User 8139ea8dbd
30-08-2007 21:32:13
I got a smiles from an external source, which contains "Rg", I think standing for R-group.
Marvin does not like it, Daylight Depict takes it fine and display the atom as "Rg". ChemDraw takes it as well.
CC(C)(C)NC(CCC(=O)[Rg])C(=O)NC(CC(=O)O)C(=O)O
I certainly can replace it with "*", just wonder if Marvin wants to support that as the other two vendors?
User f359e526a1
31-08-2007 06:24:19
Hello, we will consider your request.
ChemAxon 25dcd765a3
05-09-2007 20:11:00
As far as I see Depict can also handle the following non SMILES conform molecule :-) :
C[IsThereAnybodyOutThere]CC
We rather don't accept buggy SMILES, and warn the users.
User 8139ea8dbd
11-09-2007 22:10:29
Following the same spirit, may be it was not intentional for Mavin to support the following wrong smiles then?
CC\\\\\C=C/CN
ChemAxon 25dcd765a3
12-09-2007 07:57:20
Sure. Thank you for the report. I will correct it.
I just wonder if you agree with us. Do you also vote for warning users rather than accepting badly formed smiles?
Andras
ChemAxon 25dcd765a3
12-09-2007 08:10:16
The correction is not so simple as I suspected but we will do it.
ChemAxon 25dcd765a3
12-09-2007 12:06:01
Hi!
We have discussed it and realized that the following SMARTS is syntactically correct:
CC\\\\\C=C/CN
however it is not a syntactically correct SMILES.
During import it is imported as SMARTS (as it cannot be imported as SMILES).
You may argue that it is not correct to import something as SMARTS which cannot be imported as SMILES.
Andras
User 870ab5b546
13-09-2007 01:31:27
Hello,
Rg is the symbol for the element roentgenium, element 111. Though I doubt that someone entered a compound containing this element in an organic compounds database, it should still be accepted as legitimate SMILES.
-- Bob
ChemAxon 25dcd765a3
13-09-2007 07:21:06
Bob, you are right.
However Marvin accepts elements until atomic number 109 (Meitnerium). I think it is far enough.
Andras
User 870ab5b546
13-09-2007 12:40:28
Yes, Meitnerium is probably far enough. Though you might want to accept Dilithium, too, just for all the Trekkies out there. (Do you have Trekkies in Hungary?)
Before we realized we could invent pseudoatoms, we used Db as an atom that would be unlikely to be found in any structure drawn by a student.
ChemAxon 25dcd765a3
14-09-2007 12:49:16
If Marvin will appear in the new Star Trek version, we will do it for sure.
About Trekkies, I think not too much. I don't know any Trekkies around me. Probably because Star Trek arrived to Hungary lately. We have rather Star Wars fans.
Andras