From: <ha...@us...> - 2017-05-14 19:04:55
|
Revision: 21601 http://sourceforge.net/p/jmol/code/21601 Author: hansonr Date: 2017-05-14 19:04:52 +0000 (Sun, 14 May 2017) Log Message: ----------- Jmol.___JmolVersion="14.15.5" code: CIP: additional simplification; code: CIP status: implementation complete, including: All subrules implemented fully: 1a, 1b, 2, 3, 4a, 4b, 4c, 5 R/S, E/Z, M/P, r/s, seqCis/seqTrans (as Z/E) benzenoid (including fused benzenoid heteroaromatic) Mancude ring "Kekule weighted" atom number adjustments proposed Rule 1b amendment: A duplicate atom in a Kekule-weighted system is given a root distance equal to its sphere, not the sphere of its duplicated atom. IUPAC Blue Book 2103 errors: ,"147":"r,,,R,,,,r,,,S" // chiral phosphine -- disagrees with BB P-93.5.1.1.2 for S vs R { "id" : "148" "name_pname_pin" : "bis[(1r,4r)-4-methylcyclohexyl]phosphane" "ref_pname_pin" : "P-93.5.1.1.2" "stereo" : ",r,,,R,,,,r,,,R,,," } ,"148":"r,,,S,,,,r,,,R,,,,s,,,s" // r,,,S,,,,r,,,S,,,,s,,,S Jmol disagrees with BB P-93.5.1.1.2 or R and S p. 1243 { "id" : "149" "name_pname_pin" : "bis[(1r,4r)-4-methylcyclohexyl]-(1s,4s)-4-methylcyclohexylphosphane" "ref_pname_pin" : "P-93.5.1.1.2" "stereo" : ",r,,,S,,,,r,,,S,,,,s,,,S,,," } ,"202":"RR" // // p. 1265 disagrees with BB P-93.5.3.5 for RR vs. SS { "id" : "203" "name_pname_pin" : "(5S,8R,11S)-1,12-dioxatrispiro[4.2.2.4^{11}.2^{8}.2^{5}]nonadecane" "ref_pname_pin" : "P-93 5.3.5" } ,"227":"SrSEErS" // disagrees with BB P-93.5.7.2 for S vs. r { "id" : "228" "name_pname_pin" : "(1E)-1-{(1'S,1r,4s)-[1,1'-bi(cyclohexan)]-3'-en-4-yl}-N-[(1r,4r)-4-phenylcyclohexyl]methan-1-imine" "ref_pname_pin" : "P-93.5.7.2" "stereo" : "S,,,,,,,r,S,,,,,,,E,,r,r,,,,,,,,,,,," } ,"230":"@3D RrRsR" // p 1282 disagrees with BB P-93.6 { "id" : "231" "name_pname_pin" : "(2R)-1-[(1r,4R)-4-methylcyclohexyl]-3-[(1s,4S)-4-methylcyclohexyl]propan-2-ol" "ref_pname_pin" : "P-93.6" "stereo" : ",,,,r,,,R,,,,s,,,R,,," } Modified Paths: -------------- trunk/Jmol/src/org/jmol/viewer/Jmol.properties Modified: trunk/Jmol/src/org/jmol/viewer/Jmol.properties =================================================================== --- trunk/Jmol/src/org/jmol/viewer/Jmol.properties 2017-05-14 18:49:17 UTC (rev 21600) +++ trunk/Jmol/src/org/jmol/viewer/Jmol.properties 2017-05-14 19:04:52 UTC (rev 21601) @@ -55,8 +55,62 @@ # instead of the occupancies I tried to assign in jmol. -Jmol.___JmolVersion="14.15.4" // 2017-05-13 +Jmol.___JmolVersion="14.15.5" + +code: CIP: additional simplification; +code: CIP status: implementation complete, including: + All subrules implemented fully: 1a, 1b, 2, 3, 4a, 4b, 4c, 5 + R/S, E/Z, M/P, r/s, seqCis/seqTrans (as Z/E) + benzenoid (including fused benzenoid heteroaromatic) Mancude ring "Kekule weighted" atom number adjustments + proposed Rule 1b amendment: + A duplicate atom in a Kekule-weighted system is given a root distance equal to + its sphere, not the sphere of its duplicated atom. + +IUPAC Blue Book 2103 errors: + +,"147":"r,,,R,,,,r,,,S" // chiral phosphine -- disagrees with BB P-93.5.1.1.2 for S vs R +{ + "id" : "148" + "name_pname_pin" : "bis[(1r,4r)-4-methylcyclohexyl]phosphane" + "ref_pname_pin" : "P-93.5.1.1.2" + "stereo" : ",r,,,R,,,,r,,,R,,," + } + +,"148":"r,,,S,,,,r,,,R,,,,s,,,s" // r,,,S,,,,r,,,S,,,,s,,,S Jmol disagrees with BB P-93.5.1.1.2 or R and S p. 1243 +{ + "id" : "149" + "name_pname_pin" : "bis[(1r,4r)-4-methylcyclohexyl]-(1s,4s)-4-methylcyclohexylphosphane" + "ref_pname_pin" : "P-93.5.1.1.2" + "stereo" : ",r,,,S,,,,r,,,S,,,,s,,,S,,," + } + +,"202":"RR" // // p. 1265 disagrees with BB P-93.5.3.5 for RR vs. SS +{ + "id" : "203" + "name_pname_pin" : "(5S,8R,11S)-1,12-dioxatrispiro[4.2.2.4^{11}.2^{8}.2^{5}]nonadecane" + "ref_pname_pin" : "P-93 5.3.5" + } + +,"227":"SrSEErS" // disagrees with BB P-93.5.7.2 for S vs. r +{ + "id" : "228" + "name_pname_pin" : "(1E)-1-{(1'S,1r,4s)-[1,1'-bi(cyclohexan)]-3'-en-4-yl}-N-[(1r,4r)-4-phenylcyclohexyl]methan-1-imine" + "ref_pname_pin" : "P-93.5.7.2" + "stereo" : "S,,,,,,,r,S,,,,,,,E,,r,r,,,,,,,,,,,," + } + +,"230":"@3D RrRsR" // p 1282 disagrees with BB P-93.6 +{ + "id" : "231" + "name_pname_pin" : "(2R)-1-[(1r,4R)-4-methylcyclohexyl]-3-[(1s,4S)-4-methylcyclohexyl]propan-2-ol" + "ref_pname_pin" : "P-93.6" + "stereo" : ",,,,r,,,R,,,,s,,,R,,," + } + + +JmolVersion="14.15.4" // 2017-05-13 + bug fix: INVERTSELECTED ATOM not documented; functionality of INVERTSTEREO SELECTED folded into it, and INVERTSELECTED STEREO deprecated -- inverts ring or chain stereochemistry -- adds that keyword ATOM is optional, so INVERTSELECTED @2 works @@ -65,7 +119,7 @@ bug fix: CIP full implementation; simplified algorithm - 984 lines bug fix: CIP Rule 1b modification to ensure aromatic rings do not result in false positive for R/S (binap2) - -- specifically that the duplicate atom is given the root distance of its parent, not its duplicated atom + -- specifically that the duplicate atom is given a root distance equal to its sphere, not that of its duplicated atom bug fix: CIP chiral bridgehead N designations missing bug fix: CIP Assignment of auxiliary r/s not functional (AY-236.201,202) bug fix: CIP basic "mancude" atom number adjustment for heteroatoms This was sent by the SourceForge.net collaborative development platform, the world's largest Open Source development site. |