Update_solv_workflow

Author: mgt16-LANL

architector/io_obabel.py

@@ -6,7 +6,6 @@
 
 # Imports
 import ase
-import itertools
 from ase.io import read
 from ase import units
 import numpy as np
@@ -20,8 +19,8 @@
 from pynauty import Graph as pnGraph
 from pynauty import canon_label
 
-# ob.obErrorLog.SetOutputLevel(0) # Set warnings to only critical.
 ob.obErrorLog.StopLogging()  # Turn off ALL openbabel logging.
+# ob.obErrorLog.SetOutputLevel(0)  # Set warnings to only critical.
 
 warnings.filterwarnings('ignore')  # Supress warnings.
 
@@ -442,27 +441,27 @@ def generate_obmol_conformers(structure, rmsd_cutoff=0.4, conf_cutoff=3000,
     _, anums, graph = get_OBMol_coords_anums_graph(obmol, return_coords=False,
                                                    get_types=False)
     syms = [io_ptable.elements[x] for x in anums]
-    act_inds = [i for i,x in enumerate(syms) if x in io_ptable.actinides]
-    swapped=False
+    act_inds = [i for i, x in enumerate(syms) if x in io_ptable.actinides]
+    swapped = False
     if len(act_inds) > 0:
         an_symbols = [syms[x] for x in act_inds]
         ln_symbols = [io_ptable.lanthanides[io_ptable.actinides.index(x)] for x in an_symbols]
         j = 0
         for i, atom in enumerate(ob.OBMolAtomIter(obmol)):
             if i in act_inds:
                 atom.SetAtomicNum(io_ptable.elements.index(ln_symbols[j]))
-                j+=1
-        swapped=True
+                j += 1
+        swapped = True
     mmff94_ok = check_mmff_okay(obmol)
     if mmff94_ok:
         FF = ob.OBForceField.FindForceField("MMFF94")
-        FF.Setup(obmol) # Make sure setup works OK
+        FF.Setup(obmol)  # Make sure setup works OK
     else:
         FF = ob.OBForceField.FindForceField("UFF")
-        FF.Setup(obmol) # Make sure setup works OK
+        FF.Setup(obmol)  # Make sure setup works OK
     if fix_m_neighbors:
-        mets = [i for i,x in enumerate(syms) if x in io_ptable.all_metals]
-        if len(mets) == 1: # Freeze metal and neighbor positions - relax ligands
+        mets = [i for i, x in enumerate(syms) if x in io_ptable.all_metals]
+        if len(mets) == 1:  # Freeze metal and neighbor positions - relax ligands
             frozen_atoms = [mets[0]+1] + (np.nonzero(np.ravel(graph[mets[0]]))[0] + 1).tolist()
             constr = ob.OBFFConstraints()
             for j in frozen_atoms:

development/solubility_dev/Soldb_workflow_dev.ipynb

@@ -6,6 +6,18 @@
 
 
 def read_solv_params(file):
+    """XTB output parser for solvent parameters
+
+    Parameters
+    ----------
+    file : str
+        file to load
+
+    Returns
+    -------
+    outdict : dict
+       dictionary of output
+    """
     with open(file, "r") as file1:
         lines = file1.readlines()
     solvent_area_start_key = "generalized Born model for continuum solvation"
@@ -93,7 +105,8 @@ def xtb_solv_params(structure, solvent="water"):
             xtbPath, int(mol_charge), int(uhf), solvent
         )
 
-        sub.run(execStr, shell=True, check=True)
+        sub.run(execStr, shell=True, check=True,
+                stderr=sub.DEVNULL, stdout=sub.DEVNULL)
 
         # Read conformers from file
         result_dict = read_solv_params("output.xtb")