bioworld.h File Reference Detailed DescriptionA bridge between world structures and biological information.
Definition in file bioworld.h.
Function Documentation
Initializes a world structure from biological information.
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(), and SetAtomCoordinates(). Referenced by main().
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.
Definition at line 1470 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. 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.
Definition at line 1802 of file bioworld.c. References TBioWorld::w. Referenced by main().
Number of atoms in the molecule.
Definition at line 1807 of file bioworld.c. References TBioWorld::na. Referenced by main().
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).
Definition at line 1812 of file bioworld.c. References GetWorldNumSystemVariables(), and TBioWorld::w. Referenced by main().
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).
Definition at line 1817 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().
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).
Definition at line 1846 of file bioworld.c. References BioWordGetAtomPositionsFromConformation(), TBioWorld::m, TBioWorld::pos, and SetAtomCoordinates(). Referenced by BioWorldEnergy(), InitBioWorld(), and SaveBioWorldBioInfo().
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.
Definition at line 1854 of file bioworld.c. References Distance(), TBioWorld::linkID, TBioWorld::na, and TBioWorld::pos. Referenced by main().
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.
Definition at line 1876 of file bioworld.c. References Atoms2Transforms(), GetSolutionPointFromLinkTransforms(), HTransformDelete(), NEW, TBioWorld::nl, and TBioWorld::w. Referenced by InitBioWorld(), and main().
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).
Definition at line 1896 of file bioworld.c. References BioWordSetAtomPositionsFromConformation(), and ComputeEnergy(). Referenced by main().
Changes the atom positions and stores the resulting conformation into a molecular format.
Definition at line 1905 of file bioworld.c. References BioWordSetAtomPositionsFromConformation(), TBioWorld::m, and WriteMolecule(). Referenced by main().
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.
Definition at line 1913 of file bioworld.c. References PrintWorld(), and TBioWorld::w. Referenced by main().
Releases the memory allocated in a BioWorld structure.
Definition at line 1918 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(). |
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