embiep.c


Function embIepPkNew

Create a pK array to hold amino acid pK data

Prototype

double** embIepPkNew (
      void
);

TypeNameRead/WriteDescription
double** RETURNpK data

From EMBOSS 6.1.0


Function embIepPkNewFile

Create a pK array and read the data from a file

Prototype

AjBool embIepPkNewFile (
      AjPFile pkfile,
      double*** pK
);

TypeNameRead/WriteDescription
AjPFilepkfileModifyAmino acid pKa data file
double***pKOutputArrays of pK values
AjBool RETURNTrue on success

From EMBOSS 6.6.0


Function embIepPkDel

Delete a pK array and read the data

Prototype

void embIepPkDel (
      double*** pK
);

TypeNameRead/WriteDescription
double***pKOutputpKs
void RETURN

From EMBOSS 6.1.0


Function embIepPhToHconc

Convert pH to hydrogen ion concontration

Prototype

double embIepPhToHconc (
      double pH
);

TypeNameRead/WriteDescription
doublepHInputpH
double RETURNhydrogen ion concentrration

From EMBOSS 4.0.0


Function embIepPhFromHconc

Convert hydrogen ion concontration to pH

Prototype

double embIepPhFromHconc (
      double H
);

TypeNameRead/WriteDescription
doubleHInputH
double RETURNpH

From EMBOSS 4.0.0


Function embIepPkToK

Convert pK to dissociation constant

Prototype

double embIepPkToK (
      double pK
);

TypeNameRead/WriteDescription
doublepKInputpK
double RETURNdissociation constant

From EMBOSS 1.0.0


Function embIepPkFromK

Convert dissociation constant to pK

Prototype

double embIepPkFromK (
      double K
);

TypeNameRead/WriteDescription
doubleKInputK
double RETURNpK

From EMBOSS 4.0.0


Function embIepPkRead

Read the pK values from Epk.dat

Prototype

void embIepPkRead (
      double** pK
);

TypeNameRead/WriteDescription
double**pKOutputpK
void RETURN

From EMBOSS 1.0.0


Function embIepPkReadFile

Read the pK values from Epk.dat

Prototype

void embIepPkReadFile (
      double** pK,
      AjPFile pkfile
);

TypeNameRead/WriteDescription
double**pKOutputpK
AjPFilepkfileOutputpK data file
void RETURN

From EMBOSS 6.6.0


Function embIepCompC

Calculate the amino acid composition of a protein sequence

Prototype

void embIepCompC (
      const char* s,
      ajuint amino,
      ajuint carboxyl,
      ajuint sscount,
      ajuint modlysine,
      ajuint* c,
      ajuint* resn,
      ajuint* resc
);

TypeNameRead/WriteDescription
const char*sInputprotein sequence
ajuintaminoInputnumber of amino termini
ajuintcarboxylInputnumber of carboxyl termini
ajuintsscountInputnumber of disulphide bridges
ajuintmodlysineInputnumber of modified lysines
ajuint*cOutputarray of amino acid composition
ajuint*resnOutputN-terminal amino acid
ajuint*rescOutputC-terminal amino acid
void RETURN

From EMBOSS 4.0.0


Function embIepCompS

Calculate the amino acid composition of a protein sequence

Prototype

void embIepCompS (
      const AjPStr str,
      ajuint amino,
      ajuint carboxyl,
      ajuint sscount,
      ajuint modlysine,
      ajuint* c,
      ajuint* resn,
      ajuint* resc
);

TypeNameRead/WriteDescription
const AjPStrstrInputprotein sequence
ajuintaminoInputnumber of amino termini
ajuintcarboxylInputnumber of carboxyl termini
ajuintsscountInputnumber of disulphide bridges
ajuintmodlysineInputnumber of modified lysines
ajuint*cOutputArray of amino acid composition
ajuint*resnOutputN-terminal amino acid
ajuint*rescOutputC-terminal amino acid
void RETURN

From EMBOSS 4.0.0


Function embIepCalcK

Calculate the dissociation constants Amino acids for which there is no entry in Epk.dat have K set to 0.0

Prototype

void embIepCalcK (
      double* K,
      double** pK
);

TypeNameRead/WriteDescription
double*KOutputdissociation constants
double**pKOutputpK values
void RETURN

From EMBOSS 1.0.0


Function embIepCalcKend

Calculate the dissociation constants for the N and C termini Amino acids for which there is no entry in Epk.dat have K set to 0.0

Prototype

void embIepCalcKend (
      double* K,
      double** pK,
      ajuint resn,
      ajuint resc
);

TypeNameRead/WriteDescription
double*KOutputdissociation constants
double**pKOutputpK values
ajuintresnInputN-terminal amino acid
ajuintrescInputN-terminal amino acid
void RETURN

From EMBOSS 1.0.0


Function embIepGetProto

Calculate the number of H+ bound Amino acids for which there is no entry in Epk.dat have this set to 0.0

Prototype

void embIepGetProto (
      const double* K,
      const ajuint* c,
      ajuint* op,
      double H,
      double* pro
);

TypeNameRead/WriteDescription
const double*KInputdissociation constants
const ajuint*cInputsequence composition
ajuint*opOutputprintout flags
doubleHInputhydrogen ion concentration
double*proOutputnumber of protons bound
void RETURN

From EMBOSS 1.0.0


Function embIepGetCharge

Calculate the number of H+ bound

Prototype

double embIepGetCharge (
      const ajuint* c,
      const double* pro,
      double* total
);

TypeNameRead/WriteDescription
const ajuint*cInputsequence composition
const double*proInputnumber of protons
double*totalOutputtotal protons
double RETURNcharge

From EMBOSS 1.0.0


Function embIepPhConverge

Calculate the pH nearest the IEP or return 0.0 if one doesn't exist

Prototype

double embIepPhConverge (
      const ajuint* c,
      const double* K,
      ajuint* op,
      double* pro
);

TypeNameRead/WriteDescription
const ajuint*cInputsequence composition
const double*KInputsequence dissociation constants
ajuint*opOutputprintout flags
double*proOutputnumber of protons
double RETURNIEP or 0.0

From EMBOSS 1.0.0


Function embIepIepC

Calculate the pH nearest the IEP.

Prototype

AjBool embIepIepC (
      const char* s,
      ajuint amino,
      ajuint carboxyl,
      ajuint sscount,
      ajuint modlysine,
      double** pK,
      double* iep,
      AjBool termini
);

TypeNameRead/WriteDescription
const char*sInputsequence
ajuintaminoInputnumber of N-termini
ajuintcarboxylInputnumber of C-termini
ajuintsscountInputnumber of disulphide bridges
ajuintmodlysineInputnumber of modified lysines
double**pKOutputpK values
double*iepOutputIEP
AjBoolterminiInputuse termini
AjBool RETURNTrue if IEP exists

From EMBOSS 4.0.0


Function embIepIepS

Calculate the pH nearest the IEP.

Prototype

AjBool embIepIepS (
      const AjPStr str,
      ajuint amino,
      ajuint carboxyl,
      ajuint sscount,
      ajuint modlysine,
      double** pK,
      double* iep,
      AjBool termini
);

TypeNameRead/WriteDescription
const AjPStrstrInputsequence
ajuintaminoInputnumber of N-termini
ajuintcarboxylInputnumber of C-termini
ajuintsscountInputnumber of disulphide bridges
ajuintmodlysineInputnumber of modified lysines
double**pKOutputpK values
double*iepOutputIEP
AjBoolterminiInputuse termini
AjBool RETURNTrue if IEP exists

From EMBOSS 4.0.0