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josemduartejosemduarte
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Merge pull request biojava#790 from biocryst/master
SecStrucCalc - Logger string formatting changed to brackets.
2 parents 8a7b651 + a6012cd commit 1beedcb

1 file changed

Lines changed: 18 additions & 23 deletions

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‎biojava-structure/src/main/java/org/biojava/nbio/structure/secstruc/SecStrucCalc.java‎

Lines changed: 18 additions & 23 deletions
Original file line numberDiff line numberDiff line change
@@ -230,7 +230,7 @@ private void createLadders(){
230230

231231
private void updateSheets() {
232232

233-
logger.debug(" got " +ladders.size() + " ladders!");
233+
logger.debug(" got {} ladders!", ladders.size());
234234

235235
for (Ladder ladder : ladders){
236236
logger.debug(ladder.toString());
@@ -308,7 +308,7 @@ private void connectLadders() {
308308
if (hasBulge(l1,l2)) {
309309
l1.connectedTo = j;
310310
l2.connectedFrom = i;
311-
logger.debug("Bulge from " + i + " to " + j);
311+
logger.debug("Bulge from {} to {}", i, j);
312312
}
313313
}
314314
}
@@ -362,8 +362,7 @@ private void registerBridge(int i, int j, BridgeType btype) {
362362
boolean b2 = getSecStrucState(j).addBridge(bridge);
363363

364364
if (!b1 && !b2)
365-
logger.warn("Ignoring Bridge between residues" + i + " and " + j
366-
+ ". DSSP assignment might differ.");
365+
logger.warn("Ignoring Bridge between residues {} and {}. DSSP assignment might differ.", i, j);
367366

368367
bridges.add(bridge);
369368
}
@@ -799,11 +798,11 @@ private void checkAddHBond(int i, int j){
799798
SecStrucGroup one = groups[i];
800799

801800
if (one.getPDBName().equals("PRO")){
802-
logger.debug("Ignore: PRO " + one.getResidueNumber());
801+
logger.debug("Ignore: PRO {}", one.getResidueNumber());
803802
return;
804803
}
805804
if (!one.hasAtom("H")) {
806-
logger.debug("Residue "+one.getResidueNumber()+" has no H");
805+
logger.debug("Residue {} has no H",one.getResidueNumber());
807806
return;
808807
}
809808

@@ -817,7 +816,7 @@ private void checkAddHBond(int i, int j){
817816
logger.warn("Energy calculation failed", e);
818817
return;
819818
}
820-
logger.debug("Energy between positions ("+i+","+j+"): "+energy);
819+
logger.debug("Energy between positions ({},{}): ",i,j,energy);
821820

822821
trackHBondEnergy(i,j,energy);
823822
}
@@ -848,12 +847,9 @@ private static double calculateHBondEnergy(SecStrucGroup one,
848847
double dho = Calc.getDistance(O,H);
849848
double dnc = Calc.getDistance(C,N);
850849

851-
logger.debug(" cccc: " + one.getResidueNumber() +
852-
" " + one.getPDBName() + " " +two.getResidueNumber()+
853-
" " + two.getPDBName() + String.format(" O ("+
854-
O.getPDBserial()+")..N ("+ N.getPDBserial()+
855-
"):%4.1f | ho:%4.1f - hc:%4.1f + nc:%4.1f - no:%4.1f ",
856-
dno,dho,dhc,dnc,dno));
850+
logger.debug(" cccc: {} {} {} {} O ({})..N ({}):{} | ho:{} - hc:{} + nc:{} - no:{}",
851+
one.getResidueNumber(),one.getPDBName(),two.getResidueNumber(),two.getPDBName(),
852+
O.getPDBserial(),N.getPDBserial(),dno,dho,dhc,dnc,dno);
857853

858854
//there seems to be a contact!
859855
if ( (dno < MINDIST) || (dhc < MINDIST) ||
@@ -866,8 +862,7 @@ private static double calculateHBondEnergy(SecStrucGroup one,
866862

867863
double energy = e1 + e2;
868864

869-
logger.debug(String.format(" N (%d) O(%d): %4.1f : %4.2f ",
870-
N.getPDBserial(),O.getPDBserial(), (float) dno, energy));
865+
logger.debug(" N ({}) O({}): {} : {} ",N.getPDBserial(),O.getPDBserial(),(float) dno,energy);
871866

872867
//Avoid too strong energy
873868
if (energy > HBONDLOWENERGY) return energy;
@@ -882,7 +877,7 @@ private static double calculateHBondEnergy(SecStrucGroup one,
882877
private void trackHBondEnergy(int i, int j, double energy) {
883878

884879
if (groups[i].getPDBName().equals("PRO")) {
885-
logger.debug("Ignore: PRO " + groups[i].getResidueNumber());
880+
logger.debug("Ignore: PRO {}",groups[i].getResidueNumber());
886881
return;
887882
}
888883

@@ -897,7 +892,7 @@ private void trackHBondEnergy(int i, int j, double energy) {
897892

898893
//Acceptor: N-H-->O
899894
if (energy < acc1e) {
900-
logger.debug(energy +"<"+acc1e);
895+
logger.debug("{} < {}",energy,acc1e);
901896
stateOne.setAccept2(stateOne.getAccept1());
902897

903898
HBond bond = new HBond();
@@ -907,7 +902,7 @@ private void trackHBondEnergy(int i, int j, double energy) {
907902
stateOne.setAccept1(bond);
908903

909904
} else if ( energy < acc2e ) {
910-
logger.debug(energy +"<"+acc2e);
905+
logger.debug("{} < {}",energy,acc2e);
911906

912907
HBond bond = new HBond();
913908
bond.setEnergy(energy);
@@ -919,7 +914,7 @@ private void trackHBondEnergy(int i, int j, double energy) {
919914

920915
//The other side of the bond: donor O-->N-H
921916
if (energy < don1e) {
922-
logger.debug(energy +"<"+don1e);
917+
logger.debug("{} < {}",energy,don1e);
923918
stateTwo.setDonor2(stateTwo.getDonor1());
924919

925920
HBond bond = new HBond();
@@ -929,7 +924,7 @@ private void trackHBondEnergy(int i, int j, double energy) {
929924
stateTwo.setDonor1(bond);
930925

931926
} else if ( energy < don2e ) {
932-
logger.debug(energy +"<"+don2e);
927+
logger.debug("{} < {}",energy,don2e);
933928

934929
HBond bond = new HBond();
935930
bond.setEnergy(energy);
@@ -951,7 +946,7 @@ private void calculateTurns(){
951946

952947
//Check for H bond from NH(i+n) to CO(i)
953948
if (isBonded(i, i+turn)) {
954-
logger.debug("Turn at ("+i+","+(i+turn)+") turn "+turn);
949+
logger.debug("Turn at ({},{}) turn {}",i,(i+turn),turn);
955950
getSecStrucState(i).setTurn('>', turn);
956951
getSecStrucState(i+turn).setTurn('<', turn);
957952
//Bracketed residues get the helix number
@@ -998,7 +993,7 @@ private boolean isBonded(int i, int j) {
998993
(acc2p == i && acc2e < HBONDHIGHENERGY);
999994

1000995
if (hbond){
1001-
logger.debug("*** H-bond from CO of " + i + " to NH of " + j);
996+
logger.debug("*** H-bond from CO of {} to NH of {}", i, j);
1002997
return true;
1003998
}
1004999
return false ;
@@ -1105,7 +1100,7 @@ private void checkSetTurns() {
11051100
private void checkSetHelix(int n, SecStrucType type){
11061101

11071102
int idx = n - 3;
1108-
logger.debug("Set helix " + type + " " + n + " " + idx);
1103+
logger.debug("Set helix {} {} {}", type, n, idx);
11091104

11101105
for (int i = 1; i < groups.length-n; i++) {
11111106

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