screenmd Bad XML configuration string

User aed4f53879

24-02-2015 19:51:28

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](=[O:2])=[O:4]"/>N                    <Mol ID="sulfonate" Structure="[O-:3](=[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](=[O:2])=[O:4]"/>N                    <Mol ID="sulfonate" Structure="[O-:3](=[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)

ChemAxon d51151248d

03-03-2015 09:42:36

Dear TJ, 


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


Best regards, 


Daniel

ChemAxon 5fc3e8d7d0

06-03-2015 09:51:19

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 

User aed4f53879

06-03-2015 15:09:20

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