Ipynb idioms: Difference between revisions
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These are idioms for iPython Notebooks, also generally python. | These are idioms for iPython Notebooks, also generally python. | ||
{{TOCright}} | |||
== top of every ipynb == | == top of every ipynb == | ||
Line 9: | Line 9: | ||
import urllib | import urllib | ||
== set up | == set up to use ZINC API == | ||
(hint ask john for credentials) | (hint ask john for credentials) | ||
urlroot = 'http:// | urlroot = 'http://zinc15.docking.org' | ||
format = 'txt' | format = 'txt' | ||
Line 50: | Line 50: | ||
== working with results== | == working with results== | ||
cmd3 = urlroot + '/' + table1 + '/txt:best_purchasable,best_catalog/substance.sub_id={0}' | |||
cmd4 = urlroot + '/' + table1 + '/txt:best_purchasable,best_catalog/substance.sub_id in {0}' | |||
def getPurchasability(sub_id): | def getPurchasability(sub_id): | ||
Line 65: | Line 68: | ||
return int(zinc_id.lower().replace('zinc', '')) | return int(zinc_id.lower().replace('zinc', '')) | ||
[[Category: | [[Category:ZINC15]] | ||
[[Category:Idioms]] | [[Category:Idioms]] |
Latest revision as of 23:30, 1 October 2015
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 to use ZINC API
(hint ask john for credentials)
urlroot = 'http://zinc15.docking.org' 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
working with results
cmd3 = urlroot + '/' + table1 + '/txt:best_purchasable,best_catalog/substance.sub_id={0}' cmd4 = urlroot + '/' + table1 + '/txt:best_purchasable,best_catalog/substance.sub_id in {0}'
def getPurchasability(sub_id): R1 = requests.get(cmd3.format(sub_id)) purch,cat = R1.text.splitlines()[1].split('\t') return int(purch),cat
def getPurchasability2(*sub_ids): R1 = requests.get(cmd4.format(','.join(map(str, sub_ids)))) data_lines = [line.split('\t') for line in R1.text.splitlines()[1:]] print data_lines return [(int(purch), cat) for purch, cat in data_lines]
def to_sub_id(zinc_id): return int(zinc_id.lower().replace('zinc', ))