inclusion of simple test case to check resolution of issue MDAnalysis…

…#3419.

testsuite/MDAnalysisTests/data/atomtypes_charge.itp

@@ -0,0 +1,60 @@
+[ defaults ]
+; nbfunc        comb-rule       gen-pairs       fudgeLJ fudgeQQ
+  1             2               no              1.0     1.0
+
+
+
+[ atomtypes ]
+;name at.num  mass  charge ptype        c6             c12
+NP 	 NP 	 100.000000 	 -1.000000 	 A  	 1.00E-02  	 8.707129E-04 
+NR 	 NR 	 100.000000 	 0.000000 	 A  	 1.00E-02  	 8.707129E-04 
+NA 	 NA 	 100.000000 	 0.000000 	 A  	 1.00E-02  	 8.707129E-04 
+
+
+
+[ moleculetype ]
+; Name      nrexcl
+testmol	    2
+
+[ atoms ]
+; nr type resnr residue atom cgnr
+1 	 NP 	 1 	 A 	 NP 	 1
+2 	 NR 	 1 	 A 	 NR 	 2
+3 	 NA 	 1 	 A 	 NA 	 3
+4 	 NP 	 2 	 A 	 NP 	 4
+5 	 NR 	 2 	 A 	 NR 	 5
+6 	 NA 	 2 	 A 	 NA 	 6
+7 	 NP 	 3 	 A 	 NP 	 7
+8 	 NR 	 3 	 A 	 NR 	 8
+9 	 NA 	 3 	 A 	 NA 	 9
+
+[ bonds ]
+; i  j funct   c0       c1
+1 	 2 	 1 	 0.390 	 300000.000
+2 	 3 	 1 	 0.586 	 300000.000
+2 	 4 	 1 	 0.390 	 300000.000
+4 	 5 	 1 	 0.390 	 300000.000
+5 	 6 	 1 	 0.586 	 300000.000
+5 	 7 	 1 	 0.390 	 300000.000
+7 	 8 	 1 	 0.390 	 300000.000
+8 	 9 	 1 	 0.586 	 300000.000
+
+[ angles ]
+; ai    aj    ak     funct  table_number  k(kJ/mol)
+1 	 2 	 3 	 1 	 91.100 	 1000.000
+1 	 2 	 4 	 1 	 113.100 	 1000.000
+2 	 4 	 5 	 1 	 95.200 	 1000.000
+3 	 2 	 4 	 1 	 100.800 	 1000.000
+4 	 5 	 6 	 1 	 91.100 	 1000.000
+4 	 5 	 7 	 1 	 113.100 	 1000.000
+5 	 7 	 8 	 1 	 95.200 	 1000.000
+6 	 5 	 7 	 1 	 100.800 	 1000.000
+7 	 8 	 9 	 1 	 91.100 	 1000.000
+
+[ system ]
+; Name
+test
+
+[ molecules ]
+; Compound	#mols
+testmol    1

testsuite/MDAnalysisTests/datafiles.py

@@ -557,6 +557,7 @@
 ITP = resource_filename(__name__, 'data/gromacs_ala10.itp')
 ITP_nomass = resource_filename(__name__, 'data/itp_nomass.itp')
 ITP_atomtypes = resource_filename(__name__, 'data/atomtypes.itp')
+ITP_charges = resource_filename(__name__, 'data/atomtypes_charge.itp')
 ITP_edited = resource_filename(__name__, 'data/edited_itp.itp')
 ITP_tip5p = resource_filename(__name__, "data/tip5p.itp")
 ITP_spce = resource_filename(__name__, 'data/spce.itp')

testsuite/MDAnalysisTests/topology/test_itp.py

@@ -31,6 +31,7 @@
     ITP,  # GROMACS itp
     ITP_nomass,  # from Automated Topology Builder
     ITP_atomtypes,
+    ITP_charges,
     ITP_edited,
     ITP_tip5p,
     ITP_spce,
@@ -188,6 +189,34 @@ def test_mass_parse_or_guess(self, universe):
         assert_almost_equal(universe.atoms[2].mass, 20.989)
         assert_almost_equal(universe.atoms[3].mass, 1.008)
 
+class TestITPAtomtypes(ParserBase):
+    parser = mda.topology.ITPParser.ITPParser
+    ref_filename = ITP_charges
+    expected_attrs = ['ids', 'names', 'types', 'masses',
+                      'charges', 'chargegroups',
+                      'resids', 'resnames',
+                      'segids', 'moltypes', 'molnums',
+                      'bonds', 'angles', 'dihedrals', 'impropers']
+    guessed_attrs = []
+    expected_n_atoms = 9
+    expected_n_residues = 3
+    expected_n_segments = 1
+
+    @pytest.fixture
+    def universe(self, filename):
+        return mda.Universe(filename)
+
+    def test_charge_parse(self, universe):
+        assert_almost_equal(universe.atoms[0].charge, -1.0)
+        assert_almost_equal(universe.atoms[1].charge, 0)
+        assert_almost_equal(universe.atoms[2].charge, 0)
+        assert_almost_equal(universe.atoms[3].charge, -1.)
+
+    def test_mass_parse_or_guess(self, universe):
+        assert_almost_equal(universe.atoms[0].mass, 100.0)
+        assert_almost_equal(universe.atoms[1].mass, 100.0)
+        assert_almost_equal(universe.atoms[2].mass, 100.0)
+        assert_almost_equal(universe.atoms[3].mass, 100.0)
 
 class TestDifferentDirectivesITP(BaseITP):