OBPhModel Class Reference

#include <phmodel.h>

Inheritance diagram for OBPhModel:

Public Member Functions
	OBPhModel ()
	~OBPhModel ()
void	ParseLine (const char *)
size_t	GetSize ()
void	AssignSeedPartialCharge (OBMol &)
void	CorrectForPH (OBMol &, double pH=7.4)
void	Init ()
void	SetReadDirectory (char *dir)
void	SetEnvironmentVariable (char *var)

Protected Attributes
bool	_init
const char *	_dataptr
std::string	_filename
std::string	_dir
std::string	_subdir
std::string	_envvar

Detailed Description

Corrections for pH used by OBMol::CorrectForPH()

The data/phmodel.txt file contains transformations which are applied to correct the charges for a given pH. This function uses the Henderson-Hasselbalch equation to calculate which species (protonated/ unprotonated) is present in the highest concentration at the given pH.

For acids an entry would look like:

# carboxylic acid
O=C[OD1:1] >> O=C[O-:1] 4.0

The 4.0 is the pKa for the dissociation [HA] -> [H+] + [A-]. To calculate [HA]/[A-] we use:

[HA] / [A-] = 10^(pKa - pH)

[HA]/[A-] > 1  :  [HA] > [A-]
[HA]/[A-] < 1  :  [A-] > [HA]

For a base, an entry would look be:

# methyl amine
C[N:1] >> C[N+:1]       10.7

Here, the 10.7 is the pKa for the dissociation [BH+] -> [H+] + [B:]. To calculate [BH+]/[B:] we use:

[BH+] / [B:] = 10^(pKa - pH)

[BH+]/[B:] > 1  :  [BH+] > [B:]
[BH+]/[B:] < 1  :  [B:] > [BH+]

The transformations are all applied (if needed at the specified pH value) in the same order they are found in data/phmodel.txt.

Constructor & Destructor Documentation

OBPhModel()

OBPhModel

(

)

~OBPhModel()

~OBPhModel

(

)

Member Function Documentation

ParseLine()

void ParseLine ( const char *  )

virtual

Specified by particular table classes (parses an individual data line)

Reimplemented from OBGlobalDataBase.

GetSize()

size_t GetSize ( )

inlinevirtual

Returns

the number of chemical transformations

Reimplemented from OBGlobalDataBase.

AssignSeedPartialCharge()

void AssignSeedPartialCharge

(

OBMol &

mol

)

CorrectForPH()

void CorrectForPH	(	OBMol &	mol,
		double	pH = 7.4
	)

Init()

void Init ( )

inherited

Read in the data file, falling back as needed.

Referenced by OBRotorList::Init().

SetReadDirectory()

void SetReadDirectory ( char *  dir )

inlineinherited

Set the directory before calling Init()

SetEnvironmentVariable()

void SetEnvironmentVariable ( char *  var )

inlineinherited

Set the environment variable to use before calling Init()

Member Data Documentation

_init

bool _init

protectedinherited

Whether the data been read already.

_dataptr

const char* _dataptr

protectedinherited

Default data table if file is unreadable.

_filename

std::string _filename

protectedinherited

File to search for.

_dir

std::string _dir

protectedinherited

Data directory for file if _envvar fails.

_subdir

std::string _subdir

protectedinherited

Subdirectory (if using environment variable)

_envvar

std::string _envvar

protectedinherited

Environment variable to check first.

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

• phmodel.h
• phmodel.cpp