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native conformation not returned in lattice.confs.k_lowest_confs() #5

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JBGreisman opened this issue Dec 4, 2017 · 0 comments
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@JBGreisman
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For certain sequences, I am finding that the native conformation that is returned by lattice.native_conf(seq) is not found in the output of lattice.confs.k_lowest_confs(seq, lattice.temp, 5). I am under the impression that the native conformation should be the 0th item returned by lattice.confs.k_lowest_confs, so please let me know if I am mistaken.

seq_length = 16
temperature = 1
lattice = lp.LatticeThermodynamics.from_length(seq_length, temperature)

# Fold sequence
seq = "PQHKIFGKQMHKTETF"
print lattice.native_conf(seq)
print lattice.confs.k_lowest_confs(seq, lattice.temp, 5) # Native conf not found
URRDLDDRURRUULD
['UUURDRURDDDLLUR' 'UUURRRDLDRDLLUU' 'URRULLURRRDDDLL' 'URDRDLLDRRRUUUL'
 'UUURRRDLLDDRRUL']

For other sequences, this seems to hold:

seq = "AGRLQFQLIYMLKLAR"
print lattice.native_conf(seq)
print lattice.confs.k_lowest_confs(seq, lattice.temp, 5) # Native conf found
URRRDDLULDLDRRR
['URRRDDLULDLDRRR' 'UUURRRDLLDDRURD' 'URDDLDRRUUURDDD' 'URDRURDDLLLDRRR'
 'UURRRDLLDRRDLLL']
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