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screenmd Bad XML configuration string
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TJ

Joined: 27 Sep 2011
Posts: 9

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Link to postPosted: Tue Feb 24, 2015 8:51 pmPost subject: screenmd Bad XML configuration string Reply with quote

I'm using JChem 15.2.16.0 and got the following error.  I'm using an xml file from the example directory.  Can you help with this error?

-bash-3.2$ cp ~/ChemAxon/JChem/examples/screen/pharma-frag.xml .
-bash-3.2$ ~/ChemAxon/JChem/bin/generatemd c 10k.smi  -k PF -c pharma-frag.xml -o 10k.pfp
-bash-3.2$ ~/ChemAxon/JChem/bin/screenmd 11168293.smi -k 10k.pfp
Bad configuration: Bad XML configuration string: <?xml version="1.0" encoding="UTF-8"?>N<!-- Pharmacophore configuration file --><PharmacophoreFingerprintConfiguration Version="0.3" schemaLocation="pharmacophores.xsd">NN     <PharmacophoreDefinition>NN        <Search StereoCareChecking="false"/>NN        <Mols>N                    <Mol ID="pos" Structure="[*+]"/>N                    <Mol ID="nitro" Structure="[O:2]~[N:1]=[O:3]"/>N                    <Mol ID="amine" Structure="C[N:1]"/>N                    <Mol ID="tertamine" Structure="C[N:1](C)C"/>N                <Mol ID="aniline" Structure="c[N:1]"/>N                    <Mol ID="amide" Structure="[#7:1][C,P,S:2]=O"/>N                    <Mol ID="hydrazine" Structure="NN"/>N                    <Mol ID="phenylhydrazine" Structure="c[N:1][N:2]"/>N                    <Mol ID="hydrazide" Structure="[#7:1]NC=O"/>N                    <Mol ID="amidine" Structure="[#7:2][C,P,S:1]=[N:3]"/>N                    <Mol ID="neg" Structure="[*-]"/>N                    <Mol ID="carbox" Structure="[H][O:3][C:1]=[O:2]"/>N                    <Mol ID="carboxylate" Structure="[H][O:3][C:1]=[O:2]"/>N                    <Mol ID="sulfonyl" Structure="[H][O:3][S:1](=[O:2])=[O:4]"/>N                    <Mol ID="sulfonate" Structure="[O-:3][S:1](=[O:4])=[O:2]"/>N                    <Mol ID="phosphonyl" Structure="[H][O:4][P:1]([O:2])=[O:3]"/>N                    <Mol ID="phosphonate" Structure="[O:4][P:1]([O-:2])=[O:3]"/>N                    <Mol ID="arom" Structure="[*;a]"/>N                    <Mol ID="cx" Structure="[C,F,Cl,Br,I,At]"/>N                    <Mol ID="nos" Structure="[#7,#8,#16]"/>N                    <Mol ID="pyr" Structure="[nX3]"/>N                    <Mol ID="qh" Structure="[!#1!#6:1][H]"/>N        </Mols>NN        <Pharmacophores>N            <AtomSet ID="Aromatic" Symbol="r">arom</AtomSet>N            <AtomSet ID="Cationic" Symbol="+">N                <![CDATA[ !neg && ((pos && !nitro:1) || ((amine:1 || hydrazine || amidine:2,3) && !(tertamine:1 || amide:1 || nitro:1 || aniline:1 || phenylhydrazine:2))) ]]>N            </AtomSet>N            <AtomSet ID="Anionic" Symbol="-">N                <![CDATA[ !pos && ((neg && !nitro:2,3) || carbox:2,3 || carboxylate:2,3 || sulfonyl:2,3,4 || sulfonate || phosphonyl:2,3,4 || phosphonate) ]]>N            </AtomSet>N            <AtomSet ID="HydrogenBondDonor" Symbol="d">N                <![CDATA[ qh:1 || tertamine:1 && !{Anionic}]]>N            </AtomSet>N            <AtomSet ID="HydrogenBondAcceptor" Symbol="a">N                <![CDATA[ nos && !tertamine:1 && !pyr && !amide:1,2 && !aniline:1 && !sulfonyl:1 && !sulfonate:1 && !{Cationic} && !nitro:1 ]]>N            </AtomSet>N            <AtomSet ID="Hydrophobic" Symbol="h">N                <![CDATA[ cx && !{Aromatic} && !{Cationic} && !{Anionic} && !{HydrogenBondDonor} && !{HydrogenBondAcceptor} ]]>N            </AtomSet>N        </Pharmacophores>NN        <PharmacophoreFingerprintParameters MinimalDistance="1" MaximalDistance="10"/>N            N    </PharmacophoreDefinition>NN    <StandardizerConfiguration Version="0.1">N        <Actions>        N            <Removal ID="keepOne" Method="keepLargest" Measure="molMass"/>N            <Action ID="aromatize" Act="aromatize"/>N        </Actions>N    </StandardizerConfiguration>NN    <ScreeningConfiguration>N        <PharmacophorePointColors>N            <Color Symbol="+" Value="#cc0000"/>N            <Color Symbol="-" Value="#0000cc"/>N            <Color Symbol="r" Value="#00ff00"/>N            <Color Symbol="h" Value="#000000"/>N            <Color Symbol="d" Value="#0000ff"/>N            <Color Symbol="a" Value="#ff0000"/>N            <Color Symbol="a/d" Value="#ff00ff"/>N            <Color Symbol="+/d" Value="#cc6666"/>N            <Color Symbol="-/a" Value="#ff99cc"/>N            <Color Symbol="a/r" Value="#ffcc00"/>N            <Color Symbol="d/r" Value="#00ccff"/>N            <Color Symbol="h/r" Value="#339933"/>N            <Color Symbol="-/a/d" Value="#33ffff"/>N            <Color Symbol="other" Value="#cc9900"/>N            <Color Symbol="empty" Value="#cccccc"/>N        </PharmacophorePointColors>        N        N        <ParametrizedMetrics>N            <ParametrizedMetric Name="Tanimoto" ActiveFamily="Generic" Metric="Tanimoto" Threshold="0.2"/>N            <ParametrizedMetric Name="Euclidean" ActiveFamily="Generic" Metric="Euclidean" Threshold="15"/>N        </ParametrizedMetrics>        N    </ScreeningConfiguration>N    N</PharmacophoreFingerprintConfiguration>
chemaxon.descriptors.MDReaderException: Bad configuration: Bad XML configuration string: <?xml version="1.0" encoding="UTF-8"?>N<!-- Pharmacophore configuration file --><PharmacophoreFingerprintConfiguration Version="0.3" schemaLocation="pharmacophores.xsd">NN     <PharmacophoreDefinition>NN        <Search StereoCareChecking="false"/>NN        <Mols>N                    <Mol ID="pos" Structure="[*+]"/>N                    <Mol ID="nitro" Structure="[O:2]~[N:1]=[O:3]"/>N                    <Mol ID="amine" Structure="C[N:1]"/>N                    <Mol ID="tertamine" Structure="C[N:1](C)C"/>N                <Mol ID="aniline" Structure="c[N:1]"/>N                    <Mol ID="amide" Structure="[#7:1][C,P,S:2]=O"/>N                    <Mol ID="hydrazine" Structure="NN"/>N                    <Mol ID="phenylhydrazine" Structure="c[N:1][N:2]"/>N                    <Mol ID="hydrazide" Structure="[#7:1]NC=O"/>N                    <Mol ID="amidine" Structure="[#7:2][C,P,S:1]=[N:3]"/>N                    <Mol ID="neg" Structure="[*-]"/>N                    <Mol ID="carbox" Structure="[H][O:3][C:1]=[O:2]"/>N                    <Mol ID="carboxylate" Structure="[H][O:3][C:1]=[O:2]"/>N                    <Mol ID="sulfonyl" Structure="[H][O:3][S:1](=[O:2])=[O:4]"/>N                    <Mol ID="sulfonate" Structure="[O-:3][S:1](=[O:4])=[O:2]"/>N                    <Mol ID="phosphonyl" Structure="[H][O:4][P:1]([O:2])=[O:3]"/>N                    <Mol ID="phosphonate" Structure="[O:4][P:1]([O-:2])=[O:3]"/>N                    <Mol ID="arom" Structure="[*;a]"/>N                    <Mol ID="cx" Structure="[C,F,Cl,Br,I,At]"/>N                    <Mol ID="nos" Structure="[#7,#8,#16]"/>N                    <Mol ID="pyr" Structure="[nX3]"/>N                    <Mol ID="qh" Structure="[!#1!#6:1][H]"/>N        </Mols>NN        <Pharmacophores>N            <AtomSet ID="Aromatic" Symbol="r">arom</AtomSet>N            <AtomSet ID="Cationic" Symbol="+">N                <![CDATA[ !neg && ((pos && !nitro:1) || ((amine:1 || hydrazine || amidine:2,3) && !(tertamine:1 || amide:1 || nitro:1 || aniline:1 || phenylhydrazine:2))) ]]>N            </AtomSet>N            <AtomSet ID="Anionic" Symbol="-">N                <![CDATA[ !pos && ((neg && !nitro:2,3) || carbox:2,3 || carboxylate:2,3 || sulfonyl:2,3,4 || sulfonate || phosphonyl:2,3,4 || phosphonate) ]]>N            </AtomSet>N            <AtomSet ID="HydrogenBondDonor" Symbol="d">N                <![CDATA[ qh:1 || tertamine:1 && !{Anionic}]]>N            </AtomSet>N            <AtomSet ID="HydrogenBondAcceptor" Symbol="a">N                <![CDATA[ nos && !tertamine:1 && !pyr && !amide:1,2 && !aniline:1 && !sulfonyl:1 && !sulfonate:1 && !{Cationic} && !nitro:1 ]]>N            </AtomSet>N            <AtomSet ID="Hydrophobic" Symbol="h">N                <![CDATA[ cx && !{Aromatic} && !{Cationic} && !{Anionic} && !{HydrogenBondDonor} && !{HydrogenBondAcceptor} ]]>N            </AtomSet>N        </Pharmacophores>NN        <PharmacophoreFingerprintParameters MinimalDistance="1" MaximalDistance="10"/>N            N    </PharmacophoreDefinition>NN    <StandardizerConfiguration Version="0.1">N        <Actions>        N            <Removal ID="keepOne" Method="keepLargest" Measure="molMass"/>N            <Action ID="aromatize" Act="aromatize"/>N        </Actions>N    </StandardizerConfiguration>NN    <ScreeningConfiguration>N        <PharmacophorePointColors>N            <Color Symbol="+" Value="#cc0000"/>N            <Color Symbol="-" Value="#0000cc"/>N            <Color Symbol="r" Value="#00ff00"/>N            <Color Symbol="h" Value="#000000"/>N            <Color Symbol="d" Value="#0000ff"/>N            <Color Symbol="a" Value="#ff0000"/>N            <Color Symbol="a/d" Value="#ff00ff"/>N            <Color Symbol="+/d" Value="#cc6666"/>N            <Color Symbol="-/a" Value="#ff99cc"/>N            <Color Symbol="a/r" Value="#ffcc00"/>N            <Color Symbol="d/r" Value="#00ccff"/>N            <Color Symbol="h/r" Value="#339933"/>N            <Color Symbol="-/a/d" Value="#33ffff"/>N            <Color Symbol="other" Value="#cc9900"/>N            <Color Symbol="empty" Value="#cccccc"/>N        </PharmacophorePointColors>        N        N        <ParametrizedMetrics>N            <ParametrizedMetric Name="Tanimoto" ActiveFamily="Generic" Metric="Tanimoto" Threshold="0.2"/>N            <ParametrizedMetric Name="Euclidean" ActiveFamily="Generic" Metric="Euclidean" Threshold="15"/>N        </ParametrizedMetrics>        N    </ScreeningConfiguration>N    N</PharmacophoreFingerprintConfiguration>
    at chemaxon.descriptors.MDFileReader.createMDSet(MDFileReader.java:406)
    at chemaxon.descriptors.MDFileReader.<init>(MDFileReader.java:101)
    at chemaxon.descriptors.ScreenMD.initFileReader(ScreenMD.java:920)
    at chemaxon.descriptors.ScreenMD.initSources(ScreenMD.java:862)
    at chemaxon.descriptors.ScreenMD.main(ScreenMD.java:229)

Daniel
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Joined: 22 Jan 2012
Posts: 315

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Link to postPosted: Tue Mar 03, 2015 10:42 amPost subject: Reply with quote

Dear TJ, 

We managed to reproduce the problem. We are going to fix it ASAP.

Best regards, 

Daniel

László
ChemAxon personnel
Joined: 14 Jan 2011
Posts: 78

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Link to postPosted: Fri Mar 06, 2015 10:51 amPost subject: Reply with quote

Hi,

 

We have fixed this bug. Thanks for the report. The fix will be available next week (version 15.3.9).

Until that there is a workaround if you use the following command:

screenmd targets.smi query.smi -g -k PF -c pharma-frag.xml

 

Best regards,
Laszlo 

TJ

Joined: 27 Sep 2011
Posts: 9

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Link to postPosted: Fri Mar 06, 2015 4:09 pmPost subject: workaround Reply with quote

Thanks.  I did discover that workaround, but that recomputes the PF for both sets I think.  I'm trying to avoid doing that for the very large set in targets.smi.  I'm looking forward to the fix due next week.

TJ

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