Only 1 rigid used in synthesis

[cplateVT]

When I run the program on the example fragments (3 linkers and 4 rigids), it produces 52 molecules, and all of the molecules have only benzene bricks and I have no idea why. It was as if the other 3 rigids were ignored. Any ideas?

[wcatykid]

It is possible that no other molecules were Lipinski compliant. You could change the Tanimoto Coefficient. I haven't looked at the code in many years, so those are initial guesses.

…

On Mon, Jan 24, 2022 at 5:41 PM cplateVT ***@***.***> wrote: When I run the program on the example fragments (3 linkers and 4 rigids), it produces 52 molecules, and all of the molecules have only benzene bricks and I have no idea why. It was as if the other 3 rigids were ignored. Any ideas? — Reply to this email directly, view it on GitHub <#2>, or unsubscribe <https://github.com/notifications/unsubscribe-auth/ABUOTREM4QD2XZ3WOWG5ZXDUXXITJANCNFSM5MWU3TDA> . Triage notifications on the go with GitHub Mobile for iOS <https://apps.apple.com/app/apple-store/id1477376905?ct=notification-email&mt=8&pt=524675> or Android <https://play.google.com/store/apps/details?id=com.github.android&referrer=utm_campaign%3Dnotification-email%26utm_medium%3Demail%26utm_source%3Dgithub>. You are receiving this because you are subscribed to this thread.Message ID: ***@***.***>

[cplateVT]

Thank you for the reply. This program would be very useful in my research if I could get it to work. I lowered the TC and got the same output. Below is my input and output:

esynth -nopen -tc 0.1 l-5834.sdf l-7932.sdf l-8012.sdf r-31553.sdf r-30052.sdf r-32216.sdf r-3437.sdf
Serial execution.
Probability Filtration Level: 5
OBGEN output thread pool size: 15
C.ar
C.ar
C.ar
C.ar
C.ar
C.ar
C.ar
C.ar
C.ar
C.ar
C.ar
C.ar
C.ar
O.2
C.3
C.3
C.ar
O.2
C.ar
C.ar
C.ar
O.2
C.ar
C.ar
C.ar
C.ar
C.ar
C.ar
O.2
C.ar
C.3
C.ar
N.ar
N.ar
C.ar
C.ar
C.ar
C.2
O.2
C.ar
C.ar
C.ar
C.ar
C.ar
C.ar
Thread pool manager created.
worker 0 created
worker 1 created
worker 2 created
worker 3 created
worker 4 created
worker 5 created
worker 6 created
worker 7 created
worker 8 created
worker 9 created
worker 10 created
worker 11 created
worker 12 created
worker 13 created
worker 14 created
Will output to directory: synth_output_dir
The output directory synth_output_dir exists.
Do you wish to overwrite? (Y / N)
y
Cleaning output directory: synth_output_dir
Done creating level 2
Processing level 2
Processing molecule 1 at level 2 queue contains (1); Overall Processed Count: 1
Processing molecule 2 at level 2 queue contains (0); Overall Processed Count: 2
Processing level 3
Processing molecule 1 at level 3 queue contains (3); Overall Processed Count: 3
Processing molecule 2 at level 3 queue contains (2); Overall Processed Count: 4
Processing molecule 3 at level 3 queue contains (1); Overall Processed Count: 5
Processing molecule 4 at level 3 queue contains (0); Overall Processed Count: 6
Processing level 4
Processing molecule 1 at level 4 queue contains (6); Overall Processed Count: 7
Processing molecule 2 at level 4 queue contains (5); Overall Processed Count: 8
Processing molecule 3 at level 4 queue contains (4); Overall Processed Count: 9
Processing molecule 4 at level 4 queue contains (3); Overall Processed Count: 10
Processing molecule 5 at level 4 queue contains (2); Overall Processed Count: 11
Processing molecule 6 at level 4 queue contains (1); Overall Processed Count: 12
Processing molecule 7 at level 4 queue contains (0); Overall Processed Count: 13
Processing level 5
Processing molecule 1 at level 5 queue contains (9); Overall Processed Count: 14
Processing molecule 2 at level 5 queue contains (8); Overall Processed Count: 15
Processing molecule 3 at level 5 queue contains (7); Overall Processed Count: 16
Processing molecule 4 at level 5 queue contains (6); Overall Processed Count: 17
Processing molecule 5 at level 5 queue contains (5); Overall Processed Count: 18
Processing molecule 6 at level 5 queue contains (4); Overall Processed Count: 19
Processing molecule 7 at level 5 queue contains (3); Overall Processed Count: 20
Processing molecule 8 at level 5 queue contains (2); Overall Processed Count: 21
Processing molecule 9 at level 5 queue contains (1); Overall Processed Count: 22
Processing molecule 10 at level 5 queue contains (0); Overall Processed Count: 23
Processing level 6
Processing molecule 1 at level 6 queue contains (9); Overall Processed Count: 24
Processing molecule 2 at level 6 queue contains (8); Overall Processed Count: 25
Processing molecule 3 at level 6 queue contains (7); Overall Processed Count: 26
Processing molecule 4 at level 6 queue contains (6); Overall Processed Count: 27
Processing molecule 5 at level 6 queue contains (5); Overall Processed Count: 28
Processing molecule 6 at level 6 queue contains (4); Overall Processed Count: 29
Processing molecule 7 at level 6 queue contains (3); Overall Processed Count: 30
Processing molecule 8 at level 6 queue contains (2); Overall Processed Count: 31
Processing molecule 9 at level 6 queue contains (1); Overall Processed Count: 32
Processing molecule 10 at level 6 queue contains (0); Overall Processed Count: 33
Processing level 7
Processing level 8
Processing level 9
Processing level 10
Processing level 11
Killed level 2
Killed level 3
Killed level 4
Killed level 5
Killed level 6
Killed level 7
Killed level 8
Killed level 9
Killed level 10
Killed level 11
Killed level 12
Killed level 13
Killed level 14
Killed level 15
Killed level 16
Killed level 17
Killed level 18
Killed level 19
Killed level 20
Level # Molecules
1 7
2 2
3 4
4 7
5 10
6 10
7 9
8 6
9 3
10 1
11 0
12 0
13 0
14 0
15 0
16 0
17 0
18 0
19 0
20 0
Synthesis is complete; writing continues.
Input pool contains 0 molecules to process with obgen.
Writing of the molecules with obgen is complete.
Excluded (0); Included (52) Excluded: 0%
Validation file not specified; will not validate.
worker 0 removed
worker 1 removed
worker 2 removed
worker 3 removed
worker 4 removed
worker 5 removed
worker 6 removed
worker 7 removed
worker 8 removed
worker 9 removed
worker 10 removed
worker 11 removed
worker 12 removed
worker 13 removed
worker 14 removed
Exiting the main thread.

[wcatykid]

Try running it serially: ./esynth -nopen -serial -smi-only -prob-level 2 <files>

…

On Tue, Jan 25, 2022 at 2:22 PM cplateVT ***@***.***> wrote: Thank you for the reply. This program would be very useful in my research if I could get it to work. I lowered the TC and got the same output. Below is my input and output: esynth -nopen -tc 0.1 l-5834.sdf l-7932.sdf l-8012.sdf r-31553.sdf r-30052.sdf r-32216.sdf r-3437.sdf Serial execution. Probability Filtration Level: 5 OBGEN output thread pool size: 15 C.ar C.ar C.ar C.ar C.ar C.ar C.ar C.ar C.ar C.ar C.ar C.ar C.ar O.2 C.3 C.3 C.ar O.2 C.ar C.ar C.ar O.2 C.ar C.ar C.ar C.ar C.ar C.ar O.2 C.ar C.3 C.ar N.ar N.ar C.ar C.ar C.ar C.2 O.2 C.ar C.ar C.ar C.ar C.ar C.ar Thread pool manager created. worker 0 created worker 1 created worker 2 created worker 3 created worker 4 created worker 5 created worker 6 created worker 7 created worker 8 created worker 9 created worker 10 created worker 11 created worker 12 created worker 13 created worker 14 created Will output to directory: synth_output_dir The output directory synth_output_dir exists. Do you wish to overwrite? (Y / N) y Cleaning output directory: synth_output_dir Done creating level 2 Processing level 2 Processing molecule 1 at level 2 queue contains (1); Overall Processed Count: 1 Processing molecule 2 at level 2 queue contains (0); Overall Processed Count: 2 Processing level 3 Processing molecule 1 at level 3 queue contains (3); Overall Processed Count: 3 Processing molecule 2 at level 3 queue contains (2); Overall Processed Count: 4 Processing molecule 3 at level 3 queue contains (1); Overall Processed Count: 5 Processing molecule 4 at level 3 queue contains (0); Overall Processed Count: 6 Processing level 4 Processing molecule 1 at level 4 queue contains (6); Overall Processed Count: 7 Processing molecule 2 at level 4 queue contains (5); Overall Processed Count: 8 Processing molecule 3 at level 4 queue contains (4); Overall Processed Count: 9 Processing molecule 4 at level 4 queue contains (3); Overall Processed Count: 10 Processing molecule 5 at level 4 queue contains (2); Overall Processed Count: 11 Processing molecule 6 at level 4 queue contains (1); Overall Processed Count: 12 Processing molecule 7 at level 4 queue contains (0); Overall Processed Count: 13 Processing level 5 Processing molecule 1 at level 5 queue contains (9); Overall Processed Count: 14 Processing molecule 2 at level 5 queue contains (8); Overall Processed Count: 15 Processing molecule 3 at level 5 queue contains (7); Overall Processed Count: 16 Processing molecule 4 at level 5 queue contains (6); Overall Processed Count: 17 Processing molecule 5 at level 5 queue contains (5); Overall Processed Count: 18 Processing molecule 6 at level 5 queue contains (4); Overall Processed Count: 19 Processing molecule 7 at level 5 queue contains (3); Overall Processed Count: 20 Processing molecule 8 at level 5 queue contains (2); Overall Processed Count: 21 Processing molecule 9 at level 5 queue contains (1); Overall Processed Count: 22 Processing molecule 10 at level 5 queue contains (0); Overall Processed Count: 23 Processing level 6 Processing molecule 1 at level 6 queue contains (9); Overall Processed Count: 24 Processing molecule 2 at level 6 queue contains (8); Overall Processed Count: 25 Processing molecule 3 at level 6 queue contains (7); Overall Processed Count: 26 Processing molecule 4 at level 6 queue contains (6); Overall Processed Count: 27 Processing molecule 5 at level 6 queue contains (5); Overall Processed Count: 28 Processing molecule 6 at level 6 queue contains (4); Overall Processed Count: 29 Processing molecule 7 at level 6 queue contains (3); Overall Processed Count: 30 Processing molecule 8 at level 6 queue contains (2); Overall Processed Count: 31 Processing molecule 9 at level 6 queue contains (1); Overall Processed Count: 32 Processing molecule 10 at level 6 queue contains (0); Overall Processed Count: 33 Processing level 7 Processing level 8 Processing level 9 Processing level 10 Processing level 11 Killed level 2 Killed level 3 Killed level 4 Killed level 5 Killed level 6 Killed level 7 Killed level 8 Killed level 9 Killed level 10 Killed level 11 Killed level 12 Killed level 13 Killed level 14 Killed level 15 Killed level 16 Killed level 17 Killed level 18 Killed level 19 Killed level 20 Level # Molecules 1 7 2 2 3 4 4 7 5 10 6 10 7 9 8 6 9 3 10 1 11 0 12 0 13 0 14 0 15 0 16 0 17 0 18 0 19 0 20 0 Synthesis is complete; writing continues. Input pool contains 0 molecules to process with obgen. Writing of the molecules with obgen is complete. Excluded (0); Included (52) Excluded: 0% Validation file not specified; will not validate. worker 0 removed worker 1 removed worker 2 removed worker 3 removed worker 4 removed worker 5 removed worker 6 removed worker 7 removed worker 8 removed worker 9 removed worker 10 removed worker 11 removed worker 12 removed worker 13 removed worker 14 removed Exiting the main thread. — Reply to this email directly, view it on GitHub <#2 (comment)>, or unsubscribe <https://github.com/notifications/unsubscribe-auth/ABUOTRBTQKU25KCVSMG26P3UX3Z5XANCNFSM5MWU3TDA> . Triage notifications on the go with GitHub Mobile for iOS <https://apps.apple.com/app/apple-store/id1477376905?ct=notification-email&mt=8&pt=524675> or Android <https://play.google.com/store/apps/details?id=com.github.android&referrer=utm_campaign%3Dnotification-email%26utm_medium%3Demail%26utm_source%3Dgithub>. You are receiving this because you commented.Message ID: ***@***.***>

[cplateVT]

same output

esynth -nopen -serial -smi-only -prob-level 2 l-5834.sdf l-7932.sdf l-8012.sdf r-31553.sdf r-30052.sdf r-32216.sdf r-3437.sdf
Serial execution.
Probability Filtration Level: 2
C.ar
C.ar
C.ar
C.ar
C.ar
C.ar
C.ar
C.ar
C.ar
C.ar
C.ar
C.ar
C.ar
O.2
C.3
C.3
C.ar
O.2
C.ar
C.ar
C.ar
O.2
C.ar
C.ar
C.ar
C.ar
C.ar
C.ar
O.2
C.ar
C.3
C.ar
N.ar
N.ar
C.ar
C.ar
C.ar
C.2
O.2
C.ar
C.ar
C.ar
C.ar
C.ar
C.ar
Will output to directory: synth_output_dir
Cleaning output directory: synth_output_dir
Done creating level 2
Processing level 2
Processing molecule 1 at level 2 queue contains (1); Overall Processed Count: 1
Processing molecule 2 at level 2 queue contains (0); Overall Processed Count: 2
Processing level 3
Processing molecule 1 at level 3 queue contains (3); Overall Processed Count: 3
Processing molecule 2 at level 3 queue contains (2); Overall Processed Count: 4
Processing molecule 3 at level 3 queue contains (1); Overall Processed Count: 5
Processing molecule 4 at level 3 queue contains (0); Overall Processed Count: 6
Processing level 4
Processing molecule 1 at level 4 queue contains (6); Overall Processed Count: 7
Processing molecule 2 at level 4 queue contains (5); Overall Processed Count: 8
Processing molecule 3 at level 4 queue contains (4); Overall Processed Count: 9
Processing molecule 4 at level 4 queue contains (3); Overall Processed Count: 10
Processing molecule 5 at level 4 queue contains (2); Overall Processed Count: 11
Processing molecule 6 at level 4 queue contains (1); Overall Processed Count: 12
Processing molecule 7 at level 4 queue contains (0); Overall Processed Count: 13
Processing level 5
Processing molecule 1 at level 5 queue contains (9); Overall Processed Count: 14
Processing molecule 2 at level 5 queue contains (8); Overall Processed Count: 15
Processing molecule 3 at level 5 queue contains (7); Overall Processed Count: 16
Processing molecule 4 at level 5 queue contains (6); Overall Processed Count: 17
Processing molecule 5 at level 5 queue contains (5); Overall Processed Count: 18
Processing molecule 6 at level 5 queue contains (4); Overall Processed Count: 19
Processing molecule 7 at level 5 queue contains (3); Overall Processed Count: 20
Processing molecule 8 at level 5 queue contains (2); Overall Processed Count: 21
Processing molecule 9 at level 5 queue contains (1); Overall Processed Count: 22
Processing molecule 10 at level 5 queue contains (0); Overall Processed Count: 23
Processing level 6
Processing molecule 1 at level 6 queue contains (9); Overall Processed Count: 24
Processing molecule 2 at level 6 queue contains (8); Overall Processed Count: 25
Processing molecule 3 at level 6 queue contains (7); Overall Processed Count: 26
Processing molecule 4 at level 6 queue contains (6); Overall Processed Count: 27
Processing molecule 5 at level 6 queue contains (5); Overall Processed Count: 28
Processing molecule 6 at level 6 queue contains (4); Overall Processed Count: 29
Processing molecule 7 at level 6 queue contains (3); Overall Processed Count: 30
Processing molecule 8 at level 6 queue contains (2); Overall Processed Count: 31
Processing molecule 9 at level 6 queue contains (1); Overall Processed Count: 32
Processing molecule 10 at level 6 queue contains (0); Overall Processed Count: 33
Processing level 7
Processing level 8
Processing level 9
Processing level 10
Processing level 11
Killed level 2
Killed level 3
Killed level 4
Killed level 5
Killed level 6
Killed level 7
Killed level 8
Killed level 9
Killed level 10
Killed level 11
Killed level 12
Killed level 13
Killed level 14
Killed level 15
Killed level 16
Killed level 17
Killed level 18
Killed level 19
Killed level 20
Level # Molecules
1 7
2 2
3 4
4 7
5 10
6 10
7 9
8 6
9 3
10 1
11 0
12 0
13 0
14 0
15 0
16 0
17 0
18 0
19 0
20 0
Excluded (0); Included (52) Excluded: 0%
Validation file not specified; will not validate.
Exiting the main thread.

[cplateVT]

After some investigation, it appears that this is the correct output from the software given the set of rigids and linkers. If I change the sdf files of the rigids to add more connectivity sites, the program generates thousands of compounds.

For example: in r-3437.sdf, if just line 58 is changed from '1 O.3' to '1 C.3', then the program generates over 3000 compounds. Whether these are viable compounds or not I'm not sure, I was just messing around.

[wcatykid]

It might come down to Lipinski compliance.

…

On Tue, Jan 25, 2022 at 3:41 PM cplateVT ***@***.***> wrote: After some investigation, it appears that this is the correct output from the software given the set of rigids and linkers. If I change the sdf files of the rigids to add more connectivity sites, the program generates thousands of compounds. For example: in r-3437.sdf, if just line 58 is changed from '1 O.3' to '1 C.3', then the program generates over 3000 compounds. Whether these are viable compounds or not I'm not sure, I was just messing around. — Reply to this email directly, view it on GitHub <#2 (comment)>, or unsubscribe <https://github.com/notifications/unsubscribe-auth/ABUOTREFPNHGUV27NBXOUYTUX4DH5ANCNFSM5MWU3TDA> . Triage notifications on the go with GitHub Mobile for iOS <https://apps.apple.com/app/apple-store/id1477376905?ct=notification-email&mt=8&pt=524675> or Android <https://play.google.com/store/apps/details?id=com.github.android&referrer=utm_campaign%3Dnotification-email%26utm_medium%3Demail%26utm_source%3Dgithub>. You are receiving this because you commented.Message ID: ***@***.***>