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

#!/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

#!/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

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

baoilleach

 The lyf so short, the craft so long to lerne.
                             -- Chaucer

baoilleach

def sdfsingledata(filename, data):
    if filename.endswith(".gz"):
        input = gzip.open(filename, "r")
    else:
        input = open(filename, "r")
    fieldname = "> <%s>\n" % data
    for line in input:
        if line == fieldname:
            line = input.next().strip()
            yield line

baoilleach

# Find errors with Implicit Hs

import pybel
import glob

sdfs = glob.glob("C:\Tools\openbabel\PubChem3D\*.sdf")
print sdfs


for sdf in sdfs:

baoilleach

import time

import pybel
ob = pybel.ob

molecules = list(pybel.readfile("sdf", "pubchem_416_benzenes.sdf"))

t = time.time()

query = ob.CompileSmilesQuery("c1ccccc1")

baoilleach

from pylab import *

inputfile = open("tmp3.txt", "r")

for line in inputfile:
    if line.startswith(" ENERGY DELTA MAP(S) (W.R. TO THE LOWEST FOUND)"):
        break

blank = inputfile.next()
dash = inputfile.next()