OBPhModel Class Reference

Corrections for pH used by OBMol::CorrectForPH() More...

#include <phmodel.h>

Inheritance diagram for OBPhModel:

List of all members.

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

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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.

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Constructor & Destructor Documentation

OBPhModel

(

)

~OBPhModel

(

)

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Member Function Documentation

void ParseLine

(

const char *

)

[virtual]

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

Reimplemented from OBGlobalDataBase.

size_t GetSize

(

)

[inline, virtual]

Returns:

the number of chemical transformations

Reimplemented from OBGlobalDataBase.

void AssignSeedPartialCharge

(

OBMol &

mol )

Referenced by OBAtom::GetPartialCharge().

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

Referenced by OBMol::CorrectForPH().

void Init

(

)

[inherited]

Read in the data file, falling back as needed.

void SetReadDirectory

(

char *

dir )

[inline, inherited]

Set the directory before calling Init()

void SetEnvironmentVariable

(

char *

var )

[inline, inherited]

Set the environment variable to use before calling Init()

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Member Data Documentation

bool _init [protected, inherited]

Whether the data been read already.

const char* _dataptr [protected, inherited]

Default data table if file is unreadable.

std::string _filename [protected, inherited]

File to search for.

std::string _dir [protected, inherited]

Data directory for file if _envvar fails.

std::string _subdir [protected, inherited]

Subdirectory (if using environment variable)

std::string _envvar [protected, inherited]

Environment variable to check first.

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

• phmodel.h
• phmodel.cpp