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Fix for issue 517 #541

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Merged
andreasprlic merged 5 commits into from
Jul 28, 2016
Merged

Fix for issue 517 #541

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bdca0e1
Now testing seqres groups in roundtrip
josemduarte Jul 26, 2016
e4cf7f8
Fixing #517
josemduarte Jul 27, 2016
fefb03d
Merge branch 'master' into fixIssue517
josemduarte Jul 27, 2016
4fa6833
Fixing issue introduced in PR #537
josemduarte Jul 27, 2016
347a8fc
Replacing the very old 1tap.pdb so that test logs aren't so long
josemduarte Jul 28, 2016
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Now testing seqres groups in roundtrip
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@josemduarte
josemduarte committed Jul 26, 2016
commit bdca0e1c21a386ffbd48fb45ec45442160b61a1d
27 changes: 20 additions & 7 deletions biojava-structure/src/test/java/org/biojava/nbio/structure/io/mmtf/TestMmtfRoundTrip.java
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Original file line number Diff line number Diff line change
Expand Up @@ -82,6 +82,7 @@ private boolean checkIfAtomsSame(Structure structOne, Structure structTwo) {
Chain chainTwo = chainsTwo.get(j);
// Check they have the same chain id
assertEquals(chainOne.getId(), chainTwo.getId());
checkSeqresGroups(chainOne, chainTwo);
List<Group> groupsOne = chainOne.getAtomGroups();
List<Group> groupsTwo = chainTwo.getAtomGroups();
if(groupsOne.size()!=groupsTwo.size()){
Expand All @@ -93,19 +94,20 @@ private boolean checkIfAtomsSame(Structure structOne, Structure structTwo) {
Group groupOne = groupsOne.get(k);
Group groupTwo = groupsTwo.get(k);
// Check if the groups are of the same type
if(groupOne.getType().equals(groupTwo.getType())==false){
if(!groupOne.getType().equals(groupTwo.getType())){
System.out.println("Error - diff group type: "+structOne.getPDBCode());
System.out.println(groupOne.getPDBName() + " and type: "+groupOne.getType());
System.out.println(groupTwo.getPDBName() + " and type: "+groupTwo.getType());;
}
// Check the single letter amino aicd is correct
// Check the single letter amino acid is correct
if(groupOne.getChemComp().getOne_letter_code().length()==1 && groupTwo.getChemComp().getOne_letter_code().length()==1){
if(!groupOne.getChemComp().getOne_letter_code().equals(groupTwo.getChemComp().getOne_letter_code())){
System.out.println(groupOne.getPDBName());
}
assertEquals(groupOne.getChemComp().getOne_letter_code(), groupTwo.getChemComp().getOne_letter_code());
}
assertEquals(groupOne.getType(), groupTwo.getType());
assertEquals(groupOne.getPDBName(), groupTwo.getPDBName());
assertEquals(groupOne.getResidueNumber().getSeqNum(), groupTwo.getResidueNumber().getSeqNum());
assertEquals(groupOne.getResidueNumber().getInsCode(), groupTwo.getResidueNumber().getInsCode());
assertEquals(groupOne.getResidueNumber().getChainName(), groupTwo.getResidueNumber().getChainName());
Expand Down Expand Up @@ -142,15 +144,15 @@ private boolean checkIfAtomsSame(Structure structOne, Structure structTwo) {
for(int l=0;l<atomsOne.size();l++){
Atom atomOne = atomsOne.get(l);
Atom atomTwo = atomsTwo.get(l);
assertTrue(atomOne.getGroup().getPDBName().equals(atomTwo.getGroup().getPDBName()));
assertTrue(atomOne.getCharge()==atomTwo.getCharge());
assertEquals(atomOne.getGroup().getPDBName(), atomTwo.getGroup().getPDBName());
assertEquals(atomOne.getCharge(), atomTwo.getCharge());
// Check the coords are the same to three db
assertArrayEquals(atomOne.getCoords(), atomTwo.getCoords(), 0.0009999999);
assertEquals(atomOne.getTempFactor(), atomTwo.getTempFactor(), 0.009999999);
assertEquals(atomOne.getOccupancy(), atomTwo.getOccupancy(), 0.009999999);
assertTrue(atomOne.getElement()==atomTwo.getElement());
assertTrue(atomOne.getName().equals(atomTwo.getName()));
assertTrue(atomOne.getAltLoc()==atomTwo.getAltLoc());
assertEquals(atomOne.getElement(), atomTwo.getElement());
assertEquals(atomOne.getName(),atomTwo.getName());
assertEquals(atomOne.getAltLoc(), atomTwo.getAltLoc());
if(i==0){
if(atomOne.getBonds()==null){
if(atomTwo.getBonds()!=null){
Expand Down Expand Up @@ -246,4 +248,15 @@ public int compare(Chain o1, Chain o2) {

}

private void checkSeqresGroups(Chain chainOne, Chain chainTwo) {

assertEquals(chainOne.getSeqResGroups().size(), chainTwo.getSeqResGroups().size());

for (int i=0; i<chainOne.getSeqResGroups().size(); i++) {
Group gOne = chainOne.getSeqResGroup(i);
Group gTwo = chainTwo.getSeqResGroup(i);
assertEquals(gOne.getResidueNumber(), gTwo.getResidueNumber());
assertEquals(gOne.getPDBName(), gTwo.getPDBName());
}
}
}