ResidueChecker Class Reference
[Miscellaneous]

Residue Consistency Checker. More...

#include <residueChecker.h>

Inheritance diagram for ResidueChecker:

List of all members.

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 }
	Enum to refer to the individual tests. More...
Public Member Functions
	ResidueChecker ()
	Default constructor.
	ResidueChecker (FragmentDB &fragment_db)
	Detailed constructor.
	ResidueChecker (const ResidueChecker &residue_checker)
	Copy constructor.
virtual	~ResidueChecker ()
	Destructor.
void	enable (TestType t) throw ()
	Enable a specific test.
void	disable (TestType t) throw ()
	Disable a specific test.
void	enableSelection () throw ()
	Enable selection of problematic atoms.
void	disableSelection () throw ()
	Disable selection of problematic atoms.
bool	isSelectionEnabled () throw ()
	Return the status of the selection.
bool	getStatus () const
	Return true if the last application did not produce any warning.
bool	isEnabled (TestType t) const throw ()
	Check whether a specific test is enabled.
Processor::Result	operator() (Residue &residue)
	operator ()
bool	start ()
	start method
bool	finish ()
	finish method
Explicit tests
bool	checkAtomPositions (const Residue &res, const String &res_name) throw ()
bool	checkCharge (const Residue &res, const String &res_name) throw ()
bool	checkCompleteness (const Residue &res, const Residue &reference, const String &res_name) throw ()
bool	checkTemplate (const Residue &res, const Residue &reference, const String &res_name) throw ()
Protected Attributes
FragmentDB *	fragment_db_
bool	status_
BitVector	tests_
bool	selection_

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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.

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Member Enumeration Documentation

enum ResidueChecker::TestType

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

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Member Function Documentation

bool 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