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opls2Q.py
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opls2Q.py
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import settings as s
from subprocess import check_output
import shlex
import math
import re
import sys
import os
import argparse
import IO
import functions as f
class Run(object):
"""
Create FEP files from a common substructure for a given set of
ligands
"""
def __init__(self, lig, FF, merge, vs, AA, resname,include = ('ATOM','HETATM'), *args, **kwargs):
"""
The init method is a kind of constructor, called when an instance
of the class is created. The method serves to initialize what you
want to do with the object.
"""
supported_FFs = ['OPLS2005', 'OPLS2015']
self.lig = lig
self.FF = FF
self.merge = merge
self.vs = vs
self.AA = AA
self.ff_list = []
self.backbone = {'C':'0.500',
'O':'-0.500',
'CA':'0.140',
'N':'-0.500',
'H':'0.300',
'HA':'0.060'
}
self.pdbfiles=[self.lig + '.pdb']
self.include = include
self.resname = resname
if len(self.resname) != 3:
print('Error, resname must be three letters')
sys.exit()
# This is a test part, should be generalized for lone pairs and different
# halogen bonds. Now, it works for Bn-X, where X is a halogen
# The parameters below are extracted from:
# J. Chem. Theory Comput. 2012, 8, 10, 3895-3901
# Note: I find it quite unlikely that bond length for Cl and Br for vs
# are the same
self.virtual_site = {'Cl' :[ '1.600', # [0] X-vs bond length
-0.250, # [1] X charge
0.075, # [2] vs charge
0.175 # [3] CA charge
],
'Br' :[ '1.700', # [0] X-vs bond length
-0.270, # [1] X charge
0.100, # [2] vs charge
0.170 # [3] CA charge
],
'I' :[ '1.800', # [0] X-vs bond length
-0.260, # [1] X charge
0.110, # [2] vs charge
0.150 # [3] CA charge
]
}
# Below are potential AMBER parameter for later
# those from AMBER paper:
# DOI 10.1002/jcc.21836
#self.virtual_site = {'Cl' :[ '1.950', # [0] X-vs bond length
# -0.2679, # [1] X charge
# 0.0382, # [2] vs charge
# 0.2297 # [3] CA charge
# ],
#
# 'Br' :[ '2.220', # [0] X-vs bond length
# -0.2512, # [1] X charge
# 0.0506, # [2] vs charge
# 0.2006 # [3] CA charge
# ],
# 'I' :[ '2.350', # [0] X-vs bond length
# -0.1966, # [1] X charge
# 0.0574, # [2] vs charge
# 0.1392 # [3] CA charge
# ]
# }
if self.FF in supported_FFs:
self.FF = FF
else:
print('Forcefields ' + ','.join(supported_FFs)) + ' currently supported'
sys.exit()
def vdw_calc(self, sig, eps):
# calculate LJ types
sig = float(sig)
eps = float(eps)
Avdw1 = math.sqrt(4*eps*(sig**12))
Avdw2 = math.sqrt(4*eps*(sig**12))
Bvdw1 = math.sqrt(4*eps*(sig**6))
Avdw3 = (math.sqrt(4*eps*(sig**12)))/math.sqrt(2)
Bvdw23 = (math.sqrt(4*eps*(sig**6)))/math.sqrt(2)
# returns unparsed floats, consider changing
return[Avdw1, Avdw2, Bvdw1, Avdw3, Bvdw23]
def get_mass(self, atom):
mass_dic = {"H":"1.0080",
"C":"12.0110",
"N":"14.0070",
"O":"15.9994",
"F":"19.00",
"P":"30.97",
"S":"32.0600",
"Cl":"35.0000",
"Br":"79.90",
"CL":"35.0000",
"BR":"79.90",
"I":"126.90",
"DUM": "0.00"
}
at = re.findall('\d+|\D+', atom)
mass = mass_dic[at[0][0:len(at[0])]]
return mass
def bond_calc(self, k):
k = float(k)*2
return k
# Double function, but this might be needed for different forcefields
def angle_calc(self, k):
k = float(k)*2
return k
# FIX
def torsion_calc(self, tors):
cnt = 0
tors_Q = []
for line in tors:
cnt = cnt + 1
if cnt == 1 or cnt == 3:
Vn = (float(line))/2
Vn_Q = [Vn, -cnt, '0.000', '1.000']
tors_Q.append(Vn_Q)
if cnt == 2:
Vn = (float(line))/2
Vn_Q = [Vn, -cnt, '180.000', '1.000']
tors_Q.append(Vn_Q)
if cnt == 4:
Vn = (float(line))/2
Vn_Q = [Vn, cnt, '180.000', '1.000']
tors_Q.append(Vn_Q)
#add some debugging here (if n tors > 4)
else:
continue
return tors_Q
def improper_calc(self, imp_V2):
imp_V2 = float(imp_V2)/2
return[imp_V2]
def get_charge_groups(self, charges, bonds):
dic = {}
charge_group = []
charge_group_list = []
charge_group_dic = {}
# Generating bond dictionary
for line in bonds:
if line[0] in dic:
dic[line[0]].append(line[1])
else:
dic[line[0]] = [line[1]]
# Now first we do a naive check for X-H charge group partners
for key in dic:
for line in dic[key]:
charge = float(charges[key]) + float(charges[line])
if charge.is_integer() == True:
charge_group_list.append([key, line])
charge_group_dic[key] = line
charge = 0
charge = 0
# Now for larger groups
for line in bonds:
if line[0] in charge_group_dic or line[1] in charge_group_dic:
continue
else:
charge_a1 = float(charges[line[0]])
charge_a2 = float(charges[line[1]])
if line[0] in charge_group:
charge = round((charge + charge_a2), 5)
charge_group.append(line[1])
else:
charge = charge + charge_a1 + charge_a2
charge_group = [line[0], line[1]]
if charge.is_integer() == True:
charge_group_list.append(charge_group)
charge_group = []
charge = 0
#return charge_group_list
return []
def get_parameters(self):
for pdb in self.pdbfiles:
# Add other parameter generators later
v = 'OPLS 14'
v = v.split(' ')
if os.path.exists('/proc/sys/fs/binfmt_misc/WSLInterop') == False:
ffld_serv = s.SCHROD_DIR + 'utilities/ffld_server'
if os.path.exists('/proc/sys/fs/binfmt_misc/WSLInterop') == True:
ffld_serv = s.SCHROD_DIR + 'utilities/ffld_server.exe'
struct_conv = s.SCHROD_DIR + 'utilities/structconvert'
# Running command line tool has been moved to IO, change function!
if self.AA == True:
# First convert to .mae file to avoid reading errors
options = ' -ipdb ' + pdb + ' -omae ' + pdb[:-4] + '.mae'
args = shlex.split(struct_conv + options)
out = check_output(args,universal_newlines=True)
# Run structconvert on .mae file, write out .mae
options = ' -imae ' + pdb[:-4] + '.mae -omae ' + pdb[:-4] + '_out.mae -print_parameters -version ' + v[1]
args = shlex.split(ffld_serv + options)
out_prms = check_output(args,universal_newlines=True)
# Then move the .mae file to .pdb
options = ' -imae ' + pdb[:-4] + '_out.mae -opdb ' + pdb[:-4] + '_out.pdb'
args = shlex.split(struct_conv + options)
out = check_output(args,universal_newlines=True)
else:
options = ' -ipdb ' + pdb + ' -print_parameters -version ' + v[1]
args = shlex.split(ffld_serv + options)
out_prms = check_output(args,universal_newlines=True)
with open(pdb[:-4]+'.log', 'w') as outfile:
block = 0
cnt = 0
at_names = []
self.at_replace = {}
bonds = []
outfile.write('Forcefield: ' + v[0] + ' ' + v[1] + '\n')
out_prms = out_prms.split('\n')
for line in out_prms:
if len(line) < 2:
continue
outfile.write(line +'\n')
if self.AA == True:
# Construct for renaming atom names
line = line.split()
if line[0] == 'OPLSAA':
block = 1
continue
elif line[0] == "Stretch":
block = 2
continue
elif line[0] == "Bending":
block = 0
if block == 1:
if line[0][0] == '-':
continue
if line[0] == 'atom':
continue
else:
at_names.append(line[0])
# Find the 'fake' hydrogens that need to be removed
if block == 2:
bonds.append([line[0],line[1]])
self.h_ignore = []
if self.AA == True:
with open(pdb) as infile:
for line in infile:
if line.startswith(self.include) == False:
continue
line = IO.pdb_parse_in(line)
at_id = int(line[1]) - 1
self.at_replace[at_names[at_id]] = line[2]
for bond in bonds:
ref = ['N','C']
if self.at_replace[bond[0]] in ref \
or self.at_replace[bond[1]] in ref:
for at in bond:
if self.at_replace[at] not in self.backbone:
self.h_ignore.append(self.at_replace[at])
def read_log(self):
opls_list = []
# Read output from ffld_server
with open(self.lig + '.log', 'r') as infile:
for line in infile:
ignore_line = False
if self.AA == True:
line = IO.replace(line, self.at_replace)
if len(line) > 2:
line = line.split()
for entry in line:
if entry in self.h_ignore:
ignore_line = True
if ignore_line != True:
opls_list.append(line)
self.ff_list = opls_list
def convert_toQ(self):
ff_list = self.ff_list
halogen_cnt = 0
charge_sum = 0
charge_list = []
charge_dic = {}
vdw_list = []
bond_list = []
bonded = []
charge_group_list = []
angle_list = []
torsion_list = []
improper_list = []
block = 0
# READ BLOCKS
for line in ff_list:
if len(line) > 1:
if line[0] == "OPLSAA":
block = 1
if line[0] == "Stretch":
block = 2
if line[0] == "Bending":
block = 3
if line[0] == "proper":
block = 4
if line[0] == "improper":
block = 5
# Create lists
if len(line[0]) <= 4 and line[0] != 'atom':
if block == 1:
if line[0] in self.backbone and self.AA == True:
charge = [line[0], float(self.backbone[line[0]])]
charge_sum = charge_sum + float(self.backbone[line[0]])
else:
charge = [line[0], float(line[4])]
charge_sum = charge_sum + float(line[4])
charge_dic[line[0]] = line[4]
vdw = [line[0],
run.vdw_calc(line[5],
line[6]) + [run.get_mass(line[0])]
]
charge_list.append(charge)
vdw_list.append(vdw)
if block == 2:
bond = [line[0:2], [run.bond_calc(line[2]), line[3]]]
bond_list.append(bond)
bonded.append(line[0:2])
if block == 3:
angle = [line[0:3], [run.angle_calc(line[3]), line[4]]]
angle_list.append(angle)
if block == 4:
torsion = [line[0:4], run.torsion_calc(line[4:8])]
torsion_list.append(torsion)
if block == 5:
improper = [line[0:4], run.improper_calc(line[4]) + ['180.000']]
improper_list.append(improper)
charge_group_list = run.get_charge_groups(charge_dic, bonded)
self.Q_FF =[charge_list,
charge_sum,
vdw_list,
bond_list,
angle_list,
torsion_list,
improper_list,
charge_group_list]
def add_virtualsite(self):
self.halogens = {}
# First we find the C-X bonds, to adjust parameters accordingly
for at in self.Q_FF[0]:
element = re.findall('\d+|\D+', at[0])[0]
at_id = re.findall('\d+|\D+', at[0])[1]
if element not in self.virtual_site:
continue
# Construct dictionary to look up vs parameters
self.halogens[at[0]]=[element]
# Add the virtual site
VS = 'X' + at_id
# Add the virtual site to the atom types
VS_at = [VS, [0.0, 0.0,0.0, 0.0, 0.0, '1.0080']]
self.Q_FF[2].append(VS_at)
# Look up bond length and force, add to Q bonds
self.Q_FF[3].append([[at[0],VS],
[600.0,self.virtual_site[element][0]]])
# Store the added attomtypes
self.halogens[at[0]].append(VS)
# Add the charges of the virtual site
self.Q_FF[0].append([VS,self.virtual_site[element][2]])
for halogen in self.halogens:
# Construct the bonded list for halogens
for bond in self.Q_FF[3]:
element = re.findall('\d+|\D+', halogen)[0]
if halogen in bond[0] and self.halogens[halogen][1] not in bond[0]:
# Create the angle and store it in Q angles
at_types = [bond[0][0],bond[0][1],self.halogens[halogen][1]]
self.Q_FF[4].append([at_types,[200.0,'180.000']])
# change de charges
for at_ref in bond[0]:
for i, at in enumerate(self.Q_FF[0]):
ele = re.findall('\d+|\D+', at_ref)[0]
if at[0] == at_ref:
if ele in self.virtual_site:
self.Q_FF[0][i][1] = self.virtual_site[element][1]
else:
self.Q_FF[0][i][1] = self.virtual_site[element][3]
# Loop through angles for the atom types in torsion constructs
for angle in self.Q_FF[4]:
if halogen in angle[0] and self.halogens[halogen][1] not in angle[0]:
at_types = [angle[0][0], angle[0][1], angle[0][2], self.halogens[halogen][1]]
self.Q_FF[5].append([at_types,[[0.0, 1, '0.000', '1.000']]])
def write_lib_Q(self):
# this is just for readability, not necessary
parm = self.Q_FF
at_len = len(parm[0])
charge = parm[1]
charges = parm[0]
bonds = parm[3]
improper = parm[6]
charge_groups = parm[7]
with open(self.lig + '.lib', 'w') as outfile:
outfile.write("{%s} ! atoms no %4d total charge %.3f \n\n" % (self.resname,
at_len,
charge
)
)
#outfile.write("[info] \n SYBYLtype RESIDUE \n\n")
# atom and charge block:
outfile.write("[atoms] \n")
cnt = 0
for line in charges:
cnt = cnt + 1
outfile.write('{:>4d} {:10}X{:11}{: .4f}\n'.format(cnt,
line[0],
line[0],
line[1]
)
)
outfile.write("\n[bonds]\n")
for line in bonds:
outfile.write('{:10}{}\n'.format(line[0][0], line[0][1]))
if self.AA == True:
outfile.write('\n[connections]\n')
outfile.write('head N\n')
outfile.write('tail C\n')
outfile.write("\n[impropers]\n")
for line in improper:
outfile.write('{:10}{:10}{:10}{}\n'.format(line[0][0],
line[0][1],
line[0][2],
line[0][3]))
outfile.write("\n[charge_groups]\n")
# This charge group definition is WRONG anyway
#for i in charges:
# if i[0][0] != 'H':
# outfile.write('{}'.format(i[0]))
# for j in bonds:
# if j[0][0]==i[0] and j[0][1][0] == 'H':
# outfile.write(' {} '.format(j[0][1]))
# if j[0][1][0] == i[0] and j[0][1][0] =='H':
# outfile.write(" H%i" % j[0])
# outfile.write("\n")
def write_prm_Q(self):
parm = self.Q_FF
vdw = parm[2]
bond = parm[3]
angle = parm[4]
torsion = parm[5]
improper = parm[6]
if self.FF == 'OPLS2015' and self.merge == True:
prm_file = os.path.join(s.FF_DIR, 'OPLS2015.prm')
prm_file_out = self.FF + '_' + self.lig + '.prm'
elif self.FF == 'OPLS2005' and self.merge == True:
prm_file = os.path.join(s.FF_DIR, 'OPLS2005.prm')
prm_file_out = self.FF + '_' + self.lig + '.prm'
elif self.merge == False:
prm_file = os.path.join(s.FF_DIR, 'NOMERGE.prm')
prm_file_out = self.lig + '.prm'
with open(prm_file) as infile, open(prm_file_out, 'w') as outfile:
for line in infile:
block = 0
outfile.write(line)
if len(line) > 1:
if line == "! Ligand vdW parameters\n":
block = 1
if line == "! Ligand bond parameters\n":
block = 2
if line == "! Ligand angle parameters\n":
block = 3
if line == "! Ligand torsion parameters\n":
block = 4
if line == "! Ligand improper parameters\n":
block = 5
# Create lists
if block == 1:
for line in vdw:
outfile.write("""X{:6}{: 8.2f}{: 10.2f}{: 10.2f}{: 10.2f}{: 10.2f}{:>10s}\n""".format(line[0],
line[1][0],
line[1][1],
line[1][2],
line[1][3],
line[1][4],
line[1][5]))
if block == 2:
for line in bond:
outfile.write('X{:10}X{:10}{:10.1f}{:>10.5s}\n'.format(line[0][0],
line[0][1],
line[1][0],
line[1][1]))
if block == 3:
for line in angle:
outfile.write("""X{:10}X{:10}X{:10}{: 8.2f}{:>12.7}\n""".format(line[0][0],
line[0][1],
line[0][2],
line[1][0],
line[1][1]))
if block == 4:
for line in torsion:
for line2 in line[1]:
outfile.write("""X{:10}X{:10}X{:10}X{:10}{:<10.3f}{: d}.000{:>10s}{:>10s}\n""".format(line[0][0],
line[0][1],
line[0][2],
line[0][3],
line2[0],
line2[1],
line2[2],
line2[3]))
if block == 5:
for line in improper:
outfile.write("""X{:10}X{:10}X{:10}X{:10}{:10.3f}{:>10s}\n""".format(line[0][0],
line[0][1],
line[0][2],
line[0][3],
line[1][0],
line[1][1]))
def rename_pdb(self, include = ('ATOM', 'HETATM')):
pdb_in = self.lig + '.pdb'
pdb_out = self.lig + '_out.pdb'
index = -1
atomnames = self.Q_FF[0]
if self.vs == True:
lig_size = len(self.Q_FF[0]) - len(self.halogens)
with open(pdb_in) as infile, open(pdb_out, 'w') as outfile:
for line in infile:
line = IO.pdb_parse_in(line)
if self.AA == True and line[2] in self.h_ignore:
continue
if line[0].strip() in include:
line[4] = self.resname
index += 1
line[2] = atomnames[index][0]
line[6] = 1
outline = IO.pdb_parse_out(line)
outfile.write(outline + '\n')
# Define virtual site coordinates
if self.vs == True and line[2] in self.halogens:
self.halogens[line[2]].append(line)
if self.vs == True:
for halogen in self.halogens:
lig_size += 1
at_entry = self.halogens[halogen][2]
at_entry[1] = lig_size
at_entry[2] = self.halogens[halogen][1]
at_entry[8] = at_entry[8] + 0.001
at_entry[9] = at_entry[9] + 0.001
at_entry[10] = at_entry[10] + 0.001
at_entry[13] = ' H'
outline = IO.pdb_parse_out(at_entry)
outfile.write(outline + '\n')
os.rename(pdb_out, pdb_in)
if __name__ == "__main__":
parser = argparse.ArgumentParser(
prog='lig_prep',
formatter_class=argparse.RawDescriptionHelpFormatter,
description = ' == Generate parameter files for ligands. == ')
parser.add_argument('-l', '--ligand',
dest = "lig",
required = True,
help = "name of the ligand")
parser.add_argument('-FF', '--forcefield',
dest = "FF",
required = True,
help = "forcefield to use, OPLS2005 or OPLS2015")
parser.add_argument('-m', '--merge',
dest = "merge",
action = 'store_false',
default = True,
help = "Use this flag if you do not want the ligand prms to be merged")
parser.add_argument('-vs', '--virtual_site',
dest = "vs",
action = 'store_true',
default = False,
help = "Toggle to add virtual site Note: only Bn-X, where X is a halogen" \
" currently inlcuded. The parameters are extracted from:" \
"J. Chem. Theory Comput. 2012, 8, 10, 3895-3901"
)
parser.add_argument('-AA', '--aminoacid',
dest = "AA",
action = 'store_true',
default = False,
help = "When toggled, this module will treat the input .pdb as an AA")
parser.add_argument('-R', '--resname',
dest = "resname",
default = 'LIG',
help = "Change residue name (three letters)")
args = parser.parse_args()
run = Run(lig = args.lig,
FF = args.FF,
merge = args.merge,
vs = args.vs,
AA = args.AA,
resname = args.resname
)
run.get_parameters()
run.read_log()
run.convert_toQ()
if args.vs == True:
run.add_virtualsite()
run.write_lib_Q()
run.write_prm_Q()
run.rename_pdb()