Vparam class

Reads and assigns charge/radii parameters. More...

Data Structures
struct	sVparam_AtomData
	AtomData sub-class; stores atom data. More...
struct	Vparam_ResData
	ResData sub-class; stores residue data. More...
struct	Vparam
	Reads and assigns charge/radii parameters. More...
Files
file	vparam.h
	Contains declarations for class Vparam.
file	vparam.c
	Class Vparam methods.
Typedefs
typedef struct sVparam_AtomData	Vparam_AtomData
	Declaration of the Vparam_AtomData class as the sVparam_AtomData structure.
typedef struct Vparam_ResData	Vparam_ResData
	Declaration of the Vparam_ResData class as the Vparam_ResData structure.
typedef struct Vparam	Vparam
	Declaration of the Vparam class as the Vparam structure.
Functions
unsigned long int	Vparam_memChk (Vparam *thee)
	Get number of bytes in this object and its members.
Vparam_AtomData *	Vparam_AtomData_ctor ()
	Construct the object.
int	Vparam_AtomData_ctor2 (Vparam_AtomData *thee)
	FORTRAN stub to construct the object.
void	Vparam_AtomData_dtor (Vparam_AtomData **thee)
	Destroy object.
void	Vparam_AtomData_dtor2 (Vparam_AtomData *thee)
	FORTRAN stub to destroy object.
void	Vparam_AtomData_copyTo (Vparam_AtomData thee, Vparam_AtomData dest)
	Copy current atom object to destination.
void	Vparam_ResData_copyTo (Vparam_ResData thee, Vparam_ResData dest)
	Copy current residue object to destination.
void	Vparam_AtomData_copyFrom (Vparam_AtomData thee, Vparam_AtomData src)
	Copy current atom object from another.
Vparam_ResData *	Vparam_ResData_ctor (Vmem *mem)
	Construct the object.
int	Vparam_ResData_ctor2 (Vparam_ResData thee, Vmem mem)
	FORTRAN stub to construct the object.
void	Vparam_ResData_dtor (Vparam_ResData **thee)
	Destroy object.
void	Vparam_ResData_dtor2 (Vparam_ResData *thee)
	FORTRAN stub to destroy object.
Vparam *	Vparam_ctor ()
	Construct the object.
int	Vparam_ctor2 (Vparam *thee)
	FORTRAN stub to construct the object.
void	Vparam_dtor (Vparam **thee)
	Destroy object.
void	Vparam_dtor2 (Vparam *thee)
	FORTRAN stub to destroy object.
Vparam_ResData *	Vparam_getResData (Vparam *thee, char resName[VMAX_ARGLEN])
	Get residue data.
Vparam_AtomData *	Vparam_getAtomData (Vparam *thee, char resName[VMAX_ARGLEN], char atomName[VMAX_ARGLEN])
	Get atom data.
int	Vparam_readFlatFile (Vparam thee, const char iodev, const char iofmt, const char thost, const char *fname)
	Read a flat-file format parameter database.
int	Vparam_readXMLFile (Vparam thee, const char iodev, const char iofmt, const char thost, const char *fname)
	Read an XML format parameter database.
VPRIVATE int	readFlatFileLine (Vio sock, Vparam_AtomData atom)
	Read a single line of the flat file database.
VPRIVATE int	readXMLFileAtom (Vio sock, Vparam_AtomData atom)
	Read atom information from an XML file.
Variables
VPRIVATE char *	MCwhiteChars = " =,;\t\n\r"
	Whitespace characters for socket reads.
VPRIVATE char *	MCcommChars = "#%"
	Comment characters for socket reads.
VPRIVATE char *	MCxmlwhiteChars = " =,;\t\n\r<>"
	Whitespace characters for XML socket reads.

Detailed Description

Reads and assigns charge/radii parameters.

Function Documentation

VPRIVATE int readFlatFileLine	(	Vio *	sock,
		Vparam_AtomData *	atom
	)

Read a single line of the flat file database.

Author:: Nathan Baker

Parameters:

	sock	Socket ready for reading
	atom	Atom to hold parsed data

Returns:: 1 if successful, 0 otherwise

References sVparam_AtomData::atomName, sVparam_AtomData::charge, sVparam_AtomData::epsilon, sVparam_AtomData::radius, and sVparam_AtomData::resName.

Referenced by Vparam_readFlatFile().

VPRIVATE int readXMLFileAtom	(	Vio *	sock,
		Vparam_AtomData *	atom
	)

Read atom information from an XML file.

Author:: Todd Dolinsky

Parameters:

	sock	Socket ready for reading
	atom	Atom to hold parsed data

Returns:: 1 if successful, 0 otherwise

References sVparam_AtomData::atomName, sVparam_AtomData::charge, sVparam_AtomData::epsilon, sVparam_AtomData::radius, and Vstring_strcasecmp().

Referenced by Vparam_readXMLFile().

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void Vparam_AtomData_copyFrom	(	Vparam_AtomData *	thee,
		Vparam_AtomData *	src
	)

Copy current atom object from another.

Author:: Nathan Baker

Parameters:

	thee	Pointer to destination object
	src	Pointer to source object

References Vparam_AtomData_copyTo().

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void Vparam_AtomData_copyTo	(	Vparam_AtomData *	thee,
		Vparam_AtomData *	dest
	)

Copy current atom object to destination.

Author:: Nathan Baker

Parameters:

	thee	Pointer to source object
	dest	Pointer to destination object

References sVparam_AtomData::atomName, sVparam_AtomData::charge, sVparam_AtomData::epsilon, sVparam_AtomData::radius, and sVparam_AtomData::resName.

Referenced by Vparam_AtomData_copyFrom(), Vparam_readFlatFile(), Vparam_readXMLFile(), and Vparam_ResData_copyTo().

Vparam_AtomData* Vparam_AtomData_ctor ( )

Construct the object.

Author:: Nathan Baker

Returns:: Newly allocated object

References Vparam_AtomData_ctor2().

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int Vparam_AtomData_ctor2 ( Vparam_AtomData * thee )

FORTRAN stub to construct the object.

Author:: Nathan Baker

Parameters:

thee

Allocated memory

Returns:: 1 if successful, 0 otherwise

Referenced by Vparam_AtomData_ctor().

void Vparam_AtomData_dtor ( Vparam_AtomData ** thee )

Destroy object.

Author:: Nathan Baker

Parameters:

thee

Pointer to memory location of object

References Vparam_AtomData_dtor2().

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void Vparam_AtomData_dtor2 ( Vparam_AtomData * thee )

FORTRAN stub to destroy object.

Author:: Nathan Baker

Parameters:

thee

Pointer to object

Referenced by Vparam_AtomData_dtor().

Vparam* Vparam_ctor ( )

Construct the object.

Author:: Nathan Baker

Returns:: Newly allocated Vparam object

References Vparam_ctor2().

Referenced by loadParameter().

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int Vparam_ctor2 ( Vparam * thee )

FORTRAN stub to construct the object.

Author:: Nathan Baker

Parameters:

thee

Allocated Vparam memory

Returns:: 1 if successful, 0 otherwise

References nResData, resData, and vmem.

Referenced by Vparam_ctor().

void Vparam_dtor ( Vparam ** thee )

Destroy object.

Author:: Nathan Baker

Parameters:

thee

Pointer to memory location of object

References Vparam_dtor2().

Referenced by main().

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void Vparam_dtor2 ( Vparam * thee )

FORTRAN stub to destroy object.

Author:: Nathan Baker

Parameters:

thee

Pointer to object

References nResData, resData, vmem, and Vparam_ResData_dtor2().

Referenced by Vparam_dtor().

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Vparam_AtomData* Vparam_getAtomData	(	Vparam *	thee,
		char	resName[VMAX_ARGLEN],
		char	atomName[VMAX_ARGLEN]
	)

Get atom data.

Author:: Nathan Baker

Parameters:

	thee	Vparam object
	resName	Residue name
	atomName	Atom name

Returns:: Pointer to the desired atom object or VNULL if residue not found

Note:: Some method to initialize the database must be called before this method (e.g.,

See also:: Vparam_readFlatFile)

References Vparam_ResData::atomData, sVparam_AtomData::atomName, Vparam_ResData::nAtomData, nResData, resData, Vparam_getResData(), and Vstring_strcasecmp().

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

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Vparam_ResData* Vparam_getResData	(	Vparam *	thee,
		char	resName[VMAX_ARGLEN]
	)

Get residue data.

Author:: Nathan Baker

Parameters:

	thee	Vparam object
	resName	Residue name

Returns:: Pointer to the desired residue object or VNULL if residue not found

Note:: Some method to initialize the database must be called before this method (e.g.,

See also:: Vparam_readFlatFile)

References Vparam_ResData::name, nResData, resData, and Vstring_strcasecmp().

Referenced by Vparam_getAtomData().

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unsigned long int Vparam_memChk ( Vparam * thee )

Get number of bytes in this object and its members.

Author:: Nathan Baker

Parameters:

thee

Vparam object

Returns:: Number of bytes allocated for object

References vmem.

int Vparam_readFlatFile	(	Vparam *	thee,
		const char *	iodev,
		const char *	iofmt,
		const char *	thost,
		const char *	fname
	)

Read a flat-file format parameter database.

Author:: Nathan Baker

Parameters:

	thee	Vparam object
	iodev	Input device type (FILE/BUFF/UNIX/INET)
	iofmt	Input device format (ASCII/XDR)
	thost	Input hostname (for sockets)
	fname	Input FILE/BUFF/UNIX/INET name (see note below for format)

Returns:: 1 if successful, 0 otherwise

Note:

The database file should have the following format:

 RESIDUE ATOM CHARGE RADIUS EPSILON

where RESIDUE is the residue name string, ATOM is the atom name string, CHARGE is the charge in e, RADIUS is the van der Waals radius ( $\sigma_i$ ) in Å, and EPSILON is the van der Waals well-depth ( $\epsilon_i$ ) in kJ/mol. See the Vparam structure documentation for the precise definitions of $\sigma_i$ and $\epsilon_i$ .

ASCII-format flat files are provided with the APBS source code:

tools/conversion/vparam-amber-parm94.dat: AMBER parm94 parameters
tools/conversion/vparam-charmm-par_all27.dat: CHARMM par_all27_prot_na parameters

References Vparam_ResData::atomData, MCcommChars, Vparam_ResData::name, Vparam_ResData::nAtomData, nResData, readFlatFileLine(), resData, sVparam_AtomData::resName, vmem, Vparam_AtomData_copyTo(), Vparam_ResData_ctor2(), Vparam_ResData_dtor2(), and Vstring_strcasecmp().

Referenced by loadParameter().

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int Vparam_readXMLFile	(	Vparam *	thee,
		const char *	iodev,
		const char *	iofmt,
		const char *	thost,
		const char *	fname
	)

Read an XML format parameter database.

Author:: Todd Dolinsky

Parameters:

	thee	Vparam object
	iodev	Input device type (FILE/BUFF/UNIX/INET)
	iofmt	Input device format (ASCII/XDR)
	thost	Input hostname (for sockets)
	fname	Input FILE/BUFF/UNIX/INET name