Library DockingLib

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Classes

ACEScore

ACEScorePerResidue

AminoAcid

Container that stores Atom's of amino acid. In addition the class provides a general information about amino acid residues.

Atom

This is a general class to hold an atom as it appears in a PDB file.

AtomTypeGrid

BindingEnergyCalculator

BindingEnergyScoring

BindingForce

CharmmParams

ChemAtom

This is a class that addes additional atrributes to Atom

ChemEntry

This is a class that keeps protein atom attributes: type, radius and charge

ChemLib

This is a class that serves as a library for protein attributes: type, radius and charge.

ChemMolecule

This is a class that is a container of ChemAtoms

ChemSurface

ChemSurfacePoint

Common

ComplexEnergyCalculator

DistanceConstraint

DistanceConstraints

DockSurface

DockingEvaluator

DotSphere

Energy

EnergyAtom

EnergyCalculator

EnergyCalculator_Consts

EnergyParams

EnergyTable

ExhaustivePerturbations

FMatch

Defines a match object used to build and refine matches between Molecule type objects. Matches are build by matching pairs of Particles from each Molecule.

FastClusterer

This clustering technique is very coarse and therefore efficient in fast reduction of transformations number. FastClusterer first clusters transformations according to rotational parameters and after that applies RMSD clustering in each such cluster. TransT template should be like TransT in RMSDCluster class template < class TransT>

GeomScore

InterfaceRMSDClusterer

Class that clusters according to interface RMSD criteria. TransT is any class that extends RigidTrans3 NumTypeT is number type: int, float...

Key

MolIntersection

Class for checking sphere intersections with atoms of the molecule template< class MoleculeT>

MoleculeGrid

MultiResolution

MyMatch

Net

Patch

PatchDockSurface

ProbGrid

RMSDClusterer

Class that clusters according to RMSD criteria. TransT is any class that extends RigidTrans3 NumTypeT is number type: int, float...

RangeParams

ResidueConformer

represents residue conformer copy with chi angles and its RotamerAtoms (do not includes fixed residue backbone atoms and CB)KEYWORD

ResidueGrid

ResidueIndexedMolecule

ResiduesBuildingInfo

Result

RigidBodyMinimization

Rotamer

stores 1-4 side-chain torsional angles: chi1-chi4 and probability

RotamerAtom

for different atom's positions in residues' conformers' copiesKEYWORD

RotamerEnergyPreprocessor

RotamerLibrary

stores 1-4 side-chain torsional angles: chi1-chi4 and probability

RotamerMolecule

RotamerResidue

represents residue, with one backbone and different residue conformers

RotamerResidueBuilder

RotamersSet

stores 2 backbone angles and all possible rotamers

SASurface

Class that computes solvent accessible surface for the molecule

ScoreData

ScorePair

Segmentation

ShuoSurface

SurfaceParams

struct SurfaceParams { SurfaceParams() {} GridParams gridParams; SegmentationParams segmentationParams;

SurfacePointGrid

SurfaceSegmentation

SurfaceTriangle

Torus

TwoPointBase

VolumeGrid

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Data

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Global Functions

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FMolecule() ;

Default constructor - empty molecule.

  FMolecule() ;

Function is currently defined inline.

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int readPDBfile(istream& PDBstream, const PDB::Selector& selector ));

readPDBfile accepts an input stream (file or cin) and an atom selector. The default atom selector defined under PDB - PDB::Selector selects all atoms by default. To write different selection functions one has to define descendants to PDB::Selector() and redefine the operato()(const char* PDBrec) const function to operate as desired.

  int 
  readPDBfile(istream& PDBstream, 
	      const PDB::Selector& selector = PDB::Selector());

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void add(const ParticleT& p);

Shorthand for vector push_back. Adds a new Particle at the end of the Particle array.

  void add(const ParticleT& p);

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Vector3 operator()(unsigned int particle) const ;

The () operator returns a Particle's position according to index. The virtual operator() is declared in MoleculeBase a virtual class that serves as a base for Molecule. The operator() is used by functions recieving Molecule objects of unknown types. See for example Match.h.

  Vector3 operator()(unsigned int particle) const                              
;

Function is currently defined inline.

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Vector3 centroid() const;

Returns centroid of all particle positions.

  Vector3 centroid() const;

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void transform(const Matrix3& lt);

Transforms molecule using a linear transformation of type Matrix3.

  void transform(const Matrix3& lt);

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void translate(const Vector3& move);

Moves all atom coordinates by given vector3 move.

  inline void translate(const Vector3& move);

Function is currently defined inline.

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void rigidTrans(const RigidTrans3& rt);

Applies a rigid transformation on all molecule's Particles.

  void rigidTrans(const RigidTrans3& rt);

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void concat(const FMolecule& m);

Concating two molecules together molecule m is added at the end of *this molecule

  void concat(const FMolecule& m);

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FMolecule splitOnIndex(const int i);

Splitting a molecule on index i all the particles from 0-i (included) will stay in this molecule the other particles : i+1-end-of-molecule are returned as a different molecule

  FMolecule splitOnIndex(const int i);

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FMolecule& operator+=(const Vector3& v);

Moves all atom coordinates by given vector3 move.

  FMolecule& operator+=(const Vector3& v);

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FMolecule& operator*=(const Matrix3& lt);

Applies a linear transformation on all protein coordinates.

  FMolecule& operator*=(const Matrix3& lt);

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FMolecule& operator*=(const RigidTrans3& rt);

Applies a rigid transformation on all atom coordinates.

  FMolecule& operator*=(const RigidTrans3& rt);

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FMolecule& operator=(const FMolecule& m);

Equality operator.

  FMolecule& operator=(const FMolecule& m);

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template < class T> friend ostream& operator<<(ostream& s, const FMolecule& m);

Output operator assuming the ParticleT class has its own overload of the output operator.

  template < class T>
  friend ostream& operator<<(ostream& s, const FMolecule& m);

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struct key_comp ;

struct key_comp {
  bool operator()(const Key3& key1, const Key3& key2) const {
    if(key1[0] != key2[0]) return (key1[0] < key2[0]) ? true : false;
    if(key1[1] != key2[1]) return (key1[1] < key2[1]) ? true : false;
    if(key1[2] != key2[2]) return (key1[2] < key2[2]) ? true : false;
    return false;
  }
};

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typedef leda::UGRAPH< int, float> SurfaceNet;

typedef leda::UGRAPH< int, float> SurfaceNet;

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typedef TwoPointBase::MatchParams MatchParams;

typedef TwoPointBase::MatchParams MatchParams;

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typedef TwoPointBase::BaseParams BaseParams;

typedef TwoPointBase::BaseParams BaseParams;

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