org.jmol.dssx

Class DSSP

java.lang.Object

org.jmol.dssx.DSSP

All Implemented Interfaces:

DSSPInterface

public class DSSP
extends java.lang.Object
implements DSSPInterface

Field Summary

Fields

Modifier and Type	Field and Description
private int	bioPolymerCount
private BioPolymer[]	bioPolymers
private javajs.util.Lst<Bridge>	bridgesA
private javajs.util.Lst<Bridge>	bridgesP
private BS	bsBad
private BS[]	done
private boolean	doReport
private boolean	dsspIgnoreHydrogens
private java.util.Map<java.lang.String,Bridge>	htBridges
private java.util.Map<int[][],java.lang.Boolean>	htLadders
private char[][]	labels
private boolean	setStructure
private int[][]	sheetOffsets
private javajs.util.Lst<Bond>	vHBonds

Constructor Summary

Constructors

Constructor and Description
DSSP()

Method Summary

Modifier and Type	Method and Description
private void	addHbond(Monomer donor, Monomer acceptor, int iEnergy, int type, java.util.Map<java.lang.String,java.lang.Boolean> htTemp)
java.lang.String	calculateDssp(java.lang.Object[] objBioPolymers, int bioPolymerCount, java.lang.Object objVHBonds, boolean doReport, boolean dsspIgnoreHydrogens, boolean setStructure)
private boolean	checkBridge(Bridge bridge, boolean isAntiparallel, int n1, int n2) check to see if another bridge exists offset by n1 and n2 from the two ends of a bridge
private void	checkBulge(Bridge bridge, boolean isAntiparallel, int dir)
private void	createLadders(javajs.util.Lst<Bridge> bridges, boolean isAntiparallel) "ladder =: one or more consecutive bridges of identical type" (p.
private java.lang.String	dumpSummary(AminoPolymer ap, char[] labels)
private java.lang.String	dumpTags(AminoPolymer ap, java.lang.String lines, BS bsBad, int mode)
private java.lang.String	findHelixes(int iPolymer, int[][][] min) (p.
private java.lang.String	findHelixes2(int iPolymer, int pitch, int[][][] min, STR subtype, int type, BS bsTurn)
private Bridge	getBridge(int[][][][] min, int p1, int a, int p2, int b, javajs.util.Lst<Bridge> bridges, Atom atom1, Atom atom2, AminoPolymer ap1, AminoPolymer ap2, java.util.Map<java.lang.String,java.lang.Boolean> htTemp, boolean isAntiparallel)
private void	getBridges(int[][][][] min) (p.
private int[][][][]	getDualHydrogenBondArray() (p.
private void	getSheetStructures() "sheet =: a set of one or more ladders connected by shared residues" (p.
private int[]	isHbonded(int indexDonor, int indexAcceptor, int pDonor, int pAcceptor, int[][][][] min)
private void	setStructure(AminoPolymer ap, BS bs, STR type)
private void	setTag(char[] tags, BS bs, char ch)

Methods inherited from class java.lang.Object

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

Field Detail

bioPolymers

private BioPolymer[] bioPolymers

vHBonds

private javajs.util.Lst<Bond> vHBonds

done

private BS[] done

doReport

private boolean doReport

dsspIgnoreHydrogens

private boolean dsspIgnoreHydrogens

setStructure

private boolean setStructure

labels

private char[][] labels

bsBad

private BS bsBad

bioPolymerCount

private int bioPolymerCount

htBridges

private java.util.Map<java.lang.String,Bridge> htBridges

htLadders

private java.util.Map<int[][],java.lang.Boolean> htLadders

bridgesA

private javajs.util.Lst<Bridge> bridgesA

bridgesP

private javajs.util.Lst<Bridge> bridgesP

sheetOffsets

private int[][] sheetOffsets

Constructor Detail

DSSP

public DSSP()

Method Detail

calculateDssp

public java.lang.String calculateDssp(java.lang.Object[] objBioPolymers,
                                      int bioPolymerCount,
                                      java.lang.Object objVHBonds,
                                      boolean doReport,
                                      boolean dsspIgnoreHydrogens,
                                      boolean setStructure)

Specified by:

calculateDssp in interface DSSPInterface

Parameters:

objBioPolymers -

bioPolymerCount -

objVHBonds -

doReport -

dsspIgnoreHydrogens -

setStructure -

Returns:

helix-5, helix-4, helix-3, and SUMMARY lines

getDualHydrogenBondArray

private int[][][][] getDualHydrogenBondArray()

(p. 2579): Hydrogen bonds in proteins have little wave-function overlap and are well described by an electromodel: E = q1q2(1/r(ON) + 1/r(CH) - 1/r(OH) - 1/r(CN)) * f with q1 = 0.42e and q2 = 0.20e, e being the unit electron charge and r(AB) the interatomic distance from A to B. In chemical units, r is in angstroms, the dimensional factor f = 332, and E is in kcal/mol. We ... assign an H bond between C=O of residue i and N-H of residue j if E is less than the cutoff, i.e., "Hbond(i,j) =: [E < -0.5 kcal/mol]."

Returns:

array of dual-minmum NH-->O=C H bonds

getBridges

private void getBridges(int[][][][] min)

(p. 2581): Two nonoverlapping stretches of three residues each, i-1,i,i+1 and j-1,j,j+1, form either a parallel or antiparallel bridge, depending on which of two basic patterns (Fig. 2) is matched. We assign a bridge between residues i and j if there are two H bonds characteristic of beta-structure; in particular: Parallel Bridge(i,j) =: [Hbond(i-1,j) and Hbond(j,i+1)] or [Hbond(j-1,i) and Hbond(i,j+1)] Antiparallel Bridge(i,j) =: [Hbond(i,j) and Hbond(j,i)] or [Hbond(i-1,j+1) and Hbond(j-1,i+1)]

Parameters:

min -

getBridge

private Bridge getBridge(int[][][][] min,
                         int p1,
                         int a,
                         int p2,
                         int b,
                         javajs.util.Lst<Bridge> bridges,
                         Atom atom1,
                         Atom atom2,
                         AminoPolymer ap1,
                         AminoPolymer ap2,
                         java.util.Map<java.lang.String,java.lang.Boolean> htTemp,
                         boolean isAntiparallel)

addHbond

private void addHbond(Monomer donor,
                      Monomer acceptor,
                      int iEnergy,
                      int type,
                      java.util.Map<java.lang.String,java.lang.Boolean> htTemp)

getSheetStructures

private void getSheetStructures()

"sheet =: a set of one or more ladders connected by shared residues" (p. 2582)

createLadders

private void createLadders(javajs.util.Lst<Bridge> bridges,
                           boolean isAntiparallel)

"ladder =: one or more consecutive bridges of identical type" (p. 2582) "For beta structures, we define explicitly: a bulge-linked ladder consists of two (perfect) ladder or bridges of the same type connected by at most one extra residue on one strand and at most four extra resideus on the other strand.... all residues in bulge-linked ladders are marked "E," including the extra residues." (p. 2585)

Parameters:

bridges -

isAntiparallel -

checkBridge

private boolean checkBridge(Bridge bridge,
                            boolean isAntiparallel,
                            int n1,
                            int n2)

check to see if another bridge exists offset by n1 and n2 from the two ends of a bridge

Parameters:

bridge -

isAntiparallel -

n1 -

n2 -

Returns:

TRUE if bridge is part of a ladder

checkBulge

private void checkBulge(Bridge bridge,
                        boolean isAntiparallel,
                        int dir)

dumpSummary

private java.lang.String dumpSummary(AminoPolymer ap,
                                     char[] labels)

dumpTags

private java.lang.String dumpTags(AminoPolymer ap,
                                  java.lang.String lines,
                                  BS bsBad,
                                  int mode)

isHbonded

private int[] isHbonded(int indexDonor,
                        int indexAcceptor,
                        int pDonor,
                        int pAcceptor,
                        int[][][][] min)

findHelixes

private java.lang.String findHelixes(int iPolymer,
                                     int[][][] min)

(p. 2581): A basic turn pattern (Fig. 2) is a single H bond of type (i,i+n). We assign an n-turn at residue i if there is an H bond from CO(i) to NH(i+n).... When the pattern is found, the ends of the H bond are indicated using ">" at i and "<" at i+n...; the residues bracketed by the H bond are noted "3," "4," or "5" unless they are also end points of other H bonds. Coincidence of ">" and "<" at one residue is indicated by "X." ... Residues bracketed by the hydrogen bond are marked "T," unless they are part of an n-helix (defined below). (p. 2582): A minimal helix is defined by two consecutive n-turns.... Longer helices are defined as overlaps of minimal helices.... Residues bracketed by H bonds are labeled G, H, I.... Long helices can deviate from regularity in that not all possible H bonds are formed. This possibility is implicit in the above helix definition.

Parameters:

min -

iPolymer -

Returns:

string label

findHelixes2

private java.lang.String findHelixes2(int iPolymer,
                                      int pitch,
                                      int[][][] min,
                                      STR subtype,
                                      int type,
                                      BS bsTurn)

setTag

private void setTag(char[] tags,
                    BS bs,
                    char ch)

setStructure

private void setStructure(AminoPolymer ap,
                          BS bs,
                          STR type)