Bob, John and the group
If there is interest in starting up an ‘Open CIP’ project I can offer space on
the newly minted IUPAC GitHub account.
Let me know if that would be of use and if so who would be the admin for the
project. We can invite collaborators after that…
Stuart
On May 9, 2017, at 4:19 PM, John Mayfield
<john.wilkinson...@gmail.com<mailto:john.wilkinson...@gmail.com>> wrote:
With regards to an "Open" CIP -- I strongly suggest not going there. If you are
seriously interested in this, join/form an IUPAC project.
For me the main motivation is to not reinvent the wheel, or perhaps not
reinvent the wheel worse than it already was. The less people have to think and
worry about CIP the better.
Maybe an IUPAC project is the way to go there... but a stepping stone is to
have a 'standard/verified' implementation (i.e. Open CIP) first. You've done
well on your implementation and it may be one to recomend as a 'verified'
version but if we do nothing in 2 years time someone else will come along and
waste more time with the same bugs/corner cases.
- You've still not done the iteration quite right, you only give 4 labels for
this one:
[C@]3([C@]1([H])CC[C@@]([H])(C)CC1)([C@]2([H])CC[C@@]([H])(C)CC2)CC[C@]([H])(C)CC3
- What CIP labels do you get for
CHEBI:51439<http://www.ebi.ac.uk/chebi/searchId.do?chebiId=CHEBI%3A51439>? I
believe a correct implementation should never finish... or at least run of
memory when building the digraph.
On 9 May 2017 at 19:48, Robert Hanson
<hans...@stolaf.edu<mailto:hans...@stolaf.edu>> wrote:
OK, 967 lines. This now includes chiral bridgehead nitrogens and is just
missing a small piece of code for integrating M/P and seqCis/seqTrans into Rule
4b. The algorithm is solid. No particular issues other than that. Does not
implement atom-number averaging for mancude rings, but does remove Kekule
dependencies for aromatic rings. This last bit required a slight additional
"friendly amendment" to Rule 1b, which I don't think was crafted with aromatics
in mind. Pseudocode is still pretty much the same as initially described. There
are no issues with multi-center dependencies.
Validates on the full 236-compound Chapter 9 validation suite from ACD/Labs
except:
var skip = ({27 229}) || // ignore -- BB has E/Z only; missing chirality
({95 96 98 99 100 101 102 103 104 108 109 110 111 112 200}) || //
trigonal planar, square planar, or hypervalent
({32 33}) || // helicene
({212 213})|| // chiral conformation 1,4-benzene in a ring
({38}) || // ignoring -- Mancude for cyclopentadienyl -- will
require some thought
({170}) // failing (mixed Rule 4b)
In the process, I have found four erroneous assignments in IUPAC Blue Book
2013. These are being checked by IUPAC. There's actually quite a large errata
page for that book already.
With regards to an "Open" CIP -- I strongly suggest not going there. If you are
seriously interested in this, join/form an IUPAC project.
Bob
On Sat, Apr 29, 2017 at 2:54 PM, Robert Hanson
<hans...@stolaf.edu<mailto:hans...@stolaf.edu>> wrote:
OK, final update for a while. (816 lines, Wolf. I have no idea how that
compares to yours or others' algorithms.)
Open-source, validated IUPAC 2013 preferred IUPAC name (PIN) stereochemical
designations.
Jmol.___JmolVersion="14.15.2" // 4/29/17
-- 816 lines
-- validation data are at
https://sourceforge.net/p/jmol/code/HEAD/tree/trunk/Jmol-datafiles/cip/
-- validates for 160 structures (some duplicates; both cip_examples.zip and
stereo_test_cases.sdf)
-- validates for all cases considered:
-- simple R/S and E/Z
-- small-ring removal of E/Z
-- parallel-strand Rule 4b and Rule 5 (Mata)
-- pseudochiral r/s and m/p
-- odd and even cumulenes
-- atropisomers
-- P, S, As, Se, Sb, Te, Bi, Po trigonal pyramidal and tetrahedral
-- imine and diazine E/Z chirality
The algorithm will fail for some more complex nested aspects of Rule 4b. I
decided to be satisfied for now with only those examples in IUPAC Blue Book
2013 Chapter 9. My understanding is that even ACD/Labs did not fully implement
Rules 4 and 5 much beyond that.
Working version in JavaScript can be tested at
https://chemapps.stolaf.edu/jmol/jsmol/jsmetest2.htm
Binary and source at https://sourceforge.net/projects/jmol/files/Jmol/
A great challenge for April!
Bob
On Thu, Apr 27, 2017 at 12:21 AM, Robert Hanson
<hans...@stolaf.edu<mailto:hans...@stolaf.edu>> wrote:
Rule 5 is done. Fully validating using the first validation set that Mikko sent
me (86 compounds, roughly, some 2D/3D duplicates). I'm sure there are more
cases it needs testing with, though.
My algorithm implementation handles Rules 4 and 5 lexicographically so that a
simple Array.sort(String[]) does the job. Kind of interesting, perhaps.
763 lines, Wolf.
Bob
--
Robert M. Hanson
Larson-Anderson Professor of Chemistry
St. Olaf College
Northfield, MN
http://www.stolaf.edu/people/hansonr
If nature does not answer first what we want,
it is better to take what answer we get.
-- Josiah Willard Gibbs, Lecture XXX, Monday, February 5, 1900
--
Robert M. Hanson
Larson-Anderson Professor of Chemistry
St. Olaf College
Northfield, MN
http://www.stolaf.edu/people/hansonr
If nature does not answer first what we want,
it is better to take what answer we get.
-- Josiah Willard Gibbs, Lecture XXX, Monday, February 5, 1900
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