mirror of
https://github.com/rdkit/rdkit.git
synced 2026-06-04 21:54:27 +08:00
9249ca5cc8
* Make reaction drawings deal with padding properly. * Move large lambdas into anonymous namespace. Correct totWidth after scaling plusWidth. * Update some hashcodes. * Take out debugging setting. Bugger. * Padding on height as well. * Hash codes. * Delay padding use in flexiCanvas. * More centring. * Light grey background in side_by_side table. * Tweak agents layout for testReactionCoords. * Fully ignore missing reagents and products. * Hash codes. * Const references. --------- Co-authored-by: David Cosgrove <david@cozchemix.co.uk>
370 lines
14 KiB
C++
370 lines
14 KiB
C++
//
|
|
// Copyright (C) 2017 Greg Landrum
|
|
//
|
|
// @@ All Rights Reserved @@
|
|
// This file is part of the RDKit.
|
|
// The contents are covered by the terms of the BSD license
|
|
// which is included in the file license.txt, found at the root
|
|
// of the RDKit source tree.
|
|
//
|
|
|
|
#include <RDGeneral/test.h>
|
|
#include <RDGeneral/utils.h>
|
|
#include <RDGeneral/Invariant.h>
|
|
#include <RDGeneral/RDLog.h>
|
|
#include <GraphMol/RDKitBase.h>
|
|
#include <RDGeneral/hash/hash.hpp>
|
|
#include <GraphMol/SmilesParse/SmilesParse.h>
|
|
#include <GraphMol/ChemReactions/ReactionParser.h>
|
|
#include <GraphMol/ChemReactions/SanitizeRxn.h>
|
|
#include <GraphMol/Depictor/RDDepictor.h>
|
|
|
|
#include <RDGeneral/BoostStartInclude.h>
|
|
#include <boost/algorithm/string.hpp>
|
|
#include <boost/lexical_cast.hpp>
|
|
#include <RDGeneral/BoostEndInclude.h>
|
|
|
|
#include <GraphMol/MolDraw2D/MolDraw2D.h>
|
|
#include <GraphMol/MolDraw2D/MolDraw2DSVG.h>
|
|
#include <GraphMol/MolDraw2D/MolDraw2DUtils.h>
|
|
|
|
#include <iostream>
|
|
#include <fstream>
|
|
#include <sstream>
|
|
#include <iterator>
|
|
#include <map>
|
|
|
|
using namespace RDKit;
|
|
#ifdef RDK_BUILD_CAIRO_SUPPORT
|
|
#include <cairo.h>
|
|
#include "MolDraw2DCairo.h"
|
|
#endif
|
|
|
|
namespace {
|
|
|
|
// if the generated SVG hashes to the value we're expecting, delete
|
|
// the file. That way, only the files that need inspection will be
|
|
// left at the end of the run.
|
|
static const bool DELETE_WITH_GOOD_HASH = true;
|
|
#ifdef RDK_BUILD_FREETYPE_SUPPORT
|
|
static const std::map<std::string, std::hash_result_t> SVG_HASHES = {
|
|
{"rxn_test1_1.svg", 2645695747U}, {"rxn_test1_2.svg", 2640646320U},
|
|
{"rxn_test1_3.svg", 2781928588U}, {"rxn_test1_4.svg", 437863065U},
|
|
{"rxn_test1_5.svg", 2762972460U}, {"rxn_test1_6.svg", 3761578104U},
|
|
{"rxn_test1_7.svg", 1881564163U}, {"rxn_test2_1.svg", 3791815067U},
|
|
{"rxn_test2_2_1.svg", 2068242269U}, {"rxn_test2_2_2.svg", 269990608U},
|
|
{"rxn_test2_2_3.svg", 1544919807U}, {"rxn_test2_2_4.svg", 2015871327U},
|
|
{"rxn_test3_1.svg", 2165658826U}, {"rxn_test4_1.svg", 3239755313U},
|
|
{"rxn_test4_2.svg", 4127054729U},
|
|
};
|
|
#else
|
|
static const std::map<std::string, std::hash_result_t> SVG_HASHES = {
|
|
{"rxn_test1_1.svg", 1788608017U}, {"rxn_test1_2.svg", 823823509U},
|
|
{"rxn_test1_3.svg", 1377786051U}, {"rxn_test1_4.svg", 857944362U},
|
|
{"rxn_test1_5.svg", 4077811587U}, {"rxn_test1_6.svg", 3464747970U},
|
|
{"rxn_test1_7.svg", 2955631040U}, {"rxn_test2_1.svg", 706601656U},
|
|
{"rxn_test2_2_1.svg", 152711069U}, {"rxn_test2_2_2.svg", 1696961942U},
|
|
{"rxn_test2_2_3.svg", 4141786420U}, {"rxn_test2_2_4.svg", 793880456U},
|
|
{"rxn_test3_1.svg", 2145858565U}, {"rxn_test4_1.svg", 3386568263U},
|
|
{"rxn_test4_2.svg", 3251940560U},
|
|
};
|
|
#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
|
|
// rxn_test1_2.png rxn_test1_5.png rxn_test2_2_1.png rxn_test2_2_4.png
|
|
// rxn_test4_2.png rxn_test1_3.png rxn_test1_7.png rxn_test2_2_2.png
|
|
// rxn_test3_1.png rxn_test1_4.png rxn_test2_1.png rxn_test2_2_3.png
|
|
// rxn_test4_1.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 = {
|
|
{"rxn_test1_1.png", 1556334749U}, {"rxn_test1_2.png", 1924084263U},
|
|
{"rxn_test1_3.png", 1644921059U}, {"rxn_test1_4.png", 2471435686U},
|
|
{"rxn_test1_5.png", 1428782307U}, {"rxn_test1_6.png", 483353696U},
|
|
{"rxn_test1_7.png", 528963379U}, {"rxn_test2_1.png", 399415052U},
|
|
{"rxn_test2_2_1.png", 1215378243U}, {"rxn_test2_2_2.png", 3645141778U},
|
|
{"rxn_test2_2_3.png", 551946805U}, {"rxn_test2_2_4.png", 4234617566U},
|
|
{"rxn_test3_1.png", 4176857511U}, {"rxn_test4_1.png", 4187207676U},
|
|
{"rxn_test4_2.png", 3490081297U},
|
|
};
|
|
|
|
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 drawit(ChemicalReaction *rxn, std::string nameBase,
|
|
bool highlight_map = false,
|
|
const std::vector<DrawColour> *highlight_colors = nullptr) {
|
|
double panex = 200, paney = 150;
|
|
double width = panex * (rxn->getNumReactantTemplates() +
|
|
rxn->getNumProductTemplates() + 1);
|
|
double height = paney;
|
|
#ifdef RDK_BUILD_CAIRO_SUPPORT
|
|
{
|
|
MolDraw2DCairo drawer(width, height);
|
|
drawer.drawReaction(*rxn, highlight_map, highlight_colors);
|
|
drawer.finishDrawing();
|
|
drawer.writeDrawingText(nameBase + ".png");
|
|
check_file_hash(nameBase + ".png");
|
|
}
|
|
#endif
|
|
{
|
|
std::ofstream outs((nameBase + ".svg").c_str());
|
|
MolDraw2DSVG drawer(width, height, outs);
|
|
drawer.drawReaction(*rxn, highlight_map, highlight_colors);
|
|
drawer.finishDrawing();
|
|
outs.close();
|
|
check_file_hash(nameBase + ".svg");
|
|
}
|
|
}
|
|
} // namespace
|
|
|
|
void test1() {
|
|
std::cout << " ----------------- Test 1" << std::endl;
|
|
{
|
|
std::string smiles =
|
|
"[CH3:1][C:2](=[O:3])[OH:4].[CH3:5][NH2:6]>CC(O)C.[Pt]>[CH3:1][C:2](=["
|
|
"O:3])[NH:6][CH3:5].[OH2:4]";
|
|
std::string nameBase = "rxn_test1_1";
|
|
bool useSmiles = true;
|
|
ChemicalReaction *rxn =
|
|
RxnSmartsToChemicalReaction(smiles, nullptr, useSmiles);
|
|
TEST_ASSERT(rxn);
|
|
drawit(rxn, nameBase);
|
|
delete rxn;
|
|
}
|
|
{
|
|
std::string smiles =
|
|
"[N:1][C:2][C:3](=[O:4])[O:5].[N:6][C:7][C:8](=[O:9])[O:10]>>[N:1]1[C:"
|
|
"2][C:3](=[O:4])[N:6][C:7][C:8]1=[O:9].[O:5][O:10]";
|
|
std::string nameBase = "rxn_test1_2";
|
|
bool useSmiles = true;
|
|
ChemicalReaction *rxn =
|
|
RxnSmartsToChemicalReaction(smiles, nullptr, useSmiles);
|
|
TEST_ASSERT(rxn);
|
|
drawit(rxn, nameBase);
|
|
delete rxn;
|
|
}
|
|
{
|
|
std::string smiles =
|
|
">>[N:1]1[C:"
|
|
"2][C:3](=[O:4])[N:6][C:7][C:8]1=[O:9].[O:5][O:10]";
|
|
std::string nameBase = "rxn_test1_3";
|
|
bool useSmiles = true;
|
|
ChemicalReaction *rxn =
|
|
RxnSmartsToChemicalReaction(smiles, nullptr, useSmiles);
|
|
TEST_ASSERT(rxn);
|
|
drawit(rxn, nameBase);
|
|
delete rxn;
|
|
}
|
|
{
|
|
std::string smiles =
|
|
"[N:1][C:2][C:3](=[O:4])[O:5].[N:6][C:7][C:8](=[O:9])[O:10]>>";
|
|
std::string nameBase = "rxn_test1_4";
|
|
bool useSmiles = true;
|
|
ChemicalReaction *rxn =
|
|
RxnSmartsToChemicalReaction(smiles, nullptr, useSmiles);
|
|
TEST_ASSERT(rxn);
|
|
drawit(rxn, nameBase);
|
|
delete rxn;
|
|
}
|
|
{
|
|
std::string smiles =
|
|
"[N:1][C:2][C:3](=[O:4])[O:5].[N:6][C:7][C:8](=[O:9])[O:10]>O.ClCl>";
|
|
std::string nameBase = "rxn_test1_5";
|
|
bool useSmiles = true;
|
|
ChemicalReaction *rxn =
|
|
RxnSmartsToChemicalReaction(smiles, nullptr, useSmiles);
|
|
TEST_ASSERT(rxn);
|
|
drawit(rxn, nameBase);
|
|
delete rxn;
|
|
}
|
|
{
|
|
std::string smiles =
|
|
"[CH3:1][C:2](=[O:3])[OH:4].[CH3:5][NH2:6]>CC(O)C.[Pt]>[CH3:1][C:2](=["
|
|
"O:3])[NH:6][CH3:5].[OH2:4]";
|
|
std::string nameBase = "rxn_test1_6";
|
|
bool useSmiles = true;
|
|
ChemicalReaction *rxn =
|
|
RxnSmartsToChemicalReaction(smiles, nullptr, useSmiles);
|
|
TEST_ASSERT(rxn);
|
|
drawit(rxn, nameBase, true);
|
|
delete rxn;
|
|
}
|
|
{
|
|
// With the new code (Jan 2022) it appears that the 2nd reagent overlaps
|
|
// the + sign, but this is an optical illusion. Trust me :-).
|
|
std::string smiles =
|
|
"[N:1][C:2][C:3](=[O:4])[O:5].[N:6][C:7][C:8](=[O:9])[O:10]>>[N:1]1[C:"
|
|
"2][C:3](=[O:4])[N:6][C:7][C:8]1=[O:9].[O:5][O:10]";
|
|
std::string nameBase = "rxn_test1_7";
|
|
bool useSmiles = true;
|
|
ChemicalReaction *rxn =
|
|
RxnSmartsToChemicalReaction(smiles, nullptr, useSmiles);
|
|
TEST_ASSERT(rxn);
|
|
drawit(rxn, nameBase, true);
|
|
delete rxn;
|
|
}
|
|
std::cout << " Done" << std::endl;
|
|
}
|
|
|
|
void test2() {
|
|
std::cout << " ----------------- Test 2: some examples that caused problems "
|
|
"in testing"
|
|
<< std::endl;
|
|
{ // from the reaction role assignment paper
|
|
std::string smiles =
|
|
"[cH:5]1[cH:6][c:7]2[cH:8][n:9][cH:10][cH:11][c:12]2[c:3]([cH:4]1)[C:2]"
|
|
"(=[O:1])O.[N-:13]=[N+:14]=[N-:15]>C(Cl)Cl.C(=O)(C(=O)Cl)Cl>[cH:5]1["
|
|
"cH:6][c:7]2[cH:8][n:9][cH:10][cH:11][c:12]2[c:3]([cH:4]1)[C:2](=[O:1])"
|
|
"[N:13]=[N+:14]=[N-:15]";
|
|
std::string nameBase = "rxn_test2_1";
|
|
bool useSmiles = true;
|
|
ChemicalReaction *rxn =
|
|
RxnSmartsToChemicalReaction(smiles, nullptr, useSmiles);
|
|
TEST_ASSERT(rxn);
|
|
drawit(rxn, nameBase);
|
|
delete rxn;
|
|
}
|
|
{ // from Ed Griffen
|
|
// order is: SMIRKS substrate product
|
|
std::string indata =
|
|
"[cH:1]1[cH:2][cH:3][c:4][cH:5][cH:6]1>>CC(C)[c:1]1[cH:2][cH:3][c:4][cH:5][cH:6]1 CN1CCC(CC1)N(C)S(=O)(=O)c2ccccc2 CC(C)c1ccc(cc1)S(=O)(=O)N(C)C2CCN(CC2)C\n\
|
|
[cH:1]1[cH:2][cH:3][c:4][cH:5][cH:6]1>>[cH:3]1[cH:2][c:1]([cH:6][cH:5][c:4]1)Cl Cc1cccc(c1C)N2CCN(CC2)CCCNC(=O)c3cc([nH]c3C)c4ccccc4 Cc1cccc(c1C)N2CCN(CC2)CCCNC(=O)c3cc([nH]c3C)c4ccc(cc4)Cl\n\
|
|
Cc1c(cc([nH]1)[c:1]2[cH:2][cH:3][cH:4][cH:5][cH:6]2)[C:7](=[O:8])[NH:9][CH2:10][CH2:11]>>CCc1nc(c(n1[c:1]2[cH:2][cH:3][cH:4][cH:5][cH:6]2)C)[C:7](=[O:8])[NH:9][CH2:10][CH2:11] Cc1c(cc([nH]1)c2ccccc2)C(=O)NCCN3CCN(C\n\
|
|
C3)c4cccc(c4Cl)Cl CCc1nc(c(n1c2ccccc2)C)C(=O)NCCN3CCN(CC3)c4cccc(c4Cl)Cl\n\
|
|
[c:1][C:2](=[O:3])[NH:4]CCC[CH2:5][N:6]([CH2:7])[CH2:8]>>[c:1][C:2](=[O:3])[NH:4]C[CH2:5][N:6]([CH2:7])[CH2:8] CCCn1c(c(cc1c2ccccc2)C(=O)NCCCCN3CCN(CC3)c4cccc(c4Cl)Cl)C CCCn1c(c(cc1c2ccccc2)C(=O)NCCN3CCN(CC3)c4cccc(c4Cl)Cl)C\n\
|
|
[CH3:1]c1c(cc(n1[CH3:2])C(C)(C)C)[C:3]>>[CH3:2]c1c(c(nc(n1)[CH3:1])[C:3])OC Cc1cccc(c1C)N2CCN(CC2)CCNC(=O)c3cc(n(c3C)C)C(C)(C)C Cc1cccc(c1C)N2CCN(CC2)CCNC(=O)c3c(c(nc(n3)C)C)OC";
|
|
std::vector<std::string> lines;
|
|
boost::split(lines, indata, boost::is_any_of("\n"));
|
|
unsigned int idx = 0;
|
|
for (auto &line : lines) {
|
|
std::vector<std::string> tokens;
|
|
boost::split(tokens, line, boost::is_any_of("\t "));
|
|
std::cerr << tokens.size() << " " << line << std::endl;
|
|
if (tokens.size() > 2) {
|
|
++idx;
|
|
|
|
std::string nameBase = "rxn_test2_2_" + std::to_string(idx);
|
|
bool useSmiles = true;
|
|
ChemicalReaction *rxn =
|
|
RxnSmartsToChemicalReaction(tokens[0], nullptr, useSmiles);
|
|
TEST_ASSERT(rxn);
|
|
drawit(rxn, nameBase);
|
|
delete rxn;
|
|
}
|
|
}
|
|
}
|
|
std::cout << " Done" << std::endl;
|
|
}
|
|
|
|
void test3() {
|
|
std::cout << " ----------------- Test 3: test reactant highlighting"
|
|
<< std::endl;
|
|
{ // from the reaction role assignment paper
|
|
std::string smiles =
|
|
"[cH:5]1[cH:6][c:7]2[cH:8][n:9][cH:10][cH:11][c:12]2[c:3]([cH:4]1)[C:2]"
|
|
"(=[O:1])O.[N-:13]=[N+:14]=[N-:15]>C(Cl)Cl.C(=O)(C(=O)Cl)Cl>[cH:5]1["
|
|
"cH:6][c:7]2[cH:8][n:9][cH:10][cH:11][c:12]2[c:3]([cH:4]1)[C:2](=[O:1])"
|
|
"[N:13]=[N+:14]=[N-:15]";
|
|
std::string nameBase = "rxn_test3_1";
|
|
bool useSmiles = true;
|
|
ChemicalReaction *rxn =
|
|
RxnSmartsToChemicalReaction(smiles, nullptr, useSmiles);
|
|
TEST_ASSERT(rxn);
|
|
std::vector<DrawColour> highlight_colors;
|
|
highlight_colors.push_back(DrawColour(1., 1., .67));
|
|
highlight_colors.push_back(DrawColour(1., .71, .76));
|
|
highlight_colors.push_back(DrawColour(.8, 1., .8));
|
|
highlight_colors.push_back(DrawColour(.67, .67, 1.));
|
|
drawit(rxn, nameBase, true, &highlight_colors);
|
|
delete rxn;
|
|
}
|
|
std::cout << " Done" << std::endl;
|
|
}
|
|
|
|
void test4() {
|
|
std::cout << " ----------------- Test 4: some examples from SMARTS "
|
|
"in testing"
|
|
<< std::endl;
|
|
{ // from the reaction role assignment paper
|
|
std::string smiles =
|
|
"[cH:5]1[cH:6][c:7]2[cH:8][n:9][cH:10][cH:11][c:12]2[c:3]([cH:4]1)[C:2]"
|
|
"(=[O:1])O.[N-:13]=[N+:14]=[N-:15]>C(Cl)Cl.C(=O)(C(=O)Cl)Cl>[cH:5]1["
|
|
"cH:6][c:7]2[cH:8][n:9][cH:10][cH:11][c:12]2[c:3]([cH:4]1)[C:2](=[O:1])"
|
|
"[N:13]=[N+:14]=[N-:15]";
|
|
std::string nameBase = "rxn_test4_1";
|
|
bool useSmiles = false;
|
|
ChemicalReaction *rxn =
|
|
RxnSmartsToChemicalReaction(smiles, nullptr, useSmiles);
|
|
TEST_ASSERT(rxn);
|
|
std::cerr << "draw!" << std::endl;
|
|
drawit(rxn, nameBase, true);
|
|
std::cerr << " done" << std::endl;
|
|
delete rxn;
|
|
}
|
|
{ // from the reaction role assignment paper
|
|
std::string smiles =
|
|
"[CH3:16][CH2:15][c:14]1[c:7]([cH:6][c:5]([cH:22][c:17]1[O:18][CH2:19]["
|
|
"CH:20]=[CH2:21])[O:4][CH2:3][CH:2]=[CH2:1])[CH2:8][CH2:9][O:10][CH2:"
|
|
"11][CH2:12][O:13]C2CCCCO2.CO.C1COCCO1.C(=O)(O)[O-].O.[Na+].Cl>>[CH3:"
|
|
"16][CH2:15][c:14]1[c:7]([cH:6][c:5]([cH:22][c:17]1[O:18][CH2:19][CH:"
|
|
"20]=[CH2:21])[O:4][CH2:3][CH:2]=[CH2:1])[CH2:8][CH2:9][O:10][CH2:11]["
|
|
"CH2:12][OH:13]";
|
|
std::string nameBase = "rxn_test4_2";
|
|
bool useSmiles = false;
|
|
ChemicalReaction *rxn =
|
|
RxnSmartsToChemicalReaction(smiles, nullptr, useSmiles);
|
|
TEST_ASSERT(rxn);
|
|
drawit(rxn, nameBase, true);
|
|
delete rxn;
|
|
}
|
|
std::cout << " Done" << std::endl;
|
|
}
|
|
|
|
int main() {
|
|
RDLog::InitLogs();
|
|
#if 1
|
|
test1();
|
|
test2();
|
|
test3();
|
|
test4();
|
|
#endif
|
|
}
|