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import sys,os
sys.path.insert(0,'/global/project/projectdirs/metatlas/anaconda/lib/python2.7/site-packages' )
from metatlas import metatlas_objects as metob
import csv
curr_ld_lib_path = ''
os.environ['LD_LIBRARY_PATH'] = curr_ld_lib_path + ':/project/projectdirs/openmsi/jupyterhub_libs/boost_1_55_0/lib' + ':/project/projectdirs/openmsi/jupyterhub_libs/lib'
import sys
# sys.path.remove('/anaconda/lib/python2.7/site-packages')
sys.path.append('/global/project/projectdirs/openmsi/jupyterhub_libs/anaconda/lib/python2.7/site-packages')
sys.path.insert(0,'/project/projectdirs/openmsi/projects/meta-iq/pactolus/pactolus' )
from rdkit import Chem
# from rdkit.Chem.rdMolDescriptors import ExactMolWt
from rdkit.Chem import Descriptors
from rdkit.Chem import rdMolDescriptors
from rdkit.Chem import AllChem
from rdkit.Chem.Fingerprints import FingerprintMols
from rdkit.Chem import Draw
from rdkit import DataStructs
import numpy as np
from matplotlib import pylab as plt
# %matplotlib notebook
%matplotlib inline
%config InlineBackend.figure_format = 'retina'
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import json
from pprint import pprint
with open('network_and_view.cyjs') as data_file:
data = json.load(data_file)
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from matplotlib import collections as mplib_collections
x = []
y = []
node_id = []
for n in data['elements']['nodes']:
x.append(n['position']['x'])
y.append(n['position']['y'])
node_id.append(float(n['data']['SUID']))
fig = plt.figure(figsize=(22,18))
myMarker = 'k'#[0.99324789, 0.60615657, 0.1439362] #'aqua'# #'aqua'
myEdges = [0.26700401, 0.00487433, 0.32941519] #
plt.plot(x,y,'o',markersize=1, markeredgecolor=myMarker, markerfacecolor = myMarker)
node_id = np.asarray(node_id)
colors = []
segs = []
for e in data['elements']['edges']:
idx1 = np.argwhere(node_id == float(e['data']['source']))[0][0]
idx2 = np.argwhere(node_id == float(e['data']['target']))[0][0]
colors.append(myEdges)
segs.append(( (x[idx1], y[idx1]),
(x[idx2], y[idx2]) ))
ln_coll = mplib_collections.LineCollection(segs, colors=colors)
ax = plt.gca()
ax.add_collection(ln_coll)
# fig.set_facecolor('w')
# ax.set_xlim(0, 600)
# ax.set_ylim(0, 400)
# plt.draw()
plt.axis('off')
plt.show()
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%%javascript
var nb = IPython.notebook;
var kernel = IPython.notebook.kernel;
var command = "NOTEBOOK_FULL_PATH = '" + nb.base_url + nb.notebook_path + "'";
kernel.execute(command);
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filename = os.path.basename(NOTEBOOK_FULL_PATH)
%system cp $filename /project/projectdirs/openmsi/www/
temp = '%s/%s'%('/project/projectdirs/openmsi/www',filename)
%system chmod 775 $temp
print 'http://nbviewer.ipython.org/url/portal.nersc.gov/project/openmsi/%s?flush_cache=true'%filename
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