Mercurial > repos > bgruening > molecule_datatypes
changeset 2:e533de975501
Uploaded
| author | bgruening |
|---|---|
| date | Fri, 26 Apr 2013 11:03:19 -0400 (2013-04-26) |
| parents | 25698453d7d7 |
| children | ad5ecf08508a |
| files | molecules.py tool_dependencies.xml |
| diffstat | 2 files changed, 19 insertions(+), 7 deletions(-) [+] |
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--- a/molecules.py Sun Mar 31 13:08:00 2013 -0400 +++ b/molecules.py Fri Apr 26 11:03:19 2013 -0400 @@ -70,6 +70,19 @@ def get_mime(self): return 'text/plain' +class MOL( GenericMolFile ): + file_ext = "mol" + def sniff( self, filename ): + if count_special_lines("^M\s*END", filename) = 1: + return True + else: + return False + + def set_meta( self, dataset, **kwd ): + """ + Set the number molecules, in the case of MOL its always one. + """ + dataset.metadata.number_of_molecules = 1 class SDF( GenericMolFile ): @@ -82,9 +95,9 @@ def set_meta( self, dataset, **kwd ): """ - Set the number of lines of data in dataset. + Set the number of molecules in dataset. """ - dataset.metadata.number_of_molecules = count_special_lines("^\$\$\$\$", dataset.file_name)#self.count_data_lines(dataset.file_name) + dataset.metadata.number_of_molecules = count_special_lines("^\$\$\$\$", dataset.file_name) def split( cls, input_datasets, subdir_generator_function, split_params): """
--- a/tool_dependencies.xml Sun Mar 31 13:08:00 2013 -0400 +++ b/tool_dependencies.xml Fri Apr 26 11:03:19 2013 -0400 @@ -1,5 +1,4 @@ -<tool_dependency> - <package name="openbabel" version="2.3.2"> - <repository toolshed="http://testtoolshed.g2.bx.psu.edu/" name="package_openbabel_2_3" owner="bgruening" changeset_revision="9e07452137da" /> - </package> -</tool_dependency> +<?xml version="1.0"?> +<repositories description="This requires the OpenBabel binaries and python bindings (e.g. obabel, obgrep)."> + <repository toolshed="http://testtoolshed.g2.bx.psu.edu/" name="package_openbabel_2_3" owner="bgruening" changeset_revision="13d2ea9436b3" /> +</repositories>