changeset 4:b4ad35a9c82a

Deleted selected files

--- a/rdkit_descriptors.py	Sat May 11 17:05:26 2013 -0400
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,77 +0,0 @@
-#!/usr/bin/env python
-
-from rdkit.Chem import Descriptors
-from rdkit import Chem
-import sys, os, re
-import argparse
-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()
-            if format == 'smiles':
-                mol = Chem.MolFromSmiles( line, sanitize=True )
-            elif format == 'inchi':
-                mol = Chem.inchi.MolFromInchi( line, sanitize=True, removeHs=True, logLevel=None, treatWarningAsError=False )
-            if mol is None:
-                yield False
-            else:
-                mol.SetProp( '_Name', line.split('\t')[0] )
-                yield mol
-
-
-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
-
-
-def descriptors( mol, functions ):
-    """
-    Calculates the descriptors of a given molecule.
-    """
-    for name, function in functions:
-        yield (name, function( mol ))
-
-
-if __name__ == "__main__":
-    parser = argparse.ArgumentParser()
-    parser.add_argument('-i', '--infile', required=True, help='Path to the input file.')
-    parser.add_argument("--iformat", help="Specify the input file format.")
-
-    parser.add_argument('-o', '--outfile', type=argparse.FileType('w+'), 
-        default=sys.stdout, help="path to the result file, default it sdtout")
-
-    parser.add_argument("--header", dest="header", action="store_true",
-                    default=False,
-                    help="Write header line.")
-
-    args = parser.parse_args()
-
-    if args.iformat == 'sdf':
-        supplier = Chem.SDMolSupplier( args.infile )
-    elif args.iformat =='smi':
-        supplier = get_supplier( args.infile, format = 'smiles' )
-    elif args.iformat == 'inchi':
-        supplier = get_supplier( args.infile, format = 'inchi' )
-
-    functions = get_rdkit_descriptor_functions()
-
-    if args.header:
-        args.outfile.write( '%s\n' % '\t'.join( [name for name, f in functions] ) )
-
-    for mol in supplier:
-        if not mol:
-            continue
-        descs = descriptors( mol, functions )
-        molecule_id = mol.GetProp("_Name")
-        args.outfile.write( "%s\n" % '\t'.join( [molecule_id]+ [str(res) for name, res in descs] ) )
-

--- a/rdkit_descriptors.xml	Sat May 11 17:05:26 2013 -0400
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,49 +0,0 @@
-<tool id="ctb_rdkit_describtors" name="Descriptors" version="0.1">
-    <description>calculated with RDKit</description>
-    <parallelism method="multi" split_inputs="infile" split_mode="to_size" split_size="10000" shared_inputs="" merge_outputs="outfile"></parallelism>
-    <requirements>
-        <requirement type="package" version="2012_12_1">rdkit</requirement>
-    </requirements>
-    <command interpreter="python">rdkit_descriptors.py -i "${infile}" --iformat "${infile.ext}" -o "${outfile}" $header 2>&#38;1</command>
-    <inputs>
-        <param format="smi,sdf" name="infile" type="data" label="Molecule data in SD- or SMILES-format" help="Dataset missing? See TIP below"/>
-        <param name="header" type="boolean" label="Include the descriptor name as header" truevalue="--header" falsevalue="" checked="false" />
-    </inputs>
-    <outputs>
-        <data format="tabular" name="outfile" />
-    </outputs>
-    <tests>
-    </tests>
-    <help>
-
-.. class:: infomark
-
-**TIP:** If your data is not in SD- or SMILES format, use the pencil icon on your dataset to convert your data
-
------
-
-**Example**
-
-- Input file::
-
-    - SD-Format (http://en.wikipedia.org/wiki/Chemical_table_file)
-    - SMILES Format (http://en.wikipedia.org/wiki/Simplified_molecular_input_line_entry_specification)
-
-- Result::
-
-
-http://code.google.com/p/rdkit/wiki/DescriptorsInTheRDKit
-http://rdkit.org/Python_Docs/rdkit.Chem.Descriptors-module.html
-
-
------
-
-
-**Cite**
-
-Greg Landrum
-[1] RDKit: Open-source cheminformatics; http://www.rdkit.org
-
-
-    </help>
-</tool>

--- a/repository_dependencies.xml	Sat May 11 17:05:26 2013 -0400
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,4 +0,0 @@
-<?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="bc6a7eeb7c32" />
-</repositories> 

--- a/tool_dependencies.xml	Sat May 11 17:05:26 2013 -0400
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,46 +0,0 @@
-<tool_dependency>
-    <package name="numpy" version="1.7.1">
-        <repository toolshed="http://testtoolshed.g2.bx.psu.edu/" name="package_numpy_1_7" owner="bgruening" changeset_revision="ec80bba4bccb" prior_installation_required="True" />
-    </package>
-    <package name="boost" version="1.53.0">
-        <repository toolshed="http://testtoolshed.g2.bx.psu.edu/" name="package_boost_1_53" owner="bgruening" changeset_revision="f4209b50c801" prior_installation_required="True" />
-    </package>
-
-    <package name="rdkit" version="2013_03_2">
-        <install version="1.0">
-            <actions>
-                <!-- first action is always downloading -->
-                <action type="download_by_url">http://rdkit.googlecode.com/files/RDKit_2013_03_2.tgz</action>
-
-                <!-- populate the environment variables from the dependend repos -->
-                <action type="set_environment_for_install">
-                    <repository toolshed="http://testtoolshed.g2.bx.psu.edu/" name="package_numpy_1_7" owner="bgruening" changeset_revision="ec80bba4bccb">
-                        <package name="numpy" version="1.7.1" />
-                    </repository>
-                </action>
-                <action type="set_environment_for_install">
-                    <repository toolshed="http://testtoolshed.g2.bx.psu.edu/" name="package_boost_1_53" owner="bgruening" changeset_revision="f4209b50c801">
-                        <package name="boost" version="1.53.0" />
-                    </repository>
-                </action>
-
-                <!-- PYTHONPATH_NUMPY is set in the numpy package -->
-                <action type="shell_command">export LD_LIBRARY_PATH=$LD_LIBRARY_PATH:`pwd`/lib/ &amp;&amp;
-                    export PYTHONPATH=$PYTHONPATH:`pwd`/ &amp;&amp;
-                    mkdir build &amp;&amp;
-                    cd build &amp;&amp;
-                    cmake .. -DBOOST_ROOT=$BOOST_ROOT_DIR -DCMAKE_INSTALL_PREFIX=$INSTALL_DIR/rdkit/ -DRDK_INSTALL_INTREE=OFF -DPYTHON_NUMPY_INCLUDE_PATH=$PYTHONPATH_NUMPY/numpy/core/include/</action>
-                <action type="shell_command">cd ./build &amp;&amp; make </action>
-                <action type="shell_command">cd ./build &amp;&amp; make install</action>
-
-                <action type="set_environment">
-                    <environment_variable name="RDBASE" action="set_to">$INSTALL_DIR/rdkit</environment_variable>
-                    <environment_variable name="LD_LIBRARY_PATH" action="append_to">$INSTALL_DIR/rdkit</environment_variable>
-                    <environment_variable name="PATH" action="prepend_to">$INSTALL_DIR/rdkit/bin</environment_variable>
-                    <environment_variable name="PYTHONPATH" action="prepend_to">$INSTALL_DIR/rdkit/lib</environment_variable>
-                </action>
-            </actions>
-        </install>
-        <readme>Compiling rdkit requires cmake, python headers, sqlite3, flex and bison.</readme>
-    </package>
-</tool_dependency>