def name2id(name, outformat):
import cirpy
import chemspipy
import queryDevice
idstring = None
source = None
if idstring is None:
source = 'NCI'
idstring = cirpy.resolve(name, outformat)
if idstring is None:
source = 'ChemSpi'
chemspid = chemspipy.find_one(name)
try:
smiles = chemspid.smiles
idstring = cirpy.resolve(smiles, outformat)
except AttributeError:
idstring = None
if idstring is None:
source = 'NCI-pattern-match'
idstring = cirpy.resolve(name, outformat,['name_pattern'])
if idstring is None:
source = None
idstring = str(idstring)
try:
idstring = (idstring.rstrip(),source)
except AttributeError:
idstring = (idstring[0].rstrip(),source)
print 'There were multiple results for: ', name, ' using: ', idstring[0], '\n', idstring
return idstring
#!/usr/bin/env python # from: # http://blog.matt-swain.com/post/16893587098/chemspipy-a-python-wrapper-for-the-chemspider-api import chemspipy import re, sys if len(sys.argv) != 2: print 'usage : molecule_name.py <search string>' sys.exit(1) search = sys.argv[1] c = chemspipy.find_one(search) try: name = c.commonname except AttributeError: name = 0 print name
with open('E coli core.core metabolism.json', 'r') as f:
core_map = json.load(f)
# only look at primary metabolites
nodes = {k: node for k, node in core_map[1]['nodes'].iteritems()
if node['node_type'] == 'metabolite' and node['node_is_primary'] is True}
print 'searching for {} structures'.format(len(nodes))
for k, node in nodes.iteritems():
# check for img
structure_path = join(structures_dir, '{}.png'.format(remove_compartment(node['bigg_id'])))
if exists(structure_path):
print 'Structure image already downloaded: {}'.format(structure_path)
continue
# search for the formula
chem = chemspipy.find_one(node['name'])
if not chem:
print 'could not find match for {}'.format(node['name'])
continue
# convert to transparent
image = Image.open(StringIO(b64decode(chem.image)))
image = image.convert('RGBA')
new_data = [x if x[:3] != (255, 255, 255) else (255, 255, 255, 0) for x in image.getdata()]
image.putdata(new_data)
# save the image
print 'Found structure for {}. Saving to {}'.format(node['name'], structure_path)
image.save(structure_path, "PNG")
#import getopt
#opts = getopt.getopt(sys.argv[1])
class Logger(object):
def __init__(self, filename="Default.log"):
self.terminal = sys.stdout
self.log = open(filename, "a")
def write(self, message):
self.terminal.write(message)
self.log.write(message)
sys.stdout = Logger("log.txt")
cos = sys.argv[1]
name = sys.argv[2]
try:
chemspipy.find_one(name)
except AttributeError:
print("%s\t" % (cos))
else:
c_1 = chemspipy.find_one(name)
if c_1:
print("%s\t%s\t%s\t%s\t%s\t%s" %
(cos, name, c_1.smiles, c_1.inchi, c_1.inchikey, c_1.commonname))
else:
print("%s\t" % (cos))
import chemspipy
import sys
import fileinput
terms = []
print "Enter your search terms, one per line. When done, hit Crtl+D on an empty line to start the search."
for line in fileinput.input():
if len(line.strip()) > 0:
terms.append(line.strip())
pass
for term in terms:
d = {}
c = chemspipy.find_one(term)
if not c:
continue
d["imageurl"] = c.imageurl
d["mf"] = c.mf
d["smiles"] = c.smiles
d["inchi"] = c.inchi
d["inchikey"] = c.inchikey
d["averagemass"] = c.averagemass
d["molecularweight"] = c.molecularweight
d["monoisotopicmass"] = c.monoisotopicmass
d["nominalmass"] = c.nominalmass
d["alogp"] = c.alogp
d["xlogp"] = c.xlogp
d["commonname"] = c.commonname
#d["image"] = c.image
import chemspipy
import re
import sys
if len(sys.argv) == 1:
indfilnavn = raw_input("Filnavn med stoffer? >")
else:
indfilnavn = sys.argv[1]
fjern = re.compile('[^a-zA-Z0-9]')
print("Stof\tSumformel\tMonoisotopicmass")
with open(indfilnavn) as f:
for line in f:
c = chemspipy.find_one(line)
print line.strip(), "\t", re.sub(fjern, '', c.mf) , "\t", c.monoisotopicmass
