embprop.c

Function embPropAminoRead

Read amino acid properties from Eamino.dat

Synopsis

Prototype

void embPropAminoRead (
      AjPFile mfptr
);

Input & Output

mfptr:(Modify)Input file object

Returns

void:No return value

Description

Read amino acid properties from Eamino.dat

Usage

See source code

Example

In preparation

Errors

See source code

Dependencies

See source code

See Also

See other functions in this section

Availability

In release 3.0.0

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
);

Input

s:(Input)sequence
start:(Input)start position
end:(Input)end position

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

See Also

See other functions in this section

Availability

In release 3.0.0

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,
      double nmass,
      double cmass
);

Input

s:(Input)sequence
start:(Input)start position
end:(Input)end position
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

See Also

See other functions in this section

Availability

In release 3.0.0

Function embPropCalcMolextcoeff

Calculate the molecular extinction coefficient of a protein sequence

Synopsis

Prototype

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

Input

s:(Input)sequence
start:(Input)start position
end:(Input)end position

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

See Also

See other functions in this section

Availability

In release 3.0.0

Function embPropCharToThree

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

Synopsis

Prototype

const char* embPropCharToThree (
      char c
);

Input

c:(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

See Also

See other functions in this section

Availability

In release 3.0.0

Function embPropIntToThree

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

Synopsis

Prototype

const char* embPropIntToThree (
      ajint c
);

Input

c:(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

See Also

See other functions in this section

Availability

In release 3.0.0

Function embPropCalcFragments

Read amino acd properties

Synopsis

Prototype

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

Input

s:(Input)sequence
n:(Input)"enzyme" number
begin:(Input)sequence offset
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

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

See Also

See other functions in this section

Availability

In release 3.0.0

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
);

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

See Also

See other functions in this section

Availability

In release 3.0.0

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
);

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

See Also

See other functions in this section

Availability

In release 3.0.0

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
);

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

See Also

See other functions in this section

Availability

In release 3.0.0

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
);

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

See Also

See other functions in this section

Availability

In release 3.0.0

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
);

Input

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

Returns

AjBool:return ajTrue if this is a transversion

Description

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)

Usage

See source code

Example

In preparation

Errors

See source code

Dependencies

See source code

See Also

See other functions in this section

Availability

In release 3.0.0

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
);

Input

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

Returns

AjBool:return ajTrue if this is a transition

Description

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)

Usage

See source code

Example

In preparation

Errors

See source code

Dependencies

See source code

See Also

See other functions in this section

Availability

In release 3.0.0

Function embPropExit

Cleanup of properties data

Synopsis

Prototype

void embPropExit (
      void
);

Returns

void:No return value

Description

Cleanup of properties data

Usage

See source code

Example

In preparation

Errors

See source code

Dependencies

See source code

See Also

See other functions in this section

Availability

In release 3.0.0