embprop.c

Function embPropEaminoRead

Read amino acid properties from Eamino.dat

Synopsis

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

Input & Output

mfptr:

(Modify)

Input file object

Returns

EmbPPropAmino*:

array of amino acid properties

Description

Read amino acid properties from Eamino.dat

Usage

See source code

Example

In preparation

Errors

See source code

Dependencies

See source code

Availability

In release 5.0.0

Synopsis

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

Input & Output

mfptr:

(Modify)

Input file object

Returns

EmbPPropMolwt*:

array of amino acid molecular weights

Description

Read molecular weights from Emolwt.dat

Usage

See source code

Example

In preparation

Errors

See source code

Dependencies

See source code

Availability

In release 5.0.0

Synopsis

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

Input

prop:

(Input)

Input properties object

Returns

float:

charge

Description

Return charge value

Usage

See source code

Example

In preparation

Errors

See source code

Dependencies

See source code

Availability

In release 5.0.0

Function embPropCalcMolwt

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

Synopsis

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

Input

s:	(Input)	sequence
start:	(Input)	start position
end:	(Input)	end position
mwdata:	(Input)	molecular weight data
mono:	(Input)	true for monoisotopic values

Returns

double:

molecular weight

Description

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

Usage

See source code

Example

In preparation

Errors

See source code

Dependencies

See source code

Availability

In release 5.0.0

Function embPropCalcMolwtMod

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

Synopsis

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

Input

s:	(Input)	sequence
start:	(Input)	start position
end:	(Input)	end position
mwdata:	(Input)	molecular weight data
mono:	(Input)	true for monoisotopic values
nmass:	(Input)	mass of the N-terminal group
cmass:	(Input)	mass of the C-terminal group

Returns

double:

molecular weight

Description

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

Usage

See source code

Example

In preparation

Errors

See source code

Dependencies

See source code

Availability

In release 5.0.0

Function embPropCalcMolextcoeff

Calculate the molecular extinction coefficient of a protein sequence

Synopsis

Prototype

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

Type Name Read/Write Description

const char* s Input sequence

ajint start Input start position

ajint end Input end position

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
EmbPPropAmino const*	aadata	Input	amino acid data
double		RETURN	molar extinction coefficient

Input

s:	(Input)	sequence
start:	(Input)	start position
end:	(Input)	end position
aadata:	(Input)	amino acid data

Returns

double:

molar extinction coefficient

Description

Calculate the molecular extinction coefficient of a protein sequence

Usage

See source code

Example

In preparation

Errors

See source code

Dependencies

See source code

Availability

In release 5.0.0

Function embPropCharToThree

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

Synopsis

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

Input

(Input)

integer code

Returns

const char*:

three letter amino acid code

Description

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

Usage

See source code

Example

In preparation

Errors

See source code

Dependencies

See source code

Availability

In release 5.0.0

Function embPropIntToThree

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

Synopsis

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

Input

(Input)

integer code

Returns

const char*:

three letter amino acid code

Description

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

Usage

See source code

Example

In preparation

Errors

See source code

Dependencies

See source code

Availability

In release 5.0.0

Function embPropCalcFragments

Read amino acd properties

Synopsis

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

Input

s:	(Input)	sequence
n:	(Input)	"enzyme" number
unfavoured:	(Input)	allow unfavoured cuts
overlap:	(Input)	show overlapping partials
allpartials:	(Input)	show all possible partials
nterm:	(Input)	nterm ragging
cterm:	(Input)	cterm ragging
dorag:	(Input)	true if ragging
mwdata:	(Input)	molecular weight data
mono:	(Input)	true for monoisotopic weights

Output

l:	(Output)	list to push hits to
pa:	(Output)	list to push partial hits to
ncomp:	(Output)	number of complete digest fragments
npart:	(Output)	number of partial digest fragments
rname:	(Output)	name of reagent

Returns

void:

No return value

Description

Read amino acd properties

Usage

See source code

Example

In preparation

Errors

See source code

Dependencies

See source code

Availability

In release 5.0.0

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

Synopsis

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

Input

pad:

(Input)

number of spaces to insert at the start of the result

Input & Output

seq:

(Modify)

protein sequence to add spaces into

Returns

AjPStr:

New string with the padded sequence

Description

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

Usage

See source code

Example

In preparation

Errors

See source code

Dependencies

See source code

Availability

In release 5.0.0

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.

Synopsis

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

Input

pad:

(Input)

number of spaces to insert at the start of the result

Input & Output

seq:

(Modify)

protein sequence to convert to 3-letter codes

Returns

AjPStr:

string containing 3-letter protein sequence

Description

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.

Usage

See source code

Example

In preparation

Errors

See source code

Dependencies

See source code

Availability

In release 5.0.0

Function embPropPurine

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

Synopsis

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

Input

base:

(Input)

base

Returns

AjBool:

return ajTrue if this is a Purine

Description

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

Usage

See source code

Example

In preparation

Errors

See source code

Dependencies

See source code

Availability

In release 5.0.0

Function embPropPyrimidine

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

Synopsis

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

Input

base:

(Input)

base

Returns

AjBool:

return ajTrue if this is a Pyrimidine

Description

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

Usage

See source code

Example

In preparation

Errors

See source code

Dependencies

See source code

Availability

In release 5.0.0

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)

Synopsis

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

Input

base1:	(Input)	first base
base2:	(Input)	second base

Returns

AjBool:

return ajTrue if this is a transversion

Description

Usage

See source code

Example

In preparation

Errors

See source code

Dependencies

See source code

Availability

In release 5.0.0

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)

Synopsis

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

Input

base1:	(Input)	first base
base2:	(Input)	second base

Returns

AjBool:

return ajTrue if this is a transition

Description

Usage

See source code

Example

In preparation

Errors

See source code

Dependencies

See source code

Availability

In release 5.0.0

Function embPropFixF

Fix for missing properties data in a float array

Synopsis

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

Input

missing:

(Input)

Missing data value

Input & Output

matrix:

(Modify)

Matrix

Returns

void:

No return value

Description

Fix for missing properties data in a float array

Usage

See source code

Example

In preparation

Errors

See source code

Dependencies

See source code

Availability

In release 5.0.0

Function embPropAminoDel

Delete array of amino acid properties

Synopsis

Prototype

void embPropAminoDel (
      EmbPPropAmino** thys
);

Type Name Read/Write Description

EmbPPropAmino** thys Output amino acid properties

void RETURN

Output

thys:

(Output)

amino acid properties

Returns

void:

No return value

Description

Delete array of amino acid properties

Usage

See source code

Example

In preparation

Errors

See source code

Dependencies

See source code

Availability

In release 5.0.0

Function embPropMolwtDel

Delete array of molwts

Synopsis

Prototype

void embPropMolwtDel (
      EmbPPropMolwt** thys
);

Type Name Read/Write Description

EmbPPropMolwt** thys Output molwts

void RETURN

Output

thys:

(Output)

molwts

Returns

void:

No return value

Description

Delete array of molwts

Usage

See source code

Example

In preparation

Errors

See source code

Dependencies

See source code

Availability

In release 5.0.0

embprop.c

Synopsis

Prototype

Input & Output

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Description

Usage

Example

Errors

Dependencies

See Also

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Input & Output

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