In [2]:

    

import matplotlib as mpl
import matplotlib.pyplot as plt
from scipy.interpolate import griddata
from scipy.interpolate import interp2d
import sys
import argparse
import os
import numpy as np
from numpy.random import uniform
import pandas as pd
from itertools import product
import datetime
import glob
# %matplotlib inline
%matplotlib notebook


    

In [26]:

    

def expand_grid(dictionary):
    return pd.DataFrame([row for row in product(*dictionary.values())],
                        columns=dictionary.keys())
def readPMF(pmf_list_data, pre):
    pmf_list_data = expand_grid(pmf_list)
    all_pmf_list = []
    for index, row in pmf_list_data.iterrows():
    #     print(index)
    #     print("--")
    #     print(row)
        force = row["force"]
        temp = row["temp"]
        perturbation = row["perturbation"]
        if perturbation == 0:
            location = pre + f"/force_{force}/pmf-{temp}.dat"
            change = "none"
            upOrDown = "none"
        else:
            location = pre + f"/force_{force}/perturbation-{perturbation}-pmf-{temp}.dat"
            change = perturbation_table[perturbation].split("_")[-1]
            upOrDown = perturbation_table[perturbation].split("_")[0]
    #     print(location)
        name_list = ["f", "df", "e", "s"]
        names = ["bin", "x"] + name_list
        try:
            data = pd.read_table(location, skiprows=2, sep='\s+', names=names).assign(upOrDown=upOrDown, change=change, force=force, temp=temp, perturbation=perturbation_table[perturbation])
            all_pmf_list.append(data)
        except:
            print(row, "not available")
    return pd.concat(all_pmf_list).dropna().reset_index()


    

In [60]:

    

def expand_grid(dictionary):
    return pd.DataFrame([row for row in product(*dictionary.values())],
                        columns=dictionary.keys())
def readPMF(pre):
    perturbation_table = {0:"original", 1:"p_mem",
                          2:"m_mem", 3:"p_lipid",
                          4:"m_lipid", 5:"p_go",
                          6:"m_go", 7:"p_rg", 8:"m_rg"}
    pmf_list = {
    "perturbation":list(perturbation_table.keys()),
    "force":["0.0", "0.1", "0.2"]
    }
    pmf_list_data = expand_grid(pmf_list)
    all_pmf_list = []
    for index, row in pmf_list_data.iterrows():
    #     print(index)
    #     print("--")
    #     print(row)
        force = row["force"]
        perturbation = row["perturbation"]
        if perturbation == 0:
            location = pre + f"/force_{force}/pmf-*.dat"
            pmf_list = glob.glob(location)
            change = "none"
            upOrDown = "none"
        else:
            location = pre + f"/force_{force}/perturbation-{perturbation}-pmf-*.dat"
            pmf_list = glob.glob(location)
            change = perturbation_table[perturbation].split("_")[-1]
            upOrDown = perturbation_table[perturbation].split("_")[0]
    #     print(location)
        name_list = ["f", "df", "e", "s"]
        names = ["bin", "x"] + name_list
        for location in pmf_list:
#             print(location)
            temp = re.findall(r'pmf-(\d+)', location)
            if len(temp) != 1:
                raise ValueError('Not expected to see more than one or none')
            else:
                temp = temp[0]
            data = pd.read_table(location, skiprows=2, sep='\s+', names=names).assign(upOrDown=upOrDown, change=change, force=force, temp=temp, perturbation=perturbation_table[perturbation])
            all_pmf_list.append(data)

    return pd.concat(all_pmf_list).dropna().reset_index()


    

In [66]:

    

pre = "/Users/weilu/Research/davinci/all_freeEnergy_calculation_nov11/"
pre = pre + "next_gen_native_based_memb_3_rg_0.4_lipid_0.6_topology/1d_dis"
data = readPMF(pre)


    

In [74]:

    

import datetime


    

In [94]:

    

datetime.datetime.today().strftime("%d_%h")


    

    
Out[94]:





'14_Nov'

In [78]:

    

print(datetime.date())


    

    




---------------------------------------------------------------------------
TypeError                                 Traceback (most recent call last)
<ipython-input-78-3ccbc339ae28> in <module>()
----> 1 print(datetime.date())

TypeError: Required argument 'year' (pos 1) not found

In [ ]:

    

# pre = "/Users/weilu/Research/davinci/all_freeEnergy_calculation/rgWidth_memb_3_rg_0.1_lipid_1_extended/1d_dis/"
pre = "/Users/weilu/Research/davinci/all_freeEnergy_calculation_nov11/next_gen_native_based_memb_3_rg_0.4_lipid_0.6_topology/1d_dis"
perturbation_table = {0:"original", 1:"p_mem", 2:"m_mem", 3:"p_lipid", 4:"m_lipid", 5:"p_go", 6:"m_go", 7:"p_rg", 8:"m_rg"}
pmf_list = {
    "temp":[*range(450, 610, 10)],
    "perturbation":list(perturbation_table.keys()),
    "force":["0.0", "0.1", "0.2"]
}
data = readPMF(pmf_list, pre)
remove_columns = ['bin']
data = data.drop(remove_columns, axis=1)
data.to_feather("/Users/weilu/Research/data/pulling/nov14_pmf.feather")


    

In [27]:

    

# pre = "/Users/weilu/Research/davinci/all_freeEnergy_calculation/rgWidth_memb_3_rg_0.1_lipid_1_extended/1d_dis/"
pre = "/Users/weilu/Research/davinci/all_freeEnergy_calculation_nov11/next_gen_native_based_memb_3_rg_0.4_lipid_0.6_topology/1d_dis"
perturbation_table = {0:"original", 1:"p_mem", 2:"m_mem", 3:"p_lipid", 4:"m_lipid", 5:"p_go", 6:"m_go", 7:"p_rg", 8:"m_rg"}
pmf_list = {
    "temp":[*range(450, 610, 10)],
    "perturbation":list(perturbation_table.keys()),
    "force":["0.0", "0.1", "0.2"]
}
data = readPMF(pmf_list, pre)
remove_columns = ['bin']
data = data.drop(remove_columns, axis=1)
data.to_feather("/Users/weilu/Research/data/pulling/nov14_pmf.feather")


    

    




temp            450
perturbation      1
force           0.0
Name: 3, dtype: object not available
temp            450
perturbation      1
force           0.1
Name: 4, dtype: object not available
temp            450
perturbation      1
force           0.2
Name: 5, dtype: object not available
temp            450
perturbation      2
force           0.0
Name: 6, dtype: object not available
temp            450
perturbation      2
force           0.1
Name: 7, dtype: object not available
temp            450
perturbation      2
force           0.2
Name: 8, dtype: object not available
temp            450
perturbation      3
force           0.0
Name: 9, dtype: object not available
temp            450
perturbation      3
force           0.1
Name: 10, dtype: object not available
temp            450
perturbation      3
force           0.2
Name: 11, dtype: object not available
temp            450
perturbation      4
force           0.0
Name: 12, dtype: object not available
temp            450
perturbation      4
force           0.1
Name: 13, dtype: object not available
temp            450
perturbation      4
force           0.2
Name: 14, dtype: object not available
temp            450
perturbation      5
force           0.0
Name: 15, dtype: object not available
temp            450
perturbation      5
force           0.1
Name: 16, dtype: object not available
temp            450
perturbation      5
force           0.2
Name: 17, dtype: object not available
temp            450
perturbation      6
force           0.0
Name: 18, dtype: object not available
temp            450
perturbation      6
force           0.1
Name: 19, dtype: object not available
temp            450
perturbation      6
force           0.2
Name: 20, dtype: object not available
temp            450
perturbation      7
force           0.0
Name: 21, dtype: object not available
temp            450
perturbation      7
force           0.1
Name: 22, dtype: object not available
temp            450
perturbation      7
force           0.2
Name: 23, dtype: object not available
temp            450
perturbation      8
force           0.0
Name: 24, dtype: object not available
temp            450
perturbation      8
force           0.1
Name: 25, dtype: object not available
temp            450
perturbation      8
force           0.2
Name: 26, dtype: object not available
temp            460
perturbation      1
force           0.0
Name: 30, dtype: object not available
temp            460
perturbation      1
force           0.1
Name: 31, dtype: object not available
temp            460
perturbation      1
force           0.2
Name: 32, dtype: object not available
temp            460
perturbation      2
force           0.0
Name: 33, dtype: object not available
temp            460
perturbation      2
force           0.1
Name: 34, dtype: object not available
temp            460
perturbation      2
force           0.2
Name: 35, dtype: object not available
temp            460
perturbation      3
force           0.0
Name: 36, dtype: object not available
temp            460
perturbation      3
force           0.1
Name: 37, dtype: object not available
temp            460
perturbation      3
force           0.2
Name: 38, dtype: object not available
temp            460
perturbation      4
force           0.0
Name: 39, dtype: object not available
temp            460
perturbation      4
force           0.1
Name: 40, dtype: object not available
temp            460
perturbation      4
force           0.2
Name: 41, dtype: object not available
temp            460
perturbation      5
force           0.0
Name: 42, dtype: object not available
temp            460
perturbation      5
force           0.1
Name: 43, dtype: object not available
temp            460
perturbation      5
force           0.2
Name: 44, dtype: object not available
temp            460
perturbation      6
force           0.0
Name: 45, dtype: object not available
temp            460
perturbation      6
force           0.1
Name: 46, dtype: object not available
temp            460
perturbation      6
force           0.2
Name: 47, dtype: object not available
temp            460
perturbation      7
force           0.0
Name: 48, dtype: object not available
temp            460
perturbation      7
force           0.1
Name: 49, dtype: object not available
temp            460
perturbation      7
force           0.2
Name: 50, dtype: object not available
temp            460
perturbation      8
force           0.0
Name: 51, dtype: object not available
temp            460
perturbation      8
force           0.1
Name: 52, dtype: object not available
temp            460
perturbation      8
force           0.2
Name: 53, dtype: object not available
temp            470
perturbation      1
force           0.0
Name: 57, dtype: object not available
temp            470
perturbation      1
force           0.1
Name: 58, dtype: object not available
temp            470
perturbation      1
force           0.2
Name: 59, dtype: object not available
temp            470
perturbation      2
force           0.0
Name: 60, dtype: object not available
temp            470
perturbation      2
force           0.1
Name: 61, dtype: object not available
temp            470
perturbation      2
force           0.2
Name: 62, dtype: object not available
temp            470
perturbation      3
force           0.0
Name: 63, dtype: object not available
temp            470
perturbation      3
force           0.1
Name: 64, dtype: object not available
temp            470
perturbation      3
force           0.2
Name: 65, dtype: object not available
temp            470
perturbation      4
force           0.0
Name: 66, dtype: object not available
temp            470
perturbation      4
force           0.1
Name: 67, dtype: object not available
temp            470
perturbation      4
force           0.2
Name: 68, dtype: object not available
temp            470
perturbation      5
force           0.0
Name: 69, dtype: object not available
temp            470
perturbation      5
force           0.1
Name: 70, dtype: object not available
temp            470
perturbation      5
force           0.2
Name: 71, dtype: object not available
temp            470
perturbation      6
force           0.0
Name: 72, dtype: object not available
temp            470
perturbation      6
force           0.1
Name: 73, dtype: object not available
temp            470
perturbation      6
force           0.2
Name: 74, dtype: object not available
temp            470
perturbation      7
force           0.0
Name: 75, dtype: object not available
temp            470
perturbation      7
force           0.1
Name: 76, dtype: object not available
temp            470
perturbation      7
force           0.2
Name: 77, dtype: object not available
temp            470
perturbation      8
force           0.0
Name: 78, dtype: object not available
temp            470
perturbation      8
force           0.1
Name: 79, dtype: object not available
temp            470
perturbation      8
force           0.2
Name: 80, dtype: object not available
temp            480
perturbation      1
force           0.0
Name: 84, dtype: object not available
temp            480
perturbation      1
force           0.1
Name: 85, dtype: object not available
temp            480
perturbation      1
force           0.2
Name: 86, dtype: object not available
temp            480
perturbation      2
force           0.0
Name: 87, dtype: object not available
temp            480
perturbation      2
force           0.1
Name: 88, dtype: object not available
temp            480
perturbation      2
force           0.2
Name: 89, dtype: object not available
temp            480
perturbation      3
force           0.0
Name: 90, dtype: object not available
temp            480
perturbation      3
force           0.1
Name: 91, dtype: object not available
temp            480
perturbation      3
force           0.2
Name: 92, dtype: object not available
temp            480
perturbation      4
force           0.0
Name: 93, dtype: object not available
temp            480
perturbation      4
force           0.1
Name: 94, dtype: object not available
temp            480
perturbation      4
force           0.2
Name: 95, dtype: object not available
temp            480
perturbation      5
force           0.0
Name: 96, dtype: object not available
temp            480
perturbation      5
force           0.1
Name: 97, dtype: object not available
temp            480
perturbation      5
force           0.2
Name: 98, dtype: object not available
temp            480
perturbation      6
force           0.0
Name: 99, dtype: object not available
temp            480
perturbation      6
force           0.1
Name: 100, dtype: object not available
temp            480
perturbation      6
force           0.2
Name: 101, dtype: object not available
temp            480
perturbation      7
force           0.0
Name: 102, dtype: object not available
temp            480
perturbation      7
force           0.1
Name: 103, dtype: object not available
temp            480
perturbation      7
force           0.2
Name: 104, dtype: object not available
temp            480
perturbation      8
force           0.0
Name: 105, dtype: object not available
temp            480
perturbation      8
force           0.1
Name: 106, dtype: object not available
temp            480
perturbation      8
force           0.2
Name: 107, dtype: object not available
temp            490
perturbation      1
force           0.0
Name: 111, dtype: object not available
temp            490
perturbation      1
force           0.1
Name: 112, dtype: object not available
temp            490
perturbation      1
force           0.2
Name: 113, dtype: object not available
temp            490
perturbation      2
force           0.0
Name: 114, dtype: object not available
temp            490
perturbation      2
force           0.1
Name: 115, dtype: object not available
temp            490
perturbation      2
force           0.2
Name: 116, dtype: object not available
temp            490
perturbation      3
force           0.0
Name: 117, dtype: object not available
temp            490
perturbation      3
force           0.1
Name: 118, dtype: object not available
temp            490
perturbation      3
force           0.2
Name: 119, dtype: object not available
temp            490
perturbation      4
force           0.0
Name: 120, dtype: object not available
temp            490
perturbation      4
force           0.1
Name: 121, dtype: object not available
temp            490
perturbation      4
force           0.2
Name: 122, dtype: object not available
temp            490
perturbation      5
force           0.0
Name: 123, dtype: object not available
temp            490
perturbation      5
force           0.1
Name: 124, dtype: object not available
temp            490
perturbation      5
force           0.2
Name: 125, dtype: object not available
temp            490
perturbation      6
force           0.0
Name: 126, dtype: object not available
temp            490
perturbation      6
force           0.1
Name: 127, dtype: object not available
temp            490
perturbation      6
force           0.2
Name: 128, dtype: object not available
temp            490
perturbation      7
force           0.0
Name: 129, dtype: object not available
temp            490
perturbation      7
force           0.1
Name: 130, dtype: object not available
temp            490
perturbation      7
force           0.2
Name: 131, dtype: object not available
temp            490
perturbation      8
force           0.0
Name: 132, dtype: object not available
temp            490
perturbation      8
force           0.1
Name: 133, dtype: object not available
temp            490
perturbation      8
force           0.2
Name: 134, dtype: object not available
temp            500
perturbation      0
force           0.2
Name: 137, dtype: object not available
temp            500
perturbation      1
force           0.0
Name: 138, dtype: object not available
temp            500
perturbation      1
force           0.1
Name: 139, dtype: object not available
temp            500
perturbation      1
force           0.2
Name: 140, dtype: object not available
temp            500
perturbation      2
force           0.0
Name: 141, dtype: object not available
temp            500
perturbation      2
force           0.1
Name: 142, dtype: object not available
temp            500
perturbation      2
force           0.2
Name: 143, dtype: object not available
temp            500
perturbation      3
force           0.0
Name: 144, dtype: object not available
temp            500
perturbation      3
force           0.1
Name: 145, dtype: object not available
temp            500
perturbation      3
force           0.2
Name: 146, dtype: object not available
temp            500
perturbation      4
force           0.0
Name: 147, dtype: object not available
temp            500
perturbation      4
force           0.1
Name: 148, dtype: object not available
temp            500
perturbation      4
force           0.2
Name: 149, dtype: object not available
temp            500
perturbation      5
force           0.0
Name: 150, dtype: object not available
temp            500
perturbation      5
force           0.1
Name: 151, dtype: object not available
temp            500
perturbation      5
force           0.2
Name: 152, dtype: object not available
temp            500
perturbation      6
force           0.0
Name: 153, dtype: object not available
temp            500
perturbation      6
force           0.1
Name: 154, dtype: object not available
temp            500
perturbation      6
force           0.2
Name: 155, dtype: object not available
temp            500
perturbation      7
force           0.0
Name: 156, dtype: object not available
temp            500
perturbation      7
force           0.1
Name: 157, dtype: object not available
temp            500
perturbation      7
force           0.2
Name: 158, dtype: object not available
temp            500
perturbation      8
force           0.0
Name: 159, dtype: object not available
temp            500
perturbation      8
force           0.1
Name: 160, dtype: object not available
temp            500
perturbation      8
force           0.2
Name: 161, dtype: object not available
temp            510
perturbation      0
force           0.0
Name: 162, dtype: object not available
temp            510
perturbation      0
force           0.1
Name: 163, dtype: object not available
temp            510
perturbation      0
force           0.2
Name: 164, dtype: object not available
temp            510
perturbation      1
force           0.0
Name: 165, dtype: object not available
temp            510
perturbation      1
force           0.1
Name: 166, dtype: object not available
temp            510
perturbation      1
force           0.2
Name: 167, dtype: object not available
temp            510
perturbation      2
force           0.0
Name: 168, dtype: object not available
temp            510
perturbation      2
force           0.1
Name: 169, dtype: object not available
temp            510
perturbation      2
force           0.2
Name: 170, dtype: object not available
temp            510
perturbation      3
force           0.0
Name: 171, dtype: object not available
temp            510
perturbation      3
force           0.1
Name: 172, dtype: object not available
temp            510
perturbation      3
force           0.2
Name: 173, dtype: object not available
temp            510
perturbation      4
force           0.0
Name: 174, dtype: object not available
temp            510
perturbation      4
force           0.1
Name: 175, dtype: object not available
temp            510
perturbation      4
force           0.2
Name: 176, dtype: object not available
temp            510
perturbation      5
force           0.0
Name: 177, dtype: object not available
temp            510
perturbation      5
force           0.1
Name: 178, dtype: object not available
temp            510
perturbation      5
force           0.2
Name: 179, dtype: object not available
temp            510
perturbation      6
force           0.0
Name: 180, dtype: object not available
temp            510
perturbation      6
force           0.1
Name: 181, dtype: object not available
temp            510
perturbation      6
force           0.2
Name: 182, dtype: object not available
temp            510
perturbation      7
force           0.0
Name: 183, dtype: object not available
temp            510
perturbation      7
force           0.1
Name: 184, dtype: object not available
temp            510
perturbation      7
force           0.2
Name: 185, dtype: object not available
temp            510
perturbation      8
force           0.0
Name: 186, dtype: object not available
temp            510
perturbation      8
force           0.1
Name: 187, dtype: object not available
temp            510
perturbation      8
force           0.2
Name: 188, dtype: object not available
temp            520
perturbation      0
force           0.0
Name: 189, dtype: object not available
temp            520
perturbation      0
force           0.1
Name: 190, dtype: object not available
temp            520
perturbation      0
force           0.2
Name: 191, dtype: object not available
temp            520
perturbation      1
force           0.0
Name: 192, dtype: object not available
temp            520
perturbation      1
force           0.1
Name: 193, dtype: object not available
temp            520
perturbation      1
force           0.2
Name: 194, dtype: object not available
temp            520
perturbation      2
force           0.0
Name: 195, dtype: object not available
temp            520
perturbation      2
force           0.1
Name: 196, dtype: object not available
temp            520
perturbation      2
force           0.2
Name: 197, dtype: object not available
temp            520
perturbation      3
force           0.0
Name: 198, dtype: object not available
temp            520
perturbation      3
force           0.1
Name: 199, dtype: object not available
temp            520
perturbation      3
force           0.2
Name: 200, dtype: object not available
temp            520
perturbation      4
force           0.0
Name: 201, dtype: object not available
temp            520
perturbation      4
force           0.1
Name: 202, dtype: object not available
temp            520
perturbation      4
force           0.2
Name: 203, dtype: object not available
temp            520
perturbation      5
force           0.0
Name: 204, dtype: object not available
temp            520
perturbation      5
force           0.1
Name: 205, dtype: object not available
temp            520
perturbation      5
force           0.2
Name: 206, dtype: object not available
temp            520
perturbation      6
force           0.0
Name: 207, dtype: object not available
temp            520
perturbation      6
force           0.1
Name: 208, dtype: object not available
temp            520
perturbation      6
force           0.2
Name: 209, dtype: object not available
temp            520
perturbation      7
force           0.0
Name: 210, dtype: object not available
temp            520
perturbation      7
force           0.1
Name: 211, dtype: object not available
temp            520
perturbation      7
force           0.2
Name: 212, dtype: object not available
temp            520
perturbation      8
force           0.0
Name: 213, dtype: object not available
temp            520
perturbation      8
force           0.1
Name: 214, dtype: object not available
temp            520
perturbation      8
force           0.2
Name: 215, dtype: object not available
temp            530
perturbation      0
force           0.0
Name: 216, dtype: object not available
temp            530
perturbation      0
force           0.1
Name: 217, dtype: object not available
temp            530
perturbation      0
force           0.2
Name: 218, dtype: object not available
temp            530
perturbation      1
force           0.0
Name: 219, dtype: object not available
temp            530
perturbation      1
force           0.1
Name: 220, dtype: object not available
temp            530
perturbation      1
force           0.2
Name: 221, dtype: object not available
temp            530
perturbation      2
force           0.0
Name: 222, dtype: object not available
temp            530
perturbation      2
force           0.1
Name: 223, dtype: object not available
temp            530
perturbation      2
force           0.2
Name: 224, dtype: object not available
temp            530
perturbation      3
force           0.0
Name: 225, dtype: object not available
temp            530
perturbation      3
force           0.1
Name: 226, dtype: object not available
temp            530
perturbation      3
force           0.2
Name: 227, dtype: object not available
temp            530
perturbation      4
force           0.0
Name: 228, dtype: object not available
temp            530
perturbation      4
force           0.1
Name: 229, dtype: object not available
temp            530
perturbation      4
force           0.2
Name: 230, dtype: object not available
temp            530
perturbation      5
force           0.0
Name: 231, dtype: object not available
temp            530
perturbation      5
force           0.1
Name: 232, dtype: object not available
temp            530
perturbation      5
force           0.2
Name: 233, dtype: object not available
temp            530
perturbation      6
force           0.0
Name: 234, dtype: object not available
temp            530
perturbation      6
force           0.1
Name: 235, dtype: object not available
temp            530
perturbation      6
force           0.2
Name: 236, dtype: object not available
temp            530
perturbation      7
force           0.0
Name: 237, dtype: object not available
temp            530
perturbation      7
force           0.1
Name: 238, dtype: object not available
temp            530
perturbation      7
force           0.2
Name: 239, dtype: object not available
temp            530
perturbation      8
force           0.0
Name: 240, dtype: object not available
temp            530
perturbation      8
force           0.1
Name: 241, dtype: object not available
temp            530
perturbation      8
force           0.2
Name: 242, dtype: object not available
temp            540
perturbation      0
force           0.0
Name: 243, dtype: object not available
temp            540
perturbation      0
force           0.1
Name: 244, dtype: object not available
temp            540
perturbation      0
force           0.2
Name: 245, dtype: object not available
temp            540
perturbation      1
force           0.0
Name: 246, dtype: object not available
temp            540
perturbation      1
force           0.1
Name: 247, dtype: object not available
temp            540
perturbation      1
force           0.2
Name: 248, dtype: object not available
temp            540
perturbation      2
force           0.0
Name: 249, dtype: object not available
temp            540
perturbation      2
force           0.1
Name: 250, dtype: object not available
temp            540
perturbation      2
force           0.2
Name: 251, dtype: object not available
temp            540
perturbation      3
force           0.0
Name: 252, dtype: object not available
temp            540
perturbation      3
force           0.1
Name: 253, dtype: object not available
temp            540
perturbation      3
force           0.2
Name: 254, dtype: object not available
temp            540
perturbation      4
force           0.0
Name: 255, dtype: object not available
temp            540
perturbation      4
force           0.1
Name: 256, dtype: object not available
temp            540
perturbation      4
force           0.2
Name: 257, dtype: object not available
temp            540
perturbation      5
force           0.0
Name: 258, dtype: object not available
temp            540
perturbation      5
force           0.1
Name: 259, dtype: object not available
temp            540
perturbation      5
force           0.2
Name: 260, dtype: object not available
temp            540
perturbation      6
force           0.0
Name: 261, dtype: object not available
temp            540
perturbation      6
force           0.1
Name: 262, dtype: object not available
temp            540
perturbation      6
force           0.2
Name: 263, dtype: object not available
temp            540
perturbation      7
force           0.0
Name: 264, dtype: object not available
temp            540
perturbation      7
force           0.1
Name: 265, dtype: object not available
temp            540
perturbation      7
force           0.2
Name: 266, dtype: object not available
temp            540
perturbation      8
force           0.0
Name: 267, dtype: object not available
temp            540
perturbation      8
force           0.1
Name: 268, dtype: object not available
temp            540
perturbation      8
force           0.2
Name: 269, dtype: object not available
temp            550
perturbation      0
force           0.0
Name: 270, dtype: object not available
temp            550
perturbation      0
force           0.1
Name: 271, dtype: object not available
temp            550
perturbation      0
force           0.2
Name: 272, dtype: object not available
temp            550
perturbation      1
force           0.0
Name: 273, dtype: object not available
temp            550
perturbation      1
force           0.1
Name: 274, dtype: object not available
temp            550
perturbation      1
force           0.2
Name: 275, dtype: object not available
temp            550
perturbation      2
force           0.0
Name: 276, dtype: object not available
temp            550
perturbation      2
force           0.1
Name: 277, dtype: object not available
temp            550
perturbation      2
force           0.2
Name: 278, dtype: object not available
temp            550
perturbation      3
force           0.0
Name: 279, dtype: object not available
temp            550
perturbation      3
force           0.1
Name: 280, dtype: object not available
temp            550
perturbation      3
force           0.2
Name: 281, dtype: object not available
temp            550
perturbation      4
force           0.0
Name: 282, dtype: object not available
temp            550
perturbation      4
force           0.1
Name: 283, dtype: object not available
temp            550
perturbation      4
force           0.2
Name: 284, dtype: object not available
temp            550
perturbation      5
force           0.0
Name: 285, dtype: object not available
temp            550
perturbation      5
force           0.1
Name: 286, dtype: object not available
temp            550
perturbation      5
force           0.2
Name: 287, dtype: object not available
temp            550
perturbation      6
force           0.0
Name: 288, dtype: object not available
temp            550
perturbation      6
force           0.1
Name: 289, dtype: object not available
temp            550
perturbation      6
force           0.2
Name: 290, dtype: object not available
temp            550
perturbation      7
force           0.0
Name: 291, dtype: object not available
temp            550
perturbation      7
force           0.1
Name: 292, dtype: object not available
temp            550
perturbation      7
force           0.2
Name: 293, dtype: object not available
temp            550
perturbation      8
force           0.0
Name: 294, dtype: object not available
temp            550
perturbation      8
force           0.1
Name: 295, dtype: object not available
temp            550
perturbation      8
force           0.2
Name: 296, dtype: object not available
temp            560
perturbation      0
force           0.0
Name: 297, dtype: object not available
temp            560
perturbation      0
force           0.1
Name: 298, dtype: object not available
temp            560
perturbation      0
force           0.2
Name: 299, dtype: object not available
temp            560
perturbation      1
force           0.0
Name: 300, dtype: object not available
temp            560
perturbation      1
force           0.1
Name: 301, dtype: object not available
temp            560
perturbation      1
force           0.2
Name: 302, dtype: object not available
temp            560
perturbation      2
force           0.0
Name: 303, dtype: object not available
temp            560
perturbation      2
force           0.1
Name: 304, dtype: object not available
temp            560
perturbation      2
force           0.2
Name: 305, dtype: object not available
temp            560
perturbation      3
force           0.0
Name: 306, dtype: object not available
temp            560
perturbation      3
force           0.1
Name: 307, dtype: object not available
temp            560
perturbation      3
force           0.2
Name: 308, dtype: object not available
temp            560
perturbation      4
force           0.0
Name: 309, dtype: object not available
temp            560
perturbation      4
force           0.1
Name: 310, dtype: object not available
temp            560
perturbation      4
force           0.2
Name: 311, dtype: object not available
temp            560
perturbation      5
force           0.0
Name: 312, dtype: object not available
temp            560
perturbation      5
force           0.1
Name: 313, dtype: object not available
temp            560
perturbation      5
force           0.2
Name: 314, dtype: object not available
temp            560
perturbation      6
force           0.0
Name: 315, dtype: object not available
temp            560
perturbation      6
force           0.1
Name: 316, dtype: object not available
temp            560
perturbation      6
force           0.2
Name: 317, dtype: object not available
temp            560
perturbation      7
force           0.0
Name: 318, dtype: object not available
temp            560
perturbation      7
force           0.1
Name: 319, dtype: object not available
temp            560
perturbation      7
force           0.2
Name: 320, dtype: object not available
temp            560
perturbation      8
force           0.0
Name: 321, dtype: object not available
temp            560
perturbation      8
force           0.1
Name: 322, dtype: object not available
temp            560
perturbation      8
force           0.2
Name: 323, dtype: object not available
temp            570
perturbation      0
force           0.0
Name: 324, dtype: object not available
temp            570
perturbation      0
force           0.1
Name: 325, dtype: object not available
temp            570
perturbation      0
force           0.2
Name: 326, dtype: object not available
temp            570
perturbation      1
force           0.0
Name: 327, dtype: object not available
temp            570
perturbation      1
force           0.1
Name: 328, dtype: object not available
temp            570
perturbation      1
force           0.2
Name: 329, dtype: object not available
temp            570
perturbation      2
force           0.0
Name: 330, dtype: object not available
temp            570
perturbation      2
force           0.1
Name: 331, dtype: object not available
temp            570
perturbation      2
force           0.2
Name: 332, dtype: object not available
temp            570
perturbation      3
force           0.0
Name: 333, dtype: object not available
temp            570
perturbation      3
force           0.1
Name: 334, dtype: object not available
temp            570
perturbation      3
force           0.2
Name: 335, dtype: object not available
temp            570
perturbation      4
force           0.0
Name: 336, dtype: object not available
temp            570
perturbation      4
force           0.1
Name: 337, dtype: object not available
temp            570
perturbation      4
force           0.2
Name: 338, dtype: object not available
temp            570
perturbation      5
force           0.0
Name: 339, dtype: object not available
temp            570
perturbation      5
force           0.1
Name: 340, dtype: object not available
temp            570
perturbation      5
force           0.2
Name: 341, dtype: object not available
temp            570
perturbation      6
force           0.0
Name: 342, dtype: object not available
temp            570
perturbation      6
force           0.1
Name: 343, dtype: object not available
temp            570
perturbation      6
force           0.2
Name: 344, dtype: object not available
temp            570
perturbation      7
force           0.0
Name: 345, dtype: object not available
temp            570
perturbation      7
force           0.1
Name: 346, dtype: object not available
temp            570
perturbation      7
force           0.2
Name: 347, dtype: object not available
temp            570
perturbation      8
force           0.0
Name: 348, dtype: object not available
temp            570
perturbation      8
force           0.1
Name: 349, dtype: object not available
temp            570
perturbation      8
force           0.2
Name: 350, dtype: object not available
temp            580
perturbation      0
force           0.0
Name: 351, dtype: object not available
temp            580
perturbation      0
force           0.1
Name: 352, dtype: object not available
temp            580
perturbation      0
force           0.2
Name: 353, dtype: object not available
temp            580
perturbation      1
force           0.0
Name: 354, dtype: object not available
temp            580
perturbation      1
force           0.1
Name: 355, dtype: object not available
temp            580
perturbation      1
force           0.2
Name: 356, dtype: object not available
temp            580
perturbation      2
force           0.0
Name: 357, dtype: object not available
temp            580
perturbation      2
force           0.1
Name: 358, dtype: object not available
temp            580
perturbation      2
force           0.2
Name: 359, dtype: object not available
temp            580
perturbation      3
force           0.0
Name: 360, dtype: object not available
temp            580
perturbation      3
force           0.1
Name: 361, dtype: object not available
temp            580
perturbation      3
force           0.2
Name: 362, dtype: object not available
temp            580
perturbation      4
force           0.0
Name: 363, dtype: object not available
temp            580
perturbation      4
force           0.1
Name: 364, dtype: object not available
temp            580
perturbation      4
force           0.2
Name: 365, dtype: object not available
temp            580
perturbation      5
force           0.0
Name: 366, dtype: object not available
temp            580
perturbation      5
force           0.1
Name: 367, dtype: object not available
temp            580
perturbation      5
force           0.2
Name: 368, dtype: object not available
temp            580
perturbation      6
force           0.0
Name: 369, dtype: object not available
temp            580
perturbation      6
force           0.1
Name: 370, dtype: object not available
temp            580
perturbation      6
force           0.2
Name: 371, dtype: object not available
temp            580
perturbation      7
force           0.0
Name: 372, dtype: object not available
temp            580
perturbation      7
force           0.1
Name: 373, dtype: object not available
temp            580
perturbation      7
force           0.2
Name: 374, dtype: object not available
temp            580
perturbation      8
force           0.0
Name: 375, dtype: object not available
temp            580
perturbation      8
force           0.1
Name: 376, dtype: object not available
temp            580
perturbation      8
force           0.2
Name: 377, dtype: object not available
temp            590
perturbation      0
force           0.0
Name: 378, dtype: object not available
temp            590
perturbation      0
force           0.1
Name: 379, dtype: object not available
temp            590
perturbation      0
force           0.2
Name: 380, dtype: object not available
temp            590
perturbation      1
force           0.0
Name: 381, dtype: object not available
temp            590
perturbation      1
force           0.1
Name: 382, dtype: object not available
temp            590
perturbation      1
force           0.2
Name: 383, dtype: object not available
temp            590
perturbation      2
force           0.0
Name: 384, dtype: object not available
temp            590
perturbation      2
force           0.1
Name: 385, dtype: object not available
temp            590
perturbation      2
force           0.2
Name: 386, dtype: object not available
temp            590
perturbation      3
force           0.0
Name: 387, dtype: object not available
temp            590
perturbation      3
force           0.1
Name: 388, dtype: object not available
temp            590
perturbation      3
force           0.2
Name: 389, dtype: object not available
temp            590
perturbation      4
force           0.0
Name: 390, dtype: object not available
temp            590
perturbation      4
force           0.1
Name: 391, dtype: object not available
temp            590
perturbation      4
force           0.2
Name: 392, dtype: object not available
temp            590
perturbation      5
force           0.0
Name: 393, dtype: object not available
temp            590
perturbation      5
force           0.1
Name: 394, dtype: object not available
temp            590
perturbation      5
force           0.2
Name: 395, dtype: object not available
temp            590
perturbation      6
force           0.0
Name: 396, dtype: object not available
temp            590
perturbation      6
force           0.1
Name: 397, dtype: object not available
temp            590
perturbation      6
force           0.2
Name: 398, dtype: object not available
temp            590
perturbation      7
force           0.0
Name: 399, dtype: object not available
temp            590
perturbation      7
force           0.1
Name: 400, dtype: object not available
temp            590
perturbation      7
force           0.2
Name: 401, dtype: object not available
temp            590
perturbation      8
force           0.0
Name: 402, dtype: object not available
temp            590
perturbation      8
force           0.1
Name: 403, dtype: object not available
temp            590
perturbation      8
force           0.2
Name: 404, dtype: object not available
temp            600
perturbation      0
force           0.0
Name: 405, dtype: object not available
temp            600
perturbation      0
force           0.1
Name: 406, dtype: object not available
temp            600
perturbation      0
force           0.2
Name: 407, dtype: object not available
temp            600
perturbation      1
force           0.0
Name: 408, dtype: object not available
temp            600
perturbation      1
force           0.1
Name: 409, dtype: object not available
temp            600
perturbation      1
force           0.2
Name: 410, dtype: object not available
temp            600
perturbation      2
force           0.0
Name: 411, dtype: object not available
temp            600
perturbation      2
force           0.1
Name: 412, dtype: object not available
temp            600
perturbation      2
force           0.2
Name: 413, dtype: object not available
temp            600
perturbation      3
force           0.0
Name: 414, dtype: object not available
temp            600
perturbation      3
force           0.1
Name: 415, dtype: object not available
temp            600
perturbation      3
force           0.2
Name: 416, dtype: object not available
temp            600
perturbation      4
force           0.0
Name: 417, dtype: object not available
temp            600
perturbation      4
force           0.1
Name: 418, dtype: object not available
temp            600
perturbation      4
force           0.2
Name: 419, dtype: object not available
temp            600
perturbation      5
force           0.0
Name: 420, dtype: object not available
temp            600
perturbation      5
force           0.1
Name: 421, dtype: object not available
temp            600
perturbation      5
force           0.2
Name: 422, dtype: object not available
temp            600
perturbation      6
force           0.0
Name: 423, dtype: object not available
temp            600
perturbation      6
force           0.1
Name: 424, dtype: object not available
temp            600
perturbation      6
force           0.2
Name: 425, dtype: object not available
temp            600
perturbation      7
force           0.0
Name: 426, dtype: object not available
temp            600
perturbation      7
force           0.1
Name: 427, dtype: object not available
temp            600
perturbation      7
force           0.2
Name: 428, dtype: object not available
temp            600
perturbation      8
force           0.0
Name: 429, dtype: object not available
temp            600
perturbation      8
force           0.1
Name: 430, dtype: object not available
temp            600
perturbation      8
force           0.2
Name: 431, dtype: object not available

In [25]:

    

# pre = "/Users/weilu/Research/davinci/all_freeEnergy_calculation/rgWidth_memb_3_rg_0.1_lipid_1_extended/1d_dis/"
pre = "/Users/weilu/Research/davinci/all_freeEnergy_calculation_nov11/next_gen_native_based_memb_3_rg_0.4_lipid_0.6_extended/1d_qw"
perturbation_table = {0:"original", 1:"p_mem", 2:"m_mem", 3:"p_lipid", 4:"m_lipid", 5:"p_go", 6:"m_go", 7:"p_rg", 8:"m_rg"}
pmf_list = {
    "temp":[*range(450, 610, 10)],
    "perturbation":list(perturbation_table.keys()),
    "force":["0.0", "0.1", "0.2"]
}
data = readPMF(pmf_list, pre)
remove_columns = ['bin']
data = data.drop(remove_columns, axis=1)
data.to_feather("/Users/weilu/Research/data/pulling/nov12_pmf_qw.feather")


    

In [3]:

    

# pre = "/Users/weilu/Research/davinci/all_freeEnergy_calculation/rgWidth_memb_3_rg_0.1_lipid_1_extended/1d_dis/"
pre = "/Users/weilu/Research/davinci/all_freeEnergy_calculation_nov11/next_gen_native_based_memb_3_rg_0.4_lipid_0.6_extended/1d_dis"
perturbation_table = {0:"original", 1:"p_mem", 2:"m_mem", 3:"p_lipid", 4:"m_lipid", 5:"p_go", 6:"m_go", 7:"p_rg", 8:"m_rg"}
pmf_list = {
    "temp":[*range(450, 610, 10)],
    "perturbation":list(perturbation_table.keys()),
    "force":["0.0", "0.1", "0.2"]
}
data = readPMF(pmf_list, pre)
remove_columns = ['bin']
data = data.drop(remove_columns, axis=1)
data.to_feather("/Users/weilu/Research/data/pulling/nov12_pmf.feather")


    

    




temp            450
perturbation      7
force           0.0
Name: 21, dtype: object not available
temp            450
perturbation      7
force           0.1
Name: 22, dtype: object not available
temp            450
perturbation      7
force           0.2
Name: 23, dtype: object not available
temp            450
perturbation      8
force           0.0
Name: 24, dtype: object not available
temp            450
perturbation      8
force           0.1
Name: 25, dtype: object not available
temp            450
perturbation      8
force           0.2
Name: 26, dtype: object not available
temp            460
perturbation      7
force           0.0
Name: 48, dtype: object not available
temp            460
perturbation      7
force           0.1
Name: 49, dtype: object not available
temp            460
perturbation      7
force           0.2
Name: 50, dtype: object not available
temp            460
perturbation      8
force           0.0
Name: 51, dtype: object not available
temp            460
perturbation      8
force           0.1
Name: 52, dtype: object not available
temp            460
perturbation      8
force           0.2
Name: 53, dtype: object not available
temp            470
perturbation      7
force           0.0
Name: 75, dtype: object not available
temp            470
perturbation      7
force           0.1
Name: 76, dtype: object not available
temp            470
perturbation      7
force           0.2
Name: 77, dtype: object not available
temp            470
perturbation      8
force           0.0
Name: 78, dtype: object not available
temp            470
perturbation      8
force           0.1
Name: 79, dtype: object not available
temp            470
perturbation      8
force           0.2
Name: 80, dtype: object not available
temp            480
perturbation      7
force           0.0
Name: 102, dtype: object not available
temp            480
perturbation      7
force           0.1
Name: 103, dtype: object not available
temp            480
perturbation      7
force           0.2
Name: 104, dtype: object not available
temp            480
perturbation      8
force           0.0
Name: 105, dtype: object not available
temp            480
perturbation      8
force           0.1
Name: 106, dtype: object not available
temp            480
perturbation      8
force           0.2
Name: 107, dtype: object not available
temp            490
perturbation      7
force           0.0
Name: 129, dtype: object not available
temp            490
perturbation      7
force           0.1
Name: 130, dtype: object not available
temp            490
perturbation      7
force           0.2
Name: 131, dtype: object not available
temp            490
perturbation      8
force           0.0
Name: 132, dtype: object not available
temp            490
perturbation      8
force           0.1
Name: 133, dtype: object not available
temp            490
perturbation      8
force           0.2
Name: 134, dtype: object not available
temp            500
perturbation      7
force           0.0
Name: 156, dtype: object not available
temp            500
perturbation      7
force           0.1
Name: 157, dtype: object not available
temp            500
perturbation      7
force           0.2
Name: 158, dtype: object not available
temp            500
perturbation      8
force           0.0
Name: 159, dtype: object not available
temp            500
perturbation      8
force           0.1
Name: 160, dtype: object not available
temp            500
perturbation      8
force           0.2
Name: 161, dtype: object not available
temp            510
perturbation      6
force           0.1
Name: 181, dtype: object not available
temp            510
perturbation      7
force           0.0
Name: 183, dtype: object not available
temp            510
perturbation      7
force           0.1
Name: 184, dtype: object not available
temp            510
perturbation      7
force           0.2
Name: 185, dtype: object not available
temp            510
perturbation      8
force           0.0
Name: 186, dtype: object not available
temp            510
perturbation      8
force           0.1
Name: 187, dtype: object not available
temp            510
perturbation      8
force           0.2
Name: 188, dtype: object not available
temp            520
perturbation      6
force           0.0
Name: 207, dtype: object not available
temp            520
perturbation      6
force           0.1
Name: 208, dtype: object not available
temp            520
perturbation      6
force           0.2
Name: 209, dtype: object not available
temp            520
perturbation      7
force           0.0
Name: 210, dtype: object not available
temp            520
perturbation      7
force           0.1
Name: 211, dtype: object not available
temp            520
perturbation      7
force           0.2
Name: 212, dtype: object not available
temp            520
perturbation      8
force           0.0
Name: 213, dtype: object not available
temp            520
perturbation      8
force           0.1
Name: 214, dtype: object not available
temp            520
perturbation      8
force           0.2
Name: 215, dtype: object not available
temp            530
perturbation      6
force           0.0
Name: 234, dtype: object not available
temp            530
perturbation      6
force           0.1
Name: 235, dtype: object not available
temp            530
perturbation      6
force           0.2
Name: 236, dtype: object not available
temp            530
perturbation      7
force           0.0
Name: 237, dtype: object not available
temp            530
perturbation      7
force           0.1
Name: 238, dtype: object not available
temp            530
perturbation      7
force           0.2
Name: 239, dtype: object not available
temp            530
perturbation      8
force           0.0
Name: 240, dtype: object not available
temp            530
perturbation      8
force           0.1
Name: 241, dtype: object not available
temp            530
perturbation      8
force           0.2
Name: 242, dtype: object not available
temp            540
perturbation      6
force           0.0
Name: 261, dtype: object not available
temp            540
perturbation      6
force           0.1
Name: 262, dtype: object not available
temp            540
perturbation      6
force           0.2
Name: 263, dtype: object not available
temp            540
perturbation      7
force           0.0
Name: 264, dtype: object not available
temp            540
perturbation      7
force           0.1
Name: 265, dtype: object not available
temp            540
perturbation      7
force           0.2
Name: 266, dtype: object not available
temp            540
perturbation      8
force           0.0
Name: 267, dtype: object not available
temp            540
perturbation      8
force           0.1
Name: 268, dtype: object not available
temp            540
perturbation      8
force           0.2
Name: 269, dtype: object not available
temp            550
perturbation      6
force           0.0
Name: 288, dtype: object not available
temp            550
perturbation      6
force           0.1
Name: 289, dtype: object not available
temp            550
perturbation      6
force           0.2
Name: 290, dtype: object not available
temp            550
perturbation      7
force           0.0
Name: 291, dtype: object not available
temp            550
perturbation      7
force           0.1
Name: 292, dtype: object not available
temp            550
perturbation      7
force           0.2
Name: 293, dtype: object not available
temp            550
perturbation      8
force           0.0
Name: 294, dtype: object not available
temp            550
perturbation      8
force           0.1
Name: 295, dtype: object not available
temp            550
perturbation      8
force           0.2
Name: 296, dtype: object not available
temp            560
perturbation      6
force           0.0
Name: 315, dtype: object not available
temp            560
perturbation      6
force           0.1
Name: 316, dtype: object not available
temp            560
perturbation      6
force           0.2
Name: 317, dtype: object not available
temp            560
perturbation      7
force           0.0
Name: 318, dtype: object not available
temp            560
perturbation      7
force           0.1
Name: 319, dtype: object not available
temp            560
perturbation      7
force           0.2
Name: 320, dtype: object not available
temp            560
perturbation      8
force           0.0
Name: 321, dtype: object not available
temp            560
perturbation      8
force           0.1
Name: 322, dtype: object not available
temp            560
perturbation      8
force           0.2
Name: 323, dtype: object not available
temp            570
perturbation      6
force           0.0
Name: 342, dtype: object not available
temp            570
perturbation      6
force           0.1
Name: 343, dtype: object not available
temp            570
perturbation      6
force           0.2
Name: 344, dtype: object not available
temp            570
perturbation      7
force           0.0
Name: 345, dtype: object not available
temp            570
perturbation      7
force           0.1
Name: 346, dtype: object not available
temp            570
perturbation      7
force           0.2
Name: 347, dtype: object not available
temp            570
perturbation      8
force           0.0
Name: 348, dtype: object not available
temp            570
perturbation      8
force           0.1
Name: 349, dtype: object not available
temp            570
perturbation      8
force           0.2
Name: 350, dtype: object not available
temp            580
perturbation      6
force           0.0
Name: 369, dtype: object not available
temp            580
perturbation      6
force           0.1
Name: 370, dtype: object not available
temp            580
perturbation      6
force           0.2
Name: 371, dtype: object not available
temp            580
perturbation      7
force           0.0
Name: 372, dtype: object not available
temp            580
perturbation      7
force           0.1
Name: 373, dtype: object not available
temp            580
perturbation      7
force           0.2
Name: 374, dtype: object not available
temp            580
perturbation      8
force           0.0
Name: 375, dtype: object not available
temp            580
perturbation      8
force           0.1
Name: 376, dtype: object not available
temp            580
perturbation      8
force           0.2
Name: 377, dtype: object not available
temp            590
perturbation      6
force           0.0
Name: 396, dtype: object not available
temp            590
perturbation      6
force           0.1
Name: 397, dtype: object not available
temp            590
perturbation      6
force           0.2
Name: 398, dtype: object not available
temp            590
perturbation      7
force           0.0
Name: 399, dtype: object not available
temp            590
perturbation      7
force           0.1
Name: 400, dtype: object not available
temp            590
perturbation      7
force           0.2
Name: 401, dtype: object not available
temp            590
perturbation      8
force           0.0
Name: 402, dtype: object not available
temp            590
perturbation      8
force           0.1
Name: 403, dtype: object not available
temp            590
perturbation      8
force           0.2
Name: 404, dtype: object not available
temp            600
perturbation      6
force           0.0
Name: 423, dtype: object not available
temp            600
perturbation      6
force           0.1
Name: 424, dtype: object not available
temp            600
perturbation      6
force           0.2
Name: 425, dtype: object not available
temp            600
perturbation      7
force           0.0
Name: 426, dtype: object not available
temp            600
perturbation      7
force           0.1
Name: 427, dtype: object not available
temp            600
perturbation      7
force           0.2
Name: 428, dtype: object not available
temp            600
perturbation      8
force           0.0
Name: 429, dtype: object not available
temp            600
perturbation      8
force           0.1
Name: 430, dtype: object not available
temp            600
perturbation      8
force           0.2
Name: 431, dtype: object not available

In [75]:

    

# pre = "/Users/weilu/Research/davinci/all_freeEnergy_calculation/rgWidth_memb_3_rg_0.1_lipid_1_extended/1d_dis/"
pre = "/Users/weilu/Research/davinci/all_freeEnergy_calculation_nov11/next_gen_native_based_memb_3_rg_0.2_lipid_0.6_extended/1d_dis"
perturbation_table = {0:"original", 1:"p_mem", 2:"m_mem", 3:"p_lipid", 4:"m_lipid", 5:"p_go", 6:"m_go", 7:"p_rg", 8:"m_rg"}
pmf_list = {
    "temp":[*range(450, 610, 10)],
    "perturbation":list(perturbation_table.keys()),
    "force":["0.0", "0.1", "0.2"]
}
data = readPMF(pmf_list, pre)


    

In [71]:

    

# pre = "/Users/weilu/Research/davinci/all_freeEnergy_calculation/rgWidth_memb_3_rg_0.1_lipid_1_extended/1d_dis/"
pre = "/Users/weilu/Research/davinci/all_freeEnergy_calculation_nov11_2/next_gen_native_based_memb_3_rg_0.2_lipid_0.6_extended/1d_dis"
perturbation_table = {0:"original", 1:"p_mem", 2:"m_mem", 3:"p_lipid", 4:"m_lipid", 5:"p_go", 6:"m_go", 7:"p_rg", 8:"m_rg"}
pmf_list = {
    "temp":[*range(450, 600, 50)],
    "perturbation":list(perturbation_table.keys()),
    "force":["0.0", "0.1", "0.2"]
}
data = readPMF(pmf_list, pre)


    

    




temp            450
perturbation      3
force           0.0
Name: 9, dtype: object not available
temp            450
perturbation      3
force           0.1
Name: 10, dtype: object not available
temp            450
perturbation      3
force           0.2
Name: 11, dtype: object not available
temp            450
perturbation      4
force           0.0
Name: 12, dtype: object not available
temp            450
perturbation      4
force           0.1
Name: 13, dtype: object not available
temp            450
perturbation      4
force           0.2
Name: 14, dtype: object not available
temp            450
perturbation      5
force           0.0
Name: 15, dtype: object not available
temp            450
perturbation      5
force           0.1
Name: 16, dtype: object not available
temp            450
perturbation      5
force           0.2
Name: 17, dtype: object not available
temp            450
perturbation      6
force           0.0
Name: 18, dtype: object not available
temp            450
perturbation      6
force           0.1
Name: 19, dtype: object not available
temp            450
perturbation      6
force           0.2
Name: 20, dtype: object not available
temp            450
perturbation      7
force           0.0
Name: 21, dtype: object not available
temp            450
perturbation      7
force           0.1
Name: 22, dtype: object not available
temp            450
perturbation      7
force           0.2
Name: 23, dtype: object not available
temp            450
perturbation      8
force           0.0
Name: 24, dtype: object not available
temp            450
perturbation      8
force           0.1
Name: 25, dtype: object not available
temp            450
perturbation      8
force           0.2
Name: 26, dtype: object not available
temp            500
perturbation      3
force           0.0
Name: 36, dtype: object not available
temp            500
perturbation      3
force           0.1
Name: 37, dtype: object not available
temp            500
perturbation      3
force           0.2
Name: 38, dtype: object not available
temp            500
perturbation      4
force           0.0
Name: 39, dtype: object not available
temp            500
perturbation      4
force           0.1
Name: 40, dtype: object not available
temp            500
perturbation      4
force           0.2
Name: 41, dtype: object not available
temp            500
perturbation      5
force           0.0
Name: 42, dtype: object not available
temp            500
perturbation      5
force           0.1
Name: 43, dtype: object not available
temp            500
perturbation      5
force           0.2
Name: 44, dtype: object not available
temp            500
perturbation      6
force           0.0
Name: 45, dtype: object not available
temp            500
perturbation      6
force           0.1
Name: 46, dtype: object not available
temp            500
perturbation      6
force           0.2
Name: 47, dtype: object not available
temp            500
perturbation      7
force           0.0
Name: 48, dtype: object not available
temp            500
perturbation      7
force           0.1
Name: 49, dtype: object not available
temp            500
perturbation      7
force           0.2
Name: 50, dtype: object not available
temp            500
perturbation      8
force           0.0
Name: 51, dtype: object not available
temp            500
perturbation      8
force           0.1
Name: 52, dtype: object not available
temp            500
perturbation      8
force           0.2
Name: 53, dtype: object not available
temp            550
perturbation      3
force           0.0
Name: 63, dtype: object not available
temp            550
perturbation      3
force           0.1
Name: 64, dtype: object not available
temp            550
perturbation      3
force           0.2
Name: 65, dtype: object not available
temp            550
perturbation      4
force           0.0
Name: 66, dtype: object not available
temp            550
perturbation      4
force           0.1
Name: 67, dtype: object not available
temp            550
perturbation      4
force           0.2
Name: 68, dtype: object not available
temp            550
perturbation      5
force           0.0
Name: 69, dtype: object not available
temp            550
perturbation      5
force           0.1
Name: 70, dtype: object not available
temp            550
perturbation      5
force           0.2
Name: 71, dtype: object not available
temp            550
perturbation      6
force           0.0
Name: 72, dtype: object not available
temp            550
perturbation      6
force           0.1
Name: 73, dtype: object not available
temp            550
perturbation      6
force           0.2
Name: 74, dtype: object not available
temp            550
perturbation      7
force           0.0
Name: 75, dtype: object not available
temp            550
perturbation      7
force           0.1
Name: 76, dtype: object not available
temp            550
perturbation      7
force           0.2
Name: 77, dtype: object not available
temp            550
perturbation      8
force           0.0
Name: 78, dtype: object not available
temp            550
perturbation      8
force           0.1
Name: 79, dtype: object not available
temp            550
perturbation      8
force           0.2
Name: 80, dtype: object not available

In [72]:

    

remove_columns = ['bin']
data = data.drop(remove_columns, axis=1)
data.to_feather("/Users/weilu/Research/data/pulling/nov11_pmf_3.feather")


    

In [76]:

    

remove_columns = ['bin']
data = data.drop(remove_columns, axis=1)
data.to_feather("/Users/weilu/Research/data/pulling/nov11_pmf.feather")


    

In [55]:

    

def expand_grid(dictionary):
    return pd.DataFrame([row for row in product(*dictionary.values())],
                        columns=dictionary.keys())
def read_subfolder_PMF(pmf_list_data, pre):
    pmf_list_data = expand_grid(pmf_list)
    all_pmf_list = []
    for index, row in pmf_list_data.iterrows():
    #     print(index)
    #     print("--")
    #     print(row)
        subfolder = row["subfolder"]
        if subfolder.split("_")[0] == "force":
            force = float(subfolder.split("_")[1])
        else:
            force = 0.0
        temp = row["temp"]
        perturbation = row["perturbation"]
        if perturbation == 0:
            location = pre + f"/{subfolder}/pmf-{temp}.dat"
            change = "none"
            upOrDown = "none"
        else:
            location = pre + f"/{subfolder}/perturbation-{perturbation}-pmf-{temp}.dat"
            change = perturbation_table[perturbation].split("_")[-1]
            upOrDown = perturbation_table[perturbation].split("_")[0]
    #     print(location)
        name_list = ["f", "df", "e", "s"]
        names = ["bin", "x"] + name_list
        try:
            data = pd.read_table(location, skiprows=2, sep='\s+', names=names).assign(upOrDown=upOrDown, change=change, force=force, temp=temp, perturbation=perturbation_table[perturbation])
            all_pmf_list.append(data)
        except:
            print(row, "not available")
    return pd.concat(all_pmf_list).dropna().reset_index()


    

In [66]:

    

# pre = "/Users/weilu/Research/davinci/all_freeEnergy_calculation/rgWidth_memb_3_rg_0.1_lipid_1_extended/1d_dis/"
pre = "/Users/weilu/Research/davinci/all_freeEnergy_calculation_nov11/next_gen_native_based_memb_3_rg_0.2_lipid_0.6_extended/test/"
perturbation_table = {0:"original", 1:"p_mem", 2:"m_mem", 3:"p_lipid", 4:"m_lipid", 5:"p_go", 6:"m_go", 7:"p_rg", 8:"m_rg"}
pmf_list = {
    "temp":[*range(400, 630, 50)],
    "perturbation":list(perturbation_table.keys()),
    "subfolder":["force_0.0", "force_0.1", "force_0.2"]
}
data = read_subfolder_PMF(pmf_list, pre)


    

    




temp                  400
perturbation            0
subfolder       force_0.0
Name: 0, dtype: object not available
temp                  400
perturbation            0
subfolder       force_0.1
Name: 1, dtype: object not available
temp                  400
perturbation            0
subfolder       force_0.2
Name: 2, dtype: object not available
temp                  400
perturbation            1
subfolder       force_0.0
Name: 3, dtype: object not available
temp                  400
perturbation            1
subfolder       force_0.1
Name: 4, dtype: object not available
temp                  400
perturbation            1
subfolder       force_0.2
Name: 5, dtype: object not available
temp                  400
perturbation            2
subfolder       force_0.0
Name: 6, dtype: object not available
temp                  400
perturbation            2
subfolder       force_0.1
Name: 7, dtype: object not available
temp                  400
perturbation            2
subfolder       force_0.2
Name: 8, dtype: object not available
temp                  400
perturbation            3
subfolder       force_0.0
Name: 9, dtype: object not available
temp                  400
perturbation            3
subfolder       force_0.1
Name: 10, dtype: object not available
temp                  400
perturbation            3
subfolder       force_0.2
Name: 11, dtype: object not available
temp                  400
perturbation            4
subfolder       force_0.0
Name: 12, dtype: object not available
temp                  400
perturbation            4
subfolder       force_0.1
Name: 13, dtype: object not available
temp                  400
perturbation            4
subfolder       force_0.2
Name: 14, dtype: object not available
temp                  400
perturbation            5
subfolder       force_0.0
Name: 15, dtype: object not available
temp                  400
perturbation            5
subfolder       force_0.1
Name: 16, dtype: object not available
temp                  400
perturbation            5
subfolder       force_0.2
Name: 17, dtype: object not available
temp                  400
perturbation            6
subfolder       force_0.0
Name: 18, dtype: object not available
temp                  400
perturbation            6
subfolder       force_0.1
Name: 19, dtype: object not available
temp                  400
perturbation            6
subfolder       force_0.2
Name: 20, dtype: object not available
temp                  400
perturbation            7
subfolder       force_0.0
Name: 21, dtype: object not available
temp                  400
perturbation            7
subfolder       force_0.1
Name: 22, dtype: object not available
temp                  400
perturbation            7
subfolder       force_0.2
Name: 23, dtype: object not available
temp                  400
perturbation            8
subfolder       force_0.0
Name: 24, dtype: object not available
temp                  400
perturbation            8
subfolder       force_0.1
Name: 25, dtype: object not available
temp                  400
perturbation            8
subfolder       force_0.2
Name: 26, dtype: object not available
temp                  450
perturbation            3
subfolder       force_0.0
Name: 36, dtype: object not available
temp                  450
perturbation            3
subfolder       force_0.1
Name: 37, dtype: object not available
temp                  450
perturbation            3
subfolder       force_0.2
Name: 38, dtype: object not available
temp                  450
perturbation            4
subfolder       force_0.0
Name: 39, dtype: object not available
temp                  450
perturbation            4
subfolder       force_0.1
Name: 40, dtype: object not available
temp                  450
perturbation            4
subfolder       force_0.2
Name: 41, dtype: object not available
temp                  450
perturbation            5
subfolder       force_0.0
Name: 42, dtype: object not available
temp                  450
perturbation            5
subfolder       force_0.1
Name: 43, dtype: object not available
temp                  450
perturbation            5
subfolder       force_0.2
Name: 44, dtype: object not available
temp                  450
perturbation            6
subfolder       force_0.0
Name: 45, dtype: object not available
temp                  450
perturbation            6
subfolder       force_0.1
Name: 46, dtype: object not available
temp                  450
perturbation            6
subfolder       force_0.2
Name: 47, dtype: object not available
temp                  450
perturbation            7
subfolder       force_0.0
Name: 48, dtype: object not available
temp                  450
perturbation            7
subfolder       force_0.1
Name: 49, dtype: object not available
temp                  450
perturbation            7
subfolder       force_0.2
Name: 50, dtype: object not available
temp                  450
perturbation            8
subfolder       force_0.0
Name: 51, dtype: object not available
temp                  450
perturbation            8
subfolder       force_0.1
Name: 52, dtype: object not available
temp                  450
perturbation            8
subfolder       force_0.2
Name: 53, dtype: object not available
temp                  500
perturbation            3
subfolder       force_0.0
Name: 63, dtype: object not available
temp                  500
perturbation            3
subfolder       force_0.1
Name: 64, dtype: object not available
temp                  500
perturbation            3
subfolder       force_0.2
Name: 65, dtype: object not available
temp                  500
perturbation            4
subfolder       force_0.0
Name: 66, dtype: object not available
temp                  500
perturbation            4
subfolder       force_0.1
Name: 67, dtype: object not available
temp                  500
perturbation            4
subfolder       force_0.2
Name: 68, dtype: object not available
temp                  500
perturbation            5
subfolder       force_0.0
Name: 69, dtype: object not available
temp                  500
perturbation            5
subfolder       force_0.1
Name: 70, dtype: object not available
temp                  500
perturbation            5
subfolder       force_0.2
Name: 71, dtype: object not available
temp                  500
perturbation            6
subfolder       force_0.0
Name: 72, dtype: object not available
temp                  500
perturbation            6
subfolder       force_0.1
Name: 73, dtype: object not available
temp                  500
perturbation            6
subfolder       force_0.2
Name: 74, dtype: object not available
temp                  500
perturbation            7
subfolder       force_0.0
Name: 75, dtype: object not available
temp                  500
perturbation            7
subfolder       force_0.1
Name: 76, dtype: object not available
temp                  500
perturbation            7
subfolder       force_0.2
Name: 77, dtype: object not available
temp                  500
perturbation            8
subfolder       force_0.0
Name: 78, dtype: object not available
temp                  500
perturbation            8
subfolder       force_0.1
Name: 79, dtype: object not available
temp                  500
perturbation            8
subfolder       force_0.2
Name: 80, dtype: object not available
temp                  550
perturbation            3
subfolder       force_0.0
Name: 90, dtype: object not available
temp                  550
perturbation            3
subfolder       force_0.1
Name: 91, dtype: object not available
temp                  550
perturbation            3
subfolder       force_0.2
Name: 92, dtype: object not available
temp                  550
perturbation            4
subfolder       force_0.0
Name: 93, dtype: object not available
temp                  550
perturbation            4
subfolder       force_0.1
Name: 94, dtype: object not available
temp                  550
perturbation            4
subfolder       force_0.2
Name: 95, dtype: object not available
temp                  550
perturbation            5
subfolder       force_0.0
Name: 96, dtype: object not available
temp                  550
perturbation            5
subfolder       force_0.1
Name: 97, dtype: object not available
temp                  550
perturbation            5
subfolder       force_0.2
Name: 98, dtype: object not available
temp                  550
perturbation            6
subfolder       force_0.0
Name: 99, dtype: object not available
temp                  550
perturbation            6
subfolder       force_0.1
Name: 100, dtype: object not available
temp                  550
perturbation            6
subfolder       force_0.2
Name: 101, dtype: object not available
temp                  550
perturbation            7
subfolder       force_0.0
Name: 102, dtype: object not available
temp                  550
perturbation            7
subfolder       force_0.1
Name: 103, dtype: object not available
temp                  550
perturbation            7
subfolder       force_0.2
Name: 104, dtype: object not available
temp                  550
perturbation            8
subfolder       force_0.0
Name: 105, dtype: object not available
temp                  550
perturbation            8
subfolder       force_0.1
Name: 106, dtype: object not available
temp                  550
perturbation            8
subfolder       force_0.2
Name: 107, dtype: object not available
temp                  600
perturbation            0
subfolder       force_0.0
Name: 108, dtype: object not available
temp                  600
perturbation            0
subfolder       force_0.1
Name: 109, dtype: object not available
temp                  600
perturbation            0
subfolder       force_0.2
Name: 110, dtype: object not available
temp                  600
perturbation            1
subfolder       force_0.0
Name: 111, dtype: object not available
temp                  600
perturbation            1
subfolder       force_0.1
Name: 112, dtype: object not available
temp                  600
perturbation            1
subfolder       force_0.2
Name: 113, dtype: object not available
temp                  600
perturbation            2
subfolder       force_0.0
Name: 114, dtype: object not available
temp                  600
perturbation            2
subfolder       force_0.1
Name: 115, dtype: object not available
temp                  600
perturbation            2
subfolder       force_0.2
Name: 116, dtype: object not available
temp                  600
perturbation            3
subfolder       force_0.0
Name: 117, dtype: object not available
temp                  600
perturbation            3
subfolder       force_0.1
Name: 118, dtype: object not available
temp                  600
perturbation            3
subfolder       force_0.2
Name: 119, dtype: object not available
temp                  600
perturbation            4
subfolder       force_0.0
Name: 120, dtype: object not available
temp                  600
perturbation            4
subfolder       force_0.1
Name: 121, dtype: object not available
temp                  600
perturbation            4
subfolder       force_0.2
Name: 122, dtype: object not available
temp                  600
perturbation            5
subfolder       force_0.0
Name: 123, dtype: object not available
temp                  600
perturbation            5
subfolder       force_0.1
Name: 124, dtype: object not available
temp                  600
perturbation            5
subfolder       force_0.2
Name: 125, dtype: object not available
temp                  600
perturbation            6
subfolder       force_0.0
Name: 126, dtype: object not available
temp                  600
perturbation            6
subfolder       force_0.1
Name: 127, dtype: object not available
temp                  600
perturbation            6
subfolder       force_0.2
Name: 128, dtype: object not available
temp                  600
perturbation            7
subfolder       force_0.0
Name: 129, dtype: object not available
temp                  600
perturbation            7
subfolder       force_0.1
Name: 130, dtype: object not available
temp                  600
perturbation            7
subfolder       force_0.2
Name: 131, dtype: object not available
temp                  600
perturbation            8
subfolder       force_0.0
Name: 132, dtype: object not available
temp                  600
perturbation            8
subfolder       force_0.1
Name: 133, dtype: object not available
temp                  600
perturbation            8
subfolder       force_0.2
Name: 134, dtype: object not available

In [67]:

    

remove_columns = ['bin']
data = data.drop(remove_columns, axis=1)
data.to_feather("/Users/weilu/Research/data/pulling/nov11_pmf_2.feather")


    

In [68]:

    

data


    

    
Out[68]:







  

    

      

      
index
      
x
      
f
      
df
      
e
      
s
      
change
      
force
      
perturbation
      
temp
      
upOrDown
    
  
  

    

      
0
      
0
      
7.692
      
6.858
      
0.0
      
-847.760
      
-854.617
      
none
      
0.0
      
original
      
450
      
none
    
    

      
1
      
1
      
10.927
      
8.500
      
0.0
      
-840.592
      
-849.092
      
none
      
0.0
      
original
      
450
      
none
    
    

      
2
      
2
      
14.162
      
0.000
      
0.0
      
-930.661
      
-930.661
      
none
      
0.0
      
original
      
450
      
none
    
    

      
3
      
3
      
17.397
      
3.953
      
0.0
      
-904.304
      
-908.257
      
none
      
0.0
      
original
      
450
      
none
    
    

      
4
      
4
      
20.631
      
2.480
      
0.0
      
-928.194
      
-930.674
      
none
      
0.0
      
original
      
450
      
none
    
    

      
5
      
5
      
23.866
      
2.678
      
0.0
      
-920.745
      
-923.424
      
none
      
0.0
      
original
      
450
      
none
    
    

      
6
      
6
      
27.101
      
2.519
      
0.0
      
-933.167
      
-935.685
      
none
      
0.0
      
original
      
450
      
none
    
    

      
7
      
7
      
30.336
      
2.731
      
0.0
      
-930.538
      
-933.270
      
none
      
0.0
      
original
      
450
      
none
    
    

      
8
      
8
      
33.571
      
2.255
      
0.0
      
-953.751
      
-956.006
      
none
      
0.0
      
original
      
450
      
none
    
    

      
9
      
9
      
36.806
      
4.218
      
0.0
      
-935.416
      
-939.633
      
none
      
0.0
      
original
      
450
      
none
    
    

      
10
      
10
      
40.041
      
6.657
      
0.0
      
-922.348
      
-929.005
      
none
      
0.0
      
original
      
450
      
none
    
    

      
11
      
11
      
43.276
      
10.779
      
0.0
      
-886.182
      
-896.960
      
none
      
0.0
      
original
      
450
      
none
    
    

      
12
      
12
      
46.511
      
11.442
      
0.0
      
-901.013
      
-912.455
      
none
      
0.0
      
original
      
450
      
none
    
    

      
13
      
13
      
49.746
      
17.010
      
0.0
      
-853.484
      
-870.495
      
none
      
0.0
      
original
      
450
      
none
    
    

      
14
      
14
      
52.981
      
20.901
      
0.0
      
-824.810
      
-845.711
      
none
      
0.0
      
original
      
450
      
none
    
    

      
15
      
15
      
56.216
      
22.718
      
0.0
      
-805.163
      
-827.881
      
none
      
0.0
      
original
      
450
      
none
    
    

      
16
      
16
      
59.451
      
22.338
      
0.0
      
-814.236
      
-836.574
      
none
      
0.0
      
original
      
450
      
none
    
    

      
17
      
17
      
62.685
      
21.766
      
0.0
      
-826.127
      
-847.892
      
none
      
0.0
      
original
      
450
      
none
    
    

      
18
      
18
      
65.920
      
20.318
      
0.0
      
-857.485
      
-877.803
      
none
      
0.0
      
original
      
450
      
none
    
    

      
19
      
19
      
69.155
      
21.021
      
0.0
      
-840.674
      
-861.695
      
none
      
0.0
      
original
      
450
      
none
    
    

      
20
      
20
      
72.390
      
20.337
      
0.0
      
-869.714
      
-890.051
      
none
      
0.0
      
original
      
450
      
none
    
    

      
21
      
21
      
75.625
      
22.131
      
0.0
      
-842.329
      
-864.460
      
none
      
0.0
      
original
      
450
      
none
    
    

      
22
      
22
      
78.860
      
23.422
      
0.0
      
-837.815
      
-861.237
      
none
      
0.0
      
original
      
450
      
none
    
    

      
23
      
23
      
82.095
      
22.943
      
0.0
      
-855.354
      
-878.297
      
none
      
0.0
      
original
      
450
      
none
    
    

      
24
      
24
      
85.330
      
23.561
      
0.0
      
-868.351
      
-891.912
      
none
      
0.0
      
original
      
450
      
none
    
    

      
25
      
25
      
88.565
      
26.792
      
0.0
      
-832.696
      
-859.488
      
none
      
0.0
      
original
      
450
      
none
    
    

      
26
      
26
      
91.800
      
28.835
      
0.0
      
-835.962
      
-864.797
      
none
      
0.0
      
original
      
450
      
none
    
    

      
27
      
27
      
95.035
      
29.248
      
0.0
      
-861.191
      
-890.439
      
none
      
0.0
      
original
      
450
      
none
    
    

      
28
      
28
      
98.270
      
32.215
      
0.0
      
-1107.508
      
-1139.723
      
none
      
0.0
      
original
      
450
      
none
    
    

      
29
      
0
      
7.692
      
7.591
      
0.0
      
-847.760
      
-855.350
      
none
      
0.1
      
original
      
450
      
none
    
    

      
...
      
...
      
...
      
...
      
...
      
...
      
...
      
...
      
...
      
...
      
...
      
...
    
    

      
1207
      
19
      
69.155
      
2.886
      
0.0
      
-498.235
      
-501.121
      
mem
      
0.2
      
m_mem
      
550
      
m
    
    

      
1208
      
20
      
72.390
      
3.294
      
0.0
      
-508.098
      
-511.392
      
mem
      
0.2
      
m_mem
      
550
      
m
    
    

      
1209
      
21
      
75.625
      
3.880
      
0.0
      
-523.607
      
-527.487
      
mem
      
0.2
      
m_mem
      
550
      
m
    
    

      
1210
      
22
      
78.860
      
3.851
      
0.0
      
-525.908
      
-529.759
      
mem
      
0.2
      
m_mem
      
550
      
m
    
    

      
1211
      
23
      
82.095
      
3.884
      
0.0
      
-521.522
      
-525.406
      
mem
      
0.2
      
m_mem
      
550
      
m
    
    

      
1212
      
24
      
85.330
      
4.791
      
0.0
      
-535.351
      
-540.142
      
mem
      
0.2
      
m_mem
      
550
      
m
    
    

      
1213
      
25
      
88.565
      
4.707
      
0.0
      
-523.693
      
-528.400
      
mem
      
0.2
      
m_mem
      
550
      
m
    
    

      
1214
      
26
      
91.800
      
4.830
      
0.0
      
-524.610
      
-529.440
      
mem
      
0.2
      
m_mem
      
550
      
m
    
    

      
1215
      
27
      
95.035
      
6.075
      
0.0
      
-536.042
      
-542.117
      
mem
      
0.2
      
m_mem
      
550
      
m
    
    

      
1216
      
28
      
98.270
      
4.581
      
0.0
      
-508.547
      
-513.128
      
mem
      
0.2
      
m_mem
      
550
      
m
    
    

      
1217
      
29
      
101.505
      
6.827
      
0.0
      
-547.439
      
-554.266
      
mem
      
0.2
      
m_mem
      
550
      
m
    
    

      
1218
      
30
      
104.739
      
7.202
      
0.0
      
-534.105
      
-541.307
      
mem
      
0.2
      
m_mem
      
550
      
m
    
    

      
1219
      
31
      
107.974
      
7.115
      
0.0
      
-532.412
      
-539.527
      
mem
      
0.2
      
m_mem
      
550
      
m
    
    

      
1220
      
32
      
111.209
      
5.414
      
0.0
      
-510.420
      
-515.834
      
mem
      
0.2
      
m_mem
      
550
      
m
    
    

      
1221
      
33
      
114.444
      
6.287
      
0.0
      
-517.966
      
-524.253
      
mem
      
0.2
      
m_mem
      
550
      
m
    
    

      
1222
      
34
      
117.679
      
6.549
      
0.0
      
-516.685
      
-523.234
      
mem
      
0.2
      
m_mem
      
550
      
m
    
    

      
1223
      
35
      
120.914
      
5.044
      
0.0
      
-493.270
      
-498.313
      
mem
      
0.2
      
m_mem
      
550
      
m
    
    

      
1224
      
36
      
124.149
      
2.410
      
0.0
      
-458.757
      
-461.167
      
mem
      
0.2
      
m_mem
      
550
      
m
    
    

      
1225
      
37
      
127.384
      
2.412
      
0.0
      
-465.443
      
-467.855
      
mem
      
0.2
      
m_mem
      
550
      
m
    
    

      
1226
      
38
      
130.619
      
2.561
      
0.0
      
-480.347
      
-482.908
      
mem
      
0.2
      
m_mem
      
550
      
m
    
    

      
1227
      
39
      
133.854
      
1.943
      
0.0
      
-451.732
      
-453.675
      
mem
      
0.2
      
m_mem
      
550
      
m
    
    

      
1228
      
40
      
137.089
      
0.000
      
0.0
      
-443.737
      
-443.737
      
mem
      
0.2
      
m_mem
      
550
      
m
    
    

      
1229
      
41
      
140.324
      
3.467
      
0.0
      
-465.340
      
-468.807
      
mem
      
0.2
      
m_mem
      
550
      
m
    
    

      
1230
      
42
      
143.559
      
3.484
      
0.0
      
-481.661
      
-485.145
      
mem
      
0.2
      
m_mem
      
550
      
m
    
    

      
1231
      
43
      
146.793
      
1.575
      
0.0
      
-449.391
      
-450.967
      
mem
      
0.2
      
m_mem
      
550
      
m
    
    

      
1232
      
44
      
150.028
      
3.707
      
0.0
      
-485.360
      
-489.067
      
mem
      
0.2
      
m_mem
      
550
      
m
    
    

      
1233
      
45
      
153.263
      
2.569
      
0.0
      
-485.080
      
-487.649
      
mem
      
0.2
      
m_mem
      
550
      
m
    
    

      
1234
      
46
      
156.498
      
1.589
      
0.0
      
-470.847
      
-472.436
      
mem
      
0.2
      
m_mem
      
550
      
m
    
    

      
1235
      
47
      
159.733
      
4.046
      
0.0
      
-507.583
      
-511.628
      
mem
      
0.2
      
m_mem
      
550
      
m
    
    

      
1236
      
48
      
162.968
      
5.168
      
0.0
      
-534.138
      
-539.306
      
mem
      
0.2
      
m_mem
      
550
      
m
    
  

1237 rows × 11 columns

In [4]:

    

[*range(500, 630, 10)]


    

    
Out[4]:





[500, 510, 520, 530, 540, 550, 560, 570, 580, 590, 600, 610, 620]

In [31]:

    

perturbation_list


    

    
Out[31]:





[0, 1, 2, 3, 4, 5, 6, 7, 8]

In [32]:

    

import datetime


    

In [43]:

    

perturbation_table = {0:"original", 1:"p_mem", 2:"m_mem", 3:"p_lipid", 4:"m_lipid", 5:"p_go", 6:"m_go", 7:"p_rg", 8:"m_rg"}
pmf_list = {
    "temp":[500, 530, 560, 590],
    "perturbation":list(perturbation_table.keys()),
    "force":["0.0", "0.1", "0.2"]
}


    

In [ ]:

    




    

In [48]:

    

pmf_list_data = expand_grid(pmf_list)
pre = "/Users/weilu/Research/davinci/extended/finer"
all_pmf_list = []

for index, row in pmf_list_data.iterrows():
#     print(index)
#     print("--")
#     print(row)
    force = row["force"]
    temp = row["temp"]
    perturbation = row["perturbation"]
    if perturbation == 0:
        location = pre + f"/force_{force}/pmf-{temp}.dat"
        change = "none"
        upOrDown = "none"
    else:
        location = pre + f"/force_{force}/perturbation-{perturbation}-pmf-{temp}.dat"
        change = perturbation_table[perturbation].split("_")[-1]
        upOrDown = perturbation_table[perturbation].split("_")[0]
#     print(location)
    name_list = ["f", "df", "e", "s"]
    names = ["bin", "x"] + name_list
    data = pd.read_table(location, skiprows=2, sep='\s+', names=names).assign(upOrDown=upOrDown, change=change, force=force, temp=temp, perturbation=perturbation_table[perturbation])
    all_pmf_list.append(data)
data = pd.concat(all_pmf_list).dropna().reset_index()
data.to_feather("/Users/weilu/Research/data/pulling/nov06_pmf_2.feather")


    

In [53]:

    

def readPMF(pmf_list_data, pre):
    all_pmf_list = []
    for index, row in pmf_list_data.iterrows():
    #     print(index)
    #     print("--")
    #     print(row)
        force = row["force"]
        temp = row["temp"]
        perturbation = row["perturbation"]
        if perturbation == 0:
            location = pre + f"/force_{force}/pmf-{temp}.dat"
            change = "none"
            upOrDown = "none"
        else:
            location = pre + f"/force_{force}/perturbation-{perturbation}-pmf-{temp}.dat"
            change = perturbation_table[perturbation].split("_")[-1]
            upOrDown = perturbation_table[perturbation].split("_")[0]
    #     print(location)
        name_list = ["f", "df", "e", "s"]
        names = ["bin", "x"] + name_list
        try:
            data = pd.read_table(location, skiprows=2, sep='\s+', names=names).assign(upOrDown=upOrDown, change=change, force=force, temp=temp, perturbation=perturbation_table[perturbation])
            all_pmf_list.append(data)
        except:
            print(row, "not available")
    return pd.concat(all_pmf_list).dropna().reset_index()


    

In [84]:

    

list(range(500, 710, 10))


    

    
Out[84]:





[500,
 510,
 520,
 530,
 540,
 550,
 560,
 570,
 580,
 590,
 600,
 610,
 620,
 630,
 640,
 650,
 660,
 670,
 680,
 690,
 700]

In [85]:

    

pmf_list = {
    "temp":list(range(500, 710, 10)),
    "perturbation":list(perturbation_table.keys()),
    "force":["0.0", "0.1", "0.2"]
}
pmf_list_data = expand_grid(pmf_list)
pre = "/Users/weilu/Research/davinci/extended/coarse"
data = readPMF(pmf_list_data, pre)
# data.to_feather("/Users/weilu/Research/data/pulling/nov06_pmf_3.feather")
remove_columns = ['bin']
data = data.drop(remove_columns, axis=1)
data.to_feather("/Users/weilu/Research/data/pulling/nov07_pmf_1.feather")


    

    




temp            500
perturbation      4
force           0.1
Name: 13, dtype: object not available
temp            500
perturbation      4
force           0.2
Name: 14, dtype: object not available
temp            500
perturbation      5
force           0.0
Name: 15, dtype: object not available
temp            500
perturbation      5
force           0.1
Name: 16, dtype: object not available
temp            500
perturbation      5
force           0.2
Name: 17, dtype: object not available
temp            500
perturbation      6
force           0.0
Name: 18, dtype: object not available
temp            500
perturbation      6
force           0.1
Name: 19, dtype: object not available
temp            500
perturbation      6
force           0.2
Name: 20, dtype: object not available
temp            500
perturbation      7
force           0.0
Name: 21, dtype: object not available
temp            500
perturbation      7
force           0.1
Name: 22, dtype: object not available
temp            500
perturbation      7
force           0.2
Name: 23, dtype: object not available
temp            500
perturbation      8
force           0.0
Name: 24, dtype: object not available
temp            500
perturbation      8
force           0.1
Name: 25, dtype: object not available
temp            500
perturbation      8
force           0.2
Name: 26, dtype: object not available
temp            510
perturbation      4
force           0.0
Name: 39, dtype: object not available
temp            510
perturbation      4
force           0.1
Name: 40, dtype: object not available
temp            510
perturbation      4
force           0.2
Name: 41, dtype: object not available
temp            510
perturbation      5
force           0.0
Name: 42, dtype: object not available
temp            510
perturbation      5
force           0.1
Name: 43, dtype: object not available
temp            510
perturbation      5
force           0.2
Name: 44, dtype: object not available
temp            510
perturbation      6
force           0.0
Name: 45, dtype: object not available
temp            510
perturbation      6
force           0.1
Name: 46, dtype: object not available
temp            510
perturbation      6
force           0.2
Name: 47, dtype: object not available
temp            510
perturbation      7
force           0.0
Name: 48, dtype: object not available
temp            510
perturbation      7
force           0.1
Name: 49, dtype: object not available
temp            510
perturbation      7
force           0.2
Name: 50, dtype: object not available
temp            510
perturbation      8
force           0.0
Name: 51, dtype: object not available
temp            510
perturbation      8
force           0.1
Name: 52, dtype: object not available
temp            510
perturbation      8
force           0.2
Name: 53, dtype: object not available
temp            520
perturbation      4
force           0.0
Name: 66, dtype: object not available
temp            520
perturbation      4
force           0.1
Name: 67, dtype: object not available
temp            520
perturbation      4
force           0.2
Name: 68, dtype: object not available
temp            520
perturbation      5
force           0.0
Name: 69, dtype: object not available
temp            520
perturbation      5
force           0.1
Name: 70, dtype: object not available
temp            520
perturbation      5
force           0.2
Name: 71, dtype: object not available
temp            520
perturbation      6
force           0.0
Name: 72, dtype: object not available
temp            520
perturbation      6
force           0.1
Name: 73, dtype: object not available
temp            520
perturbation      6
force           0.2
Name: 74, dtype: object not available
temp            520
perturbation      7
force           0.0
Name: 75, dtype: object not available
temp            520
perturbation      7
force           0.1
Name: 76, dtype: object not available
temp            520
perturbation      7
force           0.2
Name: 77, dtype: object not available
temp            520
perturbation      8
force           0.0
Name: 78, dtype: object not available
temp            520
perturbation      8
force           0.1
Name: 79, dtype: object not available
temp            520
perturbation      8
force           0.2
Name: 80, dtype: object not available
temp            530
perturbation      4
force           0.0
Name: 93, dtype: object not available
temp            530
perturbation      4
force           0.1
Name: 94, dtype: object not available
temp            530
perturbation      4
force           0.2
Name: 95, dtype: object not available
temp            530
perturbation      5
force           0.0
Name: 96, dtype: object not available
temp            530
perturbation      5
force           0.1
Name: 97, dtype: object not available
temp            530
perturbation      5
force           0.2
Name: 98, dtype: object not available
temp            530
perturbation      6
force           0.0
Name: 99, dtype: object not available
temp            530
perturbation      6
force           0.1
Name: 100, dtype: object not available
temp            530
perturbation      6
force           0.2
Name: 101, dtype: object not available
temp            530
perturbation      7
force           0.0
Name: 102, dtype: object not available
temp            530
perturbation      7
force           0.1
Name: 103, dtype: object not available
temp            530
perturbation      7
force           0.2
Name: 104, dtype: object not available
temp            530
perturbation      8
force           0.0
Name: 105, dtype: object not available
temp            530
perturbation      8
force           0.1
Name: 106, dtype: object not available
temp            530
perturbation      8
force           0.2
Name: 107, dtype: object not available
temp            540
perturbation      4
force           0.0
Name: 120, dtype: object not available
temp            540
perturbation      4
force           0.1
Name: 121, dtype: object not available
temp            540
perturbation      4
force           0.2
Name: 122, dtype: object not available
temp            540
perturbation      5
force           0.0
Name: 123, dtype: object not available
temp            540
perturbation      5
force           0.1
Name: 124, dtype: object not available
temp            540
perturbation      5
force           0.2
Name: 125, dtype: object not available
temp            540
perturbation      6
force           0.0
Name: 126, dtype: object not available
temp            540
perturbation      6
force           0.1
Name: 127, dtype: object not available
temp            540
perturbation      6
force           0.2
Name: 128, dtype: object not available
temp            540
perturbation      7
force           0.0
Name: 129, dtype: object not available
temp            540
perturbation      7
force           0.1
Name: 130, dtype: object not available
temp            540
perturbation      7
force           0.2
Name: 131, dtype: object not available
temp            540
perturbation      8
force           0.0
Name: 132, dtype: object not available
temp            540
perturbation      8
force           0.1
Name: 133, dtype: object not available
temp            540
perturbation      8
force           0.2
Name: 134, dtype: object not available
temp            550
perturbation      4
force           0.0
Name: 147, dtype: object not available
temp            550
perturbation      4
force           0.1
Name: 148, dtype: object not available
temp            550
perturbation      4
force           0.2
Name: 149, dtype: object not available
temp            550
perturbation      5
force           0.0
Name: 150, dtype: object not available
temp            550
perturbation      5
force           0.1
Name: 151, dtype: object not available
temp            550
perturbation      5
force           0.2
Name: 152, dtype: object not available
temp            550
perturbation      6
force           0.0
Name: 153, dtype: object not available
temp            550
perturbation      6
force           0.1
Name: 154, dtype: object not available
temp            550
perturbation      6
force           0.2
Name: 155, dtype: object not available
temp            550
perturbation      7
force           0.0
Name: 156, dtype: object not available
temp            550
perturbation      7
force           0.1
Name: 157, dtype: object not available
temp            550
perturbation      7
force           0.2
Name: 158, dtype: object not available
temp            550
perturbation      8
force           0.0
Name: 159, dtype: object not available
temp            550
perturbation      8
force           0.1
Name: 160, dtype: object not available
temp            550
perturbation      8
force           0.2
Name: 161, dtype: object not available
temp            560
perturbation      4
force           0.0
Name: 174, dtype: object not available
temp            560
perturbation      4
force           0.1
Name: 175, dtype: object not available
temp            560
perturbation      4
force           0.2
Name: 176, dtype: object not available
temp            560
perturbation      5
force           0.0
Name: 177, dtype: object not available
temp            560
perturbation      5
force           0.1
Name: 178, dtype: object not available
temp            560
perturbation      5
force           0.2
Name: 179, dtype: object not available
temp            560
perturbation      6
force           0.0
Name: 180, dtype: object not available
temp            560
perturbation      6
force           0.1
Name: 181, dtype: object not available
temp            560
perturbation      6
force           0.2
Name: 182, dtype: object not available
temp            560
perturbation      7
force           0.0
Name: 183, dtype: object not available
temp            560
perturbation      7
force           0.1
Name: 184, dtype: object not available
temp            560
perturbation      7
force           0.2
Name: 185, dtype: object not available
temp            560
perturbation      8
force           0.0
Name: 186, dtype: object not available
temp            560
perturbation      8
force           0.1
Name: 187, dtype: object not available
temp            560
perturbation      8
force           0.2
Name: 188, dtype: object not available
temp            570
perturbation      4
force           0.0
Name: 201, dtype: object not available
temp            570
perturbation      4
force           0.1
Name: 202, dtype: object not available
temp            570
perturbation      4
force           0.2
Name: 203, dtype: object not available
temp            570
perturbation      5
force           0.0
Name: 204, dtype: object not available
temp            570
perturbation      5
force           0.1
Name: 205, dtype: object not available
temp            570
perturbation      5
force           0.2
Name: 206, dtype: object not available
temp            570
perturbation      6
force           0.0
Name: 207, dtype: object not available
temp            570
perturbation      6
force           0.1
Name: 208, dtype: object not available
temp            570
perturbation      6
force           0.2
Name: 209, dtype: object not available
temp            570
perturbation      7
force           0.0
Name: 210, dtype: object not available
temp            570
perturbation      7
force           0.1
Name: 211, dtype: object not available
temp            570
perturbation      7
force           0.2
Name: 212, dtype: object not available
temp            570
perturbation      8
force           0.0
Name: 213, dtype: object not available
temp            570
perturbation      8
force           0.1
Name: 214, dtype: object not available
temp            570
perturbation      8
force           0.2
Name: 215, dtype: object not available
temp            580
perturbation      4
force           0.0
Name: 228, dtype: object not available
temp            580
perturbation      4
force           0.1
Name: 229, dtype: object not available
temp            580
perturbation      4
force           0.2
Name: 230, dtype: object not available
temp            580
perturbation      5
force           0.0
Name: 231, dtype: object not available
temp            580
perturbation      5
force           0.1
Name: 232, dtype: object not available
temp            580
perturbation      5
force           0.2
Name: 233, dtype: object not available
temp            580
perturbation      6
force           0.0
Name: 234, dtype: object not available
temp            580
perturbation      6
force           0.1
Name: 235, dtype: object not available
temp            580
perturbation      6
force           0.2
Name: 236, dtype: object not available
temp            580
perturbation      7
force           0.0
Name: 237, dtype: object not available
temp            580
perturbation      7
force           0.1
Name: 238, dtype: object not available
temp            580
perturbation      7
force           0.2
Name: 239, dtype: object not available
temp            580
perturbation      8
force           0.0
Name: 240, dtype: object not available
temp            580
perturbation      8
force           0.1
Name: 241, dtype: object not available
temp            580
perturbation      8
force           0.2
Name: 242, dtype: object not available
temp            590
perturbation      4
force           0.0
Name: 255, dtype: object not available
temp            590
perturbation      4
force           0.1
Name: 256, dtype: object not available
temp            590
perturbation      4
force           0.2
Name: 257, dtype: object not available
temp            590
perturbation      5
force           0.0
Name: 258, dtype: object not available
temp            590
perturbation      5
force           0.1
Name: 259, dtype: object not available
temp            590
perturbation      5
force           0.2
Name: 260, dtype: object not available
temp            590
perturbation      6
force           0.0
Name: 261, dtype: object not available
temp            590
perturbation      6
force           0.1
Name: 262, dtype: object not available
temp            590
perturbation      6
force           0.2
Name: 263, dtype: object not available
temp            590
perturbation      7
force           0.0
Name: 264, dtype: object not available
temp            590
perturbation      7
force           0.1
Name: 265, dtype: object not available
temp            590
perturbation      7
force           0.2
Name: 266, dtype: object not available
temp            590
perturbation      8
force           0.0
Name: 267, dtype: object not available
temp            590
perturbation      8
force           0.1
Name: 268, dtype: object not available
temp            590
perturbation      8
force           0.2
Name: 269, dtype: object not available
temp            600
perturbation      4
force           0.0
Name: 282, dtype: object not available
temp            600
perturbation      4
force           0.1
Name: 283, dtype: object not available
temp            600
perturbation      4
force           0.2
Name: 284, dtype: object not available
temp            600
perturbation      5
force           0.0
Name: 285, dtype: object not available
temp            600
perturbation      5
force           0.1
Name: 286, dtype: object not available
temp            600
perturbation      5
force           0.2
Name: 287, dtype: object not available
temp            600
perturbation      6
force           0.0
Name: 288, dtype: object not available
temp            600
perturbation      6
force           0.1
Name: 289, dtype: object not available
temp            600
perturbation      6
force           0.2
Name: 290, dtype: object not available
temp            600
perturbation      7
force           0.0
Name: 291, dtype: object not available
temp            600
perturbation      7
force           0.1
Name: 292, dtype: object not available
temp            600
perturbation      7
force           0.2
Name: 293, dtype: object not available
temp            600
perturbation      8
force           0.0
Name: 294, dtype: object not available
temp            600
perturbation      8
force           0.1
Name: 295, dtype: object not available
temp            600
perturbation      8
force           0.2
Name: 296, dtype: object not available
temp            610
perturbation      4
force           0.0
Name: 309, dtype: object not available
temp            610
perturbation      4
force           0.1
Name: 310, dtype: object not available
temp            610
perturbation      4
force           0.2
Name: 311, dtype: object not available
temp            610
perturbation      5
force           0.0
Name: 312, dtype: object not available
temp            610
perturbation      5
force           0.1
Name: 313, dtype: object not available
temp            610
perturbation      5
force           0.2
Name: 314, dtype: object not available
temp            610
perturbation      6
force           0.0
Name: 315, dtype: object not available
temp            610
perturbation      6
force           0.1
Name: 316, dtype: object not available
temp            610
perturbation      6
force           0.2
Name: 317, dtype: object not available
temp            610
perturbation      7
force           0.0
Name: 318, dtype: object not available
temp            610
perturbation      7
force           0.1
Name: 319, dtype: object not available
temp            610
perturbation      7
force           0.2
Name: 320, dtype: object not available
temp            610
perturbation      8
force           0.0
Name: 321, dtype: object not available
temp            610
perturbation      8
force           0.1
Name: 322, dtype: object not available
temp            610
perturbation      8
force           0.2
Name: 323, dtype: object not available
temp            620
perturbation      4
force           0.0
Name: 336, dtype: object not available
temp            620
perturbation      4
force           0.1
Name: 337, dtype: object not available
temp            620
perturbation      4
force           0.2
Name: 338, dtype: object not available
temp            620
perturbation      5
force           0.0
Name: 339, dtype: object not available
temp            620
perturbation      5
force           0.1
Name: 340, dtype: object not available
temp            620
perturbation      5
force           0.2
Name: 341, dtype: object not available
temp            620
perturbation      6
force           0.0
Name: 342, dtype: object not available
temp            620
perturbation      6
force           0.1
Name: 343, dtype: object not available
temp            620
perturbation      6
force           0.2
Name: 344, dtype: object not available
temp            620
perturbation      7
force           0.0
Name: 345, dtype: object not available
temp            620
perturbation      7
force           0.1
Name: 346, dtype: object not available
temp            620
perturbation      7
force           0.2
Name: 347, dtype: object not available
temp            620
perturbation      8
force           0.0
Name: 348, dtype: object not available
temp            620
perturbation      8
force           0.1
Name: 349, dtype: object not available
temp            620
perturbation      8
force           0.2
Name: 350, dtype: object not available
temp            630
perturbation      4
force           0.0
Name: 363, dtype: object not available
temp            630
perturbation      4
force           0.1
Name: 364, dtype: object not available
temp            630
perturbation      4
force           0.2
Name: 365, dtype: object not available
temp            630
perturbation      5
force           0.0
Name: 366, dtype: object not available
temp            630
perturbation      5
force           0.1
Name: 367, dtype: object not available
temp            630
perturbation      5
force           0.2
Name: 368, dtype: object not available
temp            630
perturbation      6
force           0.0
Name: 369, dtype: object not available
temp            630
perturbation      6
force           0.1
Name: 370, dtype: object not available
temp            630
perturbation      6
force           0.2
Name: 371, dtype: object not available
temp            630
perturbation      7
force           0.0
Name: 372, dtype: object not available
temp            630
perturbation      7
force           0.1
Name: 373, dtype: object not available
temp            630
perturbation      7
force           0.2
Name: 374, dtype: object not available
temp            630
perturbation      8
force           0.0
Name: 375, dtype: object not available
temp            630
perturbation      8
force           0.1
Name: 376, dtype: object not available
temp            630
perturbation      8
force           0.2
Name: 377, dtype: object not available
temp            640
perturbation      4
force           0.0
Name: 390, dtype: object not available
temp            640
perturbation      4
force           0.1
Name: 391, dtype: object not available
temp            640
perturbation      4
force           0.2
Name: 392, dtype: object not available
temp            640
perturbation      5
force           0.0
Name: 393, dtype: object not available
temp            640
perturbation      5
force           0.1
Name: 394, dtype: object not available
temp            640
perturbation      5
force           0.2
Name: 395, dtype: object not available
temp            640
perturbation      6
force           0.0
Name: 396, dtype: object not available
temp            640
perturbation      6
force           0.1
Name: 397, dtype: object not available
temp            640
perturbation      6
force           0.2
Name: 398, dtype: object not available
temp            640
perturbation      7
force           0.0
Name: 399, dtype: object not available
temp            640
perturbation      7
force           0.1
Name: 400, dtype: object not available
temp            640
perturbation      7
force           0.2
Name: 401, dtype: object not available
temp            640
perturbation      8
force           0.0
Name: 402, dtype: object not available
temp            640
perturbation      8
force           0.1
Name: 403, dtype: object not available
temp            640
perturbation      8
force           0.2
Name: 404, dtype: object not available
temp            650
perturbation      4
force           0.0
Name: 417, dtype: object not available
temp            650
perturbation      4
force           0.1
Name: 418, dtype: object not available
temp            650
perturbation      4
force           0.2
Name: 419, dtype: object not available
temp            650
perturbation      5
force           0.0
Name: 420, dtype: object not available
temp            650
perturbation      5
force           0.1
Name: 421, dtype: object not available
temp            650
perturbation      5
force           0.2
Name: 422, dtype: object not available
temp            650
perturbation      6
force           0.0
Name: 423, dtype: object not available
temp            650
perturbation      6
force           0.1
Name: 424, dtype: object not available
temp            650
perturbation      6
force           0.2
Name: 425, dtype: object not available
temp            650
perturbation      7
force           0.0
Name: 426, dtype: object not available
temp            650
perturbation      7
force           0.1
Name: 427, dtype: object not available
temp            650
perturbation      7
force           0.2
Name: 428, dtype: object not available
temp            650
perturbation      8
force           0.0
Name: 429, dtype: object not available
temp            650
perturbation      8
force           0.1
Name: 430, dtype: object not available
temp            650
perturbation      8
force           0.2
Name: 431, dtype: object not available
temp            660
perturbation      3
force           0.2
Name: 443, dtype: object not available
temp            660
perturbation      4
force           0.0
Name: 444, dtype: object not available
temp            660
perturbation      4
force           0.1
Name: 445, dtype: object not available
temp            660
perturbation      4
force           0.2
Name: 446, dtype: object not available
temp            660
perturbation      5
force           0.0
Name: 447, dtype: object not available
temp            660
perturbation      5
force           0.1
Name: 448, dtype: object not available
temp            660
perturbation      5
force           0.2
Name: 449, dtype: object not available
temp            660
perturbation      6
force           0.0
Name: 450, dtype: object not available
temp            660
perturbation      6
force           0.1
Name: 451, dtype: object not available
temp            660
perturbation      6
force           0.2
Name: 452, dtype: object not available
temp            660
perturbation      7
force           0.0
Name: 453, dtype: object not available
temp            660
perturbation      7
force           0.1
Name: 454, dtype: object not available
temp            660
perturbation      7
force           0.2
Name: 455, dtype: object not available
temp            660
perturbation      8
force           0.0
Name: 456, dtype: object not available
temp            660
perturbation      8
force           0.1
Name: 457, dtype: object not available
temp            660
perturbation      8
force           0.2
Name: 458, dtype: object not available
temp            670
perturbation      3
force           0.2
Name: 470, dtype: object not available
temp            670
perturbation      4
force           0.0
Name: 471, dtype: object not available
temp            670
perturbation      4
force           0.1
Name: 472, dtype: object not available
temp            670
perturbation      4
force           0.2
Name: 473, dtype: object not available
temp            670
perturbation      5
force           0.0
Name: 474, dtype: object not available
temp            670
perturbation      5
force           0.1
Name: 475, dtype: object not available
temp            670
perturbation      5
force           0.2
Name: 476, dtype: object not available
temp            670
perturbation      6
force           0.0
Name: 477, dtype: object not available
temp            670
perturbation      6
force           0.1
Name: 478, dtype: object not available
temp            670
perturbation      6
force           0.2
Name: 479, dtype: object not available
temp            670
perturbation      7
force           0.0
Name: 480, dtype: object not available
temp            670
perturbation      7
force           0.1
Name: 481, dtype: object not available
temp            670
perturbation      7
force           0.2
Name: 482, dtype: object not available
temp            670
perturbation      8
force           0.0
Name: 483, dtype: object not available
temp            670
perturbation      8
force           0.1
Name: 484, dtype: object not available
temp            670
perturbation      8
force           0.2
Name: 485, dtype: object not available
temp            680
perturbation      3
force           0.1
Name: 496, dtype: object not available
temp            680
perturbation      3
force           0.2
Name: 497, dtype: object not available
temp            680
perturbation      4
force           0.0
Name: 498, dtype: object not available
temp            680
perturbation      4
force           0.1
Name: 499, dtype: object not available
temp            680
perturbation      4
force           0.2
Name: 500, dtype: object not available
temp            680
perturbation      5
force           0.0
Name: 501, dtype: object not available
temp            680
perturbation      5
force           0.1
Name: 502, dtype: object not available
temp            680
perturbation      5
force           0.2
Name: 503, dtype: object not available
temp            680
perturbation      6
force           0.0
Name: 504, dtype: object not available
temp            680
perturbation      6
force           0.1
Name: 505, dtype: object not available
temp            680
perturbation      6
force           0.2
Name: 506, dtype: object not available
temp            680
perturbation      7
force           0.0
Name: 507, dtype: object not available
temp            680
perturbation      7
force           0.1
Name: 508, dtype: object not available
temp            680
perturbation      7
force           0.2
Name: 509, dtype: object not available
temp            680
perturbation      8
force           0.0
Name: 510, dtype: object not available
temp            680
perturbation      8
force           0.1
Name: 511, dtype: object not available
temp            680
perturbation      8
force           0.2
Name: 512, dtype: object not available
temp            690
perturbation      3
force           0.1
Name: 523, dtype: object not available
temp            690
perturbation      3
force           0.2
Name: 524, dtype: object not available
temp            690
perturbation      4
force           0.0
Name: 525, dtype: object not available
temp            690
perturbation      4
force           0.1
Name: 526, dtype: object not available
temp            690
perturbation      4
force           0.2
Name: 527, dtype: object not available
temp            690
perturbation      5
force           0.0
Name: 528, dtype: object not available
temp            690
perturbation      5
force           0.1
Name: 529, dtype: object not available
temp            690
perturbation      5
force           0.2
Name: 530, dtype: object not available
temp            690
perturbation      6
force           0.0
Name: 531, dtype: object not available
temp            690
perturbation      6
force           0.1
Name: 532, dtype: object not available
temp            690
perturbation      6
force           0.2
Name: 533, dtype: object not available
temp            690
perturbation      7
force           0.0
Name: 534, dtype: object not available
temp            690
perturbation      7
force           0.1
Name: 535, dtype: object not available
temp            690
perturbation      7
force           0.2
Name: 536, dtype: object not available
temp            690
perturbation      8
force           0.0
Name: 537, dtype: object not available
temp            690
perturbation      8
force           0.1
Name: 538, dtype: object not available
temp            690
perturbation      8
force           0.2
Name: 539, dtype: object not available
temp            700
perturbation      3
force           0.1
Name: 550, dtype: object not available
temp            700
perturbation      3
force           0.2
Name: 551, dtype: object not available
temp            700
perturbation      4
force           0.0
Name: 552, dtype: object not available
temp            700
perturbation      4
force           0.1
Name: 553, dtype: object not available
temp            700
perturbation      4
force           0.2
Name: 554, dtype: object not available
temp            700
perturbation      5
force           0.0
Name: 555, dtype: object not available
temp            700
perturbation      5
force           0.1
Name: 556, dtype: object not available
temp            700
perturbation      5
force           0.2
Name: 557, dtype: object not available
temp            700
perturbation      6
force           0.0
Name: 558, dtype: object not available
temp            700
perturbation      6
force           0.1
Name: 559, dtype: object not available
temp            700
perturbation      6
force           0.2
Name: 560, dtype: object not available
temp            700
perturbation      7
force           0.0
Name: 561, dtype: object not available
temp            700
perturbation      7
force           0.1
Name: 562, dtype: object not available
temp            700
perturbation      7
force           0.2
Name: 563, dtype: object not available
temp            700
perturbation      8
force           0.0
Name: 564, dtype: object not available
temp            700
perturbation      8
force           0.1
Name: 565, dtype: object not available
temp            700
perturbation      8
force           0.2
Name: 566, dtype: object not available

In [86]:

    

data


    

    
Out[86]:







  

    

      

      
index
      
x
      
f
      
df
      
e
      
s
      
change
      
force
      
perturbation
      
temp
      
upOrDown
    
  
  

    

      
0
      
2
      
9.267
      
0.000
      
0.0
      
-763.998
      
-763.998
      
none
      
0.0
      
original
      
500
      
none
    
    

      
1
      
3
      
12.293
      
3.085
      
0.0
      
-793.759
      
-796.844
      
none
      
0.0
      
original
      
500
      
none
    
    

      
2
      
4
      
15.318
      
2.593
      
0.0
      
-765.426
      
-768.020
      
none
      
0.0
      
original
      
500
      
none
    
    

      
3
      
5
      
18.343
      
2.636
      
0.0
      
-758.124
      
-760.761
      
none
      
0.0
      
original
      
500
      
none
    
    

      
4
      
6
      
21.369
      
2.157
      
0.0
      
-755.503
      
-757.659
      
none
      
0.0
      
original
      
500
      
none
    
    

      
5
      
7
      
24.394
      
2.160
      
0.0
      
-757.645
      
-759.805
      
none
      
0.0
      
original
      
500
      
none
    
    

      
6
      
8
      
27.419
      
2.054
      
0.0
      
-758.642
      
-760.696
      
none
      
0.0
      
original
      
500
      
none
    
    

      
7
      
9
      
30.445
      
2.140
      
0.0
      
-759.274
      
-761.414
      
none
      
0.0
      
original
      
500
      
none
    
    

      
8
      
10
      
33.470
      
2.468
      
0.0
      
-760.162
      
-762.630
      
none
      
0.0
      
original
      
500
      
none
    
    

      
9
      
11
      
36.495
      
3.181
      
0.0
      
-758.039
      
-761.220
      
none
      
0.0
      
original
      
500
      
none
    
    

      
10
      
12
      
39.521
      
4.293
      
0.0
      
-757.991
      
-762.284
      
none
      
0.0
      
original
      
500
      
none
    
    

      
11
      
13
      
42.546
      
5.734
      
0.0
      
-756.959
      
-762.693
      
none
      
0.0
      
original
      
500
      
none
    
    

      
12
      
14
      
45.572
      
7.586
      
0.0
      
-755.458
      
-763.043
      
none
      
0.0
      
original
      
500
      
none
    
    

      
13
      
15
      
48.597
      
9.774
      
0.0
      
-752.978
      
-762.752
      
none
      
0.0
      
original
      
500
      
none
    
    

      
14
      
16
      
51.622
      
12.221
      
0.0
      
-748.730
      
-760.951
      
none
      
0.0
      
original
      
500
      
none
    
    

      
15
      
17
      
54.648
      
15.144
      
0.0
      
-743.760
      
-758.904
      
none
      
0.0
      
original
      
500
      
none
    
    

      
16
      
18
      
57.673
      
18.515
      
0.0
      
-734.686
      
-753.201
      
none
      
0.0
      
original
      
500
      
none
    
    

      
17
      
19
      
60.698
      
22.862
      
0.0
      
-715.316
      
-738.179
      
none
      
0.0
      
original
      
500
      
none
    
    

      
18
      
21
      
66.749
      
29.066
      
0.0
      
-656.467
      
-685.534
      
none
      
0.0
      
original
      
500
      
none
    
    

      
19
      
22
      
69.774
      
31.949
      
0.0
      
-583.868
      
-615.818
      
none
      
0.0
      
original
      
500
      
none
    
    

      
20
      
23
      
72.800
      
31.307
      
0.0
      
-673.347
      
-704.654
      
none
      
0.0
      
original
      
500
      
none
    
    

      
21
      
24
      
75.825
      
33.559
      
0.0
      
-643.972
      
-677.531
      
none
      
0.0
      
original
      
500
      
none
    
    

      
22
      
25
      
78.850
      
32.642
      
0.0
      
-721.249
      
-753.891
      
none
      
0.0
      
original
      
500
      
none
    
    

      
23
      
26
      
81.876
      
32.866
      
0.0
      
-837.164
      
-870.030
      
none
      
0.0
      
original
      
500
      
none
    
    

      
24
      
27
      
84.901
      
33.153
      
0.0
      
-686.904
      
-720.057
      
none
      
0.0
      
original
      
500
      
none
    
    

      
25
      
28
      
87.926
      
33.559
      
0.0
      
-686.904
      
-720.463
      
none
      
0.0
      
original
      
500
      
none
    
    

      
26
      
29
      
90.952
      
33.964
      
0.0
      
-965.959
      
-999.923
      
none
      
0.0
      
original
      
500
      
none
    
    

      
27
      
30
      
93.977
      
34.252
      
0.0
      
-343.452
      
-377.704
      
none
      
0.0
      
original
      
500
      
none
    
    

      
28
      
2
      
9.267
      
1.774
      
0.0
      
-764.085
      
-765.859
      
none
      
0.1
      
original
      
500
      
none
    
    

      
29
      
3
      
12.293
      
2.719
      
0.0
      
-789.856
      
-792.576
      
none
      
0.1
      
original
      
500
      
none
    
    

      
...
      
...
      
...
      
...
      
...
      
...
      
...
      
...
      
...
      
...
      
...
      
...
    
    

      
11194
      
16
      
51.622
      
8.462
      
0.0
      
-92.832
      
-101.293
      
lipid
      
0.0
      
p_lipid
      
700
      
p
    
    

      
11195
      
17
      
54.648
      
9.751
      
0.0
      
-90.022
      
-99.773
      
lipid
      
0.0
      
p_lipid
      
700
      
p
    
    

      
11196
      
18
      
57.673
      
12.457
      
0.0
      
-118.885
      
-131.342
      
lipid
      
0.0
      
p_lipid
      
700
      
p
    
    

      
11197
      
19
      
60.698
      
14.952
      
0.0
      
-124.073
      
-139.024
      
lipid
      
0.0
      
p_lipid
      
700
      
p
    
    

      
11198
      
20
      
63.724
      
16.750
      
0.0
      
-137.126
      
-153.876
      
lipid
      
0.0
      
p_lipid
      
700
      
p
    
    

      
11199
      
21
      
66.749
      
17.821
      
0.0
      
-117.726
      
-135.547
      
lipid
      
0.0
      
p_lipid
      
700
      
p
    
    

      
11200
      
22
      
69.774
      
20.082
      
0.0
      
-133.533
      
-153.615
      
lipid
      
0.0
      
p_lipid
      
700
      
p
    
    

      
11201
      
23
      
72.800
      
18.227
      
0.0
      
-95.265
      
-113.492
      
lipid
      
0.0
      
p_lipid
      
700
      
p
    
    

      
11202
      
24
      
75.825
      
18.361
      
0.0
      
-68.425
      
-86.786
      
lipid
      
0.0
      
p_lipid
      
700
      
p
    
    

      
11203
      
25
      
78.850
      
21.086
      
0.0
      
-107.199
      
-128.285
      
lipid
      
0.0
      
p_lipid
      
700
      
p
    
    

      
11204
      
26
      
81.876
      
20.610
      
0.0
      
-93.770
      
-114.381
      
lipid
      
0.0
      
p_lipid
      
700
      
p
    
    

      
11205
      
27
      
84.901
      
19.863
      
0.0
      
-79.853
      
-99.716
      
lipid
      
0.0
      
p_lipid
      
700
      
p
    
    

      
11206
      
28
      
87.926
      
20.588
      
0.0
      
-70.752
      
-91.340
      
lipid
      
0.0
      
p_lipid
      
700
      
p
    
    

      
11207
      
29
      
90.952
      
22.067
      
0.0
      
-101.930
      
-123.997
      
lipid
      
0.0
      
p_lipid
      
700
      
p
    
    

      
11208
      
30
      
93.977
      
21.770
      
0.0
      
-90.738
      
-112.508
      
lipid
      
0.0
      
p_lipid
      
700
      
p
    
    

      
11209
      
31
      
97.003
      
22.585
      
0.0
      
-85.893
      
-108.477
      
lipid
      
0.0
      
p_lipid
      
700
      
p
    
    

      
11210
      
32
      
100.028
      
22.869
      
0.0
      
-89.335
      
-112.205
      
lipid
      
0.0
      
p_lipid
      
700
      
p
    
    

      
11211
      
33
      
103.053
      
23.603
      
0.0
      
-100.228
      
-123.831
      
lipid
      
0.0
      
p_lipid
      
700
      
p
    
    

      
11212
      
34
      
106.079
      
23.583
      
0.0
      
-75.511
      
-99.094
      
lipid
      
0.0
      
p_lipid
      
700
      
p
    
    

      
11213
      
35
      
109.104
      
24.723
      
0.0
      
-93.632
      
-118.354
      
lipid
      
0.0
      
p_lipid
      
700
      
p
    
    

      
11214
      
36
      
112.129
      
24.265
      
0.0
      
-69.293
      
-93.558
      
lipid
      
0.0
      
p_lipid
      
700
      
p
    
    

      
11215
      
37
      
115.155
      
26.237
      
0.0
      
-102.128
      
-128.364
      
lipid
      
0.0
      
p_lipid
      
700
      
p
    
    

      
11216
      
38
      
118.180
      
26.192
      
0.0
      
-88.944
      
-115.136
      
lipid
      
0.0
      
p_lipid
      
700
      
p
    
    

      
11217
      
39
      
121.205
      
26.483
      
0.0
      
-78.128
      
-104.611
      
lipid
      
0.0
      
p_lipid
      
700
      
p
    
    

      
11218
      
40
      
124.231
      
27.504
      
0.0
      
-89.171
      
-116.675
      
lipid
      
0.0
      
p_lipid
      
700
      
p
    
    

      
11219
      
41
      
127.256
      
28.314
      
0.0
      
-93.816
      
-122.130
      
lipid
      
0.0
      
p_lipid
      
700
      
p
    
    

      
11220
      
42
      
130.281
      
29.441
      
0.0
      
-133.812
      
-163.254
      
lipid
      
0.0
      
p_lipid
      
700
      
p
    
    

      
11221
      
43
      
133.307
      
30.166
      
0.0
      
-173.169
      
-203.335
      
lipid
      
0.0
      
p_lipid
      
700
      
p
    
    

      
11222
      
44
      
136.332
      
31.040
      
0.0
      
-284.015
      
-315.054
      
lipid
      
0.0
      
p_lipid
      
700
      
p
    
    

      
11223
      
45
      
139.357
      
29.908
      
0.0
      
-107.528
      
-137.436
      
lipid
      
0.0
      
p_lipid
      
700
      
p
    
  

11224 rows × 11 columns

In [62]:

    

pmf_list_data = expand_grid(pmf_list)
pre = "/Users/weilu/Research/davinci/extended/finer_with_more_data"
data = readPMF(pmf_list_data, pre)
# data.to_feather("/Users/weilu/Research/data/pulling/nov06_pmf_3.feather")
remove_columns = ['bin']
data = data.drop(remove_columns, axis=1)
data.to_feather("/Users/weilu/Research/data/pulling/nov06_pmf_3.feather")


    

    




temp            500
perturbation      6
force           0.0
Name: 18, dtype: object not available
temp            500
perturbation      6
force           0.1
Name: 19, dtype: object not available
temp            500
perturbation      6
force           0.2
Name: 20, dtype: object not available
temp            500
perturbation      7
force           0.0
Name: 21, dtype: object not available
temp            500
perturbation      7
force           0.1
Name: 22, dtype: object not available
temp            500
perturbation      7
force           0.2
Name: 23, dtype: object not available
temp            500
perturbation      8
force           0.0
Name: 24, dtype: object not available
temp            500
perturbation      8
force           0.1
Name: 25, dtype: object not available
temp            500
perturbation      8
force           0.2
Name: 26, dtype: object not available
temp            530
perturbation      5
force           0.0
Name: 42, dtype: object not available
temp            530
perturbation      6
force           0.0
Name: 45, dtype: object not available
temp            530
perturbation      6
force           0.1
Name: 46, dtype: object not available
temp            530
perturbation      6
force           0.2
Name: 47, dtype: object not available
temp            530
perturbation      7
force           0.0
Name: 48, dtype: object not available
temp            530
perturbation      7
force           0.1
Name: 49, dtype: object not available
temp            530
perturbation      7
force           0.2
Name: 50, dtype: object not available
temp            530
perturbation      8
force           0.0
Name: 51, dtype: object not available
temp            530
perturbation      8
force           0.1
Name: 52, dtype: object not available
temp            530
perturbation      8
force           0.2
Name: 53, dtype: object not available
temp            560
perturbation      5
force           0.0
Name: 69, dtype: object not available
temp            560
perturbation      5
force           0.2
Name: 71, dtype: object not available
temp            560
perturbation      6
force           0.0
Name: 72, dtype: object not available
temp            560
perturbation      6
force           0.1
Name: 73, dtype: object not available
temp            560
perturbation      6
force           0.2
Name: 74, dtype: object not available
temp            560
perturbation      7
force           0.0
Name: 75, dtype: object not available
temp            560
perturbation      7
force           0.1
Name: 76, dtype: object not available
temp            560
perturbation      7
force           0.2
Name: 77, dtype: object not available
temp            560
perturbation      8
force           0.0
Name: 78, dtype: object not available
temp            560
perturbation      8
force           0.1
Name: 79, dtype: object not available
temp            560
perturbation      8
force           0.2
Name: 80, dtype: object not available
temp            590
perturbation      5
force           0.0
Name: 96, dtype: object not available
temp            590
perturbation      5
force           0.1
Name: 97, dtype: object not available
temp            590
perturbation      5
force           0.2
Name: 98, dtype: object not available
temp            590
perturbation      6
force           0.0
Name: 99, dtype: object not available
temp            590
perturbation      6
force           0.1
Name: 100, dtype: object not available
temp            590
perturbation      6
force           0.2
Name: 101, dtype: object not available
temp            590
perturbation      7
force           0.0
Name: 102, dtype: object not available
temp            590
perturbation      7
force           0.1
Name: 103, dtype: object not available
temp            590
perturbation      7
force           0.2
Name: 104, dtype: object not available
temp            590
perturbation      8
force           0.0
Name: 105, dtype: object not available
temp            590
perturbation      8
force           0.1
Name: 106, dtype: object not available
temp            590
perturbation      8
force           0.2
Name: 107, dtype: object not available

In [60]:

    




    

In [24]:

    

temp_list = [500, 530, 560, 590]
def readPMF(force_list=["0.0", "0.1", "0.2"], temp_list=[500, 530, 560, 590],perturbation_list=[0, 1, 2, 3, 4, 5, 6, 7, 8])
    for force in force_list:
        for temp in temp_list:
            for perturbation in perturbation_list:

                # pmf 
                if perturbation == 0:
                    location = pre + f"/force_{force}/pmf-{temp}.dat"
                else:
                    location = pre + \
                    "/force_{}/perturbation-{}-pmf-{}.dat".format(force, perturbation, temp)


    

    




  File "<ipython-input-24-d16f5fd7ef3a>", line 2
    def readPMF(force_list=["0.0", "0.1", "0.2"], temp_list=[500, 530, 560, 590],perturbation_list=[0, 1, 2, 3, 4, 5, 6, 7, 8]  )
                                                                                                                                 ^
SyntaxError: invalid syntax

In [ ]:

    

all_pmf_list = []
all_evpb_list = []
for folder in folder_list:
    for force in force_list:
        for temp in temp_list:
            for perturbation in perturbation_list:

                # pmf 
                if perturbation == 0:
                    location = pre + f"{folder}/1d_dis/t_all/force_{force}/pmf-{temp}.dat"
                else:
                    location = pre + \
                    "{}/1d_dis/t_all/force_{}/perturbation-{}-pmf-{}.dat".format(folder, force, perturbation, temp)

                name_list = ["f", "df", "e", "s"]
                names = ["bin", "x"] + name_list
                data = pd.read_table(location, skiprows=2, sep='\s+', names=names).assign(folder=folder, force=force, temp=temp, perturbation=perturbation_table[perturbation])
                all_pmf_list.append(data)

data = pd.concat(all_pmf_list).dropna().reset_index()
data.to_feather("/Users/weilu/Research/data/pulling/nov06_pmf.feather")


    

In [20]:

    

all_pmf_list = []
all_evpb_list = []
for folder in folder_list:
    for force in force_list:
        for temp in temp_list:
            for perturbation in perturbation_list:

                # pmf 
                if perturbation == 0:
                    location = pre + f"{folder}/1d_dis/t_all/force_{force}/pmf-{temp}.dat"
                else:
                    location = pre + \
                    "{}/1d_dis/t_all/force_{}/perturbation-{}-pmf-{}.dat".format(folder, force, perturbation, temp)

                name_list = ["f", "df", "e", "s"]
                names = ["bin", "x"] + name_list
                data = pd.read_table(location, skiprows=2, sep='\s+', names=names).assign(folder=folder, force=force, temp=temp, perturbation=perturbation_table[perturbation])
                all_pmf_list.append(data)

data = pd.concat(all_pmf_list).dropna().reset_index()
data.to_feather("/Users/weilu/Research/data/pulling/nov06_pmf.feather")


    

In [ ]:

    




    

In [114]:

    

all_pmf_list = []
all_evpb_list = []
for folder in folder_list:
    for temp in temp_list:
        for perturbation in perturbation_list:
            
            # evpb
            if perturbation == 0:
                location = pre + "{}/1d_qw/t_all/force_0.0/evpb-{}.dat".format(folder, temp)
            else:
                location = pre + \
                "{}/1d_qw/t_all/force_0.0/perturbation-{}-evpb-{}.dat".format(folder, perturbation, temp)

            name_list = ["Lipid", "Go", "Mem", "Rg"]
            names = ["bin", "q"] + name_list
            data = pd.read_table(location, skiprows=1, sep='\s+', names=names).assign(folder=folder, temp=temp, perturbation=perturbation_table[perturbation])
            all_evpb_list.append(data)
            
            # pmf 
            if perturbation == 0:
                location = pre + "{}/1d_qw/t_all/force_0.0/pmf-{}.dat".format(folder, temp)
            else:
                location = pre + \
                "{}/1d_qw/t_all/force_0.0/perturbation-{}-pmf-{}.dat".format(folder, perturbation, temp)

            name_list = ["f", "df", "e", "s"]
            names = ["bin", "q"] + name_list
            data = pd.read_table(location, skiprows=2, sep='\s+', names=names).assign(folder=folder, temp=temp, perturbation=perturbation_table[perturbation])
            all_pmf_list.append(data)

data = pd.concat(all_pmf_list).dropna().reset_index()
data.to_feather("/Users/weilu/Research/data/pulling/oct31_pmf_qw.feather")

data = pd.concat(all_evpb_list).dropna().reset_index()
data.to_feather("/Users/weilu/Research/data/pulling/oct31_evpb_qw.feather")


    

In [77]:

    

pre = "/Users/weilu/Research/server/oct_2017/23oct/"
folder_list = [
   'memb_3_rg_0.1_lipid_1_extended',
    'memb_3_rg_0.1_lipid_1_topology'
]
all_data_list = []
temp_list = [450, 500, 550]
perturbation_list = [0, 1, 2, 3, 4]
for folder in folder_list:
    for temp in temp_list:
        for perturbation in perturbation_list:
            if perturbation == 0:
                location = pre + "{}/1d_dis/t_all/force_0.0/pmf-{}.dat".format(folder, temp)
            else:
                location = pre + \
                "{}/1d_dis/t_all/force_0.0/perturbation-{}-pmf-{}.dat".format(folder, perturbation, temp)
#         location = pre + "{}/1d_dis/t_all/force_0.0/pmf-{}.dat".format(folder, temp)
            name_list = ["f", "df", "e", "s"]
            names = ["bin", "x"] + name_list
            data = pd.read_table(location, skiprows=2, sep='\s+', names=names).assign(folder=folder, temp=temp, perturbation=perturbation)
            all_data_list.append(data)
data = pd.concat(all_data_list)
data = data.dropna().reset_index()
data.to_feather("/Users/weilu/Research/data/pulling/oct31_pmf.feather")


    

In [71]:

    

fig, axes = plt.subplots(1, 2, figsize=(8,6))
i = 0
for label, group in data.groupby('folder'):
#     processed_data = group - group.mean()
#     processed_data["x"] = data["x"]
    
    group.plot('x', "f", ax=axes[i], label=label)
    i = i + 1


    

In [86]:

    

pre = "/Users/weilu/Research/server/oct_2017/23oct/"
folder_list = [
   'memb_3_rg_0.1_lipid_1_extended',
    'memb_3_rg_0.1_lipid_1_topology'
]
all_data_list = []
for folder in folder_list:
    location = pre + "{}/1d_qw/t_all/force_0.0/evpb-500.dat".format(folder)
    name_list = ["Lipid", "Go", "Mem", "Rg"]
    names = ["bin", "x"] + name_list
    data = pd.read_table(location, skiprows=1, sep='\s+', names=names).assign(folder=folder)
    all_data_list.append(data)
data = pd.concat(all_data_list)
data = data.dropna()


    

In [87]:

    

fig, axes = plt.subplots(1, 2, figsize=(8,6))
i = 0
for label, group in data.groupby('folder'):
#     processed_data = group - group.mean()
#     processed_data["x"] = data["x"]
    for name in name_list:
        group.plot('x', name, ax=axes[i], ylim=(-550,550), label=label)
    i = i + 1


    

In [ ]:

    

plotcontour.py pmf-400.dat -xmax 1 -xmin 0 -ymin 0 -ymax 150"


    

In [63]:

    

location = "/Users/weilu/Research/davinci/extended/2d_qw_dis/t_all/force_0.0/"
filename = location + "pmf-500.dat"
x = 1
y = 2
z = 3
xmin, xmax = 0, 1
ymin, ymax = 0, 150
zmin, zmax = 0, 30
xlabel, ylabel = "xlabel", "ylabel"
title = "title"
titlefontsize = 28


    

In [98]:

    

location = "/Users/weilu/Research/server/oct_2017/23oct/memb_3_rg_0.1_lipid_1_topology/2d_qw_dis/t_all/force_0.0/"
filename = location + "pmf-500.dat"
x = 1
y = 2
z = 3
xmin, xmax = 0, 1
ymin, ymax = 0, 150
zmin, zmax = 0, 30
xlabel, ylabel = "xlabel", "ylabel"
title = "title"
titlefontsize = 28


    

In [99]:

    

location = "/Users/weilu/Research/server/oct_2017/23oct/memb_3_rg_0.1_lipid_1_topology/2d_qw_dis/t_all/force_0.0/"
arguments ={
    filename : location + "pmf-500.dat",
    x : 1,
    y : 2,
    z : 3,
    xmin, xmax : 0, 1,
    ymin, ymax : 0, 150,
    zmin, zmax : 0, 30,
    xlabel, ylabel : "xlabel", "ylabel",
    title : "title",
    titlefontsize : 28
}


    

    




  File "<ipython-input-99-0e619d8b795c>", line 7
    xmin, xmax : 0, 1,
        ^
SyntaxError: invalid syntax

In [64]:

    

def plot2d(**kargs):
    data = np.loadtxt(filename)
    data = data[~np.isnan(data).any(axis=1)] # remove rows with nan
    data = data[~(data[:,z] > zmax)] # remove rows of data for z not in [zmin zmax]
    data = data[~(data[:,z] < zmin)]

    xi = np.linspace(min(data[:,x]), max(data[:,x]), 20)
    yi = np.linspace(min(data[:,y]), max(data[:,y]), 20)
    zi = griddata((data[:,x], data[:,y]), data[:,z], (xi[None,:], yi[:,None]), method='linear')
    # plt.contour(xi, yi, zi, 50, linewidths=0.25,colors='k')
    jet = cm = plt.get_cmap('jet')
    print(jet)
    # plt.contourf(xi, yi, zi, 20, cmap='rainbow')
    plt.contourf(xi, yi, zi, 30, cmap='jet')
    plt.xlim(xmin, xmax)
    plt.ylim(ymin, ymax)
    plt.clim(zmin, zmax)
    plt.colorbar()

    plt.xlabel(xlabel)
    plt.ylabel(ylabel)
    plt.title(title, y=1.02, fontsize = titlefontsize)
    #plt.tight_layout()
    #plt.axis('equal')
    #plt.axes().set_aspect('equal')
    #plt.axes().set_aspect('scaled')
    # plt.savefig(args.outname, dpi=args.dpi, bbox_inches='tight')
    plt.show()


    

In [65]:

    

location = "/Users/weilu/Research/server/oct_2017/23oct/memb_3_rg_0.1_lipid_1_topology/2d_qw_dis/t_all/force_0.0/"
filename = location + "pmf-550.dat"
data = np.loadtxt(filename)
data = data[~np.isnan(data).any(axis=1)] # remove rows with nan
data = data[~(data[:,z] > zmax)] # remove rows of data for z not in [zmin zmax]
data = data[~(data[:,z] < zmin)]

xi = np.linspace(min(data[:,x]), max(data[:,x]), 20)
yi = np.linspace(min(data[:,y]), max(data[:,y]), 20)
zi = griddata((data[:,x], data[:,y]), data[:,z], (xi[None,:], yi[:,None]), method='linear')
# plt.contour(xi, yi, zi, 50, linewidths=0.25,colors='k')
jet = cm = plt.get_cmap('jet')
print(jet)
# plt.contourf(xi, yi, zi, 20, cmap='rainbow')
plt.figure()
plt.contourf(xi, yi, zi, 30, cmap='jet')
plt.xlim(xmin, xmax)
plt.clim(zmin, zmax)
plt.colorbar()

plt.xlabel(xlabel)
plt.ylabel(ylabel)
plt.title(title, y=1.02, fontsize = titlefontsize)
#plt.tight_layout()
#plt.axis('equal')
#plt.axes().set_aspect('equal')
#plt.axes().set_aspect('scaled')
# plt.savefig(args.outname, dpi=args.dpi, bbox_inches='tight')
plt.show()


    

    




---------------------------------------------------------------------------
FileNotFoundError                         Traceback (most recent call last)
<ipython-input-65-6c95b2873410> in <module>()
      1 location = "/Users/weilu/Research/server/oct_2017/23oct/memb_3_rg_0.1_lipid_1_topology/2d_qw_dis/t_all/force_0.0/"
      2 filename = location + "pmf-550.dat"
----> 3 data = np.loadtxt(filename)
      4 data = data[~np.isnan(data).any(axis=1)] # remove rows with nan
      5 data = data[~(data[:,z] > zmax)] # remove rows of data for z not in [zmin zmax]

~/anaconda3/lib/python3.6/site-packages/numpy/lib/npyio.py in loadtxt(fname, dtype, comments, delimiter, converters, skiprows, usecols, unpack, ndmin)
    896                 fh = iter(open(fname, 'U'))
    897             else:
--> 898                 fh = iter(open(fname))
    899         else:
    900             fh = iter(fname)

FileNotFoundError: [Errno 2] No such file or directory: '/Users/weilu/Research/server/oct_2017/23oct/memb_3_rg_0.1_lipid_1_topology/2d_qw_dis/t_all/force_0.0/pmf-550.dat'

In [ ]:

    

plot2d()


    

In [9]:

    

location = "/Users/weilu/Research/davinci/dec_2017/dec04_no_side_2/no_side_contraint_memb_3_rg_0.4_lipid_0.6_extended_350-550/2d_qc_dis/force_0.0/"
filename = location + "pmf-520.dat"
x = 1
y = 2
z = 3
xmin, xmax = 0, 1
ymin, ymax = 0, 150
zmin, zmax = 0, 15
xlabel, ylabel = "xlabel", "ylabel"
title = "title"
titlefontsize = 28

data = np.loadtxt(filename)
data = data[~np.isnan(data).any(axis=1)] # remove rows with nan
data = data[~(data[:,z] > zmax)] # remove rows of data for z not in [zmin zmax]
data = data[~(data[:,z] < zmin)]

xi = np.linspace(min(data[:,x]), max(data[:,x]), 20)
yi = np.linspace(min(data[:,y]), max(data[:,y]), 20)
zi = griddata((data[:,x], data[:,y]), data[:,z], (xi[None,:], yi[:,None]), method='linear')
# plt.contour(xi, yi, zi, 50, linewidths=0.25,colors='k')
jet = cm = plt.get_cmap('jet')
print(jet)
# plt.contourf(xi, yi, zi, 20, cmap='rainbow')
plt.figure()
plt.contourf(xi, yi, zi, 30, cmap='jet')
plt.xlim(xmin, xmax)
plt.clim(zmin, zmax)
plt.colorbar()

plt.xlabel(xlabel)
plt.ylabel(ylabel)
plt.title(title, y=1.02, fontsize = titlefontsize)
#plt.tight_layout()
#plt.axis('equal')
#plt.axes().set_aspect('equal')
#plt.axes().set_aspect('scaled')
# plt.savefig(args.outname, dpi=args.dpi, bbox_inches='tight')
plt.show()


    

    




<matplotlib.colors.LinearSegmentedColormap object at 0x10aefb6a0>






    















    

In [98]:

    

location = "/Users/weilu/Research/davinci/all_freeEnergy_calculation_nov11/next_gen_native_based_memb_3_rg_0.4_lipid_0.6_topology/2d_qw_dis/force_0.0/"
filename = location + "pmf-490.dat"
x = 1
y = 2
z = 3
xmin, xmax = 0, 1
ymin, ymax = 0, 150
zmin, zmax = 0, 30
xlabel, ylabel = "xlabel", "ylabel"
title = "title"
titlefontsize = 28

data = np.loadtxt(filename)
data = data[~np.isnan(data).any(axis=1)] # remove rows with nan
data = data[~(data[:,z] > zmax)] # remove rows of data for z not in [zmin zmax]
data = data[~(data[:,z] < zmin)]

xi = np.linspace(min(data[:,x]), max(data[:,x]), 20)
yi = np.linspace(min(data[:,y]), max(data[:,y]), 20)
zi = griddata((data[:,x], data[:,y]), data[:,z], (xi[None,:], yi[:,None]), method='linear')
# plt.contour(xi, yi, zi, 50, linewidths=0.25,colors='k')
jet = cm = plt.get_cmap('jet')
print(jet)
# plt.contourf(xi, yi, zi, 20, cmap='rainbow')
plt.figure()
plt.contourf(xi, yi, zi, 30, cmap='jet')
plt.xlim(xmin, xmax)
plt.clim(zmin, zmax)
plt.colorbar()

plt.xlabel(xlabel)
plt.ylabel(ylabel)
plt.title(title, y=1.02, fontsize = titlefontsize)
#plt.tight_layout()
#plt.axis('equal')
#plt.axes().set_aspect('equal')
#plt.axes().set_aspect('scaled')
# plt.savefig(args.outname, dpi=args.dpi, bbox_inches='tight')
plt.show()


    

    




<matplotlib.colors.LinearSegmentedColormap object at 0x10f383ef0>






    















    

In [96]:

    

location = "/Users/weilu/Research/davinci/nov_14_all_freeEnergy_calculation/stronger_bias_for_expand_distance_rgWidth_memb_3_rg_0.1_lipid_1_extended/2d_qw_dis/force_0.0/"
filename = location + "pmf-500.dat"
x = 1
y = 2
z = 3
xmin, xmax = 0, 1
ymin, ymax = 0, 150
zmin, zmax = 0, 30
xlabel, ylabel = "xlabel", "ylabel"
title = "title"
titlefontsize = 28

data = np.loadtxt(filename)
data = data[~np.isnan(data).any(axis=1)] # remove rows with nan
data = data[~(data[:,z] > zmax)] # remove rows of data for z not in [zmin zmax]
data = data[~(data[:,z] < zmin)]

xi = np.linspace(min(data[:,x]), max(data[:,x]), 20)
yi = np.linspace(min(data[:,y]), max(data[:,y]), 20)
zi = griddata((data[:,x], data[:,y]), data[:,z], (xi[None,:], yi[:,None]), method='linear')
# plt.contour(xi, yi, zi, 50, linewidths=0.25,colors='k')
jet = cm = plt.get_cmap('jet')
print(jet)
# plt.contourf(xi, yi, zi, 20, cmap='rainbow')
plt.figure()
plt.contourf(xi, yi, zi, 30, cmap='jet')
plt.xlim(xmin, xmax)
plt.clim(zmin, zmax)
plt.colorbar()

plt.xlabel(xlabel)
plt.ylabel(ylabel)
plt.title(title, y=1.02, fontsize = titlefontsize)
#plt.tight_layout()
#plt.axis('equal')
#plt.axes().set_aspect('equal')
#plt.axes().set_aspect('scaled')
# plt.savefig(args.outname, dpi=args.dpi, bbox_inches='tight')
plt.show()


    

    




<matplotlib.colors.LinearSegmentedColormap object at 0x10f383ef0>






    















    

In [24]:

    

location = "/Users/weilu/Research/davinci/all_freeEnergy_calculation_nov11/next_gen_native_based_memb_3_rg_0.4_lipid_0.6_extended/low_t_2d_qw_dis/force_0.0/"
filename = location + "pmf-350.dat"
x = 1
y = 2
z = 3
xmin, xmax = 0, 1
ymin, ymax = 0, 150
zmin, zmax = 0, 30
xlabel, ylabel = "xlabel", "ylabel"
title = "title"
titlefontsize = 28

data = np.loadtxt(filename)
data = data[~np.isnan(data).any(axis=1)] # remove rows with nan
data = data[~(data[:,z] > zmax)] # remove rows of data for z not in [zmin zmax]
data = data[~(data[:,z] < zmin)]

xi = np.linspace(min(data[:,x]), max(data[:,x]), 20)
yi = np.linspace(min(data[:,y]), max(data[:,y]), 20)
zi = griddata((data[:,x], data[:,y]), data[:,z], (xi[None,:], yi[:,None]), method='linear')
# plt.contour(xi, yi, zi, 50, linewidths=0.25,colors='k')
jet = cm = plt.get_cmap('jet')
print(jet)
# plt.contourf(xi, yi, zi, 20, cmap='rainbow')
plt.figure()
plt.contourf(xi, yi, zi, 30, cmap='jet')
plt.xlim(xmin, xmax)
plt.clim(zmin, zmax)
plt.colorbar()

plt.xlabel(xlabel)
plt.ylabel(ylabel)
plt.title(title, y=1.02, fontsize = titlefontsize)
#plt.tight_layout()
#plt.axis('equal')
#plt.axes().set_aspect('equal')
#plt.axes().set_aspect('scaled')
# plt.savefig(args.outname, dpi=args.dpi, bbox_inches='tight')
plt.show()


    

    




<matplotlib.colors.LinearSegmentedColormap object at 0x10f383ef0>






    















    

In [23]:

    

location = "/Users/weilu/Research/davinci/all_freeEnergy_calculation_nov11/next_gen_native_based_memb_3_rg_0.4_lipid_0.6_extended/2d_qw_dis/force_0.0/"
filename = location + "pmf-450.dat"
x = 1
y = 2
z = 3
xmin, xmax = 0, 1
ymin, ymax = 0, 150
zmin, zmax = 0, 30
xlabel, ylabel = "xlabel", "ylabel"
title = "title"
titlefontsize = 28

data = np.loadtxt(filename)
data = data[~np.isnan(data).any(axis=1)] # remove rows with nan
data = data[~(data[:,z] > zmax)] # remove rows of data for z not in [zmin zmax]
data = data[~(data[:,z] < zmin)]

xi = np.linspace(min(data[:,x]), max(data[:,x]), 20)
yi = np.linspace(min(data[:,y]), max(data[:,y]), 20)
zi = griddata((data[:,x], data[:,y]), data[:,z], (xi[None,:], yi[:,None]), method='linear')
# plt.contour(xi, yi, zi, 50, linewidths=0.25,colors='k')
jet = cm = plt.get_cmap('jet')
print(jet)
# plt.contourf(xi, yi, zi, 20, cmap='rainbow')
plt.figure()
plt.contourf(xi, yi, zi, 30, cmap='jet')
plt.xlim(xmin, xmax)
plt.clim(zmin, zmax)
plt.colorbar()

plt.xlabel(xlabel)
plt.ylabel(ylabel)
plt.title(title, y=1.02, fontsize = titlefontsize)
#plt.tight_layout()
#plt.axis('equal')
#plt.axes().set_aspect('equal')
#plt.axes().set_aspect('scaled')
# plt.savefig(args.outname, dpi=args.dpi, bbox_inches='tight')
plt.show()


    

    




<matplotlib.colors.LinearSegmentedColormap object at 0x10f383ef0>






    















    

In [74]:

    

location = "/Users/weilu/Research/davinci/extended/2d_qw_dis/t_all/force_0.1/"
filename = location + "pmf-550.dat"
x = 1
y = 2
z = 3
xmin, xmax = 0, 1
ymin, ymax = 0, 150
zmin, zmax = 0, 30
xlabel, ylabel = "xlabel", "ylabel"
title = "title"
titlefontsize = 28

data = np.loadtxt(filename)
data = data[~np.isnan(data).any(axis=1)] # remove rows with nan
data = data[~(data[:,z] > zmax)] # remove rows of data for z not in [zmin zmax]
data = data[~(data[:,z] < zmin)]

xi = np.linspace(min(data[:,x]), max(data[:,x]), 20)
yi = np.linspace(min(data[:,y]), max(data[:,y]), 20)
zi = griddata((data[:,x], data[:,y]), data[:,z], (xi[None,:], yi[:,None]), method='linear')
# plt.contour(xi, yi, zi, 50, linewidths=0.25,colors='k')
jet = cm = plt.get_cmap('jet')
print(jet)
# plt.contourf(xi, yi, zi, 20, cmap='rainbow')
plt.figure()
plt.contourf(xi, yi, zi, 30, cmap='jet')
plt.xlim(xmin, xmax)
plt.clim(zmin, zmax)
plt.colorbar()

plt.xlabel(xlabel)
plt.ylabel(ylabel)
plt.title(title, y=1.02, fontsize = titlefontsize)
#plt.tight_layout()
#plt.axis('equal')
#plt.axes().set_aspect('equal')
#plt.axes().set_aspect('scaled')
# plt.savefig(args.outname, dpi=args.dpi, bbox_inches='tight')
plt.show()