[Debichem-devel] Bug#1082109: Bug#1082109: inchi: support for .sdf (v3000 dialect) is not functional

[Norwid Behrnd]

Dear Andrius,

In the more general case of a .mol/.sdf file about models with multiple atoms
and at least one explicit bond, the reference executable of InChI 1.07.1 is
able to process data in the v3000 dialect.  Their executable published by
August 21st, 2024 on
<https://github.com/IUPAC-InChI/InChI/releases>
for instance is able to assign pyridine (written by OpenBabel) its InChI
string.  For documentation, I attach the log of a test run in Linux Debian
13/trixie with InChI's reference executable 1.07.1.

---

Issue 52 (on InChI's GitHub repository) addresses a particular case -- .mol or
.sdf with exactly one explicit atom only.  In this instance, some programs
write a bound block (for instance the sketcher InChI's demo page currently
uses, and OpenBabel) though there is no _explicit_ second atom to bound to.
The file then reads

```
M  V30 BEGIN BOND
M  V30 END BOND
```

The reference executable of InChI 1.07.1 considers this to be an error.  Other
programs (for instance Marvin) write a bound block only if there are at least
two atoms with an explicit bound.  The current implementation in OpenBabel
3.1.1 (as packaged for Debian by September 4, 2024) can process either one of
the two forms thanks to the internal design of OpenBabel.

Best regards,

Norwid
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