Extraneous Parity Markers Added to Molecule in "Clean in 3D"

I'm attempting to draw a primary alcohol, which has no parity/chirality/etc.  When I draw the molecule myself and pass it through molConverter (see Screenshot1 for the molecule), I get the following string: [H][#8]C([H])([H])C([H])([H])C([H])([H])[H]

This string results from the following xml:

<?xml version="1.0" encoding="UTF-8"?><cml version="ChemAxon file format v5.10.0, generated by v5.12.1"><MDocument><MChemicalStruct><molecule molID="m1"><atomArray atomID="a1 a2 a3 a4 a5 a6 a7 a8 a9 a10 a11 a12" elementType="C C C O H H H H H H H H" x2="-2.219411849975586 -0.18117646872997284 -2.717647075653076 -1.5852941274642944 -4.30294132232666 -3.3064706325531006 -1.358823537826538 1.313529372215271 1.5852941274642944 -4.574706077575684 -4.438823699951172 -0.8605882525444031" y2="-2.8082354068756104 -0.99647057056427 1.358823537826538 3.6235294342041016 -3.034705877304077 -4.076470375061035 -4.212352752685547 -1.99294114112854 -0.498235285282135 1.5852941274642944 0.4076470732688904 5.163529396057129"></atomArray><bondArray><bond atomRefs2="a5 a1" order="1"></bond><bond atomRefs2="a1 a6" order="1"></bond><bond atomRefs2="a7 a1" order="1"></bond><bond atomRefs2="a1 a2" order="1"></bond><bond atomRefs2="a2 a8" order="1"></bond><bond atomRefs2="a9 a2" order="1"></bond><bond atomRefs2="a2 a3" order="1"></bond><bond atomRefs2="a3 a11" order="1"></bond><bond atomRefs2="a10 a3" order="1"></bond><bond atomRefs2="a3 a4" order="1"></bond><bond atomRefs2="a4 a12" order="1"></bond></bondArray></molecule></MChemicalStruct></MDocument></cml>

 

However, if I press the "Clean in 3D" button and then pass the molecule through molConverter (see Screenshot2 for the cleaned molecule), I get one of two different strings: [H][#8][C@]([H])([H])[C@]([H])([H])C([H])([H])[H] OR [H][#8][C@]([H])([H])[C@@]([H])([H])C([H])([H])[H]

These strings result from the following xml: 

<?xml version="1.0" encoding="UTF-8"?><cml version="ChemAxon file format v5.10.0, generated by v5.12.1"> <MDocument><MChemicalStruct><molecule molID="m1"><atomArray atomID="a1 a2 a3 a4 a5 a6 a7 a8 a9 a10 a11 a12" elementType="C C C O H H H H H H H H" x3="0.975091947031839 0.6648303290127311 1.805565560252321 1.484005425553194 2.2583586995909872 1.8836930766995577 0.1473458694603294 1.11722970008557 -0.25844338903044184 0.5043835161803841 1.9644344155865112 2.7321807244877334" y3="-0.8932905265409933 0.4651097056687462 0.9342189372842387 2.1848342489382726 2.3946639436729793 -0.820672330878338 -1.1908209135657464 -1.6654689467930528 0.37498938000649434 1.2157778255242615 0.20639156389417948 1.0526022873829437" z3="-0.3713234300409698 0.294851395043763 1.2252693193257487 1.8184273025020974 2.382826506261905 -0.9756682749698912 -1.0199404353264814 0.38999086134006977 0.8746346342730861 -0.48454505723429464 2.025349649932296 0.657404664004483"></atomArray><bondArray><bond atomRefs2="a6 a1" order="1"></bond><bond atomRefs2="a1 a7" order="1"></bond><bond atomRefs2="a8 a1" order="1"></bond><bond atomRefs2="a1 a2" order="1"></bond><bond atomRefs2="a2 a9" order="1"></bond><bond atomRefs2="a10 a2" order="1"></bond><bond atomRefs2="a2 a3" order="1"></bond><bond atomRefs2="a3 a11" order="1"></bond><bond atomRefs2="a12 a3" order="1"></bond><bond atomRefs2="a3 a4" order="1"></bond><bond atomRefs2="a4 a5" order="1"></bond></bondArray></molecule></MChemicalStruct></MDocument></cml>

As far as I can tell, these strings differ based on the orientation the molecule takes on after using Clean in 3D.

 

Now I'm not a master of chemistry by any stretch of the imagination, but it is my understanding that there is no parity/chirality present in these molecules - which is what the @ sign represents. Is there another reason why these @s are being added into the output of molConverter?

 

For reference, I'm passing the following arguments to molConverter: ":+s,+e,+l,+L,+R,-w,-d,-f,-p,-m,-N,-D"

I know already that the e adds the relative chirality flag, which I have seen returned on other molecules as |r|, but removing it from the list of flags does not solve this issue.

 

Happy to provide any other necessary details, just let me know.

Hi Cliff,

We store the local parity information from the 3D strucure because the smarts (+s option) represents a query structure and in case of substructure search the local parity of a non-chiral molecule can be important in a chiral target molecule. 

If you use smiles (remove the +s option) the parity won't be stored.

BRs,

Peter

Hey,

 

With the modified smarts string (":-s,+e,+l,+L,+R,-w,-d,-f,-p,-m,-N,-D"), I still get the following from the clean in 3D option

[H][O][C@]([H])([H])[C@@]([H])([H])C([H])([H])[H]

with the following xml

<?xml version="1.0" encoding="UTF-8"?><cml version="ChemAxon file format v5.10.0, generated by v5.12.1"><MDocument><MChemicalStruct><molecule molID="m1"><atomArray atomID="a1 a2 a3 a4 a5 a6 a7 a8 a9 a10 a11 a12" elementType="C C C O H H H H H H H H" x3="0.975091947031839 0.6648303290127311 1.805565560252321 1.484005425553194 1.8836930766995577 0.1473458694603294 1.11722970008557 -0.25844338903044184 0.5043835161803841 1.9644344155865112 2.7321807244877334 2.2583586995909872" y3="-0.8932905265409933 0.4651097056687462 0.9342189372842387 2.1848342489382726 -0.820672330878338 -1.1908209135657464 -1.6654689467930528 0.37498938000649434 1.2157778255242615 0.20639156389417948 1.0526022873829437 2.3946639436729793" z3="-0.3713234300409698 0.294851395043763 1.2252693193257487 1.8184273025020974 -0.9756682749698912 -1.0199404353264814 0.38999086134006977 0.8746346342730861 -0.48454505723429464 2.025349649932296 0.657404664004483 2.382826506261905"></atomArray><bondArray><bond atomRefs2="a5 a1" order="1"></bond><bond atomRefs2="a1 a6" order="1"></bond><bond atomRefs2="a7 a1" order="1"></bond><bond atomRefs2="a1 a2" order="1"></bond><bond atomRefs2="a2 a8" order="1"></bond><bond atomRefs2="a9 a2" order="1"></bond><bond atomRefs2="a2 a3" order="1"></bond><bond atomRefs2="a3 a10" order="1"></bond><bond atomRefs2="a11 a3" order="1"></bond><bond atomRefs2="a3 a4" order="1"></bond><bond atomRefs2="a4 a12" order="1"></bond></bondArray></molecule></MChemicalStruct></MDocument></cml>

 

I'm not sure what the s option is by default, but even leaving it out of the string entirely results in the same thing.

 

Maybe its useful to note that I do get a flag at the end of the string related to the @ signs; in this instance it was |@@:2,5|, which is confused to me as only one of those locations actually has a @@.

Yes, this seems a bit strange.

Pcseh@pcseh-t530 ~/work/java/temp/marvin-and-jchem/marvin/scripts

$ ./molconvert smiles:-s,+e,+l,+L,+R,-w,-d,-f,-p,-m,-N,-D  -3 -s "[H][#8]C([H])([H])C([H])([H])C([H])([H])[H]"

[H][#8][C@@]([H])([H])[C@@]([H])([H])C([H])([H])[H]



Pcseh@pcseh-t530 ~/work/java/temp/marvin-and-jchem/marvin/scripts

$ ./molconvert smiles:+e,+l,+L,+R,-w,-d,-f,-p,-m,-N,-D  -3 -s "[H][#8]C([H])([H])C([H])([H])C([H])([H])[H]"

[H]OC([H])([H])C([H])([H])C([H])([H])[H]

 

If I don't write the "s" option the parity disappears.

We will investigate the reason and get back to you soon.

BR,

Peter

I've read the smiles and cxsmiles documentation and found this:

http://www.chemaxon.com/marvin/help/formats/smiles-doc.html#options

http://www.chemaxon.com/marvin/help/formats/cxsmiles-doc.html#options

 

"s" is a SMILES export option, not a CXSMILES option. The +- marks have effect only on CXSMILES export options, SMILES option can be turned off by leaving it off the string. 

BRs,

Peter