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java.lang.Objectdasp.model.DaspStructure
public class DaspStructure
Constructor Summary | |
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DaspStructure(String pdbFile)
Create a new structure from a pdb file. |
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DaspStructure(String pdbFile,
String chain)
Create a new structure from a pdb file. |
Method Summary | |
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String |
getPdbId()
Return the pbd id and chain as a string for this sequence Does not account ofr a possible 'pdb' in front of the pdb id. |
Residue |
getResidue(String residueID)
Return a Residue object for a residue within this PDB file. |
int |
getSeqLength()
Returns the number of residues in the sequence. |
String |
getSequence()
Return the amino acid sequence for this PDB file. |
boolean |
hasMoreResidues()
Tests to see if there is at least one more Residue object in the sequence |
Residue |
nextResidue()
Enumerates through sequence of residues and returns the next Residue object. |
void |
resetEnum()
Resets the enumerator variable to -1 |
Methods inherited from class java.lang.Object |
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clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait |
Constructor Detail |
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public DaspStructure(String pdbFile) throws IOException
pdbFile
- the pdb identifier or path to the pdb file
IOException
public DaspStructure(String pdbFile, String chain) throws IOException
pdbFile
- the pdb identifier or path to the pdb filechain
- the chain ID
IOException
Method Detail |
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public String getSequence()
public String getPdbId()
public int getSeqLength()
public Residue nextResidue()
public boolean hasMoreResidues()
public void resetEnum()
public Residue getResidue(String residueID)
residueID
- the ID for the residue to get from the structure. The
residue ID can be the residue # as an int, or an amino acid code followed
by an integer value (e.g. A123)
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