mirror of
https://github.com/openbabel/openbabel.git
synced 2025-02-25 18:55:23 -06:00
71b835bcad
pyopenbabelapi.html: Changed all references to pyopenbabel to
pybel
(new name). Also, corrected minor typo in docstring in pybel.py.
253 lines
15 KiB
HTML
253 lines
15 KiB
HTML
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<!doctype html PUBLIC "-//W3C//DTD HTML 4.0 Transitional//EN">
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<html><head><title>Python: module pybel</title>
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</head><body bgcolor="#f0f0f8">
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<table width="100%" cellspacing=0 cellpadding=2 border=0 summary="heading">
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<tr bgcolor="#7799ee">
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<td valign=bottom> <br>
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<font color="#ffffff" face="helvetica, arial"> <br><big><big><strong>pybel</strong></big></big></font></td
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><td align=right valign=bottom
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><font color="#ffffff" face="helvetica, arial"><a href=".">index</a><br><a href="file:/home/vmware/Tools/openbabel/scripts/python/pybel.py">/home/vmware/Tools/openbabel/scripts/python/pybel.py</a></font></td></tr></table>
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<p></p>
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<p>
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<table width="100%" cellspacing=0 cellpadding=2 border=0 summary="section">
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<tr bgcolor="#aa55cc">
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<td colspan=3 valign=bottom> <br>
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<font color="#fffff" face="helvetica, arial"><big><strong>Modules</strong></big></font></td></tr>
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<tr><td bgcolor="#aa55cc"><tt> </tt></td><td> </td>
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<td width="100%"><table width="100%" summary="list"><tr><td width="25%" valign=top><a href="openbabel.html">openbabel</a><br>
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</td><td width="25%" valign=top><a href="os.html">os</a><br>
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</td><td width="25%" valign=top></td><td width="25%" valign=top></td></tr></table></td></tr></table><p>
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<table width="100%" cellspacing=0 cellpadding=2 border=0 summary="section">
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<tr bgcolor="#ee77aa">
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<td colspan=3 valign=bottom> <br>
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<font color="#ffffff" face="helvetica, arial"><big><strong>Classes</strong></big></font></td></tr>
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<tr><td bgcolor="#ee77aa"><tt> </tt></td><td> </td>
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<td width="100%"><dl>
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<dt><font face="helvetica, arial"><a href="__builtin__.html#object">__builtin__.object</a>
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</font></dt><dd>
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<dl>
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<dt><font face="helvetica, arial"><a href="pybel.html#Atom">Atom</a>
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</font></dt><dt><font face="helvetica, arial"><a href="pybel.html#Molecule">Molecule</a>
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</font></dt><dt><font face="helvetica, arial"><a href="pybel.html#Outputfile">Outputfile</a>
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</font></dt><dt><font face="helvetica, arial"><a href="pybel.html#Smarts">Smarts</a>
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</font></dt></dl>
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</dd>
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</dl>
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<p>
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<table width="100%" cellspacing=0 cellpadding=2 border=0 summary="section">
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<tr bgcolor="#ffc8d8">
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<td colspan=3 valign=bottom> <br>
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<font color="#000000" face="helvetica, arial"><a name="Atom">class <strong>Atom</strong></a>(<a href="__builtin__.html#object">__builtin__.object</a>)</font></td></tr>
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<tr bgcolor="#ffc8d8"><td rowspan=2><tt> </tt></td>
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<td colspan=2><tt>Represent a Pybel atom.<br>
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<br>
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Optional parameters:<br>
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OBAtom -- an Open Babel <a href="#Atom">Atom</a> (default is None)<br>
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index -- the index of the atom in the molecule (default is None)<br>
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<br>
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An empty <a href="#Atom">Atom</a> is created if an Open Babel atom is not provided.<br>
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<br>
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Attributes:<br>
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atomicmass, atomicnum, cidx, coords, coordidx, exactmass,<br>
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formalcharge, heavyvalence, heterovalence, hyb, idx,<br>
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implicitvalence, index, isotope, partialcharge, spin, type,<br>
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valence, vector.<br>
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<br>
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(refer to the Open Babel library documentation for more info).<br>
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<br>
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The original Open Babel atom can be accessed using the attribute:<br>
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OBAtom<br> </tt></td></tr>
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<tr><td> </td>
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<td width="100%">Methods defined here:<br>
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<dl><dt><a name="Atom-__getattr__"><strong>__getattr__</strong></a>(self, attr)</dt></dl>
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<dl><dt><a name="Atom-__init__"><strong>__init__</strong></a>(self, OBAtom<font color="#909090">=None</font>, index<font color="#909090">=None</font>)</dt></dl>
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<dl><dt><a name="Atom-__str__"><strong>__str__</strong></a>(self)</dt><dd><tt>Create a string representation of the atom.<br>
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<br>
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>>> a = <a href="#Atom">Atom</a>()<br>
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>>> print a<br>
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<a href="#Atom">Atom</a>: 0 (0.0, 0.0, 0.0)</tt></dd></dl>
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<hr>
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Data and other attributes defined here:<br>
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<dl><dt><strong>__dict__</strong> = <dictproxy object><dd><tt>dictionary for instance variables (if defined)</tt></dl>
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<dl><dt><strong>__weakref__</strong> = <attribute '__weakref__' of 'Atom' objects><dd><tt>list of weak references to the <a href="__builtin__.html#object">object</a> (if defined)</tt></dl>
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</td></tr></table> <p>
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<table width="100%" cellspacing=0 cellpadding=2 border=0 summary="section">
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<tr bgcolor="#ffc8d8">
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<td colspan=3 valign=bottom> <br>
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<font color="#000000" face="helvetica, arial"><a name="Molecule">class <strong>Molecule</strong></a>(<a href="__builtin__.html#object">__builtin__.object</a>)</font></td></tr>
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<tr bgcolor="#ffc8d8"><td rowspan=2><tt> </tt></td>
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<td colspan=2><tt>Represent a Pybel molecule.<br>
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<br>
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Optional parameters:<br>
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OBMol -- an Open Babel molecule (default is None)<br>
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<br>
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An empty <a href="#Molecule">Molecule</a> is created if an Open Babel molecule is not provided.<br>
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<br>
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Attributes:<br>
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atoms, charge, dim, energy, exactmass, flags, formula, <br>
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mod, molwt, spin, sssr, title.<br>
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(refer to the Open Babel library documentation for more info).<br>
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<br>
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Methods:<br>
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<a href="#Molecule-write">write</a>()<br>
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<br>
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The original Open Babel molecule can be accessed using the attribute:<br>
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OBMol<br> </tt></td></tr>
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<tr><td> </td>
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<td width="100%">Methods defined here:<br>
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<dl><dt><a name="Molecule-__getattr__"><strong>__getattr__</strong></a>(self, attr)</dt><dd><tt>Return the value of an attribute<br>
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<br>
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Note: The values are calculated on-the-fly. You may want to store the value in<br>
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a variable if you repeatedly access the same attribute.</tt></dd></dl>
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<dl><dt><a name="Molecule-__init__"><strong>__init__</strong></a>(self, OBMol<font color="#909090">=None</font>)</dt></dl>
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<dl><dt><a name="Molecule-__iter__"><strong>__iter__</strong></a>(self)</dt><dd><tt>Iterate over the Atoms of the <a href="#Molecule">Molecule</a>.<br>
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<br>
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This allows constructions such as the following:<br>
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for atom in mymol:<br>
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print atom</tt></dd></dl>
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<dl><dt><a name="Molecule-__str__"><strong>__str__</strong></a>(self)</dt></dl>
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<dl><dt><a name="Molecule-write"><strong>write</strong></a>(self, format<font color="#909090">='SMI'</font>, filename<font color="#909090">=None</font>, overwrite<font color="#909090">=False</font>)</dt><dd><tt>Write the molecule to a file or return a string.<br>
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<br>
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Optional parameters:<br>
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format -- default is "SMI"<br>
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filename -- default is None<br>
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overwite -- default is False<br>
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<br>
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If a filename is specified, the result is written to a file.<br>
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Otherwise, a string is returned containing the result.<br>
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The overwrite flag is ignored if a filename is not specified.<br>
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It controls whether to overwrite an existing file.</tt></dd></dl>
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<hr>
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Data and other attributes defined here:<br>
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<dl><dt><strong>__dict__</strong> = <dictproxy object><dd><tt>dictionary for instance variables (if defined)</tt></dl>
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<dl><dt><strong>__weakref__</strong> = <attribute '__weakref__' of 'Molecule' objects><dd><tt>list of weak references to the <a href="__builtin__.html#object">object</a> (if defined)</tt></dl>
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</td></tr></table> <p>
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<table width="100%" cellspacing=0 cellpadding=2 border=0 summary="section">
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<tr bgcolor="#ffc8d8">
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<td colspan=3 valign=bottom> <br>
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<font color="#000000" face="helvetica, arial"><a name="Outputfile">class <strong>Outputfile</strong></a>(<a href="__builtin__.html#object">__builtin__.object</a>)</font></td></tr>
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<tr bgcolor="#ffc8d8"><td rowspan=2><tt> </tt></td>
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<td colspan=2><tt>Represent a file to which *output* is to be sent.<br>
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<br>
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Although it's possible to write a single molecule to a file by<br>
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calling the <a href="#Outputfile-write">write</a>() method of a molecule, if multiple molecules<br>
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are to be written to the same file you should use the <a href="#Outputfile">Outputfile</a><br>
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class.<br>
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<br>
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Required parameters:<br>
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format<br>
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filename<br>
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Optional parameters:<br>
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overwrite (default is False) -- if the output file already exists,<br>
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should it be overwritten?<br>
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Methods:<br>
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<a href="#Outputfile-write">write</a>(molecule)<br> </tt></td></tr>
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<tr><td> </td>
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<td width="100%">Methods defined here:<br>
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<dl><dt><a name="Outputfile-__init__"><strong>__init__</strong></a>(self, format, filename, overwrite<font color="#909090">=False</font>)</dt></dl>
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<dl><dt><a name="Outputfile-write"><strong>write</strong></a>(self, molecule)</dt><dd><tt>Write a molecule to the output file.<br>
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<br>
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Required parameters:<br>
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molecule</tt></dd></dl>
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<hr>
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Data and other attributes defined here:<br>
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<dl><dt><strong>__dict__</strong> = <dictproxy object><dd><tt>dictionary for instance variables (if defined)</tt></dl>
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<dl><dt><strong>__weakref__</strong> = <attribute '__weakref__' of 'Outputfile' objects><dd><tt>list of weak references to the <a href="__builtin__.html#object">object</a> (if defined)</tt></dl>
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</td></tr></table> <p>
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<table width="100%" cellspacing=0 cellpadding=2 border=0 summary="section">
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<tr bgcolor="#ffc8d8">
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<td colspan=3 valign=bottom> <br>
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<font color="#000000" face="helvetica, arial"><a name="Smarts">class <strong>Smarts</strong></a>(<a href="__builtin__.html#object">__builtin__.object</a>)</font></td></tr>
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<tr bgcolor="#ffc8d8"><td rowspan=2><tt> </tt></td>
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<td colspan=2><tt>A <a href="#Smarts">Smarts</a> Pattern Matcher<br>
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<br>
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Required parameters:<br>
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smartspattern<br>
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<br>
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Methods:<br>
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<a href="#Smarts-findall">findall</a>()<br>
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<br>
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Example:<br>
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>>> mol = <a href="#-readstring">readstring</a>("smi","CCN(CC)CC") # triethylamine<br>
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>>> smarts = <a href="#Smarts">Smarts</a>("[#6][#6]") # Matches an ethyl group<br>
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>>> print smarts.<a href="#Smarts-findall">findall</a>(mol) <br>
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[(1, 2), (4, 5), (6, 7)]<br> </tt></td></tr>
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<tr><td> </td>
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<td width="100%">Methods defined here:<br>
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<dl><dt><a name="Smarts-__init__"><strong>__init__</strong></a>(self, smartspattern)</dt><dd><tt>Initialise with a SMARTS pattern.</tt></dd></dl>
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<dl><dt><a name="Smarts-findall"><strong>findall</strong></a>(self, molecule)</dt><dd><tt>Find all matches of the SMARTS pattern to a particular molecule.<br>
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<br>
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Required parameters:<br>
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molecule</tt></dd></dl>
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<hr>
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Data and other attributes defined here:<br>
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<dl><dt><strong>__dict__</strong> = <dictproxy object><dd><tt>dictionary for instance variables (if defined)</tt></dl>
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<dl><dt><strong>__weakref__</strong> = <attribute '__weakref__' of 'Smarts' objects><dd><tt>list of weak references to the <a href="__builtin__.html#object">object</a> (if defined)</tt></dl>
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</td></tr></table></td></tr></table><p>
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<table width="100%" cellspacing=0 cellpadding=2 border=0 summary="section">
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<tr bgcolor="#eeaa77">
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<td colspan=3 valign=bottom> <br>
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<font color="#ffffff" face="helvetica, arial"><big><strong>Functions</strong></big></font></td></tr>
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<tr><td bgcolor="#eeaa77"><tt> </tt></td><td> </td>
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<td width="100%"><dl><dt><a name="-readfile"><strong>readfile</strong></a>(format, filename)</dt><dd><tt>Iterate over the molecules in a file.<br>
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<br>
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Required parameters:<br>
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format<br>
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filename<br>
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<br>
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You can access the first molecule in a file using:<br>
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mol = <a href="#-readfile">readfile</a>("smi", "myfile.smi").next()<br>
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<br>
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You can make a list of the molecules in a file using:<br>
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mols = [mol for mol in <a href="#-readfile">readfile</a>("smi", "myfile.smi")]<br>
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<br>
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You can iterate over the molecules in a file as shown in the<br>
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following code snippet...<br>
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<br>
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>>> atomtotal = 0<br>
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>>> for mol in <a href="#-readfile">readfile</a>("sdf","head.sdf"):<br>
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... atomtotal += len(mol.atoms)<br>
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...<br>
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>>> print atomtotal<br>
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43</tt></dd></dl>
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<dl><dt><a name="-readstring"><strong>readstring</strong></a>(format, string)</dt><dd><tt>Read in a molecule from a string.<br>
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<br>
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Required parameters:<br>
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format<br>
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string<br>
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<br>
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>>> input = "C1=CC=CS1"<br>
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>>> mymol = <a href="#-readstring">readstring</a>("smi",input)<br>
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>>> len(mymol.atoms)<br>
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5</tt></dd></dl>
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</td></tr></table>
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</body></html> |