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rdkit/Code/GraphMol/MolStandardize/test1.cpp
Ricardo Rodriguez 680520e0ad Follow up to PR #8968 (#9168) 
* implement consistency check

* add more consistency checks

* check direction consistency accross double bond

* clean up directions for non-stereo bonds

* fix counts for second from atom dirs; add check

* handle inconconsistent bond dirs

* add more tests, pubchem cases, and update existing

* drop statics

* fix typo

* make sourceBond arg const

* fix consistency check
2026-03-20 04:28:17 +01:00

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//
// Copyright (C) 2018 Susan H. Leung
//
// @@ 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 "MolStandardize.h"
#include "Normalize.h"
#include "Fragment.h"
#include "Charge.h"
#include "Metal.h"
#include <RDGeneral/Invariant.h>
#include <GraphMol/RDKitBase.h>
#include <GraphMol/FileParsers/FileParsers.h>
#include <GraphMol/FileParsers/MolSupplier.h>
#include <GraphMol/SmilesParse/SmilesParse.h>
#include <GraphMol/SmilesParse/SmilesWrite.h>
#include <GraphMol/ROMol.h>
using namespace RDKit;
void testCleanup() {
BOOST_LOG(rdDebugLog) << "-----------------------\n test cleanup"
<< std::endl;
MolStandardize::CleanupParameters params;
// Test covalent metal is disconnected during standardize.
{
RWMOL_SPTR m = "CCC(=O)O[Na]"_smiles;
RWMOL_SPTR res(MolStandardize::cleanup(*m, params));
TEST_ASSERT(MolToSmiles(*res) == "CCC(=O)[O-].[Na+]");
}
{
// Github 5997
auto m = "CC(=O)O[Mg]OC(=O)C"_smiles;
RWMOL_SPTR res(MolStandardize::cleanup(*m, params));
TEST_ASSERT(MolToSmiles(*res) == "CC(=O)[O-].CC(=O)[O-].[Mg+2]");
}
// Test metal ion is untouched during standardize.
{
RWMOL_SPTR m = "CCC(=O)[O-].[Na+]"_smiles;
RWMOL_SPTR res(MolStandardize::cleanup(*m, params));
TEST_ASSERT(MolToSmiles(*res) == "CCC(=O)[O-].[Na+]");
}
// Test Hg is disconnected from O during standardize.
{
RWMOL_SPTR m = "CCC(=O)O[Hg]"_smiles;
RWMOL_SPTR res(MolStandardize::cleanup(*m, params));
TEST_ASSERT(MolToSmiles(*res) == "CCC(=O)[O-].[Hg+]")
}
// Test dimethylmercury is not disconnected during standardize.
{
RWMOL_SPTR m = "C[Hg]C"_smiles;
RWMOL_SPTR res(MolStandardize::cleanup(*m, params));
TEST_ASSERT(MolToSmiles(*res) == "[CH3][Hg][CH3]")
}
BOOST_LOG(rdDebugLog) << "Finished" << std::endl;
}
void testStandardizeSm() {
BOOST_LOG(rdDebugLog) << "-----------------------\n test standardize smiles"
<< std::endl;
// check aromaticity
{
std::string smi = "C1=CC=CC=C1";
std::string ss = MolStandardize::standardizeSmiles(smi);
TEST_ASSERT(ss == "c1ccccc1");
}
// both rings should be aromatic
{
std::string smi = "C[N]1C=NC2=C1C(=O)N(C)C(=O)N2C";
std::string ss = MolStandardize::standardizeSmiles(smi);
TEST_ASSERT(ss == "Cn1c(=O)c2c(ncn2C)n(C)c1=O");
}
// both rings should be aromatic
{
std::string smi = "C=Cc1ccc2c(c1)[nH]c(=O)/c/2=C\\c1ccc[nH]1";
std::string ss = MolStandardize::standardizeSmiles(smi);
TEST_ASSERT(ss == R"SMI(C=Cc1ccc2c(c1)NC(=O)/C2=C\c1ccc[nH]1)SMI");
}
// check stereochemistry is correctly perceived
{
std::string smi = "Cl\\C=C/Cl";
std::string ss = MolStandardize::standardizeSmiles(smi);
TEST_ASSERT(ss == "Cl/C=C\\Cl");
}
// Break metal-organic covalent bonds
{
std::string smi = "[Na]OC(=O)c1ccccc1";
std::string ss = MolStandardize::standardizeSmiles(smi);
TEST_ASSERT(ss == "O=C([O-])c1ccccc1.[Na+]");
}
// SMILES parsing error should stop tests
// std::string smi ="C1CCC1C(=O)O.Na";
// std::string ss6 = MolStandardize::standardizeSmiles(smi);
BOOST_LOG(rdDebugLog) << "Finished" << std::endl;
}
void testMetalDisconnector() {
BOOST_LOG(rdDebugLog) << "-----------------------\n test metal disconnector"
<< std::endl;
MolStandardize::MetalDisconnector md;
unsigned int failedOp;
{
RWMOL_SPTR m(SmilesToMol("[O-]C(=O)C.[Mg+2][O-]C(=O)C", 0, false));
MolOps::sanitizeMol(*m, failedOp, MolOps::SANITIZE_CLEANUP);
TEST_ASSERT(m);
md.disconnect(*m);
TEST_ASSERT(MolToSmiles(*m) == "CC(=O)[O-].CC(=O)[O-].[Mg+2]");
}
// testing overloaded function
{
ROMOL_SPTR m("CCC(=O)O[Na]"_smiles);
TEST_ASSERT(m);
ROMOL_SPTR nm(md.disconnect(*m));
TEST_ASSERT(MolToSmiles(*nm) == "CCC(=O)[O-].[Na+]");
}
{
RWMOL_SPTR m("[Na]OC(=O)CCC(=O)O[Na]"_smiles);
TEST_ASSERT(m);
md.disconnect(*m);
TEST_ASSERT(MolToSmiles(*m) == "O=C([O-])CCC(=O)[O-].[Na+].[Na+]");
}
{
RWMOL_SPTR m("c1ccccc1[Mg]Br"_smiles);
TEST_ASSERT(m);
md.disconnect(*m);
TEST_ASSERT(MolToSmiles(*m) == "[Br][Mg][c]1ccccc1");
}
{
RWMOL_SPTR m("C1(CCCCC1)[Zn]Br"_smiles);
TEST_ASSERT(m);
md.disconnect(*m);
TEST_ASSERT(MolToSmiles(*m) == "[Br-].[CH-]1CCCCC1.[Zn+2]");
}
{
RWMOL_SPTR m("Br[Mg]c1ccccc1CCC(=O)O[Na]"_smiles);
TEST_ASSERT(m);
md.disconnect(*m);
TEST_ASSERT(MolToSmiles(*m) == "O=C([O-])CCc1cccc[c]1[Mg][Br].[Na+]");
}
// test input own dp_metal_non, dp_metal_nof
// missing out Na
{
MolStandardize::MetalDisconnector md2;
ROMOL_SPTR metal_nof(
SmartsToMol("[Li,K,Rb,Cs,Fr,Be,Mg,Ca,Sr,Ba,Ra,Sc,Ti,V,Cr,Mn,Fe,Co,"
"Ni,Cu,Zn,Al,Ga,Y,Zr,Nb,Mo,Tc,Ru,Rh,Pd,Ag,Cd,In,Sn,Hf,Ta,"
"W,Re,Os,Ir,Pt,Au,Hg,Tl,Pb,Bi]~[#7,#8,F]"));
md2.setMetalNof(*metal_nof);
ROMOL_SPTR m("CCC(=O)O[Na]"_smiles);
TEST_ASSERT(m);
ROMOL_SPTR nm(md2.disconnect(*m));
TEST_ASSERT(MolToSmiles(*nm) == "CCC(=O)[O][Na]"); // not disconnected
}
// test that metals are not assigned excess positive charge
{
RWMOL_SPTR m(SmilesToMol("[Be](F)(F)(F)OC", 0, false));
MolOps::sanitizeMol(*m, failedOp, MolOps::SANITIZE_CLEANUP);
TEST_ASSERT(m);
md.disconnect(*m);
TEST_ASSERT(MolToSmiles(*m) == "C[O-].[Be+2].[F-].[F-].[F-]");
}
// test that badly written complexes with 4ary nitrogen
// are not assigned a negative charge nor the metal is
// stolen electrons from
{
RWMOL_SPTR m(SmilesToMol("[Ru](SC)(SC)(SC)N(C)(C)C", 0, false));
MolOps::sanitizeMol(*m, failedOp, MolOps::SANITIZE_CLEANUP);
TEST_ASSERT(m);
md.disconnect(*m);
TEST_ASSERT(MolToSmiles(*m) == "CN(C)C.C[S-].C[S-].C[S-].[Ru+3]");
}
// test that badly written salts are not assigned excess formal charges
{
RWMOL_SPTR m(SmilesToMol("[Na+][O-]C(=O)C", 0, false));
MolOps::sanitizeMol(*m, failedOp, MolOps::SANITIZE_CLEANUP);
TEST_ASSERT(m);
md.disconnect(*m);
TEST_ASSERT(MolToSmiles(*m) == "CC(=O)[O-].[Na+]");
}
// make sure that -1 as a valence is dealt with (Github 5997)
{
RWMOL_SPTR m(SmilesToMol("[O-]C(=O)C.[Mg+2][O-]C(=O)C", 0, false));
MolOps::sanitizeMol(*m, failedOp, MolOps::SANITIZE_CLEANUP);
TEST_ASSERT(m);
md.disconnect(*m);
TEST_ASSERT(MolToSmiles(*m) == "CC(=O)[O-].CC(=O)[O-].[Mg+2]");
}
// test that badly specified dative bonds are perceived as such
{
RWMOL_SPTR m(
SmilesToMol("CC1=CC=CC2=[N]1[Cu+2]3[N](=C2)NC(=[S]3)N(C)C", 0, false));
MolOps::sanitizeMol(*m, failedOp, MolOps::SANITIZE_CLEANUP);
TEST_ASSERT(m);
md.disconnect(*m);
TEST_ASSERT(MolToSmiles(*m) == "CC1=CC=CC(C=NNC(=S)N(C)C)=N1.[Cu+2]");
}
// test that carbonyl complexes are not assigned excess formal charges
{
RWMOL_SPTR m(SmilesToMol("[Ni+2]([C]=O)([C]=O)([C]=O)([C]=O)([C]=O)[C]=O",
0, false));
MolOps::sanitizeMol(
*m, failedOp, MolOps::SANITIZE_CLEANUP | MolOps::SANITIZE_FINDRADICALS);
TEST_ASSERT(m);
md.disconnect(*m);
TEST_ASSERT(MolToSmiles(*m) ==
"[C]=O.[C]=O.[C]=O.[C]=O.[C]=O.[C]=O.[Ni+2]");
}
// test that dative bonds are handled appropriately
{
RWMOL_SPTR m("O->[Fe](<-O)(O)O"_smiles);
TEST_ASSERT(m);
md.disconnect(*m);
TEST_ASSERT(MolToSmiles(*m) == "O.O.[Fe+2].[OH-].[OH-]");
}
// test that dative bonds are handled appropriately
{
RWMOL_SPTR m("[OH-]->[Co+3](<-[OH-])(<-O)<-O"_smiles);
TEST_ASSERT(m);
md.disconnect(*m);
TEST_ASSERT(MolToSmiles(*m) == "O.O.[Co+3].[OH-].[OH-]");
}
// test that pre-existing formal charges on metals are honored (github #3625)
{
RWMOL_SPTR m("[Pd+]Cl"_smiles);
TEST_ASSERT(m);
md.disconnect(*m);
TEST_ASSERT(MolToSmiles(*m) == "[Cl-].[Pd+2]");
}
{
RWMOL_SPTR m("[Pd+2]<-[Cl-]"_smiles);
TEST_ASSERT(m);
md.disconnect(*m);
TEST_ASSERT(MolToSmiles(*m) == "[Cl-].[Pd+2]");
}
{
RWMOL_SPTR m("[Al](Cl)(Cl)Cl"_smiles);
TEST_ASSERT(m);
md.disconnect(*m);
TEST_ASSERT(MolToSmiles(*m) == "[Al+3].[Cl-].[Cl-].[Cl-]");
}
{
RWMOL_SPTR m("[Al+](<-[Cl-])(Cl)Cl"_smiles);
TEST_ASSERT(m);
md.disconnect(*m);
TEST_ASSERT(MolToSmiles(*m) == "[Al+3].[Cl-].[Cl-].[Cl-]");
}
{
RWMOL_SPTR m("[Al+](Cl)Cl"_smiles);
TEST_ASSERT(m);
md.disconnect(*m);
TEST_ASSERT(MolToSmiles(*m) == "[Al+3].[Cl-].[Cl-]");
}
{
RWMOL_SPTR m("[Al+2]Cl"_smiles);
TEST_ASSERT(m);
md.disconnect(*m);
TEST_ASSERT(MolToSmiles(*m) == "[Al+3].[Cl-]");
}
BOOST_LOG(rdDebugLog) << "Finished" << std::endl;
}
void testNormalize() {
BOOST_LOG(rdDebugLog) << "-----------------------\n test normalize"
<< std::endl;
MolStandardize::CleanupParameters params;
std::string rdbase = getenv("RDBASE");
std::string transformFile =
rdbase + "/Code/GraphMol/MolStandardize/test_data/normalizations.txt";
params.normalizations = transformFile;
// Normalize nitro group.
{
RWMOL_SPTR m = "C1(=CC=CC=C1)[N+](=O)[O-]"_smiles;
RWMOL_SPTR res(MolStandardize::cleanup(*m, params));
TEST_ASSERT(MolToSmiles(*res) == "O=[N+]([O-])c1ccccc1");
}
// Normalize nitro group.
{
RWMOL_SPTR m = "O=[N](=O)c1ccccc1"_smiles;
RWMOL_SPTR res(MolStandardize::cleanup(*m, params));
TEST_ASSERT(MolToSmiles(*res) == "O=[N+]([O-])c1ccccc1");
}
// Normalize nitro group.
{
RWMOL_SPTR m = "[O-][N+](=O)c1ccccc1"_smiles;
RWMOL_SPTR res(MolStandardize::cleanup(*m, params));
TEST_ASSERT(MolToSmiles(*res) == "O=[N+]([O-])c1ccccc1");
}
// Normalize nitro group.
{
RWMOL_SPTR m = "[N](=O)(=O)O"_smiles;
RWMOL_SPTR res(MolStandardize::cleanup(*m, params));
TEST_ASSERT(MolToSmiles(*res) == "O=[N+]([O-])O");
}
// Normalize nitro group.
{
RWMOL_SPTR m = "O[N+](=O)[O-]"_smiles;
RWMOL_SPTR res(MolStandardize::cleanup(*m, params));
TEST_ASSERT(MolToSmiles(*res) == "O=[N+]([O-])O");
}
// Normalize pyridine oxide.
{
RWMOL_SPTR m = "C1=[N](C=CC=C1)=O"_smiles;
RWMOL_SPTR res(MolStandardize::cleanup(*m, params));
TEST_ASSERT(MolToSmiles(*res) == "[O-][n+]1ccccc1");
}
// Normalize pyridine oxide.
{
RWMOL_SPTR m = "O=n1ccccc1"_smiles;
RWMOL_SPTR res(MolStandardize::cleanup(*m, params));
TEST_ASSERT(MolToSmiles(*res) == "[O-][n+]1ccccc1");
}
// normalize sulfone.
{
RWMOL_SPTR m = "C[S+2]([O-])([O-])C"_smiles;
RWMOL_SPTR res(MolStandardize::cleanup(*m, params));
TEST_ASSERT(MolToSmiles(*res) == "CS(C)(=O)=O");
}
// normalize sulfone.
{
RWMOL_SPTR m = "C[S+2]([O-])([O-])O"_smiles;
RWMOL_SPTR res(MolStandardize::cleanup(*m, params));
TEST_ASSERT(MolToSmiles(*res) == "CS(=O)(=O)O");
}
// normalize sulfoxide..
{
RWMOL_SPTR m = "CS(=O)C"_smiles;
RWMOL_SPTR res(MolStandardize::cleanup(*m, params));
TEST_ASSERT(MolToSmiles(*res) == "C[S+](C)[O-]");
}
// normalize sulfoxide.
{
RWMOL_SPTR m =
"COC1=CC2=C(C=C1)[N]C(=N2)[S](=O)CC3=C(C(=C(C=N3)C)OC)C"_smiles;
RWMOL_SPTR res(MolStandardize::cleanup(*m, params));
TEST_ASSERT(MolToSmiles(*res) ==
"COc1ccc2c(c1)N=C([S+]([O-])Cc1ncc(C)c(OC)c1C)[N]2");
}
// Normalize sulfoxide.
{
RWMOL_SPTR m = "COc1ccc2c(c1)nc([nH]2)S(=O)Cc1ncc(c(c1C)OC)C"_smiles;
RWMOL_SPTR res(MolStandardize::cleanup(*m, params));
TEST_ASSERT(MolToSmiles(*res) ==
"COc1ccc2[nH]c([S+]([O-])Cc3ncc(C)c(OC)c3C)nc2c1");
}
// Normalize azide.
{
RWMOL_SPTR m = "C1(=CC=C(C=C1)N)N=[N]#N"_smiles;
RWMOL_SPTR res(MolStandardize::cleanup(*m, params));
TEST_ASSERT(MolToSmiles(*res) == "[N-]=[N+]=Nc1ccc(N)cc1");
}
// Normalize diazo.
{
RWMOL_SPTR m = "[N](#N)=C1C(NC(N=C1)=O)=O"_smiles;
RWMOL_SPTR res(MolStandardize::cleanup(*m, params));
TEST_ASSERT(MolToSmiles(*res) == "[N-]=[N+]=C1C=NC(=O)NC1=O");
}
// Normalize phosphate.
{
RWMOL_SPTR m = "C1=NC=C([N]1)CO[P+]([O-])([O-])[O-]"_smiles;
RWMOL_SPTR res(MolStandardize::cleanup(*m, params));
TEST_ASSERT(MolToSmiles(*res) == "O=P([O-])([O-])OCC1=CN=C[N]1");
}
// Normalize hydrazine-diazonium.
{
RWMOL_SPTR m = "CNNC[N+]#N"_smiles;
RWMOL_SPTR res(MolStandardize::cleanup(*m, params));
TEST_ASSERT(MolToSmiles(*res) == "CN=[NH+]CN=N");
}
// Normalize amidinium.
{
RWMOL_SPTR m = "[C+](C)(N)N"_smiles;
RWMOL_SPTR res(MolStandardize::cleanup(*m, params));
TEST_ASSERT(MolToSmiles(*res) == "CC(N)=[NH2+]");
BOOST_LOG(rdDebugLog) << "Finished" << std::endl;
}
}
void testNormalizeMultiFrags() {
BOOST_LOG(rdDebugLog)
<< "-----------------------\n test normalize multiple frags" << std::endl;
MolStandardize::CleanupParameters params;
std::string rdbase = getenv("RDBASE");
std::string transformFile =
rdbase + "/Code/GraphMol/MolStandardize/test_data/normalizations.txt";
params.normalizations = transformFile;
// All fragments should stay if one gets transformed by normalization.
{
RWMOL_SPTR m = "[Na]OC(=O)c1ccc(C[S+2]([O-])([O-]))cc1"_smiles;
RWMOL_SPTR res(MolStandardize::cleanup(*m, params));
TEST_ASSERT(MolToSmiles(*res) == "O=C([O-])c1ccc(C[S](=O)=O)cc1.[Na+]");
}
// All fragments should stay if one gets transformed by normalization.
{
RWMOL_SPTR m = "[Na+].[O-]C(=O)c1ccc(C[S+2]([O-])([O-]))cc1"_smiles;
RWMOL_SPTR res(MolStandardize::cleanup(*m, params));
TEST_ASSERT(MolToSmiles(*res) == "O=C([O-])c1ccc(C[S](=O)=O)cc1.[Na+]");
}
// Recombine non-aromatic 1,3-separated charges.
{
RWMOL_SPTR m = "C[N-]C(C)=[N+](C)C"_smiles;
RWMOL_SPTR res(MolStandardize::cleanup(*m, params));
TEST_ASSERT(MolToSmiles(*res) == "CN=C(C)N(C)C");
}
// Recombine aromatic 1,3-separated charges.
{
RWMOL_SPTR m = "[n-]1c(=[N+](C)C)cccc1"_smiles;
RWMOL_SPTR res(MolStandardize::cleanup(*m, params));
TEST_ASSERT(MolToSmiles(*res) == "CN(C)c1ccccn1");
}
// Recombine aromatic 1,3-separated charges.
{
RWMOL_SPTR m = "C[n+]1c([N-](C))cccc1"_smiles;
RWMOL_SPTR res(MolStandardize::cleanup(*m, params));
TEST_ASSERT(MolToSmiles(*res) == "CN=c1ccccn1C");
}
// Recombine aromatic 1,3-separated charges to form pyrimidone.
{
RWMOL_SPTR m = "[O-]c1[n+](C)cccc1"_smiles;
RWMOL_SPTR res(MolStandardize::cleanup(*m, params));
TEST_ASSERT(MolToSmiles(*res) == "Cn1ccccc1=O");
}
// Recombine aromatic 1,3-separated charges to form pyrimidone.
{
RWMOL_SPTR m =
"COc1cc2ccc3c4c(OC)cc(OC)c(OC)c4c([O-])[n+](C)c3c2cc1OC"_smiles;
RWMOL_SPTR res(MolStandardize::cleanup(*m, params));
TEST_ASSERT(MolToSmiles(*res) ==
"COc1cc2ccc3c4c(OC)cc(OC)c(OC)c4c(=O)n(C)c3c2cc1OC");
}
// Recombine non-aromatic 1,5-separated charges.
{
RWMOL_SPTR m = "C[N-]C=CC=[N+](C)C"_smiles;
RWMOL_SPTR res(MolStandardize::cleanup(*m, params));
TEST_ASSERT(MolToSmiles(*res) == "CN=CC=CN(C)C");
}
// Recombine aromatic 1,5-separated charges.
{
RWMOL_SPTR m = "[n-]1ccc(=[N+](C)C)cc1"_smiles;
RWMOL_SPTR res(MolStandardize::cleanup(*m, params));
TEST_ASSERT(MolToSmiles(*res) == "CN(C)c1ccncc1");
}
// Recombine aromatic 1,5-separated charges.
{
RWMOL_SPTR m = "C[n+]1ccc([N-]C)cc1"_smiles;
RWMOL_SPTR res(MolStandardize::cleanup(*m, params));
TEST_ASSERT(MolToSmiles(*res) == "CN=c1ccn(C)cc1");
}
// Shift positive charge from nonprotonated to protonated atom.
{
RWMOL_SPTR m = "CNC=[N+](C)C"_smiles;
RWMOL_SPTR res(MolStandardize::cleanup(*m, params));
TEST_ASSERT(MolToSmiles(*res) == "C[NH+]=CN(C)C");
}
// Shift positive charge from nonprotonated to protonated atom."
{
RWMOL_SPTR m = "CNC=CC=[N+](C)C"_smiles;
RWMOL_SPTR res(MolStandardize::cleanup(*m, params));
TEST_ASSERT(MolToSmiles(*res) == "C[NH+]=CC=CN(C)C");
}
// Shift positive charge from nonprotonated to protonated atom."
{
RWMOL_SPTR m = "[nH]1ccc(=[N+](C)C)cc1"_smiles;
RWMOL_SPTR res(MolStandardize::cleanup(*m, params));
TEST_ASSERT(MolToSmiles(*res) == "CN(C)c1cc[nH+]cc1");
}
// Ensure no transforms inadvertently breaks open rings.
{
RWMOL_SPTR m = "[O-]C1=CC=CC2=CC=CC=[N+]12"_smiles;
RWMOL_SPTR res(MolStandardize::cleanup(*m, params));
TEST_ASSERT(MolToSmiles(*res) == "O=c1cccc2ccccn12");
}
// Shift positive charge from nonprotonated to protonated atom.
{
RWMOL_SPTR m = "[nH]1c(=[N+](C)C)cccc1"_smiles;
RWMOL_SPTR res(MolStandardize::cleanup(*m, params));
TEST_ASSERT(MolToSmiles(*res) == "CN(C)c1cccc[nH+]1");
BOOST_LOG(rdDebugLog) << "Finished" << std::endl;
}
}
void testCharge() {
BOOST_LOG(rdDebugLog) << "-----------------------\n test charges"
<< std::endl;
// Reionization should not infinitely loop forever on these molecules.
{
std::string smi = "CCCCCCCCCCCCCCCCCC(=O)CC(=C)C(=O)O[V](=O)(OC(C)C)C(C)C";
std::string ss = MolStandardize::standardizeSmiles(smi);
TEST_ASSERT(
ss ==
"C=C(CC(=O)[CH-]CCCCCCCCCCCCCCCC)C(=O)[O-].CC(C)[O-].CCC.[O-2].[V+5]");
}
// Reionization should not infinitely loop forever on these molecules.
{
std::string smi =
"OP(=O)(O)[O-].OP(=O)([O-])[O-].[O-]S(=O)(=O)[O-].[Na+].[Na+].[Na+].["
"Mg+"
"2].[Cl-].[Cl-].[K+].[K+]";
std::string ss = MolStandardize::standardizeSmiles(smi);
TEST_ASSERT(
ss ==
"O=P([O-])(O)O.O=P([O-])([O-])O.O=S(=O)([O-])[O-].[Cl-].[Cl-].[K+"
"].[K+].[Mg+2].[Na+].[Na+].[Na+]");
}
// Charge parent!!
// Test reionizer moves proton to weaker acid.
{
std::string smi = "[Na].[Na]";
std::string ss = MolStandardize::standardizeSmiles(smi);
TEST_ASSERT(ss == "[Na+].[Na+]");
}
// TODO: Arguably should become selenite ion... O=[Se]([O-])[O-].
// Need an AcidBasePair?
{
std::string smi = "[Na].[Na].O[Se](O)=O";
std::string ss = MolStandardize::standardizeSmiles(smi);
TEST_ASSERT(ss == "O=[Se](O)O.[Na+].[Na+]");
BOOST_LOG(rdDebugLog) << "Finished" << std::endl;
}
// Test that tetrazolate salts are not neutralised
{
std::string smi = "c1nn[n-]n1.[Na+]";
std::string ss = MolStandardize::standardizeSmiles(smi);
TEST_ASSERT(ss == "[Na+].c1nn[n-]n1");
BOOST_LOG(rdDebugLog) << "Finished" << std::endl;
}
// Test that tetrazolate zwitterions are not neutralised
{
std::string smi = "CCCc1cc(-c2ccccc2)cc(CCC)[n+]1-c1nn[n-]n1";
std::string ss = MolStandardize::standardizeSmiles(smi);
TEST_ASSERT(ss == "CCCc1cc(-c2ccccc2)cc(CCC)[n+]1-c1nn[n-]n1");
BOOST_LOG(rdDebugLog) << "Finished" << std::endl;
}
}
void testEnumerateTautomerSmiles() {
BOOST_LOG(rdDebugLog)
<< "-----------------------\n test enumerate tautomer smiles"
<< std::endl;
MolStandardize::CleanupParameters params;
std::string smi = "c1(ccccc1)/C=C(/O)\\C";
std::vector<std::string> tsmiles =
MolStandardize::enumerateTautomerSmiles(smi, params);
BOOST_LOG(rdDebugLog) << "Finished" << std::endl;
}
void testMetalDisconnectorLigandExpo() {
BOOST_LOG(rdDebugLog) << "-----------------------\n test metal disconnector "
"on LigandExpo ligands"
<< std::endl;
std::list<std::pair<std::string, std::string>> ligandExpoSmiles{
{"[Be](O[P@@](=O)(O)O[P@](=O)(O)OCCCNc1ccc(cc1[N+](=O)[O-])[N+](=O)[O-])("
"F)(F)F",
"O=[N+]([O-])c1ccc(NCCCO[P@@](=O)(O)OP(=O)(O)O)c([N+](=O)[O-])c1"},
{"[Be](OP(=O)(O)OP(=O)(O)OC[C@@H]1[C@H]([C@H]([C@@H](O1)n2cnc3c2ncnc3N)O)"
"O)(F)(F)F",
"Nc1ncnc2c1ncn2[C@@H]1O[C@H](COP(=O)(O)OP(=O)(O)O)[C@@H](O)[C@H]1O"},
{"[Be-](O[P@@](=O)(O)O[P@](=O)(O)OCCNc1cccc(c1)[N+](=O)[O-])(F)(F)F",
"O=[N+]([O-])c1cccc(NCCO[P@@](=O)(O)OP(=O)(O)O)c1"},
{"[Be-](O[P@@](=O)(O)O[P@](=O)(O)OCCNc1ccccc1[N+](=O)[O-])(F)(F)F",
"O=[N+]([O-])c1ccccc1NCCO[P@@](=O)(O)OP(=O)(O)O"},
{"[Be](O[P@@](=O)(O)O[P@](=O)(O)OCCNc1ccc(cc1)[N+](=O)[O-])(F)(F)F",
"O=[N+]([O-])c1ccc(NCCO[P@@](=O)(O)OP(=O)(O)O)cc1"},
{"[Be-](O[P@@](=O)(O)O[P@](=O)(O)OCCNc1ccc(cc1[N+](=O)[O-])[N+](=O)[O-])("
"F)(F)F",
"O=[N+]([O-])c1ccc(NCCO[P@@](=O)(O)OP(=O)(O)O)c([N+](=O)[O-])c1"},
{"[Be-](O[P@@](=O)(O)O[P@](=O)(O)OCC[N@@](C)c1ccccc1[N+](=O)[O-])(F)(F)F",
"CN(CCO[P@@](=O)(O)OP(=O)(O)O)c1ccccc1[N+](=O)[O-]"},
{"c1c2c3c4c(c1NC(=O)CI)C=CC=[N]4[Ru+2]56([N]3=CC=C2)([N]7=C(C=CC=C7)C8=["
"N]5C=CC=C8)[N]9=C(C=CC=C9)C1=CC=CC=[N]61",
"O=C(CI)Nc1cc2cccnc2c2ncccc12"},
{"c1c2c(cc3c1C4=[N]([Ru]356([S]7CC[S]5CC[S]6CC7)C#[O+])C=CC=C4)C(=O)NC2="
"O",
"O=C1NC(=O)c2cc(-c3ccccn3)c([Ru])cc21"},
{"c1c2c(cc3c1C4=[N]([Ru]356([S]7CC[S]5CC[S]6CC7)N=C=S)C=CC=C4)C(=O)NC2=O",
"O=C1NC(=O)c2cc(-c3ccccn3)c([Ru])cc21"},
{"C1=C2C(=C(C3=[N]2[Fe]45n6c1c(c(c6C=C7[N]4=C(C=C8N5C(=C3)C(=C8CCC(=O)O)"
"CC(=O)O)C(=C7CC(=O)O)CCC(=O)O)CC(=O)O)CCC(=O)O)CCC(=O)O)CC(=O)O",
"O=C(O)CCC1=C(CC(=O)O)c2cc3[nH]c(cc4nc(cc5[nH]c(cc1n2)c(CC(=O)O)c5CCC(="
"O)O)C(CCC(=O)O)=C4CC(=O)O)c(CC(=O)O)c3CCC(=O)O"},
{"C1=CC23=C4([Ru+]2567892%10([CH]3=[CH]5[CH]6=[CH]74)[CH]3=[CH]8C9[CH]2=["
"CH]%103)C=C1",
"c1ccc2ccccc2c1"},
{"c1cc2c3c4c1C=CC=[N]4[Ru]5678(C3=CNC2=O)(C9=C5[C]6C7=C89)C#O",
"O=c1[nH]ccc2c1ccc1cccnc12"},
{"c1cc2c3c4c1N=CC=[N]4[Ru+2]56([N]3=CC=N2)([N]7=C8C(=CC=C7)c9c(nc1cc(c("
"cc1n9)F)F)C1=CC=C[N]5=C18)[N]1=CC=Nc2c1c1c(cc2)N=CC=[N]61",
"Fc1cc2nc3c4cccnc4c4ncccc4c3nc2cc1F"},
{"c1cc2c(cc1c3ccc4c(c3)nc5c(n4)C6=CC=C[N]7=C6C8=[N]([Ru]791([N]3=CC="
"Cc4c3c3c(cc4)C=CC=[N]93)[N]3=CC=Cc4c3c3c(cc4)C=CC=[N]13)C=CC=C58)nc1c("
"n2)C2=CC=C[N]3=C2C2=[N]([Ru]334([N]5=CC=Cc6c5c5c(cc6)C=CC=[N]35)[N]3="
"CC=Cc5c3c3c(cc5)C=CC=[N]43)C=CC=C12",
"c1cnc2c(c1)c1nc3ccc(-c4ccc5nc6c7cccnc7c7ncccc7c6nc5c4)cc3nc1c1cccnc12"},
{"c1cc2c(cc1Cl)nc3c(n2)C4=C5C6=[N](C=CC=C36)[Ru+2]78([N]5=CC=C4)([N]9=CC="
"Nc1c9c2c(cc1)N=CC=[N]72)[N]1=CC=Nc2c1c1c(cc2)N=CC=[N]81",
"Clc1ccc2nc3c4cccnc4c4ncccc4c3nc2c1"},
{"c1cc2c(cc1C(N)N)NC3=[N]2[Zn+2][N]4=C(C3=O)Nc5c4ccc(c5)C(N)N",
"NC(N)c1ccc2nc(C(=O)c3nc4ccc(C(N)N)cc4[nH]3)[nH]c2c1"},
{"c1cc2c(c(c1)[N+](=O)[OH-])nc3c4c5c6c(c3n2)C=CC=[N]6[Ru]78([N]5=CC=C4)(["
"N]9=C1C(=CC=C9)C=CC2=CC=C[N]7=C21)[N]1=C2C(=CC=C1)C=CC1=CC=C[N]8=C12",
"O=[N+]([1O-])c1cccc2nc3c4cccnc4c4ncccc4c3nc12"},
{"c1cc2c(cc1N(=O)=O)nc3c(n2)C4=CC=C[N]5=C4C6=[N]([Ru]578([N]9=CC="
"Cc1c9c2c(cc1)C=CC=[N]72)[N]1=CC=Cc2c1c1c(cc2)C=CC=[N]81)C=CC=C36",
"O=[N+]([O-])c1ccc2nc3c4cccnc4c4ncccc4c3nc2c1"},
{"c1cc2c(cc1O)c3c4c(c5c6c3n2[Ru]7891([N]6=CC=C5)([CH]2=[CH]7C8[CH]9=[CH]"
"12)C#O)C(=O)NC4=O",
"O=C1NC(=O)c2c1c1cccnc1c1[nH]c3ccc(O)cc3c21"},
{"c1cc2c(cc1O)c3c4n2[Ru]56([N]7=C4C(=CC(=C7)F)C8=C3C(=O)NC8=O)([S]9CC[S]"
"5CC[S]6CC9)[N]CS",
"O=C1NC(=O)c2c1c1cc(F)cnc1c1[nH]c3ccc(O)cc3c21"},
{"c1cc2c(cc1OCCN3CCCCC3)O[Cu]45[N](=C2)c6cc(c(cc6[N]4=Cc7ccc(cc7O5)"
"OCCN8CCCCC8)F)F",
"Oc1cc(OCCN2CCCCC2)ccc1C=Nc1cc(F)c(F)cc1N=Cc1ccc(OCCN2CCCCC2)cc1O"},
{"c1cc2c(cc1OCCN3CCCCC3)O[Ni]45[N](=C2)c6cc(c(cc6[N]4=Cc7ccc(cc7O5)"
"OCCN8CCCCC8)F)F",
"Oc1cc(OCCN2CCCCC2)ccc1C=Nc1cc(F)c(F)cc1N=Cc1ccc(OCCN2CCCCC2)cc1O"},
{"c1cc2c(cc(c(c2cc1)N)/N=N/c3ccc(cc3)c4ccc(cc4)/N=N/"
"c5c(c6c(c(c5)S(=O)(=O)[O-][Na+])cccc6)N)S(=O)(=O)[O-][Na+]",
"Nc1c(/N=N/c2ccc(-c3ccc(/N=N/"
"c4cc(S(=O)(=O)O)c5ccccc5c4N)cc3)cc2)cc(S(=O)(=O)O)c2ccccc12"},
{"c1cc2n3c1C=C4C=CC5=[N]4[Fe]36[N]7=C(C=CC7=C2)C=C8N6C(=C5)C=C8",
"C1=Cc2cc3ccc(cc4nc(cc5ccc(cc1n2)[nH]5)C=C4)[nH]3"},
{"c1cc2n3c1C(=C4C=CC5=[N]4[Zn]36N7C(=C5C(F)(F)F)C=CC7=C(C8=[N]6C(=C2C(F)("
"F)F)C=C8)C(F)(F)F)C(F)(F)F",
"FC(F)(F)c1c2nc(c(C(F)(F)F)c3ccc([nH]3)c(C(F)(F)F)c3nc(c(C(F)(F)F)"
"c4ccc1[nH]4)C=C3)C=C2"},
{"C1=CC2=[N](C=C1)[Pt]34[N]5=C(C=CC=C5)NC6=CC=CC(=[N]63)C7=[N]4C(=CC=C7)"
"N2",
"c1ccc(Nc2cccc(-c3cccc(Nc4ccccn4)n3)n2)nc1"},
{"c1ccc2c(c1)c3c4c(c5c6c3n2[Ru]7([N]6=CC(=C5)N)(NCC8=[N]7C=CC=C8)(C#O)Cl)"
"C(=O)NC4=O",
"Nc1cnc2c(c1)c1c(c3c4ccccc4[nH]c23)C(=O)NC1=O"},
{"c1ccc2c(c1)-c3c4c(c5c6c3[NH]2[Ru]7891([N]6=CC=C5)([CH]2=[CH]7[CH]8=C9=["
"CH]12)C#O)C(=O)NC4=O",
"O=C1NC(=O)c2c1c1cccnc1c1[nH]c3ccccc3c21"},
{"c1ccc2c(c1)c3c4n2[Ru]5678(C9C5C6C7C89)([N]1=C4C(=CC(=C1)F)C1=C3C(=O)"
"NC1=O)C#[O+]",
"O=C1NC(=O)c2c1c1cc(F)cnc1c1[nH]c3ccccc3c21"},
{"c1ccc2c(c1)c3n4c2N=C5c6ccccc6C7=[N]5[Ga]48N9C(=NC1=[N]8C(=N3)c2c1cccc2)"
"c1ccccc1C9=N7",
"c1ccc2c(c1)-c1nc-2nc2[nH]c(nc3nc(nc4[nH]c(n1)c1ccccc41)-c1ccccc1-3)"
"c1ccccc21"},
{"c1ccc2c(c1)C(=CC3=[N]2[Ru]4567([C]8[C]4[C]5[C]6[C]78)(OC3=O)[O])N9CCN("
"CC9)C(=O)CCCC[C@H]1[C@@H]2[C@H](CS1)NC(=O)N2",
"O=C1N[C@@H]2[C@H](CCCCC(=O)N3CCN(c4cc(C(=O)O)nc5ccccc45)CC3)SC[C@@H]"
"2N1"},
{"c1ccc2c(c1)C=[N]3c4ccc(cc4O[Cr+]3O2)CCC(=O)O",
"O=C(O)CCc1ccc(N=Cc2ccccc2O)c(O)c1"},
{"c1ccc2c(c1)nc3c4c5c6c(c3n2)C=CC=[N]6[Ru]78([N]5=CC=C4)([N]9=CC="
"Cc1c9c2c(cc1)C=CC=[N]72)[N]1=CC=Cc2c1c1c(cc2)C=CC=[N]81",
"c1ccc2nc3c4cccnc4c4ncccc4c3nc2c1"},
{"c1ccc2c(c1)nc3c4c5c6c(c3n2)C=CC=[N]6[Ru]78([N]5=CC=C4)([N]9=CC="
"Cc1c9c2c(cc1)C=CC=[N]72)[N]1=CC=Cc2c1c1c(cc2)C=CC=[N]81",
"c1ccc2nc3c4cccnc4c4ncccc4c3nc2c1"},
{"c1ccc2c(c1)nc3c(n2)C4=CC=C[N]5=C4C6=[N]([Ru+2]578([N]9=C1C(=NC=C9)C="
"CC2=NC=C[N]7=C21)[N]1=C2C(=NC=C1)C=CC1=NC=C[N]8=C12)C=CC=C36",
"c1ccc2nc3c4cccnc4c4ncccc4c3nc2c1"},
{"c1ccc2c(c1)nc3c(n2)C4=CC=C[N]5=C4C6=[N]([Ru]578([N]9=C(C=CC=C9)C1=CC="
"CC=[N]71)[N]1=CC=CC=C1C1=CC=CC=[N]81)C=CC=C36",
"c1ccc2nc3c4cccnc4c4ncccc4c3nc2c1"},
{"c1ccc2c(c1)nc3c(n2)C4=CC=C[N]5=C4C6=[N]([Ru]578([N]9=C(C=CC=C9)C1=[N]"
"7C=CC=C1)[N]1=CC=CC=C1C1=CC=CC=[N]81)C=CC=C36",
"c1ccc2nc3c4cccnc4c4ncccc4c3nc2c1"},
{"C1=CC(C=C1)[Ru@]2(N3C=CC=C4C3=C5[N]2=C6C=CC(=CC6=C5C7=C4C(=O)NC7=O)O)C#"
"O",
"O=C1NC(=O)c2c1c1ccc[nH]c1c1nc3ccc(O)cc3c21"},
{"c1c(c(cc2c1nc3c4c5c6c(c3n2)C=CC=[N]6[Ru]78([N]5=CC=C4)([N]9=C1C(=NC=C9)"
"C=CC2=NC=C[N]7=C21)[N]1=C2C(=NC=C1)C=CC1=NC=C[N]8=C12)C#N)C#N",
"N#Cc1cc2nc3c4cccnc4c4ncccc4c3nc2cc1C#N"},
{"c1ccc(cc1)C2=C3C=CC4=CC5=[N]6C(=C(c7ccc8n7[Zn]6(N43)[N]9=C2C=CC9=C8)"
"c1ccc(cc1)C(=O)O)C=C5",
"O=C(O)c1ccc(-c2c3nc(cc4ccc([nH]4)c(-c4ccccc4)c4nc(cc5ccc2[nH]5)C=C4)C="
"C3)cc1"},
{"c1ccc(cc1)C2=C3C=CC4=[N]3[Fe]56n7c2ccc7C=C8[N]5=C(C=C8)C(=C9N6C(="
"C4c1ccccc1)C=C9)c1ccccc1",
"C1=Cc2nc1cc1ccc([nH]1)c(-c1ccccc1)c1nc(c(-c3ccccc3)c3ccc([nH]3)c2-"
"c2ccccc2)C=C1"},
{"c1ccc(cc1)C2=C3C=CC4=[N]3[Fe]56n7c2ccc7C=C8[N]5=C(C=C8)C(=C9N6C(=C4)C="
"C9)c1ccccc1",
"C1=Cc2nc1cc1ccc([nH]1)c(-c1ccccc1)c1nc(cc3ccc([nH]3)c2-c2ccccc2)C=C1"},
{"c1ccc(cc1)C2=C3C=CC4=[N]3[Fe]56n7c2ccc7N=C8[N]5=C(C=C8)C(=C9N6C(=N4)C="
"C9)c1ccccc1",
"C1=Cc2nc1nc1ccc([nH]1)c(-c1ccccc1)c1nc(nc3ccc([nH]3)c2-c2ccccc2)C=C1"},
{"c1ccc(cc1)C2=C(C3=[N]4C(=C5C=CC6=C(C(=C7C=CC8=[N]7[Co]4(N56)n9c8ccc92)"
"c1ccccc1)c1ccccc1)C=C3)c1ccccc1",
"C1=Cc2nc1c(-c1ccccc1)c(-c1ccccc1)c1ccc([nH]1)c1nc(c(-c3ccccc3)c(-"
"c3ccccc3)c3ccc2[nH]3)C=C1"},
{"c1ccc(cc1)C[C@H]2C(=O)O[Cu]3[N]2=Cc4ccccc4O3",
"O=C(O)[C@H](Cc1ccccc1)N=Cc1ccccc1O"},
{"c1ccc(cc1)[C@H]2COC3=[N]2[Rh]4c5c3cccc5C6=[N]4[C@H](CO6)c7ccccc7",
"[Rh]c1c(C2=N[C@@H](c3ccccc3)CO2)cccc1C1=N[C@@H](c2ccccc2)CO1"},
{"c1cc(ccc1C[N@]23CCCN4[Ni]25N(CCCN5CC3)CC4)C[N@]67CCC[N@@]8[Ni@@]69[N@]("
"CCC[N@]9CC7)CC8",
"c1cc(CN2CCCNCCNCCCNCC2)ccc1CN1CCCNCCNCCCNCC1"},
{"c1cc(ccc1C[N@]23CCC[N@H]4[Cu@@]25[N@H](CCC[N@H]5CC3)CC4)C[N@@]67CCC[N@"
"H]8[Cu]69[N@H](CCC[N@H]9CC7)CC8",
"c1cc(CN2CCCNCCNCCCNCC2)ccc1CN1CCCNCCNCCCNCC1"},
{"c1cc(ccc1CNC(=O)C23[CH]4=[CH]5[Re]426([CH]5=[CH]63)(C#O)(C#O)C#O)S(=O)("
"=O)N",
"NS(=O)(=O)c1ccc(CNC(=O)C2C=CC=C2)cc1"},
{"c1cc(ccc1NC(=O)CCCC[C@H]2[C@@H]3[C@H](CS2)NC(=O)N3)S(=O)(=O)[N-]4CC["
"NH2][Ir+3]4",
"NCCNS(=O)(=O)c1ccc(NC(=O)CCCC[C@@H]2SC[C@@H]3NC(=O)N[C@H]23)cc1"},
{"c1cc(ccc1NC(=O)CCCC[C@H]2[C@@H]3[C@H](CS2)NC(=O)N3)S(=O)(=O)[N@@]4CCN["
"Ru]456789([CH]1=[CH]5[CH]6=[CH]7[CH]8=[CH]91)Cl",
"NCCNS(=O)(=O)c1ccc(NC(=O)CCCC[C@@H]2SC[C@@H]3NC(=O)N[C@H]23)cc1"},
{"C1CCC(CC1)[NH2][Pt+2][NH3]", "NC1CCCCC1"},
{"c1ccc(cc1)[P](c2ccccc2)(c3ccccc3)[Pt+2]4(c5ccccc5C6=CC=CC=[N]64)Cl",
"c1ccc(P(c2ccccc2)c2ccccc2)cc1"},
{"C1CC[C@@H]2[C@@H](C1)[N]34CC5=[N]([Fe]367([N]2(CC8=CC=CC=[N]68)CC(=O)"
"O7)OC(=O)C4)C=CC=C5",
"O=C(O)CN(Cc1ccccn1)[C@@H]1CCCC[C@H]1N(CC(=O)O)Cc1ccccn1"},
{"C1CC[C@@H]2[C@@H](C1)[NH2][Pt+2][NH2]2", "N[C@@H]1CCCC[C@H]1N"},
{"C1=CC=[N]2C(=C1)C3=CC=CC4=[N]3[Pt+]2([N]5=C4C=CC=C5)Cl",
"c1ccc(-c2cccc(-c3ccccn3)n2)nc1"},
{"C1=CC=[N]2C(=C1)C3=CC=CC=[N]3[Ru+2]245([N]6=C7C(=CC=C6)c8c(nc9c1c2c3c("
"c9n8)C=CC=[N]3[Ru+2]36([N]2=CC=C1)([N]1=C(C=CC=C1)C1=[N]3C=CC=C1)[N]1="
"C(C=CC=C1)C1=[N]6C=CC=C1)C1=CC=C[N]4=C17)[N]1=CC=CC=C1C1=CC=CC=[N]51",
"c1cnc2c(c1)c1nc3c4cccnc4c4ncccc4c3nc1c1cccnc12"},
{"C1=CC=[N]2C(=C1)C3=CC=CC=[N]3[Ru+2]245([N]6=C(C=CC=C6)C7=[N]4C=CC=C7)["
"N]8=C9C(=CC=C8)c1c(nc2c3c4c6c(c2n1)C=CC=[N]6[Ru+2]12([N]4=CC=C3)([N]3="
"C(C=CC=C3)C3=[N]1C=CC=C3)[N]1=C(C=CC=C1)C1=[N]2C=CC=C1)C1=C9[N]5=CC=C1",
"c1cnc2c(c1)c1nc3c4cccnc4c4ncccc4c3nc1c1cccnc12"},
{"C1=CC=[N]2C(=C1)C3=[N]4[Ru+2]25([N]6=C(C4=CC=C3)C=CC=C6)[N]7=C8C(=CC="
"C7)C=CC9=CC=C[N]5=C98",
"c1ccc(-c2cccc(-c3ccccn3)n2)nc1"},
{"C1=CC=[N]2C(=C1)N(C3=[N]([Ru]2Cl)C=CC=C3)CCCCCN",
"NCCCCCN(c1ccccn1)c1ccccn1"},
{"c1ccnc(c1)C2=[N](C=CC=C2)[Ru]([N]3=CNC=C3)[N]4=C(C=CC=C4)c5ccccn5",
"c1ccc(-c2ccccn2)nc1"},
{"C1=CC=[N](C=C1)[Pt+2]([NH3])([NH3])Cl", "c1ccncc1"},
{"C1CC(=O)N(C1=O)CCC23=[CH]4[Fe]2567891([CH]3=[CH]5[C@H]64)[CH]2=[CH]7C8["
"CH]9=[CH]12",
"O=C1CCC(=O)N1CCC1=CCC=C1"},
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{"[OH2][Ca+2]([OH2])([OH2])([OH2])([OH2])([OH2])[OH2]", "O"},
{"[OH2][Ca+2]([OH2])([OH2])([OH2])([OH2])([OH2])([OH2])[OH2]", "O"},
{"[OH2][K]([OH2])([OH2])[OH2]", "O"},
{"[OH2][Mg+2]", "O"},
{"[OH2][Mg+2][OH2]", "O"},
{"[OH2][Mg+2]([OH2])[OH2]", "O"},
{"[OH2][Mg+2]([OH2])([OH2])[OH2]", "O"},
{"[OH2][Mg+2]([OH2])([OH2])([OH2])[OH2]", "O"},
{"[OH2][Mg+2]([OH2])([OH2])([OH2])([OH2])[OH2]", "O"},
{"[OH2-][Na+]", "O"},
{"[OH2-][Na+][OH2-]", "O"},
{"[OH2-][Na+]([OH2-])[OH2-]", "O"},
{"[OH2-][Na+]([OH2-])([OH2-])([OH2-])[OH2-]", "O"},
{"[OH2-][Na+]([OH2-])([OH2-])([OH2-])([OH2-])[OH2-]", "O"},
};
std::string normalizationSmarts = R"DATA(// Name SMIRKS
// Opposite of #2.1 in InChI technical manual? Covered by RDKit Sanitization.
Nitro to N+(O-)=O [N,P,As,Sb;X3:1](=[O,S,Se,Te:2])=[O,S,Se,Te:3]>>[*+1:1]([*-1:2])=[*:3]
Sulfone to S(=O)(=O) [S+2:1]([O-:2])([O-:3])>>[S+0:1](=[O-0:2])(=[O-0:3])
Pyridine oxide to n+O- [n:1]=[O:2]>>[n+:1][O-:2]
Azide to N=N+=N- [N:2]=[N:3]#[N:4]>>[N:2]=[N+:3]=[N-:4]
Broken azide to N=N+=N- [N:2]=[N:3]=[N:4]>>[NH0:2]=[NH0+:3]=[NH0-:4]
Diazo/azo to =N+=N- [*:1]=[N:2]#[N:3]>>[*:1]=[N+:2]=[N-:3]
Sulfoxide to -S+(O-)- [!O:1][S+0;X3:2](=[O:3])[!O:4]>>[*:1][S+1:2]([O-:3])[*:4]
// Equivalent to #1.5 in InChI technical manual
Phosphate to P(O-)=O [O,S,Se,Te;-1:1][P+;D4:2][O,S,Se,Te;-1:3]>>[*+0:1]=[P+0;D5:2][*-1:3]
// Equivalent to #1.8 in InChI technical manual
C/S+N to C/S=N+ [C,S;X3+1:1]([NX3:2])[NX3!H0:3]>>[*+0:1]([N:2])=[N+:3]
// Equivalent to #1.8 in InChI technical manual
P+N to P=N+ [P;X4+1:1]([NX3:2])[NX3!H0:3]>>[*+0:1]([N:2])=[N+:3]
Normalize hydrazine-diazonium [CX4:1][NX3H:2]-[NX3H:3][CX4:4][NX2+:5]#[NX1:6]>>[CX4:1][NH0:2]=[NH+:3][C:4][N+0:5]=[NH:6]
// Equivalent to #1.3 in InChI technical manual
Recombine 1,3-separated charges [N,P,As,Sb,O,S,Se,Te;-1:1]-[A+0:2]=[N,P,As,Sb,O,S,Se,Te;+1:3]>>[*-0:1]=[*:2]-[*+0:3]
Recombine 1,3-separated charges [n,o,p,s;-1:1]:[a:2]=[N,O,P,S;+1:3]>>[*-0:1]:[*:2]-[*+0:3]
Recombine 1,3-separated charges [N,O,P,S;-1:1]-[a:2]:[n,o,p,s;+1:3]>>[*-0:1]=[*:2]:[*+0:3]
Recombine 1,5-separated charges [N,P,As,Sb,O,S,Se,Te;-1:1]-[A+0:2]=[A:3]-[A:4]=[N,P,As,Sb,O,S,Se,Te;+1:5]>>[*-0:1]=[*:2]-[*:3]=[*:4]-[*+0:5]
Recombine 1,5-separated charges [n,o,p,s;-1:1]:[a:2]:[a:3]:[c:4]=[N,O,P,S;+1:5]>>[*-0:1]:[*:2]:[*:3]:[c:4]-[*+0:5]
Recombine 1,5-separated charges [N,O,P,S;-1:1]-[c:2]:[a:3]:[a:4]:[n,o,p,s;+1:5]>>[*-0:1]=[c:2]:[*:3]:[*:4]:[*+0:5]
// Conjugated cation rules taken from Francis Atkinson's standardiser. Those that can reduce aromaticity aren't included
Normalize 1,3 conjugated cation [N,O;+0!H0:1]-[A:2]=[N!$(*[O-]),O;+1H0:3]>>[*+1:1]=[*:2]-[*+0:3]
Normalize 1,3 conjugated cation [n;+0!H0:1]:[c:2]=[N!$(*[O-]),O;+1H0:3]>>[*+1:1]:[*:2]-[*+0:3]
//Normalization('Normalize 1,3 conjugated cation', '[N,O;+0!H0:1]-[c:2]:[n!$(*[O-]),o;+1H0:3]>>[*+1:1]=[*:2]:[*+0:3]'),
Normalize 1,5 conjugated cation [N,O;+0!H0:1]-[A:2]=[A:3]-[A:4]=[N!$(*[O-]),O;+1H0:5]>>[*+1:1]=[*:2]-[*:3]=[*:4]-[*+0:5]
Normalize 1,5 conjugated cation [n;+0!H0:1]:[a:2]:[a:3]:[c:4]=[N!$(*[O-]),O;+1H0:5]>>[n+1:1]:[*:2]:[*:3]:[*:4]-[*+0:5]
// Normalization('Normalize 1,5 conjugated cation', '[N,O;+0!H0:1]-[c:2]:[a:3]:[a:4]:[n!$(*[O-]),o;+1H0:5]>>[*+1:1]=[c:2]:[*:3]:[*:4]:[*+0:5]'),
// Normalization('Normalize 1,5 conjugated cation', '[n;+0!H0:1]1:[a:2]:[a:3]:[a:4]:[n!$(*[O-]);+1H0:5]1>>[n+1:1]1:[*:2]:[*:3]:[*:4]:[n+0:5]1'),
// Normalization('Normalize 1,5 conjugated cation', '[n;+0!H0:1]:[a:2]:[a:3]:[a:4]:[n!$(*[O-]);+1H0:5]>>[n+1:1]:[*:2]:[*:3]:[*:4]:[n+0:5]'),
// Equivalent to #1.6 in InChI technical manual. RDKit Sanitization handles this for perchlorate.
Charge normalization [F,Cl,Br,I,At;-1:1]=[O:2]>>[*-0:1][O-:2]
Charge recombination [N,P,As,Sb;-1:1]=[C+;v3:2]>>[*+0:1]#[C+0:2]
Tetravalent [N] to [N+] [N+0;v4:1]>>[N+1:1]
Tetravalent [N-] to [N] [N-1;v4:1]>>[N+0:1]
[OH-] to [O-] [N,P,As,Sb,O,S,Se,Te:1][OH-:2]>>[N,P,As,Sb,O,S,Se,Te:1][OH0;1-:2]
Duplicate C=O [C:1](=[O:2])=O>>[C:1]=[O:2]
CH-C=[O,S] to C=C-[O,S] in aromatic ring [#6;H1:1][#6:2]=[#8,#16;+0:3][*:4]>>[CH0:1]=[C:2][*:3][*:4]
CH2-C=[O,S] to CH=C-[O,S] in aromatic ring [#6;H2:1][#6:2]=[#8,#16;+0:3][*:4]>>[CH1:1]=[C:2][*:3][*:4]
Negatively charged divalent O,S [O,S;v2;-1:1]>>[*;H0;-0:1]
Neutral trivalent O,S [O,S;v3;+0:1]>>[*;+1:1]
Broken 1,3-dioxol [#8,#16;v3,v4:1]=[#6:2][#8,#16:3]>>[*;+0;H0:1][C:2][*;+0;H0:3]
Positively charged tetravalent B [B;v4;+1:1]>>[*;-1:1])DATA";
std::stringstream normalizationSmartsStream(normalizationSmarts);
MolStandardize::CleanupParameters params;
MolStandardize::Normalizer normalizer(normalizationSmartsStream,
params.maxRestarts);
MolStandardize::MetalDisconnector metalDisconnector;
MolStandardize::Reionizer reionizer;
MolStandardize::LargestFragmentChooser largestFragmentChooser;
MolStandardize::Uncharger uncharger;
unsigned int failedOp;
for (const auto &pair : ligandExpoSmiles) {
RWMOL_SPTR rwmol(SmilesToMol(pair.first, 0, false));
MolOps::sanitizeMol(
*rwmol, failedOp,
MolOps::SANITIZE_CLEANUP | MolOps::SANITIZE_FINDRADICALS);
metalDisconnector.disconnect(*rwmol);
ROMOL_SPTR mol(normalizer.normalize(static_cast<const ROMol &>(*rwmol)));
rwmol.reset(new RWMol(*mol));
MolOps::sanitizeMol(*rwmol);
mol.reset(reionizer.reionize(static_cast<const ROMol &>(*rwmol)));
MolOps::assignStereochemistry(*mol);
mol.reset(largestFragmentChooser.choose(*mol));
mol.reset(uncharger.uncharge(*mol));
rwmol.reset(new RWMol(*mol));
MolOps::sanitizeMol(*rwmol);
std::unique_ptr<ROMol> refmol(SmilesToMol(pair.second));
auto refsmi = MolToSmiles(*refmol);
auto prodsmi = MolToSmiles(static_cast<const ROMol &>(*rwmol));
TEST_ASSERT(prodsmi == refsmi);
}
BOOST_LOG(rdDebugLog) << "Finished" << std::endl;
}
void testOrganometallics() {
BOOST_LOG(rdDebugLog)
<< "-----------------------\n test organometallic disconnections"
<< std::endl;
std::string rdbase = getenv("RDBASE");
std::string test_dir = rdbase + "/Code/GraphMol/MolStandardize/test_data";
std::vector<std::pair<std::string, std::string>> test_files = {
{"CPLX_0001.mol",
R"(O=C([O-])CN(CCN(CC(=O)[O-])CC(=O)[O-])CC(=O)[O-].[Mg+2].[Na+].[Na+])"},
{"CPLX_0002.mol",
R"(O=C([O-])CN(CCN(CC(=O)[O-])CC(=O)[O-])CC(=O)[O-].[Fe+2].[Na+].[Na+])"},
{"MOL_00001.mol",
R"([Pd].c1ccc(P(c2ccccc2)c2ccccc2)cc1.c1ccc(P(c2ccccc2)c2ccccc2)cc1.c1ccc(P(c2ccccc2)c2ccccc2)cc1.c1ccc(P(c2ccccc2)c2ccccc2)cc1)"},
{"MOL_00002.mol",
R"(ClCCl.[Cl-].[Cl-].[Fe+2].[Pd+2].c1ccc(P(c2ccccc2)[c-]2cccc2)cc1.c1ccc(P(c2ccccc2)[c-]2cccc2)cc1)"},
{"MOL_00003.mol",
R"([Cl-].[Cl-].[Fe+2].[Pd+2].c1ccc(P(c2ccccc2)[c-]2cccc2)cc1.c1ccc(P(c2ccccc2)[c-]2cccc2)cc1)"},
{"MOL_00004.mol",
R"(CC(C)c1cc(C(C)C)c(-c2ccccc2P(C2CCCCC2)C2CCCCC2)c(C(C)C)c1.Nc1ccccc1-c1[c-]cccc1.[Cl-].[Pd+2])"},
{"MOL_00005.mol",
R"(CCCCP(C12CC3CC(CC(C3)C1)C2)C12CC3CC(CC(C3)C1)C2.CS(=O)(=O)[O-].Nc1ccccc1-c1[c-]cccc1.[Pd+2])"},
{"MOL_00006.mol",
R"(CCCCP(C12CC3CC(CC(C3)C1)C2)C12CC3CC(CC(C3)C1)C2.CS(=O)(=O)[O-].Nc1ccccc1-c1[c-]cccc1.[Pd+2])"},
{"MOL_00007.mol",
R"(CC(C)c1cc(C(C)C)c(-c2ccccc2P(C2CCCCC2)C2CCCCC2)c(C(C)C)c1.CS(=O)(=O)[O-].Nc1ccccc1-c1[c-]cccc1.[Pd+2])"},
{"MOL_00008.mol",
R"(CC(C)(C)P([c-]1cccc1)C(C)(C)C.CC(C)(C)P([c-]1cccc1)C(C)(C)C.[Cl-].[Cl-].[Fe+2].[Pd+2])"},
{"MOL_00009.mol",
R"(CN(C)c1ccc(P(C(C)(C)C)C(C)(C)C)cc1.CN(C)c1ccc(P(C(C)(C)C)C(C)(C)C)cc1.[Cl-].[Cl-].[Pd+2])"},
{"MOL_00010.mol",
R"(Cc1cc(C(c2ccccc2)c2ccccc2)c(-n2[c-][n+](-c3c(C(c4ccccc4)c4ccccc4)cc(C)cc3C(c3ccccc3)c3ccccc3)cc2)c(C(c2ccccc2)c2ccccc2)c1.[CH2-]/C=C/c1ccccc1.[Cl-].[Pd+2])"},
{"MOL_00011.mol",
R"([Cl-].[Cl-].[Ni+2].c1ccc(P(CCCP(c2ccccc2)c2ccccc2)c2ccccc2)cc1)"},
{"MOL_00012.mol", R"(C1=C\CC/C=C\CC/1.CC1=C(C)C(=O)C(C)=C(C)C1=O.[Ni])"},
{"MOL_00013.mol", R"(CN(C)CCN(C)C.Cc1[c-]cccc1.[Cl-].[Ni+2])"},
{"MOL_00014.mol",
R"(Cc1cc(C)cc(/C=C/c2cc(C)cc(C)c2)c1.Cc1cc(C)cc(/C=C/c2cc(C)cc(C)c2)c1.Cc1cc(C)cc(/C=C/c2cc(C)cc(C)c2)c1.[Ni])"},
{"MOL_00015.mol",
R"(CC(C)(C)c1ccc(/C=C/c2ccc(C(C)(C)C)cc2)cc1.CC(C)(C)c1ccc(/C=C/c2ccc(C(C)(C)C)cc2)cc1.CC(C)(C)c1ccc(/C=C/c2ccc(C(C)(C)C)cc2)cc1.[Ni])"},
{"diethylzinc.mol", R"([CH2-]CC.[CH2-]CC.[Zn+2])"},
{"edta_case.mol",
R"(O=C([O-])CN(CCN(CC(=O)[O-])CC(=O)[O-])CC(=O)[O-].[Mg+2].[Na+].[Na+])"},
{"ferrocene.mol", R"([Fe+2].c1cc[cH-]c1.c1cc[cH-]c1)"},
{"ferrocene_1.mol", R"(C[c-]1cccc1.C[c-]1cccc1.[Fe+2])"},
{"grignard_1.mol", R"([CH3-].[Cl-].[Mg+2])"},
{"grignard_2.mol", R"([Cl-].[Mg+2].[c-]1ccccc1)"},
{"lithium_1.mol", R"([CH3-].[Li+])"},
{"lithium_2.mol", R"([Li+].[c-]1ccccc1)"},
{"phenylzincbromide.mol", R"([Br-].[Zn+2].[c-]1ccccc1)"},
{"ruthenium.mol",
R"([Cl-].[Cl-].[Cl-].[Cl-].[Ru+2].[Ru+2].c1ccccc1.c1ccccc1)"},
{"sodium_1.mol", R"([Na+].c1cc[cH-]c1)"},
{"sodium_2.mol",
R"(CN(C)CCN(C)CCN(C)C.CN(C)CCN(C)CCN(C)C.[Na+].[Na+].[c-]1ccccc1.[c-]1ccccc1)"},
{"weirdzinc_1.mol",
R"([Zn+2].[Zn+2].[c-]1ccccc1.[c-]1ccccc1.[c-]1ccccc1.[c-]1ccccc1)"},
{"weirdzinc_2.mol",
R"([Cu+].[Cu+].[Zn+2].[Zn+2].[c-]1ccccc1.[c-]1ccccc1.[c-]1ccccc1.[c-]1ccccc1.[c-]1ccccc1.[c-]1ccccc1)"}};
for (auto &test_file : test_files) {
std::string full_file = test_dir + "/" + test_file.first;
bool takeOwnership = true;
SDMolSupplier mol_supplier(full_file, takeOwnership);
std::unique_ptr<ROMol> m(mol_supplier.next());
TEST_ASSERT(m);
std::unique_ptr<ROMol> dm(MolStandardize::disconnectOrganometallics(*m));
// std::cout << test_file.first << " got : " << MolToSmiles(*dm)
// << " expected : " << test_file.second << std::endl;
TEST_ASSERT(MolToSmiles(*dm) == test_file.second);
std::unique_ptr<RWMol> em(new RWMol(*m));
MolStandardize::disconnectOrganometallics(*em);
TEST_ASSERT(MolToSmiles(*em) == test_file.second);
}
{
auto m("[CH2-](->[K+])c1ccccc1"_smiles);
TEST_ASSERT(m);
MolStandardize::disconnectOrganometallics(*m);
TEST_ASSERT(MolToSmiles(*m) == "[CH2-]c1ccccc1.[K+]");
}
}
int main() {
RDLog::InitLogs();
boost::logging::disable_logs("rdApp.info");
testCleanup();
testStandardizeSm();
testMetalDisconnector();
testNormalize();
testNormalizeMultiFrags();
testCharge();
testMetalDisconnectorLigandExpo();
testEnumerateTautomerSmiles();
testOrganometallics();
return 0;
}
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