public class DSSP extends java.lang.Object implements DSSPInterface
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 and Description |
---|
DSSP() |
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) |
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 int[][] sheetOffsets
public java.lang.String calculateDssp(java.lang.Object[] objBioPolymers, int bioPolymerCount, java.lang.Object objVHBonds, boolean doReport, boolean dsspIgnoreHydrogens, boolean setStructure)
calculateDssp
in interface DSSPInterface
objBioPolymers
- bioPolymerCount
- objVHBonds
- doReport
- dsspIgnoreHydrogens
- setStructure
- private 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 iPolymer, int pitch, int[][][] min, STR subtype, int type, BS bsTurn)
private void setTag(char[] tags, BS bs, char ch)
private void setStructure(AminoPolymer ap, BS bs, STR type)