def select_waters(self):
src = 'water.pdb'
tgt = self.directory + '/inputfiles/water.pdb'
cofactor_coordinates = []
waters_remove = []
waters = {}
if self.cofactor[0] != None:
for line in self.cofactor:
with open(line + '.pdb') as infile:
for line in infile:
if line.startswith(self.include):
line = IO.pdb_parse_in(line)
cofactor_coordinates.append(
[line[8], line[9], line[10]])
with open(src) as infile, open(tgt, 'w') as outfile:
outfile.write('{} SPHERE\n'.format(self.radius))
for line in infile:
line = IO.pdb_parse_in(line)
coord_wat = [line[8], line[9], line[10]]
try:
waters[line[6]].append(line)
except:
waters[line[6]] = [line]
for coord_co in cofactor_coordinates:
if f.euclidian_overlap(coord_wat, coord_co, 1.6) == True:
waters_remove.append(line[6])
for key in waters:
if key not in waters_remove:
for water in waters[key]:
outfile.write(IO.pdb_parse_out(water) + '\n')
def write_pdb_out(self):
waters ={'HOH': ['O', 'H1', 'H2'],
'SOL': ['OW1', 'HW1', 'HW2']
}
waters_tokeep = []
with open('top_p.pdb') as infile:
for line in infile:
if line.startswith(self.include):
line = IO.pdb_parse_in(line)
if line[4].strip() in waters and \
line[2].strip() == waters[line[4].strip()][0]:
coord1 = self.center
coord2 = [float(line[8]),
float(line[9]),
float(line[10])
]
if f.euclidian_overlap(coord1, coord2, self.radius) == True:
waters_tokeep.append(line[6])
with open('top_p.pdb') as infile, \
open('water.pdb', 'w') as watout, \
open('protein.pdb', 'w') as protout:
for line in infile:
if line.startswith(self.include):
line = IO.pdb_parse_in(line)
if line[6] in waters_tokeep:
outline = IO.pdb_parse_out(line) + '\n'
watout.write(outline)
if line[4] not in waters:
outline = IO.pdb_parse_out(line) + '\n'
protout.write(outline)
def get_CYX(self):
cys = []
cyx = []
cys_bond = 2.2
cys_mat = []
i = 0
k = -1
# Reduce coordinate array
for chain in self.PDB:
for key in self.PDB[chain]:
at = self.PDB[chain][key]
if at[4] == 'CYS' or at[4] == 'CYX' and at[2].strip() == 'SG':
cys.append([at[6], (at[8], at[9], at[10])])
# Construct S-S bond matrix
for SG_1 in cys:
cys_list = [SG_1[0]]
for SG_2 in cys:
cys_list.append(
f.euclidian_overlap(SG_1[1], SG_2[1], cys_bond))
cys_mat.append(cys_list)
# Fix to better handling
try:
total = len(cys_mat[0]) - 1
for line in cys_mat:
k += 1
for j in range(i, total):
if cys_mat[i][
j +
1] == True and cys_mat[k][0] != cys_mat[j][0]:
cyx.append(cys_mat[k][0])
cyx.append(cys_mat[j][0])
outline = '{:<10}{:<10}{:<10}{:<10}{:<10}{:<10}'.format(
self.log['QRESN'][chain][cys_mat[k][0]],
self.log['QRESN'][chain][cys_mat[j][0]],
cys_mat[k][0], chain, cys_mat[j][0], chain)
self.log['CYX'].append(outline)
i += 1
for chain in self.PDB:
for key in self.PDB[chain]:
at = self.PDB[chain][key]
if at[6] in cyx and at[4] == 'CYS':
self.PDB[chain][key][4] = 'CYX'
except:
return None
def get_mutations(self):
test = []
with open('protein.pdb') as infile:
for line in infile:
if line.startswith(self.include):
line = IO.pdb_parse_in(line)
if int(line[6]) in self.CYS:
continue
if line[4] in self.exclude:
continue
coord = (line[8], line[9], line[10])
self.prot_coord[line[1]] = [coord, line[6], line[4]]
for lig in self.lig:
self.liglist.append("'{}'".format(lig))
with open(lig + '.pdb') as infile:
for line in infile:
if line.startswith(self.include):
line = IO.pdb_parse_in(line)
coord1 = (line[8], line[9], line[10])
for at in self.prot_coord:
coord2 = self.prot_coord[at][0]
if f.euclidian_overlap(coord1,
coord2,
float(self.dist)) \
== True:
res = self.prot_coord[at][1]
if self.prot_coord[at][2] != 'ALA':
mutation = self.prot_coord[at][2] + str(
self.mapping[res]) + 'A'
else:
mutation = self.prot_coord[at][2] + str(
self.mapping[res]) + 'G'
if mutation not in self.mutations:
self.mutations.append(mutation)
def prepwizard_parse(self):
if self.origin == 'gromacs':
with open(self.prot) as infile, \
open(self.prot[:-4] + '_noH.pdb', 'w') as outfile:
for line in infile:
tmp = line
if line.startswith(self.include) == False:
continue
line = IO.pdb_parse_in(line)
if tmp[13] == 'H': # and line[4] != 'SOL':
write = False
else:
write = True
# Change residue name of waters
if line[4] == 'SOL':
line[4] = 'HOH'
if line[2] == 'OW':
line[2] = 'O'
coord1 = self.center
coord2 = [
float(line[8]),
float(line[9]),
float(line[10])
]
write = f.euclidian_overlap(
coord1, coord2, self.radius + 5)
if self.water != False:
line_out = IO.pdb_parse_out(line)
else:
continue
elif line[4] == 'ILE' and line[2] == 'CD':
line[2] = 'CD1'
line_out = IO.pdb_parse_out(line)
elif line[4] == 'CL-':
continue
line_out = IO.pdb_parse_out(line)
# Get the charges from the hydrogen connections
# NOTE: this might be more common and thus less lines of code might be
# needed, check when implementing MolProbity!!
if line[4] in IO.charged_res:
if line[2] in IO.charged_res[line[4]]:
if line[5] not in self.original_charges:
self.original_charges[line[5]] = {}
if line[2] not in IO.charged_res[line[4]]:
self.original_charges[line[5]][line[6]] = 'HIP'
else:
self.original_charges[line[5]][line[6]] = \
IO.charged_res[line[4]][line[2]]
if write == True:
outfile.write(line_out + '\n')
elif self.origin == 'maestro':
with open(self.prot) as infile, \
open(self.prot[:-4] + '_noH.pdb', 'w') as outfile:
for line in infile:
if line.startswith(self.include):
line = IO.pdb_parse_in(line)
if line[2][0] != 'H':
outline = IO.pdb_parse_out(line)
outfile.write(outline + '\n')
# Get the charges from the hydrogen connections
if line[4] in IO.charged_res:
if line[2] in IO.charged_res[line[4]]:
if line[5] not in self.original_charges:
self.original_charges[line[5]] = {}
if line[2] not in IO.charged_res[line[4]]:
self.original_charges[line[5]][
line[6]] = 'HIP'
else:
self.original_charges[line[5]][line[
6]] = IO.charged_res[line[4]][line[2]]
def decharge(self):
charged_res = {
'GLU': ['GLH', 'CD', -1],
'ASP': ['ASH', 'CG', -1],
'ARG': ['ARN', 'CZ', 1],
'LYS': ['LYN', 'NZ', 1],
'HIP': ['HID', 'CG', 1]
}
coord1 = self.center
decharge = {}
# Distance for decharging residues in boundary
rest_bound = float(self.radius) - 3.0
for chain in self.PDB:
for key in self.PDB[chain]:
at = self.PDB[chain][key]
if at[4] in charged_res:
if at[2].strip() == charged_res[at[4]][1]:
coord2 = [float(at[8]), float(at[9]), float(at[10])]
if f.euclidian_overlap(coord1, coord2,
rest_bound) == False:
if not at[5] in decharge:
decharge[at[5]] = [at[6]]
else:
decharge[at[5]].append(at[6])
outline = '{:<10}{:<10}{:<10}{:<10}'.format(
self.log['QRESN'][chain][at[6]], at[6], chain,
at[4])
self.log['DECHARGE'].append(outline)
# Check if the decharged residue is part of a salt bridge and
# neutralize this residue as well
for chain in self.PDB:
for key in self.PDB[chain]:
at = self.PDB[chain][key]
if chain not in decharge:
continue
if at[6] in decharge[chain] and at[2].strip() == charged_res[
at[4]][1]:
coord1 = [float(at[8]), float(at[9]), float(at[10])]
for chain2 in self.PDB:
for key2 in self.PDB[chain2]:
at_2 = self.PDB[chain2][key2]
if at_2[4] in charged_res:
if at_2[2].strip() == charged_res[at_2[4]][1]:
coord2 = [
float(at_2[8]),
float(at_2[9]),
float(at_2[10])
]
if at == at_2:
continue
if at_2[6] in decharge[chain]:
continue
if at_2[6] in decharge[chain2]:
continue
if f.euclidian_overlap(
coord1, coord2, 4.0) == True:
decharge[chain2].append(at_2[6])
outline = '{:<10}{:<10}{:<10}{:<10}'.format(
self.log['QRESN'][chain2][at_2[6]],
at_2[6], chain2, at_2[4])
self.log['DECHARGE'].append(outline)
# Get the charged residues in the sphere and the total charge of these residues in the sphere
for chain in self.PDB:
for key in self.PDB[chain]:
at = self.PDB[chain][key]
if chain not in decharge:
continue
if at[6] in decharge[chain]:
at[4] = charged_res[at[4]][0]
continue
else: # at[4] in charged_res:
if at[4] in charged_res:
if at[2].strip() == charged_res[at[4]][1]:
self.log['CHARGE'].append(
'{:<10}{:<10}{:<10}{:<10}'.format(
self.log['QRESN'][chain][at[6]], at[6],
chain, at[4]))
self.log['TOTAL_CHARGE'] += charged_res[at[4]][2]
