TargetStruct Class Reference

This structure holds data related to protein sequence that is to be threaded. More...

#include <open_prospect.h>

Inheritance diagram for TargetStruct:

Public Member Functions
	TargetStruct (void)
virtual	~TargetStruct ()
	Free memory structures created during the loading of the target info.
virtual void	SetLen (int new_len)
void	FreeMem (void)
	TargetStruct (const TargetStruct &rhs)
int	Setup (ProspectParam *param)
	This function setup of Target data structures for pairwise energy calculation using the tables in Prospect.
int	LoadConstraint (char *constraint_file)
	Load a distance constraint file and apply it to a Target.
int	LoadPsiPred (char *psipred_path)
int	LoadFasta (char *SeqPath)
int	LoadPHD (char *filename)
int	LoadChk (char *ChkPath)
int	LoadFreq (char *FreqPath)
int	LoadPDB (char *filename, char chain=0)
int	SetSequence (char *seq)
int	Copy (TargetStruct *template_data, int start=-1, int stop=-1)
	Copy the sequence and structure information from a TemplateStruct into the target.
int	Append (TargetStruct *rhs, int start=-1, int stop=-1)
int	LoadSSP (char *ssp_path)
	Load Target information from SSP file.
int	LoadSSPStr (char *ssp_text)
void	ReadSingleDelStr (char *text)
void	ReadSingleInsStr (char *text)
int	LoadXML (char *xml_path)
int	CopyBackBone (TemplateStruct *template_data, AlignmentStruct *align_data, int start=-1, int stop=-1)
	Given a template, and alignment copy the template backbone atom positions into the target struct.
pValType	Calc_LRET (ProspectParam *param)
int	Count_Atoms (void)
void	ReNumberAtoms (int start=0)
int	Count_SetResidues (void)
int	Count_UnSetResidues (void)
vec3 *	GetCaLocArray (void)
void	SetChain (char new_chain= ' ')
	Set the chain IDs for all of the residues that belong to this target.
int	DSSP (void)
	Do the DSSP style secondary structure prediction on the existing structure This is not verified to be accurate.
void	Calc_hloc (int residue, vec3 h_loc)
float	Calc_hval (int i, int j)
void	Setup_Hbonds (void)
void	CleanUndefinedResidues (void)
void	ChouFasman (void)
	Target Struct Choufasman secondary structure prediction code.
int	WritePDB (char *outpath=NULL, int start=-1, int stop=-1)
	Write out the atomic information as it has been assigned to this target.
char *	WritePDBText (int start=-1, int stop=-1)
char *	GetSeq (void)
int	FindResIndexFromResNum (int res_num, char res_mod= ' ')
int	SideChain_Init (ProspectParam *param)
int	SideChain_Pack (ProspectParam *param)
void	MoveMeanToOrigin (void)
TargetResidue *	GetResidue (int i)
ResidueAtoms *	GetResidueAtoms (int i)
pValType	GetTwobody (int i, int j)
char	GetBSheet (int i, int j)
void	Translate (vec3 trans)
void	Rotate (mat3 rotate)
int	GetCaCount (void)
vec3 *	GetCaArray (void)
Data Fields
int	len
int	residue_offset
	Length of the target sequence.
pValType **	twobody
	2 dimensional (lenxlen) matrix that describes twobody interactions
pValType **	hbond
char **	bsheet
TargetDistConstraint *	distconst
int	distconst_count
TargetResidue *	residue
	The list of residues. Size len.
ResidueAtoms *	structure

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Detailed Description

This structure holds data related to protein sequence that is to be threaded.

Also contains the secondary structure information and position specific profile matrix

Definition at line 636 of file open_prospect.h.

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Constructor & Destructor Documentation

TargetStruct::~TargetStruct (   )  [virtual]

Free memory structures created during the loading of the target info. Parameters: target  Definition at line 44 of file target_struct.cc. References FreeMem().

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Member Function Documentation

int TargetStruct::Copy (  TargetStruct *  template_data, int  start = -1, int  stop = -1 )

Copy the sequence and structure information from a TemplateStruct into the target. Parameters: TemplateStruct  src template data start,stop  the range of residues to be copied, by default all of them Definition at line 708 of file target_struct.cc. References len, residue, and SetLen(). Referenced by Append().

int TargetStruct::LoadConstraint (  char *  constraint_file  )

Load a distance constraint file and apply it to a Target. Parameters: constraint_file  Definition at line 370 of file target_struct.cc. References TargetDistConstraint::aa, distconst, and distconst_count.

int TargetStruct::LoadSSP (  char *  ssp_path  )

Load Target information from SSP file. Parameters: ssp_path  Definition at line 275 of file target_struct.cc. References LoadSSPStr().

int TargetStruct::Setup (  ProspectParam *  param  )

This function setup of Target data structures for pairwise energy calculation using the tables in Prospect. You only need to call it if you plan on calculating twobody energies. Parameters: param  Definition at line 141 of file target_struct.cc. References AA1toAANum(). Referenced by ProspectParam::DoThreading(), and AlignmentStruct::GetEnergies().

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The documentation for this class was generated from the following files:

• src/common/open_prospect.h
• src/common/target_struct.cc

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