clipper::MAtom Class Reference
#include <minimol.h>
Public Member Functions | |
| MAtom () | |
| null constructor | |
| MAtom (const clipper::Atom &atom) | |
| constructor: from clipper::Atom | |
| const String & | id () const |
| get atom ID, e.g. " N ", " CA ", " CG1", " CA :A" | |
| void | set_id (const String &s) |
| set atom ID | |
| String | name () const |
| get atom name, i.e. the ID, omitting any alternate conformation code | |
| void | set_name (const String s, const String altconf="") |
| set full id | |
| const String & | element () const |
| get element e.g. H, C, Zn2+ | |
| const Coord_orth & | coord_orth () const |
| get orth coordinate | |
| const ftype & | occupancy () const |
| get occupancy | |
| const ftype & | u_iso () const |
| get isotropic U | |
| const U_aniso_orth & | u_aniso_orth () const |
| get anisotropic U | |
| void | set_element (const String &s) |
| set element | |
| void | set_coord_orth (const Coord_orth &s) |
| set coord_orth | |
| void | set_occupancy (const ftype &s) |
| set occupancy | |
| void | set_u_iso (const ftype &s) |
| set u_iso | |
| void | set_u_aniso_orth (const U_aniso_orth &s) |
| set u_aniso | |
| void | transform (const RTop_orth rt) |
| apply transform to object | |
| const Atom & | atom () const |
| explicitly get atom | |
| Atom & | atom () |
| explicitly set atom | |
| MAtom & | copy (const MAtom &other, const MM::COPY &mode) |
| configureable copy function | |
Static Public Member Functions | |
| static String | id_tidy (const String &id) |
| convert ID to std format | |
| static bool | id_match (const String &id1, const String &id2, const MM::MODE &mode) |
| convert ID to std format | |
Detailed Description
MiniMol atom object.
The MiniMol atom is derived from the basic clipper::Atom, with the addition of an 'id', which is a unique identifier within a monomer in accordance with the mmCIF definition.
In addition, it is a clipper::PropertyManager, which means you can add labelled properties of any type to the object. These may be simple strings, or complex objects such as maps, function objects, or whatever.
The most commonly used properties are:
- "CID" The original CID of this atom in an MMDB heirarchy.
The id() is the unique key which identifies an atom.
Member Function Documentation
configureable copy function
copy from other atom. mode can be MM::COPY_M, COPY_P, COPY_MP, COPY_C, COPY_MC, COPY_PC, COPY_MPC, where M means copy members, P means copy PropertyMananger properties, and C means copy children. Children are copied with the same option. The values 'MEMBERS', 'PROPERTIES', 'CHILDREN' can also be used.
References atom().
The documentation for this class was generated from the following files:
- minimol.h
- minimol.cpp
