fix required resname (#26)

CHANGELOG.md

@@ -15,6 +15,8 @@ The rules for this file:
     * YYYY-MM-DD date format (following ISO 8601)
   * accompany each entry with github issue/PR number (Issue #xyz)
 -->
+## 0.2.7
+ * [Fix] Acess resname safely and test agains DCD
 
 ## 0.2.0
  * [New] Include segmentid for freesasa calculation.

mdakit_sasa/analysis/sasaanalysis.py

@@ -11,6 +11,7 @@
 from typing import Union, TYPE_CHECKING
 
 from MDAnalysis.analysis.base import AnalysisBase
+from MDAnalysis.exceptions import NoDataError
 import numpy as np
 import freesasa
 import os
@@ -90,7 +91,12 @@ def _single_frame(self):
         # FreeSasa structure accepts PDBS if not available requires to reconstruct the structure using `addAtom`
         for a in self.atomgroup:
             x,y,z = a.position
-            structure.addAtom(a.type.rjust(2), a.resname, a.resnum.item(), a.segid, x, y, z)
+            try:
+                resname = a.resname
+            except NoDataError:
+                resname = 'ANY' # Default classifier value
+
+            structure.addAtom(a.type.rjust(2), resname, a.resnum.item(), a.segid, x, y, z)
 
         # Define 1 cpu for windows avoid freesasa code to calculate it.
         parametes =  freesasa.Parameters()

mdakit_sasa/tests/analysis/test_sasaanalysis.py

@@ -75,13 +75,14 @@ def test_residue_sasa_calculation_results(self, analysis):
         assert analysis.results['residue_area'].shape == (3,25)
 
     @pytest.mark.parametrize(
-        "pdb_file_name, res_numbers",
+        "filename, res_numbers",
         [
-            ('134L.pdb', 201)
+            ('134L.pdb', 201),
+            ('image_vf.data', 1)
         ]
     )
-    def test(self, pdb_file_name, res_numbers):
-        u = mda.Universe(PARENT / 'data' / pdb_file_name)
+    def test(self, filename, res_numbers):
+        u = mda.Universe(PARENT / 'data' / filename)
         analysis = SASAAnalysis(u)
         analysis.run()
         assert(len(analysis.results.residue_area[0]) == res_numbers)

mdakit_sasa/tests/data/image_vf.data

@@ -0,0 +1,48 @@
+LAMMPS data file via write_data, version 30 Jul 2021, timestep = 0
+
+7 atoms
+2 atom types
+1 bonds
+1 bond types
+
+0 10 xlo xhi
+0 10 ylo yhi
+0 10 zlo zhi
+
+Masses
+
+1 1
+2 1
+
+Pair Coeffs # lj/cut
+
+1 1 1
+2 1 1
+
+Bond Coeffs # harmonic
+
+1 1000 1
+
+Atoms # full
+
+4 0 2 0 5.891131260960588 3.398519062578611 0.23689615365476138 0 0 0
+1 0 1 0 4.999443228802319 5.0001459354508775 5.5008776144874 0 0 0
+2 0 1 0 5.000001730605194 4.999999546244266 4.500875455656523 0 0 0
+6 0 2 0 8.27919675422795 8.459848309149896 4.670531882285388 0 0 0
+3 0 2 0 3.362012829847722 5.522388563244657 8.669485965475673 0 0 0
+5 0 2 0 6.586761886625301 3.97905466100164 9.576146361865367 0 0 0
+7 0 2 0 7.621069760835089 6.390558075605001 9.73656065860773 0 0 0
+
+Velocities
+
+4 -0.07044405565641114 0.22797649438575432 0.9964537327696037
+1 1.6773916431557685 0.920692478778414 -2.57312540408295
+2 0.6247600152168848 1.0635940922731792 -0.09111771815842719
+6 0.28742689473258004 -0.5462919186206593 -1.8993269764408356
+3 -0.9529069979679257 -0.9763723022827592 3.1367559503110862
+5 -0.7649018752874791 -2.004540572487937 0.652141765065628
+7 -0.8013256241934161 1.3149417279540099 -0.22178134946410677
+
+Bonds
+
+1 1 1 2