molSimplify 1.7.4__py3-none-any.whl

molSimplify/Classes/globalvars.py

@@ -0,0 +1,827 @@
+# @file globalvars.py
+# @file globalvars.py
+#  Contains useful constants used throughout the code.
+#
+#  Written by Kulik Group
+#
+#  Department of Chemical Engineering, MIT
+
+import os
+import inspect
+import glob
+import platform
+import sys
+import subprocess
+from typing import Dict, Tuple
+from molSimplify.utils.metaclasses import Singleton
+
+# Dictionary containing atomic mass, atomic number, covalent radius, num valence electrons
+# Data from http://www.webelements.com/ (last accessed May 13th 2015)
+amassdict = {'X': (1.0, 0, 0.77, 0), 'H': (1.0079, 1, 0.37, 1),
+             'D': (2.0141, 1, 0.37, 1), 'He': (4.002602, 2, 0.46, 2),
+             'Li': (6.94, 3, 1.33, 1), 'Be': (9.0121831, 4, 1.02, 2), 'B': (10.83, 5, 0.85, 3),
+             'C': (12.0107, 6, 0.77, 4), 'N': (14.0067, 7, 0.75, 5), 'O': (15.9994, 8, 0.73, 6),
+             'F': (18.9984, 9, 0.71, 7), 'Ne': (20.1797, 10, 0.67, 8), 'Na': (22.99, 11, 1.55, 1),
+             'Mg': (24.30, 12, 1.39, 2), 'Al': (26.98, 13, 1.26, 3), 'Si': (28.08, 14, 1.16, 4),
+             'P': (30.9738, 15, 1.06, 5), 'S': (32.065, 16, 1.02, 6), 'Cl': (35.453, 17, 0.99, 7),
+             'Ar': (39.948, 18, 0.96, 8), 'K': (39.10, 19, 1.96, 1), 'Ca': (40.08, 20, 1.71, 2),
+             'Sc': (44.96, 21, 1.7, 3), 'Ti': (47.867, 22, 1.36, 4), 'V': (50.94, 23, 1.22, 5),
+             'Cr': (51.9961, 24, 1.27, 6), 'Mn': (54.938, 25, 1.39, 7), 'Fe': (55.84526, 26, 1.25, 8),
+             'Co': (58.9332, 27, 1.26, 9), 'Ni': (58.4934, 28, 1.21, 10), 'Cu': (63.546, 29, 1.38, 11),
+             'Zn': (65.39, 30, 1.31, 12), 'Ga': (69.72, 31, 1.24, 3), 'Ge': (72.63, 32, 1.21, 4),
+             'As': (74.92, 33, 1.21, 5), 'Se': (78.96, 34, 1.16, 6), 'Br': (79.904, 35, 1.14, 7),
+             'Kr': (83.798, 36, 1.17, 8), 'Rb': (85.47, 37, 2.10, 1), 'Sr': (87.62, 38, 1.85, 2),
+             'Y': (88.91, 39, 1.63, 3), 'Zr': (91.22, 40, 1.54, 4), 'Nb': (92.91, 41, 1.47, 5),
+             'Mo': (95.96, 42, 1.38, 6), 'Tc': (98.9, 43, 1.56, 7), 'Ru': (101.1, 44, 1.25, 8),
+             'Rh': (102.9, 45, 1.25, 9), 'Pd': (106.4, 46, 1.20, 10), 'Ag': (107.9, 47, 1.28, 11),
+             'Cd': (112.4, 48, 1.48, 12), 'In': (111.818, 49, 1.42, 3), 'Sn': (118.710, 50, 1.40, 4),
+             'Sb': (121.760, 51, 1.40, 5), 'Te': (127.60, 52, 1.99, 6), 'I': (126.90447, 53, 1.40, 7),
+             'Xe': (131.293, 54, 1.31, 8), 'Cs': (132.9055, 55, 2.32, 1), 'Ba': (137.327, 56, 1.96, 2),
+             'La': (138.9, 57, 1.69, 3), 'Ce': (140.116, 58, 1.63, 4), 'Pr': (140.90766, 59, 1.76, 5),
+             'Nd': (144.242, 60, 1.74, 6), 'Pm': (145, 61, 1.73, 7), 'Sm': (150.36, 62, 1.72, 8),
+             'Eu': (151.964, 63, 1.68, 9), 'Gd': (157.25, 64, 1.69, 10), 'Tb': (158.92535, 65, 1.68, 11),
+             'Dy': (162.500, 66, 1.67, 12), 'Ho': (164.93033, 67, 1.66, 13), 'Er': (167.259, 68, 1.65, 14),
+             'Tm': (168.93422, 69, 1.64, 15), 'Yb': (173.045, 70, 1.70, 16), 'Lu': (174.9668, 71, 1.62, 3),
+             'Hf': (178.5, 72, 1.50, 8), 'Ta': (180.9, 73, 1.38, 5), 'W': (183.8, 74, 1.46, 6),
+             'Re': (186.2, 75, 1.59, 7), 'Os': (190.2, 76, 1.28, 8), 'Ir': (192.2, 77, 1.37, 9),
+             'Pt': (195.1, 78, 1.23, 10), 'Au': (197.0, 79, 1.24, 11), 'Hg': (200.6, 80, 1.49, 2),
+             'Tl': (204.38, 81, 1.44, 3), 'Pb': (207.2, 82, 1.44, 4), 'Bi': (208.9804, 83, 1.51, 5),
+             'Po': (208.98, 84, 1.90, 6), 'At': (209.99, 85, 2.00, 7), 'Rn': (222.6, 86, 142, 4),
+             'Fr': (223.02, 87, 3.48, 8), 'Ra': (226.03, 88, 2.01, 2), 'Ac': (277, 89, 1.86, 3),
+             'Th': (232.0377, 90, 1.75, 4), 'Pa': (231.04, 91, 2.00, 5), 'U': (238.02891, 92, 1.70, 6),
+             'Np': (237.05, 93, 1.90, 7), 'Pu': (244.06, 94, 1.75, 8), 'Am': (243.06, 95, 1.80, 9),
+             'Cm': (247.07, 96, 1.69, 10), 'Bk': (247.07, 97, 1.68, 11), 'Cf': (251.08, 98, 1.68, 12)}
+
+# Pa and onward should be checked
+
+
+# van der Waals radii for elements
+# Data from DOI: 10.1039/C3DT50599E, Dalton Trans., 2013, 42, 8617-8636
+vdwrad = {'H': 1.2, 'He': 1.43, 'Li': 2.12, 'Be': 1.98, 'B': 1.91,
+          'C': 1.77, 'N': 1.66, 'O': 1.50, 'F': 1.46, 'Ne': 1.58, 'Na': 2.50,
+          'Mg': 2.51, 'Al': 2.25, 'Si': 2.19, 'P': 1.90, 'S': 1.89,
+          'Cl': 1.82, 'Ar': 1.83, 'K': 2.73, 'Ca': 2.62, 'Sc': 2.58,
+          'Ti': 2.46, 'V': 2.42, 'Cr': 2.45, 'Mn': 2.45, 'Fe': 2.44,
+          'Co': 2.40, 'Ni': 2.40, 'Cu': 2.38, 'Zn': 2.39, 'Ga': 2.32,
+          'Ge': 2.29, 'As': 1.88, 'Se': 1.82, 'Br': 1.86, 'Kr': 2.25,
+          'Rb': 3.21, 'Sr': 2.84, 'Y': 2.75, 'Zr': 2.52, 'Nb': 2.56,
+          'Mo': 2.45, 'Tc': 2.44, 'Ru': 2.46, 'Rh': 2.44, 'Pd': 2.15,
+          'Ag': 2.53, 'Cd': 2.49, 'In': 2.43, 'Sn': 2.42, 'Sb': 2.47,
+          'Te': 1.99, 'I': 2.04, 'Xe': 2.06, 'Cs': 3.48, 'Ba': 3.03,
+          'La': 2.98, 'Ce': 2.88, 'Pr': 2.92, 'Nd': 2.95, 'Sm': 2.90,
+          'Eu': 2.87, 'Gd': 2.83, 'Tb': 2.79, 'Dy': 2.87, 'Ho': 2.81,
+          'Er': 2.83, 'Tm': 2.79, 'Yb': 2.80, 'Lu': 2.74, 'Hf': 2.63,
+          'Ta': 2.53, 'W': 2.57, 'Re': 2.49, 'Os': 2.48, 'Ir': 2.41,
+          'Pt': 2.29, 'Au': 2.32, 'Hg': 2.45, 'Tl': 2.47, 'Pb': 2.60,
+          'Bi': 2.54, 'Ac': 2.8, 'Th': 2.93, 'Pa': 2.88, 'U': 2.71,
+          'Np': 2.82, 'Pu': 2.81, 'Am': 2.83, 'Cm': 3.05, 'Bk': 3.4,
+          'Cf': 3.05, 'Es': 2.7}
+
+# Bondi van der Waals radii for elements
+# From: doi:10.1021/j100881a503
+# Accessed: http://www.knowledgedoor.com/2/elements_handbook/bondi_van_der_waals_radius.html 4/8/2021
+bondivdw = {'Ar': 1.88, 'As': 1.85, 'Br': 1.85, 'Cd': 1.62, 'C': 1.70,
+            'Cl': 1.75, 'Cu': 1.4, 'F': 1.47, 'Ga': 1.87, 'Au': 1.66,
+            'He': 1.40, 'H': 1.20, 'In': 1.93, 'I': 1.98, 'Kr': 2.02,
+            'Pb': 2.02, 'Li': 1.82, 'Mg': 1.73, 'Hg': 1.70, 'Ne': 1.54,
+            'Ni': 1.63, 'N': 1.55, 'O': 1.52, 'Pd': 1.63, 'P': 1.80, 'Pt': 1.7,
+            'K': 2.75, 'Se': 1.90, 'Si': 2.10, 'Ag': 1.72, 'Na': 2.27, 'S': 1.80,
+            'Te': 2.06, 'Tl': 1.96, 'Sn': 1.96, 'U': 1.86, 'Xe': 2.16, 'Zn': 1.39}
+
+# Period definitions for all element symbols
+# Data from https://en.wikipedia.org/wiki/Group_(periodic_table) (last accessed Sept. 12th 2019)
+
+period_1 = ['H', 'He']
+
+period_2 = ['Li', 'Be', 'B', 'C', 'N', 'O', 'F', 'Ne']
+
+period_3 = ['Na', 'Mg', 'Al', 'Si', 'P', 'S', 'Cl', 'Ar']
+
+period_4 = ['K', 'Ca', 'Sc', 'Ti', 'V', 'Cr', 'Mn', 'Fe', 'Co', 'Ni', 'Cu',
+            'Zn', 'Ga', 'Ge', 'As', 'Se', 'Br', 'Kr']
+
+period_5 = ['Rb', 'Sr', 'Y', 'Zr', 'Nb', 'Mo', 'Tc', 'Ru', 'Rh',
+            'Pd', 'Ag', 'Cd', 'In', 'Sn', 'Sb', ' Te', 'I', 'Xe']
+
+period_6 = ['Cs', 'Ba', 'La', 'Ce', 'Pr', 'Nd', 'Pm', 'Sm', 'Eu', 'Gd',
+            'Tb', 'Dy', 'Ho', 'Er', 'Tm', 'Yb', 'Lu', 'Hf', 'Ta', 'W', 'Re',
+            'Os', 'Ir', 'Pt', 'Au', 'Hg', 'Tl', 'Pb', 'Bi', 'Po', 'At', 'Rn']
+
+period_7 = ['Fr', 'Ra', 'Ac', 'Th', 'Pa', 'U', 'Np', 'Pu', 'Am', 'Cm', 'Bk',
+            'Cf', 'Es', 'Fm', 'Md', 'No', 'Lr', 'Rf', 'Db', 'Sg', 'Bh', 'Hs',
+            'Mt', 'Ds', 'Rg', 'Cn', 'Nh', 'Fl', 'Mc', 'Lv', 'Ts', 'Og']
+
+periods_dict = {'period_1': period_1, 'period_2': period_2, 'period_3': period_3,
+                'period_4': period_4, 'period_5': period_5, 'period_6': period_6,
+                'period_7': period_7}
+
+# Group definitions for all element symbols
+# Data from https://en.wikipedia.org/wiki/Group_(periodic_table) (last accessed Sept. 12th 2019)
+
+hydrogen = ['H']  # Note H not typically included in group 1
+
+group_1 = ['Li', 'Na', 'K', 'Rb', 'Cs', 'Fr']
+
+group_2 = ['Be', 'Mg', 'Ca', 'Sr', 'Ba', 'Ra']
+
+group_3 = ['Sc', 'Y']  # Some IUPAC Initiatives to call either 'La' and 'Ac' grp 3 or 'Lu' and 'Lr
+
+group_4 = ['Ti', 'Zr', 'Hf', 'Rf']
+
+group_5 = ['V', 'Nb', 'Ta', 'Db']
+
+group_6 = ['Cr', 'Mo', 'W', 'Sg']
+
+group_7 = ['Mn', 'Tc', 'Re', 'Bh']
+
+group_8 = ['Fe', 'Ru', 'Os', 'Hs']
+
+group_9 = ['Co', 'Rh', 'Ir', 'Mt']
+
+group_10 = ['Ni', 'Pd', 'Pt', 'Ds']
+
+group_11 = ['Cu', 'Ag', 'Au', 'Rg']
+
+group_12 = ['Zn', 'Cd', 'Hg', 'Cn']
+
+group_13 = ['B', 'Al', 'Ga', 'In', 'Tl', 'Nh']
+
+group_14 = ['C', 'Si', 'Ge', 'Sn', 'Pb', 'Fl']
+
+group_15 = ['N', 'P', 'As', 'Sb', 'Bi', 'Mc']
+
+group_16 = ['O', 'S', 'Se', 'Te', 'Po', 'Lv']
+
+group_17 = ['F', 'Cl', 'Br', 'I', 'At', 'Ts']
+
+group_18 = ['He', 'Ne', 'Ar', 'Kr', 'Xe', 'Rn', 'Og']
+
+lanthanides = ['La', 'Ce', 'Pr', 'Nd', 'Pm', 'Sm', 'Eu', 'Gd', 'Tb', 'Dy',
+               'Ho', 'Er', 'Tm', 'Yb', 'Lu']
+
+actinides = ['Ac', 'Th', 'Pa', 'U', 'Np', 'Pu', 'Am', 'Cm', 'Bk', 'Cf',
+             'Es', 'Fm', 'Md', 'No', 'Lr']
+
+groups_dict = {
+    'group_1': group_1, 'group_2': group_2, 'group_3': group_3,
+    'group_4': group_4, 'group_5': group_5, 'group_6': group_6,
+    'group_7': group_7, 'group_8': group_8, 'group_9': group_9,
+    'group_10': group_10, 'group_11': group_11, 'group_12': group_12,
+    'group_13': group_13, 'group_14': group_14, 'group_15': group_15,
+    'group_16': group_16, 'group_17': group_17, 'group_18': group_18,
+    'lanthanides': lanthanides, 'actinides': actinides, 'hydrogen': hydrogen}
+
+# Metals (includes alkali, alkaline earth, and transition metals)
+alkali_and_alkaline_earth = [
+    'Li', 'li', 'LI', 'lithium', 'Be', 'be', 'BE', 'beryllium',
+    'Na', 'na', 'NA', 'sodium', 'Mg', 'mg', 'MG', 'magnesium',
+    'K', 'k', 'potassium', 'Ca', 'ca', 'CA', 'calcium',
+    'Rb', 'rb', 'RB', 'rubidium', 'Sr', 'sr', 'SR', 'strontium',
+    'Cs', 'cs', 'CS', 'cesium', 'Ba', 'ba', 'BA', 'barium',
+    'Fr', 'fr', 'FR', 'francium', 'Ra', 'ra', 'RA', 'radium']
+
+heavy_metals_and_metalloids = [
+    'Al', 'al', 'AL', 'aluminum', 'aluminium',
+    'Ga', 'ga', 'GA', 'gallium', 'Ge', 'ge', 'GE', 'germanium',
+    'As', 'as', 'AS', 'arsenic', 'In', 'in', 'IN', 'indium',
+    'Sn', 'sn', 'SN', 'tin', 'Sb', 'sb', 'SB', 'antimony',
+    'Te', 'te', 'TE', 'tellurium', 'Tl', 'tl', 'TL', 'thallium',
+    'Pb', 'pb', 'PB', 'lead', 'Bi', 'bi', 'BI', 'bismuth',
+    'Po', 'po', 'PO', 'polonium', 'At', 'at', 'AT', 'astatine',
+    'La', 'la', 'LA', 'lanthanum',
+    'Ce', 'ce', 'CE', 'cerium', 'Pr', 'pr', 'PR', 'praseodymium',
+    'Nd', 'nd', 'ND', 'neodymium', 'Pm', 'pm', 'PM', 'promethium',
+    'Sm', 'sm', 'SM', 'samarium', 'Eu', 'eu', 'EU', 'europium',
+    'Gd', 'gd', 'GD', 'gadolinium', 'Tb', 'tb', 'TB', 'terbium',
+    'Dy', 'dy', 'DY', 'dysprosium', 'Ho', 'ho', 'HO', 'holmium',
+    'Er', 'er', 'ER', 'erbium', 'Tm', 'tm', 'TM', 'thulium',
+    'Yb', 'yb', 'YB', 'ytterbium', 'Lu', 'lu', 'LU', 'lutetium',
+    'Ac', 'ac', 'AC', 'actinium', 'Th', 'th', 'TH', 'thorium',
+    'Pa', 'pa', 'PA', 'protactinium', 'U', 'u', 'uranium',
+    'Np', 'np', 'NP', 'neptunium', 'Pu', 'pu', 'PU', 'plutonium',
+    'Am', 'am', 'AM', 'americium', 'Cm', 'cm', 'CM', 'curium',
+    'Bk', 'bk', 'BK', 'berkelium', 'Cf', 'cf', 'CF', 'californium',
+    'Es', 'es', 'ES', 'einsteinium', 'Fm', 'fm', 'FM', 'fermium',
+    'Md', 'md', 'MD', 'mendelevium', 'No', 'no', 'NO', 'nobelium',
+    'Lr', 'lr', 'LR', 'lawrencium']
+
+# ## The metals list below contains only TMs. See metalslist function for logic.
+metalslist = [
+    'Sc', 'sc', 'SC', 'scandium', 'Ti', 'ti', 'TI', 'titanium',
+    'V', 'v', 'vanadium', 'Cr', 'cr', 'CR', 'chromium',
+    'Mn', 'mn', 'MN', 'manganese', 'Fe', 'fe', 'FE', 'iron',
+    'Co', 'co', 'CO', 'cobalt', 'Ni', 'ni', 'NI', 'nickel',
+    'Cu', 'cu', 'CU', 'copper', 'Zn', 'zn', 'ZN', 'zinc',
+    'Y', 'y', 'yttrium', 'Zr', 'zr', 'ZR', 'zirconium',
+    'Nb', 'nb', 'NB', 'niobium', 'Mo', 'mo', 'MO', 'molybdenum',
+    'Tc', 'tc', 'TC', 'technetium', 'Ru', 'ru', 'RU', 'ruthenium',
+    'Rh', 'rh', 'RH', 'rhodium', 'Pd', 'pd', 'PD', 'palladium',
+    'Ag', 'ag', 'AG', 'silver', 'Cd', 'cd', 'CD', 'cadmium',
+    'Hf', 'hf', 'HF', 'hafnium', 'Ta', 'ta', 'TA', 'tantalum',
+    'W', 'w', 'tungsten', 'Re', 're', 'RE', 'rhenium',
+    'Os', 'os', 'OS', 'osmium', 'Ir', 'ir', 'IR', 'iridium',
+    'Pt', 'pt', 'PT', 'platinum', 'Au', 'au', 'AU', 'gold',
+    'Hg', 'hg', 'HG', 'mercury', 'X',
+]
+
+metals_conv = {
+    'scandium': 'Sc', 'titanium': 'Ti', 'vanadium': 'V', 'chromium': 'Cr',
+    'manganese': 'Mn', 'iron': 'Fe', 'cobalt': 'Co', 'nickel': 'Ni',
+    'copper': 'Cu', 'zinc': 'Zn', 'yttrium': 'Y', 'zirconium': 'Zr',
+    'niobium': 'Nb', 'molybdenum': 'Mo', 'technetium': 'Tc',
+    'ruthenium': 'Ru', 'rhodium': 'Rh', 'palladium': 'Pd', 'silver': 'Ag',
+    'cadmium': 'Cd', 'lanthanum': 'La', 'hafnium': 'Hf', 'tantalum': 'Ta',
+    'tungsten': 'W', 'rhenium': 'Re', 'osmium': 'Os', 'iridium': 'Ir',
+    'platinum': 'Pt', 'gold': 'Au', 'mercury': 'Hg'}
+
+# d-electron counts of transition metals
+mtlsdlist = {'sc': 1, 'ti': 2, 'v': 3, 'cr': 4, 'mn': 5, 'fe': 6, 'co': 7, 'ni': 8, 'cu': 9, 'zn': 10,
+             'y': 1, 'zr': 2, 'nb': 3, 'mo': 4, 'tc': 5, 'ru': 6, 'rh': 7, 'pd': 8, 'ag': 9, 'cd': 10,
+             'hf': 2, 'ta': 3, 'w': 4, 're': 5, 'os': 6, 'ir': 7, 'pt': 8, 'au': 9, 'hg': 10}
+
+# Default spins for each d-electron count (make this metal/oxidation state specific)
+defaultspins = {0: '1', 1: '2', 2: '3', 3: '4', 4: '5',
+                5: '6', 6: '5', 7: '4', 8: '3', 9: '2', 10: '1'}
+
+# Elements sorted by atomic number
+elementsbynum = ['H', 'He',
+                 'Li', 'Be', 'B', 'C', 'N', 'O', 'F', 'Ne',
+                 'Na', 'Mg', 'Al', 'Si', 'P', 'S', 'Cl', 'Ar',
+                 'K', 'Ca',
+                 'Sc', 'Ti', 'V', 'Cr', 'Mn', 'Fe', 'Co', 'Ni', 'Cu', 'Zn', 'Ga', 'Ge', 'As', 'Se', 'Br', 'Kr',
+                 'Rb', 'Sr', 'Y', 'Zr', 'Nb', 'Mo', 'Tc', 'Ru', 'Rh', 'Pd', 'Ag', 'Cd', 'In', 'Sn', 'Sb', 'Te', 'I',
+                 'Xe',
+                 'Cs', 'Ba', 'La', 'Ce', 'Pr', 'Nd', 'Pm', 'Sm', 'Eu', 'Gd', 'Tb', 'Dy', 'Ho', 'Er', 'Tm', 'Yb', 'Lu',
+                 'Hf', 'Ta', 'W', 'Re', 'Os', 'Ir', 'Pt', 'Au', 'Hg', 'Tl', 'Pb', 'Bi', 'Po', 'At', 'Rn',
+                 'Fr', 'Ra', 'Ac', 'Th', 'Pa', 'U', 'Np', 'Pu', 'Am', 'Cm', 'Bk', 'Cf', 'Es', 'Fm', 'Md', 'No', 'Lr',
+                 'Rf', 'Db', 'Sg', 'Bh', 'Hs', 'Mt', 'Ds', 'Rg', 'Cn', 'Uut', 'Fl', 'Uup', 'Lv', 'Uus', 'Uuo']
+
+# Electronegativity (Pauling) by atom symbol
+endict = {"H": 2.20, "He": 4.16,
+          "Li": 0.98, "Be": 1.57, "B": 2.04, "C": 2.55, "N": 3.04, "O": 3.44, "F": 3.98,
+          "Na": 0.93, "Mg": 1.31, "Al": 1.61, "Si": 1.90, "P": 2.19, "S": 2.58, "Cl": 3.16,
+          "K": 0.82, "Ca": 1.00, "Sc": 1.36, "Ti": 1.54, "V": 1.63, "Cr": 1.66,
+          "Mn": 1.55, "Fe": 1.83, "Co": 1.88, "Ni": 1.91, "Cu": 1.90, "Zn": 1.65, "Ga": 1.81,
+          "Ge": 2.01, "As": 2.18, "Se": 2.55, "Br": 2.96, "Rb": 0.82, "Sr": 0.95, "Y": 1.22,
+          "Zr": 1.33, "Nb": 1.60, "Mo": 2.16, "Tc": 2.10, "Ru": 2.20, "Rh": 2.28,
+          "Pd": 2.20, "Ag": 1.93, "Cd": 1.69, "In": 1.78, "Sn": 1.96, "Sb": 2.05, "I": 2.66,
+          "Cs": 0.79, "Ba": 0.89, "Hf": 1.30, "Ta": 1.50, "W": 2.36, "Re": 1.90, "Os": 2.20, "Ir": 2.20,
+          "Pt": 2.28, "Au": 2.54, "Hg": 2.00, "Tl": 1.62, "Pb": 2.33, "Bi": 2.02,
+          "La": 1.10, "Ce": 1.12, "Pr": 1.13, "Nd": 1.14, "Sm": 1.17,
+          "Gd": 1.20, "Dy": 1.22, "Ho": 1.23, "Er": 1.24, "Tm": 1.25, "Lu": 1.27,
+          "Fr": 0.7, "Ra": 0.9, "Ac": 1.1, "Th": 1.3, "Pa": 1.5, "U": 1.38, "Np": 1.36, "Pu": 1.28,
+          "Am": 1.3, "Cm": 1.3, "Bk": 1.3, "Cf": 1.3, "Es": 1.3, "Fm": 1.3, "Md": 1.3, "No": 1.3,
+          "Yb": 1.1, "Eu": 1.2, "Tb": 1.1, "Te": 2.10}
+
+# Polarizability (alpha) by atom symbol
+# From https://www.tandfonline.com/doi/full/10.1080/00268976.2018.1535143
+# Last accessed 4/28/20
+
+poldict = {"H": 4.50711, "He": 1.38375,
+           "Li": 164.1125, "Be": 37.74, "B": 20.5, "C": 11.3, "N": 7.4,
+           "O": 5.3, "F": 3.74, "Ne": 2.66, "Na": 162.7, "Mg": 71.2, "Al": 57.8, "Si": 37.3, "P": 25,
+           "S": 19.4, "Cl": 14.6, "Ar": 11.083, "K": 289.7, "Ca": 160.8, "Sc": 97, "Ti": 100,
+           "V": 87, "Cr": 83, "Mn": 68, "Fe": 62, "Co": 55, "Ni": 49, "Cu": 46.5, "Zn": 38.67,
+           "Ga": 50, "Ge": 40, "As": 30, "Se": 28.9, "Br": 21, "Kr": 16.78, "Rb": 319.8, "Sr": 197.2,
+           "Y": 162, "Zr": 112, "Nb": 98, "Mo": 87, "Tc": 79, "Ru": 72, "Rh": 66, "Pd": 26.14,
+           "Ag": 55, "Cd": 46, "In": 65, "Sn": 53, "Sb": 43, "Te": 38, "I": 32.9, "Xe": 27.32,
+           "Cs": 400.9, "Ba": 272, "La": 215, "Ce": 205, "Pr": 216, "Nd": 208, "Pm": 200, "Sm": 192,
+           "Eu": 184, "Gd": 158, "Tb": 170, "Dy": 163, "Ho": 156, "Er": 150, "Tm": 144,
+           "Yb": 139, "Lu": 137, "Hf": 103, "Ta": 74, "W": 68, "Re": 62, "Os": 57, "Ir": 54,
+           "Pt": 48, "Au": 36, "Hg": 33.91, "Tl": 50, "Pb": 47, "Bi": 48, "Po": 44, "At": 42,
+           "Rn": 35, "Fr": 317.8, "Ra": 246, "Ac": 203, "Pa": 154, "U": 129, "Np": 151, "Pu": 132,
+           "Am": 131, "Cm": 144, "Bk": 125, "Cf": 122, "Es": 118, "Fm": 113, "Md": 109, "No": 110,
+           "Lr": 320, "Rf": 112, "Db": 42, "Sg": 40, "Bh": 38, "Hs": 36, "Mt": 34, "Ds": 32,
+           "Rg": 32, "Cn": 28, "Nh": 29, "Fl": 31, "Mc": 71, "Ts": 76, "Og": 58}
+
+
+# Roman numerals
+romans = {'I': '1', 'II': '2', 'III': '3', 'IV': '4',
+          'V': '5', 'VI': '6', 'VII': '7', 'VIII': '8'}
+
+# bondsdict
+bondsdict = {"H": 1, "Li": 1, "Be": 2, "B": 3, "C": 4, "N": 3, "O": 2, "F": 1,
+             "Na": 1, "Mg": 2, "Al": 3, "Si": 4, "P": 3, "S": 2, "Cl": 1,
+             "As": 3, "Se": 2, "Br": 1, "I": 1, "He": 2}
+
+# triple bonds dictionry: Defined as 0.5*(double bond dist + triple bond dist)
+# bond lengths are from http://www.wiredchemist.com/chemistry/data/bond_energies_lengths.html
+tribonddict = {("C", "C"): 1.27, ("C", "N"): 1.235, ("C", "O"): 1.165, ("N", "N"): 1.175,
+               ("N", "C"): 1.235, ("O", "C"): 1.165}
+
+# Amino acids
+amino_acids = {"ALA": "ALA", "A": "ALA",
+               "ARG": "ARG", "R": "ARG", "ARN": "ARG",
+               "ASN": "ASN", "N": "ASN",
+               "ASP": "ASP", "D": "ASP", "ASH": "ASP",
+               "CYS": "CYS", "C": "CYS", "CYS2": "CYS", "CYM": "CYS",
+               "CYX": "CYS", "GLU": "GLU", "E": "GLU", "GLH": "GLU",
+               "GLN": "GLN", "Q": "GLN", 'AGLN': 'GLN', 'BGLN': 'GLN',
+               "GLY": "GLY", "G": "GLY",
+               "HIS": "HIS", 'H': "HIS", "HID": "HIS", "HIE": "HIS",
+               "HIP": "HIS", "HSE": "HIS", "HSD": "HIS", "HSP": "HIS",
+               "ILE": "ILE", "I": "ILE", "LEU": "LEU", "L": "LEU",
+               "LYS": "LYS", "K": "LYS", "LYN": "LYS",
+               "MET": "MET", "M": "MET", "AMET": "MET", "BMET": "MET",
+               "PHE": "PHE", "F": "PHE", "PRO": "PRO", "P": "PRO",
+               "SER": "SER", "S": "SER", "ASER": "SER", "BSER": "SER",
+               "THR": "THR", 'T': "THR", "TRP": "TRP", "W": "TRP",
+               "TYR": "TYR", "Y": 'TYR',
+               "VAL": "VAL", 'V': "VAL", 'AVAL': 'VAL', 'BVAL': 'VAL'
+               }
+
+# Common heteromolecules
+het_mols = ['TAU', 'AKG', 'FE2', 'HOH', 'NAG', 'BMA', 'MAN', 'ACE', 'ACY', 'FE',
+            'HEM', 'BLE', 'MG', 'BGC', 'WAT', 'CA', 'CL1']
+
+# ---Geo_Check_Metrics------
+dict_oct_check_loose = {"mono": {'num_coord_metal': 6,
+                                 'rmsd_max': 0.4, 'atom_dist_max': 0.6,
+                                 'oct_angle_devi_max': 16, 'max_del_sig_angle': 27,
+                                 'dist_del_eq': 0.45, 'dist_del_all': 1.25,
+                                 'devi_linear_avrg': 35, 'devi_linear_max': 40},
+                        "multi": {'num_coord_metal': 6,
+                                  'rmsd_max': 4, 'atom_dist_max': 0.6,
+                                  'oct_angle_devi_max': 20, 'max_del_sig_angle': 35,
+                                  'dist_del_eq': 0.45, 'dist_del_all': 1.25,
+                                  'devi_linear_avrg': 35, 'devi_linear_max': 40}
+                        }
+
+dict_oct_check_st = {"mono": {'num_coord_metal': 6,
+                              'rmsd_max': 0.3, 'atom_dist_max': 0.45,
+                              'oct_angle_devi_max': 12, 'max_del_sig_angle': 22.5,
+                              'dist_del_eq': 0.35, 'dist_del_all': 1.0,
+                              'devi_linear_avrg': 20, 'devi_linear_max': 28},
+                     "multi": {'num_coord_metal': 6,
+                               'rmsd_max': 3, 'atom_dist_max': 0.45,
+                               'oct_angle_devi_max': 20, 'max_del_sig_angle': 36,
+                               'dist_del_eq': 0.35, 'dist_del_all': 1.0,
+                               'devi_linear_avrg': 20, 'devi_linear_max': 28}
+                     }
+
+dict_oneempty_check_st = {"mono": {'num_coord_metal': 5,
+                                   'rmsd_max': 0.4, 'atom_dist_max': 0.7,
+                                   'oct_angle_devi_max': 15, 'max_del_sig_angle': 18,
+                                   'dist_del_eq': 0.5, 'dist_del_all': 1,
+                                   'devi_linear_avrg': 10, 'devi_linear_max': 20},
+                          "multi": {'num_coord_metal': 5,
+                                    'rmsd_max': 0.4, 'atom_dist_max': 0.7,
+                                    'oct_angle_devi_max': 15, 'max_del_sig_angle': 18,
+                                    'dist_del_eq': 0.5, 'dist_del_all': 1,
+                                    'devi_linear_avrg': 10, 'devi_linear_max': 20}
+                          }
+
+dict_oneempty_check_loose = {"mono": {'num_coord_metal': 5,
+                                      'rmsd_max': 0.6, 'atom_dist_max': 0.9,
+                                      'oct_angle_devi_max': 20, 'max_del_sig_angle': 27,
+                                      'dist_del_eq': 0.6, 'dist_del_all': 1.2,
+                                      'devi_linear_avrg': 15, 'devi_linear_max': 28},
+                             "multi": {'num_coord_metal': 5,
+                                       'rmsd_max': 0.6, 'atom_dist_max': 0.9,
+                                       'oct_angle_devi_max': 20, 'max_del_sig_angle': 27,
+                                       'dist_del_eq': 0.6, 'dist_del_all': 1.2,
+                                       'devi_linear_avrg': 15, 'devi_linear_max': 28}
+                             }
+
+dict_tetra_check_loose = {"mono": {'num_coord_metal': 4, 'rmsd_max': 0.4,
+                                   'oct_angle_devi_max': 16, 'max_del_sig_angle': 27,
+                                   'dist_del_all': 1.25,
+                                   'devi_linear_avrg': 35, 'devi_linear_max': 40},
+                          "multi": {'num_coord_metal': 4, 'rmsd_max': 0.4,
+                                    'oct_angle_devi_max': 16, 'max_del_sig_angle': 27,
+                                    'dist_del_all': 1.25,
+                                    'devi_linear_avrg': 35, 'devi_linear_max': 40}
+                          }
+
+dict_tetra_check_st = {"mono": {'num_coord_metal': 4, 'rmsd_max': 0.3,
+                                'oct_angle_devi_max': 12, 'max_del_sig_angle': 22.5,
+                                'dist_del_all': 1,
+                                'devi_linear_avrg': 20, 'devi_linear_max': 28},
+                       "multi": {'num_coord_metal': 4, 'rmsd_max': 0.3,
+                                 'oct_angle_devi_max': 12, 'max_del_sig_angle': 22.5,
+                                 'dist_del_all': 1,
+                                 'devi_linear_avrg': 20, 'devi_linear_max': 28}
+                       }
+
+dict_eightcoord_check = {"mono": {'num_coord_metal': 8,
+                              'rmsd_max': 0.4, 'atom_dist_max': 0.6,
+                              'oct_angle_devi_max': 16, 'max_del_sig_angle': 27,
+                              'dist_del_eq': 0.45, 'dist_del_all': 1.25,
+                              'devi_linear_avrg': 35, 'devi_linear_max': 40},
+                         "multi": {'num_coord_metal': 8,
+                               'rmsd_max': 0.4, 'atom_dist_max': 0.6,
+                               'oct_angle_devi_max': 20, 'max_del_sig_angle': 35,
+                               'dist_del_eq': 0.45, 'dist_del_all': 1.25,
+                               'devi_linear_avrg': 35, 'devi_linear_max': 40}
+                         }
+
+dict_staus = {'good': 1, 'bad': 0}
+
+oct_angle_ref = [[90, 90, 90, 90, 180] for x in range(6)]
+tetra_angle_ref = [[109.47, 109.47, 109.47] for x in range(4)]
+oneempty_angle_ref = [[90, 90, 90, 90], [180, 90, 90, 90], [180, 90, 90, 90],
+                      [180, 90, 90, 90], [180, 90, 90, 90]]
+eightcoord_angle_ref = [[73.7, 73.7, 76.8, 76.8, 116.1, 142.1, 142.1] for x in range(8)]
+geo_check_dictionary = {"dict_oct_check_loose": dict_oct_check_loose,
+                        "dict_oct_check_st": dict_oct_check_st,
+                        "dict_oneempty_check_st": dict_oneempty_check_st,
+                        "dict_oneempty_check_loose": dict_oneempty_check_loose,
+                        "dict_staus": dict_staus,
+                        "oct_angle_ref": oct_angle_ref,
+                        "oneempty_angle_ref": oneempty_angle_ref,
+                        "eightcoord_angle_ref": eightcoord_angle_ref}
+all_geometries = {
+    2: ["linear", "bent"],
+    3: ["trigonal planar", "T shape", "trigonal pyramidal"],
+    4: ["tetrahedral", "square planar", "seesaw"],
+    5: ["trigonal bipyramidal", "square pyramidal", "pentagonal planar"],
+    6: ["octahedral", "pentagonal pyramidal", "trigonal prismatic"],
+    7: ["pentagonal bipyramidal"],
+    8: ["square antiprismatic"],
+    9: ["tricapped trigonal prismatic"]
+}
+all_angle_refs = {
+    "linear": [[180] for x in range(2)],
+    "bent": [[120] for x in range(2)],
+    "trigonal planar": [[120, 120] for x in range(3)],
+    "T shape": [[90, 90], [90, 180], [90, 180]],
+    "tetrahedral": [[109.47, 109.47, 109.47] for x in range(4)],
+    "square planar": [[90, 90, 180] for x in range(4)],
+    "seesaw": [[90, 90, 180] for x in range(2)] + [[90, 90, 120] for x in range(2)],
+    "trigonal pyramidal": [[109.5, 109.5] for x in range(3)],
+    "trigonal bipyramidal": [[90, 90, 90, 180] for x in range(2)] + [[120, 120, 90, 90] for x in range(3)],
+    "square pyramidal": [[90, 90, 90, 90]] + [[180, 90, 90, 90] for x in range(4)],
+    "pentagonal planar": [[36, 36, 72, 72] for x in range(5)],
+    "octahedral": [[90, 90, 90, 90, 180] for x in range(6)],
+    "pentagonal pyramidal": [[90, 90, 90, 90, 90]] + [[36, 36, 72, 72, 90] for x in range(5)],
+    "trigonal prismatic": [[75.3, 86.5, 86.5, 133.3, 133.3] for x in range(6)],
+    "pentagonal bipyramidal": [[90, 90, 90, 90, 90, 180] for x in range(2)] +
+                              [[72, 72, 144, 144, 90, 90] for x in range(5)],
+    "square antiprismatic": [[73.7, 73.7, 76.8, 76.8, 116.1, 142.1, 142.1] for x in range(8)],
+    "tricapped trigonal prismatic": [[70.5, 70.5, 120, 67.7, 67.7, 135.5, 135.5, 120] for x in range(4)] +
+                                    [[76.3, 79, 138.2, 70.5, 67.7, 76.3, 138.2, 135.5] for x in range(4)] +
+                                    [[70.5, 70.5, 67.7, 67.7, 120, 120, 135.5, 135.5]]
+}
+
+# Module for running bash commands
+#  @param cmd String containing command to be run
+#  @return bash output string
+def mybash(cmd):
+    """Function to run a bash command.
+
+    Parameters
+    ----------
+        cmd : str
+            String containing command to be run
+
+    Returns
+    -------
+        output : str
+            bash output string
+
+    """
+    p = subprocess.Popen(
+        cmd, shell=True, stdout=subprocess.PIPE, stderr=subprocess.STDOUT)
+    stdout, stderr = p.communicate()
+    lines = stdout.decode('utf-8').splitlines()
+    lines = [line+"\n" for line in lines if line !=""]
+    return ''.join(lines)
+
+
+# Defines global variables used throughout the code
+class globalvars(metaclass=Singleton):
+    """Globalvars class. Defines global variables used throughout the code, including periodic table.
+    """
+    def __init__(self):
+        # Program name
+        self.PROGRAM = 'molSimplify'
+        s = '\nmolSimplify v1.3.3x\nFreely distributed under the GNU GPL license.\n'
+        s += 'Copyright 2017 Kulik Lab @ MIT\n'
+        s += 'Developed by: Efthymios Ioannidis (timis@mit.edu)\n'
+        s += 'Contributions by:\n\tHeather J. Kulik (hjkulik@mit.edu)\n'
+        s += '\t Terry Gani (terryg@mit.edu)\n'
+        s += '\t JP Janet (jpjanet@mit.edu)\n'
+        s += 'E. I. Ioannidis, T. Z. H. Gani, H. J. Kulik. J. Comput. Chem. 2016, 37, 2106-2117.\n'
+        s += 'J.P. Janet, Q. Zhao, E.I. Ioannidis, H.J. Kulik. Mol. Simul. 2017,43(5-6), 327-345.\n'
+        s += 'J.P. Janet, T. Z. H. Gani, A. H. Steeves, E. I. Ioannidis, H. J. Kulik. Ind. Eng. Chem. Res. 2017, 56(17), 4898-4910.\n'
+        # About message
+        self.about = s
+        # ##### GET INFORMATION ######
+        runfromcmd = False
+        try:
+            # ## check if running through commandline ###
+            if sys.stdin.isatty():
+                # running through command line
+                runfromcmd = True
+            else:
+                runfromcmd = False
+        except AttributeError:  # if sys.stdin does not have an isatty method
+            runfromcmd = True
+        # ## get running os ###
+        self.linux, self.osx = False, False
+        if platform.system().lower() in 'linux':
+            self.linux = True
+        elif platform.system().lower() in 'darwin':
+            self.osx = True
+        # get cwd
+        # script filename (usually with path)
+        _ = inspect.getfile(inspect.currentframe())
+        cdir2 = os.path.dirname(os.path.abspath(
+            inspect.getfile(inspect.currentframe())))  # script directory
+        cdir = cdir2.rsplit('/', 1)[0]
+        # unused:
+        # cdir2 = cdir
+        homedir = os.path.expanduser("~")
+        # create default molSimplify for mac
+        if self.osx and not glob.glob(homedir + '/.' + self.PROGRAM) and not runfromcmd:
+            txt = 'INSTALLDIR=/Applications/' + self.PROGRAM + '.app/Contents/Resources\n'
+            with open(homedir + '/.' + self.PROGRAM, 'w') as fout:
+                fout.write(txt)
+        self.chemdbdir = ''
+        self.multiwfn = ''
+        self.custom_path = False
+        # ##### check for ~/.molSimplify ######
+        if glob.glob(homedir + '/.' + self.PROGRAM):
+            with open(homedir + '/.' + self.PROGRAM, 'r') as fin:
+                s = [_f for _f in fin.read().splitlines() if _f]
+            d = dict()
+            for ss in s:
+                sp = [_f for _f in ss.split('=') if _f]
+                try:
+                    d[sp[0]] = sp[1]
+                except IndexError:
+                    pass
+            if 'CHEMDBDIR' in list(d.keys()):
+                self.chemdbdir = d['CHEMDBDIR']
+            if 'MULTIWFN' in list(d.keys()):
+                self.multiwfn = "'" + d['MULTIWFN'] + "'"
+            if 'CUSTOM_DATA_PATH' in list(d.keys()):
+                self.custom_path = d['CUSTOM_DATA_PATH']
+        else:
+            self.installdir = cdir
+            with open(homedir + '/.' + self.PROGRAM, 'w') as fout:
+                fout.write('CHEMDBDIR=\n')
+
+        # Home directory
+        self.homedir = homedir
+        # Number of smiles ligands
+        self.nosmiles = 0
+        # Jobs directory
+        self.rundir = homedir + '/Runs/'
+        # Number of generated structures
+        self.generated = 0
+        # Additional debug output
+        self.debug = False
+        # SMARTS patterns for forced hydrogen removal
+        self.remHsmarts = ["O=CN", "O=CO", "n", "N=CN", "nN"]
+        # Default geometries for each coordination number if none specified
+        self.defaultgeometry = {8: ('sqap', 'square_antiprismatic'), 7: ('pbp', 'pentagonal_bipyramidal'),
+                                6: ('oct', 'octahedral'), 5: ('tbp', 'trigonal bipyramidal'), 4: ('thd', 'tetrahedral'),
+                                3: ('trigonal planar', 'tpl'), 2: ('linear', 'li'), 1: ('one', 'one')}
+        # Default oxidation states for elements
+        self.defaultoxstate = {
+            'au': 'I', 'gold': 'I', 'scandium': 'III', 'sc': 'III', 'ti': 'IV', 'titanium': 'IV'}
+        # bent "linear" angle in degrees, e.g., in Fe(III)-superoxo or a bent nitrosyl
+        self.linearbentang = 45
+
+    # Returns atomic mass dictionary
+    #  @param self The object pointer
+    #  @return Atomic mass dictionary
+    def amass(self) -> Dict[str, Tuple[float, int, float, int]]:
+        """Get the atomic mass dictionary.
+
+        Returns
+        -------
+            amassdict : dict
+                Dictionary containing atomic masses.
+        """
+        return amassdict
+
+    def polarizability(self) -> Dict[str, float]:
+        """Get the polarizability dictionary.
+
+        Returns
+        -------
+            poldict : dict
+                Dictionary containing polarizabilities.
+        """
+        return poldict
+
+    def tribonddict(self):
+        """Get the triple bond dictionary.
+
+        Returns
+        -------
+            tribonddict : dict
+                Dictionary containing triple bond lengths.
+        """
+        return tribonddict
+
+    def bondsdict(self):
+        """Get the bond dictionary.
+
+        Returns
+        -------
+            bondsdict : dict
+                Dictionary containing bond lengths.
+        """
+        return bondsdict
+
+    def elementsbynum(self):
+        """Returns list of elements by number
+
+        Returns
+        -------
+            elementsbynum : list
+                List of elements by number
+        """
+        return elementsbynum
+
+    def endict(self):
+        """Returns electronegativity dictionary.
+
+        Returns
+        -------
+            endict : list
+                Electronegativity dictionary
+        """
+        return endict
+
+    def vdwrad(self):
+        """Returns VDW dictionary.
+
+        Returns
+        -------
+            vdwrad : list
+                Dictionary of VDW radii.
+        """
+        return vdwrad
+
+    def metalslist(self, transition_metals_only=True):
+        """Get the metals list.
+
+        Returns
+        -------
+            metalslist : list
+                List of available metals.
+        """
+        if not transition_metals_only:
+            return metalslist + alkali_and_alkaline_earth + heavy_metals_and_metalloids
+        else:
+            return metalslist
+
+    def groups(self):
+        """Returns dict of elements by groups.
+
+        Returns
+        -------
+            groups_dict : dict
+                Groups dictionary.
+        """
+        return groups_dict
+
+    def periods(self):
+        """Returns dict of elements by periods.
+
+        Returns
+        -------
+            periods_dict : dict
+                Periods dictionary.
+        """
+        return periods_dict
+
+    def geo_check_dictionary(self):
+        """Returns list of geo check objects dictionary.
+
+        Returns
+        -------
+            geo_check_dictionary : dict
+                Geo check measurement dictionary.
+        """
+        return geo_check_dictionary
+
+    def get_all_geometries(self):
+        """Get available geometries.
+
+        Returns
+        -------
+            all_geometries : list
+                All available geometries.
+        """
+        return all_geometries
+
+    def get_all_angle_refs(self):
+        """Get references angle dict.
+
+        Returns
+        -------
+            all_angle_refs : dict
+                Reference angles for various geometries.
+        """
+        return all_angle_refs
+
+    def add_custom_path(self, path):
+        """Record custom path in ~/.molSimplify file
+
+        Parameters
+        ----------
+            path : str
+                Path to custom data ~/.molSimplify file.
+        """
+        homedir = os.path.expanduser("~")
+        with open(homedir + '/.' + self.PROGRAM, 'a') as f:
+            f.write('CUSTOM_DATA_PATH=' + str(path) + "\n")
+
+    def bbcombs_mononuc(self):
+        """Get backbone combinations dictionary
+
+        Returns
+        -------
+            bbcombs_mononuc : dict
+                Backbone combination dictionary for different geometries.
+        """
+        bbcombs_mononuc = dict()
+        bbcombs_mononuc['one'] = [[1]]
+        bbcombs_mononuc['li'] = [[1], [2]]
+        bbcombs_mononuc['oct'] = [[1, 2, 3, 4, 5, 6],  # 6-dentate
+                                  [1, 2, 3, 4, 5], [1, 2, 3, 4, 6], [
+                                      1, 2, 3, 5, 6], [1, 2, 4, 5, 6],  # 5-dentate
+                                  [1, 3, 4, 5, 6], [2, 3, 4, 5, 6],  # 5-dentate
+                                  [1, 2, 3, 4], [2, 5, 4, 6], [
+                                      1, 5, 3, 6],  # 4-dentate
+                                  [1, 2, 3], [1, 4, 2], [1, 4, 3], [1, 5, 3], [
+                                      1, 6, 3], [2, 3, 4],  # 3-dentate
+                                  [2, 5, 4], [2, 6, 4], [5, 4, 6], [5, 1, 6], [
+                                      5, 2, 6], [5, 3, 6],  # 3-dentate
+                                  [1, 2], [1, 4], [1, 5], [1, 6], [
+                                      2, 3], [2, 5],  # 2-dentate
+                                  [2, 6], [3, 5], [3, 6], [4, 5], [
+                                      4, 6], [3, 4],  # 2-dentate
+                                  [1], [2], [3], [4], [5], [6]]  # 1-dentate
+        bbcombs_mononuc['pbp'] = [[1, 2, 3, 4, 5, 6], [1, 2, 3, 4, 6],  # 6/5-dentate
+                                  [1, 2, 3, 5],  # 4-dentate
+                                  [1, 2, 3], [1, 2, 4], [2, 1, 5], [3, 1, 6], [
+                                      5, 6, 3], [2, 6, 5],  # 3-dentate
+                                  [1, 2], [2, 3], [3, 4], [4, 5], [1, 7], [
+                                      2, 6], [5, 7], [3, 6],  # 2-dentate
+                                  [1], [2], [3], [4], [5], [6], [7]]  # 1-dentate
+        bbcombs_mononuc['spy'] = [[1, 2, 3, 4, 5], [1, 2, 3, 4], [1, 2, 3], [2, 3, 4], [3, 4, 1], [4, 1, 2],
+                                  [1, 2], [1, 4], [2, 3], [3, 4], [4, 5], [
+                                      2, 5], [3, 5], [1, 5], [1], [2], [3], [4],
+                                  [5]]
+        bbcombs_mononuc['sqp'] = [[1, 4, 2, 3], [1, 2, 3], [2, 3, 4], [3, 4, 1], [4, 1, 2], [1, 2], [1, 4], [2, 3],
+                                  [3, 4],
+                                  [1], [2], [3], [4]]
+        bbcombs_mononuc['tbp'] = [[1, 2, 3, 4, 5], [1, 3, 4, 5], [3, 2, 4], [4, 5, 3], [5, 1, 3], [4, 5], [5, 3],
+                                  [3, 4],
+                                  [1, 4], [1, 5], [1, 3], [2, 4], [2, 5], [2, 3], [1], [2], [3], [4], [5]]
+        bbcombs_mononuc['thd'] = [[1, 2, 3, 4], [3, 2, 4], [2, 4, 1], [4, 1, 3], [2, 4], [4, 3], [3, 2], [1, 3], [1, 4],
+                                  [2, 4], [1], [2], [3], [4]]
+        bbcombs_mononuc['tpl'] = [[1, 2, 3], [
+            1, 2], [2, 3], [1, 3], [1], [2], [3]]
+        bbcombs_mononuc['tpr'] = [[1, 2, 3, 4, 5, 6], [1, 2, 3, 4, 5], [1, 2, 5, 4], [5, 2, 3, 6], [1, 4, 6, 3],
+                                  [1, 2, 3], [3, 6, 5],
+                                  [2, 3], [2, 5], [5, 6], [6, 4], [4, 1], [1], [2], [3], [4], [5], [6]]
+        return bbcombs_mononuc
+
+    def testTF(self):
+        """Tests to see whether keras and tensorflow are available.
+
+        Returns
+        -------
+            tf_flag : bool
+                True if tensorflow and keras are available.
+        """
+        try:
+            os.environ['TF_CPP_MIN_LOG_LEVEL'] = '3'
+            from tensorflow.keras.models import Model  # noqa: F401
+            from tensorflow.keras.models import Sequential  # noqa: F401
+            return True
+        except ImportError:
+            return False
+
+    def testmatplotlib(self):
+        """Tests to see if matplotlib is available
+
+        Returns
+        -------
+            mpl_flag : bool
+                True if matplotlib is available
+        """
+        try:
+            # os.environ['TF_CPP_MIN_LOG_LEVEL'] = '3'
+            import matplotlib.pyplot as plt  # noqa: F401
+            import matplotlib.ticker as ticker  # noqa: F401
+            return True
+        except ImportError:
+            return False
+
+    def getAllAAs(self):
+        """ Gets all amino acids
+
+        Returns
+        -------
+            amino_acids : dictionary
+                Dictionary of standard amino acids
+        """
+        return amino_acids