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, bool output_break_records)
 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, bool output_break_records=true)
af::shared< unsigned > get_resid_sequence (af::shared< std::string > resid_list, af::shared< std::size_t > chain_break_list, std::string start, std::string stop)


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
            fp fdp
            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

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