All Questions
Tagged with notation cheminformatics
6 questions
2
votes
1
answer
53
views
What does ‘S/A’ mean in SMARTS pattern when using Chemicalize to draw the chemical structure?
I am still new to the SMARTS annotation. I am wondering what does S/A’ mean on the bond labeling drawn with Chemicalize using SMARTS [!#1]c1n[cH]nc([!#1])c1[!#1]? ...
- 131
3
votes
1
answer
204
views
What does ‘(A)’ mean in SMARTS pattern when using Chemicalize to draw the chemical structure?
I am not quite sure what ‘(A)’ could mean for the carbon atom when writing the SMARTS CCN(C)C using Chemicalize to draw the chemical structure below. Can anyone ...
- 131
4
votes
1
answer
315
views
Line Entry system like SMILES for metals?
SMILES is not designed for metallic compounds.
Is there a similar ASCII line entry notation for metallic compounds, including repeating structure in space, &c.?
- 51
10
votes
2
answers
3k
views
What databases or repositories are there that have generalized SMILES for functional groups?
Does a resource exist that has the SMILES formula of the generalized pattern that represents the group?
For instance: I have the aldehydes group, which has the pattern: ...
- 203
11
votes
1
answer
1k
views
What would be SMILES notation for a compound with delocalized bonding?
For example, the cyclopentadienyl rings in ferrocene $\ce{Fe(}\eta^5 \ce{-C5H5)2}$ are often drawn with delocalized electron circles in them instead of explicit pi bonds.
The Wikipedia article for ...
23
votes
1
answer
808
views
Structure that breaks InChI
I am currently testing a piece of software that generates the InChI for a given structure. I also want to test error situations as end users will also deliver the mol files that will be used as input ...
- 365