PQR class model to handle proteins (atoms and titratable groups). More...

#include <PQR.h>

Public Member Functions
	PQR (string _fileName)
	Constructor.
void	addInfo (INI &ini)
	Setting up some options.
void	parseSTFolder ()
	Parsing ST files folder.
void	parseSTFiles ()
	Parsing ST files folder wrapper.
int	parse ()
	Parsing the PQR file.
void	calcModel (INI &ini)
	Wrapper method to compute molecular volume model of the protein.
void	calcDeltaG ()
	Compute energy difference using NETGEN and nglib libraries.
void	calcResidues (INI &ini)
	Using the atom list from PQR file parse all residues.
void	calcExplicitModels (INI &ini)
	Molecular volume surfaces for titratable groups are computed if using the two-cycle approach.
void	writePQR (vector< Atom > &aList, string fileName)
	Write out a PQR file using a given atom list.
void	writePQR (Residue &titGroup, int stateNr)
	Overloading method to write out a given residue with a given state to a PQR file.
void	switchState (Residue &titGroup, int stateNr)
	Switches the state of a residue to a given state nr.
void	neutralState (Residue &titGroup, int stateNr)
	Switches a given residue into neutral state.
void	patch (vector< Atom > &atomList, ST &st)
	Switches a given atom list (of a residue) to another state (using ST data structure which is already in a given state).
void	patchNeutral (vector< Atom > &atomList, ST &st)
	Switches a given atom list (of a residue) to neutral state (using ST data structure).
void	writeOutW (string fileName)
	Writing out W-matrix as flat G file.
double	calcWmv (int state, Residue &ref, Residue &mref, Residue &mstat, string cycle)
	Computing the W-matrix element given a residue in reference and current state and cycle information.
void	calcW (string cycle)
	Computing the whole W-matrix for every pairwise titratable group interaction.
void	calcPkint (string cycleName, string refPQRFileName)
	Computing intrinsic pKA values.
vector< Atom >	deleteAtoms (vector< Atom > result, vector< Atom > &compareAtomList)
	Deletes from atom List "result" all atoms which are also in atom list "compareAtomList" via their atom id in PQR file.
vector< Atom >	getAtoms (Residue currentTitGroup, int stateNr)
	Returns a list of atoms from a given residue which is patched to a given state nr.
float	getCycle0Shift (string residueName, int state)
	Returns the averaged pKA value which is defined for the one-cycle approach to skip a second thermodynamic cycle computation.
void	calcPotat (string cycleName)
	Computes POTAT files which are needed to calculate intrinsic pKA values.
void	writePDE (INI &ini, string mode="explicit")
	Writes out PDE files to compute POTAT files with NGSolve.
void	writeOutPkint (string cycleName, string fileName, INI &ini)
	Writes out PKINT files to use with Monte-Carlo method, Karlsberg2.
char	getState (string residueName, int stateNr)
	Every state has a char identifier which is returned from ST file.
float	getShift (string residueName, int stateNr)
	Returns the pKA shift from reference to given state.
float	getShiftCycle0 (string residueName, int stateNr)
	Returns the averaged pKA value to skip second thermodynamic cycle.
Static Public Attributes
static bool	STparsed = false
	Are ST files already parsed.
static bool	calcNTE = false
	Do we have to compute the N-terminus.
static bool	calcCTE = false
	Do we have to compute the C-terminus.
static bool	explicitModels = false
	Are we using the two-cycle approach (compute models explicitly)
Private Attributes
string	fileName
	File name of the PQR file which has to be parsed (protein).
string	stFilesFolder
Model	molecule
	Placeholder for molecular volume mesh computation.
vector< Atom >	atomList
	Atom list of all atoms with all PQR information.
vector< Residue >	residueList
	A list of all residues in the protein.
vector< Residue >	titGroupList
vector< ST >	stList
	A list of all states in every ST file for every titratable group.
tCycle	cycle
	An abstraction of the thermodynamic cycle.
vector< vector< vector< vector < double > > > >	wmatrix
	A multidensional W-matrix vector to store pairwise interaction energies of all titratable groups with each other.

Detailed Description

PQR class model to handle proteins (atoms and titratable groups).

Reading options in config file. Parsing ST files (description of titratable groups in proteins). Titrating N- and/or C-terminus. Patching groups. Computing potential energies. pKA values (W-matrix, pkint PKINT files) using one- or two-cycle approach. Managing model generation (protein and titratable groups).

Author:: Ilkay Sakalli

Constructor & Destructor Documentation

PQR::PQR ( string _fileName ) [inline]

Constructor.

Parsing the PQR file and adding atoms to atomList.

Parameters:

string fileName of the PQR file

Member Function Documentation

void PQR::addInfo ( INI & ini ) [inline]

Setting up some options.

Here, some options are defined: ST files folder, calc termini?, use two-cycle approach?

Parameters:

INI	Options INI file.

Returns:: Void.

void PQR::calcDeltaG ( ) [inline]

Compute energy difference using NETGEN and nglib libraries.

An electrostatic solvation energy difference is computed. NETGEN and MUMPS is used.

Returns:: Void.

void PQR::calcExplicitModels ( INI & ini ) [inline]

Molecular volume surfaces for titratable groups are computed if using the two-cycle approach.

Molecular volume models are computed for titratable groups if the two-cycle approach (explicit model computation) is chosen. PQR files are written out for every titratable group in every state.

Parameters:

INI	Configuration INI file.

Returns:: Void.

void PQR::calcModel ( INI & ini ) [inline]

Wrapper method to compute molecular volume model of the protein.

Compute molecular volume model of protein depending on the configuration of the INI file.

Parameters:

INI	Configuration INI file.

Returns:: Void.

Compute the cavity

Compute the ion exclusion layer if ionc != 0

Compute the molecular surface of the protein

void PQR::calcPkint	(	string	cycleName,
		string	refPQRFileName
	)		`[inline]`

Computing intrinsic pKA values.

Intrinsic pKA values (pkint) are computed parsing PKINT files computed before. Back and Born energy parts are assigned to titratable groups.

Parameters:

string	Name of current cycle.
string	A reference PQR definition is needed (written out before).

Returns:: Void.

void PQR::calcPotat ( string cycleName ) [inline]

Computes POTAT files which are needed to calculate intrinsic pKA values.

A PDE file is written out before to control NGSolve which is a module of NETGEN. With this, POTAT files are computed which store all electrostatic potentials at every atom position of every titratable goup in every state.

Parameters:

string Name of current cycle.

Returns:: Void.

void PQR::calcResidues ( INI & ini ) [inline]

Using the atom list from PQR file parse all residues.

All residues which define a molecular model and for every titratable group are computed in the spirit of the pKA framework of Knapp et al. Also, C- and N-termini are added if defined in config INI file.

Parameters:

INI	Configuration INI file.

Returns:: Void.

void PQR::calcW ( string cycle ) [inline]

Computing the whole W-matrix for every pairwise titratable group interaction.

A multidimensional W-matrix is generated. At first diagonal elements are set to zero. Decide which cycle is computed and compute every W element using calcWmv of one to another group for every state. Then the matrix is symmetrized.

Parameters:

string Name of current cycle.

Returns:: Void.

double PQR::calcWmv	(	int	state,
		Residue &	ref,
		Residue &	mref,
		Residue &	mstat,
		string	cycle
	)		`[inline]`

Computing the W-matrix element given a residue in reference and current state and cycle information.

A W-matrix element is computed using the pKA framework defined by Knapp et al.

Parameters:

int	Current state number.
Residue	Residue in reference state (protein environment).
Residue	Residue in reference state (water environment).
Residue	Residue in current state (water environment).
string	Name of current cycle.

Returns:: double W-matrix element.

vector<Atom> PQR::deleteAtoms	(	vector< Atom >	result,
		vector< Atom > &	compareAtomList
	)		`[inline]`

Deletes from atom List "result" all atoms which are also in atom list "compareAtomList" via their atom id in PQR file.

Returns the vector "result" which contains all atoms which were in list "result" before and are not same as in "compareAtomList". If same atoms are found in "result" and "compareAtomList" this aroms are erased from "result".

Parameters:

vector<Atom>	Atom list where same atoms with compareAtomList will be erased.
vector<Atom>	Atom list where atoms from this list are erased in result list.

Returns:: vector<Atom> Returns an atom list where same atoms with compareAtomList are erased from result list.

vector<Atom> PQR::getAtoms	(	Residue	currentTitGroup,
		int	stateNr
	)		`[inline]`

Returns a list of atoms from a given residue which is patched to a given state nr.

A residue is patched to a given state by stateNr. Its atoms are returned as an atom list.

Parameters:

Residue	A titratable group which will be patched.
int	State number to patch given residue.

Returns:: vector<Atom> Returns an atom list where given residue currentTitGroup is patched to state stateNr.

float PQR::getCycle0Shift	(	string	residueName,
		int	state
	)		`[inline]`

Returns the averaged pKA value which is defined for the one-cycle approach to skip a second thermodynamic cycle computation.

Averaged pKA values are given by Sakalli et al. and are stored in ST files.

Parameters:

string	Name of residue receive an averaged pKA value.
int	State of given residue to return an averaged pKA value.

Returns:: float Averaged pKA value to skip second thermodynamic cycle computation.

float PQR::getShift	(	string	residueName,
		int	stateNr
	)		`[inline]`

Returns the pKA shift from reference to given state.

Returns a pKA shift value from experimental values (defined in ST file) which is defined from reference residue to same residue to given state.

Parameters:

string	Name of the residue
int	State of the residue to get it char identifier.

Returns:: float Returns the pKA shift from reference to given state.

float PQR::getShiftCycle0	(	string	residueName,
		int	stateNr
	)		`[inline]`

Returns the averaged pKA value to skip second thermodynamic cycle.

Returns an averaged pKA value which mimics the electrostatics part of the energy shift in the thermodynamic cycle from reference to given state of every titratable group/residue. Values are given from Sakalli et al.

Parameters:

string	Name of the residue
int	State of the residue to get it char identifier.

Returns:: float Returns the average pKA value for a given residue in a given state

char PQR::getState	(	string	residueName,
		int	stateNr
	)		`[inline]`

Every state has a char identifier which is returned from ST file.

Returns a char character which is stored in ST file for every titratable group and every state.

Parameters:

string	Name of the residue.
int	State of the residue to get it char identifier.

Returns:: char Char identifier of residue in given state.

void PQR::neutralState	(	Residue &	titGroup,
		int	stateNr
	)		`[inline]`

Switches a given residue into neutral state.

A residue which has an arbitrary state is switched into neutral/ reference state using previous ST file information and atom list information from given residue.

Parameters:

Residue	Current resdiue which holds a list of atoms.
int	State of residue to patch to neutral state.

Returns:: Void.

int PQR::parse ( ) [inline]

Parsing the PQR file.

Adding all atoms of PQR file to atomList.

Returns:: int 1 if parsing was successful.

void PQR::parseSTFiles ( ) [inline]

Parsing ST files folder wrapper.

ST files given in CHARMM format are parsed to know charges of different titration states of residues. Afterwards static variable STparsed is set to true.

Returns:: Void.

void PQR::parseSTFolder ( ) [inline]

Parsing ST files folder.

ST files given in CHARMM format are parsed to know charges of different titration states of residues.

Returns:: Void.

For every file in the ST files folder defined in INI config file If the file has extension "st"

Parse current ST file

void PQR::patch	(	vector< Atom > &	atomList,
		ST &	st
	)		`[inline]`

Switches a given atom list (of a residue) to another state (using ST data structure which is already in a given state).

An atom list (normally from a residue) is patched. Atoms in the list are patched using ST which has charge information. ST is normally one state of a titratable group.

Parameters:

vector<Atom>	An atom list.
ST	ST structure with information about charges.

Returns:: Void.

void PQR::patchNeutral	(	vector< Atom > &	atomList,
		ST &	st
	)		`[inline]`

Switches a given atom list (of a residue) to neutral state (using ST data structure).

An atom list (normally from a residue) is patched. Atoms in the list are patched using ST which has charge information.

Parameters:

vector<Atom>	An atom list.
ST	ST structure with information about charges.

Returns:: Void.

void PQR::switchState	(	Residue &	titGroup,
		int	stateNr
	)		`[inline]`

Switches the state of a residue to a given state nr.

A residue which has an arbitrary state is switched into another state with this one using previous ST file information and atom list information from given residue.

Parameters:

Residue	Current resdiue which holds a list of atoms.
int	State of residue to patch to.

Returns:: Void.

void PQR::writeOutPkint	(	string	cycleName,
		string	fileName,
		INI &	ini
	)		`[inline]`

Writes out PKINT files to use with Monte-Carlo method, Karlsberg2.

Depending on the current cycle a PKINT file is written out. Before, all pkint values where computed using POTAT files. A PKINT file contains all intrinsic pKA values for every titratable group from reference to its other states.

Parameters:

string	Current cycle name.
string	Prefix of file name to write out PKINT file.
INI	Config INI file.

Returns:: Void.

void PQR::writeOutW ( string fileName ) [inline]

Writing out W-matrix as flat G file.

A symmetric W-matrix which is computed before is written out.

Parameters:

string Prefix of filename for W-matrix

Returns:: Void.

void PQR::writePDE	(	INI &	ini,
		string	mode = `"explicit"`
	)		`[inline]`

Writes out PDE files to compute POTAT files with NGSolve.

A PDE file is written out to control NGSolve which is a module of NETGEN.

Parameters:

INI	Config INI file.
string	Approach used to compute pKA values (two-cycle approach: implicit; one-cycle approach: explicit).

Returns:: Void.

void PQR::writePQR	(	vector< Atom > &	aList,
		string	fileName
	)		`[inline]`

Write out a PQR file using a given atom list.

A PQR file is written out using a given atom list to a file as fileName.

Parameters:

vector<Atom>	Atom List to write out to PQR file.
string	File name of the resulting PQR file.

Returns:: Void.

void PQR::writePQR	(	Residue &	titGroup,
		int	stateNr
	)		`[inline]`

Overloading method to write out a given residue with a given state to a PQR file.

A PQR file is written out using a given residue with state.

Parameters:

Residue	Current resdiue which holds a list of atoms.
int	State of residue to patch to.

Returns:: Void.

Member Data Documentation

vector<Atom> PQR::atomList [private]

Atom list of all atoms with all PQR information.

bool PQR::calcCTE = false [static]

Do we have to compute the C-terminus.

bool PQR::calcNTE = false [static]

Do we have to compute the N-terminus.

tCycle PQR::cycle [private]

An abstraction of the thermodynamic cycle.

bool PQR::explicitModels = false [static]

Are we using the two-cycle approach (compute models explicitly)

string PQR::fileName [private]

File name of the PQR file which has to be parsed (protein).

Model PQR::molecule [private]

Placeholder for molecular volume mesh computation.

vector<Residue> PQR::residueList [private]

A list of all residues in the protein.

string PQR::stFilesFolder [private]

Folder of ST files, which define charge pattern for different states of every titratable group in CHARMM format.

vector<ST> PQR::stList [private]

A list of all states in every ST file for every titratable group.

bool PQR::STparsed = false [static]

Are ST files already parsed.

vector<Residue> PQR::titGroupList [private]

A list of all titratable groups in the protein (definition via framework of pKA computations from Knapp et al.).

vector< vector< vector< vector<double> > > > PQR::wmatrix [private]

A multidensional W-matrix vector to store pairwise interaction energies of all titratable groups with each other.

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

PQR.h

Public Member Functions

Static Public Attributes

Private Attributes

Detailed Description

Constructor & Destructor Documentation

Member Function Documentation

Member Data Documentation