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amberparm_dihedral_to_lt.py
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Sun, Nov 3, 23:23

amberparm_dihedral_to_lt.py
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#!/usr/bin/env python
# SOME UGLY CODE HERE
import sys
lines_gaff = sys.stdin.readlines()
dihedral_style_name = 'fourier'
in_dihedral_coeffs = []
for i in range(0, len(lines_gaff)):
line = lines_gaff[i]
atypes = line[:11].split('-')
atype1 = atypes[0].strip()
atype2 = atypes[1].strip()
atype3 = atypes[2].strip()
atype4 = atypes[3].strip()
at1 = atype1.replace('X','*')
at2 = atype2.replace('X','*')
at3 = atype3.replace('X','*')
at4 = atype4.replace('X','*')
dihedraltype = '@dihedral:'+atype1+'-'+atype2+'-'+atype3+'-'+atype4
tokens= line[11:].split()
npth = float(tokens[0])
Kn = float(tokens[1])
Kn /= npth # The coeff for each fourier term is Kn/npth
# ...I THINK (?). (Very confusing. See documentation below...)
dn = float(tokens[2])
n = int(float(tokens[3]))
comments=' # '+(' '.join(tokens[4:]))
in_dihedral_coeffs.append([dihedraltype, Kn, n, dn, comments])
#print(Kn, n, dn)
#for entry in in_dihedral_coeffs:
# print(entry)
#exit()
# ---- processing dihedral fourier series ----
# ---- (negative "n" values means the
# ---- Fourier series is not yet complete.
i = 0
while i < len(in_dihedral_coeffs):
type_str = in_dihedral_coeffs[i][0]
Kn = in_dihedral_coeffs[i][1]
n = in_dihedral_coeffs[i][2]
dn = in_dihedral_coeffs[i][3]
#if (i>0):
# sys.stderr.write('prev_n='+str(in_dihedral_coeffs[i-1][-3])+'\n')
#sys.stderr.write('n='+str(n)+'\n')
if ((i>0) and (in_dihedral_coeffs[i-1][-3] < 0)):
#sys.stdout.write('interaction_before_append: '+str(in_dihedral_coeffs[i-1])+'\n')
assert(in_dihedral_coeffs[i-1][0] == in_dihedral_coeffs[i][0])
in_dihedral_coeffs[i-1][-3] = -in_dihedral_coeffs[i-1][-3]
comments = in_dihedral_coeffs[i-1][-1]
in_dihedral_coeffs[i-1][-1] = Kn
in_dihedral_coeffs[i-1].append(n)
in_dihedral_coeffs[i-1].append(dn)
in_dihedral_coeffs[i-1].append(comments)
#sys.stdout.write('interaction_after_append: '+str(in_dihedral_coeffs[i-1])+'\n')
del in_dihedral_coeffs[i]
#elif len(in_dihedral_coeffs) < 3:
# del in_dihedral_coeffs[i]
else:
i += 1
for i in range(0, len(in_dihedral_coeffs)):
type_str = in_dihedral_coeffs[i][0]
params = in_dihedral_coeffs[i][1:]
params = map(str, params)
num_fourier_terms = (len(params)-1)/3
dihedral_coeff_str = 'dihedral_coeff '+type_str+' '+\
dihedral_style_name+' '+ \
str(num_fourier_terms)+' '+ \
' '.join(params)
in_dihedral_coeffs[i] = dihedral_coeff_str
# ---- finished processing dihedral fourier series ----
sys.stdout.write(' write_once(\"In Settings\") {\n ')
sys.stdout.write('\n '.join(in_dihedral_coeffs)+'\n')
sys.stdout.write(' } # (end of dihedral_coeffs)\n')
sys.stdout.write('\n')
sys.stdout.write(' write_once("Data Dihedrals By Type") {\n')
for i in range(0, len(lines_gaff)):
line = lines_gaff[i]
atypes = line[:11].split('-')
atype1 = atypes[0].strip()
atype2 = atypes[1].strip()
atype3 = atypes[2].strip()
atype4 = atypes[3].strip()
at1 = atype1.replace('X','*')
at2 = atype2.replace('X','*')
at3 = atype3.replace('X','*')
at4 = atype4.replace('X','*')
dihedraltype = '@dihedral:'+atype1+'-'+atype2+'-'+atype3+'-'+atype4
sys.stdout.write(' '+dihedraltype+' @atom:'+at1+' @atom:'+at2+' @atom:'+at3+' @atom:'+at4+'\n')
sys.stdout.write(' } # (end of Dihedrals By Type)\n')
sys.stdout.write('\n')
"""
- 6 - ***** INPUT FOR DIHEDRAL PARAMETERS *****
IPT , JPT , KPT , LPT , IDIVF , PK , PHASE , PN
FORMAT(A2,1X,A2,1X,A2,1X,A2,I4,3F15.2)
IPT, ... The atom symbols for the atoms forming a dihedral
angle. If IPT .eq. 'X ' .and. LPT .eq. 'X ' then
any dihedrals in the system involving the atoms "JPT" and
and "KPT" are assigned the same parameters. This is
called the general dihedral type and is of the form
"X "-"JPT"-"KPT"-"X ".
IDIVF The factor by which the torsional barrier is divided.
Consult Weiner, et al., JACS 106:765 (1984) p. 769 for
details. Basically, the actual torsional potential is
(PK/IDIVF) * (1 + cos(PN*phi - PHASE))
PK The barrier height divided by a factor of 2.
PHASE The phase shift angle in the torsional function.
The unit is degrees.
PN The periodicity of the torsional barrier.
NOTE: If PN .lt. 0.0 then the torsional potential
is assumed to have more than one term, and the
values of the rest of the terms are read from the
next cards until a positive PN is encountered. The
negative value of pn is used only for identifying
the existence of the next term and only the
absolute value of PN is kept.
The input is terminated by a blank card.
"""

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