def __init__(self, program='sander', verbosity=1):
# define instance data
self.program = program # which program we're creating the input file for
self.cntrl_obj = cntrl(
) # object with cntrl namelist vars in a dictionary
self.ewald_obj = ewald(
) # object with ewald namelist vars in a dictionary
self.pb_obj = pb() # object with pb namelist vars in a dictionary
self.qmmm_obj = qmmm(
) # object with qmmm namelist vars in a dictionary
self.verbosity = 0 # verbosity level: 0 -- print nothing
# 1 -- print errors
# 2 -- print errors and warnings
# 3 -- print errors, warnings, and notes
self.cards = [
] # array that has all of the input cards that come after namelists
self.cntrl_nml = {} # dictionary with cntrl namelist vars
self.cntrl_nml_defaults = {
} # dictionary with default cntrl namelist vars
self.ewald_nml = {} # dictionary with ewald namelist vars
self.ewald_nml_defaults = {
} # dictionary with default ewald namelist vars
self.pb_nml = {} # dictionary with pb namelist vars
self.pb_nml_defaults = {} # dictionary with default pb namelist vars
self.qmmm_nml = {} # dictionary with qmmm namelist vars
self.qmmm_nml_defaults = {
} # dictionary with default qmmm namelist vars
self.valid_namelists = [
] # array with valid namelists for each program
self.title = 'mdin prepared by mdin.py' # title for the mdin file
self.extra_lines = ''
if self.program == "sander":
self.cntrl_nml = self.cntrl_obj.sander
self.ewald_nml = self.ewald_obj.sander
self.pb_nml = self.pb_obj.sander
self.qmmm_nml = self.qmmm_obj.sander
self.valid_namelists = ['cntrl', 'ewald', 'qmmm', 'pb']
elif self.program == "sander.APBS":
self.cntrl_nml = self.cntrl_obj.sander
self.pb_nml = self.pb_obj.sanderAPBS
self.valid_namelists = ['cntrl', 'apbs']
elif self.program == "pmemd":
self.cntrl_nml = self.cntrl_obj.pmemd
self.ewald_nml = self.ewald_obj.pmemd
self.valid_namelists = ['cntrl', 'ewald']
else:
print >> stderr, 'Error: program (%s) unrecognized!' % self.program
return
self.cntrl_nml_defaults = self.cntrl_nml.copy()
self.ewald_nml_defaults = self.ewald_nml.copy()
self.pb_nml_defaults = self.pb_nml.copy()
self.qmmm_nml_defaults = self.qmmm_nml.copy()
def __init__(self, program = 'sander', verbosity = 1):
# define instance data
self.program = program # which program we're creating the input file for
self.cntrl_obj = cntrl() # object with cntrl namelist vars in a dictionary
self.ewald_obj = ewald() # object with ewald namelist vars in a dictionary
self.pb_obj = pb() # object with pb namelist vars in a dictionary
self.qmmm_obj = qmmm() # object with qmmm namelist vars in a dictionary
self.verbosity = 0 # verbosity level: 0 -- print nothing
# 1 -- print errors
# 2 -- print errors and warnings
# 3 -- print errors, warnings, and notes
self.cards = [] # array that has all of the input cards that come after namelists
self.cntrl_nml = {} # dictionary with cntrl namelist vars
self.cntrl_nml_defaults = {} # dictionary with default cntrl namelist vars
self.ewald_nml = {} # dictionary with ewald namelist vars
self.ewald_nml_defaults = {} # dictionary with default ewald namelist vars
self.pb_nml = {} # dictionary with pb namelist vars
self.pb_nml_defaults = {} # dictionary with default pb namelist vars
self.qmmm_nml = {} # dictionary with qmmm namelist vars
self.qmmm_nml_defaults = {} # dictionary with default qmmm namelist vars
self.valid_namelists = [] # array with valid namelists for each program
self.title = 'mdin prepared by mdin.py' # title for the mdin file
self.extra_lines = ''
if self.program == "sander":
self.cntrl_nml = self.cntrl_obj.sander
self.ewald_nml = self.ewald_obj.sander
self.pb_nml = self.pb_obj.sander
self.qmmm_nml = self.qmmm_obj.sander
self.valid_namelists = ['cntrl','ewald','qmmm','pb']
elif self.program == "sander.APBS":
self.cntrl_nml = self.cntrl_obj.sander
self.pb_nml = self.pb_obj.sanderAPBS
self.valid_namelists = ['cntrl','apbs']
elif self.program == "pmemd":
self.cntrl_nml = self.cntrl_obj.pmemd
self.ewald_nml = self.ewald_obj.pmemd
self.valid_namelists = ['cntrl','ewald']
else:
print >> stderr, 'Error: program (%s) unrecognized!' % self.program
return
self.cntrl_nml_defaults = self.cntrl_nml.copy()
self.ewald_nml_defaults = self.ewald_nml.copy()
self.pb_nml_defaults = self.pb_nml.copy()
self.qmmm_nml_defaults = self.qmmm_nml.copy()