#include <Residue.h>
All the information concerning atoms and bonds for each residue is stored here. To add atoms to residues, new residues, or bonds to residues, look in Residue_data.cc. There is documentation there of what you need to do.
Definition at line 42 of file Residue.h.
Public Types | |
| typedef PDB_index< Residue > | Index |
| typedef std::pair< Atom::Index, Atom::Index > | Bond |
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typedef small_map< Atom_label, Atom > | Atoms |
| typedef std::vector< Bond >::const_iterator | Bonds_iterator |
| typedef Atoms::iterator | Atoms_iterator |
| typedef Atoms::const_iterator | Const_atoms_iterator |
| enum | Type |
| enum | Atom_label |
Public Member Functions | |
| Residue () | |
| Residue (Type al) | |
| Type | type () const |
| Bonds_iterator | bonds_begin () const |
| Bonds_iterator | bonds_end () const |
| unsigned int | number_of_bonds () 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 |
| bool | has_atom (Atom_label al) const |
| bool | can_have_atom (Atom_label al) const |
| const Atom & | atom (Atom_label al) const |
| Atom_label | atom_label (Atom::Index model_index) const |
| void | set_atom (Atom_label al, const Atom &a) |
| void | set_atom_from_string (const char *str, const Atom &a) |
| Atom::Index | last_atom_index () const |
| Index | index () const |
| void | set_index (Index i) |
| void | dump (std::ostream &out) const |
| void | write (char chain, std::ostream &out) const |
| Point | sidechain_point () const |
| void | set_has_bonds (bool tf) |
| bool | has_bonds () const |
Static Public Member Functions | |
| static Type | type (const std::string &st) |
| static std::string | type_string (Type rl) |
| static Atom::Type | element (Atom_label al) |
| static std::string | atom_label_string (Atom_label al) |
| static Atom_label | atom_label (const char *c) |
Protected Member Functions | |
| Atom::Index | min_atom_index () const |
Friends | |
| class | Protein |
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An iterator to list all the atoms.
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A bond between two atoms in a residue. The ints refer the the atom index. |
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Return a list of all the bonds in the residue.
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An iterator to list all the atoms.
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The type for storing residue indices in the PDB.
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The labels of atoms within residues. These are the labels for each atom in each residue. The identifiers are attempting to following the PDB specs. Feel free to add more if needed. AL_N must be before AL_CA which must be before AL_C to get the backbone order correct. |
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The labels for the types of residues.
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Default constructor. Makes and invalid residue.
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Make a residue of a given type.
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Return the data for an atom.
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Return an atom label from a string. Note, this label may be adjusted when the atoms is added to a residue to address naming inconsistencies. |
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Return the label of the atom with this index.
Referenced by set_atom_from_string(). |
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return the string corresponding to an atom label
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Return a list of the labels of all the atoms which are present.
Definition at line 153 of file Residue.h. References dsrpdb::small_map< Key, Data >::begin(). |
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Return a list of the labels of all the atoms which are present.
Definition at line 140 of file Residue.h. References dsrpdb::small_map< Key, Data >::begin(). |
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End iterating through the atoms.
Definition at line 158 of file Residue.h. References dsrpdb::small_map< Key, Data >::end(). |
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End iterating through the atoms.
Definition at line 145 of file Residue.h. References dsrpdb::small_map< Key, Data >::end(). |
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Begin iterating through the list of all the bonds. Note that the iterator will be invalidated if the residue is changed. Note that if Residue::has_bonds() is false, this returns an empty sequence. |
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End bond iteration.
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Return true if residues of this type can have atoms of that type.
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Write it for debugging.
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Return the element corresponding to an atom label.
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Return true if the atom is in the atoms() list.
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Return whether this residue has the inter-atom bonds computed.
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The index for the residue. This is 0 based index so it is the PDB index -1. |
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The index of the last atom in the residue.
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The number of atoms present in the residue.
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The number of atoms present in the residue.
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Set an atom. If the atom is not already there, then the bonds iterators are invalidated. Referenced by set_atom_from_string(). |
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Set an atom using a string as a label.
Definition at line 188 of file Residue.h. References atom_label(), and set_atom(). |
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Set whether all the inter-atom bonds are present or not. This must be true before Residue::bonds_begin() is called. |
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Set the index for the residue.
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Return a point representing the sidechain. If the sidechain is empty this returns the CA location. Otherwise it returns the location of some atom or the average of some atom locations. |
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Convert a string for an amino acid type into a tag.
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The label for the residue.
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A string so you can write an amino acid type.
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Write the lines for a pdb file.
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