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"""Author: BKR
Copied of......hmmm... Inspired by the "fetch from webbook" plugin :-)
Ideas: Getting all alternative names from webbook and or other sources and
creating a Dialog to choose the one desired
"""
import re
try:
from urllib.request import urlopen
except ImportError:
from urllib import urlopen
import dialogs
import oasa_bridge
from main import interactors
from singleton_store import Store
# search strings for the name and the cas registry number
name_re = re.compile('(<h1><a id="Top" name="Top">)(.*)(</a></h1>)')
cas_re = re.compile('(<strong>CAS Registry Number:</strong>)(.*)(</li>)')
stereoisomers = re.compile('(<li><a href=")(.*)(">)(.*)(</a></li>)')
#create inchi
def get_inchi_for_one(u):
program = Store.pm.get_preference("inchi_program_path")
if not oasa_bridge.oasa_available:
return '',["oasa plugin error",]
sms = []
inchi_mol=""
if not interactors.check_validity(u):
return '',["validity Error",]
try:
inchi_mol,key,warning=(oasa_bridge.mol_to_inchi(u, program))
# except oasa.oasa_exceptions.oasa_inchi_error, e:
# sms = ["InChI generation failed,", "make sure the path to the InChI program is correct in 'Options/INChI program path'", "", str(e)]
except:
sms = ["Unknown error occured during INChI generation, sorry", "Please, try to make sure the path to the InChI program is correct in 'Options/INChI program path'"]
warning = []
sms=sms+warning
return inchi_mol, sms
def stereoisomers_found(streamx):
alt_mol = []
for line in streamx:
mol_addrm = stereoisomers.search(line)
if mol_addrm:
mol = mol_addrm.group(4)
if mol[-1] == "-": #When Nist changes the name around
mol = turn_name_around(mol)
addr = mol_addrm.group(2)
alt_mol.append((mol, addr))
mols=[]
for a in alt_mol:
mols.append(a[0])
#Stereoisomer selection dialog
dialog = Pmw.Dialog(App.paper,
buttons=(_('OK'), _('Cancel')),
defaultbutton=_('OK'),
title=_('The molecule was not found'))
w = Pmw.ScrolledListBox(dialog.interior(), labelpos='n', items=mols, label_text='These Stereoisomers were found')
w.pack(expand=1, fill='both', padx=4, pady=4)
dialog.activate()
for a in alt_mol:
if a[0] == w.getvalue()[0]:
return download_nist("http://webbook.nist.gov"+a[1])
#Searches nist by name using inchi instead of the name
def get_name_from_webbook(inchi):
# Escape problematic characters
searchstr = ""
for a in inchi:
if a == "+":
a = "%2B"
elif a == "/":
a = "%2F"
elif a == "(":
a = "%28"
elif a == ")":
a = "%29"
searchstr = searchstr + a
url = "http://webbook.nist.gov/cgi/cbook.cgi?Name=%s&Units=SI" % ("+".join(searchstr.split()))
return download_nist(url)
def download_nist(url):
# print url
dialog = dialogs.progress_dialog(App, title=_("Fetching progress"))
dialog.update(0, top_text = "Connecting to WebBook...", bottom_text=url)
sms=[]
try:
stream = urlopen(url)
except IOError:
dialog.close()
sms.append('Nist could not be reached.')
sms.append('Please check your internet connection')
return '','', sms
cas = ''
mol_name = ''
dialog.update(0.5, top_text = "Reading the webbook...", bottom_text=url)
stream_lines = stream.readlines()
for line in stream_lines:
line = line.decode('utf-8')
mol_namem = name_re.search(line)
if line == "<h2>No matches found</h2>\n": #When stereoisomers are found
dialog.close()
return stereoisomers_found(stream_lines)
elif line == "<h1>Name Not Found</h1>\n": #When nothing is found
dialog.close()
sms.append("The molecule was not found")
return mol_name, cas, sms
if mol_namem:
mol_name=mol_namem.group(2)
casm = cas_re.search(line)
if casm:
cas = casm.group(2)
stream.close()
dialog.close()
return mol_name, cas, sms
dialog.close()
sms.append("The molecule was not found")
return mol_name, cas, sms
import Pmw
def err_mess_box(mess): #Pops up error OK-box
message=""
for m in mess:
message=message+m+"\n"
dialog = Pmw.Dialog(App.paper, buttons=('OK',),
defaultbutton='OK', title='Error')
w = Pmw.LabeledWidget(dialog.interior(), labelpos='n', label_text=message)
w.pack(expand=1, fill='both', padx=4, pady=4)
dialog.activate()
def turn_name_around(mol_name):
bra = 0 #bracket counter
back = "" #end of name
front= "" #beginning of name
frontreached = 0
citra = "" #cis and trans are written at the end of the Nistname
if mol_name[len(mol_name)-7:] == ",trans-":
mol_name = mol_name[:len(mol_name)-7]
citra = "trans-"
elif mol_name[len(mol_name)-8:] == ", trans-": #Nist has spaces in some Names
mol_name = mol_name[:len(mol_name)-8]
citra = "trans-"
elif mol_name[len(mol_name)-5:] == ",cis-":
mol_name = mol_name[:len(mol_name)-5]
citra = "cis-"
elif mol_name[len(mol_name)-6:] == ", cis-": #Nist has spaces in some Names
mol_name = mol_name[:len(mol_name)-6]
citra = "cis-"
for a in mol_name:
if not frontreached:
#the front and the back are devided by "," that is not in a bracket
if a == "," and bra == 0:
frontreached = 1
else:
back = back + a
if a == "(":
bra = bra + 1
elif a == ")":
bra = bra -1
else:
front = front + a
if front[0] == " ": #Nist has spaces in some Names
front = front[1:]
mol_name = citra + front + back
return mol_name
a=App.paper.selected_mols
err_mess=[]
if len(a)!= 0:
for b in a:
App.paper.unselect_all()
App.paper.select(b)
App.paper.select(b.children) #select whole molekule for alignment below
App.paper.swap_sides_of_selected("horizontal")
inchi_form, mess = get_inchi_for_one(b)
App.paper.swap_sides_of_selected("horizontal")
if len(mess) != 0: #Check for Errors
err_mess = err_mess + mess
if inchi_form:
mess = []
mol_name, cas, mess = get_name_from_webbook(inchi_form)
err_mess = err_mess + mess
if mol_name: #writing Name
#sometimes Nist changes the Name around e.g.: Cyclohexane,1,2-dibromo-,cis-
if mol_name[-1] == "-":
corr_mol_name = turn_name_around(mol_name)
else:
corr_mol_name = mol_name
t1 = App.paper.new_text(300, 300, text=corr_mol_name.strip())
t1.draw()
App.paper.place_next_to_selected ("b","v",10,t1) #place below mol
App.paper.select([t1])
if cas: #writing CAS
t2 = App.paper.new_text(300, 325, text="CAS: "+cas.strip())
t2.draw()
App.paper.place_next_to_selected ("b","v",5,t2) #place below mol
App.paper.select([t2])
if len(err_mess)!= 0: #check for any error messages
err_mess_box(err_mess)
App.paper.add_bindings()
else:
err_mess_box(["Please select a molecule"])
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