On Mon, Apr 10, 2017 at 3:56 PM, John Mayfield <john.wilkinson...@gmail.com>
wrote:
> I'm pretty sure it's 1R 5R.
>
>
> 1) Firstly, there is only one stereocentre so how do you name two?
>
It's a bicyclo[3.1.0]octene system. It has two stereocenters; only one was
needed for the SMILES string. See PNG image.
Still curious: What was your logic for 1S? What was wrong with mine?
> 2) What did you get for the other test case, that one checks you have the
> ordering ranking for atomic masses.
>
>> CC[C@@](CO)([H])[14CH2]C
>
>
R.
I'll draw out the full digraph tomorrow if we can't work it out from these
tests.
Q: Is there software that does a nice job with producing digraphs from
SMILES?
To answer some other parts of the discussion.
1) Has anyone taken the CIP rules and rewritten them as formal logic (and
> machine readable) rules?
>>In general the algorithm has (bad) exponential run time for even small
cases... it really is quite poor based on current computer science
knowledge.
I guess this would matter if you had 1,000,000 compounds to check; the
100-line algorithm (Rules 1 and 2) I wrote seems quite straightforward and
suitable for my purposes. Hard to believe any molecule of interest would
push the limits for such.
>Here some Open CIP Implementations I can quickly find
- JUMBO6
<https://bitbucket.org/wwmm/jumbo6/src/e76bf83c1eaf6ec65d794b111676913c633f1112/src/main/java/org/xmlcml/cml/tools/StereochemistryTool.java?at=default&fileviewer=file-view-default>
(Notice a bug report from me 5 years ago
<https://bitbucket.org/wwmm/jumbo6/issues/1/incorrect-stereochemistry-determination>
:D)
by Peter Murray Rust
- OPSIN
<https://bitbucket.org/dan2097/opsin/src/343e6340a9ad85f68a08630f8b08de8df8f49557/opsin-core/src/main/java/uk/ac/cam/ch/wwmm/opsin/CipSequenceRules.java?at=default&fileviewer=file-view-default>
by
Daniel Lowe
- CDK
<https://github.com/cdk/cdk/blob/master/descriptor/cip/src/main/java/org/openscience/cdk/geometry/cip/CIPTool.java>
by
Egon Willighagen
- RDKit
<https://github.com/rdkit/rdkit/blob/f2c1a95c6e1548457c1b4bf4f6f8fc7defc5f1a7/Code/GraphMol/Chirality.cpp>
by Greg Landrum
- Centres <https://github.com/johnmay/centres> by Me
Q: These all implement Rule 1b and the rest of the rules? Have they been
validated in some systematic, common way, so we know they don't have any
bugs?
I also compared some commercial tools in my thesis also. When Daniel and I
did an investigation at NextMove we found OPSIN/Centres agreed the most.
Centres handles more complicate cases (e.g. decalin, para-cyclohexanes,
inositols) however I know it's still incomplete/wrong - I never bothered to
implement the fraction bond orders for mancude rings see [1].
Q: Doesn't this argue against the "Why bother doing this -- it's been done
seven times already" argument? Which one is IUPAC-2013-standard?
Anyways if anything this discussion has prompted to me submit the following
abstract to ACS Fall 2017. The main aim is to formalise the problems and
propose a way forward.
> *Comparing CIP Implementations: The Need for an Open CIP*
> *John Mayfield, Daniel Lowe and Roger Sayle*Session: Open Structures:
> Wither & Hence in the Digital Era (Oral)
>
Super! One more reason I'm bummed that I won't be there... Please say hello
to Roger and Daniel for me.
Bob
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