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()

baoilleach

Use "Fit to Printable Area", in combination with 2 pages per sheet. The default setting is "Shrink to Printable Area".

baoilleach

import pybel

def dodgywedge(sdffile):
    tot = probs = potential_probs = 0
    for mol in pybel.readfile("sdf", sdffile):
        tot += 1
        facade = pybel.ob.OBStereoFacade(mol.OBMol)
        tetcenters = [atom.OBAtom for atom in mol
                      if facade.HasTetrahedralStereo(atom.OBAtom.GetId())]
        for idx, atom_a in enumerate(tetcenters[:-1]):

baoilleach

Here's part of extconf.rb from OB after some edits to add support for --prefix. Unfortunately, this doesn't work (see discussion of mkmf2 which tries to fix some of these problems)

require 'getoptlong'
makeopts = {}
opts = GetoptLong.new(["--prefix", "-p", GetoptLong::OPTIONAL_ARGUMENT],
          ["--with-openbabel-lib", "-L", GetoptLong::OPTIONAL_ARGUMENT],
          ["--with-openbabel-include", "-I", GetoptLong::OPTIONAL_ARGUMENT]
          ).each{|o, a| makeopts[o[%r/[^-].*/]] = a}
prefix = makeopts.delete('prefix') || nil
oblib = makeopts.delete('with-openbabel-lib') || nil

baoilleach

import os

from PyQt4.QtCore import *
from PyQt4.QtGui import *

##import sys
##sys.path.append("C:\\Python26\\Lib\\site-packages")
##sys.path.append("C:\\Python26\\lib")

import Avogadro as avo

baoilleach

from PyQt4.Qt import *
import Avogadro


class Engine(QObject):
  # declare the changed() signal
  __pyqtSignals__ = ("changed()",)

  # constructor
  def __init__(self):