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

 
Modules
       
cctbx
cctbx.array_family.flex
iotbx
libtbx
cctbx.maptbx
scitbx.matrix
cctbx.miller
mmtbx
posixpath
os
scitbx
sys

 
Classes
       
__builtin__.object
geometry_restraints_manager_plus
home_restraints
residue_refine_constrained
residue_refine_restrained

 
class geometry_restraints_manager_plus(__builtin__.object)
     Methods defined here:
__init__(O, manager, home_sites_cart=None, home_restraints_list=None, home_dihedral_proxies=None)
dihedral_energies_show(O, energies_obj, f, prefix)
energies_add(O, energies_obj)
energies_show(O, energies_obj, f, prefix)
energies_sites(O, sites_cart, flags=None, custom_nonbonded_function=None, compute_gradients=False, gradients=None, disable_asu_cache=False, normalization=False)
select(O, selection=None, iselection=None)
show_sorted(O, flags=None, sites_cart=None, site_labels=None, f=None)

Data descriptors defined here:
angle_proxies
crystal_symmetry
dihedral_proxies
home_dihedral_proxies
home_restraints_list
home_sites_cart
manager
pair_proxies
plain_pair_sym_table
plain_pairs_radius
site_symmetry_table

 
class home_restraints(__builtin__.object)
     Methods defined here:
__init__(O, iselection, weight, slack)

Data descriptors defined here:
iselection
slack
weight

 
class residue_refine_constrained(__builtin__.object)
     Methods defined here:
__init__(O, pdb_hierarchy, residue, density_map, geometry_restraints_manager, real_space_target_weight, real_space_gradients_delta, lbfgs_termination_params)
compute_functional_and_gradients(O)
d_e_pot_d_sites(O, sites_moved)

Data descriptors defined here:
__dict__
dictionary for instance variables (if defined)
__weakref__
list of weak references to the object (if defined)

 
class residue_refine_restrained(__builtin__.object)
     Methods defined here:
__init__(O, pdb_hierarchy, residue, density_map, geometry_restraints_manager, real_space_target_weight, real_space_gradients_delta, lbfgs_termination_params)
compute_functional_and_gradients(O)

Data descriptors defined here:
__dict__
dictionary for instance variables (if defined)
__weakref__
list of weak references to the object (if defined)

 
Functions
       
compose_output_file_name(input_pdb_file_name, new_suffix)
compute_functional_lite(pdb_hierarchy, residue, density_map, geometry_restraints_manager, real_space_target_weight)
extract_map_coeffs(params, optional, miller_arrays)
fit_rotamers_simple(processed_pdb_file, fft_map, d_max, d_min)
get_atom_selection_bool(scope_extract, attr, processed_pdb_file, work_params)
get_best_rotamer(processed_pdb_file, fft_map, d_max, d_min)
get_master_phil()
get_rotamer_iterator(mon_lib_srv, residue, atom_selection_bool)
process_home_restraints_params(work_params, processed_pdb_file)
real_space_rigid_body_gradients_simple(unit_cell, density_map, sites_cart_0, center_of_mass, q, unit_quaternion_delta=0.01, translation_delta=0.3)
rotamer_score_and_choose_best(mon_lib_srv, density_map, pdb_hierarchy, geometry_restraints_manager, atom_selection_bool, real_space_target_weight, real_space_gradients_delta, lbfgs_termination_params, force_rotamer=False)
run(args, log=None)
run_coordinate_refinement(geometry_restraints_manager, selection_variable, density_map, real_space_gradients_delta, work_params, pdb_atoms=None, sites_cart=None, home_restraints_list=[], work_scatterers=None, unit_cell=None, d_min=None, weight_map=None, write_pdb_callback=None, log=None)
run_coordinate_refinement_driver(processed_pdb_file, geometry_restraints_manager, fft_map, real_space_gradients_delta, work_params, std_dev_weight_fft_map=None, write_pdb_callback=None, log=None)
write_pdb(file_name, input_pdb_file_name, processed_pdb_file, grm, new_suffix)

 
Data
        Auto = <libtbx.AutoType object>
coordinate_refinement_export_phil_str = 'finishing_geometry_minimization\n{\n cycles_max =...t\n }\n}\nlbfgs_max_iterations = 500\n .type = int\n'
coordinate_refinement_params_phil_str = 'coordinate_refinement {\n run = False\n .type ... }\n}\nlbfgs_max_iterations = 500\n .type = int\n\n}\n'
division = _Feature((2, 2, 0, 'alpha', 2), (3, 0, 0, 'alpha', 0), 8192)
real_space_params_phil_str = 'real_space_target_weight = 10\n .type = float\nre...ts_delta_resolution_factor = 1/3\n .type = float\n'