#425 Smiles with attachment points is not read correctly (valences are wrong)

[jblack-mestre]

Generic request

• PR name follows the pattern #1234 – issue name
• branch name does not contain '#'
• base branch (master or release/xx) is correct
• PR is linked with the issue
• task status changed to "Code review"
• code follows product standards
• regression tests updated

[jblack-mestre]

Similar bug to #2746; need to remove the old bonds before removing atoms (and thereby recalculating the implicit hydrogens)

[AliaksandrDziarkach]

Maybe better fix void BaseMolecule::removeAtoms(const Array<int>& indices) to remove bonds connected to removed atoms?
Because edges without vertex looks weird.

[jblack-mestre]

I can add some code to remove the edges in removeAtoms, however there are problems. If I put this code after line 813 (_removeAtoms), it doesn't fix this bug. If I put it before this line, then I break a some integration tests.

These tests seem to be about folding/unfolding molecules. There is a comment in Molecule::_removeAtoms about this. I suspect some other parts of the code are relying on having the 'incorrect' number of bonds to an atom.

I think this is a deeper problem that can't be solved with adding code to BaseMolecule::removeAtoms.

[jblack-mestre]

I don't understand why the tests fail with:

[AliaksandrDziarkach]

Such code cause UTs fails due to different sorting in iron python.
To avoid such fails I usually use next code:

for key in sorted(smiles.keys()):
   value = smeles[key]

[AliaksandrDziarkach]

I don't understand why the tests fail with:

It is unclear without context, but I already hit same issue - it is due to different key order in iron python, so line moved to different position.
I added comment to code.

[AliaksandrDziarkach]

Render at linux and mac could generate files different from windows so you will see fails like

rendering/render_chemaxon_smiles.py..................................[FAILED]    0.09 sec
Diff:
+ chemaxon_smiles/smiles_attachment_points_452_N.png rendering status: Problem: PNG similarity is 0.89 for alpha channel
+ 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
- chemaxon_smiles/smiles_attachment_points_452_N.png rendering status: OK

Line after rendering status: Problem: contains render result coded using base64, so you could get this string (after the + or from raw logs) and conver into corresponding png file.
I use next code for this:

#!python3
import base64
import sys

if len(sys.argv) < 3:
  print("Use b64 infile outfile")
  exit()

with open(sys.argv[1]) as b64file:
    b64data = b64file.read()

with open(sys.argv[2], 'wb') as file:
    file.write(base64.b64decode(b64data))