org.strbio.mol
Class Residue

java.lang.Object
  org.strbio.mol.Monomer
      org.strbio.mol.Residue

All Implemented Interfaces:

DLinkedList.Node

Direct Known Subclasses:

ProfRes

public class Residue
extends Monomer

Class to represent a single residue in a protein. See ProfRes as an example of how to extend this.

 Version 1.3, 12/15/04 - added molecularWeight
 Version 1.21, 11/22/00 - added translateEA
 Version 1.2, 1/14/00 - added makeVirtualCB
 Version 1.18, 1/7/00 - made isGap return more gap types
 Version 1.17, 9/28/99 - saves more env stuff in YAPF files
 Version 1.16, 11/2/98 - added isValidType function
 Version 1.15, 8/20/98 - changed readVar2 and readConv to correctly read
   coil secondary structure as a -, not a ?
 Version 1.14, 8/7/98 - changed PrintfStream to Printf
 Version 1.13, 7/20/98 - changed coding for VAR files' env code...
   values range from -2 to -5.  -1 = unknown.
 Version 1.12, 7/17/98 - added readVar
 Version 1.11, 6/10/98 - added writeCASP
 Version 1.1, 4/17/98 - based on Monomer, JMC-specific stuff moved
   to org.strbio.jmc.JMCResidue
 Version 1.0, 4/3/98 - original version
 

Version:

1.21, 11/22/00

Author:

JMC

See Also:

Atom, AtomNode, Protein, ProfRes

Field Summary

static double[]	aaMolecularWeight molecular weight of each residue above
double	cAlpha Pre-calculated alpha angle at this residue.
double	cPhi Pre-calculated phi angle at this residue.
double	cPsi Pre-calculated psi angle at this residue.
double	cTau Pre-calculated tau angle at this residue.
int	env Environment code.
double	exposedArea Area of the residue (in square angstroms) exposed to solvent, as calculated from Scott Presnell's access program.
static java.lang.String	oneLetter one letter code, in alphabetical order by 3-letter code.
static java.lang.String	oneLetterBLAST one letter code used by BLAST.
static java.lang.String	oneLetterDefay one letter code, in alphabetical order by 1-letter code.
double	pctExposed Percentage of surface-exposed area, from 0 - 100.0.
double	predE Predicted strand probability.
double	predH Predicted helix probability.
char	predStructure Predicted secondary structure.
char	structure the structure, as defined by DSSP.
static java.lang.String	threeLetter three letter code, in alphabetical order.

Fields inherited from class org.strbio.mol.Monomer

atoms, n, type

Constructor Summary

Residue()
Constructor makes structure and predStructure '?'.

Residue(char t)
Make a new residue of a given type.

Residue(Residue q)
copy another residue, including the atoms.

Residue(java.lang.String t)
Make a new residue of a given type (3-letter code).

Method Summary

double	alpha() Alpha is the bond angle between CA(n-1), CA(n), CA(n+1).
void	copyDataFrom(Monomer q) copy another residue, including the atoms.
DLinkedList.Node	copyNode() copy contents of a residue
static boolean	is3Res(java.lang.String x) Is your string a valid 3-letter code?
boolean	isGap() is the character used to represent a gap?
static boolean	isGap(char x) Is a character a gap code?
static boolean	isRes(char x) Is your character a valid 1-letter code?
boolean	isValidType() is the character in 'type' valid for this residue?
void	makeVirtualCB() Construct a virtual CB atom.
double	molecularWeight() molecular weight for residue of a residue, minus 18 for the water missing in the peptide bond
static char	num2Res(int x) Convert a number to amino acid one letter code (0-20), in the order shown in Residue.oneLetter.
static char	num2ResDefay(int x) Convert a number to amino acid one letter code (0-20), in the order shown in Residue.oneLetterDefay.
static java.lang.String	one2Three(char x) Convert your 1-letter code into 3-letter code.
double	phi() Phi is the bond angle between C(n-1), N(n), CA(n), C(n).
double	psi() Psi is the bond angle between N(n), CA(n), C(n), N(n+1).
boolean	readAccess(java.io.BufferedReader infile) Read this residue out of an Access format file (Scott Presnell's format).
void	readAccessRecord(java.lang.String buffer) Read Access record out of YAPF file.
void	readAngleRecord(java.lang.String buffer) Read pre-calc angles out of YAPF file.
boolean	readConv(java.io.BufferedReader infile) Read this residue out of a Conv format file (Tom Defay's format).
boolean	readDSSP(java.io.BufferedReader infile) Read this residue out of a DSSP (Dictionary of Secondary Structure for Proteins) format file (Kabsch & Sander's format).
void	readDSSPRecord(java.lang.String buffer) Read DSSP record out of YAPF file.
boolean	readEA(java.io.BufferedReader infile) Read this residue out of a EA (Estimated Accuracy) format file (JMC's format).
void	readJMCSTR(java.lang.String buffer) Get info for this residue out of a JMCSTR line in a PDB or YAPF file.
void	readPredSSRecord(java.lang.String buffer) Read predicted SS info out of YAPF file.
boolean	readProf(java.io.BufferedReader infile) Read this residue out of a Prof (sequence profile) format file (JMC's format).
boolean	readVar(java.io.BufferedReader infile) Read this residue out of a Var format file (Tom Defay's format).
boolean	readVar2(java.io.BufferedReader infile) Read this residue out of a Var2 format file (Tom Defay's format).
void	readVarTomRecord(java.lang.String buffer) Read VarTom record out of YAPF file.
static int	res2Num(char x) Convert an amino acid one letter code to a number (0-20), in the order shown in Residue.oneLetter.
static int	res2NumDefay(char x) Convert an amino acid one letter code to a number (0-20), in the order shown in Residue.oneLetterDefay.
void	stripAllButCA() Strip away all atoms except alpha carbons (atoms named "CA").
double	tau() Tau is the dihedral angle between CA(n-1), CA(n), CA(n+1), CA(n+2).
static char	three2One(java.lang.String x) Convert your 3-letter code into 1-letter code.
void	translateEA() Translates predH and predE into predStructure (directly).
java.lang.String	typeName() Return a long name for this monomer, based on the type.
void	writeAccessRecord(Printf outfile) Write ACCESS record to YAPF file.
void	writeAngleRecord(Printf outfile) Write ANGLE record to YAPF file.
void	writeCASP(Printf outfile) Writes out this residue in CASP format.
void	writeConv(Printf outfile) Writes out this residue in Conv format.
void	writeDSSPRecord(Printf outfile) Write DSSP record to YAPF file.
void	writeEA(Printf outfile) Writes out this residue in EA format.
void	writePDBStr(Printf outfile) Writes out PDB JMCSTR records for this residue.
void	writePredSSRecord(Printf outfile) Write PREDSS record to YAPF file.
void	writeVar2(Printf outfile) Writes out this residue in Var2 format.
void	writeVarTomRecord(Printf outfile) Write VarTom record to YAPF file.

Methods inherited from class org.strbio.mol.Monomer

atomSearch, centerOfMass, centerOfMass, copyAtoms, isValidNonGap, nAtoms, nAtomsWithCoord, next, prev, readAtomRecord, readFasta, readSeqRecord, rotate, setNext, setPrev, stripAllAtoms, stripAllBut, stripAllButFirstAtom, stripAtomsByName, transform, translate, writePDBAtom, writePts, writeSeqRecord, writeYAPFAtom

Methods inherited from class java.lang.Object

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

Field Detail

oneLetter

public static final java.lang.String oneLetter

one letter code, in alphabetical order by 3-letter code. Note 0 = NUL. This is the order used by my letter/number conversion functions.

See Also:

res2Num(char), num2Res(int), isRes(char), Constant Field Values

oneLetterDefay

public static final java.lang.String oneLetterDefay

one letter code, in alphabetical order by 1-letter code. Note 0 = NUL. This is the order used by the letter/number conversion functions which were written to read/write Tom Defay's file formats.

See Also:

res2NumDefay(char), num2ResDefay(int), Constant Field Values

threeLetter

public static final java.lang.String threeLetter

three letter code, in alphabetical order. Note 0 = NUL. This is the order used by my letter/number conversion functions. I haven't written any to convert directly; you have to convert to three <--> one <--> number.

See Also:

three2One(java.lang.String), one2Three(char), is3Res(java.lang.String), Constant Field Values

aaMolecularWeight

public static final double[] aaMolecularWeight

molecular weight of each residue above

oneLetterBLAST

public static final java.lang.String oneLetterBLAST

one letter code used by BLAST. Note that not all of these are actual residues.

See Also:

Constant Field Values

structure

public char structure

the structure, as defined by DSSP. Examples include H for helix, E for extended beta strand, T for turn. Everything not H or E is considered coil. Default is '?'.

predStructure

public char predStructure

Predicted secondary structure. Default is '?'.

predH

public double predH

Predicted helix probability. Range is 0.0 to 1.0. Coil probability is 1.0 - predH - predE. Default is 0.0.

predE

public double predE

Predicted strand probability. Range is 0.0 to 1.0. Coil probability is 1.0 - predH - predE. Default is 0.0.

cPhi

public double cPhi

Pre-calculated phi angle at this residue. This is here because some file formats like to keep track of the dihedral angles, but throw away the actual atoms they were calculated from. Default is NaN.

See Also:

phi()

cPsi

public double cPsi

Pre-calculated psi angle at this residue. This is here because some file formats like to keep track of the dihedral angles, but throw away the actual atoms they were calculated from. Default is NaN.

See Also:

psi()

cAlpha

public double cAlpha

Pre-calculated alpha angle at this residue. This is here because some file formats like to keep track of the dihedral angles, but throw away the actual atoms they were calculated from. Default is NaN.

See Also:

alpha()

cTau

public double cTau

Pre-calculated tau angle at this residue. This is here because some file formats like to keep track of the dihedral angles, but throw away the actual atoms they were calculated from. Default is NaN.

See Also:

tau()

exposedArea

public double exposedArea

Area of the residue (in square angstroms) exposed to solvent, as calculated from Scott Presnell's access program. Default is NaN.

pctExposed

public double pctExposed

Percentage of surface-exposed area, from 0 - 100.0. The default is NaN, indicating unknown environment.

env

public int env

Environment code. From Access, -1 (default) is unknown. 0=buried, 1=intermediate, 2=exposed. The boundaries used by Defay between categories are at 7.2% exposed, and 28.9% exposed. From var-tom, codes range from -5 to -2 and have to do with how much variation there is in the hydrophillic and hydrophobic residues in a profile at this position.

Constructor Detail

Residue

public Residue()

Constructor makes structure and predStructure '?'.

Residue

public Residue(char t)

Make a new residue of a given type.

Residue

public Residue(java.lang.String t)

Make a new residue of a given type (3-letter code).

Residue

public Residue(Residue q)

copy another residue, including the atoms. This makes another copy of the data.

Method Detail

isRes

public static final boolean isRes(char x)

Is your character a valid 1-letter code?

isGap

public static final boolean isGap(char x)

Is a character a gap code?

is3Res

public static final boolean is3Res(java.lang.String x)

Is your string a valid 3-letter code? Note that it has to be capitalized. There is a bug in this code; strings like "ALA ARG" or even "A A" will return true, but it works fine for all 3-letter strings without spaces.

three2One

public static final char three2One(java.lang.String x)
                            throws java.lang.IllegalArgumentException

Convert your 3-letter code into 1-letter code. Note that it has to be capitalized. There is a bug in this code; strings like "ALA ARG" or even "A A" will return values, but it works fine for all 3-letter strings without spaces. If you want to know if something can be converted, use is3Res.

Throws:

java.lang.IllegalArgumentException - if your String is not a valid AA.

See Also:

is3Res(java.lang.String)

copyDataFrom

public void copyDataFrom(Monomer q)

copy another residue, including the atoms.

Overrides:

copyDataFrom in class Monomer

copyNode

public DLinkedList.Node copyNode()

copy contents of a residue

Specified by:

copyNode in interface DLinkedList.Node

Overrides:

copyNode in class Monomer

res2Num

public static final int res2Num(char x)
                         throws java.lang.IllegalArgumentException

Convert an amino acid one letter code to a number (0-20), in the order shown in Residue.oneLetter. Also, maps B->N and Z->E. (B indicates somebody didn't know if it was a N or D, and Z indicates either E or Q). If you want to know if something can be converted, use isRes.

Throws:

java.lang.IllegalArgumentException - if your code isn't an AA.

See Also:

oneLetter, isRes(char)

res2NumDefay

public static final int res2NumDefay(char x)
                              throws java.lang.IllegalArgumentException

Convert an amino acid one letter code to a number (0-20), in the order shown in Residue.oneLetterDefay. Also, maps B->N and Z->E. (B indicates somebody didn't know if it was a N or D, and Z indicates either E or Q). If you want to know if something can be converted, use isRes.

Throws:

java.lang.IllegalArgumentException - if your code isn't an AA.

See Also:

oneLetterDefay, isRes(char)

num2Res

public static final char num2Res(int x)
                          throws java.lang.IllegalArgumentException

Convert a number to amino acid one letter code (0-20), in the order shown in Residue.oneLetter.

Throws:

java.lang.IllegalArgumentException - if your number is not 0-20.

See Also:

oneLetter

num2ResDefay

public static final char num2ResDefay(int x)
                               throws java.lang.IllegalArgumentException

Convert a number to amino acid one letter code (0-20), in the order shown in Residue.oneLetterDefay.

Throws:

java.lang.IllegalArgumentException - if your number is not 0-20.

See Also:

oneLetterDefay

one2Three

public static final java.lang.String one2Three(char x)
                                        throws java.lang.IllegalArgumentException

Convert your 1-letter code into 3-letter code. Note that it has to be capitalized. Also, maps B->ASN and Z->GLN. (B indicates somebody didn't know if it was a ASN or ASP, and Z indicates either GLU or GLN). If you want to know if something can be converted, use isRes.

Throws:

java.lang.IllegalArgumentException - if your character is not a valid AA.

See Also:

isRes(char)

typeName

public java.lang.String typeName()

Return a long name for this monomer, based on the type. The default is to just return a string of whatever's in 'type', but that should be overridden for Residues, Bases, etc. (i.e. 'C' -> "CYS" for Residues).

Overrides:

typeName in class Monomer

stripAllButCA

public final void stripAllButCA()

Strip away all atoms except alpha carbons (atoms named "CA").

readVar2

public final boolean readVar2(java.io.BufferedReader infile)

Read this residue out of a Var2 format file (Tom Defay's format). If the next line of input in the file is not in the right format, it resets the file back to before the line, and returns false. If the residue is successfully read in, the line is consumed, and the function returns true.

See Also:

Protein.readVar2(java.io.BufferedReader, org.strbio.io.Printf)

readVar

public final boolean readVar(java.io.BufferedReader infile)

Read this residue out of a Var format file (Tom Defay's format). If the next line of input in the file is not in the right format, it resets the file back to before the line, and returns false. If the residue is successfully read in, the line is consumed, and the function returns true.

See Also:

Protein.readVar(java.io.BufferedReader, org.strbio.io.Printf)

readAccess

public final boolean readAccess(java.io.BufferedReader infile)

Read this residue out of an Access format file (Scott Presnell's format). This searches for "ATOM 0 T " records, and translates the accessibility found for the residue into an environmental class using Tom Defay's scale. If a residue is successfully read in, the function returns true. If an 'END' is found first, or the end of the file, it returns false.

See Also:

Protein.readAccess(java.io.BufferedReader, org.strbio.io.Printf)

readEA

public final boolean readEA(java.io.BufferedReader infile)

Read this residue out of a EA (Estimated Accuracy) format file (JMC's format). If the next line of input in the file is not in the right format, it resets the file back to before the line, and returns false. If the residue is successfully read in, the line is consumed, and the function returns true.

See Also:

Protein.readEA(java.io.BufferedReader, org.strbio.io.Printf)

readConv

public final boolean readConv(java.io.BufferedReader infile)

Read this residue out of a Conv format file (Tom Defay's format). If the next line of input in the file is not in the right format, it resets the file back to before the line, and returns false. If the residue is successfully read in, the line is consumed, and the function returns true.

See Also:

Protein.readConv(java.io.BufferedReader, org.strbio.io.Printf)

readJMCSTR

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

Get info for this residue out of a JMCSTR line in a PDB or YAPF file.

Throws:

java.io.IOException

readPredSSRecord

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

Read predicted SS info out of YAPF file.

Throws:

java.io.IOException

writePredSSRecord

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

Write PREDSS record to YAPF file.

Throws:

java.io.IOException

readDSSPRecord

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

Read DSSP record out of YAPF file.

Throws:

java.io.IOException

writeDSSPRecord

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

Write DSSP record to YAPF file.

Throws:

java.io.IOException

readAccessRecord

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

Read Access record out of YAPF file.

Throws:

java.io.IOException

writeAccessRecord

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

Write ACCESS record to YAPF file.

Throws:

java.io.IOException

readVarTomRecord

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

Read VarTom record out of YAPF file.

Throws:

java.io.IOException

writeVarTomRecord

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

Write VarTom record to YAPF file.

Throws:

java.io.IOException

readAngleRecord

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

Read pre-calc angles out of YAPF file.

Throws:

java.io.IOException

writeAngleRecord

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

Write ANGLE record to YAPF file.

Throws:

java.io.IOException

readProf

public boolean readProf(java.io.BufferedReader infile)

Read this residue out of a Prof (sequence profile) format file (JMC's format). If the next line of input in the file is not in the right format, it resets the file back to before the line, and returns false. If the residue is successfully read in, the line is consumed, and the function returns true. All profile information is thrown away, since there's no field to store it in.

readDSSP

public final boolean readDSSP(java.io.BufferedReader infile)
                       throws java.io.IOException

Read this residue out of a DSSP (Dictionary of Secondary Structure for Proteins) format file (Kabsch & Sander's format). If the next line of input in the file is not in the right format, it resets the file back to before the line, and returns false. If the residue is successfully read in, the line is consumed, and the function returns true. Only the number, type, structure, and chainID information are paid attention to. chainID is returned in the predStructure field, and should be processed by Protein.readDSSP.

Throws:

java.io.IOException

See Also:

Protein.readDSSP(java.io.BufferedReader, org.strbio.io.Printf)

writeEA

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

Writes out this residue in EA format.

Throws:

java.io.IOException

See Also:

Protein.writeEA(org.strbio.io.Printf)

translateEA

public final void translateEA()

Translates predH and predE into predStructure (directly).

writeCASP

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

Writes out this residue in CASP format.

Throws:

java.io.IOException

See Also:

Protein.writeCASP(org.strbio.io.Printf)

writeConv

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

Writes out this residue in Conv format. If any pre-calculated angles (i.e. c_phi) are undefined (Float.NaN) then it prints 1000.000000 to the file in their place.

Throws:

java.io.IOException

See Also:

Protein.writeConv(org.strbio.io.Printf)

writeVar2

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

Writes out this residue in Var2 format.

Throws:

java.io.IOException

See Also:

Protein.writeVar2(org.strbio.io.Printf)

writePDBStr

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

Writes out PDB JMCSTR records for this residue. These records have same info as in EA files, plus pre-calculated dihedral angles. If any of the latter are Double.NaN, it indicates this by printing 1000.000000. This function is really slow and gets called a lot, so has been optimized. Original code is left in comments.

Throws:

java.io.IOException

See Also:

Protein.writePDB(org.strbio.io.Printf, boolean)

alpha

public final double alpha()

Alpha is the bond angle between CA(n-1), CA(n), CA(n+1). Returns Double.NaN if any info is missing. This info has been precalculated for some file formats.

tau

public final double tau()

Tau is the dihedral angle between CA(n-1), CA(n), CA(n+1), CA(n+2). Returns Double.NaN if any info is missing. This info has been precalculated for some file formats.

phi

public final double phi()

Phi is the bond angle between C(n-1), N(n), CA(n), C(n). Returns Double.NaN if any info is missing. This info has been precalculated for some file formats.

psi

public final double psi()

Psi is the bond angle between N(n), CA(n), C(n), N(n+1). Returns Double.NaN if any info is missing. This info has been precalculated for some file formats.

isValidType

public boolean isValidType()

is the character in 'type' valid for this residue?

Overrides:

isValidType in class Monomer

isGap

public boolean isGap()

is the character used to represent a gap?

Overrides:

isGap in class Monomer

makeVirtualCB

public void makeVirtualCB()

Construct a virtual CB atom. N, C, and CA atoms are needed.

molecularWeight

public double molecularWeight()

molecular weight for residue of a residue, minus 18 for the water missing in the peptide bond

Overrides:

molecularWeight in class Monomer