org.proteinshader.structure.exceptions
Class BondLengthException

java.lang.Object
  java.lang.Throwable
      java.lang.Exception
          org.proteinshader.structure.exceptions.BondLengthException

All Implemented Interfaces:

Serializable

public class BondLengthException
extends Exception

Can be used to report that a Bond is unacceptably short or long.

See Also:

Serialized Form

Constructor Summary

BondLengthException(double calculatedLength, double expectedLength, double toleranceFactor, AtomEnum srcAtomType, AtomEnum dstAtomType, int srcAtomSerialNo, int dstAtomSerialNo)
Sets the default message to "A Bond length was unacceptable".

BondLengthException(String message, double calculatedLength, double expectedLength, double toleranceFactor, AtomEnum srcAtomType, AtomEnum dstAtomType, int srcAtomSerialNo, int dstAtomSerialNo)
The message given this constructor can be retrieved using getMessage().

Method Summary

double	getCalculatedLength() Returns the calculated Bond length in angstroms.
int	getDstAtomSerialNo() Returns the destination Atom PDB serial number.
AtomEnum	getDstAtomType() Returns the destination Atom type as an AtomEnum.
double	getExpectedLength() Returns the expected Bond length in angstroms.
int	getSrcAtomSerialNo() Returns the source Atom PDB serial number.
AtomEnum	getSrcAtomType() Returns the source Atom type as an AtomEnum.
double	getToleranceFactor() Returns the tolerance factor used to determine that the calulated length was too far from the expected length.

Methods inherited from class java.lang.Throwable

fillInStackTrace, getCause, getLocalizedMessage, getMessage, getStackTrace, initCause, printStackTrace, printStackTrace, printStackTrace, setStackTrace, toString

Methods inherited from class java.lang.Object

clone, equals, finalize, getClass, hashCode, notify, notifyAll, wait, wait, wait

Constructor Detail

BondLengthException

public BondLengthException(double calculatedLength,
                           double expectedLength,
                           double toleranceFactor,
                           AtomEnum srcAtomType,
                           AtomEnum dstAtomType,
                           int srcAtomSerialNo,
                           int dstAtomSerialNo)

Sets the default message to "A Bond length was unacceptable". This message can be retrieved using getMessage().

Parameters:

calculatedLength - the calculated bond length in angstroms.

expectedLength - the expected bond length in angstroms.

toleranceFactor - the tolerance factor for the length.

srcAtomType - the source Atom type.

dstAtomType - the destination Atom type.

srcAtomSerialNo - the source atom PDB serial number.

dstAtomSerialNo - the destination Atom PDB serial number.

BondLengthException

public BondLengthException(String message,
                           double calculatedLength,
                           double expectedLength,
                           double toleranceFactor,
                           AtomEnum srcAtomType,
                           AtomEnum dstAtomType,
                           int srcAtomSerialNo,
                           int dstAtomSerialNo)

The message given this constructor can be retrieved using getMessage().

Parameters:

message - an error message.

calculatedLength - the calculated bonc length in angstroms.

expectedLength - the expected bond length in angstroms.

toleranceFactor - the tolerance factor for the length.

srcAtomType - the source Atom type.

dstAtomType - the destination Atom type.

srcAtomSerialNo - the source Atom PDB serial number.

dstAtomSerialNo - the destination Atom PDB serial number.

Method Detail

getCalculatedLength

public double getCalculatedLength()

Returns the calculated Bond length in angstroms.

Returns:

The calculated Bond length.

getExpectedLength

public double getExpectedLength()

Returns the expected Bond length in angstroms.

Returns:

The expected Bond length.

getToleranceFactor

public double getToleranceFactor()

Returns the tolerance factor used to determine that the calulated length was too far from the expected length. For example, if the tolerance factor is 0.15, then the calculated Bond length is only allowed to be 15 percent longer or shorter than the expected length.

Returns:

The tolerance factor as a number between 0 and 1.

getSrcAtomType

public AtomEnum getSrcAtomType()

Returns the source Atom type as an AtomEnum.

Returns:

The source Atom type.

getDstAtomType

public AtomEnum getDstAtomType()

Returns the destination Atom type as an AtomEnum.

Returns:

The destination Atom type.

getSrcAtomSerialNo

public int getSrcAtomSerialNo()

Returns the source Atom PDB serial number.

Returns:

The source Atom serial number.

getDstAtomSerialNo

public int getDstAtomSerialNo()

Returns the destination Atom PDB serial number.

Returns:

The destination Atom serial number.