clipper::MMonomer Class Reference

MiniMol monomer (e.g. residue) object. More...

#include <minimol.h>

Inheritance diagram for clipper::MMonomer:

List of all members.

Public Types
enum	TYPE { Default, Dunbrack, Richardson }
	Rotamer library type.
Public Member Functions
const String &	id () const
	get monomer ID
void	set_id (const String &s)
	set monomer ID
const String &	type () const
	get monomer type
void	set_type (const String &s)
	set monomer type, e.g. LYS, VAL, G
int	seqnum () const
	get monomer seq number
void	set_seqnum (const int s, const String inscode="")
	set full 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 atoms in monomer
const MAtom &	operator[] (const int &i) const
	get atom
MAtom &	operator[] (const int &i)
	set atom
const MAtom &	find (const String &n, const MM::MODE mode=MM::UNIQUE) const
	get atom by id
MAtom &	find (const String &n, const MM::MODE mode=MM::UNIQUE)
	set atom by id
MMonomer	select (const String &sel, const MM::MODE mode=MM::UNIQUE) const
	create selection
int	lookup (const String &str, const MM::MODE &mode) const
	lookup atom by id
void	insert (const MAtom &add, int pos=-1)
	add atom
MMonomer &	copy (const MMonomer &other, const MM::COPY &mode)
	configureable copy function
void	protein_mainchain_build_carbonyl_oxygen (const MMonomer &next)
	UTILITY: Build carbonyl oxygen, give next residue in chain.
int	protein_sidechain_number_of_rotamers (TYPE t=default_type_) const
	UTILITY: get number of rotamers for protein sidechain.
int	protein_sidechain_number_of_rotomers () const
ftype	protein_sidechain_build_rotamer (const int &n, TYPE t=default_type_)
	UTILITY: build numbered rotamer for protein sidechain.
ftype	protein_sidechain_build_rotomer (const int &n)
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
static bool	protein_peptide_bond (const MMonomer &m1, const MMonomer &m2, ftype r=1.5)
	UTILITY: test if two peptide are adjacent.
static double	protein_ramachandran_phi (const MMonomer &m1, const MMonomer &m2)
	UTILITY: return Ramachandran phi, or NaN if atoms missing.
static double	protein_ramachandran_psi (const MMonomer &m1, const MMonomer &m2)
	UTILITY: return Ramachandran psi, or NaN if atoms missing.
static TYPE &	default_type ()
Friends
MMonomer	operator& (const MMonomer &m1, const MMonomer &m2)
	and operator
MMonomer	operator| (const MMonomer &m1, const MMonomer &m2)
	or operator

---

Detailed Description

MiniMol monomer (e.g. residue) object.

The MiniMol monomer object contains a list of clipper::MAtom.

It has two properties: a sequence number and a type. The sequence number need not reflect the order in which the monomers are stored in a polymer. MResidue is an alias for 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 monomer.

---

Member Function Documentation

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

get atom by id

Lookup atom by ID. If mode=UNIQUE, the alternate conformation code must match, otherwise the first atom with the same name is returned.

Parameters:

	n	The atom ID.
	mode	The search mode.

Returns:

The atom.

References lookup(), and clipper::message.

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

set atom by id

See MMonomer::find()

References lookup(), and clipper::message.

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

create selection

Creates a copy of this monomer containing only the atoms described by the selection string. '*' copies all atoms.

The atom selection must contain an atom ID or a comma separated list of atom IDs, or '*' to select all atom. Atom IDs are described in s_mm_atom_id.

The selection string must contain an atom ID or a comma separated list of atom IDs. Atom IDs are described in s_mm_atom_id.

Parameters:

	sel	The selection string.
	mode	MM::UNIQUE forces an exact match, including alternate conformation code. MM::ANY matches every atom with the right name, ignoring alternate conformation codes.

Returns:

The selection as a new monomer.

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

MMonomer & clipper::MMonomer::copy	(	const MMonomer &	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().

void clipper::MMonomer::protein_mainchain_build_carbonyl_oxygen

(

const MMonomer &

next

)

UTILITY: Build carbonyl oxygen, give next residue in chain.

A carbonyl oxygen is added to this residue if the supplied residue contains an appriate N atom bonded to the C. Otherwise, nothing happens.

Parameters:

next

The next monomer in the chain.

References insert(), clipper::Coord_orth::lengthsq(), lookup(), clipper::Atom::null(), clipper::MAtom::set_coord_orth(), clipper::MAtom::set_element(), clipper::MAtom::set_id(), clipper::MAtom::set_occupancy(), clipper::MAtom::set_u_iso(), and clipper::Vec3< T >::unit().

int clipper::MMonomer::protein_sidechain_number_of_rotamers

(

TYPE

t = default_type_

)

const

UTILITY: get number of rotamers for protein sidechain.

Returns:

The number of stored rotamers for this residue type. 0 if unknown.

References type().

ftype clipper::MMonomer::protein_sidechain_build_rotamer	(	const int &	n,
		TYPE	t = default_type_
	)

UTILITY: build numbered rotamer for protein sidechain.

Parameters:

n

The number of the rotamer required.

Returns:

The frequency of the given rotamer.

References insert(), lookup(), clipper::Atom::null(), clipper::MAtom::set_coord_orth(), clipper::MAtom::set_element(), clipper::MAtom::set_id(), clipper::MAtom::set_occupancy(), clipper::MAtom::set_u_iso(), clipper::String::trim(), type(), and clipper::Vec3< T >::unit().

bool clipper::MMonomer::protein_peptide_bond	(	const MMonomer &	m1,
		const MMonomer &	m2,
		ftype	r = 1.5
	)			[static]

UTILITY: test if two peptide are adjacent.

Test if the C of residue 1 is bonded to the N of residue 2, within the distance r.

Parameters:

	r1	The first residue.
	r2	The second residue.
	r	The maximum allowed bond length.

Returns:

true if N and C are present and bonded.

References lookup().

double clipper::MMonomer::protein_ramachandran_phi	(	const MMonomer &	m1,
		const MMonomer &	m2
	)			[static]

UTILITY: return Ramachandran phi, or NaN if atoms missing.

Return the Ramachadran angle in radians on -pi...pi. To check the result, see clipper::Util::is_nan()

Parameters:

	r1	The first residue.
	r2	The second residue.

Returns:

The torsion angle in radians, or NaN if atoms are missing.

References lookup(), clipper::Util::nan(), and clipper::Coord_orth::torsion().

double clipper::MMonomer::protein_ramachandran_psi	(	const MMonomer &	m1,
		const MMonomer &	m2
	)			[static]

UTILITY: return Ramachandran psi, or NaN if atoms missing.

Return the Ramachadran angle in radians on -pi...pi. To check the result, see clipper::Util::is_nan()

Parameters:

	r1	The first residue.
	r2	The second residue.

Returns:

The torsion angle in radians, or NaN if atoms are missing.

References lookup(), clipper::Util::nan(), and clipper::Coord_orth::torsion().

---

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

• minimol.h
• minimol.cpp