def pdb(request, pdb_name_slug):
context_dict, sheetDict = {}, {}
sheetList, algList = [], []
try:
pdb = PDB.objects.get(slug=pdb_name_slug)
context_dict['pdb_iden'] = pdb.pdb_iden
url_target = "https://www.rcsb.org/pdb/files/{0}.pdb".format(pdb.pdb_iden)
p = protein.buildProtein(url_target)
sheetList += sheet.buildSheet(url_target, p, pdb.pdb_iden)
algorithms = pdb.algorithmdetail_set.all()
for s in sheetList:
for alg in algorithms:
if str(s.sheetIden.replace(" ", "")) == alg.sheet_iden:
algList.append(alg.algorithm)
else:
algList.append("No matching algorithms.")
break
sheetDict[str(s.sheetIden.replace(" ", ""))] = algList
algList = []
context_dict['sheetAlg'] = sheetDict
context_dict['algorithms'] = algorithms
context_dict['pdb'] = pdb
context_dict['pdb_name_slug'] = pdb_name_slug
except PDB.DoesNotExist:
pass
return render(request, 'pdb.html', context_dict)
def computeAll(path):
only100 = 0
count = 0
for filename in glob.glob(os.path.join(path, '*.pdb')):
drive, pathAndFile = os.path.splitdrive(
filename
) #http://stackoverflow.com/questions/3167154/how-to-split-a-dos-path-into-its-components-in-python
filePath, file = os.path.split(pathAndFile)
if (only100 == MAXVALUE):
break
else:
only100 += 1
p = protein.buildProtein(filename)
sheetList = sheet.buildSheet(filename, p)
print "{0} files completed...".format(only100)
listOfBridges = detectBridge(sheetList)
if listOfBridges:
print "{0} is BRIDGE".format(file)
toHTML(listOfBridges, file)
count += 1
else:
print "{0} is NOT BRIDGE".format(file)
with open("bridges.html",
'a') as output: #My quick solution to ending HTML file
output.write("</body>\n</html>")
print count
def computeOne(filename):
p = protein.buildProtein(filename)
sheetList = sheet.buildSheet(filename, p)
listOfBridges = detectBridge(sheetList)
if listOfBridges:
print "{0} is BRIDGE".format(filename)
toHTML(listOfBridges, filename)
else:
print "{0} is NOT BRIDGE".format(filename)
with open("bridges.html",
'a') as output: #My quick solution to ending HTML file
output.write("</body>\n</html>")
def computeOne(filename):
p = protein.buildProtein(filename)
sheetList = sheet.buildSheet(filename, p)
listOfTwist = detectTwist(sheetList)
if listOfTwist:
print "{0} has a Twist".format(filename)
toHTML(listOfTwist, filename)
else:
print "{0} is NOT a Twist".format(filename)
with open("twist.html",
'a') as output: #My quick solution to ending HTML file
output.write("</body>\n</html>")
def testAlgorithm(alg):
sheetList = []
url_target = "https://www.rcsb.org/pdb/files/1a1r.pdb"
p = protein.buildProtein(url_target)
sheetList += sheet.buildSheet(url_target, p, '1a1r')
algName = os.path.splitext(os.path.basename(alg.filePath.name))[0]
sys.path.append(os.path.realpath("media/content/{0}".format(alg.author)))
new_module = __import__(algName)
try:
new_module.detect(sheetList)
return True
except:
print "Unexpected Error: Probably not proper file format"
print sys.exc_info()[0]
return False
def runAlgorithm(alg, PDBList, pdb_used_testing, example_information):
sheetList = []
returnPDBSheetList = []
for pdb in PDBList:
try:
url_target = "https://www.rcsb.org/pdb/files/{0}.pdb".format(
pdb.pdb_iden)
p = protein.buildProtein(url_target)
sheetList += sheet.buildSheet(url_target, p, pdb.pdb_iden)
algName = os.path.splitext(os.path.basename(alg.filePath.name))[0]
sys.path.append(
os.path.realpath("media/content/{0}".format(alg.author)))
new_module = __import__(algName)
print "Working... {0}".format(pdb.pdb_iden)
try:
returnPDBSheetList += new_module.detect(sheetList)
sheetList = []
except:
print "Unexpected Error: Probably something went wrong with their logic"
print sys.exc_info()[0]
for PDBsheet in returnPDBSheetList:
ad = AlgorithmDetail.objects.get_or_create(
algorithm=alg,
pdb=pdb,
sheet_iden=PDBsheet.sheetIden,
test_set=False,
example=False)[0]
ad.save()
returnPDBSheetList = []
pdbDetails = pdb.algorithmdetail_set.all().filter(algorithm=alg)
for pdbDet in pdbDetails:
for each_pdb in pdb_used_testing:
if pdbDet.pdb.pdb_iden == each_pdb.pdb_iden:
pdbDet.test_set = True
for example_pdb in example_information:
if pdbDet.pdb.pdb_iden == example_pdb[
0] and pdbDet.pdb.sheet_iden == example_pdb[1]:
pdbDet.example = True
except:
print pdb.pdb_iden