Design considerations:

Definitions contained MolDef, ResidueDef, AtomDef, DihedralDef classes
Export to pyhton-readable code;
  Methods: printit()

Import/export of atom naming conventions from/to flat-atom table file is possible:
  to faciltate updating
  Methods: MolDef.importNameDefs( fileName )
           Moldef.exportNameDefs( fileName )

Internal naming is essential and cannot be changed easily
Internally now use CYANA nomenclature (from cyana.lib):
- closest to IUPAC but complete in its table,
- plus HN rather then H, and 'Q' rather then 'M' for methyls is preferable.
- Note that for Gly CYANA uses HA1,HA2 and BMRB uses HA2,HA3!! Other than that, the stereo
  nomenclature is the same (I think).

First atom table list generated from
  cyana.lib
  protein translation table of BMRB
  rna.pdb from BMRB
  dna.pdb from BMRB
Script: mkatomTable.py > file atomTable.def

Edited DNA/RNA entries atomTable.def manually

Used atomTable.def and cyana.lib data to generate first residueDefs database structure
Script: mkresidueDefs.py > residueDefs.py

* 24 Feb 2004:
Edited aa name defs for ARG+, GLU-, ASP-, HIST, HIS+ in atomTable.def

 py updateResidueDefs.py > tmp
 mv tmp residueDefs.py

* 24 Feb 2004:
Scripts used initially now in INITIAL_SCRIPTS directory


* To Do:
Clean-up referencing: everything follwing the NTstruct dictionary method
Nomenclature atoms DNA/RNA

20-25 Sep 2005
Restructuring using NTtree and saving to different file format.
1. Read residueDefs and converted to 'keyword format': dbTable.py
2. Redefined the MolDef, ResidueDef, AtomDef and DihedralDef classes; based on
   NTtree,
   used nameDict attribute to store the different names
3. File 'NTdb.py': contains classes and parser of dbTable.
   Yields NTdb as root of database
4. Conversion dictionaries initialised from nameDict entries of NTdb

Note that updating dict and list types requires first initialisation of the
NTdb-tree and then updating it. Otherwise, the changes are discarded as parsing
the dbTable involves blunt assignment of the corresponding attributes.

28 Nov 2005:
* dbTable now contains dbTable entry: update proprams that write this table.
* Using dbTableNew, added spin system SS

* Need to update initBMRB and initDynamo.

* Need to update Peaks class and routines depending on it:
exportPeaks2Xeasy, exportPeaks2sparky, updateResonancesFromPeaks .....

20-22 Jan 2006: implementing removing residue for Mark H.
* Chain.removeResidue
* Tree.removeChild
* Tree.youngerSiblings
* Tree.olderSiblings
* General rule: all refs using instances, strings only on initializing    ...


30 Jan 2006.
Included shifts info from BMRB using the addSHIFTS.py routine.
Residues CYSS, HIS+, HIST, and DNA/RNA are not yet included.

31 Jan 2006
Major overhaul of the dictonairy routines. Removed resNameTranslations,
atomNameTranslations, resNameTable, and resName2internal routine.
Now everything works from the residueDict and atomDict dictionaries.
Defined a LOOSE convention to allow for shortname or Partially caps
residue name translation
new routines:
translateAtomName, translateResidueName, NTdbGetResidue, NTdbGetAtom

31 Jan 2006
Added ION residue, to accomodate the Ca2+ in CBD structures.

23 Feb 2006:
When importing peaks from Xeasy, I now update the peak index with the
peakid from the original file

17 April 2007: fixed error in QE topology (was SD, should be CE)
18 April 2007: changed defs QR for PHE and TYR, now similar to VAL QQG and LEU QQD
24 May   2007: Reordered dihedrals for more useful output during validation:
               PHI, PSI, CHIs, OMEGA
               Introduced PRO PHI
               Renamed ILE CHI21 to CHI2
               Added cPRO residue, CB and CG shifts from Shubert et al,
               JBNMR 24, 149-54, 2002
                CYSS as CYS with HG removed
23 Jul    2007: Changed internal name HIST into HISE
 7 Sep    2007: Changed internal name ION to CA2P, included hetatm attribute for PDB
11 Sep    2007: Added properties attribute.
25 Sep    2007: Commented irrelevant dihedral of methyl containing residues:
                ALA CHI1; ILE CHI22, CHI31 ; LEU CHI31, CHI32; MET CHI4
                THR CHI22, renamed CHI21 to CHI2; VAL CHI21, CHI22
26 Sep    2007: Gave Cyana pseudo residues the cyanaPseudoResidue property
10 Oct    2007: OMEGA IUPAC
05 Dec    2007: Renamed NTdict to NTdict
19 Dec    2007: remapped BMRB nucleic acid residue names to reflect PDB;
                  added Zn, His HE2, with BMRB map. Added nucleic prop to n.a.
11 Apr    2008: Added Aqua mappings and improved others.
29 Apr    2008: Fixed entry HIS: removed HE2, now is prot HD1; deprot HE2
30 Apr    2008: Fixed entry HISH: nameDict = { ..., 'CYANA': 'HIS+', ...}
08 May    2008: Renamed RURA to URA
15 May    2008: Defined CE1 for BRMB, AQUA in HISE
20 May    2008: BRMB, AQUA atom names for HISH
01 Jun    2008: BRMB, AQUQ residue names for LYSx, ARGx

15 Jun 2008:
For changing INTERNAL format to IUPAC
- Need to use INTERNAL everywhere rather then 'INTERNAL': ccpn plugin needs adjustment (27 Sep 08: done)
- INTERNAL will map on 'INTERNAL0' string: allows for future changes ('INTERNAL1', 'INTERNAL2') etc.
- After update: Molecule._saveSequence, _saveStereoAssignments: CYANA->INTERNAL
- old cing projects will fail on restoring peaks, restraints, etc.
- For 'alias': implemented in Residue.addAtom; update Residue.mutate

18 Jul    2008: Removed quotes ("") from Q1' and Q2' of ZN2P

29 Jul 2008: change to IUPAC
- Removed HOH CYANA/CYANA2 defs (Cyana does not know waters)
- ZN2P CYANA/CYANA2 names are wrong: (Cyana only knows one ion type) => consequences for conversion from PDB
- Added HN,H and C,CO aliases
- removed CHI2 CYSS (currently undefined) and adjusted CG topology
- corrected HISE.HN: nameDict BMRB->H

- Ran script dbTableUpdate.290908
===> residue INTERNAL_0: ALA      IUPAC: ALA       CYANA2: ALA
IUPAC: MB        CYANA2: QB


===> residue INTERNAL_0: ARGx     IUPAC: ARG       CYANA2: None     ****


===> residue INTERNAL_0: ARG      IUPAC: ARG       CYANA2: ARG


===> residue INTERNAL_0: ASN      IUPAC: ASN       CYANA2: ASN
IUPAC: QD        CYANA2: QD2


===> residue INTERNAL_0: ASPH     IUPAC: ASP       CYANA2: None     ****


===> residue INTERNAL_0: ASP      IUPAC: ASP       CYANA2: ASP


===> residue INTERNAL_0: CYSS     IUPAC: CYS       CYANA2: CYSS     ****


===> residue INTERNAL_0: CYS      IUPAC: CYS       CYANA2: CYS


===> residue INTERNAL_0: GLN      IUPAC: GLN       CYANA2: GLN
IUPAC: QE        CYANA2: QE2


===> residue INTERNAL_0: GLUH     IUPAC: GLU       CYANA2: None     ****


===> residue INTERNAL_0: GLU      IUPAC: GLU       CYANA2: GLU


===> residue INTERNAL_0: GLY      IUPAC: GLY       CYANA2: GLY


===> residue INTERNAL_0: HISE     IUPAC: HIS       CYANA2: HIST     ****


===> residue INTERNAL_0: HISH     IUPAC: HIS       CYANA2: HIS      ****


===> residue INTERNAL_0: HIS      IUPAC: HIS       CYANA2: HIS


===> residue INTERNAL_0: ILE      IUPAC: ILE       CYANA2: ILE
IUPAC: MG        CYANA2: QG2
IUPAC: QG        CYANA2: QG1
IUPAC: MD        CYANA2: QD1


===> residue INTERNAL_0: LEU      IUPAC: LEU       CYANA2: LEU
IUPAC: MD1       CYANA2: QD1
IUPAC: MD2       CYANA2: QD2
IUPAC: QD        CYANA2: QQD


===> residue INTERNAL_0: LYSx     IUPAC: LYS       CYANA2: None     ****


===> residue INTERNAL_0: LYS      IUPAC: LYS       CYANA2: LYS


===> residue INTERNAL_0: MET      IUPAC: MET       CYANA2: MET
IUPAC: ME        CYANA2: QE


===> residue INTERNAL_0: PHE      IUPAC: PHE       CYANA2: PHE


===> residue INTERNAL_0: cPRO     IUPAC: PRO       CYANA2: cPRO     ****


===> residue INTERNAL_0: PRO      IUPAC: PRO       CYANA2: PRO


===> residue INTERNAL_0: SER      IUPAC: SER       CYANA2: SER


===> residue INTERNAL_0: THR      IUPAC: THR       CYANA2: THR
IUPAC: MG        CYANA2: QG2


===> residue INTERNAL_0: TRP      IUPAC: TRP       CYANA2: TRP


===> residue INTERNAL_0: TYR      IUPAC: TYR       CYANA2: TYR


===> residue INTERNAL_0: VAL      IUPAC: VAL       CYANA2: VAL
IUPAC: MG1       CYANA2: QG1
IUPAC: MG2       CYANA2: QG2
IUPAC: QG        CYANA2: QQG


===> residue INTERNAL_0: ADE      IUPAC: DA        CYANA2: ADE      ****
IUPAC: H5''      CYANA2: H5"
IUPAC: H2''      CYANA2: H2"


===> residue INTERNAL_0: RADE     IUPAC: A         CYANA2: RADE     ****
IUPAC: H5''      CYANA2: H5"


===> residue INTERNAL_0: CYT      IUPAC: DC        CYANA2: CYT      ****
IUPAC: H5''      CYANA2: H5"
IUPAC: H2''      CYANA2: H2"
IUPAC: Q2        CYANA2: Q2'


===> residue INTERNAL_0: RCYT     IUPAC: C         CYANA2: RCYT     ****
IUPAC: H5''      CYANA2: H5"


===> residue INTERNAL_0: GUA      IUPAC: DG        CYANA2: GUA      ****
IUPAC: H5''      CYANA2: H5"
IUPAC: H2''      CYANA2: H2"


===> residue INTERNAL_0: RGUA     IUPAC: G         CYANA2: RGUA     ****
IUPAC: H5''      CYANA2: H5"


===> residue INTERNAL_0: THY      IUPAC: DT        CYANA2: THY      ****
IUPAC: H5''      CYANA2: H5"
IUPAC: H2''      CYANA2: H2"
IUPAC: M7        CYANA2: Q7


===> residue INTERNAL_0: URA      IUPAC: U         CYANA2: URA      ****
IUPAC: H5''      CYANA2: H5"


===> residue INTERNAL_0: PL       IUPAC: None      CYANA2: PL       ****
IUPAC: None      CYANA2: N
IUPAC: None      CYANA2: Q1
IUPAC: None      CYANA2: Q2


===> residue INTERNAL_0: NL       IUPAC: None      CYANA2: NL       ****
IUPAC: None      CYANA2: P
IUPAC: None      CYANA2: Q1
IUPAC: None      CYANA2: Q2


===> residue INTERNAL_0: LL       IUPAC: None      CYANA2: LL       ****
IUPAC: None      CYANA2: Q3
IUPAC: None      CYANA2: Q1
IUPAC: None      CYANA2: Q2


===> residue INTERNAL_0: LL2      IUPAC: None      CYANA2: LL2      ****
IUPAC: None      CYANA2: Q3
IUPAC: None      CYANA2: Q1
IUPAC: None      CYANA2: Q2


===> residue INTERNAL_0: LL5      IUPAC: None      CYANA2: LL5      ****
IUPAC: None      CYANA2: Q3
IUPAC: None      CYANA2: Q1
IUPAC: None      CYANA2: Q2


===> residue INTERNAL_0: LP       IUPAC: None      CYANA2: LP       ****
IUPAC: None      CYANA2: Q3
IUPAC: None      CYANA2: C
IUPAC: None      CYANA2: O


===> residue INTERNAL_0: LN       IUPAC: None      CYANA2: LN       ****
IUPAC: None      CYANA2: Q3
IUPAC: None      CYANA2: C3'
IUPAC: None      CYANA2: O3'


===> residue INTERNAL_0: PLM      IUPAC: None      CYANA2: PLM      ****
IUPAC: None      CYANA2: N
IUPAC: None      CYANA2: Q1
IUPAC: None      CYANA2: Q1'
IUPAC: None      CYANA2: Q2
IUPAC: None      CYANA2: Q2'


===> residue INTERNAL_0: NLM      IUPAC: None      CYANA2: NLM      ****
IUPAC: None      CYANA2: P
IUPAC: None      CYANA2: Q1
IUPAC: None      CYANA2: Q1'
IUPAC: None      CYANA2: Q2
IUPAC: None      CYANA2: Q2'


===> residue INTERNAL_0: LLM      IUPAC: None      CYANA2: LLM      ****
IUPAC: None      CYANA2: Q3
IUPAC: None      CYANA2: Q3'
IUPAC: None      CYANA2: Q1
IUPAC: None      CYANA2: Q1'
IUPAC: None      CYANA2: Q2
IUPAC: None      CYANA2: Q2'


===> residue INTERNAL_0: LLM2     IUPAC: None      CYANA2: LLM2     ****
IUPAC: None      CYANA2: Q3
IUPAC: None      CYANA2: Q3'
IUPAC: None      CYANA2: Q1
IUPAC: None      CYANA2: Q1'
IUPAC: None      CYANA2: Q2
IUPAC: None      CYANA2: Q2'


===> residue INTERNAL_0: LLM5     IUPAC: None      CYANA2: LLM5     ****
IUPAC: None      CYANA2: Q3
IUPAC: None      CYANA2: Q3'
IUPAC: None      CYANA2: Q1
IUPAC: None      CYANA2: Q1'
IUPAC: None      CYANA2: Q2
IUPAC: None      CYANA2: Q2'


===> residue INTERNAL_0: LPM      IUPAC: None      CYANA2: LPM      ****
IUPAC: None      CYANA2: Q3
IUPAC: None      CYANA2: Q3'
IUPAC: None      CYANA2: C
IUPAC: None      CYANA2: O


===> residue INTERNAL_0: LNM      IUPAC: None      CYANA2: LNM      ****
IUPAC: None      CYANA2: Q3
IUPAC: None      CYANA2: Q3'
IUPAC: None      CYANA2: C3'
IUPAC: None      CYANA2: O3'


===> residue INTERNAL_0: LGLY     IUPAC: None      CYANA2: LGLY     ****
IUPAC: None      CYANA2: N
IUPAC: None      CYANA2: Q1
IUPAC: None      CYANA2: Q2
IUPAC: None      CYANA2: Q21
IUPAC: None      CYANA2: Q22
IUPAC: None      CYANA2: Q3
IUPAC: None      CYANA2: C
IUPAC: None      CYANA2: O


===> residue INTERNAL_0: SS       IUPAC: None      CYANA2: SS       ****


===> residue INTERNAL_0: CA2P     IUPAC: CA        CYANA2: ION      ****
IUPAC: CA        CYANA2: ME
IUPAC: None      CYANA2: Q3
IUPAC: None      CYANA2: Q3'
IUPAC: None      CYANA2: Q1
IUPAC: None      CYANA2: Q1'
IUPAC: None      CYANA2: Q2
IUPAC: None      CYANA2: Q2'


===> residue INTERNAL_0: ZN2P     IUPAC: ZN        CYANA2: ZN       ****
IUPAC: ZN        CYANA2: ME
IUPAC: None      CYANA2: Q3
IUPAC: None      CYANA2: Q3'
IUPAC: None      CYANA2: Q1
IUPAC: None      CYANA2: Q1'
IUPAC: None      CYANA2: Q2
IUPAC: None      CYANA2: Q2'


===> residue INTERNAL_0: HOH      IUPAC: HOH       CYANA2: None
IUPAC: O         CYANA2: None
IUPAC: H1        CYANA2: None
IUPAC: H2        CYANA2: None



===================================================================================
- Changing existing BMRB->IUPAC
- Changing existing INTERNAL->INTERNAL_0
- Adding INTERNAL_1 ResidueDefs:
  keep original residue names (manual check required)
- Adding INTERNAL_1 atomDefs:
  Use BMRB/IUPAC or CYANA2 if BMRB/IUPAC undefined
  Add CYANA2 names as alias if different from BMRB/IUPAC
===================================================================================

WARNING: DihedralDef.exportDef: <DihedralDef ALA.PHI> topology (-1,C) skipped translation
WARNING: DihedralDef.exportDef: <DihedralDef ALA.PSI> topology (1,N) skipped translation
WARNING: DihedralDef.exportDef: <DihedralDef ALA.OMEGA> topology (-1,CA) skipped translation
WARNING: DihedralDef.exportDef: <DihedralDef ALA.OMEGA> topology (-1,C) skipped translation
WARNING: AtomDef.exportDef: <AtomDef ALA.N> topology (-1,C) skipped translation
WARNING: AtomDef.exportDef: <AtomDef ALA.C> topology (1,N) skipped translation
WARNING: DihedralDef.exportDef: <DihedralDef ARGx.PHI> topology (-1,C) skipped translation
WARNING: DihedralDef.exportDef: <DihedralDef ARGx.PSI> topology (1,N) skipped translation
WARNING: DihedralDef.exportDef: <DihedralDef ARGx.OMEGA> topology (-1,CA) skipped translation
WARNING: DihedralDef.exportDef: <DihedralDef ARGx.OMEGA> topology (-1,C) skipped translation
WARNING: AtomDef.exportDef: <AtomDef ARGx.N> topology (-1,C) skipped translation
WARNING: AtomDef.exportDef: <AtomDef ARGx.C> topology (1,N) skipped translation
WARNING: DihedralDef.exportDef: <DihedralDef ARG.PHI> topology (-1,C) skipped translation
WARNING: DihedralDef.exportDef: <DihedralDef ARG.PSI> topology (1,N) skipped translation
WARNING: DihedralDef.exportDef: <DihedralDef ARG.OMEGA> topology (-1,CA) skipped translation
WARNING: DihedralDef.exportDef: <DihedralDef ARG.OMEGA> topology (-1,C) skipped translation
WARNING: AtomDef.exportDef: <AtomDef ARG.N> topology (-1,C) skipped translation
WARNING: AtomDef.exportDef: <AtomDef ARG.C> topology (1,N) skipped translation
WARNING: DihedralDef.exportDef: <DihedralDef ASN.PHI> topology (-1,C) skipped translation
WARNING: DihedralDef.exportDef: <DihedralDef ASN.PSI> topology (1,N) skipped translation
WARNING: DihedralDef.exportDef: <DihedralDef ASN.OMEGA> topology (-1,CA) skipped translation
WARNING: DihedralDef.exportDef: <DihedralDef ASN.OMEGA> topology (-1,C) skipped translation
WARNING: AtomDef.exportDef: <AtomDef ASN.N> topology (-1,C) skipped translation
WARNING: AtomDef.exportDef: <AtomDef ASN.C> topology (1,N) skipped translation
WARNING: DihedralDef.exportDef: <DihedralDef ASPH.PHI> topology (-1,C) skipped translation
WARNING: DihedralDef.exportDef: <DihedralDef ASPH.PSI> topology (1,N) skipped translation
WARNING: DihedralDef.exportDef: <DihedralDef ASPH.OMEGA> topology (-1,CA) skipped translation
WARNING: DihedralDef.exportDef: <DihedralDef ASPH.OMEGA> topology (-1,C) skipped translation
WARNING: AtomDef.exportDef: <AtomDef ASPH.N> topology (-1,C) skipped translation
WARNING: AtomDef.exportDef: <AtomDef ASPH.C> topology (1,N) skipped translation
WARNING: DihedralDef.exportDef: <DihedralDef ASP.PHI> topology (-1,C) skipped translation
WARNING: DihedralDef.exportDef: <DihedralDef ASP.PSI> topology (1,N) skipped translation
WARNING: DihedralDef.exportDef: <DihedralDef ASP.OMEGA> topology (-1,CA) skipped translation
WARNING: DihedralDef.exportDef: <DihedralDef ASP.OMEGA> topology (-1,C) skipped translation
WARNING: AtomDef.exportDef: <AtomDef ASP.N> topology (-1,C) skipped translation
WARNING: AtomDef.exportDef: <AtomDef ASP.C> topology (1,N) skipped translation
WARNING: DihedralDef.exportDef: <DihedralDef CYSS.PHI> topology (-1,C) skipped translation
WARNING: DihedralDef.exportDef: <DihedralDef CYSS.PSI> topology (1,N) skipped translation
WARNING: DihedralDef.exportDef: <DihedralDef CYSS.OMEGA> topology (-1,CA) skipped translation
WARNING: DihedralDef.exportDef: <DihedralDef CYSS.OMEGA> topology (-1,C) skipped translation
WARNING: AtomDef.exportDef: <AtomDef CYSS.N> topology (-1,C) skipped translation
WARNING: AtomDef.exportDef: <AtomDef CYSS.C> topology (1,N) skipped translation
WARNING: DihedralDef.exportDef: <DihedralDef CYS.PHI> topology (-1,C) skipped translation
WARNING: DihedralDef.exportDef: <DihedralDef CYS.PSI> topology (1,N) skipped translation
WARNING: DihedralDef.exportDef: <DihedralDef CYS.OMEGA> topology (-1,CA) skipped translation
WARNING: DihedralDef.exportDef: <DihedralDef CYS.OMEGA> topology (-1,C) skipped translation
WARNING: AtomDef.exportDef: <AtomDef CYS.N> topology (-1,C) skipped translation
WARNING: AtomDef.exportDef: <AtomDef CYS.C> topology (1,N) skipped translation
WARNING: DihedralDef.exportDef: <DihedralDef GLN.PHI> topology (-1,C) skipped translation
WARNING: DihedralDef.exportDef: <DihedralDef GLN.PSI> topology (1,N) skipped translation
WARNING: DihedralDef.exportDef: <DihedralDef GLN.OMEGA> topology (-1,CA) skipped translation
WARNING: DihedralDef.exportDef: <DihedralDef GLN.OMEGA> topology (-1,C) skipped translation
WARNING: AtomDef.exportDef: <AtomDef GLN.N> topology (-1,C) skipped translation
WARNING: AtomDef.exportDef: <AtomDef GLN.C> topology (1,N) skipped translation
WARNING: DihedralDef.exportDef: <DihedralDef GLUH.PHI> topology (-1,C) skipped translation
WARNING: DihedralDef.exportDef: <DihedralDef GLUH.PSI> topology (1,N) skipped translation
WARNING: DihedralDef.exportDef: <DihedralDef GLUH.OMEGA> topology (-1,CA) skipped translation
WARNING: DihedralDef.exportDef: <DihedralDef GLUH.OMEGA> topology (-1,C) skipped translation
WARNING: AtomDef.exportDef: <AtomDef GLUH.N> topology (-1,C) skipped translation
WARNING: AtomDef.exportDef: <AtomDef GLUH.C> topology (1,N) skipped translation
WARNING: DihedralDef.exportDef: <DihedralDef GLU.PHI> topology (-1,C) skipped translation
WARNING: DihedralDef.exportDef: <DihedralDef GLU.PSI> topology (1,N) skipped translation
WARNING: DihedralDef.exportDef: <DihedralDef GLU.OMEGA> topology (-1,CA) skipped translation
WARNING: DihedralDef.exportDef: <DihedralDef GLU.OMEGA> topology (-1,C) skipped translation
WARNING: AtomDef.exportDef: <AtomDef GLU.N> topology (-1,C) skipped translation
WARNING: AtomDef.exportDef: <AtomDef GLU.C> topology (1,N) skipped translation
WARNING: DihedralDef.exportDef: <DihedralDef GLY.PHI> topology (-1,C) skipped translation
WARNING: DihedralDef.exportDef: <DihedralDef GLY.PSI> topology (1,N) skipped translation
WARNING: DihedralDef.exportDef: <DihedralDef GLY.OMEGA> topology (-1,CA) skipped translation
WARNING: DihedralDef.exportDef: <DihedralDef GLY.OMEGA> topology (-1,C) skipped translation
WARNING: AtomDef.exportDef: <AtomDef GLY.N> topology (-1,C) skipped translation
WARNING: AtomDef.exportDef: <AtomDef GLY.C> topology (1,N) skipped translation
WARNING: DihedralDef.exportDef: <DihedralDef HISE.PHI> topology (-1,C) skipped translation
WARNING: DihedralDef.exportDef: <DihedralDef HISE.PSI> topology (1,N) skipped translation
WARNING: DihedralDef.exportDef: <DihedralDef HISE.OMEGA> topology (-1,CA) skipped translation
WARNING: DihedralDef.exportDef: <DihedralDef HISE.OMEGA> topology (-1,C) skipped translation
WARNING: AtomDef.exportDef: <AtomDef HISE.N> topology (-1,C) skipped translation
WARNING: AtomDef.exportDef: <AtomDef HISE.C> topology (1,N) skipped translation
WARNING: DihedralDef.exportDef: <DihedralDef HISH.PHI> topology (-1,C) skipped translation
WARNING: DihedralDef.exportDef: <DihedralDef HISH.PSI> topology (1,N) skipped translation
WARNING: DihedralDef.exportDef: <DihedralDef HISH.OMEGA> topology (-1,CA) skipped translation
WARNING: DihedralDef.exportDef: <DihedralDef HISH.OMEGA> topology (-1,C) skipped translation
WARNING: AtomDef.exportDef: <AtomDef HISH.N> topology (-1,C) skipped translation
WARNING: AtomDef.exportDef: <AtomDef HISH.C> topology (1,N) skipped translation
WARNING: DihedralDef.exportDef: <DihedralDef HIS.PHI> topology (-1,C) skipped translation
WARNING: DihedralDef.exportDef: <DihedralDef HIS.PSI> topology (1,N) skipped translation
WARNING: DihedralDef.exportDef: <DihedralDef HIS.OMEGA> topology (-1,CA) skipped translation
WARNING: DihedralDef.exportDef: <DihedralDef HIS.OMEGA> topology (-1,C) skipped translation
WARNING: AtomDef.exportDef: <AtomDef HIS.N> topology (-1,C) skipped translation
WARNING: AtomDef.exportDef: <AtomDef HIS.C> topology (1,N) skipped translation
WARNING: DihedralDef.exportDef: <DihedralDef ILE.PHI> topology (-1,C) skipped translation
WARNING: DihedralDef.exportDef: <DihedralDef ILE.PSI> topology (1,N) skipped translation
WARNING: DihedralDef.exportDef: <DihedralDef ILE.OMEGA> topology (-1,CA) skipped translation
WARNING: DihedralDef.exportDef: <DihedralDef ILE.OMEGA> topology (-1,C) skipped translation
WARNING: AtomDef.exportDef: <AtomDef ILE.N> topology (-1,C) skipped translation
WARNING: AtomDef.exportDef: <AtomDef ILE.C> topology (1,N) skipped translation
WARNING: DihedralDef.exportDef: <DihedralDef LEU.PHI> topology (-1,C) skipped translation
WARNING: DihedralDef.exportDef: <DihedralDef LEU.PSI> topology (1,N) skipped translation
WARNING: DihedralDef.exportDef: <DihedralDef LEU.OMEGA> topology (-1,CA) skipped translation
WARNING: DihedralDef.exportDef: <DihedralDef LEU.OMEGA> topology (-1,C) skipped translation
WARNING: AtomDef.exportDef: <AtomDef LEU.N> topology (-1,C) skipped translation
WARNING: AtomDef.exportDef: <AtomDef LEU.C> topology (1,N) skipped translation
WARNING: DihedralDef.exportDef: <DihedralDef LYSx.PHI> topology (-1,C) skipped translation
WARNING: DihedralDef.exportDef: <DihedralDef LYSx.PSI> topology (1,N) skipped translation
WARNING: DihedralDef.exportDef: <DihedralDef LYSx.OMEGA> topology (-1,CA) skipped translation
WARNING: DihedralDef.exportDef: <DihedralDef LYSx.OMEGA> topology (-1,C) skipped translation
WARNING: AtomDef.exportDef: <AtomDef LYSx.N> topology (-1,C) skipped translation
WARNING: AtomDef.exportDef: <AtomDef LYSx.C> topology (1,N) skipped translation
WARNING: DihedralDef.exportDef: <DihedralDef LYS.PHI> topology (-1,C) skipped translation
WARNING: DihedralDef.exportDef: <DihedralDef LYS.PSI> topology (1,N) skipped translation
WARNING: DihedralDef.exportDef: <DihedralDef LYS.OMEGA> topology (-1,CA) skipped translation
WARNING: DihedralDef.exportDef: <DihedralDef LYS.OMEGA> topology (-1,C) skipped translation
WARNING: AtomDef.exportDef: <AtomDef LYS.N> topology (-1,C) skipped translation
WARNING: AtomDef.exportDef: <AtomDef LYS.C> topology (1,N) skipped translation
WARNING: DihedralDef.exportDef: <DihedralDef MET.PHI> topology (-1,C) skipped translation
WARNING: DihedralDef.exportDef: <DihedralDef MET.PSI> topology (1,N) skipped translation
WARNING: DihedralDef.exportDef: <DihedralDef MET.OMEGA> topology (-1,CA) skipped translation
WARNING: DihedralDef.exportDef: <DihedralDef MET.OMEGA> topology (-1,C) skipped translation
WARNING: AtomDef.exportDef: <AtomDef MET.N> topology (-1,C) skipped translation
WARNING: AtomDef.exportDef: <AtomDef MET.C> topology (1,N) skipped translation
WARNING: DihedralDef.exportDef: <DihedralDef PHE.PHI> topology (-1,C) skipped translation
WARNING: DihedralDef.exportDef: <DihedralDef PHE.PSI> topology (1,N) skipped translation
WARNING: DihedralDef.exportDef: <DihedralDef PHE.OMEGA> topology (-1,CA) skipped translation
WARNING: DihedralDef.exportDef: <DihedralDef PHE.OMEGA> topology (-1,C) skipped translation
WARNING: AtomDef.exportDef: <AtomDef PHE.N> topology (-1,C) skipped translation
WARNING: AtomDef.exportDef: <AtomDef PHE.C> topology (1,N) skipped translation
WARNING: DihedralDef.exportDef: <DihedralDef cPRO.PHI> topology (-1,C) skipped translation
WARNING: DihedralDef.exportDef: <DihedralDef cPRO.PSI> topology (1,N) skipped translation
WARNING: DihedralDef.exportDef: <DihedralDef cPRO.OMEGA> topology (-1,CA) skipped translation
WARNING: DihedralDef.exportDef: <DihedralDef cPRO.OMEGA> topology (-1,C) skipped translation
WARNING: AtomDef.exportDef: <AtomDef cPRO.N> topology (-1,C) skipped translation
WARNING: AtomDef.exportDef: <AtomDef cPRO.C> topology (1,N) skipped translation
WARNING: DihedralDef.exportDef: <DihedralDef PRO.PHI> topology (-1,C) skipped translation
WARNING: DihedralDef.exportDef: <DihedralDef PRO.PSI> topology (1,N) skipped translation
WARNING: DihedralDef.exportDef: <DihedralDef PRO.OMEGA> topology (-1,CA) skipped translation
WARNING: DihedralDef.exportDef: <DihedralDef PRO.OMEGA> topology (-1,C) skipped translation
WARNING: AtomDef.exportDef: <AtomDef PRO.N> topology (-1,C) skipped translation
WARNING: AtomDef.exportDef: <AtomDef PRO.C> topology (1,N) skipped translation
WARNING: DihedralDef.exportDef: <DihedralDef SER.PHI> topology (-1,C) skipped translation
WARNING: DihedralDef.exportDef: <DihedralDef SER.PSI> topology (1,N) skipped translation
WARNING: DihedralDef.exportDef: <DihedralDef SER.OMEGA> topology (-1,CA) skipped translation
WARNING: DihedralDef.exportDef: <DihedralDef SER.OMEGA> topology (-1,C) skipped translation
WARNING: AtomDef.exportDef: <AtomDef SER.N> topology (-1,C) skipped translation
WARNING: AtomDef.exportDef: <AtomDef SER.C> topology (1,N) skipped translation
WARNING: DihedralDef.exportDef: <DihedralDef THR.PHI> topology (-1,C) skipped translation
WARNING: DihedralDef.exportDef: <DihedralDef THR.PSI> topology (1,N) skipped translation
WARNING: DihedralDef.exportDef: <DihedralDef THR.OMEGA> topology (-1,CA) skipped translation
WARNING: DihedralDef.exportDef: <DihedralDef THR.OMEGA> topology (-1,C) skipped translation
WARNING: AtomDef.exportDef: <AtomDef THR.N> topology (-1,C) skipped translation
WARNING: AtomDef.exportDef: <AtomDef THR.C> topology (1,N) skipped translation
WARNING: DihedralDef.exportDef: <DihedralDef TRP.PHI> topology (-1,C) skipped translation
WARNING: DihedralDef.exportDef: <DihedralDef TRP.PSI> topology (1,N) skipped translation
WARNING: DihedralDef.exportDef: <DihedralDef TRP.OMEGA> topology (-1,CA) skipped translation
WARNING: DihedralDef.exportDef: <DihedralDef TRP.OMEGA> topology (-1,C) skipped translation
WARNING: AtomDef.exportDef: <AtomDef TRP.N> topology (-1,C) skipped translation
WARNING: AtomDef.exportDef: <AtomDef TRP.C> topology (1,N) skipped translation
WARNING: DihedralDef.exportDef: <DihedralDef TYR.PHI> topology (-1,C) skipped translation
WARNING: DihedralDef.exportDef: <DihedralDef TYR.PSI> topology (1,N) skipped translation
WARNING: DihedralDef.exportDef: <DihedralDef TYR.OMEGA> topology (-1,CA) skipped translation
WARNING: DihedralDef.exportDef: <DihedralDef TYR.OMEGA> topology (-1,C) skipped translation
WARNING: AtomDef.exportDef: <AtomDef TYR.N> topology (-1,C) skipped translation
WARNING: AtomDef.exportDef: <AtomDef TYR.C> topology (1,N) skipped translation
WARNING: DihedralDef.exportDef: <DihedralDef VAL.PHI> topology (-1,C) skipped translation
WARNING: DihedralDef.exportDef: <DihedralDef VAL.PSI> topology (1,N) skipped translation
WARNING: DihedralDef.exportDef: <DihedralDef VAL.OMEGA> topology (-1,CA) skipped translation
WARNING: DihedralDef.exportDef: <DihedralDef VAL.OMEGA> topology (-1,C) skipped translation
WARNING: AtomDef.exportDef: <AtomDef VAL.N> topology (-1,C) skipped translation
WARNING: AtomDef.exportDef: <AtomDef VAL.C> topology (1,N) skipped translation
WARNING: DihedralDef.exportDef: <DihedralDef ADE.EPSI> topology (1,P) skipped translation
WARNING: DihedralDef.exportDef: <DihedralDef ADE.ALPHA> topology (-1,O3') skipped translation
WARNING: DihedralDef.exportDef: <DihedralDef ADE.ZETA> topology (-1,C3') skipped translation
WARNING: DihedralDef.exportDef: <DihedralDef ADE.ZETA> topology (-1,O3') skipped translation
WARNING: AtomDef.exportDef: <AtomDef ADE.P> topology (-1,O3') skipped translation
WARNING: AtomDef.exportDef: <AtomDef ADE.O3'> topology (1,P) skipped translation
WARNING: DihedralDef.exportDef: <DihedralDef RADE.EPSI> topology (1,P) skipped translation
WARNING: DihedralDef.exportDef: <DihedralDef RADE.ALPHA> topology (-1,O3') skipped translation
WARNING: DihedralDef.exportDef: <DihedralDef RADE.ZETA> topology (-1,C3') skipped translation
WARNING: DihedralDef.exportDef: <DihedralDef RADE.ZETA> topology (-1,O3') skipped translation
WARNING: AtomDef.exportDef: <AtomDef RADE.P> topology (-1,O3') skipped translation
WARNING: AtomDef.exportDef: <AtomDef RADE.O3'> topology (1,P) skipped translation
WARNING: DihedralDef.exportDef: <DihedralDef CYT.EPSI> topology (1,P) skipped translation
WARNING: DihedralDef.exportDef: <DihedralDef CYT.ALPHA> topology (-1,O3') skipped translation
WARNING: DihedralDef.exportDef: <DihedralDef CYT.ZETA> topology (-1,C3') skipped translation
WARNING: DihedralDef.exportDef: <DihedralDef CYT.ZETA> topology (-1,O3') skipped translation
WARNING: AtomDef.exportDef: <AtomDef CYT.P> topology (-1,O3') skipped translation
WARNING: AtomDef.exportDef: <AtomDef CYT.O3'> topology (1,P) skipped translation
WARNING: DihedralDef.exportDef: <DihedralDef RCYT.EPSI> topology (1,P) skipped translation
WARNING: DihedralDef.exportDef: <DihedralDef RCYT.ALPHA> topology (-1,O3') skipped translation
WARNING: DihedralDef.exportDef: <DihedralDef RCYT.ZETA> topology (-1,C3') skipped translation
WARNING: DihedralDef.exportDef: <DihedralDef RCYT.ZETA> topology (-1,O3') skipped translation
WARNING: AtomDef.exportDef: <AtomDef RCYT.P> topology (-1,O3') skipped translation
WARNING: AtomDef.exportDef: <AtomDef RCYT.O3'> topology (1,P) skipped translation
WARNING: DihedralDef.exportDef: <DihedralDef GUA.EPSI> topology (1,P) skipped translation
WARNING: DihedralDef.exportDef: <DihedralDef GUA.ALPHA> topology (-1,O3') skipped translation
WARNING: DihedralDef.exportDef: <DihedralDef GUA.ZETA> topology (-1,C3') skipped translation
WARNING: DihedralDef.exportDef: <DihedralDef GUA.ZETA> topology (-1,O3') skipped translation
WARNING: AtomDef.exportDef: <AtomDef GUA.P> topology (-1,O3') skipped translation
WARNING: AtomDef.exportDef: <AtomDef GUA.O3'> topology (1,P) skipped translation
WARNING: DihedralDef.exportDef: <DihedralDef RGUA.EPSI> topology (1,P) skipped translation
WARNING: DihedralDef.exportDef: <DihedralDef RGUA.ALPHA> topology (-1,O3') skipped translation
WARNING: DihedralDef.exportDef: <DihedralDef RGUA.ZETA> topology (-1,C3') skipped translation
WARNING: DihedralDef.exportDef: <DihedralDef RGUA.ZETA> topology (-1,O3') skipped translation
WARNING: AtomDef.exportDef: <AtomDef RGUA.P> topology (-1,O3') skipped translation
WARNING: AtomDef.exportDef: <AtomDef RGUA.O3'> topology (1,P) skipped translation
WARNING: DihedralDef.exportDef: <DihedralDef THY.EPSI> topology (1,P) skipped translation
WARNING: DihedralDef.exportDef: <DihedralDef THY.ALPHA> topology (-1,O3') skipped translation
WARNING: DihedralDef.exportDef: <DihedralDef THY.ZETA> topology (-1,C3') skipped translation
WARNING: DihedralDef.exportDef: <DihedralDef THY.ZETA> topology (-1,O3') skipped translation
WARNING: AtomDef.exportDef: <AtomDef THY.P> topology (-1,O3') skipped translation
WARNING: AtomDef.exportDef: <AtomDef THY.O3'> topology (1,P) skipped translation
WARNING: DihedralDef.exportDef: <DihedralDef URA.EPSI> topology (1,P) skipped translation
WARNING: DihedralDef.exportDef: <DihedralDef URA.ALPHA> topology (-1,O3') skipped translation
WARNING: DihedralDef.exportDef: <DihedralDef URA.ZETA> topology (-1,C3') skipped translation
WARNING: DihedralDef.exportDef: <DihedralDef URA.ZETA> topology (-1,O3') skipped translation
WARNING: AtomDef.exportDef: <AtomDef URA.P> topology (-1,O3') skipped translation
WARNING: AtomDef.exportDef: <AtomDef URA.O3'> topology (1,P) skipped translation
WARNING: DihedralDef.exportDef: <DihedralDef PL.LB> topology (-1,O) skipped translation
WARNING: DihedralDef.exportDef: <DihedralDef NL.LB> topology (-1,O3') skipped translation
WARNING: DihedralDef.exportDef: <DihedralDef LL.LB> topology (-1,Q2) skipped translation
WARNING: DihedralDef.exportDef: <DihedralDef LL2.LB> topology (-1,Q2) skipped translation
WARNING: DihedralDef.exportDef: <DihedralDef LL5.LB> topology (-1,Q2) skipped translation
WARNING: DihedralDef.exportDef: <DihedralDef LP.LB> topology (-1,Q2) skipped translation
WARNING: DihedralDef.exportDef: <DihedralDef LN.LB> topology (-1,Q2) skipped translation
WARNING: DihedralDef.exportDef: <DihedralDef PLM.LB> topology (-1,O) skipped translation
WARNING: DihedralDef.exportDef: <DihedralDef NLM.LB> topology (-1,O3') skipped translation
WARNING: DihedralDef.exportDef: <DihedralDef LLM.LB> topology (-1,Q2) skipped translation
WARNING: DihedralDef.exportDef: <DihedralDef LLM2.LB> topology (-1,Q2) skipped translation
WARNING: DihedralDef.exportDef: <DihedralDef LLM5.LB> topology (-1,Q2) skipped translation
WARNING: DihedralDef.exportDef: <DihedralDef LPM.LB> topology (-1,Q2) skipped translation
WARNING: DihedralDef.exportDef: <DihedralDef LNM.LB> topology (-1,Q2) skipped translation
WARNING: DihedralDef.exportDef: <DihedralDef LGLY.PHI> topology (-1,C) skipped translation
WARNING: DihedralDef.exportDef: <DihedralDef LGLY.PSI> topology (1,N) skipped translation
WARNING: DihedralDef.exportDef: <DihedralDef LGLY.OMEGA> topology (-1,CA) skipped translation
WARNING: DihedralDef.exportDef: <DihedralDef LGLY.OMEGA> topology (-1,C) skipped translation
WARNING: DihedralDef.exportDef: <DihedralDef SS.PHI> topology (-1,C) skipped translation
WARNING: DihedralDef.exportDef: <DihedralDef SS.PSI> topology (1,N) skipped translation
WARNING: DihedralDef.exportDef: <DihedralDef SS.OMEGA> topology (-1,CA) skipped translation
WARNING: DihedralDef.exportDef: <DihedralDef SS.OMEGA> topology (-1,C) skipped translation
WARNING: AtomDef.exportDef: <AtomDef SS.N> topology (-1,C) skipped translation
WARNING: AtomDef.exportDef: <AtomDef SS.C> topology (1,N) skipped translation
WARNING: DihedralDef.exportDef: <DihedralDef CA2P.LB> topology (-1,Q2) skipped translation
WARNING: DihedralDef.exportDef: <DihedralDef ZN2P.LB> topology (-1,Q2) skipped translation

- Saved results as dbTable.INTERNAL_0
- Manually edited nucleic acid names
- Manually edited the errors with aliases for Cys residues

- Ran mkDbTable to generate dbTable.INTERNAL_1


- 15 Jan 2009:
Added QH pseudo-atom to HOH residue

- 29 Jul 2009:
Changed to sml description of residues.

- 2 Jan 2011
Updated INTERNAL_1 directory using mkINTERNAL_1.py script
Changed to INTERNAL_1 definitions

- 8 Jan 2013 WGT
Updated Xplor N-terminal and C-terminal name conventions using updateXplorConv script
N-terminal H1/2/3 changed to HT1/2/3
C-terminal O changed to OT1
C-terminal OXT changed to OT2 
