public class DSSP
extends java.lang.Object
Modifier and Type | Field | 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 boolean |
isDSSP2 |
|
private char[][] |
labels |
|
private boolean |
setStructure |
|
private int[][] |
sheetOffsets |
|
private javajs.util.Lst<Bond> |
vHBonds |
Constructor | Description |
---|---|
DSSP() |
Modifier and Type | Method | 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,
int version) |
|
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 mmtfType,
int iPolymer,
int pitch,
int[][][] min,
STR subtype,
int type,
BS bsTurn,
boolean isFirst) |
|
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 |
setTag(char[] tags,
BS bs,
char ch) |
private BioPolymer[] bioPolymers
private javajs.util.Lst<Bond> vHBonds
private BS[] done
private boolean doReport
private boolean dsspIgnoreHydrogens
private boolean setStructure
private char[][] labels
private BS bsBad
private int bioPolymerCount
private java.util.Map<java.lang.String,Bridge> htBridges
private java.util.Map<int[][],java.lang.Boolean> htLadders
private javajs.util.Lst<Bridge> bridgesA
private javajs.util.Lst<Bridge> bridgesP
private boolean isDSSP2
private int[][] sheetOffsets
public java.lang.String calculateDssp(java.lang.Object[] objBioPolymers, int bioPolymerCount, java.lang.Object objVHBonds, boolean doReport, boolean dsspIgnoreHydrogens, boolean setStructure, int version)
objBioPolymers
- bioPolymerCount
- objVHBonds
- doReport
- dsspIgnoreHydrogens
- setStructure
- version
- can be 2.0 to reverse order of helix calculation and emphasize pi-helicesprivate int[][][][] getDualHydrogenBondArray()
private void getBridges(int[][][][] min)
min
- 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 addHbond(Monomer donor, Monomer acceptor, int iEnergy, int type, java.util.Map<java.lang.String,java.lang.Boolean> htTemp)
private void getSheetStructures()
private void createLadders(javajs.util.Lst<Bridge> bridges, boolean isAntiparallel)
bridges
- isAntiparallel
- private boolean checkBridge(Bridge bridge, boolean isAntiparallel, int n1, int n2)
bridge
- isAntiparallel
- n1
- n2
- private void checkBulge(Bridge bridge, boolean isAntiparallel, int dir)
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 int[] isHbonded(int indexDonor, int indexAcceptor, int pDonor, int pAcceptor, int[][][][] min)
private java.lang.String findHelixes(int iPolymer, int[][][] min)
min
- iPolymer
- private java.lang.String findHelixes2(int mmtfType, int iPolymer, int pitch, int[][][] min, STR subtype, int type, BS bsTurn, boolean isFirst)
private void setTag(char[] tags, BS bs, char ch)