From 107644b5311efc0fffbcde37d87dcc46aa7310ef Mon Sep 17 00:00:00 2001
From: Chris Maffeo <cmaffeo2@illinois.edu>
Date: Mon, 16 Dec 2024 17:32:38 -0600
Subject: [PATCH] Copy arbmodel commit 7ceb134 to arbdmodel/submodule
---
mrdna/arbdmodel/submodule/__init__.py | 6 +++++-
mrdna/arbdmodel/submodule/mpipi_polymer.py | 7 +++----
mrdna/arbdmodel/submodule/onck_polymer_model.py | 5 +++--
3 files changed, 11 insertions(+), 7 deletions(-)
diff --git a/mrdna/arbdmodel/submodule/__init__.py b/mrdna/arbdmodel/submodule/__init__.py
index 2b9fbe8..61ba106 100644
--- a/mrdna/arbdmodel/submodule/__init__.py
+++ b/mrdna/arbdmodel/submodule/__init__.py
@@ -479,7 +479,7 @@ class ParticleType():
if diffusivity is not None: self.diffusivity = diffusivity
self.parent = parent
self.rigid_body_potentials = rigid_body_potentials
- devlogger.info(f'Created {type(self)} {name} @ {hex(id(self))}')
+ devlogger.debug(f'Created {type(self)} {name} @ {hex(id(self))}')
for key in ParticleType.excludedAttributes:
assert( key not in kwargs )
@@ -1043,6 +1043,10 @@ class ArbdModel(PdbModel):
self.group_sites = []
+ def add(self, obj):
+ self._clear_types() # TODO: call upon (potentially nested) `child.add(add)`
+ return Parent.add(self, obj)
+
def add_group_site(self, particles, weights=None):
g = ArbdModel._GroupSite(particles, weights)
self.group_sites.append(g)
diff --git a/mrdna/arbdmodel/submodule/mpipi_polymer.py b/mrdna/arbdmodel/submodule/mpipi_polymer.py
index 61e5196..ef9cdaa 100644
--- a/mrdna/arbdmodel/submodule/mpipi_polymer.py
+++ b/mrdna/arbdmodel/submodule/mpipi_polymer.py
@@ -5,11 +5,10 @@ import numpy as np
import sys
import pandas as pd
## Local imports
-from . import logger, ParticleType, PointParticle, get_resource_path
+from . import logger, ParticleType, PointParticle
from .polymer import PolymerBeads, PolymerModel
from .interactions import AbstractPotential, HarmonicBond
-
"""Define particle types"""
_types = dict(
A = ParticleType("ALA",
@@ -150,7 +149,7 @@ class MpipiNonbonded(AbstractPotential):
def potential(self, r, types):
""" Electrostatics """
typeA, typeB = types
- ld = self.debye_length
+ ld = self.debye_length
q1 = typeA.charge*0.75
q2 = typeB.charge*0.75
D = 80 # dielectric of water
@@ -159,7 +158,7 @@ class MpipiNonbonded(AbstractPotential):
u_elec = (A*q1*q2/D)*np.exp(-r/ld) / r
"""Mpipi Wang-Frenkel Potential"""
- WF=pd.read_csv(get_resource_path("mpipi_protein_resname.csv"),index_col=0)
+ WF=pd.read_csv("mpipi_protein_resname.csv",index_col=0)
indices=list(df.columns)
if indices.index(typeA.resname)<indices.index(typeB.resname):
sigma_ij=WF[typeB.resname][typeA.resname+"_sigma"]*10
diff --git a/mrdna/arbdmodel/submodule/onck_polymer_model.py b/mrdna/arbdmodel/submodule/onck_polymer_model.py
index a59fa80..f2ababf 100644
--- a/mrdna/arbdmodel/submodule/onck_polymer_model.py
+++ b/mrdna/arbdmodel/submodule/onck_polymer_model.py
@@ -244,6 +244,7 @@ class OnckNonbonded(AbstractPotential):
u_lj = eps * (3*r8 - 4*r6)
except:
+ sigma = 6.0
r6 = (sigma/r)**6
r8 = (sigma/r)**8
@@ -251,7 +252,6 @@ class OnckNonbonded(AbstractPotential):
epsilon_hp = 3.1070746 # units "13 kJ/N_A" kcal_mol
epsilon_rep = 2.3900574 # units "10 kJ/N_A" kcal_mol
- sigma = 6.0
epsilon = epsilon_hp*np.sqrt( (typeA.epsilon*typeB.epsilon)**alpha )
u_lj = (epsilon_rep-epsilon) * r8
@@ -363,6 +363,7 @@ class OnckModel(PolymerModel):
if version not in _types_versions:
raise ValueError(f'Unkown Onck model version "{version}"')
self.version = version
+ self.types_dict = _types_versions[version]
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'
@@ -398,7 +399,7 @@ class OnckModel(PolymerModel):
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.useNonbondedScheme( interaction, typeA=type_, typeB=t )
+ self.add_nonbonded_interaction( interaction, typeA=type_, typeB=t )
def _generate_polymer_beads(self, polymer, sequence, polymer_index=None):
return OnckBeads(polymer, sequence,
--
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