<?xml version="1.0" encoding="UTF-8"?>
<!-- Pharmacophore configuration file -->

<PharmacophoreConfiguration Version ="0.3" schemaLocation="pharmacophores.xsd">

     <PharmacophoreDefinition>

        <Search StereoCareChecking="false"/>

        <Mols>
                    <Mol ID="pos" Structure="[*+]"/>
                    <Mol ID="nitro" Structure="[O:2]~[N:1]=[O:3]"/>
                    <Mol ID="amine" Structure="C[N:1]"/>
                    <Mol ID="tertamine" Structure="C[N:1](C)C"/>
	    	    <Mol ID="aniline" Structure="c[N:1]"/>
                    <Mol ID="amide" Structure="[#7:1][C,P,S:2]=O"/>
                    <Mol ID="hydrazine" Structure="NN"/>
                    <Mol ID="phenylhydrazine" Structure="c[N:1][N:2]"/>
                    <Mol ID="hydrazide" Structure="[#7:1]NC=O"/>
                    <Mol ID="amidine" Structure="[#7:2][C,P,S:1]=[N:3]"/>
                    <Mol ID="neg" Structure="[*-]"/>
                    <Mol ID="carbox" Structure="[H][O:3][C:1]=[O:2]"/>
                    <Mol ID="carboxylate" Structure="[H][O:3][C:1]=[O:2]"/>
                    <Mol ID="sulfonyl" Structure="[H][O:3][S:1](=[O:2])=[O:4]"/>
                    <Mol ID="sulfonate" Structure="[O-:3][S:1](=[O:4])=[O:2]"/>
                    <Mol ID="phosphonyl" Structure="[H][O:4][P:1]([O:2])=[O:3]"/>
                    <Mol ID="phosphonate" Structure="[O:4][P:1]([O-:2])=[O:3]"/>
                    <Mol ID="arom" Structure="[*;a]"/>
                    <Mol ID="cx" Structure="[C,F,Cl,Br,I,At]"/>
                    <Mol ID="nos" Structure="[#7,#8,#16]"/>
                    <Mol ID="pyr" Structure="[nX3]"/>
                    <Mol ID="qh" Structure="[!#1!#6:1][H]"/>
        </Mols>

        <Pharmacophores>
            <AtomSet ID="Aromatic" Symbol="r">arom</AtomSet>
            <AtomSet ID="Cationic" Symbol="+">
                <![CDATA[ !neg && ((pos && !nitro:1) || ((amine:1 || hydrazine || amidine:2,3) && !(tertamine:1 || amide:1 || nitro:1 || aniline:1 || phenylhydrazine:2))) ]]>
            </AtomSet>
            <AtomSet ID="Anionic" Symbol="-">
                <![CDATA[ !pos && ((neg && !nitro:2,3) || carbox:2,3 || carboxylate:2,3 || sulfonyl:2,3,4 || sulfonate || phosphonyl:2,3,4 || phosphonate) ]]>
            </AtomSet>
            <AtomSet ID="HydrogenBondDonor" Symbol="d">
                <![CDATA[ qh:1 || tertamine:1 && !{Anionic}]]>
            </AtomSet>
            <AtomSet ID="HydrogenBondAcceptor" Symbol="a">
                <![CDATA[ nos && !tertamine:1 && !pyr && !amide:1,2 && !aniline:1 && !sulfonyl:1 && !sulfonate:1 && !{Cationic} && !nitro:1 ]]>
            </AtomSet>
            <AtomSet ID="Hydrophobic" Symbol="h">
                <![CDATA[ cx && !{Aromatic} && !{Cationic} && !{Anionic} && !{HydrogenBondDonor} && !{HydrogenBondAcceptor} ]]>
            </AtomSet>
        </Pharmacophores>

        <PharmacophoreFingerprintParameters
            MinimalDistance="1"
            MaximalDistance="10"
            />
            
    </PharmacophoreDefinition>

    <StandardizerConfiguration Version ="0.1">
        <Actions>		
            <Removal ID="keepOne" Method="keepLargest" Measure="molMass"/>
            <Action ID="aromatize" Act="aromatize"/>
        </Actions>
    </StandardizerConfiguration>

    <ScreeningConfiguration>

        <PharmacophorePointColors>
            <Color Symbol="+" Value="red"/>
            <Color Symbol="-" Value="blue"/>
            <Color Symbol="r" Value="green"/>
            <Color Symbol="h" Value="black"/>
            <Color Symbol="d" Value="navy"/>
            <Color Symbol="a" Value="maroon"/>
            <Color Symbol="a/d" Value="purple"/>
            <Color Symbol="+/d" Value="lime"/>
            <Color Symbol="-/a" Value="aqua"/>
            <Color Symbol="empty" Value="gray"/>
            <Color Symbol="other" Value="fuchsia"/>
        </PharmacophorePointColors>        
        

        <ParametrizedMetrics>
            <ParametrizedMetric Name="Tanimoto" ActiveFamily="Generic" 
                Metric="Tanimoto" Threshold="0.2"/>
            <ParametrizedMetric Name="Euclidean" ActiveFamily="Generic" 
                Metric="Euclidean" Threshold="15" />
        </ParametrizedMetrics>        
    </ScreeningConfiguration>
    
</PharmacophoreConfiguration>