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datamol-io · Oct 27, 2023 · e281c1a · e281c1a
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commit e281c1a
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diff --git a/docs/tutorials/design-with-safe.ipynb b/docs/tutorials/design-with-safe.ipynb
@@ -49,7 +49,7 @@
     }
    ],
    "source": [
-    "designer = sf.SAFEDesign.load_default(verbose=True)\n"
+    "# designer = sf.SAFEDesign.load_default(verbose=True)\n"
    ]
   },
   {
@@ -58,13 +58,13 @@
    "metadata": {},
    "outputs": [],
    "source": [
-    "candidate_mol = \"O=C(C#CCN1CCCCC1)Nc1ccc2ncnc(Nc3cccc(Br)c3)c2c1\"\n",
+    "# candidate_mol = \"O=C(C#CCN1CCCCC1)Nc1ccc2ncnc(Nc3cccc(Br)c3)c2c1\"\n",
     "\n",
-    "scaffold = \"[*]N-c1ccc2ncnc(-N[*])c2c1\" # this is for scaffold decoration\n",
-    "superstructure = \"c1ccc2ncncc2c1\"\n",
-    "side_chains = '[1*]C(=O)C#CCN1CCCCC1.[2*]c1cccc(Br)c1' # this is for scaffold morphing\n",
-    "motif = \"[*]-N1CCCCC1\" # this is for motif extension\n",
-    "linker_generation = [\"[*]-N1CCCCC1\", \"Brc1cccc(Nc2ncnc3ccc(-[*])cc23)c1\"] # this is for linker generation\n"
+    "# scaffold = \"[*]N-c1ccc2ncnc(-N[*])c2c1\" # this is for scaffold decoration\n",
+    "# superstructure = \"c1ccc2ncncc2c1\"\n",
+    "# side_chains = '[1*]C(=O)C#CCN1CCCCC1.[2*]c1cccc(Br)c1' # this is for scaffold morphing\n",
+    "# motif = \"[*]-N1CCCCC1\" # this is for motif extension\n",
+    "# linker_generation = [\"[*]-N1CCCCC1\", \"Brc1cccc(Nc2ncnc3ccc(-[*])cc23)c1\"] # this is for linker generation\n"
    ]
   },
   {
@@ -184,7 +184,7 @@
     }
    ],
    "source": [
-    "dm.to_image(dm.to_mol(candidate_mol))\n"
+    "# dm.to_image(dm.to_mol(candidate_mol))\n"
    ]
   },
   {
@@ -193,7 +193,7 @@
    "metadata": {},
    "outputs": [],
    "source": [
-    "N_SAMPLES = 100\n"
+    "# N_SAMPLES = 100\n"
    ]
   },
   {
@@ -219,7 +219,7 @@
     }
    ],
    "source": [
-    "generated = designer.de_novo_generation(sanitize=True, n_samples_per_trial=N_SAMPLES)\n"
+    "# generated = designer.de_novo_generation(sanitize=True, n_samples_per_trial=N_SAMPLES)\n"
    ]
   },
   {
@@ -1633,7 +1633,7 @@
     }
    ],
    "source": [
-    "dm.to_image(generated[:20])\n"
+    "# dm.to_image(generated[:20])\n"
    ]
   },
   {
@@ -1710,7 +1710,7 @@
     }
    ],
    "source": [
-    "dm.to_image(scaffold)\n"
+    "# dm.to_image(scaffold)\n"
    ]
   },
   {
@@ -1727,7 +1727,7 @@
     }
    ],
    "source": [
-    "generated = designer.scaffold_decoration(scaffold=scaffold, n_samples_per_trial=N_SAMPLES, n_trials=2, sanitize=True, do_not_fragment_further=True)\n"
+    "# generated = designer.scaffold_decoration(scaffold=scaffold, n_samples_per_trial=N_SAMPLES, n_trials=2, sanitize=True, do_not_fragment_further=True)\n"
    ]
   },
   {
@@ -5996,7 +5996,7 @@
     }
    ],
    "source": [
-    "dm.viz.lasso_highlight_image([dm.to_mol(x) for x in generated[:20]], dm.from_smarts(scaffold))\n"
+    "# dm.viz.lasso_highlight_image([dm.to_mol(x) for x in generated[:20]], dm.from_smarts(scaffold))\n"
    ]
   },
   {
@@ -6061,7 +6061,7 @@
     }
    ],
    "source": [
-    "dm.to_image(superstructure)\n"
+    "# dm.to_image(superstructure)\n"
    ]
   },
   {
@@ -6078,8 +6078,8 @@
     }
    ],
    "source": [
-    "generated = designer.super_structure(core=superstructure, n_samples_per_trial=N_SAMPLES, n_trials=1, sanitize=True, do_not_fragment_further=False, attachment_point_depth=3)\n",
-    "#generated\n"
+    "# generated = designer.super_structure(core=superstructure, n_samples_per_trial=N_SAMPLES, n_trials=1, sanitize=True, do_not_fragment_further=False, attachment_point_depth=3)\n",
+    "# #generated\n"
    ]
   },
   {
@@ -7227,7 +7227,7 @@
     }
    ],
    "source": [
-    "dm.to_image(generated[:20])\n"
+    "# dm.to_image(generated[:20])\n"
    ]
   },
   {
@@ -7279,7 +7279,7 @@
     }
    ],
    "source": [
-    "dm.to_image(motif)\n"
+    "# dm.to_image(motif)\n"
    ]
   },
   {
@@ -7296,8 +7296,8 @@
     }
    ],
    "source": [
-    "# let's make some long sequence\n",
-    "generated = designer.motif_extension(motif=motif, n_samples_per_trial=N_SAMPLES, n_trials=1, sanitize=True, do_not_fragment_further=False, min_length=25, max_length=80)\n"
+    "# # let's make some long sequence\n",
+    "# generated = designer.motif_extension(motif=motif, n_samples_per_trial=N_SAMPLES, n_trials=1, sanitize=True, do_not_fragment_further=False, min_length=25, max_length=80)\n"
    ]
   },
   {
@@ -8453,7 +8453,7 @@
     }
    ],
    "source": [
-    "dm.to_image(generated[:20])\n"
+    "# dm.to_image(generated[:20])\n"
    ]
   },
   {
@@ -8543,7 +8543,7 @@
     }
    ],
    "source": [
-    "dm.to_image(side_chains)\n"
+    "# dm.to_image(side_chains)\n"
    ]
   },
   {
@@ -10007,8 +10007,8 @@
     }
    ],
    "source": [
-    "generated = designer.scaffold_morphing(side_chains=side_chains, n_samples_per_trial=N_SAMPLES, n_trials=1, sanitize=True, do_not_fragment_further=False, random_seed=100)\n",
-    "dm.to_image(generated[:20])\n"
+    "# generated = designer.scaffold_morphing(side_chains=side_chains, n_samples_per_trial=N_SAMPLES, n_trials=1, sanitize=True, do_not_fragment_further=False, random_seed=100)\n",
+    "# dm.to_image(generated[:20])\n"
    ]
   },
   {
@@ -10114,7 +10114,7 @@
     }
    ],
    "source": [
-    "dm.to_image(linker_generation)\n"
+    "# dm.to_image(linker_generation)\n"
    ]
   },
   {
@@ -12321,8 +12321,8 @@
     }
    ],
    "source": [
-    "generated = designer.linker_generation(*linker_generation, n_samples_per_trial=N_SAMPLES, n_trials=1, sanitize=True, do_not_fragment_further=False, random_seed=100)\n",
-    "dm.to_image(generated[:20])\n"
+    "# generated = designer.linker_generation(*linker_generation, n_samples_per_trial=N_SAMPLES, n_trials=1, sanitize=True, do_not_fragment_further=False, random_seed=100)\n",
+    "# dm.to_image(generated[:20])\n"
    ]
   }
  ],

diff --git a/scripts/model_trainer.py b/scripts/model_trainer.py