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Update Class_PDB.py #6

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Update Class_PDB.py #6

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18 changes: 9 additions & 9 deletions Class_PDB.py
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Original file line number Diff line number Diff line change
Expand Up @@ -833,14 +833,14 @@ def PDB2PDBwLeap(self):
leap_input.write('bond a.'+ring_num+'.N a.ASX.C\n')
leap_input.write('bond a.ASX.CG a.1.N\n') #isopeptide bond
leap_input.write('remove a a.ASX.OD2\n')
leap_input.write('remove a a.ASX.H02\n')
leap_input.write('remove a a.ASX.HB2\n')
leap_input.write('remove a a.ASX.HB3\n')
leap_input.write('remove a a.1.H1\n')
leap_input.write('remove a a.1.H2\n')
leap_input.write('remove a a.1.H3\n')
leap_input.write('remove a a.9.H1\n')
leap_input.write('remove a a.9.H2\n')
leap_input.write('remove a a.9.H3\n')
#leap_input.write('remove a a.1.H1\n')
#leap_input.write('remove a a.1.H2\n')
#leap_input.write('remove a a.1.H3\n')
#leap_input.write('remove a a.9.H1\n')
#leap_input.write('remove a a.9.H2\n')
#leap_input.write('remove a a.9.H3\n')
leap_input.write('deletebond a.ASX.CG a.'+ring_num+'.N\n')
leap_input.write('deletebond a.ASX.C a.2.N\n')
else:
Expand Down Expand Up @@ -874,7 +874,7 @@ def PDB2PDBwLeap(self):

def partition(self):
'''
partition the lasso structure into parts -Reecan
partition the lasso structure into parts
'''

a = list(self.topology_sort())
Expand Down Expand Up @@ -1317,7 +1317,7 @@ def _combine_parm(self, lig_parms, prm_out_path='', o_dir='', ifsavepdb=0, ifsol
of.write('deletebond a.ASX.CG a.'+ring_num+'.N'+line_feed)
#of.write('deletebond a.ASX.C a.2.N'+line_feed)
of.write('deletebond a.ASX.O a.10.C'+line_feed)
of.write('remove a a.ASX.OXT'+line_feed)
#of.write('remove a a.ASX.OXT'+line_feed)
of.write('remove a a.ASX.OD2'+line_feed)
of.write('remove a a.ASX.H01'+line_feed)
of.write('deletebond a.ASX.OD1 a.10.N'+line_feed)
Expand Down