After packaging 4.1 for bioconda I took a look at swapping Indigo for RDKit. Looks like all of the structure calculation is based on smiles concatenation so all indigo was used for was to:
load a smiles string from a file
calculate the structure
write out 2 PNG files.
Therefore swapping Indigo for RDKit is reasonably straightforward as you can see in this PR - the only code changes are in structure_drawer.py - everything else is removing Indigo. I tested the basic RDKit functionality in this code but haven't tested it within Antismash. I know you had mentioned wanting to swap out Indigo so maybe this can move the needle in that direction.
Kai,
After packaging 4.1 for bioconda I took a look at swapping Indigo for RDKit. Looks like all of the structure calculation is based on smiles concatenation so all indigo was used for was to:
load a smiles string from a file
calculate the structure
write out 2 PNG files.
Therefore swapping Indigo for RDKit is reasonably straightforward as you can see in this PR - the only code changes are in structure_drawer.py - everything else is removing Indigo. I tested the basic RDKit functionality in this code but haven't tested it within Antismash. I know you had mentioned wanting to swap out Indigo so maybe this can move the needle in that direction.
zach cp
draw with rdkit
remove all indigo code and binaries
small fixes for png outputs