Re: [BlueObelisk-discuss] OK, bragging -- CIP

2017-04-21 Thread John Mayfield 
Thanks for the acknowledgments, let me know where Wolf and I can send the
invoices for our consulting fees. ;-)

- John

On 21 April 2017 at 12:47, Robert Hanson  wrote:

> 570 lines; 40 methods.
> https://sourceforge.net/p/jmol/code/HEAD/tree/trunk/
> Jmol/src/org/jmol/symmetry/CIPChirality.java
>
> Limitations:
>
>  no parallel chirality paths (Mata)
>  not processing inositols correctly
>  no lone-pair business (S, P, imines)
>  standard E/Z, R/S, r/s only; no allenes, no planar asymmetry
>
> Tests passed from Mikko's collection:
>
> (2R,3r,4S)-2,3,4-trichloropentane.mol//RrS
> (2R,3s,4S)-2,3,4-trichloropentane.mol//RsS
> (2R,3r,4R,5s,6R)-2,6-dichloro-3,5-bis[(1S)-1-chloroethyl]
> heptan-4-ol_2d.sdf
> (2R,3r,4R,5s,6R)-2,6-dichloro-3,5-bis[(1S)-1-chloroethyl]
> heptan-4-ol_3d.sdf
> (2R,3s,4S,6R)-2,6-dichloro-5-[(1R)-1-chloroethyl]-3-[(1S)-1-
> chloroethyl]heptan-4-ol_2d.sdf
> (2R,3s,4S,6R)-2,6-dichloro-5-[(1R)-1-chloroethyl]-3-[(1S)-1-
> chloroethyl]heptan-4-ol_3d.sdf
> (2R,3R,4R,5S,6R)-2,3,4,5,6-pentachloroheptanedioic_acid_2d.mol//RSRRR
> (2R,3R,4R,5S,6R)-2,3,4,5,6-pentachloroheptanedioic_acid_2d.sdf//RSRRR
> (2R,3R,4R,5S,6R)-2,3,4,5,6-pentachloroheptanedioic_acid_3d.sdf//RSRRR
> (2R,3R,4S,5S,6R)-2,3,4,5,6-pentachloroheptanedioic_acid_3d.mol//RSSRR
> (1s,4s)-1,4-dimethylcyclohexane.mol//ss
> (1r,4r)-1,4-dimethylcyclohexane.mol//rr
> (1r,4r)-4-bromo-4-methylcyclohexan-1-amine.mol//rr
> (1s,4s)-4-bromo-4-methylcyclohexan-1-amine.mol//ss
> (1r,3r)-cyclobutane-1,3-diol.mol//rr
> (1s,3s)-cyclobutane-1,3-diol.mol//ss
> two_pairs_of_enantiomeric_ligands.mol//SRSR
> (2R,3r,4S)-2,3,4-trichloropentane.mol//RrS
> (2R,3s,4S)-2,3,4-trichloropentane.mol//RsS
> (2R,3r,4R,5s,6R)-2,6-dichloro-3,5-bis[(1S)-1-chloroethyl]
> heptan-4-ol_2d.sdf
> (2R,3r,4R,5s,6R)-2,6-dichloro-3,5-bis[(1S)-1-chloroethyl]
> heptan-4-ol_3d.sdf
> (2R,3s,4S,6R)-2,6-dichloro-5-[(1R)-1-chloroethyl]-3-[(1S)-1-
> chloroethyl]heptan-4-ol_2d.sdf
> (2R,3s,4S,6R)-2,6-dichloro-5-[(1R)-1-chloroethyl]-3-[(1S)-1-
> chloroethyl]heptan-4-ol_3d.sdf
> (2R,3R,4R,5S,6R)-2,3,4,5,6-pentachloroheptanedioic_acid_2d.mol//RSRRR
> (2R,3R,4R,5S,6R)-2,3,4,5,6-pentachloroheptanedioic_acid_2d.sdf//RSRRR
> (2R,3R,4R,5S,6R)-2,3,4,5,6-pentachloroheptanedioic_acid_3d.sdf//RSRRR
> (2R,3R,4S,5S,6R)-2,3,4,5,6-pentachloroheptanedioic_acid_3d.mol//RSSRR
> (1R,2R)-2-chlorocyclohexanol_2d.mol
> (1R,2R)-2-chlorocyclohexanol_2d_noH.mol
> (1R,2R)-2-chlorocyclohexanol_3d.mol
> (1R,2R)-2-chlorocyclohexanol_3d_noH.mol
> (1R,2R,4R,5R)-cyclohexane-1,2,3,4,5-pentol_2d_noH.mol//
> (1R,2R,4R,5R)-cyclohexane-1,2,3,4,5-pentol_3d.mol//
> (1S,5R)-bicyclo[3.1.0]hex-2-ene_2D.mol//SZZR
> (1S,5R)-bicyclo[3.1.0]hex-2-ene_3D.mol//SZZR
> (2R,3S,4R,5R,6S)-3-(2-bromoethyl)-1-chloro-2,6,7-trifluoro-5-(2-iodoethyl)
> heptan-4-ol_2D.mol//SRRSR
> (2R,3S,4R,5R,6S)-3-(2-bromoethyl)-1-chloro-2,6,7-trifluoro-5-(2-iodoethyl)
> heptan-4-ol_3D.mol//SRRSR
> (2R,3S,4S,5R,6S)-3-(2-bromoethyl)-1-chloro-2,6,7-trifluoro-5-(2-iodoethyl)
> heptan-4-ol_2D.mol//SRSSR
> (2R,3S,4S,5R,6S)-3-(2-bromoethyl)-1-chloro-2,6,7-trifluoro-5-(2-iodoethyl)
> heptan-4-ol_3D.mol//SRSSR
> (2S,4aS,8aS)-8a-chloro-2-fluoro-decahydronaphthalen-4a-ol.sdf
> (4aR,8aS)-8a-methyl-octahydro-1H-2-benzopyran.sdf
> one-R-one-S.sdf
> _1R,2R_-2-__S_-chloro_fluoro_methyl_cyclohexan-1- ol.sdf
> _2R,3R_-3-methylpentan-2-ol.sdf
> _2R,3S_-3-methylpentan-2-ol.sdf
> beta-eudesmol.sdf
> beta-eudesmol_3d.sdf
> gibberellin_3D_new.mol//RRRS
>
>
> --
> 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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>
>
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[BlueObelisk-discuss] OK, bragging -- CIP

2017-04-21 Thread Robert Hanson 
570 lines; 40 methods.
https://sourceforge.net/p/jmol/code/HEAD/tree/trunk/Jmol/src/org/jmol/symmetry/CIPChirality.java

Limitations:

 no parallel chirality paths (Mata)
 not processing inositols correctly
 no lone-pair business (S, P, imines)
 standard E/Z, R/S, r/s only; no allenes, no planar asymmetry

Tests passed from Mikko's collection:

(2R,3r,4S)-2,3,4-trichloropentane.mol//RrS
(2R,3s,4S)-2,3,4-trichloropentane.mol//RsS
(2R,3r,4R,5s,6R)-2,6-dichloro-3,5-bis[(1S)-1-chloroethyl]heptan-4-ol_2d.sdf
(2R,3r,4R,5s,6R)-2,6-dichloro-3,5-bis[(1S)-1-chloroethyl]heptan-4-ol_3d.sdf
(2R,3s,4S,6R)-2,6-dichloro-5-[(1R)-1-chloroethyl]-3-[(1S)-1-chloroethyl]heptan-4-ol_2d.sdf
(2R,3s,4S,6R)-2,6-dichloro-5-[(1R)-1-chloroethyl]-3-[(1S)-1-chloroethyl]heptan-4-ol_3d.sdf
(2R,3R,4R,5S,6R)-2,3,4,5,6-pentachloroheptanedioic_acid_2d.mol//RSRRR
(2R,3R,4R,5S,6R)-2,3,4,5,6-pentachloroheptanedioic_acid_2d.sdf//RSRRR
(2R,3R,4R,5S,6R)-2,3,4,5,6-pentachloroheptanedioic_acid_3d.sdf//RSRRR
(2R,3R,4S,5S,6R)-2,3,4,5,6-pentachloroheptanedioic_acid_3d.mol//RSSRR
(1s,4s)-1,4-dimethylcyclohexane.mol//ss
(1r,4r)-1,4-dimethylcyclohexane.mol//rr
(1r,4r)-4-bromo-4-methylcyclohexan-1-amine.mol//rr
(1s,4s)-4-bromo-4-methylcyclohexan-1-amine.mol//ss
(1r,3r)-cyclobutane-1,3-diol.mol//rr
(1s,3s)-cyclobutane-1,3-diol.mol//ss
two_pairs_of_enantiomeric_ligands.mol//SRSR
(2R,3r,4S)-2,3,4-trichloropentane.mol//RrS
(2R,3s,4S)-2,3,4-trichloropentane.mol//RsS
(2R,3r,4R,5s,6R)-2,6-dichloro-3,5-bis[(1S)-1-chloroethyl]heptan-4-ol_2d.sdf
(2R,3r,4R,5s,6R)-2,6-dichloro-3,5-bis[(1S)-1-chloroethyl]heptan-4-ol_3d.sdf
(2R,3s,4S,6R)-2,6-dichloro-5-[(1R)-1-chloroethyl]-3-[(1S)-1-chloroethyl]heptan-4-ol_2d.sdf
(2R,3s,4S,6R)-2,6-dichloro-5-[(1R)-1-chloroethyl]-3-[(1S)-1-chloroethyl]heptan-4-ol_3d.sdf
(2R,3R,4R,5S,6R)-2,3,4,5,6-pentachloroheptanedioic_acid_2d.mol//RSRRR
(2R,3R,4R,5S,6R)-2,3,4,5,6-pentachloroheptanedioic_acid_2d.sdf//RSRRR
(2R,3R,4R,5S,6R)-2,3,4,5,6-pentachloroheptanedioic_acid_3d.sdf//RSRRR
(2R,3R,4S,5S,6R)-2,3,4,5,6-pentachloroheptanedioic_acid_3d.mol//RSSRR
(1R,2R)-2-chlorocyclohexanol_2d.mol
(1R,2R)-2-chlorocyclohexanol_2d_noH.mol
(1R,2R)-2-chlorocyclohexanol_3d.mol
(1R,2R)-2-chlorocyclohexanol_3d_noH.mol
(1R,2R,4R,5R)-cyclohexane-1,2,3,4,5-pentol_2d_noH.mol//
(1R,2R,4R,5R)-cyclohexane-1,2,3,4,5-pentol_3d.mol//
(1S,5R)-bicyclo[3.1.0]hex-2-ene_2D.mol//SZZR
(1S,5R)-bicyclo[3.1.0]hex-2-ene_3D.mol//SZZR
(2R,3S,4R,5R,6S)-3-(2-bromoethyl)-1-chloro-2,6,7-trifluoro-5-(2-iodoethyl)heptan-4-ol_2D.mol//SRRSR
(2R,3S,4R,5R,6S)-3-(2-bromoethyl)-1-chloro-2,6,7-trifluoro-5-(2-iodoethyl)heptan-4-ol_3D.mol//SRRSR
(2R,3S,4S,5R,6S)-3-(2-bromoethyl)-1-chloro-2,6,7-trifluoro-5-(2-iodoethyl)heptan-4-ol_2D.mol//SRSSR
(2R,3S,4S,5R,6S)-3-(2-bromoethyl)-1-chloro-2,6,7-trifluoro-5-(2-iodoethyl)heptan-4-ol_3D.mol//SRSSR
(2S,4aS,8aS)-8a-chloro-2-fluoro-decahydronaphthalen-4a-ol.sdf
(4aR,8aS)-8a-methyl-octahydro-1H-2-benzopyran.sdf
one-R-one-S.sdf
_1R,2R_-2-__S_-chloro_fluoro_methyl_cyclohexan-1- ol.sdf
_2R,3R_-3-methylpentan-2-ol.sdf
_2R,3S_-3-methylpentan-2-ol.sdf
beta-eudesmol.sdf
beta-eudesmol_3d.sdf
gibberellin_3D_new.mol//RRRS


-- 
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
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