Talk:AtomSets

This page started by AngelHerraez, 5 June 2006. Initial clue came from Tim Driscoll, who pointed me to JmolConstants.java as the source for this information.

This needs an update and fixes (e.g. purine and pyrimidine seem to be based on structure, not IDs). Also, the current subsections are somewhat confusing. Maybe change them into

• by chemical structure
• by atom IDs

--AngelHerraez 18:05, 23 January 2010 (UTC)

Draft for 'carbohydrate' atom set

[AFL] = <fucose> obsolete, replaced with FUL
[AGC] = <glucose> obsolete, replaced with GLC
[AHR] = alpha-L-arabinofuranose
[ARA] = alpha-L-arabinopyranose
[ARB] = beta-L-arabinopyranose
[ASF] = 3-(butylsulfonyl)propanoic acid ##must be suppressed, not a carbohydrate
[BDF] = beta-D-fructopyranose  (see also FRU)
[BDR] = beta-D-ribofuranose
[BGC] = beta-D-glucopyranose  (see also GLC)
[BMA] = beta-D-mannopyranose  (see also MAN)
[CBI] = cellobiose
[CT3] = beta-cellotriose
[CTR] = cellotriose
[CTT] = cellotetraose
[FCA] = alpha-D-fucose  (see also FCB, FUC, FUL)
[FCB] = beta-D-fucose  (see also FCA, FUC, FUL)
[FRU] = beta-D-fructofuranose  (see also BDF)
[FUC] = alpha-L-fucose  (see also FCA, FCB, FUL)
[FUL] = beta-L-fucose  (see also FCA, FCB, FUC)
[GAL] = beta-D-galactopyranose  (see also GLA)
[GCU] = alpha-D-glucopyranuronic acid (glucuronic acid)
[GLA] = alpha-D-galactopyranose  (see also GAL)
[GLB] = <galactose> obsolete, replaced with GAL
[GLC] = alpha-D-glucopyranose  (see also BGC)
[GUP] = alpha-L-gulopyranose
[LAT] = beta-lactose
[LXC] = beta-L-xylopyranose
[MAB] = mannobiose
[MAL] = maltose
[MAN] = alpha-D-mannopyranose  (see also BMA)
[MLR] = maltotriose
[MTL] = D-mannitol
[MTT] = maltotetraose
[NAG] = N-acetylglucosamine = GlcNAc = 2-(acetylamino)-2-deoxy-beta-D-glucopyranose)
[NAM] = naphthylaminoalanine ##must be suppressed, not a carbohydrate
[RAA] = <rhamnose> obsolete, replaced with RAM
[RAM] = alpha-L-rhamnose
[RHA] = 6-deoxy-mannose-1'-phosphate
[RIB] = alpha-D-ribofuranose
[RIP] = beta-D-ribopyranose
[SOR] = D-glucitol = D-sorbitol
[SUC] = sucrose
[TRE] = trehalose
[XYL] = D-xylitol
[XYP] = beta-D-xylopyranose
[XYS] = alpha-D-xylopyranose

Not currently recognized by Jmol:

[A2G] = N-acetyl-alpha-D-galactosamine = GalNAc = 2-(acetylamino)-2-deoxy-alpha-D-galactopyranose  (see also NGA)
[NGA] = N-acetyl-beta-D-galactosamine = GalNAc = 2-(acetylamino)-2-deoxy-beta-D-galactopyranose  (see also A2G)
[NAN] = obsolete, replaced with SIA
[SIA] = 5-N-acetyl-alpha-D-neuraminic acid  (see also SLB)
[SLB] = 5-N-acetyl-beta-D-neuraminic acid  (see also SIA)

Contributors

AngelHerraez