tests for csearch and cmin

Author: shreesowndarya

.gitignore

@@ -1,5 +1,4 @@
 Example_workflows_BEGINNING/
-tests/
 # Byte-compiled / optimized / DLL files
 __pycache__/
 *.py[cod]

tests/test_cmin.py

@@ -0,0 +1,83 @@
+#!/usr/bin/env python
+
+######################################################.
+# 		        Testing with pytest: 	             #
+#                   CMIN module                      #
+######################################################.
+
+import os
+import pytest
+import subprocess
+from aqme.cmin import cmin
+import glob
+from pathlib import Path
+import rdkit
+
+# saves the working directory
+w_dir_main = os.getcwd()
+cmin_methods_dir = w_dir_main + "/tests/cmin_methods"
+cmin_xtb_dir = w_dir_main + "/tests/cmin_xtb"
+
+# tests for parameters of csearch random initialzation
+@pytest.mark.parametrize(
+	"program, sdf, ani_method, xtb_method, opt_steps, opt_fmax, output_nummols",
+	[
+		# tests for conformer generation with RDKit
+		("ani", "pentane_rdkit_methods.sdf",'ANI1ccx', None, 100, 0.08, 4),
+		("xtb", "pentane_rdkit_methods.sdf",None, 'GFN2-xTB', 400, 0.03, 4),
+	],
+)
+def test_cmin_methods(program, sdf, ani_method, xtb_method, opt_steps, opt_fmax, output_nummols ):
+	os.chdir(cmin_methods_dir)
+	# runs the program with the different tests
+	if program =='ani':
+		cmin(w_dir_main=cmin_methods_dir,ani_method=ani_method, program=program, files=sdf, opt_steps=opt_steps, opt_fmax=opt_fmax)
+	elif program =='xtb':
+		cmin(w_dir_main=cmin_methods_dir,xtb_method=xtb_method, program=program, files=sdf, opt_steps=opt_steps, opt_fmax=opt_fmax)
+
+	#tests here
+	file = str("CMIN/" + program + "/" + sdf.split('.')[0] + "_" + program + ".sdf")
+	file2 = str("CMIN/" + program + "/" + sdf.split('.')[0] + "_" + program + "_all_confs.sdf")
+	assert os.path.exists(file)
+	assert os.path.exists(file2)
+
+	mols = rdkit.Chem.SDMolSupplier(file,removeHs=False)
+	assert len(mols) == output_nummols
+	os.chdir(w_dir_main)
+
+# tests for parameters of cmin paramters
+@pytest.mark.parametrize(
+	"program, sdf, metal_complex,metal,metal_oxi,complex_type, charge, mult, xtb_solvent, ewin_cmin, initial_energy_threshold, energy_threshold,rms_threshold,xtb_accuracy,xtb_electronic_temperature, xtb_max_iterations, output_nummols",
+	[
+		# tests for conformer generation with RDKit
+		("xtb", "pentane_rdkit.sdf",False,None,None,None, 0, 1, 'Chloroform', 5,0.003, 0.4,0.5,0.01,298,500,4 ),
+		("xtb", "Pd_complex_0_rdkit.sdf",True,['Pd'],[2],'squareplanar',0,1,"none",8,0.004,0.3,0.2,0.02,300,400, 2),
+	],
+)
+def test_cmin_xtb_parameters(program, sdf, metal_complex,metal,metal_oxi,complex_type,charge, mult, xtb_solvent, ewin_cmin, initial_energy_threshold, energy_threshold,rms_threshold,xtb_accuracy,xtb_electronic_temperature, xtb_max_iterations, output_nummols ):
+	os.chdir(cmin_xtb_dir)
+	# runs the program with the different tests
+	if not metal_complex:
+		cmin(w_dir_main=cmin_xtb_dir, program=program, files=sdf,
+		charge=charge, mult=mult, xtb_solvent=xtb_solvent, ewin_cmin=ewin_cmin, initial_energy_threshold=initial_energy_threshold,
+		energy_threshold=energy_threshold,rms_threshold=rms_threshold,
+		xtb_accuracy=xtb_accuracy,xtb_electronic_temperature=xtb_electronic_temperature, xtb_max_iterations=xtb_max_iterations)
+	else:
+		cmin(w_dir_main=cmin_xtb_dir, program=program, files=sdf, metal_complex=metal_complex,metal=metal,metal_oxi=metal_oxi,complex_type=complex_type,
+		charge=charge, mult=mult, xtb_solvent=xtb_solvent, ewin_cmin=ewin_cmin, initial_energy_threshold=initial_energy_threshold,
+		energy_threshold=energy_threshold,rms_threshold=rms_threshold,
+		xtb_accuracy=xtb_accuracy,xtb_electronic_temperature=xtb_electronic_temperature, xtb_max_iterations=xtb_max_iterations)
+
+	#tests here
+	file = str("CMIN/" + program + "/" + sdf.split('.')[0] + "_" + program + ".sdf")
+	file2 = str("CMIN/" + program + "/" + sdf.split('.')[0] + "_" + program + "_all_confs.sdf")
+	assert os.path.exists(file)
+	assert os.path.exists(file2)
+
+	mols = rdkit.Chem.SDMolSupplier(file,removeHs=False)
+	assert len(mols) == output_nummols
+
+	assert int(mols[0].GetProp('Real charge')) == charge
+	assert int(mols[0].GetProp('Mult')) == mult
+
+	os.chdir(w_dir_main)