In [1]:
import os
import sys
import random
import time
from random import seed, randint
import argparse
import platform
from datetime import datetime
import imp
import numpy as np
import fileinput
from itertools import product
import pandas as pd
from scipy.interpolate import griddata
from scipy.interpolate import interp2d
import seaborn as sns
from os import listdir
import matplotlib.pyplot as plt
import seaborn as sns
from scipy.interpolate import griddata
import matplotlib as mpl
# sys.path.insert(0,'..')
# from notebookFunctions import *
# from .. import notebookFunctions
from Bio.PDB.Polypeptide import one_to_three
from Bio.PDB.Polypeptide import three_to_one
from Bio.PDB.PDBParser import PDBParser
from pyCodeLib import *
from small_script.myFunctions import *
from collections import defaultdict
%matplotlib inline
# plt.rcParams['figure.figsize'] = (10,6.180) #golden ratio
# %matplotlib notebook
%load_ext autoreload
%autoreload 2
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plt.rcParams['figure.figsize'] = [16.18033, 10] #golden ratio
plt.rcParams['figure.facecolor'] = 'w'
plt.rcParams['figure.dpi'] = 100
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dataset = {}
dataset["may13"] = ['1r69', '3icb', '256b', '4cpv', '2mhr', '1mba', '2fha', '1fc2', '1enh', '2gb1', '2cro', '1ctf', '4icb']
pdb_list = dataset["may13"]
folder_list = []
folder_list_1 = ["original", "multi_iter0"]
folder_list_2 = ["multi_constant_tc_frag", "multi_constant_tc", "original_fragMemory", "multi_iter0_fragMemory"]
folder_list_3 = ["iter1_30", "iter1_90", "iter1_30_frag", "iter1_90_frag"]
folder_list_4 = ["iter2_30", "iter2_90", "iter2_30_frag", "iter2_90_frag"]
folder_list_5 = ["iter3_30", "iter3_90", "iter3_30_frag", "iter3_90_frag"]
folder_list_6 = ["iter1_30_correct", "iter1_30_correct_frag", "iter1_80_correct", "iter1_80_correct_frag"]
folder_list_7 = ["iter2_30_correct", "iter2_30_correct_frag", "iter2_80_correct", "iter2_80_correct_frag"]
folder_list_8 = ["iter3_30_correct", "iter3_30_correct_frag", "iter3_80_correct", "iter3_80_correct_frag"]
In [35]:
folder_list = []
# folder_list = folder_list_1 + folder_list_2
# folder_list = folder_list_1 + folder_list_2
# folder_list += folder_list_3
# folder_list += folder_list_4
# folder_list += folder_list_5
folder_list += folder_list_8
# folder_list = [a for a in folder_list if a[-4:] == "frag"]
simulation_location_list_dic = defaultdict(list)
for p in pdb_list:
# name = p.lower()[:4]
name = p
simulation_location_list_dic[name] += folder_list
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decoy_n = 2000
n = len(folder_list)
os.chdir("/Users/weilu/Research/server/may_2019/iteration_optimization/optimization/")
# gamma_file_name = "gamma_iter1_combined_mar06.dat"
gamma_file_name = "/Users/weilu/Research/server/may_2019/gammas/original_gamma"
data = validate_hamiltonian_wei("phi_list_contact.txt", "proteins_name_list.txt", gamma_file_name, "lammps", n*decoy_n, mode=2, simulation_location_list_dic=simulation_location_list_dic)
data
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In [38]:
decoy_n = 200
all_data = []
n = len(folder_list)
os.chdir("/Users/weilu/Research/server/may_2019/iteration_optimization/optimization/")
for g_name in ["original_gamma", "multi_constraint_tc_constant", "iter1_cutoff_600", "iter2_cutoff_600", "iter3_cutoff_600", "iter4_cutoff_600", "iter4_cutoff_644", "iter4_cutoff_644_constant_tc"]:
gamma_file_name = f"/Users/weilu/Research/server/may_2019/correct_gammas/{g_name}"
data = validate_hamiltonian_wei("phi_list_contact.txt", "proteins_name_list.txt", gamma_file_name, "lammps", n*decoy_n, mode=2, simulation_location_list_dic=simulation_location_list_dic)
all_data.append(data.assign(Gamma=g_name))
data = pd.concat(all_data).reset_index()
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data.sort_values("Protein").query("Protein == '1mba'")
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In [30]:
decoy_n = 2000
all_data = []
n = len(folder_list)
os.chdir("/Users/weilu/Research/server/may_2019/iteration_optimization/optimization/")
for g_name in ["iter4_cutoff_600", "iter4_cutoff_644", "iter4_cutoff_644_constant_tc"]:
gamma_file_name = f"/Users/weilu/Research/server/may_2019/correct_gammas/{g_name}"
data = validate_hamiltonian_wei("phi_list_contact.txt", "proteins_name_list.txt", gamma_file_name, "lammps", n*decoy_n, mode=2, simulation_location_list_dic=simulation_location_list_dic)
all_data.append(data.assign(Gamma=g_name))
data = pd.concat(all_data).reset_index()
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data_1_2 = data
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fg = sns.FacetGrid(data=data, hue='Gamma', aspect=3)
fg.map(plt.scatter, 'Protein', 'Z_scores').add_legend()
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data.sort_values(["Protein", "Gamma"])
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data.sort_values(["Protein", "Gamma"])
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y_show = "Z_scores"
g = sns.FacetGrid(a, col="Name",col_wrap=4, hue="Folder", sharey=False, sharex=False)
g = (g.map(plt.scatter, "Qw", y_show, alpha=0.5).add_legend())
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data
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decoy_n = 200
n = len(folder_list)
os.chdir("/Users/weilu/Research/server/may_2019/iteration_optimization/optimization/")
# gamma_file_name = "gamma_iter1_combined_mar06.dat"
gamma_file_name = "/Users/weilu/Research/server/may_2019/gammas/original_gamma"
data = validate_hamiltonian_wei("phi_list_contact.txt", "proteins_name_list.txt", gamma_file_name, "lammps", n*decoy_n, mode=2, simulation_location_list_dic=simulation_location_list_dic)
data
Out[6]:
In [36]:
decoy_n = 2000
n = len(folder_list)
os.chdir("/Users/weilu/Research/server/may_2019/iter1_optimization_decoys_2000/optimization_3")
# gamma_file_name = "gamma_iter1_combined_mar06.dat"
gamma_file_name = "/Users/weilu/Research/server/may_2019/gammas/iter1_constant_tc_filtered"
data = validate_hamiltonian_wei("phi_list_contact.txt", "proteins_name_list.txt", gamma_file_name, "lammps", n*decoy_n, mode=2, simulation_location_list_dic=simulation_location_list_dic)
data
Out[36]:
In [37]:
folder_list = []
# folder_list = folder_list_1 + folder_list_2
# folder_list = folder_list_1 + folder_list_2
folder_list += folder_list_3
# folder_list += folder_list_4
# folder_list += folder_list_5
# folder_list = [a for a in folder_list if a[-4:] == "frag"]
simulation_location_list_dic = defaultdict(list)
for p in pdb_list:
# name = p.lower()[:4]
name = p
simulation_location_list_dic[name] += folder_list
In [38]:
decoy_n = 2000
n = len(folder_list)
os.chdir("/Users/weilu/Research/server/may_2019/iter1_optimization_decoys_2000/optimization_3")
# gamma_file_name = "gamma_iter1_combined_mar06.dat"
gamma_file_name = "/Users/weilu/Research/server/may_2019/gammas/original_gamma"
data = validate_hamiltonian_wei("phi_list_contact.txt", "proteins_name_list.txt", gamma_file_name, "lammps", n*decoy_n, mode=2, simulation_location_list_dic=simulation_location_list_dic)
data
Out[38]:
In [39]:
decoy_n = 2000
n = len(folder_list)
os.chdir("/Users/weilu/Research/server/may_2019/iter1_optimization_decoys_2000/optimization_3")
# gamma_file_name = "gamma_iter1_combined_mar06.dat"
gamma_file_name = "/Users/weilu/Research/server/may_2019/gammas/iter1_constant_tc_filtered"
data = validate_hamiltonian_wei("phi_list_contact.txt", "proteins_name_list.txt", gamma_file_name, "lammps", n*decoy_n, mode=2, simulation_location_list_dic=simulation_location_list_dic)
data
Out[39]:
In [40]:
decoy_n = 2000
n = len(folder_list)
os.chdir("/Users/weilu/Research/server/may_2019/iter1_optimization_decoys_2000/optimization_3")
# gamma_file_name = "gamma_iter1_combined_mar06.dat"
gamma_file_name = "/Users/weilu/Research/server/may_2019/gammas/iter2_constant_tc_cutoff600"
data = validate_hamiltonian_wei("phi_list_contact.txt", "proteins_name_list.txt", gamma_file_name, "lammps", n*decoy_n, mode=2, simulation_location_list_dic=simulation_location_list_dic)
data
Out[40]:
In [44]:
folder_list = []
# folder_list = folder_list_1 + folder_list_2
# folder_list = folder_list_1 + folder_list_2
# folder_list += folder_list_3
folder_list += folder_list_4
# folder_list += folder_list_5
folder_list = [a for a in folder_list if a[-4:] == "frag"]
print(folder_list)
simulation_location_list_dic = defaultdict(list)
for p in pdb_list:
# name = p.lower()[:4]
name = p
simulation_location_list_dic[name] += folder_list
In [45]:
decoy_n = 2000
n = len(folder_list)
os.chdir("/Users/weilu/Research/server/may_2019/iter1_optimization_decoys_2000/optimization_3")
# gamma_file_name = "gamma_iter1_combined_mar06.dat"
gamma_file_name = "/Users/weilu/Research/server/may_2019/gammas/iter2_constant_tc_cutoff600"
data = validate_hamiltonian_wei("phi_list_contact.txt", "proteins_name_list.txt", gamma_file_name, "lammps", n*decoy_n, mode=2, simulation_location_list_dic=simulation_location_list_dic)
data
Out[45]:
In [46]:
decoy_n = 2000
n = len(folder_list)
os.chdir("/Users/weilu/Research/server/may_2019/iter1_optimization_decoys_2000/optimization_3")
# gamma_file_name = "gamma_iter1_combined_mar06.dat"
gamma_file_name = "/Users/weilu/Research/server/may_2019/gammas/iter_2_30"
data = validate_hamiltonian_wei("phi_list_contact.txt", "proteins_name_list.txt", gamma_file_name, "lammps", n*decoy_n, mode=2, simulation_location_list_dic=simulation_location_list_dic)
data
Out[46]:
In [47]:
decoy_n = 2000
n = len(folder_list)
os.chdir("/Users/weilu/Research/server/may_2019/iter1_optimization_decoys_2000/optimization_3")
# gamma_file_name = "gamma_iter1_combined_mar06.dat"
gamma_file_name = "/Users/weilu/Research/server/may_2019/gammas/iter_2_30"
data = validate_hamiltonian_wei("phi_list_contact.txt", "proteins_name_list.txt", gamma_file_name, "lammps", n*decoy_n, mode=2, simulation_location_list_dic=simulation_location_list_dic)
data
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In [32]:
decoy_n = 2000
n = len(folder_list)
os.chdir("/Users/weilu/Research/server/may_2019/iter1_optimization_decoys_2000/optimization_3")
# gamma_file_name = "gamma_iter1_combined_mar06.dat"
gamma_file_name = "/Users/weilu/Research/server/may_2019/gammas/original_gamma"
data = validate_hamiltonian_wei("phi_list_contact.txt", "proteins_name_list.txt", gamma_file_name, "lammps", n*decoy_n, mode=2, simulation_location_list_dic=simulation_location_list_dic)
data
Out[32]:
In [17]:
os.chdir("/Users/weilu/Research/server/may_2019/iter1_optimization_decoys_2000/optimization_3")
# gamma_file_name = "gamma_iter1_combined_mar06.dat"
gamma_file_name = "/Users/weilu/Research/server/may_2019/iter1_optimization_decoys_2000/optimization_3/gammas/cutoff_600"
data = validate_hamiltonian_wei("phi_list_contact.txt", "proteins_name_list.txt", gamma_file_name, "lammps", n*decoy_n, mode=2, simulation_location_list_dic=simulation_location_list_dic)
data
Out[17]:
In [19]:
decoy_n = 2000
n = len(folder_list)
os.chdir("/Users/weilu/Research/server/may_2019/iter1_optimization_decoys_2000/optimization_3")
# gamma_file_name = "gamma_iter1_combined_mar06.dat"
gamma_file_name = "/Users/weilu/Research/server/may_2019/iter1_optimization_decoys_2000/optimization_3/gammas/cutoff_600"
data = validate_hamiltonian_wei("phi_list_contact.txt", "proteins_name_list.txt", gamma_file_name, "lammps", n*decoy_n, mode=2, simulation_location_list_dic=simulation_location_list_dic)
data
Out[19]:
In [25]:
decoy_n = 2000
n = len(folder_list)
os.chdir("/Users/weilu/Research/server/may_2019/iter1_optimization_decoys_2000/optimization_3")
# gamma_file_name = "gamma_iter1_combined_mar06.dat"
# gamma_file_name = "/Users/weilu/Research/server/may_2019/iter1_optimization_decoys_2000/optimization_3/gammas/cutoff_600"
gamma_file_name = "/Users/weilu/Research/server/may_2019/gammas/multi_constraint_tc_constant"
data = validate_hamiltonian_wei("phi_list_contact.txt", "proteins_name_list.txt", gamma_file_name, "lammps", n*decoy_n, mode=2, simulation_location_list_dic=simulation_location_list_dic)
data
Out[25]:
In [30]:
decoy_n = 500
n = len(folder_list)
os.chdir("/Users/weilu/Research/server/may_2019/iter1_optimization_decoys_2000/optimization_3")
# gamma_file_name = "gamma_iter1_combined_mar06.dat"
# gamma_file_name = "/Users/weilu/Research/server/may_2019/iter1_optimization_decoys_2000/optimization_3/gammas/cutoff_600"
gamma_file_name = "/Users/weilu/Research/server/may_2019/gammas/multi_constraint_tc_constant"
data = validate_hamiltonian_wei("phi_list_contact.txt", "proteins_name_list.txt", gamma_file_name, "lammps", n*decoy_n, mode=2, simulation_location_list_dic=simulation_location_list_dic)
data
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In [29]:
decoy_n = 50
n = len(folder_list)
os.chdir("/Users/weilu/Research/server/may_2019/iter1_optimization_decoys_2000/optimization_3")
# gamma_file_name = "gamma_iter1_combined_mar06.dat"
# gamma_file_name = "/Users/weilu/Research/server/may_2019/iter1_optimization_decoys_2000/optimization_3/gammas/cutoff_600"
gamma_file_name = "/Users/weilu/Research/server/may_2019/gammas/multi_constraint_tc_constant"
data = validate_hamiltonian_wei("phi_list_contact.txt", "proteins_name_list.txt", gamma_file_name, "lammps", n*decoy_n, mode=2, simulation_location_list_dic=simulation_location_list_dic)
data
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