# global_cutoff = float(sys.argv[3])
# carpeta destino
directory = '/home/serch/pdbmani/Serch/pdbs/'
# Ya moficamos la cadenaa darle atomos
chain1 = 'A'
chain2 = 'A'
global_cutoff = 7 # modificar si quieres cambiar de cutoff!!! en filtro dihedral
# numero de cliques, preguntar en el software para generalizarlo INPUT...
number_elements_clique = 3
# se define la estructura
trj1 = rpt.Trajectory(file1)
trj2 = rpt.Trajectory(file2)
# se lee el pdb y se agrega al objeto
trj1.ReadTraj("%s" % file1)
trj2.ReadTraj("%s" % file2)
trj11 = trj1.frames
trj22 = trj2.frames
num_samples1 = int(len(trj11) * 0.05)
num_samples2 = int(len(trj22) * 0.05)
num_samples = num_samples1
if num_samples1 > num_samples2:
num_samples = num_samples2
#!/usr/bin/env python
import numpy as np
import sys
sys.path.append("math_tricks/")
sys.path.append("graphs/")
import read_pdb_tools as rpt
import math_vect_tools as mymath
import network_hb_from_md_traj as pdbnet
assert (len(sys.argv) > 1)
infile = sys.argv[1]
outfile = open('hh_%s.txt' % infile.split('.')[0], 'w')
trj = rpt.Trajectory("first")
trj.ReadTraj("%s" % infile, every=1)
trj.PrintTrajInfo()
while trj.current < trj.length:
ref = trj.next()
net = pdbnet.Network("first")
net.set_nodes_on_frame(ref, mute=True)
net.set_arists_on_nodes()
#line = "# frame: %-4s Nodes: %-6s Edges: %-10s"%(trj.current ,net.count_nodes() ,net.count_arists())
#print line
#outfile.write('%s\n# Edge Distance[A]\n'%line)
net.write_arist_short(outfile, trj.current, short=True)
# networks
import networkx as nx
# filtro distancia minima
# from scipy.spatial.distance import euclidean
# por si no jala
import os
os.chdir('/home/serch/pdbmani/Serch')
# multiprocessing
# import multiprocessing
# from functools import partial
# lectura de archivo
file1 = '/home/serch/pdbmani/Serch/pdbs/trj_0.pdb' # sys.argv[1]
# se define la estructura
trj1 = rpt.Trajectory(file1)
# se lee el pdb y se agrega al objeto
trj1.ReadTraj("%s" % file1)
trj11 = trj1.frames[:3]
# set center_mass
for pdbstruct in trj11:
pdbstruct.set_center_mass()
def get_df_distancias(ref):
"""Funcion para obtener los enlaces de distancias de cada residuo
Dudas en codigo pueden revisar fc.distancia_entre_atomos en ese se basa