MoleculeGraph.clean() 2D options

In the GUI, there is a separate "Wedge bond" clean 2D option from the three Optimize options. In the API, there appear to be only the three optimize options (see this help page). Even the O0 option causes wedge bonds to be optimized. Is there a way to turn off this option? It is not working well for this compound:

Code:

<?xml version="1.0" ?> <MDocument>   <MChemicalStruct>     <molecule molID="m1">       <atomArray>         <atom id="a1" elementType="C" mrvMap="2"               x2="-6.400625228881836" y2="1.6843750476837158" />         <atom id="a2" elementType="C" mrvMap="1"               x2="-5.0669461070538" y2="2.454375047683716" />         <atom id="a3" elementType="C" mrvMap="3"               x2="-6.400625228881836" y2="0.14437504768371578" />         <atom id="a4" elementType="C" mrvMap="4"               x2="-5.0669461070538" y2="-0.6256249523162841" />         <atom id="a5" elementType="C"               x2="-7.734304350709872" y2="-0.6256249523162845" />         <atom id="a6" elementType="C"               x2="-5.0669461070538" y2="3.994375047683716" />         <atom id="a7" elementType="C"               x2="-5.0669461070538" y2="-2.1656249523162843" />         <atom id="a8" elementType="C" mrvMap="6"               x2="-0.8662499785423279" y2="1.443750023841858" />         <atom id="a9" elementType="C" mrvMap="5"               x2="-0.8662499785423278" y2="-0.09624997615814213" />         <atom id="a10" elementType="C"               x2="0.46742914328570795" y2="-0.866249976158142" />         <atom id="a11" elementType="C"               x2="0.46742914328570784" y2="2.213750023841858" />         <atom id="a12" elementType="O"               x2="0.46742914328570795" y2="3.753750023841858" />         <atom id="a13" elementType="O"               x2="0.46742914328570806" y2="-2.406249976158142" />         <atom id="a14" elementType="O"               x2="1.8287500143051147" y2="0.6256250143051147" />         <atom id="a15" elementType="C"               x2="-1.6362499785423275" y2="2.7774291456698936" />       </atomArray>       <bondArray>         <bond atomRefs2="a1 a3" order="2">           <bondStereo>T</bondStereo>         </bond>         <bond atomRefs2="a2 a1" order="1">           <bondStereo>W</bondStereo>         </bond>         <bond atomRefs2="a2 a6" order="1" />         <bond atomRefs2="a8 a2" order="1">           <bondStereo>W</bondStereo>         </bond>         <bond atomRefs2="a3 a5" order="1" />         <bond atomRefs2="a4 a3" order="1">           <bondStereo>W</bondStereo>         </bond>         <bond atomRefs2="a4 a7" order="1" />         <bond atomRefs2="a9 a4" order="1">           <bondStereo>W</bondStereo>         </bond>         <bond atomRefs2="a8 a11" order="1" />         <bond atomRefs2="a8 a15" order="1" />         <bond atomRefs2="a9 a8" order="1" />         <bond atomRefs2="a9 a10" order="1" />         <bond atomRefs2="a10 a13" order="2" />         <bond atomRefs2="a14 a10" order="1" />         <bond atomRefs2="a11 a12" order="2" />         <bond atomRefs2="a14 a11" order="1" />       </bondArray>     </molecule>   </MChemicalStruct> </MDocument>

After cleaning I want configurations to be indicated at four stereocenters (where the four wedge bonds originate), but only two are being indicated. (Same thing happens, BTW, when I convert the structure into SMILES.) I know the structure is not drawn in the most optimal way, but the origination points of the wedges should show the intention.

We will check it.

Clean has no option to keep the wedges in the original form as it may change the chirality of the molecule. (See attached images for an example. The atomic indexes are also shown on the picture.)





The other problem is related to the chirality perception:


If a molecule has one up and one down wedge then it is usually ambiguous stereo information. This is the case in your molecule and in the attached one also.





In the next major release the user can select from the API which wedge interpretation to follow. Wheter to interpret both (narrow and wide) endpoints of the wedge as chiral center or just the first node (which is the narrow end of the wedge).