HashInterface

The class can build Interface object efficiently by using Geometric Hashing for the particles of the first molecule. template< class MoleculeT>

[ GAMB | Source | Keywords | Summary | Ancestors | All Members | Descendants ]

Quick Index

AUTHORS

CHANGES LOG

GOALS

USAGE

Class Summary

Back to the top of HashInterface

AUTHORS

Copyright: SAMBA group, Tel-Aviv Univ. Israel, 1997-9.

Back to the top of HashInterface

CHANGES LOG

• 23.11.03 Dina Implementation of probe interface definition. <\LI>
• 23.11.03 Dina Option to compute together two Interface objects (one for each molecule) <\LI>

Back to the top of HashInterface

GOALS

The class supports 2 interface definitions: 1. If the distance between two atoms, one from each of the molecules, is less than distance_threshold, the two corresponding atoms are marked as interface atom pair. 2. If the distance between two atoms, one from each of the molecules, is less than the sum of their vdW radii and probe diameter, the two corresponding atoms are marked as interface atom pair. Intutively, two atoms are interface pair, if the probe sphere can't be placed between them.

Back to the top of HashInterface

USAGE

The class has several options to build the interface. First the user should pick the interface definition he needs (see Goals). For each of the two definitions, 8 functions with different arguments are provided. Below we summarize different options:

The first molecule remains the same in all cases. The second molecule can be the same that was given in constructor or can be specified by the user. In some cases, like generating docking results interfaces, the second molecule is always the same, however the orientation is different. In this case the user may specufy the 3D transformation to apply to the second molecule.

Since the Interface object is not symmetric, it is possible to specify which molecule will be used as first index in the Interface. The first molecule MOL1 is the default. Also it is possible to generate both interfaces at once.

The following example demonstrates how two Interfaces are created for one complex. The complex in the example is composed of an Antibody=Ab and an Antigen=Ag. Ab and Ab are of type Molecule<Atom>.

  HashInterface<Molecule<Atom> > hashInterface(Ab,Ag);
  Interface face1, face2;
  hashInterface.buildInterface(face1, face2);
  for(Interface::iterator it=face2.begin(); it!=face2.end(); ++it) {
    cout << "serial:  " << *it << endl;    
    cout << "pdb first atom:  " << Ab[(*it).second()]<<endl;
    cout << "pdb second atom:  " << Ag[(*it).first()]<<endl;
  }

Back to the top of HashInterface

HashInterface(const MoleculeT& iMol1, const MoleculeT& iMol2, const unsigned short d , const float cs );

  HashInterface(const MoleculeT& iMol1, const MoleculeT& iMol2,
                const unsigned short d=hashParam_d, const float cs=hashParam_cs);

Back to the top of HashInterface

void buildInterface(Interface& face, const float distThr , const MOL_INDEX molIndex );

  void buildInterface(Interface& face,
		      const float distThr=defaultThreshold, const MOL_INDEX molIndex=MOL1);

Back to the top of HashInterface

void buildInterface(Interface& face, const RigidTrans3& trans2, const float distThr , const MOL_INDEX molIndex );

  void buildInterface(Interface& face, const RigidTrans3& trans2,
		      const float distThr=defaultThreshold, const MOL_INDEX molIndex=MOL1);

Back to the top of HashInterface

void buildInterface(Interface& face, const MoleculeT& iMol2, const float distThr , const MOL_INDEX molIndex );

  void buildInterface(Interface& face, const MoleculeT& iMol2,
		      const float distThr=defaultThreshold, const MOL_INDEX molIndex=MOL1);

Back to the top of HashInterface

void buildInterface(Interface& face, const MoleculeT& iMol2, const RigidTrans3& trans2, const float distThr , const MOL_INDEX molIndex );

  void buildInterface(Interface& face, const MoleculeT& iMol2, const RigidTrans3& trans2,
		      const float distThr=defaultThreshold, const MOL_INDEX molIndex=MOL1);

Back to the top of HashInterface

void buildInterface(Interface& face1, Interface& face2, const float distThr );

  void buildInterface(Interface& face1, Interface& face2, const float distThr=defaultThreshold);

Back to the top of HashInterface

void buildInterface(Interface& face1, Interface& face2, const RigidTrans3& trans2, const float distThr );

  void buildInterface(Interface& face1, Interface& face2,
		      const RigidTrans3& trans2, const float distThr=defaultThreshold);

Back to the top of HashInterface

void buildInterface(Interface& face1, Interface& face2, const MoleculeT& iMol2, const float distThr );

  void buildInterface(Interface& face1, Interface& face2,
		      const MoleculeT& iMol2, const float distThr=defaultThreshold);

Back to the top of HashInterface

void buildInterface(Interface& face1, Interface& face2, const MoleculeT& iMol2, const RigidTrans3& trans2, const float distThr );

  void buildInterface(Interface& face1, Interface& face2, const MoleculeT& iMol2,
		      const RigidTrans3& trans2, const float distThr=defaultThreshold);

Back to the top of HashInterface

void buildProbeInterface(Interface& face, const float probeRadius, const MOL_INDEX molIndex );

  void buildProbeInterface(Interface& face, const float probeRadius, const MOL_INDEX molIndex=MOL1);

Back to the top of HashInterface

void buildProbeInterface(Interface& face, const RigidTrans3& trans2, const float probeRadius, const MOL_INDEX molIndex );

  void buildProbeInterface(Interface& face, const RigidTrans3& trans2,
			   const float probeRadius, const MOL_INDEX molIndex=MOL1);

Back to the top of HashInterface

void buildProbeInterface(Interface& face, const MoleculeT& iMol2, const float probeRadius, const MOL_INDEX molIndex );

  void buildProbeInterface(Interface& face, const MoleculeT& iMol2,
			   const float probeRadius, const MOL_INDEX molIndex=MOL1);

Back to the top of HashInterface

void buildProbeInterface(Interface& face, const MoleculeT& iMol2, const RigidTrans3& trans2, const float probeRadius, const MOL_INDEX molIndex );

  void buildProbeInterface(Interface& face, const MoleculeT& iMol2, const RigidTrans3& trans2,
			   const float probeRadius, const MOL_INDEX molIndex=MOL1);

Back to the top of HashInterface

void buildProbeInterface(Interface& face1, Interface& face2, const float probeRadius);

  void buildProbeInterface(Interface& face1, Interface& face2, const float probeRadius);

Back to the top of HashInterface

void buildProbeInterface(Interface& face1, Interface& face2, const RigidTrans3& trans2, const float probeRadius);

  void buildProbeInterface(Interface& face1, Interface& face2,
			   const RigidTrans3& trans2, const float probeRadius);

Back to the top of HashInterface

void buildProbeInterface(Interface& face1, Interface& face2, const MoleculeT& iMol2, const float probeRadius);

  void buildProbeInterface(Interface& face1, Interface& face2,
			   const MoleculeT& iMol2, const float probeRadius);

Back to the top of HashInterface

void buildProbeInterface(Interface& face1, Interface& face2, const MoleculeT& iMol2, const RigidTrans3& trans2, const float probeRadius);

  void buildProbeInterface(Interface& face1, Interface& face2, const MoleculeT& iMol2,
			   const RigidTrans3& trans2, const float probeRadius);

Back to the top of HashInterface

void internalBuildInterface(Interface& face, const MoleculeT& secondMol, const float distThr , const MOL_INDEX molIndex );

  void internalBuildInterface(Interface& face, const MoleculeT& secondMol,
			      const float distThr=defaultThreshold, const MOL_INDEX molIndex=MOL1);

Back to the top of HashInterface

void internalBuildInterface(Interface& face1, Interface& face2, const MoleculeT& secondMol, const float distThr );

  void internalBuildInterface(Interface& face1, Interface& face2,
			      const MoleculeT& secondMol, const float distThr=defaultThreshold);

Back to the top of HashInterface

void internalBuildProbeInterface(Interface& face, const MoleculeT& secondMol, const float probeRadius, const MOL_INDEX molIndex );

  void internalBuildProbeInterface(Interface& face, const MoleculeT& secondMol,
				   const float probeRadius, const MOL_INDEX molIndex=MOL1);

Back to the top of HashInterface

void internalBuildProbeInterface(Interface& face, Interface& face2, const MoleculeT& secondMol, const float probeRadius);

  void internalBuildProbeInterface(Interface& face, Interface& face2,
				   const MoleculeT& secondMol, const float probeRadius);

Back to the top of HashInterface

const MoleculeT& mol1;

  const MoleculeT& mol1;

Back to the top of HashInterface

const MoleculeT& mol2;

  const MoleculeT& mol2;

Back to the top of HashInterface

GeomHash< Vector3, unsigned int> gHash1;

  GeomHash< Vector3, unsigned int> gHash1;

Back to the top of HashInterface

All Members

Back to the top of HashInterface

Ancestors

Back to the top of HashInterface

Descendants

Back to the top of HashInterface