Add tests: minimizing

pyproject.toml

@@ -73,6 +73,7 @@ testpaths = ["tests"]
 markers = [
     "exe: test requires third-party executable",
     "web: test requires internet access",
+    "rdkit: test requires RDKit",
 ]
 filterwarnings = [
     'ignore:.*xdrlib.*:DeprecationWarning:mdtraj.formats',

tests/test_mcsalign.py

@@ -1,7 +1,9 @@
 import psico.mcsalign
 from pymol import cmd
+import pytest
 
 
+@pytest.mark.rdkit
 def test_mcsalign():
     cmd.reinitialize()
     cmd.fragment("his")

tests/test_minimizing.py

@@ -0,0 +1,43 @@
+import psico.minimizing
+from pymol import cmd
+import pytest
+from pytest import approx
+
+
+def test_get_fixed_indices():
+    cmd.reinitialize()
+    cmd.fragment("gly", "m1")
+    cmd.flag("fix", "elem N+O")
+    r = psico.minimizing.get_fixed_indices("m1", 1, _self=cmd)
+    assert r == [0, 3]
+    r = psico.minimizing.get_fixed_indices("m1 & elem C+O", 1, _self=cmd)
+    assert r == [2]
+
+
+def test_load_or_update():
+    cmd.reinitialize()
+    cmd.fragment("gly", "m1")
+    molstr = cmd.get_str("mol", "m1")
+    psico.minimizing.load_or_update(molstr, "m2", "m1", 1, _self=cmd)
+    assert cmd.rms_cur("m2", "m1", matchmaker=-1) == approx(0.0)
+    cmd.alter_state(1, "m1", "(x,y,z) = (x*2, y*2, z*2)")
+    assert cmd.rms("m2", "m1", matchmaker=-1) > 1
+    psico.minimizing.load_or_update(molstr, "", "m1", 1, _self=cmd)
+    assert cmd.get_names() == ["m1", "m2"]
+    assert cmd.rms("m2", "m1", matchmaker=-1) == approx(0.0)
+
+
+# def minimize_ob(selection='enabled', state=-1, ff='UFF', nsteps=500,
+
+
+@pytest.mark.rdkit
+def test_minimize_rdkit():
+    cmd.reinitialize()
+    cmd.fab("ACD", "m1")
+    cmd.copy("m2", "m1")
+    psico.minimizing.minimize_rdkit("m2", nsteps=100)
+    r = cmd.rms("m2", "m1")
+    assert r == approx(0.7118, abs=1e-2)
+
+
+# def clean_ob(selection, present='', state=-1, fix='', restrain='',