This may not be happening for 0.6.0, but will not change the logics of current template matching. The changes will be just about the template files:
First, available Amber residue names will be added to default chemical template. Instead of finding the best match from CCD, they will be parsed directly from leap dat files. These names are the expected residue names from Amber compliant input. They will be the parents to lead a new item in the ambiguous dict, if they're never registered.
Then, CCD ligands whose names coincide with Amber residue names (HIE, T1P) will be added to default chemical template. These templates are added as possible matches for the residue names in the ambiguous dict.
rwxayheee
commented
3 weeks ago
This may not be happening for 0.6.0, but will not change the logics of current template matching. The changes will be just about the template files:
First, available Amber residue names will be added to default chemical template. Instead of finding the best match from CCD, they will be parsed directly from leap dat files. These names are the expected residue names from Amber compliant input. They will be the parents to lead a new item in the ambiguous dict, if they're never registered.
Then, CCD ligands whose names coincide with Amber residue names (HIE, T1P) will be added to default chemical template. These templates are added as possible matches for the residue names in the ambiguous dict.