IMP::atom::AtomType Class Reference

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Detailed Description

The type of an atom.

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 heterogen 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 heterogen 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

Public Member Functions
	AtomType (std::string nm)
Related Functions
(Note that these are not member functions.)
AtomType	add_atom_type (std::string name, Element e)
	Create a new AtomType.
const AtomType	AT_CA
const AtomType	AT_N
const AtomType	AT_UNKNOWN

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Friends And Related Function Documentation

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

Create a new AtomType.

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]

const AtomType AT_N [related]

const AtomType AT_UNKNOWN [related]

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

• Atom.h
• atom/__init__.py