Mercurial > repos > bgruening > rdkit
changeset 1:45b822b9d522
Uploaded
| author | bgruening |
|---|---|
| date | Sat, 27 Apr 2013 13:15:27 -0400 |
| parents | 764340994e71 |
| children | ba209f6d2fac |
| files | rdkit_descriptors.py repository_dependencies.xml tool_dependencies.xml |
| diffstat | 3 files changed, 11 insertions(+), 5 deletions(-) [+] |
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--- a/rdkit_descriptors.py Sat Apr 27 09:01:41 2013 -0400 +++ b/rdkit_descriptors.py Sat Apr 27 13:15:27 2013 -0400 @@ -7,6 +7,10 @@ import inspect def get_supplier( infile, format = 'smiles' ): + """ + Returns a generator over a SMILES or InChI file. Every element is of RDKit + molecule and has its original string as _Name property. + """ with open(infile) as handle: for line in handle: line = line.strip() @@ -22,6 +26,9 @@ def get_rdkit_descriptor_functions(): + """ + Returns all descriptor functions under the Chem.Descriptors Module as tuple of (name, function) + """ ret = [ (name, f) for name, f in inspect.getmembers( Descriptors ) if inspect.isfunction( f ) and not name.startswith( '_' ) ] ret.sort() return ret @@ -31,7 +38,6 @@ """ Calculates the descriptors of a given molecule. """ - for name, function in functions: yield (name, function( mol )) @@ -66,6 +72,6 @@ if not mol: continue descs = descriptors( mol, functions ) - name = mol.GetProp("_Name") - args.outfile.write( "%s\n" % '\t'.join( [name]+ [str(res) for name, res in descs] ) ) + molecule_id = mol.GetProp("_Name") + args.outfile.write( "%s\n" % '\t'.join( [molecule_id]+ [str(res) for name, res in descs] ) )
--- a/repository_dependencies.xml Sat Apr 27 09:01:41 2013 -0400 +++ b/repository_dependencies.xml Sat Apr 27 13:15:27 2013 -0400 @@ -1,4 +1,4 @@ <?xml version="1.0"?> <repositories description="This requires the Molecule datatype definitions (e.g. SMILES, InChI, SD-format)."> - <repository toolshed="http://testtoolshed.g2.bx.psu.edu/" name="molecule_datatypes" owner="bgruening" changeset_revision="e533de975501" /> + <repository toolshed="http://testtoolshed.g2.bx.psu.edu/" name="molecule_datatypes" owner="bgruening" changeset_revision="31d2baa37efe" /> </repositories>
--- a/tool_dependencies.xml Sat Apr 27 09:01:41 2013 -0400 +++ b/tool_dependencies.xml Sat Apr 27 13:15:27 2013 -0400 @@ -1,5 +1,5 @@ <tool_dependency> <package name="rdkit" version="2012_12_1"> - <repository toolshed="http://testtoolshed.g2.bx.psu.edu/" name="package_rdkit_2012_12" owner="bgruening" changeset_revision="0adc830e7d71" prior_installation_required="True" /> + <repository toolshed="http://testtoolshed.g2.bx.psu.edu/" name="package_rdkit_2013_03" owner="bgruening" changeset_revision="2afc5219c053" prior_installation_required="True" /> </package> </tool_dependency>