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Perl

Installation

The Perl bindings are available only on MacOSX and Linux. (We could not get them to work on Windows.) See Compile language bindings for information on how to configure CMake to compile and install the Perl bindings.

Using Chemistry::OpenBabel

The Chemistry::OpenBabel module is designed to allow Perl scripts to use the C++ Open Babel library. The bindings are generated using the SWIG package and provides access to almost all of the Open Babel interfaces via Perl, including the base classes OBMol, OBAtom, OBBond, and OBResidue, as well as the conversion framework OBConversion.

As such, essentially any call in the C++ API is available to Perl access with very little difference in syntax. This guide is designed to give examples of common Perl syntax for Chemistry::OpenBabel and pointers to the appropriate sections of the API documentation.

The example script below creates atoms and bonds one-by-one using the OBMol, OBAtom, and OBBond classes.

#!/usr/bin/perl

use Chemistry::OpenBabel;

my $obMol = new Chemistry::OpenBabel::OBMol;

$obMol->NewAtom();
$numAtoms = $obMol->NumAtoms(); # now 1 atom

my $atom1 = $obMol->GetAtom(1); # atoms indexed from 1
$atom1->SetVector(0.0, 1.0, 2.0);
$atom1->SetAtomicNum(6); # carbon atom

$obMol->NewAtom();
$obMol->AddBond(1, 2, 1); # bond between atoms 1 and 2 with bond order 1
$numBonds = $obMol->NumBonds(); # now 1 bond

$obMol->Clear();

More commonly, Open Babel can be used to read in molecules using the OBConversion framework. The following script reads in molecular information from a SMILES string, adds hydrogens, and writes out an MDL file as a string.

#!/usr/bin/perl

use Chemistry::OpenBabel;

my $obMol = new Chemistry::OpenBabel::OBMol;
my $obConversion = new Chemistry::OpenBabel::OBConversion;
$obConversion->SetInAndOutFormats("smi", "mdl");
$obConversion->ReadString($obMol, "C1=CC=CS1");

$numAtoms = $obMol->NumAtoms(); # now 5 atoms

$obMol->AddHydrogens();
$numAtoms = $obMol->NumAtoms(); # now 9 atoms

my $outMDL = $obConversion->WriteString($obMol);

The following script writes out a file using a filename, rather than reading and writing to a Perl string.

#!/usr/bin/perl

use Chemistry::OpenBabel;

my $obMol = new Chemistry::OpenBabel::OBMol;
my $obConversion = new Chemistry::OpenBabel::OBConversion;
$obConversion->SetInAndOutFormats("pdb", "mol2");
$obConversion->ReadFile($obMol, "1ABC.pdb");

$obMol->AddHydrogens();

print "# of atoms: $obMol->NumAtoms()";
print "# of bonds: $obMol->NumBonds()";
print "# of residues: $obMol->NumResidues()";

$obConversion->WriteFile($obMol, "1abc.mol2");

Examples

Output Molecular Weight for a Multi-Molecule SDF File

Let’s say we want to print out the molecular weights of every molecule in an SD file. Why? Well, we might want to plot a histogram of the distribution, or see whether the average of the distribution is significantly different (in the statistical sense) compared to another SD file.

use Chemistry::OpenBabel;

my $obconversion = new Chemistry::OpenBabel::OBConversion;
$obconversion->SetInFormat("sdf");
my $obmol = new Chemistry::OpenBabel::OBMol;

my $notatend = $obconversion->ReadFile($obmol, "../xsaa.sdf");
while ($notatend) {
    print $obmol->GetMolWt(), "\n";
    $obmol->Clear();
    $notatend = $obconversion->Read($obmol);
}

Add and Delete Atoms

This script shows an example of deleting and modifying atoms to transform one structure to a related one. It operates on a set of substituted thiophenes, deletes the sulfur atom (note that R1 and R2 may contain sulfur, so the SMARTS pattern is designed to constrain to the ring sulfur), etc. The result is a substituted ethylene, as indicated in the diagrams.

../_images/Tutorial-Thiophene2.png ../_images/Tutorial-Transform2.png
use Chemistry::OpenBabel;

my $obMol = new Chemistry::OpenBabel::OBMol;
my $obConversion = new Chemistry::OpenBabel::OBConversion;
my $filename = shift @ARGV;

$obConversion->SetInAndOutFormats("xyz", "mol");
$obConversion->ReadFile($obMol, $filename);

for (1..$obMol->NumAtoms()) {
    $atom = $obMol->GetAtom($_);
    # look to see if this atom is a thiophene sulfur atom
    if ($atom->MatchesSMARTS("[#16D2]([#6D3H1])[#6D3H1]")) {
        $sulfurIdx = $atom->GetIdx();
    # see if this atom is one of the carbon atoms bonded to a thiophene sulfur
    } elsif ($atom->MatchesSMARTS("[#6D3H1]([#16D2][#6D3H1])[#6]") ) {
        if ($c2Idx == 0) { $c2Idx = $atom->GetIdx(); }
        else {$c5Idx = $atom->GetIdx(); }
    }
}

# Get the actual atom objects -- indexing will change as atoms are added and deleted!
$sulfurAtom = $obMol->GetAtom($sulfurIdx);
$c2Atom = $obMol->GetAtom($c2Idx);
$c5Atom = $obMol->GetAtom($c5Idx);

$obMol->DeleteAtom($sulfurAtom);

$obMol->DeleteHydrogens($c2Atom);
$obMol->DeleteHydrogens($c5Atom);

$c2Atom->SetAtomicNum(1);
$c5Atom->SetAtomicNum(1);

$obConversion->WriteFile($obMol, "$filename.mol");