Create a data file for residue/value mappings

[Barry Grant]

This would be called by aa2mass() and possibly aa321() and aa123().

File should be called resid.mat and contain "aa1", "aa3", and "aaMass" cols, It should be placed in the "bio3d/inst/matrices/" dir.

We then need to update the previously mentioned functions aa2mass() and possibly aa321() and aa123()*.

[Lars Skjærven]

I tried with a version in inst/matrices. Sure we shouldn't put in data/?

Also, I put previously atom.index.R and sdENM.RData in data/. Is this ok?

[Barry Grant]

Depends, if they are binary .rda or as I call them .RData files then put them in data/ if they are scripts, tables or text etc. put them matrices/ Does this not sound sensible?

[Lars Skjærven]

aa.mass was included some time ago for this purpose. it's looked up by aa2mass(), but not aa321 and aa123.

> aa.mass
    aa3 aa1  aaMass       formula                             name
ALA ALA   A  71.078    C3 H5 N O1                          Alanine
ARG ARG   R 157.194  C6 H13 N4 O1                         Arginine
ASN ASN   N 114.103   C4 H6 N2 O2                       Asparagine
ASP ASP   D 114.079    C4 H4 N O3                    Aspartic Acid
CYS CYS   C 103.143  C3 H5 N O1 S                          Cystein
GLN GLN   Q 117.126   C4 H9 N2 O2                        Glutamine
GLU GLU   E 128.106    C5 H6 N O3                    Glutamic Acid
GLY GLY   G  57.051    C2 H3 N O1                          Glycine
HIS HIS   H 137.139   C6 H7 N3 O1                        Histidine
ILE ILE   I 113.158   C6 H11 N O1                       Isoleucine
LEU LEU   L 113.158   C6 H11 N O1                          Leucine
LYS LYS   K 129.180  C6 H13 N2 O1                           Lysine
MET MET   M 131.196  C5 H9 N O1 S                       Methionine
PHE PHE   F 147.174    C9 H9 N O1                    Phenylalanine
PRO PRO   P  97.115    C5 H7 N O1                          Proline
SER SER   S  87.077    C3 H5 N O2                           Serine
THR THR   T 101.104    C4 H7 N O2                        Threonine
TRP TRP   W 186.210 C11 H10 N2 O1                       Tryptophan
TYR TYR   Y 163.173    C9 H9 N O2                         Tyrosine
VAL VAL   V  99.131    C5 H9 N O1                           Valine
ABA ABA   C  85.104   C4 H7 N1 O1          alpha-aminobutyric acid
ASH ASH   X 115.087    C4 H5 N O3            Aspartic acid Neutral
CME CME   C 179.260 C5 H9 N O2 S2 s,s-(2-hydroxyethyl)thiocysteine
CMT CMT   C 117.169  C4 H7 N O1 S                 o-methylcysteine
CSD CSD   C 133.126  C3 H3 N O3 S          s-cysteinesulfinic acid
CSO CSO   C 119.142  C3 H5 N O2 S                s-hydroxycysteine
CSW CSW   X 135.142  C3 H5 N O3 S               cysteine-s-dioxide
CSX CSX   C 119.142  C3 H5 N O2 S                   s-oxy cysteine
CYM CYM   C 102.135  C3 H4 N O1 S                 Cystein Negative
CYX CYX   C 102.135  C3 H4 N O1 S                   Cystein SSbond
GLH GLH   X 129.114    C5 H7 N O3           Glutatmic acid Neutral
HID HID   H 137.139   C6 H7 N3 O1                        Histidine
HIE HIE   H 137.139   C6 H7 N3 O1                        Histidine
HIP HIP   H 138.147   C6 H8 N3 O1               Histidine Positive
HSD HSD   H 137.139   C6 H7 N3 O1                        Histidine
HSE HSE   H 137.139   C6 H7 N3 O1                        Histidine
HSP HSP   H 138.147   C6 H8 N3 O1               Histidine Positive
IAS IAS   D 115.087    C4 H5 N O3                    beta-aspartyl
KCX KCX   X 172.182  C7 H12 N2 O3        lysine nz-carboxylic acid
LYN LYN   X 128.172  C6 H12 N2 O1                   Lysine Neutral
MHO MHO   M 147.195  C5 H9 N O2 S                  s-oxymethionine
MLY MLY   K 156.225  C8 H16 N2 O1                n-dimethyl-lysine
MSE MSE   M 131.196 C5 H9 N O1 SE                 selenomethionine
OCS OCS   X 169.156  C3 H7 N O5 S            cysteinesulfonic acid
PFF PFF   Y 165.164  C9 H8 F N O1         4-fluoro-l-phenylalanine
PTR PTR   X 243.153 C9 H10 N O5 P                o-phosphotyrosine
SEP SEP   S 167.057  C3 H6 N O5 P                    phosphoserine
TPO TPO   T 181.084  C4 H8 N O5 P                 phosphothreonine

[Barry Grant]

I guess they should all point to the same file/table. However, aa321 etc. are not broken currently so I sugest we just leave this migration on the back burner for whenever we next need to update for other reasons here. One reason to hold off is that for aa123 the table pasted above contains multiple "X" mapping to different residues where is shoukd rtn UNK I think

[Lars Skjærven]

right, but can map KCX to K, LYN to L, etc in this table? (as we apparently do here for TPO to T)

[Barry Grant]

Yes, if we want to use this for aa321() we should have KCX to K and all the other common non-standard modified residue mappings we have in aa321() currently.

Note that we can do the mapping of 3-to-1 like this but not uniquely the other way (1 to 3) unless we demand that only the first instance of a single amino acid code maps to the standard 3 letter version (i.e. H to HIS before H to HSD etc. (as it is in the pasted table in the earlier message)).

I see you have linked this issue to issue #82, for that are you proposing that atom.select() use this list of of protein resid's also in place of the hardcoded 'prot.aa' variable on line 71 of that function?

[Lars Skjærven]

The list of residue names should perhaps primarily be used for sequence stuff (e.g. mapping 321), while the VMD approach for atom.select(). We should anyway aim to have only one list of residue names which I was hoping would solve some of these issues, and at the same time be easier to maintain. In the current version there are three slightly deviating lists (atom.select, aa321/aa123, and table aa.mass).

[Barry Grant]

Lets start by using this list for atom.select() and 321 conversion. Migrating atom.select() to the VMD approach, which is based on atom names within a residue, will likely cause other issues. Having a single consistent list as you say will be an improvement.

[Lars Skjærven]

I think this is solved with the aa.table data file. aa321() has been updated