org.strbio.mol
Class Protein

java.lang.Object
  org.strbio.mol.Molecule
      org.strbio.mol.Polymer
          org.strbio.mol.Protein

Direct Known Subclasses:

Profile, RAFProtein

public class Protein
extends Polymer

Class to represent a single protein. For an example of how to extend this class, see Profile or ProfilePSI

 Version 1.7, 7/1/05 - added readSwissProt
 Version 1.64, 12/15/04 - added molecularWeight
 Version 1.63, 1/8/02 - change in getInfo; moved some code to parent class
 Version 1.62, 2/12/02 - made findPDB look for matching chain ID.
 Version 1.61, 11/22/00 - moved translateEA to Residue
 Version 1.6, 3/31/00 - split PRECALC_ANGLES into PRECALC_PHIPSI and
   PRECALC_ALPHATAU
 Version 1.5, 1/14/00 - added makeVirtualCB
 Version 1.48, 1/7/00 - added fixDistanceGaps
 Version 1.47, 1/3/00 - added makeMonDistanceCB
 Version 1.46, 12/6/99 - added isCATHMatch function
 Version 1.45, 10/28/99 - recognises PDB HEADER lines
 Version 1.44, 9/28/99 - made getInfo(env) get exposedArea, pctExposed
 Version 1.43, 7/22/99 - changed getPDBInfo to getInfo
 Version 1.42, 6/4/99 - added predictSS
 Version 1.41, 3/30/99 - made printfs consistent, limited names to 4096 chars
 Version 1.4, 2/10/99 - added YAPF format
 Version 1.38, 1/4/99 - added readCASP
 Version 1.37, 11/23/98 - fixed readDSSP for no-HEADER cases
 Version 1.36, 8/20/98 - gets secondary structure predcition if present
   in VAR2 file.  Added translateEA from org.strbio.jmc.TPSet.
 Version 1.35, 8/17/98 - changed all JMC.fatal() calls to exceptions,
   since they aren't always fatal.
 Version 1.34, 8/7/98 - changed PrintfStream to Printf
 Version 1.33, 7/22/98 - fixed bug in reading SEQRES records in generic PDB
 Version 1.32, 7/17/98 - added readVar
 Version 1.31, 6/10/98 - added writeCASP
 Version 1.3, 5/21/98 - added transparent reading of gzipped files
   ending in .gz.
 Version 1.2, 4/20/98 - extends Polymer, removed JMC-specific methods
 Version 1.1, 4/8/98 - added static alignment methods, getPDBInfo, readList
 Version 1.01, 4/3/98 - added methods to setup JMCPotential's with
   default offset and scale.
 Version 1.0, 3/31/98 - original version
 

Version:

1.63, 1/8/03

Author:

JMC

See Also:

Atom, Residue, ProteinSet, Profile, ProfilePSI

Field Summary

Fields inherited from class org.strbio.mol.Polymer

chainID, includeFile, includingFile, monDistance, monomers, properties

Fields inherited from class org.strbio.mol.Molecule

atoms, data, MAX_NAME_LENGTH, name

Constructor Summary

Protein()
Create a new protein with no information known about it.

Protein(Protein q)
Copy another Protein, making copies of all data fields.

Protein(java.lang.String sequence)
Make a new protein from a string representing a sequence.

Method Summary

Residue	AA(int i) returns the N'th residue in the sequence.
double	actualAccuracy() The actual accuracy of the secondary structure prediction that's been done on this protein.
Polymer	copy() Return a copy of yourself.
void	copyPredSSFrom(Protein q) Copy predicted secondary structure info from another protein.
double	expectedAccuracy() Expected accuracy of the secondary structure prediction that's been done on this protein.
void	filterPred() filters predStructure predictions in a protein's residues according to DSSP rules: no helix shorter than 4, no strand shorter than 2.
void	filterPred(boolean frishman) filters predStructure predictions in a protein's residues according to DSSP rules: no helix shorter than 4, no strand shorter than 2.
void	filterReal() filters DSSP structure in a protein's residues according to DSSP rules: no helix shorter than 4, no strand shorter than 2.
void	filterReal(boolean frishman) filters DSSP structure in a protein's residues according to DSSP rules: no helix shorter than 4, no strand shorter than 2.
Protein	findAccess(Printf outfile) find a protein in a PDB file which should be this one, based on the name.
Protein	findDSSP(Printf outfile) finds a protein in a PDB file which should be this one, based on the name.
protected Protein	findDSSPResult(ProteinSet q, Printf outfile) returns the appropriate protein from a set of DSSP results, aligned to this one.
Protein	findPDB(Printf outfile) find a protein in a PDB file which should be this one, based on the name.
Residue	firstRes() Return first residue if there is one.
ProteinSet	fixDistanceGaps() Filter out distance gaps (inter-CA > 4 A or < 3.6 A), returning a new set of proteins consisting of this protein broken into fragments everywhere there is a problem.
ProteinSet	getDSSPResults(Printf outfile) runs DSSP on a protein, returning a ProteinSet containing results from DSSP.
void	getInfo(Printf outfile, boolean getSequence, boolean getAngles, boolean getAtoms, boolean getStructure, boolean getEnv, boolean getPDB, boolean getCATH) Get info for a protein out of local databases.
boolean	hasGaps() Are any residues missing?
boolean	isCATHMatch(Protein y) Does this protein match another at the H level or below, according to CATH codes?
void	makeMonDistance() calculate inter-residue distance matrix (CA-CA distances) for use in threading functions.
void	makeMonDistanceCB() calculate inter-residue distance matrix (CB-CB distances, or CA for Gly residues) for use in threading functions.
void	makeVirtualCB() Add a virtual CB atom for residues that don't have one.
double	molecularWeight() Calculate molecular weight; add back the last water
Monomer	newMonomer() This should return a new monomer of whatever type this polymer is made of (i.e.
Monomer	newMonomer(char t) This should return a new monomer of whatever type this polymer is made of (i.e.
Monomer	newMonomer(java.lang.String s) This should return a new monomer of whatever type this polymer is made of (i.e.
void	preCalculateAlphaTau() pre-calculates cAlpha and cTau for all residues.
void	preCalculateAngles() pre-calculates cPhi, cPsi, cAlpha, and cTau for all residues.
void	preCalculatePhiPsi() pre-calculates cPhi and cPsi for all residues.
void	predictSS(Printf outfile) Predict the secondary structure of this protein, using the default method (Pred2ary, with large jury).
void	predictSS(Printf outfile, SSPredictor method) Predict the secondary structure of this protein, using a specified prediction method.
void	processYAPF(java.lang.String buffer) Process a line from a YAPF file... this should ignore the line if it doesn't know what it is.
void	readAccess(java.io.BufferedReader infile, Printf outfile) read a protein out of an Access file.
void	readCASP(java.io.BufferedReader infile, Printf outfile) read a protein out of a CASP file.
void	readConv(java.io.BufferedReader infile, Printf outfile) read a protein out of a Conv file.
void	readDSSP(java.io.BufferedReader infile, Printf outfile) read a protein out of a DSSP file.
void	readEA(java.io.BufferedReader infile, Printf outfile) read a protein out of an EA file.
void	readPDB(java.io.BufferedReader infile, Printf outfile) read a protein out of a PDB file.
void	readPDBAtom(java.io.BufferedReader infile, Printf outfile) read a protein out of a PDB file with no SEQRES records.
void	readProf(java.io.BufferedReader infile, Printf outfile) read a protein out of a Prof file.
void	readSwissProt(java.io.BufferedReader infile, Printf outfile) read a protein out of a SwissProt file.
void	readVar(java.io.BufferedReader infile, Printf outfile) read a protein out of a Var file.
void	readVar2(java.io.BufferedReader infile, Printf outfile) read a protein out of a Var2 file.
protected boolean	recognizeAndRead(java.lang.String buffer, java.io.BufferedReader infile, Printf outfile) This looks for a protein and reads it in.
int	residues() How many residues do we have?
void	reverse() Reverse yourself.
void	runDSSP(Printf outfile) Runs DSSP on this protein (which must have atomic coordinates).
void	showGaps(Printf outfile) Print out possible gaps in the sequence.
void	smoothHE() Do one round of 'diffusive smoothing' on the predH and predE values in a protein's residues.
protected Polymer	splitCopy() This should return a copy of all data which should be copied during AutoSplit (not including monomers, monDistance, name).
void	stripAllButCA() go to each residue, and remove all atoms except alpha carbons (CA).
ThreadResults	thread(Printf outfile) Thread, using the default method.
ThreadResults	thread(Printf outfile, ThreadMethod method) Thread the protein, using a specified threading method.
void	translateEA() Translates predH and predE into predStructure (directly).
void	writeCASP(Printf outfile) Write in CASP format.
void	writeConv(Printf outfile) Write in Conv format.
void	writeEA(Printf outfile) Write in EA format.
void	writePDB(Printf outfile) Write in PDB format, including SEQRES, JMCSTR, and ATOM records.
void	writePDB(Printf outfile, boolean vanillaPDB) Write in PDB format, which includes SEQRES and ATOM records.
void	writeVar2(Printf outfile) Write in Var2 format.
protected void	writeYAPFInfo(Printf outfile) Write applicable sections of YAPF info.

Methods inherited from class org.strbio.mol.Polymer

alignToArray, alignToInverseArray, autoSplit, centerOfMass, centerOfMass, clear, clearProperties, clearProperty, copyAtoms, correctAlignFold, correctAlignSeq, deleteMonDistance, firstMon, getGlobalAlignment, getMonomers, getNonGapMonomers, getProperty, getValidNonGapMonomers, globalAlign, globalAlign, globalCompare, globalCompare, keepMonomers, kludgeChainID, lastMon, length, makeMonDistanceAllAtomMin, minareaSuperimpose, monomer, nMonomers, nMonomers, nonGapMonomers, pad, printSequence, quickAlign, quickAlign, quickCompare, quickCompare, read, read, read, readFasta, readList, readSequence, readYAPF, renumberMonomers, renumberValidNonGapMonomers, reverseCopy, rotate, sequence, sequenceNonGap, sequenceValidNonGap, setProperty, stripAllAtoms, stripAllBut, stripAllButFirstAtom, stripAtomsByName, stripCommonGaps, stripGaps, stripInvalidAndGaps, stripNoAtoms, stripType, transform, translate, trimEnds, validNonGapMonomers, writeFasta, writePDBAtom, writePDBSeqres, writePTS, writeYAPF, writeYAPFAtom, YAPFGetNextMonomer

Methods inherited from class org.strbio.mol.Molecule

atomSearch, copyAtoms

Methods inherited from class java.lang.Object

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

Constructor Detail

Protein

public Protein()

Create a new protein with no information known about it.

Protein

public Protein(Protein q)

Copy another Protein, making copies of all data fields.

Protein

public Protein(java.lang.String sequence)

Make a new protein from a string representing a sequence.

Method Detail

residues

public int residues()

How many residues do we have?

firstRes

public Residue firstRes()

Return first residue if there is one.

newMonomer

public Monomer newMonomer()

This should return a new monomer of whatever type this polymer is made of (i.e. Residue, Base). By default, this is just Monomer.

Overrides:

newMonomer in class Polymer

newMonomer

public Monomer newMonomer(char t)

This should return a new monomer of whatever type this polymer is made of (i.e. Residue, Base), and initialize the type from a character.

Overrides:

newMonomer in class Polymer

newMonomer

public Monomer newMonomer(java.lang.String s)

This should return a new monomer of whatever type this polymer is made of (i.e. Residue, Base), and initialize the type from a string.

Overrides:

newMonomer in class Polymer

splitCopy

protected Polymer splitCopy()

Description copied from class: Polymer

This should return a copy of all data which should be copied during AutoSplit (not including monomers, monDistance, name).

Overrides:

splitCopy in class Polymer

AA

public final Residue AA(int i)

returns the N'th residue in the sequence. This starts from zero and counts gaps, so it has no relation to the residue (if it exists) with residue number N. This function is slow the first time it gets called after loading the protein in or making insertions/deletions, but otherwise fast.

makeMonDistance

public void makeMonDistance()

calculate inter-residue distance matrix (CA-CA distances) for use in threading functions.

Overrides:

makeMonDistance in class Polymer

makeMonDistanceCB

public void makeMonDistanceCB()

calculate inter-residue distance matrix (CB-CB distances, or CA for Gly residues) for use in threading functions.

readPDB

public final void readPDB(java.io.BufferedReader infile,
                          Printf outfile)
                   throws java.io.IOException

read a protein out of a PDB file. It will complain if the ATOM records don't match the sequence in SEQRES records. If that happens, curse the crystallographer, grep out just the ATOM records, and try again.

Parameters:

infile - an open PDB file

outfile - if non-null, will print info on what's going on

Throws:

java.io.IOException

See Also:

Polymer.read(java.io.BufferedReader, org.strbio.io.Printf, boolean)

readPDBAtom

public final void readPDBAtom(java.io.BufferedReader infile,
                              Printf outfile)
                       throws java.io.IOException

read a protein out of a PDB file with no SEQRES records. It figures out the sequence based on the ATOM records, I suggest renumbering the sequence afterwards.

Parameters:

infile - an open PDB file

outfile - if non-null, will print info on what's going on

Throws:

java.io.IOException

See Also:

Polymer.read(java.io.BufferedReader, org.strbio.io.Printf, boolean)

readVar2

public final void readVar2(java.io.BufferedReader infile,
                           Printf outfile)
                    throws java.io.IOException

read a protein out of a Var2 file.

Parameters:

infile - an open Var2 file

outfile - if non-null, will print info on what's going on

Throws:

java.io.IOException

See Also:

Polymer.read(java.io.BufferedReader, org.strbio.io.Printf, boolean), Residue.readVar2(java.io.BufferedReader)

readVar

public final void readVar(java.io.BufferedReader infile,
                          Printf outfile)
                   throws java.io.IOException

read a protein out of a Var file.

Parameters:

infile - an open Var file

outfile - if non-null, will print info on what's going on

Throws:

java.io.IOException

See Also:

Polymer.read(java.io.BufferedReader, org.strbio.io.Printf, boolean), Residue.readVar(java.io.BufferedReader)

readEA

public final void readEA(java.io.BufferedReader infile,
                         Printf outfile)
                  throws java.io.IOException

read a protein out of an EA file.

Parameters:

infile - an open EA file

outfile - if non-null, will print info on what's going on

Throws:

java.io.IOException

See Also:

Polymer.read(java.io.BufferedReader, org.strbio.io.Printf, boolean), Residue.readEA(java.io.BufferedReader)

readProf

public final void readProf(java.io.BufferedReader infile,
                           Printf outfile)
                    throws java.io.IOException

read a protein out of a Prof file.

Parameters:

infile - an open Prof file

outfile - if non-null, will print info on what's going on

Throws:

java.io.IOException

See Also:

Polymer.read(java.io.BufferedReader, org.strbio.io.Printf, boolean), Residue.readProf(java.io.BufferedReader), ProfRes.readProf(java.io.BufferedReader)

readConv

public final void readConv(java.io.BufferedReader infile,
                           Printf outfile)
                    throws java.io.IOException

read a protein out of a Conv file.

Parameters:

infile - an open Conv file

outfile - if non-null, will print info on what's going on

Throws:

java.io.IOException

See Also:

Polymer.read(java.io.BufferedReader, org.strbio.io.Printf, boolean), Residue.readConv(java.io.BufferedReader)

readCASP

public final void readCASP(java.io.BufferedReader infile,
                           Printf outfile)
                    throws java.io.IOException

read a protein out of a CASP file.

Parameters:

infile - an open CASP file

outfile - if non-null, will print info on what's going on

Throws:

java.io.IOException

See Also:

Polymer.read(java.io.BufferedReader, org.strbio.io.Printf, boolean)

readSwissProt

public final void readSwissProt(java.io.BufferedReader infile,
                                Printf outfile)
                         throws java.io.IOException

read a protein out of a SwissProt file.

Parameters:

infile - an open SwissProt file

outfile - if non-null, will print info on what's going on

Throws:

java.io.IOException

See Also:

Polymer.read(java.io.BufferedReader, org.strbio.io.Printf, boolean)

readDSSP

public final void readDSSP(java.io.BufferedReader infile,
                           Printf outfile)
                    throws java.io.IOException

read a protein out of a DSSP file.

Parameters:

infile - an open DSSP file

outfile - if non-null, will print info on what's going on

Throws:

java.io.IOException

See Also:

Polymer.read(java.io.BufferedReader, org.strbio.io.Printf, boolean), Residue.readDSSP(java.io.BufferedReader)

readAccess

public final void readAccess(java.io.BufferedReader infile,
                             Printf outfile)
                      throws java.io.IOException

read a protein out of an Access file. This format is not autodetected.

Parameters:

infile - an open Access file

outfile - if non-null, will print info on what's going on

Throws:

java.io.IOException

See Also:

Residue.readAccess(java.io.BufferedReader)

recognizeAndRead

protected boolean recognizeAndRead(java.lang.String buffer,
                                   java.io.BufferedReader infile,
                                   Printf outfile)
                            throws java.io.IOException

This looks for a protein and reads it in.

Overrides:

recognizeAndRead in class Polymer

Throws:

java.io.IOException

See Also:

Polymer.recognizeAndRead(java.lang.String, java.io.BufferedReader, org.strbio.io.Printf)

expectedAccuracy

public final double expectedAccuracy()

Expected accuracy of the secondary structure prediction that's been done on this protein. It assumes you've done one.

translateEA

public final void translateEA()

Translates predH and predE into predStructure (directly).

actualAccuracy

public final double actualAccuracy()

The actual accuracy of the secondary structure prediction that's been done on this protein. It assumes you've done one.

writePDB

public final void writePDB(Printf outfile,
                           boolean vanillaPDB)
                    throws java.io.IOException

Write in PDB format, which includes SEQRES and ATOM records.

Parameters:

outfile - where to write to

vanillaPDB - if true, won't write JMCSTR records

Throws:

java.io.IOException

writePDB

public final void writePDB(Printf outfile)
                    throws java.io.IOException

Write in PDB format, including SEQRES, JMCSTR, and ATOM records.

Overrides:

writePDB in class Polymer

Parameters:

outfile - where to write to

Throws:

java.io.IOException

writeEA

public final void writeEA(Printf outfile)
                   throws java.io.IOException

Write in EA format.

Parameters:

outfile - where to write to

Throws:

java.io.IOException

writeCASP

public final void writeCASP(Printf outfile)
                     throws java.io.IOException

Write in CASP format.

Parameters:

outfile - where to write to

Throws:

java.io.IOException

writeConv

public final void writeConv(Printf outfile)
                     throws java.io.IOException

Write in Conv format.

Parameters:

outfile - where to write to

Throws:

java.io.IOException

writeVar2

public final void writeVar2(Printf outfile)
                     throws java.io.IOException

Write in Var2 format.

Parameters:

outfile - where to write to

Throws:

java.io.IOException

processYAPF

public void processYAPF(java.lang.String buffer)
                 throws java.io.IOException

Process a line from a YAPF file... this should ignore the line if it doesn't know what it is.

Overrides:

processYAPF in class Polymer

Throws:

java.io.IOException

writeYAPFInfo

protected void writeYAPFInfo(Printf outfile)
                      throws java.io.IOException

Write applicable sections of YAPF info.

Overrides:

writeYAPFInfo in class Polymer

Throws:

java.io.IOException

filterPred

public final void filterPred(boolean frishman)

filters predStructure predictions in a protein's residues according to DSSP rules: no helix shorter than 4, no strand shorter than 2. Set frishman to eliminate helices of length 4 and strands of length 2, making secondary structure prediction much easier than it really is.

filterPred

public final void filterPred()

filters predStructure predictions in a protein's residues according to DSSP rules: no helix shorter than 4, no strand shorter than 2.

filterReal

public final void filterReal(boolean frishman)

filters DSSP structure in a protein's residues according to DSSP rules: no helix shorter than 4, no strand shorter than 2. Set frishman to use Dmitri Frishman's idea of what DSSP's minimum lengths should be.

filterReal

public final void filterReal()

filters DSSP structure in a protein's residues according to DSSP rules: no helix shorter than 4, no strand shorter than 2.

smoothHE

public final void smoothHE()

Do one round of 'diffusive smoothing' on the predH and predE values in a protein's residues. Values from each residue get averaged with values from adjacent residues.

stripAllButCA

public final void stripAllButCA()

go to each residue, and remove all atoms except alpha carbons (CA).

See Also:

Residue.stripAllButCA()

makeVirtualCB

public final void makeVirtualCB()

Add a virtual CB atom for residues that don't have one.

copy

public Polymer copy()

Return a copy of yourself.

Overrides:

copy in class Polymer

hasGaps

public final boolean hasGaps()

Are any residues missing? Inter-CA distances greater than 4.0 or less than 3.6 angstroms are considered gaps. For lo-res PDB files, this is usually true.

fixDistanceGaps

public final ProteinSet fixDistanceGaps()

Filter out distance gaps (inter-CA > 4 A or < 3.6 A), returning a new set of proteins consisting of this protein broken into fragments everywhere there is a problem. Also, residues without CA are deleted. If there are no gaps, returns null.

showGaps

public final void showGaps(Printf outfile)
                    throws java.io.IOException

Print out possible gaps in the sequence. Inter-CA distances greater than 4.0 or less than 3.6 angstroms are considered gaps. For lo-res PDB files, this is usually true.

Throws:

java.io.IOException

preCalculatePhiPsi

public final void preCalculatePhiPsi()

pre-calculates cPhi and cPsi for all residues.

preCalculateAlphaTau

public final void preCalculateAlphaTau()

pre-calculates cAlpha and cTau for all residues.

preCalculateAngles

public final void preCalculateAngles()

pre-calculates cPhi, cPsi, cAlpha, and cTau for all residues.

findPDB

public final Protein findPDB(Printf outfile)
                      throws java.io.IOException

find a protein in a PDB file which should be this one, based on the name. Returns that protein aligned to this one. All residues which do not match (except Cys) have their atom information removed. If this protein has no residue information, the function does not do the alignment or remove any atom information.

Throws:

java.io.IOException

getDSSPResults

public final ProteinSet getDSSPResults(Printf outfile)
                                throws java.io.IOException

runs DSSP on a protein, returning a ProteinSet containing results from DSSP.

Throws:

java.io.IOException

See Also:

ProteinSet.findDSSP(java.lang.String, org.strbio.io.Printf)

findDSSPResult

protected final Protein findDSSPResult(ProteinSet q,
                                       Printf outfile)
                                throws java.io.IOException

returns the appropriate protein from a set of DSSP results, aligned to this one. All residues which do not match (except Cys) have their structure information removed (set to '-'). If this protein has no residue information, the function does not do the alignment or remove any structure information.

Throws:

java.io.IOException

runDSSP

public final void runDSSP(Printf outfile)
                   throws java.io.IOException

Runs DSSP on this protein (which must have atomic coordinates). As a side affect, all gaps are removed.

Throws:

java.io.IOException

findDSSP

public final Protein findDSSP(Printf outfile)
                       throws java.io.IOException

finds a protein in a PDB file which should be this one, based on the name. Does DSSP on it. Returns that protein aligned to this one. All residues which do not match (except Cys) have their structure information removed (set to '-'). If this protein has no residue information, the function does not do the alignment or remove any structure information.

Throws:

java.io.IOException

findAccess

public final Protein findAccess(Printf outfile)
                         throws java.io.IOException

find a protein in a PDB file which should be this one, based on the name. Run Access on it to get the environmental classes for each residue, and load it in. Returns that protein aligned to this one. All residues which do not match (except Cys) have their environment information removed. If this protein has no residue information, the function does not do the alignment or remove any atom information.

Throws:

java.io.IOException

copyPredSSFrom

public final void copyPredSSFrom(Protein q)

Copy predicted secondary structure info from another protein.

predictSS

public void predictSS(Printf outfile,
                      SSPredictor method)
               throws java.io.IOException

Predict the secondary structure of this protein, using a specified prediction method.

Throws:

java.io.IOException

predictSS

public void predictSS(Printf outfile)
               throws java.io.IOException

Predict the secondary structure of this protein, using the default method (Pred2ary, with large jury).

Throws:

java.io.IOException

thread

public ThreadResults thread(Printf outfile,
                            ThreadMethod method)
                     throws java.io.IOException

Thread the protein, using a specified threading method.

Throws:

java.io.IOException

thread

public ThreadResults thread(Printf outfile)
                     throws java.io.IOException

Thread, using the default method.

Throws:

java.io.IOException

getInfo

public final void getInfo(Printf outfile,
                          boolean getSequence,
                          boolean getAngles,
                          boolean getAtoms,
                          boolean getStructure,
                          boolean getEnv,
                          boolean getPDB,
                          boolean getCATH)
                   throws java.io.IOException

Get info for a protein out of local databases. Writes some progress reports to outfile, if non-null. For residue based properties, this does a simple sequence alignment before copying things over; residues that don't match don't have their info copied (except for Cys, which is often incorrectly stored in protein sequences).

Parameters:

outfile - write progress reports here

getSequence - get sequence out of PDB

getAngles - get precalculated dihedral angels

getAtoms - get atomic coordinates

getStructure - get secondary structure using DSSP

getEnv - get environmental class using Access

getPDB - get records like title, header from PDB

getCATH - get records like title, header from CATH

Throws:

java.io.IOException

isCATHMatch

public final boolean isCATHMatch(Protein y)

Does this protein match another at the H level or below, according to CATH codes? CATH data must be present for both proteins, or false is returned.

reverse

public void reverse()

Reverse yourself. Name is prepended with an 'R' character. Also, ProteinInfo is removed.

Overrides:

reverse in class Polymer

molecularWeight

public double molecularWeight()

Calculate molecular weight; add back the last water

Overrides:

molecularWeight in class Polymer