From a77aa990660f31c3e92f7f6bcb964c69fc4091c1 Mon Sep 17 00:00:00 2001 From: Jim Procter Date: Tue, 15 Feb 2022 16:54:26 +0000 Subject: [PATCH] JAL-3551 patch test for altloc handling atom spec in superposition code --- test/jalview/ext/pymol/PymolCommandsTest.java | 10 +++++----- 1 file changed, 5 insertions(+), 5 deletions(-) diff --git a/test/jalview/ext/pymol/PymolCommandsTest.java b/test/jalview/ext/pymol/PymolCommandsTest.java index f6bad92..bc12542 100644 --- a/test/jalview/ext/pymol/PymolCommandsTest.java +++ b/test/jalview/ext/pymol/PymolCommandsTest.java @@ -122,16 +122,16 @@ public class PymolCommandsTest toAlign.addRange("2", 20, 21, "B"); toAlign.addRange("2", 22, 22, "C"); List commands = testee.superposeStructures(ref, - toAlign); + toAlign, false); assertEquals(commands.size(), 2); - String refSpecCA = "1//A/12-14/CA 1//B/18+22-23/CA"; - String toAlignSpecCA = "2//B/15-17+20-21/CA 2//C/22/CA"; + String refSpecCA = "(1//A/12-14/CA 1//B/18+22-23/CA"; + String toAlignSpecCA = "(2//B/15-17+20-21/CA 2//C/22/CA"; String refSpec = "1//A/12-14/ 1//B/18+22-23/"; String toAlignSpec = "2//B/15-17+20-21/ 2//C/22/"; - + String altLoc = " and (altloc '' or altloc 'a'))"; // super command: separate arguments for regions to align assertEquals(commands.get(0), - new StructureCommand("super", refSpecCA, toAlignSpecCA)); + new StructureCommand("pair_fit", toAlignSpecCA+altLoc, refSpecCA+altLoc)); // show aligned regions: one argument for combined atom specs assertEquals(commands.get(1), new StructureCommand("show", "cartoon", refSpec + " " + toAlignSpec)); -- 1.7.10.2