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Linking subtypes are explicitly restricted by smiles and linker_labels in chem templates #2

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rwxayheee opened this issue Oct 7, 2024 · 0 comments

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@rwxayheee
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rwxayheee commented Oct 7, 2024

Because the linking subtypes are explicitly restricted by smiles (atoms with implicit hydrogens) and the linker_labels. A new subtype needs to be created for a different type of linking.

To have a distinguishable subtype name, the 5' to 3' notation needs to include:
p <-- phosphate, if any
5' <-- intramol linker position to phosphate
DA <-- type of base name
3' <-- linker position to next nucleotide

p5'DA3' will be the standard embedded form of Adenosine in DNA. A short sequence may consist of:

(5'DT3') - (p5'DA3') - (p5'DC3') - (p5'DG3')

Currently they're named:

(DT5) - (DA) - (DC) - (DG3)

@rwxayheee rwxayheee changed the title X5p can have a unique residue name X3p can have a unique residue name Oct 7, 2024
@rwxayheee rwxayheee changed the title X3p can have a unique residue name Linking subtypes are explicitly restricted by smiles and linker_labels in chem templates Oct 14, 2024
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