mnowotka

from chembl_webresource_client.new_client import new_client

# Get Molecules with ATC 'A10' classification
molecules    = new_client.molecule.filter(atc_classifications__level5__startswith='A10')
molecule_ids = list(set(map(lambda d: d['molecule_chembl_id'], molecules)))
print molecule_ids


# Get Targets for Molecules
activities = new_client.activity.filter(molecule_chembl_id__in=molecule_ids).filter(pchembl_value__gte=6)

mnowotka

from chembl_webresource_client.new_client import new_client
 
# Get Molecules with ATC 'A10' classification
molecules = new_client.molecule.filter(atc_classifications__level5__startswith='A10')
molecule_ids = [mol['molecule_chembl_id'] for mol in molecules]
 
 
# Get Targets for Molecules
activities = new_client.activity.filter(molecule_chembl_id__in=molecule_ids).filter(pchembl_value__gte=6)
target_ids = set([act['target_chembl_id'] for act in activities])

mnowotka

from chembl_webresource_client.new_client import new_client

molecules = new_client.molecule
clean_mols = molecules.filter(molecule_properties__full_mwt__isnull=False)
len(clean_mols)
weights = [x['molecule_properties']['full_mwt'] for x in clean_mols[0:1000]]

mnowotka

data_directory = '/var/lib/postgresql/9.4/main'		# use data in another directory
hba_file = '/etc/postgresql/9.4/main/pg_hba.conf'	# host-based authentication file
ident_file = '/etc/postgresql/9.4/main/pg_ident.conf'	# ident configuration file
external_pid_file = '/var/run/postgresql/9.4-main.pid'			# write an extra PID file
listen_addresses = '*' # what IP address(es) to listen on;
port = 5432				# (change requires restart)
max_connections = 100			# (change requires restart)
unix_socket_directories = '/var/run/postgresql'	# comma-separated list of directories
ssl = true				# (change requires restart)
ssl_cert_file = '/etc/ssl/certs/ssl-cert-snakeoil.pem'		# (change requires restart)

mnowotka

#!/bin/sh

wmctrl -o 0,0

setsid gnome-terminal -t "PIPELINE"  -e "ssh pipeline -t \"htop\"" --geometry=71x15+0+0 &
setsid gnome-terminal -t "API1" -e "ssh api1 -t \"htop\"" --geometry=71x15+640+0 &
setsid gnome-terminal -t "API2" -e "ssh api2 -t \"htop\"" --geometry=71x15+1280+0 &
setsid gnome-terminal -t "UI" -e "ssh ui -t \"htop\"" --geometry=71x15+0+325 &
setsid gnome-terminal -t "UI3" -e "ssh ui3 -t \"htop\"" --geometry=71x15+640+325 &
setsid gnome-terminal -t "MYSQL" -e "ssh mysql -t \"htop\"" --geometry=71x15+1280+325 &

mnowotka

#!/bin/sh

wmctrl -o 0,0
setsid firefox -new-window -url "http://sark.ebi.ac.uk:9000/chembl/chembl_new_webservices/" &
sleep 5
wmctrl -o 1920,0
setsid firefox -new-window -url "http://ves-ebi-56.ebi.ac.uk/surechemblmonitor/#/dashboard/db/overview" &
sleep 5
wmctrl -o 0,1200
setsid firefox -new-window -url "https://uptimerobot.com/dashboard#tvMode" &

mnowotka

#!/bin/sh

wmctrl -o 0,0

setsid gnome-terminal -t "PIPELINE SHANDLERS.LOG" -e "ssh pipeline -t \"tail -f /srv/pipelinelogs/shandlers-1.log | ccze\"" --geometry=215x15+640+0 &
setsid gnome-terminal -t "PIPELINE ATT-REAPER.LOG" -e "ssh pipeline -t \"tail -f /srv/surechem-pipeline/shared/log/att-reaper.log | ccze\"" --geometry=215x15+640+325 &
setsid gnome-terminal -t "PIPELINE BATCH_MAPPER.LOG" -e "ssh pipeline -t \"tail -f /srv/surechem-pipeline/shared/log/batch-mapper.log | ccze\"" --geometry=215x15+640+625 &
setsid gnome-terminal -t "PIPELINE PIPELINE-REAPER-RESTART.LOG" -e "ssh pipeline -t \"tail -f /srv/surechem-pipeline/shared/log/pipeline-reaper-restart.log | ccze\"" --geometry=215x15+640+960 &

sleep 5

mnowotka

Copyright (c) 2015, Shahar Evron
All rights reserved.

Redistribution and use in source and binary forms, with or without modification, 
are permitted provided that the following conditions are met:

1. Redistributions of source code must retain the above copyright notice, this 
list of conditions and the following disclaimer.

2. Redistributions in binary form must reproduce the above copyright notice, 

mnowotka

# This scripts reads a list of compounds, identified by their chembl ids from a CSV file 
# given as an input. For each compound it find related targets, optionally filtered by
# organism. It saves a mepping between the compound and targets in the output CSV file.

# import libraries for reading csv files, parsing command line arguments
# and the python client library
import csv
import argparse
from chembl_webresource_client.new_client import new_client

mnowotka

#!/bin/bash

# This script will get a list of targets related to a compound.
# Each compound, identified by its chembl id will be read from
# the CSV file specified as the first argument.

# This script assumes that you have a 'jq' command line tool installed.
# Installation instructions can be found here: 
# https://stedolan.github.io/jq/download/