def run_poreblazer(pkl_file):
print('Processing pkl file: {} '.format(pkl_file))
mycell = ab_util.cellFromPickle(pkl_file, paramsDir=params_dir)
mycell.poreblazer(poreblazer_exe)
#!/usr/bin/env python
import sys
sys.path.append("/opt/ambuild.git")
from ambuild import ab_util
paramsDir = '/home/pierre/Dropbox/Ambuild_Files/Parameters'
mycell = ab_util.cellFromPickle('step_1.pkl.gz', paramsDir=paramsDir)
poreblazerExe = '/opt/poreblazer/src/poreblazer.exe'
mycell.poreblazer(poreblazerExe)
#!/usr/bin/env python
import os, sys
ambuild_home = "/opt/ambuild.git"
sys.path.insert(0, ambuild_home)
# This imports the builder cell module - this is the only module that should be required
from ambuild import ab_util
mycell = ab_util.cellFromPickle("step_628.pkl")
def pkl_step_num(pkl_filename):
return re.match('step_([0-9]+)\.pkl.*',pkl_filename).group(1)
paramsDir = '/home/pierre/Dropbox/Ambuild_Files/Parameters'
ignore = ['DMF', 'TEA', 'cat']
prev_block_data = {}
with open('blocks.csv', 'w') as csvfile:
w = csv.writer(csvfile, delimiter=',')
w.writerow(['nstep','nblocks','max_mass', 'zip_bonds'])
for p in sorted(glob.glob("*.pkl*"), key=pkl_step_num):
print("Processing: {}".format(p))
nstep = pkl_step_num(p)
try:
mycell = ab_util.cellFromPickle(p, paramsDir=paramsDir)
except EOFError:
print("Picklefile: {} was empty!".format(p))
continue
nblocks = 0
max_mass = 0
zip_bonds = 0
current_block_data = {}
for k, b in mycell.blocks.items():
if len(b.fragments) == 1 and b.fragments[0].fragmentType in ignore:
continue
current_block_data[k] = len(b.blockBonds())
if k in prev_block_data and prev_block_data[k] < current_block_data[k]:
zip_bonds += current_block_data[k] - prev_block_data[k]
nblocks += 1
max_mass = max(max_mass, b.blockMass())