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openbabel/test/smilestest.cpp
T
Noel O'Boyle c047a594ae Everything else
2019-04-04 20:20:04 +01:00

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#include "obtest.h"
#include <openbabel/mol.h>
#include <openbabel/obconversion.h>
#include <openbabel/stereo/tetrahedral.h>
#include <openbabel/stereo/cistrans.h>
#include <openbabel/stereo/squareplanar.h>
#include <openbabel/graphsym.h>
#include <openbabel/canon.h>
#include <openbabel/atom.h>
using namespace std;
using namespace OpenBabel;
/*
* Stereo classes have their own tests. This file tests if the smiles
* format uses them correctly.
*/
void testTetrahedralStereo1()
{
cout << "testTetrahedralStereo1()" << endl;
// read a smiles string
OBMol mol;
OBConversion conv;
OB_REQUIRE( conv.SetInFormat("smi") );
cout << "smiles: C[C@H](O)N" << endl;
OB_REQUIRE( conv.ReadString(&mol, "C[C@H](O)N") );
// get the stereo data
OB_REQUIRE( mol.HasData(OBGenericDataType::StereoData) );
std::vector<OBGenericData *> stereoData = mol.GetAllData(OBGenericDataType::StereoData);
OB_REQUIRE( stereoData.size() == 1 );
// convert to tetrahedral data
OB_REQUIRE( ((OBStereoBase*)stereoData[0])->GetType() == OBStereo::Tetrahedral );
OBTetrahedralStereo *ts = dynamic_cast<OBTetrahedralStereo*>(stereoData[0]);
OB_REQUIRE( ts );
// print the configuration
cout << *ts << endl;
// construct a valid configuration here
//
// C[C@H](O)N
// 0 1 2 3 4 <- ids
//
OBTetrahedralStereo::Config cfg(1, 0, OBStereo::MakeRefs(4, 3, 2), OBStereo::Clockwise);
// compare stereochemistry
OB_REQUIRE( ts->GetConfig() == cfg );
cout << endl;
}
void genericSmilesCanonicalTest(const std::string &smiles)
{
cout << "Testing generic smiles <-> canonical smiles" << endl;
// read a smiles string
OBMol mol;
OBConversion conv;
OB_REQUIRE( conv.SetInFormat("smi") );
OB_REQUIRE( conv.SetOutFormat("can") );
cout << "smiles: " << smiles << endl;
// read a smiles string
OB_REQUIRE( conv.ReadString(&mol, smiles) );
// store the stereo data for the smiles string using unique symmetry ids
std::vector<OBTetrahedralStereo::Config> tetrahedral1;
std::vector<OBCisTransStereo::Config> cistrans1;
std::vector<OBSquarePlanarStereo::Config> squareplanar1;
// get the stereo data
OB_ASSERT( mol.HasData(OBGenericDataType::StereoData) );
std::vector<OBGenericData *> stereoData = mol.GetAllData(OBGenericDataType::StereoData);
std::vector<unsigned int> canlbls;
std::vector<unsigned int> symclasses;
OBGraphSym gs1(&mol);
gs1.GetSymmetry(symclasses);
CanonicalLabels(&mol, symclasses, canlbls);
cout << "mol.NumAtoms = " << mol.NumAtoms() << endl;
for (std::vector<OBGenericData*>::iterator data = stereoData.begin(); data != stereoData.end(); ++data) {
if (((OBStereoBase*)*data)->GetType() == OBStereo::Tetrahedral) {
// convert to tetrahedral data
OBTetrahedralStereo *ts = dynamic_cast<OBTetrahedralStereo*>(*data);
OB_REQUIRE( ts );
OB_ASSERT( ts->IsValid() );
if (!ts->IsValid())
continue;
OBTetrahedralStereo::Config config = ts->GetConfig();
// convert atom ids to symmetry ids
if (mol.GetAtomById(config.center))
config.center = canlbls.at( mol.GetAtomById(config.center)->GetIdx() - 1 );
if (mol.GetAtomById(config.from))
config.from = canlbls.at( mol.GetAtomById(config.from)->GetIdx() - 1 );
if (mol.GetAtomById(config.refs[0]))
config.refs[0] = canlbls.at( mol.GetAtomById(config.refs[0])->GetIdx() - 1 );
if (mol.GetAtomById(config.refs[1]))
config.refs[1] = canlbls.at( mol.GetAtomById(config.refs[1])->GetIdx() - 1 );
if (mol.GetAtomById(config.refs[2]))
config.refs[2] = canlbls.at( mol.GetAtomById(config.refs[2])->GetIdx() - 1 );
cout << "Config with symmetry ids: " << config << endl;
tetrahedral1.push_back(config);
} else
if (((OBStereoBase*)*data)->GetType() == OBStereo::CisTrans) {
// convert to tetrahedral data
OBCisTransStereo *ct = dynamic_cast<OBCisTransStereo*>(*data);
OB_REQUIRE( ct );
OB_ASSERT( ct->IsValid() );
OBCisTransStereo::Config config = ct->GetConfig();
// convert atom ids to symmetry ids
config.begin = canlbls.at( mol.GetAtomById(config.begin)->GetIdx() - 1 );
config.end = canlbls.at( mol.GetAtomById(config.end)->GetIdx() - 1 );
if (mol.GetAtomById(config.refs[0]))
config.refs[0] = canlbls.at( mol.GetAtomById(config.refs[0])->GetIdx() - 1 );
if (mol.GetAtomById(config.refs[1]))
config.refs[1] = canlbls.at( mol.GetAtomById(config.refs[1])->GetIdx() - 1 );
if (mol.GetAtomById(config.refs[2]))
config.refs[2] = canlbls.at( mol.GetAtomById(config.refs[2])->GetIdx() - 1 );
if (mol.GetAtomById(config.refs[3]))
config.refs[3] = canlbls.at( mol.GetAtomById(config.refs[3])->GetIdx() - 1 );
cout << "Config with symmetry ids: " << config << endl;
cistrans1.push_back(config);
} else
if (((OBStereoBase*)*data)->GetType() == OBStereo::SquarePlanar) {
// convert to tetrahedral data
OBSquarePlanarStereo *sp = dynamic_cast<OBSquarePlanarStereo*>(*data);
OB_REQUIRE( sp );
OB_ASSERT( sp->IsValid() );
if (!sp->IsValid())
continue;
OBSquarePlanarStereo::Config config = sp->GetConfig();
// convert atom ids to symmetry ids
if (mol.GetAtomById(config.center))
config.center = canlbls.at( mol.GetAtomById(config.center)->GetIdx() - 1 );
if (mol.GetAtomById(config.refs[0]))
config.refs[0] = canlbls.at( mol.GetAtomById(config.refs[0])->GetIdx() - 1 );
if (mol.GetAtomById(config.refs[1]))
config.refs[1] = canlbls.at( mol.GetAtomById(config.refs[1])->GetIdx() - 1 );
if (mol.GetAtomById(config.refs[2]))
config.refs[2] = canlbls.at( mol.GetAtomById(config.refs[2])->GetIdx() - 1 );
if (mol.GetAtomById(config.refs[3]))
config.refs[3] = canlbls.at( mol.GetAtomById(config.refs[3])->GetIdx() - 1 );
cout << "Config with symmetry ids: " << config << endl;
squareplanar1.push_back(config);
}
}
// write to can smiles
std::string canSmiles = conv.WriteString(&mol);
cout << "canSmiles: " << canSmiles;
// read can smiles in again
OB_REQUIRE( conv.ReadString(&mol, canSmiles) );
// store the stereo data for the smiles string using unique symmetry ids
std::vector<OBTetrahedralStereo::Config> tetrahedral2;
std::vector<OBCisTransStereo::Config> cistrans2;
std::vector<OBSquarePlanarStereo::Config> squareplanar2;
// get the stereo data
OB_ASSERT( mol.HasData(OBGenericDataType::StereoData) );
stereoData = mol.GetAllData(OBGenericDataType::StereoData);
OBGraphSym gs2(&mol);
gs2.GetSymmetry(symclasses);
CanonicalLabels(&mol, symclasses, canlbls);
cout << "mol.NumAtoms = " << mol.NumAtoms() << endl;
for (std::vector<OBGenericData*>::iterator data = stereoData.begin(); data != stereoData.end(); ++data) {
if (((OBStereoBase*)*data)->GetType() == OBStereo::Tetrahedral) {
// convert to tetrahedral data
OBTetrahedralStereo *ts = dynamic_cast<OBTetrahedralStereo*>(*data);
OB_REQUIRE( ts );
OB_ASSERT( ts->IsValid() );
OBTetrahedralStereo::Config config = ts->GetConfig();
// convert atom ids to symmetry ids
if (mol.GetAtomById(config.center))
config.center = canlbls.at( mol.GetAtomById(config.center)->GetIdx() - 1 );
if (mol.GetAtomById(config.from))
config.from = canlbls.at( mol.GetAtomById(config.from)->GetIdx() - 1 );
if (mol.GetAtomById(config.refs[0]))
config.refs[0] = canlbls.at( mol.GetAtomById(config.refs[0])->GetIdx() - 1 );
if (mol.GetAtomById(config.refs[1]))
config.refs[1] = canlbls.at( mol.GetAtomById(config.refs[1])->GetIdx() - 1 );
if (mol.GetAtomById(config.refs[2]))
config.refs[2] = canlbls.at( mol.GetAtomById(config.refs[2])->GetIdx() - 1 );
cout << "Config with symmetry ids: " << config << endl;
tetrahedral2.push_back(config);
}
if (((OBStereoBase*)*data)->GetType() == OBStereo::CisTrans) {
// convert to tetrahedral data
OBCisTransStereo *ct = dynamic_cast<OBCisTransStereo*>(*data);
OB_REQUIRE( ct );
OB_ASSERT( ct->IsValid() );
OBCisTransStereo::Config config = ct->GetConfig();
// convert atom ids to symmetry ids
config.begin = canlbls.at( mol.GetAtomById(config.begin)->GetIdx() - 1 );
config.end = canlbls.at( mol.GetAtomById(config.end)->GetIdx() - 1 );
if (mol.GetAtomById(config.refs[0]))
config.refs[0] = canlbls.at( mol.GetAtomById(config.refs[0])->GetIdx() - 1 );
if (mol.GetAtomById(config.refs[1]))
config.refs[1] = canlbls.at( mol.GetAtomById(config.refs[1])->GetIdx() - 1 );
if (mol.GetAtomById(config.refs[2]))
config.refs[2] = canlbls.at( mol.GetAtomById(config.refs[2])->GetIdx() - 1 );
if (mol.GetAtomById(config.refs[3]))
config.refs[3] = canlbls.at( mol.GetAtomById(config.refs[3])->GetIdx() - 1 );
cout << "Config with symmetry ids: " << config << endl;
cistrans2.push_back(config);
} else
if (((OBStereoBase*)*data)->GetType() == OBStereo::SquarePlanar) {
// convert to tetrahedral data
OBSquarePlanarStereo *sp = dynamic_cast<OBSquarePlanarStereo*>(*data);
OB_REQUIRE( sp );
OB_ASSERT( sp->IsValid() );
OBSquarePlanarStereo::Config config = sp->GetConfig();
// convert atom ids to symmetry ids
if (mol.GetAtomById(config.center))
config.center = canlbls.at( mol.GetAtomById(config.center)->GetIdx() - 1 );
if (mol.GetAtomById(config.refs[0]))
config.refs[0] = canlbls.at( mol.GetAtomById(config.refs[0])->GetIdx() - 1 );
if (mol.GetAtomById(config.refs[1]))
config.refs[1] = canlbls.at( mol.GetAtomById(config.refs[1])->GetIdx() - 1 );
if (mol.GetAtomById(config.refs[2]))
config.refs[2] = canlbls.at( mol.GetAtomById(config.refs[2])->GetIdx() - 1 );
if (mol.GetAtomById(config.refs[3]))
config.refs[3] = canlbls.at( mol.GetAtomById(config.refs[3])->GetIdx() - 1 );
cout << "Config with symmetry ids: " << config << endl;
squareplanar2.push_back(config);
}
}
// compare the tetrahedral structs
OB_ASSERT( tetrahedral1.size() == tetrahedral2.size() );
for (unsigned int i = 0; i < tetrahedral1.size(); ++i) {
for (unsigned int j = 0; j < tetrahedral2.size(); ++j) {
if (tetrahedral1[i].center == tetrahedral2[j].center)
OB_ASSERT( tetrahedral1[i] == tetrahedral2[j] );
if ( tetrahedral1[i] != tetrahedral2[j] ) {
cout << "1 = " << tetrahedral1[i] << endl;
cout << "2 = " << tetrahedral2[j] << endl;
}
}
}
// compare the cistrans structs
OB_ASSERT( cistrans1.size() == cistrans2.size() );
for (unsigned int i = 0; i < cistrans1.size(); ++i) {
for (unsigned int j = 0; j < cistrans2.size(); ++j) {
if ((cistrans1[i].begin == cistrans2[j].begin) && (cistrans1[i].end == cistrans2[j].end))
OB_ASSERT( cistrans1[i] == cistrans2[j] );
if ((cistrans1[i].begin == cistrans2[j].end) && (cistrans1[i].end == cistrans2[j].begin))
OB_ASSERT( cistrans1[i] == cistrans2[j] );
}
}
// compare the square-planar structs
OB_ASSERT( squareplanar1.size() == squareplanar2.size() );
for (unsigned int i = 0; i < squareplanar1.size(); ++i) {
for (unsigned int j = 0; j < squareplanar2.size(); ++j) {
if (squareplanar1[i].center == squareplanar2[j].center)
OB_ASSERT( squareplanar1[i] == squareplanar2[j] );
if ( squareplanar1[i] != squareplanar2[j] ) {
cout << "1 = " << squareplanar1[i] << endl;
cout << "2 = " << squareplanar2[j] << endl;
}
}
}
cout << "." << endl << endl;
}
int smilestest(int argc, char* argv[])
{
int defaultchoice = 1;
int choice = defaultchoice;
if (argc > 1) {
if(sscanf(argv[1], "%d", &choice) != 1) {
printf("Couldn't parse that input as a number\n");
return -1;
}
}
// Define location of file formats for testing
#ifdef FORMATDIR
char env[BUFF_SIZE];
snprintf(env, BUFF_SIZE, "BABEL_LIBDIR=%s", FORMATDIR);
putenv(env);
#endif
switch(choice) {
case 1:
testTetrahedralStereo1();
// Tetrahedral
genericSmilesCanonicalTest("C[C@H](O)N");
genericSmilesCanonicalTest("Cl[C@@](CCl)(I)Br");
// CisTrans
genericSmilesCanonicalTest("Cl/C=C/F");
break;
case 2:
// SquarePlanar
genericSmilesCanonicalTest("F[Po@SP1](Cl)(Br)I");
genericSmilesCanonicalTest("F[Po@SP2](Br)(Cl)I");
genericSmilesCanonicalTest("F[Po@SP3](Cl)(I)Br");
break;
case 3:
// Mixed
genericSmilesCanonicalTest("CCC[C@@H](O)CC\\C=C\\C=C\\C#CC#C\\C=C\\CO");
genericSmilesCanonicalTest("OC[C@@H](O1)[C@@H](O)[C@H](O)[C@@H](O)[C@@H](O)1");
genericSmilesCanonicalTest("OC[C@@H](O1)[C@@H](O)[C@H](O)[C@@H]2[C@@H]1c3c(O)c(OC)c(O)cc3C(=O)O2");
genericSmilesCanonicalTest("CC(=O)OCCC(/C)=C\\C[C@H](C(C)=C)CCC=C");
genericSmilesCanonicalTest("CC[C@H](O1)CC[C@@]12CCCO2");
genericSmilesCanonicalTest("CN1CCC[C@H]1c2cccnc2");
genericSmilesCanonicalTest("CC(C)[C@@]12C[C@@H]1[C@@H](C)C(=O)C2");
genericSmilesCanonicalTest("CC(C)[C@H]1CC[C@]([C@@H]2[C@@H]1C=C(COC2=O)C(=O)O)(CCl)O");
genericSmilesCanonicalTest("C(CS[14CH2][14C@@H]1[14C@H]([14C@H]([14CH](O1)O)O)O)[C@@H](C(=O)O)N");
genericSmilesCanonicalTest("CCC[C@@H]1C[C@H](N(C1)C)C(=O)NC([C@@H]2[C@@H]([C@@H]([C@H]([C@H](O2)SC)OP(=O)(O)O)O)O)C(C)Cl");
break;
// this structure fails but this is an error in genericSmilesCanonicalTest (It should sort the centers). However, this is
// extensivily tested in other tests.
//genericSmilesCanonicalTest("O1C=C[C@H]([C@H]1O2)c3c2cc(OC)c4c3OC(=O)C5=C4CCC(=O)5");
// FAILING: need to fix graphsymtest first!!
// ring gets converted to aromatic ring, adding H on n (i.e. N -> [nH])
//genericSmilesCanonicalTest("CC1=CN(C(=O)NC1=O)[C@H]2C[C@@H]([C@H](O2)CNCC3=CC=CC=C3)O");
default:
cout << "Test number " << choice << " does not exist!\n";
return -1;
}
return 0;
}
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