Re: [BlueObelisk-discuss] Fwd: Cahn-Ingold-Prelog rules into Jmol

[John Mayfield]

Please read back in the discussion Henry,

I've linked multiple comparisons - and am planning on doing a more
comprehensive one for the next ACS (I'll add Gaussview to the list).
ChemDraw's is more advanced than ChemDoodle's. CIP should not be used for
finding stereocenters, canonicalizing, or comparing (matching) - as said
before *InChI does not, should not, and will never include or need a CIP
implementation*.

John

On 12 April 2017 at 14:11, Rzepa, Henry S  wrote:

> Can I ask a more general question?  Quite a number of codes, including
> various commercial,to detect and assign  CIP.  Three that  I use
> are Gaussview, ChemDraw and  ChemDoodle.  There are I am sure many others.
> I presume InChI in the stereochemical layer might have a go as well (?)
>
> Rarely declared however are the heuristics behind such detection, and in
> particular how the  “difficult” cases are handled.  Might we assume caveat
> emptor when it comes to all these codes?  I suppose  one should really test
> them against each other?
>
> I am sure  Jmol when its entry into this fold is mature will compete with
> the best of them,  but how many of these other codes have been tested
> against proper validation sets and the results reported?
>
> Henry Rzepa, http://orcid.org/-0002-8635-8390
>
>
>
> 
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Re: [BlueObelisk-discuss] Fwd: Cahn-Ingold-Prelog rules into Jmol

[Rzepa, Henry S]

Can I ask a more general question?  Quite a number of codes, including various 
commercial,to detect and assign  CIP.  Three that  I use are 
Gaussview, ChemDraw and  ChemDoodle.  There are I am sure many others. I 
presume InChI in the stereochemical layer might have a go as well (?)

Rarely declared however are the heuristics behind such detection, and in 
particular how the  “difficult” cases are handled.  Might we assume caveat 
emptor when it comes to all these codes?  I suppose  one should really test 
them against each other?

I am sure  Jmol when its entry into this fold is mature will compete with the 
best of them,  but how many of these other codes have been tested against 
proper validation sets and the results reported?

Henry Rzepa, http://orcid.org/-0002-8635-8390




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Re: [BlueObelisk-discuss] Fwd: Cahn-Ingold-Prelog rules into Jmol

[Robert Hanson]

On Wed, Apr 12, 2017 at 7:54 AM, Wolf Ihlenfeldt  wrote:

> On Wed, Apr 12, 2017 at 1:44 PM, Robert Hanson  wrote:
> > (and I wish they had thought of seqR and seqS)
> >
> > In case anyone is interested, here is my pseudocode. The actual methods
> > aren't much longer than this.
> > John, do you agree this is the appropriate approach?
> >
> > Bob
> >
> > https://sourceforge.net/p/jmol/code/HEAD/tree/trunk/
> Jmol/src/org/jmol/symmetry/CIPChirality.java
> >
> >   //
> >   // getChirality(atom) {
> >   //  if (atom.getCovalentBondCount() != 4) exit NO_CHIRALITY
>
> Insufficient. Chiral atoms where a FEP is substituting for a ligand
> are certainly important, in real-life chemistry. But of course that
> heavily depends on the atom type - not every FEP stays locked in
> place. Also geometry matters - you want to treat square planar
> different from tetrahedral, so there needs to be at least some kind of
> VSEPR analysis of prospective chiral centers.
>

"Insufficient" is a relative term. I'm just showing what my algorithm does
in Jmol.

I don't know what "FEP" means.


>
> Also I do not see any iteration here.


This is only for Rules 1-3 right now. One thing at a time...



> Cases where the chirality or
> non-chirality of an atom can only be determined after this has been
> done in its substituent sphere (say, identical substituents but one
> with a stereogenic cis-DB and one with a stereogenic trans-DB, or with
> a R and a S center in the substituents) are important - and can of
> course be nested to any depth, and they can appear in any atom or bond
> order, so there needs to be iteration as long as anything can be
> resolved, which then can lead to a possibility to resolve more
> centers. Furthermode, you need to interweave CIP atomic and bond
> stereodescriptor determination, they cannot be handled independently.
>

I don't  doubt that. Next up is Rules 4 and 5, where this will surely
become an issue.

Revisions to the pseudocode are welcome.

Bob
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Re: [BlueObelisk-discuss] Fwd: Cahn-Ingold-Prelog rules into Jmol

[Wolf Ihlenfeldt]

On Wed, Apr 12, 2017 at 1:44 PM, Robert Hanson <hans...@stolaf.edu> wrote:
> (and I wish they had thought of seqR and seqS)
>
> In case anyone is interested, here is my pseudocode. The actual methods
> aren't much longer than this.
> John, do you agree this is the appropriate approach?
>
> Bob
>
> https://sourceforge.net/p/jmol/code/HEAD/tree/trunk/Jmol/src/org/jmol/symmetry/CIPChirality.java
>
>   //
>   // getChirality(atom) {
>   //  if (atom.getCovalentBondCount() != 4) exit NO_CHIRALITY

Insufficient. Chiral atoms where a FEP is substituting for a ligand
are certainly important, in real-life chemistry. But of course that
heavily depends on the atom type - not every FEP stays locked in
place. Also geometry matters - you want to treat square planar
different from tetrahedral, so there needs to be at least some kind of
VSEPR analysis of prospective chiral centers.

Also I do not see any iteration here. Cases where the chirality or
non-chirality of an atom can only be determined after this has been
done in its substituent sphere (say, identical substituents but one
with a stereogenic cis-DB and one with a stereogenic trans-DB, or with
a R and a S center in the substituents) are important - and can of
course be nested to any depth, and they can appear in any atom or bond
order, so there needs to be iteration as long as anything can be
resolved, which then can lead to a possibility to resolve more
centers. Furthermode, you need to interweave CIP atomic and bond
stereodescriptor determination, they cannot be handled independently.

>   //  for (each Rule){
>   //sortSubstituents()
>   //if (done) exit getHandedness();
>   //  }
>   //  exit NO_CHIRALITY
>   // }
>   //
>   // sortSubstituents() {
>   //   for (all pairs of substituents a and b) {
>   // score = a.compareTo(b, currentRule)
>   // if (score == TIED)
>   //   score = breakTie(a,b)
>   // }
>   //
>   // breakTie(a,b) {
>   //score = compareShallowly(a, b)
>   //if (score != TIED) return score
>   //a.sortSubstituents(), b.sortSubstituents()
>   //return compareDeeply(a, b)
>   // }
>   //
>   // compareShallowly(a, b) {
>   //for (each substituent pairing i in a and b) {
>   //  score = applyCurrentRule(a_i, b_i)
>   //  if (score != TIED) return score
>   //}
>   //return TIED
>   // }
>   //
>   // compareDeeply(a, b) {
>   //for (each substituent pairing i in a and b) {
>   //  score = breakTie(a_i, b_i)
>   //  if (score != TIED) return score
>   //}
>   //return TIED
>   // }
>   //
>
>
>
>
>
> On Tue, Apr 11, 2017 at 5:17 PM, Bob <hans...@stolaf.edu> wrote:
>>
>> Wow.  I love seqcis! Rule 3 was trivial
>>
>> Robert M. Hanson
>> St. Olaf College Chemistry
>> from my Windows phone
>> 
>> From: Robert Hanson
>> Sent: ‎4/‎11/‎2017 7:30 AM
>> To: BlueObelisk-Discuss
>> Subject: Fwd: [BlueObelisk-discuss] Fwd: Cahn-Ingold-Prelog rules into
>> Jmol
>>
>> [sorry - forgot that this list requires "reply-all"]
>> -- Forwarded message --
>> From: Robert Hanson <hans...@stolaf.edu>
>> Date: Tue, Apr 11, 2017 at 7:29 AM
>> Subject: Re: [BlueObelisk-discuss] Fwd: Cahn-Ingold-Prelog rules into Jmol
>> To: John Mayfield <john.wilkinson...@gmail.com>
>>
>>
>>
>>
>> On Tue, Apr 11, 2017 at 2:37 AM, John Mayfield
>> <john.wilkinson...@gmail.com> wrote:
>>>
>>>
>>> On 11 April 2017 at 04:37, Robert Hanson <hans...@stolaf.edu> wrote:
>>>>>
>>>>> 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.
>>>
>>>
>>> There you go, that should also be S, ordering is: *CO, *[14CH2]C, *CC,
>>> *[H]
>>> https://nextmovesoftware.com/blog/2015/01/21/r-or-s-lets-vote/.
>>>
>>
>> John, what basis in the IUPAC rules leads you to this reading? It suggests
>> that atoms in the nth sphere cannot be ranked until atoms in the (n+1)th
>> sphere are checked after application of Rule 1, even if they could be
>> distinguished by Rule 2. Are you suggesting that after each rule is checked
>> (Rule 1a, Rule 1b, Rule 2 -- or is it Rule 1(a and b), Rule 2,...?) one must
>> expand to the next sphere before making a decision? That seems to me (a)
>> unsupportable by the IUPAC rules and (b) just asking for extremely complex
>> code and a whole lot 

Re: [BlueObelisk-discuss] Fwd: Cahn-Ingold-Prelog rules into Jmol

[Robert Hanson]

(and I wish they had thought of seqR and seqS)

In case anyone is interested, here is my pseudocode. The actual methods
aren't much longer than this.
John, do you agree this is the appropriate approach?

Bob

https://sourceforge.net/p/jmol/code/HEAD/tree/trunk/Jmol/src/org/jmol/symmetry/CIPChirality.java

  //
  // getChirality(atom) {
  //  if (atom.getCovalentBondCount() != 4) exit NO_CHIRALITY
  //  for (each Rule){
  //sortSubstituents()
  //if (done) exit getHandedness();
  //  }
  //  exit NO_CHIRALITY
  // }
  //
  // sortSubstituents() {
  //   for (all pairs of substituents a and b) {
  // score = a.compareTo(b, currentRule)
  // if (score == TIED)
  //   score = breakTie(a,b)
  // }
  //
  // breakTie(a,b) {
  //score = compareShallowly(a, b)
  //if (score != TIED) return score
  //a.sortSubstituents(), b.sortSubstituents()
  //return compareDeeply(a, b)
  // }
  //
  // compareShallowly(a, b) {
  //for (each substituent pairing i in a and b) {
  //  score = applyCurrentRule(a_i, b_i)
  //  if (score != TIED) return score
  //}
  //return TIED
  // }
  //
  // compareDeeply(a, b) {
  //for (each substituent pairing i in a and b) {
  //  score = breakTie(a_i, b_i)
  //  if (score != TIED) return score
  //}
  //return TIED
  // }
  //





On Tue, Apr 11, 2017 at 5:17 PM, Bob <hans...@stolaf.edu> wrote:

> Wow.  I love seqcis! Rule 3 was trivial
>
> Robert M. Hanson
> St. Olaf College Chemistry
> from my Windows phone
> --
> From: Robert Hanson <hans...@stolaf.edu>
> Sent: ‎4/‎11/‎2017 7:30 AM
> To: BlueObelisk-Discuss <blueobelisk-discuss@lists.sourceforge.net>
> Subject: Fwd: [BlueObelisk-discuss] Fwd: Cahn-Ingold-Prelog rules into
> Jmol
>
> [sorry - forgot that this list requires "reply-all"]
> -- Forwarded message --
> From: Robert Hanson <hans...@stolaf.edu>
> Date: Tue, Apr 11, 2017 at 7:29 AM
> Subject: Re: [BlueObelisk-discuss] Fwd: Cahn-Ingold-Prelog rules into Jmol
> To: John Mayfield <john.wilkinson...@gmail.com>
>
>
>
>
> On Tue, Apr 11, 2017 at 2:37 AM, John Mayfield <
> john.wilkinson...@gmail.com> wrote:
>
>>
>> On 11 April 2017 at 04:37, Robert Hanson <hans...@stolaf.edu> wrote:
>>
>>> 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.
>>>
>>
>> There you go, that should also be S, ordering is: *CO, *[14CH2]C, *CC,
>> *[H]
>> https://nextmovesoftware.com/blog/2015/01/21/r-or-s-lets-vote/.
>>
>>
> John, what basis in the IUPAC rules leads you to this reading? It suggests
> that atoms in the nth sphere cannot be ranked until atoms in the (n+1)th
> sphere are checked after application of Rule 1, even if they could be
> distinguished by Rule 2. Are you suggesting that after each rule is checked
> (Rule 1a, Rule 1b, Rule 2 -- or is it Rule 1(a and b), Rule 2,...?) one
> must expand to the next sphere before making a decision? That seems to me
> (a) unsupportable by the IUPAC rules and (b) just asking for extremely
> complex code and a whole lot of unnecessary checks.
>
> My understanding is that exhaustive application of all rules are done
> within the sphere first, then the process is repeated at the next sphere.
> What I read is this:
>
>
>
>
>
> *The ranking of each atom in the nth sphere depends in the first place on
> theranking of atoms of the same branch in (n − 1)th sphere, and then by
> theapplication of the Sequence Rules to it; the smaller the number, the
> higher therelative ranking. (Ranking Rule 2).*
> This is certainly my understanding from all the reading I have done. You
> have three atoms connected to an atom. You rank those three atoms based on
> the rules.  Atoms that are tied are taken to  the next sphere, but not
> until that process is completed.
>
> To me that is pretty clear: We apply all rules to rank all atoms in a
> single sphere. Nothing here says, "Atoms in a sphere are compared pairwise,
> and if they are identical, then the comparison of this pair is continued to
> the next sphere. Once this depth-first relative ranking is determined, the
> procedure is repeated with all pairs of the sphere." I can certainly see
> where *that* reading could drive one mad.
>
>
>
>
>
>> Q: Is there software that does a nice job with producing digraphs from
>>> SMILES?
>>
>>
>> I think I added a utility in Centres, however I've barely looked at the
>> code in 5 years - but am planning to brush it off and clean u

Re: [BlueObelisk-discuss] Fwd: Cahn-Ingold-Prelog rules into Jmol

[Bob]

Wow.  I love seqcis! Rule 3 was trivial

Robert M. Hanson
St. Olaf College Chemistry 
from my Windows phone 

-Original Message-
From: "Robert Hanson" <hans...@stolaf.edu>
Sent: ‎4/‎11/‎2017 7:30 AM
To: "BlueObelisk-Discuss" <blueobelisk-discuss@lists.sourceforge.net>
Subject: Fwd: [BlueObelisk-discuss] Fwd: Cahn-Ingold-Prelog rules into Jmol

[sorry - forgot that this list requires "reply-all"]

-- Forwarded message --
From: Robert Hanson <hans...@stolaf.edu>
Date: Tue, Apr 11, 2017 at 7:29 AM
Subject: Re: [BlueObelisk-discuss] Fwd: Cahn-Ingold-Prelog rules into Jmol
To: John Mayfield <john.wilkinson...@gmail.com>







On Tue, Apr 11, 2017 at 2:37 AM, John Mayfield <john.wilkinson...@gmail.com> 
wrote:



On 11 April 2017 at 04:37, Robert Hanson <hans...@stolaf.edu> wrote:

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. 
 
There you go, that should also be S, ordering is: *CO, *[14CH2]C, *CC, *[H]
https://nextmovesoftware.com/blog/2015/01/21/r-or-s-lets-vote/.




John, what basis in the IUPAC rules leads you to this reading? It suggests that 
atoms in the nth sphere cannot be ranked until atoms in the (n+1)th sphere are 
checked after application of Rule 1, even if they could be distinguished by 
Rule 2. Are you suggesting that after each rule is checked (Rule 1a, Rule 1b, 
Rule 2 -- or is it Rule 1(a and b), Rule 2,...?) one must expand to the next 
sphere before making a decision? That seems to me (a) unsupportable by the 
IUPAC rules and (b) just asking for extremely complex code and a whole lot of 
unnecessary checks.


My understanding is that exhaustive application of all rules are done within 
the sphere first, then the process is repeated at the next sphere.  What I read 
is this: 

The ranking of each atom in the nth sphere depends in the first place on the
ranking of atoms of the same branch in (n − 1)th sphere, and then by the
application of the Sequence Rules to it; the smaller the number, the higher the
relative ranking. (Ranking Rule 2).


This is certainly my understanding from all the reading I have done. You have 
three atoms connected to an atom. You rank those three atoms based on the 
rules.  Atoms that are tied are taken to  the next sphere, but not until that 
process is completed. 

 

To me that is pretty clear: We apply all rules to rank all atoms in a single 
sphere. Nothing here says, "Atoms in a sphere are compared pairwise, and if 
they are identical, then the comparison of this pair is continued to the next 
sphere. Once this depth-first relative ranking is determined, the procedure is 
repeated with all pairs of the sphere." I can certainly see where that reading 
could drive one mad.





 
Q: Is there software that does a nice job with producing digraphs from SMILES?


I think I added a utility in Centres, however I've barely looked at the code in 
5 years - but am planning to brush it off and clean up now though. BTW if you 
look closely, Centres is abstract and wraps around existing toolkits - I only 
wrapped it around CDK though in theory you could do the same with JMol.


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 don't think so. IIRC 1b was introduced to fix this case: 
O[C@H](C(CCC1CC1)(CCC1CC1)CCC1CC1)C12CCC(CC1)CC2. If you use that molecule you 
can tell whether it does/doesn't implement that rule. Without rule 1b it should 
not be possible to label it. In centres you can change the rules of the 
ranking: CDKPerceptor.java.


Yes, that's one of the models Mikko sent me. I used it for checking Rule 1b.
 



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?


It wasn't me who said that, I'd only say don't do it because the implementation 
will drive you mad :-). The "blessed" version would allow everyone to confirm 
against it, as your original question asks - you want to test yours it would be 
much simpler just to point to a complete one leave it there. However from my 
previous testing I don't know if a complete one exists anywhere (maybe the 
LHASA one: http://pubs.acs.org/doi/abs/10.1021/ci00019a004 but of course this 
maybe doesn't exist anymore, will ask them).


Supposedly ACD/Labs has a compliant CIP-determining algorithm. 
http://bulletin.acscinf.org/PDFs/247nm44.pdf

Is ACD/Labs represented on this list?




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. 


CHEBI:51439, whether that's of interest or not is of course subjective 

That's a n

Re: [BlueObelisk-discuss] Fwd: Cahn-Ingold-Prelog rules into Jmol

[John Mayfield]

On 11 April 2017 at 04:37, Robert Hanson  wrote:

> 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.
>

There you go, that should also be S, ordering is: *CO, *[14CH2]C, *CC, *[H]
https://nextmovesoftware.com/blog/2015/01/21/r-or-s-lets-vote/.

Q: Is there software that does a nice job with producing digraphs from
> SMILES?


I think I added a utility in Centres, however I've barely looked at the
code in 5 years - but am planning to brush it off and clean up now though.
BTW if you look closely, Centres is abstract and wraps around existing
toolkits - I only wrapped it around CDK though in theory you could do the
same with JMol.

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 don't think so. IIRC 1b was introduced to fix this case:
O[C@H](C(CCC1CC1)(CCC1CC1)CCC1CC1)C12CCC(CC1)CC2.
If you use that molecule you can tell whether it does/doesn't implement
that rule. Without rule 1b it should not be possible to label it. In
centres you can change the rules of the ranking: CDKPerceptor.java

.

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?
>

It wasn't me who said that, I'd only say don't do it because the
implementation will drive you mad :-). The "blessed" version would allow
everyone to confirm against it, as your original question asks - you want
to test yours it would be much simpler just to point to a complete one
leave it there. However from my previous testing I don't know if a complete
one exists anywhere (maybe the LHASA one:
http://pubs.acs.org/doi/abs/10.1021/ci00019a004 but of course this maybe
doesn't exist anymore, will ask them).

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.


CHEBI:51439, whether that's of interest or not is of course subjective

John
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Re: [BlueObelisk-discuss] Fwd: Cahn-Ingold-Prelog rules into Jmol

[Robert Hanson]

OK. That's fine. Point me to the algorithm. I'll say no more.

On Mon, Apr 10, 2017 at 7:10 AM, Noel O'Boyle  wrote:

> Sorry, but I have to call you out on this, especially as this is the
> Blue Obelisk mailing list.
>
> I've no problem anyone reimplementing anything for fun or profit, but
> I have to disagree with the suggestion that having an N'th
> implementation of the same algorithm is progress, or good for this
> community. At a recent meeting at the EBI, I think there were at least
> 7 attendees who had written versions of this algorithm. The whole goal
> of the Blue Obelisk is to pool our expertise to develop common
> resources, to avoid exactly this situation.
>
> - Noel
>
> On 9 April 2017 at 23:53, Robert Hanson  wrote:
> > "re" implementing is a great way to find additional bugs and compare
> > strategies. This (to this point) took me two days. And if I started with
> a
> > "libRS" in Java, I would still have to modify it extensively to fit Jmol.
> > That said, I wouldn't mind taking a look at how other have implemented
> it.
> >
> > In the mean time, is it OK for me to continue this discussion without
> libRS?
> >
> > Q: What do you say for the stereochemistry of [13CH@@]12C3C1.C2=CC3  ?
> >
> >
> >
> >
> > On Sun, Apr 9, 2017 at 1:53 PM, Noel O'Boyle 
> wrote:
> >>
> >> We need libRS. Everyone reimplementing these rules is some type of
> >> madness.
> >>
> >> On 9 Apr 2017 7:05 p.m., "Robert Hanson"  wrote:
> >>>
> >>> OK, I don't get the logic of this:
> >>>
> >>>
> >>> Rule 1 (a) Higher atomic number precedes lower;
> >>> (b) A duplicated atom, with its predecessor node having the same label
> >>> closer
> >>> to the root, ranks higher than a duplicated atom, with its predecessor
> >>> node
> >>> having the same label farther from the root, which ranks higher than
> any
> >>> nonduplicated-atom-node (proposed by Custer, ref. 36)
> >>>
> >>> Rule 2 Higher atomic mass number precedes lower;
> >>>
> >>>
> >>> Seriously? root distance is checked before isotope. Sure seems odd to
> me.
> >>> Why would that distance check not be after atomic number and mass??
> >>>
> >>> Whatever...
> >>>
> >>> Bob
> >>>
> >>>
> >>>
> >>>
> >>> On Sun, Apr 9, 2017 at 12:11 PM, Robert Hanson 
> >>> wrote:
> 
>  OK, so I am reading Chapter 9 now to see the gory details. I didn't
> know
>  about the root-distance check, and so now
> 
> 
>  1-(bicyclo[2.2.2]octan-1-yl)-1-[1,5-dicyclopropyl-3(2-
> cyclopropylethyl)-pentan-3-yl]methan-1-ol.mol
> 
>  is working. So all of this is easy enough. That's probably it for
>  independent stereochemistry.  Where there is a dependency  of one
>  stereochemical determination from another -- R/S after E/Z; E/Z after
> R/S,
>  E/Z after E/Z, R/S after R/S -- obviously that takes some sort of more
>  general iteration.
> 
>  I think I will have to tackle that another day.
> 
>  Bob
> 
> 
> 
> 
> 
>  On Sun, Apr 9, 2017 at 11:03 AM, John Mayfield
>   wrote:
> >
> > Good good,
> >
> > Fake news before fake news - a paper published in the CCG journal by
> > the CCG.
> >
> > John
> >
> > On 9 April 2017 at 16:51, Robert Hanson  wrote:
> >>
> >> No, John. Don't worry.  I just happened to look at that page prior
> to
> >> designing my own.
> >>
> >> On Sun, Apr 9, 2017 at 10:44 AM, John Mayfield
> >>  wrote:
> >>>
> >>> Hi Bob,
> >>>
> >>> On 9 April 2017 at 13:42, Robert Hanson 
> wrote:
> 
>  [I actually do know it is Cahn; pulled "Cohen" without thinking
> from
>  https://www.chemcomp.com/journal/chiral.htm. Serves me right.
> Duh!]
> >>>
> >>>
> >>> Was that the algorithm you implemented because it's not correct -
> it
> >>> doesn't (and can't) handle ghost atoms. Trying to track down the
> example but
> >>> Daniel Lowe constructed a small reproducible example to
> demonstrate why this
> >>> can never work.
> >>>
> >>> John
> >>>
> >>>
> >>>
> >>> 
> --
> >>> Check out the vibrant tech community on one of the world's most
> >>> engaging tech sites, Slashdot.org! http://sdm.link/slashdot
> >>> ___
> >>> Blueobelisk-discuss mailing list
> >>> Blueobelisk-discuss@lists.sourceforge.net
> >>> https://lists.sourceforge.net/lists/listinfo/blueobelisk-discuss
> >>>
> >>
> >>
> >>
> >> --
> >> Robert M. Hanson
> >> Larson-Anderson Professor of Chemistry
> >> St. Olaf College
> >> Northfield, MN
> >> http://www.stolaf.edu/people/hansonr
> >>
> >>
> >> If nature does 

Re: [BlueObelisk-discuss] Fwd: Cahn-Ingold-Prelog rules into Jmol

[John Mayfield]

Noel pointed out I only sent this back to Bob.

On 10 April 2017 at 08:40, John Mayfield 
wrote:

> On 9 April 2017 at 23:53, Robert Hanson  wrote:
>
>> [13CH@@]12C3C1.C2=CC3
>
>
> Well if you make it valid (Open) SMILES:
>
> [13C@@H]12C3C1.C2=CC3
>
> Also why so many dots, that's considered "not good form" in SMILES
>
> C1C2CC=C[13C@@H]12
>
> Anyways, it should be S. A simpler example is:
>
> CC[C@](CO)([H])[14CH2]C R
> CC[C@@](CO)([H])[14CH2]C S
>
>
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Re: [BlueObelisk-discuss] Fwd: Cahn-Ingold-Prelog rules into Jmol

[Robert Hanson]

"re" implementing is a great way to find additional bugs and compare
strategies. This (to this point) took me two days. And if I started with a
"libRS" in Java, I would still have to modify it extensively to fit Jmol.
That said, I wouldn't mind taking a look at how other have implemented it.

In the mean time, is it OK for me to continue this discussion without libRS?

Q: What do you say for the stereochemistry of [13CH@@]12C3C1.C2=CC3  ?




On Sun, Apr 9, 2017 at 1:53 PM, Noel O'Boyle  wrote:

> We need libRS. Everyone reimplementing these rules is some type of madness.
>
> On 9 Apr 2017 7:05 p.m., "Robert Hanson"  wrote:
>
>> OK, I don't get the logic of this:
>>
>>
>> Rule 1 (a) Higher atomic number precedes lower;
>> (b) A duplicated atom, with its predecessor node having the same label
>> closer
>> to the root, ranks higher than a duplicated atom, with its predecessor
>> node
>> having the same label farther from the root, which ranks higher than any
>> nonduplicated-atom-node (proposed by Custer, ref. 36)
>>
>> Rule 2 Higher atomic mass number precedes lower;
>>
>>
>> Seriously? root distance is checked before isotope. Sure seems odd to me.
>> Why would that distance check not be after atomic number and mass??
>>
>> Whatever...
>>
>> Bob
>>
>>
>>
>>
>> On Sun, Apr 9, 2017 at 12:11 PM, Robert Hanson 
>> wrote:
>>
>>> OK, so I am reading Chapter 9 now to see the gory details. I didn't know
>>> about the root-distance check, and so now
>>>
>>> 1-(bicyclo[2.2.2]octan-1-yl)-1-[1,5-dicyclopropyl-3(2-cyclop
>>> ropylethyl)-pentan-3-yl]methan-1-ol.mol
>>>
>>> is working. So all of this is easy enough. That's probably it for
>>> independent stereochemistry.  Where there is a dependency  of one
>>> stereochemical determination from another -- R/S after E/Z; E/Z after R/S,
>>> E/Z after E/Z, R/S after R/S -- obviously that takes some sort of more
>>> general iteration.
>>>
>>> I think I will have to tackle that another day.
>>>
>>> Bob
>>>
>>>
>>>
>>>
>>>
>>> On Sun, Apr 9, 2017 at 11:03 AM, John Mayfield <
>>> john.wilkinson...@gmail.com> wrote:
>>>
 Good good,

 Fake news before fake news - a paper published in the CCG journal by
 the CCG.

 John

 On 9 April 2017 at 16:51, Robert Hanson  wrote:

> No, John. Don't worry.  I just happened to look at that page prior to
> designing my own.
>
> On Sun, Apr 9, 2017 at 10:44 AM, John Mayfield <
> john.wilkinson...@gmail.com> wrote:
>
>> Hi Bob,
>>
>> On 9 April 2017 at 13:42, Robert Hanson  wrote:
>>
>>> [I actually do know it is Cahn; pulled "Cohen" without thinking from
>>> https://www.chemcomp.com/journal/chiral.htm. Serves me right. Duh!]
>>>
>>
>> Was that the algorithm you implemented because it's not correct - it
>> doesn't (and can't) handle ghost atoms. Trying to track down the example
>> but Daniel Lowe constructed a small reproducible example to demonstrate 
>> why
>> this can never work.
>>
>> John
>>
>>
>> 
>> --
>> Check out the vibrant tech community on one of the world's most
>> engaging tech sites, Slashdot.org! http://sdm.link/slashdot
>> ___
>> Blueobelisk-discuss mailing list
>> Blueobelisk-discuss@lists.sourceforge.net
>> https://lists.sourceforge.net/lists/listinfo/blueobelisk-discuss
>>
>>
>
>
> --
> 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
>>>
>>>
>>
>>
>> --
>> 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
>>
>>
>> 
>> --
>> Check out the vibrant tech community on one of the world's most
>> engaging tech sites, Slashdot.org! http://sdm.link/slashdot
>> ___
>> Blueobelisk-discuss mailing list
>> Blueobelisk-discuss@lists.sourceforge.net

Re: [BlueObelisk-discuss] Fwd: Cahn-Ingold-Prelog rules into Jmol

[Noel O'Boyle]

We need libRS. Everyone reimplementing these rules is some type of madness.

On 9 Apr 2017 7:05 p.m., "Robert Hanson"  wrote:

> OK, I don't get the logic of this:
>
>
> Rule 1 (a) Higher atomic number precedes lower;
> (b) A duplicated atom, with its predecessor node having the same label
> closer
> to the root, ranks higher than a duplicated atom, with its predecessor node
> having the same label farther from the root, which ranks higher than any
> nonduplicated-atom-node (proposed by Custer, ref. 36)
>
> Rule 2 Higher atomic mass number precedes lower;
>
>
> Seriously? root distance is checked before isotope. Sure seems odd to me.
> Why would that distance check not be after atomic number and mass??
>
> Whatever...
>
> Bob
>
>
>
>
> On Sun, Apr 9, 2017 at 12:11 PM, Robert Hanson  wrote:
>
>> OK, so I am reading Chapter 9 now to see the gory details. I didn't know
>> about the root-distance check, and so now
>>
>> 1-(bicyclo[2.2.2]octan-1-yl)-1-[1,5-dicyclopropyl-3(2-cyclop
>> ropylethyl)-pentan-3-yl]methan-1-ol.mol
>>
>> is working. So all of this is easy enough. That's probably it for
>> independent stereochemistry.  Where there is a dependency  of one
>> stereochemical determination from another -- R/S after E/Z; E/Z after R/S,
>> E/Z after E/Z, R/S after R/S -- obviously that takes some sort of more
>> general iteration.
>>
>> I think I will have to tackle that another day.
>>
>> Bob
>>
>>
>>
>>
>>
>> On Sun, Apr 9, 2017 at 11:03 AM, John Mayfield <
>> john.wilkinson...@gmail.com> wrote:
>>
>>> Good good,
>>>
>>> Fake news before fake news - a paper published in the CCG journal by the
>>> CCG.
>>>
>>> John
>>>
>>> On 9 April 2017 at 16:51, Robert Hanson  wrote:
>>>
 No, John. Don't worry.  I just happened to look at that page prior to
 designing my own.

 On Sun, Apr 9, 2017 at 10:44 AM, John Mayfield <
 john.wilkinson...@gmail.com> wrote:

> Hi Bob,
>
> On 9 April 2017 at 13:42, Robert Hanson  wrote:
>
>> [I actually do know it is Cahn; pulled "Cohen" without thinking from
>> https://www.chemcomp.com/journal/chiral.htm. Serves me right. Duh!]
>>
>
> Was that the algorithm you implemented because it's not correct - it
> doesn't (and can't) handle ghost atoms. Trying to track down the example
> but Daniel Lowe constructed a small reproducible example to demonstrate 
> why
> this can never work.
>
> John
>
>
> 
> --
> Check out the vibrant tech community on one of the world's most
> engaging tech sites, Slashdot.org! http://sdm.link/slashdot
> ___
> Blueobelisk-discuss mailing list
> Blueobelisk-discuss@lists.sourceforge.net
> https://lists.sourceforge.net/lists/listinfo/blueobelisk-discuss
>
>


 --
 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
>>
>>
>
>
> --
> 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
>
>
> 
> --
> Check out the vibrant tech community on one of the world's most
> engaging tech sites, Slashdot.org! http://sdm.link/slashdot
> ___
> Blueobelisk-discuss mailing list
> Blueobelisk-discuss@lists.sourceforge.net
> https://lists.sourceforge.net/lists/listinfo/blueobelisk-discuss
>
>
--
Check out the vibrant tech community on one of the world's most
engaging tech sites, Slashdot.org! http://sdm.link/slashdot___
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Re: [BlueObelisk-discuss] Fwd: Cahn-Ingold-Prelog rules into Jmol

[Robert Hanson]

OK, I don't get the logic of this:


Rule 1 (a) Higher atomic number precedes lower;
(b) A duplicated atom, with its predecessor node having the same label
closer
to the root, ranks higher than a duplicated atom, with its predecessor node
having the same label farther from the root, which ranks higher than any
nonduplicated-atom-node (proposed by Custer, ref. 36)

Rule 2 Higher atomic mass number precedes lower;


Seriously? root distance is checked before isotope. Sure seems odd to me.
Why would that distance check not be after atomic number and mass??

Whatever...

Bob




On Sun, Apr 9, 2017 at 12:11 PM, Robert Hanson  wrote:

> OK, so I am reading Chapter 9 now to see the gory details. I didn't know
> about the root-distance check, and so now
>
> 1-(bicyclo[2.2.2]octan-1-yl)-1-[1,5-dicyclopropyl-3(2-cyclop
> ropylethyl)-pentan-3-yl]methan-1-ol.mol
>
> is working. So all of this is easy enough. That's probably it for
> independent stereochemistry.  Where there is a dependency  of one
> stereochemical determination from another -- R/S after E/Z; E/Z after R/S,
> E/Z after E/Z, R/S after R/S -- obviously that takes some sort of more
> general iteration.
>
> I think I will have to tackle that another day.
>
> Bob
>
>
>
>
>
> On Sun, Apr 9, 2017 at 11:03 AM, John Mayfield <
> john.wilkinson...@gmail.com> wrote:
>
>> Good good,
>>
>> Fake news before fake news - a paper published in the CCG journal by the
>> CCG.
>>
>> John
>>
>> On 9 April 2017 at 16:51, Robert Hanson  wrote:
>>
>>> No, John. Don't worry.  I just happened to look at that page prior to
>>> designing my own.
>>>
>>> On Sun, Apr 9, 2017 at 10:44 AM, John Mayfield <
>>> john.wilkinson...@gmail.com> wrote:
>>>
 Hi Bob,

 On 9 April 2017 at 13:42, Robert Hanson  wrote:

> [I actually do know it is Cahn; pulled "Cohen" without thinking from
> https://www.chemcomp.com/journal/chiral.htm. Serves me right. Duh!]
>

 Was that the algorithm you implemented because it's not correct - it
 doesn't (and can't) handle ghost atoms. Trying to track down the example
 but Daniel Lowe constructed a small reproducible example to demonstrate why
 this can never work.

 John


 
 --
 Check out the vibrant tech community on one of the world's most
 engaging tech sites, Slashdot.org! http://sdm.link/slashdot
 ___
 Blueobelisk-discuss mailing list
 Blueobelisk-discuss@lists.sourceforge.net
 https://lists.sourceforge.net/lists/listinfo/blueobelisk-discuss


>>>
>>>
>>> --
>>> 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
>
>


-- 
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
--
Check out the vibrant tech community on one of the world's most
engaging tech sites, Slashdot.org! http://sdm.link/slashdot___
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Re: [BlueObelisk-discuss] Fwd: Cahn-Ingold-Prelog rules into Jmol

[Robert Hanson]

OK, so I am reading Chapter 9 now to see the gory details. I didn't know
about the root-distance check, and so now

1-(bicyclo[2.2.2]octan-1-yl)-1-[1,5-dicyclopropyl-3(2-cyclo
propylethyl)-pentan-3-yl]methan-1-ol.mol

is working. So all of this is easy enough. That's probably it for
independent stereochemistry.  Where there is a dependency  of one
stereochemical determination from another -- R/S after E/Z; E/Z after R/S,
E/Z after E/Z, R/S after R/S -- obviously that takes some sort of more
general iteration.

I think I will have to tackle that another day.

Bob





On Sun, Apr 9, 2017 at 11:03 AM, John Mayfield 
wrote:

> Good good,
>
> Fake news before fake news - a paper published in the CCG journal by the
> CCG.
>
> John
>
> On 9 April 2017 at 16:51, Robert Hanson  wrote:
>
>> No, John. Don't worry.  I just happened to look at that page prior to
>> designing my own.
>>
>> On Sun, Apr 9, 2017 at 10:44 AM, John Mayfield <
>> john.wilkinson...@gmail.com> wrote:
>>
>>> Hi Bob,
>>>
>>> On 9 April 2017 at 13:42, Robert Hanson  wrote:
>>>
 [I actually do know it is Cahn; pulled "Cohen" without thinking from
 https://www.chemcomp.com/journal/chiral.htm. Serves me right. Duh!]

>>>
>>> Was that the algorithm you implemented because it's not correct - it
>>> doesn't (and can't) handle ghost atoms. Trying to track down the example
>>> but Daniel Lowe constructed a small reproducible example to demonstrate why
>>> this can never work.
>>>
>>> John
>>>
>>>
>>> 
>>> --
>>> Check out the vibrant tech community on one of the world's most
>>> engaging tech sites, Slashdot.org! http://sdm.link/slashdot
>>> ___
>>> Blueobelisk-discuss mailing list
>>> Blueobelisk-discuss@lists.sourceforge.net
>>> https://lists.sourceforge.net/lists/listinfo/blueobelisk-discuss
>>>
>>>
>>
>>
>> --
>> 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
--
Check out the vibrant tech community on one of the world's most
engaging tech sites, Slashdot.org! http://sdm.link/slashdot___
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Re: [BlueObelisk-discuss] Fwd: Cahn-Ingold-Prelog rules into Jmol

[John Mayfield]

Good good,

Fake news before fake news - a paper published in the CCG journal by the
CCG.

John

On 9 April 2017 at 16:51, Robert Hanson  wrote:

> No, John. Don't worry.  I just happened to look at that page prior to
> designing my own.
>
> On Sun, Apr 9, 2017 at 10:44 AM, John Mayfield <
> john.wilkinson...@gmail.com> wrote:
>
>> Hi Bob,
>>
>> On 9 April 2017 at 13:42, Robert Hanson  wrote:
>>
>>> [I actually do know it is Cahn; pulled "Cohen" without thinking from
>>> https://www.chemcomp.com/journal/chiral.htm. Serves me right. Duh!]
>>>
>>
>> Was that the algorithm you implemented because it's not correct - it
>> doesn't (and can't) handle ghost atoms. Trying to track down the example
>> but Daniel Lowe constructed a small reproducible example to demonstrate why
>> this can never work.
>>
>> John
>>
>>
>> 
>> --
>> Check out the vibrant tech community on one of the world's most
>> engaging tech sites, Slashdot.org! http://sdm.link/slashdot
>> ___
>> Blueobelisk-discuss mailing list
>> Blueobelisk-discuss@lists.sourceforge.net
>> https://lists.sourceforge.net/lists/listinfo/blueobelisk-discuss
>>
>>
>
>
> --
> 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
>
>
--
Check out the vibrant tech community on one of the world's most
engaging tech sites, Slashdot.org! http://sdm.link/slashdot___
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Re: [BlueObelisk-discuss] Fwd: Cahn-Ingold-Prelog rules into Jmol

[Robert Hanson]

No, John. Don't worry.  I just happened to look at that page prior to
designing my own.

On Sun, Apr 9, 2017 at 10:44 AM, John Mayfield 
wrote:

> Hi Bob,
>
> On 9 April 2017 at 13:42, Robert Hanson  wrote:
>
>> [I actually do know it is Cahn; pulled "Cohen" without thinking from
>> https://www.chemcomp.com/journal/chiral.htm. Serves me right. Duh!]
>>
>
> Was that the algorithm you implemented because it's not correct - it
> doesn't (and can't) handle ghost atoms. Trying to track down the example
> but Daniel Lowe constructed a small reproducible example to demonstrate why
> this can never work.
>
> John
>
>
> 
> --
> Check out the vibrant tech community on one of the world's most
> engaging tech sites, Slashdot.org! http://sdm.link/slashdot
> ___
> Blueobelisk-discuss mailing list
> Blueobelisk-discuss@lists.sourceforge.net
> https://lists.sourceforge.net/lists/listinfo/blueobelisk-discuss
>
>


-- 
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
--
Check out the vibrant tech community on one of the world's most
engaging tech sites, Slashdot.org! http://sdm.link/slashdot___
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Re: [BlueObelisk-discuss] Fwd: Cahn-Ingold-Prelog rules into Jmol

[John Mayfield]

Hi Bob,

On 9 April 2017 at 13:42, Robert Hanson  wrote:

> [I actually do know it is Cahn; pulled "Cohen" without thinking from
> https://www.chemcomp.com/journal/chiral.htm. Serves me right. Duh!]
>

Was that the algorithm you implemented because it's not correct - it
doesn't (and can't) handle ghost atoms. Trying to track down the example
but Daniel Lowe constructed a small reproducible example to demonstrate why
this can never work.

John
--
Check out the vibrant tech community on one of the world's most
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