#include <Protein.h>
It probably should be called chain, but it is not :-)
check_protein.cc, pdb_align.cc, pdb_align_points.cc, pdb_distance.cc, and pdb_split.cc.
Definition at line 41 of file Protein.h.
Public Types | |
| typedef std::pair< Atom::Index, Atom::Index > | Bond |
| typedef std::vector< Residue > ::iterator | Residues_iterator |
| typedef std::vector< Residue > ::const_iterator | Const_residues_iterator |
Public Member Functions | |
| Protein (std::istream &in, bool print_errors=false) | |
| Protein () | |
| char | chain () const |
| void | set_chain (char c) |
| Residues_iterator | residues_begin () |
| Residues_iterator | residues_end () |
| Const_residues_iterator | residues_begin () const |
| Const_residues_iterator | residues_end () const |
| Atoms_iterator | atoms_begin () |
| Atoms_iterator | atoms_end () |
| Const_atoms_iterator | atoms_begin () const |
| Const_atoms_iterator | atoms_end () const |
| unsigned int | number_of_atoms () const |
| Bonds_iterator | bonds_begin () const |
| Bonds_iterator | bonds_end () const |
| unsigned int | number_of_bonds () const |
| const Residue & | residue_containing_atom (Atom::Index atom_index) const |
| Residue & | residue_containing_atom (Atom::Index atom_index) |
| const Atom & | atom (Atom::Index atom_index) const |
| void | set_atom (Atom::Index atom_index, const Atom &a) |
| std::vector< Residue::Type > | sequence () const |
| void | write (std::ostream &out) const |
| void | write_pdb (std::ostream &out) const |
| void | dump (std::ostream &out) const |
| const Residue & | residue (Residue::Index i) const |
| bool | has_residue (Residue::Index i) const |
| bool | has_bonds () const |
| void | set_has_bonds (bool tf) |
Classes | |
| class | Atoms_iterator |
| An iterator through the atoms of a dsrpdb::Protein. More... | |
| class | Bonds_iterator |
| An iterator through the bonds of a dsrpdb::Protein. More... | |
| class | Const_atoms_iterator |
| An iterator through the atoms of a dsrpdb::Protein. More... | |
| typedef std::pair<Atom::Index,Atom::Index> dsrpdb::Protein::Bond |
| typedef std::vector<Residue>::iterator dsrpdb::Protein::Residues_iterator |
| typedef std::vector<Residue>::const_iterator dsrpdb::Protein::Const_residues_iterator |
| dsrpdb::Protein::Protein | ( | std::istream & | in, | |
| bool | print_errors = false | |||
| ) |
Build a protein from a pdb file. See check_protein.cc for an example of using this to read a pdb file.
The optional bool controls whether errors (such as unparsable PDB lines). Set it to false to disable printing errors.
| dsrpdb::Protein::Protein | ( | ) |
Default.
| char dsrpdb::Protein::chain | ( | ) | const |
| void dsrpdb::Protein::set_chain | ( | char | c | ) |
Set the chain id.
| Residues_iterator dsrpdb::Protein::residues_begin | ( | ) | [inline] |
Iterate through all the residues.
Definition at line 73 of file Protein.h.
Referenced by dsrpdb::simplified_coordinates_and_bonds().
| Residues_iterator dsrpdb::Protein::residues_end | ( | ) | [inline] |
End iterator through the residues.
Definition at line 77 of file Protein.h.
Referenced by dsrpdb::simplified_coordinates_and_bonds().
| Const_residues_iterator dsrpdb::Protein::residues_begin | ( | ) | const [inline] |
| Const_residues_iterator dsrpdb::Protein::residues_end | ( | ) | const [inline] |
| Atoms_iterator dsrpdb::Protein::atoms_begin | ( | ) |
Begin iterating through the atoms.
Referenced by dsrpdb::all_coordinates_begin(), dsrpdb::backbone_coordinates_begin(), dsrpdb::ca_coordinates_begin(), and dsrpdb::protein_backbone_indices_begin().
| Atoms_iterator dsrpdb::Protein::atoms_end | ( | ) |
End iterating through the atoms.
Referenced by dsrpdb::all_coordinates_begin(), dsrpdb::all_coordinates_end(), dsrpdb::backbone_coordinates_begin(), dsrpdb::backbone_coordinates_end(), dsrpdb::ca_coordinates_begin(), dsrpdb::ca_coordinates_end(), dsrpdb::protein_backbone_indices_begin(), and dsrpdb::protein_backbone_indices_end().
| Const_atoms_iterator dsrpdb::Protein::atoms_begin | ( | ) | const |
Begin iterating through the atoms.
| Const_atoms_iterator dsrpdb::Protein::atoms_end | ( | ) | const |
End iterating through the atoms.
| unsigned int dsrpdb::Protein::number_of_atoms | ( | ) | const |
This is non-const time.
| Bonds_iterator dsrpdb::Protein::bonds_begin | ( | ) | const |
Begin iterating through all the bonds
| Bonds_iterator dsrpdb::Protein::bonds_end | ( | ) | const |
| unsigned int dsrpdb::Protein::number_of_bonds | ( | ) | const |
This is non-const time.
| const Residue& dsrpdb::Protein::residue_containing_atom | ( | Atom::Index | atom_index | ) | const |
Return the dsrpdb::Residue which contains the atoms with a particular index.
This operation is currently linear in the number of residues. Making it logrighmic should be easy, but it isn't done.
| Residue& dsrpdb::Protein::residue_containing_atom | ( | Atom::Index | atom_index | ) |
Return the dsrpdb::Residue which contains the atom witha particular index.
| const Atom& dsrpdb::Protein::atom | ( | Atom::Index | atom_index | ) | const |
| void dsrpdb::Protein::set_atom | ( | Atom::Index | atom_index, | |
| const Atom & | a | |||
| ) |
Return the atom which has the pdb index passed.
| std::vector<Residue::Type> dsrpdb::Protein::sequence | ( | ) | const |
The sequence of residue types.
| void dsrpdb::Protein::write | ( | std::ostream & | out | ) | const |
Write as part of pdb file.
| void dsrpdb::Protein::write_pdb | ( | std::ostream & | out | ) | const |
Write a pdb file.
See check_protein.cc for an example of using this to write a pdb file.
| void dsrpdb::Protein::dump | ( | std::ostream & | out | ) | const |
Dump as human readable.
| const Residue& dsrpdb::Protein::residue | ( | Residue::Index | i | ) | const |
Return the residue with a particular index.
| bool dsrpdb::Protein::has_residue | ( | Residue::Index | i | ) | const |
Return true if there is a residue with that index.
| bool dsrpdb::Protein::has_bonds | ( | ) | const [inline] |
| void dsrpdb::Protein::set_has_bonds | ( | bool | tf | ) | [inline] |