refactor print into logging, added checks for atoms and bonds

tests/check_file.py

@@ -1,50 +1,87 @@
+import logging
+import sys
 from math import isclose, isnan
+from openbabel import openbabel
 from openbabel import pybel
-import sys
+
+
+class CIFComparer:
+    def __init__(self, path_to_file1, path_to_file2):
+        logging.basicConfig(format="%(levelname)s: %(message)s", level=logging.WARNING)
+        self.obmol1 = self._get_OBMol_from_CIF(path_to_file1)
+        self.obmol2 = self._get_OBMol_from_CIF(path_to_file2)
+        self.mol1 = self._get_mol_from_CIF(path_to_file1)
+        self.mol2 = self._get_mol_from_CIF(path_to_file2)
+        self.mismatch = False
+
+    def compare(self):
+        self._compare_descriptors()
+        self._compare_atoms()
+        self._compare_bonds()
+        self._compare_molecules()
+        if (self.mismatch):
+            sys.exit(1)
+        else:
+            sys.exit()
+
+    def _get_OBMol_from_CIF(self, path_to_file):
+        ob_conversion = openbabel.OBConversion()
+        ob_conversion.SetInAndOutFormats("cif", "mol")
+        mol = openbabel.OBMol()
+        ob_conversion.ReadFile(mol, path_to_file)
+        return mol
+
+    def _get_mol_from_CIF(self, path_to_file):
+        if ((not path_to_file1.lower().endswith("cif")) or (not path_to_file2.lower().endswith("cif"))):
+            sys.exit("Unexpected file type, expected CIF files")
+        return next(pybel.readfile("cif", path_to_file))
+
+    def _compare_descriptors(self):
+        desc1 = self.mol1.calcdesc()
+        desc2 = self.mol2.calcdesc()
+        for k in desc1.keys():
+            if (isnan(desc1[k]) and isnan(desc2[k])):
+                continue
+            if ((type(desc1[k]) is float) and (type(desc2[k]) is float)):
+                if (not isclose(desc1[k], desc2[k])):
+                    logging.warning(f"molecule %s self.mismatch, %s vs. %s", k, desc1[k], desc2[k])
+                    self.mismatch = True
+            elif (desc1[k] != desc2[k]):
+                logging.warning(f"molecule %s self.mismatch, %s vs. %s", k, desc1[k], desc2[k])
+                self.mismatch = True
+
+    def _compare_atoms(self):
+        if (len(self.mol1.atoms) != len(self.mol2.atoms)):
+            logging.warning("atom count self.mismatch, %s vs. %s", len(self.mol1.atoms), len(self.mol2.atoms))
+            self.mismatch = True
+        else:
+            for i in range(len(self.mol1.atoms)):
+                atom1 = self.mol1.atoms[i]
+                atom2 = self.mol2.atoms[i]
+                for (attr1, attr2, message) in zip((atom1.atomicnum, atom1.exactmass, atom1.formalcharge, atom1.heavydegree, atom1.heterodegree, atom1.hyb, atom1.isotope, atom1.partialcharge, atom1.spin, atom1.type, atom1.degree), (atom2.atomicnum, atom2.exactmass, atom2.formalcharge, atom2.heavydegree, atom2.heterodegree, atom2.hyb, atom2.isotope, atom2.partialcharge, atom2.spin, atom2.type, atom2.degree), ("number", "exact mass", "formal charge", "attached non-hydrogens", "attached heteroatoms", "hybridization", "isotope", "partial charge", "spin", "type", "explicit connections")):
+                    if (attr1 != attr2):
+                        logging.warning("atom %s %s mismatch, %s vs. %s", i, message, attr1, attr2)
+                        self.mismatch = True
+
+    def _compare_bonds(self):
+        i = 0
+        for (bond1, bond2) in zip(openbabel.OBMolBondIter(self.obmol1), openbabel.OBMolBondIter(self.obmol2)):
+            i += 1
+            for (attr1, attr2, message) in zip((bond1.GetBondOrder(), round(bond1.GetLength(), 9), bond1.GetBeginAtom().GetAtomicNum(), bond1.GetEndAtom().GetAtomicNum()), (bond2.GetBondOrder(), round(bond2.GetLength(), 9), bond2.GetBeginAtom().GetAtomicNum(), bond2.GetEndAtom().GetAtomicNum()), ("order", "length", "begin atom", "end atom")):
+                if (attr1 != attr2):
+                    logging.warning("bond %s %s mismatch, %s vs. %s", i, message, attr1, attr2)
+                    self.mismatch = True
+
+    def _compare_molecules(self):
+        for (attr1, attr2, message) in zip((self.mol1.calcfp().bits, self.mol1.energy, self.mol1.formula, self.mol1.exactmass, self.mol1.molwt, self.mol1.spin, self.mol1.charge), (self.mol2.calcfp().bits, self.mol2.energy, self.mol2.formula, self.mol2.exactmass, self.mol2.molwt, self.mol2.spin, self.mol2.charge), ("fingerprint (FP2)", "energy", "formula", "mass", "weight", "spin multiplicity", "charge")):
+            if (attr1 != attr2):
+                logging.warning("atom %s %s mismatch, %s vs. %s", i, message, attr1, attr2)
+                self.mismatch = True
 
 if __name__ == "__main__":
     if (len(sys.argv) != 3):
         sys.exit("Usage: python check_file.py path_to_file_1 path_to_file_2")
-    file1 = sys.argv[1]
-    file2 = sys.argv[2]
-    if ((not file1.lower().endswith("cif")) or (not file2.lower().endswith("cif"))):
-        sys.exit("Unexpected file type, expected CIF files")
-    mol1 = next(pybel.readfile("cif", file1))
-    mol2 = next(pybel.readfile("cif", file2))
-    mismatch = False
-    desc1 = mol1.calcdesc()
-    desc2 = mol2.calcdesc()
-    for k in desc1.keys():
-        if (isnan(desc1[k]) and isnan(desc2[k])):
-            continue
-        if ((type(desc1[k]) is float) and (type(desc2[k]) is float)):
-            if (not isclose(desc1[k], desc2[k])):
-                print(f"Molecule {k} mismatch: {desc1[k]} vs. {desc2[k]}")
-                mismatch = True
-        elif (desc1[k] != desc2[k]):
-            print(f"Molecule {k} mismatch: {desc1[k]} vs. {desc2[k]}")
-            mismatch = True
-    if (len(mol1.atoms) != len(mol2.atoms)):
-        print(f"Atom count mismatch: {len(mol1.atoms)} vs. {len(mol2.atoms)}")
-        mismatch = True
-    if (mol1.calcfp().bits != mol2.calcfp().bits):
-        print(f"Molecular fingerprint (FP2) mismatch: {mol1.calcfp().bits} vs. {mol2.calcfp().bits}")
-        mismatch = True
-    if (mol1.energy != mol2.energy):
-        print(f"Molecular energy mismatch: {mol1.energy} vs. {mol2.energy}")
-        mismatch = True
-    if (mol1.formula != mol2.formula):
-        print(f"Molecular formula mismatch: {mol1.formula} vs. {mol2.formula}")
-        mismatch = True
-    if (mol1.exactmass != mol2.exactmass):
-        print(f"Molecular mass mismatch: {mol1.exactmass} vs. {mol2.exactmass}")
-    if (mol1.molwt != mol2.molwt):
-        print(f"Molecular weight mismatch: {mol1.molwt} vs. {mol2.molwt}")
-    if (mol1.spin != mol2.spin):
-        print(f"Spin multiplicity mismatch: {mol1.spin} vs. {mol2.spin}")
-    if (mol1.charge != mol2.charge):
-        print(f"Molecule charge mismatch: {mol1.charge} vs. {mol2.charge}")
-    if (mismatch):
-        sys.exit(1)
-    else:
-        sys.exit()
+    path_to_file1 = sys.argv[1]
+    path_to_file2 = sys.argv[2]
+    comparer = CIFComparer(path_to_file1, path_to_file2)
+    comparer.compare()