BALL::ResidueChecker Class Reference

#include <BALL/STRUCTURE/residueChecker.h>

Inheritance diagram for BALL::ResidueChecker:

Public Types
enum	TestType {   MISSING_ATOMS = 0, EXTRA_ATOMS, ELEMENTS, SUSPECT_BOND_LENGTHS,   NON_INTEGRAL_NET_CHARGE, LARGE_CHARGES, LARGE_NET_CHARGE, NAN_POSITIONS,   OVERLAPPING_ATOMS, STRONGLY_OVERLAPPING_ATOMS, DUPLICATE_ATOM_NAMES, UNKNOWN_RESIDUES,   NUMBER_OF_TESTS }

Public Member Functions
	ResidueChecker ()
	ResidueChecker (FragmentDB &fragment_db)
	ResidueChecker (const ResidueChecker &residue_checker)
virtual	~ResidueChecker ()
void	enable (TestType t)
void	disable (TestType t)
void	enableSelection ()
void	disableSelection ()
bool	isSelectionEnabled ()
bool	getStatus () const
bool	isEnabled (TestType t) const
Processor::Result	operator() (Residue &residue)
bool	start ()
bool	finish ()
Explicit tests
bool	checkAtomPositions (const Residue &res, const String &res_name)
bool	checkCharge (const Residue &res, const String &res_name)
bool	checkCompleteness (const Residue &res, const Residue &reference, const String &res_name)
bool	checkTemplate (const Residue &res, const Residue &reference, const String &res_name)
Public Member Functions inherited from BALL::UnaryProcessor< Residue >
	UnaryProcessor ()
	UnaryProcessor (const UnaryProcessor &)
virtual	~UnaryProcessor ()

Protected Attributes
FragmentDB *	fragment_db_
bool	status_
BitVector	tests_
bool	selection_

Detailed Description

Residue Consistency Checker. This processor checks residues for internal consistency. It identifies missing or superfluous atoms, suspect bond lengths and non-integral or extremely large charges on the residue. Atom positions are checked as well: a warning is printed, if any of the atom's coordinates is not a number (NaN). Warnings are emitted to Log .

The individual tests can be enabled/disabled using the enable and disable methods. Please use the enum TestTypes to refer to the appropriate tests. By default all tests are enabled except for OVERLAPPING_ATOMS.

The following tests are currently implemented:

• missing atoms in a residue

  This test checks whether all atoms contained in the fragment database for this type of residue are present in each of the residues.

• extra atoms

  This test checks whether all atoms contained in the current residue are also present in the template from the fragment database.

• correct elements

  Check that all atoms in a residue are of the same element as the corresponding atoms in the template from the fragment database.

• suspect bond lengths

  Check that the bond lengths encountered in each of the residues agree within 15% with the bond length in the template from the reference database.

• non-integral net charge

  Check that the sum of charges of a residue is integral, i.e. the sum of all charges is an integer (+/- 0.05 elementary charges).

• large charges

  Check that the none of the atoms bears a charge with an absolute value above 4.0 elementary charges.

• large net charge

  Check that the net charge of the residue is between -2 and +2 elementary charges.

• NaN atom positions

  Check whether any atom has NaN (not a number) as any of its corrdinates. This is a frequent source of error after failing simulations, minimizations, etc.

• strongly overlapping atoms

  Check whether any pair of atoms within a residue is closer than 0.5 Angstrom.

• overlapping atoms

  Check whether any pair of atoms not sharing a bond is further apart then the sum of their vdW radii minus 0.4 Ansgtrom

• duplicate atom names

  Check whether two atoms within the residue have the same name.

• unknown residues

  If unknown residues are encountered (i.e. residues for which no reference template exists in the fragment database), an error occurs. If this test is disabled, the tests requiring a template (missing atoms, extra atoms, suspectr bond lengths, elements) will not be executed for unknown residues.

Definition at line 126 of file residueChecker.h.

Member Enumeration Documentation

enum BALL::ResidueChecker::TestType

EnumsEnum to refer to the individual tests. The values of this enum are used by enable , disable , and isEnabled .

Enumerator
MISSING_ATOMS
EXTRA_ATOMS
ELEMENTS
SUSPECT_BOND_LENGTHS
NON_INTEGRAL_NET_CHARGE
LARGE_CHARGES
LARGE_NET_CHARGE
NAN_POSITIONS
OVERLAPPING_ATOMS
STRONGLY_OVERLAPPING_ATOMS
DUPLICATE_ATOM_NAMES
UNKNOWN_RESIDUES
NUMBER_OF_TESTS

Definition at line 141 of file residueChecker.h.

Constructor & Destructor Documentation

BALL::ResidueChecker::ResidueChecker

(

)

Constructors and DestructorsDefault constructor

BALL::ResidueChecker::ResidueChecker

(

FragmentDB &

fragment_db

)

Detailed constructor

BALL::ResidueChecker::ResidueChecker

(

const ResidueChecker &

residue_checker

)

Copy constructor

virtual BALL::ResidueChecker::~ResidueChecker ( )

virtual

Destructor

Member Function Documentation

bool BALL::ResidueChecker::checkAtomPositions	(	const Residue &	res,
		const String &	res_name
	)

bool BALL::ResidueChecker::checkCharge	(	const Residue &	res,
		const String &	res_name
	)

bool BALL::ResidueChecker::checkCompleteness	(	const Residue &	res,
		const Residue &	reference,
		const String &	res_name
	)

bool BALL::ResidueChecker::checkTemplate	(	const Residue &	res,
		const Residue &	reference,
		const String &	res_name
	)

void BALL::ResidueChecker::disable

(

TestType

t

)

Disable a specific test

void BALL::ResidueChecker::disableSelection ( )

inline

Disable selection of problematic atoms

Definition at line 211 of file residueChecker.h.

void BALL::ResidueChecker::enable

(

TestType

t

)

AccessorsEnable a specific test

void BALL::ResidueChecker::enableSelection ( )

inline

Enable selection of problematic atoms

Definition at line 207 of file residueChecker.h.

bool BALL::ResidueChecker::finish ( )

virtual

finish method

Reimplemented from BALL::UnaryProcessor< Residue >.

bool BALL::ResidueChecker::getStatus

(

)

const

Return true if the last application did not produce any warning. The getStatus method may be called after applying the ResidueChecker to a kernel object.

Returns

bool true if no warnings occured, false otherwise

bool BALL::ResidueChecker::isEnabled

(

TestType

t

)

const

Check whether a specific test is enabled

bool BALL::ResidueChecker::isSelectionEnabled ( )

inline

Return the status of the selection

Definition at line 215 of file residueChecker.h.

Processor::Result BALL::ResidueChecker::operator() ( Residue &  residue )

virtual

Processor-related methods

Reimplemented from BALL::UnaryProcessor< Residue >.

bool BALL::ResidueChecker::start ( )

virtual

start method

Reimplemented from BALL::UnaryProcessor< Residue >.

Member Data Documentation

FragmentDB* BALL::ResidueChecker::fragment_db_

protected

Definition at line 277 of file residueChecker.h.

bool BALL::ResidueChecker::selection_

protected

Definition at line 286 of file residueChecker.h.

bool BALL::ResidueChecker::status_

protected

Definition at line 280 of file residueChecker.h.

BitVector BALL::ResidueChecker::tests_

protected

Definition at line 283 of file residueChecker.h.