Mercurial > repos > bitlab > plidflow
diff PLIDflow/scripts/cluster_to_vina_cluster.R @ 6:795e11fac81b draft default tip
Included new tools for standardization
author | bitlab |
---|---|
date | Wed, 22 Apr 2020 06:12:00 -0400 |
parents | 6fcfa4756040 |
children |
line wrap: on
line diff
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/PLIDflow/scripts/cluster_to_vina_cluster.R Wed Apr 22 06:12:00 2020 -0400 @@ -0,0 +1,100 @@ +#cluster_to_vina_clusters.R introduces the x, y,z, coordenates of the cluster/-s identified in the vina file configuration how many cluster/-s identified + +#!/usr/bin/env Rscript +args = commandArgs(trailingOnly=TRUE) + +if(length(args) < 8){ + stop("USE: Rscript cluster_to_vina_clusters.R <receptor_name> <ligand_name> <out_PDBQT> <log_file> <eboxsizedata> <session_dir> <receptor_filename> <ligand_filename>") + #stop("USE: Rscript cluster_to_vina_clusters.R <receptor_name> <ligand_name> <out_PDBQT> <log_file> <eboxsizedata> <out_conf_file>") +} + +#Arguments definition +receptor_name <- args[1] +ligand_name <- args[2] +out_PDBQT <- args[3] +log_file <- args[4] +eboxsizedata <- args[5] +session_dir <- args[6] +#out_conf_file <- args[6] +receptor_filename <- args[7] +ligand_filename <- args[8] + +setwd(session_dir) + +#print("before reading table") +clusters_file <- read.table("clusterscoordenates.txt", header = TRUE) +#print("After reading table") + +value <- 0 +el_b_que_me_quedo <- 1 +for(v in 1: nrow(clusters_file)){ + coo_x <- clusters_file[v,2] + coo_y <- clusters_file[v,3] + coo_z <- clusters_file[v,4] + + + #<receptor_PDBQT> <ligand_PDBQT> <out_PDBQT> <log_file> <coo_x > <coo_y> <coo_z> <eboxsizedata> <galaxy out> <v> + argumentos <- paste(args[1],args[2], args[3], args[4], coo_x, coo_y, coo_z, args[5], v, session_dir, sep = " ") + script_argumentos <- paste("Rscript vinafilemarkerclusters.R", argumentos, sep = " ") + + system (script_argumentos) + system (paste("vina --config ", paste(v, "_vinaconfig", sep = ""), sep ="")) + #system (paste("/home/eugenia/workflowsoftware/autodock_vina_1_1_2_linux_x86/bin/vina --config ", paste(v, "_vinaconfig", sep = ""), sep ="")) + #write(paste("/home/eugenia/workflowsoftware/autodock_vina_1_1_2_linux_x86/bin/vina --config ", paste(v, "_vinaconfig", sep = ""), sep =""), file = "commands", append = TRUE) + # + + #Save out pdbqt from Vina 30julio2018 + #print("before scanning") + outlog_vina <- scan (paste(v, "_vinaconfig", sep = ""), what = character(), quiet = TRUE) + #print("after scanning") + + pegar_mv_out9 <- paste("mv", outlog_vina[9], sep = " ") + pegar_v_out <- paste(v,"_", receptor_filename, "_", ligand_filename, "_out_vina.pdbqt", sep = "") + pegar_dos_outs <- paste(pegar_mv_out9, pegar_v_out, sep = " ") + + + #print(pegar_dos_outs) + system(pegar_dos_outs) + + #Save log pdbqt from Vina 30julio2018 + pegar_mv_out12 <- paste("mv", outlog_vina[12], sep = " ") + pegar_v_log <- paste(v,"_", receptor_filename, "_", ligand_filename, "_log_vina.log", sep = "") + pegar_dos_logs <- paste(pegar_mv_out12, pegar_v_log, sep = " ") + + system(pegar_dos_logs) + + # + + #binding_mode1_energy <- scan(args[4], what = character(), quiet = TRUE)[122] + #if(v == 1) value <- binding_mode1_energy + #if(value > as.numeric(binding_mode1_energy)){ + # value <- as.numeric(binding_mode1_energy) + # el_b_que_me_quedo <- v + #} +} + +#copiador <- paste(el_b_que_me_quedo, "_vinaconfig", sep="") +#argumentos <- paste("mv", copiador, out_conf_file, sep=" ") +#print(argumentos) +#system(argumentos) + +#system(paste("zip all-vinas-out.zip", "*_out_vina", sep = " ")) #antes del 31julio +#system(paste("mv", "all-vinas-out.zip", args[3] , sep = " ")) #antes del 31julio + +#system(paste("zip all-vinas-log.zip", "*_log_vina", sep = " ")) #antes del 31julio +#system(paste("mv", "all-vinas-log.zip", args[4] , sep = " ")) #antes del 31julio + +#31julio2018 ----> creo que hay que cambiar los guiones porque hoy se ha quedado pillado en los zip que no lo ha hecho +#30agosto2018 -----> voy a hacer el cambio + +# USE THIS FOR keeping stdout but removing stderr +# { cmd 2>&1 >&3 3>&- | logger 3>&-; } 3>&1 + +system(paste("zip all_vinas_out.zip", "*_out_vina.pdbqt", sep = " ")) #30agosto +system(paste("mv", "all_vinas_out.zip", args[3] , sep = " ")) #30agosto + +system(paste("zip all_vinas_log.zip", "*_log_vina.log", sep = " ")) #30agosto +system(paste("mv", "all_vinas_log.zip", args[4] , sep = " ")) #30agosto + + +