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

 
Modules
       
cctbx.adp_restraints
cctbx.adptbx
cctbx.array_family.flex
cctbx.geometry_restraints
mmtbx.ias
iotbx
math
mmtbx
mmtbx.model_statistics
iotbx.pdb
scitbx
sys
mmtbx.utils
cctbx.xray

 
Classes
       
__builtin__.object
manager
xh_connectivity_table
xh_connectivity_table2

 
class manager(__builtin__.object)
     Methods defined here:
__init__(self, xray_structure, pdb_hierarchy, processed_pdb_files_srv=None, reference_sites_cart=None, restraints_manager=None, ias_xray_structure=None, refinement_flags=None, selection_moving=None, ias_manager=None, wilson_b=None, tls_groups=None, anomalous_scatterer_groups=None, log=None)
add_hydrogens(self, element='H', neutron=False, occupancy=0.01)
add_ias(self, fmodel=None, ias_params=None, file_name=None, build_only=False)
add_solvent(self, solvent_xray_structure, atom_name='O', residue_name='HOH', chain_id=' ', refine_occupancies=False, refine_adp=None)
adp_statistics(self)
append_single_atoms(self, new_xray_structure, atom_names, residue_names, nonbonded_types, refine_adp, refine_occupancies=None, nonbonded_charges=None, segids=None, i_seq_start=0, chain_id=' ', reset_labels=False)
backbone_selections(self, bool=True)
convert_atom(self, i_seq, scattering_type, atom_name, element, charge, residue_name, initial_occupancy=None, initial_b_iso=None, chain_id=None, segid=None, refine_occupancies=True, refine_adp=None)
Convert a single atom (usually water) to a different type, including
adjustment of the xray structure and geometry restraints.
deep_copy(self)
energies_adp(self, iso_restraints, compute_gradients, use_hd)
extend_xh_bonds(self, value=1.1)
extract_ncs_groups(self)
extract_water_residue_groups(self)
geometry_minimization(self, max_number_of_iterations=500, number_of_macro_cycles=5, selection=None, bond=False, nonbonded=False, angle=False, dihedral=False, chirality=False, planarity=False, generic_restraints=False, rmsd_bonds_termination_cutoff=0, rmsd_angles_termination_cutoff=0)
geometry_statistics(self, ignore_hd, molprobity_scores=False, cdl_restraints=False)
h_counts(self)
hd_group_selections(self)
idealize_h(self, selection=None, show=True)
isolated_atoms_selection(self)
number_of_ordered_solvent_molecules(self)
pdb_hierarchy(self, sync_with_xray_structure=False)
reference_model_restraints_manager(self, sites_cart, gradient_array, sigma=0.25)
reference_model_restraints_manager2(self, sites_cart, gradient_array, sigma=0.5)
remove_ias(self)
remove_solvent(self)
renumber_water(self)
reprocess_pdb_hierarchy_inefficient(self)
reset_adp_for_hydrogens(self)
reset_adp_of_hd_sites_to_be_equal(self)
reset_coordinates_for_exchangable_hd(self)
reset_occupancies_for_hydrogens(self)
restore_xh_bonds(self)
restraints_manager_energies_sites(self, geometry_flags=None, custom_nonbonded_function=None, compute_gradients=False, gradients=None, disable_asu_cache=False)
rms_b_iso_or_b_equiv_bonded(self)
rotatable_hd_selection(self)
scale_adp(self, scale_max, scale_min)
select(self, selection)
set_refine_individual_adp(self, selection_iso=None, selection_aniso=None)
set_refine_individual_sites(self, selection=None)
show_adp_statistics(self, prefix='', padded=False, pdb_deposition=False, out=None)
show_geometry_statistics(self, ignore_hd, message='', out=None)
show_groups(self, rigid_body=None, tls=None, out=None, text='Information about rigid groups')
show_h_counts(self, prefix='')
show_occupancy_statistics(self, out=None, text='')
show_rigid_bond_test(self, out=None, use_id_str=False, prefix='')
solvent_selection(self, include_ions=False)
sync_pdb_hierarchy_with_xray_structure(self)
update_anomalous_groups(self, out=<open file '<stdout>', mode 'w'>)
write_pdb_file(self, out=None, selection=None, xray_structure=None, return_pdb_string=False)
xh_connectivity_table(self)
xh_connectivity_table2(self)
xray_structure_macromolecule(self)

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

 
class xh_connectivity_table(__builtin__.object)
     Methods defined here:
__init__(self, geometry, xray_structure)
# XXX need angle information as well

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

 
class xh_connectivity_table2(__builtin__.object)
     Methods defined here:
__init__(self, geometry, xray_structure)

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

 
Functions
       
find_common_water_resseq_max(pdb_hierarchy)

 
Data
        division = _Feature((2, 2, 0, 'alpha', 2), (3, 0, 0, 'alpha', 0), 8192)
time_model_show = 0.0