mmtbx.pdbtools
index
/net/chevy/raid1/nat/src/cctbx_project/mmtbx/pdbtools.py

Common manipulations of (macromolecular) model files.  This module is used
as a standalone program, phenix.pdbtools, but some components are also used
in phenix.refine, and it is also a dumping ground for individual related
functions.

 
Modules
       
cStringIO
cctbx.crystal
iotbx.crystal_symmetry_from_any
libtbx.easy_run
cctbx.array_family.flex
iotbx
libtbx
mmtbx
mmtbx.model_statistics
mmtbx.monomer_library
os
iotbx.pdb
random
mmtbx.refinement.rigid_body
libtbx.runtime_utils
scitbx
sys
mmtbx.utils

 
Classes
       
__builtin__.object
modify
libtbx.runtime_utils.target_with_save_result(__builtin__.object)
launcher
interpreter

 
class interpreter
     Methods defined here:
__init__(self, command_name, args, log)
process_args(self)
set_ppf(self)

 
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 modify(__builtin__.object)
     Methods defined here:
__init__(self, xray_structure, params, all_chain_proxies, log=None)
report_number_of_atoms_to_be_removed(self)

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

 
Functions
       
convert_semet_to_met(pdb_hierarchy, xray_structure)
Change the chemical identity of MSE residues to MET, without changing
coordinates.
finish_job(result)
move_waters(pdb_hierarchy, xray_structure, out)
Re-arranges the PDB hierarchy so that waters are located at the end of the
atom list.  This is done automatically in phenix.refine if water picking is
enabled, but the routine here is more flexible.  (Note that there is some
overlap in functionality with mmtbx.command_line.sort_hetatms, but the
latter module is significantly more complicated.)
normalize_occupancies(hierarchy, selection=None, xray_structure=None, log=None)
Reset the sum of occupancies for each residue_group to 1.0.  This will fail
if any (selected) atom_group has non-uniform occupancies.
remove_alt_confs(hierarchy, always_keep_one_conformer=False)
Remove all alternate conformers from the hierarchy.  Depending on the
value of always_keep_one_conformer, this will either remove any atom_group
with altloc other than blank or 'A', or it will remove any atom_group
beyond the first conformer found.
rename_chain_id(hierarchy, params, log)
renumber_residues(pdb_hierarchy, renumber_from=None, atom_selection=None, log=None)
run(args, command_name='phenix.pdbtools', out=<open file '<stdout>', mode 'w'>, replace_stderr=True)
set_atomic_charge(hierarchy, xray_structure, pdb_atoms, selection, charge, log=None)
Set the charge for selected atoms.  Note that both the hierarchy and the
xray_structure must be passed here - in the context of the pdbtools app,
the scattering_type attributes will override the atom's element and charge
when the structure is written out.
truncate_to_poly_ala(hierarchy)
Remove all protein sidechain atoms beyond C-alpha (as well as all hydrogens).
Does not change the chemical identity of the residues.
validate_params(params, callback=None)
write_model_file(pdb_hierarchy, crystal_symmetry, file_name, output_format)

 
Data
        division = _Feature((2, 2, 0, 'alpha', 2), (3, 0, 0, 'alpha', 0), 8192)
master_params = <libtbx.phil.scope object>
modify_params = <libtbx.phil.scope object>
modify_params_str = 'selection = None\n .type = atom_selection\n .hel..._seed = None\n .type = int\n .help = Random seed\n'