def get_opm_file(arg_pdbid):
"""
Ensure the flatfile with annotations from OPM for the given PDB id is present
and return the path to it.
Search order: 1:Locally in fetch_path, 2:OPM Remote
"""
path = setting.get('fetch_path') #Path also used by the 'fetch' command. If not set in pymolrc, it's probably ~
localfn = os.path.join(path, arg_pdbid.upper() + '.opm')
if not os.access(localfn, os.R_OK):
#Retrieve the file from OPM website
try:
#Retrieve all segments at once
opm_segments_urlobj = urllib2.urlopen(OPM_SUBUNITS_WEBSITE)
opm_segments_html = opm_segments_urlobj.read()
#Get the relevant part from that site
soup = BeautifulSoup.BeautifulSoup(opm_segments_html)
opm_segments_div = str(soup.find("div", {"id": "body"}))
if opm_segments_div is not None:
opm_segments = opm_segments_div.split('<br />')
pdb_id = ''
arg_pdbid_lines = []
for segment in opm_segments:
match = re.search('(\w{4}) <b>(\w)</b>', segment)
if match:
pdb_id = match.group(1)
if pdb_id == arg_pdbid.lower():
arg_pdbid_lines.append(segment)
#Write all relevant lines to output file
if len(arg_pdbid_lines) > 0:
output = open(localfn,'wb')
output.write('\n'.join(arg_pdbid_lines) + '\n')
output.close()
else:
print 'Could not find any annotation for pdbid %s in OPM' % (arg_pdbid)
exit(1)
else:
print 'Error during accession or retrieval of OPM file. Cannot find segment annotations in page.'
exit(1)
except:
print 'Error during accession or retrieval of OPM file'
raise
else:
print 'Found local file'
return localfn
def get_pdbtm_xml(arg_pdbid):
"""
Make sure the XML file for the given pdbid is present and return its path
Search order: 1:Locally in fetch_path, 2:PDBTM Remote
"""
path = setting.get('fetch_path') #Path also used by the 'fetch' command. If not set in pymolrc, it's probably ~
localfn = os.path.join(path, arg_pdbid.upper() + '.xml')
if not os.access(localfn, os.R_OK):
#Retrieve file from remote
try:
xmlfile = urllib2.urlopen('http://pdbtm.enzim.hu/data/database/' + arg_pdbid[1:3] + '/' + arg_pdbid.lower() + '.xml')
output = open(localfn,'wb')
output.write(xmlfile.read())
output.close()
except:
print 'Error during accession or retrieval of XML file'
raise
return localfn