# Example ModXNA parent fragments for the timap tests.
#
# These 11 fragments are consensus parents from the ModXNA library
# (https://github.com/modna-ff). They are test data, not files the timap
# command loads, and they are not installed under dat/.
#
# From this directory:
#   parm DAA.mol2 name DAA
#   timap analog template DAA out analog.lib
#
# Combined nucleotides are mapped to a user residue (for example FLE = rA
# onto ERN = dA), not to these fragments. Use naorder on that residue to
# freeze a full-nucleotide template. For amino acids, aaorder walks the
# residue in ff19SB amino19.lib order without reading that library. A
# smaller amino-acid library already in the test tree is
# test/Test_Build/amino12.lib. Small molecules: generate your own parent.
#
# file   class                    notes
# -----  -----------------------  ------------------------------------------
# 5PO    backbone, no phosphate   5'-OH cap
# DPO    backbone, phosphate      canonical phosphodiester
# DAA    purine base              deoxyadenine nucleobase
# DTT    pyrimidine base          deoxythymine nucleobase
# TMC    purine base + phosphate  rare combined fragment; 1 corpus member
# UFB    sugar, 2'-F
# A9Z    sugar, 2'-HH             bulky analog; prefer a real d-ribose if you have one
# DDD    sugar, 2'-HH + phosphate rare combined fragment; 1 corpus member
# RUR    sugar, 2'-OH             ribose
# OME    sugar, 2'-OMe
# RBO    sugar, 2'-OR             2'-O-benzyl, not plain ribose
