fredrikw

benz
  ChemDraw03281210432D

  6  6  0  0  0  0  0  0  0  0999 V2000
   -0.7145    0.4125    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.7145   -0.4125    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.0000   -0.8250    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.7145   -0.4125    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.7145    0.4125    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.0000    0.8250    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0

fredrikw

#!/usr/bin/python

# CLI program to control the mediakeys on OS X. Used to emulate the mediakey on a keyboard with no such keys.
# Easiest used in combination with a launcher/trigger software such as Quicksilver.
# Main part taken from http://stackoverflow.com/questions/11045814/emulate-media-key-press-on-mac
# Glue to make it into cli program by Fredrik Wallner http://www.wallner.nu/fredrik/

import Quartz
import sys

fredrikw

--- ../scripts/python/pybel.py  2012-10-03 21:08:52.000000000 +0200
+++ /usr/local/lib/pybel.py     2013-06-24 22:40:30.024896494 +0200
@@ -495,7 +495,9 @@
 
         Tkinter and Python Imaging Library are required for image display.
         """
-        if not "png2" in outformats:
+        obconversion = ob.OBConversion()
+        formatok = obconversion.SetOutFormat("_png2")
+        if not formatok:

fredrikw

CREATE DATABASE mychem_match_test;
USE mychem_match_test;
CREATE TABLE `compound_mol` (
   `compound_id` int(11) NOT NULL AUTO_INCREMENT,
   `mol` text,
   PRIMARY KEY (`compound_id`)
) ENGINE=MyISAM DEFAULT CHARSET=utf8;
INSERT INTO `compound_mol` (`mol`) VALUES (SMILES_TO_MOLECULE('c1ccccc1')), (SMILES_TO_MOLECULE('c1ccccc1O')), (SMILES_TO_MOLECULE('c1cnccc1'));
CREATE TABLE `compound_ser_mol` (
   `compound_id` int(11) NOT NULL,

fredrikw

import re
import itertools
import pybel


def permuteSMILESStereo(smile):
    stereo = re.search(r"(\[[^\]]+@+[^\]]*\]|[/\\])", smile)
    if stereo:
        left = smile[:stereo.start()]
        rights = permuteSMILESStereo(smile[stereo.end():])

fredrikw

FROM python

WORKDIR /usr/src/app
RUN pip install pandas
# Change the above line for the following to get the expected table not found error
# RUN pip install pandas sqlalchemy
RUN echo 'import pandas as pd\n\
saconnstring="sqlite:///test.db"\n\
print(pd.read_sql_table("test", saconnstring))\n\
print("Done")\n' >> testscript.py