Use IUPAC for the internal residue and atom nomenclature

GoogleCodeExporter commented 9 years ago

Easy change from BMRB according to:

t is probably a good idea to have the cing internal nomenclature adhere to
IUPAC defs as much as we can (soem residues to not exists in IUPAC) before
we release it. So we should add a IUPAC definition in the dbTable and
update the INTERNAL one (rendering all the old projects unreadable!),
probably rename PDB to PDB2 to indicate the old format and set the default
for PDB reading to IUPAC.

I checked for the differences between BRMB (which we already have and is
close?? to IUPAC) and internal:

<ResidueDef ALA> <AtomDef HN> BMRB H
<ResidueDef ALA> <AtomDef QB> BMRB MB
<ResidueDef ARGx> <AtomDef HN> BMRB H
<ResidueDef ARG> <AtomDef HN> BMRB H
<ResidueDef ASN> <AtomDef HN> BMRB H
<ResidueDef ASN> <AtomDef QD2> BMRB QD
<ResidueDef ASPH> <AtomDef HN> BMRB H
<ResidueDef ASP> <AtomDef HN> BMRB H
<ResidueDef CYSS> <AtomDef HN> BMRB H
<ResidueDef CYS> <AtomDef HN> BMRB H
<ResidueDef GLN> <AtomDef HN> BMRB H
<ResidueDef GLN> <AtomDef QE2> BMRB QE
<ResidueDef GLUH> <AtomDef HN> BMRB H
<ResidueDef GLU> <AtomDef HN> BMRB H
<ResidueDef GLY> <AtomDef HN> BMRB H
<ResidueDef GLY> <AtomDef HA1> BMRB HA2
<ResidueDef GLY> <AtomDef HA2> BMRB HA3
<ResidueDef HIS> <AtomDef HN> BMRB H
<ResidueDef ILE> <AtomDef HN> BMRB H
<ResidueDef ILE> <AtomDef QG2> BMRB MG
<ResidueDef ILE> <AtomDef QG1> BMRB QG
<ResidueDef ILE> <AtomDef QD1> BMRB MD
<ResidueDef LEU> <AtomDef HN> BMRB H
<ResidueDef LEU> <AtomDef QD1> BMRB MD1
<ResidueDef LEU> <AtomDef QD2> BMRB MD2
<ResidueDef LEU> <AtomDef QQD> BMRB QD
<ResidueDef LYSx> <AtomDef HN> BMRB H
<ResidueDef LYS> <AtomDef HN> BMRB H
<ResidueDef MET> <AtomDef HN> BMRB H
<ResidueDef MET> <AtomDef QE> BMRB ME
<ResidueDef PHE> <AtomDef HN> BMRB H
<ResidueDef SER> <AtomDef HN> BMRB H
<ResidueDef THR> <AtomDef HN> BMRB H
<ResidueDef THR> <AtomDef QG2> BMRB MG
<ResidueDef TRP> <AtomDef HN> BMRB H
<ResidueDef TYR> <AtomDef HN> BMRB H
<ResidueDef VAL> <AtomDef HN> BMRB H
<ResidueDef VAL> <AtomDef QG1> BMRB MG1
<ResidueDef VAL> <AtomDef QG2> BMRB MG2
<ResidueDef VAL> <AtomDef QQG> BMRB QG
<ResidueDef ADE> <AtomDef H5"> BMRB H5''
<ResidueDef ADE> <AtomDef H2"> BMRB H2''
<ResidueDef RADE> <AtomDef H5"> BMRB H5''
<ResidueDef RADE> <AtomDef Q5'> BMRB Q5''
<ResidueDef CYT> <AtomDef H5"> BMRB H5''
<ResidueDef CYT> <AtomDef Q5'> BMRB Q5
<ResidueDef CYT> <AtomDef H2"> BMRB H2''
<ResidueDef CYT> <AtomDef Q2'> BMRB Q2
<ResidueDef RCYT> <AtomDef H5"> BMRB H5''
<ResidueDef GUA> <AtomDef H5"> BMRB H5''
<ResidueDef GUA> <AtomDef Q5'> BMRB Q4
<ResidueDef GUA> <AtomDef H2"> BMRB H2''
<ResidueDef RGUA> <AtomDef H5"> BMRB H5''
<ResidueDef RGUA> <AtomDef Q5'> BMRB Q5
<ResidueDef THY> <AtomDef H5"> BMRB H5''
<ResidueDef THY> <AtomDef Q5'> BMRB Q5
<ResidueDef THY> <AtomDef H2"> BMRB H2''
<ResidueDef THY> <AtomDef Q7> BMRB M7
<ResidueDef URA> <AtomDef H5"> BMRB H5''
<ResidueDef SS> <AtomDef HN> BMRB H
<ResidueDef CA2P> <AtomDef CA2P> BMRB CA

mainly HN, Gly and single-double-quote of DNA/RNA (which is a bit a mess
anyway).

and those without BMRB:

<ResidueDef HISE> <AtomDef N> no BMRB:
<ResidueDef HISE> <AtomDef HN> no BMRB:
<ResidueDef HISE> <AtomDef CA> no BMRB:
<ResidueDef HISE> <AtomDef HA> no BMRB:
<ResidueDef HISE> <AtomDef CB> no BMRB:
<ResidueDef HISE> <AtomDef HB2> no BMRB:
<ResidueDef HISE> <AtomDef HB3> no BMRB:
<ResidueDef HISE> <AtomDef QB> no BMRB:
<ResidueDef HISE> <AtomDef CG> no BMRB:
<ResidueDef HISE> <AtomDef ND1> no BMRB:
<ResidueDef HISE> <AtomDef CD2> no BMRB:
<ResidueDef HISE> <AtomDef HD2> no BMRB:
<ResidueDef HISE> <AtomDef NE2> no BMRB:
<ResidueDef HISE> <AtomDef CE1> no BMRB:
<ResidueDef HISE> <AtomDef HE1> no BMRB:
<ResidueDef HISE> <AtomDef HE2> no BMRB:
<ResidueDef HISE> <AtomDef C> no BMRB:
<ResidueDef HISE> <AtomDef O> no BMRB:
<ResidueDef HISH> <AtomDef N> no BMRB:
<ResidueDef HISH> <AtomDef HN> no BMRB:
<ResidueDef HISH> <AtomDef CA> no BMRB:
<ResidueDef HISH> <AtomDef HA> no BMRB:
<ResidueDef HISH> <AtomDef CB> no BMRB:
<ResidueDef HISH> <AtomDef HB2> no BMRB:
<ResidueDef HISH> <AtomDef HB3> no BMRB:
<ResidueDef HISH> <AtomDef QB> no BMRB:
<ResidueDef HISH> <AtomDef CG> no BMRB:
<ResidueDef HISH> <AtomDef ND1> no BMRB:
<ResidueDef HISH> <AtomDef CD2> no BMRB:
<ResidueDef HISH> <AtomDef HD1> no BMRB:
<ResidueDef HISH> <AtomDef CE1> no BMRB:
<ResidueDef HISH> <AtomDef NE2> no BMRB:
<ResidueDef HISH> <AtomDef HD2> no BMRB:
<ResidueDef HISH> <AtomDef HE1> no BMRB:
<ResidueDef HISH> <AtomDef HE2> no BMRB:
<ResidueDef HISH> <AtomDef C> no BMRB:
<ResidueDef HISH> <AtomDef O> no BMRB:
<ResidueDef PL> <AtomDef N> no BMRB:
<ResidueDef PL> <AtomDef Q1> no BMRB:
<ResidueDef PL> <AtomDef Q2> no BMRB:
<ResidueDef NL> <AtomDef P> no BMRB:
<ResidueDef NL> <AtomDef Q1> no BMRB:
<ResidueDef NL> <AtomDef Q2> no BMRB:
<ResidueDef LL> <AtomDef Q3> no BMRB:
<ResidueDef LL> <AtomDef Q1> no BMRB:
<ResidueDef LL> <AtomDef Q2> no BMRB:
<ResidueDef LL2> <AtomDef Q3> no BMRB:
<ResidueDef LL2> <AtomDef Q1> no BMRB:
<ResidueDef LL2> <AtomDef Q2> no BMRB:
<ResidueDef LL5> <AtomDef Q3> no BMRB:
<ResidueDef LL5> <AtomDef Q1> no BMRB:
<ResidueDef LL5> <AtomDef Q2> no BMRB:
<ResidueDef LP> <AtomDef Q3> no BMRB:
<ResidueDef LP> <AtomDef C> no BMRB:
<ResidueDef LP> <AtomDef O> no BMRB:
<ResidueDef LN> <AtomDef Q3> no BMRB:
<ResidueDef LN> <AtomDef C3'> no BMRB:
<ResidueDef LN> <AtomDef O3'> no BMRB:
<ResidueDef PLM> <AtomDef N> no BMRB:
<ResidueDef PLM> <AtomDef Q1> no BMRB:
<ResidueDef PLM> <AtomDef Q1'> no BMRB:
<ResidueDef PLM> <AtomDef Q2> no BMRB:
<ResidueDef PLM> <AtomDef Q2'> no BMRB:
<ResidueDef NLM> <AtomDef P> no BMRB:
<ResidueDef NLM> <AtomDef Q1> no BMRB:
<ResidueDef NLM> <AtomDef Q1'> no BMRB:
<ResidueDef NLM> <AtomDef Q2> no BMRB:
<ResidueDef NLM> <AtomDef Q2'> no BMRB:
<ResidueDef LLM> <AtomDef Q3> no BMRB:
<ResidueDef LLM> <AtomDef Q3'> no BMRB:
<ResidueDef LLM> <AtomDef Q1> no BMRB:
<ResidueDef LLM> <AtomDef Q1'> no BMRB:
<ResidueDef LLM> <AtomDef Q2> no BMRB:
<ResidueDef LLM> <AtomDef Q2'> no BMRB:
<ResidueDef LLM2> <AtomDef Q3> no BMRB:
<ResidueDef LLM2> <AtomDef Q3'> no BMRB:
<ResidueDef LLM2> <AtomDef Q1> no BMRB:
<ResidueDef LLM2> <AtomDef Q1'> no BMRB:
<ResidueDef LLM2> <AtomDef Q2> no BMRB:
<ResidueDef LLM2> <AtomDef Q2'> no BMRB:
<ResidueDef LLM5> <AtomDef Q3> no BMRB:
<ResidueDef LLM5> <AtomDef Q3'> no BMRB:
<ResidueDef LLM5> <AtomDef Q1> no BMRB:
<ResidueDef LLM5> <AtomDef Q1'> no BMRB:
<ResidueDef LLM5> <AtomDef Q2> no BMRB:
<ResidueDef LLM5> <AtomDef Q2'> no BMRB:
<ResidueDef LPM> <AtomDef Q3> no BMRB:
<ResidueDef LPM> <AtomDef Q3'> no BMRB:
<ResidueDef LPM> <AtomDef C> no BMRB:
<ResidueDef LPM> <AtomDef O> no BMRB:
<ResidueDef LNM> <AtomDef Q3> no BMRB:
<ResidueDef LNM> <AtomDef Q3'> no BMRB:
<ResidueDef LNM> <AtomDef C3'> no BMRB:
<ResidueDef LNM> <AtomDef O3'> no BMRB:
<ResidueDef LGLY> <AtomDef N> no BMRB:
<ResidueDef LGLY> <AtomDef Q1> no BMRB:
<ResidueDef LGLY> <AtomDef Q2> no BMRB:
<ResidueDef LGLY> <AtomDef Q21> no BMRB:
<ResidueDef LGLY> <AtomDef Q22> no BMRB:
<ResidueDef LGLY> <AtomDef Q3> no BMRB:
<ResidueDef LGLY> <AtomDef C> no BMRB:
<ResidueDef LGLY> <AtomDef O> no BMRB:
<ResidueDef CA2P> <AtomDef Q3> no BMRB:
<ResidueDef CA2P> <AtomDef Q3'> no BMRB:
<ResidueDef CA2P> <AtomDef Q1> no BMRB:
<ResidueDef CA2P> <AtomDef Q1'> no BMRB:
<ResidueDef CA2P> <AtomDef Q2> no BMRB:
<ResidueDef CA2P> <AtomDef Q2'> no BMRB:

Again, the HIS residue and of course the CYANA pseudoresidues and the
Calciums

I also would like synomyms implemented (e.g. HN for H). I still think H was
very poor choice as ALL other protons do have a heavy atom designator to
their name. Alas,

Original issue reported on code.google.com by jurge...@gmail.com on 14 May 2008 at 6:04

GoogleCodeExporter commented 9 years ago

Original comment by g.vuis...@gmail.com on 15 May 2008 at 9:42

Added labels: Priority-High
Removed labels: Priority-Medium

GoogleCodeExporter commented 9 years ago

Original comment by jurge...@gmail.com on 20 May 2008 at 12:03

Added labels: Component-CING

GoogleCodeExporter commented 9 years ago

- I also would like synomyms implemented (e.g. HN for H). I still think H was
Fixed now in code. Closing this old issue as we cover it elsewhere, right?

Original comment by jurge...@gmail.com on 17 Oct 2008 at 12:58

Changed state: Fixed

AlphaBetaTest / cing

Use IUPAC for the internal residue and atom nomenclature #41