<tool id="ctb_alignit_create_db" name="Pharmacophore" version="0.1">
    <description>generation (Align-it)</description>
    <requirements>
        <requirement type="package" version="1.0.1">silicos_it</requirement>
        <requirement type="package" version="2.3.2">openbabel</requirement>
    </requirements>
    <command>
        align-it 
            --dbType ${database.ext}
            --dbase $database
            --pharmacophore $pharmacophores
            $merge 
            $noHybrid

            2>&#38;1
    </command>
    <inputs>
        <param name="database" type="data" format='mol,mol2,sdf,smi' label="Defines the database of molecules that will be converted to pharmacophores" />
        <param name='merge' type='boolean' truevalue='--merge' falsevalue='' label='Merge pharmacophore points' />
        <param name='noHybrid' type='boolean' truevalue='--noHybrid' falsevalue='' label='Disable the use of hybrid pharmacophore points' help="Using this flag will increase the number of pharmacophore points."/>
    </inputs>
    <outputs>
        <data name="pharmacophores" format="phar" label="${tool.name} on ${on_string} (scores)"/>
    </outputs>
    <tests>
        <test>
        </test>
    </tests>
    <help>

.. class:: infomark

**What this tool does**

Align-it_ is a tool to align molecules according to their pharmacophores.
A pharmacophore is an abstract concept based on the specific interactions 
observed in drug-receptor interactions: hydrogen bonding, 
charge transfer, electrostatic and hydrophobic interactions. 
Molecular modeling and/or screening based on pharmacophore similarities 
has been proven to be an important and useful method in drug discovery.

The functionality of Align-it_ consists mainly of two parts. 
The first functionality is the generation of pharmacophores from molecules
(the function of this tool). Secondly, pairs of pharmacophores 
can be aligned (use the tool **Pharmacophore Alignment**). The resulting 
score is calculated from the volume overlap resulting of the alignments.

.. _Align-it: http://www.silicos-it.com/software/align-it/1.0.3/align-it.html

-----

.. class:: infomark

**Input**

* Example::

    - database

     30 31  0     0  0  0  0  0  0999 V2000
        1.9541    1.1500   -2.5078 Cl  0  0  0  0  0  0  0  0  0  0  0  0
        1.1377   -1.6392    2.1136 Cl  0  0  0  0  0  0  0  0  0  0  0  0
       -3.2620   -2.9284   -1.0647 O   0  0  0  0  0  0  0  0  0  0  0  0
       -2.7906   -1.9108    0.9092 O   0  0  0  0  0  0  0  0  0  0  0  0
        0.2679   -0.2051   -0.3990 N   0  0  0  0  0  0  0  0  0  0  0  0
       -2.0640    0.5139   -0.3769 C   0  0  0  0  0  0  0  0  0  0  0  0
       -0.7313    0.7178   -0.0192 C   0  0  0  0  0  0  0  0  0  0  0  0
       -2.4761   -0.6830   -1.1703 C   0  0  0  0  0  0  0  0  0  0  0  0
        1.6571   -0.2482   -0.1795 C   0  0  0  0  0  0  0  0  0  0  0  0
       -3.0382    1.4350    0.0081 C   0  0  0  0  0  0  0  0  0  0  0  0
       -0.3728    1.8429    0.7234 C   0  0  0  0  0  0  0  0  0  0  0  0
       -2.6797    2.5600    0.7506 C   0  0  0  0  0  0  0  0  0  0  0  0
       -1.3470    2.7640    1.1083 C   0  0  0  0  0  0  0  0  0  0  0  0
        2.5353    0.3477   -1.0918 C   0  0  0  0  0  0  0  0  0  0  0  0
        2.1740   -0.8865    0.9534 C   0  0  0  0  0  0  0  0  0  0  0  0
       -2.8480   -1.8749   -0.3123 C   0  0  0  0  0  0  0  0  0  0  0  0
        3.9124    0.3058   -0.8739 C   0  0  0  0  0  0  0  0  0  0  0  0
        3.5511   -0.9285    1.1713 C   0  0  0  0  0  0  0  0  0  0  0  0
        4.4203   -0.3324    0.2576 C   0  0  0  0  0  0  0  0  0  0  0  0
       -1.7086   -0.9792   -1.8930 H   0  0  0  0  0  0  0  0  0  0  0  0
       -3.3614   -0.4266   -1.7676 H   0  0  0  0  0  0  0  0  0  0  0  0
       -0.0861   -1.1146   -0.6780 H   0  0  0  0  0  0  0  0  0  0  0  0
       -4.0812    1.2885   -0.2604 H   0  0  0  0  0  0  0  0  0  0  0  0
        0.6569    2.0278    1.0167 H   0  0  0  0  0  0  0  0  0  0  0  0
       -3.4382    3.2769    1.0511 H   0  0  0  0  0  0  0  0  0  0  0  0
       -1.0683    3.6399    1.6868 H   0  0  0  0  0  0  0  0  0  0  0  0
        4.6037    0.7654   -1.5758 H   0  0  0  0  0  0  0  0  0  0  0  0
        3.9635   -1.4215    2.0480 H   0  0  0  0  0  0  0  0  0  0  0  0
        5.4925   -0.3651    0.4274 H   0  0  0  0  0  0  0  0  0  0  0  0
       -3.5025   -3.7011   -0.5102 H   0  0  0  0  0  0  0  0  0  0  0  0

    - cutoff : 0.0

-----

.. class:: infomark

**Output**

* Example::
    
    - aligned Pharmacophores 

        3033
        HYBL    -1.98494    1.9958    0.532089    0.7    0    0    0    0
        HYBL    3.52122    -0.309347    0.122783    0.7    0    0    0    0
        HYBH    -3.262    -2.9284    -1.0647    1    1    -3.5666    -3.7035    -1.61827
        HDON    0.2679    -0.2051    -0.399    1    1    -0.076102    -0.981133    -0.927616
        HACC    -2.7906    -1.9108    0.9092    1    1    -2.74368    -1.94015    1.90767
        $$$$    

-----

.. class:: infomark

**Cite**

`Silicos-it`_ - align-it

.. _Silicos-it: http://www.silicos-it.com/software/align-it/1.0.3/align-it.html

    </help>
</tool>