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# Package: Bios2cor
# This file is part of Bios2cor R package.
# Bios2cor is free software: you can redistribute it and/or modify
# it under the terms of the GNU General Public License as published by
# the Free Software Foundation, either version 2 of the License, or
# any later version.
#
# This program is distributed in the hope that it will be useful,
# but WITHOUT ANY WARRANTY; without even the implied warranty of
# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
# GNU General Public License for more details.
#
# See the GNU General Public License at:
# http://www.gnu.org/licenses/
#
write.pca.pdb <- function(corr_pca, filepathroot, trio_comp= c(1:3)){
if (missing(corr_pca)) {
stop("A PCA object created by the centered_pca function is required")
}
pca_coord <- corr_pca$coord
pca_1 <- trio_comp[1]
pca_2 <- trio_comp[2]
pca_3 <- trio_comp[3]
if (is.null(filepathroot)) {
pdb_filepath <- paste(tempdir(), "/PCA_", pca_1, "_",pca_2, "_",pca_3, ".pdb", sep ="")
pml_filepath <- paste(tempdir(), "/PCA_", pca_1, "_",pca_2, "_",pca_3, ".pml", sep ="")
} else {
pdb_filepath <- paste(filepathroot, "_PCA_", pca_1, "_",pca_2, "_",pca_3, ".pdb", sep ="")
pml_filepath <- paste(filepathroot, "_PCA_", pca_1, "_",pca_2, "_",pca_3, ".pml", sep ="")
}
pca_positions <- rownames(pca_coord)
pca_size <- length(pca_positions)
#check whether data are from a MSA or a trajectory
numbering <- grep(".", pca_positions, fixed= TRUE)
alpha <- c("A","B","C","D")
colors <- c("blue", "red", "green", "orange", "white")
background_color <- paste("bg_color", colors[5])
write(background_color, file= pml_filepath, append= FALSE)
for(i in 1:4){
chain_coloration <- paste("color", colors[i], ", chain", alpha[i])
write(chain_coloration, file= pml_filepath, append= TRUE)
}
#Configuring elements
as_sphere <- "as sphere"
sphere_scale <- "set sphere_scale, 1"
write(as_sphere, file= pml_filepath, append= TRUE)
write(sphere_scale, file= pml_filepath, append= TRUE)
## Writing PDB file
pdb_line <- "REMARK PDB file created for visualization of PCA analysis"
write(pdb_line, file= pdb_filepath, append= FALSE)
##fields required in each line
#fields without change
head <- "HETATM"
atom_name <- "O"
res_type <- "HOH"
occupation <- "1.00"
B_factor <- 100.00
atom_type <- "O"
format <- "%6s%5s %-4s%3s %1s%4s %8s%8s%8s %4s%6s %4s"
#fields with changes
if(length(numbering) == 0){
for(pos in 1:pca_size){
x <- pca_coord[pos, pca_1]
y <- pca_coord[pos, pca_2]
z <- pca_coord[pos, pca_3]
if (!is.na(x) & !is.na(y) & !is.na(z)) {
residue_number <- pca_positions[pos]
chain_ID <- "A"
pdb_line <- sprintf(format, head, pos, atom_name, res_type, chain_ID, residue_number, round(x,digits=3), round(y,digits=3), round(z,digits=3), occupation, B_factor, atom_type)
write(pdb_line, file= pdb_filepath, append= TRUE)
}
}
last_number <- as.numeric(residue_number)
}else{
resno <- sub("\\..*$", "", pca_positions)
angle <- sub("^[0-9]*\\.","", pca_positions)
for(pos in 1:pca_size){
x <- pca_coord[pos, pca_1]
y <- pca_coord[pos, pca_2]
z <- pca_coord[pos, pca_3]
if (!is.na(x) & !is.na(y) & !is.na(z)) {
residue_number <- resno[pos]
angle_ID <- angle[pos]
if (angle_ID == "chi1") {chain_ID <- "A"}
if (angle_ID == "chi2") {chain_ID <- "B"}
if (angle_ID == "chi3") {chain_ID <- "C"}
if (angle_ID == "chi4") {chain_ID <- "D"}
pdb_line <- sprintf(format, head, pos, atom_name, res_type, chain_ID, residue_number, round(x,digits=3), round(y,digits=3), round(z,digits=3), occupation, B_factor, atom_type)
write(pdb_line, file= pdb_filepath, append= TRUE)
}
}
last_number <- as.numeric(residue_number)
}
#Creating elements used to create axis
max_x <- max(abs(na.omit(pca_coord[,1])))
norm <- round(max_x*2, digits=3)
axis_fake_atoms <- c("O","C","N", "Pb")
axis_fake_chain_ID <- "Z"
x_pos <- pca_size+1
y_pos <- pca_size+2
z_pos <- pca_size+3
origin_pos <- pca_size+4
x_residue <- last_number+1
y_residue <- last_number+2
z_residue <- last_number+3
origin_residue <- last_number+4
x_name <- "XXX"
y_name <- "YYY"
z_name <- "ZZZ"
origin_name <- "000"
x_axis <- sprintf(format, head, x_residue, axis_fake_atoms[1], x_name, axis_fake_chain_ID, x_residue, norm, 0, 0, occupation, B_factor, axis_fake_atoms[1])
y_axis <- sprintf(format, head, y_residue, axis_fake_atoms[2], y_name, axis_fake_chain_ID, y_residue, 0, norm, 0, occupation, B_factor, axis_fake_atoms[2])
z_axis <- sprintf(format, head, z_residue, axis_fake_atoms[3], z_name, axis_fake_chain_ID, z_residue, 0, 0, norm, occupation, B_factor, axis_fake_atoms[3])
origin <- sprintf(format, head, origin_residue, axis_fake_atoms[4], origin_name, axis_fake_chain_ID, origin_residue, 0, 0, 0, occupation, B_factor, axis_fake_atoms[4])
write(x_axis, file= pdb_filepath, append= TRUE)
write(y_axis, file= pdb_filepath, append= TRUE)
write(z_axis, file= pdb_filepath, append= TRUE)
write(origin, file= pdb_filepath, append= TRUE)
#Connecting x, y and z to origin
connect_x <- paste("CONECT", x_residue, origin_residue)
connect_y <- paste("CONECT", y_residue, origin_residue)
connect_z <- paste("CONECT", z_residue, origin_residue)
write(connect_x, file= pdb_filepath, append= TRUE)
write(connect_y, file= pdb_filepath, append= TRUE)
write(connect_z, file= pdb_filepath, append= TRUE)
write("END", file= pdb_filepath, append= TRUE)
#Display CONECT elements when loading pml file
enable_connections <- "show lines"
write(enable_connections, file= pml_filepath, append= TRUE)
hidden_spheres <- "hide spheres, chain Z"
write(hidden_spheres, file= pml_filepath, append= TRUE)
}
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