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girke-lab / ChemmineOB

OpenBabel wrapper package for R
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fingerprintOB fails with MACCS #27

Closed eerisman closed 1 year ago

eerisman commented 2 years ago

I cannot get fingerprintOB to calculate the "MACCS" fingerprint. I can calculate other openbabel fringerprints just fine (eg "FP2", "FP4", "ECFP10", etc...) I get the following error: "Error in fingerprint_OB(obmol(sdfSet), fingerprintName) : fingerprint MACCS not found"

ChemmineOB version 1.34.0 ChemmineR version 3.48.0 openbabel version 3.1.1 I can calculate "MACCS" fingerprints via openbabel command line

tgirke commented 2 years ago

What OS are you using? It works on my systems. Perhaps send the output of sessionInfo() after observing the error.

On Thu, Jun 30, 2022 at 10:19 AM Edward Erisman @.***> wrote:

I cannot get fingerprintOB to calculate the "MACCS" fingerprint. I can calculate other openbabel fringerprints just fine (eg "FP2", "FP4", "ECFP10", etc...) I get the following error: "Error in fingerprint_OB(obmol(sdfSet), fingerprintName) : fingerprint MACCS not found"

ChemmineOB version 1.34.0 ChemmineR version 3.48.0 openbabel version 3.1.1 I can calculate "MACCS" fingerprints via openbabel command line

— Reply to this email directly, view it on GitHub https://github.com/girke-lab/ChemmineOB/issues/27, or unsubscribe https://github.com/notifications/unsubscribe-auth/AAKGMVFE3VMXJPSYJCZAINLVRXJATANCNFSM52KCOTCQ . You are receiving this because you are subscribed to this thread.Message ID: @.***>

-- Thomas Girke, Ph.D. Professor of Bioinformatics 1207F Genomics Building University of California Riverside, CA 92521

E-mail: @.*** URL: https://girke.bioinformatics.ucr.edu Phone/Cell/Text: 951-732-7072 Fax: 951-827-4437

eerisman commented 2 years ago

I am using Windows 10.

Output for sessionInfo(): R version 4.2.1 (2022-06-23 ucrt) Platform: x86_64-w64-mingw32/x64 (64-bit) Running under: Windows 10 x64 (build 19042)

Matrix products: default

locale: [1] LC_COLLATE=English_United States.1252 LC_CTYPE=English_United States.1252 LC_MONETARY=English_United States.1252 LC_NUMERIC=C [5] LC_TIME=English_United States.1252

attached base packages: [1] stats graphics grDevices utils datasets methods base

other attached packages: [1] fmcsR_1.38.0 dbscan_1.1-10 ChemmineOB_1.34.0 ChemmineR_3.48.0

loaded via a namespace (and not attached): [1] Rcpp_1.0.8.3 pillar_1.7.0 compiler_4.2.1 zlibbioc_1.42.0 bitops_1.0-7 base64enc_0.1-3 tools_4.2.1 digest_0.6.29 [9] evaluate_0.15 lifecycle_1.0.1 tibble_3.1.7 gtable_0.3.0 pkgconfig_2.0.3 png_0.1-7 rlang_1.0.2 DBI_1.1.3 [17] cli_3.3.0 yaml_2.3.5 parallel_4.2.1 xfun_0.31 fastmap_1.1.0 gridExtra_2.3 knitr_1.39 dplyr_1.0.9 [25] generics_0.1.2 vctrs_0.4.1 htmlwidgets_1.5.4 grid_4.2.1 DT_0.23 tidyselect_1.1.2 glue_1.6.2 R6_2.5.1 [33] fansi_1.0.3 rmarkdown_2.14 ggplot2_3.3.6 purrr_0.3.4 magrittr_2.0.3 scales_1.2.0 ellipsis_0.3.2 htmltools_0.5.2 [41] colorspace_2.0-3 rsvg_2.3.1 utf8_1.2.2 RCurl_1.98-1.7 munsell_0.5.0 crayon_1.5.1 rjson_0.2.21

From: Thomas Girke @.> Sent: Thursday, June 30, 2022 1:34 PM To: girke-lab/ChemmineOB @.> Cc: Erisman, Edward P. (Fed) @.>; Author @.> Subject: Re: [girke-lab/ChemmineOB] fingerprintOB fails with MACCS (Issue #27)

What OS are you using? It works on my systems. Perhaps send the output of sessionInfo() after observing the error.

On Thu, Jun 30, 2022 at 10:19 AM Edward Erisman @.***> wrote:

I cannot get fingerprintOB to calculate the "MACCS" fingerprint. I can calculate other openbabel fringerprints just fine (eg "FP2", "FP4", "ECFP10", etc...) I get the following error: "Error in fingerprint_OB(obmol(sdfSet), fingerprintName) : fingerprint MACCS not found"

ChemmineOB version 1.34.0 ChemmineR version 3.48.0 openbabel version 3.1.1 I can calculate "MACCS" fingerprints via openbabel command line

- Reply to this email directly, view it on GitHub https://github.com/girke-lab/ChemmineOB/issues/27, or unsubscribe https://github.com/notifications/unsubscribe-auth/AAKGMVFE3VMXJPSYJCZAINLVRXJATANCNFSM52KCOTCQ . You are receiving this because you are subscribed to this thread.Message ID: @.***>

-- Thomas Girke, Ph.D. Professor of Bioinformatics 1207F Genomics Building University of California Riverside, CA 92521

E-mail: @.*** URL: https://girke.bioinformatics.ucr.edu Phone/Cell/Text: 951-732-7072 Fax: 951-827-4437

- Reply to this email directly, view it on GitHubhttps://github.com/girke-lab/ChemmineOB/issues/27#issuecomment-1171496886, or unsubscribehttps://github.com/notifications/unsubscribe-auth/AZ2GRITCK2YDWYRZ2MDJQ4DVRXLCLANCNFSM52KCOTCQ. You are receiving this because you authored the thread.Message ID: @.***>

tgirke commented 2 years ago

Might be specific to Windows. We need to run some tests to be sure. As an intermediate solution you could generate the fingerprints with OpenBabel then import them into R, store them in matrix, and then convert to the expected FPset object class as outlined here https://www.bioconductor.org/packages/release/bioc/vignettes/ChemmineR/inst/doc/ChemmineR.html#FPFPset_Classes_for_Storing_Fingerprints. We can report back here once the issue is fixed.

On Thu, Jun 30, 2022 at 10:40 AM Edward Erisman @.***> wrote:

I am using Windows 10.

Output for sessionInfo(): R version 4.2.1 (2022-06-23 ucrt) Platform: x86_64-w64-mingw32/x64 (64-bit) Running under: Windows 10 x64 (build 19042)

Matrix products: default

locale: [1] LC_COLLATE=English_United States.1252 LC_CTYPE=English_United States.1252 LC_MONETARY=English_United States.1252 LC_NUMERIC=C [5] LC_TIME=English_United States.1252

attached base packages: [1] stats graphics grDevices utils datasets methods base

other attached packages: [1] fmcsR_1.38.0 dbscan_1.1-10 ChemmineOB_1.34.0 ChemmineR_3.48.0

loaded via a namespace (and not attached): [1] Rcpp_1.0.8.3 pillar_1.7.0 compiler_4.2.1 zlibbioc_1.42.0 bitops_1.0-7 base64enc_0.1-3 tools_4.2.1 digest_0.6.29 [9] evaluate_0.15 lifecycle_1.0.1 tibble_3.1.7 gtable_0.3.0 pkgconfig_2.0.3 png_0.1-7 rlang_1.0.2 DBI_1.1.3 [17] cli_3.3.0 yaml_2.3.5 parallel_4.2.1 xfun_0.31 fastmap_1.1.0 gridExtra_2.3 knitr_1.39 dplyr_1.0.9 [25] generics_0.1.2 vctrs_0.4.1 htmlwidgets_1.5.4 grid_4.2.1 DT_0.23 tidyselect_1.1.2 glue_1.6.2 R6_2.5.1 [33] fansi_1.0.3 rmarkdown_2.14 ggplot2_3.3.6 purrr_0.3.4 magrittr_2.0.3 scales_1.2.0 ellipsis_0.3.2 htmltools_0.5.2 [41] colorspace_2.0-3 rsvg_2.3.1 utf8_1.2.2 RCurl_1.98-1.7 munsell_0.5.0 crayon_1.5.1 rjson_0.2.21

From: Thomas Girke @.> Sent: Thursday, June 30, 2022 1:34 PM To: girke-lab/ChemmineOB @.> Cc: Erisman, Edward P. (Fed) @.>; Author @.> Subject: Re: [girke-lab/ChemmineOB] fingerprintOB fails with MACCS (Issue

27)

What OS are you using? It works on my systems. Perhaps send the output of sessionInfo() after observing the error.

On Thu, Jun 30, 2022 at 10:19 AM Edward Erisman @.***> wrote:

I cannot get fingerprintOB to calculate the "MACCS" fingerprint. I can calculate other openbabel fringerprints just fine (eg "FP2", "FP4", "ECFP10", etc...) I get the following error: "Error in fingerprint_OB(obmol(sdfSet), fingerprintName) : fingerprint MACCS not found"

ChemmineOB version 1.34.0 ChemmineR version 3.48.0 openbabel version 3.1.1 I can calculate "MACCS" fingerprints via openbabel command line

- Reply to this email directly, view it on GitHub https://github.com/girke-lab/ChemmineOB/issues/27, or unsubscribe < https://github.com/notifications/unsubscribe-auth/AAKGMVFE3VMXJPSYJCZAINLVRXJATANCNFSM52KCOTCQ

. You are receiving this because you are subscribed to this thread.Message ID: @.***>

-- Thomas Girke, Ph.D. Professor of Bioinformatics 1207F Genomics Building University of California Riverside, CA 92521

E-mail: @.*** URL: https://girke.bioinformatics.ucr.edu Phone/Cell/Text: 951-732-7072 Fax: 951-827-4437

- Reply to this email directly, view it on GitHub< https://github.com/girke-lab/ChemmineOB/issues/27#issuecomment-1171496886>, or unsubscribe< https://github.com/notifications/unsubscribe-auth/AZ2GRITCK2YDWYRZ2MDJQ4DVRXLCLANCNFSM52KCOTCQ

. You are receiving this because you authored the thread.Message ID: @.***>

— Reply to this email directly, view it on GitHub https://github.com/girke-lab/ChemmineOB/issues/27#issuecomment-1171500827, or unsubscribe https://github.com/notifications/unsubscribe-auth/AAKGMVBUQFATVQN7R2NADXTVRXLTXANCNFSM52KCOTCQ . You are receiving this because you commented.Message ID: @.***>

-- Thomas Girke, Ph.D. Professor of Bioinformatics 1207F Genomics Building University of California Riverside, CA 92521

E-mail: @.*** URL: https://girke.bioinformatics.ucr.edu Phone/Cell/Text: 951-732-7072 Fax: 951-827-4437

khoran commented 1 year ago

"MACCS" is not supported on Windows. This is now documented in the fingerprint_OB man page.