def __init__(self, command='PALES', verbose=False, debug=False, **free):
#euler, noeuler, qDa, qRms, qStd, w, excl, incl, verb, noverb, yzInv, noyzInv, rem, fixedDI, nofixedDI): pass
self.args, self.options = self.__parse_free__(free)
self.command = str(command)
self.verbose = bool(verbose)
self.debug = bool(debug)
if debug: loki.setLevel(logging.DEBUG)
elif verbose: loki.setLevel(logging.INFO)
def __init__(self, input, output=None, fixed_angles=None, rg_limits=None,
use_limits=True, seed=None, state=None, jump=None, tally=0,
tally_digits=3, name=None, verbose=False, debug=False):
# store and/or process inputs
self.input = str(input)
self.rg_limits = rg_limits
self.use_limits = bool(use_limits)
self.tally = int(tally)
self.tally_digits = int(tally_digits)
if output != None:
self.output = str(output)
else:
self.output = self.input + '-'
self.fixed_angles = fixed_angles
if fixed_angles != None:
if type(fixed_angles) != list:
if type(fixed_angles) == tuple:
self.fixed_angles = list(fixed_angles)
else:
self.fixed_angles = [fixed_angles]
for i in range(len(self.fixed_angles)):
if type(self.fixed_angles[i]) in [list, tuple]:
lo, hi = str(self.fixed_angles[i][0]), \
str(self.fixed_angles[i][1])
elif re.search('([0-9]+).+([0-9]+)', str(self.fixed_angles[i])):
lo, hi = re.search('([0-9]+).+([0-9]+)', \
str(self.fixed_angles[i])).groups()
else:
lo = hi = str(self.fixed_angles[i])
self.fixed_angles[i] = '%s..%s'%(lo,hi)
if name is None:
self.name = 'temp-%d'%os.getpid()
else:
self.name = str(name)
if debug: loki.setLevel(logging.DEBUG)
elif verbose: loki.setLevel(logging.INFO)
# check that required input files exist
if not os.path.isfile(self.input+'.seq'):
raise ArgumentError, ('No sequence file found.', 'Cyana')
if self.fixed_angles and not os.path.isfile(self.input + '.pdb'):
raise ArgumentError, ('No model PDB file found for angle fixes.',
'Cyana')
# setup temporary files
os.system('cp -f %s.seq %s.seq'%(self.input, self.name))
loki.info('Readied the sequence file for further use.')
if self.use_limits:
for suffix in ['lol', 'upl', 'aco', 'xplor']:
if os.path.isfile(self.input + '.' + suffix):
os.system('cp -f %s.%s %s.%s'%(self.input, suffix,
self.name, suffix))
loki.info("Readied a '%s' file for further use."%suffix)
if self.fixed_angles:
os.system('cp -f %s.pdb %s.pdb'%(self.input, self.name))
# initialise the random generator
self.randgen = Random(seed)
if state == None:
if jump != None:
if sys.version < '2.2':
loki.warn('Python older than 2.2. Problems may arise.')
elif sys.version > '2.2' and sys.version < '2.3':
# this should provide enough room for each run to be in
# unique state space
self.randgen.jumpahead(jump*self.amount*1.1)
else:
self.randgen.jumpahead(jump)
else:
self.randgen.setstate(state)
self.__last_macro_size__ = None
