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" .
Methods inherited from class java.lang.Object |
equals, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait |
ATO
public static final int ATO
- See Also:
- Constant Field Values
CHAIN_ID
public static final int CHAIN_ID
- See Also:
- Constant Field Values
ATOM
public static final int ATOM
- See Also:
- Constant Field Values
HEAD
public static final int HEAD
- See Also:
- Constant Field Values
COMP
public static final int COMP
- See Also:
- Constant Field Values
SOUR
public static final int SOUR
- See Also:
- Constant Field Values
ENDM
public static final int ENDM
- See Also:
- Constant Field Values
CONE
public static final int CONE
- See Also:
- Constant Field Values
REMA
public static final int REMA
- See Also:
- Constant Field Values
TER
public static final int TER
- See Also:
- Constant Field Values
HETA
public static final int HETA
- See Also:
- Constant Field Values
TITL
public static final int TITL
- See Also:
- Constant Field Values
HELI
public static final int HELI
- See Also:
- Constant Field Values
MODR
public static final int MODR
- See Also:
- Constant Field Values
SHEE
public static final int SHEE
- See Also:
- Constant Field Values
PDB_Parser
public PDB_Parser()
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)
'The most important classes are StrapAlign, Protein and StrapEvent.'