Tim,
I have a couple of comments/questions about the definitions of DNA & RNA
for the predefined sets.
The relevant definitions are as follows:
"@nucleic within(group,(_a>=8 & _a<=30))",
"@dna nucleic & !within(group,(_a=15,_a=30))",
"@rna nucleic & within(group,_a=15)",
_a=8 is P
_a=15 is O2*
_a=30 is 2HO*
Q: Why is it that dna refers to 2HO* and rna does not?
Second issue ... I think we need to modify the definition of nucleic.
SpecialAtomID == 8 is Phosphorus, 'P'. With this definition, anything that
has a phosphorus atom will be nucleic. I think we need to include some
reference to the group identifiers (A/G/ADP, etc) in order to further
narrow the definition of 'nucleic'.
Miguel
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