Commit
This commit does not belong to any branch on this repository, and may belong to a fork outside of the repository.
Unit test to verify that wedge bond information is properly read
Change-Id: Iaeef3089f6bb077aa7fe266182eb594481c51d60 Signed-off-by: John May <john.wilkinsonmay@gmail.com>
- Loading branch information
Showing
2 changed files
with
267 additions
and
6 deletions.
There are no files selected for viewing
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
Original file line number | Diff line number | Diff line change |
---|---|---|
@@ -0,0 +1,224 @@ | ||
<?xml version="1.0" encoding="ISO-8859-1"?> | ||
<list convention="cdk:model" id="model1" xmlns="http://www.xml-cml.org/schema"> | ||
<moleculeList convention="cdk:moleculeSet" id="molSet1"> | ||
<molecule id="m1"> | ||
<atomArray> | ||
<atom id="a1" elementType="C" x2="-4.589285714285712" y2="3.1500000000000004" formalCharge="0" hydrogenCount="1"> | ||
<scalar dictRef="cdk:aromaticAtom"/> | ||
<atomType convention="bioclipse:atomType">C.sp2</atomType> | ||
</atom> | ||
<atom id="a2" elementType="C" x2="-3.376850148987499" y2="2.4499999999999984" formalCharge="0" hydrogenCount="0"> | ||
<scalar dictRef="cdk:aromaticAtom"/> | ||
<atomType convention="bioclipse:atomType">C.sp2</atomType> | ||
</atom> | ||
<atom id="a3" elementType="C" x2="-3.376850148987501" y2="1.0499999999999983" formalCharge="0" hydrogenCount="0"> | ||
<scalar dictRef="cdk:aromaticAtom"/> | ||
<atomType convention="bioclipse:atomType">C.sp2</atomType> | ||
</atom> | ||
<atom id="a4" elementType="C" x2="-4.589285714285716" y2="0.34999999999999987" formalCharge="0" hydrogenCount="1"> | ||
<scalar dictRef="cdk:aromaticAtom"/> | ||
<atomType convention="bioclipse:atomType">C.sp2</atomType> | ||
</atom> | ||
<atom id="a5" elementType="C" x2="-5.801721279583929" y2="1.0500000000000007" formalCharge="0" hydrogenCount="1"> | ||
<scalar dictRef="cdk:aromaticAtom"/> | ||
<atomType convention="bioclipse:atomType">C.sp2</atomType> | ||
</atom> | ||
<atom id="a6" elementType="C" x2="-5.801721279583928" y2="2.4500000000000006" formalCharge="0" hydrogenCount="0"> | ||
<scalar dictRef="cdk:aromaticAtom"/> | ||
<atomType convention="bioclipse:atomType">C.sp2</atomType> | ||
</atom> | ||
<atom id="a7" elementType="C" x2="-1.9768501489874986" y2="2.4499999999999984" formalCharge="0" hydrogenCount="1"> | ||
<scalar dictRef="cdk:aromaticAtom"/> | ||
<atomType convention="bioclipse:atomType">C.sp2</atomType> | ||
</atom> | ||
<atom id="a8" elementType="N" x2="-1.544226356862572" y2="1.1185208771867827" formalCharge="0" hydrogenCount="0"> | ||
<scalar dictRef="cdk:aromaticAtom"/> | ||
<atomType convention="bioclipse:atomType">N.sp2</atomType> | ||
</atom> | ||
<atom id="a9" elementType="N" x2="-2.6768501489874987" y2="0.29562152397732033" formalCharge="0" hydrogenCount="0"> | ||
<scalar dictRef="cdk:aromaticAtom"/> | ||
<atomType convention="bioclipse:atomType">N.planar3</atomType> | ||
</atom> | ||
<atom id="a10" elementType="C" x2="-2.6768501489874987" y2="-1.0672904230981437" formalCharge="0" hydrogenCount="0"> | ||
<scalar dictRef="cdk:aromaticAtom"/> | ||
<atomType convention="bioclipse:atomType">C.sp2</atomType> | ||
</atom> | ||
<atom id="a11" elementType="C" x2="-1.4965337796988356" y2="-1.7487463966358776" formalCharge="0" hydrogenCount="1"> | ||
<scalar dictRef="cdk:aromaticAtom"/> | ||
<atomType convention="bioclipse:atomType">C.sp2</atomType> | ||
</atom> | ||
<atom id="a12" elementType="C" x2="-1.4965337796988376" y2="-3.1116583437113414" formalCharge="0" hydrogenCount="1"> | ||
<scalar dictRef="cdk:aromaticAtom"/> | ||
<atomType convention="bioclipse:atomType">C.sp2</atomType> | ||
</atom> | ||
<atom id="a13" elementType="C" x2="-2.6768501489875023" y2="-3.7931143172490724" formalCharge="0" hydrogenCount="0"> | ||
<scalar dictRef="cdk:aromaticAtom"/> | ||
<atomType convention="bioclipse:atomType">C.sp2</atomType> | ||
</atom> | ||
<atom id="a14" elementType="C" x2="-3.857166518276166" y2="-3.1116583437113396" formalCharge="0" hydrogenCount="1"> | ||
<scalar dictRef="cdk:aromaticAtom"/> | ||
<atomType convention="bioclipse:atomType">C.sp2</atomType> | ||
</atom> | ||
<atom id="a15" elementType="C" x2="-3.8571665182761654" y2="-1.7487463966358754" formalCharge="0" hydrogenCount="1"> | ||
<scalar dictRef="cdk:aromaticAtom"/> | ||
<atomType convention="bioclipse:atomType">C.sp2</atomType> | ||
</atom> | ||
<atom id="a16" elementType="O" x2="-6.982037648872593" y2="3.1314559735377325" formalCharge="0" hydrogenCount="0"> | ||
<atomType convention="bioclipse:atomType">O.sp3</atomType> | ||
</atom> | ||
<atom id="a17" elementType="C" x2="-8.162354018161258" y2="2.4500000000000006" formalCharge="0" hydrogenCount="1"> | ||
<atomType convention="bioclipse:atomType">C.sp3</atomType> | ||
</atom> | ||
<atom id="a18" elementType="C" x2="-8.162354018161258" y2="1.0870880529245364" formalCharge="0" hydrogenCount="0"> | ||
<scalar dictRef="cdk:aromaticAtom"/> | ||
<atomType convention="bioclipse:atomType">C.sp2</atomType> | ||
</atom> | ||
<atom id="a19" elementType="C" x2="-6.982037648872594" y2="0.40563207938680235" formalCharge="0" hydrogenCount="1"> | ||
<scalar dictRef="cdk:aromaticAtom"/> | ||
<atomType convention="bioclipse:atomType">C.sp2</atomType> | ||
</atom> | ||
<atom id="a20" elementType="C" x2="-6.982037648872597" y2="-0.957279867688662" formalCharge="0" hydrogenCount="0"> | ||
<scalar dictRef="cdk:aromaticAtom"/> | ||
<atomType convention="bioclipse:atomType">C.sp2</atomType> | ||
</atom> | ||
<atom id="a21" elementType="C" x2="-8.162354018161261" y2="-1.6387358412263926" formalCharge="0" hydrogenCount="1"> | ||
<scalar dictRef="cdk:aromaticAtom"/> | ||
<atomType convention="bioclipse:atomType">C.sp2</atomType> | ||
</atom> | ||
<atom id="a22" elementType="C" x2="-9.342670387449925" y2="-0.9572798676886596" formalCharge="0" hydrogenCount="1"> | ||
<scalar dictRef="cdk:aromaticAtom"/> | ||
<atomType convention="bioclipse:atomType">C.sp2</atomType> | ||
</atom> | ||
<atom id="a23" elementType="C" x2="-9.342670387449925" y2="0.40563207938680457" formalCharge="0" hydrogenCount="1"> | ||
<scalar dictRef="cdk:aromaticAtom"/> | ||
<atomType convention="bioclipse:atomType">C.sp2</atomType> | ||
</atom> | ||
<atom id="a24" elementType="O" x2="-5.8017212795839335" y2="-1.6387358412263957" formalCharge="0" hydrogenCount="0"> | ||
<atomType convention="bioclipse:atomType">O.sp3</atomType> | ||
</atom> | ||
<atom id="a25" elementType="C" x2="-5.8017212795839335" y2="-3.0016477883018604" formalCharge="0" hydrogenCount="3"> | ||
<atomType convention="bioclipse:atomType">C.sp3</atomType> | ||
</atom> | ||
<atom id="a26" elementType="C" x2="-9.342670387449923" y2="3.1314559735377334" formalCharge="0" hydrogenCount="1"> | ||
<atomType convention="bioclipse:atomType">C.sp3</atomType> | ||
</atom> | ||
<atom id="a27" elementType="N" x2="-10.522986756738588" y2="2.450000000000002" formalCharge="0" hydrogenCount="1"> | ||
<atomType convention="bioclipse:atomType">N.amide</atomType> | ||
</atom> | ||
<atom id="a28" elementType="C" x2="-9.342670387449923" y2="4.494367920613199" formalCharge="0" hydrogenCount="3"> | ||
<atomType convention="bioclipse:atomType">C.sp3</atomType> | ||
</atom> | ||
<atom id="a29" elementType="C" x2="-11.703303126027253" y2="3.1314559735377343" formalCharge="0" hydrogenCount="0"> | ||
<atomType convention="bioclipse:atomType">C.sp2</atomType> | ||
</atom> | ||
<atom id="a30" elementType="C" x2="-12.883619495315918" y2="2.450000000000003" formalCharge="0" hydrogenCount="0"> | ||
<atomType convention="bioclipse:atomType">C.sp3</atomType> | ||
</atom> | ||
<atom id="a31" elementType="O" x2="-11.70330312602725" y2="4.4943679206131995" formalCharge="0" hydrogenCount="0"> | ||
<atomType convention="bioclipse:atomType">O.sp2</atomType> | ||
</atom> | ||
<atom id="a32" elementType="F" x2="-2.6768501489875036" y2="-5.156026264324538" formalCharge="0" hydrogenCount="0"> | ||
<atomType convention="bioclipse:atomType">F</atomType> | ||
</atom> | ||
<atom id="a33" elementType="F" x2="-14.063935864604582" y2="3.1314559735377365" formalCharge="0" hydrogenCount="0"> | ||
<atomType convention="bioclipse:atomType">F</atomType> | ||
</atom> | ||
<atom id="a34" elementType="F" x2="-12.883619495315918" y2="1.0870880529245377" formalCharge="0" hydrogenCount="0"> | ||
<atomType convention="bioclipse:atomType">F</atomType> | ||
</atom> | ||
<atom id="a35" elementType="F" x2="-14.063935864604582" y2="1.7685440264622705" formalCharge="0" hydrogenCount="0"> | ||
<atomType convention="bioclipse:atomType">F</atomType> | ||
</atom> | ||
</atomArray> | ||
<bondArray> | ||
<bond id="b1" atomRefs2="a1 a2" order="D"> | ||
<bondType dictRef="cdk:aromaticBond"/> | ||
</bond> | ||
<bond id="b2" atomRefs2="a2 a3" order="S"> | ||
<bondType dictRef="cdk:aromaticBond"/> | ||
</bond> | ||
<bond id="b3" atomRefs2="a3 a4" order="D"> | ||
<bondType dictRef="cdk:aromaticBond"/> | ||
</bond> | ||
<bond id="b4" atomRefs2="a4 a5" order="S"> | ||
<bondType dictRef="cdk:aromaticBond"/> | ||
</bond> | ||
<bond id="b5" atomRefs2="a5 a6" order="D"> | ||
<bondType dictRef="cdk:aromaticBond"/> | ||
</bond> | ||
<bond id="b6" atomRefs2="a6 a1" order="S"> | ||
<bondType dictRef="cdk:aromaticBond"/> | ||
</bond> | ||
<bond id="b7" atomRefs2="a7 a8" order="D"> | ||
<bondType dictRef="cdk:aromaticBond"/> | ||
</bond> | ||
<bond id="b8" atomRefs2="a8 a9" order="S"> | ||
<bondType dictRef="cdk:aromaticBond"/> | ||
</bond> | ||
<bond id="b9" atomRefs2="a9 a3" order="S"> | ||
<bondType dictRef="cdk:aromaticBond"/> | ||
</bond> | ||
<bond id="b10" atomRefs2="a2 a7" order="S"> | ||
<bondType dictRef="cdk:aromaticBond"/> | ||
</bond> | ||
<bond id="b11" atomRefs2="a9 a10" order="S"/> | ||
<bond id="b12" atomRefs2="a10 a11" order="D"> | ||
<bondType dictRef="cdk:aromaticBond"/> | ||
</bond> | ||
<bond id="b13" atomRefs2="a11 a12" order="S"> | ||
<bondType dictRef="cdk:aromaticBond"/> | ||
</bond> | ||
<bond id="b14" atomRefs2="a12 a13" order="D"> | ||
<bondType dictRef="cdk:aromaticBond"/> | ||
</bond> | ||
<bond id="b15" atomRefs2="a13 a14" order="S"> | ||
<bondType dictRef="cdk:aromaticBond"/> | ||
</bond> | ||
<bond id="b16" atomRefs2="a14 a15" order="D"> | ||
<bondType dictRef="cdk:aromaticBond"/> | ||
</bond> | ||
<bond id="b17" atomRefs2="a15 a10" order="S"> | ||
<bondType dictRef="cdk:aromaticBond"/> | ||
</bond> | ||
<bond id="b18" atomRefs2="a6 a16" order="S"/> | ||
<bond id="b19" atomRefs2="a16 a17" order="S"/> | ||
<bond id="b20" atomRefs2="a17 a18" order="S"> | ||
<bondStereo dictRef="cml:H">H</bondStereo> | ||
</bond> | ||
<bond id="b21" atomRefs2="a18 a19" order="D"> | ||
<bondType dictRef="cdk:aromaticBond"/> | ||
</bond> | ||
<bond id="b22" atomRefs2="a19 a20" order="S"> | ||
<bondType dictRef="cdk:aromaticBond"/> | ||
</bond> | ||
<bond id="b23" atomRefs2="a20 a21" order="D"> | ||
<bondType dictRef="cdk:aromaticBond"/> | ||
</bond> | ||
<bond id="b24" atomRefs2="a21 a22" order="S"> | ||
<bondType dictRef="cdk:aromaticBond"/> | ||
</bond> | ||
<bond id="b25" atomRefs2="a22 a23" order="D"> | ||
<bondType dictRef="cdk:aromaticBond"/> | ||
</bond> | ||
<bond id="b26" atomRefs2="a23 a18" order="S"> | ||
<bondType dictRef="cdk:aromaticBond"/> | ||
</bond> | ||
<bond id="b27" atomRefs2="a20 a24" order="S"/> | ||
<bond id="b28" atomRefs2="a24 a25" order="S"/> | ||
<bond id="b29" atomRefs2="a17 a26" order="S"/> | ||
<bond id="b30" atomRefs2="a26 a27" order="S"/> | ||
<bond id="b31" atomRefs2="a26 a28" order="S"> | ||
<bondStereo dictRef="cml:W">W</bondStereo> | ||
</bond> | ||
<bond id="b32" atomRefs2="a27 a29" order="S"/> | ||
<bond id="b33" atomRefs2="a29 a30" order="S"/> | ||
<bond id="b34" atomRefs2="a29 a31" order="D"/> | ||
<bond id="b35" atomRefs2="a13 a32" order="S"/> | ||
<bond id="b36" atomRefs2="a30 a33" order="S"/> | ||
<bond id="b37" atomRefs2="a30 a34" order="S"/> | ||
<bond id="b38" atomRefs2="a30 a35" order="S"/> | ||
</bondArray> | ||
<scalar dictRef="cdk:molecularProperty" title="net.bioclipse.cdk.domain.property.SMILES" dataType="xsd:string">O=C(NC(C)C(Oc3ccc2c(cnn2(c1ccc(F)cc1))c3)c4cccc(OC)c4)C(F)(F)F</scalar> | ||
</molecule> | ||
</moleculeList> | ||
</list> |
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters