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abradleabradle
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Added some tests on the structures.
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‎biojava-structure/src/test/java/org/biojava/nbio/structure/io/mmtf/TestMmtfRoundTrip.java‎

Lines changed: 208 additions & 1 deletion
Original file line numberDiff line numberDiff line change
@@ -1,7 +1,19 @@
11
package org.biojava.nbio.structure.io.mmtf;
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import static org.junit.Assert.assertArrayEquals;
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import static org.junit.Assert.assertEquals;
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import static org.junit.Assert.assertTrue;
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import java.io.IOException;
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import java.util.ArrayList;
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import java.util.Collections;
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import java.util.Comparator;
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import java.util.List;
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import org.biojava.nbio.structure.Atom;
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import org.biojava.nbio.structure.Bond;
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import org.biojava.nbio.structure.Chain;
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import org.biojava.nbio.structure.Group;
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import org.biojava.nbio.structure.Structure;
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import org.biojava.nbio.structure.StructureException;
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import org.biojava.nbio.structure.StructureIO;
@@ -28,6 +40,201 @@ public void testRoundTrip() throws IOException, StructureException {
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new MmtfStructureWriter(structure, writerToEncoder);
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MmtfStructureReader mmtfStructureReader = new MmtfStructureReader();
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new StructureDataToAdapter(writerToEncoder, mmtfStructureReader);
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mmtfStructureReader.getStructure();
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assertTrue(checkIfAtomsSame(structure,mmtfStructureReader.getStructure()));
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}
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/**
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* Broad test of atom similarity
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* @param structOne the first input structure
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* @param structTwo the second input structure
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* @param mmtfParams
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* @return
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*/
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private boolean checkIfAtomsSame(Structure structOne, Structure structTwo) {
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int numModels = structOne.nrModels();
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if(numModels!=structTwo.nrModels()){
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System.out.println("Error - diff number models: "+structOne.getPDBCode());
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return false;
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}
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for(int i=0;i<numModels;i++){
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List<Chain> chainsOne = structOne.getChains(i);
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List<Chain> chainsTwo = structTwo.getChains(i);
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if(chainsOne.size()!=chainsTwo.size()){
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System.out.println("Error - diff number chains: "+structOne.getPDBCode());
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return false;
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}
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// Now make sure they're sorted in the right order
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sortChains(chainsOne, chainsTwo);
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// Check that each one has the same number of poly, non-poly and water chains
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checkDiffChains(structOne, structTwo, i);
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// Now loop over
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for(int j=0; j<chainsOne.size();j++){
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Chain chainOne = chainsOne.get(j);
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Chain chainTwo = chainsTwo.get(j);
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// Check they have the same chain id
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assertEquals(chainOne.getId(), chainTwo.getId());
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List<Group> groupsOne = chainOne.getAtomGroups();
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List<Group> groupsTwo = chainTwo.getAtomGroups();
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if(groupsOne.size()!=groupsTwo.size()){
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System.out.println("Error - diff number groups: "+structOne.getPDBCode());
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System.out.println(chainOne.getId()+":"+groupsOne.size()+" "+groupsTwo.size());
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return false;
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}
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for(int k=0; k<groupsOne.size();k++){
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Group groupOne = groupsOne.get(k);
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Group groupTwo = groupsTwo.get(k);
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// Check if the groups are of the same type
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if(groupOne.getType().equals(groupTwo.getType())==false){
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System.out.println("Error - diff group type: "+structOne.getPDBCode());
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System.out.println(groupOne.getPDBName() + " and type: "+groupOne.getType());
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System.out.println(groupTwo.getPDBName() + " and type: "+groupTwo.getType());;
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}
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// Check the single letter amino aicd is correct
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if(groupOne.getChemComp().getOne_letter_code().length()==1 && groupTwo.getChemComp().getOne_letter_code().length()==1){
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if(!groupOne.getChemComp().getOne_letter_code().equals(groupTwo.getChemComp().getOne_letter_code())){
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System.out.println(groupOne.getPDBName());
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}
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assertEquals(groupOne.getChemComp().getOne_letter_code(), groupTwo.getChemComp().getOne_letter_code());
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}
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assertEquals(groupOne.getType(), groupTwo.getType());
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assertEquals(groupOne.getResidueNumber().getSeqNum(), groupTwo.getResidueNumber().getSeqNum());
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assertEquals(groupOne.getResidueNumber().getInsCode(), groupTwo.getResidueNumber().getInsCode());
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assertEquals(groupOne.getResidueNumber().getChainName(), groupTwo.getResidueNumber().getChainName());
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if(groupTwo.getAltLocs().size()!=groupOne.getAltLocs().size()){
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System.out.println("Error - diff number alt locs: "+structOne.getPDBCode()+" "+groupOne.getPDBName()+" "+groupOne.getResidueNumber().getSeqNum());
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System.out.println(groupOne.getAltLocs().size());
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System.out.println(groupTwo.getAltLocs().size());
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108+
}
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// Get the first conf
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List<Atom> atomsOne = new ArrayList<>(groupOne.getAtoms());
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List<Atom> atomsTwo = new ArrayList<>(groupTwo.getAtoms());
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for(Group altLocOne: groupOne.getAltLocs()){
114+
for(Atom atomAltLocOne: altLocOne.getAtoms()){
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atomsOne.add(atomAltLocOne);
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}
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}
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for(Group altLocTwo: groupTwo.getAltLocs()){
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for(Atom atomAltLocTwo: altLocTwo.getAtoms()){
120+
atomsTwo.add(atomAltLocTwo);
121+
}
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}
123+
if(atomsOne.size()!=atomsTwo.size()){
124+
System.out.println("Error - diff number atoms: "+structOne.getPDBCode());
125+
System.out.println(groupOne.getResidueNumber());
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System.out.println(groupOne.getPDBName()+" vs "+groupTwo.getPDBName());
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System.out.println(atomsOne.size()+" vs "+atomsTwo.size());
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return false;
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}
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// Now sort the atoms
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sortAtoms(atomsOne, atomsTwo);
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// Now loop through the atoms
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for(int l=0;l<atomsOne.size();l++){
134+
Atom atomOne = atomsOne.get(l);
135+
Atom atomTwo = atomsTwo.get(l);
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assertTrue(atomOne.getGroup().getPDBName().equals(atomTwo.getGroup().getPDBName()));
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assertTrue(atomOne.getCharge()==atomTwo.getCharge());
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// Check the coords are the same to three db
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assertArrayEquals(atomOne.getCoords(), atomTwo.getCoords(), 0.0009999999);
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assertEquals(atomOne.getTempFactor(), atomTwo.getTempFactor(), 0.009999999);
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assertEquals(atomOne.getOccupancy(), atomTwo.getOccupancy(), 0.009999999);
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assertTrue(atomOne.getElement()==atomTwo.getElement());
143+
assertTrue(atomOne.getName().equals(atomTwo.getName()));
144+
assertTrue(atomOne.getAltLoc()==atomTwo.getAltLoc());
145+
if(i==0){
146+
if(atomOne.getBonds()==null){
147+
if(atomTwo.getBonds()!=null){
148+
System.out.println("Null bonds in one and not the other");
149+
return false;
150+
}
151+
}
152+
else if(atomTwo.getBonds()==null){
153+
System.out.println("Null bonds in one and not the other");
154+
return false;
155+
}
156+
else if(atomOne.getBonds().size()!=atomTwo.getBonds().size()){
157+
System.out.println("Error different number of bonds: "+structOne.getPDBCode());
158+
System.out.println(atomOne.getBonds().size()+" vs. "+atomTwo.getBonds().size());
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System.out.println(atomOne);
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System.out.println(atomTwo);
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for(Bond bond : atomOne.getBonds()) {
162+
System.out.println(bond);
163+
}
164+
for(Bond bond : atomTwo.getBonds()) {
165+
System.out.println(bond);
166+
}
167+
return false;
168+
}
169+
}
170+
}
171+
}
172+
}
173+
}
174+
return true;
175+
}
176+
/**
177+
* Check both structures have the same number of poly,non-poly and water chains
178+
* @param structOne the first structure
179+
* @param structTwo the second structure
180+
* @param i the model index
181+
*/
182+
private void checkDiffChains(Structure structOne, Structure structTwo, int i) {
183+
assertEquals(structOne.getPolyChains(i).size(), structTwo.getPolyChains(i).size());
184+
assertEquals(structOne.getNonPolyChains(i).size(), structTwo.getNonPolyChains(i).size());
185+
assertEquals(structOne.getWaterChains(i).size(), structTwo.getWaterChains(i).size());
32186
}
187+
/**
188+
* Sort the atom based on PDB serial id
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* @param atomsOne the first list
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* @param atomsTwo the second list
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*/
192+
private void sortAtoms(List<Atom> atomsOne, List<Atom> atomsTwo) {
193+
atomsOne.sort(new Comparator<Atom>() {
194+
@Override
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public int compare(Atom o1, Atom o2) {
196+
//
197+
if (o1.getPDBserial()<o2.getPDBserial()){
198+
return -1;
199+
}
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else{
201+
return 1;
202+
}
203+
}
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});
205+
atomsTwo.sort(new Comparator<Atom>() {
206+
@Override
207+
public int compare(Atom o1, Atom o2) {
208+
//
209+
if (o1.getPDBserial()<o2.getPDBserial()){
210+
return -1;
211+
}
212+
else{
213+
return 1;
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}
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}
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});
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}
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/**
220+
* Sort the chains based on chain id.
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* @param chainsOne the first list of chains
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* @param chainsTwo the second list of chains
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*/
224+
private void sortChains(List<Chain> chainsOne, List<Chain> chainsTwo) {
225+
Collections.sort(chainsOne, new Comparator<Chain>() {
226+
@Override
227+
public int compare(Chain o1, Chain o2) {
228+
return o1.getId().compareTo(o2.getId());
229+
}
230+
});
231+
Collections.sort(chainsTwo, new Comparator<Chain>() {
232+
@Override
233+
public int compare(Chain o1, Chain o2) {
234+
return o1.getId().compareTo(o2.getId());
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}
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});
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}
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33240
}

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