PDB

The PDB class defines a set of tools used for reading the Protein Data Bank file format, used to describe molecular structures, like proteins, drugs and Nucleic Acids

Quick Index

AUTHORS

CHANGES LOG

GOALS

USAGE

Class Summary

class PDB
{

public:

	// PDB record type determination methods.
static bool	isATOMrec(const char *const PDBrec);
static bool	isHETATMrec(const char *const PDBrec);
static bool	isCaATOMrec(const char *const PDBrec);
static bool	isNucleicRecord(const char *const PDBrec);
static bool	isNucleicAcid(const char *const residueName);
static bool	isCONECTrec(const char *const PDBrec);

	// ATOM record costants and methods.
static float	atomXCoord(const char *const PDBrec);
static float	atomYCoord(const char *const PDBrec);
static float	atomZCoord(const char *const PDBrec);
static int	atomIndex(const char *const PDBrec);
static const char*	atomType(const char *const PDBrec);
static char	atomAltLocIndicator(const char *const PDBrec);
static char	atomChainId(const char *const PDBrec);
static short	atomResidueIndex(const char *const PDBrec);
static char	atomResidueICode(const char *const PDBrec);
static char	atomResidueType(const char *const PDBrec);
static const char* const	residueLongName(const char resChar);
static string const	nucleicAcidLongName(const char resChar);
static const char*	getAtomResidueLongName(const char *const PDBrec);
static AtomEntryType	getAtomEntryType(const char *const PDBrec);
static float	getOccupancy(const char *const PDBrec);
static float	getTempFactor(const char *const PDBrec);
static char	residueShortName(const char *const resName);
static vector< unsigned short>	connectedAtoms(const char *const PDBrec);
class	Selector ;
class	CAlphaSelector ;
class	CBetaSelector;
class	CSelector;
class	NSelector;
class	AllSelector ;
class	ChainSelector ;
class	WaterSelector ;
class	HydrogenSelector ;
class	WaterHydrogenUnSelector ;
class	WaterUnSelector ;
class	PSelector ;
class	NucleicSelector ;
class	IgnoreAlternativesSelector ;
protected:

}; // PDB

Back to the top of PDB

AUTHORS

Meir Fuchs. (meirfux@math.tau.ac.il)

Back to the top of PDB

CHANGES LOG

23/03/08 Dina: nucleic acid long names added, isNucleicAcid added
23/03/08 Dina: WaterUnSelector added
13/11/07 Elad Donsky: adding support for alternative location indicator adding selector IgnoreAlternativesSelector
10/05/05 Nelly Bluvshtein: Adding "isCONECTrec" method Adding "atomResidueICode" method Removing "atomResidueSequenceID" method (needed only by Atom)
21/9/04 Oranit Dror: (i) updating the 'NucleicAcidSelector' and the 'CBetaSelector; inner classes; (ii) updating the 'residueLongName', 'atomResidueType' and 'getAtomEntryType' methods; and (iii) adding the 'isNucleicRecord' method.
25/8/04 Oranit Dror: Adding the 'NucleicAcidSelector' inner class
10/6/04 Oranit Dror: Supporting Nucleic Acid PDB files
17/3/04 Selectors added.

Back to the top of PDB

GOALS

Class PDB is designed to encapsulate a set of methods used for reading the PDB file format. Methods are static requiring no object instantiation before their use.

Back to the top of PDB

USAGE

A PDB file is comprised of 80-char lines called records. These records describe different properties of a molecular structure (mainly proteins). A record can describe an atom coordinate, an amino-acid sequence, an alpha helix or some other chemical or geometrical properties of the molecule, depending on the record's type. For more information see the Protein Data Bank home page.

Class PDB's methods are all static. Hence the class's constructor was declared private so that no objects of type PDB will be declared. PDB's methods recieve a PDB record line as an argument and return requested data found in the record.

    char rec[81];    pdbFile.getline(line, 81);         // read line from stream.
    if (PDB::isATOMrec(rec))             // if record is of type ATOM
      Vector3 v(PDB::atomXCoord(rec),    // instantiate a vector with
                PDB::atomYCoord(rec),    // atom's coordinates.
                PDB::atomZCoord(rec));

Note that one must make sure the record is of the correct type before asking for data found in the record. For example you cannot ask for an x-coordinate of an atom before making sure that you are dealing with an ATOM record. Method names are prefixed by the type of record they are meant to handle (e.g. atomXCoord is meant to extract the X coordinate from an ATOM record). Methods beginning with the is prefix (e.g. isATOMrec) check for record type.

Back to the top of PDB

bool isATOMrec(const char *const PDBrec);

Returns true if the given record is an ATOM record.

  static bool isATOMrec(const char *const PDBrec);

Back to the top of PDB

bool isHETATMrec(const char *const PDBrec);

Returns true if the given record is a HETATM record.

  static bool isHETATMrec(const char *const PDBrec);

Back to the top of PDB

bool isCaATOMrec(const char *const PDBrec);

Returns true if the given record is an ATOM record of a C-alpha atom.

  static bool isCaATOMrec(const char *const PDBrec);

Back to the top of PDB

bool isNucleicRecord(const char *const PDBrec);

Returns true if the given record is a record of a nucleic acid residue
Author: Oranit Dror (oranit@tau.ac.il)

  static bool isNucleicRecord(const char *const PDBrec);

Back to the top of PDB

bool isNucleicAcid(const char *const residueName);

returns true if the residue name is of nucleic acid

  static bool isNucleicAcid(const char *const residueName);

Back to the top of PDB

bool isCONECTrec(const char *const PDBrec);

Returns true if the given record is a record of a connection between atoms
Author: Bluvshtein Nelly (bluvsh@post.tau.ac.il)

  static bool isCONECTrec(const char *const PDBrec);

Back to the top of PDB

float atomXCoord(const char *const PDBrec);

Returns an ATOM record's X coordinate.

  static float atomXCoord(const char *const PDBrec);

Back to the top of PDB

float atomYCoord(const char *const PDBrec);

Returns an ATOM record's Y coordinate.

  static float atomYCoord(const char *const PDBrec);

Back to the top of PDB

float atomZCoord(const char *const PDBrec);

Returns an ATOM record's Z coordinate.

  static float atomZCoord(const char *const PDBrec);

Back to the top of PDB

int atomIndex(const char *const PDBrec);

Returns an ATOM record's atom index number.

  static int atomIndex(const char *const PDBrec);

Back to the top of PDB

const char* atomType(const char *const PDBrec);

Returns a pointer to an ATOM's record atom type string. The atom type is a 4 charachter long field. A pointer is returned to the correct position withing the given string PDBrec. Hence the pointer should not be freed or deleted.

  static const char* atomType(const char *const PDBrec);

Back to the top of PDB

char atomAltLocIndicator(const char *const PDBrec);

Returns an ATOM record's alternative location indicator.

  static char  atomAltLocIndicator(const char *const PDBrec);

Back to the top of PDB

char atomChainId(const char *const PDBrec);

Returns an ATOM record's chain id.

  static char  atomChainId(const char *const PDBrec);

Back to the top of PDB

short atomResidueIndex(const char *const PDBrec);

Returns an ATOM record's residue index.

  static short atomResidueIndex(const char *const PDBrec);

Back to the top of PDB

char atomResidueICode(const char *const PDBrec);

code for insertion of residues Returns the value stored in the atomResIndexCharField of the given PDB record (column 26).
ATOM 279 CA SER 60 8.961 9.167 37.481 1.00 20.10 1SGT 477
ATOM 285 CA GLY 60A 5.640 10.901 38.407 1.00 21.41 1SGT 483
In this case for atom no. 285 the atomResidueICode method will return 'A' and for the atom no. 279 it will return ' '

  static char atomResidueICode(const char *const PDBrec);

Back to the top of PDB

char atomResidueType(const char *const PDBrec);

Gets a PDB record of an atom and returns a one-letter abbreviation of the type of the residue that the atom belongs to.
For a nucleic acid atom returns A for adenine, G for guanine, T for thymine, U for uracil and X for unknown type.

  static char atomResidueType(const char *const PDBrec);

Back to the top of PDB

const char* const residueLongName(const char resChar);

Gets a one-letter abbreviation of the type of the residue that the atom belongs to
For a protein atom the method returns the 3-letter abbreviation of its residue. Returns 0 for other types of atoms.

  static const char* const residueLongName(const char resChar);

Back to the top of PDB

string const nucleicAcidLongName(const char resChar);

the same for nucleic acid

  static string const nucleicAcidLongName(const char resChar);

Back to the top of PDB

const char* getAtomResidueLongName(const char *const PDBrec);

Returns the full string of the Residue Name field

  static const char* getAtomResidueLongName(const char *const PDBrec);

Back to the top of PDB

AtomEntryType getAtomEntryType(const char *const PDBrec);

Return the type of the PDB entry, currently only ATOM and HETATM are identified.

  static AtomEntryType getAtomEntryType(const char *const PDBrec);

Back to the top of PDB

float getOccupancy(const char *const PDBrec);

Returns the occupancy, which is a measure of the fraction of molecules in the crystal in which the current atom actually occupies the specified position

  static float getOccupancy(const char *const PDBrec);

Back to the top of PDB

float getTempFactor(const char *const PDBrec);

Returns the temperature factor, which is a measure of how much an atom oscillates or vibrates around the specified position

  static float getTempFactor(const char *const PDBrec);

Back to the top of PDB

char residueShortName(const char *const resName);

Given a charachter string with a PDB residue type code, the method returns a one-letter abbreviation of the type of the residue that the atom belongs to:
- For a nucleic acid atom returns A for adenine, G for guanine, T for thymine, U for uracil and X for unknown type.
- For a protein atom, returns a 3-letter abbreviation of the residue name

  static char residueShortName(const char *const resName);

Back to the top of PDB

vector< unsigned short> connectedAtoms(const char *const PDBrec);

  static vector< unsigned short> connectedAtoms(const char *const PDBrec);

Back to the top of PDB

class Selector ;

Selector is a general purpose class used to select records from a PDB file. Using descendants of this class one may implement arbitrary selection functions with operator() and pass them to PDB reading functions for object selection. (See Molecule for examples).

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

Function is currently defined inline.

Back to the top of PDB

class CAlphaSelector ;

Defines a selector that will pick only C-alpha atoms.

  class CAlphaSelector : public Selector{  
   public:
    bool operator()(const char *PDBrec)const{
      const char *type = atomType(PDBrec);
      if(*(type+1) == 'C' && *(type+2) == 'A' && *(type+3) == ' '
	 && (*(type+4) == ' ' || *(type+4) == 'A')){
	return true;
      }else
	return false;
    }
  };

Function is currently defined inline.

Back to the top of PDB

class CBetaSelector;

Defines a selector that will pick only C-beta atoms.

  class CBetaSelector: public Selector{  
   public:
    bool operator()(const char *PDBrec) const {
      const char* residueName = getAtomResidueLongName(PDBrec);
      if (*(residueName) == 'G' && *(residueName+1) == 'L' && *(residueName+2) == 'Y') {
	return CAlphaSelector()(PDBrec);
      }

Back to the top of PDB

class CSelector;

Defines a selector that will pick only C atoms. (not Ca or Cb)

  class CSelector: public Selector{  
     public:
    bool operator()(const char *PDBrec) const {
      const char *type = atomType(PDBrec);
      return (*(type+1) == 'C' && *(type+2) == ' ');
    }
  };

Function is currently defined inline.

Back to the top of PDB

class NSelector;

Defines a selector that will pick only N atoms.

  class NSelector: public Selector{  
   public:
    bool operator()(const char *PDBrec) const {
      const char *type = atomType(PDBrec);
      return (*(type+1) == 'N' && *(type+2) == ' ');
    }
  };

Function is currently defined inline.

Back to the top of PDB

class AllSelector ;

Defines a selector that will pick every atom.

  class AllSelector : public Selector{  
   public:
    bool operator()(const char *PDBrec)const{
      return true;
    }
  };

Function is currently defined inline.

Back to the top of PDB

class ChainSelector ;

Selector that picks atoms of a given chain.

  class ChainSelector : public Selector {
   public:
    // constructor
    ChainSelector(const string& chainID): chains(chainID) {}
    virtual ~ChainSelector() {}
    bool operator()(const char* PDBrec) const {
      for(int i=0; i< (int)chains.length(); i++)
	if(atomChainId(PDBrec) == chains[i])
	  return true;
      return false;
    }
   private:
    string chains;
  };

Function is currently defined inline.

Back to the top of PDB

class WaterSelector ;

Selector that check if the line is water record

  class WaterSelector : public Selector {
   public:
    bool operator()(const char* PDBrec) const {
      return ((PDBrec[17]=='H' && PDBrec[18]=='O' && PDBrec[19]=='H') ||
	      (PDBrec[17]=='D' && PDBrec[18]=='O' && PDBrec[19]=='D'));
    }
  };

Function is currently defined inline.

Back to the top of PDB

class HydrogenSelector ;

Selector that check if the line is hydrogen record

  class HydrogenSelector : public Selector {
   public:
    bool operator()(const char* PDBrec) const {
      return (PDBrec[13] == 'H' || PDBrec[13] == 'D');
    }
  };

Function is currently defined inline.

Back to the top of PDB

class WaterHydrogenUnSelector ;

Selector that picks non water and non hydrogen atoms

  class WaterHydrogenUnSelector : public Selector {
   public:
    bool operator()(const char* PDBrec) const {
      return( !((PDBrec[17]=='H' && PDBrec[18]=='O' && PDBrec[19]=='H') ||
		(PDBrec[17]=='D' && PDBrec[18]=='O' && PDBrec[19]=='D')) &&
	      ! (PDBrec[13] == 'H' || PDBrec[13] == 'D' || PDBrec[12] == 'H' || PDBrec[12] == 'D') );
    }
  };

Function is currently defined inline.

Back to the top of PDB

class WaterUnSelector ;

Selector that picks non water atoms

  class WaterUnSelector : public Selector {
   public:
    bool operator()(const char* PDBrec) const {
      return( !((PDBrec[17]=='H' && PDBrec[18]=='O' && PDBrec[19]=='H') ||
		(PDBrec[17]=='D' && PDBrec[18]=='O' && PDBrec[19]=='D'))); 
	}
  };

Function is currently defined inline.

Back to the top of PDB

class PSelector ;

A PDB Selector that picks only Phosphate atoms.

  class PSelector : public Selector {  
  public:
    bool operator()(const char *PDBrec) const {
      const char *type = PDB::atomType(PDBrec);
      return (*(type+1) == 'P' && *(type+2) == ' ');
    }
  };

Function is currently defined inline.

Back to the top of PDB

class NucleicSelector ;

A PDB Selector that picks only nucleic acid atoms.

  class NucleicSelector : public Selector {  
  public:
    bool operator()(const char *PDBrec) const {
      return PDB::isNucleicRecord(PDBrec);
    }
  };

Function is currently defined inline.

Back to the top of PDB

class IgnoreAlternativesSelector ;

A PDB Selector that ignores all alternative location atoms.

  class IgnoreAlternativesSelector : public Selector {
  public:
    bool operator()(const char *PDBrec) const {
      return ((PDB::atomAltLocIndicator(PDBrec) == ' ') ||
	      (PDB::atomAltLocIndicator(PDBrec) == 'A'));
    }
  };

Function is currently defined inline.

Back to the top of PDB

All Members

public:

	// PDB record type determination methods.
static bool	isATOMrec(const char *const PDBrec);
static bool	isHETATMrec(const char *const PDBrec);
static bool	isCaATOMrec(const char *const PDBrec);
static bool	isNucleicRecord(const char *const PDBrec);
static bool	isNucleicAcid(const char *const residueName);
static bool	isCONECTrec(const char *const PDBrec);

	// ATOM record costants and methods.
static float	atomXCoord(const char *const PDBrec);
static float	atomYCoord(const char *const PDBrec);
static float	atomZCoord(const char *const PDBrec);
static int	atomIndex(const char *const PDBrec);
static const char*	atomType(const char *const PDBrec);
static char	atomAltLocIndicator(const char *const PDBrec);
static char	atomChainId(const char *const PDBrec);
static short	atomResidueIndex(const char *const PDBrec);
static char	atomResidueICode(const char *const PDBrec);
static char	atomResidueType(const char *const PDBrec);
static const char* const	residueLongName(const char resChar);
static string const	nucleicAcidLongName(const char resChar);
static const char*	getAtomResidueLongName(const char *const PDBrec);
static AtomEntryType	getAtomEntryType(const char *const PDBrec);
static float	getOccupancy(const char *const PDBrec);
static float	getTempFactor(const char *const PDBrec);
static char	residueShortName(const char *const resName);
static vector< unsigned short>	connectedAtoms(const char *const PDBrec);
class	Selector ;
class	CAlphaSelector ;
class	CBetaSelector;
class	CSelector;
class	NSelector;
class	AllSelector ;
class	ChainSelector ;
class	WaterSelector ;
class	HydrogenSelector ;
class	WaterHydrogenUnSelector ;
class	WaterUnSelector ;
class	PSelector ;
class	NucleicSelector ;
class	IgnoreAlternativesSelector ;
protected:

Back to the top of PDB

Ancestors

Class does not inherit from any other class.

Back to the top of PDB

Descendants

Class is not inherited by any others.

Back to the top of PDB

Generated from source by the Cocoon utilities on Sun Nov 15 13:35:26 2009 .

Report problems to jkotula@unimax.com