iotbx::pdb::hierarchy Namespace Reference

Hierarchy organizing PDB atom objects. More...

Classes
class	root_data
	Holder for root attributes (to be held by a shared_ptr). More...
class	model_data
	Holder for model attributes (to be held by a shared_ptr). More...
class	chain_data
	Holder for chain attributes (to be held by a shared_ptr). More...
class	residue_group_data
	Holder for residue_group attributes (to be held by a shared_ptr). More...
class	atom_group_data
	Holder for atom_group attributes (to be held by a shared_ptr). More...
class	atom_data
	Holder for atom attributes (to be held by a shared_ptr). More...
class	conformer_data
	Holder for conformer attributes (to be held by a shared_ptr). More...
class	residue_data
	Holder for residue attributes (to be held by a shared_ptr). More...
struct	atom_label_columns_formatter
	Not available in Python. More...
class	atom
	Atom attributes. More...
class	atom_group
	atom_group attributes. More...
class	residue_group
	residue_group attributes. More...
class	chain
	Chain attributes. More...
class	model
	Model attributes. More...
class	root
	Root attributes. More...
struct	overall_counts
struct	atom_selection_cache
class	residue
	Residue attributes. More...
class	conformer
	Conformer attributes. More...
class	atom_with_labels
Functions
void	residue_groups_as_pdb_string (stream_write &write, atom_label_columns_formatter &label_formatter, std::vector< residue_group > const &residue_groups, int interleaved_conf, bool atom_hetatm, bool sigatm, bool anisou, bool siguij)
	label_formatter chain_id must be set before this function is called.
void	models_as_pdb_string (stream_write &write, std::vector< model > const &models, bool append_end, int interleaved_conf, bool atom_hetatm, bool sigatm, bool anisou, bool siguij)

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Detailed Description

Hierarchy organizing PDB atom objects.

Data hierarchy:

  model
    parent
    id
    chain(s)
      parent
      id
      residue_group(s)
        parent
        resseq
        icode
        link_to_previous
        atom_group(s)
          parent
          altloc
          resname
          atom(s)
            parent
            name
            segid
            element
            charge
            serial
            xyz sigxyz
            occ sigocc
            b sigb
            uij siguij
            hetero

Convenience objects:

  residue
    parent
    resname
    resseq
    icode
    link_to_previous
    is_pure_main_conf
    atoms

A residue object is NOT a parent of the atoms.

  conformer
    parent
    altloc
    residues