Skip to content

Instantly share code, notes, and snippets.

View jp-um's full-sized avatar

JP jp-um

View GitHub Profile
@jp-um
jp-um / jabel
Created June 16, 2017 10:53
cheminformatics primer
{
"cells": [
{
"cell_type": "code",
"execution_count": 1,
"metadata": {},
"outputs": [
{
"name": "stderr",
"output_type": "stream",
{
"cells": [
{
"cell_type": "code",
"execution_count": null,
"metadata": {
"collapsed": true
},
"outputs": [],
"source": [
{"cells":[{"cell_type":"code","source":["from pyspark.sql.functions import udf, col, lit\nfrom pyspark.sql.types import IntegerType, StringType\nfrom datetime import datetime, date\nimport calendar\nfrom re import match\n\ncrimes = sqlContext.read.format('com.databricks.spark.csv').options(header='true', delimiter=',').load('/tmp/data/uk_crimes.csv')"],"metadata":{},"outputs":[],"execution_count":1},{"cell_type":"code","source":["def clean_month_col(value):\n if value is not None:\n if match(r'\\d{4}-\\d{2}', value):\n return value\n return None\n\nudf_clean_month_col = udf(clean_month_col, StringType())\ncrimes = crimes.withColumn('Month', udf_clean_month_col('Month'))"],"metadata":{},"outputs":[],"execution_count":2},{"cell_type":"code","source":["def month_from_date(value):\n value = datetime.strptime(value, '%Y-%m')\n return value.month\n\nudf_month_from_date = udf(month_from_date, IntegerType())\nmonth_df = crimes.where(col('Month').isNotNull()).withColumn('Month', udf_month_from_date('Month'
{
"cells": [
{
"cell_type": "markdown",
"metadata": {
"collapsed": false
},
"source": [
"# A very short tutorial for ipython \n"
]
{
"cells": [
{
"cell_type": "code",
"execution_count": 3,
"metadata": {},
"outputs": [],
"source": [
"from rdkit import Chem\n",
"from rdkit.Chem import AllChem\n",

Keybase proof

I hereby claim:

  • I am jp-um on github.
  • I am drjpe (https://keybase.io/drjpe) on keybase.
  • I have a public key ASCzx7aB-lKTJNkyBnqaU3YYoguZxPo4EuoolQ0XcPRWrQo

To claim this, I am signing this object:

Keybase proof

I hereby claim:

  • I am jp-um on github.
  • I am drjpe (https://keybase.io/drjpe) on keybase.
  • I have a public key ASCzx7aB-lKTJNkyBnqaU3YYoguZxPo4EuoolQ0XcPRWrQo

To claim this, I am signing this object:

Sorry, something went wrong. Reload?
Sorry, we cannot display this file.
Sorry, this file is invalid so it cannot be displayed.
Sorry, something went wrong. Reload?
Sorry, we cannot display this file.
Sorry, this file is invalid so it cannot be displayed.
{
"cells": [
{
"cell_type": "code",
"execution_count": 1,
"id": "76c3eddf",
"metadata": {},
"outputs": [],
"source": [
"from rdkit import Chem\n",