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Test that we can make a sample molecule for every atom type. #1661

Merged
merged 9 commits into from
May 17, 2023
Merged

Test that we can make a sample molecule for every atom type. #1661

merged 9 commits into from
May 17, 2023

Commits on May 16, 2023

  1. Test that we can make a sample molecule for every atom type. 

    This unit test was inspired by efforts to debug something in some
changes to the database, which caused a segfault when running
the database Tests, but was in fact caused by an undetected bug in RMG. This should detect similar bugs.
The idea is that for every atomType, such as 'Cds', the
method Group().make_sample_molecule() can create a molecule
from the group definition, eg.
  1  Cd  ux
should make the molecule
  1 C u0 p0 c0 {2,D} {3,S} {4,S}
  2 C u0 p0 c0 {1,D} {5,S} {6,S}
  3 H u0 p0 c0 {1,S}
  4 H u0 p0 c0 {1,S}
  5 H u0 p0 c0 {2,S}
  6 H u0 p0 c0 {2,S}

Many work, but quite a few fail.
Updated to RMG3/Python3.
    @rwest
    rwest committed May 16, 2023
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  2. Add undeclared charged atom type in group.make_sample_molecule() 

    We have a hard-coded list of charged atom types here. It was missing one.
    @rwest
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  3. Replace hard-coded list of charged atomtypes with check for charge. 

    The atomtypes each have a charge list - let's just see if it matches.
    @rwest
    rwest committed May 16, 2023
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  4. Include N5bd as a benzene "carbon" when generating sample molecules. 

    When you create a molecule from a functional group definition that 
declares implicit benzene rings by using a "benzene" atom type,
it creates benzene rings.

This algorithm contains a list of "benzene" atom types.
It's hard-coded. And missing some. This adds one, to check that 
adding one fixes things.

With this fix, the following line works:

rmgpy.molecule.Group().from_adjacency_list('1 N5bd ux').make_sample_molecule()
    @rwest
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  5. Group.is_benzene_explicit() checks more benzenic atom types. 

    Before it had a hard-coded list (that was missing some).
Now any atomtype that is declared as having at least one benzene bond
is counted.
    @rwest
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  6. Added more aromatic atom types to classify_benzene_carbons() 

    This helps generating sample molecules for certain atomtypes.
Now lines like this work:
rmgpy.molecule.Group().from_adjacency_list('1 P3b ux').make_sample_molecule()
    @rwest
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  7. Make failing atomtype tests into "work in progress" 

    Fixing O4b and S4b will be nontrivial, so rather than fix them
I'm marking them as "work in progress" (expected to fail)
    @rwest
    rwest committed May 16, 2023
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  8. Fix typo

    @rwest
    rwest committed May 16, 2023
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  9. Added a work in progress atomtype test: make sample molecule. 

    Ideally we could make a molecule from every atom type definition
that matches that atom type. 

This is a work in progress test, because we can't.
Two (marked in previous tests) crash. Some others create molecules,
but they don't seem to match the functional group they were designed
to match.
    @rwest
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