view align-it/align-it_create_db.xml @ 11:c904022ce8e2

updates to silicos-it

<tool id="ctb_alignit_create_db" name="Pharmacophore">
    <description>generation (Align-it)</description>
    <requirements>
        <requirement type="package" version="1.0.0">silicos_it</requirement>
        <requirement type="package" version="2.3.2">openbabel</requirement>
    </requirements>
    <command>
        align-it 
            #if str($database.ext).strip() == 'phar':
                --dbType PHAR
            #else:
                --dbType MOL
            #end if
            --dbase $database
            --pharmacophore $pharmacophores
            $merge 
            $noHybrid

            2>&#38;1
    </command>
    <inputs>
        <param name="database" type="data" format='mol,mol2,sdf,smi,phar' 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>

**What it does**

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

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


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


-----

**Example**

* input::

    - 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

* output::
    
    - 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
        $$$$    



    </help>
</tool>