public class MIFHandler
extends org.xml.sax.helpers.DefaultHandler
Constructor and Description |
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MIFHandler()
Constructs a new MIFHandler.
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Modifier and Type | Method and Description |
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void |
applyOPMAlignmentTo(Molecule_3D newProt)
This methods adjust the rotation and the position of the given
Protein to the actual membrane which it is placed into.
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void |
comparePDBTMtoOPM()
Use this method to compare both database entries to each other.
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void |
endElement(java.lang.String uri,
java.lang.String localName,
java.lang.String qName) |
javax.vecmath.Matrix3f |
getTransformMatrixOf(java.lang.String pdbID)
Obtains the transform matrix of a given PDB-Id.
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javax.vecmath.Vector3f |
getTransformVectorOf(java.lang.String pdbID)
Obtains the transformation vector of a given PDB-Id.
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boolean |
isElementOfMIF(java.lang.String pdbID)
Checks whether the given PDB-Id in the MIFile exists.
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boolean |
isElementOfOPM(java.lang.String pdbID)
Checks whether the given PDB-Id in the OPM entry of the MIFile exists.
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boolean |
isElementOfPDBTM(java.lang.String pdbID)
Checks whether the given PDB-Id in the PDBTM entry of the MIFile exists.
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void |
startElement(java.lang.String uri,
java.lang.String localName,
java.lang.String qName,
org.xml.sax.Attributes attributes) |
public void startElement(java.lang.String uri, java.lang.String localName, java.lang.String qName, org.xml.sax.Attributes attributes)
startElement
in interface org.xml.sax.ContentHandler
startElement
in class org.xml.sax.helpers.DefaultHandler
public void endElement(java.lang.String uri, java.lang.String localName, java.lang.String qName)
endElement
in interface org.xml.sax.ContentHandler
endElement
in class org.xml.sax.helpers.DefaultHandler
public boolean isElementOfMIF(java.lang.String pdbID)
pdbID
- The PDB-Id of the protein for looking at.true
if the PDB-Id in the MIFile existspublic boolean isElementOfPDBTM(java.lang.String pdbID)
pdbID
- The PDB-Id of the protein for looking at.true
if the PDB-Id in the MIFile existspublic boolean isElementOfOPM(java.lang.String pdbID)
pdbID
- The PDB-Id of the protein for looking at.true
if the PDB-Id in the MIFile existspublic javax.vecmath.Matrix3f getTransformMatrixOf(java.lang.String pdbID)
pdbID
- The PDB-Id of the protein.public javax.vecmath.Vector3f getTransformVectorOf(java.lang.String pdbID)
pdbID
- The PDB-Id of the protein.public void applyOPMAlignmentTo(Molecule_3D newProt)
newProt
- The Protein_3D to alignpublic void comparePDBTMtoOPM()