Move microservice WAMP test from MDStudio/tests to package

tests/wamp_test/test_lie_structures.py

@@ -0,0 +1,200 @@
+from  __future__ import print_function
+
+from mdstudio.deferred.chainable import chainable
+from mdstudio.component.session import ComponentSession
+from mdstudio.runner import main
+from os.path import join
+import numpy as np
+import os
+import pybel
+import shutil
+
+file_path = os.path.realpath(__file__)
+root = os.path.split(file_path)[0]
+
+
+def create_workdir(name, path="/tmp/mdstudio/lie_structures"):
+    """Create temporal workdir dir"""
+    workdir = join(path, name)
+    if not os.path.isdir(workdir):
+        os.makedirs(workdir)
+    return workdir
+
+
+def read_mol(mol, fmt="mol2"):
+    """Read a molecular object either from a file or string"""
+    if not os.path.isfile(mol):
+        name = '/tmp/structure.{}'.format(fmt)
+        with open(name, 'w') as f:
+            f.write(mol)
+        mol = name
+
+    return pybel.readfile(fmt, mol).next()
+
+
+def copy_to_workdir(file_path, workdir):
+    shutil.copy(file_path, workdir)
+    base = os.path.basename(file_path)
+    return join(workdir, base)
+
+
+def compare_molecules(mol1, mol2, rtol=1e-5, atol=1e-8):
+    """Compare the coordinates of two molecules"""
+    m1 = read_mol(mol1)
+    m2 = read_mol(mol2)
+
+    arr = np.array([x.coords for x in m1])
+    brr = np.array([x.coords for x in m2])
+
+    return np.allclose(arr, brr, rtol, atol)
+
+
+dict_convert = {
+    "output_format": "mol2",
+    "workdir": create_workdir("convert"),
+    "input_format": "smi",
+    "mol": "O1[C@@H](CCC1=O)CCC",
+    "from_file": False,
+    "to_file": True
+}
+
+dict_make3d = {
+    "from_file": True,
+    "workdir": create_workdir("make3d"),
+    "input_format": "mol2",
+    "output_format": "mol2",
+    "mol": join(root, 'files/structure.mol2')
+}
+
+dict_addh = {
+    "from_file": True,
+    "workdir": create_workdir("addh"),
+    "input_format": "mol2",
+    "output_format": "mol2",
+    "mol": join(root, "files/structure3D.mol2"),
+    "pH": 7.4,
+    "correctForPH": False
+}
+
+dict_info = {
+    "mol": join(root, "files/structure3D.mol2"),
+    "workdir": create_workdir("info"),
+    "input_format": "mol2",
+}
+
+dict_rotate = {
+    "from_file": True,
+    "workdir": create_workdir("rotate"),
+    "input_format": "mol2",
+    "output_format": "mol2",
+    "rotations": [
+        [1, 0, 0, 90], [1, 0, 0, -90], [0, 1, 0, 90],
+        [0, 1, 0, -90], [0, 0, 1, 90], [0, 0, 1, -90]],
+    "mol": join(root, "files/structureHs.mol2"),
+}
+
+dict_similarity = {
+    "mol_format": "smi",
+    "ci_cutoff": 0.3617021276595745,
+    "workdir": create_workdir('similarity'),
+    "test_set": ["O1[C@@H](CCC1=O)CCC"],
+    "reference_set": [
+      "c1(c(cccc1Nc1c(cccc1)C(=O)O)C)C",
+      "c12ccccc1nc1c(c2N)CCCC1",
+      "c1ccc(c(c1)[N+](=O)[O-])[C@H]1C(=C(NC(=C1C(=O)OC)C)C)C(=O)OC",
+      "c1cc(ccc1OCC)NC(=O)C",
+      "c12c3c(ccc1c(=O)cc(o2)c1ccccc1)cccc3",
+      "c1cc(cc(c1N/C=N/O)C)CCCC",
+      "c1(cccnc1Nc1cc(ccc1)C(F)(F)F)C(=O)O",
+      "c1ccc(c(c1C)OC[C@H](C)N)C",
+      "c1(OC[C@H](CNC(C)C)O)c2c(ccc1)cccc2",
+      "c12ccccc1cccc2",
+      "c12ccccc1cccc2C",
+      "c12ccccc1ccc(c2)C",
+      "c12ccccc1ccc(c2)F",
+      "c12ccccc1cc(cc2C)C",
+      "c12ccccc1c(ccc2C)C",
+      "c12cccc(c1cccc2Cl)Cl",
+      "c12cc(ccc1cc(cc2)C)C",
+      "C1CCC(=O)OCC1",
+      "O1[C@@H](CCC1=O)C",
+      "O1[C@@H](CCC1=O)CC",
+      "O1[C@@H](CCC1=O)CCC",
+      "O1[C@@H](CCC1=O)CCCCC",
+      "O1[C@@H](CCC1=O)CCCCCC",
+      "O1[C@@H](CCC1=O)CCCCCCC",
+      "C1C[C@@H](OC(=O)C1)CCCCC",
+      "c1c2c(ccc1)OC(=O)C2",
+      "c1c2c(ccc1)CC(=O)C2",
+      "c1c2c(ccc1)OCC2",
+      "c1c2c(ccc1)oc(=O)[nH]2",
+      "c1(ccccc1)c1ccccc1",
+      "c1c(cccc1)c1ccc(cc1)Cl",
+      "C1CCCC(C1)CCCC",
+      "[C@@H]1(OC(=O)CC1)c1ccccc1",
+      "c1(cc(oc(=O)c1)C)C",
+      "C1CC(=O)N([C@H]1c1cccnc1)C"
+    ]
+}
+
+
+class Run_structures(ComponentSession):
+
+    def authorize_request(self, uri, claims):
+        return True
+
+    @chainable
+    def on_run(self):
+        with self.group_context('mdgroup'):
+            toolkits = yield self.call(
+                "mdgroup.lie_structures.endpoint.supported_toolkits",
+                {})
+            assert "pybel" in toolkits["toolkits"]
+            print("toolkits available: {}".format(toolkits['toolkits']))
+
+            convert = yield self.call(
+                "mdgroup.lie_structures.endpoint.convert", dict_convert)
+            print(convert)
+            assert compare_molecules(convert['mol'], join(root, 'files/structure.mol2'))
+            print("converting {} from smile to mol2 succeeded!".format(
+                dict_convert['mol']))
+
+            dict_make3d['mol'] = copy_to_workdir(dict_make3d['mol'], dict_make3d['workdir'])
+            make3d = yield self.call(
+                "mdgroup.lie_structures.endpoint.make3d", dict_make3d)
+            # assert compare_molecules(make3d['mol'], join(root, 'files/structure3D.mol2'), atol=1e-2)
+            print(make3d)
+            print("successful creation of a 3D structure for {}".format(
+                dict_convert['mol']))
+
+            dict_addh['mol'] = copy_to_workdir(dict_addh['mol'], dict_addh['workdir'])
+            addh = yield self.call(
+                "mdgroup.lie_structures.endpoint.addh", dict_addh)
+            print(addh)
+            assert compare_molecules(addh['mol'], join(root, 'files/structureHs.mol2'))
+            print("added hydrogens sucessfully!")
+
+            dict_info['mol'] = copy_to_workdir(dict_info['mol'], dict_info['workdir'])
+            info = yield self.call(
+                "mdgroup.lie_structures.endpoint.info", dict_info)
+            print("info", info)
+            atts = info['attributes']
+            assert all((
+                atts['formula'] == 'C7H12O2', atts['exactmass'] - 128.083729624 < 1e-5))
+            print('attributes information successfully retrieved!')
+
+            dict_rotate['mol'] = copy_to_workdir(dict_rotate['mol'], dict_info['workdir'])
+            rotate = yield self.call(
+                "mdgroup.lie_structures.endpoint.rotate", dict_rotate)
+            print("rotate: ", rotate)
+            assert compare_molecules(rotate['mol'], join(root, 'files/rotations.mol2'))
+            print("rotatation method succeeded!")
+
+            similarity = yield self.call(
+                "mdgroup.lie_structures.endpoint.chemical_similarity",
+                dict_similarity)
+            print("similarity: ", similarity)
+
+
+if __name__ == "__main__":
+    main(Run_structures)