Updates

Author: alsinmr

Data/Data.py

@@ -10,7 +10,7 @@
 import numpy as np
 from pyDR import Defaults,clsDict
 from ..IO import write_file
-from .Plotting import plot_fit,DataPlots
+from .Plotting import plot_fit,DataPlots,plot_fit_md
 from ..Fitting import fit,opt2dist
 from matplotlib.figure import Figure
 from copy import copy
@@ -426,7 +426,6 @@ def plot(self, errorbars=False, style='canvas', fig=None, index=None,
 
 
     def plot_fit(self,index=None, exp_index=None, fig=None):
-        # todo maybe worth to remove the args and put them all into kwargs? -K
         assert self.src_data is not None and hasattr(self, 'Rc') and self.Rc is not None,\
             "Plotting a fit requires the source data(src_data) and Rc"
         info = self.src_data.info.copy()
@@ -437,6 +436,10 @@ def plot_fit(self,index=None, exp_index=None, fig=None):
             Rin=np.concatenate((Rin,np.atleast_2d(1-self.src_data.S2).T),axis=1)
             Rc=np.concatenate((Rc,np.atleast_2d(1-self.S2c).T),axis=1)
             Rin_std=np.concatenate((Rin_std,np.atleast_2d(self.src_data.S2std).T),axis=1)
+            
+        if self.src_data.sens.__class__.__name__=='MD':
+            return plot_fit_md(lbl,Rin,Rc,index=index,info=info)
+            
 
         return plot_fit(lbl=lbl,Rin=Rin,Rc=Rc,Rin_std=Rin_std,\
                     info=info,index=index,exp_index=exp_index,fig=fig)

Data/Plotting.py

@@ -602,7 +602,37 @@ def plot_fit(lbl,Rin,Rc,Rin_std=None,info=None,index=None,exp_index=None,fig=Non
                 string=r'$\nu_r$={0} kHz, $\nu_1$={1} kHz'.format(i['vr'],i['v1'])
                 a.text(np.min(lbl),a.get_ylim()[1]*0.73,string,fontsize=8)
 #    fig.show()            
-    return ax 
+    return ax
+
+def plot_fit_md(lbl,Rin,Rc,info=None,index=None,fig=None):
+    
+    if index is not None:
+        lbl=lbl[index]
+        Rin=Rin[index]
+        Rc=Rc[index]
+    
+    if fig is None:
+        fig=plt.figure(figsize=[12,9])
+    ax,*_=subplot_setup(len(lbl),fig)
+    
+    t=info['t']
+    
+    for lbl0,Rin0,Rc0,a in zip(lbl,Rin,Rc,ax):
+        a.plot(t,Rin0,color='red')
+        a.plot(t,Rc0,color='black',linestyle=':')
+        a.text(t[1],0.1,lbl0)
+        a.set_ylim([-.1,1])
+        if a.is_first_col():
+            a.set_ylabel(r'$C(t)$')
+        else:
+            a.set_yticklabels('')
+        if a.is_last_row():
+            a.set_xlabel(r'$t$ / ns')
+        else:
+            a.set_xticklabels('')
+        
+    return ax
+        
 
 def subplot_setup(nexp,fig=None):
     """

Fitting/fit.py

@@ -13,6 +13,7 @@
 from ._fitfun import fit0,dist_opt
 from copy import copy
 from pyDR.misc.tools import linear_ex
+from ..misc import ProgressBar
 
 dtype=Defaults['dtype']
 
@@ -375,8 +376,9 @@ def model_free(data,nz:int=None,fixz:list=None,fixA:list=None,Niter:int=None,inc
             A.append(np.array(fixA[k]) if hasattr(fixA[k],'__len__') else np.ones(nb)*fixA[k])
 
     zswp=np.linspace(z0[0],z0[-1],nsteps);
+    ProgressBar(0, Niter,prefix='Iterations',suffix=f' of {Niter} steps',length=30,decimals=0)
     for q in range(Niter):
-        print('{0} of {1} iterations'.format(q+1,Niter))
+        # print('{0} of {1} iterations'.format(q+1,Niter))
         for k in range(nz):
             R0=np.zeros(R.shape)
             for m in range(nz):
@@ -429,6 +431,7 @@ def model_free(data,nz:int=None,fixz:list=None,fixA:list=None,Niter:int=None,inc
                 else:
                     #All parameters fixed (no operations)
                     pass
+        ProgressBar(q+1, Niter,prefix='Iterations',suffix=f' of {Niter} steps')
     #Calculate the fit
 
     Rc=np.zeros(data.R.shape)

Frames/user_frames.py

@@ -80,3 +80,67 @@ def sub()
 from pyDR.MDtools import vft
 from pyDR.Selection import select_tools as selt
 
+def bondXY(molecule,sel1=1,sel2=2,resids=None,segids=None,filter_str:str=None,sigma:float=0):
+    """
+    
+
+    Parameters
+    ----------
+    molecule : TYPE
+        Selection object.
+    sel1 : TYPE, optional
+        First atom defining the bond. The default is 1.
+    sel2 : TYPE, optional
+        Second atom defining the bond. The default is 2.
+    resids : TYPE, optional
+        List of residues for which we should return aromatic planes. 
+        The default is None.
+    segids : TYPE, optional
+        List of segments for which we should return aromatic planes.
+        The default is None.
+    filter_str : str, optional
+        string which filters the selection using MDAnalysis format. 
+        The default is None.
+    sigma : float, optional
+        Parameter to determine Gaussian moving average in post processing. 
+        The default is 0 (no post processing).
+
+    Returns
+    -------
+    None.
+
+    """
+    
+    if not(hasattr(sel1,'__len__')):
+        sel1=(sel1+sel1)[:1]
+    if not(hasattr(sel2,'__len__')):
+        sel2=(sel2+sel2)[:1]
+    
+    sel1=selt.sel_simple(molecule,sel1,resids,segids,filter_str)
+    sel2=selt.sel_simple(molecule,sel2,resids,segids,filter_str)
+    
+    
+
+    
+    if len(sel1)==1:
+        frame_index=np.zeros(len(molecule.sel1),dtype=int)
+    elif len(sel1)==len(molecule.sel1):
+        frame_index=np.arange(len(sel1))
+    else:
+        frame_index=None
+        
+    def sub():
+        box=molecule.box
+        vXZ=sel1.positions-sel2.positions
+        vXZ[:,2]=0
+        vXZ=vft.pbc_corr(vXZ.T,box)
+        vZ=np.zeros(vXZ.shape)
+        vZ[2]=1
+        return vZ,vXZ
+    
+    return sub,frame_index,{'PPfun':'AvgGauss','sigma':sigma}
+        
+        
+    
+    
+    

Selection/MolSys.py

@@ -87,9 +87,10 @@ def __init__(self,topo:str,traj_files:list=None,t0:int=0,tf:int=None,step:int=1,
         self._traj=Trajectory(self.uni.trajectory,t0=t0,tf=tf,step=step,dt=dt) \
             if hasattr(self.uni,'trajectory') else None
 
+        self.project=project
         self.make_pdb()
 
-        self.project=project
+        
 
         self._movie=None