Error parsing Query file format

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Error parsing Query file format

Postby vinay » February 13th, 2012, 2:55 am

1. There is an error parsing with the file. Please have a look.

<?xml version="1.0" encoding="UTF-8"?>

<pharmacophore name="Model-5" pharmacophoreType="LIGAND_SCOUT">

<plane name="AR" featureId="1680674462600215364" optional="false" disabled="false" weight="1.0">

<position x3="3.0204692" y3="5.1243186" z3="-3.1123083" tolerance="0.8999999" />

<normal x3="0.7162458" y3="0.4583211" z3="-0.526245" tolerance="0.43633232" />

<environmentFeature />

</plane>

<plane name="AR" featureId="1680674462497815363" optional="true" disabled="false" weight="0.84210527">

<position x3="4.2483907" y3="5.350168" z3="-1.31564" tolerance="0.8999999" />

<normal x3="-0.70570755" y3="-0.47215265" z3="0.5282506" tolerance="0.43633232" />

<environmentFeature />

</plane>

<point name="HBA" featureId="1680671843817115134" optional="false" disabled="false" weight="0.94736844">

<position x3="2.6730192" y3="4.398619" z3="-4.2397957" tolerance="1.5" />

<environmentFeature />

</point>

<point name="HBD" featureId="16997908618135523393" optional="false" disabled="false" weight="0.94736844">

<position x3="4.162103" y3="2.707027" z3="-3.7023792" tolerance="1.5" />

<environmentFeature />

</point>

<volume type="exclusion" featureId="17081574900819335886" optional="false" disabled="false" weight="1.0">

<position x3="6.4952564" y3="6.2270274" z3="-5.211296" tolerance="1.5" />

<environmentFeature />

</volume>

<volume type="exclusion" featureId="17081573015529335882" optional="false" disabled="false" weight="1.0">

<position x3="-3.4258432" y3="1.9172231" z3="-3.7121725" tolerance="1.5" />

<environmentFeature />

</volume>

<volume type="exclusion" featureId="17081573035430935883" optional="false" disabled="false" weight="1.0">

<position x3="-2.4026442" y3="3.9414065" z3="-0.12668142" tolerance="1.5" />

<environmentFeature />

</volume>

<volume type="exclusion" featureId="17081574549123135885" optional="false" disabled="false" weight="1.0">

<position x3="4.5497684" y3="7.728" z3="-9.268655" tolerance="1.5" />

<environmentFeature />

</volume>

<volume type="exclusion" featureId="17081573225077535884" optional="false" disabled="false" weight="1.0">

<position x3="-1.0534874" y3="-1.9001307" z3="-3.4891536" tolerance="1.5" />

<environmentFeature />

</volume>

<volume type="exclusion" featureId="17081575300800235887" optional="false" disabled="false" weight="1.0">

<position x3="10.152539" y3="2.5204008" z3="-6.6725287" tolerance="1.5" />

<environmentFeature />

</volume>

</pharmacophore>



2. Is the tolerance value somehow related to Radius???



Thanks,

Vinay
vinay
 
Posts: 6
Joined: June 21st, 2011, 1:34 am

Re: Error parsing Query file format

Postby dkoes » February 13th, 2012, 9:34 am

Hi Vinay,

1. The pml parser was expecting the pharmacophore definition to be wrapped in a MolecularEnvironment tag. I have modified it to not require this and the query should work fine now.
2. The tolerance is the radius.

-Dave
dkoes
Site Admin
 
Posts: 24
Joined: May 27th, 2011, 11:29 am

Re: Error parsing Query file format

Postby vinay » February 13th, 2012, 11:37 pm

Dear Dr. David,

Thanks for the kind support, now everything is working fine.


regards,

Vinay
vinay
 
Posts: 6
Joined: June 21st, 2011, 1:34 am


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