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New interface finder functionality #867

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Merged
josemduarte merged 6 commits into from
Apr 18, 2020
Merged

New interface finder functionality #867

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3747377
Initial implementation and tests
josemduarte Jan 25, 2020
496daf0
With bounding box optimization
josemduarte Jan 25, 2020
d4dc323
Docs
josemduarte Jan 25, 2020
e70f0ef
Fixes
josemduarte Jan 25, 2020
2807d3d
Cleanup
josemduarte Jan 25, 2020
0df3813
Merge branch 'master' into interface-finder
josemduarte Jan 25, 2020
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@josemduarte
josemduarte committed Jan 25, 2020
commit e70f0ef8131897137cc2f6b201b2eca4ff9c662f
4 changes: 2 additions & 2 deletions biojava-structure/src/main/java/org/biojava/nbio/structure/contact/InterfaceFinder.java
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Expand Up @@ -20,7 +20,7 @@ public class InterfaceFinder {

public static final double DEFAULT_CONTACT_CUTOFF = 6;

private static final CrystalTransform IDENTITY_TRANSFORM = new CrystalTransform(SpaceGroup.parseSpaceGroup("P1"));
private static final CrystalTransform IDENTITY_TRANSFORM = new CrystalTransform((SpaceGroup) null);
private static final boolean INCLUDE_HETATOMS = true;

private Structure structure;
Expand All @@ -43,7 +43,7 @@ public void setCutoff(double cutoff) {

/**
* Find all inter polymer-chain interfaces in the structure.
* Two chains will be considered in contact if at least a pair of atoms from each is within the
* Two chains will be considered in contact if at least a pair of atoms (one from each chain) is within the
* contact cutoff.
* @return the list of all interfaces
*/
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