embprop.c

Function embPropEaminoRead

Read amino acid properties from Eamino.dat

Synopsis

Prototype
EmbPPropAmino* embPropEaminoRead (
      AjPFile mfptr
);

TypeNameRead/WriteDescription
AjPFilemfptrModifyInput file object
EmbPPropAmino* RETURNarray 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

See Also

See other functions in this section

Availability

In release 6.4.0

Function embPropGetProperties

Returns a string containing a list of defined properties

Synopsis

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

TypeNameRead/WriteDescription
const EmbPPropAminopropInputInput properties object
AjPStr*PstrOutputString of properties separated by commas
AjBool RETURNTrue if properties are defined

Input
prop:(Input)Input properties object
Output
Pstr:(Output)String of properties separated by commas
Returns
AjBool:True if properties are defined

Description

Returns a string containing a list of defined 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 6.4.0

Function embPropEmolwtRead

Read molecular weights from Emolwt.dat

Synopsis

Prototype
EmbPPropMolwt* embPropEmolwtRead (
      AjPFile mfptr
);

TypeNameRead/WriteDescription
AjPFilemfptrModifyInput file object
EmbPPropMolwt* RETURNarray 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

See Also

See other functions in this section

Availability

In release 6.4.0

Function embPropMolwtGetMolwt

Return charge value

Synopsis

Prototype
float embPropMolwtGetMolwt (
      const EmbPPropMolwt prop
);

TypeNameRead/WriteDescription
const EmbPPropMolwtpropInputInput mOlecular weights object
float RETURNcharge

Input
prop:(Input)Input mOlecular weights object
Returns
float:charge

Description

Return charge value

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 6.4.0

Function embPropGetCharge

Return charge value

Synopsis

Prototype
float embPropGetCharge (
      const EmbPPropAmino prop
);

TypeNameRead/WriteDescription
const EmbPPropAminopropInputInput properties object
float RETURNcharge

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

See Also

See other functions in this section

Availability

In release 6.4.0

Function embPropGetTiny

Return tiny value

Synopsis

Prototype
ajint embPropGetTiny (
      const EmbPPropAmino prop
);

TypeNameRead/WriteDescription
const EmbPPropAminopropInputInput properties object
ajint RETURNtiny

Input
prop:(Input)Input properties object
Returns
ajint:tiny

Description

Return tiny value

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 6.4.0

Function embPropGetSmall

Return small value

Synopsis

Prototype
ajint embPropGetSmall (
      const EmbPPropAmino prop
);

TypeNameRead/WriteDescription
const EmbPPropAminopropInputInput properties object
ajint RETURNsmall

Input
prop:(Input)Input properties object
Returns
ajint:small

Description

Return small value

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 6.4.0

Function embPropGetAliphatic

Return aliphatic value

Synopsis

Prototype
ajint embPropGetAliphatic (
      const EmbPPropAmino prop
);

TypeNameRead/WriteDescription
const EmbPPropAminopropInputInput properties object
ajint RETURNaliphatic

Input
prop:(Input)Input properties object
Returns
ajint:aliphatic

Description

Return aliphatic value

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 6.4.0

Function embPropGetAromatic

Return aromatic value

Synopsis

Prototype
ajint embPropGetAromatic (
      const EmbPPropAmino prop
);

TypeNameRead/WriteDescription
const EmbPPropAminopropInputInput properties object
ajint RETURNaromatic

Input
prop:(Input)Input properties object
Returns
ajint:aromatic

Description

Return aromatic value

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 6.4.0

Function embPropGetNonpolar

Return nonpolar value

Synopsis

Prototype
ajint embPropGetNonpolar (
      const EmbPPropAmino prop
);

TypeNameRead/WriteDescription
const EmbPPropAminopropInputInput properties object
ajint RETURNnonpolar

Input
prop:(Input)Input properties object
Returns
ajint:nonpolar

Description

Return nonpolar value

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 6.4.0

Function embPropGetPolar

Return polar value

Synopsis

Prototype
ajint embPropGetPolar (
      const EmbPPropAmino prop
);

TypeNameRead/WriteDescription
const EmbPPropAminopropInputInput properties object
ajint RETURNpolar

Input
prop:(Input)Input properties object
Returns
ajint:polar

Description

Return polar value

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 6.4.0

Function embPropGetPve

Return pve value

Synopsis

Prototype
ajint embPropGetPve (
      const EmbPPropAmino prop
);

TypeNameRead/WriteDescription
const EmbPPropAminopropInputInput properties object
ajint RETURNpve

Input
prop:(Input)Input properties object
Returns
ajint:pve

Description

Return pve value

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 6.4.0

Function embPropGetNve

Return nve value

Synopsis

Prototype
ajint embPropGetNve (
      const EmbPPropAmino prop
);

TypeNameRead/WriteDescription
const EmbPPropAminopropInputInput properties object
ajint RETURNnve

Input
prop:(Input)Input properties object
Returns
ajint:nve

Description

Return nve value

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 6.4.0

Function embPropGetExtcoeff

Return extcoeff value

Synopsis

Prototype
ajint embPropGetExtcoeff (
      const EmbPPropAmino prop
);

TypeNameRead/WriteDescription
const EmbPPropAminopropInputInput properties object
ajint RETURNextcoeff

Input
prop:(Input)Input properties object
Returns
ajint:extcoeff

Description

Return extcoeff value

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 6.4.0

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
);

TypeNameRead/WriteDescription
const char*sInputsequence
ajintstartInputstart position
ajintendInputend position
EmbPPropMolwt const*mwdataInputmolecular weight data
AjBoolmonoInputtrue for monoisotopic values
double RETURNmolecular 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

See Also

See other functions in this section

Availability

In release 6.4.0

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
);

TypeNameRead/WriteDescription
const char*sInputsequence
ajintstartInputstart position
ajintendInputend position
EmbPPropMolwt const*mwdataInputmolecular weight data
AjBoolmonoInputtrue for monoisotopic values
doublenmassInputmass of the N-terminal group
doublecmassInputmass of the C-terminal group
double RETURNmolecular 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

See Also

See other functions in this section

Availability

In release 6.4.0

Function embPropCalcMolextcoeff

Calculate the molecular extinction coefficient of a protein sequence

Synopsis

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

TypeNameRead/WriteDescription
const char*sInputsequence
ajintstartInputstart position
ajintendInputend position
AjBoolcystineInputTreat C residues as cystine pairs
EmbPPropAmino const*aadataInputamino acid data
double RETURNmolar extinction coefficient

Input
s:(Input)sequence
start:(Input)start position
end:(Input)end position
cystine:(Input)Treat C residues as cystine pairs
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

See Also

See other functions in this section

Availability

In release 6.4.0

Function embPropCharToThree

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

Synopsis

Prototype
const char* embPropCharToThree (
      char c
);

TypeNameRead/WriteDescription
charcInputinteger code
const char* RETURNthree letter amino acid code

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 6.4.0

Function embPropIntToThree

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

Synopsis

Prototype
const char* embPropIntToThree (
      ajint c
);

TypeNameRead/WriteDescription
ajintcInputinteger code
const char* RETURNthree letter amino acid code

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 6.4.0

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
);

TypeNameRead/WriteDescription
const char*sInputsequence
ajintnInput"enzyme" number
AjPList*lOutputlist to push hits to
AjPList*paOutputlist to push partial hits to
AjBoolunfavouredInputallow unfavoured cuts
AjBooloverlapInputshow overlapping partials
AjBoolallpartialsInputshow all possible partials
ajint*ncompOutputnumber of complete digest fragments
ajint*npartOutputnumber of partial digest fragments
AjPStr*rnameOutputname of reagent
AjBoolntermInputnterm ragging
AjBoolctermInputcterm ragging
AjBooldoragInputtrue if ragging
EmbPPropMolwt const*mwdataInputmolecular weight data
AjBoolmonoInputtrue 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

See Also

See other functions in this section

Availability

In release 6.4.0

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
);

TypeNameRead/WriteDescription
AjPSeqseqModifyprotein sequence to add spaces into
ajintpadInputnumber of spaces to insert at the start of the result
AjPStr RETURNNew 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

See Also

See other functions in this section

Availability

In release 6.4.0

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
);

TypeNameRead/WriteDescription
AjPSeqseqModifyprotein sequence to convert to 3-letter codes
ajintpadInputnumber of spaces to insert at the start of the result
AjPStr RETURNstring 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

See Also

See other functions in this section

Availability

In release 6.4.0

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.

Synopsis

Prototype
AjPStr embPropProt1to3Rev (
      AjPSeq seq,
      ajint pad
);

TypeNameRead/WriteDescription
AjPSeqseqModifyprotein sequence to convert to 3-letter codes
ajintpadInputnumber of characters to skip at the start of the result
AjPStr RETURNstring containing 3-letter protein sequence

Input
pad:(Input)number of characters to skip 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 in the reverse direction. 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 6.4.0

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
);

TypeNameRead/WriteDescription
charbaseInputbase
AjBool RETURNreturn 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

See Also

See other functions in this section

Availability

In release 6.4.0

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
);

TypeNameRead/WriteDescription
charbaseInputbase
AjBool RETURNreturn 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

See Also

See other functions in this section

Availability

In release 6.4.0

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
);

TypeNameRead/WriteDescription
charbase1Inputfirst base
charbase2Inputsecond base
AjBool RETURNreturn 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

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 6.4.0

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
);

TypeNameRead/WriteDescription
charbase1Inputfirst base
charbase2Inputsecond base
AjBool RETURNreturn 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

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 6.4.0

Function embPropFixF

Fix for missing properties data in a float array

Synopsis

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

TypeNameRead/WriteDescription
float[]matrixModifyMatrix
floatmissingInputMissing 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

See Also

See other functions in this section

Availability

In release 6.4.0

Function embPropNormalF

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

Assume the data values represent all values for a population (e.g. values for all standard amino acids) and use new value = (old value - mean) / standard deviation

Synopsis

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

TypeNameRead/WriteDescription
float[]matrixModifyMatrix
floatmissingInputMissing data value
void RETURN

Input
missing:(Input)Missing data value
Input & Output
matrix:(Modify)Matrix
Returns
void:No return value

Description

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

Assume the data values represent all values for a population (e.g. values for all standard amino acids) and use new value = (old value - mean) / standard deviation

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 6.4.0

Function embPropAminoDel

Delete array of amino acid properties

Synopsis

Prototype
void embPropAminoDel (
      EmbPPropAmino** thys
);

TypeNameRead/WriteDescription
EmbPPropAmino**thysOutputamino 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

See Also

See other functions in this section

Availability

In release 6.4.0

Function embPropMolwtDel

Delete array of molwts

Synopsis

Prototype
void embPropMolwtDel (
      EmbPPropMolwt** thys
);

TypeNameRead/WriteDescription
EmbPPropMolwt**thysOutputmolwts
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

See Also

See other functions in this section

Availability

In release 6.4.0