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openbabel/test/regressionstest.cpp
T
Noel O'Boyle 2bfe5daa73 Add basic tests
2019-02-27 20:15:55 +00:00

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#include "obtest.h"
#include <openbabel/mol.h>
#include <openbabel/obconversion.h>
#include <openbabel/phmodel.h>
#include <openbabel/elements.h>
#include <iostream>
#include <string>
#include <vector>
#include <algorithm>
using namespace std;
using namespace OpenBabel;
void test_Fix1912_PDBReading()
{
// Reading from a PDB file should set the residues
// and mark chains as perceived
OBMolPtr mol = OBTestUtil::ReadFile("00T_ideal_het.pdb");
OB_ASSERT(mol->HasChainsPerceived());
OBAtom* atom = mol->GetAtom(1);
OBResidue* res = atom->GetResidue();
OB_REQUIRE(res != (OBResidue*)0);
OB_COMPARE(res->GetAtomID(atom), " N19");
OB_COMPARE(res->GetChain(), 'A');
}
std::string remove_slashr(const char* smi)
{
// Remove \r if present to normalise across platforms
std::string ans;
const char *p = smi;
while (*p) {
if (*p != '\r')
ans += *p;
p++;
}
return ans;
}
struct CdxData {
const char* fname;
const char* smi;
};
// Some basic reading of ChemDraw files
// Note that we don't correctly read radicals - TODO
// Also, converting ChemDraw doesn't work with the Read() interface, only Convert()
void test_ChemDraw_Basic()
{
static const CdxData cdxData[] = {
{ "ethanol.cdx", "CCO\t\n" },
// cyclohexane -> benzene reaction, plus another cyclohexane drawn on its own
{ "molrxnmix.cdx", "C1CCCCC1>>c1ccccc1\t\nC1CCCCC1\t\n" },
};
ios_base::openmode imode = ios_base::in | ios_base::binary;
unsigned int size = sizeof(cdxData) / sizeof(CdxData);
OBConversion conv;
OB_REQUIRE(conv.SetInAndOutFormats("cdx", "smi"));
std::stringstream outs;
conv.SetOutStream(&outs);
for (int i=0; i<size; ++i) {
std::string fname = OBTestUtil::GetFilename(cdxData[i].fname);
std::ifstream ifs(fname.c_str(), imode);
OB_REQUIRE(ifs.good());
conv.SetInStream(&ifs);
outs.str("");
conv.Convert();
std::string out = outs.str();
OB_COMPARE(remove_slashr(out.c_str()), cdxData[i].smi);
}
}
// A basic test of functionality
void test_OBChemTsfm()
{
OBMol mol;
OBConversion conv;
conv.SetInFormat("smi");
conv.SetOutFormat("smi");
// Notes to self: Problems with OBChemTsfm:
// tsfm.Init("Cl[C:1]-[C:2]", "[C:1]=[C:2]"); // TODO: Need to change the API to take const char
// Init should wipe the state so that OBChemTsfm can safely be reused
conv.ReadString(&mol, "NCCBr");
OBChemTsfm tsfm;
std::string start("[N:1]-C-C");
std::string end("[N+:1]");
tsfm.Init(start, end);
tsfm.Apply(mol);
std::string out = conv.WriteString(&mol, true);
OB_COMPARE(out, "[NH3+]CCBr");
conv.ReadString(&mol, "ClCCBr");
start = "Cl[C:1]-[C:2]";
end = "[C:1]=[C:2]";
OBChemTsfm b;
b.Init(start, end);
b.Apply(mol);
out = conv.WriteString(&mol, true);
OB_COMPARE(out, "ClC=CBr");
conv.ReadString(&mol, "ClC(=O)[O]");
start = "[#6]-[OD1:1]";
end = "[#6]-[O-1:1]";
OBChemTsfm c;
c.Init(start, end);
c.Apply(mol);
out = conv.WriteString(&mol, true);
OB_COMPARE(out, "ClC(=O)[O-]");
conv.ReadString(&mol, "Cl[C]CBr");
start = "Cl[C:1]-[C:2]";
end = "[C:1]=[C:2]";
OBChemTsfm d;
d.Init(start, end);
d.Apply(mol);
out = conv.WriteString(&mol, true);
OB_COMPARE(out, "Cl[C]=CBr");
}
// Open Babel was previously disappearing triple bonds when provided with SMILES
// containing a triple bond in an aromatic ring
void test_AromaticTripleBond()
{
const char* smis[] = {
"CCc1n[c]#[c]n1CC2CC(C(=O)O2)(c3ccccc3)c4ccccc4",
"CCc1nc#cn1CC2CC(C(=O)O2)(c3ccccc3)c4ccccc4" };
OBConversion conv;
conv.SetInFormat("smi");
for(int i=0; i<2; ++i) {
OBMol mol;
conv.ReadString(&mol, smis[i]);
bool hasTripleBond = false;
FOR_BONDS_OF_MOL(bond, mol) {
if (bond->GetBondOrder()==3)
hasTripleBond = true;
}
OB_ASSERT(hasTripleBond);
}
}
// 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->GetAtomicNum() == OBElements::Hydrogen)
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->GetAtomicNum() == OBElements::Hydrogen)
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]");
OBPairInteger *ac = new OBPairInteger();
ac->SetAttribute("Atom Class");
ac->SetValue(99);
mol.GetAtom(2)->SetData(ac); // Assign the hydrogen (atom 2) a class of 99
mol.DeleteHydrogens();
int myNumHs = 0;
FOR_ATOMS_OF_MOL(atom, mol)
if (atom->GetAtomicNum() == OBElements::Hydrogen)
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
}
struct SmilesData {
const char* inp;
const char* out;
const char* out_hoption; // if you specify -xh, i.e. "output explicit Hydrogens as such"
const char* out_addh_hoption; // if you add hydrogens and then specify "-xh"
const char* out_soption; // if you specify -xs, create SMARTS for substructure searching
};
void test_SMILES_Valence()
{
static const SmilesData smilesData[] = {
{ "[H]", "", "", "", "[#1]" }, // SMARTS perhaps should be [*H], but not implemented at the moment
{ "[H][H]", "", "", "","[#1][#1]" },
{ "[HH]", "", "", "[H][H]", "[#1]" },
{ "C", "", "", "C([H])([H])([H])[H]", "" },
{ "[C]", "", "", "", "C" },
{ "[CH]", "", "", "[C][H]", "C" },
{ "[CH3]", "", "", "[C]([H])([H])[H]", "C" },
{ "[CH4]", "C", "C", "C([H])([H])([H])[H]", "C" },
{ "[CH5]", "", "", "[C]([H])([H])([H])([H])[H]", "C" },
{ "C[H]", "C", "", "C([H])([H])([H])[H]", "[C!H0]" },
{ "[C][H]", "[CH]", "", "", "[C!H0]" },
{ "[CH3][H]", "C", "C[H]", "C([H])([H])([H])[H]", "[C!H0]" },
{ "[CH2]([H])[H]", "C", "C([H])[H]", "C([H])([H])([H])[H]", "[C!H0!H1]" },
{ "[U][H]", "[UH]", "", "", "[U!H0]" },
{ "[UH2]", "", "", "[U]([H])[H]", "[U]" },
{ "[C@@H](Br)(Cl)I", "", "", "[C@](Br)(Cl)(I)[H]", "[C](Br)(Cl)I" }, // Note: if OB supported it, SMARTS should be [C@@?](Br)(Cl)I
{ "Br[C@@H](Cl)I", "", "", "Br[C@@](Cl)(I)[H]", "Br[C](Cl)I" }, // Note: if OB supported it, SMARTS should be Br[C@@?](Cl)I
{ "[C@@](F)(Br)(Cl)I", "", "", "", "" },
{ "F[C@@](Br)(Cl)I", "", "", "", "" },
{ "[H][C@@](Br)(Cl)I", "[C@@H](Br)(Cl)I", "", "", "[C@@H](Br)(Cl)I" },
{ "C[H:1]", "C", "C[H]", "C([H])([H])([H])[H]", "[C!H0]" }, // atom class only shown with -xa
{ "C[2H]", "", "", "C([2H])([H])([H])[H]", "C[2#1]" },
{ "c1ccccc1", "", "", "c1(c(c(c(c(c1[H])[H])[H])[H])[H])[H]", "" },
{ "c1cnccc1", "", "", "c1(c(nc(c(c1[H])[H])[H])[H])[H]", "" },
{ "c1c[nH]cc1", "", "", "c1(c(n(c(c1[H])[H])[H])[H])[H]", "c1cncc1" },
{ "F[I]F", "", "", "", "FIF" },
};
unsigned int size = (unsigned int)(sizeof(smilesData) / sizeof(smilesData[0]));
for (unsigned int rep = 0; rep < 4; ++rep) {
printf("Rep: %d\n", rep);
OBConversion conv;
OB_ASSERT(conv.SetInAndOutFormats("smi", "smi"));
switch (rep) {
case 1: case 2: conv.SetOptions("h", conv.OUTOPTIONS); break;
case 3: conv.SetOptions("s", conv.OUTOPTIONS); break;
}
for (unsigned int i = 0; i < size; ++i) {
OBMol mol;
OB_ASSERT(conv.ReadString(&mol, smilesData[i].inp));
if (rep == 2)
mol.AddHydrogens();
std::string out = conv.WriteString(&mol, true);
const char* mout;
switch (rep) {
case 0: mout = smilesData[i].out; break;
case 1: mout = smilesData[i].out_hoption; break;
case 2: mout = smilesData[i].out_addh_hoption; break;
case 3: mout = smilesData[i].out_soption; break;
}
std::string ans = mout[0] ? mout : smilesData[i].inp;
printf(" %d %s --> %s (%s)\n", i, smilesData[i].inp, ans.c_str(), out.c_str());
OB_COMPARE(out, ans);
}
}
OBConversion conv;
OB_ASSERT(conv.SetInAndOutFormats("smi", "smi"));
conv.SetOptions("ah", conv.OUTOPTIONS); // write out alias explicitly
OBMol mol;
conv.ReadString(&mol, "C[H:1]");
OB_COMPARE(conv.WriteString(&mol, true), "C[H:1]");
}
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 225:
test_AromaticTripleBond();
break;
case 226:
test_SMILES_Valence();
break;
case 227:
test_OBChemTsfm();
break;
case 228:
test_ChemDraw_Basic();
break;
case 240:
test_Fix1912_PDBReading();
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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