IMP  2.0.1
The Integrative Modeling Platform
IMP::atom::AtomType Class Reference

The type of an atom. More...

#include <IMP/atom/Atom.h>

Related Functions

(Note that these are not member functions.)

AtomType add_atom_type (std::string name, Element e)
 Create a new AtomType. More...
 
const AtomType AT_CA
 
const AtomType AT_N
 
const AtomType AT_UNKNOWN
 

Detailed Description

The standard Atom names in IMP are derived from the PDB names as follows:

  • the AtomType of a protein, DNA or RNA atom is the AtomType created from the PDB atom name string with spaces removed. For example, a protein C-alpha has the name AtomType("CA").
  • the AtomType for a hetero (HETATM) atom is the AtomType created by prefixing "HET:" to the PBD atom name string (this time without spaces removed). For example, a calcium atom is AtomType("HET:CA ").

We provide an AtomType instance for each of the standard PDB atom types. These have names such as IMP::atom::AT_N. The full list is elided for readability.

An AtomType implies an element (and hence a mass). While we have the associations set up for protein, DNA and RNA atoms, it may be necessary to add them for hetero atoms. You can use the add_atom_type() function to do this.

All atoms have the mass stored internally using a Mass decorator.

See Also
IMP::atom::Atom

Friends And Related Function Documentation

AtomType add_atom_type ( std::string  name,
Element  e 
)
related

This creates a new AtomType (returned) and sets up the mapping between the AtomType and the proper element.

Note
This method has not been tested. If you use it, please write a test and remove this comment.
See Also
atom_type_exists()
const AtomType AT_CA
related

Definition at line 62 of file atom/Atom.h.

const AtomType AT_N
related

Definition at line 60 of file atom/Atom.h.

const AtomType AT_UNKNOWN
related

Definition at line 58 of file atom/Atom.h.


The documentation for this class was generated from the following file: