bool OBConformerSearch::Setup(const OBMol &mol, int numConformers, int numChildren, int mutability, int convergence)
{
// copy some variables
m_mol = mol;
m_numConformers = numConformers;
m_numChildren = numChildren;
m_mutability = mutability;
m_convergence = convergence;
if (m_mol.GetCoordinates() == NULL)
return false;
// Initialize the OBRotorList
m_rotorList.SetFixedBonds(m_fixedBonds);
m_rotorList.Setup(m_mol);
if (!m_rotorList.Size()) { // only one conformer
return false;
}
// create initial population
OBRandom generator;
generator.TimeSeed();
RotorKey rotorKey(m_rotorList.Size() + 1, 0); // indexed from 1
if (IsGood(rotorKey))
m_rotorKeys.push_back(rotorKey);
else {
cout << "Initial conformer does not pass filter!" << endl;
}
int tries = 0;
while (m_rotorKeys.size() < m_numConformers && tries < numConformers * 1000) {
tries++;
// perform random mutation(s)
OBRotorIterator ri;
OBRotor *rotor = m_rotorList.BeginRotor(ri);
for (int i = 1; i < m_rotorList.Size() + 1; ++i, rotor = m_rotorList.NextRotor(ri)) {
if (generator.NextInt() % m_mutability == 0)
rotorKey[i] = generator.NextInt() % rotor->GetResolution().size();
}
// duplicates are always rejected
if (!IsUniqueKey(m_rotorKeys, rotorKey))
continue;
// execute filter(s)
if (!IsGood(rotorKey))
continue;
// add the key
m_rotorKeys.push_back(rotorKey);
}
// print out initial conformers
cout << "Initial conformer count: " << m_rotorKeys.size() << endl;
for (unsigned int i = 0; i < m_rotorKeys.size(); ++i) {
for (unsigned int j = 1; j < m_rotorKeys[i].size(); ++j)
std::cout << m_rotorKeys[i][j] << " ";
std::cout << std::endl;
}
return true;
}
int math(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;
}
}
cout << "# math: repeating each test " << REPEAT << " times" << endl;
randomizer.TimeSeed();
cout << "# Testing MMFF94 Force Field..." << endl;
switch(choice) {
case 1:
TEST( testBasics_vector3 );
TEST( testBasics_matrix3x3 );
break;
case 2:
TEST( testArithmeticOperators );
TEST( testDistancesAnglesOrthogonality );
break;
case 3:
TEST( testInversion );
break;
case 4:
TEST( testEigenvalues );
TEST( testEigenvectors );
break;
default:
cout << "Test number " << choice << " does not exist!\n";
return -1;
}
cout << "1.." << testCount << endl;
if( failedCount == 0 ) cout << "# math: all tests are successful" << endl;
else cout << "# math: " << failedCount << " out of "
<< testCount << " tests failed." << endl;
return 0;
}
void OBConformerSearch::NextGeneration()
{
// create next generation population
OBRandom generator;
generator.TimeSeed();
// generate the children
int numConformers = m_rotorKeys.size();
for (int c = 0; c < numConformers; ++c) {
for (int child = 0; child < m_numChildren; ++child) {
bool foundKey = false;
int tries = 0;
while (!foundKey) {
tries++;
if (tries > 1000)
foundKey = true;
RotorKey rotorKey = m_rotorKeys[c]; // copy parent gene
// perform random mutation(s)
OBRotorIterator ri;
OBRotor *rotor = m_rotorList.BeginRotor(ri);
for (int i = 1; i < m_rotorList.Size() + 1; ++i, rotor = m_rotorList.NextRotor(ri)) {
if (generator.NextInt() % m_mutability == 0)
rotorKey[i] = generator.NextInt() % rotor->GetResolution().size(); // permutate gene
}
// duplicates are always rejected
if (!IsUniqueKey(m_rotorKeys, rotorKey))
continue;
// execute the filter(s)
if (!IsGood(rotorKey))
continue;
// add the key
m_rotorKeys.push_back(rotorKey); // append child to population
// set foundKey to generate the next child
foundKey = true;
}
}
}
}
int main(int argc,char *argv[])
{
if (argc != 2)
{
cout << "Usage: obrotamer <file>" << endl;
cout << " Outputs the number of rotable bonds and generate a random"
<< " rotamer" << endl;
return(-1);
}
ifstream ifs(argv[1]);
if (!ifs)
{
cerr << "Error! Cannot read input file!" << endl;
return(-1);
}
OBConversion conv(&ifs, &cout);
OBFormat* pFormat;
pFormat = conv.FormatFromExt(argv[1]);
if ( pFormat == NULL )
{
cerr << "Error! Cannot read file format!" << endl;
return(-1);
}
// Finally, we can do some work!
OBMol mol;
if (! conv.SetInAndOutFormats(pFormat, pFormat))
{
cerr << "Error! File format isn't loaded" << endl;
return (-1);
}
OBRotorList rl;
OBRotamerList rotamers;
int *rotorKey = NULL;
OBRandom rand;
rand.TimeSeed();
while(ifs.peek() != EOF && ifs.good())
{
mol.Clear();
conv.Read(&mol);
rl.Setup(mol);
cerr << " Number of rotatable bonds: " << rl.Size() << endl;
// indexed from 1, rotorKey[0] = 0
std::vector<int> rotorKey(rl.Size() + 1, 0);
// each entry represents the configuration of a rotor
// e.g. indexes into OBRotor::GetResolution()
// (the different angles to sample from the OBRotorRules database)
OBRotorIterator ri;
OBRotor *rotor = rl.BeginRotor(ri);
for (int i = 1; i < rl.Size() + 1; ++i, rotor = rl.NextRotor(ri))
rotorKey[i] = rand.NextInt() % rotor->GetResolution().size();
rotamers.SetBaseCoordinateSets(mol);
rotamers.Setup(mol, rl);
rotamers.AddRotamer(rotorKey);
// This is more useful when you have added many rotamers
// rather than the one in this example
rotamers.ExpandConformerList(mol, mol.GetConformers());
// Change the molecule conformation -- from 0 .. rotamers.NumRotamers()
mol.SetConformer(0);
conv.Write(&mol);
} // while reading molecules
return(0);
}