charite.christo.protein
Interface Superimpose3D

All Superinterfaces:

NeedsProteins

All Known Implementing Classes:

Superimpose_CE, Superimpose_CEPROXY, Superimpose_GangstaPlus, Superimpose_Goede, Superimpose_GoedePROXY, Superimpose_LajollaProtein, Superimpose_LajollaProteinPROXY, Superimpose_LajollaRNA, Superimpose_native_CE, Superimpose_TM_align

public interface Superimpose3D
extends NeedsProteins

Implemented by plugins that perform a 3D-superposition of the C-alpha atoms of two protein chains. Before the method compute() is invoked, the reference and mobile proteins must be set with setProteins();

Nested Class Summary

static class

Superimpose3D.Result

Field Summary

static int	COLUMN_SEQUENCE
static byte[]	NO_BYTE The Result class bundles the result returned after computation
static long	PARSE_ALIGNMENT
static long	PARSE_MATRIX
static long	PARSE_MSA_START_S
static long	PARSE_SCORE
static long	PRINT_HUMAN_READABLE

Method Summary

void	compute()
long	getOptions()
Protein[]	getProteins()
Superimpose3D.Result	getResult() returns a 3X3 rotation matrix and a translation vector.
void	setOptions(long optionFlags)

Methods inherited from interface charite.christo.protein.NeedsProteins

setProteins

Field Detail

PRINT_HUMAN_READABLE

static final long PRINT_HUMAN_READABLE

See Also:

Constant Field Values

PARSE_ALIGNMENT

static final long PARSE_ALIGNMENT

See Also:

Constant Field Values

PARSE_MATRIX

static final long PARSE_MATRIX

See Also:

Constant Field Values

PARSE_SCORE

static final long PARSE_SCORE

See Also:

Constant Field Values

PARSE_MSA_START_S

static final long PARSE_MSA_START_S

See Also:

Constant Field Values

COLUMN_SEQUENCE

static final int COLUMN_SEQUENCE

See Also:

Constant Field Values

NO_BYTE

static final byte[] NO_BYTE

The Result class bundles the result returned after computation

Method Detail

setOptions

void setOptions(long optionFlags)

getOptions

long getOptions()

getProteins

Protein[] getProteins()

Returns:

the reference and the mobile protein

compute

void compute()

getResult

Superimpose3D.Result getResult()

returns a 3X3 rotation matrix and a translation vector. returns a {dx,dy,dz} translation vector This method is invoked by STRAP after the compute() method returned.