1.0) {
num_matched++;
break;
}
}
}
TEST_ASSERT(num_matched == 4);
};
{
MolDraw2DSVG drawer(200, 200);
options.scaleHighlightBondWidth = true;
drawer.drawOptions() = options;
drawer.drawMolecule(*m, &highlight_atoms, &highlight_colors);
drawer.finishDrawing();
std::string text = drawer.getDrawingText();
std::ofstream outs(nameBase + "4.svg");
outs << text;
outs.flush();
outs.close();
#if DO_TEST_ASSERT
// as seen in Github5899, we don't always get the rectangle corners
// in the same order. Make sure they all turn up, within a tolerance.
// This seems to work for Freetype and non-Freetype builds.
std::regex regex(
R"(class='bond-6 atom-6 atom-7' d='M ([\d.]*),([\d.]*) L ([\d.]*),([\d.]*) L ([\d.]*),([\d.]*) L ([\d.]*),([\d.]*) Z' style='fill:#FF7F7F;)");
std::vector<Point2D> expected{
Point2D(138.7, 116.8), Point2D(141.9, 116.8), Point2D(134.7, 129.2),
Point2D(133.1, 126.5)};
check_corners(text, regex, expected);
check_file_hash(nameBase + "4.svg");
#endif
}
#ifdef RDK_BUILD_CAIRO_SUPPORT
{
MolDraw2DCairo drawer(200, 200);
options.scaleHighlightBondWidth = false;
drawer.drawOptions() = options;
drawer.drawMolecule(*m, &highlight_atoms, &highlight_colors);
drawer.finishDrawing();
drawer.writeDrawingText(nameBase + "5.png");
check_file_hash(nameBase + "5.png");
}
#endif
{
// This picture has very wide bond highlights as a test - it
// looks pretty unsavoury. I mention it so that when you flick
// through the test images you don't panic and start searching
// for the bug. Been there, done that!
MolDraw2DSVG drawer(200, 200);
options.scaleHighlightBondWidth = false;
drawer.drawOptions() = options;
drawer.drawMolecule(*m, &highlight_atoms, &highlight_colors);
drawer.finishDrawing();
std::string text = drawer.getDrawingText();
std::ofstream outs((nameBase + "5.svg").c_str());
outs << text;
outs.flush();
outs.close();
#if DO_TEST_ASSERT
std::regex regex(
R"(class='bond-6 atom-6 atom-7' d='M ([\d.]*),([\d.]*) L ([\d.]*),([\d.]*) L ([\d.]*),([\d.]*) L ([\d.]*),([\d.]*) Z' style='fill:#FF7F7F;)");
std::vector<Point2D> expected{
Point2D(131.1, 120.8), Point2D(149.5, 120.8), Point2D(138.5, 139.8),
Point2D(129.3, 123.8)};
check_corners(text, regex, expected);
#endif
check_file_hash(nameBase + "5.svg");
}
options.continuousHighlight = false;
#ifdef RDK_BUILD_CAIRO_SUPPORT
{
MolDraw2DCairo drawer(200, 200);
options.scaleHighlightBondWidth = true;
drawer.drawOptions() = options;
drawer.drawMolecule(*m, &highlight_atoms, &highlight_colors);
drawer.finishDrawing();
drawer.writeDrawingText(nameBase + "6.png");
check_file_hash(nameBase + "6.png");
}
#endif
{
MolDraw2DSVG drawer(200, 200);
options.scaleHighlightBondWidth = true;
drawer.drawOptions() = options;
drawer.drawMolecule(*m, &highlight_atoms, &highlight_colors);
drawer.finishDrawing();
std::ofstream outs((nameBase + "6.svg").c_str());
std::string text = drawer.getDrawingText();
outs << text;
outs.flush();
outs.close();
#if DO_TEST_ASSERT
TEST_ASSERT(text.find("stroke:#FF7F7F;stroke-width:0.7") !=
std::string::npos);
TEST_ASSERT(text.find("stroke:#FF7F7F;stroke-width:4.0px") ==
std::string::npos);
#endif
check_file_hash(nameBase + "6.svg");
}
#ifdef RDK_BUILD_CAIRO_SUPPORT
{
MolDraw2DCairo drawer(200, 200);
options.scaleHighlightBondWidth = false;
drawer.drawOptions() = options;
drawer.drawMolecule(*m, &highlight_atoms, &highlight_colors);
drawer.finishDrawing();
drawer.writeDrawingText(nameBase + "7.png");
check_file_hash(nameBase + "7.png");
}
#endif
{
MolDraw2DSVG drawer(200, 200);
options.scaleHighlightBondWidth = false;
drawer.drawOptions() = options;
drawer.drawMolecule(*m, &highlight_atoms, &highlight_colors);
drawer.finishDrawing();
std::ofstream outs((nameBase + "7.svg").c_str());
std::string text = drawer.getDrawingText();
outs << text;
outs.flush();
outs.close();
#if DO_TEST_ASSERT
TEST_ASSERT(text.find("stroke:#FF7F7F;stroke-width:0.7") ==
std::string::npos);
TEST_ASSERT(text.find("stroke:#FF7F7F;stroke-width:4.0px") !=
std::string::npos);
#endif
check_file_hash(nameBase + "7.svg");
}
}
std::cerr << "Done" << std::endl;
}
void testGithub3391() {
std::cout
<< " ----------------- Test Github 3391 - maxFontSize interacting badly"
" with DrawMolecules."
<< std::endl;
auto m = "C"_smiles;
auto m2 = "CCOC(=O)Nc1ccc(SCC2COC(Cn3ccnc3)(c3ccc(Cl)cc3Cl)O2)cc1"_smiles;
auto m3 = "CCl"_smiles;
{
MolDraw2DSVG drawer(400, 200, 200, 200);
drawer.drawOptions().maxFontSize = 14;
std::vector<ROMol *> mols;
mols.push_back(m.get());
mols.push_back(m.get());
drawer.drawMolecules(mols);
drawer.finishDrawing();
std::string text = drawer.getDrawingText();
std::ofstream outs("testGithub3391_1.svg");
outs << text;
outs.flush();
outs.close();
check_file_hash("testGithub3391_1.svg");
}
{
MolDraw2DSVG drawer(400, 200, 200, 200);
drawer.drawOptions().maxFontSize = 14;
std::vector<ROMol *> mols;
mols.push_back(m.get());
mols.push_back(m2.get());
drawer.drawMolecules(mols);
drawer.finishDrawing();
std::string text = drawer.getDrawingText();
std::ofstream outs("testGithub3391_2.svg");
outs << text;
outs.flush();
outs.close();
check_file_hash("testGithub3391_2.svg");
}
{
MolDraw2DSVG drawer(400, 200, 200, 200);
drawer.drawOptions().maxFontSize = 14;
std::vector<ROMol *> mols;
mols.push_back(m2.get());
mols.push_back(m.get());
drawer.drawMolecules(mols);
drawer.finishDrawing();
std::string text = drawer.getDrawingText();
std::ofstream outs("testGithub3391_3.svg");
outs << text;
outs.flush();
outs.close();
check_file_hash("testGithub3391_3.svg");
}
{
MolDraw2DSVG drawer(600, 200, 200, 200);
drawer.drawOptions().maxFontSize = 14;
drawer.drawOptions().minFontSize = 8;
std::vector<ROMol *> mols;
auto m1 = "CO"_smiles;
auto m2 = "CCCCCCCCCCO"_smiles;
auto m3 = "CCCCCCCCCCCCCCCCCCCCCCO"_smiles;
mols.push_back(m3.get());
mols.push_back(m2.get());
mols.push_back(m1.get());
drawer.drawMolecules(mols);
drawer.finishDrawing();
std::string text = drawer.getDrawingText();
std::ofstream outs("testGithub3391_4.svg");
outs << text;
outs.flush();
outs.close();
check_file_hash("testGithub3391_4.svg");
}
std::cerr << "Done" << std::endl;
}
void testGithub4156() {
std::cout
<< " ----------------- Test Github 4156 - bad scale for radicals in grid"
<< std::endl;
auto m1 = "C1[CH]C1[C@H](F)C1CCC1"_smiles;
auto m2 = "F[C@H]1CC[C@H](O)CC1"_smiles;
#ifdef RDK_BUILD_FREETYPE_SUPPORT
{
std::vector<ROMol *> mols;
mols.push_back(m1.get());
mols.push_back(m2.get());
MolDraw2DSVG drawer(500, 200, 250, 200);
drawer.drawMolecules(mols);
drawer.finishDrawing();
std::string text = drawer.getDrawingText();
std::ofstream outs("testGithub4156_1.svg");
outs << text;
outs.flush();
outs.close();
// this is the start of the radical spot.
std::regex qry(
"<path class='atom-1' d='M 23.[0-9]*,76.[0-9]* L 23.[0-9]*,76.[0-9]*");
#if DO_TEST_ASSERT
TEST_ASSERT(std::regex_search(text, qry));
#endif
check_file_hash("testGithub4156_1.svg");
}
{
std::vector<ROMol *> mols;
mols.push_back(m2.get());
mols.push_back(m1.get());
MolDraw2DSVG drawer(500, 200, 250, 200);
drawer.drawMolecules(mols);
drawer.finishDrawing();
std::string text = drawer.getDrawingText();
std::ofstream outs("testGithub4156_2.svg");
outs << text;
outs.flush();
outs.close();
// this is the start of the radical spot.
std::regex qry(
"<path class='atom-1' d='M 273.[0-9]*,76.[0-9]* L "
"273.[0-9]*,76.[0-9]*");
#if DO_TEST_ASSERT
TEST_ASSERT(std::regex_search(text, qry));
#endif
check_file_hash("testGithub4156_2.svg");
}
#endif
std::cerr << " Done" << std::endl;
}
void test23JSONAtomColourPalette() {
std::cerr << " ----------------- Test JSON atomColourPalette" << std::endl;
{
auto m = "c1cncs1"_smiles;
TEST_ASSERT(m);
MolDraw2DUtils::prepareMolForDrawing(*m);
MolDraw2DSVG drawer(250, 200);
const char *json =
R"JSON({"atomColourPalette": {"7": [0.2, 0.4, 0.9], "16": [0.9, 0.6, 0.0]},
"rotate": 90, "bondLineWidth": 5})JSON";
MolDraw2DUtils::updateDrawerParamsFromJSON(drawer, json);
drawer.drawMolecule(*m);
drawer.finishDrawing();
std::string text = drawer.getDrawingText();
std::ofstream outs("test23_1.svg");
outs << text;
outs.close();
#if DO_TEST_ASSERT
#ifdef RDK_BUILD_FREETYPE_SUPPORT
TEST_ASSERT(text.find("' fill='#3366E5") != std::string::npos);
TEST_ASSERT(text.find("' fill='#E59900") != std::string::npos);
#else
TEST_ASSERT(text.find("fill:#3366E5") != std::string::npos);
TEST_ASSERT(text.find("fill:#E59900") != std::string::npos);
#endif
std::regex regex(
R"regex(path d='M \d+.\d+,\d+.\d+ L \d+.\d+,\d+.\d+ L \d+.\d+,\d+.\d+)regex");
auto match_count(
std::distance(std::sregex_iterator(text.begin(), text.end(), regex),
std::sregex_iterator()));
TEST_ASSERT(match_count == 3);
#endif
check_file_hash("test23_1.svg");
}
std::cerr << " Done" << std::endl;
}
void testGithub4496() {
std::cerr << " ----------------- Test draw aromatic OR queries" << std::endl;
auto m = "[c,n]1[c,n][c,n][c,n][c,n][c,n]1"_smarts;
MolDraw2DSVG drawer(200, 200);
MolDrawOptions options;
options.prepareMolsBeforeDrawing = false;
drawer.drawOptions() = options;
MolDraw2DUtils::prepareMolForDrawing(*m, false);
drawer.drawMolecule(*m);
drawer.finishDrawing();
std::ofstream outs("testGithub4496_1.svg");
std::string text = drawer.getDrawingText();
outs << text;
outs.flush();
outs.close();
check_file_hash("testGithub4496_1.svg");
std::cerr << " Done" << std::endl;
}
void testGithub5006() {
std::cerr << " ----------------- Test AND queries" << std::endl;
auto m = "[c,nH1]"_smarts;
MolDraw2DSVG drawer(200, 200);
drawer.drawMolecule(*m);
drawer.finishDrawing();
std::ofstream outs("testGithub5006_1.svg");
std::string text = drawer.getDrawingText();
#ifndef RDK_BUILD_FREETYPE_SUPPORT
TEST_ASSERT(text.find(">?</text>") != std::string::npos);
#endif
outs << text;
outs.flush();
outs.close();
check_file_hash("testGithub5006_1.svg");
std::cerr << " Done" << std::endl;
}
int main() {
#ifdef RDK_BUILD_COORDGEN_SUPPORT
RDDepict::preferCoordGen = false;
#endif
RDLog::InitLogs();
#if 1
test1();
test2();
test4();
test5();
test6();
test7();
test8PrepareMolForDrawing();
testMultiThreaded();
testGithub781();
test3();
testGithub774();
test9MolLegends();
testGithub852();
testGithub860();
testGithub910();
testGithub932();
testGithub953();
testGithub983();
testDeuteriumTritium();
testCrossedBonds();
test10DrawSecondMol();
test11DrawMolGrid();
test12DrawMols();
test13JSONConfig();
testGithub1090();
testGithub1035();
testGithub1271();
testGithub1322();
test14BWPalette();
test15ContinuousHighlightingWithGrid();
test17MaxMinFontSize();
testGithub1829();
test18FixedScales();
test19RotateDrawing();
test16MoleculeMetadata();
testGithub2063();
testGithub2151();
testGithub2762();
testGithub2931();
test20Annotate();
test21FontFile();
test22ExplicitMethyl();
testGithub3112();
testGithub3305();
testGithub3391();
testGithub4156();
test23JSONAtomColourPalette();
testGithub4496();
testGithub5006();
#endif
}
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