Ipynb idioms
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These are idioms for iPython Notebooks, also generally python.
top of every ipynb
%matplotlib inline import matplotlib.pyplot as plt import numpy as np import requests import urllib
set up variables for webapi
(hint ask john for credentials)
urlroot = 'http://x.ucsf.bkslab.org:y' format = 'txt'
execute a command, with optional limits
R = requests.get(cmd + '?count=10000') lines = list(R.iter_lines()) print len(lines) print R.text
setup
from rdkit.Chem.Draw import IPythonConsole import rdkit.Chem.Draw as D import rdkit.Chem as C import rdkit.Chem.Descriptors as CD from rdkit.Chem import SmilesMolSupplier
activate zinc api
import zinc.api api=zinc.api.make_api()
Display mols
path = '/nfs/home/jji/ipynb/data/test.smi' mols = SmilesMolSupplier(path, titleLine=False) D.MolsToGridImage( mols, legends=[m.GetProp('_Name') for m in mols])
drill down on mol
s1 =api.substances.get(110341849) [(ci.supplier_code,ci.catalog.name) for ci in s1.catalog_items]
stuff about sets
from sets import Set
https://docs.python.org/2/library/sets.html
employees = engineers | programmers | managers # union engineering_management = engineers & managers # intersection fulltime_management = managers - engineers - programmers # difference engineers.add('Marvin') # add element