diff --git a/docs/releasehistory.rst b/docs/releasehistory.rst
index cd1e561b..3f959641 100644
--- a/docs/releasehistory.rst
+++ b/docs/releasehistory.rst
@@ -7,6 +7,19 @@ Releases follow the ``major.minor.micro`` scheme recommended by `PEP440 <https:/
 * ``minor`` increments add features but do not break API compatibility
 * ``micro`` increments represent bugfix releases or improvements in documentation
 
+1.3.3 - Explicit hydrogens support
+---------------------------------------------------------
+
+This is a micro release of peleffy that includes support for the new OpenFF flag to manage explicit and implicit hydrogen atoms.
+
+New features
+""""""""""""
+- `PR #146 <https://github.com/martimunicoy/peleffy/pull/146>`_: Adds support for the new explicit hydrogens flag
+
+Tests added
+"""""""""""
+- `PR #146 <https://github.com/martimunicoy/peleffy/pull/146>`_: New test to check new explicit hydrogens flag
+
 
 1.3.2 - Migration and support for openff.toolkit
 ---------------------------------------------------------
diff --git a/examples/OFF_parameterization/parameterize.ipynb b/examples/OFF_parameterization/parameterize.ipynb
index 56f02590..6ef0af67 100644
--- a/examples/OFF_parameterization/parameterize.ipynb
+++ b/examples/OFF_parameterization/parameterize.ipynb
@@ -66,34 +66,42 @@
       "   - Assigning stereochemistry from 3D coordinates\n",
       "   - Setting molecule name to 'benzene'\n",
       "   - Setting molecule tag to 'BNZ'\n",
-      "   - Representing molecule with the Open Force Field Toolkit\n"
-     ]
-    },
-    {
-     "data": {
-      "application/vnd.jupyter.widget-view+json": {
-       "model_id": "2b60a5496a7e4336a5a3b88b2b7d3c6a",
-       "version_major": 2,
-       "version_minor": 0
-      },
-      "text/plain": []
-     },
-     "metadata": {},
-     "output_type": "display_data"
-    },
-    {
-     "name": "stderr",
-     "output_type": "stream",
-     "text": [
+      "   - Representing molecule with the Open Force Field Toolkit\n",
       " - Generating rotamer library\n",
       "   - Core set to the center of the molecule\n"
      ]
     },
     {
      "data": {
-      "image/png": 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+       "<path class=\"bond-10 atom-4 atom-10\" d=\"M 195.7,155.949 L 151.142,78.7736\" style=\"fill:none;fill-rule:evenodd;stroke:#000000;stroke-width:4.0px;stroke-linecap:butt;stroke-linejoin:miter;stroke-opacity:1\"/>\n",
+       "<path class=\"bond-11 atom-5 atom-11\" d=\"M 304.3,155.949 L 348.858,78.7736\" style=\"fill:none;fill-rule:evenodd;stroke:#000000;stroke-width:4.0px;stroke-linecap:butt;stroke-linejoin:miter;stroke-opacity:1\"/>\n",
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+       "<path class=\"atom-8\" d=\"M 130.32 423.941 L 134.16 423.941 L 134.16 435.981 L 148.64 435.981 L 148.64 423.941 L 152.48 423.941 L 152.48 452.261 L 148.64 452.261 L 148.64 439.181 L 134.16 439.181 L 134.16 452.261 L 130.32 452.261 L 130.32 423.941 \" fill=\"#000000\"/>\n",
+       "<path class=\"atom-9\" d=\"M 21.7192 235.84 L 25.5592 235.84 L 25.5592 247.88 L 40.0392 247.88 L 40.0392 235.84 L 43.8792 235.84 L 43.8792 264.16 L 40.0392 264.16 L 40.0392 251.08 L 25.5592 251.08 L 25.5592 264.16 L 21.7192 264.16 L 21.7192 235.84 \" fill=\"#000000\"/>\n",
+       "<path class=\"atom-10\" d=\"M 130.32 47.7386 L 134.16 47.7386 L 134.16 59.7786 L 148.64 59.7786 L 148.64 47.7386 L 152.48 47.7386 L 152.48 76.0586 L 148.64 76.0586 L 148.64 62.9786 L 134.16 62.9786 L 134.16 76.0586 L 130.32 76.0586 L 130.32 47.7386 \" fill=\"#000000\"/>\n",
+       "<path class=\"atom-11\" d=\"M 347.52 47.7386 L 351.36 47.7386 L 351.36 59.7786 L 365.84 59.7786 L 365.84 47.7386 L 369.68 47.7386 L 369.68 76.0586 L 365.84 76.0586 L 365.84 62.9786 L 351.36 62.9786 L 351.36 76.0586 L 347.52 76.0586 L 347.52 47.7386 \" fill=\"#000000\"/>\n",
+       "</svg>"
+      ],
       "text/plain": [
-       "<rdkit.Chem.rdchem.Mol at 0x7f8b5e81b440>"
+       "<IPython.core.display.SVG object>"
       ]
      },
      "metadata": {},
@@ -210,7 +218,7 @@
      "name": "stderr",
      "output_type": "stream",
      "text": [
-      " - Loading solvent parameters\n"
+      " - Generating solvent parameters\n"
      ]
     }
    ],
@@ -281,9 +289,107 @@
     },
     {
      "data": {
-      "image/png": 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       "text/plain": [
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      "metadata": {},
@@ -398,7 +504,7 @@
      "name": "stderr",
      "output_type": "stream",
      "text": [
-      " - Loading solvent parameters\n"
+      " - Generating solvent parameters\n"
      ]
     }
    ],
@@ -450,9 +556,44 @@
     },
     {
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+       "<path class=\"bond-6 atom-6 atom-7\" d=\"M 360.687,290.976 L 306.766,311.633\" style=\"fill:none;fill-rule:evenodd;stroke:#000000;stroke-width:4.0px;stroke-linecap:butt;stroke-linejoin:miter;stroke-opacity:1\"/>\n",
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+       "<path class=\"atom-10\" d=\"M 138.754 181.313 L 141.922 181.313 L 141.922 191.245 L 153.867 191.245 L 153.867 181.313 L 157.034 181.313 L 157.034 204.674 L 153.867 204.674 L 153.867 193.884 L 141.922 193.884 L 141.922 204.674 L 138.754 204.674 L 138.754 181.313 \" fill=\"#000000\"/>\n",
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+       "<path class=\"atom-12\" d=\"M 330.849 75.3885 L 334.017 75.3885 L 334.017 85.3202 L 345.961 85.3202 L 345.961 75.3885 L 349.129 75.3885 L 349.129 98.7496 L 345.961 98.7496 L 345.961 87.9599 L 334.017 87.9599 L 334.017 98.7496 L 330.849 98.7496 L 330.849 75.3885 \" fill=\"#000000\"/>\n",
+       "<path class=\"atom-13\" d=\"M 458.993 179.299 L 462.161 179.299 L 462.161 189.231 L 474.105 189.231 L 474.105 179.299 L 477.273 179.299 L 477.273 202.66 L 474.105 202.66 L 474.105 191.87 L 462.161 191.87 L 462.161 202.66 L 458.993 202.66 L 458.993 179.299 \" fill=\"#000000\"/>\n",
+       "<path class=\"atom-14\" d=\"M 433.076 342.23 L 436.243 342.23 L 436.243 352.162 L 448.188 352.162 L 448.188 342.23 L 451.355 342.23 L 451.355 365.591 L 448.188 365.591 L 448.188 354.801 L 436.243 354.801 L 436.243 365.591 L 433.076 365.591 L 433.076 342.23 \" fill=\"#000000\"/>\n",
+       "<path class=\"atom-15\" d=\"M 279.015 401.25 L 282.182 401.25 L 282.182 411.182 L 294.127 411.182 L 294.127 401.25 L 297.294 401.25 L 297.294 424.612 L 294.127 424.612 L 294.127 413.822 L 282.182 413.822 L 282.182 424.612 L 279.015 424.612 L 279.015 401.25 \" fill=\"#000000\"/>\n",
+       "</svg>"
+      ],
       "text/plain": [
-       "<rdkit.Chem.rdchem.Mol at 0x7f8b5c749490>"
+       "<IPython.core.display.SVG object>"
       ]
      },
      "metadata": {},
@@ -460,7 +601,7 @@
     }
    ],
    "source": [
-    "molecule = Molecule(smiles='COc1ccccc1')\n",
+    "molecule = Molecule(smiles='COc1ccccc1', hydrogens_are_explicit=False)\n",
     "display(molecule)"
    ]
   },
@@ -582,7 +723,7 @@
      "name": "stderr",
      "output_type": "stream",
      "text": [
-      " - Loading solvent parameters\n"
+      " - Generating solvent parameters\n"
      ]
     }
    ],
@@ -608,7 +749,7 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 16,
+   "execution_count": 34,
    "metadata": {},
    "outputs": [],
    "source": [
@@ -626,7 +767,7 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 17,
+   "execution_count": 35,
    "metadata": {},
    "outputs": [],
    "source": [
@@ -635,7 +776,7 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 18,
+   "execution_count": 36,
    "metadata": {},
    "outputs": [
     {
@@ -658,59 +799,59 @@
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        "<!-- END OF HEADER -->\n",
        "<rect height=\"500\" style=\"opacity:1.0;fill:#FFFFFF;stroke:none\" width=\"500\" x=\"0\" y=\"0\"> </rect>\n",
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-       "<path class=\"bond-0\" d=\"M 245.488,290.191 L 262.943,282.787\" style=\"fill:none;fill-rule:evenodd;stroke:#000000;stroke-width:4.0px;stroke-linecap:butt;stroke-linejoin:miter;stroke-opacity:1\"/>\n",
-       "<path class=\"bond-1\" d=\"M 213.897,295.264 L 199.226,284.203\" style=\"fill:none;fill-rule:evenodd;stroke:#FF0000;stroke-width:4.0px;stroke-linecap:butt;stroke-linejoin:miter;stroke-opacity:1\"/>\n",
-       "<path class=\"bond-1\" d=\"M 199.226,284.203 L 184.555,273.142\" style=\"fill:none;fill-rule:evenodd;stroke:#000000;stroke-width:4.0px;stroke-linecap:butt;stroke-linejoin:miter;stroke-opacity:1\"/>\n",
-       "<path class=\"bond-2\" d=\"M 328.694,332.361 L 314.023,321.3\" style=\"fill:none;fill-rule:evenodd;stroke:#FF0000;stroke-width:4.0px;stroke-linecap:butt;stroke-linejoin:miter;stroke-opacity:1\"/>\n",
-       "<path class=\"bond-2\" d=\"M 314.023,321.3 L 299.352,310.238\" style=\"fill:none;fill-rule:evenodd;stroke:#000000;stroke-width:4.0px;stroke-linecap:butt;stroke-linejoin:miter;stroke-opacity:1\"/>\n",
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-       "<path class=\"bond-3\" d=\"M 332.948,360.554 L 331.103,375.548\" style=\"fill:none;fill-rule:evenodd;stroke:#000000;stroke-width:4.0px;stroke-linecap:butt;stroke-linejoin:miter;stroke-opacity:1\"/>\n",
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-       "<path class=\"bond-4\" d=\"M 258.387,263.922 L 258.383,282.786\" style=\"fill:none;fill-rule:evenodd;stroke:#000000;stroke-width:4.0px;stroke-linecap:butt;stroke-linejoin:miter;stroke-opacity:1\"/>\n",
-       "<path class=\"bond-4\" d=\"M 267.511,245.06 L 267.507,263.924\" style=\"fill:none;fill-rule:evenodd;stroke:#FF0000;stroke-width:4.0px;stroke-linecap:butt;stroke-linejoin:miter;stroke-opacity:1\"/>\n",
-       "<path class=\"bond-4\" d=\"M 267.507,263.924 L 267.503,282.788\" style=\"fill:none;fill-rule:evenodd;stroke:#000000;stroke-width:4.0px;stroke-linecap:butt;stroke-linejoin:miter;stroke-opacity:1\"/>\n",
-       "<path class=\"bond-5\" d=\"M 326.804,273.829 L 299.352,310.238\" style=\"fill:none;fill-rule:evenodd;stroke:#000000;stroke-width:4.0px;stroke-linecap:butt;stroke-linejoin:miter;stroke-opacity:1\"/>\n",
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-       "<path class=\"bond-8\" d=\"M 326.804,273.829 L 357.021,296.611\" style=\"fill:none;fill-rule:evenodd;stroke:#000000;stroke-width:4.0px;stroke-linecap:butt;stroke-linejoin:miter;stroke-opacity:1\"/>\n",
-       "<path class=\"bond-9\" d=\"M 299.352,310.238 L 262.943,282.787\" style=\"fill:none;fill-rule:evenodd;stroke:#000000;stroke-width:4.0px;stroke-linecap:butt;stroke-linejoin:miter;stroke-opacity:1\"/>\n",
-       "<path class=\"bond-10\" d=\"M 294.279,315.452 L 295.736,316.55\" style=\"fill:none;fill-rule:evenodd;stroke:#000000;stroke-width:1.0px;stroke-linecap:butt;stroke-linejoin:miter;stroke-opacity:1\"/>\n",
-       "<path class=\"bond-10\" d=\"M 289.206,320.665 L 292.119,322.861\" style=\"fill:none;fill-rule:evenodd;stroke:#000000;stroke-width:1.0px;stroke-linecap:butt;stroke-linejoin:miter;stroke-opacity:1\"/>\n",
-       "<path class=\"bond-10\" d=\"M 284.134,325.879 L 288.503,329.173\" style=\"fill:none;fill-rule:evenodd;stroke:#000000;stroke-width:1.0px;stroke-linecap:butt;stroke-linejoin:miter;stroke-opacity:1\"/>\n",
-       "<path class=\"bond-10\" d=\"M 279.061,331.092 L 284.886,335.485\" style=\"fill:none;fill-rule:evenodd;stroke:#000000;stroke-width:1.0px;stroke-linecap:butt;stroke-linejoin:miter;stroke-opacity:1\"/>\n",
-       "<path class=\"bond-10\" d=\"M 273.988,336.306 L 281.27,341.796\" style=\"fill:none;fill-rule:evenodd;stroke:#000000;stroke-width:1.0px;stroke-linecap:butt;stroke-linejoin:miter;stroke-opacity:1\"/>\n",
-       "<path class=\"bond-11\" d=\"M 354.255,237.419 L 336.449,195.441\" style=\"fill:none;fill-rule:evenodd;stroke:#000000;stroke-width:4.0px;stroke-linecap:butt;stroke-linejoin:miter;stroke-opacity:1\"/>\n",
-       "<path class=\"bond-11\" d=\"M 359.98,227.561 L 347.515,198.177\" style=\"fill:none;fill-rule:evenodd;stroke:#000000;stroke-width:4.0px;stroke-linecap:butt;stroke-linejoin:miter;stroke-opacity:1\"/>\n",
-       "<path class=\"bond-12\" d=\"M 354.255,237.419 L 399.512,242.988\" style=\"fill:none;fill-rule:evenodd;stroke:#000000;stroke-width:4.0px;stroke-linecap:butt;stroke-linejoin:miter;stroke-opacity:1\"/>\n",
-       "<path class=\"bond-13\" d=\"M 336.449,195.441 L 363.9,159.032\" style=\"fill:none;fill-rule:evenodd;stroke:#000000;stroke-width:4.0px;stroke-linecap:butt;stroke-linejoin:miter;stroke-opacity:1\"/>\n",
-       "<path class=\"bond-14\" d=\"M 336.449,195.441 L 297.384,190.634\" style=\"fill:none;fill-rule:evenodd;stroke:#000000;stroke-width:4.0px;stroke-linecap:butt;stroke-linejoin:miter;stroke-opacity:1\"/>\n",
-       "<path class=\"bond-15\" d=\"M 399.512,242.988 L 426.963,206.578\" style=\"fill:none;fill-rule:evenodd;stroke:#000000;stroke-width:4.0px;stroke-linecap:butt;stroke-linejoin:miter;stroke-opacity:1\"/>\n",
-       "<path class=\"bond-15\" d=\"M 396.348,232.036 L 415.564,206.55\" style=\"fill:none;fill-rule:evenodd;stroke:#000000;stroke-width:4.0px;stroke-linecap:butt;stroke-linejoin:miter;stroke-opacity:1\"/>\n",
-       "<path class=\"bond-16\" d=\"M 399.512,242.988 L 414.096,277.369\" style=\"fill:none;fill-rule:evenodd;stroke:#000000;stroke-width:4.0px;stroke-linecap:butt;stroke-linejoin:miter;stroke-opacity:1\"/>\n",
-       "<path class=\"bond-17\" d=\"M 184.555,273.142 L 148.146,245.691\" style=\"fill:none;fill-rule:evenodd;stroke:#000000;stroke-width:4.0px;stroke-linecap:butt;stroke-linejoin:miter;stroke-opacity:1\"/>\n",
-       "<path class=\"bond-18\" d=\"M 184.555,273.142 L 162.831,301.955\" style=\"fill:none;fill-rule:evenodd;stroke:#000000;stroke-width:4.0px;stroke-linecap:butt;stroke-linejoin:miter;stroke-opacity:1\"/>\n",
-       "<path class=\"bond-19\" d=\"M 184.555,273.142 L 206.279,244.329\" style=\"fill:none;fill-rule:evenodd;stroke:#000000;stroke-width:4.0px;stroke-linecap:butt;stroke-linejoin:miter;stroke-opacity:1\"/>\n",
-       "<path class=\"bond-20\" d=\"M 148.146,245.691 L 153.714,200.433\" style=\"fill:none;fill-rule:evenodd;stroke:#000000;stroke-width:4.0px;stroke-linecap:butt;stroke-linejoin:miter;stroke-opacity:1\"/>\n",
-       "<path class=\"bond-20\" d=\"M 139.929,237.788 L 143.828,206.108\" style=\"fill:none;fill-rule:evenodd;stroke:#000000;stroke-width:4.0px;stroke-linecap:butt;stroke-linejoin:miter;stroke-opacity:1\"/>\n",
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+       "<path class=\"bond-35 atom-18 atom-34\" d=\"M 75.3265,190.788 L 45.1093,168.006\" style=\"fill:none;fill-rule:evenodd;stroke:#000000;stroke-width:4.0px;stroke-linecap:butt;stroke-linejoin:miter;stroke-opacity:1\"/>\n",
        "<path class=\"atom-0\" d=\"M 215.037 300.629 Q 215.037 297.529, 216.569 295.796 Q 218.101 294.063, 220.965 294.063 Q 223.828 294.063, 225.36 295.796 Q 226.892 297.529, 226.892 300.629 Q 226.892 303.767, 225.342 305.554 Q 223.792 307.323, 220.965 307.323 Q 218.119 307.323, 216.569 305.554 Q 215.037 303.785, 215.037 300.629 M 220.965 305.864 Q 222.934 305.864, 223.992 304.551 Q 225.068 303.219, 225.068 300.629 Q 225.068 298.094, 223.992 296.817 Q 222.934 295.522, 220.965 295.522 Q 218.995 295.522, 217.919 296.799 Q 216.861 298.076, 216.861 300.629 Q 216.861 303.238, 217.919 304.551 Q 218.995 305.864, 220.965 305.864 \" fill=\"#FF0000\"/>\n",
        "<path class=\"atom-1\" d=\"M 329.834 337.726 Q 329.834 334.625, 331.366 332.893 Q 332.898 331.16, 335.762 331.16 Q 338.625 331.16, 340.158 332.893 Q 341.69 334.625, 341.69 337.726 Q 341.69 340.863, 340.139 342.651 Q 338.589 344.42, 335.762 344.42 Q 332.916 344.42, 331.366 342.651 Q 329.834 340.881, 329.834 337.726 M 335.762 342.961 Q 337.732 342.961, 338.79 341.647 Q 339.866 340.316, 339.866 337.726 Q 339.866 335.191, 338.79 333.914 Q 337.732 332.619, 335.762 332.619 Q 333.792 332.619, 332.716 333.896 Q 331.658 335.172, 331.658 337.726 Q 331.658 340.334, 332.716 341.647 Q 333.792 342.961, 335.762 342.961 \" fill=\"#FF0000\"/>\n",
        "<path class=\"atom-2\" d=\"M 257.026 237.225 Q 257.026 234.124, 258.558 232.392 Q 260.09 230.659, 262.953 230.659 Q 265.817 230.659, 267.349 232.392 Q 268.881 234.124, 268.881 237.225 Q 268.881 240.362, 267.331 242.15 Q 265.78 243.919, 262.953 243.919 Q 260.108 243.919, 258.558 242.15 Q 257.026 240.38, 257.026 237.225 M 262.953 242.46 Q 264.923 242.46, 265.981 241.146 Q 267.057 239.815, 267.057 237.225 Q 267.057 234.69, 265.981 233.413 Q 264.923 232.118, 262.953 232.118 Q 260.983 232.118, 259.907 233.395 Q 258.849 234.672, 258.849 237.225 Q 258.849 239.833, 259.907 241.146 Q 260.983 242.46, 262.953 242.46 \" fill=\"#FF0000\"/>\n",
@@ -755,7 +896,7 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 19,
+   "execution_count": 37,
    "metadata": {},
    "outputs": [],
    "source": [
@@ -764,7 +905,7 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 20,
+   "execution_count": 38,
    "metadata": {},
    "outputs": [],
    "source": [
@@ -784,7 +925,7 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 21,
+   "execution_count": 39,
    "metadata": {},
    "outputs": [],
    "source": [
@@ -795,7 +936,7 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 22,
+   "execution_count": 40,
    "metadata": {},
    "outputs": [],
    "source": [
@@ -804,7 +945,7 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 23,
+   "execution_count": 41,
    "metadata": {},
    "outputs": [],
    "source": [
@@ -815,7 +956,7 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 24,
+   "execution_count": 42,
    "metadata": {},
    "outputs": [],
    "source": [
@@ -824,7 +965,7 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 25,
+   "execution_count": 43,
    "metadata": {},
    "outputs": [],
    "source": [
@@ -842,7 +983,7 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 26,
+   "execution_count": 44,
    "metadata": {},
    "outputs": [],
    "source": [
@@ -851,7 +992,7 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 27,
+   "execution_count": 45,
    "metadata": {},
    "outputs": [
     {
@@ -866,13 +1007,6 @@
     "solvent = OBC2(topology)\n",
     "solvent.to_file('ligandParams.txt')"
    ]
-  },
-  {
-   "cell_type": "code",
-   "execution_count": null,
-   "metadata": {},
-   "outputs": [],
-   "source": []
   }
  ],
  "metadata": {
diff --git a/examples/OPLS_parameterization/parameterize.ipynb b/examples/OPLS_parameterization/parameterize.ipynb
index 5d036916..543385ec 100644
--- a/examples/OPLS_parameterization/parameterize.ipynb
+++ b/examples/OPLS_parameterization/parameterize.ipynb
@@ -31,7 +31,7 @@
    "outputs": [],
    "source": [
     "import os\n",
-    "os.environ['SCHRODINGER'] = '/opt/schrodinger/suites2020-2/'"
+    "os.environ['SCHRODINGER'] = '/opt/schrodinger/suites2021-1/'"
    ]
   },
   {
@@ -62,34 +62,64 @@
       " - Initializing molecule from a SMILES tag\n",
       "   - Loading molecule from RDKit\n",
       "   - Setting molecule name to 'c1ccc2cc3ccccc3cc2c1'\n",
-      "   - Representing molecule with the Open Force Field Toolkit\n"
-     ]
-    },
-    {
-     "data": {
-      "application/vnd.jupyter.widget-view+json": {
-       "model_id": "041ae9aeaa3a4d58b8c0c6accf25a71f",
-       "version_major": 2,
-       "version_minor": 0
-      },
-      "text/plain": []
-     },
-     "metadata": {},
-     "output_type": "display_data"
-    },
-    {
-     "name": "stderr",
-     "output_type": "stream",
-     "text": [
+      "   - Representing molecule with the Open Force Field Toolkit\n",
       " - Generating rotamer library\n",
       "   - Core set to the center of the molecule\n"
      ]
     },
     {
      "data": {
-      "image/png": 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+       "<path class=\"bond-21 atom-7 atom-19\" d=\"M 415.172,218.213 L 461.595,191.41\" style=\"fill:none;fill-rule:evenodd;stroke:#000000;stroke-width:4.0px;stroke-linecap:butt;stroke-linejoin:miter;stroke-opacity:1\"/>\n",
+       "<path class=\"bond-8 atom-8 atom-9\" d=\"M 415.172,281.787 L 360.114,313.575\" style=\"fill:none;fill-rule:evenodd;stroke:#000000;stroke-width:4.0px;stroke-linecap:butt;stroke-linejoin:miter;stroke-opacity:1\"/>\n",
+       "<path class=\"bond-8 atom-8 atom-9\" d=\"M 400.555,275.544 L 362.015,297.795\" style=\"fill:none;fill-rule:evenodd;stroke:#000000;stroke-width:4.0px;stroke-linecap:butt;stroke-linejoin:miter;stroke-opacity:1\"/>\n",
+       "<path class=\"bond-22 atom-8 atom-20\" d=\"M 415.172,281.787 L 461.595,308.59\" style=\"fill:none;fill-rule:evenodd;stroke:#000000;stroke-width:4.0px;stroke-linecap:butt;stroke-linejoin:miter;stroke-opacity:1\"/>\n",
+       "<path class=\"bond-9 atom-9 atom-10\" d=\"M 360.114,313.575 L 305.057,281.787\" style=\"fill:none;fill-rule:evenodd;stroke:#000000;stroke-width:4.0px;stroke-linecap:butt;stroke-linejoin:miter;stroke-opacity:1\"/>\n",
+       "<path class=\"bond-23 atom-9 atom-21\" d=\"M 360.114,313.575 L 360.114,366.558\" style=\"fill:none;fill-rule:evenodd;stroke:#000000;stroke-width:4.0px;stroke-linecap:butt;stroke-linejoin:miter;stroke-opacity:1\"/>\n",
+       "<path class=\"bond-10 atom-10 atom-11\" d=\"M 305.057,281.787 L 250,313.575\" style=\"fill:none;fill-rule:evenodd;stroke:#000000;stroke-width:4.0px;stroke-linecap:butt;stroke-linejoin:miter;stroke-opacity:1\"/>\n",
+       "<path class=\"bond-10 atom-10 atom-11\" d=\"M 290.441,275.544 L 251.901,297.795\" style=\"fill:none;fill-rule:evenodd;stroke:#000000;stroke-width:4.0px;stroke-linecap:butt;stroke-linejoin:miter;stroke-opacity:1\"/>\n",
+       "<path class=\"bond-11 atom-11 atom-12\" d=\"M 250,313.575 L 194.943,281.787\" style=\"fill:none;fill-rule:evenodd;stroke:#000000;stroke-width:4.0px;stroke-linecap:butt;stroke-linejoin:miter;stroke-opacity:1\"/>\n",
+       "<path class=\"bond-24 atom-11 atom-22\" d=\"M 250,313.575 L 250,366.558\" style=\"fill:none;fill-rule:evenodd;stroke:#000000;stroke-width:4.0px;stroke-linecap:butt;stroke-linejoin:miter;stroke-opacity:1\"/>\n",
+       "<path class=\"bond-12 atom-12 atom-13\" d=\"M 194.943,281.787 L 139.886,313.575\" style=\"fill:none;fill-rule:evenodd;stroke:#000000;stroke-width:4.0px;stroke-linecap:butt;stroke-linejoin:miter;stroke-opacity:1\"/>\n",
+       "<path class=\"bond-12 atom-12 atom-13\" d=\"M 180.327,275.544 L 141.787,297.795\" style=\"fill:none;fill-rule:evenodd;stroke:#000000;stroke-width:4.0px;stroke-linecap:butt;stroke-linejoin:miter;stroke-opacity:1\"/>\n",
+       "<path class=\"bond-25 atom-13 atom-23\" d=\"M 139.886,313.575 L 139.886,366.558\" style=\"fill:none;fill-rule:evenodd;stroke:#000000;stroke-width:4.0px;stroke-linecap:butt;stroke-linejoin:miter;stroke-opacity:1\"/>\n",
+       "<path class=\"atom-14\" d=\"M 22.7273 304.572 L 25.1685 304.572 L 25.1685 312.227 L 34.3741 312.227 L 34.3741 304.572 L 36.8154 304.572 L 36.8154 322.577 L 34.3741 322.577 L 34.3741 314.261 L 25.1685 314.261 L 25.1685 322.577 L 22.7273 322.577 L 22.7273 304.572 \" fill=\"#000000\"/>\n",
+       "<path class=\"atom-15\" d=\"M 22.7273 177.423 L 25.1685 177.423 L 25.1685 185.078 L 34.3741 185.078 L 34.3741 177.423 L 36.8154 177.423 L 36.8154 195.428 L 34.3741 195.428 L 34.3741 187.112 L 25.1685 187.112 L 25.1685 195.428 L 22.7273 195.428 L 22.7273 177.423 \" fill=\"#000000\"/>\n",
+       "<path class=\"atom-16\" d=\"M 132.842 113.849 L 135.283 113.849 L 135.283 121.503 L 144.488 121.503 L 144.488 113.849 L 146.93 113.849 L 146.93 131.853 L 144.488 131.853 L 144.488 123.538 L 135.283 123.538 L 135.283 131.853 L 132.842 131.853 L 132.842 113.849 \" fill=\"#000000\"/>\n",
+       "<path class=\"atom-17\" d=\"M 242.956 113.849 L 245.397 113.849 L 245.397 121.503 L 254.603 121.503 L 254.603 113.849 L 257.044 113.849 L 257.044 131.853 L 254.603 131.853 L 254.603 123.538 L 245.397 123.538 L 245.397 131.853 L 242.956 131.853 L 242.956 113.849 \" fill=\"#000000\"/>\n",
+       "<path class=\"atom-18\" d=\"M 353.07 113.849 L 355.512 113.849 L 355.512 121.503 L 364.717 121.503 L 364.717 113.849 L 367.158 113.849 L 367.158 131.853 L 364.717 131.853 L 364.717 123.538 L 355.512 123.538 L 355.512 131.853 L 353.07 131.853 L 353.07 113.849 \" fill=\"#000000\"/>\n",
+       "<path class=\"atom-19\" d=\"M 463.185 177.423 L 465.626 177.423 L 465.626 185.078 L 474.831 185.078 L 474.831 177.423 L 477.273 177.423 L 477.273 195.428 L 474.831 195.428 L 474.831 187.112 L 465.626 187.112 L 465.626 195.428 L 463.185 195.428 L 463.185 177.423 \" fill=\"#000000\"/>\n",
+       "<path class=\"atom-20\" d=\"M 463.185 304.572 L 465.626 304.572 L 465.626 312.227 L 474.831 312.227 L 474.831 304.572 L 477.273 304.572 L 477.273 322.577 L 474.831 322.577 L 474.831 314.261 L 465.626 314.261 L 465.626 322.577 L 463.185 322.577 L 463.185 304.572 \" fill=\"#000000\"/>\n",
+       "<path class=\"atom-21\" d=\"M 353.07 368.147 L 355.512 368.147 L 355.512 375.801 L 364.717 375.801 L 364.717 368.147 L 367.158 368.147 L 367.158 386.151 L 364.717 386.151 L 364.717 377.836 L 355.512 377.836 L 355.512 386.151 L 353.07 386.151 L 353.07 368.147 \" fill=\"#000000\"/>\n",
+       "<path class=\"atom-22\" d=\"M 242.956 368.147 L 245.397 368.147 L 245.397 375.801 L 254.603 375.801 L 254.603 368.147 L 257.044 368.147 L 257.044 386.151 L 254.603 386.151 L 254.603 377.836 L 245.397 377.836 L 245.397 386.151 L 242.956 386.151 L 242.956 368.147 \" fill=\"#000000\"/>\n",
+       "<path class=\"atom-23\" d=\"M 132.842 368.147 L 135.283 368.147 L 135.283 375.801 L 144.488 375.801 L 144.488 368.147 L 146.93 368.147 L 146.93 386.151 L 144.488 386.151 L 144.488 377.836 L 135.283 377.836 L 135.283 386.151 L 132.842 386.151 L 132.842 368.147 \" fill=\"#000000\"/>\n",
+       "</svg>"
+      ],
       "text/plain": [
-       "<rdkit.Chem.rdchem.Mol at 0x7fc4b4d5c0d0>"
+       "<IPython.core.display.SVG object>"
       ]
      },
      "metadata": {},
@@ -97,7 +127,7 @@
     }
    ],
    "source": [
-    "molecule = Molecule(smiles='c1ccc2cc3ccccc3cc2c1')\n",
+    "molecule = Molecule(smiles='c1ccc2cc3ccccc3cc2c1', hydrogens_are_explicit=False)\n",
     "display(molecule)"
    ]
   },
@@ -173,7 +203,7 @@
    "outputs": [],
    "source": [
     "import os\n",
-    "os.environ['SCHRODINGER'] = '/opt/schrodinger/suites2020-2/'"
+    "os.environ['SCHRODINGER'] = '/opt/schrodinger/suites2021-1/'"
    ]
   },
   {
@@ -211,9 +241,71 @@
     },
     {
      "data": {
-      "image/png": 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+       "<path class=\"bond-2 atom-1 atom-3\" d=\"M 324.474,261.793 L 304.599,322.948\" style=\"fill:none;fill-rule:evenodd;stroke:#000000;stroke-width:4.0px;stroke-linecap:butt;stroke-linejoin:miter;stroke-opacity:1\"/>\n",
+       "<path class=\"bond-9 atom-1 atom-10\" d=\"M 324.474,261.793 L 332.595,236.804\" style=\"fill:none;fill-rule:evenodd;stroke:#000000;stroke-width:4.0px;stroke-linecap:butt;stroke-linejoin:miter;stroke-opacity:1\"/>\n",
+       "<path class=\"bond-9 atom-1 atom-10\" d=\"M 332.595,236.804 L 340.717,211.814\" style=\"fill:none;fill-rule:evenodd;stroke:#CCCC00;stroke-width:4.0px;stroke-linecap:butt;stroke-linejoin:miter;stroke-opacity:1\"/>\n",
+       "<path class=\"bond-14 atom-2 atom-15\" d=\"M 385.629,281.668 L 399.16,264.964\" style=\"fill:none;fill-rule:evenodd;stroke:#000000;stroke-width:4.0px;stroke-linecap:butt;stroke-linejoin:miter;stroke-opacity:1\"/>\n",
+       "<path class=\"bond-15 atom-2 atom-16\" d=\"M 385.629,281.668 L 375.439,334.077\" style=\"fill:none;fill-rule:evenodd;stroke:#000000;stroke-width:4.0px;stroke-linecap:butt;stroke-linejoin:miter;stroke-opacity:1\"/>\n",
+       "<path class=\"bond-16 atom-2 atom-17\" d=\"M 385.629,281.668 L 438.051,298.706\" style=\"fill:none;fill-rule:evenodd;stroke:#000000;stroke-width:4.0px;stroke-linecap:butt;stroke-linejoin:miter;stroke-opacity:1\"/>\n",
+       "<path class=\"bond-3 atom-3 atom-4\" d=\"M 304.599,322.948 L 277.406,328.726\" style=\"fill:none;fill-rule:evenodd;stroke:#000000;stroke-width:4.0px;stroke-linecap:butt;stroke-linejoin:miter;stroke-opacity:1\"/>\n",
+       "<path class=\"bond-3 atom-3 atom-4\" d=\"M 277.406,328.726 L 250.213,334.504\" style=\"fill:none;fill-rule:evenodd;stroke:#0000FF;stroke-width:4.0px;stroke-linecap:butt;stroke-linejoin:miter;stroke-opacity:1\"/>\n",
+       "<path class=\"bond-3 atom-3 atom-4\" d=\"M 293.768,312.102 L 274.733,316.146\" style=\"fill:none;fill-rule:evenodd;stroke:#000000;stroke-width:4.0px;stroke-linecap:butt;stroke-linejoin:miter;stroke-opacity:1\"/>\n",
+       "<path class=\"bond-3 atom-3 atom-4\" d=\"M 274.733,316.146 L 255.698,320.191\" style=\"fill:none;fill-rule:evenodd;stroke:#0000FF;stroke-width:4.0px;stroke-linecap:butt;stroke-linejoin:miter;stroke-opacity:1\"/>\n",
+       "<path class=\"bond-17 atom-3 atom-18\" d=\"M 304.599,322.948 L 333.977,364.913\" style=\"fill:none;fill-rule:evenodd;stroke:#000000;stroke-width:4.0px;stroke-linecap:butt;stroke-linejoin:miter;stroke-opacity:1\"/>\n",
+       "<path class=\"bond-4 atom-4 atom-5\" d=\"M 233.185,326.856 L 220.755,313.049\" style=\"fill:none;fill-rule:evenodd;stroke:#0000FF;stroke-width:4.0px;stroke-linecap:butt;stroke-linejoin:miter;stroke-opacity:1\"/>\n",
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+       "<path class=\"bond-6 atom-6 atom-7\" d=\"M 129.66,299.901 L 121.48,325.07\" style=\"fill:none;fill-rule:evenodd;stroke:#000000;stroke-width:4.0px;stroke-linecap:butt;stroke-linejoin:miter;stroke-opacity:1\"/>\n",
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+       "<path class=\"bond-6 atom-6 atom-7\" d=\"M 141.891,303.876 L 133.711,329.045\" style=\"fill:none;fill-rule:evenodd;stroke:#000000;stroke-width:4.0px;stroke-linecap:butt;stroke-linejoin:miter;stroke-opacity:1\"/>\n",
+       "<path class=\"bond-6 atom-6 atom-7\" d=\"M 133.711,329.045 L 125.531,354.215\" style=\"fill:none;fill-rule:evenodd;stroke:#FF0000;stroke-width:4.0px;stroke-linecap:butt;stroke-linejoin:miter;stroke-opacity:1\"/>\n",
+       "<path class=\"bond-7 atom-6 atom-8\" d=\"M 135.776,301.888 L 118.52,282.722\" style=\"fill:none;fill-rule:evenodd;stroke:#000000;stroke-width:4.0px;stroke-linecap:butt;stroke-linejoin:miter;stroke-opacity:1\"/>\n",
+       "<path class=\"bond-7 atom-6 atom-8\" d=\"M 118.52,282.722 L 101.265,263.555\" style=\"fill:none;fill-rule:evenodd;stroke:#0000FF;stroke-width:4.0px;stroke-linecap:butt;stroke-linejoin:miter;stroke-opacity:1\"/>\n",
+       "<path class=\"bond-8 atom-8 atom-9\" d=\"M 96.2332,243.385 L 104.43,218.164\" style=\"fill:none;fill-rule:evenodd;stroke:#0000FF;stroke-width:4.0px;stroke-linecap:butt;stroke-linejoin:miter;stroke-opacity:1\"/>\n",
+       "<path class=\"bond-8 atom-8 atom-9\" d=\"M 104.43,218.164 L 112.627,192.943\" style=\"fill:none;fill-rule:evenodd;stroke:#000000;stroke-width:4.0px;stroke-linecap:butt;stroke-linejoin:miter;stroke-opacity:1\"/>\n",
+       "<path class=\"bond-18 atom-8 atom-19\" d=\"M 84.2377,255.907 L 61.3023,260.781\" style=\"fill:none;fill-rule:evenodd;stroke:#0000FF;stroke-width:4.0px;stroke-linecap:butt;stroke-linejoin:miter;stroke-opacity:1\"/>\n",
+       "<path class=\"bond-18 atom-8 atom-19\" d=\"M 61.3023,260.781 L 38.367,265.654\" style=\"fill:none;fill-rule:evenodd;stroke:#000000;stroke-width:4.0px;stroke-linecap:butt;stroke-linejoin:miter;stroke-opacity:1\"/>\n",
+       "<path class=\"bond-19 atom-9 atom-20\" d=\"M 112.627,192.943 L 60.2042,175.906\" style=\"fill:none;fill-rule:evenodd;stroke:#000000;stroke-width:4.0px;stroke-linecap:butt;stroke-linejoin:miter;stroke-opacity:1\"/>\n",
+       "<path class=\"bond-20 atom-9 atom-21\" d=\"M 112.627,192.943 L 160.865,202.322\" style=\"fill:none;fill-rule:evenodd;stroke:#000000;stroke-width:4.0px;stroke-linecap:butt;stroke-linejoin:miter;stroke-opacity:1\"/>\n",
+       "<path class=\"bond-21 atom-9 atom-22\" d=\"M 112.627,192.943 L 129.02,142.501\" style=\"fill:none;fill-rule:evenodd;stroke:#000000;stroke-width:4.0px;stroke-linecap:butt;stroke-linejoin:miter;stroke-opacity:1\"/>\n",
+       "<path class=\"bond-10 atom-10 atom-11\" d=\"M 351.795,199.056 L 379.522,193.165\" style=\"fill:none;fill-rule:evenodd;stroke:#CCCC00;stroke-width:4.0px;stroke-linecap:butt;stroke-linejoin:miter;stroke-opacity:1\"/>\n",
+       "<path class=\"bond-10 atom-10 atom-11\" d=\"M 379.522,193.165 L 407.248,187.273\" style=\"fill:none;fill-rule:evenodd;stroke:#000000;stroke-width:4.0px;stroke-linecap:butt;stroke-linejoin:miter;stroke-opacity:1\"/>\n",
+       "<path class=\"bond-22 atom-11 atom-23\" d=\"M 407.248,187.273 L 396.16,135.087\" style=\"fill:none;fill-rule:evenodd;stroke:#000000;stroke-width:4.0px;stroke-linecap:butt;stroke-linejoin:miter;stroke-opacity:1\"/>\n",
+       "<path class=\"bond-23 atom-11 atom-24\" d=\"M 407.248,187.273 L 414.944,209.626\" style=\"fill:none;fill-rule:evenodd;stroke:#000000;stroke-width:4.0px;stroke-linecap:butt;stroke-linejoin:miter;stroke-opacity:1\"/>\n",
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+       "<path class=\"atom-4\" d=\"M 237.674 327.208 L 243.641 336.853 Q 244.233 337.805, 245.184 339.528 Q 246.136 341.252, 246.188 341.355 L 246.188 327.208 L 248.605 327.208 L 248.605 345.419 L 246.11 345.419 L 239.706 334.873 Q 238.96 333.638, 238.163 332.224 Q 237.391 330.809, 237.159 330.372 L 237.159 345.419 L 234.793 345.419 L 234.793 327.208 L 237.674 327.208 \" fill=\"#0000FF\"/>\n",
+       "<path class=\"atom-5\" d=\"M 190.316 288.575 Q 190.316 284.202, 192.476 281.759 Q 194.637 279.315, 198.675 279.315 Q 202.713 279.315, 204.874 281.759 Q 207.035 284.202, 207.035 288.575 Q 207.035 292.999, 204.848 295.519 Q 202.662 298.014, 198.675 298.014 Q 194.663 298.014, 192.476 295.519 Q 190.316 293.025, 190.316 288.575 M 198.675 295.957 Q 201.453 295.957, 202.945 294.105 Q 204.462 292.227, 204.462 288.575 Q 204.462 284.999, 202.945 283.199 Q 201.453 281.373, 198.675 281.373 Q 195.897 281.373, 194.38 283.173 Q 192.888 284.974, 192.888 288.575 Q 192.888 292.253, 194.38 294.105 Q 195.897 295.957, 198.675 295.957 \" fill=\"#FF0000\"/>\n",
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+       "<path class=\"atom-15\" d=\"M 400.014 246.008 L 402.483 246.008 L 402.483 253.751 L 411.795 253.751 L 411.795 246.008 L 414.264 246.008 L 414.264 264.219 L 411.795 264.219 L 411.795 255.808 L 402.483 255.808 L 402.483 264.219 L 400.014 264.219 L 400.014 246.008 \" fill=\"#000000\"/>\n",
+       "<path class=\"atom-16\" d=\"M 366.232 335.685 L 368.701 335.685 L 368.701 343.427 L 378.012 343.427 L 378.012 335.685 L 380.481 335.685 L 380.481 353.895 L 378.012 353.895 L 378.012 345.485 L 368.701 345.485 L 368.701 353.895 L 366.232 353.895 L 366.232 335.685 \" fill=\"#000000\"/>\n",
+       "<path class=\"atom-17\" d=\"M 439.659 292.438 L 442.128 292.438 L 442.128 300.18 L 451.439 300.18 L 451.439 292.438 L 453.909 292.438 L 453.909 310.649 L 451.439 310.649 L 451.439 302.238 L 442.128 302.238 L 442.128 310.649 L 439.659 310.649 L 439.659 292.438 \" fill=\"#000000\"/>\n",
+       "<path class=\"atom-18\" d=\"M 334.352 366.521 L 336.821 366.521 L 336.821 374.263 L 346.132 374.263 L 346.132 366.521 L 348.601 366.521 L 348.601 384.732 L 346.132 384.732 L 346.132 376.321 L 336.821 376.321 L 336.821 384.732 L 334.352 384.732 L 334.352 366.521 \" fill=\"#000000\"/>\n",
+       "<path class=\"atom-19\" d=\"M 22.7273 258.358 L 25.1965 258.358 L 25.1965 266.1 L 34.5077 266.1 L 34.5077 258.358 L 36.977 258.358 L 36.977 276.569 L 34.5077 276.569 L 34.5077 268.158 L 25.1965 268.158 L 25.1965 276.569 L 22.7273 276.569 L 22.7273 258.358 \" fill=\"#000000\"/>\n",
+       "<path class=\"atom-20\" d=\"M 44.3469 163.963 L 46.8162 163.963 L 46.8162 171.705 L 56.1273 171.705 L 56.1273 163.963 L 58.5966 163.963 L 58.5966 182.174 L 56.1273 182.174 L 56.1273 173.763 L 46.8162 173.763 L 46.8162 182.174 L 44.3469 182.174 L 44.3469 163.963 \" fill=\"#000000\"/>\n",
+       "<path class=\"atom-21\" d=\"M 162.311 194.883 L 164.781 194.883 L 164.781 202.625 L 174.092 202.625 L 174.092 194.883 L 176.561 194.883 L 176.561 213.094 L 174.092 213.094 L 174.092 204.683 L 164.781 204.683 L 164.781 213.094 L 162.311 213.094 L 162.311 194.883 \" fill=\"#000000\"/>\n",
+       "<path class=\"atom-22\" d=\"M 125.377 122.683 L 127.846 122.683 L 127.846 130.425 L 137.158 130.425 L 137.158 122.683 L 139.627 122.683 L 139.627 140.894 L 137.158 140.894 L 137.158 132.483 L 127.846 132.483 L 127.846 140.894 L 125.377 140.894 L 125.377 122.683 \" fill=\"#000000\"/>\n",
+       "<path class=\"atom-23\" d=\"M 386.759 115.268 L 389.228 115.268 L 389.228 123.011 L 398.539 123.011 L 398.539 115.268 L 401.008 115.268 L 401.008 133.479 L 398.539 133.479 L 398.539 125.068 L 389.228 125.068 L 389.228 133.479 L 386.759 133.479 L 386.759 115.268 \" fill=\"#000000\"/>\n",
+       "<path class=\"atom-24\" d=\"M 411.248 210.48 L 413.717 210.48 L 413.717 218.222 L 423.028 218.222 L 423.028 210.48 L 425.498 210.48 L 425.498 228.691 L 423.028 228.691 L 423.028 220.28 L 413.717 220.28 L 413.717 228.691 L 411.248 228.691 L 411.248 210.48 \" fill=\"#000000\"/>\n",
+       "<path class=\"atom-25\" d=\"M 463.023 164.803 L 465.492 164.803 L 465.492 172.545 L 474.803 172.545 L 474.803 164.803 L 477.273 164.803 L 477.273 183.014 L 474.803 183.014 L 474.803 174.603 L 465.492 174.603 L 465.492 183.014 L 463.023 183.014 L 463.023 164.803 \" fill=\"#000000\"/>\n",
+       "</svg>"
+      ],
       "text/plain": [
-       "<rdkit.Chem.rdchem.Mol at 0x7fc4b5444bc0>"
+       "<IPython.core.display.SVG object>"
       ]
      },
      "metadata": {},
@@ -221,7 +313,7 @@
     }
    ],
    "source": [
-    "molecule = Molecule(smiles='CC(C)(/C=N\\OC(=O)NC)SC')\n",
+    "molecule = Molecule(smiles='CC(C)(/C=N\\OC(=O)NC)SC', hydrogens_are_explicit=False)\n",
     "display(molecule)"
    ]
   },
@@ -333,7 +425,7 @@
    "outputs": [],
    "source": [
     "import os\n",
-    "os.environ['SCHRODINGER'] = '/opt/schrodinger/suites2020-2/'"
+    "os.environ['SCHRODINGER'] = '/opt/schrodinger/suites2021-1/'"
    ]
   },
   {
@@ -373,9 +465,100 @@
     },
     {
      "data": {
-      "image/png": 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+       "<path class=\"atom-37\" d=\"M 276.608 104.142 L 278.392 104.142 L 278.392 109.736 L 285.12 109.736 L 285.12 104.142 L 286.904 104.142 L 286.904 117.3 L 285.12 117.3 L 285.12 111.223 L 278.392 111.223 L 278.392 117.3 L 276.608 117.3 L 276.608 104.142 \" fill=\"#000000\"/>\n",
+       "<path class=\"atom-38\" d=\"M 328.827 144.023 L 330.611 144.023 L 330.611 149.617 L 337.339 149.617 L 337.339 144.023 L 339.123 144.023 L 339.123 157.181 L 337.339 157.181 L 337.339 151.104 L 330.611 151.104 L 330.611 157.181 L 328.827 157.181 L 328.827 144.023 \" fill=\"#000000\"/>\n",
+       "<path class=\"atom-39\" d=\"M 236.727 156.362 L 238.511 156.362 L 238.511 161.956 L 245.239 161.956 L 245.239 156.362 L 247.023 156.362 L 247.023 169.52 L 245.239 169.52 L 245.239 163.442 L 238.511 163.442 L 238.511 169.52 L 236.727 169.52 L 236.727 156.362 \" fill=\"#000000\"/>\n",
+       "</svg>"
+      ],
       "text/plain": [
-       "<rdkit.Chem.rdchem.Mol at 0x7fc4b54991c0>"
+       "<IPython.core.display.SVG object>"
       ]
      },
      "metadata": {},
@@ -383,7 +566,8 @@
     }
    ],
    "source": [
-    "molecule = Molecule(smiles='CCOP(=S)(OCC)Oc1cc(nc(n1)C(C)C)C')\n",
+    "molecule = Molecule(smiles='CCOP(=S)(OCC)Oc1cc(nc(n1)C(C)C)C',\n",
+    "                    hydrogens_are_explicit=False)\n",
     "display(molecule)"
    ]
   },
diff --git a/examples/molecular_representations/PDB-SMILES_comparison.ipynb b/examples/molecular_representations/PDB-SMILES_comparison.ipynb
index 412296e7..27cfe925 100644
--- a/examples/molecular_representations/PDB-SMILES_comparison.ipynb
+++ b/examples/molecular_representations/PDB-SMILES_comparison.ipynb
@@ -54,34 +54,35 @@
       "   - Assigning stereochemistry from 3D coordinates\n",
       "   - Setting molecule name to 'ammonium'\n",
       "   - Setting molecule tag to 'UNL'\n",
-      "   - Representing molecule with the Open Force Field Toolkit\n"
-     ]
-    },
-    {
-     "data": {
-      "application/vnd.jupyter.widget-view+json": {
-       "model_id": "67b6b888b5a143b08e6d612f92203b66",
-       "version_major": 2,
-       "version_minor": 0
-      },
-      "text/plain": []
-     },
-     "metadata": {},
-     "output_type": "display_data"
-    },
-    {
-     "name": "stderr",
-     "output_type": "stream",
-     "text": [
+      "   - Representing molecule with the Open Force Field Toolkit\n",
       " - Generating rotamer library\n",
       "   - Core set to the center of the molecule\n"
      ]
     },
     {
      "data": {
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       "text/plain": [
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      "metadata": {},
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     {
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+      "image/svg+xml": [
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+       "<path class=\"bond-3 atom-0 atom-4\" d=\"M 250,357.445 L 250,445.37\" style=\"fill:none;fill-rule:evenodd;stroke:#000000;stroke-width:4.0px;stroke-linecap:butt;stroke-linejoin:miter;stroke-opacity:1\"/>\n",
+       "<path class=\"atom-0\" d=\"M 243.74 235.84 L 253.02 250.84 Q 253.94 252.32, 255.42 255 Q 256.9 257.68, 256.98 257.84 L 256.98 235.84 L 260.74 235.84 L 260.74 264.16 L 256.86 264.16 L 246.9 247.76 Q 245.74 245.84, 244.5 243.64 Q 243.3 241.44, 242.94 240.76 L 242.94 264.16 L 239.26 264.16 L 239.26 235.84 L 243.74 235.84 \" fill=\"#0000FF\"/>\n",
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+       "<path class=\"atom-1\" d=\"M 453.322 235.84 L 457.162 235.84 L 457.162 247.88 L 471.642 247.88 L 471.642 235.84 L 475.482 235.84 L 475.482 264.16 L 471.642 264.16 L 471.642 251.08 L 457.162 251.08 L 457.162 264.16 L 453.322 264.16 L 453.322 235.84 \" fill=\"#000000\"/>\n",
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+      ],
       "text/plain": [
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      },
      "metadata": {},
@@ -122,7 +142,7 @@
     }
    ],
    "source": [
-    "m = Molecule(smiles='[NH4+]')\n",
+    "m = Molecule(smiles='[NH4+]', hydrogens_are_explicit=False)\n",
     "display(m)"
    ]
   },
@@ -154,9 +174,40 @@
     },
     {
      "data": {
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\n",
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+       "<path class=\"atom-7\" d=\"M 206.848 336.281 L 210.688 336.281 L 210.688 348.321 L 225.168 348.321 L 225.168 336.281 L 229.008 336.281 L 229.008 364.601 L 225.168 364.601 L 225.168 351.521 L 210.688 351.521 L 210.688 364.601 L 206.848 364.601 L 206.848 336.281 \" fill=\"#000000\"/>\n",
+       "<path class=\"atom-8\" d=\"M 172.097 134.999 L 175.937 134.999 L 175.937 147.039 L 190.417 147.039 L 190.417 134.999 L 194.257 134.999 L 194.257 163.319 L 190.417 163.319 L 190.417 150.239 L 175.937 150.239 L 175.937 163.319 L 172.097 163.319 L 172.097 134.999 \" fill=\"#000000\"/>\n",
+       "<path class=\"atom-9\" d=\"M 456.121 279.359 L 459.961 279.359 L 459.961 291.399 L 474.441 291.399 L 474.441 279.359 L 478.281 279.359 L 478.281 307.679 L 474.441 307.679 L 474.441 294.599 L 459.961 294.599 L 459.961 307.679 L 456.121 307.679 L 456.121 279.359 \" fill=\"#000000\"/>\n",
+       "</svg>"
+      ],
       "text/plain": [
-       "<rdkit.Chem.rdchem.Mol at 0x7fee028efd50>"
+       "<IPython.core.display.SVG object>"
       ]
      },
      "metadata": {},
@@ -197,7 +279,7 @@
     }
    ],
    "source": [
-    "m = Molecule(smiles='O=C([O-])CC(O)=O')\n",
+    "m = Molecule(smiles='O=C([O-])CC(O)=O', hydrogens_are_explicit=False)\n",
     "display(m)"
    ]
   },
@@ -229,9 +311,56 @@
     },
     {
      "data": {
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+       "<path class=\"bond-13 atom-3 atom-14\" d=\"M 372.66,241.662 L 454.313,234.46\" style=\"fill:none;fill-rule:evenodd;stroke:#000000;stroke-width:4.0px;stroke-linecap:butt;stroke-linejoin:miter;stroke-opacity:1\"/>\n",
+       "<path class=\"bond-14 atom-3 atom-15\" d=\"M 372.66,241.662 L 381.186,281.631\" style=\"fill:none;fill-rule:evenodd;stroke:#000000;stroke-width:4.0px;stroke-linecap:butt;stroke-linejoin:miter;stroke-opacity:1\"/>\n",
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+       "<path class=\"bond-16 atom-4 atom-17\" d=\"M 183.577,258.338 L 182.167,299.508\" style=\"fill:none;fill-rule:evenodd;stroke:#000000;stroke-width:4.0px;stroke-linecap:butt;stroke-linejoin:miter;stroke-opacity:1\"/>\n",
+       "<path class=\"bond-17 atom-4 atom-18\" d=\"M 183.577,258.338 L 167.15,181.33\" style=\"fill:none;fill-rule:evenodd;stroke:#000000;stroke-width:4.0px;stroke-linecap:butt;stroke-linejoin:miter;stroke-opacity:1\"/>\n",
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+       "<path class=\"bond-6 atom-5 atom-7\" d=\"M 72.7263,301.717 L 56.4166,336.757\" style=\"fill:none;fill-rule:evenodd;stroke:#FF0000;stroke-width:4.0px;stroke-linecap:butt;stroke-linejoin:miter;stroke-opacity:1\"/>\n",
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+       "<path class=\"atom-15\" d=\"M 373.836 283.032 L 377.48 283.032 L 377.48 294.459 L 391.223 294.459 L 391.223 283.032 L 394.867 283.032 L 394.867 309.91 L 391.223 309.91 L 391.223 297.496 L 377.48 297.496 L 377.48 309.91 L 373.836 309.91 L 373.836 283.032 \" fill=\"#000000\"/>\n",
+       "<path class=\"atom-16\" d=\"M 364.062 172.213 L 367.706 172.213 L 367.706 183.64 L 381.449 183.64 L 381.449 172.213 L 385.094 172.213 L 385.094 199.091 L 381.449 199.091 L 381.449 186.677 L 367.706 186.677 L 367.706 199.091 L 364.062 199.091 L 364.062 172.213 \" fill=\"#000000\"/>\n",
+       "<path class=\"atom-17\" d=\"M 171.143 300.909 L 174.788 300.909 L 174.788 312.336 L 188.531 312.336 L 188.531 300.909 L 192.175 300.909 L 192.175 327.787 L 188.531 327.787 L 188.531 315.373 L 174.788 315.373 L 174.788 327.787 L 171.143 327.787 L 171.143 300.909 \" fill=\"#000000\"/>\n",
+       "<path class=\"atom-18\" d=\"M 153.261 152.079 L 156.906 152.079 L 156.906 163.506 L 170.648 163.506 L 170.648 152.079 L 174.293 152.079 L 174.293 178.957 L 170.648 178.957 L 170.648 166.543 L 156.906 166.543 L 156.906 178.957 L 153.261 178.957 L 153.261 152.079 \" fill=\"#000000\"/>\n",
+       "</svg>"
+      ],
       "text/plain": [
-       "<rdkit.Chem.rdchem.Mol at 0x7fee029187b0>"
+       "<IPython.core.display.SVG object>"
       ]
      },
      "metadata": {},
@@ -272,7 +448,7 @@
     }
    ],
    "source": [
-    "m = Molecule(smiles='C[N+](C)(C)CC(=O)[O-]')\n",
+    "m = Molecule(smiles='C[N+](C)(C)CC(=O)[O-]', hydrogens_are_explicit=False)\n",
     "display(m)"
    ]
   }
@@ -293,7 +469,7 @@
    "name": "python",
    "nbconvert_exporter": "python",
    "pygments_lexer": "ipython3",
-   "version": "3.7.8"
+   "version": "3.7.10"
   }
  },
  "nbformat": 4,
diff --git a/examples/rotamers/core_constraints.ipynb b/examples/rotamers/core_constraints.ipynb
index 049e7683..a78588f0 100644
--- a/examples/rotamers/core_constraints.ipynb
+++ b/examples/rotamers/core_constraints.ipynb
@@ -37,33 +37,15 @@
       " - Initializing molecule from a SMILES tag\n",
       "   - Loading molecule from RDKit\n",
       "   - Representing molecule with the Open Force Field Toolkit\n",
-      "Warning: Unable to load toolkit 'OpenEye Toolkit'. The Open Force Field Toolkit does not require the OpenEye Toolkits, and can use RDKit/AmberTools instead. However, if you have a valid license for the OpenEye Toolkits, consider installing them for faster performance and additional file format support: https://docs.eyesopen.com/toolkits/python/quickstart-python/linuxosx.html OpenEye offers free Toolkit licenses for academics: https://www.eyesopen.com/academic-licensing\n"
-     ]
-    },
-    {
-     "data": {
-      "application/vnd.jupyter.widget-view+json": {
-       "model_id": "f963188257ca4e30872f4d49f993d777",
-       "version_major": 2,
-       "version_minor": 0
-      },
-      "text/plain": []
-     },
-     "metadata": {},
-     "output_type": "display_data"
-    },
-    {
-     "name": "stderr",
-     "output_type": "stream",
-     "text": [
       " - Generating rotamer library\n",
-      "   - Core forced to contain atom C1\n"
+      "   - Core forced to contain atom:  C1 \n"
      ]
     }
    ],
    "source": [
     "mol = Molecule(smiles='CCCC', name='butane', tag='BUT',\n",
-    "               exclude_terminal_rotamers=False, core_constraint=0)"
+    "               exclude_terminal_rotamers=False, core_constraints=[0, ],\n",
+    "               hydrogens_are_explicit=False)"
    ]
   },
   {
@@ -73,9 +55,37 @@
    "outputs": [
     {
      "data": {
-      "image/png": "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\n",
+      "image/svg+xml": [
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+       "<!-- END OF HEADER -->\n",
+       "<rect height=\"500\" style=\"opacity:1.0;fill:#FFFFFF;stroke:none\" width=\"500\" x=\"0\" y=\"0\"> </rect>\n",
+       "<path class=\"bond-0 atom-0 atom-1\" d=\"M 119.424,250 L 206.475,250\" style=\"fill:none;fill-rule:evenodd;stroke:#000000;stroke-width:4.0px;stroke-linecap:butt;stroke-linejoin:miter;stroke-opacity:1\"/>\n",
+       "<path class=\"bond-3 atom-0 atom-4\" d=\"M 119.424,250 L 44.194,250\" style=\"fill:none;fill-rule:evenodd;stroke:#000000;stroke-width:4.0px;stroke-linecap:butt;stroke-linejoin:miter;stroke-opacity:1\"/>\n",
+       "<path class=\"bond-4 atom-0 atom-5\" d=\"M 119.424,250 L 119.424,177.452\" style=\"fill:none;fill-rule:evenodd;stroke:#000000;stroke-width:4.0px;stroke-linecap:butt;stroke-linejoin:miter;stroke-opacity:1\"/>\n",
+       "<path class=\"bond-5 atom-0 atom-6\" d=\"M 119.424,250 L 119.424,322.548\" style=\"fill:none;fill-rule:evenodd;stroke:#000000;stroke-width:4.0px;stroke-linecap:butt;stroke-linejoin:miter;stroke-opacity:1\"/>\n",
+       "<path class=\"bond-1 atom-1 atom-2\" d=\"M 206.475,250 L 293.525,250\" style=\"fill:none;fill-rule:evenodd;stroke:#000000;stroke-width:4.0px;stroke-linecap:butt;stroke-linejoin:miter;stroke-opacity:1\"/>\n",
+       "<path class=\"bond-6 atom-1 atom-7\" d=\"M 206.475,250 L 206.475,322.548\" style=\"fill:none;fill-rule:evenodd;stroke:#000000;stroke-width:4.0px;stroke-linecap:butt;stroke-linejoin:miter;stroke-opacity:1\"/>\n",
+       "<path class=\"bond-7 atom-1 atom-8\" d=\"M 206.475,250 L 206.475,177.452\" style=\"fill:none;fill-rule:evenodd;stroke:#000000;stroke-width:4.0px;stroke-linecap:butt;stroke-linejoin:miter;stroke-opacity:1\"/>\n",
+       "<path class=\"bond-2 atom-2 atom-3\" d=\"M 293.525,250 L 380.576,250\" style=\"fill:none;fill-rule:evenodd;stroke:#000000;stroke-width:4.0px;stroke-linecap:butt;stroke-linejoin:miter;stroke-opacity:1\"/>\n",
+       "<path class=\"bond-8 atom-2 atom-9\" d=\"M 293.525,250 L 293.525,177.452\" style=\"fill:none;fill-rule:evenodd;stroke:#000000;stroke-width:4.0px;stroke-linecap:butt;stroke-linejoin:miter;stroke-opacity:1\"/>\n",
+       "<path class=\"bond-9 atom-2 atom-10\" d=\"M 293.525,250 L 293.525,322.548\" style=\"fill:none;fill-rule:evenodd;stroke:#000000;stroke-width:4.0px;stroke-linecap:butt;stroke-linejoin:miter;stroke-opacity:1\"/>\n",
+       "<path class=\"bond-10 atom-3 atom-11\" d=\"M 380.576,250 L 455.806,250\" style=\"fill:none;fill-rule:evenodd;stroke:#000000;stroke-width:4.0px;stroke-linecap:butt;stroke-linejoin:miter;stroke-opacity:1\"/>\n",
+       "<path class=\"bond-11 atom-3 atom-12\" d=\"M 380.576,250 L 380.576,322.548\" style=\"fill:none;fill-rule:evenodd;stroke:#000000;stroke-width:4.0px;stroke-linecap:butt;stroke-linejoin:miter;stroke-opacity:1\"/>\n",
+       "<path class=\"bond-12 atom-3 atom-13\" d=\"M 380.576,250 L 380.576,177.452\" style=\"fill:none;fill-rule:evenodd;stroke:#000000;stroke-width:4.0px;stroke-linecap:butt;stroke-linejoin:miter;stroke-opacity:1\"/>\n",
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+       "<path class=\"atom-7\" d=\"M 196.829 324.725 L 200.172 324.725 L 200.172 335.206 L 212.777 335.206 L 212.777 324.725 L 216.12 324.725 L 216.12 349.377 L 212.777 349.377 L 212.777 337.991 L 200.172 337.991 L 200.172 349.377 L 196.829 349.377 L 196.829 324.725 \" fill=\"#000000\"/>\n",
+       "<path class=\"atom-8\" d=\"M 196.829 150.623 L 200.172 150.623 L 200.172 161.104 L 212.777 161.104 L 212.777 150.623 L 216.12 150.623 L 216.12 175.275 L 212.777 175.275 L 212.777 163.889 L 200.172 163.889 L 200.172 175.275 L 196.829 175.275 L 196.829 150.623 \" fill=\"#000000\"/>\n",
+       "<path class=\"atom-9\" d=\"M 283.88 150.623 L 287.223 150.623 L 287.223 161.104 L 299.828 161.104 L 299.828 150.623 L 303.171 150.623 L 303.171 175.275 L 299.828 175.275 L 299.828 163.889 L 287.223 163.889 L 287.223 175.275 L 283.88 175.275 L 283.88 150.623 \" fill=\"#000000\"/>\n",
+       "<path class=\"atom-10\" d=\"M 283.88 324.725 L 287.223 324.725 L 287.223 335.206 L 299.828 335.206 L 299.828 324.725 L 303.171 324.725 L 303.171 349.377 L 299.828 349.377 L 299.828 337.991 L 287.223 337.991 L 287.223 349.377 L 283.88 349.377 L 283.88 324.725 \" fill=\"#000000\"/>\n",
+       "<path class=\"atom-11\" d=\"M 457.982 237.674 L 461.325 237.674 L 461.325 248.155 L 473.93 248.155 L 473.93 237.674 L 477.273 237.674 L 477.273 262.326 L 473.93 262.326 L 473.93 250.94 L 461.325 250.94 L 461.325 262.326 L 457.982 262.326 L 457.982 237.674 \" fill=\"#000000\"/>\n",
+       "<path class=\"atom-12\" d=\"M 370.931 324.725 L 374.274 324.725 L 374.274 335.206 L 386.879 335.206 L 386.879 324.725 L 390.222 324.725 L 390.222 349.377 L 386.879 349.377 L 386.879 337.991 L 374.274 337.991 L 374.274 349.377 L 370.931 349.377 L 370.931 324.725 \" fill=\"#000000\"/>\n",
+       "<path class=\"atom-13\" d=\"M 370.931 150.623 L 374.274 150.623 L 374.274 161.104 L 386.879 161.104 L 386.879 150.623 L 390.222 150.623 L 390.222 175.275 L 386.879 175.275 L 386.879 163.889 L 374.274 163.889 L 374.274 175.275 L 370.931 175.275 L 370.931 150.623 \" fill=\"#000000\"/>\n",
+       "</svg>"
+      ],
       "text/plain": [
-       "<rdkit.Chem.rdchem.Mol at 0x7fd194caa120>"
+       "<IPython.core.display.SVG object>"
       ]
      },
      "metadata": {},
@@ -105,7 +115,7 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 2,
+   "execution_count": 5,
    "metadata": {},
    "outputs": [
     {
@@ -115,45 +125,55 @@
       " - Initializing molecule from a SMILES tag\n",
       "   - Loading molecule from RDKit\n",
       "   - Representing molecule with the Open Force Field Toolkit\n",
-      "Warning: Unable to load toolkit 'OpenEye Toolkit'. The Open Force Field Toolkit does not require the OpenEye Toolkits, and can use RDKit/AmberTools instead. However, if you have a valid license for the OpenEye Toolkits, consider installing them for faster performance and additional file format support: https://docs.eyesopen.com/toolkits/python/quickstart-python/linuxosx.html OpenEye offers free Toolkit licenses for academics: https://www.eyesopen.com/academic-licensing\n"
-     ]
-    },
-    {
-     "data": {
-      "application/vnd.jupyter.widget-view+json": {
-       "model_id": "f963188257ca4e30872f4d49f993d777",
-       "version_major": 2,
-       "version_minor": 0
-      },
-      "text/plain": []
-     },
-     "metadata": {},
-     "output_type": "display_data"
-    },
-    {
-     "name": "stderr",
-     "output_type": "stream",
-     "text": [
       " - Generating rotamer library\n",
-      "   - Core forced to contain atom C1\n"
+      "   - Core forced to contain atom:  C1 \n"
      ]
     }
    ],
    "source": [
     "mol = Molecule(smiles='CCCC', name='butane', tag='BUT',\n",
-    "               exclude_terminal_rotamers=False, core_constraint=' C1 ')"
+    "               exclude_terminal_rotamers=False, core_constraints=[' C1 ', ],\n",
+    "               hydrogens_are_explicit=False)"
    ]
   },
   {
    "cell_type": "code",
-   "execution_count": 3,
+   "execution_count": 6,
    "metadata": {},
    "outputs": [
     {
      "data": {
-      "image/png": "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\n",
+      "image/svg+xml": [
+       "<svg baseProfile=\"full\" height=\"500px\" version=\"1.1\" viewBox=\"0 0 500 500\" width=\"500px\" xml:space=\"preserve\" xmlns=\"http://www.w3.org/2000/svg\" xmlns:rdkit=\"http://www.rdkit.org/xml\" xmlns:xlink=\"http://www.w3.org/1999/xlink\">\n",
+       "<!-- END OF HEADER -->\n",
+       "<rect height=\"500\" style=\"opacity:1.0;fill:#FFFFFF;stroke:none\" width=\"500\" x=\"0\" y=\"0\"> </rect>\n",
+       "<path class=\"bond-0 atom-0 atom-1\" d=\"M 119.424,250 L 206.475,250\" style=\"fill:none;fill-rule:evenodd;stroke:#000000;stroke-width:4.0px;stroke-linecap:butt;stroke-linejoin:miter;stroke-opacity:1\"/>\n",
+       "<path class=\"bond-3 atom-0 atom-4\" d=\"M 119.424,250 L 44.194,250\" style=\"fill:none;fill-rule:evenodd;stroke:#000000;stroke-width:4.0px;stroke-linecap:butt;stroke-linejoin:miter;stroke-opacity:1\"/>\n",
+       "<path class=\"bond-4 atom-0 atom-5\" d=\"M 119.424,250 L 119.424,177.452\" style=\"fill:none;fill-rule:evenodd;stroke:#000000;stroke-width:4.0px;stroke-linecap:butt;stroke-linejoin:miter;stroke-opacity:1\"/>\n",
+       "<path class=\"bond-5 atom-0 atom-6\" d=\"M 119.424,250 L 119.424,322.548\" style=\"fill:none;fill-rule:evenodd;stroke:#000000;stroke-width:4.0px;stroke-linecap:butt;stroke-linejoin:miter;stroke-opacity:1\"/>\n",
+       "<path class=\"bond-1 atom-1 atom-2\" d=\"M 206.475,250 L 293.525,250\" style=\"fill:none;fill-rule:evenodd;stroke:#000000;stroke-width:4.0px;stroke-linecap:butt;stroke-linejoin:miter;stroke-opacity:1\"/>\n",
+       "<path class=\"bond-6 atom-1 atom-7\" d=\"M 206.475,250 L 206.475,322.548\" style=\"fill:none;fill-rule:evenodd;stroke:#000000;stroke-width:4.0px;stroke-linecap:butt;stroke-linejoin:miter;stroke-opacity:1\"/>\n",
+       "<path class=\"bond-7 atom-1 atom-8\" d=\"M 206.475,250 L 206.475,177.452\" style=\"fill:none;fill-rule:evenodd;stroke:#000000;stroke-width:4.0px;stroke-linecap:butt;stroke-linejoin:miter;stroke-opacity:1\"/>\n",
+       "<path class=\"bond-2 atom-2 atom-3\" d=\"M 293.525,250 L 380.576,250\" style=\"fill:none;fill-rule:evenodd;stroke:#000000;stroke-width:4.0px;stroke-linecap:butt;stroke-linejoin:miter;stroke-opacity:1\"/>\n",
+       "<path class=\"bond-8 atom-2 atom-9\" d=\"M 293.525,250 L 293.525,177.452\" style=\"fill:none;fill-rule:evenodd;stroke:#000000;stroke-width:4.0px;stroke-linecap:butt;stroke-linejoin:miter;stroke-opacity:1\"/>\n",
+       "<path class=\"bond-9 atom-2 atom-10\" d=\"M 293.525,250 L 293.525,322.548\" style=\"fill:none;fill-rule:evenodd;stroke:#000000;stroke-width:4.0px;stroke-linecap:butt;stroke-linejoin:miter;stroke-opacity:1\"/>\n",
+       "<path class=\"bond-10 atom-3 atom-11\" d=\"M 380.576,250 L 455.806,250\" style=\"fill:none;fill-rule:evenodd;stroke:#000000;stroke-width:4.0px;stroke-linecap:butt;stroke-linejoin:miter;stroke-opacity:1\"/>\n",
+       "<path class=\"bond-11 atom-3 atom-12\" d=\"M 380.576,250 L 380.576,322.548\" style=\"fill:none;fill-rule:evenodd;stroke:#000000;stroke-width:4.0px;stroke-linecap:butt;stroke-linejoin:miter;stroke-opacity:1\"/>\n",
+       "<path class=\"bond-12 atom-3 atom-13\" d=\"M 380.576,250 L 380.576,177.452\" style=\"fill:none;fill-rule:evenodd;stroke:#000000;stroke-width:4.0px;stroke-linecap:butt;stroke-linejoin:miter;stroke-opacity:1\"/>\n",
+       "<path class=\"atom-4\" d=\"M 22.7273 237.674 L 26.07 237.674 L 26.07 248.155 L 38.675 248.155 L 38.675 237.674 L 42.0178 237.674 L 42.0178 262.326 L 38.675 262.326 L 38.675 250.94 L 26.07 250.94 L 26.07 262.326 L 22.7273 262.326 L 22.7273 237.674 \" fill=\"#000000\"/>\n",
+       "<path class=\"atom-5\" d=\"M 109.778 150.623 L 113.121 150.623 L 113.121 161.104 L 125.726 161.104 L 125.726 150.623 L 129.069 150.623 L 129.069 175.275 L 125.726 175.275 L 125.726 163.889 L 113.121 163.889 L 113.121 175.275 L 109.778 175.275 L 109.778 150.623 \" fill=\"#000000\"/>\n",
+       "<path class=\"atom-6\" d=\"M 109.778 324.725 L 113.121 324.725 L 113.121 335.206 L 125.726 335.206 L 125.726 324.725 L 129.069 324.725 L 129.069 349.377 L 125.726 349.377 L 125.726 337.991 L 113.121 337.991 L 113.121 349.377 L 109.778 349.377 L 109.778 324.725 \" fill=\"#000000\"/>\n",
+       "<path class=\"atom-7\" d=\"M 196.829 324.725 L 200.172 324.725 L 200.172 335.206 L 212.777 335.206 L 212.777 324.725 L 216.12 324.725 L 216.12 349.377 L 212.777 349.377 L 212.777 337.991 L 200.172 337.991 L 200.172 349.377 L 196.829 349.377 L 196.829 324.725 \" fill=\"#000000\"/>\n",
+       "<path class=\"atom-8\" d=\"M 196.829 150.623 L 200.172 150.623 L 200.172 161.104 L 212.777 161.104 L 212.777 150.623 L 216.12 150.623 L 216.12 175.275 L 212.777 175.275 L 212.777 163.889 L 200.172 163.889 L 200.172 175.275 L 196.829 175.275 L 196.829 150.623 \" fill=\"#000000\"/>\n",
+       "<path class=\"atom-9\" d=\"M 283.88 150.623 L 287.223 150.623 L 287.223 161.104 L 299.828 161.104 L 299.828 150.623 L 303.171 150.623 L 303.171 175.275 L 299.828 175.275 L 299.828 163.889 L 287.223 163.889 L 287.223 175.275 L 283.88 175.275 L 283.88 150.623 \" fill=\"#000000\"/>\n",
+       "<path class=\"atom-10\" d=\"M 283.88 324.725 L 287.223 324.725 L 287.223 335.206 L 299.828 335.206 L 299.828 324.725 L 303.171 324.725 L 303.171 349.377 L 299.828 349.377 L 299.828 337.991 L 287.223 337.991 L 287.223 349.377 L 283.88 349.377 L 283.88 324.725 \" fill=\"#000000\"/>\n",
+       "<path class=\"atom-11\" d=\"M 457.982 237.674 L 461.325 237.674 L 461.325 248.155 L 473.93 248.155 L 473.93 237.674 L 477.273 237.674 L 477.273 262.326 L 473.93 262.326 L 473.93 250.94 L 461.325 250.94 L 461.325 262.326 L 457.982 262.326 L 457.982 237.674 \" fill=\"#000000\"/>\n",
+       "<path class=\"atom-12\" d=\"M 370.931 324.725 L 374.274 324.725 L 374.274 335.206 L 386.879 335.206 L 386.879 324.725 L 390.222 324.725 L 390.222 349.377 L 386.879 349.377 L 386.879 337.991 L 374.274 337.991 L 374.274 349.377 L 370.931 349.377 L 370.931 324.725 \" fill=\"#000000\"/>\n",
+       "<path class=\"atom-13\" d=\"M 370.931 150.623 L 374.274 150.623 L 374.274 161.104 L 386.879 161.104 L 386.879 150.623 L 390.222 150.623 L 390.222 175.275 L 386.879 175.275 L 386.879 163.889 L 374.274 163.889 L 374.274 175.275 L 370.931 175.275 L 370.931 150.623 \" fill=\"#000000\"/>\n",
+       "</svg>"
+      ],
       "text/plain": [
-       "<rdkit.Chem.rdchem.Mol at 0x7fd194caa120>"
+       "<IPython.core.display.SVG object>"
       ]
      },
      "metadata": {},
@@ -166,7 +186,7 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 4,
+   "execution_count": 7,
    "metadata": {},
    "outputs": [],
    "source": [
@@ -191,7 +211,7 @@
    "name": "python",
    "nbconvert_exporter": "python",
    "pygments_lexer": "ipython3",
-   "version": "3.7.8"
+   "version": "3.7.10"
   }
  },
  "nbformat": 4,
diff --git a/peleffy/data/tests/ethane_noH.pdb b/peleffy/data/tests/ethane_noH.pdb
new file mode 100644
index 00000000..050d9e85
--- /dev/null
+++ b/peleffy/data/tests/ethane_noH.pdb
@@ -0,0 +1,5 @@
+HETATM    1  C1  UNK     1       0.755   0.000   0.000  1.00  0.00           C  
+HETATM    2  C2  UNK     1      -0.755   0.000   0.000  1.00  0.00           C  
+CONECT    1    2
+END
+
diff --git a/peleffy/forcefield/forcefield.py b/peleffy/forcefield/forcefield.py
index fa1e6112..bafae21c 100644
--- a/peleffy/forcefield/forcefield.py
+++ b/peleffy/forcefield/forcefield.py
@@ -404,9 +404,7 @@ def _get_parameters(self, molecule):
 
         openff_parameters = self._openff.parameterize(molecule,
                                                       charge_method='dummy')
-        print(openff_parameters['sigmas'])
         oplsff_parameters = self._oplsff.parameterize(molecule)
-        print(oplsff_parameters['sigmas'])
 
         if self._nonbonding == 'openff':
             hybrid_parameters['atom_names'] = openff_parameters['atom_names']
diff --git a/peleffy/tests/test_molecule.py b/peleffy/tests/test_molecule.py
index 341742d7..0cec6a97 100644
--- a/peleffy/tests/test_molecule.py
+++ b/peleffy/tests/test_molecule.py
@@ -32,7 +32,7 @@ def test_smiles_initialization(self):
         """
         It checks the initialization from a SMILES tag.
         """
-        molecule = Molecule(smiles='c1ccccc1')
+        molecule = Molecule(smiles='c1ccccc1', hydrogens_are_explicit=False)
 
         # Save it
         with tempfile.TemporaryDirectory() as tmpdir:
@@ -59,12 +59,13 @@ def test_molecule_name_assignment(self):
         assert molecule.name == 'benzene', 'Unexpected atom name'
 
         # Look for the SMILES name when a Molecule is loaded from a SMILES tag
-        molecule = Molecule(smiles='c1ccccc1')
+        molecule = Molecule(smiles='c1ccccc1', hydrogens_are_explicit=False)
         assert molecule.name == 'c1ccccc1', 'Unexpected atom name'
 
         # Look for benzene name when a Molecule is loaded from a SMILES tag
         # with a custom name
-        molecule = Molecule(smiles='c1ccccc1', name='benzene')
+        molecule = Molecule(smiles='c1ccccc1', name='benzene',
+                            hydrogens_are_explicit=False)
         assert molecule.name == 'benzene', 'Unexpected atom name'
 
     def test_molecule_tag_assignment(self):
@@ -88,12 +89,13 @@ def test_molecule_tag_assignment(self):
         assert molecule.tag == 'BEN', 'Unexpected atom tag'
 
         # Look for UNK tag when a Molecule is loaded from a SMILES tag
-        molecule = Molecule(smiles='c1ccccc1')
+        molecule = Molecule(smiles='c1ccccc1', hydrogens_are_explicit=False)
         assert molecule.tag == 'UNK', 'Unexpected atom tag'
 
         # Look for BNZ tag when a Molecule is loaded from a SMILES tag with
         # a custom tag
-        molecule = Molecule(smiles='c1ccccc1', tag='BNZ')
+        molecule = Molecule(smiles='c1ccccc1', tag='BNZ',
+                            hydrogens_are_explicit=False)
         assert molecule.tag == 'BNZ', 'Unexpected atom tag'
 
     def test_PDB_connectivity_template(self):
@@ -198,7 +200,7 @@ def check_residue_name(name):
                 check_residue_name('TAG')
 
         # Checking default tag assignment from SMILES
-        molecule = Molecule(smiles='c1ccccc1')
+        molecule = Molecule(smiles='c1ccccc1', hydrogens_are_explicit=False)
         with tempfile.TemporaryDirectory() as tmpdir:
             with temporary_cd(tmpdir):
                 assert molecule.tag == 'UNK', 'Unexpected molecule tag'
@@ -206,7 +208,8 @@ def check_residue_name(name):
                 check_residue_name('UNK')
 
         # Checking custom tag assignment from SMILES
-        molecule = Molecule(smiles='c1ccccc1', tag='BEN')
+        molecule = Molecule(smiles='c1ccccc1', tag='BEN',
+                            hydrogens_are_explicit=False)
         with tempfile.TemporaryDirectory() as tmpdir:
             with temporary_cd(tmpdir):
                 assert molecule.tag == 'BEN', 'Unexpected molecule tag'
@@ -214,7 +217,7 @@ def check_residue_name(name):
                 check_residue_name('BEN')
 
         # Checking second custom tag assignment from SMILES
-        molecule = Molecule(smiles='c1ccccc1')
+        molecule = Molecule(smiles='c1ccccc1', hydrogens_are_explicit=False)
         with tempfile.TemporaryDirectory() as tmpdir:
             with temporary_cd(tmpdir):
                 molecule.set_tag('BNZ')
@@ -281,11 +284,13 @@ def test_undefined_stereo(self):
 
         # This should crash due to an undefined stereochemistry error
         with pytest.raises(UndefinedStereochemistryError):
-            mol = Molecule(smiles='CN(C)CCC=C1c2ccccc2CCc3c1cccc3')
+            mol = Molecule(smiles='CN(C)CCC=C1c2ccccc2CCc3c1cccc3',
+                           hydrogens_are_explicit=False)
 
         # This now should work
         mol = Molecule(smiles='CN(C)CCC=C1c2ccccc2CCc3c1cccc3',
-                       allow_undefined_stereo=True)
+                       allow_undefined_stereo=True,
+                       hydrogens_are_explicit=False)
 
         # And we can parameterize it
         ff = OpenForceField('openff_unconstrained-1.2.1.offxml')
@@ -330,7 +335,9 @@ def test_from_openff(self):
         """
         from openff.toolkit.topology import Molecule as OpenFFMolecule
 
-        openff_molecule = OpenFFMolecule.from_smiles('C(C(=O)[O-])C(=O)[OH]')
+        openff_molecule = \
+            OpenFFMolecule.from_smiles('C(C(=O)[O-])C(=O)[OH]',
+                                       hydrogens_are_explicit=False)
 
         molecule = Molecule.from_openff(openff_molecule)
 
@@ -350,6 +357,75 @@ def test_from_openff(self):
         assert molecule.graph is not None, \
             'Molecule\' graph should be initialized'
 
+    def test_explicit_hydrogens(self):
+        """
+        It checks initialization of a Molecule with the explicit hydrogens
+        flag.
+        """
+
+        # Load ethane from SMILES with implicit hydrogen atoms
+        molecule = Molecule(smiles='CC')
+        atom_names = molecule.get_pdb_atom_names()
+
+        for atom_name in atom_names:
+            assert 'H' not in atom_name, 'Unexpected H in molecule without ' \
+                + 'explicit hydrogen atoms and hydrogens_are_explicit ' \
+                + 'set to True'
+
+        # Load ethane from SMILES without explicit hydrogen atoms
+        molecule = Molecule(smiles='CC', hydrogens_are_explicit=False)
+        atom_names = molecule.get_pdb_atom_names()
+
+        found_hydrogen = False
+        for atom_name in atom_names:
+            if 'H' in atom_name:
+                found_hydrogen = True
+                break
+        
+        assert found_hydrogen, 'Hydrogen not found regardless of setting ' \
+            + 'hydrogens_are_explicit to False'
+
+        # Load ethane from SMILES with explicit hydrogen atoms
+        molecule = Molecule(smiles='[H]C([H])([H])C([H])([H])([H])',
+                            hydrogens_are_explicit=True)
+        atom_names = molecule.get_pdb_atom_names()
+
+        found_hydrogen = False
+        for atom_name in atom_names:
+            if 'H' in atom_name:
+                found_hydrogen = True
+                break
+
+        assert found_hydrogen, 'Hydrogen not found regardless of being ' \
+                               + 'explicitly defined in the SMILES tag'
+
+        # Load ethane from PDB with implicit hydrogen atoms
+        pdb_path = get_data_file_path('tests/ethane_noH.pdb')
+        molecule = Molecule(pdb_path,
+                            hydrogens_are_explicit=True)
+        atom_names = molecule.get_pdb_atom_names()
+
+        for atom_name in atom_names:
+            assert 'H' not in atom_name, 'Unexpected H in molecule without ' \
+                + 'explicit hydrogen atoms and hydrogens_are_explicit ' \
+                + 'set to True'
+
+        # Load ethane from PDB without explicit hydrogen atoms
+        pdb_path = get_data_file_path('tests/ethane_noH.pdb')
+        molecule = Molecule(pdb_path,
+                            hydrogens_are_explicit=False)
+        atom_names = molecule.get_pdb_atom_names()
+
+        found_hydrogen = False
+        for atom_name in atom_names:
+            if 'H' in atom_name:
+                found_hydrogen = True
+                break
+
+        assert found_hydrogen, 'Hydrogen not found regardless of setting ' \
+            + 'hydrogens_are_explicit to False'
+
+
     def test_pdb_fixer(self):
         """
         It checks the PDB fixer prior parsing a PDB input file for
@@ -443,7 +519,7 @@ def test_molecule_display(self):
 
         from IPython.display import display
 
-        molecule = Molecule(smiles='c1ccccc1')
+        molecule = Molecule(smiles='c1ccccc1', hydrogens_are_explicit=False)
 
         # This should not raise any Exception
         display(molecule)
diff --git a/peleffy/tests/test_parameters.py b/peleffy/tests/test_parameters.py
index 1ee641cf..a996b127 100644
--- a/peleffy/tests/test_parameters.py
+++ b/peleffy/tests/test_parameters.py
@@ -314,7 +314,7 @@ def test_OFF_parameters(self):
         MAX_THRESHOLD = 1e-3
 
         # Load benzene ring
-        molecule = Molecule(smiles='c1ccccc1')
+        molecule = Molecule(smiles='c1ccccc1', hydrogens_are_explicit=False)
 
         # Parameterize
         ff = OpenForceField(FORCEFIELD_NAME)
@@ -369,7 +369,7 @@ def test_Impact_writable_parameters(self):
         """
 
         # Load benzene ring
-        molecule = Molecule(smiles='CC=O')
+        molecule = Molecule(smiles='CC=O', hydrogens_are_explicit=False)
 
         # Parameterize
         ff = OpenForceField(FORCEFIELD_NAME)
@@ -407,7 +407,7 @@ def test_OFF_parameters(self):
         MAX_THRESHOLD = 1e-3
 
         # Load benzene ring
-        molecule = Molecule(smiles='c1ccccc1')
+        molecule = Molecule(smiles='c1ccccc1', hydrogens_are_explicit=False)
 
         # Parameterize
         ff = OpenForceField(FORCEFIELD_NAME)
@@ -475,7 +475,7 @@ def test_Impact_writable_parameters(self):
         """
 
         # Load benzene ring
-        molecule = Molecule(smiles='CC=O')
+        molecule = Molecule(smiles='CC=O', hydrogens_are_explicit=False)
 
         # Parameterize
         ff = OpenForceField(FORCEFIELD_NAME)
@@ -515,7 +515,7 @@ def test_OFF_parameters(self):
         """
 
         # Load molecule
-        molecule = Molecule(smiles='C=CC(=O)O')
+        molecule = Molecule(smiles='C=CC(=O)O', hydrogens_are_explicit=False)
 
         # Parameterize
         ff = OpenForceField(FORCEFIELD_NAME)
@@ -635,7 +635,7 @@ def test_Impact_writable_parameters(self):
         """
 
         # Load benzene ring
-        molecule = Molecule(smiles='CC=O')
+        molecule = Molecule(smiles='CC=O', hydrogens_are_explicit=False)
 
         # Parameterize
         ff = OpenForceField(FORCEFIELD_NAME)
@@ -793,7 +793,8 @@ def test_nonstandard_dihedrals_writable_parameters(self):
         It checks the writable representation of non standard dihedrals.
         """
         # Load molecule
-        molecule = Molecule(smiles='c1c(c(n(n1)S(=O)(=O)C))O')
+        molecule = Molecule(smiles='c1c(c(n(n1)S(=O)(=O)C))O',
+                            hydrogens_are_explicit=False)
 
         # Parameterize
         ff = OpenForceField(FORCEFIELD_NAME)
diff --git a/peleffy/tests/test_toolkits.py b/peleffy/tests/test_toolkits.py
index 1e460131..31d28d29 100644
--- a/peleffy/tests/test_toolkits.py
+++ b/peleffy/tests/test_toolkits.py
@@ -110,7 +110,7 @@ def test_get_Schrodinger_parameters(self):
         from peleffy.utils.toolkits import ToolkitUnavailableException
 
         # Load benzene ring
-        molecule = Molecule(smiles='c1ccccc1')
+        molecule = Molecule(smiles='c1ccccc1', hydrogens_are_explicit=False)
 
         # Load OPLS2005 force field
         opls2005 = OPLS2005ForceField()
diff --git a/peleffy/tests/test_utils.py b/peleffy/tests/test_utils.py
index 22142674..def730cf 100644
--- a/peleffy/tests/test_utils.py
+++ b/peleffy/tests/test_utils.py
@@ -172,7 +172,8 @@ def test_non_datalocal_paths(self):
         from peleffy.forcefield import OpenForceField
 
         # Load benzene molecule
-        molecule = Molecule(smiles='c1ccccc1', name='benzene', tag='BNZ')
+        molecule = Molecule(smiles='c1ccccc1', name='benzene', tag='BNZ',
+                            hydrogens_are_explicit=False)
 
         # Load force field
         openff = OpenForceField('openff_unconstrained-1.2.1.offxml')
@@ -225,7 +226,8 @@ def test_datalocal_paths_for_openff(self):
         from peleffy.forcefield import OpenForceField
 
         # Load benzene molecule
-        molecule = Molecule(smiles='c1ccccc1', name='benzene', tag='BNZ')
+        molecule = Molecule(smiles='c1ccccc1', name='benzene', tag='BNZ',
+                            hydrogens_are_explicit=False)
 
         # Load force field
         openff = OpenForceField('openff_unconstrained-1.2.1.offxml')
@@ -289,7 +291,8 @@ def test_datalocal_paths_for_opls(self):
         from peleffy.forcefield import OPLS2005ForceField
 
         # Load benzene molecule
-        molecule = Molecule(smiles='c1ccccc1', name='benzene', tag='BNZ')
+        molecule = Molecule(smiles='c1ccccc1', name='benzene', tag='BNZ',
+                            hydrogens_are_explicit=False)
 
         # Load force field
         opls2005 = OPLS2005ForceField()
@@ -358,7 +361,8 @@ def test_datalocal_paths_for_offopls(self):
         from peleffy.forcefield import OpenFFOPLS2005ForceField
 
         # Load benzene molecule
-        molecule = Molecule(smiles='c1ccccc1', name='benzene', tag='BNZ')
+        molecule = Molecule(smiles='c1ccccc1', name='benzene', tag='BNZ',
+                            hydrogens_are_explicit=False)
         molecule._forcefield = OpenFFOPLS2005ForceField('OPLS2005')
 
         # Load force field
@@ -484,7 +488,8 @@ def test_folder_creation(self):
         from peleffy.forcefield import OpenForceField
 
         # Load benzene molecule
-        molecule = Molecule(smiles='c1ccccc1', name='benzene', tag='BNZ')
+        molecule = Molecule(smiles='c1ccccc1', name='benzene', tag='BNZ',
+                            hydrogens_are_explicit=False)
 
         # Load force field
         openff = OpenForceField('openff_unconstrained-1.2.1.offxml')
diff --git a/peleffy/topology/molecule.py b/peleffy/topology/molecule.py
index a11ada18..c1391569 100644
--- a/peleffy/topology/molecule.py
+++ b/peleffy/topology/molecule.py
@@ -19,7 +19,8 @@ class Molecule(object):
     def __init__(self, path=None, smiles=None, pdb_block=None,
                  rotamer_resolution=30,exclude_terminal_rotamers=True, name='',
                  tag='UNK', connectivity_template=None, core_constraints=[],
-                 allow_undefined_stereo=False, fix_pdb=True):
+                 allow_undefined_stereo=False, hydrogens_are_explicit=True,
+                 fix_pdb=True):
         """
         It initializes a Molecule object through a PDB file or a SMILES
         tag.
@@ -52,6 +53,10 @@ def __init__(self, path=None, smiles=None, pdb_block=None,
             Whether to allow a molecule with undefined stereochemistry
             to be defined or try to assign the stereochemistry and
             raise a complaint if not possible. Default is False
+        hydrogens_are_explicit : bool
+            Whether the input molecule has explicit information about
+            hydrogen atoms or not. Otherwise, they will be added when
+            the molecule is built. Default is True
         fix_pdb : bool
             Activates or deactivate the PDB fixer that is executed
             prior parsing it
@@ -113,6 +118,14 @@ def __init__(self, path=None, smiles=None, pdb_block=None,
         >>> molecule = Molecule('molecule_with_undefined_stereochemistry.pdb',
                                 allow_undefined_stereo=True)
 
+        Load a molecule with no explicit hydrogen atoms and ask the builder
+        to add them
+
+        >>> from peleffy.topology import Molecule
+
+        >>> molecule = Molecule('molecule_with_implicit_hydrogen.pdb',
+                                hydrogens_are_explicit=False)
+
         Display the molecular representation in a Jupyter Notebook
 
         >>> from peleffy.topology import Molecule
@@ -129,6 +142,7 @@ def __init__(self, path=None, smiles=None, pdb_block=None,
         self._connectivity_template = connectivity_template
         self._core_constraints = core_constraints
         self._allow_undefined_stereo = allow_undefined_stereo
+        self._hydrogens_are_explicit = hydrogens_are_explicit
         self._fix_pdb = fix_pdb
 
         # Deactivate OpenForceField toolkit warnings
@@ -299,7 +313,9 @@ def _initialize_from_pdb(self, path):
 
         logger.info('   - Loading molecule from RDKit')
         rdkit_toolkit = RDKitToolkitWrapper()
-        self._rdkit_molecule = rdkit_toolkit.from_pdb_block(pdb_block)
+        self._rdkit_molecule = \
+            rdkit_toolkit.from_pdb_block(pdb_block,
+                                         self.hydrogens_are_explicit)
 
         # Use RDKit template, if any, to assign the connectivity to
         # the current Molecule object
@@ -328,7 +344,9 @@ def _initialize_from_pdb(self, path):
         logger.info('   - Representing molecule with the Open Force Field '
                     + 'Toolkit')
         openforcefield_toolkit = OpenForceFieldToolkitWrapper()
-        self._off_molecule = openforcefield_toolkit.from_rdkit(self)
+        self._off_molecule = \
+            openforcefield_toolkit.from_rdkit(self,
+                                              self.hydrogens_are_explicit)
 
     def _initialize_from_smiles(self, smiles):
         """
@@ -345,7 +363,8 @@ def _initialize_from_smiles(self, smiles):
 
         logger.info('   - Loading molecule from RDKit')
         rdkit_toolkit = RDKitToolkitWrapper()
-        self._rdkit_molecule = rdkit_toolkit.from_smiles(smiles)
+        self._rdkit_molecule = \
+            rdkit_toolkit.from_smiles(smiles, self.hydrogens_are_explicit)
 
         # TODO not sure if stereochemistry assignment from 3D is still necessary
         # RDKit must generate stereochemistry specifically from 3D coords
@@ -359,7 +378,9 @@ def _initialize_from_smiles(self, smiles):
         logger.info('   - Representing molecule with the Open Force Field '
                     + 'Toolkit')
         openforcefield_toolkit = OpenForceFieldToolkitWrapper()
-        self._off_molecule = openforcefield_toolkit.from_rdkit(self)
+        self._off_molecule = \
+            openforcefield_toolkit.from_rdkit(self,
+                                              self.hydrogens_are_explicit)
 
     def _initialize_from_pdb_block(self, pdb_block):
         """
@@ -377,7 +398,9 @@ def _initialize_from_pdb_block(self, pdb_block):
 
         logger.info('   - Loading molecule from RDKit')
         rdkit_toolkit = RDKitToolkitWrapper()
-        self._rdkit_molecule = rdkit_toolkit.from_pdb_block(pdb_block)
+        self._rdkit_molecule = \
+            rdkit_toolkit.from_pdb_block(pdb_block,
+                                         self.hydrogens_are_explicit)
 
         # Use RDKit template, if any, to assign the connectivity to
         # the current Molecule object
@@ -399,7 +422,9 @@ def _initialize_from_pdb_block(self, pdb_block):
         logger.info('   - Representing molecule with the Open Force Field '
                     + 'Toolkit')
         openforcefield_toolkit = OpenForceFieldToolkitWrapper()
-        self._off_molecule = openforcefield_toolkit.from_rdkit(self)
+        self._off_molecule = \
+            openforcefield_toolkit.from_rdkit(self,
+                                              self.hydrogens_are_explicit)
 
     def _build_rotamers(self):
         """It builds the rotamers of the molecule."""
@@ -508,7 +533,8 @@ def get_conformer(self):
     def from_rdkit(rdkit_molecule, rotamer_resolution=30,
                    exclude_terminal_rotamers=True, name='', tag='UNK',
                    connectivity_template=None, core_constraints=[],
-                   allow_undefined_stereo=False):
+                   allow_undefined_stereo=False,
+                   hydrogens_are_explicit=True):
         """
         It initializes and returns a peleffy Molecule representation
         from an RDKit molecular representation.
@@ -540,6 +566,10 @@ def from_rdkit(rdkit_molecule, rotamer_resolution=30,
             Whether to allow a molecule with undefined stereochemistry
             to be defined or try to assign the stereochemistry and
             raise a complaint if not possible. Default is False
+        hydrogens_are_explicit : bool
+            Whether the input molecule has explicit information about
+            hydrogen atoms or not. Otherwise, they will be added when
+            the molecule is built. Default is True
 
         Returns
         -------
@@ -566,7 +596,8 @@ def from_rdkit(rdkit_molecule, rotamer_resolution=30,
             name=name, tag=tag,
             connectivity_template=connectivity_template,
             core_constraints=core_constraints,
-            allow_undefined_stereo=allow_undefined_stereo)
+            allow_undefined_stereo=allow_undefined_stereo,
+            hydrogens_are_explicit=hydrogens_are_explicit)
 
         logger = Logger()
 
@@ -578,7 +609,9 @@ def from_rdkit(rdkit_molecule, rotamer_resolution=30,
         logger.info('   - Representing molecule with the Open Force Field '
                     + 'Toolkit')
         openforcefield_toolkit = OpenForceFieldToolkitWrapper()
-        molecule._off_molecule = openforcefield_toolkit.from_rdkit(molecule)
+        molecule._off_molecule = \
+            openforcefield_toolkit.from_rdkit(molecule,
+                                              hydrogens_are_explicit)
 
         molecule._build_rotamers()
 
@@ -588,7 +621,8 @@ def from_rdkit(rdkit_molecule, rotamer_resolution=30,
     def from_openff(openff_molecule, rotamer_resolution=30,
                     exclude_terminal_rotamers=True, name='', tag='UNK',
                     connectivity_template=None, core_constraints=[],
-                    allow_undefined_stereo=False):
+                    allow_undefined_stereo=False,
+                    hydrogens_are_explicit=True):
         """
         It initializes and returns a peleffy Molecule representation
         from an OpenForceField molecular representation.
@@ -620,6 +654,10 @@ def from_openff(openff_molecule, rotamer_resolution=30,
             Whether to allow a molecule with undefined stereochemistry
             to be defined or try to assign the stereochemistry and
             raise a complaint if not possible. Default is False
+        hydrogens_are_explicit : bool
+            Whether the input molecule has explicit information about
+            hydrogen atoms or not. Otherwise, they will be added when
+            the molecule is built. Default is True
 
         Returns
         -------
@@ -649,7 +687,8 @@ def from_openff(openff_molecule, rotamer_resolution=30,
             name=name, tag=tag,
             connectivity_template=connectivity_template,
             core_constraints=core_constraints,
-            allow_undefined_stereo=allow_undefined_stereo)
+            allow_undefined_stereo=allow_undefined_stereo,
+            hydrogens_are_explicit=hydrogens_are_explicit)
 
         logger = Logger()
 
@@ -722,6 +761,21 @@ def allow_undefined_stereo(self):
         """
         return self._allow_undefined_stereo
 
+    @property
+    def hydrogens_are_explicit(self):
+        """
+        Whether the input molecule has explicit information about
+        hydrogen atoms or not. Otherwise, they will be added when
+        the molecule is built
+
+        Returns
+        -------
+        allow_undefined_stereo : bool
+            The current configuration towards the hydrogen treatment
+            of this molecule
+        """
+        return self._hydrogens_are_explicit
+
     @property
     def fix_pdb(self):
         """
diff --git a/peleffy/utils/toolkits.py b/peleffy/utils/toolkits.py
index 4b0cc6e2..8cf07420 100644
--- a/peleffy/utils/toolkits.py
+++ b/peleffy/utils/toolkits.py
@@ -98,7 +98,7 @@ def is_available():
         except ImportError:
             return False
 
-    def from_pdb(self, path):
+    def from_pdb(self, path, hydrogens_are_explicit=True):
         """
         It initializes an RDKit's Molecule object from a PDB file.
 
@@ -106,6 +106,10 @@ def from_pdb(self, path):
         ----------
         path : str
             The path to the molecule's PDB file
+        hydrogens_are_explicit : bool
+            Whether the SMILES tag has explicit information about
+            hydrogen atoms or not. Otherwise, they will be added when
+            the molecule is built. Default is True
 
         Returns
         -------
@@ -114,9 +118,15 @@ def from_pdb(self, path):
         """
         from rdkit import Chem
 
-        return Chem.rdmolfiles.MolFromPDBFile(path, removeHs=False)
+        molecule = Chem.rdmolfiles.MolFromPDBFile(path, removeHs=False)
 
-    def from_pdb_block(self, pdb_block):
+        # Add hydrogens to molecule
+        if not hydrogens_are_explicit:
+            molecule = Chem.AddHs(molecule)
+
+        return molecule
+
+    def from_pdb_block(self, pdb_block, hydrogens_are_explicit=True):
         """
         It initializes an RDKit's Molecule object from a PDB block.
 
@@ -124,6 +134,10 @@ def from_pdb_block(self, pdb_block):
         ----------
         pdb_block : str
             The PDB block to built the molecule with
+        hydrogens_are_explicit : bool
+            Whether the SMILES tag has explicit information about
+            hydrogen atoms or not. Otherwise, they will be added when
+            the molecule is built. Default is True
 
         Returns
         -------
@@ -132,16 +146,26 @@ def from_pdb_block(self, pdb_block):
         """
         from rdkit import Chem
 
-        return Chem.rdmolfiles.MolFromPDBBlock(pdb_block, removeHs=False)
+        molecule = Chem.rdmolfiles.MolFromPDBBlock(pdb_block, removeHs=False)
 
-    def from_smiles(self, smiles):
+        # Add hydrogens to molecule
+        if not hydrogens_are_explicit:
+            molecule = Chem.AddHs(molecule)
+
+        return molecule
+
+    def from_smiles(self, smiles, hydrogens_are_explicit=True):
         """
         It initializes an RDKit's Molecule object from a SMILES tag.
 
         Parameters
         ----------
         smiles : str
-            The SMILES tag to construct the molecule structure with.
+            The SMILES tag to construct the molecule structure with
+        hydrogens_are_explicit : bool
+            Whether the SMILES tag has explicit information about
+            hydrogen atoms or not. Otherwise, they will be added when
+            the molecule is built. Default is True
 
         Returns
         -------
@@ -150,10 +174,14 @@ def from_smiles(self, smiles):
         """
         from rdkit.Chem import AllChem as Chem
 
-        molecule = Chem.MolFromSmiles(smiles)
+        molecule = Chem.MolFromSmiles(smiles, sanitize=False)
+
+        Chem.SanitizeMol(molecule,
+                         Chem.SANITIZE_ALL ^ Chem.SANITIZE_ADJUSTHS ^ Chem.SANITIZE_SETAROMATICITY)
 
         # Add hydrogens to molecule
-        molecule = Chem.AddHs(molecule)
+        if not hydrogens_are_explicit:
+            molecule = Chem.AddHs(molecule)
 
         # Generate 3D coordinates
         Chem.EmbedMolecule(molecule)
@@ -787,7 +815,7 @@ def is_available():
         except ImportError:
             return False
 
-    def from_rdkit(self, molecule):
+    def from_rdkit(self, molecule, hydrogens_are_explicit=True):
         """
         It initializes an OpenForceField's Molecule object from an RDKit
         molecule.
@@ -796,6 +824,10 @@ def from_rdkit(self, molecule):
         ----------
         molecule : an peleffy.topology.Molecule
             The peleffy's Molecule object
+        hydrogens_are_explicit : bool
+            Whether the SMILES tag has explicit information about
+            hydrogen atoms or not. Otherwise, they will be added when
+            the molecule is built. Default is True
 
         Returns
         -------
@@ -807,7 +839,8 @@ def from_rdkit(self, molecule):
         rdkit_molecule = molecule.rdkit_molecule
         return Molecule.from_rdkit(
             rdkit_molecule,
-            allow_undefined_stereo=molecule.allow_undefined_stereo)
+            allow_undefined_stereo=molecule.allow_undefined_stereo,
+            hydrogens_are_explicit=molecule.hydrogens_are_explicit)
 
     def get_forcefield(self, forcefield_name):
         """