def __init__(self, form):
'''Gleans all information about the user selected options and uploaded files.
Also validates the user input. Raises WebOptionsError if there is any problems.'''
#options to pass to runPDB2PQR
self.runoptions = {}
#Additional options to pass to google analytics along with the run options.
#These are included in has_key(), __contains__(), and __getitem__() calls.
self.otheroptions = {}
self.runoptions['debump'] = "DEBUMP" in form
self.runoptions['opt'] = "OPT" in form
if 'FF' in form:
self.ff = form["FF"].value.lower()
else:
raise WebOptionsError('Force field type missing from form.')
if "PDBID" in form and form["PDBID"].value and form["PDBSOURCE"].value == 'ID':
self.pdbfile = utilities.getPDBFile(form["PDBID"].value)
if self.pdbfile is None:
raise WebOptionsError('The pdb ID provided is invalid.')
self.pdbfilestring = self.pdbfile.read()
self.pdbfile = StringIO(self.pdbfilestring)
self.pdbfilename = form["PDBID"].value
elif "PDB" in form and form["PDB"].filename and form["PDBSOURCE"].value == 'UPLOAD':
self.pdbfilestring = form["PDB"].value
self.pdbfile = StringIO(self.pdbfilestring)
self.pdbfilename = sanitizeFileName(form["PDB"].filename)
else:
raise WebOptionsError('You need to specify a pdb ID or upload a pdb file.')
if "PKACALCMETHOD" in form:
if form["PKACALCMETHOD"].value != 'none':
if 'PH' not in form:
raise WebOptionsError('Please provide a pH value.')
phHelp = 'Please choose a pH between 0.0 and 14.0.'
try:
ph = float(form["PH"].value)
except ValueError:
raise WebOptionsError('The pH value provided must be a number! ' + phHelp)
if ph < 0.0 or ph > 14.0:
text = "The entered pH of %.2f is invalid! " % ph
text += phHelp
raise WebOptionsError(text)
self.runoptions['ph'] = ph
#build propka and pdb2pka options
if form['PKACALCMETHOD'].value == 'propka':
self.runoptions['ph_calc_method'] = 'propka'
self.runoptions['ph_calc_options'] = utilities.createPropkaOptions(ph, False)
if form['PKACALCMETHOD'].value == 'pdb2pka':
self.runoptions['ph_calc_method'] = 'pdb2pka'
self.runoptions['ph_calc_options'] = {'output_dir': 'pdb2pka_output',
'clean_output': True,
'pdie': 8,
'sdie': 80,
'pairene': 1.0}
self.otheroptions['apbs'] = "INPUT" in form
self.otheroptions['whitespace'] = "WHITESPACE" in form
if self.ff == 'user':
if "USERFF" in form and form["USERFF"].filename:
self.userfffilename = sanitizeFileName(form["USERFF"].filename)
self.userffstring = form["USERFF"].value
self.runoptions['userff'] = StringIO(form["USERFF"].value)
else:
text = "A force field file must be provided if using a user created force field."
raise WebOptionsError(text)
if "USERNAMES" in form and form["USERNAMES"].filename:
self.usernamesfilename = sanitizeFileName(form["USERNAMES"].filename)
self.usernamesstring = form["USERNAMES"].value
self.runoptions['usernames'] = StringIO(form["USERNAMES"].value)
else:
text = "A names file must be provided if using a user created force field."
raise WebOptionsError(text)
if "FFOUT" in form and form["FFOUT"].value != "internal":
self.runoptions['ffout'] = form["FFOUT"].value
self.runoptions['chain'] = "CHAIN" in form
self.runoptions['typemap'] = "TYPEMAP" in form
self.runoptions['neutraln'] = "NEUTRALN" in form
self.runoptions['neutralc'] = "NEUTRALC" in form
self.runoptions['drop_water'] = "DROPWATER" in form
if (self.runoptions['neutraln'] or self.runoptions['neutraln']) and \
self.ff != 'parse':
raise WebOptionsError('Neutral N-terminus and C-terminus require the PARSE forcefield.')
if "LIGAND" in form and form['LIGAND'].filename:
self.ligandfilename=sanitizeFileName(form["LIGAND"].filename)
ligandfilestring = form["LIGAND"].value
# for Windows and Mac style newline compatibility for pdb2pka
ligandfilestring = ligandfilestring.replace('\r\n', '\n')
self.ligandfilestring = ligandfilestring.replace('\r', '\n')
self.runoptions['ligand'] = StringIO(self.ligandfilestring)
if self.pdbfilename[-4:]==".pdb":
self.pqrfilename = "%s.pqr" % self.pdbfilename[:-4]
else:
self.pqrfilename = "%s.pqr" % self.pdbfilename
#Always turn on summary and verbose.
self.runoptions['verbose'] = True
self.runoptions['selectedExtensions'] = ['summary']
def __init__(self, form):
'''Gleans all information about the user selected options and uploaded files.
Also validates the user input. Raises WebOptionsError if there is any problems.'''
#options to pass to runPDB2PQR
self.runoptions = {}
#Additional options to pass to google analytics along with the run options.
#These are included in has_key(), __contains__(), and __getitem__() calls.
self.otheroptions = {}
self.runoptions['debump'] = form.has_key("DEBUMP")
self.runoptions['opt'] = form.has_key("OPT")
if form.has_key('FF'):
self.ff = form["FF"].value.lower()
else:
raise WebOptionsError('Force field type missing from form.')
if form.has_key("PDBID") and form["PDBID"].value and form[
"PDBSOURCE"].value == 'ID':
self.pdbfile = utilities.getPDBFile(form["PDBID"].value)
if self.pdbfile is None:
raise WebOptionsError('The pdb ID provided is invalid.')
self.pdbfilestring = self.pdbfile.read()
self.pdbfile = StringIO(self.pdbfilestring)
self.pdbfilename = form["PDBID"].value
elif form.has_key("PDB") and form["PDB"].filename and form[
"PDBSOURCE"].value == 'UPLOAD':
self.pdbfilestring = form["PDB"].value
self.pdbfile = StringIO(self.pdbfilestring)
self.pdbfilename = sanitizeFileName(form["PDB"].filename)
else:
raise WebOptionsError(
'You need to specify a pdb ID or upload a pdb file.')
if form.has_key("PROPKA"):
if not form.has_key('PH'):
raise WebOptionsError('Please provide a pH value.')
phHelp = 'Please choose a pH between 0.0 and 14.0.'
try:
ph = float(form["PH"].value)
except ValueError:
raise WebOptionsError(
'The pH value provided must be a number! ' + phHelp)
if ph < 0.0 or ph > 14.0:
text = "The entered pH of %.2f is invalid! " % ph
text += phHelp
raise WebOptionsError(text)
self.runoptions['ph'] = ph
#build propka options
self.runoptions['propkaOptions'] = utilities.createPropkaOptions(
ph, True)
self.otheroptions['apbs'] = form.has_key("INPUT")
self.otheroptions['whitespace'] = form.has_key("WHITESPACE")
if self.ff == 'user':
if form.has_key("USERFF") and form["USERFF"].filename:
self.userfffilename = sanitizeFileName(form["USERFF"].filename)
self.userffstring = form["USERFF"].value
self.runoptions['userff'] = StringIO(form["USERFF"].value)
else:
text = "A force field file must be provided if using a user created force field."
raise WebOptionsError(text)
if form.has_key("USERNAMES") and form["USERNAMES"].filename:
self.usernamesfilename = sanitizeFileName(
form["USERNAMES"].filename)
self.usernamesstring = form["USERNAMES"].value
self.runoptions['usernames'] = StringIO(
form["USERNAMES"].value)
else:
text = "A names file must be provided if using a user created force field."
raise WebOptionsError(text)
if form.has_key("FFOUT") and form["FFOUT"].value != "internal":
self.runoptions['ffout'] = form["FFOUT"].value
self.runoptions['chain'] = form.has_key("CHAIN")
self.runoptions['typemap'] = form.has_key("TYPEMAP")
self.runoptions['neutraln'] = form.has_key("NEUTRALN")
self.runoptions['neutralc'] = form.has_key("NEUTRALC")
if (self.runoptions['neutraln'] or self.runoptions['neutraln']) and \
self.ff != 'parse':
raise WebOptionsError(
'Neutral N-terminus and C-terminus require the PARSE forcefield.'
)
if form.has_key("LIGAND") and form['LIGAND'].filename:
self.ligandfilename = sanitizeFileName(form["LIGAND"].filename)
ligandfilestring = form["LIGAND"].value
# for Windows and Mac style newline compatibility for pdb2pka
ligandfilestring = ligandfilestring.replace('\r\n', '\n')
self.ligandfilestring = ligandfilestring.replace('\r', '\n')
self.runoptions['ligand'] = StringIO(self.ligandfilestring)
if self.pdbfilename[-4:] == ".pdb":
self.pqrfilename = "%s.pqr" % self.pdbfilename[:-4]
else:
self.pqrfilename = "%s.pqr" % self.pdbfilename
#Always turn on summary and verbose.
self.runoptions['verbose'] = True
self.runoptions['selectedExtensions'] = ['summary']