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Structure's bonds cannot be seen in ACME [Beta-6] #44

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tomyan112 opened this issue Mar 5, 2020 · 6 comments
Closed

Structure's bonds cannot be seen in ACME [Beta-6] #44

tomyan112 opened this issue Mar 5, 2020 · 6 comments
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Bug Something isn't working Fixed Fixed, but may not be released yet Show Stopper

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@tomyan112
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tomyan112 commented Mar 5, 2020 •
edited by MikeWilliams-UK
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I cannot see the structure when I am trying to edit it.
image

<cml:cml xmlns:conventions="http://www.xml-cml.org/convention/" xmlns:cml="http://www.xml-cml.org/schema" xmlns:cmlDict="http://www.xml-cml.org/dictionary/cml/" xmlns:nameDict="http://www.xml-cml.org/dictionary/cml/name/" xmlns:c4w="http://www.chem4word.com/cml" conventions="convention:molecular">
  <c4w:customXmlPartGuid>291db9d831f34b3fbf16112b96841054</c4w:customXmlPartGuid>
  <cml:molecule id="m1">
    <cml:formula id="m1.f0" concise="C 16 H 17 O 3 N 2 Ts 1" />
    <cml:formula id="m1.f1" convention="chem4word:ResolvedFormula" inline="Not found" concise="C 16 H 17 O 3 N 2 Ts 1" />
    <cml:formula id="m1.f2" convention="chem4word:ResolvedSmiles" inline="Not found" concise="C 16 H 17 O 3 N 2 Ts 1" />
    <cml:name id="m1.n1" dictRef="chem4word:CalculatedInchi">1S/C16H17N2O3.Ts/c19-8-15(20)10-4-12-11-2-1-3-13-16(11)9(6-17-13)5-14(12)18(21)7-10;/h1-4,6,12,14-15,19-21H,5,7-8H2;/q-1;+1/t12-,14+,15+;/m0./s1</cml:name>
    <cml:name id="m1.n2" dictRef="chem4word:CalculatedAuxInfo">1/0/N:18,14,19,7,15,21,8,2,17,5,11,9,16,12,4,13,20,10,1,6,3;24/it:im;/CRV:17-1;/rA:24nOCOCCOCCCNCCCCCCCCCNCHHTs/rB:s1;;s2;s4;P4;d5;s5;s7;s3s8;s9;s9s10;s11;d11;s12;d13;s13s15;s14;s16d18;s16;d17s20;P9;P12;s20;/rC:24.7946,-17.0293,0;26.1179,-17.7932,0;32.734,-17.0293,0;27.4411,-17.0293,0;28.7643,-17.7932,0;27.4411,-15.5013,0;28.7643,-19.3212,0;30.0876,-17.0293,0;30.0876,-20.0851,0;31.4108,-17.7932,0;30.0876,-21.6131,0;31.4108,-19.3212,0;31.4108,-22.377,0;28.7643,-22.377,0;32.734,-20.0851,0;31.4108,-23.905,0;32.734,-21.6131,0;28.7643,-23.905,0;30.0876,-24.6689,0;33.248,-24.0313,0;33.8695,-22.6355,0;28.7643,-20.8491,0;32.734,-18.5572,0;33.248,-25.5713,0;</cml:name>
    <cml:name id="m1.n3" dictRef="chem4word:CalculatedInchikey">IQNAFIKWMRSYJD-SQFLUBDYSA-N</cml:name>
    <cml:name id="m1.n4" dictRef="chem4word:ResolvedIupacname">Not found</cml:name>
    <cml:atomArray>
      <cml:atom id="a1" elementType="O" x2="483.0126" y2="331.7388" />
      <cml:atom id="a2" elementType="C" x2="508.7899" y2="346.6212" />
      <cml:atom id="a3" elementType="O" x2="637.6761" y2="331.7388" />
      <cml:atom id="a4" elementType="C" x2="534.5671" y2="331.7388" />
      <cml:atom id="a5" elementType="C" x2="560.3443" y2="346.6212" />
      <cml:atom id="a6" elementType="O" x2="534.5671" y2="301.9737" />
      <cml:atom id="a7" elementType="C" x2="560.3443" y2="376.3862" />
      <cml:atom id="a8" elementType="C" x2="586.1217" y2="331.7388" />
      <cml:atom id="a9" elementType="C" x2="586.1217" y2="391.2688" />
      <cml:atom id="a10" elementType="N" x2="611.8989" y2="346.6212" />
      <cml:atom id="a11" elementType="C" x2="586.1217" y2="421.0338" />
      <cml:atom id="a12" elementType="C" x2="611.8989" y2="376.3862" />
      <cml:atom id="a13" elementType="C" x2="611.8989" y2="435.9163" />
      <cml:atom id="a14" elementType="C" x2="560.3443" y2="435.9163" />
      <cml:atom id="a15" elementType="C" x2="637.6761" y2="391.2688" />
      <cml:atom id="a16" elementType="C" x2="611.8989" y2="465.6813" />
      <cml:atom id="a17" elementType="C" x2="637.6761" y2="421.0338" />
      <cml:atom id="a18" elementType="C" x2="560.3443" y2="465.6813" />
      <cml:atom id="a19" elementType="C" x2="586.1217" y2="480.5638" />
      <cml:atom id="a20" elementType="N" x2="647.6894" y2="468.1421" />
      <cml:atom id="a21" elementType="C" x2="659.7958" y2="440.9505" />
      <cml:atom id="a22" elementType="H" x2="560.3443" y2="406.1513" />
      <cml:atom id="a23" elementType="H" x2="637.6761" y2="361.5037" />
      <cml:atom id="a24" elementType="Ts" x2="647.6894" y2="498.1421" />
    </cml:atomArray>
    <cml:bondArray>
      <cml:bond id="b1" atomRefs2="a2 a1" order="S" />
      <cml:bond id="b2" atomRefs2="a2 a4" order="S" />
      <cml:bond id="b3" atomRefs2="a4 a5" order="S" />
      <cml:bond id="b4" atomRefs2="a4 a6" order="S">
        <cml:bondStereo atomRefs2="a4 a6">W</cml:bondStereo>
      </cml:bond>
      <cml:bond id="b5" atomRefs2="a7 a5" order="D" />
      <cml:bond id="b6" atomRefs2="a5 a8" order="S" />
      <cml:bond id="b7" atomRefs2="a9 a7" order="S" />
      <cml:bond id="b8" atomRefs2="a8 a10" order="S" />
      <cml:bond id="b9" atomRefs2="a11 a9" order="S" />
      <cml:bond id="b10" atomRefs2="a9 a12" order="S" />
      <cml:bond id="b11" atomRefs2="a10 a12" order="S" />
      <cml:bond id="b12" atomRefs2="a11 a13" order="S" />
      <cml:bond id="b13" atomRefs2="a14 a11" order="D" />
      <cml:bond id="b14" atomRefs2="a12 a15" order="S" />
      <cml:bond id="b15" atomRefs2="a13 a16" order="D" />
      <cml:bond id="b16" atomRefs2="a17 a13" order="S" />
      <cml:bond id="b17" atomRefs2="a18 a14" order="S" />
      <cml:bond id="b18" atomRefs2="a15 a17" order="S" />
      <cml:bond id="b19" atomRefs2="a16 a19" order="S" />
      <cml:bond id="b20" atomRefs2="a16 a20" order="S" />
      <cml:bond id="b21" atomRefs2="a17 a21" order="D" />
      <cml:bond id="b22" atomRefs2="a19 a18" order="D" />
      <cml:bond id="b23" atomRefs2="a21 a20" order="S" />
      <cml:bond id="b24" atomRefs2="a9 a22" order="S">
        <cml:bondStereo atomRefs2="a9 a22">W</cml:bondStereo>
      </cml:bond>
      <cml:bond id="b25" atomRefs2="a12 a23" order="S">
        <cml:bondStereo atomRefs2="a12 a23">W</cml:bondStereo>
      </cml:bond>
      <cml:bond id="b26" atomRefs2="a10 a3" order="S" />
      <cml:bond id="b27" atomRefs2="a20 a24" order="S" />
    </cml:bondArray>
  </cml:molecule>
  <cml:molecule id="m2">
    <cml:formula id="m2.f0" concise="H 2 T 1 B 1 S 1" />
    <cml:formula id="m2.f1" convention="chem4word:ResolvedFormula" inline="Not found" concise="H 2 T 1 B 1 S 1" />
    <cml:formula id="m2.f2" convention="chem4word:ResolvedSmiles" inline="Not found" concise="H 2 T 1 B 1 S 1" />
    <cml:name id="m2.n1" dictRef="chem4word:CalculatedInchi">1S/BH3S/c1-2/h2H,1H2/i1T</cml:name>
    <cml:name id="m2.n2" dictRef="chem4word:CalculatedAuxInfo">1/0/N:2,3/rA:3nH.i3BS/rB:s1;s2;/rC:17.6127,-12.9287,0;19.1527,-12.9287,0;20.6927,-12.9287,0;</cml:name>
    <cml:name id="m2.n3" dictRef="chem4word:CalculatedInchikey">DBYVFGSEJWZZCZ-CNRUNOGKSA-N</cml:name>
    <cml:name id="m2.n4" dictRef="chem4word:ResolvedIupacname">Not found</cml:name>
    <cml:atomArray>
      <cml:atom id="a25" elementType="T" x2="343.1042" y2="251.8579" />
      <cml:atom id="a26" elementType="B" x2="373.1042" y2="251.8579" />
      <cml:atom id="a27" elementType="S" x2="403.1042" y2="251.8579" />
    </cml:atomArray>
    <cml:bondArray>
      <cml:bond id="b28" atomRefs2="a25 a26" order="S" />
      <cml:bond id="b29" atomRefs2="a26 a27" order="S" />
    </cml:bondArray>
  </cml:molecule>
  <cml:molecule id="m3">
    <cml:formula id="m3.f0" concise="H 2 T 1 B 1 S 1" />
    <cml:formula id="m3.f1" convention="chem4word:ResolvedFormula" inline="Not found" concise="H 2 T 1 B 1 S 1" />
    <cml:formula id="m3.f2" convention="chem4word:ResolvedSmiles" inline="Not found" concise="H 2 T 1 B 1 S 1" />
    <cml:name id="m3.n1" dictRef="chem4word:CalculatedInchi">1S/BH3S/c1-2/h2H,1H2/i1T</cml:name>
    <cml:name id="m3.n2" dictRef="chem4word:CalculatedAuxInfo">1/0/N:2,3/rA:3nH.i3BS/rB:s1;s2;/rC:17.9515,-14.8691,0;19.4915,-14.8691,0;21.0315,-14.8691,0;</cml:name>
    <cml:name id="m3.n3" dictRef="chem4word:CalculatedInchikey">DBYVFGSEJWZZCZ-CNRUNOGKSA-N</cml:name>
    <cml:name id="m3.n4" dictRef="chem4word:ResolvedIupacname">Not found</cml:name>
    <cml:atomArray>
      <cml:atom id="a28" elementType="T" x2="349.7042" y2="289.6579" />
      <cml:atom id="a29" elementType="B" x2="379.7042" y2="289.6579" />
      <cml:atom id="a30" elementType="S" x2="409.7042" y2="289.6579" />
    </cml:atomArray>
    <cml:bondArray>
      <cml:bond id="b30" atomRefs2="a28 a29" order="S" />
      <cml:bond id="b31" atomRefs2="a29 a30" order="S" />
    </cml:bondArray>
  </cml:molecule>
  <cml:molecule id="m4">
    <cml:formula id="m4.f0" concise="H 2 B 1 No 1" />
    <cml:formula id="m4.f1" convention="chem4word:ResolvedFormula" inline="Not found" concise="H 2 B 1 No 1" />
    <cml:formula id="m4.f2" convention="chem4word:ResolvedSmiles" inline="Not found" concise="H 2 B 1 No 1" />
    <cml:name id="m4.n1" dictRef="chem4word:CalculatedInchi">1S/BH2.No/h1H2;/q+1;-1</cml:name>
    <cml:name id="m4.n2" dictRef="chem4word:CalculatedAuxInfo">1/0/N:1;2/CRV:1+1;/rA:2nBNo/rB:s1;/rC:18.1055,-16.6247,0;19.6455,-16.6247,0;</cml:name>
    <cml:name id="m4.n3" dictRef="chem4word:CalculatedInchikey">HIADIOABJGXRRY-UHFFFAOYSA-N</cml:name>
    <cml:name id="m4.n4" dictRef="chem4word:ResolvedIupacname">Not found</cml:name>
    <cml:atomArray>
      <cml:atom id="a31" elementType="B" x2="352.7042" y2="323.8579" />
      <cml:atom id="a32" elementType="No" x2="382.7042" y2="323.8579" />
    </cml:atomArray>
    <cml:bondArray>
      <cml:bond id="b32" atomRefs2="a31 a32" order="S" />
    </cml:bondArray>
  </cml:molecule>
  <cml:molecule id="m5">
    <cml:formula id="m5.f0" concise="Ac 1" />
    <cml:formula id="m5.f1" convention="chem4word:ResolvedFormula" inline="Ac" concise="Ac 1" />
    <cml:formula id="m5.f2" convention="chem4word:ResolvedSmiles" inline="[Ac]" concise="Ac 1" />
    <cml:name id="m5.n1" dictRef="chem4word:CalculatedInchi">1S/Ac</cml:name>
    <cml:name id="m5.n2" dictRef="chem4word:CalculatedAuxInfo">1/0/N:1/rA:1nAc/rB:/rC:376.7042,-346.6579,0;</cml:name>
    <cml:name id="m5.n3" dictRef="chem4word:CalculatedInchikey">QQINRWTZWGJFDB-UHFFFAOYSA-N</cml:name>
    <cml:name id="m5.n4" dictRef="chem4word:ResolvedIupacname">actinium</cml:name>
    <cml:atomArray>
      <cml:atom id="a33" elementType="Ac" x2="376.7042" y2="346.6579" />
    </cml:atomArray>
  </cml:molecule>
</cml:cml>

Edit: Add markup to tidy structure
@MikeWilliams-UK
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Hi Tom,

I have found that this is a new issue with elements Ts, No and Ac in our periodic table definition.

I am consulting our chemistry expert @deadlyvices to see how to fix this properly.

With a temporary fix in code this is how your cml shows in the editor.

image

@MikeWilliams-UK MikeWilliams-UK changed the title Structure cannot be seen Structure's bonds cannot be seen Mar 5, 2020
@MikeWilliams-UK MikeWilliams-UK changed the title Structure's bonds cannot be seen Structure's bonds cannot be seen in ACME Mar 5, 2020
@MikeWilliams-UK
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@deadlyvices I think that this is the list of elements which are affected
image

Valencies string is empty.

@MikeWilliams-UK
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@tomyan112 as your structure does not include Functional groups nor nested molecules you should be able to temporarily switch to the previous editor (ChemDoodle Web) to edit this structure.

@MikeWilliams-UK MikeWilliams-UK added Bug Something isn't working Show Stopper Fixed Fixed, but may not be released yet labels Mar 5, 2020
@MikeWilliams-UK
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This is fixed in beta-7, which I am intending to release today.

@MikeWilliams-UK MikeWilliams-UK changed the title Structure's bonds cannot be seen in ACME Structure's bonds cannot be seen in ACME [Beta-6] Mar 6, 2020
MikeWilliams-UK added a commit that referenced this issue Mar 6, 2020
@MikeWilliams-UK
Merged PR 339: V3.1.7 Beta 7
11ac126 
* Structure's bonds cannot be seen in ACME #44
* ChEBI Search broken #45

Related work items: #703
@tomyan112
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Thank you for your fix.
I just want to show what I was doing with that. I removed the content control to get the letters for the protecting group.
image

@MikeWilliams-UK
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@tomyan112 very clever :-)

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