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/**********************************************************************
aliastest.cpp - unit testing code for alias.h and alias.cpp
Copyright (C) 2019 by Alex Ustinov
This program is free software; you can redistribute it and/or modify
it under the terms of the GNU General Public License as published by
the Free Software Foundation version 2 of the License.
This program is distributed in the hope that it will be useful,
but WITHOUT ANY WARRANTY; without even the implied warranty of
MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
GNU General Public License for more details.
***********************************************************************/
#include "obtest.h"
#include <openbabel/mol.h>
#include <openbabel/obconversion.h>
#include <openbabel/atom.h>
#include <openbabel/obiter.h>
#include <openbabel/alias.h>
using namespace std;
using namespace OpenBabel;
// a class for a test case should contain smiles of the molecule, number of aliases that
// are expected to be produced, and number of unaliasable atoms that are not parts of aliases
// note this test uses standard superatom.txt file included in OpenBabel
class AliasTestExample {
string _smiles;
unsigned int _num_aliases;
unsigned int _num_nonaliased;
public:
AliasTestExample(const string smiles, const unsigned int num_aliases, const unsigned int num_nonaliased):
_smiles(smiles), _num_aliases(num_aliases), _num_nonaliased(num_nonaliased) {};
// this will create aliases in the molecule, then remove all atoms present in aliases,
// count aliases and atoms that are not present in aliases, and compare with the expected result
void test() {
OBMol mol;
AliasData ad;
OBConversion conv;
OB_REQUIRE( conv.SetInFormat("smi") );
OB_REQUIRE( conv.ReadString(&mol, _smiles) );
ad.AddAliases(&mol);
AliasData::RevertToAliasForm(mol);
unsigned int alias_count = 0;
unsigned int nonaliased_count = 0;
FOR_ATOMS_OF_MOL(a, mol)
{
AliasData* ad = nullptr;
if ( static_cast<AliasData*>(a->GetData(AliasDataType)) )
alias_count++;
else
nonaliased_count++;
}
//cout << "Testing smiles " << _smiles << endl;
//cout << "number of aliases " << alias_count << ", number of nonaliased atoms " << nonaliased_count << endl;
OB_ASSERT( nonaliased_count == _num_nonaliased );
OB_ASSERT( alias_count == _num_aliases );
}
};
void testAliases()
{
AliasTestExample test_set[] = {
// methyl tert-butyl ether -> MeOtBu
AliasTestExample("COC(C)(C)C", 2, 0),
// diethylmalonate -> EtO2CCCO2Et
AliasTestExample("CCOC(=O)CC(=O)OCC", 2, 1),
// thioanisole -> PhSMe
AliasTestExample("c1ccccc1SC", 1, 6),
// oxalate dianion -> -O2CCO2-
AliasTestExample("[O-]C(=O)C(=O)[O-]", 2, 0),
// diphenyl - nothing to alias
AliasTestExample("c1ccccc1c2ccccc2", 0, 12)
};
for (auto i : test_set) {
i.test();
}
cout << endl;
}
int aliastest(int argc, char* argv[])
{
// Define location of file formats for testing
#ifdef FORMATDIR
char env[BUFF_SIZE];
snprintf(env, BUFF_SIZE, "BABEL_LIBDIR=%s", FORMATDIR);
putenv(env);
#endif
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;
}
}
switch(choice) {
case 1:
testAliases();
break;
default:
cout << "Test number " << choice << " does not exist!\n";
return -1;
}
return 0;
}
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