mmtbx.kinemage package

Submodules

mmtbx.kinemage.validation module

mmtbx.kinemage.validation.add_fan(sites, delta, num_sigmas, angle_key)

mmtbx.kinemage.validation.add_spring(sites, num_sigmas, bond_key)

mmtbx.kinemage.validation.angle_outlier_as_kinemage(self)

Represent the angle outlier as a kinemage ‘fan’.

mmtbx.kinemage.validation.bond_outlier_as_kinemage(self)

Represent the bond outlier as a kinemage spring.

mmtbx.kinemage.validation.build_name_hash(pdb_hierarchy)

mmtbx.kinemage.validation.cbeta_dev(outliers, chain_id=None)

mmtbx.kinemage.validation.chiral_outlier_as_kinemage(self)

Represent a chiral volume outlier in kinemage

mmtbx.kinemage.validation.export_molprobity_result_as_kinemage(result, pdb_hierarchy, geometry, probe_file, keep_hydrogens=False, pdbID='PDB')

mmtbx.kinemage.validation.get_altid_controls(hierarchy)

mmtbx.kinemage.validation.get_angle_outliers(angle_proxies, chain, sites_cart, hierarchy)

mmtbx.kinemage.validation.get_bond_outliers(bond_proxies, chain, sites_cart, hierarchy)

mmtbx.kinemage.validation.get_chain_color(index)

mmtbx.kinemage.validation.get_default_header()

mmtbx.kinemage.validation.get_footer()

mmtbx.kinemage.validation.get_ions(ion_list)

mmtbx.kinemage.validation.get_kin_lots(chain, bond_hash, i_seq_name_hash, pdbID=None, index=0, show_hydrogen=True)

mmtbx.kinemage.validation.get_master_phil()

mmtbx.kinemage.validation.get_residue_bonds(residue)

mmtbx.kinemage.validation.make_multikin(f, processed_pdb_file, pdbID=None, keep_hydrogens=False)

mmtbx.kinemage.validation.make_probe_dots(hierarchy, keep_hydrogens=False)

mmtbx.kinemage.validation.midpoint(p1, p2)

mmtbx.kinemage.validation.pperp_outliers(hierarchy, chain)

mmtbx.kinemage.validation.rama_outliers(chain, pdbID, ram_outliers)

mmtbx.kinemage.validation.rotamer_outliers(chain, pdbID, rot_outliers)

mmtbx.kinemage.validation.run(args, pdb_interpretation_params=None)

mmtbx.kinemage.validation.usage()

Module contents

mmtbx.kinemage.kin_vec(start_key, start_xyz, end_key, end_xyz, width=None)