raymolecule v0.5.2: Fix CRAN issues and update dependencies

DESCRIPTION

@@ -1,20 +1,22 @@
 Package: raymolecule
 Type: Package
 Title: Parse and Render Molecular Structures in 3D
-Version: 0.5.1
-Date: 2022-12-09
+Version: 0.5.2
+Date: 2024-2-18
 Authors@R: c(person("Tyler", "Morgan-Wall", email = "[email protected]",
     role = c("aut", "cph", "cre"), comment = c(ORCID = "0000-0002-3131-3814")))
 Maintainer: Tyler Morgan-Wall <[email protected]>
 Description: Downloads and parses 'SDF' (Structural Description Format) and 'PDB' (Protein Database) files for 3D rendering.
 License: GPL-3
 Encoding: UTF-8
 Imports:
-    rayrender,
+    rayrender (>= 0.31.2),
     magrittr,
     PeriodicTable, 
     httr,
-    rayvertex
+    rayvertex (>= 0.10.4)
 LazyData: true
-RoxygenNote: 7.1.2
-URL: http://www.raymolecule.com/
+RoxygenNote: 7.3.0
+URL: http://www.raymolecule.com/,
+     https://github.com/tylermorganwall/raymolecule
+BugReports: https://github.com/tylermorganwall/raymolecule/issues

R/convert_color.R

@@ -10,7 +10,7 @@
 #' #none
 convert_color = function(color, as_hex = FALSE) {
   if(inherits(color,"character")) {
-    color = as.vector(col2rgb(color))/255
+    color = as.vector(grDevices::col2rgb(color))/255
   }
   stopifnot(all(color <= 1))
   stopifnot(all(color >= 0))

R/generate_atom_scene.R

@@ -47,6 +47,7 @@ generate_atom_scene = function(model, x=0, y=0, z=0, scale = 1, center = TRUE,
                                material = rayrender::glossy,
                                material_vertex = material_list(type="phong")) {
   mat_info = material()
+  mat_info = mat_info[[1]]
   if(!mat_info$type %in% c("glossy","diffuse", "dielectric")) {
     stop("material() must be either `glossy`, `diffuse`, or `dielectric`")
   }
@@ -78,7 +79,7 @@ generate_atom_scene = function(model, x=0, y=0, z=0, scale = 1, center = TRUE,
                                     material=material(color=atomcol))
       counter = counter + 1
     }
-    return(do.call(rbind, scenelist))
+    return(do.call("rbind", scenelist))
   } else {
     scene = list()
     for (i in 1:nrow(atoms)) {
@@ -89,8 +90,8 @@ generate_atom_scene = function(model, x=0, y=0, z=0, scale = 1, center = TRUE,
         atomcol = "grey5"
       }
       material_atom = material_vertex
-      material_atom$diffuse = atomcol
-      material_atom$ambient = atomcol
+      material_atom$diffuse = as.numeric(grDevices::col2rgb(atomcol))/255
+      material_atom$ambient = as.numeric(grDevices::col2rgb(atomcol))/255
       material_atom$ambient_intensity = 0.3
       atomsize = (PeriodicTable::mass(atoms$type[i])/14)^(1/3)
       scene = add_shape(scene, sphere_mesh(position = c(atoms$x[i],atoms$y[i], atoms$z[i]),

R/generate_bond_scene.R

@@ -47,6 +47,7 @@ generate_bond_scene = function(model, x=0, y=0, z=0, scale = 1, center = TRUE,
                                                                type = "phong",
                                                                ambient_intensity=0.3)) {
   mat_info = material()
+  mat_info = mat_info[[1]]
   if(!mat_info$type %in% c("glossy","diffuse", "dielectric")) {
     stop("material() must be either `glossy`, `diffuse`, or `dielectric`")
   }

R/generate_full_scene.R

@@ -62,6 +62,7 @@ generate_full_scene = function(model, x=0,y=0,z=0, scale = 1, center = TRUE, pat
                                force_single_bonds = FALSE, material = rayrender::glossy,
                                material_vertex = material_list(type="phong")) {
   mat_info = material()
+  mat_info = mat_info[[1]]
   if(!mat_info$type %in% c("glossy","diffuse", "dielectric")) {
     stop("material() must be either `glossy`, `diffuse`, or `dielectric`")
   }

R/render_model.R

@@ -77,12 +77,14 @@ render_model = function(scene, fov = NULL, angle = c(0,0,0), order_rotation = c(
   }
   pathtraced = suppressWarnings(is.null(scene$vertices))
   if(pathtraced) {
-    scene_model = scene[is.na(scene$lightintensity) &
+    is_not_light = unlist(lapply(scene$material, \(x) x$type)) != "light"
+
+    scene_model = scene[is_not_light &
                         (scene$shape == "cylinder" | scene$shape == "sphere"),]
     bbox_x = range(scene_model$x,na.rm=TRUE)
     bbox_y = range(scene_model$y,na.rm=TRUE)
     bbox_z = range(scene_model$z,na.rm=TRUE)
-    spheresizes = scene[(scene$shape == "sphere" & scene$type != "light"),4]
+    spheresizes = unlist(lapply(scene$shape_info, \(x) x[[1]]$radius))[is_not_light]
     if(length(spheresizes) > 0) {
       max_sphere_radii = max(spheresizes,na.rm=TRUE)
     } else {

R/util.R

@@ -19,7 +19,6 @@ unit_vector = function(v) {
 
 #'@title Create Orthonormal Basis from w (z)
 #'
-#'@param v Numeric vector.
 #'@keywords internal
 onb_from_w = function(n) {
   a1 = unit_vector(n)