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

Generic wrapper for bootstrapping high-level applications which rely on some
combination of model and data, with special attention to geometry restraints
interpretation and f_model setup.  All of the bookkeeping required to
disambiguate crystal symmetry and Miller array conventions is performed
automatically.  This is superficially similar to the setup for phenix.refine
(and re-uses many of the methods in mmtbx.utils), but is somewhat simpler
(single-dataset only) and more general-purpose.

 
Package Contents
       
altloc_remediate
analyze_peptides
analyze_static_disorder
angle
anneal_real_space
b_factor_statistics
build_alt_confs
cablam_training
cablam_validate
cbetadev
cc_star
cdl_lookup
cif_as_mtz
clashscore
compare_ligands
compute_map_coefficients
density_modification
development_fem
distance_difference
dssp
dynamics
ensemble_validation
estimate_bijvoet_ratio
estimate_resolution_cutoff
extend_sidechains
f000
fab_elbow_angle
fake_f_obs
fest
fetch_pdb
find_peaks_holes
find_residue_in_pdb
find_tls_groups
find_torsion_angle_ncs_groups
flip_peptides
fmodel
fmodel_simple
fobs_minus_fobs_map
generate_disorder
geometry_minimization
get_related_ensemble
grow_density
interpolate
kinemage
lockit
map_box
map_to_model_histogram
map_to_structure_factors
map_value_at_point
maps
maximum_entropy_map
model_model_distances
model_vs_data
model_vs_sequence
molprobity
mon_lib_cif_triage
mp_geo
mtz2map
nqh_minimize
pdb_atom_selection
pdb_interpretation
pdb_view_ad_hoc
pdbtools
prepare_pdb_deposition
prune_model
r_factor_statistics
ramalyze
real_space_correlation
real_space_refine
rebuild_rotarama_cache
reciprocal_space_arrays
refine_anomalous_substructure
remove_outliers
rigid_bond_test
ringer
rna_validate
rotalyze
search_pdb_symmetry
secondary_structure_restraints
select_best_starting_model
show_r_factors_by_shell
show_suspicious_residues
simulate_low_res_data
sort_hetatms
ssm_rmsd_for_chains
strip_model
super
superpose
table_one
tls
tls_as_xyz
twin_map_utils
validate_ions
validate_ligands
validate_waters
validation_summary
verify_mon_lib_data
water_screen
xmanip
xtriage

 
Classes
       
__builtin__.object
load_model_and_data

 
class load_model_and_data(__builtin__.object)
    Class for processing command-line input and creating necessary objects.
The master_phil object should include cmdline_input_phil_str above, plus
any application-specific parameters.  Programs which use this can be invoked
using simple file arguments or explicit parameters, e.g.
 
  mmtbx.some_program model.pdb data.mtz
 
This class performs the following functions (mostly using other wrappers
elsewhere in mmtbx.utils):
  1. Process all arguments and extract as Python parameters
  2. Read in data and R-free flags
  3. Filter data and flags to be consistent if necessary
  4. Read in PDB file, either using the iotbx.pdb API, or if process_pdb_file
     is True, mmtbx.monomer_library.pdb_interpretation (using any CIF files
     included in the inputs)
  5. Extract the pdb_hierarchy and xray_structure objects.
  6. Create an mmtbx.f_model.manager object using the data, flags, and
     xray_structure.
If at any point the inputs are ambiguous, hopefully the program will stop
and raise an interpretable error.
 
  Methods defined here:
__init__(self, args, master_phil, update_f_part1_for='refinement', out=<open file '<stdout>', mode 'w'>, process_pdb_file=True, use_conformation_dependent_library=False, require_data=True, create_fmodel=True, prefer_anomalous=None, force_non_anomalous=False, set_wavelength_from_model_header=False, set_inelastic_form_factors=None, usage_string=None, create_log_buffer=False, remove_unknown_scatterers=False)
start_log_file(self, file_name)

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

 
Functions
       
StringIO(...)
StringIO([s]) -- Return a StringIO-like stream for reading or writing
generate_master_phil_with_inputs(phil_string, enable_twin_law=True, enable_automatic_twin_detection=False, enable_experimental_phases=False, enable_pdb_interpretation_params=False, enable_stop_for_unknowns=None, enable_full_geometry_params=False, enable_unmerged_data=False, as_phil_string=False)
generic_simple_input_phil()
load_and_validate_unmerged_data(f_obs, file_name, data_labels, log=<open file '<stdout>', mode 'w'>)
show_symmetry_error(file1, file2, symm1, symm2)
validate_input_params(params)

 
Data
        Auto = <libtbx.AutoType object>
cmdline_input_phil_base_str = '\ninput {\n include scope mmtbx.utils.xray_data_s...s_flag)s\n %(twin_law)s\n}\n%(pdb_interpretation)s\n'
division = _Feature((2, 2, 0, 'alpha', 2), (3, 0, 0, 'alpha', 0), 8192)