openbabel/scripts/python/Examples.html

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<h1>Using the openbabel module with Python</h1>

<p>
The <code>openbabel</code> module is designed to allow Python scripts to use the C++ Open Babel library. The wrapper is generated using the SWIG package and provides access to almost all of the Open Babel interfaces via Python, including the base
classes OBMol, OBAtom, OBBond, and OBResidue, as well as the conversion framework OBConversion.
</p>

<p>
As such, essentially any call in the C++ API is available to Python scripts with very little difference in syntax. This guide is designed to give examples of common Python syntax for the <code>openbabel</code> module and pointers to the appropriate sections of the API documentation.
</p>

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

<pre>
from openbabel import openbabel

mol = openbabel.OBMol()
print 'Should print 0 (atoms)'
print mol.NumAtoms()

a = mol.NewAtom()
a.SetAtomicNum(6)   # carbon atom
a.SetVector(0.0, 1.0, 2.0) # coordinates

b = mol.NewAtom()
mol.AddBond(1, 2, 1)   # atoms indexed from 1
print 'Should print 2 (atoms)'
print mol.NumAtoms()
print 'Should print 1 (bond)'
print mol.NumBonds()

mol.Clear();
</pre>

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

<pre>
from openbabel import openbabel

mol = openbabel.OBMol()
obConversion = openbabel.OBConversion()
obConversion.SetInAndOutFormats("smi", "mdl")

obConversion.ReadString(mol, "C1=CC=CS1")

print 'Should print 5 (atoms)'
print mol.NumAtoms()

mol.AddHydrogens()
print 'Should print 9 (atoms) after adding hydrogens'
print mol.NumAtoms()

outMDL = obConversion.WriteString(mol)
</pre>

<p>
The following script writes out a file using a filename, rather than reading and writing to a Python string.
</p>

<pre>
from openbabel import openbabel

mol = openbabel.OBMol()
obConversion = openbabel.OBConversion()
obConversion.SetInAndOutFormats("pdb", "mol2")

obConversion.ReadFile(mol, "1ABC.pdb.gz")   # Open Babel will uncompress automatically

mol.AddHydrogens()

print mol.NumAtoms()
print mol.NumBonds()
print mol.NumResidues()

obConversion.WriteFile(mol, '1abc.mol2')
</pre>

<p>
That's it! There's more information on particular calls in the <a href="http://openbabel.org/api/">library API</a>. Feel free to address questions to the <a href="mailto:openbabel-scripting@lists.sourceforge.net">openbabel-scripting</a> mailing list.
</p>

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Updated mainline with openbabel-new-framework branch. Will create a new openbabel-2-0-x release branch soon. 2005-11-18 00:53:15 +00:00			`<!DOCTYPE html PUBLIC "-//W3C//DTD XHTML 1.0 Transitional//EN" "http://www.w3.or`
			`g/TR/xhtml1/DTD/xhtml1-transitional.dtd">`
			`<html xmlns="http://www.w3.org/1999/xhtml">`
			`<head>`
			`<title>Open Babel: Python Scripting</title>`
			`<meta http-equiv="Content-Type" content="text/html; charset=ISO-8859-1" />`

Update website to openbabel.org (long overdue). 2010-10-10 01:24:39 +00:00			`<link rel="top" href="http://openbabel.org/" />`
Updated mainline with openbabel-new-framework branch. Will create a new openbabel-2-0-x release branch soon. 2005-11-18 00:53:15 +00:00			`<link rel="stylesheet" href="site.css" type="text/css" media="all" />`
			`</head>`
			`<body bgcolor="#ffffff">`

			`<div id="header">`
			`<img src="babel130.png" width=130 height=124 alt="Babel Logo" id="logo" />`
			`<h1><img src="OBTitle.jpg" width=333 height=92 alt="Open Babel" /></h1>`
			`</div>`

			`<div id="content">`

			`<h1>Using the openbabel module with Python</h1>`

			`<p>`
			`The <code>openbabel</code> module is designed to allow Python scripts to use the C++ Open Babel library. The wrapper is generated using the SWIG package and provides access to almost all of the Open Babel interfaces via Python, including the base`
			`classes OBMol, OBAtom, OBBond, and OBResidue, as well as the conversion framework OBConversion.`
			`</p>`

			`<p>`
			`As such, essentially any call in the C++ API is available to Python scripts with very little difference in syntax. This guide is designed to give examples of common Python syntax for the <code>openbabel</code> module and pointers to the appropriate sections of the API documentation.`
			`</p>`

			`<p>`
			`The example script below creates atoms and bonds one-by-one using the OBMol, OBAtom, and OBBond classes.`
			`</p>`

			`<pre>`
Fix import of openbabel 2019-10-10 16:54:59 +09:00			`from openbabel import openbabel`
Updated mainline with openbabel-new-framework branch. Will create a new openbabel-2-0-x release branch soon. 2005-11-18 00:53:15 +00:00
			`mol = openbabel.OBMol()`
			`print 'Should print 0 (atoms)'`
			`print mol.NumAtoms()`

			`a = mol.NewAtom()`
			`a.SetAtomicNum(6) # carbon atom`
			`a.SetVector(0.0, 1.0, 2.0) # coordinates`

			`b = mol.NewAtom()`
			`mol.AddBond(1, 2, 1) # atoms indexed from 1`
			`print 'Should print 2 (atoms)'`
			`print mol.NumAtoms()`
			`print 'Should print 1 (bond)'`
			`print mol.NumBonds()`

			`mol.Clear();`
			`</pre>`

			`<p>`
			`More commonly, Open Babel can be used to read in molecules using the OBConversion framework. The following script reads in molecular information (a SMI file) from a string, adds hydrogens, and writes out an MDL file as a string.`
			`</p>`

			`<pre>`
Fix import of openbabel 2019-10-10 16:54:59 +09:00			`from openbabel import openbabel`
Updated mainline with openbabel-new-framework branch. Will create a new openbabel-2-0-x release branch soon. 2005-11-18 00:53:15 +00:00
clarified required use of OBMol object While running the code as given originally would work, the re`import` of openbabel made it seem that the second and third examples would work independently when in fact they won't without defining `mol = openbabel.OBMol()`. 2017-10-06 15:00:39 -04:00			`mol = openbabel.OBMol()`
Updated mainline with openbabel-new-framework branch. Will create a new openbabel-2-0-x release branch soon. 2005-11-18 00:53:15 +00:00			`obConversion = openbabel.OBConversion()`
			`obConversion.SetInAndOutFormats("smi", "mdl")`

			`obConversion.ReadString(mol, "C1=CC=CS1")`

			`print 'Should print 5 (atoms)'`
			`print mol.NumAtoms()`

			`mol.AddHydrogens()`
			`print 'Should print 9 (atoms) after adding hydrogens'`
			`print mol.NumAtoms()`

			`outMDL = obConversion.WriteString(mol)`
			`</pre>`

			`<p>`
			`The following script writes out a file using a filename, rather than reading and writing to a Python string.`
			`</p>`

			`<pre>`
Fix import of openbabel 2019-10-10 16:54:59 +09:00			`from openbabel import openbabel`
Updated mainline with openbabel-new-framework branch. Will create a new openbabel-2-0-x release branch soon. 2005-11-18 00:53:15 +00:00
clarified required use of OBMol object While running the code as given originally would work, the re`import` of openbabel made it seem that the second and third examples would work independently when in fact they won't without defining `mol = openbabel.OBMol()`. 2017-10-06 15:00:39 -04:00			`mol = openbabel.OBMol()`
Updated mainline with openbabel-new-framework branch. Will create a new openbabel-2-0-x release branch soon. 2005-11-18 00:53:15 +00:00			`obConversion = openbabel.OBConversion()`
			`obConversion.SetInAndOutFormats("pdb", "mol2")`

			`obConversion.ReadFile(mol, "1ABC.pdb.gz") # Open Babel will uncompress automatically`

			`mol.AddHydrogens()`

			`print mol.NumAtoms()`
			`print mol.NumBonds()`
			`print mol.NumResidues()`

			`obConversion.WriteFile(mol, '1abc.mol2')`
			`</pre>`

			`<p>`
Update website to openbabel.org (long overdue). 2010-10-10 01:24:39 +00:00			`That's it! There's more information on particular calls in the <a href="http://openbabel.org/api/">library API</a>. Feel free to address questions to the <a href="mailto:openbabel-scripting@lists.sourceforge.net">openbabel-scripting</a> mailing list.`
Updated mainline with openbabel-new-framework branch. Will create a new openbabel-2-0-x release branch soon. 2005-11-18 00:53:15 +00:00			`</p>`

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