Template Tool Key Shortcuts

Development Design & Interface
1

Previous discussion was found in this thread

I put together a table - starting with ChemDraw shortcuts and adding some that made sense to me (e.g. typing c# gives you a straight-chain alkyl because those are a pain). Also for some reason ChemDraw doesn’t have a nitrile / cyano group and for mysterious reasons a t-butyl group is “K” rather than “t”.

Other common groups that I missed?

Key Name Key Name Key Name Key Name
a phenyl A acyl 1
b Br B BH2 2 carbonyl
c methyl C Cl 3 phenyl
d deuterium D 4
e ethyl E CO2Me ester 5
f fluorine F CF3 6 cyclohexane
g G 7 cyclopentane
h hydrogen H Cbz 8 -C=CH2
i iodine I isopropyl 9 isopropyl
j J 0 methyl
k sulfone SO2-CH3 K t-butyl
l Cl L Li cn nitrile / cyano nc isocyano
m methyl M MgBr no nitroso ep epoxide
n NH2 N NO2 im imine
o OH O OMe so sulfoxide
p PH2 P phenyl cs C=S thiocarbonyl
q OH Q FMoc nn N=N azo
r R n3 N3 azide
s SH S SiH3
t t-butyl T c2 ethyl Rings
u cyclobutane U c3 propyl C3 cyclopropyl
v cyclopropane V c4 butyl C4 cyclobutyl
w NH2 W c5 pentyl C5 cyclopentyl
x X c6 hexyl C6 cyclohexyl
y Boc Y … etc. …
z ≡CH Z N3 c0 decyl C0 cyclodecyl
  • deuterium is currently ignored because I haven’t added isotope support.
2

Here are some suggestions for common ligands. Ideally I’d like to keep these to 3-4 characters?

I guess in light of previous discussions, keeping single-atom ligands like F, Cl, Br, etc. should also be retained.

Other suggestions?

Abbrev. Ligand Abbrev. Ligand Abbrev. Ligand
n ammonia en ethylenediamine edta EDTA
a / o aqua ox oxalate
co carbonyl bpy bipyiridine e2 \eta^2 ethylene
cn cyano acac acetylacetonate e3 \eta^3 allyl
nc isocyano dmpe dimethylphosphinoethane e4 \eta^4 cyclo-octadiene
ncs isothiocyano dppe diphenylphosphinoethane e5 / cp \eta^5 cyclopentadienyl
p phosphine phen phenanthrolene e6 \eta^6 benzene
s thiol
scn thiocyano tpy terpyridine
porph porphin
phth phthalocyanine
salen salen
3

And part of my reason for making the tables is to insert into the documentation. :slight_smile:

4

E.g., dmg (dimethylglyoxime), pc (phthalocyanine), por (porphyrin).

5

I’ve been doing quite a lot of thinking on this because I think it could be a really nice interface and powerfully enabling. Big wall of text so for the TL;DR skip to the tables that summarize my proposal…

My general thoughts first of all:

  • I like the fact that shortcuts are generally mirrored between the groups and ligands, and I think that’s a good principle to stick to

  • While taking the ChemDraw hotkeys as a starting point is good, I think we shouldn’t be afraid to change it to make it more sensible – just as you suggested yourself

  • I think we should at minimum get rid of the various cases of redundancy, even if that means diverging from ChemDraw

  • I think we should avoid overriding the meaning of the hotkeys for the Draw Tool i.e. the element symbols – at least for the single letters and common double letters

  • We should stick to fragments/radicals rather than saturated molecules. So don’t have a hotkey for cyclohexane, just have cyclohexyl. Ideally they wouldn’t even be available in the groups selection. This keeps it more conceptually consistent and clear, and therefore predictable, for the user.

    • Note that actually the current behaviour of Avogadro already works perfectly for this principle: clicking on an atom replaces the atom with that fragment, while clicking on empty space creates the fragment with an extra hydrogen atom, so for example, adding an phenyl fragment to empty space creates benzene.

So, to cut redundancy in groups:

  • Keep l for Cl, lose C (prefer the easier to type and more commonly used of the two ChemDraw hotkeys)
  • Keep o for OH, lose q
  • Keep n for NH2, lose w
  • Keep a for Ph, lose 3 and P (so that it can be used for phosphorus, see below)
  • Keep c for methyl by analogy with the other organic elements, but put it at c1 too for consistency (my single exception to my anti-redundancy stance), drop 0 and m
  • Similarly, drop e for ethyl
  • Keep I for iPr, drop 9
  • Maybe keep K for tBu to match ChemDraw and drop the other two options
  • This means we can then use T for Troc
  • Drop u and v for cyclobutane/-propane
  • We should pick just one of the azide shortcuts – I favour n3 because then it matches the alkyl chains nicely

My further proposals for groups:

  • Keep the numerical keys free for now, as it’d be very useful to have them available to the user to set custom hotkeys in future
  • Use c# for the complete range of straight-chain alkyl groups methyl through dodecyl (extend the range)
  • It’s fine to use C# for the complete range of cycloalkyl groups starting at cyclopropyl, but have y# as an alternative because it is easier to type (no shift release between the letter and number)
  • Move vinyl to V
  • Move acetylenyl to W so that it’s paired with vinyl and the two can be remembered as number of bonds = number of vertical lines in the letter
  • Move carbonyl to co so it’s consistent with no and so
  • Make capital O OOH, and in general have shift + organic element letters be an oxidized form
  • Move silicon to z so that S and Si can each have oxidized forms with shift
  • Move bromine to r since it’s unused, and have b as boron so that it can have an oxidized form with shift
  • Move Li to li so that it matches the Draw Tool
  • Extend the f/F for F/CF3 to the other halogens, and to deuterium (even though it’s not yet implemented)
  • I would suggest some extra protecting groups such as Bn/Bz, Ms/Ts/Ns/Tf

This would be the result:

Single stroke

Key Name Key Name
a phenyl A acyl
b BH2 B B(OH)2
c CH3 C CH2OH
d D D CD3
e E
f fluorine F CF3
g G
h (hydrogen) H Cbz
i iodine I isopropyl
j J
k (potassium) K tert-butyl
l chlorine L CCl3
m M MgBr
n NH2 N NHOH
o OH O OOH
p PH2 P P(OH)2
q Q FMoc
r bromine R CBr3
s SH S SSH
t T Troc
u (uranium) U
v (vanadium) V –C=CH2
w (tungsten) W –C≡CH
x X
y (yttrium) Y Boc
z SiH3 Z Si(OH)3

2-stroke carbon chains and rings

Key Name Key Name
c1 methyl
c2 ethyl
c3 propyl C3 or y3 cyclopropyl
c4 butyl C4 or y4 cyclobutyl
c5 pentyl C5 or y5 cyclopentyl
c6 hexyl C6 or y6 cyclohexyl
… etc. …
c10 or c0 decyl C10/C0/y10/y0 cyclodecyl
c11 undecyl C11 or y11 cycloundecyl
c12 dodecyl C12 or y12 cyclododecyl

Organic functional groups

Combo Formula Name Combo Formula Name
co C(=O)H carbonyl CO C(=O)OH carboxylic acid
no N=O nitroso NO NO2 nitro
so S(=O)H sulfoxide
cn CH=NH imine CN C≡N cyano/nitrile
nc N=CH2 imine NC N≡C isocyano/isonitrile
cs C(=S)H thiocarbonyl
nn N=NH azo

Miscellaneous 2- and 3-stroke hotkeys

Key Name
a3 azide
bn benzyl
bz benzoyl
ep epoxide
li Li
mes mesityl
ms mesyl
ns nosyl
piv Piv
tf triflyl
tr trityl
ts tosyl

You might say “Where’s the ester, the sulfone, why take them out? And why get rid of OMe, surely that’s useful?”. I have a proposal on how to handle organic functional groups in a nice and mostly systematic way – I’ll post it tomorrow.

Oh and I reckon the reasoning behind ChemDraw’s K for t-Bu is that it looks like it visually :slight_smile:

6

By the way, assuming the hotkeys would be hard-coded somewhere, I’d be more than happy to help with doing the tedious leg work of specifying all the combinations. Also with generating reasonable structures for the fragments repo for anything that’s missing.

Actually writing a hotkey mechanism for the Template Tool is probably beyond me though.

7

I definitely want to have some discussion because a few of the ChemDraw choices seem weird and they leave out a wide range of groups. (No nitrile, no phosphate, etc.). Some of your suggestions seem reasonable.

On the other hand, some redundancy seems okay, and a few cases the more common functional group requires a shift key.

no (or no2) = nitro .. way more common than nitroso IMHO
cn = cyano / nitrile

And I can see that generally you’re trying to have the more oxidized form with shift, but is NHOH that common? I think NO2 is much more useful as “N”

It does, but I still don’t understand why they didn’t use t which seems way easier to remember.

And of course anything you want to propose needs to be added to the fragments repository.

Most of the code is already there. It’s mostly going to be a big switch statement, e.g avogadrolibs/avogadro/qtplugins/templatetool/templatetool.cpp at de4dbfe7c48ddf734a653c241f522de82bf2cb39 · OpenChemistry/avogadrolibs · GitHub

I can certainly add in a few of the easy cases to get things started.

8

Naturally I agree on the relative frequency of the two. But the logic of having it map to NHOH is part of my idea for a wider, systematic scheme:

  • For the key organic elements C, O, N, S, P, and B, the basic saturated functional group is selected using the normal hotkey. Si is accessed using the z key.
  • Following the first key with the o key increases the oxidation state by adding a double bonded oxygen atom to the first atom.
    • For sulfur, following this with a further o will add a second =O to the first sulfur atom.
  • Following the first element key with the n, s, or c key adds a doubly bonded N, S, or C atom to the first atom (if it creates a sensible combination).
  • There are a few special 3-stroke combinations that don’t follow this, where the typed elements are instead bonded in a line e.g. ono selects a nitrite –O–N=O
  • Holding Shift also causes the first atom to be oxidized but without the addition of double bonds to oxygen.
    • This generally means the replacement of hydrogen atoms with hydroxy groups or an increase in bond order, with the exact effect being whatever is most chemically appropriate/frequently encountered.
    • Shift is held while entering the entire sequence, for ease of input.

To demonstrate:

Combo Formula Name Combo Formula Name
carbon
c CH3 methyl C CH2OH hydroxymethyl
co C(=O)H carbonyl CO C(=O)OH carboxylic acid
cn CH=NH imine CN C≡N cyano/nitrile
nc N=CH2 imine NC N≡C isocyano/isonitrile
cs C(=S)H thiocarbonyl CS C(=S)OH thioacid
cno CH=N–OH oxime
oxygen
o OH hydroxy O OOH peroxide
ono O–N=O nitrite
nitrogen
n NH2 amino N NHOH hydroxyamino
no N=O nitroso NO NO2 nitro
nn N=NH azo NN N+≡N diazo
sulfur
s SH thiyl S SSH disulfide
so S(=O)H sulfoxide SO S(=O)OH sulfinic acid
soo S(=O)2H sulfone SOO S(=O)2OH sulfonic acid
phosphorus
p PH2 phosphine P P(OH)2 phosphite
po P(=O)H2 phosphine oxide PO P(=O)(OH)2 phosphonic acid
pn P(=NH)H2 phosphine imide
silicon
z SiH3 silyl Z SiH2OH silanol
boron
b BH2 boryl B B(OH)2 boronic acid

To extend this, additionally, following a combo by m gives a version of the combo where methyl groups have replaced hydrogens e.g. a sulfide instead of a thiol or an ester instead of a carboxylic acid:

Combo Result Combo Result
cm CMe3 CM CH2OMe
com C(=O)Me COM C(=O)OMe
cnm C(=NH)Me
csm C(=S)Me CSM C(=S)OMe
om OMe OM OOMe
nm NMe2 NM NHOMe
nnm N=NMe
sm SMe SM SSMe
som S(=O)Me SOM S(=O)OMe
soom S(=O)2Me SOOM S(=O)2OMe
pm PMe2 PM P(OMe)2
pom P(=O)Me2 POM P(=O)(OMe)2
pnm P(=NH)Me2
zm SiMe3 ZM SiH2OMe
bm BMe2 BM B(OMe)2

Similarly, the combo can be followed by the a key in order to get a version with phenyl groups – a few examples only:

Combo Result Combo Result
coa C(=O)Ph COA C(=O)OPh
oa OPh OA OOPh
soa S(=O)Ph SOA S(=O)OPh
sooa S(=O)2Ph SOOA S(=O)2OPh
poa P(=O)Ph2 POA P(=O)(OPh)2
ba BPh2 BA B(OPh)2

It probably sounds complicated when shown like this in a big table. The idea is that by making it predictable and systematic, users could have a feeling for what combinations would produce what without having to reference a table at all. And by having it systematic, having a large number of combinations becomes viable, whereas with arbitrary combos I don’t think you’d want to go very far beyond the obvious and simple ones you already suggested.

Would be interested to know what you/people think.

9

A systematic system is a reasonable long-term goal, although I suspect with everything you’ve outlined, we’d might want to assemble SMILES on-the-fly to insert rather than the pre-defined CJSON templates. After all, you have ~20 basic sets, plus the oxidized form, so that’s 40 times methyl and phenyl, or like 120 different small functional groups. (And I’m not going to ask if “nma = N(Me)(Ph)”.)

I guess what I mean to say is that my main priority right now will be to add some common cases that fit general expectations (e.g., c1-c0). I’ll try to avoid cases which might conflict with the systematic approach you mention (e.g., for now N is undefined rather than nitro).

But I’d also say that there’s no reason not to have some duplication where it makes sense. For example “no2” seems like a pretty useful and discoverable case for nitro.

Anyone who wants to help can add complex functional groups (e.g., mesityl, Piv, triflyl, trityl) to the fragments repository.

10

Yeah, I think if you actually wanted to implement it in full that would be pretty much necessary. It was more to demonstrate the suggested guiding principle for how the hotkeys for things we already have should be assigned, rather than a suggestion of fragments we should add.

Haha, my thinking was actually that only one such “modifier” at the end of a combo would be possible. But yes, it could easily get silly.

You are right though, nitro is extremely useful, and as you say, a hydroxyamine is not all that common – and the same goes for some of the other ones I suggested. As an alternative, we could simply make the Shift + element combo the fully oxidized form?

Hydroxymethyl and hydroxyamino could go, and disulfide could be ss instead since that’s unambiguous.

And then maybe restrict multi-letter combos to lowercase only, which would simplify things.

The basic element + m combos are worth having even if we don’t bother with the rest of the +methyl versions. If we keep methyl ester at E then we then have most of the useful ones covered tbh.

11

For reference, that would give the following, which doesn’t seem all that unwieldy:

Key Result Key Result Combo Result Combo Result
a phenyl A acyl C(=O)Me
b BH2 B B(OH)2 bm BMe2
c CH3 C COOH co C(=O)H cm CMe3
d D D CD3 cn C≡N nc N≡C
e CO2Et ester E CO2Me ester im CH=NH cno CH=N–OH
f fluorine F CF3 cs C(=S)H cso C(=S)OH
g G
h (hydrogen) H Cbz bn benzyl bz benzoyl
i iodine I isopropyl ep epoxide li Li
j J mes mesityl tr trityl
k (potassium) K tert-butyl ms mesyl tf triflyl
l chlorine L CCl3 ts tosyl piv Piv
m M MgBr
n NH2 N NO2 no N=O ono O–N=O
o OH O OOH nn N=NH nm NMe2
p PH2 P PO(OH)2 n2 N+≡N n3 N=N+=N-
q Q FMoc oo OOH om OMe
r bromine R CBr3 pm PMe2
s SH S SO2OH po P(=O)H2 pn P(=NH)H2
t T Troc ss SSH sm SMe
u (uranium) U so S(=O)H so2 S(=O)2H
v (vanadium) V –C=CH2 ncs N=C=S scn S–C≡N
w (tungsten) W –C≡CH
x X
y (yttrium) Y Boc
z SiH3 Z Si(OH)3 zm SiMe3
c1 methyl
c2 ethyl
c3 propyl y3 cyclopropyl
c4 butyl y4 cyclobutyl
c5 pentyl y5 cyclopentyl
c6 hexyl y6 cyclohexyl
… etc. …
c10 or c0 decyl y10 or y0 cyclodecyl
c11 undecyl y11 cycloundecyl
c12 dodecyl y12 cyclododecyl

The only thing that would still bother me there is that cn doesn’t fit logically with co, cs, so, po, pn. But I guess if we consider what a user would actually expect when they press cn, you’re surely right that it’s got to give a nitrile, it’s literally a CN group…

Without all the COM nonsense I think the methyl ester as E is then useful, and also thought that the ethyl ester might be a good counterpart, especially since it’s often abbreviated with ε, what do you think?

14

I marked this table as “solved” although I’m using “C” for cycloalkanes and I’m only going up to c0 = decyl or cyclodecyl for now.

This thread seems to get a lot of hits, so I’ll simply indicate that the vast majority of these are now implemented (e.g. for v1.103 / 2.0 releases)

Add key shortcuts for functional groups and ligands by ghutchis · Pull Request #2585 · OpenChemistry/avogadrolibs · GitHub

The main file for the ‘keymap’ is the new ‘templatetoolkeymap.h’ .. which should be fairly self-explanatory. One set of keys for ligands (e.g. en, cp, acac, etc.) and one set of keys for functional groups (e.g., c8 = octyl)

15

The website documentation is now updated for 1.103: