notebook.community

Edit and run 





In [7]:



    


import numpy as np
import pandas as pd
import matplotlib.pyplot as plt
import seaborn as sns
from small_script.myFunctions import *

plt.rcParams['figure.figsize'] = [16.18033, 10]

%matplotlib inline
%load_ext autoreload
%autoreload 2



    


















    






The autoreload extension is already loaded. To reload it, use:
  %reload_ext autoreload

















In [ ]:



    






    











In [3]:



    


def get_data(pre, pdb_list):
    # to get last 20 frame of each run
    _all = []
    for p in pdb_list:
        name = p.lower()[:4]
        for i in range(20):
            for ii in range(3):
                location = pre + f"all_simulations/{name}/simulation/{i}/{ii}/wham.dat"
                try:
                    tmp = pd.read_csv(location).tail(50).reset_index()
                    tmp.columns = tmp.columns.str.strip()
                    _all.append(tmp.assign(Run=i, Name=name, Rerun=ii))
                except Exception as e: 
                    print(e)
    data = pd.concat(_all)
    data["Run"] = "Run" + data["Run"].astype(str)
    return data

perfect frag memory, no mediated interaction





In [13]:



    


pre = "/Users/weilu/Research/server/jan_2019/iterative_optimization_4_no_gamma/"
pdb_list = "1R69, 1UTG, 3ICB, 256BA, 4CPV, 1CCR, 2MHR, 1MBA, 2FHA".split(", ")
data = get_data(pre, pdb_list)
data.reset_index(drop=True).to_csv("/Users/weilu/Research/data/optimization/single_memory_no_gamma.csv")



    


















    






File b'/Users/weilu/Research/server/jan_2019/iterative_optimization_4_no_gamma/all_simulations/4cpv/simulation/8/1/wham.dat' does not exist
File b'/Users/weilu/Research/server/jan_2019/iterative_optimization_4_no_gamma/all_simulations/4cpv/simulation/8/2/wham.dat' does not exist
File b'/Users/weilu/Research/server/jan_2019/iterative_optimization_4_no_gamma/all_simulations/4cpv/simulation/9/1/wham.dat' does not exist
File b'/Users/weilu/Research/server/jan_2019/iterative_optimization_4_no_gamma/all_simulations/4cpv/simulation/9/2/wham.dat' does not exist
File b'/Users/weilu/Research/server/jan_2019/iterative_optimization_4_no_gamma/all_simulations/4cpv/simulation/15/1/wham.dat' does not exist
File b'/Users/weilu/Research/server/jan_2019/iterative_optimization_4_no_gamma/all_simulations/4cpv/simulation/15/2/wham.dat' does not exist
File b'/Users/weilu/Research/server/jan_2019/iterative_optimization_4_no_gamma/all_simulations/2mhr/simulation/18/1/wham.dat' does not exist
File b'/Users/weilu/Research/server/jan_2019/iterative_optimization_4_no_gamma/all_simulations/2mhr/simulation/18/2/wham.dat' does not exist
File b'/Users/weilu/Research/server/jan_2019/iterative_optimization_4_no_gamma/all_simulations/1mba/simulation/3/1/wham.dat' does not exist
File b'/Users/weilu/Research/server/jan_2019/iterative_optimization_4_no_gamma/all_simulations/1mba/simulation/3/2/wham.dat' does not exist
File b'/Users/weilu/Research/server/jan_2019/iterative_optimization_4_no_gamma/all_simulations/1mba/simulation/4/1/wham.dat' does not exist
File b'/Users/weilu/Research/server/jan_2019/iterative_optimization_4_no_gamma/all_simulations/1mba/simulation/4/2/wham.dat' does not exist
File b'/Users/weilu/Research/server/jan_2019/iterative_optimization_4_no_gamma/all_simulations/1mba/simulation/6/1/wham.dat' does not exist
File b'/Users/weilu/Research/server/jan_2019/iterative_optimization_4_no_gamma/all_simulations/1mba/simulation/6/2/wham.dat' does not exist
File b'/Users/weilu/Research/server/jan_2019/iterative_optimization_4_no_gamma/all_simulations/1mba/simulation/11/1/wham.dat' does not exist
File b'/Users/weilu/Research/server/jan_2019/iterative_optimization_4_no_gamma/all_simulations/1mba/simulation/11/2/wham.dat' does not exist
File b'/Users/weilu/Research/server/jan_2019/iterative_optimization_4_no_gamma/all_simulations/1mba/simulation/12/1/wham.dat' does not exist
File b'/Users/weilu/Research/server/jan_2019/iterative_optimization_4_no_gamma/all_simulations/1mba/simulation/12/2/wham.dat' does not exist
File b'/Users/weilu/Research/server/jan_2019/iterative_optimization_4_no_gamma/all_simulations/2fha/simulation/0/1/wham.dat' does not exist
File b'/Users/weilu/Research/server/jan_2019/iterative_optimization_4_no_gamma/all_simulations/2fha/simulation/0/2/wham.dat' does not exist
File b'/Users/weilu/Research/server/jan_2019/iterative_optimization_4_no_gamma/all_simulations/2fha/simulation/3/1/wham.dat' does not exist
File b'/Users/weilu/Research/server/jan_2019/iterative_optimization_4_no_gamma/all_simulations/2fha/simulation/3/2/wham.dat' does not exist
File b'/Users/weilu/Research/server/jan_2019/iterative_optimization_4_no_gamma/all_simulations/2fha/simulation/9/1/wham.dat' does not exist
File b'/Users/weilu/Research/server/jan_2019/iterative_optimization_4_no_gamma/all_simulations/2fha/simulation/9/2/wham.dat' does not exist
File b'/Users/weilu/Research/server/jan_2019/iterative_optimization_4_no_gamma/all_simulations/2fha/simulation/14/1/wham.dat' does not exist
File b'/Users/weilu/Research/server/jan_2019/iterative_optimization_4_no_gamma/all_simulations/2fha/simulation/14/2/wham.dat' does not exist

















In [45]:



    


data = pd.read_csv("/Users/weilu/Research/data/optimization/single_memory_no_gamma.csv", index_col=0)
data2 = pd.read_csv("/Users/weilu/Research/data/optimization/single_memory_old_gamma.csv", index_col=0)
data3 = pd.read_csv("/Users/weilu/Research/data/optimization/single_memory_new_gamma.csv", index_col=0)
d = pd.concat([data.assign(Scheme="no_gamma")
              , data3.assign(Scheme="new_gamma"), data2.assign(Scheme="old_gamma")])
sns.boxplot("Name", "Qw", hue="Scheme", data=d)



    


















    
Out[45]:








<matplotlib.axes._subplots.AxesSubplot at 0x1a28ff8fd0>










    
























In [30]:



    


data.groupby("Name")["Qw"].max()



    


















    
Out[30]:








Name
1ccr    0.489935
1mba    0.483023
1r69    0.859345
1utg    0.882923
256b    0.775495
2fha    0.460386
2mhr    0.644547
3icb    0.818924
4cpv    0.660385
Name: Qw, dtype: float64

perfect frag memory. new gamma





In [43]:



    


pre = "/Users/weilu/Research/server/jan_2019/iterative_optimization_4_new_gamma/"
pdb_list = "1R69, 1UTG, 3ICB, 256BA, 4CPV, 1CCR, 2MHR, 1MBA, 2FHA".split(", ")
data = get_data(pre, pdb_list)
data.reset_index(drop=True).to_csv("/Users/weilu/Research/data/optimization/single_memory_new_gamma.csv")



    


















    






File b'/Users/weilu/Research/server/jan_2019/iterative_optimization_4_new_gamma/all_simulations/4cpv/simulation/4/1/wham.dat' does not exist
File b'/Users/weilu/Research/server/jan_2019/iterative_optimization_4_new_gamma/all_simulations/4cpv/simulation/4/2/wham.dat' does not exist
File b'/Users/weilu/Research/server/jan_2019/iterative_optimization_4_new_gamma/all_simulations/4cpv/simulation/19/1/wham.dat' does not exist
File b'/Users/weilu/Research/server/jan_2019/iterative_optimization_4_new_gamma/all_simulations/4cpv/simulation/19/2/wham.dat' does not exist
File b'/Users/weilu/Research/server/jan_2019/iterative_optimization_4_new_gamma/all_simulations/1mba/simulation/7/1/wham.dat' does not exist
File b'/Users/weilu/Research/server/jan_2019/iterative_optimization_4_new_gamma/all_simulations/1mba/simulation/7/2/wham.dat' does not exist
File b'/Users/weilu/Research/server/jan_2019/iterative_optimization_4_new_gamma/all_simulations/1mba/simulation/8/1/wham.dat' does not exist
File b'/Users/weilu/Research/server/jan_2019/iterative_optimization_4_new_gamma/all_simulations/1mba/simulation/8/2/wham.dat' does not exist
File b'/Users/weilu/Research/server/jan_2019/iterative_optimization_4_new_gamma/all_simulations/1mba/simulation/14/1/wham.dat' does not exist
File b'/Users/weilu/Research/server/jan_2019/iterative_optimization_4_new_gamma/all_simulations/1mba/simulation/14/2/wham.dat' does not exist
File b'/Users/weilu/Research/server/jan_2019/iterative_optimization_4_new_gamma/all_simulations/1mba/simulation/16/1/wham.dat' does not exist
File b'/Users/weilu/Research/server/jan_2019/iterative_optimization_4_new_gamma/all_simulations/1mba/simulation/16/2/wham.dat' does not exist
File b'/Users/weilu/Research/server/jan_2019/iterative_optimization_4_new_gamma/all_simulations/2fha/simulation/1/1/wham.dat' does not exist
File b'/Users/weilu/Research/server/jan_2019/iterative_optimization_4_new_gamma/all_simulations/2fha/simulation/1/2/wham.dat' does not exist
File b'/Users/weilu/Research/server/jan_2019/iterative_optimization_4_new_gamma/all_simulations/2fha/simulation/7/1/wham.dat' does not exist
File b'/Users/weilu/Research/server/jan_2019/iterative_optimization_4_new_gamma/all_simulations/2fha/simulation/7/2/wham.dat' does not exist
File b'/Users/weilu/Research/server/jan_2019/iterative_optimization_4_new_gamma/all_simulations/2fha/simulation/8/1/wham.dat' does not exist
File b'/Users/weilu/Research/server/jan_2019/iterative_optimization_4_new_gamma/all_simulations/2fha/simulation/8/2/wham.dat' does not exist
File b'/Users/weilu/Research/server/jan_2019/iterative_optimization_4_new_gamma/all_simulations/2fha/simulation/15/1/wham.dat' does not exist
File b'/Users/weilu/Research/server/jan_2019/iterative_optimization_4_new_gamma/all_simulations/2fha/simulation/15/2/wham.dat' does not exist
File b'/Users/weilu/Research/server/jan_2019/iterative_optimization_4_new_gamma/all_simulations/2fha/simulation/17/1/wham.dat' does not exist
File b'/Users/weilu/Research/server/jan_2019/iterative_optimization_4_new_gamma/all_simulations/2fha/simulation/17/2/wham.dat' does not exist
File b'/Users/weilu/Research/server/jan_2019/iterative_optimization_4_new_gamma/all_simulations/2fha/simulation/19/1/wham.dat' does not exist
File b'/Users/weilu/Research/server/jan_2019/iterative_optimization_4_new_gamma/all_simulations/2fha/simulation/19/2/wham.dat' does not exist

















In [12]:



    


sns.boxplot("Name", "Qw", data=data)



    


















    
Out[12]:








<matplotlib.axes._subplots.AxesSubplot at 0x10ec0bf28>

with perfect frag memory.(single memory), old gamma





In [31]:



    


pre = "/Users/weilu/Research/server/jan_2019/iterative_optimization_4/"
pdb_list = "1R69, 1UTG, 3ICB, 256BA, 4CPV, 1CCR, 2MHR, 1MBA, 2FHA".split(", ")
data = get_data(pre, pdb_list)
data.reset_index(drop=True).to_csv("/Users/weilu/Research/data/optimization/single_memory_old_gamma.csv")



    


















    






File b'/Users/weilu/Research/server/jan_2019/iterative_optimization_4/all_simulations/4cpv/simulation/8/1/wham.dat' does not exist
File b'/Users/weilu/Research/server/jan_2019/iterative_optimization_4/all_simulations/4cpv/simulation/8/2/wham.dat' does not exist
File b'/Users/weilu/Research/server/jan_2019/iterative_optimization_4/all_simulations/4cpv/simulation/9/1/wham.dat' does not exist
File b'/Users/weilu/Research/server/jan_2019/iterative_optimization_4/all_simulations/4cpv/simulation/9/2/wham.dat' does not exist
File b'/Users/weilu/Research/server/jan_2019/iterative_optimization_4/all_simulations/4cpv/simulation/17/1/wham.dat' does not exist
File b'/Users/weilu/Research/server/jan_2019/iterative_optimization_4/all_simulations/4cpv/simulation/17/2/wham.dat' does not exist
File b'/Users/weilu/Research/server/jan_2019/iterative_optimization_4/all_simulations/1mba/simulation/4/1/wham.dat' does not exist
File b'/Users/weilu/Research/server/jan_2019/iterative_optimization_4/all_simulations/1mba/simulation/4/2/wham.dat' does not exist
File b'/Users/weilu/Research/server/jan_2019/iterative_optimization_4/all_simulations/1mba/simulation/5/1/wham.dat' does not exist
File b'/Users/weilu/Research/server/jan_2019/iterative_optimization_4/all_simulations/1mba/simulation/5/2/wham.dat' does not exist
File b'/Users/weilu/Research/server/jan_2019/iterative_optimization_4/all_simulations/1mba/simulation/8/1/wham.dat' does not exist
File b'/Users/weilu/Research/server/jan_2019/iterative_optimization_4/all_simulations/1mba/simulation/8/2/wham.dat' does not exist
File b'/Users/weilu/Research/server/jan_2019/iterative_optimization_4/all_simulations/1mba/simulation/14/1/wham.dat' does not exist
File b'/Users/weilu/Research/server/jan_2019/iterative_optimization_4/all_simulations/1mba/simulation/14/2/wham.dat' does not exist
File b'/Users/weilu/Research/server/jan_2019/iterative_optimization_4/all_simulations/1mba/simulation/16/1/wham.dat' does not exist
File b'/Users/weilu/Research/server/jan_2019/iterative_optimization_4/all_simulations/1mba/simulation/16/2/wham.dat' does not exist
File b'/Users/weilu/Research/server/jan_2019/iterative_optimization_4/all_simulations/2fha/simulation/4/1/wham.dat' does not exist
File b'/Users/weilu/Research/server/jan_2019/iterative_optimization_4/all_simulations/2fha/simulation/4/2/wham.dat' does not exist

















In [10]:



    


sns.boxplot("Name", "Qw", data=data)



    


















    
Out[10]:








<matplotlib.axes._subplots.AxesSubplot at 0x10df02390>

with new gamma from first iteration





In [5]:



    


pre = "/Users/weilu/Research/server/jan_2019/iterative_optimization_3_again/"
pdb_list = "1R69, 1UTG, 3ICB, 256BA, 4CPV, 1CCR, 2MHR, 1MBA, 2FHA".split(", ")
data = get_data(pre, pdb_list)



    


















    






File b'/Users/weilu/Research/server/jan_2019/iterative_optimization_3_again/all_simulations/4cpv/simulation/1/1/wham.dat' does not exist
File b'/Users/weilu/Research/server/jan_2019/iterative_optimization_3_again/all_simulations/4cpv/simulation/1/2/wham.dat' does not exist
File b'/Users/weilu/Research/server/jan_2019/iterative_optimization_3_again/all_simulations/2mhr/simulation/6/2/wham.dat' does not exist
File b'/Users/weilu/Research/server/jan_2019/iterative_optimization_3_again/all_simulations/2mhr/simulation/14/1/wham.dat' does not exist
File b'/Users/weilu/Research/server/jan_2019/iterative_optimization_3_again/all_simulations/2mhr/simulation/14/2/wham.dat' does not exist
File b'/Users/weilu/Research/server/jan_2019/iterative_optimization_3_again/all_simulations/1mba/simulation/1/1/wham.dat' does not exist
File b'/Users/weilu/Research/server/jan_2019/iterative_optimization_3_again/all_simulations/1mba/simulation/1/2/wham.dat' does not exist
File b'/Users/weilu/Research/server/jan_2019/iterative_optimization_3_again/all_simulations/1mba/simulation/5/1/wham.dat' does not exist
File b'/Users/weilu/Research/server/jan_2019/iterative_optimization_3_again/all_simulations/1mba/simulation/5/2/wham.dat' does not exist
File b'/Users/weilu/Research/server/jan_2019/iterative_optimization_3_again/all_simulations/1mba/simulation/7/1/wham.dat' does not exist
File b'/Users/weilu/Research/server/jan_2019/iterative_optimization_3_again/all_simulations/1mba/simulation/7/2/wham.dat' does not exist
File b'/Users/weilu/Research/server/jan_2019/iterative_optimization_3_again/all_simulations/1mba/simulation/18/1/wham.dat' does not exist
File b'/Users/weilu/Research/server/jan_2019/iterative_optimization_3_again/all_simulations/1mba/simulation/18/2/wham.dat' does not exist
File b'/Users/weilu/Research/server/jan_2019/iterative_optimization_3_again/all_simulations/1mba/simulation/19/1/wham.dat' does not exist
File b'/Users/weilu/Research/server/jan_2019/iterative_optimization_3_again/all_simulations/1mba/simulation/19/2/wham.dat' does not exist
File b'/Users/weilu/Research/server/jan_2019/iterative_optimization_3_again/all_simulations/2fha/simulation/5/1/wham.dat' does not exist
File b'/Users/weilu/Research/server/jan_2019/iterative_optimization_3_again/all_simulations/2fha/simulation/5/2/wham.dat' does not exist
File b'/Users/weilu/Research/server/jan_2019/iterative_optimization_3_again/all_simulations/2fha/simulation/6/1/wham.dat' does not exist
File b'/Users/weilu/Research/server/jan_2019/iterative_optimization_3_again/all_simulations/2fha/simulation/6/2/wham.dat' does not exist
File b'/Users/weilu/Research/server/jan_2019/iterative_optimization_3_again/all_simulations/2fha/simulation/10/2/wham.dat' does not exist
File b'/Users/weilu/Research/server/jan_2019/iterative_optimization_3_again/all_simulations/2fha/simulation/11/0/wham.dat' does not exist
File b'/Users/weilu/Research/server/jan_2019/iterative_optimization_3_again/all_simulations/2fha/simulation/11/1/wham.dat' does not exist
File b'/Users/weilu/Research/server/jan_2019/iterative_optimization_3_again/all_simulations/2fha/simulation/11/2/wham.dat' does not exist
File b'/Users/weilu/Research/server/jan_2019/iterative_optimization_3_again/all_simulations/2fha/simulation/13/1/wham.dat' does not exist
File b'/Users/weilu/Research/server/jan_2019/iterative_optimization_3_again/all_simulations/2fha/simulation/13/2/wham.dat' does not exist
File b'/Users/weilu/Research/server/jan_2019/iterative_optimization_3_again/all_simulations/2fha/simulation/15/0/wham.dat' does not exist
File b'/Users/weilu/Research/server/jan_2019/iterative_optimization_3_again/all_simulations/2fha/simulation/15/1/wham.dat' does not exist
File b'/Users/weilu/Research/server/jan_2019/iterative_optimization_3_again/all_simulations/2fha/simulation/15/2/wham.dat' does not exist
File b'/Users/weilu/Research/server/jan_2019/iterative_optimization_3_again/all_simulations/2fha/simulation/16/0/wham.dat' does not exist
File b'/Users/weilu/Research/server/jan_2019/iterative_optimization_3_again/all_simulations/2fha/simulation/16/1/wham.dat' does not exist
File b'/Users/weilu/Research/server/jan_2019/iterative_optimization_3_again/all_simulations/2fha/simulation/16/2/wham.dat' does not exist

















In [8]:



    


sns.boxplot("Name", "Qw", data=data)



    


















    
Out[8]:








<matplotlib.axes._subplots.AxesSubplot at 0x1a2340d6d8>










    
























In [151]:



    


pre = "/Users/weilu/Research/server_backup/jan_2019/iterative_optimization_3/"
pdb_list = "1R69, 1UTG, 3ICB, 256BA, 4CPV, 1CCR, 2MHR, 1MBA, 2FHA".split(", ")
data = get_data(pre, pdb_list)



    


















    






File b'/Users/weilu/Research/server_backup/jan_2019/iterative_optimization_3/all_simulations/4cpv/simulation/6/1/wham.dat' does not exist
File b'/Users/weilu/Research/server_backup/jan_2019/iterative_optimization_3/all_simulations/4cpv/simulation/6/2/wham.dat' does not exist
File b'/Users/weilu/Research/server_backup/jan_2019/iterative_optimization_3/all_simulations/4cpv/simulation/8/1/wham.dat' does not exist
File b'/Users/weilu/Research/server_backup/jan_2019/iterative_optimization_3/all_simulations/4cpv/simulation/8/2/wham.dat' does not exist
File b'/Users/weilu/Research/server_backup/jan_2019/iterative_optimization_3/all_simulations/4cpv/simulation/11/1/wham.dat' does not exist
File b'/Users/weilu/Research/server_backup/jan_2019/iterative_optimization_3/all_simulations/4cpv/simulation/11/2/wham.dat' does not exist
File b'/Users/weilu/Research/server_backup/jan_2019/iterative_optimization_3/all_simulations/4cpv/simulation/12/1/wham.dat' does not exist
File b'/Users/weilu/Research/server_backup/jan_2019/iterative_optimization_3/all_simulations/4cpv/simulation/12/2/wham.dat' does not exist
File b'/Users/weilu/Research/server_backup/jan_2019/iterative_optimization_3/all_simulations/4cpv/simulation/16/1/wham.dat' does not exist
File b'/Users/weilu/Research/server_backup/jan_2019/iterative_optimization_3/all_simulations/4cpv/simulation/16/2/wham.dat' does not exist
File b'/Users/weilu/Research/server_backup/jan_2019/iterative_optimization_3/all_simulations/2mhr/simulation/0/1/wham.dat' does not exist
File b'/Users/weilu/Research/server_backup/jan_2019/iterative_optimization_3/all_simulations/2mhr/simulation/0/2/wham.dat' does not exist
File b'/Users/weilu/Research/server_backup/jan_2019/iterative_optimization_3/all_simulations/2mhr/simulation/1/1/wham.dat' does not exist
File b'/Users/weilu/Research/server_backup/jan_2019/iterative_optimization_3/all_simulations/2mhr/simulation/1/2/wham.dat' does not exist
File b'/Users/weilu/Research/server_backup/jan_2019/iterative_optimization_3/all_simulations/2mhr/simulation/17/1/wham.dat' does not exist
File b'/Users/weilu/Research/server_backup/jan_2019/iterative_optimization_3/all_simulations/2mhr/simulation/17/2/wham.dat' does not exist
File b'/Users/weilu/Research/server_backup/jan_2019/iterative_optimization_3/all_simulations/1mba/simulation/1/1/wham.dat' does not exist
File b'/Users/weilu/Research/server_backup/jan_2019/iterative_optimization_3/all_simulations/1mba/simulation/1/2/wham.dat' does not exist
File b'/Users/weilu/Research/server_backup/jan_2019/iterative_optimization_3/all_simulations/1mba/simulation/5/1/wham.dat' does not exist
File b'/Users/weilu/Research/server_backup/jan_2019/iterative_optimization_3/all_simulations/1mba/simulation/5/2/wham.dat' does not exist
File b'/Users/weilu/Research/server_backup/jan_2019/iterative_optimization_3/all_simulations/2fha/simulation/5/2/wham.dat' does not exist
File b'/Users/weilu/Research/server_backup/jan_2019/iterative_optimization_3/all_simulations/2fha/simulation/8/1/wham.dat' does not exist
File b'/Users/weilu/Research/server_backup/jan_2019/iterative_optimization_3/all_simulations/2fha/simulation/8/2/wham.dat' does not exist

















In [152]:



    


sns.boxplot("Name", "Qw", data=data)



    


















    
Out[152]:








<matplotlib.axes._subplots.AxesSubplot at 0x1a3b239860>

not nice. all going down (because all gamma is inversed)





In [150]:



    


sns.boxplot("Name", "Qw", data=data)



    


















    
Out[150]:








<matplotlib.axes._subplots.AxesSubplot at 0x125114a20>










    
























In [ ]:

The original gamma.





In [147]:



    


pre = "/Users/weilu/Research/server_backup/jan_2019/iterative_optimization_2/"
pdb_list = "1R69, 1UTG, 3ICB, 256BA, 4CPV, 1CCR, 2MHR, 1MBA, 2FHA".split(", ")
data = get_data(pre, pdb_list)



    


















    






File b'/Users/weilu/Research/server_backup/jan_2019/iterative_optimization_2/all_simulations/1mba/simulation/3/1/wham.dat' does not exist
File b'/Users/weilu/Research/server_backup/jan_2019/iterative_optimization_2/all_simulations/1mba/simulation/3/2/wham.dat' does not exist
File b'/Users/weilu/Research/server_backup/jan_2019/iterative_optimization_2/all_simulations/1mba/simulation/9/1/wham.dat' does not exist
File b'/Users/weilu/Research/server_backup/jan_2019/iterative_optimization_2/all_simulations/1mba/simulation/9/2/wham.dat' does not exist
File b'/Users/weilu/Research/server_backup/jan_2019/iterative_optimization_2/all_simulations/1mba/simulation/15/1/wham.dat' does not exist
File b'/Users/weilu/Research/server_backup/jan_2019/iterative_optimization_2/all_simulations/1mba/simulation/15/2/wham.dat' does not exist
File b'/Users/weilu/Research/server_backup/jan_2019/iterative_optimization_2/all_simulations/1mba/simulation/19/1/wham.dat' does not exist
File b'/Users/weilu/Research/server_backup/jan_2019/iterative_optimization_2/all_simulations/1mba/simulation/19/2/wham.dat' does not exist
File b'/Users/weilu/Research/server_backup/jan_2019/iterative_optimization_2/all_simulations/2fha/simulation/0/1/wham.dat' does not exist
File b'/Users/weilu/Research/server_backup/jan_2019/iterative_optimization_2/all_simulations/2fha/simulation/0/2/wham.dat' does not exist
File b'/Users/weilu/Research/server_backup/jan_2019/iterative_optimization_2/all_simulations/2fha/simulation/3/1/wham.dat' does not exist
File b'/Users/weilu/Research/server_backup/jan_2019/iterative_optimization_2/all_simulations/2fha/simulation/3/2/wham.dat' does not exist
File b'/Users/weilu/Research/server_backup/jan_2019/iterative_optimization_2/all_simulations/2fha/simulation/14/1/wham.dat' does not exist
File b'/Users/weilu/Research/server_backup/jan_2019/iterative_optimization_2/all_simulations/2fha/simulation/14/2/wham.dat' does not exist
File b'/Users/weilu/Research/server_backup/jan_2019/iterative_optimization_2/all_simulations/2fha/simulation/15/1/wham.dat' does not exist
File b'/Users/weilu/Research/server_backup/jan_2019/iterative_optimization_2/all_simulations/2fha/simulation/15/2/wham.dat' does not exist
File b'/Users/weilu/Research/server_backup/jan_2019/iterative_optimization_2/all_simulations/2fha/simulation/16/1/wham.dat' does not exist
File b'/Users/weilu/Research/server_backup/jan_2019/iterative_optimization_2/all_simulations/2fha/simulation/16/2/wham.dat' does not exist

















In [148]:



    


sns.boxplot("Name", "Qw", data=data)



    


















    
Out[148]:








<matplotlib.axes._subplots.AxesSubplot at 0x1a3886cf98>

actually below is all 1r69.





In [ ]:



    


# to get last 20 frame of each run
_all = []
for p in pdb_list:
    name = p.lower()[:4]
    for i in range(20):
        for ii in range(3):
            location = pre + f"iterative_optimization/all_simulations/{name}/simulation/{i}/{ii}/wham.dat"
            tmp = pd.read_csv(location).tail(50).reset_index()
            tmp.columns = tmp.columns.str.strip()
            _all.append(tmp.assign(Run=i, Name=name, Rerun=ii))
data = pd.concat(_all)
data["Run"] = "Run" + data["Run"].astype(str)



    











In [140]:



    


data["Qw"].describe()



    


















    
Out[140]:








count    27000.000000
mean         0.519708
std          0.103103
min          0.278139
25%          0.424369
50%          0.547636
75%          0.612597
max          0.740108
Name: Qw, dtype: float64

















In [136]:



    


sns.boxplot("Name", "Qw", data=data)



    


















    
Out[136]:








<matplotlib.axes._subplots.AxesSubplot at 0x1a36c5abe0>










    
























In [133]:



    


sns.boxplot("Rerun", "Qw", data=test)



    


















    
Out[133]:








<matplotlib.axes._subplots.AxesSubplot at 0x1a3950d6a0>










    
























In [134]:



    


sns.boxplot("Run", "Qw", data=test)



    


















    
Out[134]:








<matplotlib.axes._subplots.AxesSubplot at 0x1a394d2080>










    
























In [86]:



    


t1.plot.box()



    


















    
Out[86]:








<matplotlib.axes._subplots.AxesSubplot at 0x1267b3160>










    
























In [76]:



    


test.groupby("Run")["Qw"].describe()



    


















    
Out[76]:











  
    

      
      count
      mean
      std
      min
      25%
      50%
      75%
      max
    

    

      Run
      
      
      
      
      
      
      
      
    

  
  
    

      Run0
      60.0
      0.492063
      0.093653
      0.352099
      0.417506
      0.460681
      0.593940
      0.643896
    

    

      Run1
      60.0
      0.613469
      0.033499
      0.489589
      0.595621
      0.618510
      0.636664
      0.674489
    

    

      Run10
      60.0
      0.588040
      0.048928
      0.447847
      0.566146
      0.599418
      0.618321
      0.676286
    

    

      Run11
      60.0
      0.587644
      0.065438
      0.434903
      0.584271
      0.611547
      0.629385
      0.666405
    

    

      Run12
      60.0
      0.557059
      0.097539
      0.371032
      0.461230
      0.604372
      0.633267
      0.688444
    

    

      Run13
      60.0
      0.575532
      0.077769
      0.406862
      0.498207
      0.612705
      0.632616
      0.671788
    

    

      Run14
      60.0
      0.508262
      0.073219
      0.415144
      0.455677
      0.472969
      0.581952
      0.672595
    

    

      Run15
      60.0
      0.604550
      0.041980
      0.420115
      0.594624
      0.611072
      0.629712
      0.666170
    

    

      Run16
      60.0
      0.609762
      0.038675
      0.501425
      0.593483
      0.616208
      0.636611
      0.690865
    

    

      Run17
      60.0
      0.491577
      0.091607
      0.373193
      0.422707
      0.462378
      0.587385
      0.685718
    

    

      Run18
      60.0
      0.546189
      0.107946
      0.335089
      0.430784
      0.602315
      0.628165
      0.670491
    

    

      Run19
      60.0
      0.480945
      0.105122
      0.353187
      0.402410
      0.430124
      0.580008
      0.705537
    

    

      Run2
      60.0
      0.601997
      0.051857
      0.428726
      0.575047
      0.612330
      0.637639
      0.677871
    

    

      Run3
      60.0
      0.628324
      0.043587
      0.492678
      0.604332
      0.627939
      0.650766
      0.740108
    

    

      Run4
      60.0
      0.612680
      0.027122
      0.542264
      0.596803
      0.611940
      0.629090
      0.694046
    

    

      Run5
      60.0
      0.414978
      0.068990
      0.289961
      0.338529
      0.443743
      0.476276
      0.522907
    

    

      Run6
      60.0
      0.634158
      0.046563
      0.528628
      0.603651
      0.642405
      0.669669
      0.712608
    

    

      Run7
      60.0
      0.510316
      0.115215
      0.312644
      0.378945
      0.545967
      0.606870
      0.667881
    

    

      Run8
      60.0
      0.536624
      0.115425
      0.346724
      0.394899
      0.595567
      0.625726
      0.669929
    

    

      Run9
      60.0
      0.540470
      0.101121
      0.360576
      0.439092
      0.590581
      0.616552
      0.666440
    

  




















In [68]:



    


sns.scatterplot("Steps", "Qw", hue="Run", data=test)



    


















    
Out[68]:








<matplotlib.axes._subplots.AxesSubplot at 0x126029ac8>










    
























In [ ]:



    






    











In [16]:



    


# to get complete data
_all = []
for p in pdb_list:
    name = p.lower()[:4]
    for i in range(20):
        for ii in range(3):
            location = pre + f"iterative_optimization/all_simulations/{name}/simulation/{i}/{ii}/wham.dat"
            tmp = pd.read_csv(location)
            tmp.columns = tmp.columns.str.strip()
            _all.append(tmp.assign(Run=i, Name=name))
data = pd.concat(_all)



    











In [55]:



    






    











In [56]:



    


test = data.query("Name == '1r69'")



    











In [63]:



    


sns.scatterplot("Steps", "Qw", hue="Run", data=test)



    


















    
Out[63]:








<matplotlib.axes._subplots.AxesSubplot at 0x1265130f0>










    
























In [ ]:

Content source: luwei0917/awsemmd_script

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