from pyquery import PyQuery as pq
import re

r = re.compile('10.(\d+)/')

def get_contents(doi):
    DX_DOI = "http://dx.doi.org/"
    doi_url = DX_DOI + doi
    d = None
    try:
        d = pq(doi_url)
    except:
        pass

    return _extract(d,doi)

def _extract(d,doi):
    registrant_prefix = r.search(doi).group(1)    
    if registrant_prefix == '1021':
        return _extractACS(d,doi)
    else:
        return "no extractor"

#    SQLAlchemy
#    title            = Column(String(256), unique=True)
#    pubmed_id        = Column(Integer, unique=True)
#    doi              = Column(String(128), unique=True)
#    abstract         = Column(Text())

def _extractACS(d,doi):
    title = d("h1.articleTitle").text()
    abstract = d("p.articleBody_abstractText").text()
    return {'doi': doi, 'title': title, 'abstract': abstract}

>>> doi.get_contents('10.1021/ci900416a')
{'abstract': u'We introduce SARANEA, ... freely available under the GNU \
General Public License.', 'doi': '10.1021/ci900416a', 'title': u'SARANEA:\
A Freely Available Program To Mine Structure\u2212Activity and \
Structure\u2212Selectivity Relationship Information in Compound Data Sets'}

>>> doi.get_contents('10.1021/jo1025157')
{'abstract': u'The stereoselectivity of glycosylation reactions is affected \
by many factors. Synthesis of 1,2- cis glycosidic ... effects of the acetyl \
groups.', 'doi': '10.1021/jo1025157', 'title': 'Study of the \
Stereoselectivity of 2-Azido-2-deoxygalactosyl Donors: Remote Protecting \
Group Effects and Temperature Dependency'}

{{ bookmark.comments.count() }}

TypeError: count() takes exactly one argument (0 given)

$ pmid2doi.py 20053000
10.1021/ci900416a

<script type="text/javascript" src="{{ url_for('static', filename='jquery-1.6.min.js') }}"></script> 
<script type="text/javascript" src="{{ url_for('static', filename='jquery.form.js') }}"></script> 
<script type="text/javascript"> 
        // wait for the DOM to be loaded 
        $(document).ready(function() { 
            // bind 'myForm' and provide a simple callback function 
            $('#flaskr_form').ajaxForm(function() { 
            $(document.body).load("/");
                alert("Thank you for your comment!"); 
            }); 
        }); 
    </script>

import base64,re,Image
from random import randint

def glitch(infile,outfile):
    jpg_text = base64.encodestring(open(infile,"rb").read())
    glitched_text = ""
    width,height = Image.open(infile).size
    num = width * height / 10000
    for c in jpg_text:
        if c == '0':
            if randint(0,num) == 0:
                count += 1
                glitched_text += str(randint(0,9))
            else:
                glitched_text += c
        else:
            glitched_text += c
    glitched_jpg = base64.decodestring(glitched_text)
    open(outfile,"wb").write(glitched_jpg)
    return ""

from sqlalchemy import *
import networkx as nx
import matplotlib.pyplot as plt

G=nx.Graph()

db = create_engine('sqlite:////Users/kzfm/python/DJUtil/djutil.db')
metadata = MetaData(bind=db, reflect=True)
music_table = metadata.tables['music']
graph_table = metadata.tables['graph']

music = [m.title for m in music_table.select().execute()]

stmt = graph_table.select()
result = stmt.execute()
for row in result:
    G.add_edge(music[row.head-1], music[row.tail-1])

pos=nx.spring_layout(G)
ith_labels=False)
nx.draw(G,pos,node_color='#A0CBE2',width=1,node_size=200,alpha=0.4,edge_cmap=plt.cm.Blues,font_size=8)
plt.savefig("path.png")

import Image
from binascii import hexlify
from random import randint

def text2rgb(text,length):
   hex = hexlify(text)
   hex_length = len(hex)
   buf = hex
   result = []
   while len(result) < length:
       if len(buf) < 6:
           start = randint(1,hex_length)
           end   = randint(1,hex_length)
           if start > end:
               buf += hex[end:start]
           else:
               buf += hex[start:end]
       else:
           r = buf[:2]
           g = buf[2:4]
           b = buf[4:6]
           buf = buf[6:]
           #for t in range(10):
           result.append((int(r,16),int(g,16),int(b,16)))
   return result

if __name__ == '__main__':
   WIDTH = 480
   HEIGHT = 480

   text = open('/Users/kzfm/PKPD.dot','rb').read()

   rgb = text2rgb(text,WIDTH*HEIGHT)

   im = Image.new( "RGB", ( HEIGHT, WIDTH ), ( 0, 0, 0 ) )
   pix = im.load()
   for h in range(HEIGHT):
       for w in range(WIDTH):
           try:
               pix[w,h] = rgb[w]
           except IndexError:
               pass
   im.save("test.png")

import urllib
import sys
pdblist = sys.argv[1:]

proxies = {'http': 'http://[hostname]:[port]/'}
opener = urllib.FancyURLopener(proxies)

for pdbid in pdblist:
   f = opener.open('http://www.rcsb.org/pdb/files/%s.pdb.gz' % pdbid.upper())
   data = f.read()
   with open('%s.pdb.gz' % pdbid.upper(),'wb') as wf:
       wf.write(data)

use strict;
use Net::FTP;

die "usage:$0 [pdb_id] ...\n" unless @ARGV;

my $ftp = Net::FTP->new("[hostname]", Debug => 0)
    or die "Cannot connect to [hostname]: $@";
$ftp->login("pdb",'pdb')
  or die "Cannot login ", $ftp->message;

$ftp->binary();

for my $pdbid (@ARGV){
  $pdbid =~ tr/[A-Z]/[a-z]/;
  my $pdbdir = substr($pdbid,1,2);
  my $pdbfile = "pdb" . $pdbid . ".ent.gz";

  $ftp->cwd($pdbdir)
    or warn "Cannot change PDB directory ", $ftp->message;

  $ftp->get($pdbfile)
    or warn "$pdbfile : ", $ftp->message;

  $ftp->cwd('..')
    or warn "Cannot change PDB directory ", $ftp->message;
}

$ftp->quit;

def trunc_whitespace(app, doctree, docname):
    from docutils.nodes import Text, paragraph
    if not app.config.japanesesupport_trunc_whitespace:
        return
    for node in doctree.traverse(Text):
        if isinstance(node.parent, paragraph):
            newtext = node.astext()
            for c in "\n\r\t":
                newtext = newtext.replace(c, "")
            newtext = newtext.strip()
            node.parent.replace(node, Text(newtext))

def setup(app):
    app.add_config_value('japanesesupport_trunc_whitespace', True, True)
    app.connect("doctree-resolved", trunc_whitespace)