Detailed Description

A bridge between world structures and biological information.

See Also: bioworld.c

Definition in file bioworld.h.

Data Structures
struct	TBioWorld
	Structure with the molecular and the mechanical information. More...

Functions
boolean	InitBioWorld (Tparameters p, char filename, unsigned int maxAtomsLink, double *conformation, TBioWorld bw)
	Initializes a world form a biomolecule. More...

void	AdjustBioWorldGeometry (Tparameters p, TBioWorld bw)
	Enforces all bond lengths and angles to be the same. More...

Tworld *	BioWorldWorld (TBioWorld *bw)
	Returns a pointer to the world generated from the bio-information. More...

unsigned int	BioWorldNAtoms (TBioWorld *bw)
	Number of atoms in the molecule. More...

unsigned int	BioWorldConformationSize (TBioWorld *bw)
	Number of variables used to represent a conformation. More...

void	BioWordGetAtomPositionsFromConformation (Tparameters p, boolean simp, double conformation, double pos, TBioWorld bw)
	Computes the position of the atoms. More...

void	BioWordSetAtomPositionsFromConformation (Tparameters p, boolean simp, double conformation, TBioWorld *bw)
	Changes the position of the atoms. More...

double	BioWorldRMSE (double pos, TBioWorld bw)
	Computes the RMSE. More...

unsigned int	BioWordConformationFromAtomPositions (Tparameters p, double atoms, double *conformation, TBioWorld bw)
	Produces the internal coordinates from the atom positions. More...

double	BioWorldEnergy (Tparameters p, boolean simp, double conformation, void *bw)
	Computes the energy of a given configuration. More...

void	SaveBioWorldBioInfo (Tparameters p, char fname, boolean simp, double conformation, TBioWorld bw)
	Stores the BioWorld information in a molecular format (eg. pdb). More...

void	PrintBioWorld (Tparameters p, char fname, int argc, char *arg, TBioWorld bw)
	Prints the BioWorld information into a file. More...

void	DeleteBioWorld (TBioWorld *bw)
	Destructor. More...

Function Documentation

boolean InitBioWorld	(	Tparameters *	p,
		char *	filename,
		unsigned int	maxAtomsLink,
		double **	conformation,
		TBioWorld *	bw
	)

Initializes a world structure from biological information.

Parameters

p	The set of parameters.
filename	The name for the file with the biological information. All formats available in babel can be used.
maxAtomsLink	Links with more atoms than this limit are represented in wireframe. This is faster for visualization but it does not allow to detect collisions with the link. This is to be used only for visualization. Use NO_UINT for no limit (all in facy).
conformation	Configuration of the molecule (space allocated internally).
bw	The BioWorld to initialize.

Returns: TRUE if the BioWorld could be initialized.

Definition at line 1394 of file bioworld.c.

References BioWordConformationFromAtomPositions(), BioWordSetAtomPositionsFromConformation(), DetectLinksAndJoints(), DetectLinksAndJointsFromResidues(), DetectLinksAndJointsFromRigidsAndHinges(), FALSE, GetAtomPositions(), GetMoleculeBasicInfo(), InitWorldFromMolecule(), TBioWorld::m, TBioWorld::na, TBioWorld::nb, TBioWorld::nbAtom, NEW, TBioWorld::pos, ReadMolecule(), ReadResidueList(), ReadRigidsAndHinges(), RemoveBond(), SetAtomCoordinates(), and TRUE.

Referenced by main().

void AdjustBioWorldGeometry	(	Tparameters *	p,
		TBioWorld *	bw
	)

Enforces all bond lengths and angles to be the same for each pair or triplet of atoms of different type.

We set up a set of constraints and finds a point that holds them form the current conformation using a local procedure. The new point is used to change the atom positions in the given bioworld.

Parameters

p	The set of parameters.
bw	The BioWorld to initialize.

Definition at line 1475 of file bioworld.c.

References AddCt2Monomial(), AddEquation2CS(), AddMonomial(), AddVariable2CS(), AddVariable2Monomial(), DeleteBondIterator(), DeleteBox(), DeleteCuikSystem(), DeleteEquation(), DeleteMonomial(), DeleteVariable(), DifferenceVector(), Distance(), DotProduct(), DUMMY_EQ, DUMMY_VAR, EQU, Error(), GenerateDotProductEquation(), GenerateNormEquation(), GetAtomicNumber(), GetCSSystemVars(), GetCSVariableID(), GetCSVariableNames(), GetFirstNeighbour(), GetNextNeighbour(), InitBoxFromPoint(), InitCuikSystem(), InitEquation(), InitMonomial(), TBioWorld::m, TBioWorld::na, TBioWorld::nb, TBioWorld::nba, NEW, NewInterval(), NewVariable(), NFUN, NO_UINT, TBioWorld::pos, PrintBoxSubset(), PrintCuikSystem(), ResetMonomial(), SetEquationCmp(), SetEquationType(), SetEquationValue(), SetVariableInterval(), SYSTEM_EQ, and SYSTEM_VAR.

Tworld* BioWorldWorld ( TBioWorld * bw )

Returns a pointer to the world generated from the bio-information.

This function is provided for convenience but caution must be taken not to modify this internal structure.

Parameters

bw	The BioWorld to query.

Returns: A pointer to the internal world structure.

Definition at line 1807 of file bioworld.c.

References TBioWorld::w.

Referenced by main().

unsigned int BioWorldNAtoms ( TBioWorld * bw )

Number of atoms in the molecule.

Parameters

bw	The BioWorld to query.

Returns: The number of atoms in the molecule.

Definition at line 1812 of file bioworld.c.

References TBioWorld::na.

Referenced by main().

unsigned int BioWorldConformationSize ( TBioWorld * bw )

Number of variables used to represent a conformation. This changes for different representations (see CT_REPRESENTATION) In any case this function returns the number of system varibles used to represent a conformation. This is the number of variables appearing in the output files. Internally, though, a different number of variables migth be used (resulting from the simplification and dummification of the equations, if applied).

Parameters

bw	The BioWorld to query.

Returns: The number of variables representing a conformation.

Definition at line 1817 of file bioworld.c.

References GetWorldNumSystemVariables(), and TBioWorld::w.

Referenced by main().

void BioWordGetAtomPositionsFromConformation	(	Tparameters *	p,
		boolean	simp,
		double *	conformation,
		double *	pos,
		TBioWorld *	bw
	)

Computes the position of the atoms in a molecule from the conformation encoded in the conformation vector. The contents of this vector changes according to the representation used for the equations (see CT_REPRESENTATION).

Parameters

p	The set of parameters.
simp	TRUE if the sample is given in the simplified system.
conformation	The configuration.
pos	Array where to store the new positions (3 entries per atom).
bw	The BioWorld information.

Definition at line 1822 of file bioworld.c.

References DeleteLinkTransforms(), GetLinkTransformsFromSolutionPoint(), GetVectorElement(), HTransformApply(), TBioWorld::linkList, TBioWorld::links, TBioWorld::localPos, TBioWorld::nl, NO_UINT, and TBioWorld::w.

Referenced by BioWordSetAtomPositionsFromConformation(), and main().

void BioWordSetAtomPositionsFromConformation	(	Tparameters *	p,
		boolean	simp,
		double *	conformation,
		TBioWorld *	bw
	)

Changes the position of the atoms in a molecule. The new position is computed from the conformation encoded in the conformation vector. The contents of this vector changes according to the representation used for the equations (see CT_REPRESENTATION).

Parameters

p	The set of parameters.
simp	TRUE if the sample is given in the simplified system.
conformation	The configuration.
bw	The BioWorld information.

Definition at line 1852 of file bioworld.c.

References BioWordGetAtomPositionsFromConformation(), TBioWorld::m, TBioWorld::pos, and SetAtomCoordinates().

Referenced by BioWorldEnergy(), InitBioWorld(), and SaveBioWorldBioInfo().

double BioWorldRMSE	(	double *	pos,
		TBioWorld *	bw
	)

Computes the Root Mean Square Error (RMSE) between the current the atom positions stored int he BioWorld structure and the atom position corresponding to another conformation. These atom postiions can be computed form conformations using BioWordGetAtomPositionsFromConformation.

If the flexibility of the molecule is reduced to only few residues only those are considered for the error.

Parameters

pos	The atom positions for the new conformation.
bw	The BioWorld to be used as a reference.

Returns: The RMSE.

Definition at line 1860 of file bioworld.c.

References Distance(), TBioWorld::linkID, TBioWorld::na, and TBioWorld::pos.

Referenced by main().

unsigned int BioWordConformationFromAtomPositions	(	Tparameters *	p,
		double *	atoms,
		double **	conformation,
		TBioWorld *	bw
	)

Generates a conformation (internal coordinates) from the atom positions). The exact form of the internal coordinates depend on the CT_REPRESENTATION value in the file of parameters. If DOF is used, the conformation is represented in the tradional internal coordinates in molecular modeling (dihedral angles). Other representations are not typical in bio-engineering but in Robotics.

Parameters

p	The set of parameters.
atoms	The 3d positions of the atoms.
conformation	The output conformation. Space is allocated internally.
bw	The BioWorld to query.

Returns: The size of the conformation.

Definition at line 1882 of file bioworld.c.

References Atoms2Transforms(), GetSolutionPointFromLinkTransforms(), HTransformDelete(), NEW, TBioWorld::nl, and TBioWorld::w.

Referenced by InitBioWorld(), and main().

double BioWorldEnergy	(	Tparameters *	p,
		boolean	simp,
		double *	conformation,
		void *	bw
	)

Computes the energy of a given configuraion. This is used to implement T-RRT like algorithms on biomolecules. The signature of this function is generic for all cost function (see EvaluateCSCost).

Parameters

p	The set of parameters.
simp	TRUE if the conformation is given in the simplified system.
conformation	Array giving the conformation.
bw	The BioWorld information.

Definition at line 1902 of file bioworld.c.

References BioWordSetAtomPositionsFromConformation(), and ComputeEnergy().

Referenced by main().

void SaveBioWorldBioInfo	(	Tparameters *	p,
		char *	fname,
		boolean	simp,
		double *	conformation,
		TBioWorld *	bw
	)

Changes the atom positions and stores the resulting conformation into a molecular format.

Parameters

p	The set of parameters.
fname	The name for the output file. The format of the file is infered from the extension of the filename. All the formats available in OpenBabel can be used.
simp	TRUE if the conformation is given in the simplified system.
conformation	Array giving the conformation.
bw	The BioWorld information store.

Definition at line 1911 of file bioworld.c.

References BioWordSetAtomPositionsFromConformation(), TBioWorld::m, and WriteMolecule().

Referenced by main().

void PrintBioWorld	(	Tparameters *	p,
		char *	fname,
		int	argc,
		char **	arg,
		TBioWorld *	bw
	)

Store the world information (stored into the BioWorld structure) into a file so that it can be read as

Moreover we generate a conformation deduced from the atom positions. This can be given it is already available to the caller (for instance as an output of InitBioWorld).

The world and the conformation file can be used to generate the atlas or to plan.

Parameters

p	The set of parameters.
fname	Name of the file where to store the information (different extensions are used for the world and the sample files).
argc	Number of strings to be added to the world file header as comments.
arg	Strings to be added to the world file as comments. Right now, this is used to store in the command line used to create it.
bw	The BioWorld with the information to save.

Definition at line 1919 of file bioworld.c.

References PrintWorld(), and TBioWorld::w.

Referenced by main().

void DeleteBioWorld ( TBioWorld * bw )

Releases the memory allocated in a BioWorld structure.

Parameters

bw	The BioWorld information.

Definition at line 1924 of file bioworld.c.

References TBioWorld::cut, TBioWorld::cutB, DeleteBox(), DeleteMolecule(), DeleteVector(), DeleteWorld(), TBioWorld::g2l, HTransformDelete(), TBioWorld::joint1, TBioWorld::joint2, TBioWorld::linkID, TBioWorld::linkList, TBioWorld::links, TBioWorld::localPos, TBioWorld::m, TBioWorld::nbAtom, TBioWorld::nl, TBioWorld::pos, and TBioWorld::w.

Referenced by main().

Institut de Robòtica i Informàtica Industrial

Detailed Description

Data Structures

Functions

Function Documentation

Institut de Robòtica
i Informàtica Industrial