Removed a check for hydrogen-containing selections and fixed a unit t…

…est that wasn't assigning end states or milestoning calculation types for a markov monte carlo test.

seekr2/modules/check.py

@@ -942,7 +942,9 @@ def check_pre_simulation_all(model):
         # Skipping MD/BD salt conc. check because the best results seem to 
         # come from using no salt in BD.
         #check_passed_list.append(check_pre_sim_MD_and_BD_salt_concentration(model))
-        check_passed_list.append(check_atom_selections_dont_contain_hydrogen(model))
+        # Skipping this test because doesn't actually cause numerical 
+        # instabilities...
+        #check_passed_list.append(check_atom_selections_dont_contain_hydrogen(model))
         check_passed_list.append(check_atom_selections_on_same_molecule(model))
         check_passed_list.append(check_atom_selections_MD_BD(model))
         check_passed_list.append(check_pqr_residues(model))

seekr2/tests/test_markov_chain_monte_carlo.py

@@ -160,13 +160,15 @@ def test_mcmc_3x3_mmvt(tmpdir_factory):
     model = base.Model()
     model.num_milestones = n_milestones
     model.num_anchors = n_anchors
+    model.calculation_type = "mmvt"
     anchor0 = mmvt_cv_base.MMVT_toy_anchor()
     anchor0.index = 0
     milestone_0_0 = base.Milestone()
     milestone_0_0.index = 0
     milestone_0_0.neighbor_anchor_index = 1
     milestone_0_0.alias_index = 1
     anchor0.milestones = [milestone_0_0]
+    anchor0.endstate = True
 
     anchor1 = mmvt_cv_base.MMVT_toy_anchor()
     anchor1.index = 1
@@ -199,6 +201,7 @@ def test_mcmc_3x3_mmvt(tmpdir_factory):
     milestone_3_0.neighbor_anchor_index = 2
     milestone_3_0.alias_index = 1
     anchor3.milestones = [milestone_3_0]
+    anchor3.endstate = True
 
     model.anchors = [anchor0, anchor1, anchor2, anchor3]