Formal charges

[aerkiaga]

This Pull Requests improves Avogadro's support for formal charges. First of all, it implements reading them from CML, which also extends to other formats (e.g. SMILES, which is internally converted to CML). Those charges are then passed down the class hierarchy. Secondly, since PDB files can contain quaternary ammonium (e.g. acetylcholine, various drug ligands) or tertiary sulfonium (S-adenosylmethionine), or even quaternary arsonium (https://www.rcsb.org/structure/5NXY) groups, and those cannot be eliminated by hydrogen adjustment, specific code was added to detect those.

Then, the code was made more convergent with other paths so as to allow the various optimization PRs to act on it.

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[ghutchis]

The other part of this would be writing to CJSON since we're now using that preferentially over CML.

See io/cjsonformat.cpp

[ghutchis]

I think the question would be more on the generality - whether it's worth expanding beyond the simple cations to a slightly larger formal charge perception method.

I also don't remember if I added formal charges to the native mdlformat code -- it looks like not.

[ghutchis]

This fixes your problems for sure, but it would be great to have a slightly broader patch to address CJSON and SDF support too and ideally also handle negative formal charges.

[aerkiaga]

Regarding CJSON and SDF... How are new features introduced in CJSON; can I just send a Pull Request to them? Also, I'm not familiar with SDF at all; never used it. Where could I find the specification?

[ghutchis]

For CJSON, you're just adding an extension for atom formal charges, so it's backwards-compatible still.

In CjsonFormat::read - I'd do something like this for formal charges:

  json labels = atoms["labels"];
  if (labels.is_array() && labels.size() == atomCount) {
    for (size_t i = 0; i < atomCount; ++i) {
      molecule.atom(i).setLabel(labels[i]);
    }
  }

In write I'd look at something like:

  // labels
  json labels;
  for (size_t i = 0; i < molecule.atomCount(); ++i) {
    labels.push_back(molecule.label(i));
  }
  root["atoms"]["labels"] = labels;

[ghutchis]

For SDF, there are two parts - in the atom block itself and the M CHG parts:

atom block:

xxxxx.xxxxyyyyy.yyyyzzzzz.zzzz aaaddcccssshhhbbbvvvHHHrrriiimmmnnneee

The "ccc" part is the formal charge code (characters 36-38): 0 = uncharged or other, 1 = +3, 2 = +2, 3 = +1, 5 = -1, 6 = -2, 7 = -3
(this is for backwards compatibility - M CHG if present take priority)

M CHG fields indicate the number of formal charges on the line (up to 8), then the atom number and the charge, e.g.

M  CHG  2   8  -1  10   1

So 2 atoms with charges, atom 8 has a -1 charge, atom 10 has a +1 charge.

test.txt

[github-actions]

Here are the build results
Avogadro2.AppImage
macOS.dmg
Ubuntu-2004.tar.gz
Win64.exe
Artifacts will only be retained for 90 days.

[github-actions]

Here are the build results
Avogadro2.AppImage
macOS.dmg
Ubuntu-2004.tar.gz
Win64.exe
Artifacts will only be retained for 90 days.

[github-actions]

Here are the build results
Avogadro2.AppImage
macOS.dmg
Ubuntu-2004.tar.gz
Win64.exe
Artifacts will only be retained for 90 days.

[ghutchis]

Otherwise, this looks good. I was able to read in the test file, and adding hydrogens generated R-NH3+ and R-CO2- properly, which is great.

[github-actions]

Here are the build results
Avogadro2.AppImage
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[ghutchis]

Thanks, the SDF fix looks good. Anything else or is this good to merge?

[aerkiaga]

Well, there's that thing with halogen-substituted anions, but at this point it would only be added to PDB, and I'm not aware of any drugs or research ligands with such structures...

So... yes, good to merge!

[aerkiaga]

Well, maybe I should add support in CJSON? Looks small enough to me that you could merge it with that support tomorrow...

[github-actions]

Here are the build results
Avogadro2.AppImage
macOS.dmg
Ubuntu-2004.tar.gz
Win64.exe
Artifacts will only be retained for 90 days.

[github-actions]

Here are the build results
Avogadro2.AppImage
macOS.dmg
Ubuntu-2004.tar.gz
Win64.exe
Artifacts will only be retained for 90 days.