def _parse_bias_file(bias_filename):
"""
Return a list of bias positions and force constants from a "bias file" of
the format:
bias_position1 force_constant1 bias_position2 force_constant2 ...
where any number of bias specifications are permitted.
"""
bias_positions = []
force_constants = []
for i,line in enumerate(open(bias_filename,'r')):
try:
line = line[:line.index('#')] # ignore comments
except ValueError:
pass
if len(line) > 0: # ignore empty lines
tokens = line.strip().split()
if len(bias_positions) == len(force_constants) == 0:
dim = len(tokens)/2
else:
if len(tokens)/2 != dim:
_exit('Bad harmonic bias specification on line %d of %s'
%(i+1,bias_filename))
bias_positions.append([float(r0) for r0 in tokens[0::2]])
force_constants.append([float(k0) for k0 in tokens[1::2]])
return bias_positions,force_constants
def _checkInput(self):
pj_amber_job._checkInput(self)
# Check that all umbrellas are the same temperature. The reduced
# energies calculated in this module do not account for replicas
# running at different temperatures.
#
temp0 = self.states.state_params_are_same('cntrl','temp0')
if not temp0:
_exit('All temperatures MUST be the same when using AMBER-US.')
self.beta = 1./(at.KB*temp0)
# Umbrella sampling state information.
#
setup_us_states_from_configobj(self.states,self.keywords,self.verbose)
def setup_us_states_from_configobj(states, keywords, verbose=False):
"""
Augment a set of AMBER states to include umbrella sampling state
information (i.e. restraint information) from a ConfigObj.
"""
# Umbrella Sampling Parameters
#
nreplicas = len(states)
bias_filename = keywords.get('BIAS_FILE')
if bias_filename is not None:
try:
bias_positions,force_constants = _parse_bias_file(bias_filename)
except IOError:
_exit('Problem reading BIAS_FILE = %s'%bias_filename)
elif (keywords.get('FORCE_CONSTANTS') is not None
and keywords.get('BIAS_POSITIONS') is not None):
force_constants = _parse_state_params(
keywords.get('FORCE_CONSTANTS'))
bias_positions = _parse_state_params(
keywords.get('BIAS_POSITIONS'))
else:
_exit('No bias specifications! Either BIAS_FILE or BIAS_POSITIONS and '
'FORCE_CONSTANTS must be specified.')
if len(bias_positions) != len(force_constants):
_exit('Number of FORCE_CONSTANTS not equal to number of BIAS_POSITIONS')
if (len(bias_positions) != nreplicas
or len(force_constants) != nreplicas):
_exit('Expected %d umbrella parameter sets, but instead found %d '
'FORCE_CONSTANTS and %d BIAS_POSITIONS'
%(nreplicas,len(force_constants),len(bias_positions)))
# Look for a restraint template (try the basename?)
basename = keywords.get('ENGINE_INPUT_BASENAME')
if keywords.get('AMBER_RESTRAINT_TEMPLATE') is not None:
restraint_template = keywords.get('AMBER_RESTRAINT_TEMPLATE')
else:
restraint_template = '%s.RST'%basename
if verbose:
print 'Using restraint template file: %s'%restraint_template
# Read the restraint template and then modify the restraint objects.
for n,state in enumerate(states):
state.add_restraints(restraint_template)
state.mdin.nmr_vars['DISANG'] = DISANG_NAME
state.rstr.set_restraint_params(r0=bias_positions[n],
k0=force_constants[n])