Add cyclic_peptides cells (5 models × 6 motifs) + AVG table + grid

cyclic_peptides/_reference/_summary.json

@@ -0,0 +1,26 @@
+{
+  "benzene": {
+    "smarts": "c1ccccc1",
+    "n_ref": 100
+  },
+  "pyridine": {
+    "smarts": "c1ccncc1",
+    "n_ref": 55
+  },
+  "naphthalene": {
+    "smarts": "c1ccc2ccccc2c1",
+    "n_ref": 100
+  },
+  "indole": {
+    "smarts": "c1ccc2[nH]ccc2c1",
+    "n_ref": 42
+  },
+  "cyclohexane": {
+    "smarts": "C1CCCCC1",
+    "n_ref": 100
+  },
+  "cyclopentane": {
+    "smarts": "C1CCCC1",
+    "n_ref": 0
+  }
+}

cyclic_peptides/_reference/benzene.txt

@@ -0,0 +1,100 @@
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cyclic_peptides/_reference/cyclohexane.txt

@@ -0,0 +1,100 @@
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cyclic_peptides/_reference/indole.txt

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cyclic_peptides/_reference/naphthalene.txt

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cyclic_peptides/_reference/pyridine.txt

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cyclic_peptides/benzene/hdt/generated_metadata.json

@@ -0,0 +1,27 @@
+{
+  "dataset": "cyclic_peptides",
+  "tokenizer_type": "hdt",
+  "motif_name": "benzene",
+  "motif_smiles_prompt": "c1ccccc1",
+  "motif_smarts": "c1ccccc1",
+  "checkpoint": "eval_outputs/cyclic_peptides_hdt_motif_community_xs/last.ckpt",
+  "prompt_length_tokens": 42,
+  "k_target_decodable": 100,
+  "max_attempts": 800,
+  "num_attempted": 128,
+  "num_decodable": 100,
+  "num_decode_failures": 24,
+  "num_rdkit_valid": 100,
+  "num_motif_match": 98,
+  "decode_rate": 0.78125,
+  "rdkit_validity_of_decodable": 1.0,
+  "motif_retention_of_valid": 0.98,
+  "elapsed_sec": 23.151994228363037,
+  "sampling": {
+    "top_k": 10,
+    "temperature": 1.0,
+    "max_length": 2048,
+    "batch_size": 64,
+    "seed": 42
+  }
+}

cyclic_peptides/benzene/hdt/generated_smiles.txt

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cyclic_peptides/benzene/hdt/metrics.json

@@ -0,0 +1,35 @@
+{
+  "n_generated_decodable": 100,
+  "n_reference": 100,
+  "motif": {
+    "n_decodable": 100,
+    "n_rdkit_valid": 100,
+    "n_motif_match": 98,
+    "rdkit_validity": 1.0,
+    "motif_retention": 0.98,
+    "motif_retention_of_decodable": 0.98
+  },
+  "bertz": {
+    "bertz_gen_mean": 2585.6970734348615,
+    "bertz_ref_mean": 1907.4896699419344,
+    "bertz_delta": 678.2074034929271,
+    "bertz_n_gen": 100,
+    "bertz_n_ref": 100
+  },
+  "molecular": {
+    "validity": 1.0,
+    "uniqueness": 0.79,
+    "novelty": 1.0,
+    "vun": 0.79,
+    "snn": 0.6268910243882027,
+    "frag_similarity": 0.9291600678391504,
+    "scaff_similarity": 0.0,
+    "internal_diversity": 0.5741306826340069
+  },
+  "motif_distribution": {
+    "motif_fg_mmd": 0.08090040686476731,
+    "motif_smarts_mmd": 0.19530533921498788,
+    "motif_ring_mmd": 0.15051137608447734,
+    "motif_brics_mmd": 0.1183088320209239
+  }
+}

cyclic_peptides/benzene/hdt_hac/generated_metadata.json

@@ -0,0 +1,27 @@
+{
+  "dataset": "cyclic_peptides",
+  "tokenizer_type": "hdt",
+  "motif_name": "benzene",
+  "motif_smiles_prompt": "c1ccccc1",
+  "motif_smarts": "c1ccccc1",
+  "checkpoint": "eval_outputs/cyclic_peptides_hdt_hac_avg_xs_lr8.49e-4/last.ckpt",
+  "prompt_length_tokens": 50,
+  "k_target_decodable": 100,
+  "max_attempts": 800,
+  "num_attempted": 832,
+  "num_decodable": 61,
+  "num_decode_failures": 771,
+  "num_rdkit_valid": 61,
+  "num_motif_match": 61,
+  "decode_rate": 0.0733173076923077,
+  "rdkit_validity_of_decodable": 1.0,
+  "motif_retention_of_valid": 1.0,
+  "elapsed_sec": 117.45433950424194,
+  "sampling": {
+    "top_k": 10,
+    "temperature": 1.0,
+    "max_length": 2048,
+    "batch_size": 64,
+    "seed": 42
+  }
+}

cyclic_peptides/benzene/hdt_hac/generated_smiles.txt

@@ -0,0 +1,61 @@
+c1ccccc1
+c1ccccc1
+c1ccccc1
+c1ccccc1
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+c1ccccc1
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+c1ccccc1
+c1ccccc1
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+c1ccccc1
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+c1ccccc1
+c1ccccc1

cyclic_peptides/benzene/hdt_hac/metrics.json

@@ -0,0 +1,35 @@
+{
+  "n_generated_decodable": 61,
+  "n_reference": 100,
+  "motif": {
+    "n_decodable": 61,
+    "n_rdkit_valid": 61,
+    "n_motif_match": 61,
+    "rdkit_validity": 1.0,
+    "motif_retention": 1.0,
+    "motif_retention_of_decodable": 1.0
+  },
+  "bertz": {
+    "bertz_gen_mean": 71.96100505779538,
+    "bertz_ref_mean": 1907.4896699419344,
+    "bertz_delta": -1835.528664884139,
+    "bertz_n_gen": 61,
+    "bertz_n_ref": 100
+  },
+  "molecular": {
+    "validity": 1.0,
+    "uniqueness": 0.03278688524590164,
+    "novelty": 1.0,
+    "vun": 0.03278688524590164,
+    "snn": 0.06514914848121806,
+    "frag_similarity": 0.0,
+    "scaff_similarity": 0.0,
+    "internal_diversity": 0.023770491803278688
+  },
+  "motif_distribution": {
+    "motif_fg_mmd": 1.0546467730758078,
+    "motif_smarts_mmd": 1.217817727239841,
+    "motif_ring_mmd": 1.146431707561696,
+    "motif_brics_mmd": 1.0003849953407946
+  }
+}

cyclic_peptides/benzene/hdt_lou/generated_metadata.json

@@ -0,0 +1,27 @@
+{
+  "dataset": "cyclic_peptides",
+  "tokenizer_type": "hdt",
+  "motif_name": "benzene",
+  "motif_smiles_prompt": "c1ccccc1",
+  "motif_smarts": "c1ccccc1",
+  "checkpoint": "eval_outputs/cyclic_peptides_hdt_louvain_xs_lr8.49e-4/last.ckpt",
+  "prompt_length_tokens": 50,
+  "k_target_decodable": 100,
+  "max_attempts": 800,
+  "num_attempted": 832,
+  "num_decodable": 0,
+  "num_decode_failures": 832,
+  "num_rdkit_valid": 0,
+  "num_motif_match": 0,
+  "decode_rate": 0.0,
+  "rdkit_validity_of_decodable": 0.0,
+  "motif_retention_of_valid": 0.0,
+  "elapsed_sec": 106.83552575111389,
+  "sampling": {
+    "top_k": 10,
+    "temperature": 1.0,
+    "max_length": 2048,
+    "batch_size": 64,
+    "seed": 42
+  }
+}

cyclic_peptides/benzene/hdt_lou/metrics.json

@@ -0,0 +1,35 @@
+{
+  "n_generated_decodable": 0,
+  "n_reference": 100,
+  "motif": {
+    "n_decodable": 0,
+    "n_rdkit_valid": 0,
+    "n_motif_match": 0,
+    "rdkit_validity": 0.0,
+    "motif_retention": 0.0,
+    "motif_retention_of_decodable": 0.0
+  },
+  "bertz": {
+    "bertz_gen_mean": NaN,
+    "bertz_ref_mean": 1907.4896699419344,
+    "bertz_delta": NaN,
+    "bertz_n_gen": 0,
+    "bertz_n_ref": 100
+  },
+  "molecular": {
+    "validity": 0.0,
+    "uniqueness": 0.0,
+    "novelty": 0.0,
+    "vun": 0.0,
+    "snn": 0.0,
+    "frag_similarity": 0.0,
+    "scaff_similarity": 0.0,
+    "internal_diversity": 0.0
+  },
+  "motif_distribution": {
+    "motif_fg_mmd": Infinity,
+    "motif_smarts_mmd": Infinity,
+    "motif_ring_mmd": Infinity,
+    "motif_brics_mmd": Infinity
+  }
+}

cyclic_peptides/benzene/hdtc/generated_metadata.json

@@ -0,0 +1,27 @@
+{
+  "dataset": "cyclic_peptides",
+  "tokenizer_type": "hdtc",
+  "motif_name": "benzene",
+  "motif_smiles_prompt": "c1ccccc1",
+  "motif_smarts": "c1ccccc1",
+  "checkpoint": "eval_outputs/cyclic_peptides_hdtc_xs/last.ckpt",
+  "prompt_length_tokens": 39,
+  "k_target_decodable": 100,
+  "max_attempts": 800,
+  "num_attempted": 186,
+  "num_decodable": 100,
+  "num_decode_failures": 79,
+  "num_rdkit_valid": 100,
+  "num_motif_match": 55,
+  "decode_rate": 0.5376344086021505,
+  "rdkit_validity_of_decodable": 1.0,
+  "motif_retention_of_valid": 0.55,
+  "elapsed_sec": 32.347288370132446,
+  "sampling": {
+    "top_k": 10,
+    "temperature": 1.0,
+    "max_length": 2048,
+    "batch_size": 64,
+    "seed": 42
+  }
+}

cyclic_peptides/benzene/hdtc/generated_smiles.txt

@@ -0,0 +1,100 @@
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cyclic_peptides/benzene/hdtc/metrics.json

@@ -0,0 +1,35 @@
+{
+  "n_generated_decodable": 100,
+  "n_reference": 100,
+  "motif": {
+    "n_decodable": 100,
+    "n_rdkit_valid": 100,
+    "n_motif_match": 55,
+    "rdkit_validity": 1.0,
+    "motif_retention": 0.55,
+    "motif_retention_of_decodable": 0.55
+  },
+  "bertz": {
+    "bertz_gen_mean": 2077.688399914016,
+    "bertz_ref_mean": 1907.4896699419344,
+    "bertz_delta": 170.19872997208154,
+    "bertz_n_gen": 100,
+    "bertz_n_ref": 100
+  },
+  "molecular": {
+    "validity": 1.0,
+    "uniqueness": 0.18,
+    "novelty": 1.0,
+    "vun": 0.18,
+    "snn": 0.6083521629668401,
+    "frag_similarity": 0.505120437894638,
+    "scaff_similarity": 0.0,
+    "internal_diversity": 0.42920461791223236
+  },
+  "motif_distribution": {
+    "motif_fg_mmd": 0.3793782785147675,
+    "motif_smarts_mmd": 0.5139613184188352,
+    "motif_ring_mmd": 0.42115669765675134,
+    "motif_brics_mmd": 0.2827016977843816
+  }
+}

cyclic_peptides/benzene/sent/generated_metadata.json

@@ -0,0 +1,27 @@
+{
+  "dataset": "cyclic_peptides",
+  "tokenizer_type": "sent",
+  "motif_name": "benzene",
+  "motif_smiles_prompt": "c1ccccc1",
+  "motif_smarts": "c1ccccc1",
+  "checkpoint": "eval_outputs/cyclic_peptides_sent_xs/last.ckpt",
+  "prompt_length_tokens": 22,
+  "k_target_decodable": 100,
+  "max_attempts": 800,
+  "num_attempted": 246,
+  "num_decodable": 100,
+  "num_decode_failures": 146,
+  "num_rdkit_valid": 100,
+  "num_motif_match": 94,
+  "decode_rate": 0.4065040650406504,
+  "rdkit_validity_of_decodable": 1.0,
+  "motif_retention_of_valid": 0.94,
+  "elapsed_sec": 7.757506608963013,
+  "sampling": {
+    "top_k": 10,
+    "temperature": 1.0,
+    "max_length": 2048,
+    "batch_size": 64,
+    "seed": 42
+  }
+}

cyclic_peptides/benzene/sent/generated_smiles.txt

@@ -0,0 +1,100 @@
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cyclic_peptides/benzene/sent/metrics.json

@@ -0,0 +1,35 @@
+{
+  "n_generated_decodable": 100,
+  "n_reference": 100,
+  "motif": {
+    "n_decodable": 100,
+    "n_rdkit_valid": 100,
+    "n_motif_match": 94,
+    "rdkit_validity": 1.0,
+    "motif_retention": 0.94,
+    "motif_retention_of_decodable": 0.94
+  },
+  "bertz": {
+    "bertz_gen_mean": 1580.3253442356959,
+    "bertz_ref_mean": 1907.4896699419344,
+    "bertz_delta": -327.1643257062385,
+    "bertz_n_gen": 100,
+    "bertz_n_ref": 100
+  },
+  "molecular": {
+    "validity": 1.0,
+    "uniqueness": 1.0,
+    "novelty": 1.0,
+    "vun": 1.0,
+    "snn": 0.13918115996185995,
+    "frag_similarity": 0.3986361266640217,
+    "scaff_similarity": 0.0,
+    "internal_diversity": 0.7982559791085614
+  },
+  "motif_distribution": {
+    "motif_fg_mmd": 0.1442298341057899,
+    "motif_smarts_mmd": 1.1734344917354003,
+    "motif_ring_mmd": 0.18938682407489224,
+    "motif_brics_mmd": 0.2834845179120009
+  }
+}

cyclic_peptides/cyclohexane/hdt/generated_metadata.json

@@ -0,0 +1,27 @@
+{
+  "dataset": "cyclic_peptides",
+  "tokenizer_type": "hdt",
+  "motif_name": "cyclohexane",
+  "motif_smiles_prompt": "C1CCCCC1",
+  "motif_smarts": "C1CCCCC1",
+  "checkpoint": "eval_outputs/cyclic_peptides_hdt_motif_community_xs/last.ckpt",
+  "prompt_length_tokens": 42,
+  "k_target_decodable": 100,
+  "max_attempts": 800,
+  "num_attempted": 144,
+  "num_decodable": 100,
+  "num_decode_failures": 38,
+  "num_rdkit_valid": 100,
+  "num_motif_match": 5,
+  "decode_rate": 0.6944444444444444,
+  "rdkit_validity_of_decodable": 1.0,
+  "motif_retention_of_valid": 0.05,
+  "elapsed_sec": 26.78412103652954,
+  "sampling": {
+    "top_k": 10,
+    "temperature": 1.0,
+    "max_length": 2048,
+    "batch_size": 64,
+    "seed": 42
+  }
+}

cyclic_peptides/cyclohexane/hdt/generated_smiles.txt

@@ -0,0 +1,100 @@
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cyclic_peptides/cyclohexane/hdt/metrics.json

@@ -0,0 +1,35 @@
+{
+  "n_generated_decodable": 100,
+  "n_reference": 100,
+  "motif": {
+    "n_decodable": 100,
+    "n_rdkit_valid": 100,
+    "n_motif_match": 5,
+    "rdkit_validity": 1.0,
+    "motif_retention": 0.05,
+    "motif_retention_of_decodable": 0.05
+  },
+  "bertz": {
+    "bertz_gen_mean": 2412.438598316042,
+    "bertz_ref_mean": 1752.7281402509043,
+    "bertz_delta": 659.7104580651376,
+    "bertz_n_gen": 100,
+    "bertz_n_ref": 100
+  },
+  "molecular": {
+    "validity": 1.0,
+    "uniqueness": 0.93,
+    "novelty": 1.0,
+    "vun": 0.93,
+    "snn": 0.5893672681722827,
+    "frag_similarity": 0.7092999329955041,
+    "scaff_similarity": 0.0,
+    "internal_diversity": 0.5543584563338771
+  },
+  "motif_distribution": {
+    "motif_fg_mmd": 0.09586301032559108,
+    "motif_smarts_mmd": 0.12257999910656608,
+    "motif_ring_mmd": 0.20380429194138533,
+    "motif_brics_mmd": 0.18719530714055657
+  }
+}

cyclic_peptides/cyclohexane/hdt_hac/generated_metadata.json

@@ -0,0 +1,27 @@
+{
+  "dataset": "cyclic_peptides",
+  "tokenizer_type": "hdt",
+  "motif_name": "cyclohexane",
+  "motif_smiles_prompt": "C1CCCCC1",
+  "motif_smarts": "C1CCCCC1",
+  "checkpoint": "eval_outputs/cyclic_peptides_hdt_hac_avg_xs_lr8.49e-4/last.ckpt",
+  "prompt_length_tokens": 50,
+  "k_target_decodable": 100,
+  "max_attempts": 800,
+  "num_attempted": 832,
+  "num_decodable": 61,
+  "num_decode_failures": 771,
+  "num_rdkit_valid": 61,
+  "num_motif_match": 61,
+  "decode_rate": 0.0733173076923077,
+  "rdkit_validity_of_decodable": 1.0,
+  "motif_retention_of_valid": 1.0,
+  "elapsed_sec": 117.35070633888245,
+  "sampling": {
+    "top_k": 10,
+    "temperature": 1.0,
+    "max_length": 2048,
+    "batch_size": 64,
+    "seed": 42
+  }
+}

cyclic_peptides/cyclohexane/hdt_hac/generated_smiles.txt

@@ -0,0 +1,61 @@
+C1CCCCC1
+C1CCCCC1
+C1CCCCC1
+C1CCCCC1
+C1CCCCC1
+C1CCCCC1
+C1CCCCC1
+C1CCCCC1
+C1CCCCC1
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+C1CCCCC1
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+C1CCCCC1
+C1CCCCC1
+C.C1CCCCC1
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+C.C1CCCCC1
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+C1CCCCC1
+C1CCCCC1
+C1CCCCC1
+C1CCCCC1
+C1CCCCC1
+C1CCCCC1
+C1CCCCC1
+C1CCCCC1

cyclic_peptides/cyclohexane/hdt_hac/metrics.json

@@ -0,0 +1,35 @@
+{
+  "n_generated_decodable": 61,
+  "n_reference": 100,
+  "motif": {
+    "n_decodable": 61,
+    "n_rdkit_valid": 61,
+    "n_motif_match": 61,
+    "rdkit_validity": 1.0,
+    "motif_retention": 1.0,
+    "motif_retention_of_decodable": 1.0
+  },
+  "bertz": {
+    "bertz_gen_mean": 15.509775004326936,
+    "bertz_ref_mean": 1752.7281402509043,
+    "bertz_delta": -1737.2183652465774,
+    "bertz_n_gen": 61,
+    "bertz_n_ref": 100
+  },
+  "molecular": {
+    "validity": 1.0,
+    "uniqueness": 0.03278688524590164,
+    "novelty": 1.0,
+    "vun": 0.03278688524590164,
+    "snn": 0.05449755162869918,
+    "frag_similarity": 0.0,
+    "scaff_similarity": 0.0,
+    "internal_diversity": 0.023770491803278688
+  },
+  "motif_distribution": {
+    "motif_fg_mmd": 1.0782951578978657,
+    "motif_smarts_mmd": 1.1937416760097757,
+    "motif_ring_mmd": 1.1868683248632623,
+    "motif_brics_mmd": 0.9833992272015537
+  }
+}

cyclic_peptides/cyclohexane/hdt_lou/generated_metadata.json

@@ -0,0 +1,27 @@
+{
+  "dataset": "cyclic_peptides",
+  "tokenizer_type": "hdt",
+  "motif_name": "cyclohexane",
+  "motif_smiles_prompt": "C1CCCCC1",
+  "motif_smarts": "C1CCCCC1",
+  "checkpoint": "eval_outputs/cyclic_peptides_hdt_louvain_xs_lr8.49e-4/last.ckpt",
+  "prompt_length_tokens": 50,
+  "k_target_decodable": 100,
+  "max_attempts": 800,
+  "num_attempted": 832,
+  "num_decodable": 0,
+  "num_decode_failures": 832,
+  "num_rdkit_valid": 0,
+  "num_motif_match": 0,
+  "decode_rate": 0.0,
+  "rdkit_validity_of_decodable": 0.0,
+  "motif_retention_of_valid": 0.0,
+  "elapsed_sec": 103.02270102500916,
+  "sampling": {
+    "top_k": 10,
+    "temperature": 1.0,
+    "max_length": 2048,
+    "batch_size": 64,
+    "seed": 42
+  }
+}

cyclic_peptides/cyclohexane/hdt_lou/metrics.json

@@ -0,0 +1,35 @@
+{
+  "n_generated_decodable": 0,
+  "n_reference": 100,
+  "motif": {
+    "n_decodable": 0,
+    "n_rdkit_valid": 0,
+    "n_motif_match": 0,
+    "rdkit_validity": 0.0,
+    "motif_retention": 0.0,
+    "motif_retention_of_decodable": 0.0
+  },
+  "bertz": {
+    "bertz_gen_mean": NaN,
+    "bertz_ref_mean": 1752.7281402509043,
+    "bertz_delta": NaN,
+    "bertz_n_gen": 0,
+    "bertz_n_ref": 100
+  },
+  "molecular": {
+    "validity": 0.0,
+    "uniqueness": 0.0,
+    "novelty": 0.0,
+    "vun": 0.0,
+    "snn": 0.0,
+    "frag_similarity": 0.0,
+    "scaff_similarity": 0.0,
+    "internal_diversity": 0.0
+  },
+  "motif_distribution": {
+    "motif_fg_mmd": Infinity,
+    "motif_smarts_mmd": Infinity,
+    "motif_ring_mmd": Infinity,
+    "motif_brics_mmd": Infinity
+  }
+}

cyclic_peptides/cyclohexane/hdtc/generated_metadata.json

@@ -0,0 +1,27 @@
+{
+  "dataset": "cyclic_peptides",
+  "tokenizer_type": "hdtc",
+  "motif_name": "cyclohexane",
+  "motif_smiles_prompt": "C1CCCCC1",
+  "motif_smarts": "C1CCCCC1",
+  "checkpoint": "eval_outputs/cyclic_peptides_hdtc_xs/last.ckpt",
+  "prompt_length_tokens": 39,
+  "k_target_decodable": 100,
+  "max_attempts": 800,
+  "num_attempted": 494,
+  "num_decodable": 100,
+  "num_decode_failures": 394,
+  "num_rdkit_valid": 100,
+  "num_motif_match": 17,
+  "decode_rate": 0.20242914979757085,
+  "rdkit_validity_of_decodable": 1.0,
+  "motif_retention_of_valid": 0.17,
+  "elapsed_sec": 92.77223491668701,
+  "sampling": {
+    "top_k": 10,
+    "temperature": 1.0,
+    "max_length": 2048,
+    "batch_size": 64,
+    "seed": 42
+  }
+}

cyclic_peptides/cyclohexane/hdtc/generated_smiles.txt

@@ -0,0 +1,100 @@
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cyclic_peptides/cyclohexane/hdtc/metrics.json

@@ -0,0 +1,35 @@
+{
+  "n_generated_decodable": 100,
+  "n_reference": 100,
+  "motif": {
+    "n_decodable": 100,
+    "n_rdkit_valid": 100,
+    "n_motif_match": 17,
+    "rdkit_validity": 1.0,
+    "motif_retention": 0.17,
+    "motif_retention_of_decodable": 0.17
+  },
+  "bertz": {
+    "bertz_gen_mean": 2170.005249965014,
+    "bertz_ref_mean": 1752.7281402509043,
+    "bertz_delta": 417.2771097141099,
+    "bertz_n_gen": 100,
+    "bertz_n_ref": 100
+  },
+  "molecular": {
+    "validity": 1.0,
+    "uniqueness": 0.71,
+    "novelty": 1.0,
+    "vun": 0.71,
+    "snn": 0.4274626609658347,
+    "frag_similarity": 0.5914112509986291,
+    "scaff_similarity": 0.0,
+    "internal_diversity": 0.7057069056910681
+  },
+  "motif_distribution": {
+    "motif_fg_mmd": 0.10970281697359578,
+    "motif_smarts_mmd": 0.16501547261758584,
+    "motif_ring_mmd": 0.18429193291167356,
+    "motif_brics_mmd": 0.20771647645828412
+  }
+}

cyclic_peptides/cyclohexane/sent/generated_metadata.json

@@ -0,0 +1,27 @@
+{
+  "dataset": "cyclic_peptides",
+  "tokenizer_type": "sent",
+  "motif_name": "cyclohexane",
+  "motif_smiles_prompt": "C1CCCCC1",
+  "motif_smarts": "C1CCCCC1",
+  "checkpoint": "eval_outputs/cyclic_peptides_sent_xs/last.ckpt",
+  "prompt_length_tokens": 22,
+  "k_target_decodable": 100,
+  "max_attempts": 800,
+  "num_attempted": 192,
+  "num_decodable": 100,
+  "num_decode_failures": 88,
+  "num_rdkit_valid": 100,
+  "num_motif_match": 100,
+  "decode_rate": 0.5208333333333334,
+  "rdkit_validity_of_decodable": 1.0,
+  "motif_retention_of_valid": 1.0,
+  "elapsed_sec": 5.349858999252319,
+  "sampling": {
+    "top_k": 10,
+    "temperature": 1.0,
+    "max_length": 2048,
+    "batch_size": 64,
+    "seed": 42
+  }
+}

cyclic_peptides/cyclohexane/sent/generated_smiles.txt

@@ -0,0 +1,100 @@
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cyclic_peptides/cyclohexane/sent/metrics.json

@@ -0,0 +1,35 @@
+{
+  "n_generated_decodable": 100,
+  "n_reference": 100,
+  "motif": {
+    "n_decodable": 100,
+    "n_rdkit_valid": 100,
+    "n_motif_match": 100,
+    "rdkit_validity": 1.0,
+    "motif_retention": 1.0,
+    "motif_retention_of_decodable": 1.0
+  },
+  "bertz": {
+    "bertz_gen_mean": 1391.449483039359,
+    "bertz_ref_mean": 1752.7281402509043,
+    "bertz_delta": -361.27865721154535,
+    "bertz_n_gen": 100,
+    "bertz_n_ref": 100
+  },
+  "molecular": {
+    "validity": 1.0,
+    "uniqueness": 1.0,
+    "novelty": 1.0,
+    "vun": 1.0,
+    "snn": 0.1350256849111159,
+    "frag_similarity": 0.47258699283216504,
+    "scaff_similarity": 0.0,
+    "internal_diversity": 0.7903673107721726
+  },
+  "motif_distribution": {
+    "motif_fg_mmd": 0.2088240297688253,
+    "motif_smarts_mmd": 1.1937416760097757,
+    "motif_ring_mmd": 0.22278962052976597,
+    "motif_brics_mmd": 0.22234133563647288
+  }
+}

cyclic_peptides/indole/hdt/generated_metadata.json

@@ -0,0 +1,27 @@
+{
+  "dataset": "cyclic_peptides",
+  "tokenizer_type": "hdt",
+  "motif_name": "indole",
+  "motif_smiles_prompt": "c1ccc2[nH]ccc2c1",
+  "motif_smarts": "c1ccc2[nH]ccc2c1",
+  "checkpoint": "eval_outputs/cyclic_peptides_hdt_motif_community_xs/last.ckpt",
+  "prompt_length_tokens": 62,
+  "k_target_decodable": 100,
+  "max_attempts": 800,
+  "num_attempted": 128,
+  "num_decodable": 100,
+  "num_decode_failures": 6,
+  "num_rdkit_valid": 100,
+  "num_motif_match": 0,
+  "decode_rate": 0.78125,
+  "rdkit_validity_of_decodable": 1.0,
+  "motif_retention_of_valid": 0.0,
+  "elapsed_sec": 14.806169033050537,
+  "sampling": {
+    "top_k": 10,
+    "temperature": 1.0,
+    "max_length": 2048,
+    "batch_size": 64,
+    "seed": 42
+  }
+}

cyclic_peptides/indole/hdt/generated_smiles.txt

@@ -0,0 +1,100 @@
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cyclic_peptides/indole/hdt/metrics.json

@@ -0,0 +1,35 @@
+{
+  "n_generated_decodable": 100,
+  "n_reference": 42,
+  "motif": {
+    "n_decodable": 100,
+    "n_rdkit_valid": 100,
+    "n_motif_match": 0,
+    "rdkit_validity": 1.0,
+    "motif_retention": 0.0,
+    "motif_retention_of_decodable": 0.0
+  },
+  "bertz": {
+    "bertz_gen_mean": 2742.2457483247786,
+    "bertz_ref_mean": 2424.893044296103,
+    "bertz_delta": 317.35270402867536,
+    "bertz_n_gen": 100,
+    "bertz_n_ref": 42
+  },
+  "molecular": {
+    "validity": 1.0,
+    "uniqueness": 0.12,
+    "novelty": 1.0,
+    "vun": 0.12,
+    "snn": 0.31360930467357123,
+    "frag_similarity": 0.39321292942560016,
+    "scaff_similarity": 0.0,
+    "internal_diversity": 0.1413663602465673
+  },
+  "motif_distribution": {
+    "motif_fg_mmd": 0.4609348143793616,
+    "motif_smarts_mmd": 0.4876604459192313,
+    "motif_ring_mmd": 0.6638047948242106,
+    "motif_brics_mmd": 0.2997203851750401
+  }
+}

cyclic_peptides/indole/hdt_hac/generated_metadata.json

@@ -0,0 +1,27 @@
+{
+  "dataset": "cyclic_peptides",
+  "tokenizer_type": "hdt",
+  "motif_name": "indole",
+  "motif_smiles_prompt": "c1ccc2[nH]ccc2c1",
+  "motif_smarts": "c1ccc2[nH]ccc2c1",
+  "checkpoint": "eval_outputs/cyclic_peptides_hdt_hac_avg_xs_lr8.49e-4/last.ckpt",
+  "prompt_length_tokens": 72,
+  "k_target_decodable": 100,
+  "max_attempts": 800,
+  "num_attempted": 832,
+  "num_decodable": 0,
+  "num_decode_failures": 832,
+  "num_rdkit_valid": 0,
+  "num_motif_match": 0,
+  "decode_rate": 0.0,
+  "rdkit_validity_of_decodable": 0.0,
+  "motif_retention_of_valid": 0.0,
+  "elapsed_sec": 120.45352363586426,
+  "sampling": {
+    "top_k": 10,
+    "temperature": 1.0,
+    "max_length": 2048,
+    "batch_size": 64,
+    "seed": 42
+  }
+}

cyclic_peptides/indole/hdt_hac/metrics.json

@@ -0,0 +1,35 @@
+{
+  "n_generated_decodable": 0,
+  "n_reference": 42,
+  "motif": {
+    "n_decodable": 0,
+    "n_rdkit_valid": 0,
+    "n_motif_match": 0,
+    "rdkit_validity": 0.0,
+    "motif_retention": 0.0,
+    "motif_retention_of_decodable": 0.0
+  },
+  "bertz": {
+    "bertz_gen_mean": NaN,
+    "bertz_ref_mean": 2424.893044296103,
+    "bertz_delta": NaN,
+    "bertz_n_gen": 0,
+    "bertz_n_ref": 42
+  },
+  "molecular": {
+    "validity": 0.0,
+    "uniqueness": 0.0,
+    "novelty": 0.0,
+    "vun": 0.0,
+    "snn": 0.0,
+    "frag_similarity": 0.0,
+    "scaff_similarity": 0.0,
+    "internal_diversity": 0.0
+  },
+  "motif_distribution": {
+    "motif_fg_mmd": Infinity,
+    "motif_smarts_mmd": Infinity,
+    "motif_ring_mmd": Infinity,
+    "motif_brics_mmd": Infinity
+  }
+}