def processDelPhiParams(self):
# Storing DelPhi parameters and Creates DelPhi data structures
logfile = "LOG_readFiles"
delphimol = DelPhi4py(
Config.pypka_params["f_crg"],
Config.pypka_params["f_siz"],
"delphi_in_stmod.pdb",
Config.delphi_params["gsize"],
Config.delphi_params["scaleM"],
Config.delphi_params["precision"],
epsin=Config.delphi_params["epsin"],
epsout=Config.delphi_params["epssol"],
conc=Config.delphi_params["ionicstr"],
ibctyp=Config.delphi_params["bndcon"],
res2=Config.delphi_params["maxc"],
nlit=Config.delphi_params["nlit"],
nonit=Config.delphi_params["nonit"],
relfac=0.0,
relpar=0.0,
pbx=Config.delphi_params["pbx"],
pby=Config.delphi_params["pby"],
isurftype=Config.delphi_params["nanoshaper"],
debug=Config.debug,
outputfile=logfile,
)
if Config.pypka_params["f_structure_out"]:
with open("delphi_in_stmod.pdb") as f:
self.delphi_input_content = f.readlines()
if Config.pypka_params["save_pdb"]:
with open("delphi_in_stmod.pdb") as f, open(
Config.pypka_params["save_pdb"], "w") as f_new:
content = f.read()
f_new.write(content)
if not Config.debug:
os.remove("delphi_in_stmod.pdb")
log.checkDelPhiErrors(logfile, "readFiles")
lookup_atoms = {}
for molecule in Config.titration.molecules.values():
for atom_name, atom_id, atom_position in molecule.iterAtoms():
lookup_atoms[atom_position] = (atom_id, atom_name)
# Stores DelPhi4py object and attributes
Config.delphi_params.store_run_params(delphimol)
Config.delphi_params.lookup_atoms = lookup_atoms
if Config.debug:
for chain, molecule in self.molecules.items():
print("### CHAIN {chain} ###".format(chain=chain))
molecule.printAllSites()
molecule.printAllTautomers()
print(delphimol)
def CalcPotentialTautomer(self):
"""Run DelPhi simulation of single site tautomer
Ensures:
self.esolvation (float): tautomer solvation energy
self.p_sitpot (list): potential on site atoms
"""
if Config.debug:
t0 = time.process_time()
print((self.name))
print((self.charge_set))
molecule = self.molecule
delphimol, acent = self.setDetailsFromTautomer()
if Config.delphi_params["bndcon"] == 3:
ibctyp = 4
else:
ibctyp = Config.delphi_params["bndcon"]
filename = "{0}_{1}.prm".format(self.name, self.site.res_number)
logfile = "LOG_runDelPhi_{0}_{1}_modelcompound".format(
self.name, self.site.res_number)
if Config.debug:
print(
("started", self.name, self.site.res_number, "modelcompound"))
delphimol.runDelPhi(
scale=Config.delphi_params["scaleM"],
nonit=0,
nlit=500,
relpar=0,
relfac=0,
acent=acent,
pbx=False,
pby=False,
debug=Config.debug,
filename=filename,
ibctyp=ibctyp,
outputfile=logfile,
)
if Config.debug:
print(("ended", self.name, self.site.res_number, "modelcompound"))
log.checkDelPhiErrors(logfile, "runDelPhi")
self.esolvation = delphimol.getSolvation()
self.p_sitpot = delphimol.getSitePotential()
if Config.debug:
t1 = time.process_time() - t0
filename = "{0}_{1}.profl".format(self.name,
self.getSiteResNumber())
with open(filename, "a") as f_new:
f_new.write("time -> {0:10} {1:10}\n".format(t0, t1))
return self.esolvation, self.p_sitpot[:]
def processDelPhiParams(self):
# Storing DelPhi parameters and Creates DelPhi data structures
logfile = 'LOG_readFiles'
delphimol = DelPhi4py(Config.pypka_params['f_crg'],
Config.pypka_params['f_siz'],
'delphi_in_stmod.pdb',
Config.delphi_params['gsize'],
Config.delphi_params['scaleM'],
Config.delphi_params['precision'],
epsin=Config.delphi_params['epsin'],
epsout=Config.delphi_params['epssol'],
conc=Config.delphi_params['ionicstr'],
ibctyp=Config.delphi_params['bndcon'],
res2=Config.delphi_params['maxc'],
nlit=Config.delphi_params['nlit'],
nonit=Config.delphi_params['nonit'],
relfac=0.0,
relpar=0.0,
pbx=Config.delphi_params['pbx'],
pby=Config.delphi_params['pby'],
isurftype=Config.delphi_params['nanoshaper'],
debug=Config.debug, outputfile=logfile)
if Config.pypka_params['f_structure_out']:
with open('delphi_in_stmod.pdb') as f:
self.delphi_input_content = f.readlines()
if not Config.debug:
os.remove('delphi_in_stmod.pdb')
log.checkDelPhiErrors(logfile, 'readFiles')
lookup_atoms = {}
for molecule in Config.titration.molecules.values():
for atom_name, atom_id, atom_position in molecule.iterAtoms():
lookup_atoms[atom_position] = (atom_id, atom_name)
# Stores DelPhi4py object and attributes
Config.delphi_params.store_run_params(delphimol)
Config.delphi_params.lookup_atoms = lookup_atoms
if Config.debug:
for chain, molecule in self.molecules.items():
print('### CHAIN {chain} ###'.format(chain=chain))
molecule.printAllSites()
molecule.printAllTautomers()
print(delphimol)
def cleanPDB(molecules, chains_res, inputpqr, outputpqr):
"""
"""
pdb_filename = Config.pypka_params['f_in']
pdb2pqr_path = Config.pypka_params['pdb2pqr']
inputpdbfile = removeMembrane(pdb_filename)
logfile = 'LOG_pdb2pqr'
#errfile = 'LOG_pdb2pqr_err'
#log.redirectOutput("start", logfile)
#log.redirectErr("start", errfile)
# CTR O1/O2 will be deleted and a O/OXT will be added
os.system('python2 {0} {1} {2} --ff {4} --ffout {4} '
'--drop-water -v --chain > {5} 2>&1 '.format(
pdb2pqr_path, inputpdbfile, inputpqr,
Config.pypka_params['ffinput'],
Config.pypka_params['ff_family'], logfile))
if Config.pypka_params['f_structure_out']:
ff_out = Config.pypka_params['ff_structure_out']
if ff_out == 'gromos_cph':
ff_out = 'gromos'
os.system('python2 {0} {1} Hs.pqr --ff {3} --ffout {3} '
'--drop-water -v --chain >> {2} 2>&1 '.format(
pdb2pqr_path, inputpdbfile, logfile, ff_out))
#log.redirectOutput("stop", logfile)
#log.redirectErr("stop", errfile)
if Config.pypka_params['f_structure_out']:
with open('Hs.pqr') as f:
for line in f:
if line.startswith('ATOM '):
(aname, anumb, resname, chain, resnumb, x, y, z, charge,
radius) = read_pqr_line(line)
if resnumb in chains_res['A'] and \
resname in AMBER_Hs and \
aname in AMBER_Hs[resname] and \
aname not in AMBER_mainchain_Hs:
continue
elif aname[0] == 'H' and aname not in ('H1', 'H2', 'H3'):
if not resnumb in mainchain_Hs:
mainchain_Hs[resnumb] = []
mainchain_Hs[resnumb].append(
(aname, anumb, resname, chain, x, y, z))
CYS_bridges = {}
with open('LOG_pdb2pqr') as f:
for line in f:
if 'patched with CYX' in line:
parts = line.split('patched')[0].replace('PATCH INFO: ',
'').split()
resname, chain, resnumb = parts
chain = chain.replace('_', ' ')
if not chain in CYS_bridges:
CYS_bridges[chain] = []
cys_res_numb = int(parts[-1])
if cys_res_numb not in CYS_bridges[chain]:
CYS_bridges[chain].append(cys_res_numb)
for chain, molecule in molecules.items():
if chain in CYS_bridges:
molecule.saveCYSBridges(CYS_bridges[chain])
new_pdb_text = ''
removed_pdb_text = ''
removed_pdb_lines = []
#ntr_trigger = True
resnumb_max = 0
chains = list(molecules.keys())
with open(inputpqr) as f:
for line in f:
if "ATOM" in line[:4]:
(aname, anumb, resname, original_chain, resnumb, x, y, z,
charge, radius) = read_pqr_line(line)
if original_chain == '_':
chain = ' '
else:
chain = original_chain
termini_trigger = False
if chain in chains:
molecule = molecules[chain]
NTR_numb = molecule.NTR
CTR_numb = molecule.CTR
sites_numbs = molecule.sites.keys()
aname, resname = correct_names(resnumb, resname, aname,
sites_numbs, NTR_numb,
CTR_numb)
resnumb_max = resnumb
if resnumb in (NTR_numb, CTR_numb):
termini_trigger = True
if aname in ('O1', 'O2',
'OT1', 'OT2',
'H1', 'H2', 'H3') and \
not termini_trigger and resname in PROTEIN_RESIDUES:
if aname == 'O1':
aname = 'O'
elif aname == 'H1':
aname = 'H'
else:
continue
if line[26] != ' ':
resnumb += TERMINAL_OFFSET
new_line = new_pqr_line(anumb,
aname,
resname,
resnumb,
x,
y,
z,
charge,
radius,
chain=original_chain)
if chain in molecules:
new_pdb_text += new_line
elif aname not in ('O1', 'O2', 'OT1', 'OT2', 'H1', 'H2', 'H3'):
if resname in ('SER', 'THR') and aname == 'HG1':
aname = 'HG'
removed_pdb_lines.append(new_line)
resnumb_old = resnumb_max + 1
for line in removed_pdb_lines:
(aname, anumb_old, resname, chain, resnumb, x, y, z, charge,
radius) = read_pqr_line(line)
anumb += 1
resnumb += resnumb_old
while resnumb < resnumb_max:
resnumb += resnumb_old
removed_pdb_text += new_pqr_line(anumb, aname, resname, resnumb, x, y,
z, charge, radius)
resnumb_max = resnumb
# if ntr_trigger and :
# config.tit_mole._NTR = resnumb
#chains = copy(chains_res['A'])
#for res in chains:
# if str(res) > config.terminal_offset:
# print((res, chains_res['A'][res]))
# del chains_res['A'][res]
#chains_res['A'][config.tit_mole._NTR] = 'NTR'
#chains_res['A'][config.tit_mole._CTR] = 'CTR'
with open('cleaned.pqr', 'w') as f_new:
f_new.write(new_pdb_text)
with open('removed.pqr', 'w') as f_new:
f_new.write(removed_pdb_text)
sites_addHtaut = ''
for chain in molecules:
for res in chains_res[chain]:
if chains_res[chain][res] == 'NTR' or \
(chain in CYS_bridges and res in CYS_bridges[chain]):
continue
sites_addHtaut += '{0}-{1}-{2},'.format(res,
chains_res[chain][res],
chain.replace(' ', '_'))
if len(sites_addHtaut) > 0 and sites_addHtaut[-1] == ',':
sites_addHtaut = sites_addHtaut[:-1]
logfile = 'LOG_addHtaut'
#log.redirectErr("start", logfile)
script_dir = Config.pypka_params['script_dir']
os.system('{}/addHtaut_{} cleaned.pqr {} > {} 2> {}'.format(
script_dir, Config.pypka_params['ff_family'], sites_addHtaut,
outputpqr, logfile))
#log.redirectErr("stop", logfile)
log.checkDelPhiErrors(logfile, 'addHtaut')
with open(outputpqr) as f:
content = f.read()
with open(outputpqr, 'w') as f_new:
f_new.write(content + removed_pdb_text)
with open(pdb_filename) as f:
box = None
for line in f:
if line.startswith('CRYST1'):
tmp = line.split()[1:4]
box = (float(tmp[0]), float(tmp[1]), float(tmp[2]))
if not box:
box = (1.0, 1.0, 1.0)
#pdb2gro(outputpqr, "TMP.gro", chains_res, box, pqr=True, fix_termini=False)
with open(outputpqr) as f,\
open('TMP.pdb', 'w') as fnew:
counter = 0
new_pdb_text = "CRYST1 {:3.3f} {:3.3f} {:3.3f} "\
"60.00 60.00 90.00 P 1 1\n".format(box[0],
box[1], box[2])
for line in f:
counter += 1
(aname, anumb_old, resname, chain, resnumb, x, y, z, charge,
radius) = read_pqr_line(line)
if chain == '_':
chain = ' '
new_pdb_text += new_pdb_line(counter,
aname,
resname,
resnumb,
x,
y,
z,
chain=chain)
fnew.write(new_pdb_text)
keep_membrane = False
keep_ions = False
if Config.delphi_params['pbc_dim'] == 2:
keep_membrane = True
if Config.pypka_params['keep_ions']:
keep_ions = True
if keep_ions or keep_membrane:
add_non_protein(pdb_filename,
'TMP.pdb',
keep_membrane=keep_membrane,
keep_ions=keep_ions)
tmpfiles = ('LOG_pdb2pqr', 'LOG_pdb2pqr_err', 'clean.pqr', 'cleaned.pqr',
'cleaned_tau.pqr', 'input_clean.pdb', 'removed.pqr', 'Hs.pqr')
for filename in tmpfiles:
if not Config.debug and os.path.isfile(filename):
os.remove(filename)
def CalcPotentialTitratingMolecule(self):
"""Run DelPhi simulation of the site tautomer
within the whole molecule
Ensures:
self.esolvation (float): tautomer solvation energy
self.p_sitpot (list): potential on site atoms
"""
if Config.debug:
start = time.process_time()
molecule = self.molecule
delphimol, acent = self.setDetailsFromWholeMolecule()
if Config.debug:
t0 = time.process_time() - start
print((self.name, 'starting'))
p_atpos = delphimol.get_atpos()
p_rad3 = delphimol.get_rad3()
p_chrgv4 = delphimol.get_chrgv4()
atinf = delphimol.get_atinf()
#for atom_name, atom_id, atom_position in molecule.iterAtoms():
# print (atinf[atom_position].value, p_chrgv4[atom_position], p_rad3[atom_position],
# p_atpos[atom_position][0], p_atpos[atom_position][1], p_atpos[atom_position][2])
filename = '{0}_{1}.prm'.format(self.name, self.site.res_number)
logfile = 'LOG_runDelPhi_{0}_{1}_wholeprotein'.format(
self.name, self.site.res_number)
if Config.debug:
print(('started', self.name, self.site.res_number, 'wholeprotein'))
if Config.delphi_params['pbc_dim'] == 2:
delphimol.runDelPhi(scale_prefocus=Config.delphi_params['scaleP'],
scale=Config.delphi_params['scaleM'],
nlit_prefocus=Config.delphi_params['nlit'],
nonit=Config.delphi_params['nonit'],
nlit=500,
acent=acent,
nonit_focus=0,
relfac_focus=0.0,
relpar_focus=0.0,
relpar=Config.delphi_params['relpar'],
relfac=Config.delphi_params['relfac'],
pbx=True,
pby=True,
pbx_focus=False,
pby_focus=False,
ibctyp=4,
debug=Config.debug,
filename=filename,
outputfile=logfile)
elif Config.delphi_params['pbc_dim'] == 0 and Config.delphi_params[
'bndcon'] == 3:
delphimol.runDelPhi(scale_prefocus=Config.delphi_params['scaleP'],
scale=Config.delphi_params['scaleM'],
nlit_prefocus=Config.delphi_params['nlit'],
nonit=0,
nlit=500,
acent=acent,
nonit_focus=0,
relfac_focus=0.0,
relpar_focus=0.0,
relpar=Config.delphi_params['relpar'],
relfac=Config.delphi_params['relfac'],
pbx=False,
pby=False,
pbx_focus=False,
pby_focus=False,
ibctyp=4,
debug=Config.debug,
filename=filename,
outputfile=logfile)
else:
delphimol.runDelPhi(scale=Config.delphi_params['scaleM'],
nonit=0,
nlit=500,
relpar=0,
relfac=0,
acent=acent,
pbx=False,
pby=False,
debug=Config.debug,
filename=filename,
outputfile=logfile)
if Config.debug:
print(('ended', self.name, self.site.res_number, 'wholeprotein'))
log.checkDelPhiErrors(logfile, 'runDelPhi')
self.esolvation = delphimol.getSolvation()
self.p_sitpot = delphimol.getSitePotential()
if Config.debug:
filename = '{0}_{1}.frc'.format(self.name, self.site.res_number)
with open(filename, 'w') as f:
text = ''
for atom_name, atom_id, atom_position in molecule.iterAtoms():
text += '{0} {1} {2} '\
'{3} {4} {5} {6}\n'.format(atinf[atom_position].value,
round(p_chrgv4[atom_position], 3),
round(p_rad3[atom_position], 4),
round(p_atpos[atom_position][0], 3),
round(p_atpos[atom_position][1], 3),
round(p_atpos[atom_position][2], 3),
self.p_sitpot[atom_position])
f.write(text)
t1 = time.process_time() - start
filename = '{0}_{1}.profl'.format(self.name,
self.getSiteResNumber())
with open(filename, 'a') as f_new:
f_new.write('time -> {0:10} {1:10}\n'.format(t0, t1))
print((self.esolvation, self.name))
return self.esolvation, self.p_sitpot[:]
def cleanPDB(molecules, chains_res, inputpqr, outputpqr):
""""""
pdb_filename = Config.pypka_params["f_in"]
pdb2pqr_path = Config.pypka_params["pdb2pqr"]
inputpdbfile = removeMembrane(pdb_filename)
logfile = "LOG_pdb2pqr"
# errfile = 'LOG_pdb2pqr_err'
# log.redirectOutput("start", logfile)
# log.redirectErr("start", errfile)
# CTR O1/O2 will be deleted and a O/OXT will be added
os.system(
"python2 {0} {1} {2} --ff {3} --ffout {4} "
"--drop-water -v --chain > {5} 2>&1 ".format(
pdb2pqr_path,
inputpdbfile,
inputpqr,
Config.pypka_params["ffinput"],
Config.pypka_params["ff_family"],
logfile,
)
)
if Config.pypka_params["f_structure_out"]:
ff_out = Config.pypka_params["ff_structure_out"]
if ff_out == "gromos_cph":
ff_out = "gromos"
os.system(
"python2 {0} {1} Hs.pqr --ff {3} --ffout {3} "
"--drop-water -v --chain >> {2} 2>&1 ".format(
pdb2pqr_path, inputpdbfile, logfile, ff_out
)
)
# log.redirectOutput("stop", logfile)
# log.redirectErr("stop", errfile)
if Config.pypka_params["f_structure_out"]:
with open("Hs.pqr") as f:
for line in f:
if line.startswith("ATOM "):
(
aname,
anumb,
resname,
chain,
resnumb,
x,
y,
z,
charge,
radius,
) = read_pqr_line(line)
if (
resnumb in chains_res["A"]
and resname in AMBER_Hs
and aname in AMBER_Hs[resname]
and aname not in AMBER_mainchain_Hs
):
continue
elif aname[0] == "H" and aname not in ("H1", "H2", "H3"):
if not resnumb in mainchain_Hs:
mainchain_Hs[resnumb] = []
mainchain_Hs[resnumb].append(
(aname, anumb, resname, chain, x, y, z)
)
CYS_bridges = {}
with open("LOG_pdb2pqr") as f:
for line in f:
if "patched with CYX" in line:
parts = line.split("patched")[0].replace("PATCH INFO: ", "").split()
resname, chain, resnumb = parts
chain = chain.replace("_", " ")
if not chain in CYS_bridges:
CYS_bridges[chain] = []
cys_res_numb = int(parts[-1])
if cys_res_numb not in CYS_bridges[chain]:
CYS_bridges[chain].append(cys_res_numb)
for chain, molecule in molecules.items():
if chain in CYS_bridges:
molecule.saveCYSBridges(CYS_bridges[chain])
new_pdb_text = ""
removed_pdb_text = ""
removed_pdb_lines = []
# ntr_trigger = True
resnumb_max = 0
chains = list(molecules.keys())
with open(inputpqr) as f:
for line in f:
if "ATOM" in line[:4]:
(
aname,
anumb,
resname,
original_chain,
resnumb,
x,
y,
z,
charge,
radius,
) = read_pqr_line(line)
if original_chain == "_":
chain = " "
else:
chain = original_chain
termini_trigger = False
if chain in chains:
molecule = molecules[chain]
NTR_numb = molecule.NTR
CTR_numb = molecule.CTR
sites_numbs = molecule.sites.keys()
aname, resname = correct_names(
resnumb, resname, aname, sites_numbs, NTR_numb, CTR_numb
)
resnumb_max = resnumb
if resnumb in (NTR_numb, CTR_numb):
termini_trigger = True
if (
aname in ("O1", "O2", "OT1", "OT2", "H1", "H2", "H3")
and not termini_trigger
and resname in PROTEIN_RESIDUES
):
if aname == "O1":
aname = "O"
elif aname == "H1":
aname = "H"
else:
continue
if line[26] != " ":
resnumb += TERMINAL_OFFSET
new_line = new_pqr_line(
anumb,
aname,
resname,
resnumb,
x,
y,
z,
charge,
radius,
chain=original_chain,
)
if chain in molecules:
new_pdb_text += new_line
elif aname not in ("O1", "O2", "OT1", "OT2", "H1", "H2", "H3"):
if resname in ("SER", "THR") and aname == "HG1":
aname = "HG"
removed_pdb_lines.append(new_line)
resnumb_old = resnumb_max + 1
for line in removed_pdb_lines:
(
aname,
anumb_old,
resname,
chain,
resnumb,
x,
y,
z,
charge,
radius,
) = read_pqr_line(line)
anumb += 1
resnumb += resnumb_old
while resnumb < resnumb_max:
resnumb += resnumb_old
removed_pdb_text += new_pqr_line(
anumb, aname, resname, resnumb, x, y, z, charge, radius
)
resnumb_max = resnumb
# if ntr_trigger and :
# config.tit_mole._NTR = resnumb
# chains = copy(chains_res['A'])
# for res in chains:
# if str(res) > config.terminal_offset:
# print((res, chains_res['A'][res]))
# del chains_res['A'][res]
# chains_res['A'][config.tit_mole._NTR] = 'NTR'
# chains_res['A'][config.tit_mole._CTR] = 'CTR'
with open("cleaned.pqr", "w") as f_new:
f_new.write(new_pdb_text)
with open("removed.pqr", "w") as f_new:
f_new.write(removed_pdb_text)
sites_addHtaut = ""
for chain in molecules:
for res in chains_res[chain]:
if chains_res[chain][res] == "NTR" or (
chain in CYS_bridges and res in CYS_bridges[chain]
):
continue
sites_addHtaut += "{0}-{1}-{2},".format(
res, chains_res[chain][res], chain.replace(" ", "_")
)
if len(sites_addHtaut) > 0 and sites_addHtaut[-1] == ",":
sites_addHtaut = sites_addHtaut[:-1]
logfile = "LOG_addHtaut"
# log.redirectErr("start", logfile)
script_dir = Config.pypka_params["script_dir"]
os.system(
"{}/addHtaut_{} cleaned.pqr {} > {} 2> {}".format(
script_dir,
Config.pypka_params["ff_family"],
sites_addHtaut,
outputpqr,
logfile,
)
)
# log.redirectErr("stop", logfile)
log.checkDelPhiErrors(logfile, "addHtaut")
with open(outputpqr) as f:
content = f.read()
with open(outputpqr, "w") as f_new:
f_new.write(content + removed_pdb_text)
with open(pdb_filename) as f:
box = None
for line in f:
if line.startswith("CRYST1"):
tmp = line.split()[1:4]
box = (float(tmp[0]), float(tmp[1]), float(tmp[2]))
if not box:
box = (1.0, 1.0, 1.0)
# pdb2gro(outputpqr, "TMP.gro", chains_res, box, pqr=True, fix_termini=False)
with open(outputpqr) as f, open("TMP.pdb", "w") as fnew:
counter = 0
new_pdb_text = (
"CRYST1 {:3.3f} {:3.3f} {:3.3f} "
"60.00 60.00 90.00 P 1 1\n".format(box[0], box[1], box[2])
)
for line in f:
counter += 1
(
aname,
anumb_old,
resname,
chain,
resnumb,
x,
y,
z,
charge,
radius,
) = read_pqr_line(line)
if chain == "_":
chain = " "
new_pdb_text += new_pdb_line(
counter, aname, resname, resnumb, x, y, z, chain=chain
)
fnew.write(new_pdb_text)
keep_membrane = False
keep_ions = False
if Config.delphi_params["pbc_dim"] == 2:
keep_membrane = True
if Config.pypka_params["keep_ions"]:
keep_ions = True
if keep_ions or keep_membrane:
add_non_protein(
pdb_filename, "TMP.pdb", keep_membrane=keep_membrane, keep_ions=keep_ions
)
tmpfiles = (
"LOG_pdb2pqr",
"LOG_pdb2pqr_err",
"clean.pqr",
"cleaned.pqr",
"cleaned_tau.pqr",
"input_clean.pdb",
"removed.pqr",
"Hs.pqr",
)
for filename in tmpfiles:
if not Config.debug and os.path.isfile(filename):
os.remove(filename)