mmtbx.conformation_dependent_library package

Submodules

mmtbx.conformation_dependent_library.altloc_weighting module

mmtbx.conformation_dependent_library.altloc_weighting.run(filename)

mmtbx.conformation_dependent_library.altloc_weighting.update_restraints(hierarchy, restraints_manager, altloc_weights_object={}, min_occ=0.5, sqrt_func=False, func_factor=1.0, bond_weighting=True, angle_weighting=True, log=None, verbose=False)

mmtbx.conformation_dependent_library.bond_angle_registry module

class mmtbx.conformation_dependent_library.bond_angle_registry.bond_angle_registry

Bases: dict

mmtbx.conformation_dependent_library.cdl_database module

class mmtbx.conformation_dependent_library.cdl_database.custom_cdl_dict

Bases: dict

mmtbx.conformation_dependent_library.cdl_database.run(args)

mmtbx.conformation_dependent_library.rdl_database module

mmtbx.conformation_dependent_library.rdl_database.get_rdl_database(truncate_restaints_to_gamma=False, apply_unrestrained_dihedrals=False, verbose=False)

mmtbx.conformation_dependent_library.rdl_database.run(args)

mmtbx.conformation_dependent_library.rotamers module

mmtbx.conformation_dependent_library.tst_cdl module

mmtbx.conformation_dependent_library.tst_cdl.convert_dict_to_excel(keys_number=4, column_number=6)

mmtbx.conformation_dependent_library.tst_cdl.convert_dict_to_gnuplot(keys_number=4, column_number=6, dales_format=False)

mmtbx.conformation_dependent_library.tst_cdl.convert_dict_to_kin2Dcont(keys_number=4, column_number=6)

mmtbx.conformation_dependent_library.tst_cdl.convert_dict_to_scilab(keys_number=4, column_number=6)

mmtbx.conformation_dependent_library.tst_cdl.get_managers(filename, testing=False, verbose=False)

mmtbx.conformation_dependent_library.tst_cdl.get_min_max_table()

mmtbx.conformation_dependent_library.tst_cdl.run(filename=None)

mmtbx.conformation_dependent_library.tst_cdl.run_apply(filename, testing=False, verbose=False)

mmtbx.conformation_dependent_library.tst_cdl.test_average(hierarchy, filename, restraints_manager)

mmtbx.conformation_dependent_library.tst_cdl.test_cdl_lookup(hierarchy, filename, restraints_manager)

mmtbx.conformation_dependent_library.tst_cdl.test_cis_trans_peptide(hierarchy, filename, restraints_manager)

mmtbx.conformation_dependent_library.tst_cdl.test_phi_psi_key(hierarchy, filename, restraints_manager)

mmtbx.conformation_dependent_library.tst_cdl.test_res_type(hierarchy, filename, restraints_manager)

mmtbx.conformation_dependent_library.tst_cdl.test_threes_methods()

mmtbx.conformation_dependent_library.test_interpolation module

mmtbx.conformation_dependent_library.tst_rdl module

mmtbx.conformation_dependent_library.utils module

mmtbx.conformation_dependent_library.utils.get_db_result(db, key, column)

mmtbx.conformation_dependent_library.utils.get_grid_values(residue_type, phi, psi, column=2)

mmtbx.conformation_dependent_library.utils.get_index(phi, psi)

mmtbx.conformation_dependent_library.utils.interpolate_2d(values, coords)

Given a 2-dimensional (4x4) grid of values and fractional coordinates, compute the value at these coordinates. Assumes that the grid covers the points from -1 to 2 in both dimensions, and the fracional coordinates are between 0 and 1.

mmtbx.conformation_dependent_library.utils.interpolate_at_point(p0, p1, p2, p3, t)

http://en.wikipedia.org/wiki/Cubic_Hermite_spline http://www.mvps.org/directx/articles/catmull

mmtbx.conformation_dependent_library.utils.print_grid(grid, phi, psi)

mmtbx.conformation_dependent_library.utils.round_to_ten(d)

Module contents

mmtbx.conformation_dependent_library.generate_dna_rna_fragments(hierarchy, geometry, length, include_non_linked=False, backbone_only=False, include_non_standard_bases=False, retain_selection='all', verbose=False)

mmtbx.conformation_dependent_library.generate_protein_fragments(hierarchy, geometry, length, include_non_linked=False, backbone_only=True, include_non_standard_peptides=False, include_d_amino_acids=False, allow_poly_ca=False, verbose=False)

mmtbx.conformation_dependent_library.generate_protein_threes(hierarchy, geometry, include_non_linked=False, backbone_only=True, include_non_standard_peptides=False, include_d_amino_acids=False, include_linked_via_restraints_manager=False, allow_poly_ca=False, cdl_class=False, omega_cdl=False, retain_selection='name ca or name c or name n or name o or name cb or name h', verbose=False)

mmtbx.conformation_dependent_library.generate_protein_tuples(hierarchy, geometry, length, include_non_linked=False, backbone_only=True, include_non_standard_peptides=False, include_d_amino_acids=False, allow_poly_ca=False, include_linked_via_restraints_manager=False, cdl_class=False, omega_cdl=False, retain_selection='name ca or name c or name n or name o or name cb or name h', verbose=False)

mmtbx.conformation_dependent_library.generate_residue_tuples(hierarchy, geometry, length, dna_rna_residues=False, include_non_linked=False, backbone_only=True, include_non_standard_residues=False, include_d_amino_acids=False, allow_poly_ca=False, cdl_class=False, omega_cdl=False, retain_selection='name ca or name c or name n or name o or name cb or name h', verbose=False)

mmtbx.conformation_dependent_library.get_restraint_values(threes, cdl_svl=False, interpolate=False)

mmtbx.conformation_dependent_library.restraints_show(restraints_values)

mmtbx.conformation_dependent_library.run(filename)

mmtbx.conformation_dependent_library.update_restraints(hierarchy, geometry, current_geometry=None, sites_cart=None, cdl_proxies=None, cis_pro_eh99=False, cdl_svl=False, ideal=True, esd=True, esd_factor=1.0, interpolate=False, log=None, verbose=False)