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Fixing issue in bonds between atoms with different alt locs #854

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Merged
josemduarte merged 8 commits into from
Dec 19, 2019
Merged

Fixing issue in bonds between atoms with different alt locs #854

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761799b
Fixing issue: no bonds between different altloc atoms
josemduarte Nov 10, 2019
408c8ac
Extending test
josemduarte Nov 10, 2019
7c7caa2
Now all tests pass
josemduarte Nov 12, 2019
0ff1823
Clarifying docs and some more cleanup
josemduarte Nov 12, 2019
a29f881
Covering another alt loc bond edge case
josemduarte Nov 13, 2019
b889140
Extracted common method, now covering nucleotide bonds
josemduarte Nov 13, 2019
7180aeb
Consolidating on a single method call for all alt loc bond business
josemduarte Nov 13, 2019
c363396
Docs
josemduarte Nov 13, 2019
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Now all tests pass
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@josemduarte
josemduarte committed Nov 12, 2019
commit 7c7caa274420e3399d4c969b0feb795979e6d71d
9 changes: 7 additions & 2 deletions biojava-structure/src/main/java/org/biojava/nbio/structure/io/BondMaker.java
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Original file line number Diff line number Diff line change
Expand Up @@ -214,9 +214,14 @@ private void formIntraResidueBonds() {
Atom b = getAtom(chemCompBond.getAtom_id_2(), group);
if ( a != null && b != null){

// if they are different altlocs there must be no bond
if (a.getAltLoc() != b.getAltLoc())
// if they are different altlocs (when different from the '.' case) there must be no bond
if (a.getAltLoc() != null && b.getAltLoc()!=null &&
a.getAltLoc()!=' ' && b.getAltLoc()!=' ' &&
a.getAltLoc() != b.getAltLoc()) {
logger.debug("Skipping bond between atoms with differently named alt locs {} (altLoc '{}') -- {} (altLoc '{}')",
a.toString(), a.getAltLoc(), b.toString(), b.getAltLoc());
continue;
}

int bondOrder = chemCompBond.getNumericalBondOrder();
logger.debug("Forming bond between atoms {}-{} and {}-{} with bond order {}",
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4 changes: 2 additions & 2 deletions biojava-structure/src/test/java/org/biojava/nbio/structure/TestAltLocs.java
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Original file line number Diff line number Diff line change
Expand Up @@ -838,8 +838,8 @@ public void testBondsBetweenAltlocs() throws IOException {
for (Bond b : a.getBonds()) {
// if (b.getAtomA().getAltLoc() != b.getAtomB().getAltLoc()) {
// System.out.println(
// b.getAtomA().toString() + ":" + b.getAtomA().getAltLoc() + " --- " +
// b.getAtomB().toString() + ":" + b.getAtomB().getAltLoc());
// b.getAtomA().toString() + ": '" + b.getAtomA().getAltLoc() + "' --- " +
// b.getAtomB().toString() + ": '" + b.getAtomB().getAltLoc() + "'");
// }
// no bonds between atoms with different alt locs
assertEquals(b.getAtomA().toString() + " --- " + b.getAtomB().toString(),
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