clipper::MModel Class Reference

MiniMol model object. More...

#include <minimol.h>

Inheritance diagram for clipper::MModel:

List of all members.

Public Member Functions
Atom_list	atom_list () const
	return list of contained atoms
void	transform (const RTop_orth rt)
	apply transformation to object
int	size () const
	number of polymers in model
const MPolymer &	operator[] (const int &i) const
	get polymer
MPolymer &	operator[] (const int &i)
	set polymer
const MPolymer &	find (const String &n, const MM::MODE mode=MM::UNIQUE) const
	get polymer by id
MPolymer &	find (const String &n, const MM::MODE mode=MM::UNIQUE)
	set polymer by id
MModel	select (const String &sel, const MM::MODE mode=MM::UNIQUE) const
	create selection
int	lookup (const String &str, const MM::MODE &mode) const
	lookup polymer by id
void	insert (const MPolymer &add, int pos=-1)
	add polymer
MModel &	copy (const MModel &other, const MM::COPY &mode)
	configureable copy function
Friends
MModel	operator& (const MModel &m1, const MModel &m2)
	and operator
MModel	operator| (const MModel &m1, const MModel &m2)
	or operator

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Detailed Description

MiniMol model object.

The MiniMol model object constains a list of clipper::MPolymer.

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.

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Member Function Documentation

const MPolymer & clipper::MModel::find	(	const String &	n,
		const MM::MODE	mode = MM::UNIQUE
	)			const

get polymer by id

Lookup polymer by ID. Currently, mode is ignored.

Parameters:

	n	The monomer ID.
	mode	The search mode.

Returns:

The polymer.

References lookup(), and clipper::message.

MPolymer & clipper::MModel::find	(	const String &	n,
		const MM::MODE	mode = MM::UNIQUE
	)

set polymer by id

See MModel::find()

References lookup(), and clipper::message.

MModel clipper::MModel::select	(	const String &	sel,
		const MM::MODE	mode = MM::UNIQUE
	)			const

create selection

Creates a copy of this model containing only the polymers, monomers and atoms described by the selection string.

The selection string must be of the form 'X/Y/Z' where X is a polymer selection, Y is a monomer selection described under MMonomer::select(), and Z is an atom selection described under MAtom::select(). The polymer selection must contain a polymer ID or a comma separated list of polymer IDs, or '*' to select all polymers. Polymer IDs are described in s_mm_monomer_id.

See s_mm_selections for examples.

Parameters:

	sel	The selection string.
	mode	No effect.

Returns:

The selection as a new model.

References copy(), clipper::MPolymer::id_match(), clipper::MPolymer::id_tidy(), insert(), and clipper::String::split().

MModel & clipper::MModel::copy	(	const MModel &	other,
		const MM::COPY &	mode
	)

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 size().

Referenced by select().

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

• minimol.h
• minimol.cpp