clipper::MPolymer Class Reference

MiniMol polymer (e.g. chain) object. More...

#include <minimol.h>

Inheritance diagram for clipper::MPolymer:

List of all members.

Public Member Functions
const String &	id () const
	get polymer ID
void	set_id (const String &s)
	set polymer ID
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 monomers in polymer
const MMonomer &	operator[] (const int &i) const
	get monomer
MMonomer &	operator[] (const int &i)
	set monomer
const MMonomer &	find (const String &n, const MM::MODE mode=MM::UNIQUE) const
	get monomer by id
MMonomer &	find (const String &n, const MM::MODE mode=MM::UNIQUE)
	set monomer by id
MPolymer	select (const String &sel, const MM::MODE mode=MM::UNIQUE) const
	create selection
int	lookup (const String &str, const MM::MODE &mode) const
	lookup monomer by id
void	insert (const MMonomer &add, int pos=-1)
	add monomer
MPolymer &	copy (const MPolymer &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
Friends
MPolymer	operator& (const MPolymer &m1, const MPolymer &m2)
	and operator
MPolymer	operator| (const MPolymer &m1, const MPolymer &m2)
	or operator

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Detailed Description

MiniMol polymer (e.g. chain) object.

The MiniMol polymer object has one property: an identifying name.

It contains a list of clipper::MMonomer.

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 a polymer.

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Member Function Documentation

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

get monomer by id

Lookup monomer by ID. If mode=UNIQUE, the insertion code must match, otherwise the first monomer with the same sequence number is returned.

Parameters:

	n	The monomer ID.
	mode	The search mode.

Returns:

The monomer.

References lookup(), and clipper::message.

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

set monomer by id

See MPolymer::find()

References lookup(), and clipper::message.

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

create selection

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

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

Parameters:

	sel	The selection string.
	mode	MM::UNIQUE forces an exact match, including insertion code. MM::ANY matches any monomer with the right sequence number, ignoring insertion code.

Returns:

The selection as a new polymer.

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

MPolymer & clipper::MPolymer::copy	(	const MPolymer &	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