1. LGTM fixes

jvalegre · Jan 24, 2022 · 4b35552 · 4b35552
1 parent 080d8e8
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diff --git a/Example_workflows.zip b/Example_workflows.zip
diff --git a/README.md b/README.md
@@ -2,13 +2,13 @@
 [![Build Status](https://img.shields.io/travis/com/jvalegre/aqme?label=Linux%20CI&logo=Travis)](https://travis-ci.com/github/jvalegre/aqme)
 [![Tests](https://img.shields.io/static/v1?label=Tests&message=104&color=green&logo=Travis)](https://travis-ci.com/github/jvalegre/aqme)
 [![Codecov](https://img.shields.io/codecov/c/github/jvalegre/aqme?label=Codecov&logo=codecov)](https://codecov.io/gh/jvalegre/aqme)
+
 [![CodeFactor](https://img.shields.io/codefactor/grade/github/jvalegre/aqme?label=Codefactor%20grade&logo=codefactor)](https://www.codefactor.io/repository/github/jvalegre/aqme/overview/master)
-[![Codacy](https://img.shields.io/codacy/grade/047e9c6001a84713a82e180669e14c98?label=Codacy%20grade&logo=codacy)](https://www.codacy.com/manual/jvalegre/aqme?utm_source=github.com&amp;utm_medium=referral&amp;utm_content=jvalegre/aqme&amp;utm_campaign=Badge_Grade)
+[![Codacy](https://img.shields.io/codacy/grade/047e9c6001a84713a82e180669e14c98?label=Codacy%20grade&logo=codacy)](https://www.codacy.com/gh/jvalegre/aqme/dashboard?utm_source=github.com&amp;utm_medium=referral&amp;utm_content=jvalegre/aqme&amp;utm_campaign=Badge_Grade)
 [![lgtm](https://img.shields.io/lgtm/grade/python/github/jvalegre/aqme?label=LGTM%20grade&logo=lgtm)](https://lgtm.com/projects/g/jvalegre/aqme/context:python)
 
-![Size](https://img.shields.io/github/repo-size/jvalegre/aqme?label=Size)
-![PyPI](https://img.shields.io/pypi/v/aqme?label=PyPI&logo=pypi)
-![PyPI Downloads](https://img.shields.io/pypi/dm/aqme?label=PyPI%20downloads&logo=pypi&style=social)
+![Size](https://img.shields.io/github/languages/code-size/jvalegre/aqme)
+[![PyPI](https://img.shields.io/pypi/v/aqme?color=blue&label=PyPI&logo=pypi)](https://pypi.org/project/aqme)
 
 # Automated Quantum Mechanical Environments (AQME)
 
@@ -68,7 +68,7 @@ Descriptor generator from multiple input types such as SMILES, log files, xyz, e
 
 ## Quickstart
 ### Using AQME in Jupyter Notebooks
-There are multiple ready-to-use workflows presented as jupyter notebooks in the 'Example_workflows' folder. Some examples are:
+There are multiple ready-to-use workflows presented as jupyter notebooks in the 'Example_workflows.zip' file. Some examples are:
 * QCORR_workflows.ipynb (QCORR analysis of Gaussian output files):
 1) Analyze optimized QM ground and transition states and create json files of normally terminated files with no errors, extra imaginary frequencies, duplicates, etc. 
 2) Use json files to generate single-point energy corrections with multiple levels of theory, charge and multiplicity through for loops:

diff --git a/aqme/aqme.py b/aqme/aqme.py
@@ -26,16 +26,13 @@
 
 import os
 import time
-import json
-import pandas as pd
 from pathlib import Path
 from aqme.argument_parser import parser_args
 
 from aqme.mainf import (
     csearch_main,
     geom_rules_main,
     qprep_main,
-    move_sdf_main,
     graph_main,
     geom_par_main,
     nmr_main,
@@ -46,9 +43,8 @@
     cclib_main,
     cmin_main,
 )
-from aqme.utils import Logger, get_filenames
+from aqme.utils import Logger
 from aqme.qcorr import qcorr, json2input
-from aqme.qprep import qprep
 
 
 def main():

diff --git a/aqme/cheshire_lookup.py b/aqme/cheshire_lookup.py
diff --git a/aqme/cmin.py b/aqme/cmin.py
@@ -3,7 +3,6 @@
 #    in conformer minimization with xTB and ANI      #
 #####################################################.
 
-from operator import itemgetter
 import os
 import sys
 import numpy as np
@@ -13,7 +12,6 @@
 from rdkit.Geometry import Point3D
 import time
 from aqme.argument_parser import set_options
-from aqme.filter import CompoundFilter, EnergyFilter, RMSDFilter
 from aqme.utils import (
     set_metal_atomic_number,
     Logger,
@@ -53,12 +51,15 @@ def __init__(
         w_dir_initial=os.getcwd(),
         varfile=None,
         charge_default=0,
+        program=None,
         **kwargs,
     ):
+
         self.mols = mols
         self.name = name
         self.w_dir_initial = w_dir_initial
         self.charge_default = charge_default
+        self.program = program
 
         if "options" in kwargs:
             self.args = kwargs["options"]
@@ -640,7 +641,8 @@ def mult_min(name, args, program, charge, log, w_dir_initial):
     name_mol = os.path.basename(name).split("_" + args.CSEARCH)[0]
 
     # bar.next()
-    obj = cmin(inmols, name_mol, w_dir_initial, args.varfile, charge, program)
+    obj = cmin(mols=inmols, name=name_mol, w_dir_initial=w_dir_initial, varfile=args.varfile,
+            charge_default=charge, program=program)
     total_data = obj.compute_cmin()
 
     return total_data
diff --git a/aqme/crest.py b/aqme/crest.py
@@ -6,11 +6,9 @@
 #######################################################################
 
 # Python Libraries
-import sys, os
+import os
 from rdkit.Chem import rdMolTransforms
-import numpy as np
 import glob
-from optparse import OptionParser
 import subprocess
 import rdkit
 from rdkit.Chem import AllChem
@@ -125,7 +123,7 @@ def run_xtb(
                     + ","
                     + str(dihedral[4])
                 )
-        xtb_result = subprocess.run(command)
+        subprocess.run(command)
 
 
 def crest_opt(mol, name, dup_data, dup_data_idx, sdwriter, args, log):
@@ -223,7 +221,7 @@ def crest_opt(mol, name, dup_data, dup_data_idx, sdwriter, args, log):
             command.append("--cbonds")
             command.append(str(cbonds))
 
-        crest_result = subprocess.run(command)
+        subprocess.run(command)
 
     if cregen:
         xyzcregenensemble = xyzoutall.split(".xyz")[0] + "_cregen.xyz"
@@ -255,7 +253,7 @@ def crest_opt(mol, name, dup_data, dup_data_idx, sdwriter, args, log):
                 "--ewin",
                 str(cregen_ewin),
             ]
-            cregen_result = subprocess.run(command)
+            subprocess.run(command)
 
             # converting multiple xyz to single
             command_run_1 = [
@@ -292,7 +290,7 @@ def crest_opt(mol, name, dup_data, dup_data_idx, sdwriter, args, log):
 
     dup_data.at[dup_data_idx, "crest-conformers"] = len(xyz_files)
 
-    for f in glob.glob(os.getcwd() + "/" + name + "*.xyz"):
-        os.remove(f)
+#     for f in glob.glob(os.getcwd() + "/" + name + "*.xyz"):
+#         os.remove(f)
 
     return 1
diff --git a/aqme/csearch.py b/aqme/csearch.py
@@ -9,14 +9,12 @@
 import subprocess
 import time
 from pathlib import Path
-import concurrent.futures as futures  # RAUL: This is for the main
 
 import numpy as np
 import pandas as pd
 from rdkit.Chem import AllChem as Chem
 
 from rdkit.Chem import rdMolTransforms, PropertyMol, rdDistGeom, Lipinski
-from progress.bar import IncrementalBar  # RAUL: This is for the main
 
 from aqme.filter import filters, ewin_filter, pre_E_filter, RMSD_and_E_filter
 from aqme.tmbuild import template_embed