Molecule * OpenbabelWrapper::openFile(const QString &fileName,
const QString &fileType,
const QString &fileOptions)
{
// Check that the file can be read from disk
if (!canOpen(fileName, QFile::ReadOnly | QFile::Text))
return 0;
// Construct the OpenBabel objects, set the file type
OBConversion conv;
OBFormat *inFormat;
if (!fileType.isEmpty() && !conv.SetInFormat(fileType.toAscii().data()))
// Input format not supported
return 0;
else {
inFormat = conv.FormatFromExt(fileName.toAscii().data());
if (!conv.SetInFormat(inFormat))
// Input format not supported
return 0;
}
// set any options
if (!fileOptions.isEmpty()) {
foreach(const QString &option,
fileOptions.split('\n', QString::SkipEmptyParts)) {
conv.AddOption(option.toAscii().data(), OBConversion::INOPTIONS);
}
}
// Helper function to read molecule from file
shared_ptr<OBMol> GetMol(const std::string &filename)
{
// Create the OBMol object.
shared_ptr<OBMol> mol(new OBMol);
// Create the OBConversion object.
OBConversion conv;
OBFormat *format = conv.FormatFromExt(filename.c_str());
if (!format || !conv.SetInFormat(format)) {
std::cout << "Could not find input format for file " << filename << std::endl;
return mol;
}
// Open the file.
std::ifstream ifs(filename.c_str());
if (!ifs) {
std::cout << "Could not open " << filename << " for reading." << std::endl;
return mol;
}
// Read the molecule.
if (!conv.Read(mol.get(), &ifs)) {
std::cout << "Could not read molecule from file " << filename << std::endl;
return mol;
}
return mol;
}
bool MakeQueriesFromMolInFile(vector<OBQuery*>& queries, const std::string& filename, int* pnAtoms, bool noH)
{
OBMol patternMol;
patternMol.SetIsPatternStructure();
OBConversion patternConv;
OBFormat* pFormat;
//Need to distinguish between filename and SMARTS. Not infallable...
if( filename.empty() ||
filename.find('.')==string::npos ||
!(pFormat = patternConv.FormatFromExt(filename.c_str())) ||
!patternConv.SetInFormat(pFormat) ||
!patternConv.ReadFile(&patternMol, filename) ||
patternMol.NumAtoms()==0)
return false;
if(noH)
patternMol.DeleteHydrogens();
do
{
*pnAtoms = patternMol.NumHvyAtoms();
queries.push_back(CompileMoleculeQuery(&patternMol));
}while(patternConv.Read(&patternMol));
return true;
}
void InputFileExtension::readOutputFile(const QString filename)
{
QApplication::setOverrideCursor(Qt::WaitCursor);
OBConversion conv;
OBFormat *inFormat = conv.FormatFromExt( filename.toAscii() );
if ( !inFormat || !conv.SetInFormat( inFormat ) ) {
QApplication::restoreOverrideCursor();
QMessageBox::warning(m_widget, tr("Avogadro"),
tr("Cannot read file format of file %1.").arg(filename));
return;
}
// TODO: Switch to MoleculeFile
ifstream ifs;
ifs.open(QFile::encodeName(filename));
if (!ifs) { // shouldn't happen, already checked file above
QApplication::restoreOverrideCursor();
QMessageBox::warning(m_widget, tr("Avogadro"),
tr("Cannot read file %1.").arg( filename ) );
return;
}
OBMol *obmol = new OBMol;
if (conv.Read(obmol, &ifs)) {
Molecule *mol = new Molecule;
mol->setOBMol(obmol);
mol->setFileName(filename);
emit moleculeChanged(mol, Extension::DeleteOld);
m_molecule = mol;
}
QApplication::restoreOverrideCursor();
}
int main(int argc,char **argv)
{
char *program_name= argv[0];
int c;
char *FileIn = NULL;
if (argc != 2) {
cerr << " Usage: " << program_name << " <input file>\n";
exit(-1);
}
else {
FileIn = argv[1];
}
// Find Input filetype
OBConversion conv;
OBFormat *inFormat = conv.FormatFromExt(FileIn);
if (!inFormat || !conv.SetInFormat(inFormat)) {
cerr << program_name << ": cannot read input format!" << endl;
exit (-1);
}
ifstream ifs;
// Read the file
ifs.open(FileIn);
if (!ifs) {
cerr << program_name << ": cannot read input file!" << endl;
exit (-1);
}
OBMol mol;
OBPointGroup pg;
for (c = 1;; ++c)
{
mol.Clear();
conv.Read(&mol, &ifs);
if (mol.Empty())
break;
// not needed by OBPointGroup, but useful for external programs
mol.Center();
mol.ToInertialFrame();
pg.Setup(&mol);
cout << "Point Group: " << pg.IdentifyPointGroup() << endl;
} // end for loop
return(1);
}
int main(int argc, char **argv)
{
OBFunctionFactory *factory = OBFunctionFactory::GetFactory("MMFF94");
OBFunction *function = factory->NewInstance();
if (!function) {
cout << "ERROR: could not find MMFF94 function" << endl;
return -1;
}
if (argc < 2) {
cout << "Usage: " << argv[0] << " <filename>" << endl;
return -1;
}
OBMol mol;
OBConversion conv;
OBFormat *format = conv.FormatFromExt(argv[1]);
if (!format || !conv.SetInFormat(format)) {
cout << "ERROR: could not find format for file " << argv[1] << endl;
return -1;
}
std::ifstream ifs;
ifs.open(argv[1]);
conv.Read(&mol, &ifs);
ifs.close();
cout << "# atoms = " << mol.NumAtoms() << endl;
function->GetLogFile()->SetOutputStream(&std::cout);
function->GetLogFile()->SetLogLevel(OBLogFile::Low);
// read options file
if (argc == 3) {
std::ifstream cifs;
cifs.open(argv[2]);
std::stringstream options;
std::string line;
while (std::getline(cifs, line))
options << line << std::endl;
function->SetOptions(options.str());
}
function->Setup(mol);
OBMinimize minimize(function);
minimize.SteepestDescent(50);
}
int main(int argc, char **argv)
{
if (argc < 2) {
std::cerr << "Usage: " << argv[0] << " filename" << std::endl;
return -1;
}
// read a molecule
OBConversion conv;
OBFormat *format = conv.FormatFromExt(argv[1]);
conv.SetInFormat(format);
std::string filename(argv[1]);
std::ifstream ifs;
ifs.open(filename.c_str());
if (!ifs) {
std::cerr << "Could not open " << filename << std::endl;
return -1;
}
CairoPainter *painter = new CairoPainter;
OBDepict depictor(painter);
string::size_type pos = filename.find_last_of(".");
if (pos != string::npos)
filename = filename.substr(0, pos);
OBMol mol;
unsigned int count = 1;
while (conv.Read(&mol, &ifs)) {
// depict the molecule
depictor.DrawMolecule(&mol);
depictor.AddAtomLabels(OBDepict::AtomSymmetryClass);
std::stringstream ss;
ss << filename << count << ".png";
painter->WriteImage(ss.str());
count++;
}
return 0;
}
bool verifyLSSR(const std::string &filename, const LSSR &ref)
{
cout << "Verify LSSR: " << filename << endl;
std::string file = OBTestUtil::GetFilename(filename);
// read a smiles string
OBMol mol;
OBConversion conv;
OBFormat *format = conv.FormatFromExt(file.c_str());
OB_REQUIRE( format );
OB_REQUIRE( conv.SetInFormat(format) );
std::ifstream ifs;
ifs.open(file.c_str());
OB_REQUIRE( ifs );
OB_REQUIRE( conv.Read(&mol, &ifs) );
std::vector<int> ringSizeCount(20, 0);
std::vector<OBRing*> lssr = mol.GetLSSR();
for (unsigned int i = 0; i < lssr.size(); ++i) {
ringSizeCount[lssr[i]->_path.size()]++;
}
/*
cout << "ringSize: ringCount" << endl;
cout << "3: " << ringSizeCount[3] << endl;
cout << "4: " << ringSizeCount[4] << endl;
cout << "5: " << ringSizeCount[5] << endl;
cout << "6: " << ringSizeCount[6] << endl;
*/
bool fail = false;
for (unsigned int i = 0; i < ref.size_count.size(); ++i) {
const LSSR::Size_Count &size_count = ref.size_count[i];
OB_ASSERT( ringSizeCount[size_count.ringSize] == size_count.ringCount );
}
return true;
}
bool doShuffleTestMultiFile(const std::string &filename)
{
cout << "Shuffling: " << filename << endl;
std::string file = OBTestUtil::GetFilename(filename);
// read a smiles string
OBMol mol;
OBConversion conv;
OBFormat *format = conv.FormatFromExt(file.c_str());
OB_REQUIRE( format );
OB_REQUIRE( conv.SetInFormat(format) );
std::ifstream ifs;
ifs.open(file.c_str());
OB_REQUIRE( ifs );
bool result = true;
while (conv.Read(&mol, &ifs)) {
bool res = doShuffleTestMolecule(mol);
if (!res)
result = res;
}
return result;
}
int main(int argc,char **argv)
{
char *program_name= argv[0];
int c;
int verbose = 0;
bool hydrogens = false;
string basename, filename = "", option, option2, ff = "";
OBConversion conv;
if (argc < 2) {
cout << "Usage: obenergy [options] <filename>" << endl << endl;
cout << "options: description:" << endl << endl;
cout << " -v verbose: print out indivual energy interactions" << endl << endl;
cout << " -h add hydrogens before calculating energy" << endl << endl;
cout << " -ff ffid select a forcefield" << endl << endl;
cout << " available forcefields:" << endl << endl;
OBPlugin::List("forcefields", "verbose");
exit(-1);
} else {
int ifile = 1;
for (int i = 1; i < argc; i++) {
option = argv[i];
if (option == "-v") {
verbose = 1;
ifile++;
break;
}
if (option == "-h") {
hydrogens = true;
ifile++;
}
if ((option == "-ff") && (argc > (i+1))) {
ff = argv[i+1];
ifile += 2;
}
}
basename = filename = argv[ifile];
size_t extPos = filename.rfind('.');
size_t startPos = 0;
if (extPos!= string::npos) {
basename = filename.substr(startPos, extPos);
}
}
// Find Input filetype
OBFormat *format_in = conv.FormatFromExt(filename.c_str());
if (!format_in || !conv.SetInFormat(format_in)) {
cerr << program_name << ": cannot read input format!" << endl;
exit (-1);
}
ifstream ifs;
ofstream ofs;
// Read the file
ifs.open(filename.c_str());
if (!ifs) {
cerr << program_name << ": cannot read input file!" << endl;
exit (-1);
}
OBForceField* pFF = OBForceField::FindForceField(ff);
if (!pFF) {
cerr << program_name << ": could not find forcefield '" << ff << "'." <<endl;
exit (-1);
}
pFF->SetLogFile(&cout);
pFF->SetLogLevel(OBFF_LOGLVL_NONE);
// if (verbose)
// pFF->SetLogLevel(OBFF_LOGLVL_HIGH);
// else
// pFF->SetLogLevel(OBFF_LOGLVL_MEDIUM);
Timer totalTimer, readTimer, setupTimer, computeTimer;
double totalTime, readTime, setupTime, computeTime;
int nthreads = 1; // single core is just one thread
unsigned int totalSteps = 1; // total steps is only used when doing minimization
#ifdef _OPENMP // START OPENMP DEBUG
#pragma omp parallel default(none) shared(nthreads)
{
nthreads = omp_get_num_threads(); // determine the number of threads
} // parallel region completes
#endif // END OPENMP DEBUG
// This code only deals with creating a file to store the timings for
// the execution of the program along with other interesting statistics
char cwd[1024]; // a reasonably large current working directory (cwd)
char filepath[1100]; // a reasonably large file name plus cwd
const char * statsfile = "obenergy_runstats";
std::ofstream output;
if (getcwd(cwd, sizeof (cwd)) != NULL) {
std::cout << "Current working dir: " << cwd << std::endl;
} else {
std::cout << "The getcwd() method failed. Aborting." << std::endl;
exit(1);
}//if(getcwd()
sprintf(filepath, "%s/%s_%s_t%d.mat", cwd, statsfile, ff.c_str(), nthreads);
std::cout << "Writing output file to: " << filepath << std::endl;
output.open(filepath, ios::out | ios::app ); // The file is open in append mode
// 1 2 3 4 5 6 7 8 9 10 11 12
output << "#METHOD: " << ff << " DATASET: " << filename.c_str() << std::endl;
output << "#THREADS ENERGY MOL_MASS NUM_ATOMS NUM_ROTORS NUM_CONF TOT_TIME TIME_READ TIME_SETUP TIME_COMPUTE STEPS #MOL_NAME " << std::endl;
// A second file is created to store information on the timings of specific parts
// from the MMFF94 calculation routines. breakdown of time spent in calculations
char filepath2[1100];
std::ofstream output2;
sprintf(filepath2, "%s/%s_%s_t%d_compute.mat", cwd, statsfile, ff.c_str(), nthreads);
std::cout << "Writing method breakdown detail file to: " << filepath2 << std::endl;
output2.open(filepath2, ios::out | ios::app ); // The file is open in append mode
// 1 2 3 4 5 6 7 8 9 10 11 12
output2 << "#METHOD: " << ff << " THREADS: " << nthreads << " DATASET: " << filename.c_str() << std::endl;
output2 << "#E_BOND E_ANGLE E_STRBND E_TORSION E_OOP E_VDW E_ELEC N_ATOMS PAIRS_VDW PAIRS_ELEC MEM_VDW MEM_ELEC " << std::endl;
// A third file is created to store information on the memory allocation of data structures
// from the MMFF94 calculation routines. breakdown of memory allocated for each calculation type
char filepath3[1100];
std::ofstream output3;
sprintf(filepath3, "%s/%s_%s_t%d_malloc.mat", cwd, statsfile, ff.c_str(), nthreads);
std::cout << "Writing memory allocation breakdown detail file to: " << filepath3 << std::endl;
output3.open(filepath3, ios::out | ios::app ); // The file is open in append mode
// 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15
output3 << "#METHOD: " << ff << " THREADS: " << nthreads << " DATASET: " << filename.c_str() << std::endl;
output3 << "#ATOMS M_BOND M_ANGLE M_STRBND M_TORSION M_OOP M_VDW M_ELEC C_BOND C_ANGLE C_STRBND C_TORSION C_OOP C_VDW C_ELEC" << std::endl;
double bondCalcTime, angleCalcTime, strbndCalcTime, torsionCalcTime, oopCalcTime, vdwCalcTime, electrostaticCalcTime;
int numPairsVDW, numPairsElectrostatic;
OBMol mol;
double energy;
for (c=1;;c++) {
mol.Clear();
totalTimer.start();
readTimer.start();
if (!conv.Read(&mol, &ifs))
break;
if (mol.Empty())
break;
if (hydrogens)
mol.AddHydrogens();
readTime = readTimer.get();
setupTimer.start();
if (!pFF->Setup(mol)) {
cerr << program_name << ": could not setup force field." << endl;
exit (-1);
}
setupTime = setupTimer.get();
computeTimer.start();
energy = pFF->Energy(false);
computeTime = computeTimer.get();
totalTime = totalTimer.get();
// THREADS ENERGY MOL_MASS NUM_ATOMS NUM_ROTORS NUM_CONF TOT_TIME TIME_READ TIME_SETUP TIME_COMPUTE STEPS #MOL_NAME
output << nthreads << " " << energy << " " << mol.GetExactMass() << " " << mol.NumAtoms()
<< " " << mol.NumRotors() << " " << mol.NumConformers() << " "
<< totalTime << " " << readTime << " " << " " << setupTime << " " << computeTime << " "
<< totalSteps << " #" << mol.GetTitle() // comment added to avoid errors when reading matrix in Octave
<< std::endl;
map<string, double> timings = pFF->getTimings();
map<string, size_t> memalloc = pFF->getAllocatedMemory();
MapKeys mk;
// 1 2 3 4 5 6 7 8 9 10 11 12
// E_BOND E_ANGLE E_STRBND E_TORSION E_OOP E_VDW E_ELEC N_ATOMS PAIRS_VDW PAIRS_ELEC MEM_VDW MEM_ELEC
output2 << timings[mk.TIME_BOND_CALCULATIONS] << " " // 1
<< timings[mk.TIME_ANGLE_CALCULATIONS] << " " // 2
<< timings[mk.TIME_STRBND_CALCULATIONS] << " " // 3
<< timings[mk.TIME_TORSION_CALCULATIONS] << " " // 4
<< timings[mk.TIME_OOP_CALCULATIONS] << " " // 5
<< timings[mk.TIME_VDW_CALCULATIONS] << " " // 6
<< timings[mk.TIME_ELECTROSTATIC_CALCULATIONS] << " " // 7
<< mol.NumAtoms() << " " // 8
<< timings[mk.TOTAL_VDW_CALCULATIONS] << " " // 9
<< timings[mk.TOTAL_ELECTROSTATIC_CALCULATIONS] << " " // 10
<< memalloc[mk.MEM_VDW_CALCULATIONS] << " " // 11
<< memalloc[mk.MEM_ELECTROSTATIC_CALCULATIONS] << std::endl; // 12
// 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15
// ATOMS M_BOND M_ANGLE M_STRBND M_TORSION M_OOP M_VDW M_ELEC C_BOND C_ANGLE C_STRBND C_TORSION C_OOP C_VDW C_ELEC
output3 << mol.NumAtoms() << " " // 1
<< memalloc[mk.MEM_BOND_CALCULATIONS] << " " // 2
<< memalloc[mk.MEM_ANGLE_CALCULATIONS] << " " // 3
<< memalloc[mk.MEM_STRBND_CALCULATIONS] << " " // 4
<< memalloc[mk.MEM_TORSION_CALCULATIONS] << " " // 5
<< memalloc[mk.MEM_OOP_CALCULATIONS] << " " // 6
<< memalloc[mk.MEM_VDW_CALCULATIONS] << " " // 7
<< memalloc[mk.MEM_ELECTROSTATIC_CALCULATIONS] << " " // 8
<< timings[mk.TOTAL_BOND_CALCULATIONS] << " " // 9
<< timings[mk.TOTAL_ANGLE_CALCULATIONS] << " " // 10
<< timings[mk.TOTAL_STRBND_CALCULATIONS] << " " // 11
<< timings[mk.TOTAL_TORSION_CALCULATIONS] << " " // 12
<< timings[mk.TOTAL_OOP_CALCULATIONS] << " " // 13
<< timings[mk.TOTAL_VDW_CALCULATIONS] << " " // 14
<< timings[mk.TOTAL_ELECTROSTATIC_CALCULATIONS] << " " // 15
<< std::endl;
if (!isfinite(energy)) {
cerr << " Title: " << mol.GetTitle() << endl;
FOR_ATOMS_OF_MOL(atom, mol) {
cerr << " x: " << atom->x() << " y: " << atom->y() << " z: " << atom->z() << endl;
}
}
} // end for loop
int main(int argc, char **argv)
{
if (argc < 3) {
std::cerr << "Usage: " << argv[0] << " <molecule_file> <output_score_file>" << std::endl;
return 1;
}
unsigned long numAtoms = 0;
unsigned long numAromaticAtoms = 0;
unsigned long numCyclicAtoms = 0;
std::map<int, unsigned long> mass;
std::map<int, unsigned long> elem;
std::map<int, unsigned long> aromelem;
std::map<int, unsigned long> aliphelem;
std::map<int, unsigned long> hcount;
std::map<int, unsigned long> charge;
std::map<int, unsigned long> connect;
std::map<int, unsigned long> degree;
std::map<int, unsigned long> implicit;
std::map<int, unsigned long> rings;
std::map<int, unsigned long> size;
std::map<int, unsigned long> valence;
std::map<int, unsigned long> chiral;
std::map<int, unsigned long> hyb;
std::map<int, unsigned long> ringconnect;
unsigned long numBonds = 0;
unsigned long numSingleBonds = 0;
unsigned long numDoubleBonds = 0;
unsigned long numTripleBonds = 0;
unsigned long numAromaticBonds = 0;
unsigned long numRingBonds = 0;
OBConversion conv;
conv.SetInFormat(conv.FormatFromExt(argv[1]));
std::ifstream ifs(argv[1]);
conv.SetInStream(&ifs);
OBMol mol;
unsigned long molecule = 0;
while (conv.Read(&mol)) {
++molecule;
//if ((molecule % 1000) == 0)
// std::cout << molecule << std::endl;
FOR_ATOMS_OF_MOL (atom, mol) {
numAtoms++;
if (atom->IsAromatic()) {
numAromaticAtoms++;
aromelem[atom->GetAtomicNum()]++;
} else
aliphelem[atom->GetAtomicNum()]++;
if (atom->IsInRing())
numCyclicAtoms++;
mass[atom->GetIsotope()]++;
elem[atom->GetAtomicNum()]++;
hcount[atom->ExplicitHydrogenCount() + atom->ImplicitHydrogenCount()]++;
charge[atom->GetFormalCharge()]++;
connect[atom->GetImplicitValence()]++;
degree[atom->GetValence()]++;
implicit[atom->ImplicitHydrogenCount()]++;
rings[atom->MemberOfRingCount()]++;
for (int i = 3; i < 25; ++i)
if (atom->IsInRingSize(i))
size[i]++;
valence[atom->KBOSum() - (atom->GetSpinMultiplicity() ? atom->GetSpinMultiplicity() - 1 : 0)]++;
hyb[atom->GetHyb()]++;
ringconnect[atom->CountRingBonds()]++;
}
FOR_BONDS_OF_MOL (bond, mol) {
numBonds++;
if (bond->IsSingle())
numSingleBonds++;
else if (bond->IsDouble())
numDoubleBonds++;
else if (bond->IsTriple())
numTripleBonds++;
if (bond->IsAromatic())
numAromaticBonds++;
if (bond->IsInRing())
numRingBonds++;;
}
///////////////////////////////////////////////////////////////////////////////
//! \brief Generate rough 3D coordinates for SMILES (or other 0D files).
//
int main(int argc,char **argv)
{
char *program_name= argv[0];
int c;
string basename, filename = "", option, option2, ff = "MMFF94";
list<string> argl(argv+1, argv+argc);
list<string>::iterator optff = find(argl.begin(), argl.end(), "-ff");
if (optff != argl.end()) {
list<string>::iterator optffarg = optff;
++optffarg;
if (optffarg != argl.end()) {
ff = *optffarg;
argl.erase(optff,++optffarg);
} else {
argl.erase(optff);
}
}
if (argl.empty()) {
cout << "Usage: obgen <filename> [options]" << endl;
cout << endl;
cout << "options: description:" << endl;
cout << endl;
cout << " -ff select a forcefield" << endl;
cout << endl;
OBPlugin::List("forcefields", "verbose");
exit(-1);
}
basename = filename = *argl.begin();
size_t extPos = filename.rfind('.');
if (extPos!= string::npos) {
basename = filename.substr(0, extPos);
}
// Find Input filetype
OBConversion conv;
OBFormat *format_in = conv.FormatFromExt(filename.c_str());
OBFormat *format_out = conv.FindFormat("sdf");
if (!format_in || !format_out || !conv.SetInAndOutFormats(format_in, format_out)) {
cerr << program_name << ": cannot read input/output format!" << endl;
exit (-1);
}
ifstream ifs;
ofstream ofs;
// Read the file
ifs.open(filename.c_str());
if (!ifs) {
cerr << program_name << ": cannot read input file!" << endl;
exit (-1);
}
OBMol mol;
for (c=1;;c++) {
mol.Clear();
if (!conv.Read(&mol, &ifs))
break;
if (mol.Empty())
break;
OBForceField* pFF = OBForceField::FindForceField(ff);
if (!pFF) {
cerr << program_name << ": could not find forcefield '" << ff << "'." <<endl;
exit (-1);
}
//mol.AddHydrogens(false, true); // hydrogens must be added before Setup(mol) is called
pFF->SetLogFile(&cerr);
pFF->SetLogLevel(OBFF_LOGLVL_LOW);
//pFF->GenerateCoordinates();
OBBuilder builder;
builder.Build(mol);
mol.AddHydrogens(false, true); // hydrogens must be added before Setup(mol) is called
if (!pFF->Setup(mol)) {
cerr << program_name << ": could not setup force field." << endl;
exit (-1);
}
pFF->SteepestDescent(500, 1.0e-4);
pFF->WeightedRotorSearch(250, 50);
pFF->SteepestDescent(500, 1.0e-6);
pFF->UpdateCoordinates(mol);
//pFF->ValidateGradients();
//pFF->SetLogLevel(OBFF_LOGLVL_HIGH);
//pFF->Energy();
//char FileOut[32];
//sprintf(FileOut, "%s_obgen.pdb", basename.c_str());
//ofs.open(FileOut);
//conv.Write(&mol, &ofs);
//ofs.close();
conv.Write(&mol, &cout);
} // end for loop
return(0);
}
int main(int argc,char **argv)
{
char *program_name= argv[0];
int c;
char *FileIn = NULL;
if (argc != 2)
{
string err = "Usage: ";
err += program_name;
err += " <filename>\n"
"Output format:\n"
"name NAME\n"
"formula FORMULA\n"
"mol_weight MOLECULAR_WEIGHT\n"
"exact_mass ISOTOPIC MASS\n"
"canonical_SMILES STRING\n"
"InChI STRING\n"
"num_atoms NUM\n"
"num_bonds NUM\n"
"num_residues NUM\n"
"num_rotors NUM\n"
"sequence RESIDUE_SEQUENCE\n"
"num_rings NUMBER_OF_RING_(SSSR)\n"
"logP NUM\n"
"PSA POLAR_SURFACE_AREA\n"
"MR MOLAR REFRACTIVITY";
err += "$$$$";
// ThrowError(err); wasn't being output because error level too low
cerr << err; //Why not do directly
exit(-1);
}
else
{
FileIn = argv[1];
}
// Find Input filetype
OBConversion conv;
OBFormat *format = conv.FormatFromExt(FileIn);
if (!format || !conv.SetInFormat(format))
{
cerr << program_name << ": cannot read input format!" << endl;
exit (-1);
}
ifstream ifs;
// Read the file
ifs.open(FileIn);
if (!ifs)
{
cerr << program_name << ": cannot read input file!" << endl;
exit (-1);
}
OBMol mol;
OBFormat *canSMIFormat = conv.FindFormat("can");
OBFormat *inchiFormat = conv.FindFormat("inchi");
////////////////////////////////////////////////////////////////////////////
// List of properties
// Name
// Molecular weight (Standard molar mass given by IUPAC atomic masses)
// Number of rings : the size of the smallest set of smallest rings (SSSR)
//.....ADD YOURS HERE.....
for (c = 1;; ++c)
{
mol.Clear();
conv.Read(&mol, &ifs);
if (mol.Empty())
break;
if (!mol.HasHydrogensAdded())
mol.AddHydrogens();
// Print the properties
if (strlen(mol.GetTitle()) != 0)
cout << "name " << mol.GetTitle() << endl;
else
cout << "name " << FileIn << " " << c << endl;
cout << "formula " << mol.GetFormula() << endl;
cout << "mol_weight " << mol.GetMolWt() << endl;
cout << "exact_mass " << mol.GetExactMass() << endl;
string smilesString = "-";
if (canSMIFormat) {
conv.SetOutFormat(canSMIFormat);
smilesString = conv.WriteString(&mol);
if ( smilesString.length() == 0 )
{
smilesString = "-";
}
}
cout << "canonical_SMILES " << smilesString << endl;
string inchiString = "-";
if (inchiFormat) {
conv.SetOutFormat(inchiFormat);
inchiString = conv.WriteString(&mol);
if ( inchiString.length() == 0 )
{
inchiString = "-";
}
}
cout << "InChI " << inchiString << endl;
cout << "num_atoms " << mol.NumAtoms() << endl;
cout << "num_bonds " << mol.NumBonds() << endl;
cout << "num_residues " << mol.NumResidues() << endl;
cout << "num_rotors " << mol.NumRotors() << endl;
if (mol.NumResidues() > 0)
cout << "sequence " << sequence(mol) << endl;
else
cout << "sequence " << "-" << endl;
cout << "num_rings " << nrings(mol) << endl;
OBDescriptor* pDesc;
pDesc= OBDescriptor::FindType("logP");
if(pDesc)
cout << "logP " << pDesc->Predict(&mol) << endl;
pDesc = OBDescriptor::FindType("TPSA");
if(pDesc)
cout << "PSA " << pDesc->Predict(&mol) << endl;
pDesc = OBDescriptor::FindType("MR");
if(pDesc)
cout << "MR " << pDesc->Predict(&mol) << endl;
cout << "$$$$" << endl; // SDF like end of compound descriptor list
//Other OBDescriptors could be output here, even ones that were rarely
// used. Since these are plugin classes, they may not be loaded, but
// then with code like the above they are just ignored.
} // end for loop
return(0);
}
bool FastSearchFormat::ObtainTarget(OBConversion* pConv, vector<OBMol>& patternMols, const string& indexname)
{
//Obtains an OBMol from:
// the filename in the -s option or
// the SMARTS string in the -s option or
// by converting the file in the -S or -aS options (deprecated).
// If there is no -s -S or -aS option, information on the index file is displayed.
OBMol patternMol;
patternMol.SetIsPatternStructure();
const char* p = pConv->IsOption("s",OBConversion::GENOPTIONS);
bool OldSOption=false;
//If no -s option, make OBMol from file in -S option or -aS option (both deprecated)
if(!p)
{
p = pConv->IsOption("S",OBConversion::GENOPTIONS);
if(!p)
p = pConv->IsOption("S",OBConversion::INOPTIONS);//for GUI mainly
OldSOption = true;
}
if(p)
{
vector<string> vec;
tokenize(vec, p);
//ignore leading ~ (not relevant to fastsearch)
if(vec[0][0]=='~')
vec[0].erase(0,1);
if(vec.size()>1 && vec[1]=="exact")
pConv->AddOption("e", OBConversion::INOPTIONS);
OBConversion patternConv;
OBFormat* pFormat;
//Interpret as a filename if possible
string& txt =vec [0];
if( txt.empty() ||
txt.find('.')==string::npos ||
!(pFormat = patternConv.FormatFromExt(txt.c_str())) ||
!patternConv.SetInFormat(pFormat) ||
!patternConv.ReadFile(&patternMol, txt) ||
patternMol.NumAtoms()==0)
//if false, have a valid patternMol from a file
{
//is SMARTS/SMILES
//Replace e.g. [#6] in SMARTS by C so that it can be converted as SMILES
//for the fingerprint phase, but allow more generality in the SMARTS phase.
for(;;)
{
string::size_type pos1, pos2;
pos1 = txt.find("[#");
if(pos1==string::npos)
break;
pos2 = txt.find(']');
int atno;
if(pos2!=string::npos && (atno = atoi(txt.substr(pos1+2, pos2-pos1-2).c_str())) && atno>0)
txt.replace(pos1, pos2-pos1+1, etab.GetSymbol(atno));
else
{
obErrorLog.ThrowError(__FUNCTION__,"Ill-formed [#n] atom in SMARTS", obError);
return false;
}
}
bool hasTildeBond;
if( (hasTildeBond = (txt.find('~')!=string::npos)) ) // extra parens to indicate truth value
{
//Find ~ bonds and make versions of query molecule with a single and aromatic bonds
//To avoid having to parse the SMILES here, replace ~ by $ (quadruple bond)
//and then replace this in patternMol. Check first that there are no $ already
//Sadly, isocynanides may have $ bonds.
if(txt.find('$')!=string::npos)
{
obErrorLog.ThrowError(__FUNCTION__,
"Cannot use ~ bonds in patterns with $ (quadruple) bonds.)", obError);
return false;
}
replace(txt.begin(),txt.end(), '~' , '$');
}
//read as standard SMILES
patternConv.SetInFormat("smi");
if(!patternConv.ReadString(&patternMol, vec[0]))
{
obErrorLog.ThrowError(__FUNCTION__,"Cannot read the SMILES string",obError);
return false;
}
if(hasTildeBond)
{
AddPattern(patternMols, patternMol, 0); //recursively add all combinations of tilde bond values
return true;
}
}
else
{
// target(s) are in a file
patternMols.push_back(patternMol);
while(patternConv.Read(&patternMol))
patternMols.push_back(patternMol);
return true;
}
}
if(OldSOption) //only when using deprecated -S and -aS options
{
//make -s option for later SMARTS test
OBConversion conv;
if(conv.SetOutFormat("smi"))
{
string optiontext = conv.WriteString(&patternMol, true);
pConv->AddOption("s", OBConversion::GENOPTIONS, optiontext.c_str());
}
}
if(!p)
{
//neither -s or -S options provided. Output info rather than doing search
const FptIndexHeader& header = fs.GetIndexHeader();
string id(header.fpid);
if(id.empty())
id = "default";
clog << indexname << " is an index of\n " << header.datafilename
<< ".\n It contains " << header.nEntries
<< " molecules. The fingerprint type is " << id << " with "
<< OBFingerprint::Getbitsperint() * header.words << " bits.\n"
<< "Typical usage for a substructure search:\n"
<< "obabel indexfile.fs -osmi -sSMILES\n"
<< "(-s option in GUI is 'Convert only if match SMARTS or mols in file')" << endl;
return false;
}
patternMols.push_back(patternMol);
return true;
}
int main(int argc,char **argv)
{
char *program_name = argv[0];
int Nsymm = 0, Nrot = 0;
bool bKJ = false;
double dBdT = 0;
string filename, option;
OBConversion conv;
double unit_factor = 1;
string e_unit("kcal/mol");
string s_unit("cal/mol K");
if (argc < 2) {
cout << "Usage: obthermo [options] <filename>" << endl;
cout << endl;
cout << "options: description:" << endl;
cout << endl;
cout << " --symm N override symmetry number used in input file" << endl;
cout << endl;
cout << " --nrot N number of rotatable bonds for conformational entropy" << endl;
cout << endl;
cout << " --dbdt x temperature derivative of second virial coefficient for cp calculation" << endl;
cout << endl;
cout << " --kj output kJ/mol related units (default kcal/mol)" << endl;
cout << endl;
exit(-1);
} else {
int i;
for (i = 1; i < argc; ) {
option = argv[i];
if ((option == "--symm") && (argc > (i+1))) {
Nsymm = atoi(argv[i+1]);
if (Nsymm < 1) {
cerr << program_name << ": the symmetry number should be >= 1!" << endl;
exit(-1);
}
i += 2;
}
else if ((option == "--nrot") && (argc > (i+1))) {
Nrot = atoi(argv[i+1]);
if (Nrot < 0) {
cerr << program_name << ": the number of rotatable bonds should be >= 0!" << endl;
exit(-1);
}
i += 2;
}
else if ((option == "--dbdt") && (argc > (i+1))) {
dBdT = atof(argv[i+1]);
if (dBdT < 0) {
cerr << program_name << ": the derivative of the second virial coefficient with respect to temperature should be >= 0!" << endl;
exit(-1);
}
i += 2;
}
else if (option == "--kj") {
bKJ = true;
unit_factor = 4.184;
e_unit.assign("kJ/mol");
s_unit.assign("J/mol K");
i += 1;
}
else {
filename.assign(argv[i]);
i += 1;
}
}
}
if (filename.size() == 0) {
cerr << program_name << ": no filename specified" << endl;
exit (-1);
}
// Find Input filetype
OBFormat *format_in = conv.FormatFromExt(filename.c_str());
if (!format_in || !conv.SetInFormat(format_in)) {
cerr << program_name << ": cannot read input format in file \"" << filename << "\"" << endl;
exit (-1);
}
ifstream ifs;
// Read the file
ifs.open(filename.c_str());
if (!ifs) {
cerr << program_name << ": cannot read input file!" << endl;
exit (-1);
}
OBMol mol;
if ((conv.Read(&mol, &ifs)) && ! mol.Empty())
{
OBPointGroup obPG;
double temperature, DeltaHf0, DeltaHfT, DeltaGfT, DeltaSfT, S0T, CVT, CPT, ZPVE;
std::vector<double> Scomponents;
obPG.Setup(&mol);
printf("obthermo - extract thermochemistry data from quantum chemistry logfiles\n");
printf("Number of rotatable bonds: %d\n", Nrot);
if (dBdT == 0)
{
printf("Please supply --dbdt option to get reliable heat capacity at constant pressure.\n");
}
printf("Point group according to OpenBabel: %s\n",
obPG.IdentifyPointGroup());
bool bVerbose = true;
if (extract_thermochemistry(mol,
bVerbose,
&Nsymm,
Nrot,
dBdT,
&temperature,
&DeltaHf0,
&DeltaHfT,
&DeltaGfT,
&DeltaSfT,
&S0T,
&CVT,
&CPT,
Scomponents,
&ZPVE))
{
double Rgas = 1.9872041; // cal/mol K
printf("DeltaHform(0K) %10g %s\n", DeltaHf0*unit_factor, e_unit.c_str());
printf("Temperature %10g K\n", temperature);
printf("DeltaHform(T) %10g %s\n", DeltaHfT*unit_factor, e_unit.c_str());
printf("DeltaGform(T) %10g %s\n", DeltaGfT*unit_factor, e_unit.c_str());
printf("DeltaSform(T) %10g %s\n", DeltaSfT*unit_factor, s_unit.c_str());
printf("cv(T) %10g %s\n", CVT*unit_factor, s_unit.c_str());
printf("cp(T) %10g %s\n", CPT*unit_factor, s_unit.c_str());
printf("Strans(T) %10g %s\n", Scomponents[0]*unit_factor, s_unit.c_str());
printf("Srot(T) %10g %s\n", Scomponents[1]*unit_factor, s_unit.c_str());
printf("Svib(T) %10g %s\n", Scomponents[2]*unit_factor, s_unit.c_str());
if (Scomponents[3] != 0)
{
printf("Ssymm %10g %s\n", Scomponents[3]*unit_factor, s_unit.c_str());
}
if (Scomponents[4] != 0)
{
printf("Sconf %10g %s\n", Scomponents[4]*unit_factor, s_unit.c_str());
}
printf("S0(T) %10g %s\n", S0T*unit_factor, s_unit.c_str());
}
else
{
printf("Could not find all necessary information to determine thermochemistry values.\n");
}
}
ifs.close();
return 0;
}
bool OBReader::readFile(QString fileName)
{
using namespace OpenBabel;
OBConversion conv;
OBFormat *format = conv.FormatFromExt(fileName.toStdString());
if (!format || !conv.SetInFormat(format))
{
qDebug() << "Unsupported File Format.";
return false;
}
std::ifstream ifs;
ifs.open(fileName.toStdString());
if (!ifs)
{
qDebug() << "Could not open the file.";
return false;
}
OBMol obMol;
if (!conv.Read(&obMol, &ifs))
{
qDebug() << "Error occured while reading the file.";
return false;
}
if (!obMol.Has3D())
{
static bool showMsgBox = true;
if (showMsgBox)
{
QMessageBox msgBox;
msgBox.setWindowTitle(tr("OBReader"));
msgBox.setText(tr("No 3D coordinate values present in this file."));
msgBox.setInformativeText(tr("OBReader will generate the rough molecular geometry."));
msgBox.setCheckBox(new QCheckBox(tr("Don’t show this message again.")));
msgBox.setIcon(QMessageBox::Information);
msgBox.exec();
showMsgBox = !msgBox.checkBox()->isChecked();
}
if (!buildGeometry(&obMol))
{
qDebug() << "Error in buildGeometry()";
return false;
}
}
if (!toMolecule(&obMol))
{
qDebug() << "Could not convert OBMol to Molecule.";
return false;
}
return true;
}
int main(int argc,char **argv)
{
char *program_name= argv[0];
int c;
int verbose = 0;
bool hydrogens = false;
string basename, filename = "", option, option2, ff = "";
if (argc < 2) {
cout << "Usage: obenergy [options] <filename>" << endl;
cout << endl;
cout << "options: description:" << endl;
cout << endl;
cout << " -v verbose: print out indivual energy interactions" << endl;
cout << endl;
cout << " -h add hydrogens before calculating energy" << endl;
cout << endl;
cout << " -ff ffid select a forcefield" << endl;
cout << endl;
cout << " available forcefields:" << endl;
cout << endl;
OBPlugin::List("forcefields", "verbose");
exit(-1);
} else {
int ifile = 1;
for (int i = 1; i < argc; i++) {
option = argv[i];
if (option == "-v") {
verbose = 1;
ifile++;
break;
}
if (option == "-h") {
hydrogens = true;
ifile++;
}
if ((option == "-ff") && (argc > (i+1))) {
ff = argv[i+1];
ifile += 2;
}
}
basename = filename = argv[ifile];
size_t extPos = filename.rfind('.');
if (extPos!= string::npos) {
basename = filename.substr(0, extPos);
}
}
// Find Input filetype
OBConversion conv;
OBFormat *format_in = conv.FormatFromExt(filename.c_str());
if (!format_in || !conv.SetInFormat(format_in)) {
cerr << program_name << ": cannot read input format!" << endl;
exit (-1);
}
ifstream ifs;
ofstream ofs;
// Read the file
ifs.open(filename.c_str());
if (!ifs) {
cerr << program_name << ": cannot read input file!" << endl;
exit (-1);
}
OBForceField* pFF = OBForceField::FindForceField(ff);
if (!pFF) {
cerr << program_name << ": could not find forcefield '" << ff << "'." <<endl;
exit (-1);
}
pFF->SetLogFile(&cout);
if (verbose)
pFF->SetLogLevel(OBFF_LOGLVL_HIGH);
else
pFF->SetLogLevel(OBFF_LOGLVL_MEDIUM);
OBMol mol;
double energy;
for (c=1;;c++) {
mol.Clear();
if (!conv.Read(&mol, &ifs))
break;
if (mol.Empty())
break;
if (hydrogens)
mol.AddHydrogens();
if (!pFF->Setup(mol)) {
cerr << program_name << ": could not setup force field." << endl;
exit (-1);
}
energy = pFF->Energy(false);
if (!isfinite(energy)) {
cerr << " Title: " << mol.GetTitle() << endl;
FOR_ATOMS_OF_MOL(atom, mol) {
cerr << " x: " << atom->x() << " y: " << atom->y() << " z: " << atom->z() << endl;
}
}
} // end for loop
///////////////////////////////////////////////////////////////////////////////
//! \brief compute rms between chemically identical molecules
int main(int argc, char **argv)
{
bool firstOnly = false;
if (argc != 3 && argc != 4)
{
cerr << "Usage: " << argv[0]
<< " [-firstonly] <reference structure(s)> <comparison structure(s)>\n";
cerr << "Computes the heavy-atom RMSD of identical compound structures.\n";
cerr << "Structures in multi-structure files are compared one-by-one unless -firstonly\n"
<< "is passed, in which case only the first structure in the reference file is used.\n";
exit(-1);
}
char *fileRef = argv[1];
char *fileTest = argv[2];
if (argc == 4)
{
//if iterate is passed as first command, try to match structures in first file to strucutres in second
if (strcmp("-firstonly", argv[1]) != 0)
{
cerr << "Usage: " << argv[0]
<< " [-firstonly] <reference structure(s)> <comparison structure(s)>\n";
exit(-1);
}
fileRef = argv[2];
fileTest = argv[3];
firstOnly = true;
}
//open mols
OBConversion refconv;
OBFormat *refFormat = refconv.FormatFromExt(fileRef);
if (!refFormat || !refconv.SetInFormat(refFormat)
|| !refconv.SetOutFormat("SMI"))
{
cerr << "Cannot read reference molecule format!" << endl;
exit(-1);
}
OBConversion testconv;
OBFormat *testFormat = testconv.FormatFromExt(fileTest);
if (!testFormat || !testconv.SetInAndOutFormats(testFormat, testFormat))
{
cerr << "Cannot read reference molecule format!" << endl;
exit(-1);
}
//read reference
ifstream ifsref;
OBMol molref;
ifsref.open(fileRef);
if (!ifsref)
{
cerr << "Cannot read fixed molecule file: " << fileRef << endl;
exit(-1);
}
//check comparison file
ifstream ifstest;
ifstest.open(fileTest);
if (!ifstest)
{
cerr << "Cannot read file: " << fileTest << endl;
exit(-1);
}
while (refconv.Read(&molref, &ifsref))
{
processMol(molref);
Matcher matcher(molref);// create the matcher
OBMol moltest;
while (testconv.Read(&moltest, &ifstest))
{
if (moltest.Empty())
break;
processMol(moltest);
double rmsd = matcher.computeRMSD(moltest);
cout << "RMSD " << moltest.GetTitle() << " " << rmsd << "\n";
if (!firstOnly)
{
break;
}
}
}
return (0);
}
int main(int argc,char **argv)
{
char *program_name= argv[0];
char *FileIn = NULL;
if (argc != 2)
{
cout << "Usage: " << program_name << " <filename>" << endl;
exit(-1);
}
else
{
FileIn = argv[1];
// const char* p = strrchr(FileIn,'.');
}
// Find Input filetype
OBConversion conv;
OBFormat *format = conv.FormatFromExt(FileIn);
if (!format || !conv.SetInAndOutFormats(format, format))
{
cerr << program_name << ": cannot read input format!" << endl;
exit (-1);
}
ifstream ifs;
// Read the file
ifs.open(FileIn);
if (!ifs)
{
cerr << program_name << ": cannot read input file!" << endl;
exit (-1);
}
OBMol mol;
OBAtom *atom;
for (int c=1;;++c) // big for loop (replace with do while?)
{
mol.Clear();
conv.Read(&mol, &ifs);
if (mol.Empty())
break;
cout << "Molecule "<< c << ": " << mol.GetTitle() << endl;
//mol.FindChiralCenters(); // labels all chiral atoms
vector<OBAtom*>::iterator i; // iterate over all atoms
for (atom = mol.BeginAtom(i);atom;atom = mol.NextAtom(i))
{
if(!atom->IsChiral())continue; // aborts if atom isn't chiral
cout << "Atom " << atom->GetIdx() << " Is Chiral ";
cout << atom->GetType()<<endl;
OBChiralData* cd = (OBChiralData*)atom->GetData(OBGenericDataType::ChiralData);
if (cd){
vector<unsigned int> x=cd->GetAtom4Refs(input);
size_t n=0;
cout <<"Atom4refs:";
for (n=0;n<x.size();++n)
cout <<" "<<x[n];
cout <<endl;
}
else{cd=new OBChiralData;atom->SetData(cd);}
vector<unsigned int> _output;
unsigned int n;
for(n=1;n<5;++n) _output.push_back(n);
cd->SetAtom4Refs(_output,output);
/* // MOLV3000 uses 1234 unless an H then 123H
if (atom->GetHvyValence()==3)
{
OBAtom *nbr;
int Hid=1000;// max Atom ID +1 should be used here
vector<unsigned int> nbr_atms;
vector<OBBond*>::iterator i;
for (nbr = atom->BeginNbrAtom(i);nbr;nbr = atom->NextNbrAtom(i))
{
if (nbr->IsHydrogen()){Hid=nbr->GetIdx();continue;}
nbr_atms.push_back(nbr->GetIdx());
}
sort(nbr_atms.begin(),nbr_atms.end());
nbr_atms.push_back(Hid);
OBChiralData* cd=(OBChiralData*)atom->GetData(OBGenericDataType::ChiralData);
cd->SetAtom4Refs(nbr_atms,output);
}
else if (atom->GetHvyValence()==4)
{
OBChiralData* cd=(OBChiralData*)atom->GetData(OBGenericDataType::ChiralData);
vector<unsigned int> nbr_atms;
int n;
for(n=1;n<5;++n)nbr_atms.push_back(n);
cd->SetAtom4Refs(nbr_atms,output);
} */
/* FIXME
if (!mol.HasNonZeroCoords())
{
cout << "Calcing 0D chirality "<< CorrectChirality(mol,atom)<<endl;
}
else {
cout << "Volume= "<< CalcSignedVolume(mol,atom) << endl;
OBChiralData* cd=(OBChiralData*)atom->GetData(OBGenericDataType::ChiralData);
size_t n;
vector<unsigned int> refs=cd->GetAtom4Refs(output);
cout<<"Atom refs=";
for(n=0;n<refs.size();++n)cout<<" "<<refs[n];
cout<<endl;
}
cout << "Clockwise? " << atom->IsClockwise() << endl;
*/
} // end iterating over atoms
} // end big for loop
return(0);
} // end main
int main(int argc,char *argv[])
{
// turn off slow sync with C-style output (we don't use it anyway).
std::ios::sync_with_stdio(false);
OBConversion conv;
OBFormat *inFormat, *canFormat;
OBMol mol;
ifstream ifs;
vector<OBMol> fragments;
unsigned int fragmentCount = 0; // track how many in library -- give a running count
map<string, int> index; // index of cansmi
string currentCAN;
unsigned int size;
OBAtom *atom;
OBBond *bond;
bool nonRingAtoms, nonRingBonds;
char buffer[BUFF_SIZE];
canFormat = conv.FindFormat("can");
conv.SetOutFormat(canFormat);
if (argc < 2)
{
cout << "Usage: obfragment <file>" << endl;
return(-1);
}
for (int i = 1; i < argc; i++) {
cerr << " Reading file " << argv[i] << endl;
inFormat = conv.FormatFromExt(argv[i]);
if(inFormat==NULL || !conv.SetInFormat(inFormat))
{
cerr << " Cannot read file format for " << argv[i] << endl;
continue; // try next file
}
ifs.open(argv[i]);
if (!ifs)
{
cerr << "Cannot read input file: " << argv[i] << endl;
continue;
}
while(ifs.peek() != EOF && ifs.good())
{
conv.Read(&mol, &ifs);
if (!mol.Has3D()) continue; // invalid coordinates!
mol.DeleteHydrogens(); // remove these before we do anything else
do {
nonRingAtoms = false;
size = mol.NumAtoms();
for (unsigned int i = 1; i <= size; ++i)
{
atom = mol.GetAtom(i);
if (!atom->IsInRing()) {
mol.DeleteAtom(atom);
nonRingAtoms = true;
break; // don't know how many atoms there are
}
// Previously, we changed atoms to carbon here.
// Now we perform this alchemy in terms of string-rewriting
// once the canonical SMILES is generated
}
} while (nonRingAtoms);
if (mol.NumAtoms() < 3)
continue;
if (mol.NumBonds() == 0)
continue;
do {
nonRingBonds = false;
size = mol.NumBonds();
for (unsigned int i = 0; i < size; ++i)
{
bond = mol.GetBond(i);
if (!bond->IsInRing()) {
mol.DeleteBond(bond);
nonRingBonds = true;
break; // don't know how many bonds there are
}
}
} while (nonRingBonds);
fragments = mol.Separate();
for (unsigned int i = 0; i < fragments.size(); ++i)
{
if (fragments[i].NumAtoms() < 3) // too small to care
continue;
currentCAN = conv.WriteString(&fragments[i], true);
currentCAN = RewriteSMILES(currentCAN); // change elements to "a/A" for compression
if (index.find(currentCAN) != index.end()) { // already got this
index[currentCAN] += 1; // add to the count for bookkeeping
continue;
}
index[currentCAN] = 1; // don't ever write this ring fragment again
// OK, now retrieve the canonical ordering for the fragment
vector<string> canonical_order;
if (fragments[i].HasData("Canonical Atom Order")) {
OBPairData *data = (OBPairData*)fragments[i].GetData("Canonical Atom Order");
tokenize(canonical_order, data->GetValue().c_str());
}
// Write out an XYZ-style file with the CANSMI as the title
cout << fragments[i].NumAtoms() << '\n';
cout << currentCAN << '\n'; // endl causes a flush
vector<string>::iterator can_iter;
unsigned int order;
OBAtom *atom;
fragments[i].Center();
fragments[i].ToInertialFrame();
for (unsigned int index = 0; index < canonical_order.size();
++index) {
order = atoi(canonical_order[index].c_str());
atom = fragments[i].GetAtom(order);
snprintf(buffer, BUFF_SIZE, "C%8.3f%8.3f%8.3f\n",
atom->x(), atom->y(), atom->z());
cout << buffer;
}
}
fragments.clear();
if (index.size() > fragmentCount) {
fragmentCount = index.size();
cerr << " Fragments: " << fragmentCount << endl;
}
} // while reading molecules (in this file)
ifs.close();
ifs.clear();
} // while reading files
// loop through the map and output frequencies
map<string, int>::const_iterator indexItr;
for (indexItr = index.begin(); indexItr != index.end(); ++indexItr) {
cerr << (*indexItr).second << " INDEX " << (*indexItr).first << "\n";
}
return(0);
}
int main(int argc,char **argv)
{
char *program_name= argv[0];
int c;
int steps = 2500;
double crit = 1e-6;
bool sd = false;
bool cut = false;
bool newton = false;
bool hydrogens = false;
double rvdw = 6.0;
double rele = 10.0;
int freq = 10;
string basename, filename = "", option, option2, ff = "MMFF94";
char *oext;
OBConversion conv;
OBFormat *format_out = conv.FindFormat("pdb"); // default output format
if (argc < 2) {
cout << "Usage: obminimize [options] <filename>" << endl;
cout << endl;
cout << "options: description:" << endl;
cout << endl;
cout << " -c crit set convergence criteria (default=1e-6)" << endl;
cout << endl;
cout << " -cg use conjugate gradients algorithm (default)" << endl;
cout << endl;
cout << " -sd use steepest descent algorithm" << endl;
cout << endl;
cout << " -newton use Newton2Num linesearch (default=Simple)" << endl;
cout << endl;
cout << " -ff ffid select a forcefield:" << endl;
cout << endl;
cout << " -h add hydrogen atoms" << endl;
cout << endl;
cout << " -n steps specify the maximum numer of steps (default=2500)" << endl;
cout << endl;
cout << " -cut use cut-off (default=don't use cut-off)" << endl;
cout << endl;
cout << " -rvdw rvdw specify the VDW cut-off distance (default=6.0)" << endl;
cout << endl;
cout << " -rele rele specify the Electrostatic cut-off distance (default=10.0)" << endl;
cout << endl;
cout << " -pf freq specify the frequency to update the non-bonded pairs (default=10)" << endl;
cout << endl;
OBPlugin::List("forcefields", "verbose");
exit(-1);
} else {
int ifile = 1;
for (int i = 1; i < argc; i++) {
option = argv[i];
// steps
if ((option == "-n") && (argc > (i+1))) {
steps = atoi(argv[i+1]);
ifile += 2;
}
// vdw cut-off
if ((option == "-rvdw") && (argc > (i+1))) {
rvdw = atof(argv[i+1]);
ifile += 2;
}
// ele cut-off
if ((option == "-rele") && (argc > (i+1))) {
rele = atof(argv[i+1]);
ifile += 2;
}
// pair update frequency
if ((option == "-pf") && (argc > (i+1))) {
freq = atoi(argv[i+1]);
ifile += 2;
}
// steepest descent
if (option == "-sd") {
sd = true;
ifile++;
}
// enable cut-off
if (option == "-cut") {
cut = true;
ifile++;
}
// enable Newton2Num
if (option == "-newton") {
newton = true;
ifile++;
}
if (strncmp(option.c_str(), "-o", 2) == 0) {
oext = argv[i] + 2;
if(!*oext) {
oext = argv[++i]; //space left after -o: use next argument
ifile++;
}
format_out = conv.FindFormat(oext);
ifile++;
}
if (option == "-h") {
hydrogens = true;
ifile++;
}
if (option == "-cg") {
sd = false;
ifile++;
}
if ((option == "-c") && (argc > (i+1))) {
crit = atof(argv[i+1]);
ifile += 2;
}
if ((option == "-ff") && (argc > (i+1))) {
ff = argv[i+1];
ifile += 2;
}
}
basename = filename = argv[ifile];
size_t extPos = filename.rfind('.');
if (extPos!= string::npos) {
basename = filename.substr(0, extPos);
}
}
// Find Input filetype
OBFormat *format_in = conv.FormatFromExt(filename.c_str());
if (!format_in || !format_out || !conv.SetInAndOutFormats(format_in, format_out)) {
cerr << program_name << ": cannot read input/output format!" << endl;
exit (-1);
}
ifstream ifs;
ofstream ofs;
// Read the file
ifs.open(filename.c_str());
if (!ifs) {
cerr << program_name << ": cannot read input file!" << endl;
exit (-1);
}
OBForceField* pFF = OBForceField::FindForceField(ff);
if (!pFF) {
cerr << program_name << ": could not find forcefield '" << ff << "'." <<endl;
exit (-1);
}
// set some force field variables
pFF->SetLogFile(&cerr);
pFF->SetLogLevel(OBFF_LOGLVL_LOW);
pFF->SetVDWCutOff(rvdw);
pFF->SetElectrostaticCutOff(rele);
pFF->SetUpdateFrequency(freq);
pFF->EnableCutOff(cut);
if (newton)
pFF->SetLineSearchType(LineSearchType::Newton2Num);
OBMol mol;
for (c=1;;c++) {
mol.Clear();
if (!conv.Read(&mol, &ifs))
break;
if (mol.Empty())
break;
if (hydrogens)
mol.AddHydrogens();
if (!pFF->Setup(mol)) {
cerr << program_name << ": could not setup force field." << endl;
exit (-1);
}
bool done = true;
OBStopwatch timer;
timer.Start();
if (sd) {
pFF->SteepestDescentInitialize(steps, crit);
} else {
pFF->ConjugateGradientsInitialize(steps, crit);
}
unsigned int totalSteps = 1;
while (done) {
if (sd)
done = pFF->SteepestDescentTakeNSteps(1);
else
done = pFF->ConjugateGradientsTakeNSteps(1);
totalSteps++;
if (pFF->DetectExplosion()) {
cerr << "explosion has occured!" << endl;
conv.Write(&mol, &cout);
return(1);
} else
pFF->GetCoordinates(mol);
}
double timeElapsed = timer.Elapsed();
pFF->GetCoordinates(mol);
conv.Write(&mol, &cout);
cerr << "Time: " << timeElapsed << "seconds. Iterations per second: " << double(totalSteps) / timeElapsed << endl;
} // end for loop
return(0);
}
///////////////////////////////////////////////////////////////////////////////
//! \brief Set a tortional bond to a given angle
int main(int argc,char **argv)
{
const char *Pattern=NULL;
unsigned int i, t, errflg = 0;
int c;
char flags[255];
string err;
bool graphOutput=false;
// parse the command line -- optional -a flag to change all matching torsions
if (argc < 3 || argc > 4) {
errflg++;
} else {
FileIn = argv[1];
Pattern = "[!$(*#*)&!D1]-!@[!$(*#*)&!D1]";
// Read the atom position
c = sscanf(argv[2], "%d", &angleSum);
angle = 360./angleSum;
if (argc == 4)
{
c = sscanf(argv[3], "%s", flags);
int flagid=1;
while (flags[flagid]!=0)
switch (flags[flagid++])
{
case 'g':
graphOutput=true;
case 'e':
forceField=OBForceField::FindForceField("MMFF94");
isEnergyCalcing=true;
break;
}
}
}
if (errflg) {
cerr << "Usage: rkrotate <filename> <angle> [options]" << endl;
exit(-1);
}
// create pattern
OBSmartsPattern sp;
sp.Init(Pattern);
OBFormat* format = conv.FormatFromExt(FileIn);
if(!(format && conv.SetInAndOutFormats(format, format))) { //in and out formats same
cerr << "obrotate: cannot read and/or write this file format!" << endl;
exit (-1);
} //...NF
//Open the molecule file
ifstream ifs;
// Read the file
ifs.open(FileIn);
if (!ifs) {
cerr << "obrotate: cannot read input file!" << endl;
exit (-1);
}
OBMol mol;
vector< vector <int> > maplist; // list of matched atoms
// vector< vector <int> >::iterator m; // and its iterators
// int tindex;
// Set the angles
for (;;) {
mol.Clear();
//NF ifs >> mol; // Read molecule
conv.Read(&mol,&ifs); //NF
if (mol.Empty())
break;
if (sp.Match(mol)) {
// if match perform rotation
maplist = sp.GetUMapList(); // get unique matches
if (maplist.size() > 1)
cerr << "obrotate: Found " << maplist.size() << " matches." << endl;
energySheet=new MultiVector<double>(degrees=maplist.size(),angleSum);
indexSheet=new int[maplist.size()];
for (int EXO=0;EXO<maplist.size();++EXO)
totalSum*=angleSum+EXO;
// look at all the mapping atom but save only the last one.
turnMol(mol,maplist,maplist.size()-1);
if (graphOutput)
{
ofstream ofs("energyGraph.mlog");
int ind[degrees];
for (int i=0;i<degrees;++i)
ind[i]=0;
do
{
for (int i=0;i<degrees;++i)
ofs<<ind[i]<<'\t';
ofs<<energySheet->getVectorValue(ind)<<endl;
}
while(energySheet->incressIndex(ind));
}
if (isEnergyCalcing)
{
std::vector<int*> lowEnergySheet;
totalSum=energySheet->getMinValues(lowEnergySheet);
if (totalSum)
outputMol(lowEnergySheet,mol,maplist,maplist.size()-1);
else
cerr << "rkrotate: No low energy conformation found." << endl;
}
cout << sum;
} else {
cerr << "obrotate: Found 0 matches for the SMARTS pattern." << endl;
exit(-1);
}
//NF cout << mol;
}
return(0);
}
int main(int argc,char **argv)
{
OBForceField* pFF = OBForceField::FindForceField("Ghemical");
pFF->SetLogFile(&cout);
pFF->SetLogLevel(OBFF_LOGLVL_LOW);
OBMol mol;
mol.Clear();
char commandline[100];
vector<string> vs;
cout << endl;
cout << "openbabel " << endl;
cout << "M O L E C U L A R M E C H A N I C S" << endl;
cout << " program" << endl;
cout << " v 0.1 " << endl << endl;
while (1) {
cout << "command > ";
cin.getline(commandline, 100);
//
// commands with no parameters
//
if (EQn(commandline, "quit", 4) || cin.eof()) {
cout << "bye." << endl;
exit(0);
}
if (EQn(commandline, "help", 4) || cin.eof()) {
cout << endl;
cout << "commands: description:" << endl;
cout << "load <filename> load a molecule from filename" << endl;
cout << "save <filename> save currently loaded molecule to filename" << endl;
cout << "ff <forcefield> select the force field" << endl;
cout << "forcefields print the available forcefields" << endl;
cout << endl;
cout << "energy calculate the energy" << endl;
cout << "ebond calculate the bond stretching energy" << endl;
cout << "eangle calculate the angle bending energy" << endl;
cout << "estrbnd calculate the stretch-bending enregy" << endl;
cout << "eoop calculate the out-of-plane bending energy" << endl;
cout << "etorsion calculate the torsional energy" << endl;
cout << "evdw calculate the Van der Waals energy" << endl;
cout << "eeq calculate the electrostatic energy" << endl;
cout << endl;
cout << "sd <n> steepest descent energy minimization for n steps" << endl;
cout << "cg <n> conjugate gradients energy minimization for n steps" << endl;
cout << "" << endl;
cout << "addH add hydrogens" << endl;
cout << "delH delete hydrogens" << endl;
cout << endl;
cout << "gen generate/minimize a (random) structure" << endl;
cout << "rs rotate around all rotatable bonds" << endl;
cout << "nconf print the number of conformers" << endl;
cout << "conf <n> select conformer n" << endl;
cout << endl;
cout << "quit quit" << endl;
cout << endl;
continue;
}
// calculate the energy
if (EQn(commandline, "energy", 6)) {
if (mol.Empty()) {
cout << "no molecule loaded." << endl;
continue;
}
cout << endl << " total energy = " << pFF->Energy() << " " << pFF->GetUnit() << endl << endl;
continue;
}
if (EQn(commandline, "ebond", 5)) {
if (mol.Empty()) {
cout << "no molecule loaded." << endl;
continue;
}
cout << endl << " bond stretching energy = " << pFF->E_Bond() << " " << pFF->GetUnit() << endl << endl;
continue;
}
if (EQn(commandline, "eangle", 6)) {
if (mol.Empty()) {
cout << "no molecule loaded." << endl;
continue;
}
cout << endl << " angle bending energy = " << pFF->E_Angle() << " " << pFF->GetUnit() << endl << endl;
continue;
}
if (EQn(commandline, "estrbnd", 7)) {
if (mol.Empty()) {
cout << "no molecule loaded." << endl;
continue;
}
cout << endl << " stretch-bending energy = " << pFF->E_StrBnd() << " " << pFF->GetUnit() << endl << endl;
continue;
}
if (EQn(commandline, "eoop", 4)) {
if (mol.Empty()) {
cout << "no molecule loaded." << endl;
continue;
}
cout << endl << " out-of-plane bending energy = " << pFF->E_OOP() << " " << pFF->GetUnit() << endl << endl;
continue;
}
if (EQn(commandline, "etorsion", 8)) {
if (mol.Empty()) {
cout << "no molecule loaded." << endl;
continue;
}
cout << endl << " torsional energy = " << pFF->E_Torsion() << " " << pFF->GetUnit() << endl << endl;
continue;
}
if (EQn(commandline, "evdw", 4)) {
if (mol.Empty()) {
cout << "no molecule loaded." << endl;
continue;
}
cout << endl << " Van der Waals energy = " << pFF->E_VDW() << " " << pFF->GetUnit() << endl << endl;
continue;
}
if (EQn(commandline, "eeq", 3)) {
if (mol.Empty()) {
cout << "no molecule loaded." << endl;
continue;
}
cout << endl << " electrostatic energy = " << pFF->E_Electrostatic() << " " << pFF->GetUnit() << endl << endl;
continue;
}
if (EQn(commandline, "addH", 4)) {
int num1, num2;
num1 = mol.NumAtoms();
mol.AddHydrogens(false, true);
num2 = mol.NumAtoms();
cout << (num2 - num1) << " hydrogens added." << endl;
if (!pFF->Setup(mol)) {
cout << "error while initializing the force field for this molecule." <<endl;
continue;
}
continue;
}
if (EQn(commandline, "delH", 4)) {
int num1, num2;
num1 = mol.NumAtoms();
mol.DeleteHydrogens();
num2 = mol.NumAtoms();
cout << (num1 - num2) << " hydrogens deleted." << endl;
if (!pFF->Setup(mol)) {
cout << "error while initializing the force field for this molecule." <<endl;
continue;
}
continue;
}
if (EQn(commandline, "gen", 3)) {
//pFF->GenerateCoordinates();
pFF->UpdateCoordinates(mol);
continue;
}
if (EQn(commandline, "rs", 2)) {
pFF->SystematicRotorSearch();
pFF->UpdateCoordinates(mol);
continue;
}
if (EQn(commandline, "nconf", 5)) {
cout << endl << " number of conformers = " << mol.NumConformers() << endl << endl;
continue;
}
//
// commands with parameters
//
tokenize(vs, commandline);
// select forcefield
if (EQn(commandline, "ff", 2)) {
if (vs.size() < 2) {
cout << "no <forcefield> specified." << endl;
continue;
}
pFF = OBForceField::FindForceField(vs[1]);
if (!mol.Empty())
if (!pFF->Setup(mol))
cout << "error while initializing the force field (" << vs[1] << ") for this molecule." <<endl;
continue;
}
// load <filename>
if (EQn(commandline, "load", 4)) {
if (vs.size() < 2) {
cout << "no <filename> specified." << endl;
continue;
}
ifstream ifs;
OBConversion conv;
OBFormat *format_in = conv.FormatFromExt(vs[1].c_str());
if (!format_in || !conv.SetInFormat(format_in)) {
cout << "could not detect format." << endl;
continue;
}
ifs.open(vs[1].c_str());
if (!ifs) {
cout << "could not open '" << vs[1] << "'." <<endl;
continue;
}
mol.Clear();
if (!conv.Read(&mol, &ifs)) {
cout << "could not read a molecule from '" << vs[1] << "'." <<endl;
continue;
}
if (mol.Empty()) {
cout << "this molecule is empty." <<endl;
continue;
}
if (!pFF->Setup(mol)) {
cout << "error while initializing the force field for this molecule." <<endl;
continue;
}
cout << "molecule succesfully loaded." << endl;
cout << " " << mol.NumAtoms() << " atoms" << endl;
cout << " " << mol.NumBonds() << " bonds" << endl;
ifs.close();
continue;
}
// save <filename>
if (EQn(commandline, "save", 4)) {
if (vs.size() < 2) {
cout << "no <filename> specified." << endl;
continue;
}
ofstream ofs;
OBConversion conv;
OBFormat *format_out = conv.FormatFromExt(vs[1].c_str());
if (!format_out || !conv.SetOutFormat(format_out)) {
cout << "could not detect format." << endl;
continue;
}
ofs.open(vs[1].c_str());
if (!ofs) {
cout << "could not open '" << vs[1] << "'." <<endl;
continue;
}
if (!conv.Write(&mol, &ofs)) {
cout << "could not read a molecule from '" << vs[1] << "'." <<endl;
continue;
}
cout << "molecule succesfully saved." << endl;
cout << " " << mol.NumAtoms() << " atoms" << endl;
cout << " " << mol.NumBonds() << " bonds" << endl;
ofs.close();
continue;
}
// steepest descent
if (EQn(commandline, "sd", 2)) {
if (vs.size() < 2) {
cout << "no <n> steps specified." << endl;
continue;
}
pFF->SteepestDescent(atoi(vs[1].c_str()), OBFF_ANALYTICAL_GRADIENT);
pFF->UpdateCoordinates(mol);
continue;
}
// conjugate gradients
if (EQn(commandline, "cg", 2)) {
if (vs.size() < 2) {
cout << "no <n> steps specified." << endl;
continue;
}
pFF->ConjugateGradients(atoi(vs[1].c_str()), OBFF_ANALYTICAL_GRADIENT);
pFF->UpdateCoordinates(mol);
continue;
}
cout << "invalid command." << endl;
}
return(1);
}
