Increase unit test coverage for strucreader. Close #5

src/kallisto/console.py

@@ -57,7 +57,7 @@ def cli(config, verbose: bool, shift: int):
 def cns(config, inp: str, out: click.File, cntype: str):
     """Atomic coordination numbers."""
 
-    molecule = ksr.constructMolecule(geometry=inp)
+    molecule = ksr.constructMolecule(geometry=inp, out=out)
     cns = molecule.get_cns(cntype)
     verbosePrinter(config.verbose, cns, out)
 
@@ -85,7 +85,7 @@ def cns(config, inp: str, out: click.File, cntype: str):
 def cnsp(config, inp: str, out: click.File, cntype: str):
     """Atomic coordination number spheres."""
 
-    molecule = ksr.constructMolecule(geometry=inp)
+    molecule = ksr.constructMolecule(geometry=inp, out=out)
     nat = molecule.get_number_of_atoms()
     cnsp = molecule.get_cnspheres(cntype)
     for i in range(nat):
@@ -119,7 +119,7 @@ def bonds(config, inp: str, partner: int, constrain: bool, out: click.File):
 
     import os
 
-    molecule = ksr.constructMolecule(geometry=inp)
+    molecule = ksr.constructMolecule(geometry=inp, out=out)
 
     if partner == "X":
         # Get index table of covalent bonding partners
@@ -174,14 +174,14 @@ def sort(config, inp: str, start: str, out: click.File):
     start defines on which atom we start the sorting process.
     """
 
-    molecule = ksr.constructMolecule(geometry=inp)
+    molecule = ksr.constructMolecule(geometry=inp, out=out)
     bonds = molecule.get_bonds()
     nat = molecule.get_number_of_atoms()
 
     # construct graph
     from kallisto.sort import Graph
 
-    g = Graph(inp)
+    g = Graph(inp, out)
 
     for i in range(nat):
         partners = bonds[i]
@@ -218,7 +218,7 @@ def sort(config, inp: str, start: str, out: click.File):
 def eeq(config, inp: str, out: click.File, chrg: int):
     """Electronegativity equilibration atomic partial charges."""
 
-    molecule = ksr.constructMolecule(geometry=inp)
+    molecule = ksr.constructMolecule(geometry=inp, out=out)
     nat = molecule.get_number_of_atoms()
     eeq = molecule.get_eeq(chrg)
     for i in range(nat):
@@ -248,7 +248,7 @@ def eeq(config, inp: str, out: click.File, chrg: int):
 def alp(config, inp: str, out: click.File, chrg: int, molecular: bool):
     """Static atomic polarizabilities in Bohr^3."""
 
-    molecule = ksr.constructMolecule(geometry=inp)
+    molecule = ksr.constructMolecule(geometry=inp, out=out)
     nat = molecule.get_number_of_atoms()
     alp = molecule.get_alp(charge=chrg)
     if molecular:
@@ -291,7 +291,7 @@ def alp(config, inp: str, out: click.File, chrg: int, molecular: bool):
 def vdw(config, inp: str, out: click.File, chrg: int, vdwtype: str, angstrom: bool):
     """Charge-dependent atomic van der Waals radii in Bohr."""
 
-    molecule = ksr.constructMolecule(geometry=inp)
+    molecule = ksr.constructMolecule(geometry=inp, out=out)
     nat = molecule.get_number_of_atoms()
     vdw = np.zeros(shape=(nat,), dtype=np.float64)
 
@@ -327,20 +327,19 @@ def rms(config, compare: Tuple[str, str], out: click.File):
 
     from kallisto.rmsd import rmsd
 
-    mol1 = ksr.constructMolecule(geometry=compare[0])
+    mol1 = ksr.constructMolecule(geometry=compare[0], out=out)
     nat1 = mol1.get_number_of_atoms()
-    mol2 = ksr.constructMolecule(geometry=compare[1])
+    mol2 = ksr.constructMolecule(geometry=compare[1], out=out)
     nat2 = mol2.get_number_of_atoms()
 
     # for RMSD comparison both coordinates need the same atom count
     if nat1 != nat2:
-        click.echo(
+        errorbye(
             "Error: number of atoms do not match in {} and in {}".format(
                 compare[0], compare[1]
             ),
-            file=out,  # type: ignore
+            out,
         )
-        errorbye(out)
 
     coord1 = mol1.get_positions()
     coord2 = mol2.get_positions()
@@ -377,7 +376,7 @@ def lig(config, inp: str, center: int, out: click.File):
     """Get all substructures (or ligands) that are bound to the center atom."""
 
     # setup reference molecular structure
-    ref = ksr.constructMolecule(geometry=inp)
+    ref = ksr.constructMolecule(geometry=inp, out=out)
     nat = ref.get_number_of_atoms()
 
     # get all covalent bonding partner in reference complex
@@ -455,8 +454,8 @@ def exs(
     Calculate the RMSD between two structures using quaternions."""
 
     # setup reference molecular structure
-    ref = ksr.constructMolecule(geometry=inp[0])
-    substrate = ksr.constructMolecule(geometry=inp[1])
+    ref = ksr.constructMolecule(geometry=inp[0], out=out)
+    substrate = ksr.constructMolecule(geometry=inp[1], out=out)
     nat = ref.get_number_of_atoms()
 
     # get all covalent bonding partner in reference complex
@@ -511,7 +510,7 @@ def stm(config, inp: str, origin: int, partner: int, out: click.File):
     """Calculate sterimol descriptors using kallisto van der Waals radii."""
 
     # setup molecular structure
-    mol = ksr.constructMolecule(geometry=inp)
+    mol = ksr.constructMolecule(geometry=inp, out=out)
 
     # calculate Sterimol descriptors: L, bmin, bmax
     from kallisto.sterics import getClassicalSterimol

src/kallisto/reader/strucreader.py

@@ -1,31 +1,27 @@
 # src/kallisto/reader/strucreader.py
 
-from kallisto.atom import Atom
+import click
+
 from kallisto.molecule import Molecule
 import kallisto.reader.turbomole as tm
 import kallisto.reader.xyz as xyz
+from kallisto.utils import errorbye
 
 
-def constructMolecule(geometry: str) -> Molecule:
+def constructMolecule(geometry: str, out: click.File) -> Molecule:
     """Helper function to construct a Molecule."""
     try:
         with open(geometry, "r+") as fileObject:
             # read atoms from input file
             atoms = read(fileObject)
-
             # create molecule from atoms
             molecule = Molecule(symbols=atoms)
     except FileNotFoundError:
-        print(" Error: Input file '" + geometry + "' not found.")
-        exit()
+        errorbye('Error: Inpt file "{0}" not found.'.format(geometry), out)
 
     return molecule
 
 
-def construct_atom():
-    return Atom()
-
-
 def read(fileObject):
     """Method to first check the file type and then read
 
@@ -48,10 +44,7 @@ def read(fileObject):
 
     fileObject.close()
 
-    atoms = None
-
-    if atoms is None:
-        atoms = []
+    atoms = []
 
     newfile = open(fname, "r+")
 
@@ -60,8 +53,8 @@ def read(fileObject):
     elif filetp == "xyz":
         atoms = xyz.read(newfile)
     else:
-        print("Error: file type of input '" + fname + "' not recognized")
-        quit()
+        print('Error: file type of input "{0}" not recognized'.format(fname))
+        exit(1)
 
     newfile.close()
 

src/kallisto/sort.py

@@ -3,6 +3,7 @@
 
 from collections import defaultdict
 
+import click
 
 from kallisto.data import chemical_symbols
 import kallisto.reader.strucreader as ksr
@@ -12,11 +13,11 @@
 class Graph:
     """Define a molecular graph."""
 
-    def __init__(self, inp: str):
+    def __init__(self, inp: str, out: click.File):
 
         self.inp = inp
         self.graph = defaultdict(list)  # type: ignore
-        self.molecule = ksr.constructMolecule(geometry=self.inp)
+        self.molecule = ksr.constructMolecule(geometry=self.inp, out=out)
         self.nat = self.molecule.get_number_of_atoms()
         self.at = self.molecule.get_atomic_numbers()
         self.coordinates = self.molecule.get_positions()

src/kallisto/utils/__init__.py

@@ -16,9 +16,10 @@ def verbosePrinter(config: bool, message: str, out: click.File):
         click.echo(message, file=out)  # type: ignore
 
 
-def errorbye(out: click.File):
+def errorbye(message: str, out: click.File):
     """Exit application due to error."""
     click.echo("", file=out)  # type: ignore
+    click.echo(message)  # type: ignore
     click.echo(
         """-> kallisto was terminated due to an error.
         Please check the output.""",

tests/test_strucreader.py

@@ -3,6 +3,8 @@
 import os
 import tempfile
 
+import pytest
+
 from kallisto.atom import Atom
 import kallisto.reader.strucreader as ksr
 
@@ -11,7 +13,7 @@
 
 
 # turbomole coord files can be read
-def test_a_user_can_read_a_TMfile():
+def test_a_user_can_read_coord():
     with tempfile.NamedTemporaryFile(mode="w+", encoding="utf-8") as f:
         f.write("$coord" + s)
         f.write("  1.87167924 -0.101043656  0.1596818582  c" + s)
@@ -26,3 +28,16 @@ def test_a_user_can_read_a_TMfile():
         got = type(atoms[0])
         want = Atom
         assert got is want
+
+
+def test_a_user_cannot_read_invalid_coord():
+    with tempfile.NamedTemporaryFile(mode="w+", encoding="utf-8") as f:
+        f.write("$xoord" + s)
+        f.write("  1.87167924 -0.101043656  0.1596818582  c" + s)
+        f.write("$end")
+        f.flush()
+        fname = open(f.name, "r+")
+        with pytest.raises(SystemExit) as error:
+            ksr.read(fname)
+        assert error.value.args[0] == 1
+        fname.close()