Class DSSP

Method Details

• calculateDssp

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

  Parameters:

  objBioPolymers -

  bioPolymerCount -

  objVHBonds -

  doReport -

  dsspIgnoreHydrogens -

  setStructure -

  version - can be 2.0 to reverse order of helix calculation and emphasize pi-helices

  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, Map<String,Boolean> htTemp, boolean isAntiparallel)

• addHbond

  private void addHbond(Monomer donor, Monomer acceptor, int iEnergy, int type, Map<String,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 String dumpSummary(AminoPolymer ap, char[] labels)

• dumpTags

  private String dumpTags(AminoPolymer ap, String lines, javajs.util.BS bsBad, int mode)

• isHbonded

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

• findHelixes

  private 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 String findHelixes2(int mmtfType, int iPolymer, int pitch, int[][][] min, STR subtype, int type, javajs.util.BS bsTurn, boolean isFirst)

• setTag

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