1. // Automatic format perception // Molecular formula
Open Babel 2.3 std::ifstream ifs(filename);
OBConversion conv;
(std::string) mol.GetFormula();
C++ API OBFormat* inFormat = conv.FormatFromExt(filename);
OBFormat* outFormat = conv.SetFormat("SDF");
// Conformations
(int) mol.NumConformers();
if (inFormat && outFormat)
Quick reference guide {
conv.SetInAndOutFormats(inFormat, outFormat);
// Smallest set of smallest rings
(std::vector<OBRing*>) mol.GetSSSR();
}
// Hydrogen manipulations
(bool) mol.DeleteHydrogens(); // All H
(bool) mol.AddPolarHydrogens(); // Polar H
Namespace Looping over atoms and bonds (bool) mol.AddHydrogens(); // All H
// Generic data
using namespace OpenBabel; #include <openbabel/obiter.h> std::vector<OBGenericData*>::iterator k;
#include <openbabel/mol.h> std::vector<OBGenericData*> vdata = mol.GetData();
for (k = vdata.begin(); k != vdata.end(); ++k)
using namespace OpenBabel; if ((*k)->GetDataType() == OBGenericDataType::PairData)
Reading and writing OBMol mol;
{
std::cout << "> <" << (*k)->GetAttribute();
OBAtom* atom; std::cout << ">" << std::endl;
#include <openbabel/mol.h> OBAtom* nbrAtom; std::cout << ((OBPairData*)(*k))->GetValue();
#include <openbabel/obconversion.h> OBBond* bond; std::cout << std::endl;
}
int main(int argc, char **argv) // Looping over all atoms
{ double exactMass(0.0); // Remove all but the largest fragments
OBMol mol; FOR_ATOMS_OF_MOL(atom, mol) (bool) mol.StripSalts(0);
{
// Read from standard input and write to exactMass += atom->GetExactMass(); // Clear molecule for re-use
// standard output } (bool) mol.Clear();
OBConversion conv(&std::cin, &std::cout);
// Looping over all bonds
// Input format is sd-file, output format unsigned int totalBondOrder(0);
// is canonical smiles
if (conv.SetInAndOutFormats("sdf", "can"))
FOR_BONDS_OF_MOL(bond, mol)
{
Atoms
{ totalBondOrder += bond->GetBondOrder();
if (conv.Read(&mol)) } #include <openbabel/atom.h>
{ // Looping over all neighbor atoms of given atom
// Print number of atoms unsigned int nAtoms(0); OBAtom atom;
std::cerr << "Molecule has: " << FOR_NBORS_OF_ATOM(nbrAtom, atom) ++nAtoms;
mol.NumAtoms() << " atoms.n"; // Properties
} (int) atom.GetFormalCharge();
conv->Write(&mol); (unsigned int) atom.GetAtomicNum();
}
mol.Clear(); Element table (double) atom.GetAtomicMass();
return 0; // Explicit and maximum expected connections
} #include <openbabel/data.h> (unsigned int) atom.GetValence();
(unsigned int) atom.GetImplicitValence();
OBElementTable etab;
// Non-hydrogen connections
Conversion (char*)
(int)
etab.GetSymbol(6);
etab.GetAtomicNum("C");
(unsigned int) atom.GetHvyValence();
(double) etab.GetVdwRad(7); // Implicit and explicit hydrogens
#include <openbabel/obconversion.h> (double) etab.GetCovalentRad(8); (unsigned int) atom.ImplicitHydrogenCount();
#include <openbabel/mol.h> (double) etab.GetMass(1); (unsigned int) atom.ExplicitHydrogenCount();
// Create molecule from SMILES string // Is atom in ring of size 6?
std::string SmilesString("c1ccccc1"); (bool) atom.IsInRing() && atom.IsInRingSize(6);
OBMol mol;
stringstream ss(SmilesString)
Molecules // Size of smallest ring that contains the atom
OBConversion conv(&ss); (unsigned int) atom.MemberOfRingSize();
if (conv.SetInFormat("smi") && conv.Read(&mol)) #include <openbabel/mol.h>
{ /* ... */ } #include <openbabel/generic.h> // Number of rings that contain the atom
(unsigned int) atom.MemberOfRingCount();
// Conversion without manipulation OBMol mol;
OBConversion conv(&is, &os);
if (conv.SetInAndOutFormats("SMI", "MOL")) // Number of atoms and bonds
{
// Option "h" adds explicit hydrogens
(unsigned
(unsigned
int) mol.NumAtoms(); // All atoms
int) mol.NumHvyAtoms(); // Non-H atoms
Bonds
conv.AddOption("h", OBConversion::GENOPTIONS); (unsigned int) mol.NumBonds(); // All bonds
conv.Convert(); #include <openbabel/bond.h>
} // Molecular weight with implicit hydrogens #include <openbabel/atom.h>
(double) mol.GetMolWt(true);
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2. OBBond bond; // Set calculation parameters
spec.SetResolution(3.0); Energy calculations
// Properties spec.SetAccuracy(AngStepSize20);
(unsigned int) bond.GetBondOrder(); spec.SetStereo(NoStereoSpecificProbes); #include <openbabel/forcefield.h>
(bool) bond.IsPrimaryAmide(); // and 2 and 3... spec.SetNormalization(NormalizationTowardsZeroMean); #include <openbabel/mol.h>
(bool) bond.IsSingle(); // and 2 and 3...
(bool) bond.IsRotor(); // Calculate and print OBMol mol;
std::vector<double> sphore; /* ... */
// Flanking atoms sphore = spec.GetSpectrophore(&mol);
(OBAtom*) bond.GetBeginAtom(); for (int i(0); i < sphore.size(); ++i) // Select the MMFF94 forcefield
(OBAtom*) bond.GetEndAtom(); { OBForceField* pFF;
OBAtom* atom; (OBAtom*) bond.GetNbrAtom(atom); std::cout << sphore[i] << "t"; pFF = OBForceField::FindForceField("MMFF94");
} if (!pFF) exit(1);
// Is bond in ring? std::cout << std::endl;
(bool) bond.IsInRing(); // Set the logfile
pFF->SetLogFile(&std::cerr);
Stereochemistry // Assign atom types, parameters, ...
Substructure search pFF->Setup(mol);
#include <openbabel/mol.h> // Calculate the energy
#include <openbabel/parsmart.h> #include <openbabel/obconversion.h> pFF->Energy();
#include <openbabel/mol.h> #include <openbabel/stereo/tetrahedral.h>
#include <openbabel/atom.h> // Perform maximum 1000 steps of minimization
OBMol mol; pFF->ConjugateGradients(1000);
OBMol mol; OBConversion conv;
OBAtom* atom; conv.SetInFormat("smi");
/* ... */ conv.ReadString(&mol, "C[C@H](Cl)Br");
// Create a SMARTS pattern of a phenyl ring // Stereofacade object
OBSmartsPattern sp; OBStereoFacade facade(&mol); Open Babel
sp.Init("c1ccccc1"); (unsigned int) facade.NumTetrahedralStereo();
(unsigned int) facade.NumCisTransStereo(); This documentation is part of the Open Babel project. For more information,
// Properties of the substructure (unsigned int) facade.SquarePlanarStereo(); see www.openbabel.org. Open Babel is free software; you can redistribute
if (sp.IsValid()) it and/or modify it under the terms of the GNU General Public License as
{ // Loop over all atoms to check if stereocenter published by the Free Software Foundation version 2 of the License. Open
std::cout << sp.NumAtoms(); FOR_ATOMS_OF_MOL(atom, mol) Babel is distributed in the hope that it will be useful, but without any
std::cout << sp.NumBonds(); {
std::cout << sp.GetSmarts(); std::cout << atom->GetId() << ": "; warranty; without even the implied warranty of merchantability or fitness for
} if (facade.HasTetrahedralStereo(atom->GetId())) a particular purpose. See the GNU General Public License for more details.
std::cout << ": stereo";
// Matching else
(bool) sp.Match(mol, true); // Single matching std::cout << ": no stereo"; Spectrophore™
(bool) sp.Match(mol, false); // Complete matching std::cout << std::endl;
} Spectrophore™ is a trademark of Silicos NV and the technology is part of
// Substructure mapping the Open Babel project.
std::vector<std::vector<int> > mapListA;
mapListA = sp.GetMapList(); // Non-unique matches
std::vector<std::vector<int> > mapListU; Rings Silicos NV
mapListU = sp.GetUMapList(); // Unique matches
for (int m(0); m < mapListU.size(); ++m) Silicos is a fee-for-service company empowering open source chemo-
{ #include <openbabel/mol.h> informatics virtual screening technologies for the discovery of novel lead
std::cout << "Unique match " << m << std::endl; #include <openbabel/ring.h> compounds and database characterization. Silicos fully endorses the
for (int a(0); a < mapListU[m].size(); ++a) #include <openbabel/math/vector3.h> concept of open innovation and open source software development, and
{ provides its clients with a wide variety of computational chemistry-based
atom = mol.GetAtom(mapListU[m][a]); OBMol mol; lead discovery services, including Open Babel support, training and code
std::cout << atom->GetAtomicNum() << std::endl; /* ... */
} development. Please visit www.silicos.com for more details.
} // Get the smallest-set-of-smallest-rings
std::vector<OBRing*> rings = mol.GetSSSR();
vector3 center;
vector3 normal_up;
Spectrophores™ vector3 normal_down;
for (int i(0); i < rings.size(); ++i)
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{ Silicos NV
#include <openbabel/obspectrophore.h> (bool) rings[i].IsAromatic();
#include <openbabel/mol.h> (int) rings[i].Size(); Wetenschapspark 7,
(bool) rings[i].findCenterAndNormal(center, B-3590 Diepenbeek
OBMol mol; normal_up, Belgium
/* ... */ normal_down);
} www.silicos.com
// Create a Spectrophore object www.openbabel.org
OBSpectrophore spec;
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