2 different canonical SMILES/SMARTS for 2-butene

I'm running into a problem with canonical SMILES/SMARTS retrieved from 2-butene with an undefined double bond "Cis or Trans Double" specified in MSketch.

Depending on how a student draws in the structure I get either of these SMILES, that appear to be identical when imported into MSketch.

[H]C(C([H])([H])[H])=C([H])C([H])([H])[H]

[H]C(=C([H])C([H])([H])[H])C([H])([H])[H]

Why do I get two different "canonical" SMILES/SMARTS for the same structure?

MSketch: 5.2.4.

OS: XP SP3

Hi,

At the first sight I don't know, but I will examine the problem.

On the other hand you should get unique smiles with 'u' export option, but this option removes the explicit Hydrogen atoms.

Andras

I asked our sysadmin and he said this was generated using the following syntax:

cxsmarts:+q+s+e+l+L+R-d

q = double bond equivalence

s = query SMARTS

e = stereo configuration

l = atom labels

L = lone pairs

R = radicals

d = (ignore) ring bond indexes

This is for a course on Lewis structures. Apparently it matters if you write the C atoms all in one line (some simple Lewis structures are written like that) or whether somewhat realistic angles are used for drawing the Lewis structure.

Thanks for the example.

Hi,

Could you please attach a molecule file which reproduces the bug.

I have drawn the ones which are given in your picture but without any success.

molconvert cxsmarts:+q+s+e+l+L+R-d cistransbug.mrv 
[H]C(=C([H])C([H])([H])[H])C([H])([H])[H]
[H]C(=C([H])C([H])([H])[H])C([H])([H])[H]
[H]C(=C([H])C([H])([H])[H])C([H])([H])[H]
[H]C(=C([H])C([H])([H])[H])C([H])([H])[H]

molconvert cxsmarts:+q+s+e+l+L+R-d cistransbug.mrv 
[H]C(=C([H])C([H])([H])[H])C([H])([H])[H]
[H]C(=C([H])C([H])([H])[H])C([H])([H])[H]
[H]C(=C([H])C([H])([H])[H])C([H])([H])[H]
[H]C(=C([H])C([H])([H])[H])C([H])([H])[H]

I'll have to get back with my sysadmin on this. I can't manually (with my local copy of MSketch/molconvert.exe) reproduce this either.

molconvert cxsmarts:+q+s+e+l+L+R-d cistransbug.mrv 
[H]C(=C([H])C([H])([H])[H])C([H])([H])[H]
[H]C(=C([H])C([H])([H])[H])C([H])([H])[H]
[H]C(=C([H])C([H])([H])[H])C([H])([H])[H]
[H]C(=C([H])C([H])([H])[H])C([H])([H])[H]

Sorry for taking your time on this. The problem appears to be on our server.

Thanks.

The good news is that you found the problem and it is not in Marvin.

Andras