Custom keybindings in OS X

Since I keep forgetting how to customize keyboard navigation, here's a pointer to the documentation:
http://developer.apple.com/documentation/Cocoa/Conceptual/EventOverview/TextDefaultsBindings/chapter_9_section_2.html

And here are the bindings I'm currently using in my ~/Library/KeyBindings/DefaultKeyBinding.dict file. Basically they cause the "Home" and "End" keys on the Apple keyboard to move the cursor to the beginning and end of the current text line. Hitting these keys while holding "Shift" will also select all text covered by the move. And the page up/down keys do what you'd expect.

{
    "$\Uf729" = "moveToBeginningOfLineAndModifySelection:";
    "$\Uf72b" = "moveToEndOfLineAndModifySelection:";
    "\Uf729" = "moveToBeginningOfLine:";
    "\Uf72b" = "moveToEndOfLine:";
    "\Uf72c" = "pageUp:";
    "\Uf72d" = "pageDown:";
}

Twenty-year-old Civics got 57 miles per gallon - Dec. 19, 2007

Twenty-year-old Civics got 57 miles per gallon - Dec. 19, 2007:

"Even in its base HF trim, the CRX was considered a fun car to drive because it was small and responsive. Its zero-to-sixty time, though - about 12 seconds by some estimates - would put it well behind even a large, sedate family sedan like the Ford Taurus today."

I owned a red 1990 CRX HF for about 11 years. I drove it off the lot just a few days before Saddam Hussein invaded Kuwait. Boy, did I feel smug.

It was a great little car. On long trips it often averaged 60-62 mpg.

I finally gave it up after moving to Santa Fe. It had trouble climbing La Bajada. And it started pulling to the left after a local mechanic installed new front-end ball joints. Okay, and it had no air conditioning, which made for stinking hot desert travel.

But it was a great little car...

CDK, Jython and chemical structure format conversion

These days I'm learning how to work with some new (to me) Java cheminformatics toolkits. Google, Jython 2.2.1, and VoodooPad are helping me get up to speed:

• Google to find the documentation for the Java APIs


• Jython to learn API nuances without an edit/compile/test cycle


• VoodooPad as a scratchpad for sample scripts -- it's easy to save them in pages that sit alongside my worklog

During initial exploration I just bang up the script in VoodooPad, then repeatedly select all (Cmd-A), copy (Cmd-C), switch to a Terminal session running Jython (Cmd-Tab), and paste (Cmd-V).

The "learnings" are going into proper Jython scripts maintained with TextMate.

It's nice to be able to deploy using Jython instead of pure Java. Since almost all of the heavy lifting is being done inside the cheminformatics jars, I don't need to worry about the overhead of running a Python interpreter inside a JVM...

Here's a simple example using CDK, to transform an SD string into a SMILES string.

#! /usr/bin/env jython
# You must have set your CLASSPATH to pick up the CDK jar.
# encoding: utf-8

import java.io
from org.openscience import cdk

def getCDKMol(sdf):
reader = cdk.io.MDLReader(java.io.StringReader(sdf))
result = cdk.Molecule()
result = reader.read(result)
return result

def getSmiles(cdkMol):
result = java.io.StringWriter()
writer = cdk.io.SMILESWriter(result)
writer.write(cdkMol)
return str(result)

def sdfToSmiles(sdf):
return getSmiles(getCDKMol(sdf))

# Example:
print sdfToSmiles("""1-7


42 44 0 0 0 0 999 V2000
-0.8349 0.9908 0.0000 N 0 0 0 0 0 0 0 0 0 0 0 0
-0.0502 1.2457 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
-0.0502 2.0707 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
-0.8349 2.3257 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
-1.3198 1.6582 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
0.6172 0.7608 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
-1.0898 0.2062 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
0.5310 -0.0597 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
1.1984 -0.5446 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
1.9521 -0.2090 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
2.0383 0.6114 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
1.3709 1.0964 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
-1.8968 0.0346 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
-2.1517 -0.7500 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
-1.5997 -1.3631 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
-0.7927 -1.1915 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
-0.5378 -0.4069 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
-2.1448 1.6582 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
2.6195 -0.6940 0.0000 S 0 0 0 0 0 0 0 0 0 0 0 0
3.1044 -0.0265 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0
2.1346 -1.3614 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0
3.2869 -1.1789 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
-1.8546 -2.1477 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
0.6172 2.5557 0.0000 H 0 0 0 0 0 0 0 0 0 0 0 0
-1.0898 3.1103 0.0000 H 0 0 0 0 0 0 0 0 0 0 0 0
-0.2227 -0.3952 0.0000 H 0 0 0 0 0 0 0 0 0 0 0 0
1.1122 -1.3651 0.0000 H 0 0 0 0 0 0 0 0 0 0 0 0
2.7920 0.9470 0.0000 H 0 0 0 0 0 0 0 0 0 0 0 0
1.4571 1.9168 0.0000 H 0 0 0 0 0 0 0 0 0 0 0 0
-2.4488 0.6477 0.0000 H 0 0 0 0 0 0 0 0 0 0 0 0
-2.9587 -0.9215 0.0000 H 0 0 0 0 0 0 0 0 0 0 0 0
-0.2407 -1.8046 0.0000 H 0 0 0 0 0 0 0 0 0 0 0 0
-0.1632 -1.1420 0.0000 H 0 0 0 0 0 0 0 0 0 0 0 0
-2.1448 0.8332 0.0000 H 0 0 0 0 0 0 0 0 0 0 0 0
-2.1448 2.4832 0.0000 H 0 0 0 0 0 0 0 0 0 0 0 0
-2.9698 1.6582 0.0000 H 0 0 0 0 0 0 0 0 0 0 0 0
3.7719 -0.5114 0.0000 H 0 0 0 0 0 0 0 0 0 0 0 0
2.8020 -1.8463 0.0000 H 0 0 0 0 0 0 0 0 0 0 0 0
3.9544 -1.6638 0.0000 H 0 0 0 0 0 0 0 0 0 0 0 0
-1.0700 -2.4026 0.0000 H 0 0 0 0 0 0 0 0 0 0 0 0
-2.6392 -1.8928 0.0000 H 0 0 0 0 0 0 0 0 0 0 0 0
-2.1096 -2.9323 0.0000 H 0 0 0 0 0 0 0 0 0 0 0 0
1 2 1 0 0 0 0
1 5 1 0 0 0 0
1 7 1 0 0 0 0
2 3 2 0 0 0 0
2 6 1 0 0 0 0
3 4 1 0 0 0 0
3 24 1 0 0 0 0
4 5 2 0 0 0 0
4 25 1 0 0 0 0
5 18 1 0 0 0 0
6 8 2 0 0 0 0
6 12 1 0 0 0 0
7 13 2 0 0 0 0
7 17 1 0 0 0 0
8 9 1 0 0 0 0
8 26 1 0 0 0 0
9 10 2 0 0 0 0
9 27 1 0 0 0 0
10 11 1 0 0 0 0
10 19 1 0 0 0 0
11 12 2 0 0 0 0
11 28 1 0 0 0 0
12 29 1 0 0 0 0
13 14 1 0 0 0 0
13 30 1 0 0 0 0
14 15 2 0 0 0 0
14 31 1 0 0 0 0
15 16 1 0 0 0 0
15 23 1 0 0 0 0
16 17 2 0 0 0 0
16 32 1 0 0 0 0
17 33 1 0 0 0 0
18 34 1 0 0 0 0
18 35 1 0 0 0 0
18 36 1 0 0 0 0
19 20 2 0 0 0 0
19 21 2 0 0 0 0
19 22 1 0 0 0 0
22 37 1 0 0 0 0
22 38 1 0 0 0 0
22 39 1 0 0 0 0
23 40 1 0 0 0 0
23 41 1 0 0 0 0
23 42 1 0 0 0 0
M END
$$$$
""")

SQLElixir/SQLAlchemy/SQLite3 and ISO-8859 content

See here for the full discussion. The upshot is that, if you are storing string data into an SQLite3 database via Python, and if you suspect that the data may contain non-ASCII characters, you need to ensure that it's properly converted to (Python) Unicode before inserting.

#!/usr/bin/env python
# encoding: utf-8
"""Explores a problem importing a chemical structure file into an
SQLElixir/SQLAlchemy/SQLite3 database.

The file was in SD format. One of the tags contained ISO-8859 characters.
Python read the file contents without trouble; SQLite3 stored the contents.
But on retrieval SQLite3 raised an OperationalError:
Could not decode to UTF-8 column '[...]' with text '[...]'

This script explores the problem, and demonstrates two successful
Unicode encodings: utf-8/replaced and utf-8/ignored.

NB: Only the latter actually worked with SQLElixir:
s = unicode(s, encoding='utf-8', errors='ignore')
"""
import unittest, sqlite3

class TestCase(unittest.TestCase):
def setUp(self):
self.conn = sqlite3.connect(":memory:")
self.conn.cursor().execute('CREATE TABLE demo (value TEXT)')

def insertAndDump(self, encoding, errors, expectFailure=False):
caseName = repr([encoding, errors])
data = 'K\xf6 1366'
try:
if encoding is not None:
data = unicode(data, encoding=encoding, errors=errors)
cursor = self.conn.cursor()
cursor.execute("INSERT INTO demo (value) VALUES (?)", [data])
cursor.execute('SELECT * FROM demo')
self.failUnless(len(cursor.fetchall()) == 1)
self.failIf(expectFailure, "Unexpected success for %s" % caseName)
except Exception, info:
self.failUnless(expectFailure, "Failed %s: %s" % (caseName, info))

def testCannotRetrieveUnencoded(self):
self.insertAndDump(None, None, True)

def testCannotEncodeStrict(self):
self.insertAndDump("utf-8", "strict", True)

def testCanRetrieve8859Strict(self):
self.insertAndDump("8859", "strict")

def testCanRetrieveUTF8Ignored(self):
self.insertAndDump("utf-8", "ignore")

def testCanRetrieveUTF8Replaced(self):
self.insertAndDump("utf-8", "replace")

unittest.main()