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package foo.examples;

import org.apache.camel.CamelContext;
import org.apache.camel.impl.DefaultCamelContext;
import org.apache.camel.impl.SimpleRegistry;
import org.apache.camel.builder.RouteBuilder;
import org.apache.camel.model.rest.RestBindingMode;

import org.eclipse.jetty.server.handler.ContextHandler;
import org.eclipse.jetty.server.handler.ResourceHandler;

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package foo;

import java.io.IOException;
import javax.servlet.ServletException;
import javax.servlet.http.HttpServlet;
import javax.servlet.http.HttpServletRequest;
import javax.servlet.http.HttpServletResponse;
import org.apache.camel.builder.RouteBuilder;
import org.apache.camel.impl.DefaultCamelContext;
import org.apache.camel.impl.SimpleRegistry;

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import org.openscience.cdk.ChemFile
import org.openscience.cdk.interfaces.IAtomContainer
import org.openscience.cdk.io.ISimpleChemObjectReader
import org.openscience.cdk.io.MDLV2000Reader
import org.openscience.cdk.io.MDLV3000Reader
import org.openscience.cdk.tools.manipulator.ChemFileManipulator

String v2000 = '''
  Mrv0541 02231512112D

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import sys
from rdkit import Chem
from rdkit.Chem import AllChem, TorsionFingerprints
from rdkit.ML.Cluster import Butina


def gen_conformers(mol, numConfs=100, maxAttempts=1000, pruneRmsThresh=0.1, useExpTorsionAnglePrefs=True, useBasicKnowledge=True, enforceChirality=True):
	ids = AllChem.EmbedMultipleConfs(mol, numConfs=numConfs, maxAttempts=maxAttempts, pruneRmsThresh=pruneRmsThresh, useExpTorsionAnglePrefs=useExpTorsionAnglePrefs, useBasicKnowledge=useBasicKnowledge, enforceChirality=enforceChirality, numThreads=0)
	return list(ids)
	

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#! /usr/bin/env python

"""A Python wrapper around the Informatics Matters Fragnet service REST API.

Workflow is to create a FragnetSearch instance, authenticate
and then use the FragnetSearch query methods, like search_neighbourhood(): -

    fs = FragnetSearch(fragnet_url, username, password)
    fs.authenticate()
    fs.search_neighbourhood(...)

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#!/bin/bash
# head-setup.sh
#
# Copies the configuration files and enables, but does not start the services.
# Use the services-start/stop.sh scripts to start and stop the munge and slurmd services.  

set -e

echo "Copying munge key"
cp ~/slurm/munge.key /tmp/

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numbers = 0..10

// Create the log file and write something to it as soon as we can.
// The file is located in the workflow directory.
File logfile = new File('status.log')
logfile << 'MSG Workflow started\n'

// This process writes the input to a file that is fed to the second process.
// The status message is generated using the process variable named status.
process p1 {

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#! /usr/bin/env python

"""A Python wrapper around the Informatics Matters Fragnet service REST API.

Workflow is to create a FragnetSearch instance, authenticate
and then use the FragnetSearch query methods, like search_neighbourhood(): -

    fs = FragnetSearch(fragnet_url, username, password)
    fs.authenticate()
    fs.search_neighbourhood(...)

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