def test_api_penta_lys(self):
os.system("rm -rf LOG* *out *gro *pdb *pqr *crg *sites cent "
"contributions interactions.dat pkint LOG* __pycache__ *pyc")
results = """
LYS 4 None ('undefined', 'pk Not In Range') (2, (0.651625, 0.219385)) 3 {10.7: 0.348375}
"""
params = {
"structure": "penta/LYS/protein_000.gro",
"ncpus": ncpus,
"epsin": 2,
"ionicstr": 0.1,
"pbc_dimensions": 0,
"pH": "10.7",
"clean_pdb": False,
"sts": "sts_cphmd",
}
sites = {"A": ["4"]}
pKa = Titration(params, sites=sites)
checkAPIResult(pKa, results, pH=10.7, extended=True)
results = """
LYS 4 None ('undefined', 'pk Not In Range') (2, (0.898065, 0.71377)) 3 {10.7: 0.101935}
"""
params["structure"] = "penta/LYS/protein_006.gro"
pKa = Titration(params, sites=sites)
checkAPIResult(pKa, results, pH=10.7, extended=True)
def test_api_penta_ntr(self):
os.system("rm -rf LOG* *out *gro *pdb *pqr *crg *sites cent "
"contributions interactions.dat pkint LOG* __pycache__ *pyc")
results = """
NTR 5001 None ('undefined', 'pk Not In Range') (4, (0.608115, 0.608115)) 3 {7.7: 0.608115}
"""
params = {
"structure": "penta/NTR/protein_000.gro",
"ncpus": ncpus,
"epsin": 2,
"ionicstr": 0.1,
"pbc_dimensions": 0,
"pH": "7.7",
"clean_pdb": False,
"sts": "sts_cphmd",
}
sites = {"A": ["1N"]}
pKa = Titration(params, sites=sites)
checkAPIResult(pKa, results, pH=7.7, extended=True)
results = """
NTR 5001 None ('undefined', 'pk Not In Range') (2, (0.736045, 0.447095)) 2 {7.7: 0.263955}
"""
params["structure"] = "penta/NTR/protein_007.gro"
pKa = Titration(params, sites=sites)
checkAPIResult(pKa, results, pH=7.7, extended=True)
def test_api_penta_tyr(self):
os.system("rm -rf LOG* *out *gro *pdb *pqr *crg *sites cent "
"contributions interactions.dat pkint LOG* __pycache__ *pyc")
results = """
TYR 4 None ('undefined', 'pk Not In Range') (3, (0.52272, 0.52272)) 0 {9.5: 0.47728}
"""
params = {
"structure": "penta/TYR/protein_001.gro",
"ncpus": ncpus,
"epsin": 2,
"ionicstr": 0.1,
"pbc_dimensions": 0,
"pH": "9.5",
"clean_pdb": False,
"sts": "sts_cphmd",
}
sites = {"A": ["4"]}
pKa = Titration(params, sites=sites)
checkAPIResult(pKa, results, pH=9.5, extended=True)
results = """
TYR 4 None ('undefined', 'pk Not In Range') (2, (0.7652749999999999, 0.390635)) 0 {9.5: 0.765275}
"""
params["structure"] = "penta/TYR/protein_005.gro"
pKa = Titration(params, sites=sites)
checkAPIResult(pKa, results, pH=9.5, extended=True)
def test_api_penta_asp(self):
os.system("rm -rf LOG* *out *gro *pdb *pqr *crg *sites cent "
"contributions interactions.dat pkint LOG* __pycache__ *pyc")
results = """
ASP 4 None ('undefined', 'pk Not In Range') (5, (0.879815, 0.879815)) 4 {4.2: 0.120185}
"""
params = {
"structure": "penta/ASP/asp1.gro",
"ncpus": ncpus,
"epsin": 2,
"ionicstr": 0.1,
"pbc_dimensions": 0,
"pH": "4.2",
"clean_pdb": False,
"sts": "sts_cphmd",
}
sites = {"A": [4]}
pKa = Titration(params, sites=sites)
checkAPIResult(pKa, results, pH=4.2, extended=True)
results = """
ASP 4 None ('undefined', 'pk Not In Range') (1, (0.5596, 0.33636)) 4 {4.2: 0.5596}
"""
params["structure"] = "penta/ASP/asp2.gro"
pKa = Titration(params, sites=sites)
checkAPIResult(pKa, results, pH=4.2, extended=True)
def test_api_penta_glu(self):
os.system("rm -rf LOG* *out *gro *pdb *pqr *crg *sites cent "
"contributions interactions.dat pkint LOG* __pycache__ *pyc")
results = """
GLU 4 None ('undefined', 'pk Not In Range') (5, (0.73255, 0.73255)) 4 {4.5: 0.26745}
"""
params = {
"structure": "penta/GLU/protein_000.gro",
"ncpus": ncpus,
"epsin": 2,
"ionicstr": 0.1,
"pbc_dimensions": 0,
"pH": "4.5",
"clean_pdb": False,
"sts": "sts_cphmd",
}
sites = {"A": ["4"]}
pKa = Titration(params, sites=sites)
checkAPIResult(pKa, results, pH=4.5, extended=True)
results = """
GLU 4 None ('undefined', 'pk Not In Range') (5, (0.55045, 0.55045)) 4 {4.5: 0.44955}
"""
params["structure"] = "penta/GLU/protein_003.gro"
pKa = Titration(params, sites=sites)
checkAPIResult(pKa, results, pH=4.5, extended=True)
def test_api_penta_his(self):
os.system("rm -rf LOG* *out *gro *pdb *pqr *crg *sites cent "
"contributions interactions.dat pkint LOG* __pycache__ *pyc")
results = """
HIS 4 None ('undefined', 'pk Not In Range') (3, (0.859865, 0.859865)) 0 {6.2: 0.859865}
"""
params = {
"structure": "penta/HIS/protein_000.gro",
"ncpus": ncpus,
"epsin": 2,
"ionicstr": 0.1,
"pbc_dimensions": 0,
"pH": "6.2",
"clean_pdb": False,
"sts": "sts_cphmd",
}
sites = {"A": ["4"]}
pKa = Titration(params, sites=sites)
checkAPIResult(pKa, results, pH=6.2, extended=True)
results = """
HIS 4 None ('undefined', 'pk Not In Range') (2, (0.933485, 0.900285)) 1 {6.2: 0.066515}
"""
params["structure"] = "penta/HIS/protein_003.gro"
pKa = Titration(params, sites=sites)
checkAPIResult(pKa, results, pH=6.2, extended=True)
def test_api_penta_cys(self):
os.system("rm -rf LOG* *out *gro *pdb *pqr *crg *sites cent "
"contributions interactions.dat pkint LOG* __pycache__ *pyc")
results = """
CYS 4 None ('undefined', 'pk Not In Range') (3, (0.925685, 0.479055)) 2 {8.2: 0.925685}
"""
params = {
"structure": "penta/CYS/protein_000.gro",
"ncpus": ncpus,
"epsin": 2,
"ionicstr": 0.1,
"pbc_dimensions": 0,
"pH": "8.2",
"clean_pdb": False,
"sts": "sts_cphmd",
}
sites = {"A": ["4"]}
pKa = Titration(params, sites=sites)
checkAPIResult(pKa, results, pH=8.2, extended=True)
results = """
CYS 4 None ('undefined', 'pk Not In Range') (2, (0.61114, 0.28937)) 3 {8.2: 0.61114}
"""
params["structure"] = "penta/CYS/protein_001.gro"
pKa = Titration(params, sites=sites)
checkAPIResult(pKa, results, pH=8.2, extended=True)
def test_api_penta_ctr(self):
os.system("rm -rf LOG* *out *gro *pdb *pqr *crg *sites cent "
"contributions interactions.dat pkint LOG* __pycache__ *pyc")
results = """
CTR 5006 None ('undefined', 'pk Not In Range') (5, (0.886665, 0.886665)) 4 {4.0: 0.113335}
"""
params = {
"structure": "penta/CTR/ctr1.gro",
"ncpus": ncpus,
"epsin": 2,
"ionicstr": 0.1,
"pbc_dimensions": 0,
"pH": "4.0",
"clean_pdb": False,
"sts": "sts_cphmd",
}
sites = {"A": ["6C"]}
pKa = Titration(params, sites=sites)
checkAPIResult(pKa, results, pH=4.0, extended=True)
results = """
CTR 5006 None ('undefined', 'pk Not In Range') (5, (0.57106, 0.57106)) 4 {4.0: 0.42894}
"""
params["structure"] = "penta/CTR/ctr2.gro"
pKa = Titration(params, sites=sites)
checkAPIResult(pKa, results, pH=4.0, extended=True)
def test_api_ktp_pdb_onlytermini_noclean(self):
os.system("rm -rf LOG* *out *gro *pdb *pqr *crg *sites cent "
"contributions interactions.dat pkint LOG* __pycache__ *pyc")
results = """
NTR 5001 8.199054937290231 ('protonated', 0.9405274528487423)
CTR 5002 3.099830508474576 ('deprotonated', 0.00012582758427877238)
"""
parameters = {
"structure":
"ktp/ktp_pdb_onlytermini_noclean/ktp_noclean.pdb", # MANDATORY
"clean_pdb": "no",
"epsin": 2,
"ionicstr": 0.1,
"pbc_dimensions": 0,
"temp": 310,
"grid_fill": 0.8, # FUTURE VERSION
"ncpus": ncpus,
"pH": "0,15",
"pHstep": 0.25,
"logfile": "LOGFILE",
"scaleM": 4,
"scaleP": 1,
"gsize": 81,
"convergence": 0.01,
"nlit": 300,
"cutoff": -1,
"relfac": 0.0,
"output": "pKas.out",
"clean_pdb": False,
}
sites = {" ": ("1N", "2C")}
pKa = Titration(parameters, sites=sites)
checkAPIResult(pKa, results)
def test_api_ktp_pdb_onlytermini(self):
os.system("rm -rf LOG* *out *gro *pdb *pqr *crg *sites cent "
"contributions interactions.dat pkint LOG* __pycache__ *pyc")
results = """
NTR 5001 7.931056701030927 ('undefined', 0.8950914882162796)
CTR 5002 3.0073796144818266 ('deprotonated', 0.00010170339324314826)
"""
parameters = {
"structure": "ktp/ktp_pdb_onlytermini/ktp.pdb", # MANDATORY
"clean_pdb": "yes",
"epsin": 2,
"ionicstr": 0.1,
"pbc_dimensions": 0,
"temp": 310,
"grid_fill": 0.8, # FUTURE VERSION
"ncpus": ncpus,
"pH": "0,15",
"pHstep": 0.25,
"logfile": "LOGFILE",
"scaleM": 4,
"scaleP": 1,
"gsize": 81,
"convergence": 0.01,
"nlit": 300,
"cutoff": -1,
"relfac": 0.0,
"output": "pKas.out",
"clean_pdb": True,
"remove_hs": False,
}
sites = {" ": ("1N", "2C")}
pKa = Titration(parameters, sites=sites)
checkAPIResult(pKa, results)
def test_api_ktp_gro(self):
os.system(
"rm -f LOG* *out *gro *pdb *pqr *crg *sites cent contributions interactions.dat pkint"
)
results = """
NTR 5001 7.932515230635335 ('undefined', 0.8954064318344567)
TYR 1 9.884779718110096 ('protonated', 0.9986978698182121)
CTR 5002 2.8373655675051106 ('deprotonated', 6.875997409570579e-05)
"""
parameters = {
"structure": "ktp/ktp_gro/ktp.gro",
"epsin": 2,
"ionicstr": 0.1,
"pbc_dimensions": 0,
"temp": 310,
"grid_fill": 0.8, # FUTURE VERSION
"ncpus": ncpus,
"pH": "-5,15",
"pHstep": 0.2,
"logfile": "LOGFILE",
"scaleM": 4,
"scaleP": 1,
"gsize": 81,
"convergence": 0.01,
"nlit": 500,
"cutoff": -1,
"relfac": 0.0,
"output": "pKas.out",
"clean_pdb": False,
}
sites = {"A": ("1N", "1", "2C")}
pKa = Titration(parameters, sites=sites)
checkAPIResult(pKa, results)
def save_residues(tit: pypka.Titration, pid: int) -> pypka.Titration:
# Save residue-level details
(
all_sites,
_,
_,
_,
) = tit.getSiteInteractions()
for site in all_sites:
residue_details = {
"pid": pid,
"residue_number": site.getResNumber(),
"residue_type": site.res_name,
"chain": site.molecule.chain,
}
res_insert = insert(Residue).values(residue_details)
res_insert = res_insert.on_conflict_do_update(
index_elements=["pid", "residue_number", "residue_type", "chain"],
set_={
"pid": pid
},
).returning(Residue.resid)
result = session.execute(res_insert)
resid = result.fetchall()[0][0]
site.resid = resid
session.commit()
return tit
def test_api_antibody(self):
os.system("rm -rf LOG* *out *gro *pdb *pqr *crg *sites cent "
"contributions interactions.dat pkint LOG* __pycache__ *pyc")
results = """
NTR 5001 None ('undefined', 'pk Not In Range') (4, (0.883505, 0.883505)) 3 {7.0: 0.883505}
GLU 6 None ('undefined', 'pk Not In Range') (5, (0.998505, 0.998505)) 4 {7.0: 0.001495}
SER 7 None ('undefined', 'pk Not In Range') (3, (1.0, 0.45602)) 2 {7.0: 1.0}
SER 17 None ('undefined', 'pk Not In Range') (1, (1.0, 0.33859)) 0 {7.0: 1.0}
SER 21 None ('undefined', 'pk Not In Range') (3, (1.0, 0.46141)) 1 {7.0: 1.0}
CYS 22 None ('undefined', 'pk Not In Range') (2, (0.99653, 0.360205)) 1 {7.0: 0.99653}
SER 25 None ('undefined', 'pk Not In Range') (2, (1.0, 0.460985)) 1 {7.0: 1.0}
LYS 218 None ('undefined', 'pk Not In Range') (4, (0.999715, 0.999715)) 3 {7.0: 0.999715}
SER 219 None ('undefined', 'pk Not In Range') (1, (0.9999999999999999, 0.44376)) 0 {7.0: 1.0}
CTR 5220 None ('undefined', 'pk Not In Range') (5, (0.999825, 0.999825)) 4 {7.0: 0.000175}
CYS 220 None ('undefined', 'pk Not In Range') (3, (0.9984500000000001, 0.376525)) 2 {7.0: 0.99845}
NTR 5001 None ('undefined', 'pk Not In Range') (4, (0.89596, 0.89596)) 3 {7.0: 0.89596}
THR 5 None ('undefined', 'pk Not In Range') (3, (1.0, 0.50905)) 0 {7.0: 1.0}
SER 7 None ('undefined', 'pk Not In Range') (1, (1.0, 0.44146)) 1 {7.0: 1.0}
SER 9 None ('undefined', 'pk Not In Range') (3, (1.0, 0.41821)) 2 {7.0: 1.0}
SER 12 None ('undefined', 'pk Not In Range') (3, (1.0, 0.36406)) 0 {7.0: 1.0}
SER 14 None ('undefined', 'pk Not In Range') (2, (1.0, 0.382485)) 2 {7.0: 1.0}
ASP 17 None ('undefined', 'pk Not In Range') (5, (0.99974, 0.99974)) 4 {7.0: 0.00026}
THR 20 None ('undefined', 'pk Not In Range') (2, (1.0, 0.39265)) 0 {7.0: 1.0}
THR 22 None ('undefined', 'pk Not In Range') (3, (1.0, 0.365115)) 2 {7.0: 1.0}
CYS 23 None ('undefined', 'pk Not In Range') (2, (0.99302, 0.358615)) 2 {7.0: 0.99302}
GLU 214 None ('undefined', 'pk Not In Range') (5, (0.99813, 0.99813)) 4 {7.0: 0.00187}
CTR 5215 None ('undefined', 'pk Not In Range') (5, (0.999775, 0.999775)) 4 {7.0: 0.000225}
CYS 215 None ('undefined', 'pk Not In Range') (2, (0.99854, 0.37496)) 1 {7.0: 0.99854}
NTR 5332 None ('undefined', 'pk Not In Range') (4, (0.854645, 0.854645)) 3 {7.0: 0.854645}
HIS 332 None ('undefined', 'pk Not In Range') (2, (0.875545, 0.70737)) 1 {7.0: 0.124455}
THR 333 None ('undefined', 'pk Not In Range') (2, (1.0, 0.46669)) 2 {7.0: 1.0}
CYS 336 None ('undefined', 'pk Not In Range') (3, (0.985125, 0.336865)) 0 {7.0: 0.985125}
GLU 340 None ('undefined', 'pk Not In Range') (5, (0.99765, 0.99765)) 4 {7.0: 0.00235}
CYS 525 None ('undefined', 'pk Not In Range') (1, (0.9649099999999999, 0.335965)) 0 {7.0: 0.96491}
CTR 5527 None ('undefined', 'pk Not In Range') (5, (0.99998, 0.99998)) 4 {7.0: 2e-05}
LYS 527 None ('undefined', 'pk Not In Range') (4, (0.999805, 0.999805)) 3 {7.0: 0.999805}
"""
params = {
"structure": "proteins/Ab269/Ab269-RBD.pdb",
"ncpus": ncpus,
"epsin": 15,
"ionicstr": 0.1,
"pbc_dimensions": 0,
"pH": "7",
"structure_output": ("proteins/Ab269/Ab269-RBD_7.pdb", 7, "AMBER"),
}
pKa = Titration(params)
checkAPIResult(pKa, results, extended=True)
check_file_diff("builder/Ab269-RBD_7.pdb",
"proteins/Ab269/Ab269-RBD_7.pdb")
def test_lyso_pH12_gromos(self):
outfile = "gromos12.pdb"
parameters = {
"structure": "builder/4lzt.pdb",
"epsin": 15,
"ionicstr": 0.1,
"pbc_dimensions": 0,
"ncpus": ncpus,
"output": "pKas.out",
"titration_output": "titration.out",
"structure_output": (outfile, 12, "gromos_CpH"),
}
pKa = Titration(parameters)
checkStructureOutput(outfile)
def test_api_ktp_pdb_allsites_clean(self):
os.system(
"rm -f *out *gro *pdb *pqr *crg *sites cent contributions interactions.dat pkint"
)
results = """
NTR 5001 7.934819040827242 ('undefined', 0.8959021976401332)
TYR 1 9.78114442380826 ('protonated', 0.9983475157921265)
CTR 5002 3.010253456221198 ('deprotonated', 0.00010237855405755827)
"""
parameters = {
"structure": "ktp/ktp_pdb_allsites/ktp.pdb",
"clean_pdb": "yes",
"epsin": 2,
"ionicstr": 0.1,
"pbc_dimensions": 0,
"temp": 310,
"grid_fill": 0.8,
"ncpus": ncpus,
"pH": "0,15",
"pHstep": 0.2,
"logfile": "LOGFILE",
"scaleM": 4,
"scaleP": 1,
"gsize": 81,
"convergence": 0.01,
"nlit": 300,
"cutoff": -1,
"relfac": 0.0,
"output": "pKas.out",
"clean_pdb": True,
"remove_hs": False,
}
sites = "all"
pKa = Titration(parameters, sites=sites)
checkAPIResult(pKa, results)
"ionicstr": 0.1,
"pbc_dimensions": 0,
"ncpus": sys.argv[1],
"output": "pKas.out",
"titration_output": "titration.out",
"ser_thr_titration": False,
"structure_output": ("out4.pdb", 4.5, "gromos_cph"),
}
#'gsize' : 91,
#'bndcon' : 4,
#'nanoshaper' : 0,
#'precision' : 'single'}
sites = {"A": ["1N", 1, 7, 15, 18, 35, 48, 52, 66, 87, 101, 119, "129C"]}
pKa = Titration(parameters, sites=sites) # , debug=True)
# exit()
# Run each step separately
# pKa = Titration(parameters, run='preprocess')
# pKa.DelPhiLaunch()
# pKa.calcSiteInteractionsParallel()
# pKa.run_mc()
# print(pKa)
# from IPython import embed; embed()
# for pH in pKa.getTitrationCurve('total').keys():
# print(pH, pKa.getTitrationCurve('total')[pH])
# for site in pKa:
def save_settings(tit: pypka.Titration) -> None:
# Save settings
pypka_params, delphi_params, mc_params = tit.getParametersDict()
to_keep = [
"CpHMD_mode",
"ffID",
"ff_family",
"ffinput",
"clean_pdb",
"LIPIDS",
"keep_ions",
"ser_thr_titration",
"cutoff",
"slice",
]
pypka_params = {
key: value
for key, value in pypka_params.items() if key in to_keep
}
pypka_params["version"] = pypka_version
mc_params["pH_values"] = list(mc_params["pH_values"])
bool_params = [
"CpHMD_mode",
"ser_thr_titration",
"clean_pdb",
"keep_ions",
"pbx",
"pby",
]
query = session.query(Sim_settings.settid)
for param in pypka_params:
to_compare = str(pypka_params[param])
if param in bool_params:
to_compare = to_compare.lower()
query = query.filter(
Sim_settings.pypka_params[param].as_string() == to_compare)
for param in delphi_params:
to_compare = str(delphi_params[param])
if param in bool_params:
to_compare = to_compare.lower()
query = query.filter(
Sim_settings.delphi_params[param].as_string() == to_compare)
for param in mc_params:
to_compare = str(mc_params[param])
if param in bool_params:
to_compare = to_compare.lower()
query = query.filter(
Sim_settings.mc_params[param].as_string() == to_compare)
settid = query.first()
if not settid:
new_sim_settings = Sim_settings(pypka_params=pypka_params,
delphi_params=delphi_params,
mc_params=mc_params)
session.add(new_sim_settings)
session.flush()
settid = new_sim_settings.settid
else:
settid = settid[0]
NEW_PK_SIM.settid = settid
session.commit()
from pypka import Titration
params = {
"structure": "4lzt.pdb", # Input structure file name
"ncpus": -1, # Number of processes (-1 for maximum allowed)
"epsin": 15, # Dielectric constant of the protein
"ionicstr": 0.1, # Ionic strength of the medium (M)
"pbc_dimensions":
0, # PB periodic boundary conditions (0 for solvated proteins and 2 for lipidic systems)
}
tit = Titration(params)
pH = 7.0
for site in tit:
state = site.getProtState(pH)[0]
print(site.res_name, site.res_number, site.pK, state)
#import os
#pdbl = PDBList()
#pdbl.retrieve_pdb_file('1LSE', file_format="pdb", pdir=".")
#pdbl.retrieve_pdb_file('4LZT', file_format="pdb", pdir=".")
#os.rename('pdb1lse.ent', '1lse.pdb')
#os.rename('pdb4lzt.ent', '4lzt.pdb')
import sys
sys.path.insert(1, '../../')
from pypka import Titration
parameters = {'structure' : '4lzt.pdb',
'epsin' : 10,
'ionicstr' : 0.1,
'pbc_dimensions': 0,
'temp' : 100,
'grid_fill' : 0.8, # FUTURE VERSION
'ncpus' : 4,
'pH' : '0, 15',
'maxc' : 0.01,
'pHstep' : 0.5,
'output': 'pkas.out'}
sites = {'A': ('1N', '18', '35', '48', '66', '129C')}
pKa = Titration(parameters, sites=sites, debug=True)
for site in pKa:
print site, pKa[site], pKa.getProtState(site, 7)
print pKa.getParameters()
'epsin': 10,
'ionicstr': 0.1,
'pbc_dimensions': 0,
'ncpus': 2,
'output': 'pKas.out',
'titration_output': 'titration.out',
'structure_output': ('gromos.pdb', pH, 'amber'),
'gsize': 41,
'convergence': 0.2,
'pHstep': 1.0,
'clean_pdb': True
}
#pKa = Titration(parameters, sites={'A': ['1N', '1', '7', '129C']})
tit = Titration(parameters)
for site in tit:
pK = site.pK
#taut = site.getMostProbTaut(pH)
state = site.getProtState(pH)[0]
#site.molecule.chain,
print(site.res_name, site.res_number, pK, state)
#
# print(site.getFinalState(pH))
# print(site.getTitrationCurve())
#print(tit.getTitrationCurve())
#print(tit.getParameters())
import matplotlib.pyplot as plt