@@ -148,9 +156,9 @@ for k, m, e, q in [l.split() for l in __si_data.split('\n')]:
epsilon=float(e),charge=float(q),version=1.1)
assert(t.charge==t0.charge)
ift0.epsilon!=t.epsilon:
devlogger.info('Updating epsilon for 1BPA-1.1 {k}: {t0.epsilon} -> {t.epsilon}')
devlogger.info(f'Updating epsilon for 1BPA-1.1 {k}: {t0.epsilon} -> {t.epsilon}')
devlogger.info('Onck model version 1BPA-1.1 has {[t0.epsilon != _types_versions[1.1][k].epsilon for k,t0 in _types_versions[1.0].items()].sum()} different epsilon parameters compared to 1BPA')
devlogger.info(f'Onck model version 1BPA-1.1 has {np.sum([t0.epsilon!=_types_versions[1.1][k].epsilonfork,t0in_types_versions[1.0].items()])} different epsilon parameters compared to 1BPA')
author='A. Fragasso, H.W. de Vries, J. Andersson, et al',
title='A designer FG-Nup that reconstitutes the selective transport barrier of the nuclear pore complex',
journal='Nat Commun',
volume=12,
year=2021,
doi='10.1038/s41467-021-22293-y'
)
__ref1=Citation(
author='A. Fragasso, H.W. de Vries, J. Andersson, et al',
title='Transport receptor occupancy in nuclear pore complex mimics',
journal='Nano Res',
volume=15,
pages='9689–9703',
year=2022,
doi='10.1007/s12274-022-4647-1'
)
__ref2=Citation(
author="M. Dekker, E. Van der Giessen, and P.R. Onck",
title="Phase separation of intrinsically disordered FG-Nups is driven by highly dynamic FG motifs",
journal='PNAS',
volume=120,
number=25,
pages='e2221804120',
year=2023,
doi='10.1073/pnas.2221804120'
)
version_refs={1.0:(__base_ref,),
'1.0cp':(__base_ref,__ref1),
1.1:(__base_ref,__ref2),
}
## Default to the latest
_types=_types_versions[1.1]
...
...
@@ -192,8 +234,7 @@ class OnckNonbonded(AbstractPotential):
""" Rather than interacting through the hydrophobic
potential phi_hp, cationic residues interact with aromatic
residues through an 8–6 Lennard Jones potential """
assert(typeA.version==1.1andtypeB.version==1.1)
assert(all(t.versionin('1.0cp',1.1)fortintypes))
key=tuple((typeA.name[:3],typeB.name[:3]))
eps=eps_cp_dict[key]
...
...
@@ -226,7 +267,6 @@ class OnckBeads(PolymerBeads):
spring_constant=38.422562,# units "8038 kJ / (N_A nm**2)" "0.5 * kcal_mol/AA**2"
rest_length=3.8,version=None,**kwargs):
ifversion==None:
logger.warning(f'No Onck model version specified; using version 1BPA-1.1 from 2023')
version=1.1
...
...
@@ -234,7 +274,7 @@ class OnckBeads(PolymerBeads):
raiseValueError(f'Unkown Onck model version "{version}"')
self.version=version
self.types_dict=_types_versions[version]
_types=_types_versions[version]# Update global _types convenience variable
_types=_types_versions[version]# Update global _types convenience variable
self.peptide_bond=HarmonicBond(k=spring_constant,
r0=rest_length,
...
...
@@ -313,12 +353,20 @@ class OnckModel(PolymerModel):
"""
[debye_length]: angstroms
[damping_coefficient]: ns
"""
logger.info("""You are using an implementation of the Onck model for disordered FG-Nup peptides based on:
Fragasso, A., de Vries, H.W., Andersson, J. et al. A designer FG-Nup that reconstitutes the selective transport barrier of the nuclear pore complex. Nat Commun 12, 2010 (2021). https://doi.org/10.1038/s41467-021-22293-y
ifversion==None:
logger.warning(f'No Onck model version specified; using version 1BPA-1.1 from 2023')
version=1.1
ifversionnotin_types_versions:
raiseValueError(f'Unkown Onck model version "{version}"')
self.version=version
Please cite all appropriate articles!""")
logger.info(f'Using an implementation of the Onck model {version_name[self.version]} for disordered FG-Nup peptides.')
_msg='Please cite all appropriate articles, including:\n'