From f80eefa3a5e20b54d469fd3f3047580eed31de55 Mon Sep 17 00:00:00 2001
From: pinyili2 <pinyili2@illinois.edu>
Date: Wed, 2 Oct 2024 16:36:37 -0500
Subject: [PATCH] add arbdmodel
---
mrdna/RELEASE-VERSION | 2 +-
mrdna/__init__.py | 5 +-
mrdna/coords.py | 2 +-
mrdna/model/CanonicalNucleotideAtoms.py | 8 +-
mrdna/model/nbPot_arbd.py | 475 ++++++++++++++++++++++++
5 files changed, 487 insertions(+), 5 deletions(-)
create mode 100644 mrdna/model/nbPot_arbd.py
diff --git a/mrdna/RELEASE-VERSION b/mrdna/RELEASE-VERSION
index 1510856..7e7193f 100644
--- a/mrdna/RELEASE-VERSION
+++ b/mrdna/RELEASE-VERSION
@@ -1 +1 @@
-1.0a.dev165
+1.0a.dev166
diff --git a/mrdna/__init__.py b/mrdna/__init__.py
index 386e405..303fff6 100644
--- a/mrdna/__init__.py
+++ b/mrdna/__init__.py
@@ -32,7 +32,10 @@ def get_resource_path(relative_path):
return _RESOURCE_DIR / relative_path
## Import useful messsages
-from arbdmodel.coords import readArbdCoords
+try:
+ from arbdmodel.coords import readArbdCoords
+except:
+ from marbdmodel.coords import readArbdCoords
from .segmentmodel import SegmentModel, SingleStrandedSegment, DoubleStrandedSegment
from .simulate import multiresolution_simulation
from .model.dna_sequence import read_sequence_file
diff --git a/mrdna/coords.py b/mrdna/coords.py
index 363ab96..720165d 100644
--- a/mrdna/coords.py
+++ b/mrdna/coords.py
@@ -1,4 +1,4 @@
-from .arbdmodel.coords import *
+from .marbdmodel.coords import *
from sys import stderr
stderr.write("WARNING: the module 'mrdna.coords' has been deprecated. Please change your scripts to use 'mrdna.arbdmodel.coords'\n")
diff --git a/mrdna/model/CanonicalNucleotideAtoms.py b/mrdna/model/CanonicalNucleotideAtoms.py
index 4cade46..fa28af0 100644
--- a/mrdna/model/CanonicalNucleotideAtoms.py
+++ b/mrdna/model/CanonicalNucleotideAtoms.py
@@ -1,8 +1,12 @@
import json
import numpy as np
import copy
-from arbdmodel.coords import rotationAboutAxis
-from arbdmodel import Group, PointParticle, ParticleType
+try:
+ from arbdmodel.coords import rotationAboutAxis
+ from arbdmodel import Group, PointParticle, ParticleType
+except:
+ from ..marbdmodel.coords import rotationAboutAxis
+ from ..marbdmodel import Group, PointParticle, ParticleType
from .. import get_resource_path
seqComplement = dict(A='T',G='C')
diff --git a/mrdna/model/nbPot_arbd.py b/mrdna/model/nbPot_arbd.py
new file mode 100644
index 0000000..f564a72
--- /dev/null
+++ b/mrdna/model/nbPot_arbd.py
@@ -0,0 +1,475 @@
+import numpy as np
+import scipy.optimize as opt
+from scipy.interpolate import interp1d
+from scipy.signal import savgol_filter as savgol
+
+from arbdmodel.interactions import AbstractPotential
+from .. import get_resource_path
+from ..config import CACHE_DIR
+
+from scipy.optimize import curve_fit
+from pathlib import Path
+
+## TODO: clean this file up a bit, make things protected
+
+## units "291 k K" kcal_mol
+kT = 0.57827709
+
+def _round_bp(bp):
+ return 10**(np.around(np.log10(bp)*100)/100.0)
+
+class AbstractNbDnaPotential(AbstractPotential):
+
+ def __init__(self, *args,**kwargs):
+ AbstractPotential.__init__(self,*args,**kwargs)
+
+ self.debye_length = self.debye_length0 # set by child class
+
+ x,y = self.load_pmf()
+ self.target_x = x
+ self.target_y = y
+ base = 4
+ self.param_x = np.logspace(np.log(15)/np.log(base),np.log(120)/np.log(base),80,base=base)
+ # print(self.param_x)
+
+ self.target_x_interp = np.linspace(np.min(x),np.max(x),2*len(x)) # interpolate potential
+ self.target_x_interp = np.arange(23.5,38,0.1) # interpolate potential
+ self.target_y_interp = interp1d(x,y)(self.target_x_interp)
+
+ self.bead_distribution_y = None
+
+ """ Initialize caches """
+ try:
+ self.single_bp_pair_pot = np.loadtxt( self.get_package_cache_file() ).T
+ self.param_x = self.single_bp_pair_pot[0,:]
+ assert( len(self.param_x > 2) )
+ except:
+ pass
+
+ def get_package_cache_file(self):
+ raise NotImplementedError()
+
+ def load_pmf(self):
+ raise NotImplementedError()
+
+ def load_bead_distributions(self):
+ raise NotImplementedError()
+
+ def potential(self, r, typeA, typeB):
+ """ Implements interface for AbstractPotential """
+
+ if typeA.name[0] == "O" or typeB.name[0] == "O":
+ u = np.zeros( r.shape )
+ else:
+ u = self.nbPot(r, 0.5*typeA.nts, 0.5*typeB.nts)
+ return u
+
+ """ Remainder has to do with nbPot """
+ def load_np(self,filename):
+ return np.load(filename)['arr_0'].tolist()
+
+ def parametric_potential(self,x,*parms):
+ x0 = self.param_x
+ x = np.array(x)
+ u = interp1d(x0, np.array(parms),
+ bounds_error = False, fill_value="extrapolate",
+ assume_sorted=True)(x).T
+ u[x<13] = u[x<13] + 0.5 * (x[x<13]-13)**2
+
+ ## Debye correction
+ if self.debye_length != self.debye_length0:
+ ## units "e**2/(4 * pi * 80 epsilon0 AA)" kcal_mol
+ A = 4.1507964
+ with np.errstate(divide='ignore',invalid='ignore'):
+ du = (A/x) * (np.exp(-x/self.debye_length) - np.exp(-x/self.debye_length0))
+
+ du[x < 10] = du[x>=10][0]
+ u = u + du
+
+ return u-u[-1]
+
+ def get_bead_distributions(self, interhelical_distances):
+ if self.bead_distribution_y is None:
+ self.load_bead_distributions()
+ return self.bead_distribution_x, self.bead_distribution_y(interhelical_distances)
+
+ def iterative_fit(self):
+ try:
+ import bead_dist_data as bdd
+ x = bdd.bead_centers.x
+ except:
+ ## First iteration
+ x = np.arange(0,200,0.2)
+ f = self.get_target_force(x+2)
+ f[f>0.5] = 0.5
+ u = np.cumsum(f[::-1])[::-1]
+ u = 0.5* u / (10*20)
+ np.savetxt("pair-pot.dat", np.array((x,u)).T)
+ return interp1d(x,u,
+ bounds_error = False, fill_value="extrapolate",
+ assume_sorted=True)(self.param_x).T
+
+ x = x[x<50]
+ data = np.loadtxt("last/pair-pot.dat")
+ u_last = interp1d(data[:,0], data[:,1],
+ bounds_error = False, fill_value="extrapolate",
+ assume_sorted=True)(x).T
+
+ particle_force = np.diff(u_last) / np.diff(x)
+
+ for b in bdd.bead_dists:
+ ids = bdd.bead_centers < 10
+ b[:,ids] = 0
+
+ R = bdd.interhelical_spacing
+ R,y = self.load_rau_pressure()
+
+ P = self.get_pressure(R)
+ P_t = self.get_target_pressure(R)
+ dP = P_t-P
+
+ np.savetxt("raw_pressure.dat", self.get_raw_pressure())
+ np.savetxt("pressure.dat", np.array((R,P)).T)
+ np.savetxt("target_pressure.dat", np.array((R,P_t)).T)
+
+ def fitFun(R,*uvals):
+ df_interp = dfFun(*uvals)
+ dP_local = self.get_virial_pressure(R, df_interp)
+ print( np.std(dP_local-dP) )
+ return dP_local
+
+ def duFun(x,*popt):
+ f = dfFun(*popt)(x)
+ u = -np.cumsum(f) * np.mean( np.diff(x) )
+ u = u - u[-1]
+ return u
+
+ def dfFun(x0,f0,x1_par,x2):
+ x1 = (1-x1_par)*x0 + x1_par*x2
+ t = np.linspace(0,1,100)
+ x = x0*(1-t)**2 + 2*x1*(1-t)*t + x2*t**2
+ f = f0*(1-t)**2
+ return interp1d(x, f,
+ bounds_error = False,
+ fill_value=0,
+ assume_sorted=True)
+
+ dP_sofar = np.zeros(dP.shape)
+ popt_list = []
+ for i in range(3):
+ popt, pcov = opt.curve_fit(fitFun, R, dP-dP_sofar,
+ bounds=((10,-0.1,0.1,35),
+ (34,0.1,0.9,50)),
+ p0=(20,0,0.25,50))
+ popt_list.append(popt)
+ dP_sofar += fitFun(R,*popt)
+
+ du = np.zeros(x.shape)
+ for popt in popt_list:
+ du = du + duFun(x,*popt)
+
+ du = savgol(du,int(2.5/(x[1]-x[0]))*2+1,3)
+ u = u_last+0.75*du
+ u = u-u[-1]
+
+ np.savetxt("pair-pot.dat", np.array((x,u)).T)
+
+ return interp1d(x,u,
+ bounds_error = False, fill_value="extrapolate",
+ assume_sorted=True)(self.param_x).T
+
+
+ def get_virial_pressure(self, R, bead_force):
+ """ Return pressure as fn of interhelical spacing """
+ import bead_dist_data as bdd
+
+ interhelical_spacing = bdd.interhelical_spacing
+ volume = (np.pi*np.array(bdd.radii)**2) * bdd.height
+
+ # units "kcal_mol/AA**3" atm
+ # * 68568.409
+
+ xy = bdd.bead_centers[np.newaxis,:]
+ r = bdd.bead_centers[:,np.newaxis]
+ force = bead_force(r)
+
+ """ Pxy = 1/(4V) Sum_ij (xy_ij)**2 * bead_force(r_ij) / r_ij """
+ ## 2*count because count only includes i < j
+ pressure = [68568.409*np.sum( 2*count * (xy**2) * force / r ) / (4 * vol)
+ for vol,count in zip(volume,bdd.bead_dists)]
+ return pchip_interpolate(interhelical_spacing, pressure, R)
+ """
+ return interp1d(interhelical_spacing, pressure,
+ bounds_error = False,
+ kind='cubic',
+ fill_value="extrapolate",
+ assume_sorted=True)(R)
+
+ ## Fit double exponential
+
+ try:
+ def fitfn(x,A,a,b):
+ return A*a**(-b**x)
+ def fit_wrap(x,*popt):
+ print("pressure:",pressure)
+ print(" ",fitfn(interhelical_spacing, *popt) - pressure)
+ return fitfn(x,*popt)
+ popt, pcov = opt.curve_fit(fit_wrap, interhelical_spacing, pressure,
+ bounds=((-np.inf,0,0),
+ (np.inf,np.inf,np.inf)),
+ p0=(0,1,1))
+ return fitfn(R,*popt)
+ except:
+ return interp1d(interhelical_spacing, pressure,
+ bounds_error = False,
+ fill_value="extrapolate",
+ assume_sorted=True)(R)
+ """
+
+
+ def get_interhelical_density(self,R):
+ data = np.loadtxt("last/density.dat")
+ r,rho = data.T
+ rho = rho / r**2
+ rho = rho/np.trapz(rho,r)
+ filter_points = int(2.5/(r[1]-r[0]))*2 + 1
+ rho = savgol(rho, filter_points, 3) # smooth density
+ return interp1d(r,rho,
+ bounds_error = False, fill_value=0,
+ assume_sorted=True)(R).T
+
+ def get_raw_pressure(self):
+ from bead_dist_data import interhelical_spacing, pressure
+ distance = interhelical_spacing
+ assert( len(distance) > 2 )
+ return distance,pressure
+
+ def get_pressure(self,R):
+ distance,pressure = self.get_raw_pressure()
+ # distance,pressure = np.loadtxt("last/pressure.dat")
+ return pchip_interpolate(distance, pressure, R)
+ return interp1d(distance, pressure,
+ bounds_error = False,
+ kind='cubic',
+ fill_value="extrapolate",
+ assume_sorted=True)(R)
+ def fitfn(x,a,b):
+ return a**(-b**x)
+
+ popt, pcov = opt.curve_fit(fitfn, distance, pressure,
+ bounds=(0,np.inf),
+ p0=(1,1))
+ return fitfn(R,*popt)
+
+
+ def get_interhelical_force(self,R):
+ y = pressure = self.get_pressure(R)
+ x = R
+ force = (x*y / np.sqrt(3)) * 34 * 1.4583976e-05 # convert atm AA**2 to kcal/mol AA
+ return force
+
+ def get_target_interhelical_density(self,R):
+ r,u = self.load_pmf()
+ rho = np.exp( -u/kT )
+ rho = rho / np.trapz(rho,r)
+ return interp1d(r,rho,
+ bounds_error = False, fill_value=0,
+ assume_sorted=True)(R).T
+
+ def get_target_force(self,R):
+ x,y = self.load_rau_force()
+ # return pchip_interpolate(x, y, R)
+ # return interp1d(x,y,
+ # bounds_error = False,
+ # # kind='cubic',
+ # fill_value="extrapolate",
+ # assume_sorted=True)(R)
+
+ def fitfn(x,A,a):
+ return A * np.exp(-(x-18)/a)
+ popt,pcov = curve_fit(fitfn, x,y, p0=(10,20))
+ return fitfn(R,*popt)
+
+ def get_target_pressure(self,R):
+ x,y = self.load_rau_pressure()
+ return pchip_interpolate(x, y, R)
+ return interp1d(x,y,
+ bounds_error = False,
+ kind='cubic',
+ fill_value="extrapolate",
+ assume_sorted=True)(R)
+ def fitfn(x,A,a):
+ return A * np.exp(-(x-18)/a)
+ popt,pcov = curve_fit(fitfn, x,y, p0=(10,20))
+ return fitfn(R,*popt)
+
+ def load_rau_force(self):
+ x,y = self.load_rau_pressure()
+ y = (x*y / np.sqrt(3)) * 34 * 1.4583976e-05 # convert atm AA**2 to kcal/mol AA
+ return x,y
+
+ def get_rounded_bp(self,bps1,bps2):
+ larger = np.max([bps1,bps2])
+ smaller = np.min([bps1,bps2])
+ smaller_shift, larger_shift = [_round_bp(bp) for bp in (smaller,larger)]
+
+ key = (smaller_shift,larger_shift)
+ return smaller,larger,smaller_shift,larger_shift
+
+ def nbPot(self, x, bps1, bps2):
+ x0,u0 = self.single_bp_pair_pot
+ u = self.parametric_potential(x,*u0)
+ u = u * bps1 * bps2
+ assert(np.sum(np.isnan(u)) == 0)
+ return u
+
+
+def _add_parameter_to_cache_dict( args ):
+ obj, dict_, key = args
+ cache_key = '{}:{}'.format(*key)
+ dict_[cache_key] = obj.fit_potential(*key)
+ return True
+
+
+class nbDnaPotential100Mg(AbstractNbDnaPotential):
+
+ def __init__(self,*args,**kwargs):
+ ## units "sqrt( 80 epsilon0 295 k K / ((4*100 mM + 200 mM) e**2/particle) )" AA
+ self.debye_length0 = 5.5771297
+ AbstractNbDnaPotential.__init__(self,*args,**kwargs)
+
+ def get_package_cache_file(self):
+ return get_resource_path("nbPot.rau_refined_100Mg.dat")
+
+ def load_rau_pressure(self):
+ data = np.loadtxt("rau-data-100Mg.dat")
+ x = data[:,0]
+ y0 = data[:,1]
+ y = (10**y0) * 9.8692327e-07 # convert dyne/cm^2 to atm
+ return x,y
+
+ def load_pmf(self):
+ d = np.loadtxt(get_resource_path("jj-nar-dna-pmf-100Mg.dat"))
+ x0 = d[:,1]
+ y0 = d[:,0] # kcal/mol for 10bp with 10bp, according to JY
+ y0 = y0 - np.mean(y0[x0 > 38.5]) # set 0 to tail of potential
+ filter_points = int(2.5/(x0[1]-x0[0]))*2 + 1
+ y0 = savgol(y0, filter_points, 3) # smooth potential
+ return x0,y0
+
+ def load_bead_distributions(self):
+ from bead_dist_data import helix_bins, bead_bins
+ from bead_dist_data import helix_centers, bead_centers
+ import bead_dist_data as bdd
+
+ self.bead_distribution_x = x = bdd.bead_centers
+
+ all_x = []
+ all_y = []
+ for i in range(0,len(bdd.helix_centers),1):
+ y = bdd.bead_dists_for_helix_dist[i]
+
+ # if y.sum() == 0: continue
+ if bdd.helix_centers[i] < 20: continue
+ all_x.append( bdd.helix_centers[i] )
+ filter_points = int(5/(x[1]-x[0]))*2 + 1
+ y = savgol( y, filter_points, 3) # smooth and normalize data
+ y[y<0] = 0 # ensure positive
+ y = 10*20 * y/np.trapz(y,x) # normalize
+ all_y.append( y )
+
+ self.bead_distribution_y = interp1d( np.array(all_x), np.array(all_y),
+ axis=0,
+ kind='linear',
+ bounds_error = False, fill_value="extrapolate",
+ assume_sorted=True)
+
+
+class nbDnaPotential20Mg(AbstractNbDnaPotential):
+
+ def __init__(self,*args,**kwargs):
+ ## units "sqrt( 80 epsilon0 295 k K / ((4*25 mM + 50 mM) e**2/particle) )" nm
+ ## 25 mM MgCl2, sorry about name of this class/files
+ self.debye_length0 = 11.154259
+ AbstractNbDnaPotential.__init__(self,*args,**kwargs)
+
+ def get_package_cache_file(self):
+ return get_resource_path("nbPot.rau_refined_20Mg_200Na.dat")
+
+ def load_rau_pressure(self):
+ data = np.loadtxt("rau-data-20Mg.dat")
+ x = data[:,0]
+ y0 = data[:,1]
+ y = (10**y0) * 9.8692327e-07 # convert dyne/cm^2 to atm
+ return x,y
+
+ def load_pmf(self):
+ d = np.loadtxt(get_resource_path("jj-nar-dna-pmf-20Mg-200Na.dat"))
+ x0 = d[:,1]
+ y0 = d[:,0] # kcal/mol for 10bp with 10bp, according to JY
+ y0 = y0 - np.mean(y0[x0 > 38.5]) # set 0 to tail of potential
+ filter_points = int(2.5/(x0[1]-x0[0]))*2 + 1
+ y0 = savgol(y0, filter_points, 3) # smooth potential
+ return x0,y0
+
+ def load_bead_distributions(self):
+ import bead_dist_data as bdd
+
+ self.bead_distribution_centers = bdd.bead_centers
+ self.bead_distribution_radii = bdd.radii
+ self.bead_distribution_counts = bdd.bead_dists
+ ...
+
+
+ for i in range(0,len(bdd.helix_centers),1):
+ y = bdd.bead_dists_for_helix_dist[i]
+
+ # if y.sum() == 0: continue
+ if bdd.helix_centers[i] < 20: continue
+ all_x.append( bdd.helix_centers[i] )
+ filter_points = int(5/(x[1]-x[0]))*2 + 1
+ y = savgol( y, filter_points, 3) # smooth and normalize data
+ y[y<0] = 0 # ensure positive
+ y = 10*20 * y/np.trapz(y,x) # normalize
+ all_y.append( y )
+
+ self.bead_distribution_y = interp1d( np.array(all_x), np.array(all_y),
+ axis=0,
+ bounds_error = False, fill_value="extrapolate",
+ assume_sorted=True)
+
+
+# nbDnaPotential100MgObj = nbDnaPotential100Mg()
+nbDnaPotential = nbDnaPotential20MgObj = nbDnaPotential20Mg()
+
+
+if __name__ == "__main__":
+ # import cProfile
+ # cProfile.run("_run()")
+ # _generate_cache()
+ # tmp = nbDnaPotential20Mg()
+ # tmp._write_cache()
+ # pass
+
+ tmp = nbDnaPotential20Mg()
+
+ # dR = 1
+ # for R in np.arange(22,35,2):
+ # x,ys = tmp.get_bead_distributions(np.array([R-0.5*dR,R+0.5*dR]))
+ # y1,y2 = ys
+ # d_rho_dR = (y2-y1)/dR
+ # # plt.plot(x,d_rho_dR)
+
+ # x = np.arange(20,50,1)
+ # tmp.nbPot(x,1,1)
+
+
+ # plt.gca().set_xlim((10,40))
+ # plt.savefig("test.pdf")
+
+ # x = np.arange(20,50,1)
+ # tmp.nbPot(x,1,1)
+
+ nb = nbDnaPotential20MgObj
+ x = np.arange(10,50,1)
+ u = nb.nbPot(x,1,1)
--
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