Molecule

Template defines a collection of Particles that make up a Molecule. Among others class hosts a PDB file readr and linear algebra operators.

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AUTHORS

Class Summary

class Molecule :
public vector< ParticleT>
{

public:

	// Constructors
	Molecule() ;

	// Adding Particles.
template< class StreamT> int readPDBfile(StreamT& PDBstream, const	PDB::Selector& selector ));
template< class StreamT> int readHetAtomsFromPDBfile(StreamT& PDBstream, const	PDB::Selector& selector ));
int readAllPDBfile(const string& pdbFile, const	PDB::Selector& selector ));
template< class StreamT> int readAllPDBfile(StreamT& PDBstream, const	PDB::Selector& selector ));
class	Selector ;
class	ChainSelector ;
class	WaterHydrogenUnSelector ;
class	CaSelector ;
class	BackboneSelector ;
int	select (const Selector& selector);
int	select (const Selector& selector, Molecule< ParticleT>& m) const;
void	add(const ParticleT& p);
vector< Vector3>	getDiameterTriple() const;

	// Inspection.
Vector3	operator()(unsigned int particle) const;
Vector3	centroid() const;

	// Operators.
void	transform(const Matrix3& lt);
void	translate(const Vector3& move);
void	rigidTrans(const RigidTrans3& rt);
void	concat(const Molecule& m);
Molecule	splitOnIndex(const int i);
Molecule&	operator+=(const Vector3& v);
Molecule&	operator*=(const Matrix3& lt);
Molecule&	operator*=(const RigidTrans3& rt);
Molecule&	operator=(const Molecule& m);
template< class T> friend ostream&	operator<< (ostream& s, const Molecule& m);
protected:

}; // Molecule

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AUTHORS

Meir Fuchs. (meirfux@math.tau.ac.il) and Zipi Fligelman (zipo@math.tau.ac.il)

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CHANGES LOG

6.04.08, Dina: Adding BackboneSelector
20.06.06, Dina: Adding CaSelector
10.05.05, Nelly Bluvshtein: Adding WaterHydrogenUnSelector
7.11.04, Alex Shulman: Changing the methods that read PDB to templates of general streams (e.g zipped or regular files). Removing the repositioning of file pointer to the beginning of the file with seekg. If the user does not want to manage the file pointer by itself, functions that receive the name of the file must be used.
21.09.04, Oranit Dror: Adding a new 'readAllPDBfile' method.
25.08.04, Oranit Dror: Adding a new 'readPDBfile' method.
3.03.04 readPDB functions: line, 85 was changed to MAX_LINE_LENGTH = 1000
13.01.03 PDBstream.getline(line,85); //PDBstream.get(line, 85, '\n');
New readPDB functions. One of them reads only HETATM (it was not possible with previous readPDBFile function). The second function reads all atoms: both ATOM and HETATM. The selectors can be used with them like with readPDBFile. 8.01.03 Alex and Dina
The istream pointer in readPDBfile is set to the beggining of the file in the beggining of this method. It enables multiple readings of the same stream. 11.11.2002 Inbal Halperin.
Added a Selector. This selector is different from the PDB::Selector. The PDB::Selector can be operated only when a molecule is read. This selector can either select particles from a given Molecule object which was already created, thereby changing the molecule or can select particles into a new molecule without changing the operating object molecule. 7.11.2002 Inbal Halperin.
getline is changes to StringUtils::getLine

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GOALS

Serves as a container to a set of similarly typed class Particle descendants. The Molecule container hosts all methods of the STL vector container. It allows linear transfomrations to be applied to all Particles in the molecule. A PDB reader, enabling selected atoms to be read off a PDB format file is also supplied.

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USAGE

Construction is done using the default constructor. An empty Molecule object is returned.

The Molecule may be built using the add method or using any other method supplied by the STL vector. Alternatively Particles may be added from a PDB format file using the readPDBfile method. This method may recieve a function object which will determine which of the atoms are loaded into memory.

Matrices, rigid transformations, vector additions may be applied to all particles simultaneously. See the operators.

The following is an example of using a Molecule<Particle> object to read in all C-alpha atom from a PDB file and print their coordinates after a rigid-transformation is applied to all the particles.

  class CAlphaSelector : public PDB::Selector
  {  // This class defines a selector that will pick only C-alpha atoms.
  public:
  bool operator()(const char *PDBrec) const {
  const char *type = PDB::atomType(PDBrec);
  return (*(type+1) == 'C' && *(type+2) == 'A');
  }
  };

  main() {
  Molecule<Particle> M;
  ifstream pdb("pdb1tpo.ent");  
  M.readPDBfile(pdb, CAlphaSelector());
  pdb.close();
  RigidTrans3 rt(Whatever);
  M*= rt;
  for (Molecule<Particle>::iterator i= M.begin(); i != M.end(); i++)
  cout << *i << '\n';

  }

Note that Molecule has 2 base classes. The MolculeBase class is a virtual class that has a sole virtual method - the () operator. This class may be used to pass Molecule objects of unknown type T into functions that access Molecule vector positions only. This tool is used in the Match class.

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EXAMPLE

main() { Molecule<Atom> mol; Molecule<Atom> antibody;

ifstream pdb("complex.pdb"); mol.readPDBfile(pdb); pdb.close();

Molecule<Atom>::ChainSelector selectorAntibody("LH"); Molecule<Atom>::ChainSelector selectorAntigen("A");

mol.select(selectorAntibody,antibody); mol.select(selectorAntigen); } END

Note: If the complex contained chains L,H,A than after the first select mol contains L,H,A and antibody contains L,H after the second select mol contains A.

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Molecule() ;

Default constructor - empty molecule.

  Molecule() ;

Function is currently defined inline.

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template< class StreamT> int readPDBfile(StreamT& PDBstream, const PDB::Selector& selector ));

Reads all ATOM records from the given PDB file according to the given atom selector and returns the number of read atoms (a negative value is returned in case of an error).
The default atom selector is PDB::Selector that selects all records. To write a different selection function one has to define a descendant of PDB::Selector() and redefine the 'operator()(const char* PDBrec) const' function to operate as desired.

  template< class StreamT>
  int readPDBfile(StreamT& PDBstream, const PDB::Selector& selector = PDB::Selector());

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template< class StreamT> int readHetAtomsFromPDBfile(StreamT& PDBstream, const PDB::Selector& selector ));

readHetAtomsFromPDBfile accepts an input stream (file or cin) a PDB file format. Only HETATM records are read.

  template< class StreamT>
  int readHetAtomsFromPDBfile(StreamT& PDBstream, const PDB::Selector& selector = PDB::Selector());

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int readAllPDBfile(const string& pdbFile, const PDB::Selector& selector ));

Reads all ATOM and HETATM records from the given PDB file according to the given atom selector and returns the number of read atoms (a negative value is returned in case of an error).
The default atom selector is PDB::Selector that selects all records. To write a different selection function one has to define a descendant of PDB::Selector() and redefine the 'operator()(const char* PDBrec) const' function to operate as desired.
Note that to filter out hydrogen, water molecules or anything else, use the PDB::WaterHydrogenUnSelector

  int readAllPDBfile(const string& pdbFile, const PDB::Selector& selector = PDB::Selector());

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template< class StreamT> int readAllPDBfile(StreamT& PDBstream, const PDB::Selector& selector ));

  template< class StreamT>
  int readAllPDBfile(StreamT& PDBstream, const PDB::Selector& selector = PDB::Selector());

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class Selector ;

Enables to create selectors that can operate on a Molecule after the Molecule object was created. For example a pdb file containing several chains can be read only once to create a Molecule. Each chain would be selected into a new Molecule object. The selector can be operated on a Molecule using the select function.

  class Selector {
  public:
    virtual bool operator()(const ParticleT*) const {  return true;}
    virtual ~Selector() {}
  };

Function is currently defined inline.

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class ChainSelector ;

Selects particles from a Molecule according to their chainId.

  class ChainSelector : public Selector {
  public:
    ChainSelector(const string& chainID): chains(chainID) {}
    bool operator()(const ParticleT* particle) const {
      for (int i=0; i< (int)chains.length(); i++)
	if (particle->chainId() == chains[i])
	  return true;
      return false;
    }
  private:
    string chains;
  };

Function is currently defined inline.

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class WaterHydrogenUnSelector ;

Selects particles from a Molecule, which are not water or hydrogens atoms.

  class WaterHydrogenUnSelector : public Selector {
  public:
    bool operator()(const ParticleT* particle) const {
      if (!(particle->isWater() || particle->isH()))
	return true;
      return false;
    }
  };

Function is currently defined inline.

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class CaSelector ;

Selects CA atoms Molecule

  class CaSelector : public Selector {
  public:
    bool operator()(const ParticleT* particle) const {
      if (particle->isCA())
	return true;
      return false;
    }
  };

Function is currently defined inline.

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class BackboneSelector ;

Selects backbone atoms Molecule

  class BackboneSelector : public Selector {
  public:
    bool operator()(const ParticleT* particle) const {
      if (particle->isBackbone())
	return true;
      return false;
    }
  };

Function is currently defined inline.

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int select (const Selector& selector);

Excludes particles that are not selected by the Selector. The operating Molecule object may be changed as a result of this function.

  int select (const Selector& selector);

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int select (const Selector& selector, Molecule< ParticleT>& m) const;

Adds particles that are selected by the Selector to the input Molecule. The operating Molecule object is NOT changed as a result of this function.

  int select (const Selector& selector, Molecule< ParticleT>& m) const;

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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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vector< Vector3> getDiameterTriple() const;

Return a triple of the positions of the most distant atoms

  vector< Vector3> getDiameterTriple() const;

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Vector3 operator()(unsigned int particle) const;

The () operator returns a Particle's position according to index.

  Vector3 operator()(unsigned int particle) const;

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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 Molecule& m);

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

  void concat(const Molecule& m);

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Molecule 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

  Molecule splitOnIndex(const int i);

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

Moves all atom coordinates by given vector3 move.

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

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

Applies a linear transformation on all protein coordinates.

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

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

Applies a rigid transformation on all atom coordinates.

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

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Molecule& operator=(const Molecule& m);

Equality operator.

  Molecule& operator=(const Molecule& m);

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

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

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

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All Members

public:

	// Adding Particles.
template< class StreamT> int readPDBfile(StreamT& PDBstream, const	PDB::Selector& selector ));
template< class StreamT> int readHetAtomsFromPDBfile(StreamT& PDBstream, const	PDB::Selector& selector ));
int readAllPDBfile(const string& pdbFile, const	PDB::Selector& selector ));
template< class StreamT> int readAllPDBfile(StreamT& PDBstream, const	PDB::Selector& selector ));
class	Selector ;
class	ChainSelector ;
class	WaterHydrogenUnSelector ;
class	CaSelector ;
class	BackboneSelector ;
int	select (const Selector& selector);
int	select (const Selector& selector, Molecule< ParticleT>& m) const;
void	add(const ParticleT& p);
vector< Vector3>	getDiameterTriple() const;

	// Inspection.
Vector3	operator()(unsigned int particle) const;
Vector3	centroid() const;

	// Operators.
void	transform(const Matrix3& lt);
void	translate(const Vector3& move);
void	rigidTrans(const RigidTrans3& rt);
void	concat(const Molecule& m);
Molecule	splitOnIndex(const int i);
Molecule&	operator+=(const Vector3& v);
Molecule&	operator*=(const Matrix3& lt);
Molecule&	operator*=(const RigidTrans3& rt);
Molecule&	operator=(const Molecule& m);
template< class T> friend ostream&	operator<< (ostream& s, const Molecule& m);
protected:

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Ancestors

Inheritance chain for Molecule:

vector

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Descendants

Surface

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