unable to generate

[Neo-Flash]

Hi ！
thanks for sharing your excellent work！

I am unable to do the final step of generate after modifying part of your code to successfully train and get pockets, could you please upload the latest and correct full code?

Thanks!

[longlongman]

Sorry to hear that. Right now, I am kind of busy with another project. I don't have time to check the code entirely. But I am willing to help you solve the problems. Could you give a more specific description (code snippet, screenshot) of your problems?

[CNDOTA]

Hello, longlongman. I meet the same problem, when running the "bash generator.sh" command, it shows that there is no "ShapePretrainingTaskNoRegressionPocket.py" in the shape_pretaining folder. However, in the generating.yaml, the task class is configured as "ShapePretrainingTaskNoRegressionPocket". Could you provide "ShapePretrainingTaskNoRegressionPocket.py" or help fix it? Thanks very much and very nice work!

[longlongman]

Hello, longlongman. I meet the same problem, when running the "bash generator.sh" command, it shows that there is no "ShapePretrainingTaskNoRegressionPocket.py" in the shape_pretaining folder. However, in the generating.yaml, the task class is configured as "ShapePretrainingTaskNoRegressionPocket". Could you provide "ShapePretrainingTaskNoRegressionPocket.py" or help fix it? Thanks very much and very nice work!

Sorry for the missing file. Already uploaded.

[CNDOTA]

Hello, longlongman. I meet the same problem, when running the "bash generator.sh" command, it shows that there is no "ShapePretrainingTaskNoRegressionPocket.py" in the shape_pretaining folder. However, in the generating.yaml, the task class is configured as "ShapePretrainingTaskNoRegressionPocket". Could you provide "ShapePretrainingTaskNoRegressionPocket.py" or help fix it? Thanks very much and very nice work!

Sorry for the missing file. Already uploaded.

Thanks very much!

[CNDOTA]

Hello, longlongman. I meet the same problem, when running the "bash generator.sh" command, it shows that there is no "ShapePretrainingTaskNoRegressionPocket.py" in the shape_pretaining folder. However, in the generating.yaml, the task class is configured as "ShapePretrainingTaskNoRegressionPocket". Could you provide "ShapePretrainingTaskNoRegressionPocket.py" or help fix it? Thanks very much and very nice work!

Sorry for the missing file. Already uploaded.

Hello, longlongman. I could run the "generator.sh" script successfully but I cannot find where the generated molecule is after running. Before running "generator.sh", I run "sketching.py" and get the "sample_shapes" and "sample_n_o_f" files and configure "task.data.valid.path.samples" and "task.data.test.path.samples" as the same "sample_shapes" file.

I also find that the "shape_pretraining_search_forward_sampling_dock_dedup_iterative_no_regression.py" need to be configured with the file names such as "_vocab_h_nei_nof" in Line 55 and "'--PDBQT PATH FOR DOCKING--', '--LIGAND PATH FOR CALCULATE CENTER--'" in the functions "_get_top_dock_fast" and "_get_top_dock_dedup". But I do not change them as I have no idea of how to config them.

For your reference, the console outputs information as below:

[13:26:04] UFFTYPER: Warning: hybridization set to SP3 for atom 18
[13:26:06] Explicit valence for atom # 0 N, 4, is greater than permitted
[13:26:07] Explicit valence for atom # 0 O, 3, is greater than permitted
[13:26:09] Explicit valence for atom # 7 N, 4, is greater than permitted
[13:26:11] Can't kekulize mol. Unkekulized atoms: 2 3 4 6 7
[13:26:11] Explicit valence for atom # 0 O, 3, is greater than permitted
[13:26:11] Explicit valence for atom # 2 C, 5, is greater than permitted
[13:26:15] Explicit valence for atom # 0 O, 3, is greater than permitted
[13:26:15] Explicit valence for atom # 14 N, 5, is greater than permitted
[13:26:17] Explicit valence for atom # 0 N, 4, is greater than permitted
50%|██████████████████████████████████████████████████████████████████████████████████████████████████████████████ | 1/2 [02:23<02:23, 143.33s/it][13:27:36] Can't kekulize mol. Unkekulized atoms: 6 7 9
[13:27:37] Can't kekulize mol. Unkekulized atoms: 1 2 3
[13:27:38] Can't kekulize mol. Unkekulized atoms: 5 7 8
[13:27:40] Explicit valence for atom # 5 N, 4, is greater than permitted
[13:27:42] Can't kekulize mol. Unkekulized atoms: 0 1 2 3 4 6 7
[13:27:42] Can't kekulize mol. Unkekulized atoms: 1 3 4
[13:27:43] Explicit valence for atom # 16 C, 5, is greater than permitted
[13:27:44] Explicit valence for atom # 4 C, 5, is greater than permitted
[13:27:44] Can't kekulize mol. Unkekulized atoms: 1 2 3
[13:27:44] UFFTYPER: Unrecognized atom type: S_5+4 (2)
2022-10-25,13:27:52 ｜ INFO | bycha.evaluators.evaluator |
Hypothesis: []

Hypothesis: []

Hypothesis: []

Hypothesis: []

Hypothesis: []

2022-10-25,13:27:52 ｜ INFO | bycha.evaluators.evaluator | acc: 0.0

Could you please provide more information? Thank you very much!

[longlongman]

• Before running "sketching.py", you need to use CAVITY to generate the cavity PDB file (the file name is usually like "thischains_vacant_xx.pdb").
• Please ignore "sample_n_o_f". It is not required in our final method. We only use it when we try to combine the chemical information of proteins.
• "_vocab_h_nei_nof" in Line 55 is the same situation with "sample_n_o_f". We already set "for_protein_decode" in Line 54 as "False" to block it.
• "--PDBQT PATH FOR DOCKING--" is the PDBQT file prepared for vina docking. You can use "Open Babel" to convert your PDB file to PDBQT like this.
• "--LIGAND PATH FOR CALCULATE CENTER--" is the SDF file of the ligand. We use it to set up the center of the box which is required by vina. We can also replace it with the SDF file of any molecule as long as its centroid falls into the pocket.

[CNDOTA]

• Before running "sketching.py", you need to use CAVITY to generate the cavity PDB file (the file name is usually like "thischains_vacant_xx.pdb").
• Please ignore "sample_n_o_f". It is not required in our final method. We only use it when we try to combine the chemical information of proteins.
• "_vocab_h_nei_nof" in Line 55 is the same situation with "sample_n_o_f". We already set "for_protein_decode" in Line 54 as "False" to block it.
• "--PDBQT PATH FOR DOCKING--" is the PDBQT file prepared for vina docking. You can use "Open Babel" to convert your PDB file to PDBQT like this.
• "--LIGAND PATH FOR CALCULATE CENTER--" is the SDF file of the ligand. We use it to set up the center of the box which is required by vina. We can also replace it with the SDF file of any molecule as long as its centroid falls into the pocket.

Thanks very much for your reply! After configuring the description, I found it seems to run normally.

I found the file "test.hypo" stores data as below. It is the generated molecule and how could I convert it to mol2 or sdf format?

[[(2, 0, 0), (1228, 16032, 3922), (1021, 9761, 1393), (4013, 9761, 4182), (4, 9111, 1596), (5713, 6573, 4198), (5, 10467, 7189), (14, 10467, 2870), (3, 10467, 6889), (3, 16033, 7189), (3, 16033, 7189), (3, 16033, 7189), (3, 16033, 7459), (3, 16033, 7185), (3, 16033, 7185), (3, 16033, 7185), (3, 16033, 7185), (3, 16033, 7185), (3, 10761, 7185), (3, 10761, 4959), (3, 5947, 4959)], [(2, 0, 0), (65205, 16032, 3922), (15058, 12897, 6953), (10, 8953, 4182), (1749, 8926, 6659), (8772, 9003, 6614), (4, 9111, 1387), (6, 5919, 4378), (3, 5947, 4160), (3, 10761, 4160), (3, 10761, 3652), (3, 10761, 3652), (3, 5947, 3652), (3, 5947, 3676), (3, 5947, 3929), (3, 5947, 3929), (3, 5947, 3929), (3, 5947, 3652), (3, 5947, 3652), (3, 5947, 3652), (3, 5947, 3652)], [(2, 0, 0), (68292, 16032, 3922), (82684, 12897, 6953), (114, 8953, 4182), (4, 9710, 7197), (703, 5789, 3923), (5, 9683, 7185), (436, 8926, 1393), (232, 9683, 2684), (2108, 8926, 1343), (515, 9031, 1596), (1581, 8300, 4176), (3148, 11432, 564), (3, 5947, 3253), (3, 5947, 3000), (3, 5947, 3000), (3, 5947, 3000), (3, 5947, 3000), (3, 5947, 3000), (3, 5947, 6243), (3, 10761, 6243)], [(2, 0, 0), (42, 16032, 3922), (316, 16030, 6959), (15679, 14464, 6959), (283, 9030, 4182), (50, 9761, 4182), (218, 8141, 4128), (10, 6573, 4125), (219, 5789, 334), (3, 5789, 6658), (3, 10467, 7185), (3, 9683, 6634), (3, 9683, 6634), (3, 9683, 6634), (3, 9683, 6611), (3, 8953, 6634), (53, 9787, 7424), (35050, 9030, 5279), (53, 9950, 1460), (19, 9977, 3112), (3, 10761, 6288)], [(2, 0, 0), (22, 16032, 3922), (7535, 16032, 1393), (1316, 12113, 1), (4, 9788, 1), (199, 6573, 3922), (5, 10467, 6960), (11, 9003, 5279), (10, 9030, 4332), (14757, 9111, 3485), (3, 5919, 3945), (3, 5919, 3253), (3, 5947, 3253), (3, 5947, 3253), (3, 5947, 6955), (3, 5947, 7185), (3, 5947, 7185), (3, 5947, 7185), (3, 5947, 7185), (3, 5947, 7185), (3, 5947, 7185)], [(2, 0, 0), (89918, 16032, 3922), (1561, 12897, 6953), (4, 9787, 4182), (114, 8953, 1393), (4, 10494, 6386), (1086, 6573, 3923), (5, 9059, 7189), (27, 9710, 6089), (22, 11224, 2223), (3, 1, 2495), (3, 10761, 4959), (3, 10761, 7232), (3, 5919, 6243), (3, 5919, 83), (3, 5919, 6243), (3, 5947, 6243), (3, 10761, 7185), (3, 10761, 7185), (3, 10761, 7185), (3, 10761, 7185)], [(2, 0, 0), (13199, 16032, 3922), (673, 12113, 6959), (876, 9761, 4182), (4, 8953, 1393), (4, 5789, 3945), (171, 5789, 3945), (5, 11250, 7211), (18321, 9031, 1642), (114, 9922, 1393), (4, 10761, 7672), (171, 5947, 1835), (5, 10761, 7189), (250, 9949, 3737), (3, 10761, 3630), (3, 10761, 3630), (3, 10761, 3630), (3, 10761, 3630), (3, 5947, 3630), (3, 5919, 3630), (3, 5919, 3630)], [(2, 0, 0), (7569, 16032, 3922), (152, 13680, 6959), (3822, 11329, 1), (4, 9111, 1387), (6, 5919, 1116), (5, 5948, 7189), (1294, 6573, 6153), (3, 10467, 3917), (3, 10467, 4147), (3, 10467, 2495), (3, 10467, 7185), (3, 10467, 7185), (3, 10467, 7185), (3, 8926, 1343), (3, 9084, 1343), (686, 5947, 3423), (3, 5947, 7185), (3, 5947, 7185), (3, 5947, 7185), (3, 5947, 7185)], [(2, 0, 0), (9404, 16032, 3922), (386, 12113, 1393), (4, 9789, 4182), (429, 8141, 1670), (4, 10467, 6089), (2773, 10467, 3945), (5, 6572, 4959), (19, 6573, 4176), (5, 6572, 7143), (10, 9003, 1273), (5161, 8301, 6959), (3, 12217, 3652), (3, 12216, 2454), (3, 12216, 3253), (3, 10761, 2248), (3, 5919, 3253), (3, 5919, 3253), (3, 5919, 3253), (3, 5919, 3253), (3, 5919, 3253)], [(2, 0, 0), (125, 16032, 3922), (17224, 12113, 1393), (8319, 8953, 1393), (53, 9003, 7149), (19903, 8300, 1387), (3, 5919, 588), (3, 5947, 3676), (3, 5947, 7185), (3, 5947, 7185), (3, 10761, 7185), (3, 10761, 1343), (3, 10761, 1343), (42, 10761, 1343), (3, 9081, 1343), (3, 12188, 1343), (3, 12188, 3929), (3, 12188, 1343), (3, 10761, 3400), (3, 10761, 3400), (3, 10761, 3400)], [(2, 0, 0), (3549, 16032, 3922), (11, 13680, 127), (23734, 9761, 4182), (6, 9084, 1116), (26869, 9111, 1387), (3, 5919, 1343), (3, 5919, 335), (3, 5947, 4125), (3, 5947, 6919), (3, 5947, 3676), (3, 5947, 3652), (3, 5947, 3652), (3, 5947, 3652), (3, 5947, 3652), (3, 5947, 3652), (3, 5947, 3652), (3, 5947, 3652), (3, 5947, 7185), (3, 10761, 1343), (6, 16033, 1343)], [(2, 0, 0), (4008, 16032, 3922), (8057, 12113, 1), (2665, 9031, 1393), (2307, 8953, 1647), (3, 5789, 3945), (3, 5789, 4148), (3, 10467, 3917), (3, 10467, 2495), (3, 10467, 6360), (3, 8926, 6360), (42, 9084, 1343), (11286, 9111, 4182), (3, 10761, 3652), (3, 10761, 3652), (3, 10761, 3652), (3, 5947, 3652), (3, 5919, 335), (3, 5947, 3676), (3, 11432, 3652), (3, 10761, 3652)], [(2, 0, 0), (58695, 16032, 3922), (15222, 12897, 6953), (225, 9737, 4182), (4, 9762, 3897), (4, 6573, 3918), (129, 5789, 4125), (5, 11250, 7211), (10, 10467, 1343), (3, 10467, 6405), (3, 9683, 2495), (3, 10467, 2495), (3, 10467, 2495), (3, 10467, 2495), (3, 10467, 4959), (3, 5920, 4959), (3, 10761, 4959), (3, 10761, 3353), (3, 11433, 7185), (3, 5947, 3000), (3, 5947, 39)], [(2, 0, 0), (31181, 16032, 3922), (31445, 12897, 6953), (257, 8953, 4182), (42, 6573, 6614), (3, 8926, 3929), (3, 5920, 5671), (3, 9950, 3929), (3, 5947, 588), (3, 5947, 4160), (3, 5947, 4160), (3, 5947, 4160), (3, 5947, 4160), (3, 10761, 4160), (3, 9950, 3652), (6, 12217, 7208), (3, 12217, 3928), (3, 14465, 1343), (10, 10494, 7192), (22, 10467, 329), (3, 9683, 6657)], [(2, 0, 0), (70, 16032, 3922), (21509, 14464, 6959), (9330, 9031, 4182), (134, 8953, 1393), (4, 5789, 3918), (22, 5789, 3917), (5, 9683, 4148), (4, 10467, 1366), (3, 10467, 3894), (3, 9683, 3918), (3, 5789, 3918), (3, 6573, 4959), (3, 9084, 7185), (3, 9950, 7185), (3, 12216, 2248), (3, 12216, 2248), (3, 10761, 2248), (3, 10761, 7185), (3, 10761, 7185), (22, 10761, 7185)], [(2, 0, 0), (13094, 16032, 3922), (875, 12113, 6953), (4, 9789, 4182), (42, 6573, 6682), (5, 8925, 6959), (9, 9787, 1642), (316, 9111, 6959), (5302, 9949, 7419), (3, 10761, 3253), (3, 5947, 6243), (3, 5947, 3000), (3, 5947, 6243), (3, 5947, 6243), (3, 5947, 6243), (3, 5947, 6243), (3, 5947, 3000), (3, 5947, 6243), (3, 5947, 6243), (3, 5947, 6243), (3, 5947, 6243)], [(2, 0, 0), (66716, 16032, 3922), (38910, 12897, 6953), (499, 8953, 4182), (14, 5920, 151), (3, 10733, 3929), (3, 5947, 335), (3, 5947, 3929), (3, 5947, 83), (3, 5947, 3929), (3, 5947, 5968), (3, 6731, 3929), (3, 12217, 7208), (3, 12217, 1343), (6, 16033, 1343), (3, 16033, 7212), (4, 15249, 6960), (6, 16033, 1071), (5, 16816, 7211), (4, 14465, 6962), (1254, 16033, 1343)], [(2, 0, 0), (3836, 16032, 3922), (11, 13680, 127), (28988, 9761, 1393), (4, 9084, 1116), (3, 5919, 1341), (3, 5947, 3929), (3, 10761, 3652), (3, 10761, 3652), (3, 10761, 3652), (3, 5919, 3652), (3, 5919, 3676), (3, 5919, 3676), (3, 5947, 3676), (3, 5947, 3652), (3, 10761, 3929), (3, 16033, 1343), (70, 15249, 6960), (3, 16033, 1072), (3, 16033, 1072), (3, 15249, 1072)], [(2, 0, 0), (29074, 16032, 3922), (13210, 12897, 6953), (3715, 9737, 4182), (876, 9003, 2703), (2307, 9111, 4182), (3, 5947, 588), (3, 5947, 6919), (3, 5947, 6938), (3, 5947, 3652), (3, 10761, 3652), (3, 10761, 3652), (3, 10761, 3652), (3, 9977, 3652), ...

Thanks again for your help!

[longlongman]

Sorry for replying late. Yes, it is the sequence of the fragment tuple (the whole thing represents a molecule). For the converting, you can check out the code here.

[CNDOTA]

Thank you very much!

Sorry for replying late. Yes, it is the sequence of the fragment tuple (the whole thing represents a molecule). For the converting, you can check out the code here.