Mercurial > repos > bgruening > openbabel
changeset 10:cc63a42fd22e
Uploaded
| author | bgruening |
|---|---|
| date | Sat, 25 May 2013 12:54:40 -0400 |
| parents | d051544e94da |
| children | 77b82f259298 |
| files | convert/ob_convert.xml filter/ob_filter.xml filter/ob_remDuplicates.xml modify/ob_genProp.xml repository_dependencies.xml search/ob_spectrophore_search.py search/ob_spectrophore_search.xml tool_dependencies.xml |
| diffstat | 8 files changed, 11 insertions(+), 4 deletions(-) [+] |
line wrap: on
line diff
--- a/convert/ob_convert.xml Thu May 23 17:29:11 2013 -0400 +++ b/convert/ob_convert.xml Sat May 25 12:54:40 2013 -0400 @@ -28,9 +28,9 @@ -o "$format" -e -O ${os.path.join($outfile.extra_files_path,'molecule.fs')} #if int($oformat.fs_fold) > 0: - $oformat.fs_fold + -xN$oformat.fs_fold #end if - -xN$#str(${oformat.fs_fptype}).strip() + ${oformat.fs_fptype} #else: "${infile}" -o "$format"
--- a/filter/ob_filter.xml Thu May 23 17:29:11 2013 -0400 +++ b/filter/ob_filter.xml Sat May 25 12:54:40 2013 -0400 @@ -3,6 +3,7 @@ <parallelism method="multi" split_inputs="infile" split_mode="to_size" split_size="10000" shared_inputs="" merge_outputs="outfile"></parallelism> <requirements> <requirement type="package" version="2.3.2">openbabel</requirement> + <requirement type="package" version="0.1">cheminfolib</requirement> </requirements> <command interpreter="python"> ob_filter.py
--- a/filter/ob_remDuplicates.xml Thu May 23 17:29:11 2013 -0400 +++ b/filter/ob_remDuplicates.xml Sat May 25 12:54:40 2013 -0400 @@ -7,7 +7,7 @@ <command> obabel -i"${infile.ext}" - "${infile} + "${infile}" -ocopy --unique "${descriptor}" -O "${outfile}"
--- a/modify/ob_genProp.xml Thu May 23 17:29:11 2013 -0400 +++ b/modify/ob_genProp.xml Sat May 25 12:54:40 2013 -0400 @@ -3,6 +3,7 @@ <parallelism method="multi" split_inputs="infile" split_mode="to_size" split_size="10000" shared_inputs="" merge_outputs="outfile"></parallelism> <requirements> <requirement type="package" version="2.3.2">openbabel</requirement> + <requirement type="package" version="0.1">cheminfolib</requirement> </requirements> <command interpreter="python"> ob_genProp.py
--- a/repository_dependencies.xml Thu May 23 17:29:11 2013 -0400 +++ b/repository_dependencies.xml Sat May 25 12:54:40 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 changeset_revision="bd886859b184" name="molecule_datatypes" owner="bgruening" toolshed="http://testtoolshed.g2.bx.psu.edu" /> + <repository changeset_revision="c5383bd4d006" name="molecule_datatypes" owner="bgruening" toolshed="http://testtoolshed.g2.bx.psu.edu" /> </repositories>
--- a/search/ob_spectrophore_search.py Thu May 23 17:29:11 2013 -0400 +++ b/search/ob_spectrophore_search.py Sat May 25 12:54:40 2013 -0400 @@ -10,6 +10,7 @@ openbabel.obErrorLog.StopLogging() import pybel import math +import numpy as np #TODO get rid of eval()
--- a/search/ob_spectrophore_search.xml Thu May 23 17:29:11 2013 -0400 +++ b/search/ob_spectrophore_search.xml Sat May 25 12:54:40 2013 -0400 @@ -2,6 +2,7 @@ <description>similarity search based on 1D chemical features</description> <requirements> <requirement type="package" version="2.3.2">openbabel</requirement> + <requirement type="package" version="1.7.1">numpy</requirement> </requirements> <command interpreter="python"> ob_spectrophore_search.py
--- a/tool_dependencies.xml Thu May 23 17:29:11 2013 -0400 +++ b/tool_dependencies.xml Sat May 25 12:54:40 2013 -0400 @@ -3,6 +3,9 @@ <package name="openbabel" version="2.3.2"> <repository changeset_revision="ccda1b8ebc72" name="package_openbabel_2_3" owner="bgruening" toolshed="http://testtoolshed.g2.bx.psu.edu" /> </package> + <package name="numpy" version="1.7.1"> + <repository changeset_revision="7283651b62fe" name="package_numpy_1_7" owner="bgruening" prior_installation_required="True" toolshed="http://testtoolshed.g2.bx.psu.edu" /> + </package> <package name="cheminfolib" version="0.1"> <install version="1.0"> <actions>