#Sample script for generating a set of pdb files
import numpy as np
import sys
import r2pdb
import os
input_folder = '../../data'
output_folder = 'pdb/test'
#define topology ('linear' or 'circular')
topo = 'linear'
#define index range for coordinate files
file_inds = range(1,101)
os.system('rm -r %s/*' %output_folder)
for ind in file_inds:
#load file
r = np.loadtxt('%s/r%s' %(input_folder,ind))
#get pdb lines
lines = r2pdb.mkpdb(r, topology = topo)
#save pdb file
r2pdb.save_pdb('%s/snap%0.3d.pdb' %(output_folder,ind),lines)
import numpy as np
import sys
import r2pdb
import os
input_folder = '../../data'
output_folder = 'pdb'
#define topology ('linear' or 'circular')
topo = 'circular'
#define index range for coordinate files
file_inds = range(1, 101, 1)
#Define range of linking numbers
LKs = range(0, 4)
#loop over files and save to pdb
for lk in LKs:
#Create output folder if it does not exists
os.system('mkdir %s/LK_%s/' % (output_folder, lk))
#clear output folder
os.system('rm -r %s/LK_%s/*' % (output_folder, lk))
for ind in file_inds:
#load file
r = np.loadtxt('%s/LK_%s/r%s' % (input_folder, lk, ind))
#get pdb lines
lines = r2pdb.mkpdb(r, topology=topo)
#save pdb file
r2pdb.save_pdb('%s/LK_%s/snap%0.3d.pdb' % (output_folder, lk, ind),
lines)