gbranden pushed a commit to branch master
in repository groff.
commit d7eb1ce9dae4fcaf228ca337d48fcb281f2e6f88
Author: Norwid Behrnd <[email protected]>
AuthorDate: Thu Jan 1 15:17:03 2026 +0100
[chem]: Reorganize penicillin example.
* contrib/chem/examples/penicillin.chem: Reorganize file.
- Improve use of the ring templates.
- Prevent partial overwrite of N in lactam moiety and alkyl amide.
- Explicitly designate stereochemistry. If available, future versions
of chem should replace `backbond` by a wegde shaped variant of this
bond.
...for better visual representation similar to the one currently used on
Wikipedia.[1]
Fixes <https://savannah.gnu.org/bugs/?67877>.
[1] https://en.wikipedia.org/wiki/Benzylpenicillin
Signed-off-by: Norwid Behrnd <[email protected]>
---
contrib/chem/ChangeLog | 17 +++++++++++++++
contrib/chem/examples/penicillin.chem | 41 +++++++++++++++++------------------
2 files changed, 37 insertions(+), 21 deletions(-)
diff --git a/contrib/chem/ChangeLog b/contrib/chem/ChangeLog
index fe5714c09..8654333e3 100644
--- a/contrib/chem/ChangeLog
+++ b/contrib/chem/ChangeLog
@@ -1,3 +1,20 @@
+2026-01-01 Norwid Behrnd <[email protected]>
+
+ * examples/penicillin.chem: Reorganize file.
+ - Improve use of the ring templates.
+ - Prevent partial overwrite of N in lactam moiety and alkyl
+ amide.
+ - Explicitly designate stereochemistry. If available, future
+ versions of chem should replace `backbond` by a wegde shaped
+ variant of this bond.
+
+ ...for better visual representation similar to the one currently
+ used on Wikipedia.[1]
+
+ Fixes <https://savannah.gnu.org/bugs/?67877>.
+
+ [1] https://en.wikipedia.org/wiki/Benzylpenicillin
+
2026-01-01 Norwid Behrnd <[email protected]>
* examples/ethamivan.chem: Improve visual representation.
diff --git a/contrib/chem/examples/penicillin.chem
b/contrib/chem/examples/penicillin.chem
index b785ad245..c6648cc14 100644
--- a/contrib/chem/examples/penicillin.chem
+++ b/contrib/chem/examples/penicillin.chem
@@ -2,31 +2,30 @@ penicillin.chem:
.cstart
# Example file for chem:
-# Penicillin or C16_H18_N2_O4_S or
-# 3,3-dimethyl-6-oxo-7-(2-phenylacetyl)amino-2-thia-5-
-# azabicyclo[3.2.0]heptane-4-carboxylic acid
+# benzylpenicillin or C16_H18_N2_O4_S or
+# (2S,5R,6R)-3,3-Dimethyl-7-oxo-6-(2-phenylacetamido)-4-thia-
+# 1-azabicyclo[3.2.0]heptane-2-carboxylic acid (CAS-RN: 61-33-6)
#
-# Found at http://www.chemindustry.com/apps/chemicals.
+# Found at https://en.wikipedia.org/wiki/Benzylpenicillin
#
-# Prepared by Bernd Warken <[email protected]>.
+# Prepared by Bernd Warken <[email protected]>,
+# partial rewrite by Norwid Behrnd <[email protected]>.
-R1: flatring5 pointing up put S at 1 put N at 4
- bond 45 at R1.V2
- bond 135 at R1.V2
- bond 120 at R1.V3
-D1: doublebond 45 ; O
- bond 135 at D1.start ; OH
- bond left at R1.N
- doublebond -135 ; O
- bond left at R1.V5
-B1: bond down length .3
- bond -60 at B1.start ; N
- bond up ; H
- bond -120 at N
-D2: doublebond down ; O
- bond -60 at D2.start
+R1: ring4 pointing 45 put N at 2
+R2: ring5 pointing right with .V3 at R1.V2 put N at 3 put S at 5
+
+ doublebond -130 at R1.V3 ; O
+ frontbond -60 at R1.V4 ; N
+B1: bond -120
+ doublebond down ; O
+ bond -60 at B1.end
bond -120
- benzene
+ ring6 double 1,2 3,4 5,6
+ H above N
+
+ bond 60 at R2.V1
+ bond 120 at R2.V1
+ backbond 160 at R2.V2 ; CO2H
# Local Variables:
# mode: Nroff
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