comparison filter/ob_filter.xml @ 2:125da3a296ca draft default tip

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1:b52872a1755a

  <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
      -i "${infile}"
      -o "${outfile}"
      -iformat "${infile.ext}"
      -oformat "${infile.ext}"

            #set $filter_max = $filter_selected + "_max"
            "$filter_selected" : [$filter.filter_sel[$filter_min], $filter.filter_sel[$filter_max] ],
          #end for
        #end if
      }'
  </command>
  <inputs>
    <param name="infile" type="data" format="sdf,smi,mol,mol2,cml,inchi" label="Select input file previously created with the 'Compute physico-chemical properties' tool"/>
    <conditional name="filter_methods">
      <param name="filter_methods_opts" type="select" label="Select a pre-defined filtering set">

        <output name="outfile" ftype="smi" file="ob_filter_on_CID2244_2.smi" />
    </test>
    -->
  </tests>
  <help>


.. class:: infomark

**What this tool does**

Filters a library of compounds based on user-defined physico-chemical parameters or predefined options (e.g. Ro5, lead-like properties, etc.). Multiple parameters can be selected for more specific queries. 

-----

.. class:: warningmark

**Hint**

| If your input file is in SDF format you can use the *Compute physico-chemical properties* tool to precalulate the properties and use the filter on that precomputed dataset. It should be faster and can be reused but it's bigger than a SMILES file.
| 
| For exact matches please use the target value for both minimum and maximum parameters (e.g. a selection of exactly 4 rotatable bonds can be performed by selecting 4 as minimum and maximum value).
| 
| Selecting the same property multiple times with different parameters will result in querying the largest overlapping subset of values for the parameter (e.g. a selection of between 0 and 3 rotatable bonds plus a selection between 2 and 4 will result in a query for compounds between 2 and 3 rotatable bonds).

-----

.. class:: infomark

**Definition of the pre-defined filtering rules**

  **# Lipinski's Rule of Five:**
    =&lt; 5 Hydrogen-bond donor groups

    =&lt; 10 Hydrogen-bond acceptor groups

    =&lt; 500 Molecular weight

    =&lt; 5 octanol/water partition coefficient (log P)

  **# Lead Like properties** (Teague, Davis, Leeson, Oprea, Angew Chem Int Ed Engl. 1999 Dec 16;38(24):3743-3748):
    =&lt; 7 rotatable bonds

    =&lt; 350 Molecular weight

    =&lt; 3.5 octanol/water partition coefficient (log P)

  **# Drug Like properties** (Lipinski, J Pharmacol Toxicol Methods. 2000 Jul-Aug;44(1):235-49):
    =&lt; 10 Hydrogen-bond acceptor groups

    =&lt; 8 rotatable bonds

    150 =&lt; Molecular weight =&lt; 500

    =&lt; 150 Polar Surface Area

    =&lt; 5 octanol/water partition coefficient (log P)

  **# Fragment Like properties** (Carr RA, Congreve M, Murray CW, Rees DC, Drug Discov Today. 2005 Jul 15;10(14):987):
    =&lt; 5 rotatable bonds

    =&lt; 250 Molecular weight

    =&lt; 2.5 octanol/water partition coefficient (log P)

-----

.. class:: infomark

-----

.. class:: infomark

**Output** 

| SDF formatted coordinates of the molecules, with selected properties stored as meta-data for each compound.
| 
| SMILES, InChI or mol2 formatted files containing the 1D strings or 3D coordinates of each compound.

-----

.. class:: infomark

`Open Babel`_

.. _`Open Babel`: http://openbabel.org/wiki/Main_Page

  </help>
</tool>

2:125da3a296ca

  <requirements>
    <requirement type="package" version="2.3.2">openbabel</requirement>
    <requirement type="package" version="0.1">cheminfolib</requirement>
  </requirements>
  <command interpreter="python">
<![CDATA[
    ob_filter.py
      -i "${infile}"
      -o "${outfile}"
      -iformat "${infile.ext}"
      -oformat "${infile.ext}"

            #set $filter_max = $filter_selected + "_max"
            "$filter_selected" : [$filter.filter_sel[$filter_min], $filter.filter_sel[$filter_max] ],
          #end for
        #end if
      }'
]]>
  </command>
  <inputs>
    <param name="infile" type="data" format="sdf,smi,mol,mol2,cml,inchi" label="Select input file previously created with the 'Compute physico-chemical properties' tool"/>
    <conditional name="filter_methods">
      <param name="filter_methods_opts" type="select" label="Select a pre-defined filtering set">

        <output name="outfile" ftype="smi" file="ob_filter_on_CID2244_2.smi" />
    </test>
    -->
  </tests>
  <help>
<![CDATA[


.. class:: infomark

**What this tool does**

Filters a library of compounds based on user-defined physico-chemical parameters or predefined options (e.g. Ro5, lead-like properties, etc.). Multiple parameters can be selected for more specific queries.

-----

.. class:: warningmark

**Hint**

| If your input file is in SDF format you can use the *Compute physico-chemical properties* tool to precalulate the properties and use the filter on that precomputed dataset. It should be faster and can be reused but it's bigger than a SMILES file.
|
| For exact matches please use the target value for both minimum and maximum parameters (e.g. a selection of exactly 4 rotatable bonds can be performed by selecting 4 as minimum and maximum value).
|
| Selecting the same property multiple times with different parameters will result in querying the largest overlapping subset of values for the parameter (e.g. a selection of between 0 and 3 rotatable bonds plus a selection between 2 and 4 will result in a query for compounds between 2 and 3 rotatable bonds).

-----

.. class:: infomark

**Definition of the pre-defined filtering rules**

  **# Lipinski's Rule of Five:**
    =< 5 Hydrogen-bond donor groups

    =< 10 Hydrogen-bond acceptor groups

    =< 500 Molecular weight

    =< 5 octanol/water partition coefficient (log P)

  **# Lead Like properties** (Teague, Davis, Leeson, Oprea, Angew Chem Int Ed Engl. 1999 Dec 16;38(24):3743-3748):
    =< 7 rotatable bonds

    =< 350 Molecular weight

    =< 3.5 octanol/water partition coefficient (log P)

  **# Drug Like properties** (Lipinski, J Pharmacol Toxicol Methods. 2000 Jul-Aug;44(1):235-49):
    =< 10 Hydrogen-bond acceptor groups

    =< 8 rotatable bonds

    150 =< Molecular weight =< 500

    =< 150 Polar Surface Area

    =< 5 octanol/water partition coefficient (log P)

  **# Fragment Like properties** (Carr RA, Congreve M, Murray CW, Rees DC, Drug Discov Today. 2005 Jul 15;10(14):987):
    =< 5 rotatable bonds

    =< 250 Molecular weight

    =< 2.5 octanol/water partition coefficient (log P)

-----

.. class:: infomark

-----

.. class:: infomark

**Output**

| SDF formatted coordinates of the molecules, with selected properties stored as meta-data for each compound.
|
| SMILES, InChI or mol2 formatted files containing the 1D strings or 3D coordinates of each compound.

-----

.. class:: infomark

`Open Babel`_

.. _`Open Babel`: http://openbabel.org/wiki/Main_Page

]]>
  </help>
</tool>