/**
* Returns the chemical property string for this chain in the 5 types system, but considers only
* AA residues which are part of an SSE (ignores ligands and AAs in coiled regions).
*
* @param sseSeparator the String (most likely a single character) to add between two SSEs. You
* can specify the empty String if you do not want anything inserted, of course.
* @return the chemical property string, 5 types system
*/
public String[] getChainChemPropsStringSSEResiduesOnly(String sseSeparator) {
StringBuilder sbChemProp = new StringBuilder();
StringBuilder sbSSE = new StringBuilder();
SSE s;
String sseString = null;
String sseStringlast = null;
int numSeps = 0;
// some basic stat stuff, just a quick test
int numSSETypes = 2;
int H = 0;
int E = 1; // helix and strand
int numResH = 0;
int numResE = 0;
Integer[][] chemPropsBySSEType = new Integer[numSSETypes][AminoAcid.ALL_CHEM_PROPS5.length];
for (int i = 0; i < numSSETypes; i++) {
Arrays.fill(chemPropsBySSEType[i], 0);
}
for (Residue r : this.residues) {
if (r.isAA()) {
s = r.getSSE();
if (s != null) {
if (s.isOtherSSE()) {
continue;
}
sseString = s.getSSEClass();
if (sseStringlast != null
&& (sseString == null ? sseStringlast != null : !sseString.equals(sseStringlast))) {
sbChemProp.append(sseSeparator);
sbSSE.append(sseSeparator);
numSeps++;
}
sbChemProp.append(r.getChemicalProperty5OneLetterString());
if (sseString.equals("H")) {
numResH++;
chemPropsBySSEType[H][r.getChemicalProperty5Type()]++;
}
if (sseString.equals("E")) {
numResE++;
chemPropsBySSEType[E][r.getChemicalProperty5Type()]++;
}
sbSSE.append(s.getSSEClass());
}
sseStringlast = sseString;
}
}
// stat stuff
Boolean doStats = false;
if (doStats) {
float[] sharesH = new float[AminoAcid.ALL_CHEM_PROPS5.length];
float[] sharesE = new float[AminoAcid.ALL_CHEM_PROPS5.length];
for (int i = 0; i < AminoAcid.ALL_CHEM_PROPS5.length; i++) {
sharesH[i] = (float) numResH / (float) chemPropsBySSEType[H][i];
sharesE[i] = (float) numResE / (float) chemPropsBySSEType[E][i];
}
System.out.println(
"Chain: chemType by SSEtype[H]: totalH="
+ numResH
+ ", shares: "
+ IO.floatArrayToString(sharesH));
System.out.println(
"Chain: chemType by SSEtype[E]: totalE="
+ numResE
+ ", shares: "
+ IO.floatArrayToString(sharesE));
}
// System.out.println("Added " + numSeps + " separators.");
return new String[] {sbChemProp.toString(), sbSSE.toString()};
}
/**
* Change the value of a constraint
*
* @param c the integer representation of the constraint as defined in ConstraintParam
* @param v whether the constraint should be enabled or disabled
*/
public void put(int c, boolean v) {
if (constraints.containsKey(c)) constraints.put(c, v);
else IO.error("Warning: trying to add a constraint that has a undefined description. Ignored");
}