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Commit 3cee99f5 authored by cmaffeo2's avatar cmaffeo2
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Add Citation class and citation information for various Onck model versions

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arbdmodel/RELEASE-VERSION
+ 1
− 1
View file @ 3cee99f5
0.1.dev61
0.2.dev37
arbdmodel/onck_polymer_model.py
+ 65
− 15
View file @ 3cee99f5
......@@ -5,9 +5,10 @@ import numpy as np
import sys
## Local imports
from . import logger, ParticleType, PointParticle, get_resource_path
from . import devlogger, logger, ParticleType, PointParticle, get_resource_path
from .polymer import PolymerBeads, PolymerModel
from .interactions import AbstractPotential, HarmonicBond
from .version import Citation
"""Define particle types"""
_types = dict(
......@@ -121,20 +122,27 @@ for k,t in _types.items():
_types_versions = {1.0: _types}
_types_versions[1.1] = dict()
## https://link.springer.com/article/10.1007/s12274-022-4647-1
_types_versions['1.0cp'] = {k:ParticleType(t.name,
mass = t.mass,
charge = t.charge,
epsilon = t.epsilon) for k,t in _types.items()}
for k in 'R D E K'.split(): _types_versions['1.0cp'][k].epsilon = 0.005
_types_versions[1.1] = dict() # https://www.pnas.org/doi/10.1073/pnas.2221804120
__si_data = """A 71.07 0.7 0
L 113.16 1 0
R 156.19 0.005 +1
K 128.17 0.005 +1
N 114.10 0.41 0
M 131.20 0.78 0
D 115.09 0.005 −1
D 115.09 0.005 -1
F 147.18 1 0
C 103.14 0.68 0
P 97.12 0.65 0
Q 128.13 0.33 0
S 87.08 0.45 0
E 129.11 0.005 −1
E 129.11 0.005 -1
T 101.11 0.51 0
G 57.05 0.48 0
W 186.22 0.96 0
......@@ -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)
if t0.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].epsilon for k,t0 in _types_versions[1.0].items()])} different epsilon parameters compared to 1BPA')
""" Cation-Pi interactions """
eps_cp_dict = {('ARG','PHE'): 4.3,
......@@ -162,6 +170,40 @@ eps_cp_dict = {('ARG','PHE'): 4.3,
eps_cp_dict = {k:v*0.23900574 for k,v in eps_cp_dict.items()} # convert to kcal/mol
for k,v in list(eps_cp_dict.items()): eps_cp_dict[(k[1],k[0])] = v # add reversed keys to dictionary
version_name = {1.0:'1BPA', '1.0cp':'1BPA-CP', 1.1:'1BPA-1.1'}
__base_ref = Citation(
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 == 1.1 and typeB.version == 1.1)
assert( all( t.version in ('1.0cp',1.1) for t in types ) )
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):
if version == 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):
raise ValueError(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
if version == None:
logger.warning(f'No Onck model version specified; using version 1BPA-1.1 from 2023')
version = 1.1
if version not in _types_versions:
raise ValueError(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'
_msg = _msg + "\n and\n".join(ref.display() for ref in version_refs[self.version])
print(_msg)
if debye_length != 12.7:
logger.warning("""Deviating from the model published by Onck by choosing a Debye length differing from 1.27 nm.
......@@ -348,12 +396,14 @@ Fragasso, A., de Vries, H.W., Andersson, J. et al. A designer FG-Nup that recons
def _add_nonbonded_interaction(self, interaction, type_):
i = self.types.index(type_) if type_ in self.types else 0
for t in self.types[i:]:
self.add_nonbonded_interaction( interaction, typeA=type_, typeB=t )
# self.add_nonbonded_interaction( interaction, typeA=type_, typeB=t )
self.useNonbondedScheme( interaction, typeA=type_, typeB=t )
def _generate_polymer_beads(self, polymer, sequence, polymer_index=None):
return OnckBeads(polymer, sequence,
monomers_per_bead_group = self.monomers_per_bead_group,
poymer_index = polymer_index
poymer_index = polymer_index,
version = self.version
)
def set_damping_coefficient(self, damping_coefficient):
......
arbdmodel/version.py
+ 29
− 1
View file @ 3cee99f5
......@@ -139,7 +139,35 @@ def read_version_file(filename):
with open(filename) as fh:
version = fh.readlines()[0].strip()
return version
class Citation():
def __init__(self, author=None, title=None, journal=None, volume=None, number=None, pages=None, year=None, doi=None):
self.author = author
self.title = title
self.journal = journal
self.volume = volume
self.number = number
self.pages = pages
self.year = year
self.doi = doi
def display(self):
msg = ''
if self.author: msg = f'{self.author}. '
if self.title: msg = f'{msg}{self.title}. '
if self.journal: msg = f'{msg}{self.journal} '
if self.volume:
msg = f'{msg} {self.volume}{"," if any((self.number, self.pages, self.year)) else "."} '
if self.number:
msg = f'{msg}({self.number}){"" if any((self.pages,self.year)) else "."} '
if self.pages: msg = f'{msg}{self.pages}{"" if self.year else "."} '
if self.year: msg = f'{msg}({self.year}). '
if self.doi:
if self.doi[:4] == 'http':
msg = f'{msg}{self.doi}'
else:
msg = f'{msg}https://doi.org/{self.doi}'
return msg
try:
version = read_version_file(_version_file)
......
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