ChemMolecule

This is a class that is a container of ChemAtoms

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KEYWORD
AUTHORS
GOALS
CHANGES LOG
USAGE

Class Summary

class ChemMolecule
: public ResidueIndexedMolecule<ChemAtom>
{
public:
void loadMolecule(istream& molFile, const ChemLib& chemLib, const PDB::Selector& selector ));
void readAllPDBfile(istream& molFile, const PDB::Selector& selector ));
void computeSteadyProbs();
unsigned int readBindingSite(const string fileName);
unsigned int readBlockingSite(const string fileName);
const set< unsigned int>& getBindingSite(unsigned int siteNumber ) const;
const set< unsigned int>& getBlockingSite(unsigned int siteNumber ) const;
const ChemAtom& getChemAtom(int atomIndex) const;
const Vector3& getCentroid() const ;
protected:
vector< set< unsigned int> > bindingSites_;
vector< set< unsigned int> > blockingSites_;
Vector3 centroid_;
bool isProtein_;
}; // ChemMolecule

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KEYWORD

ChemAtom, radius, charge, type

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AUTHORS

Dina Schneidman (duhovka@tau.ac.il)

copyright: GAMBA Group , Tel-Aviv Univ. Israel, 2004.

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GOALS

ChemMolecule is a molecule of ChemAtoms. ChemAtom extends Atom and has 4 additional attributes: chemical type, radius, charge and probability of the atom of being steady. The type, radius and charge are taken from ChemLib. This library is initiated with chem.lib file. The chemical types are from: Zhang,C., Cornette,J.L. and DeLisi,C. (1997) Determination of atomic desolvation energies from the structures of crystallized proteins. J. Mol. Biol., 267, 707 726. This types are only for protein atoms! The radii are taken from CHARMM, however they are slightly bigger to account for missing hydrogens. The charges are from CHARMM too. The probabilities of being steady were computed based on the maximal distance between C-alpha and side-chain atoms of that residue. The lower the distance the higher is the prob. of being steady.

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CHANGES LOG

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USAGE

ChemMolecule chemMolecule; ifstream pdbFile("mol.pdb"); ChemLib chemLib("chem.lib"); chemMolecule.loadMolecule(pdbFile, chemLib);

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void loadMolecule(istream& molFile, const ChemLib& chemLib, const PDB::Selector& selector ));

load molecule from PDB file, using chemLib for attributes. 

  void loadMolecule(istream& molFile, const ChemLib& chemLib, const PDB::Selector& selector = PDB::WaterHydrogenUnSelector());

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void readAllPDBfile(istream& molFile, const PDB::Selector& selector ));

reads and assigns default values for radius, charge and chemType 

  void readAllPDBfile(istream& molFile, const PDB::Selector& selector = PDB::WaterHydrogenUnSelector());

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void computeSteadyProbs();

compute probabilities of being steady 

  void computeSteadyProbs();

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unsigned int readBindingSite(const string fileName);

read and save binding site, returns number of residues in site 

  unsigned int readBindingSite(const string fileName);

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unsigned int readBlockingSite(const string fileName);

read and save blocking site, returns number of residues in site 

  unsigned int readBlockingSite(const string fileName);

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const set< unsigned int>& getBindingSite(unsigned int siteNumber ) const;

  const set< unsigned int>& getBindingSite(unsigned int siteNumber = 0) const;

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const set< unsigned int>& getBlockingSite(unsigned int siteNumber ) const;

  const set< unsigned int>& getBlockingSite(unsigned int siteNumber = 0) const;

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const ChemAtom& getChemAtom(int atomIndex) const;

  const ChemAtom& getChemAtom(int atomIndex) const;

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const Vector3& getCentroid() const ;

  const Vector3& getCentroid() const                      
;

Function is currently defined inline.


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vector< set< unsigned int> > bindingSites_;

entries of binding site residues according to ResidueIndexedMolecule 

  vector< set< unsigned int> > bindingSites_;

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vector< set< unsigned int> > blockingSites_;

entries of blocking site residues according to ResidueIndexedMolecule 

  vector< set< unsigned int> > blockingSites_;

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Vector3 centroid_;

  Vector3 centroid_;

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bool isProtein_;

  bool isProtein_;

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All Members

public:
bool isInitialized() const ;
void resetResEntries();
int residueEntry(char chainId, string resSequenceID ) const ;
int getFirstAtomEntryForResEntry(unsigned int entry) const ;
int getFirstAtomEntryForResIndex(char chainId, string resSequenceID) const ;
int atomEntryToResEntry(unsigned int entry) const ;
unsigned int numberOfRes() const ;
void loadMolecule(istream& molFile, const ChemLib& chemLib, const PDB::Selector& selector ));
void readAllPDBfile(istream& molFile, const PDB::Selector& selector ));
void computeSteadyProbs();
unsigned int readBindingSite(const string fileName);
unsigned int readBlockingSite(const string fileName);
const set< unsigned int>& getBindingSite(unsigned int siteNumber ) const;
const set< unsigned int>& getBlockingSite(unsigned int siteNumber ) const;
const ChemAtom& getChemAtom(int atomIndex) const;
const Vector3& getCentroid() const ;
protected:
vector< set< unsigned int> > bindingSites_;
vector< set< unsigned int> > blockingSites_;
Vector3 centroid_;
bool isProtein_;

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Ancestors

Inheritance chain for ChemMolecule:

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Descendants

Class is not inherited by any others.

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