libball1.4-dev 1.4.3~beta1-4 / usr / include / BALL / STRUCTURE / residueChecker.h

// -*- Mode: C++; tab-width: 2; -*-
// vi: set ts=2:
//

#ifndef BALL_STRUCTURE_RESIDUECHECKER_H
#define BALL_STRUCTURE_RESIDUECHECKER_H

#ifndef BALL_MATHS_COMMON_H
#	include <BALL/MATHS/common.h>
#endif

#ifndef BALL_COMMON_H
#	include <BALL/common.h>
#endif

#ifndef BALL_CONCEPT_PROCESSOR_H
# include <BALL/CONCEPT/processor.h>
#endif

#ifndef BALL_DATATYPE_BITVECTOR_H
# include <BALL/DATATYPE/bitVector.h>
#endif

namespace BALL
{
	class FragmentDB;
	class Residue;

	/**	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  \link LogStream Log \endlink .  \par
			The individual tests can be enabled/disabled using the \link ResidueChecker::enable enable \endlink
			and \link ResidueChecker::disable disable \endlink methods. Please use the enum
			\link ResidueChecker::TestTypes TestTypes \endlink to refer to the appropriate tests.
			By default all tests are enabled except for OVERLAPPING_ATOMS.
			
			The following tests are currently implemented:
			<ul>
				<li> 
					missing atoms in a residue
				</li>
				<p>
					This test checks whether all atoms contained in the fragment database for
					this type of residue are present in each of the residues.
				</p>
				<li>
					extra atoms
				</li>
				<p>
					This test checks whether all atoms contained in the current residue are also	
					present in the template from the fragment database.
				</p>
				<li>
					correct elements
				</li>
				<p>
					Check that all atoms in a residue are of the same element as the corresponding 
					atoms in the template from the fragment database.
				</p>
				<li>
					suspect bond lengths
				</li>
				<p>
					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.
				</p>
				<li>
					non-integral net charge
				</li>
				<p>
					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).
				</p>
				<li>
					large charges
				</li>
				<p>
					Check that the none of the atoms bears a charge with an absolute value above
					4.0 elementary charges.
				</p>
				<li>
					large net charge
				</li>
				<p>
					Check that the net charge of the residue is between -2 and +2 elementary charges.
				</p>
				<li>
					NaN atom positions
				</li>
				<p>
					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.
				</p>
				<li>
					strongly overlapping atoms
				</li>
				<p>
					Check whether any pair of atoms within a residue is closer than 0.5 Angstrom.
				</p>
				<li> overlapping atoms
				</li>
				<p>
					Check whether any pair of atoms not sharing a bond is further apart then the sum of their vdW radii minus 0.4 Ansgtrom
				</p>
				<li>
					duplicate atom names
				</li>
				<p>
					Check whether two atoms within the residue have the same name.
				</p>
				<li>
					unknown residues
				</li>
				<p>
					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.
			</ul>
	\ingroup StructureMiscellaneous		
	*/
	class BALL_EXPORT ResidueChecker
		:	public UnaryProcessor<Residue>
	{
		public:

		BALL_CREATE(ResidueChecker)

		/**	Enums
		*/
		//@{
			
		/**	Enum to refer to the individual tests.
				The values of this enum are used by \link ResidueChecker::enable enable \endlink,
				\link ResidueChecker::disable disable \endlink, and \link ResidueChecker::isEnabled isEnabled \endlink.
		*/
		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
		};
		//@}

		/**	Constructors and Destructors
		*/
		//@{

		/**	Default constructor
		*/
		ResidueChecker();

		/** Detailed constructor
		*/
		ResidueChecker(FragmentDB& fragment_db);

		/**	Copy constructor
		*/
		ResidueChecker(const ResidueChecker& residue_checker);

		/**	Destructor
		*/
		virtual ~ResidueChecker();
		//@}

		/**	Accessors
		*/
		//@{

		/**	Enable a specific test
		*/
		void enable(TestType t, bool enable = true) ;

		/**	Disable a specific test
		*/
		void disable(TestType t) ;

		/**	Enable selection of problematic atoms
		*/
		void enableSelection()  { selection_ = true; }

		/**	Disable selection of problematic atoms
		*/
		void disableSelection()  { selection_ = false; }

		/**	Return the status of the selection
		*/
		bool isSelectionEnabled()  { return selection_; }

		/**	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. 
				@return bool <b>true</b> if no warnings occured, <b>false</b> otherwise
		*/
		bool getStatus() const;



		/**	Check whether a specific test is enabled
		*/
		bool isEnabled(TestType t) const ;
		//@}

		/**	Processor-related methods
		*/
		//@{

		/**
		*/
		Processor::Result operator () (Residue& residue);

		/**
		*/
		bool start();

		/**
		*/
		bool finish();

		//@}

		/**@name	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:
		
		// The fragment database
		FragmentDB*	fragment_db_;

		// Bool flag indicating whether any of the tests failed
		bool				status_;

		// A bitvector containing the flags for the tests
		BitVector		tests_;

		// If this flag is set, all atoms/residues having problems will be selected
		bool				selection_;
	}; 
  					
} // namespace BALL

#endif // BALL_STRUCTURE_RESIDUE_CHECKER