charite.christo.protein
Class PDB_Parser

java.lang.Object
  charite.christo.protein.PDB_Parser

All Implemented Interfaces:

ProteinParser

public class PDB_Parser
extends java.lang.Object
implements ProteinParser

HELP Those lines containing CA in the third column describe C-alpha atoms. Initially, STRAP loads only the C-alpha atoms, but side chain atoms are read on demand. For a short explanation of the PDB-format see WIKI:Protein_Data_Bank_(file_format). There might be residues in a protein model without corresponding ATOM-lines but which are recorded in the SEQRES lines of the pdb-file. These residues are written in lower case in the alignment panel indicating that they have no 3D-coordinates. The interpretation of SEQRES-lines can be deactivated by unselecting CB:charite.christo.strap.StrapAlign#ACTION_ignoreSEQRES or with the command line option "-noSeqres" .

Field Summary

static int	ATO
static int	ATOM
static int	CHAIN_ID
static int	COMP
static int	CONE
static int	ENDM
static int	HEAD
static int	HELI
static int	HETA
static int	MODR
static int	REMA
static int	SHEE
static int	SOUR
static int	TER
static int	TITL

Fields inherited from interface charite.christo.protein.ProteinParser

IGNORE_SEQRES, SEQUENCE_FEATURES, SIDE_CHAIN_ATOMS

Constructor Summary

PDB_Parser()

Method Summary

boolean	parse(Protein protein, long options, BA byteArray)
static java.lang.String	simplifyTitle(java.lang.String s0)

Methods inherited from class java.lang.Object

equals, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait

Field Detail

ATO

public static final int ATO

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Constant Field Values

CHAIN_ID

public static final int CHAIN_ID

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ATOM

public static final int ATOM

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HEAD

public static final int HEAD

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COMP

public static final int COMP

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SOUR

public static final int SOUR

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ENDM

public static final int ENDM

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CONE

public static final int CONE

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REMA

public static final int REMA

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TER

public static final int TER

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HETA

public static final int HETA

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TITL

public static final int TITL

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HELI

public static final int HELI

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MODR

public static final int MODR

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SHEE

public static final int SHEE

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Constructor Detail

PDB_Parser

public PDB_Parser()

Method Detail

parse

public boolean parse(Protein protein,
                     long options,
                     BA byteArray)

Specified by:

parse in interface ProteinParser

byteArray - the entire file contents It is a byte array and not a String Object for performance reasons.

Returns:

true: success, false: inappropriate file format

simplifyTitle

public static java.lang.String simplifyTitle(java.lang.String s0)