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amberparm_bond_to_lt.py
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Sat, Oct 19, 02:27

amberparm_bond_to_lt.py
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#!/usr/bin/env python
import sys
lines_gaff = sys.stdin.readlines()
bond_style_name = 'harmonic'
sys.stdout.write(' write_once("In Settings") {\n')
for i in range(0, len(lines_gaff)):
line = lines_gaff[i]
tokens= line.split()
atypes = line[:6].split('-')
atype1 = atypes[0].strip()
atype2 = atypes[1].strip()
at1 = atype1.replace('X','*')
at2 = atype2.replace('X','*')
bondtype = '@bond:'+atype1+'-'+atype2
tokens= line[5:].split()
keq = tokens[0]
req = tokens[1]
comments=' '.join(tokens[2:])
sys.stdout.write(' bond_coeff '+bondtype+' '+bond_style_name+' '+keq+' '+req+' # '+comments+'\n')
sys.stdout.write(' } # (end of bond_coeffs)\n')
sys.stdout.write('\n')
sys.stdout.write(' write_once("Data Bonds By Type") {\n')
for i in range(0, len(lines_gaff)):
line = lines_gaff[i]
atypes = line[:6].split('-')
atype1 = atypes[0].strip()
atype2 = atypes[1].strip()
at1 = atype1.replace('X','*')
at2 = atype2.replace('X','*')
bondtype = '@bond:'+atype1+'-'+atype2
#tokens= line[5:].split()
#keq = tokens[0]
#req = tokens[1]
#comments=' '.join(tokens[2:])
sys.stdout.write(' '+bondtype+' @atom:'+at1+' @atom:'+at2+'\n')
sys.stdout.write(' } # (end of Bonds By Type)\n')
sys.stdout.write('\n')

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