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rdkit/Code/GraphMol/MolDraw2D/test1.cpp

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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 <algorithm>
#include <cstdio>
#include <iosfwd>
#include <iostream>
#include <iterator>
#include <map>
#include <fstream>
#include <sstream>
#ifdef RDKIT_USE_BOOST_REGEX
#include <boost/regex.hpp>
using boost::regex;
using boost::regex_search;
#else
#include <regex>
using std::regex;
using std::regex_search;
#endif
// 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", 3113938861U},
{"test1_2.svg", 94669297U},
{"test1_3.svg", 2548256503U},
{"test1_4.svg", 2036254482U},
{"test1_5.svg", 787343273U},
{"test1_6.svg", 2725213945U},
{"test1_7.svg", 923829929U},
{"test4_1.svg", 1830084315U},
{"test5_1.svg", 4218143958U},
{"test5_2.svg", 1453910928U},
{"test5_3.svg", 3415240862U},
{"test6_1.svg", 1194058816U},
{"test6_2.svg", 3509581388U},
{"test6_3.svg", 2358886761U},
{"test7_1.svg", 602351070U},
{"test7_2.svg", 1022417818U},
{"testGithub781_1.svg", 3080997483U},
{"testGithub781_2.svg", 2164237918U},
{"testGithub781_3.svg", 3655151266U},
{"testGithub781_4.svg", 2963167941U},
{"testGithub781_5.svg", 2840696942U},
{"testGithub781_6.svg", 2469528418U},
{"test3_1.svg", 1621669208U},
{"test3_2.svg", 3739243117U},
{"test3_3.svg", 4209036462U},
{"test3_4.svg", 234934996U},
{"test3_5.svg", 715914516U},
{"test3_6.svg", 3806061398U},
{"test3_7.svg", 2511914961U},
{"test774_1.svg", 2641469654U},
{"test774_2.svg", 568348710U},
{"test9_1.svg", 1037255840U},
{"test852_1.svg", 158641809U},
{"test852_2.svg", 239253461U},
{"test852_2a.svg", 4270721163U},
{"test852_2b.svg", 786035561U},
{"test852_2c.svg", 263980967U},
{"test852_2d.svg", 3989607891U},
{"test860_1.svg", 150940515U},
{"test860_2.svg", 3354751138U},
{"test860_3.svg", 363558801U},
{"test910_1.svg", 1586190483U},
{"test910_2.svg", 1045945973U},
{"test983_1.svg", 3330975144U},
{"test983_2.svg", 152080733U},
{"testNoDeuterium.svg", 978533211U},
{"testNoTritium.svg", 1367911514U},
{"testDeuterium.svg", 4089922801U},
{"testTritium.svg", 3762235788U},
{"crossed_bonds.svg", 4064206667U},
{"test10_1.svg", 3323929696U},
{"test10_2.svg", 150233603U},
{"test10_3.svg", 1929234659U},
{"test10_4.svg", 1411925001U},
{"test10_5.svg", 1988570733U},
{"test10_6.svg", 3454197083U},
{"test11_1.svg", 352029742U},
{"test11_2.svg", 2223723861U},
{"test12_1.svg", 3993224976U},
{"test12_5.svg", 1004111871U},
{"test12_3.svg", 195908813U},
{"test12_4.svg", 195908813U},
{"test12_2.svg", 3671149443U},
{"test13_1.svg", 2742552224U},
{"testGithub1090_1.svg", 101922948U},
{"test1271_1.svg", 3344708082U},
{"test1271_2.svg", 3059809816U},
{"test1271_3.svg", 2354035380U},
{"test1271_4.svg", 2354035380U},
{"test1271_5.svg", 372064348U},
{"test1322_1.svg", 3135367689U},
{"test1322_2.svg", 4005358140U},
{"test14_1.svg", 3564456084U},
{"test14_2.svg", 3910116450U},
{"test15_1.svg", 1451152049U},
{"test15_2.svg", 897342575U},
{"test17_1.svg", 299659569U},
{"test17_2.svg", 4269918050U},
{"test17_3.svg", 3686942802U},
{"test17_4.svg", 1165258183U},
{"test18_1.svg", 2006926306U},
{"test18_2.svg", 1059521378U},
{"test18_3.svg", 2476234962U},
{"test18_4.svg", 2307905334U},
{"test18_5.svg", 3813135781U},
{"test18_6.svg", 4066225946U},
{"test18_7.svg", 2159645153U},
{"test19_1.svg", 1554391501U},
{"test19_2.svg", 2637911287U},
{"test16_1.svg", 3439177658U},
{"test16_2.svg", 3915356332U},
{"testGithub2063_1.svg", 2185501652U},
{"testGithub2063_2.svg", 2185501652U},
{"testGithub2151_1.svg", 3638120408U},
{"testGithub2151_2.svg", 3354257096U},
{"testGithub2762.svg", 168469294U},
{"testGithub2931_1.svg", 298969290U},
{"testGithub2931_2.svg", 922872904U},
{"testGithub2931_3.svg", 2823954159U},
{"test20_1.svg", 2394223373U},
{"test20_2.svg", 3739838435U},
{"test20_3.svg", 2641474171U},
{"test20_4.svg", 4249232030U},
{"test21_1.svg", 1074495878U},
{"test21_2.svg", 566215580U},
{"test22_1.svg", 2151815275U},
{"test22_2.svg", 2372731585U},
{"testGithub3112_1.svg", 2657556514U},
{"testGithub3112_2.svg", 2085437875U},
{"testGithub3112_3.svg", 1902029396U},
{"testGithub3112_4.svg", 3605529183U},
{"testGithub3305_1.svg", 2151815275U},
{"testGithub3305_2.svg", 3973016396U},
{"testGithub3305_3.svg", 1169182745U},
{"testGithub3305_4.svg", 715914516U},
{"testGithub3305_5.svg", 3377515019U},
{"testGithub3305_6.svg", 2803663571U},
{"testGithub3305_7.svg", 168127666U},
{"testGithub3391_1.svg", 2537248999U},
{"testGithub3391_2.svg", 3751504500U},
{"testGithub3391_3.svg", 2544939276U},
{"testGithub3391_4.svg", 327641375U},
{"testGithub4156_1.svg", 1849893282U},
{"testGithub4156_2.svg", 3547810764U},
{"test23_1.svg", 3900878023U},
{"testGithub4496_1.svg", 746049636U},
{"testGithub5006_1.svg", 484020409U},
};
#else
static const std::map<std::string, std::hash_result_t> SVG_HASHES = {
{"test1_1.svg", 17882343U},
{"test1_2.svg", 2018870875U},
{"test1_3.svg", 3929393842U},
{"test1_4.svg", 669955328U},
{"test1_5.svg", 939765106U},
{"test1_6.svg", 2581265326U},
{"test1_7.svg", 2259213431U},
{"test4_1.svg", 1180178511U},
{"test5_1.svg", 2366643605U},
{"test5_2.svg", 1453910928U},
{"test5_3.svg", 1107383262U},
{"test6_1.svg", 1119388153U},
{"test6_2.svg", 3509581388U},
{"test6_3.svg", 3890471193U},
{"test7_1.svg", 602351070U},
{"test7_2.svg", 1022417818U},
{"testGithub781_1.svg", 3207306052U},
{"testGithub781_2.svg", 654027269U},
{"testGithub781_3.svg", 1406186712U},
{"testGithub781_4.svg", 1077101569U},
{"testGithub781_5.svg", 2840696942U},
{"testGithub781_6.svg", 2700448827U},
{"test3_1.svg", 185347742U},
{"test3_2.svg", 630095031U},
{"test3_3.svg", 1227367667U},
{"test3_4.svg", 1100667496U},
{"test3_5.svg", 4259273141U},
{"test3_6.svg", 3300797533U},
{"test3_7.svg", 2337710286U},
{"test774_1.svg", 2100192513U},
{"test774_2.svg", 3451445580U},
{"test9_1.svg", 2594385297U},
{"test852_1.svg", 2585851230U},
{"test852_2.svg", 2002950078U},
{"test852_2a.svg", 1518484056U},
{"test852_2b.svg", 3993611607U},
{"test852_2c.svg", 1363089666U},
{"test852_2d.svg", 1651090742U},
{"test860_1.svg", 740240442U},
{"test860_2.svg", 3486368908U},
{"test860_3.svg", 3382493739U},
{"test910_1.svg", 727377666U},
{"test910_2.svg", 1953921556U},
{"test983_1.svg", 2884442763U},
{"test983_2.svg", 105610357U},
{"testNoDeuterium.svg", 1004401828U},
{"testNoTritium.svg", 2757848600U},
{"testDeuterium.svg", 2768836206U},
{"testTritium.svg", 1944598332U},
{"crossed_bonds.svg", 4064206667U},
{"test10_1.svg", 3330748573U},
{"test10_2.svg", 3864984751U},
{"test10_3.svg", 4107747066U},
{"test10_4.svg", 961927042U},
{"test10_5.svg", 1619495344U},
{"test10_6.svg", 2229853397U},
{"test11_1.svg", 3204552666U},
{"test11_2.svg", 443828916U},
{"test12_1.svg", 121561307U},
{"test12_5.svg", 2652536373U},
{"test12_3.svg", 2850489014U},
{"test12_4.svg", 2850489014U},
{"test12_2.svg", 1823632585U},
{"test13_1.svg", 3050327511U},
{"testGithub1090_1.svg", 3202892343U},
{"test1271_1.svg", 3344708082U},
{"test1271_2.svg", 3059809816U},
{"test1271_3.svg", 1332755355U},
{"test1271_4.svg", 1332755355U},
{"test1271_5.svg", 2751210223U},
{"test1322_1.svg", 3994558723U},
{"test1322_2.svg", 742631954U},
{"test14_1.svg", 2682635437U},
{"test14_2.svg", 34596589U},
{"test15_1.svg", 3343879210U},
{"test15_2.svg", 1080125425U},
{"test17_1.svg", 2021974679U},
{"test17_2.svg", 1982675305U},
{"test17_3.svg", 2726010452U},
{"test17_4.svg", 669144902U},
{"test18_1.svg", 623880911U},
{"test18_2.svg", 2829021357U},
{"test18_3.svg", 1981527496U},
{"test18_4.svg", 3856599456U},
{"test18_5.svg", 2285263698U},
{"test18_6.svg", 99755875U},
{"test18_7.svg", 992293488U},
{"test19_1.svg", 1710391789U},
{"test19_2.svg", 725512425U},
{"test16_1.svg", 3097818490U},
{"test16_2.svg", 4078512567U},
{"testGithub2063_1.svg", 108931418U},
{"testGithub2063_2.svg", 108931418U},
{"testGithub2151_1.svg", 519358907U},
{"testGithub2151_2.svg", 3102378492U},
{"testGithub2762.svg", 2006115844U},
{"testGithub2931_1.svg", 3001628989U},
{"testGithub2931_2.svg", 3664574077U},
{"testGithub2931_3.svg", 35507527U},
{"test20_1.svg", 2324941307U},
{"test20_2.svg", 457598277U},
{"test20_3.svg", 1187217942U},
{"test20_4.svg", 3479670855U},
{"test22_1.svg", 2151815275U},
{"test22_2.svg", 2026302466U},
{"testGithub3112_1.svg", 477831513U},
{"testGithub3112_2.svg", 1805767733U},
{"testGithub3112_3.svg", 3766118446U},
{"testGithub3112_4.svg", 244160302U},
{"testGithub3305_1.svg", 2151815275U},
{"testGithub3305_2.svg", 3973016396U},
{"testGithub3305_3.svg", 1169182745U},
{"testGithub3305_4.svg", 4259273141U},
{"testGithub3305_5.svg", 3128781134U},
{"testGithub3305_6.svg", 379495450U},
{"testGithub3305_7.svg", 2011619515U},
{"testGithub3391_1.svg", 4243890317U},
{"testGithub3391_2.svg", 3058304314U},
{"testGithub3391_3.svg", 1146107029U},
{"testGithub3391_4.svg", 1343702587U},
{"test23_1.svg", 1351566708U},
{"testGithub4496_1.svg", 4130500721U},
};
#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", 971078492U},
{"test2_2.png", 2496148757U},
{"test2_3.png", 2179746375U},
{"test3_1.png", 1170536022U},
{"test3_2.png", 1032821596U},
{"test3_3.png", 885386832U},
{"test3_4.png", 3688119914U},
{"test3_5.png", 687841644U},
{"test3_6.png", 777149828U},
{"test3_7.png", 1470346128U},
{"test4_1.png", 1519573413U},
{"test5_1.png", 4099878968U},
{"test5_2.png", 455957375U},
{"test5_3.png", 3369257680U},
{"test7_1.png", 1722944047U},
{"test7_2.png", 435326497U},
{"test774_1.png", 1512858255U},
{"test774_2.png", 1820438693U},
{"test852_1.png", 2239409891U},
{"test852_2.png", 4120574352U},
{"test860_1.png", 1123622564U},
{"test860_2.png", 821482019U},
{"test860_3.png", 3772870014U},
{"test20_1.png", 1671273091U},
{"test20_2.png", 4014074794U},
{"test20_3.png", 3118790846U},
{"test20_4.png", 3857678453U},
{"testGithub3305_1.png", 3055401857U},
{"testGithub3305_2.png", 1405637787U},
{"testGithub3305_3.png", 774264151U},
{"testGithub3305_4.png", 687841644U},
{"testGithub3305_5.png", 402607644U},
{"testGithub3305_6.png", 1157397108U},
{"testGithub3305_7.png", 2220979057U},
};
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);
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);
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);
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);
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);
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);
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);
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);
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);
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);
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);
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);
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);
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);
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);
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);
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);
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);
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);
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 270.1,148.0") !=
std::string::npos);
// start of first radical spot
TEST_ASSERT(
txt.find("<path class='atom-0' d='M 284.1,152.0 L 284.1,152.2") !=
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 191.5,116.9") !=
std::string::npos);
// start of first radical spot
TEST_ASSERT(txt.find("<path class='atom-1' d='M 43.1,192.1 L 43.1,192.3") !=
std::string::npos);
#else
TEST_ASSERT(
txt.find("<path class='bond-0 atom-0 atom-1' d='M 187.2,117.4") !=
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 118.3 143.0") !=
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 117.1 128.9") !=
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 34.7 194.4") !=
std::string::npos);
// start of l
TEST_ASSERT(txt.find("<path class='atom-3' d='M 43.7 77.3") !=
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 88.9 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);
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));
std::cout << dcoords << std::endl;
Point2D acoords = drawer.getDrawCoords(dcoords);
std::cout << acoords << std::endl;
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);
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");
// 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);
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);
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 74.0,85.5 L "
"25.1,120.7 L 19.1,110.3 Z' style='fill:#000000;") !=
std::string::npos);
#endif
#else
TEST_ASSERT(text.find("<path class='bond-1 atom-2 atom-4' d='M 125.6,110.7 "
"L 173.7,76.1 L 179.6,86.4 Z' "
"style='fill:#000000;fill-rule:evenodd;fill-opacity:"
"1;stroke:#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 104.2,117.6 "
"L 72.7,99.7 L 77.2,93.5 Z' style='fill:#000000;") !=
std::string::npos);
#endif
#else
TEST_ASSERT(text.find("<path class='bond-3 atom-2 atom-4' d='M 105.1,114.8 "
"L 74.0,97.2 L 78.4,91.0 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='246.6' 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='246.6' 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);
MolDraw2DUtils::prepareMolForDrawing(*m);
MolDraw2DSVG drawer(250, 200);
const char *json =
"{\"legendColour\":[1.0,0.5,1.0], \"rotate\": 90, "
"\"bondLineWidth\": 5}";
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 120.0,8.2 L "
"163.5,83.6'") != 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 119.8,8.2"
" L 162.1,81.5'") != 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");
}
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");
TEST_ASSERT(text.find("stroke:#FF7F7F;stroke-width:4.0px;") ==
std::string::npos);
}
{
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");
TEST_ASSERT(text.find("stroke:#FF7F7F;stroke-width:4.3px") !=
std::string::npos);
}
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 256.5 204.0") !=
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 252.7 199.4") !=
std::string::npos);
#endif
#else
TEST_ASSERT(text.find("font-size:53px") != 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 262.3 211.1") !=
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 166.6 92.6") !=
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;
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 283.2 121.9") !=
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 184.7 131.6") !=
std::string::npos);
#endif
#else
TEST_ASSERT(text.find("font-size:9px") != 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 72.1 176.7") !=
std::string::npos);
#endif
#else
TEST_ASSERT(text.find("font-size:10px") != 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 104.0 155.3") !=
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 73.3 168.9") !=
std::string::npos);
#endif
#else
TEST_ASSERT(text.find("font-size:10px") != 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 71.1 166.6") !=
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 74.2 169.9") !=
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 263.0 150.8") !=
std::string::npos);
#endif
#else
TEST_ASSERT(text.find("<text x='256.8' y='166.9' 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 140.6 273.8") !=
std::string::npos);
#endif
#else
TEST_ASSERT(text.find("<text x='139.8' y='286.4' 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();
TEST_ASSERT(text.find("<path class='bond-0 atom-0 atom-1' d='M "
"65.9,100.9 L 134.1,79.1'") != std::string::npos);
TEST_ASSERT(text.find("<path class='bond-1 atom-0 atom-2' d='M "
"69.7,107.5 L 9.1,72.5'") != std::string::npos);
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();
TEST_ASSERT(text.find("<path class='bond-0 atom-0 atom-1' d='M "
"65.9,100.9 L 134.1,79.1'") != std::string::npos);
TEST_ASSERT(text.find("<path class='bond-1 atom-0 atom-2' d='M "
"69.7,107.5 L 9.1,72.5'") != std::string::npos);
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();
TEST_ASSERT(text.find("stroke-width:2.0px") != std::string::npos);
TEST_ASSERT(text.find("stroke-width:3.0px") == std::string::npos);
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();
TEST_ASSERT(text.find("stroke-width:2.0px") == std::string::npos);
TEST_ASSERT(text.find("stroke-width:8.0px") != std::string::npos);
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();
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);
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);
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();
#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='242.6' cy='348.6' rx='9.9' ry='10.1' "
"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='242.6' cy='297.0' rx='9.8' ry='9.8' "
"class='atom-5' style='fill:none;stroke:#00FF00;") !=
std::string::npos);
#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();
#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='242.6' cy='348.2' rx='9.9' ry='9.9' "
"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='242.6' cy='296.7' rx='9.8' ry='9.8' "
"class='atom-5' style='fill:none;stroke:#00FF00;") !=
std::string::npos);
#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);
TEST_ASSERT(
text.find("<ellipse cx='242.6' cy='297.0' rx='9.8' ry='9.8' "
"class='atom-5' style='fill:none;stroke:#00FF00;") !=
std::string::npos);
#endif
check_file_hash("testGithub2931_3.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
TEST_ASSERT(text.find("<path class='legend' d='M 129.7 184.1") !=
std::string::npos);
#endif
#else
TEST_ASSERT(text.find("<text x='121.0' y='195.0' class='legend' "
"style='font-size:15px;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 121.3 190.2") !=
std::string::npos);
#endif
#else
TEST_ASSERT(text.find("<text x='113.8' y='195.0' 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' >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 1.0 186.1") !=
std::string::npos);
#endif
#else
TEST_ASSERT(text.find("<text x='-2.5' y='195.0' class='legend' "
"style='font-size:10px;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 74.8 180.4") !=
std::string::npos);
#endif
#else
TEST_ASSERT(text.find("<text x='68.9' y='187.5' 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_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 49.6 120.8") !=
std::string::npos);
#endif
#else
// first one of atom note 11
TEST_ASSERT(text.find("<text x='394.3' y='215.2' 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='note' d='M 273.3 236.3") !=
std::string::npos);
#endif
#else
// this is the (E)
TEST_ASSERT(text.find("<text x='260.4' y='232.0' class='note' "
"style='font-size:20px;font-style:normal;font-weight:"
"normal;fill-opacity:1;stroke:none;font-family:sans-"
"serif;text-anchor:start;fill:#000000' >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 159.1 177.0") !=
std::string::npos);
#endif
#else
// f of foolish
TEST_ASSERT(text.find("<text x='145.2' y='181.8' 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 19.8 48.3") !=
std::string::npos);
#endif
#else
// first one of atom note 11
TEST_ASSERT(text.find("<text x='157.7' y='86.1' 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);
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);
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();
TEST_ASSERT(text.find("stroke-width:4.1px") != std::string::npos);
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);
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
{
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();
TEST_ASSERT(text.find("stroke:#FF7F7F;stroke-width:2.7") !=
std::string::npos);
TEST_ASSERT(text.find("stroke:#FF7F7F;stroke-width:16.0px") ==
std::string::npos);
check_file_hash(nameBase + "4.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 + "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();
TEST_ASSERT(text.find("stroke:#FF7F7F;stroke-width:2.7") ==
std::string::npos);
TEST_ASSERT(text.find("stroke:#FF7F7F;stroke-width:16.0px") !=
std::string::npos);
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();
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);
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();
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);
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.
regex qry(
"<path class='atom-1' d='M 21.[0-9]*,75.[0-9]* L 21.[0-9]*,75.[0-9]*");
TEST_ASSERT(regex_search(text, qry));
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.
regex qry(
"<path class='atom-1' d='M 271.[0-9]*,75.[0-9]* L "
"271.[0-9]*,75.[0-9]*");
TEST_ASSERT(regex_search(text, qry));
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();
#ifdef RDK_BUILD_FREETYPE_SUPPORT
#if DO_TEST_ASSERT
TEST_ASSERT(text.find("' fill='#3366E5") != std::string::npos);
TEST_ASSERT(text.find("' fill='#E59900") != std::string::npos);
#endif
#else
TEST_ASSERT(text.find("fill:#3366E5") != std::string::npos);
TEST_ASSERT(text.find("fill:#E59900") != std::string::npos);
#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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