aalist.c File Reference

Amino acid linked lists. More...

#include <stdlib.h>
#include "macros.h"
#include "aalist.h"

Go to the source code of this file.

Functions
AA *	blInsertNextResiduesInAAList (AA *a, char res, int nres)
AA *	blInsertNextResidueInAAList (AA *a, char res)
char *	blBuildSeqFromAAList (AA *aa)
AA *	blInsertResidueInAAListAt (AA *aa, char res, int pos)
AA *	blInsertResiduesInAAListAt (AA *aa, char res, int nres, int pos)
AA *	blBuildAAList (char *seq)
int	blFindAAListOffsetByResnum (AA *aa, int resnum)
AA *	blFindAAListItemByResnum (AA *aa, int resnum)
void	blSetAAListFlagByResnum (AA *aa, int resnum)
char *	blBuildFlagSeqFromAAList (AA *aa, char ch)
int	blGetAAListLen (AA *aa)

Detailed Description

Amino acid linked lists.

Version

V3.1

Date

07.07.14

Copyright

(c) UCL / Dr. Andrew C.R. Martin 2006-2014

Author

Dr. Andrew C.R. Martin

Institute of Structural & Molecular Biology, University College London, Gower Street, London. WC1E 6BT.

andre.nosp@m.w@bi.nosp@m.oinf..nosp@m.org..nosp@m.uk andre.nosp@m.w.ma.nosp@m.rtin@.nosp@m.ucl..nosp@m.ac.uk

This code is NOT IN THE PUBLIC DOMAIN, but it may be copied according to the conditions laid out in the accompanying file COPYING.DOC.

The code may be modified as required, but any modifications must be documented so that the person responsible can be identified.

The code may not be sold commercially or included as part of a commercial product except as described in the file COPYING.DOC.

Description:

Usage:

#include "bioplib/aalist.h" to define AA datatype.

Revision History:

• V1.0 21.08.06 Original By: ACRM
• V3.0 06.11.08 Incorporated into ProFit V3 By: CTP
• V3.0 18.02.09 Moved to bioplib. By: CTP
• V3.1 07.07.14 Use bl prefix for functions By: CTP

Definition in file aalist.c.

Function Documentation

AA* blBuildAAList

(

char *

seq

)

Parameters

[in]

*seq

The sequence as a string

Returns

A linked list representation

Converts a sequence string into a linked list

• 21.08.06 Original By: ACRM
• 07.07.14 Use bl prefix for functions By: CTP

Definition at line 359 of file aalist.c.

char* blBuildFlagSeqFromAAList	(	AA *	aa,
		char	ch
	)

Parameters

[in]	*aa	Sequence linked list
[in]	ch	Character to use in the sequence

Returns

Sequence string (malloc'd)

Builds a sequence string with blanks except where the flag in the sequence structure is set. At these positions the character specified in ch is used instead.

• 21.08.06 Original By: ACRM
• 07.07.14 Use bl prefix for functions By: CTP

Definition at line 494 of file aalist.c.

char* blBuildSeqFromAAList

(

AA *

aa

)

Parameters

[in]

*aa

Sequence linked list

Returns

Sequence as a string (malloc'd)

Converts the linked list back into a string which is malloc'd

• 21.08.06 Original By: ACRM
• 07.07.14 Use bl prefix for functions By: CTP

Definition at line 221 of file aalist.c.

AA* blFindAAListItemByResnum	(	AA *	aa,
		int	resnum
	)

Parameters

[in]	*aa	Sequence linked list
[in]	resnum	Residue number

Returns

Linked list item

Searches the linked list of the specified resnum (i.e. the original residue number in the sequence before any insertions were made) and returns a pointer to that item in the list.

• 21.08.06 Original By: ACRM
• 07.07.14 Use bl prefix for functions By: CTP

Definition at line 441 of file aalist.c.

int blFindAAListOffsetByResnum	(	AA *	aa,
		int	resnum
	)

Parameters

[in]	*aa	Sequence linked list
[in]	resnum	Residue number

Returns

Linked list offset

Searches the linked list of the specified resnum (i.e. the original residue number in the sequence before any insertions were made) and returns the position of that residue in the list (numbered from 1)

• 21.08.06 Original By: ACRM
• 07.07.14 Use bl prefix for functions By: CTP

Definition at line 406 of file aalist.c.

int blGetAAListLen

(

AA *

aa

)

Parameters

[in]

*aa

Sequence linked list

Returns

Length of sequence linked list

Returns the number of items in the linked list

• 21.08.06 Original By: ACRM
• 07.07.14 Use bl prefix for functions By: CTP

Definition at line 527 of file aalist.c.

AA* blInsertNextResidueInAAList	(	AA *	a,
		char	res
	)

Parameters

[in]	*a	Sequence linked list
[in]	res	Residue to insert

Returns

Pointer to the residue that has just been inserted

Inserts a residues after the current position in the linked list. The returned value is the residue which has been inserted so this can be called again on the returned aa to insert another aa

• 21.08.06 Original By: ACRM
• 07.07.14 Use bl prefix for functions By: CTP

Definition at line 182 of file aalist.c.

AA* blInsertNextResiduesInAAList	(	AA *	a,
		char	res,
		int	nres
	)

Parameters

[in]	*a	Sequence linked list
[in]	res	Residue to insert
[in]	nres	Number of residues to insert

Returns

Pointer to the residue that has just been inserted

Inserts a set of identical residues after the current position in the linked list. The returned value is the last residue which has been inserted so this can be called again on the returned aa to insert another aa

• 21.08.06 Original By: ACRM
• 07.07.14 Use bl prefix for functions By: CTP

Definition at line 154 of file aalist.c.

AA* blInsertResidueInAAListAt	(	AA *	aa,
		char	res,
		int	pos
	)

Parameters

[in]	*aa	Sequence linked list
[in]	res	Residue to insert
[in]	pos	Position at which to insert (from 1...)

Returns

Updated sequence linked list

Inserts a residue after the specified position in the list. Residues are numbered from 1. If the position is > length of the list then the residue will be added at the end. If the position is zero, it will be at the start of the list in which case the return value for the list will be different from the input value.

• 21.08.06 Original By: ACRM
• 18.06.08 Set inserted residue's flag to FALSE. By: CTP
• 07.07.14 Use bl prefix for functions By: CTP

Definition at line 261 of file aalist.c.

AA* blInsertResiduesInAAListAt	(	AA *	aa,
		char	res,
		int	nres,
		int	pos
	)

Parameters

[in]	*aa	Sequence linked list
[in]	res	Residue to insert
[in]	nres	Number of residues to insert
[in]	pos	Position at which to insert (from 1...)

Returns

Updated sequence linked list

Inserts a set of residues after the specified position in the list. Residues are numbered from 1. If the position is > length of the list then the residue will be added at the end. If the position is zero, it will be at the start of the list in which case the return value for the list will be different from the input value.

• 21.08.06 Original By: ACRM
• 07.07.14 Use bl prefix for functions By: CTP

Definition at line 335 of file aalist.c.

void blSetAAListFlagByResnum	(	AA *	aa,
		int	resnum
	)

Parameters

[in]	*aa	Sequence linked list
[in]	resnum	Residue number

Searches the linked list of the specified resnum (i.e. the original residue number in the sequence before any insertions were made) and sets the flag in that item in the linked list

• 21.08.06 Original By: ACRM
• 07.07.14 Use bl prefix for functions By: CTP

Definition at line 470 of file aalist.c.