ClusPro output pdb file gives read.pdb error

Issue #866 resolved
Shoumo Bhattacharya created an issue

Hello,

On using read.pdb to import a ClusPro output pdb file I get an error, how should I fix this please? An example ClusPro file model.000.00.pdb is provided. Many thanks for your help!

code

test.pdb <- read.pdb("model.000.00.pdb")

Warning message:
In read.pdb("model.000.00.pdb") :
duplicated element numbers ('eleno') detected

session info:

R version 4.1.2 (2021-11-01)
Platform: x86_64-apple-darwin17.0 (64-bit)
Running under: macOS Monterey 12.1

Matrix products: default
LAPACK: /Library/Frameworks/R.framework/Versions/4.1/Resources/lib/libRlapack.dylib

locale:
[1] en_GB.UTF-8/en_GB.UTF-8/en_GB.UTF-8/C/en_GB.UTF-8/en_GB.UTF-8

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

other attached packages:
[1] bio3d_2.4-2 R.utils_2.11.0 R.oo_1.24.0 R.methodsS3_1.8.1 forcats_0.5.1 stringr_1.4.0 dplyr_1.0.7
[8] purrr_0.3.4 readr_2.1.1 tidyr_1.1.4 tibble_3.1.6 ggplot2_3.3.5 tidyverse_1.3.1

loaded via a namespace (and not attached):
[1] tidyselect_1.1.1 janitor_2.1.0 haven_2.4.3 snakecase_0.11.0 colorspace_2.0-2 vctrs_0.3.8 generics_0.1.1 utf8_1.2.2
[9] rlang_0.4.12 pillar_1.6.4 glue_1.6.0 withr_2.4.3 DBI_1.1.2 dbplyr_2.1.1 modelr_0.1.8 readxl_1.3.1
[17] lifecycle_1.0.1 munsell_0.5.0 gtable_0.3.0 cellranger_1.1.0 rvest_1.0.2 tzdb_0.2.0 parallel_4.1.2 fansi_0.5.0
[25] broom_0.7.10 Rcpp_1.0.7 scales_1.1.1 backports_1.4.1 writexl_1.4.0 jsonlite_1.7.2 fs_1.5.2 hms_1.1.1
[33] stringi_1.7.6 grid_4.1.2 cli_3.1.0 tools_4.1.2 magrittr_2.0.1 crayon_1.4.2 pkgconfig_2.0.3 ellipsis_0.3.2
[41] xml2_1.3.3 reprex_2.0.1 lubridate_1.8.0 assertthat_0.2.1 httr_1.4.2 rstudioapi_0.13 R6_2.5.1 compiler_4.1.2

Comments (2)

  1. Xinqiu Yao

    Hi,

    I don’t see any error messages. It should be fine. You can safely ignore the ‘warning’ message.

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