This is a temporary script file.
"""
import matplotlib.pyplot as plt
import numpy as np
filename = 'chromo2019_11_13_time_15_35'
velname = filename + '_vels_forces.txt'
pdbname = filename + '.pdb'
from Python_functions.import_vel_force import read_file
from Python_functions.import_pdb import import_trajectories_from_pdb
#vel_data, time = read_file(velname)
data, time = import_trajectories_from_pdb(pdbname)
from scipy.spatial.distance import pdist, squareform
d = squareform(pdist(data[151, 162:, :]))
ind1, ind2 = np.where(d < 2)
unique = (ind1 < ind2)
ind1 = ind1[unique]
ind2 = ind2[unique]
for i1, i2 in zip(ind1, ind2):
if abs(i1 - i2) != 1:
print(i1, i2)
d = d < 2
fig, ax = plt.subplots()
soft_pdbs = ['chromo2019_12_06_time_22_53.pdb']
hard_pdbs = [
'chromo2019_12_18_time_23_20.pdb', 'chromo2019_12_19_time_17_48.pdb'
]
#pdbname = ['chromo2019_12_06_time_22_53.pdb']
#pdbname = str(sys.argv[1]) + '.pdb'
longname = str(sys.argv[1] + '.pdb')
fig, (ax1, ax2) = plt.subplots(1, 2, figsize=(12, 5.5))
fig2, ax3 = plt.subplots(1, 1)
mem_nodes = 162
ini_t = int(400 / 0.4)
fin_t = int(800 / 0.4)
data, time = import_trajectories_from_pdb(soft_pdbs[0])
sr2n = [R2N(data[ini_t:fin_t, mem_nodes:1000 + mem_nodes, :], None, ax2)]
sr2n = np.concatenate(
(sr2n,
[R2N(data[ini_t:fin_t, mem_nodes + 1000:2000 + mem_nodes, :], None,
ax2)]))
sr2n = np.concatenate(
(sr2n,
[R2N(data[ini_t:fin_t, mem_nodes + 2000:3000 + mem_nodes, :], None,
ax2)]))
sr2n = np.concatenate(
(sr2n, [R2N(data[ini_t:fin_t, mem_nodes + 3000:, :], None, ax2)]))
data, time = import_trajectories_from_pdb(hard_pdbs[0])