Closed davidfarinajr closed 1 year ago
Will keeping the charge in to_single_bonds
be correct and solve this, and can we think of cases where it won't be correct to keep them?
Will keeping the charge in
to_single_bonds
be correct and solve this, and can we think of cases where it won't be correct to keep them?
Yes, however I think the to_single_bonds
method is primarily used to check isomorphism with a QC calc, where it is difficult to determine formal charges on the atoms. That's why I decided to add 0 to allowable atomtype charges instead of conserve atom charges with to_single_bonds
method. We could keep the charges with to_single_bonds
, and add an option to neglect charge with is_isomorphic
method when comparing with molecule initiated with from_xyz
.
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Bug Description
The
to_single_bonds
method raises anAtomTypeError
when used for molecules withN5sc
atomtype.How To Reproduce
Expected Behavior
I'm using the
to_single_bonds
method in AutoTST to check isomorphism from quantum chem calculations. We get the atomtype error because theto_single_bonds
method does not conserve formal charges for the atoms, andN5sc
is only allowed +1/+2 charges. The work around I am using now is adding 0 to allowedN5sc
atomtype charges.Installation Information
Describe your installation method and system information.
Additional Context