Re: [chem] more on bonds and arrows

Dear Norwid, Branden en others,

Long overdue, but I've made some adjustments.

I think it solves the issue when using 'put Mol at N' in ring structures.

Norwid would you be so kind to check if this is the case?

To put chem to the test, would it be a good idea to try and recreate the preferred examples as shown in this article?[1]

My workflow is slow but when I have some spare time I would be happy to work on it.

Kind regards,

Hans

[1] https://publications.iupac.org/pac/pdf/2008/pdf/8002x0277.pdf

> 
> Op Mon Dec 08 2025 schreef Hans Bezemer via GNU roff typesetting system
> discussion <[email protected]>: ---------- Oorspronkelijk bericht ----------
> 
> Thanks Branden and Norwid for the replies.
> 
> I hope to be able to revise my
> adjustments in the beginning of January and will post them here.
> 
> Kind
> regards,
> 
> Hans
> 
> On December 7, 2025 8:53:46 AM GMT+01:00, "G. Branden
> Robinson" <[email protected]> wrote:
> >Hi Norwid,
> >
> >At
> 2025-11-12T19:38:49+0100, Norwid Behrnd wrote:
> >> While browsing though
> the examples of `chem` Linux Debian provides in
> >> path
> `/usr/share/doc/groff-base/examples/chem`, I noticed a chemical
> >> error
> in file `ATP.chem`, i.e., a missing nitrogen atom.
> >
> >Well, _that's_ not
> good...
> >
> >> This lead to an observation of maybe a second one.
> >> 
> >>
> Given Hans' preliminary modifications of `chem` as shared in his email
> >>
> by September 27th, I used the archived he included for a gradual
> >>
> correction / modification of `ATP.chem` in question.  To best of my
> >>
> knowledge, the new bond types proposed were not yet added to the
> >> commit
> history of groff.  This is the reason why this email includes a
> >> .zip
> archive the most relevant files to ease a replication by Hans and
> >> other
> volunteers interested.
> >
> >Correct, nothing along those lines has been
> committed yet.  When there
> >is consensus regarding a code change to groff,
> two good procedures for
> >people who aren't already committers are (1) mail
> this list with a
> >"[PATCH]" annotation in the subject line; or (2) file a
> Savannah ticket.
> >
> >https://savannah.gnu.org/bugs/?group=groff
> >
> >Sometimes a patch proposal is a good idea even for people who _are_
> >committers; observe
> >
> >https://lists.gnu.org/archive/html/groff/2025-11/msg00003.html
> >
> >...for
> example.
> >
> >> Revisions `atp_r03.chem` and above build on Hans' work (->
> >> `Chem.pdf`), hence can not be rendered by the current original `chem`
> >> preprocessor (-> `ChemO.pdf`).
> >> 
> >> @Hans, and interested volunteers:
> Contrary to the examples compiled by
> >> Hans, I observe the proposed new
> bond types `wedge` and `rwedge` work
> >> will within a plain cycle, e.g.
> `ring5` in code block `atp_r03.chem:`.
> >> They however appear to be
> incompatible with an additional explicit
> >> definition of a non-C atom
> (`put O at 1`, block `atp_r04.chem:`
> >> because `chem` now interprets them
> to belong to keyword `double`.
> >> 
> >> This might represent a bug in Hans'
> proposition, separate from the
> >> missing nitrogen atom in `ATP.chem`
> (last commit by 11 Novembre 2020).
> >
> >The foregoing sounds like solid peer
> review of Hans's proposal.  We
> >don't want to catch only mere typos, but
> design errors.
> >
> >> @Branden:  My preference is to address the bond issue
> in `ATP.chem`
> >> first,
> >
> >I agree.  However, the ZIP file you attached
> appears to contain only
> >additional ATP molecule examples, not a patch,
> properly considered, to
> >the existing one.
> >
> >I propose the following
> minimal correction of the existing file:
> >
> >$ git diff
> >diff --git
> a/contrib/chem/examples/atp.chem b/contrib/chem/examples/atp.chem
> >index
> 738c4da3c..d36c5175d 100644
> >--- a/contrib/chem/examples/atp.chem
> >+++
> b/contrib/chem/examples/atp.chem
> >@@ -25,8 +25,11 @@ atp.chem:
> > # The
> GPL2 license text is available in the internet at
> > #
> <http://www.gnu.org/licenses/gpl-2.0.html>.
> >
> >-R1:    ring5 pointing left
> double 1,2 3,4 put N at 2 put N at 5
> >-B:     benzene put N at 2 with .V6
> at R1.V3 with .V5 at R1.V4
> >+# corrected missing nitrogen atom, Norwid
> Behrnd 2025-11-11
> >+
> >+R1:    ring5 pointing left double 1,2 put N at 2
> put N at 5
> >+B:     benzene put N at 2 put N at 4 double 1,2 3,4 5,6 \
> >+ 
> with .V6 at R1.V3 with .V5 at R1.V4
> >        bond up ; NH2
> >       
> backbond 170 length .7 from R1.V5
> > R2:    ring5 pointing down with .V2
> put O at 1
> >
> >I reduced the change to not omit the "Thiele ring".  I am
> unfamiliar
> >with this term and the English Wikipedia is no help; I assume
> you refer
> >to what my limited education calls a "benzene ring".
> >
> >I
> attach screenshots of the PostScript generated by the unpatched and
> >patched files.  To my minimally trained eye your corrected version
> >looks, uh, topologically equivalent to Wikipedia's info box for ATP.
> >
> >But please correct me if I am mistaken.
> >
> >> subsequently consider filing
> a PR with a revised `ATP.chem` to the git
> >> history of groff.
> >
> >More or
> less.  We don't use a GitHub/GitLab-style system, so our "pull
> >requests"
> are either Savannah tickets or emails to this list, as noted
> >above.
> >
> >Thanks for giving your attention to this under-appreciated component of
> >groff!
> >
> >Regards,
> >Branden
> 
> 
>