URL: <https://savannah.gnu.org/bugs/?68127>
Summary: [chem] bond lengths in simple bonds vs cyclic
templates
Group: GNU roff
Submitter: nbehrnd
Submitted: Fri 06 Mar 2026 11:43:18 AM UTC
Category: Preprocessor - others/general
Severity: 3 - Normal
Item Group: Feature change
Status: None
Privacy: Public
Assigned to: None
Open/Closed: Open
Discussion Lock: Unlocked
Planned Release: None
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Follow-up Comments:
-------------------------------------------------------
Date: Fri 06 Mar 2026 11:43:18 AM UTC By: Norwid Behrnd <nbehrnd>
Self declaration: this is a bug with a severity less or equal to level 3.
In section setparams, file chem.pl defines parameters which affect the
eventual visual result. This includes normal bonds
$Params{'db'} = $scale * 0.2;
as well as the bonds in the cyclic templates (ring3, ring4, ..., ring8)
$Params{'ringside'} = $scale * 0.3
Because the scale factor differs, so differ the plotted bond lengths. For
bonds outside the cyclic templates with implicit carbon bonds, this is
annoying because they are consistently too short. See attached
01_next.chem/01_next.pdf for an illustration of the result with current chem
1.0.6 vs ACDChemSketch_bondlengths_check.pdf with a GUI based molecule
editor.
The preferred adjustment of chem would
- draw simple bonds with the same scale factor of 0.3 (i.e., length) as are
the sides of the ring templates
- draw bonds with the current scaling factor of 0.2 only if their definition
includes an explicit atom / atom group as in
```
bond 120 ; OH
```
I have not the necessary experience in Perl to provide a correction myself but
hope to draw attention to this proposition by an additional post to the normal
user list.
_______________________________________________________
File Attachments:
Name: 01_next.chem Size: 456B
<https://file.savannah.gnu.org/file/01_next.chem?file_id=58312>
Name: 01_next.chem.pdf Size: 6.6KiB
<https://file.savannah.gnu.org/file/01_next.chem.pdf?file_id=58313>
Name: ACDChemSketch_bondlengths_check.pdf Size: 33KiB
<https://file.savannah.gnu.org/file/ACDChemSketch_bondlengths_check.pdf?file_id=58314>
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