A C D F G H L M N O P R S

A

ActiveSiteProfile - Class in dasp.model
 
ActiveSiteProfile(List<ActiveSiteSignature>, Align) - Constructor for class dasp.model.ActiveSiteProfile
 
ActiveSiteSignature - Class in dasp.model
 
ActiveSiteSignature(String) - Constructor for class dasp.model.ActiveSiteSignature
 
ActiveSiteSignature(DaspStructure, List<Residue>) - Constructor for class dasp.model.ActiveSiteSignature
 
addFragRes(Residue) - Method in class dasp.model.Fragment
 
addSequence(String) - Method in class dasp.model.Alignment
addSequence can be used to add an addtional sequence to the alignment.
addSequences(List<String>) - Method in class dasp.model.Alignment
addSequences can be used to add a list of addtional sequences to the alignment.
Align - Interface in dasp.algorithms
 
align(List<String>) - Method in interface dasp.algorithms.Align
align actually performs the alignment.
align(List<String>) - Method in class dasp.algorithms.ClustalAlign
align actually performs the alignment.
Alignment - Class in dasp.model
 
Alignment() - Constructor for class dasp.model.Alignment
 
Alignment(List<String>, Align) - Constructor for class dasp.model.Alignment
 
alignment - Variable in class dasp.model.Alignment
 

C

ClustalAlign - Class in dasp.algorithms
 
ClustalAlign() - Constructor for class dasp.algorithms.ClustalAlign
Will need to store the alignment or files the alignemnt is saved to?

D

dasp - package dasp
 
Dasp - Class in dasp
 
Dasp() - Constructor for class dasp.Dasp
 
dasp.algorithms - package dasp.algorithms
 
dasp.model - package dasp.model
 
DaspStructure - Class in dasp.model
 
DaspStructure(String) - Constructor for class dasp.model.DaspStructure
Create a new structure from a pdb file.
DaspStructure(String, String) - Constructor for class dasp.model.DaspStructure
Create a new structure from a pdb file.
deleteSequence(String) - Method in class dasp.model.Alignment
deleteSequence can be used to remove a sequence from the alignment.
dist(Residue, Residue) - Method in class dasp.model.ActiveSiteSignature
Calculates the Euclidean distance between two residue centers
doAlign() - Method in class dasp.model.Alignment
 

F

Fragment - Class in dasp.model
 
Fragment() - Constructor for class dasp.model.Fragment
 

G

getAA() - Method in class dasp.model.Residue
 
getAlignment() - Method in interface dasp.algorithms.Align
Return the alignment itself as a list of aligned sequences with dashes to account for insertions.
getAlignment() - Method in class dasp.algorithms.ClustalAlign
Return the alignment itself with each sequence as a single string and with dashes inserted to account for insertions.
getAlignment() - Method in class dasp.model.Alignment
Return the alignment itself as a list of strings with dashes inserted to account for insertions.
getAlignmentAsString() - Method in class dasp.model.Alignment
Return the alignment itself as a string with newlines between sequences and dashes inserted to account for insertions.
getAlignmentByIndex(int) - Method in class dasp.model.Alignment
Return the alignment string for just one of the proteins in the alignment.
getAlignmentByName(String) - Method in class dasp.model.Alignment
Return the alignment string for just one of the proteins in the alignment.
getASPscore(String, int) - Method in interface dasp.algorithms.Align
Return the ASP score as defined in Cammer et al for this alignment.
getASPscore(String, int) - Method in class dasp.algorithms.ClustalAlign
Return the ASP score as defined in Cammer et al for this alignment.
getCenter() - Method in class dasp.model.Residue
 
getFragFormattedAlignment() - Method in class dasp.model.ActiveSiteProfile
Modify alignment to reflect fragments of signatures.
getFragmentsInContext() - Method in class dasp.model.ActiveSiteSignature
 
getFragRes(int) - Method in class dasp.model.Fragment
 
getHTMLAlignment(List<String>) - Method in interface dasp.algorithms.Align
Return the alignment itself as an HTML-formatted string to account for insertions.
getHTMLAlignment(List<String>) - Method in class dasp.algorithms.ClustalAlign
Return the alignment itself as an HTML-formatted string to account for insertions.
getHTMLAlignment() - Method in class dasp.model.Alignment
Return the alignment itself as an HTML-formatted string to account for insertions.
getIdentity() - Method in interface dasp.algorithms.Align
Return the % identity for all of the sequences in the alignment.
getIdentity() - Method in class dasp.algorithms.ClustalAlign
Return the % identity for all of the sequences in the alignment.
getIdentity() - Method in class dasp.model.Alignment
Return the % identity for all of the sequences in the alignment.
GetOpt - Class in dasp
 
GetOpt(String[], String) - Constructor for class dasp.GetOpt
 
getopt() - Method in class dasp.GetOpt
 
getOptLetter() - Method in class dasp.GetOpt
 
getPdbId() - Method in class dasp.model.ActiveSiteSignature
 
getPdbId() - Method in class dasp.model.DaspStructure
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.
getResidue(String) - Method in class dasp.model.DaspStructure
Return a Residue object for a residue within this PDB file.
getScore() - Method in class dasp.model.Alignment
Return the alignment score that results from the alignment.
getSeqLength() - Method in class dasp.model.DaspStructure
Returns the number of residues in the sequence.
getSequence() - Method in class dasp.model.DaspStructure
Return the amino acid sequence for this PDB file.
getSequence(boolean) - Method in class dasp.model.Fragment
 
getSequences() - Method in class dasp.model.Alignment
Return all of the sequences as FASTA-formatted strings
getSignature(int) - Method in class dasp.model.ActiveSiteSignature
 
getX() - Method in class dasp.model.Location
 
getY() - Method in class dasp.model.Location
 
getZ() - Method in class dasp.model.Location
 

H

hasMoreResidues() - Method in class dasp.model.DaspStructure
Tests to see if there is at least one more Residue object in the sequence

L

Location - Class in dasp.model
 
Location(double, double, double) - Constructor for class dasp.model.Location
 

M

main(String[]) - Static method in class dasp.Dasp
 
main(String[]) - Static method in class dasp.model.ActiveSiteSignature
 
makeUpper(String) - Method in class dasp.model.Fragment
 
method - Variable in class dasp.model.Alignment
 

N

nameMap - Variable in class dasp.model.Alignment
 
nextResidue() - Method in class dasp.model.DaspStructure
Enumerates through sequence of residues and returns the next Residue object.

O

optArg - Variable in class dasp.GetOpt
 
optInd - Variable in class dasp.GetOpt
 

P

PSSM - Class in dasp.model
 
PSSM() - Constructor for class dasp.model.PSSM
 

R

resetEnum() - Method in class dasp.model.DaspStructure
Resets the enumerator variable to -1
Residue - Class in dasp.model
 
Residue(AminoAcid) - Constructor for class dasp.model.Residue
 

S

seqs - Variable in class dasp.model.Alignment
 
sortN2C(List<Fragment>) - Static method in class dasp.model.Fragment
 

A C D F G H L M N O P R S