embprop.c

Function embPropEaminoRead

Read amino acid properties from Eamino.dat

Prototype

EmbPPropAmino* embPropEaminoRead (
      AjPFile mfptr
);

Type Name Read/Write Description

AjPFile mfptr Modify Input file object

EmbPPropAmino* RETURN array of amino acid properties

Type	Name	Read/Write	Description
`AjPFile`	`mfptr`	Modify	Input file object
`EmbPPropAmino*`		RETURN	array of amino acid properties

From EMBOSS 6.0.0

Function embPropGetProperties

Returns a string containing a list of defined properties

Prototype

AjBool embPropGetProperties (
      const EmbPPropAmino prop,
      AjPStr* Pstr
);

Type Name Read/Write Description

const EmbPPropAmino prop Input Input properties object

AjPStr* Pstr Output String of properties separated by commas

AjBool RETURN True if properties are defined

Type	Name	Read/Write	Description
`const EmbPPropAmino`	`prop`	Input	Input properties object
`AjPStr*`	`Pstr`	Output	String of properties separated by commas
`AjBool`		RETURN	True if properties are defined

From EMBOSS 6.0.0

Function embPropEmolwtRead

Read molecular weights from Emolwt.dat

Prototype

EmbPPropMolwt* embPropEmolwtRead (
      AjPFile mfptr
);

Type Name Read/Write Description

AjPFile mfptr Modify Input file object

EmbPPropMolwt* RETURN array of amino acid molecular weights

Type	Name	Read/Write	Description
`AjPFile`	`mfptr`	Modify	Input file object
`EmbPPropMolwt*`		RETURN	array of amino acid molecular weights

From EMBOSS 6.0.0

Function embPropMolwtGetMolwt

Return charge value

Prototype

float embPropMolwtGetMolwt (
      const EmbPPropMolwt prop
);

Type Name Read/Write Description

const EmbPPropMolwt prop Input Input mOlecular weights object

float RETURN charge

Type	Name	Read/Write	Description
`const EmbPPropMolwt`	`prop`	Input	Input mOlecular weights object
`float`		RETURN	charge

From EMBOSS 6.0.0

Function embPropGetCharge

Return charge value

Prototype

float embPropGetCharge (
      const EmbPPropAmino prop
);

Type Name Read/Write Description

const EmbPPropAmino prop Input Input properties object

float RETURN charge

Type	Name	Read/Write	Description
`const EmbPPropAmino`	`prop`	Input	Input properties object
`float`		RETURN	charge

From EMBOSS 6.0.0

Function embPropGetTiny

Return tiny value

Prototype

ajint embPropGetTiny (
      const EmbPPropAmino prop
);

Type Name Read/Write Description

const EmbPPropAmino prop Input Input properties object

ajint RETURN tiny

Type	Name	Read/Write	Description
`const EmbPPropAmino`	`prop`	Input	Input properties object
`ajint`		RETURN	tiny

From EMBOSS 6.0.0

Function embPropGetSmall

Return small value

Prototype

ajint embPropGetSmall (
      const EmbPPropAmino prop
);

Type Name Read/Write Description

const EmbPPropAmino prop Input Input properties object

ajint RETURN small

Type	Name	Read/Write	Description
`const EmbPPropAmino`	`prop`	Input	Input properties object
`ajint`		RETURN	small

From EMBOSS 6.0.0

Function embPropGetAliphatic

Return aliphatic value

Prototype

ajint embPropGetAliphatic (
      const EmbPPropAmino prop
);

Type Name Read/Write Description

const EmbPPropAmino prop Input Input properties object

ajint RETURN aliphatic

Type	Name	Read/Write	Description
`const EmbPPropAmino`	`prop`	Input	Input properties object
`ajint`		RETURN	aliphatic

From EMBOSS 6.0.0

Function embPropGetAromatic

Return aromatic value

Prototype

ajint embPropGetAromatic (
      const EmbPPropAmino prop
);

Type Name Read/Write Description

const EmbPPropAmino prop Input Input properties object

ajint RETURN aromatic

Type	Name	Read/Write	Description
`const EmbPPropAmino`	`prop`	Input	Input properties object
`ajint`		RETURN	aromatic

From EMBOSS 6.0.0

Function embPropGetNonpolar

Return nonpolar value

Prototype

ajint embPropGetNonpolar (
      const EmbPPropAmino prop
);

Type Name Read/Write Description

const EmbPPropAmino prop Input Input properties object

ajint RETURN nonpolar

Type	Name	Read/Write	Description
`const EmbPPropAmino`	`prop`	Input	Input properties object
`ajint`		RETURN	nonpolar

From EMBOSS 6.0.0

Function embPropGetPolar

Return polar value

Prototype

ajint embPropGetPolar (
      const EmbPPropAmino prop
);

Type Name Read/Write Description

const EmbPPropAmino prop Input Input properties object

ajint RETURN polar

Type	Name	Read/Write	Description
`const EmbPPropAmino`	`prop`	Input	Input properties object
`ajint`		RETURN	polar

From EMBOSS 6.0.0

Function embPropGetPve

Return pve value

Prototype

ajint embPropGetPve (
      const EmbPPropAmino prop
);

Type Name Read/Write Description

const EmbPPropAmino prop Input Input properties object

ajint RETURN pve

Type	Name	Read/Write	Description
`const EmbPPropAmino`	`prop`	Input	Input properties object
`ajint`		RETURN	pve

From EMBOSS 6.0.0

Function embPropGetNve

Return nve value

Prototype

ajint embPropGetNve (
      const EmbPPropAmino prop
);

Type Name Read/Write Description

const EmbPPropAmino prop Input Input properties object

ajint RETURN nve

Type	Name	Read/Write	Description
`const EmbPPropAmino`	`prop`	Input	Input properties object
`ajint`		RETURN	nve

From EMBOSS 6.0.0

Function embPropGetExtcoeff

Return extcoeff value

Prototype

ajint embPropGetExtcoeff (
      const EmbPPropAmino prop
);

Type Name Read/Write Description

const EmbPPropAmino prop Input Input properties object

ajint RETURN extcoeff

Type	Name	Read/Write	Description
`const EmbPPropAmino`	`prop`	Input	Input properties object
`ajint`		RETURN	extcoeff

From EMBOSS 6.0.0

Function embPropCalcMolwt

Calculate the molecular weight of a protein sequence This is a shell around embPropCalcMolwtMod using water as the modifier.

Prototype

double embPropCalcMolwt (
      const char* s,
      ajint start,
      ajint end,
      EmbPPropMolwt const* mwdata,
      AjBool mono
);

Type Name Read/Write Description

const char* s Input sequence

ajint start Input start position

ajint end Input end position

EmbPPropMolwt const* mwdata Input molecular weight data

AjBool mono Input true for monoisotopic values

double RETURN molecular weight

Type	Name	Read/Write	Description
`const char*`	`s`	Input	sequence
`ajint`	`start`	Input	start position
`ajint`	`end`	Input	end position
`EmbPPropMolwt const*`	`mwdata`	Input	molecular weight data
`AjBool`	`mono`	Input	true for monoisotopic values
`double`		RETURN	molecular weight

From EMBOSS 1.0.0

Function embPropCalcMolwtMod

Calculate the molecular weight of a protein sequence with chemically modified termini

Prototype

double embPropCalcMolwtMod (
      const char* s,
      ajint start,
      ajint end,
      EmbPPropMolwt const* mwdata,
      AjBool mono,
      double nmass,
      double cmass
);

Type	Name	Read/Write	Description
`const char*`	`s`	Input	sequence
`ajint`	`start`	Input	start position
`ajint`	`end`	Input	end position
`EmbPPropMolwt const*`	`mwdata`	Input	molecular weight data
`AjBool`	`mono`	Input	true for monoisotopic values
`double`	`nmass`	Input	mass of the N-terminal group
`double`	`cmass`	Input	mass of the C-terminal group
`double`		RETURN	molecular weight

From EMBOSS 2.1.0

Function embPropCalcMolextcoeff

Calculate the molecular extinction coefficient of a protein sequence

Prototype

double embPropCalcMolextcoeff (
      const char* s,
      ajint start,
      ajint end,
      AjBool cystine,
      EmbPPropAmino const* aadata
);

Type Name Read/Write Description

const char* s Input sequence

ajint start Input start position

ajint end Input end position

AjBool cystine Input Treat C residues as cystine pairs

EmbPPropAmino const* aadata Input amino acid data

double RETURN molar extinction coefficient

Type	Name	Read/Write	Description
`const char*`	`s`	Input	sequence
`ajint`	`start`	Input	start position
`ajint`	`end`	Input	end position
`AjBool`	`cystine`	Input	Treat C residues as cystine pairs
`EmbPPropAmino const*`	`aadata`	Input	amino acid data
`double`		RETURN	molar extinction coefficient

From EMBOSS 2.8.0

Function embPropCharToThree

Return 3 letter amino acid code A=Ala B=Asx C=Cys etc

Prototype

const char* embPropCharToThree (
      char c
);

Type Name Read/Write Description

char c Input integer code

const char* RETURN three letter amino acid code

Type	Name	Read/Write	Description
`char`	`c`	Input	integer code
`const char*`		RETURN	three letter amino acid code

From EMBOSS 1.0.0

Function embPropIntToThree

Return 3 letter amino acid code 0=Ala 1=Asx 2=Cys etc

Prototype

const char* embPropIntToThree (
      ajint c
);

Type Name Read/Write Description

ajint c Input integer code

const char* RETURN three letter amino acid code

Type	Name	Read/Write	Description
`ajint`	`c`	Input	integer code
`const char*`		RETURN	three letter amino acid code

From EMBOSS 1.0.0

Function embPropCalcFragments

Read amino acd properties

Prototype

void embPropCalcFragments (
      const char* s,
      ajint n,
      AjPList* l,
      AjPList* pa,
      AjBool unfavoured,
      AjBool overlap,
      AjBool allpartials,
      ajint* ncomp,
      ajint* npart,
      AjPStr* rname,
      AjBool nterm,
      AjBool cterm,
      AjBool dorag,
      EmbPPropMolwt const* mwdata,
      AjBool mono
);

Type Name Read/Write Description

const char* s Input sequence

ajint n Input "enzyme" number

AjPList* l Output list to push hits to

AjPList* pa Output list to push partial hits to

AjBool unfavoured Input allow unfavoured cuts

AjBool overlap Input show overlapping partials

AjBool allpartials Input show all possible partials

ajint* ncomp Output number of complete digest fragments

ajint* npart Output number of partial digest fragments

AjPStr* rname Output name of reagent

AjBool nterm Input nterm ragging

AjBool cterm Input cterm ragging

AjBool dorag Input true if ragging

EmbPPropMolwt const* mwdata Input molecular weight data

AjBool mono Input true for monoisotopic weights

void RETURN

Type	Name	Read/Write	Description
`const char*`	`s`	Input	sequence
`ajint`	`n`	Input	"enzyme" number
`AjPList*`	`l`	Output	list to push hits to
`AjPList*`	`pa`	Output	list to push partial hits to
`AjBool`	`unfavoured`	Input	allow unfavoured cuts
`AjBool`	`overlap`	Input	show overlapping partials
`AjBool`	`allpartials`	Input	show all possible partials
`ajint*`	`ncomp`	Output	number of complete digest fragments
`ajint*`	`npart`	Output	number of partial digest fragments
`AjPStr*`	`rname`	Output	name of reagent
`AjBool`	`nterm`	Input	nterm ragging
`AjBool`	`cterm`	Input	cterm ragging
`AjBool`	`dorag`	Input	true if ragging
`EmbPPropMolwt const*`	`mwdata`	Input	molecular weight data
`AjBool`	`mono`	Input	true for monoisotopic weights
`void`		RETURN

From EMBOSS 1.0.0

Function embPropProtGaps

Creates a string of a protein sequence which has been padded out with two spaces after every residue to aid aligning a translation under a nucleic sequence

Prototype

AjPStr embPropProtGaps (
      AjPSeq seq,
      ajint pad
);

Type Name Read/Write Description

AjPSeq seq Modify protein sequence to add spaces into

ajint pad Input number of spaces to insert at the start of the result

AjPStr RETURN New string with the padded sequence

Type	Name	Read/Write	Description
`AjPSeq`	`seq`	Modify	protein sequence to add spaces into
`ajint`	`pad`	Input	number of spaces to insert at the start of the result
`AjPStr`		RETURN	New string with the padded sequence

From EMBOSS 1.0.0

Function embPropProt1to3

Creates a a 3-letter sequence protein string from single-letter sequence EMBOSS is bad at reading 3-letter sequences, but this may be useful when displaying translations.

Prototype

AjPStr embPropProt1to3 (
      AjPSeq seq,
      ajint pad
);

Type Name Read/Write Description

AjPSeq seq Modify protein sequence to convert to 3-letter codes

ajint pad Input number of spaces to insert at the start of the result

AjPStr RETURN string containing 3-letter protein sequence

Type	Name	Read/Write	Description
`AjPSeq`	`seq`	Modify	protein sequence to convert to 3-letter codes
`ajint`	`pad`	Input	number of spaces to insert at the start of the result
`AjPStr`		RETURN	string containing 3-letter protein sequence

From EMBOSS 1.0.0

Function embPropProt1to3Rev

Creates a a 3-letter sequence protein string from single-letter sequence in the reverse direction. EMBOSS is bad at reading 3-letter sequences, but this may be useful when displaying translations.

Prototype

AjPStr embPropProt1to3Rev (
      AjPSeq seq,
      ajint pad
);

Type Name Read/Write Description

AjPSeq seq Modify protein sequence to convert to 3-letter codes

ajint pad Input number of characters to skip at the start of the result

AjPStr RETURN string containing 3-letter protein sequence

Type	Name	Read/Write	Description
`AjPSeq`	`seq`	Modify	protein sequence to convert to 3-letter codes
`ajint`	`pad`	Input	number of characters to skip at the start of the result
`AjPStr`		RETURN	string containing 3-letter protein sequence

From EMBOSS 6.1.0

Function embPropPurine

Returns ajTrue if the input base is a Purine. Returns ajFalse if it is a Pyrimidine or it is ambiguous.

Prototype

AjBool embPropPurine (
      char base
);

Type Name Read/Write Description

char base Input base

AjBool RETURN return ajTrue if this is a Purine

Type	Name	Read/Write	Description
`char`	`base`	Input	base
`AjBool`		RETURN	return ajTrue if this is a Purine

From EMBOSS 1.4.3

Function embPropPyrimidine

Returns ajTrue if the input base is a Pyrimidine. Returns ajFalse if it is a Purine or it is ambiguous.

Prototype

AjBool embPropPyrimidine (
      char base
);

Type Name Read/Write Description

char base Input base

AjBool RETURN return ajTrue if this is a Pyrimidine

Type	Name	Read/Write	Description
`char`	`base`	Input	base
`AjBool`		RETURN	return ajTrue if this is a Pyrimidine

From EMBOSS 1.4.3

Function embPropTransversion

Returns ajTrue if the input two bases have undergone a tranversion. (Pyrimidine to Purine, or vice versa) Returns ajFalse if this is not a transversion or it can not be determined (e.g. no change A->A, transition C->T, unknown A->N)

Prototype

AjBool embPropTransversion (
      char base1,
      char base2
);

Type Name Read/Write Description

char base1 Input first base

char base2 Input second base

AjBool RETURN return ajTrue if this is a transversion

Type	Name	Read/Write	Description
`char`	`base1`	Input	first base
`char`	`base2`	Input	second base
`AjBool`		RETURN	return ajTrue if this is a transversion

From EMBOSS 1.4.3

Function embPropTransition

Returns ajTrue if the input two bases have undergone a transition. (Pyrimidine to Pyrimidine, or Purine to Purine) Returns ajFalse if this is not a transition or it can not be determined (e.g. no change A->A, transversion A->T, unknown A->N)

Prototype

AjBool embPropTransition (
      char base1,
      char base2
);

Type Name Read/Write Description

char base1 Input first base

char base2 Input second base

AjBool RETURN return ajTrue if this is a transition

Type	Name	Read/Write	Description
`char`	`base1`	Input	first base
`char`	`base2`	Input	second base
`AjBool`		RETURN	return ajTrue if this is a transition

From EMBOSS 1.4.3

Function embPropFixF

Fix for missing properties data in a float array

Prototype

void embPropFixF (
      float[] matrix,
      float missing
);

Type Name Read/Write Description

float[] matrix Modify Matrix

float missing Input Missing data value

void RETURN

Type	Name	Read/Write	Description
`float[]`	`matrix`	Modify	Matrix
`float`	`missing`	Input	Missing data value
`void`		RETURN

From EMBOSS 4.1.0

Function embPropNormalF

Normalize data values in a float array to have mean 0.0 and standard deviation 1.0

Prototype

void embPropNormalF (
      float[] matrix,
      float missing
);

Type Name Read/Write Description

float[] matrix Modify Matrix

float missing Input Missing data value

void RETURN

Type	Name	Read/Write	Description
`float[]`	`matrix`	Modify	Matrix
`float`	`missing`	Input	Missing data value
`void`		RETURN

From EMBOSS 6.1.0

Function embPropAminoDel

Delete array of amino acid properties

Prototype

void embPropAminoDel (
      EmbPPropAmino** thys
);

Type Name Read/Write Description

EmbPPropAmino** thys Output amino acid properties

void RETURN

Type	Name	Read/Write	Description
`EmbPPropAmino**`	`thys`	Output	amino acid properties
`void`		RETURN

From EMBOSS 6.0.0

Function embPropMolwtDel

Delete array of molwts

Prototype

void embPropMolwtDel (
      EmbPPropMolwt** thys
);

Type Name Read/Write Description

EmbPPropMolwt** thys Output molwts

void RETURN

Type	Name	Read/Write	Description
`EmbPPropMolwt**`	`thys`	Output	molwts
`void`		RETURN

From EMBOSS 6.0.0