PdbLoader Class Reference

Loads components (Atoms, Groups, Spacer, etc.) in standard PDB format. More...

Inheritance diagram for PdbLoader:

Collaboration diagram for PdbLoader:

Public Member Functions
	PdbLoader (istream &_input=cin, bool _permissive=false, bool _noHAtoms=false, bool _noHetAtoms=false, bool _noSecondary=false, bool _noConnection=false, bool _noWater=true, bool _verb=true, bool _allChains=false, string _NULL="", bool _onlyMetal=false, bool _noNucleotideChains=true)
void	checkAndSetChain ()
void	checkModel ()
vector< char >	getAllChains ()
unsigned int	getMaxModels ()
unsigned int	getMaxModelsFast ()
virtual void	loadProtein (Protein &prot)

Protected Member Functions
void	assignSecondary (Spacer &sp)
bool	inSideChain (const AminoAcid &aa, const Atom &at)
int	parsePDBline (string atomLine, string tag, Ligand *lig, AminoAcid *aa)
bool	setBonds (Spacer &sp)

Detailed Description

Loads components (Atoms, Groups, Spacer, etc.) in standard PDB format.

Constructor & Destructor Documentation

PdbLoader	(	istream &	_input = cin,
		bool	_permissive = false,
		bool	_noHAtoms = false,
		bool	_noHetAtoms = false,
		bool	_noSecondary = false,
		bool	_noConnection = false,
		bool	_noWater = true,
		bool	_verb = true,
		bool	_allChains = false,
		string	_NULL = "",
		bool	_onlyMetal = false,
		bool	_noNucleotideChains = true
	)

Constructor.

Parameters

_input	= the PDB file object
_permissive	= if true, allows loading residues with missing atoms
_noHAtoms	= if true, doesn't load Hydrogens
_noHetAtoms	= if true, doesn't load het atoms
_noSecondary	= if true, doesn't load secondary structure (neither the one calculated from torsional angles nor the DSSP)
_noConnection	= if true, doesn't connect residues
_noWater	= if true, doesn't load water atoms
_verb	= if true, verbose mode
_allChains	= if true, loads all chains
_NULL	= the name of the chain to be loaded, if not provided only loads the first chain
_onlyMetal	= if true, load only metals as ligands
_noNucleotideChains	= if true, doesn't load DNA/RNA chains

Member Function Documentation

void assignSecondary ( Spacer &  sp )

protected

Try to assigns the secondary structure from the PDB header. If not present uses Spacer's setStateFromTorsionAngles().

Parameters

Spacer

reference

void checkAndSetChain

(

)

If user selected a chain, it check validity of this choice, otherwise it select first available chain.

Parameters

void

Returns

void

void checkModel

(

)

If user selected a Model, it check validity of this choice, otherwise it select first available chain.

Parameters

void

Returns

void

vector< char > getAllChains

(

)

Returns all available chain IDs for a PDB file.

Parameters

void

Returns

vector of chars

unsigned int getMaxModels

(

)

Reads in the maximum allowed number of NMR models, zero otherwise

Parameters

none

unsigned int getMaxModelsFast

(

)

Reads in the maximum allowed number of NMR models, zero otherwise. This is a faster version because we only need to read the line with EXPDTA

Parameters

void

Returns

unsigned int

bool inSideChain ( const AminoAcid &  aa, const Atom &  at  )

protected

Private helper function to determine if atom is backbone or sidechain.

Parameters

Spacer

reference

Returns

bool

void loadProtein ( Protein &  prot )

virtual

Core function for PDB file parsing.

Parameters

prot	(Protein&)

Reimplemented from Loader.

int parsePDBline ( string  atomLine, string  tag, Ligand *  lig, AminoAcid *  aa  )

protected

Parse a single line of a PDB file.

Parameters

atomLine	(string) the whole PDB line as it is
tag	(string) = the first field (keyword) in a PDB line
lig	(Ligand) pointer
aa	(AminoAcid) pointer

Returns

Residue number read from the PDB line (int)

bool setBonds ( Spacer &  sp )

protected

Private helper function to set bond structure after loading the spacer.

Parameters

Spacer

reference

Returns

bool

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The documentation for this class was generated from the following files:

• Biopool/Sources/PdbLoader.h
• Biopool/Sources/PdbLoader.cc