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#include "obtest.h"
#include <openbabel/mol.h>
#include <openbabel/atomclass.h>
#include <openbabel/obconversion.h>
#include <iostream>
#include <string>
#include <vector>
#include <algorithm>
using namespace std;
using namespace OpenBabel;
// A segfault was occuring when a Universal SMILES was output after an InChIfied SMILES.
// This was due to short-circuit caching of InChIs on reading. The fix was to limit
// the situations when the cached value was used, but also to delete the cached value
// in this particular instance.
void test_Issue135_UniversalSmiles()
{
// Test writing U smiles after I smiles
OBConversion conv;
conv.SetInFormat("smi");
OBMol mol;
conv.ReadString(&mol, "C(=O)([O-])C(=O)O");
conv.SetOutFormat("smi");
conv.SetOptions("I", OBConversion::OUTOPTIONS);
std::string res = conv.WriteString(&mol, true);
OB_COMPARE(res, "C(=O)(C(=O)O)[O-]");
conv.SetOptions("U", OBConversion::OUTOPTIONS);
res = conv.WriteString(&mol, true);
OB_COMPARE(res, "C(=O)(C(=O)[O-])O");
}
// Reading an InChI and then adding hydrogens messed up the structure
void test_Issue134_InChI_addH()
{
OBConversion conv;
conv.SetInFormat("inchi");
OBMol mol;
conv.ReadString(&mol, "InChI=1S/C2H7NO/c1-2(3)4/h2,4H,3H2,1H3/t2-/m0/s1");
OB_ASSERT(!mol.HasData(OBGenericDataType::VirtualBondData));
mol.AddHydrogens();
conv.SetOutFormat("smi");
std::string res = conv.WriteString(&mol, true);
OB_COMPARE(res, "C[C@@H](N)O");
}
// Delete hydrogens should not remove charged or isotopic hydrogens or [H][H] or [Cu][H][Cu]
// or hydrogens with assigned atom classes
void test_Issue178_DeleteHydrogens()
{
OBConversion conv;
conv.SetInFormat("smi");
OBMol mol;
// Test DeleteHydrogens() and DeleteNonPolarHydrogens()
static const char *smi[] = { "C[H]", "[H][H]", "C[1H]", "C[H]C", "C[H+]" };
int numHs[] = { 0, 2, 1, 1, 1 };
for (int i = 0; i < 5; ++i) {
for (int j = 0; j < 2; ++j) {
conv.ReadString(&mol, smi[i]);
if (j == 0)
mol.DeleteHydrogens();
else
mol.DeleteNonPolarHydrogens();
int myNumHs = 0;
FOR_ATOMS_OF_MOL(atom, mol)
if (atom->IsHydrogen())
myNumHs++;
OB_COMPARE(myNumHs, numHs[i]);
}
}
// Test DeletePolarHydrogens()
static const char *smiB[] = { "N[H]", "[H][H]", "N[1H]", "N[H]C", "N[H+]" };
int numHsB[] = { 0, 2, 1, 1, 1 };
for (int i = 0; i < 5; ++i) {
conv.ReadString(&mol, smiB[i]);
mol.DeletePolarHydrogens();
int myNumHs = 0;
FOR_ATOMS_OF_MOL(atom, mol)
if (atom->IsHydrogen())
myNumHs++;
OB_COMPARE(myNumHs, numHsB[i]);
}
// Test atom class
// Currently, the SMILES parser does not retain atom classes for hydrogens on reading so...
conv.ReadString(&mol, "C[H]");
OBAtomClassData *ac = new OBAtomClassData;
ac->Add(2, 99); // Assign the hydrogen (atom 2) a class of 99
mol.SetData(ac);
mol.DeleteHydrogens();
int myNumHs = 0;
FOR_ATOMS_OF_MOL(atom, mol)
if (atom->IsHydrogen())
myNumHs++;
OB_COMPARE(myNumHs, 1);
}
void test_Issue305_NumRotors()
{
OBMolPtr mol = OBTestUtil::ReadFile("regressiontest_numrotors.mol");
OB_COMPARE(mol->NumRotors(), 9); // was returning 4
}
void test_PR329_Molfile_RGroups()
{
// There are several way to get an R Group into a mol file
// 1. The existing use of atom maps on dummy atoms in SMILES
OBConversion conv;
OBMol mol;
conv.SetInAndOutFormats("smi", "mol");
conv.ReadString(&mol, "C([*:1]CO[*:2]");
obErrorLog.SetOutputLevel(obError); // avoid warning about no 2D or 3D coords
std::string molfileWithRGP = conv.WriteString(&mol);
obErrorLog.SetOutputLevel(obWarning);
OB_ASSERT( molfileWithRGP.find("R#") != std::string::npos );
OB_ASSERT( molfileWithRGP.find("M RGP 2 2 1 5 2") != std::string::npos); // i.e. atom 2 is labelled R1, atom 5 is labelled R2
// Check negative case
conv.ReadString(&mol, "C([*]CO[*]");
std::string molfileb = conv.WriteString(&mol);
OB_ASSERT( molfileb.find("R#") == std::string::npos );
OB_ASSERT( molfileb.find("M RGP") == std::string::npos);
// 2. By reading a molfile that use the R#, RGP notation
conv.SetInAndOutFormats("mol", "mol");
conv.ReadString(&mol, molfileWithRGP);
molfileb = conv.WriteString(&mol);
OB_ASSERT( molfileb.find("R#") != std::string::npos );
OB_ASSERT( molfileb.find("M RGP 2 2 1 5 2") != std::string::npos); // i.e. atom 2 is labelled R1, atom 5 is labelled R2
// 3. By reading a molfile that specifies the atom alias as Rn, where n is an integer
std::string molfileWithAlias = "\n"
" OpenBabel07211621152D\n"
"\n"
" 2 1 0 0 0 0 0 0 0 0999 V2000\n"
" 1.0000 0.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0\n"
" 0.0000 1.0000 0.0000 * 0 0 0 0 0 0 0 0 0 0 0 0\n"
" 1 2 1 0 0 0 0\n"
"A 2\n"
"R1\n"
"M END";
conv.SetInAndOutFormats("mol", "mol");
conv.ReadString(&mol, molfileWithAlias);
std::string molfile = conv.WriteString(&mol);
OB_ASSERT( molfile.find("R#") != std::string::npos );
OB_ASSERT( molfile.find("M RGP 1 2 1") != std::string::npos); // i.e. atom 2 is labelled R1
// Check negative case
molfileWithAlias = "\n"
" OpenBabel07211621152D\n"
"\n"
" 2 1 0 0 0 0 0 0 0 0999 V2000\n"
" 1.0000 0.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0\n"
" 0.0000 1.0000 0.0000 * 0 0 0 0 0 0 0 0 0 0 0 0\n"
" 1 2 1 0 0 0 0\n"
"A 2\n"
"R\n"
"M END";
conv.SetInAndOutFormats("mol", "mol");
obErrorLog.SetOutputLevel(obError); // avoid warning "Alias R was not chemically interpreted"
conv.ReadString(&mol, molfileWithAlias);
obErrorLog.SetOutputLevel(obWarning);
molfile = conv.WriteString(&mol);
OB_ASSERT( molfile.find("R#") == std::string::npos );
OB_ASSERT( molfile.find("M RGP") == std::string::npos);
// 4. By reading a molfile that specifies the element name as R1, etc.
std::string molfileWithRGroupElementName = "\n"
" OpenBabel07211621152D\n"
"\n"
" 2 1 0 0 0 0 0 0 0 0999 V2000\n"
" 1.0000 0.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0\n"
" 0.0000 1.0000 0.0000 R1 0 0 0 0 0 0 0 0 0 0 0 0\n"
" 1 2 1 0 0 0 0\n"
"M END";
conv.SetInAndOutFormats("mol", "mol");
conv.ReadString(&mol, molfileWithRGroupElementName);
molfile = conv.WriteString(&mol);
OB_ASSERT( molfile.find("R#") != std::string::npos );
OB_ASSERT( molfile.find("M RGP 1 2 1") != std::string::npos); // i.e. atom 2 is labelled R1
}
int regressionstest(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:
test_Issue135_UniversalSmiles();
break;
case 221:
test_Issue134_InChI_addH();
break;
case 222:
test_Issue178_DeleteHydrogens();
break;
case 223:
test_Issue305_NumRotors();
break;
case 224:
test_PR329_Molfile_RGroups();
break;
//case N:
// YOUR_TEST_HERE();
// Remember to update CMakeLists.txt with the number of your test
// break;
default:
cout << "Test number " << choice << " does not exist!\n";
return -1;
}
return 0;
}
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