baoilleach

import math
import pybel

def sqr_dist(a, b):
    ac = a.coords
    bc = b.coords
    return (ac[0]-bc[0])**2 + (ac[1]-bc[1])**2 + (ac[2]-bc[2])**2

# Definitions taken from
#    http://baoilleach.blogspot.com/2007/07/pybel-hack-that-sd-file.html

baoilleach

import os
import glob
import subprocess

testprogram = """
#include <openbabel/parsmart.h>

using namespace OpenBabel;

int main(int argc, char *argv[]) {

baoilleach

import urllib
import random
import pdb
import pybel
 
def getfromPubChem(N = 100, filenames = None):
    """Download N random PubChem molecules as 2D and 3D"""
    
    if filenames == None:
        filenames = ["2Ddataset.sdf", "3Ddataset.sdf"]

baoilleach

# Requires PyActiveResource (http://code.google.com/p/pyactiveresource/)
from pyactiveresource.activeresource import ActiveResource

registry_id = "16" # Replace this with your registry_id
password = "password"
user = "baoilleach@gmail.com"
site = "https://chemcaster.com/registries/$registry_id/"

class Structure(ActiveResource):
    _site = site

baoilleach

Generate the enol from the ketone...OBChemTsfm..not quite..

>>> t.Init("[C:2](C)(=[O:1])[CH2]", "[C:2](C)([O:1])=C")
True

Chris says:
[*:2][C:3](=[O:1])[C:4] >> [*:2][C:3]([O:1])=[C:4]
works for ketones, except t-butyl ketones are wrong.

baoilleach

"""sdfdatareader.py

Super fast skimmer over sdf files just to return the data
fields
"""

def sdf(filename):
    input = open(filename, "r")
    data = {}
    for line in input:

baoilleach

/server freenode
/nick baoilleach
/msg NickServ identify ******
/join openbabel

baoilleach

#!/usr/bin/python

import os, os.path
import sys
import smtplib
import datetime

nightly_dir = '/home/oboyle/not-backed-up'

output = open(os.path.join(nightly_dir, 'log.txt'),"a")

baoilleach

#!/bin/bash
root=/home/oboyle/not-backed-up
prefix=$root/tree

if [ ! -d $root ]
then
        echo "Cannot find the autobuild folder: $root"
        exit 1
fi

baoilleach

Download Visual C++ 2008 Express Edition.

C:\Tools\OpenBabel\trunk>"C:\Program Files\CMake 2.6\bin\cmake.exe" -DCMAKE_BUILD_TYPE=Debug -DCMAKE_INSTALL_PREFIX=..\buildtrunk -G "Visual Studio 9 2008" -DLIBXML2_LIBRARIES=windows-vc2005\libxml2.lib -DZLIB_LIBRARY=windows-vc2005\zlib1.lib -DLIBXML2_INCLUDE_DIR=windows-vc2005 -DZLIB_INCLUDE_DIR=windows-vc2005

Open openbabel.sln and build