Valist class

Container class for list of atom objects. More...

Data Structures
struct	sValist
	Container class for list of atom objects. More...
Files
file	valist.h
	Contains declarations for class Valist.
Typedefs
typedef struct sValist	Valist
	Declaration of the Valist class as the Valist structure.
Functions
Vatom *	Valist_getAtomList (Valist *thee)
	Get actual array of atom objects from the list.
double	Valist_getCenterX (Valist *thee)
	Get x-coordinate of molecule center.
double	Valist_getCenterY (Valist *thee)
	Get y-coordinate of molecule center.
double	Valist_getCenterZ (Valist *thee)
	Get z-coordinate of molecule center.
int	Valist_getNumberAtoms (Valist *thee)
	Get number of atoms in the list.
Vatom *	Valist_getAtom (Valist *thee, int i)
	Get pointer to particular atom in list.
unsigned long int	Valist_memChk (Valist *thee)
	Get total memory allocated for this object and its members.
Valist *	Valist_ctor ()
	Construct the atom list object.
Vrc_Codes	Valist_ctor2 (Valist *thee)
	FORTRAN stub to construct the atom list object.
void	Valist_dtor (Valist **thee)
	Destroys atom list object.
void	Valist_dtor2 (Valist *thee)
	FORTRAN stub to destroy atom list object.
Vrc_Codes	Valist_readPQR (Valist thee, Vparam param, Vio *sock)
	Fill atom list with information from a PQR file.
Vrc_Codes	Valist_readPDB (Valist thee, Vparam param, Vio *sock)
	Fill atom list with information from a PDB file.
Vrc_Codes	Valist_readXML (Valist thee, Vparam param, Vio *sock)
	Fill atom list with information from an XML file.
Vrc_Codes	Valist_getStatistics (Valist *thee)
	Load up Valist with various statistics.

Detailed Description

Container class for list of atom objects.

Function Documentation

Valist* Valist_ctor ( )

Construct the atom list object.

Author:: Nathan Baker

Returns:: Pointer to newly allocated (empty) atom list

References Valist_ctor2(), and VRC_SUCCESS.

Referenced by loadMolecules().

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Vrc_Codes Valist_ctor2 ( Valist * thee )

FORTRAN stub to construct the atom list object.

Author:: Nathan Baker, Yong Huang

Returns:: Success enumeration

Parameters:

thee

Storage for new atom list

References sValist::atoms, sValist::number, sValist::vmem, and VRC_SUCCESS.

Referenced by Valist_ctor().

void Valist_dtor ( Valist ** thee )

Destroys atom list object.

Author:: Nathan Baker

Parameters:

thee

Pointer to storage for atom list

References Valist_dtor2().

Referenced by killMolecules().

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void Valist_dtor2 ( Valist * thee )

FORTRAN stub to destroy atom list object.

Author:: Nathan Baker

Parameters:

thee

Pointer to atom list object

References sValist::atoms, sValist::number, and sValist::vmem.

Referenced by Valist_dtor().

Vatom* Valist_getAtom	(	Valist *	thee,
		int	i
	)

Get pointer to particular atom in list.

Author:: Nathan Baker

Returns:: Pointer to atom object i

Parameters:

	thee	Atom list object
	i	Index of atom in list

References sValist::atoms, and sValist::number.

Referenced by energyMG(), extEnergy(), fillcoChargeSpline1(), fillcoChargeSpline2(), fillcoCoefMolDielNoSmooth(), fillcoCoefMolIon(), fillcoCoefSpline(), fillcoCoefSpline3(), fillcoCoefSpline4(), fillcoPermanentMultipole(), forceAPOL(), initAPOL(), initMG(), qfForceSpline1(), qfForceSpline2(), qfForceSpline4(), storeAtomEnergy(), Vacc_SASA(), Vacc_storeParms(), Vcsm_getAtom(), Vcsm_init(), Vcsm_update(), Vfetk_getAtomColor(), Vfetk_setAtomColors(), Vgreen_coulomb_direct(), Vgreen_coulombD_direct(), Vpbe_ctor2(), Vpbe_getCoulombEnergy1(), Vpmg_dbForce(), Vpmg_ibForce(), Vpmg_polarizEnergy(), Vpmg_qfEnergyPoint(), Vpmg_setPart(), and Vpmg_unsetPart().

Vatom* Valist_getAtomList ( Valist * thee )

Get actual array of atom objects from the list.

Author:: Nathan Baker

Returns:: Array of atom objects

Parameters:

thee

Atom list object

References sValist::atoms.

double Valist_getCenterX ( Valist * thee )

Get x-coordinate of molecule center.

Author:: Nathan Baker

Returns:: X-coordinate of molecule center

Parameters:

thee

Atom list object

References sValist::center.

double Valist_getCenterY ( Valist * thee )

Get y-coordinate of molecule center.

Author:: Nathan Baker

Returns:: Y-coordinate of molecule center

Parameters:

thee

Atom list object

References sValist::center.

double Valist_getCenterZ ( Valist * thee )

Get z-coordinate of molecule center.

Author:: Nathan Baker

Returns:: Z-coordinate of molecule center

Parameters:

thee

Atom list object

References sValist::center.

int Valist_getNumberAtoms ( Valist * thee )

Get number of atoms in the list.

Author:: Nathan Baker

Returns:: Number of atoms in list

Parameters:

thee

Atom list object

References sValist::number.

Referenced by energyMG(), extEnergy(), fillcoChargeSpline1(), fillcoChargeSpline2(), fillcoCoefMolDielNoSmooth(), fillcoCoefMolIon(), fillcoCoefSpline(), fillcoCoefSpline3(), fillcoCoefSpline4(), fillcoPermanentMultipole(), forceAPOL(), forceMG(), initAPOL(), initMG(), loadMolecules(), storeAtomEnergy(), Vacc_allocate(), Vacc_dtor2(), Vacc_SASA(), Vacc_storeParms(), Vacc_wcaEnergy(), Vcsm_init(), Vfetk_getAtomColor(), Vfetk_qfEnergy(), Vfetk_setAtomColors(), Vgreen_coulomb(), Vgreen_coulomb_direct(), Vgreen_coulombD(), Vgreen_coulombD_direct(), Vpbe_ctor2(), Vpbe_getCoulombEnergy1(), Vpmg_polarizEnergy(), Vpmg_qfEnergyPoint(), Vpmg_setPart(), and Vpmg_unsetPart().

Vrc_Codes Valist_getStatistics ( Valist * thee )

Load up Valist with various statistics.

Author:: Nathan Baker, Yong Huang

Returns:: Success enumeration

References sValist::atoms, sValist::center, sVatom::charge, sValist::charge, sValist::maxcrd, sValist::maxrad, sValist::mincrd, sValist::number, sVatom::position, sVatom::radius, VRC_FAILURE, and VRC_SUCCESS.

Referenced by Valist_readPDB(), Valist_readPQR(), and Valist_readXML().

unsigned long int Valist_memChk ( Valist * thee )

Get total memory allocated for this object and its members.

Author:: Nathan Baker

Returns:: Total memory in bytes

Parameters:

thee

Atom list object

References sValist::vmem.

Vrc_Codes Valist_readPDB	(	Valist *	thee,
		Vparam *	param,
		Vio *	sock
	)

Fill atom list with information from a PDB file.

Author:: Nathan Baker, Todd Dolinsky, Yong Huang

Returns:: Success enumeration

Note:: We don't actually respect PDB format; instead recognize whitespace- or tab-delimited fields which allows us to deal with structures with coordinates > 999 or < -999.

Parameters:

	thee	Atom list object
	param	A pre-initialized parameter object
	sock	Socket read for reading PDB file

References sVparam_AtomData::charge, sVparam_AtomData::epsilon, sValist::number, sVparam_AtomData::radius, Valist_getStatistics(), Vatom_setAtomID(), Vatom_setAtomName(), Vatom_setCharge(), Vatom_setEpsilon(), Vatom_setPosition(), Vatom_setRadius(), Vatom_setResName(), sValist::vmem, Vparam_getAtomData(), VRC_FAILURE, and Vstring_strcasecmp().

Referenced by loadMolecules().

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Vrc_Codes Valist_readPQR	(	Valist *	thee,
		Vparam *	param,
		Vio *	sock
	)

Fill atom list with information from a PQR file.

Author:: Nathan Baker, Yong Huang

Returns:: Success enumeration

Note:

A PQR file has PDB structure with charge and radius in the last two columns instead of weight and occupancy
We don't actually respect PDB format; instead recognize whitespace- or tab-delimited fields which allows us to deal with structures with coordinates > 999 or < -999.

Parameters:

	thee	Atom list object
	param	A pre-initialized parameter object
	sock	Socket reading for reading PQR file

References sVparam_AtomData::charge, sVparam_AtomData::epsilon, sValist::number, sVparam_AtomData::radius, Valist_getStatistics(), Vatom_setAtomID(), Vatom_setAtomName(), Vatom_setCharge(), Vatom_setEpsilon(), Vatom_setPosition(), Vatom_setRadius(), Vatom_setResName(), sValist::vmem, Vparam_getAtomData(), VRC_FAILURE, and Vstring_strcasecmp().

Referenced by loadMolecules().

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Vrc_Codes Valist_readXML	(	Valist *	thee,
		Vparam *	param,
		Vio *	sock
	)

Fill atom list with information from an XML file.

Author:: Todd Dolinsky, Yong Huang

Returns:: Success enumeration

Note:

The XML file must adhere to some guidelines, notably the presence of an <atom> tag with all other useful information (x, y, z, charge, and radius) as nested elements.

Parameters:

	thee	Atom list object
	param	A pre-initialized parameter object
	sock	Socket reading for reading PQR file

References sValist::number, Valist_getStatistics(), Vatom_setAtomID(), Vatom_setCharge(), Vatom_setPosition(), Vatom_setRadius(), sValist::vmem, VRC_FAILURE, and Vstring_strcasecmp().

Referenced by loadMolecules().

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Valist class

Data Structures

Files

Typedefs

Functions

Detailed Description

Function Documentation