Added tests for rotate_substituent

kmlefran · Jan 29, 2024 · 4d41919 · 4d41919
1 parent 3828f7a
commit 4d41919
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Showing 70 changed files with 414,730 additions and 1 deletion.
diff --git a/.DS_Store b/.DS_Store
diff --git a/subproptools/__pycache__/__init__.cpython-311.pyc b/subproptools/__pycache__/__init__.cpython-311.pyc
diff --git a/subproptools/sub_reor.py b/subproptools/sub_reor.py
@@ -677,6 +677,8 @@ def rotate_substituent_aiida(
         molecule_xaxis = _set_xaxis(_set_origin(xyz_w_y_pt, originAtom), negXAtom)
         final_y = molecule_xaxis[posYAtom - 1]
         final_orientation = _set_yaxis(molecule_xaxis[0:-1], final_y)
+    elif posYAtom:
+        posYPoint = molecule_xyz["xyz"][posYAtom - 1]
     else:
         molecule_xaxis = _set_xaxis(
             _set_origin(molecule_xyz["xyz"], originAtom), negXAtom
@@ -745,9 +747,13 @@ def rotate_substituent(sumFileNoExt, originAtom, negXAtom, posYAtom=0):
     # perform reorientation
     if not posYAtom and len(molecule_xyz["Atoms"]) > 2:
         posYPoint = _get_posy_point(sumFileNoExt, atomDict, attachedAtom, negXAtomLabel)
+    elif posYAtom:
+        posYPoint = molecule_xyz["xyz"][posYAtom - 1]
     else:
         posYPoint = []
     if len(posYPoint) > 0:
+        print(molecule_xyz["xyz"])
+        print(posYPoint)
         xyz_w_y_pt = np.append(molecule_xyz["xyz"], [posYPoint], axis=0)
         # perform reorientation
         molecule_xaxis = _set_xaxis(_set_origin(xyz_w_y_pt, originAtom), negXAtom)
@@ -856,7 +862,7 @@ def rotate_sheet(
         Substituent: string label for substituent
         originAtom: numerical index(starting form 1) of atom to use as origin
         negXAtom: numerical index(starting form 1) of atom to place on -x
-        posYAtom: usually 0, but if override desired, numerical index(starting form 1) of atom to place on +y
+        posYAtom: usually 0, but override if desired, numerical index(starting form 1) of atom to place on +y
         charge: charge of the molecule
         multiplicity: multiplicity of the molecule
         label1, label2... label depicting situation for molecule(substrate, method) e.g. "SubH", "B3LYP/cc-pvDZ" etc

diff --git a/tests/test_data/CFHCH3.sum b/tests/test_data/CFHCH3.sum
diff --git a/tests/test_data/CFHCH3_atomicfiles/c1.agpviz b/tests/test_data/CFHCH3_atomicfiles/c1.agpviz
diff --git a/tests/test_data/CFHCH3_atomicfiles/c1.inp b/tests/test_data/CFHCH3_atomicfiles/c1.inp
@@ -0,0 +1,16 @@
+ Title Card Required
+C1
+Auto
+Critical Point Data
+  4  0  0
+ -1.07200447546262E+00  2.75078304057096E-01 -6.77683736037888E-10 C5
+  2.99115721546819E-01  1.79733970154982E+00  1.05756656144443E+00 H2
+  2.99115732727216E-01  1.79733974888736E+00 -1.05756653094508E+00 H3
+  9.14689442262505E-01  4.56991519494873E-01  6.56510350176200E-10 F4
+0 0
+Options
+Integer  3
+42 1
+48 2
+52 1
+Real  0
diff --git a/tests/test_data/CFHCH3_atomicfiles/c1.int b/tests/test_data/CFHCH3_atomicfiles/c1.int