tylermorganwall / raymolecule Goto Github PK
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error with new version for toon shading
Dear Dr Morgan-Wall,
I am sorry to bother you. I am just having a bit of trouble with the latest version or raymolecule. With the latest version the example Raymolecule code at https://github.com/tylermorganwall/raymolecule for using using the cel-shading and the toon shading no longer seem to work. They used to but now if I run for example,
shiny_toon_material = material_list(type="toon_phong",
toon_levels=,
toon_outline_width=0.1)
get_example_molecule("morphine") |>
read_sdf() |>
generate_full_scene(pathtrace=FALSE, material_vertex = shiny_toon_material) |>
render_model(width=800,height=800,background="grey66")
It gives an error "-Error in apply(single_obj$vertices, 2, range) :
dim(X) must have a positive length
Basically anything on https://github.com/tylermorganwall/raymolecule with a black background still works but the ones with a grey background don’t - unless I use the old version of Rayshader on my laptop.
I have tried to work it out but I’m stuck.
Many thanks
Oliver
Noise and 360 views
Hello,
the package is awesome. Could you please explain how can I make the 360 view video with raymolecule?
Also, there'll always have some noise in the image? how much can we remove?
read_pdb fails in Linux when using a gzip compressed file in R 4.1.0
An example of this error:
> p = read_pdb("1kys.pdb.gz")
Error in readChar(con, nchars = 6) : invalid UTF-8 input in readChar()
In addition: Warning message:
In readChar(con, nchars = 6) : truncating string with embedded nuls
Seems like the issue is in
Line 25 in 159959d
con = file(filename,"rb")Subsequently, it fails when trying to execute:
type = trimws(readChar(con,nchars=6))Not sure if it is an issue with the new version of R (which I've updated today), or "raymolecule" (which I've installed today).
FWIW, when trying to read the file w/o using "rb", it works:
> con = file("1kys.pdb.gz")
> readChar(con, n = 6)
[1] "HEADER"
As a reference. here is my sessionInfo() output
> sessionInfo()
R version 4.1.0 (2021-05-18)
Platform: x86_64-pc-linux-gnu (64-bit)
Running under: Ubuntu 20.04.2 LTS
Matrix products: default
BLAS: /usr/lib/x86_64-linux-gnu/openblas-pthread/libblas.so.3
LAPACK: /usr/lib/x86_64-linux-gnu/openblas-pthread/liblapack.so.3
locale:
[1] LC_CTYPE=en_US.UTF-8 LC_NUMERIC=C
[3] LC_TIME=en_US.UTF-8 LC_COLLATE=en_US.UTF-8
[5] LC_MONETARY=en_US.UTF-8 LC_MESSAGES=en_US.UTF-8
[7] LC_PAPER=en_US.UTF-8 LC_NAME=C
[9] LC_ADDRESS=C LC_TELEPHONE=C
[11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C
attached base packages:
[1] stats graphics grDevices utils datasets methods base
other attached packages:
[1] forcats_0.5.1 stringr_1.4.0 dplyr_1.0.6 purrr_0.3.4
[5] readr_1.4.0 tidyr_1.1.3 tibble_3.1.2 ggplot2_3.3.3
[9] tidyverse_1.3.1 raymolecule_0.3.2
loaded via a namespace (and not attached):
[1] Rcpp_1.0.6 lubridate_1.7.10 lattice_0.20-44
[4] prettyunits_1.1.1 ps_1.6.0 assertthat_0.2.1
[7] rprojroot_2.0.2 utf8_1.2.1 cellranger_1.1.0
[10] R6_2.5.0 backports_1.2.1 reprex_2.0.0
[13] httr_1.4.2 pillar_1.6.1 rlang_0.4.11.9000
[16] readxl_1.3.1 curl_4.3.1 rstudioapi_0.13
[19] callr_3.7.0 raster_3.4-10 desc_1.3.0
[22] devtools_2.4.1 munsell_0.5.0 broom_0.7.6
[25] modelr_0.1.8 compiler_4.1.0 pkgconfig_2.0.3
[28] pkgbuild_1.2.0 tidyselect_1.1.1 rayrender_0.21.2
[31] codetools_0.2-18 fansi_0.4.2 crayon_1.4.1
[34] dbplyr_2.1.1 withr_2.4.2 grid_4.1.0
[37] jsonlite_1.7.2 gtable_0.3.0 lifecycle_1.0.0
[40] PeriodicTable_0.1.2 DBI_1.1.1 magrittr_2.0.1
[43] scales_1.1.1 stringi_1.6.2 cli_2.5.0
[46] cachem_1.0.5 fs_1.5.0 remotes_2.3.0
[49] sp_1.4-5 testthat_3.0.2 xml2_1.3.2
[52] ellipsis_0.3.2 generics_0.1.0 vctrs_0.3.8
[55] tools_4.1.0 glue_1.4.2 rayimage_0.5.1
[58] hms_1.1.0 processx_3.5.2 pkgload_1.2.1
[61] parallel_4.1.0 fastmap_1.1.0 colorspace_2.0-1
[64] sessioninfo_1.1.1 rvest_1.0.0 memoise_2.0.0
[67] haven_2.4.1 usethis_2.0.1
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