Marvin stereochemistry bug & shortcuts

User 870ab5b546

01-11-2005 21:53:13

Check out Marvin 4.0.1's R/S assignment of stereocenters in the following two files, which are identical except that one uses the Et shortccut group, and the other does not.

Code:

<?xml version="1.0" encoding="MacRoman" ?>

<MDocument>

<MChemicalStruct>

<molecule molID="m1">

<atomArray

atomID="a1 a2 a3 a4 a5 a6 a7 a8"

elementType="C C H H Br C R R"

mrvMap="2 1 0 0 0 0 0 0"

sgroupRef="0 0 0 0 0 0 sg1 sg2"

x3="-1.9788 -2.197 -2.8537 -2.2131 -1.6918 -0.7102 -1.1882 -3.584894001567392"

y3="0.6044 0.1809 1.2316 -0.9065 -0.6459 1.4671 0.5663 0.7736974379488073"

z3="-0.4203 0.4103 -0.5913 0.3367 -1.8219 -0.2867 1.5082 0.7167986753227217"

/>

<bondArray>

<bond atomRefs2="a3 a1" order="1" />

<bond atomRefs2="a1 a2" order="1" />

<bond atomRefs2="a1 a5" order="1" />

<bond atomRefs2="a1 a6" order="1" />

<bond atomRefs2="a2 a4" order="1" />

<bond atomRefs2="a2 a7" order="1" />

<bond atomRefs2="a2 a8" order="1" />

</bondArray>

<molecule id="sg1" role="SuperatomSgroup" title="Ph" molID="m2">

<atomArray

atomID="a9 a10 a11 a12 a13 a14"

elementType="C C C C C C"

attachmentPoint="1 0 0 0 0 0"

x2="-1.1882 0.0071 1.4457 1.689 0.4937 -0.9449"

y2="0.5663 -0.4048 0.1448 1.6655 2.6366 2.087"

/>

<bondArray>

<bond atomRefs2="a9 a10" order="2" />

<bond atomRefs2="a9 a14" order="1" />

<bond atomRefs2="a10 a11" order="1" />

<bond atomRefs2="a11 a12" order="2" />

<bond atomRefs2="a12 a13" order="1" />

<bond atomRefs2="a13 a14" order="2" />

</bondArray>

</molecule>

<molecule id="sg2" role="SuperatomSgroup" title="Et" molID="m3">

<atomArray

atomID="a15 a16"

elementType="C C"

attachmentPoint="1 0"

x2="2.31 0.77"

y2="0.0 0.0"

/>

<bondArray>

<bond atomRefs2="a16 a15" order="1" />

</bondArray>

</molecule>

</molecule>

</MChemicalStruct>

</MDocument>

<?xml version="1.0" encoding="MacRoman" ?>

<MDocument>

<MChemicalStruct>

<molecule molID="m1">

<atomArray

atomID="a1 a2 a3 a4 a5 a6 a7 a8 a9"

elementType="C C H H Br C R C C"

mrvMap="2 1 0 0 0 0 0 0 0"

sgroupRef="0 0 0 0 0 0 sg1 0 0"

x3="-1.9788 -2.197 -2.8537 -2.2131 -1.6918 -0.7102 -1.1882 -3.5849 -4.6738"

y3="0.6044 0.1809 1.2316 -0.9065 -0.6459 1.4671 0.5663 0.7737 -0.3152"

z3="-0.4203 0.4103 -0.5913 0.3367 -1.8219 -0.2867 1.5082 0.7168 0.7168"

/>

<bondArray>

<bond atomRefs2="a3 a1" order="1" />

<bond atomRefs2="a1 a2" order="1" />

<bond atomRefs2="a1 a5" order="1" />

<bond atomRefs2="a1 a6" order="1" />

<bond atomRefs2="a2 a4" order="1" />

<bond atomRefs2="a2 a8" order="1" />

<bond atomRefs2="a8 a9" order="1" />

<bond atomRefs2="a2 a7" order="1" />

</bondArray>

<molecule id="sg1" role="SuperatomSgroup" title="Ph" molID="m2">

<atomArray

atomID="a10 a11 a12 a13 a14 a15"

elementType="C C C C C C"

attachmentPoint="1 0 0 0 0 0"

x2="-1.1882 0.0071 1.4457 1.689 0.4937 -0.9449"

y2="0.5663 -0.4048 0.1448 1.6655 2.6366 2.087"

/>

<bondArray>

<bond atomRefs2="a10 a11" order="2" />

<bond atomRefs2="a10 a15" order="1" />

<bond atomRefs2="a11 a12" order="1" />

<bond atomRefs2="a12 a13" order="2" />

<bond atomRefs2="a13 a14" order="1" />

<bond atomRefs2="a14 a15" order="2" />

</bondArray>

</molecule>

</molecule>

</MChemicalStruct>

</MDocument>

ChemAxon a3d59b832c

02-11-2005 08:50:34

Bob,

Thanks for the bug report, we are already working on this problem.

Best regards,

Szabolcs

User 870ab5b546

02-11-2005 19:17:36

OK, here's another one.

See the PNG file. The molecule on the left was loaded into Marvin; the one on the right was drawn. They are identical, except Marvin incorrectly labels one of the stereocenters on the left, S.

I attach the XML below.

Code:

<?xml version="1.0" encoding="MacRoman" ?>

<MDocument>

<MChemicalStruct>

<molecule molID="m1">

<atomArray

atomID="a1 a2 a3 a4 a5 a6 a7 a8 a9 a10 a11 a12 a13 a14 a15 a16 a17 a18"

elementType="C C H H Br C R C C C C H H Br C R C C"

mrvMap="1 2 0 0 0 0 0 0 0 1 2 0 0 0 0 0 0 0"

sgroupRef="0 0 0 0 0 0 sg1 0 0 0 0 0 0 0 0 sg2 0 0"

x3="-5.6602 -5.4399 -6.148 -4.9135 -5.6255 -7.0589 -5.4404 -4.029 -2.9401 0.8731121021244252 1.0934358928790786 0.3853117698167985 1.61980410016033 0.9078442417310894 -0.5255357963074696 1.0929138737910142 2.5043284413620466 3.5932728843893296"

y3="1.827 2.4645 2.4628 1.8994 0.0385 2.123 3.88 2.1869 3.2758 1.7687133905318682 2.406172453634163 2.4044426652217243 1.8410441726667912 -0.019824280853127485 2.0647133998920717 3.8217142140974483 2.1285356676074523 3.2174801106347353"

z3="0.3227 -0.3519 -1.1805 1.1731 -0.3176 0.8952 0.2546 -0.9031 -0.9031 0.32270163827600645 -0.3518517763374682 -1.180548558370453 1.1730528085832197 -0.3175535268847915 0.8952119444459505 0.25464740081001536 -0.9031230631645576 -0.9031230631645576"

/>

<bondArray>

<bond atomRefs2="a1 a2" order="1" />

<bond atomRefs2="a1 a6" order="1" />

<bond atomRefs2="a1 a4" order="1" />

<bond atomRefs2="a1 a5" order="1" />

<bond atomRefs2="a2 a3" order="1" />

<bond atomRefs2="a2 a8" order="1" />

<bond atomRefs2="a8 a9" order="1" />

<bond atomRefs2="a10 a11" order="1" />

<bond atomRefs2="a10 a15" order="1" />

<bond atomRefs2="a10 a13" order="1" />

<bond atomRefs2="a10 a14" order="1" />

<bond atomRefs2="a11 a12" order="1" />

<bond atomRefs2="a11 a17" order="1" />

<bond atomRefs2="a17 a18" order="1" />

<bond atomRefs2="a2 a7" order="1" />

<bond atomRefs2="a11 a16" order="1" />

</bondArray>

<molecule id="sg1" role="SuperatomSgroup" title="Ph" molID="m2">

<atomArray

atomID="a19 a20 a21 a22 a23 a24"

elementType="C C C C C C"

attachmentPoint="1 0 0 0 0 0"

x2="-5.4404 -4.107 -4.1076 -5.4416 -6.775 -6.7744"

y2="3.88 4.6505 6.1905 6.96 6.1896 4.6496"

/>

<bondArray>

<bond atomRefs2="a19 a20" order="2" />

<bond atomRefs2="a19 a24" order="1" />

<bond atomRefs2="a20 a21" order="1" />

<bond atomRefs2="a21 a22" order="2" />

<bond atomRefs2="a22 a23" order="1" />

<bond atomRefs2="a23 a24" order="2" />

</bondArray>

</molecule>

<molecule id="sg2" role="SuperatomSgroup" title="Ph" molID="m3">

<atomArray

atomID="a25 a26 a27 a28 a29 a30"

elementType="C C C C C C"

attachmentPoint="1 0 0 0 0 0"

x2="-8.881784197001252E-16 1.3336791218280366 1.3336791218280366 1.1102230246251565E-15 -1.3336791218280348 -1.3336791218280357"

y2="-1.5400000000000005 -0.7700000000000004 0.7699999999999997 1.54 0.7700000000000006 -0.7699999999999995"

/>

<bondArray>

<bond atomRefs2="a25 a26" order="2" />

<bond atomRefs2="a25 a30" order="1" />

<bond atomRefs2="a26 a27" order="1" />

<bond atomRefs2="a27 a28" order="2" />

<bond atomRefs2="a28 a29" order="1" />

<bond atomRefs2="a29 a30" order="2" />

</bondArray>

</molecule>

</molecule>

</MChemicalStruct>

</MDocument>

The XML of the structure I used to start the second drawing:

Code:

<?xml version="1.0" encoding="MacRoman" ?>

<MDocument>

<MChemicalStruct>

<molecule molID="m1">

<atomArray

atomID="a1 a2 a3 a4 a5 a6 a7 a8"

elementType="C C H H H H H H"

mrvMap="1 2 0 0 0 0 0 0"

x3="-3.326887826350001 -3.1065640355953485 -3.306963226488211 -3.814688158657628 -3.1069484330203343 -2.0676659283323504 -2.580195828314096 -4.356752594125821"

y3="2.352046882810921 2.9895059459132156 1.326026089284964 2.987776157500777 4.031863630001091 2.7850705820579975 2.424377664945844 2.570000222778158"

z3="0.32270163827600645 -0.3518517763374682 -0.04459010129841188 -1.180548558370453 0.09475396525912515 -0.7577754571230105 1.1730528085832197 0.744257481010992"

/>

<bondArray>

<bond atomRefs2="a1 a2" order="1" />

<bond atomRefs2="a1 a8" order="1" />

<bond atomRefs2="a1 a7" order="1" />

<bond atomRefs2="a1 a3" order="1" />

<bond atomRefs2="a2 a4" order="1" />

<bond atomRefs2="a2 a5" order="1" />

<bond atomRefs2="a2 a6" order="1" />

</bondArray>

</molecule>

</MChemicalStruct>

</MDocument>

ChemAxon a3d59b832c

03-11-2005 07:42:47

Thanks. These will be useful testing the solution.