Re: [Open Babel] Tidying up files

Chris Morley Mon, 26 Nov 2012 04:53:26 -0800

Chris

My apologies also for the slow response.

OB will already read MDL files with abbreviations in the A (alias) line,like in the attached file. (But not in the S or R structures.) So


  obabel alias2.mol -O expanded2.mol -r

will expand the abbreviations and also remove all disconnected moleculesapart from the largest. Is this close to what you wanted?

The data (SMILES) to do the expansions in in /data/superatoms.txt. Onlyunivalent abbreviated groups are possible at the moment. There arecurrently about a hundred entries but the your list would expand thisconsiderably. Is there anybody who would like to add the additional entries?


Chris

On 25/11/2012 09:57, Chris Swain wrote:

Hi,

Here is a list of abbreviations I have compiled over the years.

Ac, Ace, Acetate, Acetyl, Acyl
AcAc acetoacetyl
ACN = acetonitrile
Ad = 1-adamantyl
Alloc, AOC = allyoxycarbonyl
All, Allyl

Bam = benzamidomethyl
BDMS = biphenyldimethylsilyl
BOC, Boc, t-boc = t-butoxycarbonyl
BOM = benzyloxymethyl
Bn, Benzyl
Bz, Benzoyl
Bromo
Bu, Butyl
Bs = Brosylate

Carboxy
Cbz, Z = benzyloxycarbonyl
CE, Cne = cyanoethyl
Cp = cyclopentadienyl
cinnamyl

Chloro

Dan, dansyl
DEM = diethoxyethyl
DEIPS = diethylisopropylsilyl
Dip = 2,6-diisopropylphenyl
Dmb = 2,4-dimethoxybenzyl
DNP = 2,4-dinitrophenyl
DPA = diphenylacetyl
DPhAc = diphenylacetyl
DTBMS = di-t-butylmethylsilyl


Ethyl
EE = ethoxyethyl
EOM = ethoxymethyl

Formyl, formate
FMOC, Fmoc = 9-fluorenylmethoxycarbonyl

HBn = 2-hydroxybenzyl
heptyl
hexyl

Iodo
IPDMS = Isopropyldimethylsilyl

Me, Methyl
MEM = 2-methoxyethoxymethyl
Mes, Mesityl = 2,4,6-trimethylphenyl
MOM = methoxymethyl
Ms, mesyl = methanesulphonyl

NBOM = nitrobenzyloxymethyl
Ns = p-nitrophenylsulphonyl
Nitro


PAB = p-aminobenzyl
Pentyl
Ph, Phe, Phenyl
PMB = p-methoxybenzyl
PMP = p-methoxyphenyl
Pv, pivaloyl

Proparyl
Propyl
Py = Pyridyl

SEM = 2-(trimethylsilyl)ethoxymethyl

THP = Tetrahydropyranyl
THF = tetrahydrofuranyl
TMS = Trimethylsilyl
TBDMS, TBS = t-butyldimethlysilyl
TBDPS = t-butyldiphenylsilyl
TES = Triethylsilyl
TF, triflyl = trifluoromethylsulphonyl
TFA = trifluoroacetyl
TIBS = trisopropylsilyl
Tol, p-Tolyl
Tos, Tosyl = Toluenesuphonyl
Tr, trityl = triphenylmethyl
Troc = 2,2,2 -trichloroethoxycarbonyl

vinyl
Voc = vinyloxycarbonyl

nEt, Pr, But, pent, hex, hept, oct, non
nEthyl, Propyl, Butyl, pentyl, hexyl, heptyl, octyl, nonyl
n-Et, Pr, But, pent, hex, hept, oct, non
n-Ethyl, Propyl, Butyl, pentyl, hexyl, heptyl, heptyl, octyl, nonyl

cPr, But, pent, hex, hept, oct, non
cPropyl, Butyl, pentyl, hexyl, heptyl,  octyl, nonyl
c-Pr, But, pent, hex, hept, oct, non
c-Propyl, Butyl, pentyl, hexyl, heptyl,  octyl, nonyl

iPro, Propyl
i-Pro, Propyl
iso-Pro, Propyl
s-But, Butyl
sec-But, Butyl

tBut, Butyl
t-But, Butyl


o, m,p ortho, meta, para

Cheers,

Chris



On 24 Nov 2012, at 20:55, Geoff Hutchison <ge...@geoffhutchison.net> wrote:

I often end up editing files using a text editor because they contain features 
that are not compatible with other programs. In particular removing salts 
and/or solvents and expanding fragment labels e.g TMS, t-butyl etc.


Sorry Chris -- a pile of things stopped me from getting back to this. I think 
it's a good idea.

Want to draft a list of what you'd like "tidy'ed?"

-Geoff



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  ACD/Labs11261212372D

 14 13  0  0  0  0  0  0  0  0  8 V2000
   14.1653  -10.2875    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   12.1463  -12.6751    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   12.9955  -11.5053    0.0000 N   0  3  0  0  0  0  0  0  0  0  0  0
    7.8839   -8.0441    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   10.6560  -13.2199    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   11.8720   -9.1578    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   11.8720  -10.4878    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   10.7201   -8.4928    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   10.7201  -11.1528    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    9.5683   -9.1578    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    9.5683  -10.4878    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   13.7967   -8.1563    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   14.1653  -12.4187    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   16.6170  -11.5534    0.0000 Cl  0  5  0  0  0  0  0  0  0  0  0  0
  7  6  1  0  0  0  0
  8  6  2  0  0  0  0
  9  7  2  0  0  0  0
 10  8  1  0  0  0  0
 11  9  1  0  0  0  0
 11 10  2  0  0  0  0
  6 12  1  0  0  0  0
  5  9  1  0  0  0  0
  4 10  1  0  0  0  0
  3  7  1  0  0  0  0
  2  3  1  0  0  0  0
  1  3  1  0  0  0  0
  3 13  1  0  0  0  0
M  CHG  2   3   1  14  -1
A    4
OAc
A    5
CN
A   12
COOEt
M  END

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Re: [Open Babel] Tidying up files

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