pub_soft/rdkit
3
0
Fork 0
mirror of https://github.com/rdkit/rdkit.git synced 2026-06-04 21:54:27 +08:00
Code Issues Packages Projects Releases Wiki Activity
Files
Release_2024_09
rdkit/Code/GraphMol/catch_canon.cpp
tadhurst-cdd ab5483dc51 Fix canonicalization of stereogroups (#7041) 
* atropisomer handling added

* fixed non-used variables,  linking directives

* BOOST LIB start/stop fixes, linking fix

* Fixes for RDKIT CI errors

* minimalLib fix

* changed vector<enum> for java builds

* check for extra chars in CIP labeling

* removed wrong deprecated message

* fix ostrstream output error?

* restored _ChiralAtomRank to lowercase first letter

* changes for merged master

* Fixed catch label for new Catch package

* update expected psql results

* get swig wrappers building

* restore MolFileStereochem to FileParsers

* fix java wrapper for reapplyMolBlockWedging

* test changes

* some suggestions

* move a couple functions out of Bond

* Merge branch 'master' into pr/atropisomers2

* merged master

* Renamed setStereoanyFromSquiggleBond

* atropisomers in cdxml, rationalize atrop wedging, stereoGroups in drawMol

* Merge branch 'master' into pr/specialQueries

* changes from previous PR

* Iclude false chiral

* rigorous enhnced stereo canoncalization

* Added more tests and clenup

* removed commented out code

* corrected init of SmilesWriteParams

* added MolFileStereoChem.h to the header files

* Renamed Rxn parser to MrvBlockToChemicalReaction

* To make catch2 work, and match the checksum

* Fixed Structchecker errors

* fix CI for DetermineBonds catch test

* error in catch_test for CI

* Allow custom  smileWriteParams  in GetMolLayers

* misnamed entry point

* ReactionFromMrvString change name

* remove adding writeParams to GetMolLayers

* make rigorous enhanced stereo the default, and fix tests

* only one abs group no longer needs Rigorous Enhanced treatment

* changed string_view to string in catch test

* Canonicalize Enhnaced Stereo only resturne unique smiles

* Now allows or and and groups together

* internal routines inside detail scope

* fix test error

* changed string back to string_view and fixed a CHECK

* Fixes for PR review tests

* Fix RDKit_Book.rst failure on build test

* fix xqm sql test

* updated expected files for cxsmiles_test

* Fixed removal of atom attrs

* Fixed tests after merge of master

* More efficient version of Stereo Groups Canonicalization

* Fixes for ctests

* removed debug code

* readded cipLabel test

* fix generalizedSubstruct/catch_tests.cpp error

* hueristics to improve speed

* Rationaized control of abs groups

* removed unused routine

* added rigorous stereo group treatment to test

* some suggested changes

* Changes per PR review and removed some changes to smiles

* Fixed CI errors

* changes per PR review

* more PR review vhanges and cleanup

* Fixed PSql PKL change

* changes as per PR review

* Restored error type for bad mols for canonicalizeStereoGroups and added a test

* Merge master and fix test in MolDraw2D

* Fix for randomize test error and other PR review comments

* Removed unsued variable to fix mac CI

* do not force aromatization in canonicalizeStereoGroups

* changes as per PR review

---------

Co-authored-by: greg landrum <greg.landrum@gmail.com>
2024-10-25 05:09:30 +02:00

1111 lines
41 KiB
C++
Raw Permalink Blame History

//
// Copyright (C) 2022 Greg Landrum and other RDKit contributors
//
// @@ All Rights Reserved @@
// This file is part of the RDKit.
// The contents are covered by the terms of the BSD license
// which is included in the file license.txt, found at the root
// of the RDKit source tree.
//
#include <catch2/catch_all.hpp>
#include <GraphMol/RDKitBase.h>
#include <GraphMol/StereoGroup.h>
#include <GraphMol/Chirality.h>
#include <GraphMol/new_canon.h>
#include <GraphMol/MolOps.h>
#include <GraphMol/Canon.h>
#include <GraphMol/test_fixtures.h>
#include <GraphMol/FileParsers/FileParsers.h>
#include <GraphMol/FileParsers/MolFileStereochem.h>
#include <GraphMol/FileParsers/MolSupplier.h>
#include <GraphMol/SmilesParse/SmilesParse.h>
#include <GraphMol/SmilesParse/SmilesWrite.h>
#include <GraphMol/SmilesParse/CanonicalizeStereoGroups.h>
#include <random>
using namespace RDKit;
TEST_CASE("chirality and canonicalization") {
SECTION("basics") {
auto mol = "F[C@](O)(Cl)C[C@](F)(O)Cl"_smiles;
REQUIRE(mol);
bool cleanIt = true;
bool force = true;
MolOps::assignStereochemistry(*mol, cleanIt, force);
std::string cip;
CHECK(mol->getAtomWithIdx(1)->getPropIfPresent(common_properties::_CIPCode,
cip));
CHECK(cip == "S");
CHECK(mol->getAtomWithIdx(5)->getPropIfPresent(common_properties::_CIPCode,
cip));
CHECK(cip == "R");
std::vector<unsigned int> ranks;
bool breakTies = false;
Canon::rankMolAtoms(*mol, ranks, breakTies);
CHECK(ranks[1] > ranks[5]);
mol->getAtomWithIdx(1)->clearProp(common_properties::_CIPCode);
mol->getAtomWithIdx(5)->clearProp(common_properties::_CIPCode);
Canon::rankMolAtoms(*mol, ranks, breakTies);
CHECK(ranks[1] > ranks[5]);
}
SECTION("same") {
auto mol = "F[C@](O)(Cl)C[C@](O)(F)Cl"_smiles;
REQUIRE(mol);
bool cleanIt = true;
bool force = true;
MolOps::assignStereochemistry(*mol, cleanIt, force);
std::string cip;
CHECK(mol->getAtomWithIdx(1)->getPropIfPresent(common_properties::_CIPCode,
cip));
CHECK(cip == "S");
CHECK(mol->getAtomWithIdx(5)->getPropIfPresent(common_properties::_CIPCode,
cip));
CHECK(cip == "S");
std::vector<unsigned int> ranks;
bool breakTies = false;
Canon::rankMolAtoms(*mol, ranks, breakTies);
CHECK(ranks[1] == ranks[5]);
mol->getAtomWithIdx(1)->clearProp(common_properties::_CIPCode);
mol->getAtomWithIdx(5)->clearProp(common_properties::_CIPCode);
Canon::rankMolAtoms(*mol, ranks, breakTies);
CHECK(ranks[1] == ranks[5]);
}
SECTION("dependent") {
auto mol = "F[C@](O)(Cl)[C@](F)(O)[C@](F)(O)Cl"_smiles;
REQUIRE(mol);
bool cleanIt = true;
bool force = true;
MolOps::assignStereochemistry(*mol, cleanIt, force);
std::string cip;
CHECK(mol->getAtomWithIdx(1)->getPropIfPresent(common_properties::_CIPCode,
cip));
CHECK(cip == "S");
CHECK(mol->getAtomWithIdx(7)->getPropIfPresent(common_properties::_CIPCode,
cip));
CHECK(cip == "R");
CHECK(mol->getAtomWithIdx(4)->getPropIfPresent(common_properties::_CIPCode,
cip));
CHECK(cip == "R");
std::vector<unsigned int> ranks;
bool breakTies = false;
Canon::rankMolAtoms(*mol, ranks, breakTies);
CHECK(ranks[1] > ranks[7]);
mol->getAtomWithIdx(1)->clearProp(common_properties::_CIPCode);
mol->getAtomWithIdx(4)->clearProp(common_properties::_CIPCode);
mol->getAtomWithIdx(7)->clearProp(common_properties::_CIPCode);
Canon::rankMolAtoms(*mol, ranks, breakTies);
CHECK(ranks[1] > ranks[7]);
}
SECTION("dependent non-chiral") {
auto mol = "F[C@](O)(Cl)[C@](F)(O)[C@](O)(F)Cl"_smiles;
REQUIRE(mol);
bool cleanIt = false;
bool force = true;
mol->getAtomWithIdx(4)->setChiralTag(Atom::ChiralType::CHI_TETRAHEDRAL_CCW);
MolOps::assignStereochemistry(*mol, cleanIt, force);
std::string cip;
CHECK(mol->getAtomWithIdx(1)->getPropIfPresent(common_properties::_CIPCode,
cip));
CHECK(cip == "S");
CHECK(mol->getAtomWithIdx(7)->getPropIfPresent(common_properties::_CIPCode,
cip));
CHECK(cip == "S");
std::vector<unsigned int> ranks;
bool breakTies = false;
Canon::rankMolAtoms(*mol, ranks, breakTies);
CHECK(ranks[1] == ranks[7]);
mol->getAtomWithIdx(1)->clearProp(common_properties::_CIPCode);
mol->getAtomWithIdx(7)->clearProp(common_properties::_CIPCode);
Canon::rankMolAtoms(*mol, ranks, breakTies);
CHECK(ranks[1] == ranks[7]);
}
SECTION("swap parity") {
auto mol = "F[C@](O)(Cl)C[C@@](O)(Cl)F"_smiles;
REQUIRE(mol);
bool cleanIt = false;
bool force = true;
MolOps::assignStereochemistry(*mol, cleanIt, force);
std::string cip;
CHECK(mol->getAtomWithIdx(1)->getPropIfPresent(common_properties::_CIPCode,
cip));
CHECK(cip == "S");
CHECK(mol->getAtomWithIdx(5)->getPropIfPresent(common_properties::_CIPCode,
cip));
CHECK(cip == "S");
std::vector<unsigned int> ranks;
bool breakTies = false;
Canon::rankMolAtoms(*mol, ranks, breakTies);
CHECK(ranks[1] == ranks[5]);
mol->getAtomWithIdx(1)->clearProp(common_properties::_CIPCode);
mol->getAtomWithIdx(5)->clearProp(common_properties::_CIPCode);
Canon::rankMolAtoms(*mol, ranks, breakTies);
CHECK(ranks[1] == ranks[5]);
}
}
TEST_CASE("double bond stereo and canonicalization") {
SECTION("basics") {
auto mol = "CC=C(F)C(B)C(F)=CC"_smiles;
REQUIRE(mol);
mol->getBondWithIdx(1)->setStereoAtoms(0, 4);
mol->getBondWithIdx(1)->setStereo(Bond::BondStereo::STEREOTRANS);
mol->getBondWithIdx(7)->setStereoAtoms(4, 9);
mol->getBondWithIdx(7)->setStereo(Bond::BondStereo::STEREOCIS);
bool breakTies = false;
std::vector<unsigned int> ranks;
Canon::rankMolAtoms(*mol, ranks, breakTies);
mol->getBondWithIdx(1)->setStereo(Bond::BondStereo::STEREOCIS);
mol->getBondWithIdx(7)->setStereo(Bond::BondStereo::STEREOTRANS);
std::vector<unsigned int> ranks2;
Canon::rankMolAtoms(*mol, ranks2, breakTies);
CHECK(ranks[0] == ranks2[9]);
CHECK(ranks[1] == ranks2[8]);
CHECK(ranks[2] == ranks2[6]);
CHECK(ranks[3] == ranks2[7]);
CHECK(ranks[4] == ranks2[4]);
CHECK(ranks[5] == ranks2[5]);
// same as previous example, different controlling atoms
mol->getBondWithIdx(7)->setStereoAtoms(7, 9);
mol->getBondWithIdx(7)->setStereo(Bond::BondStereo::STEREOCIS);
std::vector<unsigned int> ranks3;
Canon::rankMolAtoms(*mol, ranks3, breakTies);
CHECK(ranks2 == ranks3);
}
SECTION("STEREOANY is higher priority than STEREONONE") {
auto mol = "CC=C(F)C(B)C(F)=CC"_smiles;
REQUIRE(mol);
mol->getBondWithIdx(7)->setStereoAtoms(4, 9);
mol->getBondWithIdx(7)->setStereo(Bond::BondStereo::STEREOANY);
bool breakTies = false;
std::vector<unsigned int> ranks;
Canon::rankMolAtoms(*mol, ranks, breakTies);
CHECK(ranks[0] < ranks[9]);
}
}
TEST_CASE("enhanced stereo canonicalization") {
SECTION("simple chiral tags") {
std::vector<std::pair<std::string, std::string>> tests = {
{"C[C@H](F)Cl |&1:1|", "C[C@@H](F)Cl |&1:1|"},
{"C[C@H](F)Cl |o1:1|", "C[C@@H](F)Cl |o1:1|"},
};
for (const auto &[smi1, smi2] : tests) {
INFO(smi1 + " : " + smi2);
std::unique_ptr<RWMol> mol1{SmilesToMol(smi1)};
REQUIRE(mol1);
std::unique_ptr<RWMol> mol2{SmilesToMol(smi2)};
REQUIRE(mol2);
Canon::canonicalizeEnhancedStereo(*mol1);
Canon::canonicalizeEnhancedStereo(*mol2);
CHECK(mol1->getAtomWithIdx(1)->getChiralTag() ==
mol2->getAtomWithIdx(1)->getChiralTag());
}
}
SECTION("abs groups are not modified") {
std::vector<std::pair<std::string, std::string>> tests = {
{"C[C@H](F)Cl |a:1|", "C[C@@H](F)Cl |a:1|"},
};
for (const auto &[smi1, smi2] : tests) {
INFO(smi1 + " : " + smi2);
std::unique_ptr<RWMol> mol1{SmilesToMol(smi1)};
REQUIRE(mol1);
std::unique_ptr<RWMol> mol2{SmilesToMol(smi2)};
REQUIRE(mol2);
Canon::canonicalizeEnhancedStereo(*mol1);
Canon::canonicalizeEnhancedStereo(*mol2);
CHECK(mol1->getAtomWithIdx(1)->getChiralTag() !=
mol2->getAtomWithIdx(1)->getChiralTag());
}
}
SECTION("relative chiral tags") {
std::vector<std::pair<std::string, std::string>> tests = {
{"C[C@H](F)[C@H](Br)O |&1:1,3|", "C[C@@H](F)[C@@H](Br)O |&1:1,3|"},
{"C[C@H](F)[C@@H](Br)O |&1:1,3|", "C[C@@H](F)[C@H](Br)O |&1:1,3|"},
{"O[C@H](Br)[C@H](F)C |&1:1,3|", "O[C@@H](Br)[C@@H](F)C |&1:1,3|"},
{"O[C@H](Br)[C@@H](F)C |&1:1,3|", "O[C@@H](Br)[C@H](F)C |&1:1,3|"},
};
for (const auto &[smi1, smi2] : tests) {
INFO(smi1 + " : " + smi2);
std::unique_ptr<RWMol> mol1{SmilesToMol(smi1)};
REQUIRE(mol1);
std::unique_ptr<RWMol> mol2{SmilesToMol(smi2)};
REQUIRE(mol2);
Canon::canonicalizeEnhancedStereo(*mol1);
Canon::canonicalizeEnhancedStereo(*mol2);
CHECK(mol1->getAtomWithIdx(1)->getChiralTag() ==
mol2->getAtomWithIdx(1)->getChiralTag());
CHECK(mol1->getAtomWithIdx(3)->getChiralTag() ==
mol2->getAtomWithIdx(3)->getChiralTag());
}
}
SECTION("multiple groups") {
std::vector<std::pair<std::string, std::string>> tests = {
{"C[C@H](F)[C@H](Br)O |&1:1,o2:3|",
"C[C@@H](F)[C@@H](Br)O |&1:1,o2:3|"},
{"C[C@H](F)[C@H](Br)O |&1:1,o2:3|",
"C[C@@H](F)[C@@H](Br)O |o1:3,&1:1|"},
};
for (const auto &[smi1, smi2] : tests) {
INFO(smi1 + " : " + smi2);
std::unique_ptr<RWMol> mol1{SmilesToMol(smi1)};
REQUIRE(mol1);
std::unique_ptr<RWMol> mol2{SmilesToMol(smi2)};
REQUIRE(mol2);
Canon::canonicalizeEnhancedStereo(*mol1);
Canon::canonicalizeEnhancedStereo(*mol2);
CHECK(mol1->getAtomWithIdx(1)->getChiralTag() ==
mol2->getAtomWithIdx(1)->getChiralTag());
CHECK(mol1->getAtomWithIdx(3)->getChiralTag() ==
mol2->getAtomWithIdx(3)->getChiralTag());
}
}
}
TEST_CASE("chiralRandomTest") {
SECTION("chiralRandomTest") {
std::vector<std::string> tests = {
"CNC(=O)[C@@H](NC(=O)[C@H](OCc1cc(F)ccc1F)[C@@H](O)[C@@H](O)[C@H](OCc1cc(F)ccc1F)C(=O)N[C@H](C(=O)NC)C(C)C)C(C)C |o1:19,23,&1:8,37|",
"CNC(=O)C(NC(=O)[C@H](OCc1ccccc1)[C@@H](O)[C@@H](O)[C@H](OCc1ccccc1)C(=O)NC(C(=O)NC)[C@@H](C)O)[C@H](C)O o1:38,41,&1:17,21|",
"CCC(=O)NC[C@H]1CN(c2cc(F)c(N3C[C@H]4[C@H](N)[C@H]4C3)c(F)c2)C(=O)O1 |o1:16,17,&1:6,19|",
"Cc1cc(O)c([C@@]2(C)CC[C@@H]3C[C@@]32C)cc1-c1cc([C@]2(C)CC[C@H]3C[C@@]32C)c(O)cc1C |o1:6,23,&1:19,25|",
"C[N+]12CC[C@@]34c5ccccc5N5[C@@H]6OCC=C7C[N+]8(C)CC[C@]9%10c%11ccccc%11N([C@@H]%11OCC=C(C1)[C@H](C[C@@H]32)[C@@H]%11[C@H]54)[C@H]9[C@H]6[C@H]7C[C@@H]%108.[Cl-].[Cl-] |o1:42,45,&1:22,41|",
"Cl.Oc1ccc2c3c1O[C@H]1c4[nH]c5c(c4C[C@@]4(O)[C@@H](C2)N(CC2CC2)CC[C@]314)C[C@]1(O)[C@H]2Cc3ccc(O)c4c3[C@]1(CCN2CC1CC1)[C@H]5O4 |o1:29,40,&1:16,48|",
"O=C1NC(=O)c2c1c1c3ccccc3n3c1c1c2c2ccccc2n1[C@@H]1[C@H](O)[C@H](O)[C@H](O)[C@H]3N1Cc1ccccc1 |o1:26,32,&1:25,30|",
"CC1=C(N2C=CC=C2[C@H](C)Cl)C(C)CCC1 |(2.679,0.4142,;1.3509,1.181,;0.0229,0.4141,;0.0229,-1.1195,;1.2645,-2.0302,;0.7901,-3.4813,;-0.7446,-3.4813,;-1.219,-2.0302,;-2.679,-1.5609,;-3.0039,-0.0556,;-3.8202,-2.595,;-1.3054,1.1809,;-2.6335,0.4141,;-1.3054,2.7145,;0.0229,3.4813,;1.3509,2.7146,),wD:2.11,wU:8.10,&1:8|",
"O=C(CCCc1ccccc1)OC[C@H]1C[C@@H]2O[C@H]1[C@@H]1[C@H]2C(=O)OC1=O |a:18,19,o1:13,15,17|",
"CC1=CC[C@H]2[C@H](C1)c1c(O)cc(C=C3C4CC5CC(C4)CC3C5)cc1OC2(C)C |&1:4,5|",
"O=C(O)C(F)(F)F.O=C(O)[C@@]1(N(CCn2cnc3ncncc32)S(=O)(=O)c2ccc(-c3ccc(Cl)cc3)cc2)C[C@H]1c1ccccc1 |o1:10,40|",
"CCCCNC1N[C@H](CO)[C@@H](O)[C@@H](O)[C@H](CO)N1 |a:12,&2:10,&1:7,14|",
"CCCCNC1N[C@H](CO)[C@@H](O)[C@@H](O)[C@H](CO)N1 |a:10,12,&1:7,14|",
"CCCCNC1N[C@H](CO)C(O)[C@@H](O)[C@H](CO)N1 |a:12,&1:7,14|",
"CCNC(=O)c1ccc(/C(=C2/C[C@H]3CC[C@@H](C2)N3CCc2ccccc2)c2ccccc2)cc1 |&1:12,15|",
"C[C@H](O)[C@@H](C)[C@H](C)[C@H](C)O |&1:1,&2:3,5,&3:7|",
"C[C@@H](Cl)C[C@H](C)Cl |a:1,4,|",
"C[C@H](Cl)C[C@@H](C)Cl |a:1,4,|",
"N[C@H]1CC[C@@H](O)CC1 |a:1,4|",
"N[C@H]1CC[C@@H](O)CC1 |a:1,4|",
"N[C@H]1CC[C@@H](O)CC1 |a:1,4|",
"N[C@H]1CC[C@@H](O)CC1 |a:1,4|",
"N[C@H]1CC[C@@H](O)CC1 |a:1,4|",
"C[C@H]1CC[C@H](CC1)C1CC(CC(C1)[C@@H]1CC[C@H](C)CC1)[C@@H]1CC[C@H](C)CC1 |o1:23,o2:20,o3:13,o4:16,o5: ,&6:1|",
"C[C@H]1CC[C@H](CC1)C1CC(CC(C1)[C@@H]1CC[C@H](C)CC1)[C@@H]1CC[C@H](C)CC1 |o1:23,o2:20,o3:13,o4:16,o5:4,o6:1|",
"C[C@H]1CC[C@@H](C[C@@H]2CC[C@H](C)CC2)CC1 |a:9,o1:6,&1:4,&2:1|",
"C[C@H]1CC[C@@H](C[C@@H]2CC[C@H](C)CC2)CC1 |o1:6,o2:1,9,o3:4|",
"C[C@H]1CC[C@@H](C[C@@H]2CC[C@H](C)CC2)CC1 |o1:6,o2:1,9,o3:4|",
"N[C@H]1CC[C@@H](O)CC1",
"N[C@H]1CC[C@@H](O)CC1 |o2:1,4|",
"N[C@H]1CC[C@@H](O)CC1 |&2:1,4|",
"N[C@H]1CC[C@@H](O)CC1 |a:1,4|",
// no enhanced stereo
"CC(C)[C@H]1CCCCN1C(=O)[C@H]1CC[C@@H](C)CC1",
// enhance stereo abs,abs,abs
"CC(C)[C@H]1CCCCN1C(=O)[C@H]1CC[C@@H](C)CC1 |a:3,11,14|",
// abs, abs, or and abs, or abs
"CC(C)[C@H]1CCCCN1C(=O)[C@H]1CC[C@@H](C)CC1 |a:3,11,o1:14|",
"CC(C)[C@H]1CCCCN1C(=O)[C@H]1CC[C@@H](C)CC1 |a:3,11,o1:14|",
"CC(C)[C@H]1CCCCN1C(=O)[C@H]1CC[C@@H](C)CC1 |a:3,11,o1:14|",
"CC(C)[C@H]1CCCCN1C(=O)[C@H]1CC[C@@H](C)CC1 |a:3,11,&1:14|",
"CC(C)[C@H]1CCCCN1C(=O)[C@H]1CC[C@@H](C)CC1 |a:3,11,&1:14|",
"CC(C)[C@H]1CCCCN1C(=O)[C@H]1CC[C@@H](C)CC1 |a:3,11,&1:14|",
};
UseLegacyStereoPerceptionFixture reset_stereo_perception{false};
for (const auto &smi1 : tests) {
INFO(smi1);
SmilesParserParams rps;
rps.sanitize = true;
rps.removeHs = false;
std::unique_ptr<ROMol> mol1{SmilesToMol(smi1, rps)};
REQUIRE(mol1);
std::vector<unsigned int> idxV(mol1->getNumAtoms());
for (unsigned int i = 0; i < mol1->getNumAtoms(); ++i) {
idxV[i] = i;
}
std::string smiExpected = "";
auto randomGen = std::mt19937(0xf00d);
for (auto i = 0; i < 100; ++i) {
std::vector<unsigned int> nVect(idxV);
if (i > 0) {
std::shuffle(nVect.begin(), nVect.end(), randomGen);
}
std::unique_ptr<ROMol> nmol{MolOps::renumberAtoms(*mol1, nVect)};
RDKit::canonicalizeStereoGroups(nmol);
auto outSmi1 = MolToCXSmiles(*nmol);
if (smiExpected == "") {
smiExpected = outSmi1;
} else {
CHECK(outSmi1 == smiExpected);
}
}
}
}
}
TEST_CASE("pseudoTestCanonFailure") {
SECTION("canonFailure") {
UseLegacyStereoPerceptionFixture reset_stereo_perception{false};
std::string smi1 = "C[C@H]1CC[C@@H](C[C@@H]2CC[C@H](C)CC2)CC1 |&1:4,&2:1|";
SmilesParserParams rps;
rps.sanitize = true;
rps.removeHs = false;
std::unique_ptr<ROMol> mol1{SmilesToMol(smi1, rps)};
REQUIRE(mol1);
std::vector<unsigned int> idxV(mol1->getNumAtoms());
for (unsigned int i = 0; i < mol1->getNumAtoms(); ++i) {
idxV[i] = i;
}
auto randomGen = std::mt19937(0xf00d);
std::vector<unsigned int> nVect(idxV);
std::shuffle(nVect.begin(), nVect.end(), randomGen);
std::unique_ptr<ROMol> nmol{MolOps::renumberAtoms(*mol1, nVect)};
RDKit::canonicalizeStereoGroups(mol1);
RDKit::canonicalizeStereoGroups(nmol);
SmilesWriteParams wp;
wp.canonical = false;
auto outSmi1Check = MolToCXSmiles(*mol1, wp);
auto outSmi1Check2 = MolToCXSmiles(*nmol, wp);
CHECK(outSmi1Check == outSmi1Check2);
wp.canonical = true;
outSmi1Check = MolToCXSmiles(*mol1, wp);
outSmi1Check2 = MolToCXSmiles(*nmol, wp);
CHECK(outSmi1Check == outSmi1Check2);
}
}
TEST_CASE("pseudoTest1") {
SECTION("pseudoTest1") {
std::vector<std::tuple<std::string, std::string, std::string>> tests = {
{"CC1=C(N2C=CC=C2[C@H](C)Cl)C(C)CCC1 |(2.679,0.4142,;1.3509,1.181,;0.0229,0.4141,;0.0229,-1.1195,;1.2645,-2.0302,;0.7901,-3.4813,;-0.7446,-3.4813,;-1.219,-2.0302,;-2.679,-1.5609,;-3.0039,-0.0556,;-3.8202,-2.595,;-1.3054,1.1809,;-2.6335,0.4141,;-1.3054,2.7145,;0.0229,3.4813,;1.3509,2.7146,),wD:2.11,wU:8.10,&1:8|",
"CC1=C(N2C=CC=C2[C@H](C)Cl)C(C)CCC1 |(2.679,0.4142,;1.3509,1.181,;0.0229,0.4141,;0.0229,-1.1195,;1.2645,-2.0302,;0.7901,-3.4813,;-0.7446,-3.4813,;-1.219,-2.0302,;-2.679,-1.5609,;-3.0039,-0.0556,;-3.8202,-2.595,;-1.3054,1.1809,;-2.6335,0.4141,;-1.3054,2.7145,;0.0229,3.4813,;1.3509,2.7146,),wD:2.11,wU:8.10,a:2,&1:8|",
"CC1=C(n2cccc2[C@H](C)Cl)C(C)CCC1 |(2.679,0.4142,;1.3509,1.181,;0.0229,0.4141,;0.0229,-1.1195,;1.2645,-2.0302,;0.7901,-3.4813,;-0.7446,-3.4813,;-1.219,-2.0302,;-2.679,-1.5609,;-3.0039,-0.0556,;-3.8202,-2.595,;-1.3054,1.1809,;-2.6335,0.4141,;-1.3054,2.7145,;0.0229,3.4813,;1.3509,2.7146,),wD:8.9,2.11,a:2,&1:8|"},
{"O=C(CCCc1ccccc1)OC[C@H]1C[C@@H]2O[C@H]1[C@@H]1[C@H]2C(=O)OC1=O |a:18,19,o1:13,15,17|",
"O=C(CCCc1ccccc1)OC[C@@H]1C[C@H]2O[C@@H]1[C@@H]1[C@H]2C(=O)OC1=O |a:18,19,o1:13,15,17|",
"O=C(CCCc1ccccc1)OC[C@@H]1C[C@H]2O[C@@H]1[C@H]1C(=O)OC(=O)[C@H]12 |a:18,24,o1:13,15,17|"},
{"CC1=CC[C@H]2[C@H](C1)c1c(O)cc(C=C3C4CC5CC(C4)CC3C5)cc1OC2(C)C |&1:4,5|",
"CC1=CC[C@@H]2[C@@H](C1)c1c(O)cc(C=C3C4CC5CC(C4)CC3C5)cc1OC2(C)C |&1:4,5|",
"CC1=CC[C@H]2[C@H](C1)c1c(O)cc(C=C3C4CC5CC(C4)CC3C5)cc1OC2(C)C |&1:4,5|"},
{"O=C(O)C(F)(F)F.O=C(O)[C@@]1(N(CCn2cnc3ncncc32)S(=O)(=O)c2ccc(-c3ccc(Cl)cc3)cc2)C[C@H]1c1ccccc1 |o1:10,40|",
"O=C(O)[C@@]1(N(CCn2cnc3ncncc32)S(=O)(=O)c2ccc(-c3ccc(Cl)cc3)cc2)C[C@H]1c1ccccc1.O=C(O)C(F)(F)F |o1:3,33|",
"O=C(O)C(F)(F)F.O=C(O)[C@@]1(N(CCn2cnc3ncncc32)S(=O)(=O)c2ccc(-c3ccc(Cl)cc3)cc2)C[C@H]1c1ccccc1 |o1:10,40|"},
{"CCCCNC1N[C@H](CO)[C@@H](O)[C@@H](O)[C@H](CO)N1 |a:12,&2:10,&1:7,14|",
"CCCCNC1N[C@@H](CO)[C@H](O)[C@H](O)[C@@H](CO)N1 |a:7,14,&1:10,&2:12|",
"CCCCNC1N[C@@H](CO)[C@H](O)[C@H](O)[C@@H](CO)N1 |a:7,14,&1:10,&2:12|"},
{"CCCCNC1N[C@H](CO)[C@@H](O)[C@@H](O)[C@H](CO)N1 |a:10,12,&1:7,14|",
"CCCCNC1N[C@@H](CO)[C@@H](O)[C@@H](O)[C@@H](CO)N1 |a:10,12,&1:7,14|",
"CCCCNC1N[C@@H](CO)[C@H](O)[C@H](O)[C@@H](CO)N1 |a:7,14,&1:10,12|"},
{"CCCCNC1N[C@H](CO)C(O)[C@@H](O)[C@H](CO)N1 |a:12,&1:7,14|",
"CCCCNC1N[C@@H](CO)C(O)[C@@H](O)[C@@H](CO)N1 |a:12,&1:7,14|",
"CCCCNC1N[C@H](CO)C(O)[C@@H](O)[C@H](CO)N1 |a:12,&1:7,14|"},
{"CCNC(=O)c1ccc(/C(=C2/C[C@H]3CC[C@@H](C2)N3CCc2ccccc2)c2ccccc2)cc1 |&1:12,15|",
"CCNC(=O)c1ccc(\\C(=C2/C[C@@H]3CC[C@H](C2)N3CCc2ccccc2)c2ccccc2)cc1 |&1:12,15|",
"CCNC(=O)c1ccc(/C(=C2/C[C@H]3CC[C@@H](C2)N3CCc2ccccc2)c2ccccc2)cc1"},
{"C[C@H](O)[C@@H](C)[C@H](C)[C@H](C)O |&1:1,&2:3,5,&3:7|",
"C[C@H](O)[C@H](C)[C@@H](C)[C@H](C)O |&1:1,&2:3,5,&3:7|",
"C[C@H](O)[C@H](C)[C@@H](C)[C@H](C)O |&1:1,&2:3,5,&3:7|"},
{"C[C@@H](Cl)C[C@H](C)Cl |a:1,4,|", "C[C@@H](Cl)C[C@H](C)Cl |o1:1,4,|",
"C[C@H](Cl)C[C@@H](C)Cl"},
{"C[C@H](Cl)C[C@@H](C)Cl |a:1,4,|", "C[C@@H](Cl)C[C@H](C)Cl |&1:1,4,|",
"C[C@H](Cl)C[C@@H](C)Cl"},
{"N[C@H]1CC[C@@H](O)CC1 |a:1,4|", "N[C@H]1CC[C@@H](O)CC1 |o1:1,4|",
"N[C@@H]1CC[C@H](O)CC1"},
{"N[C@H]1CC[C@@H](O)CC1 |a:1,4|", "N[C@H]1CC[C@@H](O)CC1 |&1:1,4|",
"N[C@@H]1CC[C@H](O)CC1"},
{"N[C@H]1CC[C@@H](O)CC1 |a:1,4|", "N[C@@H]1CC[C@H](O)CC1 |a:1,4|",
"N[C@@H]1CC[C@H](O)CC1"},
{"N[C@H]1CC[C@@H](O)CC1 |a:1,4|", "N[C@@H]1CC[C@H](O)CC1 |o1:1,4|",
"N[C@@H]1CC[C@H](O)CC1"},
{"N[C@H]1CC[C@@H](O)CC1 |a:1,4|", "N[C@@H]1CC[C@H](O)CC1 |&1:1,4|",
"N[C@@H]1CC[C@H](O)CC1"},
// {"C[C@H]1C[C@@H](C)C[C@@H](C)C1 |o1:1,o2:6,o3:3|",
// "C[C@@H]1C[C@H](C)C[C@@H](C)C1 |a:3,o1:6,o3:1|",
// "CC1CC(C)CC(C)C1"}, // this excercises a bug in the new canon -
// these
// // are ring stereo atoms but the chiral
// markers
// // are removed!
{"C[C@H]1CC[C@H](CC1)C1CC(CC(C1)[C@@H]1CC[C@H](C)CC1)[C@@H]1CC[C@H](C)CC1 |o1:23,o2:20,o3:13,o4:16,o5:4,&6:1|",
"C[C@H]1CC[C@@H](CC1)C1CC(CC(C1)[C@H]1CC[C@H](C)CC1)[C@H]1CC[C@H](C)CC1 |a:1,13,20,o2:4,o6:16,&4:23|",
"C[C@H]1CC[C@@H](C2CC([C@@H]3CC[C@H](C)CC3)CC([C@@H]3CC[C@H](C)CC3)C2)CC1 |a:4,8,17,o1:1,o2:11,&1:20|"},
{"C[C@H]1CC[C@H](CC1)C1CC(CC(C1)[C@@H]1CC[C@H](C)CC1)[C@@H]1CC[C@H](C)CC1 |o1:23,o2:20,o3:13,o4:16,o5:4,o6:1|",
"C[C@H]1CC[C@@H](CC1)C1CC(CC(C1)[C@H]1CC[C@H](C)CC1)[C@H]1CC[C@H](C)CC1 |a:4,13,23,o2:20,o4:16,o6:1|",
"C[C@H]1CC[C@@H](C2CC([C@@H]3CC[C@H](C)CC3)CC([C@@H]3CC[C@H](C)CC3)C2)CC1 |a:4,8,17,o1:1,o2:11,o3:20|"},
{"C[C@H]1CC[C@@H](C[C@@H]2CC[C@H](C)CC2)CC1 |a:9,o1:6,&1:4,&2:1|",
"C[C@H]1CC[C@H](C[C@H]2CC[C@H](C)CC2)CC1 |a:4,9,&1:6,o2:1|",
"C[C@H]1CC[C@H](C[C@@H]2CC[C@H](C)CC2)CC1 |a:4,6,o1:1,&1:9|"},
{"C[C@H]1CC[C@@H](C[C@@H]2CC[C@H](C)CC2)CC1 |o1:6,o2:1,9,o3:4|",
"C[C@H]1CC[C@H](C[C@H]2CC[C@H](C)CC2)CC1 |o1:6,o2:1,9,o3:4|",
"C[C@H]1CC[C@@H](C[C@@H]2CC[C@H](C)CC2)CC1 |a:4,6,o1:1,o2:9|"},
{"C[C@H]1CC[C@@H](C[C@@H]2CC[C@H](C)CC2)CC1 |o1:6,o2:1,9,o3:4|",
"C[C@H]1CC[C@H](C[C@H]2CC[C@H](C)CC2)CC1 |a:4,9,o1:6,o2:1|",
"C[C@H]1CC[C@@H](C[C@@H]2CC[C@H](C)CC2)CC1 |a:4,6,o1:1,o2:9|"},
{"N[C@H]1CC[C@@H](O)CC1", "N[C@@H]1CC[C@H](O)CC1",
"N[C@@H]1CC[C@H](O)CC1"},
{"N[C@H]1CC[C@@H](O)CC1 |o2:1,4|", "N[C@@H]1CC[C@H](O)CC1 |o2:1,4|",
"N[C@@H]1CC[C@H](O)CC1"},
{"N[C@H]1CC[C@@H](O)CC1 |&2:1,4|", "N[C@@H]1CC[C@H](O)CC1 |&2:1,4|",
"N[C@@H]1CC[C@H](O)CC1"},
{"N[C@H]1CC[C@@H](O)CC1 |a:1,4|", "N[C@@H]1CC[C@H](O)CC1 |a:1,4|",
"N[C@@H]1CC[C@H](O)CC1"},
// no enhanced stereo
{"CC(C)[C@H]1CCCCN1C(=O)[C@H]1CC[C@@H](C)CC1",
"CC(C)[C@H]1CCCCN1C(=O)[C@@H]1CC[C@H](C)CC1",
"CC(C)[C@H]1CCCCN1C(=O)[C@@H]1CC[C@H](C)CC1"},
// enhance stereo abs,abs,abs
{"CC(C)[C@H]1CCCCN1C(=O)[C@H]1CC[C@@H](C)CC1 |a:3,11,14|",
"CC(C)[C@H]1CCCCN1C(=O)[C@@H]1CC[C@H](C)CC1 |a:3,11,14|",
"CC(C)[C@H]1CCCCN1C(=O)[C@@H]1CC[C@H](C)CC1"},
// abs, abs, or and abs, or abs
{"CC(C)[C@H]1CCCCN1C(=O)[C@H]1CC[C@@H](C)CC1 |a:3,11,o1:14|",
"CC(C)[C@H]1CCCCN1C(=O)[C@H]1CC[C@H](C)CC1 |a:3,11,o1:14|",
"CC(C)[C@H]1CCCCN1C(=O)[C@@H]1CC[C@H](C)CC1 |a:3,11,o1:14|"},
{"CC(C)[C@H]1CCCCN1C(=O)[C@H]1CC[C@@H](C)CC1 |a:3,11,o1:14|",
"CC(C)[C@H]1CCCCN1C(=O)[C@H]1CC[C@H](C)CC1 |a:3,14,o1:11|",
"CC(C)[C@H]1CCCCN1C(=O)[C@@H]1CC[C@H](C)CC1 |a:3,11,o1:14|"},
{"CC(C)[C@H]1CCCCN1C(=O)[C@H]1CC[C@@H](C)CC1 |a:3,11,o1:14|",
"CC(C)[C@H]1CCCCN1C(=O)[C@H]1CC[C@@H](C)CC1 |a:3,o1:11,o2:14|",
"CC(C)[C@H]1CCCCN1C(=O)[C@@H]1CC[C@H](C)CC1 |a:3,11,o1:14|"},
{"CC(C)[C@H]1CCCCN1C(=O)[C@H]1CC[C@@H](C)CC1 |a:3,11,&1:14|",
"CC(C)[C@H]1CCCCN1C(=O)[C@H]1CC[C@H](C)CC1 |a:3,11,&1:14|",
"CC(C)[C@H]1CCCCN1C(=O)[C@@H]1CC[C@H](C)CC1 |a:3,11,&1:14|"},
{"CC(C)[C@H]1CCCCN1C(=O)[C@H]1CC[C@@H](C)CC1 |a:3,11,&1:14|",
"CC(C)[C@H]1CCCCN1C(=O)[C@H]1CC[C@H](C)CC1 |a:3,14,&1:11|",
"CC(C)[C@H]1CCCCN1C(=O)[C@@H]1CC[C@H](C)CC1 |a:3,11,&1:14|"},
{"CC(C)[C@H]1CCCCN1C(=O)[C@H]1CC[C@@H](C)CC1 |a:3,11,&1:14|",
"CC(C)[C@H]1CCCCN1C(=O)[C@H]1CC[C@@H](C)CC1 |a:3,&1:11,&2:14|",
"CC(C)[C@H]1CCCCN1C(=O)[C@@H]1CC[C@H](C)CC1 |a:3,11,&1:14|"},
};
UseLegacyStereoPerceptionFixture reset_stereo_perception{false};
for (const auto &[smi1, smi2, smiExpected] : tests) {
INFO(smi1 + " : " + smi2 + " : " + smiExpected);
SmilesParserParams rps;
rps.sanitize = true;
rps.removeHs = false;
std::unique_ptr<ROMol> mol1{SmilesToMol(smi1, rps)};
REQUIRE(mol1);
std::unique_ptr<ROMol> mol2{SmilesToMol(smi2, rps)};
REQUIRE(mol2);
std::vector<unsigned int> idxV(mol1->getNumAtoms());
for (unsigned int i = 0; i < mol1->getNumAtoms(); ++i) {
idxV[i] = i;
}
auto randomGen = std::mt19937(0xf00d);
for (auto i = 0; i < 100; ++i) {
INFO("i: " << i);
std::vector<unsigned int> nVect(idxV);
std::shuffle(nVect.begin(), nVect.end(), randomGen);
std::unique_ptr<ROMol> nmol{MolOps::renumberAtoms(*mol1, nVect)};
RDKit::canonicalizeStereoGroups(nmol);
RDKit::canonicalizeStereoGroups(mol2);
auto outSmi1 = MolToCXSmiles(*nmol);
auto outSmi2 = MolToCXSmiles(*mol2);
CHECK(outSmi1 == outSmi2);
CHECK(outSmi1 == smiExpected);
CHECK(outSmi2 == smiExpected);
}
}
}
SECTION("pseudoTestFails") {
std::vector<std::string> tests = {
"CNC(=O)[C@@H](NC(=O)[C@H](OCc1cc(F)ccc1F)[C@@H](O)[C@@H](O)[C@H](OCc1cc(F)ccc1F)C(=O)N[C@H](C(=O)NC)C(C)C)C(C)C |o1:19,23,&1:8,37|",
"CNC(=O)C(NC(=O)[C@H](OCc1ccccc1)[C@@H](O)[C@@H](O)[C@H](OCc1ccccc1)C(=O)NC(C(=O)NC)[C@@H](C)O)[C@H](C)O |o1:38,41,&1:17,21|",
"CCC(=O)NC[C@H]1CN(c2cc(F)c(N3C[C@H]4[C@H](N)[C@H]4C3)c(F)c2)C(=O)O1 |o1:16,17,&1:6,19|",
"Cc1cc(O)c([C@@]2(C)CC[C@@H]3C[C@@]32C)cc1-c1cc([C@]2(C)CC[C@H]3C[C@@]32C)c(O)cc1C |o1:6,23,&1:19,25|",
"C[N+]12CC[C@@]34c5ccccc5N5[C@@H]6OCC=C7C[N+]8(C)CC[C@]9%10c%11ccccc%11N([C@@H]%11OCC=C(C1)[C@H](C[C@@H]32)[C@@H]%11[C@H]54)[C@H]9[C@H]6[C@H]7C[C@@H]%108.[Cl-].[Cl-] |o1:42,45,&1:22,41|",
"Cl.Oc1ccc2c3c1O[C@H]1c4[nH]c5c(c4C[C@@]4(O)[C@@H](C2)N(CC2CC2)CC[C@]314)C[C@]1(O)[C@H]2Cc3ccc(O)c4c3[C@]1(CCN2CC1CC1)[C@H]5O4 |o1:29,40,&1:16,48|",
"O=C1NC(=O)c2c1c1c3ccccc3n3c1c1c2c2ccccc2n1[C@@H]1[C@H](O)[C@H](O)[C@H](O)[C@H]3N1Cc1ccccc1 |o1:26,32,&1:25,30|",
};
UseLegacyStereoPerceptionFixture reset_stereo_perception{false};
for (const auto &smi1 : tests) {
INFO(smi1);
SmilesParserParams rps;
rps.sanitize = true;
rps.removeHs = false;
std::unique_ptr<ROMol> mol1{SmilesToMol(smi1, rps)};
REQUIRE(mol1);
std::vector<unsigned int> idxV(mol1->getNumAtoms());
for (unsigned int i = 0; i < mol1->getNumAtoms(); ++i) {
idxV[i] = i;
}
for (auto i = 0; i < 100; ++i) {
std::vector<unsigned int> nVect(idxV);
std::shuffle(nVect.begin(), nVect.end(), std::mt19937(0xf00d));
std::unique_ptr<ROMol> nmol{MolOps::renumberAtoms(*mol1, nVect)};
RDKit::canonicalizeStereoGroups(nmol);
auto outSmi1 = MolToCXSmiles(*nmol);
CHECK(outSmi1 == smi1);
}
}
}
}
TEST_CASE("using enhanced stereo in rankMolAtoms") {
SECTION("basics: different ranks") {
std::vector<std::string> smis{
"C[C@H](F)[C@@H](F)C |a:1|",
"C[C@H](F)[C@@H](F)C |&1:1|"
"C[C@H](F)[C@@H](F)C |o1:1|",
"C[C@H](F)[C@@H](F)C |o1:1,a:3|",
"C[C@H](F)[C@@H](F)C |o1:1,&:3|",
"C[C@H](F)[C@@H](F)C |a:1,&2:3|",
};
for (auto &smi : smis) {
INFO(smi);
std::unique_ptr<RWMol> mol{SmilesToMol(smi)};
REQUIRE(mol);
bool breakTies = false;
std::vector<unsigned int> atomRanks;
Canon::rankMolAtoms(*mol, atomRanks, breakTies);
CHECK(atomRanks[1] != atomRanks[3]);
}
}
SECTION("basics: same ranks") {
std::vector<std::string> smis{
"C[C@H](F)[C@@H](F)C |o1:1,o2:3|",
"C[C@H](F)[C@@H](F)C |&1:1,&2:3|",
"C[C@H](F)[C@@H](F)C |a:1,a:3|",
};
for (auto &smi : smis) {
INFO(smi);
std::unique_ptr<RWMol> mol{SmilesToMol(smi)};
REQUIRE(mol);
bool breakTies = false;
std::vector<unsigned int> atomRanks;
Canon::rankMolAtoms(*mol, atomRanks, breakTies);
CHECK(atomRanks[1] == atomRanks[3]);
}
}
SECTION("more complex, include group membership") {
auto m1 =
"C[C@@H]1CC(C[C@@H](C)[C@@H](C)O)C[C@H](C)C1 |o1:1,7,o2:5,11|"_smiles;
REQUIRE(m1);
std::vector<unsigned int> atomRanks;
bool breakTies = false;
Canon::rankMolAtoms(*m1, atomRanks, breakTies);
CHECK(atomRanks[11] > atomRanks[1]);
auto m2 =
"C[C@H](O)[C@H](C)CC1C[C@H](C)C[C@@H](C)C1 |o1:1,8;o2:3,11|"_smiles;
REQUIRE(m2);
Canon::rankMolAtoms(*m2, atomRanks, breakTies);
CHECK(atomRanks[11] > atomRanks[8]);
}
}
TEST_CASE("more enhanced stereo canonicalization") {
// FIX: add tests for ring stereo in an s group
SECTION("case 1") {
auto m1 =
"C[C@@H](O)[C@H](C)[C@@H](C)[C@@H](C)F |a:3,&1:1,7,&2:5,r|"_smiles;
REQUIRE(m1);
auto m2 = "C[C@H](O)[C@H](C)[C@@H](C)[C@H](C)F |a:3,&1:1,7,&2:5,r|"_smiles;
REQUIRE(m2);
Canon::canonicalizeEnhancedStereo(*m1);
Canon::canonicalizeEnhancedStereo(*m2);
CHECK(MolToCXSmiles(*m1) == MolToCXSmiles(*m2));
}
SECTION("case 2") {
auto m1 =
"C[C@@H](O)[C@H](C)[C@@H](C)[C@@H](C)O |&3:3,5,o1:7,&2:1,r|"_smiles;
REQUIRE(m1);
auto m2 =
"C[C@@H](O)[C@H](C)[C@@H](C)[C@@H](C)O |&3:3,5,&2:7,o1:1,r|"_smiles;
REQUIRE(m2);
Canon::canonicalizeEnhancedStereo(*m1);
Canon::canonicalizeEnhancedStereo(*m2);
CHECK(MolToCXSmiles(*m1) == MolToCXSmiles(*m2));
}
SECTION("case 3") {
auto m1 =
"C[C@@H](O)[C@H](C)[C@@H](C)[C@@H](C)O |&8:3,5,o1:7,&7:1,r|"_smiles;
REQUIRE(m1);
auto m2 =
"C[C@@H](O)[C@H](C)[C@@H](C)[C@@H](C)O |&3:3,5,&2:7,o1:1,r|"_smiles;
REQUIRE(m2);
Canon::canonicalizeEnhancedStereo(*m1);
Canon::canonicalizeEnhancedStereo(*m2);
CHECK(MolToCXSmiles(*m1) == MolToCXSmiles(*m2));
}
SECTION("case 4") {
auto m1 =
"C[C@@H](O)[C@H](C)[C@@H](C)[C@@H](C)O |&8:3,5,o1:7,&7:1,r|"_smiles;
REQUIRE(m1);
auto m2 =
"C[C@@H](O)[C@H](C)[C@@H](C)[C@@H](C)O |&3:3,5,&2:7,o1:1,r|"_smiles;
REQUIRE(m2);
CHECK(MolToCXSmiles(*m1) == MolToCXSmiles(*m2));
}
SECTION("case 5") {
auto m1 =
"C[C@@H](O)[C@H](C)[C@@H](C)[C@@H](C)O |&8:3,5,o1:7,&7:1,r|"_smiles;
REQUIRE(m1);
auto m2 =
"C[C@@H](O)[C@H](C)[C@@H](C)[C@@H](C)O |&3:3,5,&2:7,o1:1,r|"_smiles;
REQUIRE(m2);
forwardStereoGroupIds(*m1);
forwardStereoGroupIds(*m2);
auto cx1 = MolToCXSmiles(*m1);
auto cx2 = MolToCXSmiles(*m2);
CHECK(cx1 == "C[C@H](O)[C@H](C)[C@@H](C)[C@H](C)O |o1:1,&7:7,&8:3,5|");
CHECK(cx2 == "C[C@H](O)[C@H](C)[C@@H](C)[C@H](C)O |o1:1,&2:7,&3:3,5|");
}
SECTION("case 5a") {
std::unique_ptr<ROMol> m1 =
"C[C@@H](O)[C@H](C)[C@@H](C)[C@@H](C)O |&8:3,5,o1:7,&7:1,r|"_smiles;
REQUIRE(m1);
std::unique_ptr<ROMol> m2 =
"C[C@@H](O)[C@H](C)[C@@H](C)[C@@H](C)O |&3:3,5,&2:7,o1:1,r|"_smiles;
REQUIRE(m2);
forwardStereoGroupIds(*m1);
forwardStereoGroupIds(*m2);
RDKit::canonicalizeStereoGroups(m1);
RDKit::canonicalizeStereoGroups(m2);
auto cx1 = MolToCXSmiles(*m1);
auto cx2 = MolToCXSmiles(*m2);
CHECK(cx1 == "C[C@H](O)[C@H](C)[C@@H](C)[C@H](C)O |o1:1,&1:3,5,&2:7|");
CHECK(cx2 == "C[C@H](O)[C@H](C)[C@@H](C)[C@H](C)O |o1:1,&1:3,5,&2:7|");
}
SECTION("case 6") {
auto m1 =
"C[C@@H](O)[C@H](C)[C@@H](C)[C@@H](C)O |&8:3,5,o1:7,&7:1,r|"_smiles;
REQUIRE(m1);
auto m2 =
"C[C@@H](O)[C@H](C)[C@@H](C)[C@@H](C)O |&3:3,5,&2:7,o1:1,r|"_smiles;
REQUIRE(m2);
forwardStereoGroupIds(*m1);
forwardStereoGroupIds(*m2);
// Canonicalization resets the Stereo Group IDs
Canon::canonicalizeEnhancedStereo(*m1);
Canon::canonicalizeEnhancedStereo(*m2);
CHECK(MolToCXSmiles(*m1) == MolToCXSmiles(*m2));
// "read" ids are also reset!
forwardStereoGroupIds(*m1);
forwardStereoGroupIds(*m2);
CHECK(MolToCXSmiles(*m1) == MolToCXSmiles(*m2));
}
}
TEST_CASE("ensure unused features are not used") {
SECTION("isotopes") {
auto mol = "[13CH3]OC"_smiles;
REQUIRE(mol);
std::vector<unsigned int> ranks;
bool breakTies = false;
bool includeChirality = true;
bool includeIsotopes = true;
Canon::rankMolAtoms(*mol, ranks, breakTies, includeChirality,
includeIsotopes);
CHECK(ranks[0] != ranks[2]);
includeIsotopes = false;
Canon::rankMolAtoms(*mol, ranks, breakTies, includeChirality,
includeIsotopes);
CHECK(ranks[0] == ranks[2]);
}
SECTION("chirality") {
auto mol = "F[C@H](Cl)OC(F)Cl"_smiles;
REQUIRE(mol);
std::vector<unsigned int> ranks;
bool breakTies = false;
bool includeChirality = true;
bool includeIsotopes = true;
Canon::rankMolAtoms(*mol, ranks, breakTies, includeChirality,
includeIsotopes);
CHECK(ranks[1] != ranks[4]);
includeChirality = false;
Canon::rankMolAtoms(*mol, ranks, breakTies, includeChirality,
includeIsotopes);
CHECK(ranks[1] == ranks[4]);
}
SECTION("chirality and stereogroups") {
auto mol = "F[C@H](Cl)O[C@H](F)Cl |o1:1|"_smiles;
REQUIRE(mol);
std::vector<unsigned int> ranks;
bool breakTies = false;
bool includeChirality = true;
bool includeIsotopes = true;
Canon::rankMolAtoms(*mol, ranks, breakTies, includeChirality,
includeIsotopes);
CHECK(ranks[1] != ranks[4]);
includeChirality = false;
Canon::rankMolAtoms(*mol, ranks, breakTies, includeChirality,
includeIsotopes);
CHECK(ranks[1] == ranks[4]);
}
}
TEST_CASE(
"GitHub Issue #6633: Pre-condition violation in canonicalization of dative bond adjacent to double bond",
"[bug][canonicalization]") {
auto mb = R"CTAB(
3D
0 0 0 0 0 999 V3000
M V30 BEGIN CTAB
M V30 COUNTS 16 16 0 0 0
M V30 BEGIN ATOM
M V30 1 C -2.0033 -1.4133 -0.0473 0
M V30 2 C -2.9101 -0.3985 -0.2677 0
M V30 3 O -2.7092 0.8645 -0.2504 0
M V30 4 Ir -0.9429 1.8106 0.2184 0
M V30 5 N 0.0151 -0.0816 0.3618 0
M V30 6 C 1.4929 -0.0477 0.5631 0
M V30 7 C -0.6236 -1.2309 0.2291 0
M V30 8 C -4.3730 -0.7437 -0.5877 0
M V30 9 H -2.3752 -2.4232 -0.1048 0
M V30 10 H 1.8628 -0.9806 0.9803 0
M V30 11 H 1.6928 0.7152 1.3165 0
M V30 12 H 2.0044 0.1878 -0.3701 0
M V30 13 H -4.9409 0.1756 -0.7308 0
M V30 14 H -4.4149 -1.3416 -1.4982 0
M V30 15 H -4.8022 -1.3104 0.2386 0
M V30 16 H 0.0202 -2.0891 0.3538 0
M V30 END ATOM
M V30 BEGIN BOND
M V30 1 1 1 7
M V30 2 2 1 2
M V30 3 1 1 9
M V30 4 1 2 3
M V30 5 1 2 8
M V30 6 1 3 4
M V30 7 9 5 4
M V30 8 1 5 6
M V30 9 2 5 7
M V30 10 1 6 10
M V30 11 1 6 11
M V30 12 1 6 12
M V30 13 1 7 16
M V30 14 1 8 13
M V30 15 1 8 14
M V30 16 1 8 15
M V30 END BOND
M V30 END CTAB
M END)CTAB";
auto countStereoBonds = [](const auto &mol) {
unsigned num_stereo_bonds = 0;
for (const auto bond : mol.bonds()) {
if (bond->getBondType() == Bond::BondType::DOUBLE &&
bond->getStereo() != Bond::BondStereo::STEREONONE) {
++num_stereo_bonds;
}
}
return num_stereo_bonds;
};
auto sanitize = true;
auto removeHs = false;
std::unique_ptr<ROMol> mol(MolBlockToMol(mb, sanitize, removeHs));
REQUIRE(mol);
REQUIRE(mol->getNumAtoms() == 16);
REQUIRE(countStereoBonds(*mol) == 2);
CHECK_NOTHROW(MolToSmiles(*mol));
CHECK(countStereoBonds(*mol) == 2);
}
TEST_CASE("atom mapping in canonicalization") {
SECTION("basics") {
auto m = "[F:1]C([F:2])O"_smiles;
REQUIRE(m);
std::vector<unsigned int> ranks;
bool breakTies = false;
bool includeChirality = true;
bool includeIsotopes = true;
bool includeAtomMaps = true;
Canon::rankMolAtoms(*m, ranks, breakTies, includeChirality, includeIsotopes,
includeAtomMaps);
CHECK(ranks[0] != ranks[2]);
includeAtomMaps = false;
Canon::rankMolAtoms(*m, ranks, breakTies, includeChirality, includeIsotopes,
includeAtomMaps);
CHECK(ranks[0] == ranks[2]);
}
}
TEST_CASE(
"GitHub Issue #7023: \"Inconsistent state\" when manually sanitizing and assigning stereo when using the new stereo algorithm",
"[bug]") {
UseLegacyStereoPerceptionFixture reset_stereo_perception{false};
const auto molb = R"CTAB("
RDKit 2D
0 0 0 0 0 0 0 0 0 0999 V3000
M V30 BEGIN CTAB
M V30 COUNTS 40 47 0 0 1
M V30 BEGIN ATOM
M V30 1 C -1.412000 -2.520800 0.000000 0
M V30 2 N -2.236600 -2.495700 0.000000 0
M V30 3 N -3.801500 -2.612400 0.000000 0
M V30 4 C -4.626200 -2.587400 0.000000 0
M V30 5 C -4.904800 -3.363900 0.000000 0
M V30 6 C -5.696800 -3.595000 0.000000 0
M V30 7 C -4.966800 -0.807100 0.000000 0
M V30 8 N -4.155000 -0.660100 0.000000 0
M V30 9 C -4.044000 0.157400 0.000000 0
M V30 10 C -3.039200 0.506000 0.000000 0
M V30 11 C -2.237800 0.310100 0.000000 0
M V30 12 N -2.176500 -0.512600 0.000000 0
M V30 13 C -1.375100 -0.708600 0.000000 0
M V30 14 C -0.941100 -0.006900 0.000000 0
M V30 15 C -0.118400 0.054400 0.000000 0
M V30 16 C -1.474300 0.622600 0.000000 0
M V30 17 C -0.910300 1.224700 0.000000 0
M V30 18 C -1.697100 1.417000 0.000000 0
M V30 19 C -5.077900 -1.624600 0.000000 0
M V30 20 C -5.893400 -1.749400 0.000000 0
M V30 21 C -1.133400 -1.744200 0.000000 0
M V30 22 C -0.309800 -1.791700 0.000000 0
M V30 23 C -2.515200 -3.272300 0.000000 0
M V30 24 C -3.570500 -3.404400 0.000000 0
M V30 25 C -3.278900 -4.176100 0.000000 0
M V30 26 C 0.225100 -3.058100 0.000000 0
M V30 27 C -0.404400 -3.591300 0.000000 0
M V30 28 C -1.181000 -3.312700 0.000000 0
M V30 29 C -1.076700 -4.131100 0.000000 0
M V30 30 Co -0.633100 -1.614100 0.000000 0 CHG=1 VAL=6
M V30 31 C -4.787100 0.515600 0.000000 0
M V30 32 C -4.934100 1.327400 0.000000 0
M V30 33 C -1.862800 -3.777200 0.000000 0
M V30 34 C -1.887800 -4.601800 0.000000 0
M V30 35 C -4.252300 -3.868900 0.000000 0
M V30 36 C -4.678900 -4.575000 0.000000 0
M V30 37 C -3.869300 -4.599600 0.000000 0
M V30 38 C -5.357500 -0.080500 0.000000 0
M V30 39 C -6.124200 -0.385000 0.000000 0
M V30 40 C -6.015200 0.417600 0.000000 0
M V30 END ATOM
M V30 BEGIN BOND
M V30 1 2 21 1
M V30 2 1 1 2
M V30 3 1 28 1
M V30 4 1 23 2 CFG=3
M V30 5 1 2 30
M V30 6 1 23 33
M V30 7 1 23 24
M V30 8 1 33 28
M V30 9 1 24 3
M V30 10 1 24 35
M V30 11 2 3 4
M V30 12 1 5 4
M V30 13 1 4 19
M V30 14 1 5 6 CFG=3
M V30 15 1 35 5
M V30 16 2 19 7
M V30 17 1 7 8
M V30 18 1 38 7
M V30 19 2 8 9
M V30 20 1 9 10
M V30 21 1 31 9
M V30 22 2 10 11
M V30 23 1 11 12
M V30 24 1 11 16
M V30 25 2 12 13
M V30 26 1 14 13
M V30 27 1 14 15 CFG=3
M V30 28 1 14 16
M V30 29 1 16 17
M V30 30 1 16 18
M V30 31 1 31 38
M V30 32 9 8 30
M V30 33 9 3 30
M V30 34 9 12 30
M V30 35 1 19 20
M V30 36 1 21 22
M V30 37 1 24 25 CFG=3
M V30 38 1 27 26
M V30 39 1 28 27
M V30 40 1 28 29 CFG=1
M V30 41 1 21 13
M V30 42 1 31 32 CFG=3
M V30 43 1 33 34 CFG=1
M V30 44 1 35 36
M V30 45 1 35 37
M V30 46 1 38 39
M V30 47 1 38 40
M V30 END BOND
M V30 END CTAB
M END
)CTAB";
bool sanitize = false;
bool removeHs = false;
std::unique_ptr<RWMol> m(MolBlockToMol(molb, sanitize, removeHs));
MolOps::sanitizeMol(*m);
MolOps::assignStereochemistry(*m);
// This should not throw an invariant violation
auto smiles = MolToSmiles(*m);
CHECK(
smiles ==
R"SMI(CC[C@@]1(C)/C2=C(C)/C3=N4->[CoH2+]56N2[C@H]([C@@H]1C)[C@]1(C)N->5=C(/C(C)=C2N->6=C(/C=C4/C(C)(C)[C@@H]3C)[C@@H](C)C\2(C)C)[C@@H](C)C1(C)C)SMI");
}
TEST_CASE("chiral presence and ranking") {
SECTION("basics") {
auto mol = "OC(F)C([C@H](F)O)[C@@H](F)O"_smiles;
REQUIRE(mol);
std::vector<unsigned int> ranks;
bool breakTies = false;
// default: all three centers are different
Canon::rankMolAtoms(*mol, ranks, breakTies);
CHECK(ranks[1] != ranks[4]);
CHECK(ranks[1] != ranks[7]);
CHECK(ranks[4] != ranks[7]);
// if we don't include chirality, the ranks should be the same
bool includeChirality = false;
Canon::rankMolAtoms(*mol, ranks, breakTies, includeChirality);
CHECK(ranks[1] == ranks[4]);
CHECK(ranks[1] == ranks[7]);
// if we include chiral presence, 4 and 7 are the same, but 1 is
// different
includeChirality = false;
bool includeChiralPresence = true;
bool includeIsotopes = true;
bool includeAtomMaps = true;
const bool includeStereoGroups = includeChirality;
const bool useNonStereoRanks = false;
Canon::rankMolAtoms(*mol, ranks, breakTies, includeChirality,
includeIsotopes, includeAtomMaps, includeChiralPresence,
includeStereoGroups, useNonStereoRanks);
CHECK(ranks[1] != ranks[4]);
CHECK(ranks[1] != ranks[7]);
CHECK(ranks[4] == ranks[7]);
}
}
TEST_CASE("meso impact on atom ranking") {
SECTION("basics") {
{
auto m = "C1[C@H](O)C[C@@H]1[C@H](F)[C@@H]1C[C@H](O)C1"_smiles;
REQUIRE(m);
std::vector<unsigned int> ranks;
bool breakTies = false;
Canon::rankMolAtoms(*m, ranks, breakTies);
CHECK(ranks[4] == ranks[7]);
}
{
auto m = "C1[C@H](O)C[C@@H]1[C@H](F)[C@@H]1C[C@@H](O)C1"_smiles;
REQUIRE(m);
std::vector<unsigned int> ranks;
bool breakTies = false;
Canon::rankMolAtoms(*m, ranks, breakTies);
CHECK(ranks[4] != ranks[7]);
}
{
auto m =
"C[C@@H](Cl)C1[C@H](C)Cl.C[C@@H](Cl)C2[C@H](C)Cl.[C@H]12F"_smiles;
REQUIRE(m);
std::vector<unsigned int> ranks;
bool breakTies = false;
Canon::rankMolAtoms(*m, ranks, breakTies);
CHECK(ranks[3] == ranks[10]);
}
{
auto m =
"C[C@@H](Cl)C1[C@@H](C)Cl.C[C@@H](Cl)C2[C@H](C)Cl.[C@H]12F"_smiles;
REQUIRE(m);
std::vector<unsigned int> ranks;
bool breakTies = false;
Canon::rankMolAtoms(*m, ranks, breakTies);
CHECK(ranks[3] != ranks[10]);
}
}
}
Reference in New Issue View Git Blame Copy Permalink