mmtbx.command_line.dynamics
index
/net/chevy/raid1/nat/src/cctbx_project/mmtbx/command_line/dynamics.py

# LIBTBX_SET_DISPATCHER_NAME phenix.dynamics

 
Modules
       
scitbx.array_family.flex
mmtbx.command_line.geometry_minimization
iotbx
os
libtbx.runtime_utils
sys

 
Classes
       
libtbx.runtime_utils.target_with_save_result(__builtin__.object)
launcher
mmtbx.command_line.geometry_minimization.run(__builtin__.object)
run

 
class launcher(libtbx.runtime_utils.target_with_save_result)
    
Method resolution order:
launcher
libtbx.runtime_utils.target_with_save_result
__builtin__.object

Methods defined here:
run(self)

Methods inherited from libtbx.runtime_utils.target_with_save_result:
__call__(self)
__init__(self, args, file_name, output_dir=None, log_file=None, job_title=None)

Data descriptors inherited from libtbx.runtime_utils.target_with_save_result:
__dict__
dictionary for instance variables (if defined)
__weakref__
list of weak references to the object (if defined)

 
class run(mmtbx.command_line.geometry_minimization.run)
    
Method resolution order:
run
mmtbx.command_line.geometry_minimization.run
__builtin__.object

Methods defined here:
atom_selection(self, prefix)
dynamics(self, prefix)
format_usage_message(self)
master_params(self)

Methods inherited from mmtbx.command_line.geometry_minimization.run:
__init__(self, args, log, use_directory_prefix=True)
addcbetar(self, prefix)
caller(self, func, prefix)
exclude_outliers_from_reference_restraints_selection(self)
generate_reference_restraints_selection(self)
get_restraints(self, prefix)
initialize(self, prefix)
min_max_mean_shift(self)
minimization(self, prefix)
process_inputs(self, prefix)
reference_restraints(self, prefix)
show_times(self)
write_geo_file(self, prefix)
write_pdb_file(self, prefix)

Data descriptors inherited from mmtbx.command_line.geometry_minimization.run:
__dict__
dictionary for instance variables (if defined)
__weakref__
list of weak references to the object (if defined)

 
Functions
       
finish_job(result)
master_params()
run_cartesian_dynamics(xray_structure, restraints_manager, params, log)
validate_params(params)

 
Data
        division = _Feature((2, 2, 0, 'alpha', 2), (3, 0, 0, 'alpha', 0), 8192)
master_params_str = '\nsilent = False\n .type = bool\nwrite_geo_file = ...mmtbx.dynamics.cartesian_dynamics.master_params\n}'