BALL::ResidueChecker Class Reference
[Miscellaneous]

#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)
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.

Member Enumeration Documentation

enum BALL::ResidueChecker::TestType

Enums Enum 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

Constructor & Destructor Documentation

BALL::ResidueChecker::ResidueChecker ( )

Constructors and Destructors Default 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

void BALL::ResidueChecker::enable ( TestType t )

Accessors Enable a specific test

void BALL::ResidueChecker::enableSelection ( ) [inline]

Enable selection of problematic atoms

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.