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Uses of Class
org.strbio.mol.Protein

Packages that use Protein
org.strbio.local These classes are for running or exchanging data with local programs (other programs installed on your computer). 
org.strbio.mol These classes represent objects or concepts useful to structural biologists. 
org.strbio.mol.lib These classes represent conceptual objects used in structural biology algorithms. 
org.strbio.mol.lib.pred2ary These classes represent conceptual objects used in the Pred2ary program, which are probably not very useful for other purposes. 
org.strbio.net These classes are for running or exchanging data with non-local programs (i.e., programs that you run by submitting data to a web page). 
org.strbio.raf These classes are related to the RAF file format used by the ASTRAL database. 
org.strbio.util.db These classes are a primitive interface to store and manipulate protein structure information from various commonly used databases. 
org.strbio.util.ui These classes are general purpose utility functions related to a program's user interface. 
 

Uses of Protein in org.strbio.local
 

Fields in org.strbio.local declared as Protein
protected  Protein BlastPAdapter.query
           
 

Methods in org.strbio.local that return Protein
 Protein Modeller.model(Alignment al)
          Make a model for a given alignment
 

Methods in org.strbio.local with parameters of type Protein
 MaxSub.Results MaxSub.run(Protein model, Protein correct)
          Run maxsub on two proteins, default cutoff is 3.5
 MaxSub.Results MaxSub.run(Protein model, Protein correct, double cutoff)
          Run maxsub on two proteins
 MinareaResults Minarea.runOnProteins(Protein a, Protein b)
          Return a set of results, including alignment.
 MinareaResults Malfe.runOnProteins(Protein a, Protein b)
          Return a set of results, including alignment.
 void BlastPAdapter.setQuery(Protein p)
          Sets a query protein.
 

Constructors in org.strbio.local with parameters of type Protein
BlastClient(Protein p)
          Initialize with a given protein.
BlastP(Protein p)
          Initialize with a given protein.
PSIBlastP(Protein p)
          Initialize with a given protein.
PSIBlastP2(Protein p)
          Initialize with a given protein.
TBlastN(Protein p)
          Initialize with a given protein.
 

Uses of Protein in org.strbio.mol
 

Subclasses of Protein in org.strbio.mol
 class Profile
          Class to represent a protein with profile information.
 class ProfilePSI
          Class to represent a profile with position specific information (PSI), such as PSI-BLAST info and JMC's backbone potential.
 

Methods in org.strbio.mol that return Protein
 Protein Profile.doVarTom(Printf outfile)
          Do var-tom on this profile.
 Protein Protein.findAccess(Printf outfile)
          find a protein in a PDB file which should be this one, based on the name.
 Protein Protein.findDSSP(Printf outfile)
          finds a protein in a PDB file which should be this one, based on the name.
protected  Protein Protein.findDSSPResult(ProteinSet q, Printf outfile)
          returns the appropriate protein from a set of DSSP results, aligned to this one.
 Protein Protein.findPDB(Printf outfile)
          find a protein in a PDB file which should be this one, based on the name.
 Protein ProteinSet.protein(int i)
          Return the i'th protein in the array.
 

Methods in org.strbio.mol with parameters of type Protein
 void Protein.copyPredSSFrom(Protein q)
          Copy predicted secondary structure info from another protein.
 boolean Protein.isCATHMatch(Protein y)
          Does this protein match another at the H level or below, according to CATH codes?
static Alignment Alignment.makeFromSuperposition(Protein seq, Protein fold)
          Make from 2 superimposed proteins, using JDB's method. 1) Make table of everything in (fold) which is <= CUTOFF angstroms from each residue in (seq). 2) Get longest consecutive stretch, and set them as aligned; remove these residues from future consideration. 3) Repeat until nothing is left that has any matches.
static Alignment Alignment.makeFromSuperpositionDP(Protein seq, Protein fold)
          Make from a superposition, using dynamic programming.
 

Constructors in org.strbio.mol with parameters of type Protein
Profile(Protein q)
          Make a Profile from a Protein, copying all data.
ProfilePSI(Protein q)
          Create from a single protein.
Protein(Protein q)
          Copy another Protein, making copies of all data fields.
 

Uses of Protein in org.strbio.mol.lib
 

Fields in org.strbio.mol.lib declared as Protein
protected  Protein BlastAdapter.query
           
 Protein ThreadResults.target
          The protein that was threaded.
 

Methods in org.strbio.mol.lib with parameters of type Protein
 void Pred2ary.predict(Protein p, Printf outfile)
          Predicts on a given protein.
 void SSPredictor.predict(Protein p, Printf outfile)
          Predicts on a given protein.
 double Sippl90.selfEnergy(Protein p)
          return the total self energy for a protein.
 double Sippl90.selfEnergy(Protein p, int kMin, int kMax)
          return the self-energy for a protein for a range of k's (including both ends of the range)
 double Sippl90.selfEnergyLR1(Protein p)
          return the long range (1) energy for a protein (k=31..60)
 double Sippl90.selfEnergyLR2(Protein p)
          return the long range (2) energy for a protein (k=61..100)
 double Sippl90.selfEnergyLR3(Protein p)
          return the long range (3) energy for a protein (k=101..150)
 double Sippl90.selfEnergyLR4(Protein p)
          return the long range (4) energy for a protein (k=151+)
 double Sippl90.selfEnergyMR(Protein p)
          return the medium range energy for a protein (k=11..30)
 double Sippl90.selfEnergySR(Protein p)
          return the short range energy for a protein (k=1..10)
 void BlastAdapter.setQuery(Protein p)
          Sets a query protein.
 void PSIBlastMatrices.setQuery(Protein p)
          Set the query sequence to a given string.
 void Blast.setQuery(Protein p)
          Sets a query protein.
 ThreadResults JMCThreadMethod2.thread(Protein p, Printf outfile)
          Thread a given protein, returning a ThreadResults object.
 ThreadResults JMCThreadMethod.thread(Protein p, Printf outfile)
          Thread a given protein, returning a ThreadResults object.
 ThreadResults ThreadMethod.thread(Protein p, Printf outfile)
          Thread a given protein, returning a ThreadResults object.
 

Constructors in org.strbio.mol.lib with parameters of type Protein
PSIBlastMatrices(Protein query)
          Create with given protein as query.
 

Uses of Protein in org.strbio.mol.lib.pred2ary
 

Subclasses of Protein in org.strbio.mol.lib.pred2ary
 class PredClassProfile
          Class to represent a single protein, with class routines and lots of stats.
 

Constructors in org.strbio.mol.lib.pred2ary with parameters of type Protein
PredClassProfile(Protein q)
           
 

Uses of Protein in org.strbio.net
 

Methods in org.strbio.net that return Protein
static Protein Entrez.getProtein(java.lang.String id, Printf outfile)
          Searches on a given protein identifier.
 

Methods in org.strbio.net with parameters of type Protein
static java.lang.String ProtParam.getAnnot(Protein p, Printf outfile)
          gets annot for a protein... returns null error processing or reading sequence.
static java.lang.String ProtParam.getCheckedAnnot(Protein p, Printf outfile)
          gets raw annot for a protein... returns null error processing or reading sequence
static java.lang.String ThreeDPSSM.submit(Protein p, Printf outfile)
          Query the server
 

Constructors in org.strbio.net with parameters of type Protein
BlastNCBI(Protein p)
          Initialize with a given protein.
BlastNCBI2(Protein p)
          Initialize with a given protein.
BlastWeb(Protein p)
          Initialize with a given protein.
PSIBlastNCBI(Protein p)
          Initialize with a given protein.
PSIBlastWeb(Protein p)
          Initialize with a given protein.
 

Uses of Protein in org.strbio.raf
 

Subclasses of Protein in org.strbio.raf
 class RAFProtein
          Modified version of org.strbio.mol.Protein... part of this might might be ported back to Protein.
 

Uses of Protein in org.strbio.util.db
 

Fields in org.strbio.util.db declared as Protein
 Protein ProteinInfo.protein
          A Protein object associated with this info, or null if it doesn't exist.
 

Uses of Protein in org.strbio.util.ui
 

Methods in org.strbio.util.ui with parameters of type Protein
static void ProteinTools.draw2aryStructure(java.awt.Graphics g, int drawX, int drawY, int fontWidth, int fontHeight, int fontLeading, Protein pr, int startRes, int n)
          This draws a line of letters showing the actual 2ary structure of a protein, from residue startRes (expressed in the protein's internal numbering scheme; 0 = first residue, etc).
static void ProteinTools.drawPred2aryGraph(java.awt.Graphics g, int drawX, int drawY, int fontWidth, int fontHeight, Protein pr, int startRes, int n)
          This draws a graph of the secondary structure probabilities.
static void ProteinTools.drawPred2aryStructure(java.awt.Graphics g, int drawX, int drawY, int fontWidth, int fontHeight, int fontLeading, Protein pr, int startRes, int n)
          This draws a line of letters showing the actual 2ary structure of a protein, from residue startRes to startRes+n (expressed in the protein's internal numbering scheme; 0 = first residue, etc).
 

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