# HG changeset patch # User bitlab # Date 1579006368 18000 # Node ID afd5b5ffc38fee31213dad9d9b3d72daa74e116a # Parent eda62adfc85882f6a201f74b45527d74d40ebd7d Uploaded diff -r eda62adfc858 -r afd5b5ffc38f PLIDflow/autodocktools_lig_plidflow.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/PLIDflow/autodocktools_lig_plidflow.xml Tue Jan 14 07:52:48 2020 -0500 @@ -0,0 +1,17 @@ + + AutoDock is a suite of automated docking tools. It is designed to predict how small molecules, such as substrates or drug candidates, bind to a receptor of known 3D structure. + + + + + + + + diff -r eda62adfc858 -r afd5b5ffc38f PLIDflow/autodocktools_rec_plidflow.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/PLIDflow/autodocktools_rec_plidflow.xml Tue Jan 14 07:52:48 2020 -0500 @@ -0,0 +1,22 @@ + + AutoDock is a suite of automated docking tools. It is designed to predict how small molecules, such as substrates or drug candidates, bind to a receptor of known 3D structure + + + + + + + + + + + + diff -r eda62adfc858 -r afd5b5ffc38f PLIDflow/confmaker_multiple_plidflow.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/PLIDflow/confmaker_multiple_plidflow.xml Tue Jan 14 07:52:48 2020 -0500 @@ -0,0 +1,33 @@ + + is a tool to select optimal Vina mode 1 energy. + + + + + + + + + + + + + + + + + + + + diff -r eda62adfc858 -r afd5b5ffc38f PLIDflow/eboxsize_plidflow.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/PLIDflow/eboxsize_plidflow.xml Tue Jan 14 07:52:48 2020 -0500 @@ -0,0 +1,15 @@ + + is a tool to customize the box size for individual query ligands in order to maximize the accuracy of molecular docking. + + + + $eboxsizedata ; + rm ${ligand_pdbqt}.pdbqt ; + ]]> + + + + diff -r eda62adfc858 -r afd5b5ffc38f PLIDflow/launch_confmaker_multiple.sh --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/PLIDflow/launch_confmaker_multiple.sh Tue Jan 14 07:52:48 2020 -0500 @@ -0,0 +1,76 @@ +receptor_pdbqt=$1 +receptor_pdbqt_modified=$2 +receptor_pdbqt_modified2=$3 +ligand_pdbqt=$4 +size_x=$5 +out=$6 +log=$7 +receptor_name=$8 +ligand_name=$9 +# This one is to extract the protein code and to check whether the fillouts have already been done +# This is for the parallel version, ignore +receptor_file=${10} +receptorTypes=${11} +toolsDirectory=${12} + +# Configuration variables // This is not really necessary anymore +MYRAND=$(( ( RANDOM % 10000000 ) + 1 )) +RANDDIR=${MYRAND} + + + + + +mkdir $RANDDIR + + +cp -r ${toolsDirectory}/scripts/* $RANDDIR +echo "$toolsDirectory" + +cp $receptorTypes $RANDDIR +NOMBRERECEPTOR=$(basename $receptorTypes) +mv $RANDDIR/$NOMBRERECEPTOR $RANDDIR/receptor_atm_types.txt + +MYPWD=$PWD + + +cd $RANDDIR + +source ADT_VENV/bin/activate + +#echo "[RUNNING] - (Rscript pdbcenter_npts_finder.R $receptor_pdbqt_modified $RANDDIR) &>/dev/null" +Rscript pdbcenter_npts_finder.R $receptor_pdbqt_modified2 $MYPWD/$RANDDIR + +#echo "[RUNNING] - (Rscript gpffilemaker.R $receptor_pdbqt $RANDDIR) " +Rscript gpffilemaker.R $receptor_pdbqt_modified2 $MYPWD/$RANDDIR + +#echo "[RUNNING] - (Rscript glgfilemaker.R $receptor_pdbqt $RANDDIR) " +Rscript glgfilemaker.R $receptor_pdbqt_modified2 $MYPWD/$RANDDIR + +#echo "[RUNNING] - (Rscript envelopesmaker.R $receptor_pdbqt $RANDDIR) " +#(Rscript envelopesmaker.R $receptor_pdbqt $RANDDIR) &>/dev/null +pathLigand=$(which AutoLigand.py) +Rscript envelopesmaker.R $receptor_pdbqt_modified2 $MYPWD/$RANDDIR $pathLigand + +#cp ~/proteindb/2E9U_PH7/FILL* . + +#echo "[RUNNING] - (Rscript envelopesmaker.R $receptor_pdbqt $RANDDIR) " +#(Rscript envelopesmaker.R $receptor_pdbqt $RANDDIR) &>/dev/null + + +#echo "[RUNNING] - (Rscript clusterfilemaker.R $RANDDIR) " +Rscript clusterfilemaker.R $MYPWD/$RANDDIR + + +#echo "[RUNNING] - (Rscript clusterfinder_Auto.R $RANDDIR) " +Rscript clusterfinder_Auto.R $MYPWD/$RANDDIR + + +#echo "[RUNNING] - (Rscript cluster_to_vina_cluster.R $receptor_pdbqt_modified2 $ligand_pdbqt $out $log $size_x $RANDDIR $receptor_name $ligand_name) " +Rscript cluster_to_vina_cluster.R $receptor_pdbqt_modified2 $ligand_pdbqt $out $log $size_x $MYPWD/$RANDDIR $receptor_name $ligand_name + + +cd $MYPWD + + +deactivate diff -r eda62adfc858 -r afd5b5ffc38f PLIDflow/modeller_plidflow.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/PLIDflow/modeller_plidflow.xml Tue Jan 14 07:52:48 2020 -0500 @@ -0,0 +1,10 @@ + + Modeller description + + + + mod9.19 $pdbFile $mutantPdbFile0 + + + + diff -r eda62adfc858 -r afd5b5ffc38f PLIDflow/openbabel_SDF_plidflow.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/PLIDflow/openbabel_SDF_plidflow.xml Tue Jan 14 07:52:48 2020 -0500 @@ -0,0 +1,10 @@ + + Open Babel converts chemical structures from one file format to another. Use Open Babel to convert SDF files to PDF files + + + + (obabel -i sdf $ligand_sdf -o pdb -O $ligand_pdb) &>/dev/null + + + + diff -r eda62adfc858 -r afd5b5ffc38f PLIDflow/openbabel_SMI_plidflow.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/PLIDflow/openbabel_SMI_plidflow.xml Tue Jan 14 07:52:48 2020 -0500 @@ -0,0 +1,10 @@ + + Open Babel converts chemical structures from one file format to another. Use Open Babel to convert SMI files to SDF files + + + + (obabel -i smi $ligand_smi -o sdf -O $ligand_sdf --gen3D) &>/dev/null + + + + diff -r eda62adfc858 -r afd5b5ffc38f PLIDflow/pdb2pqr_plidflow.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/PLIDflow/pdb2pqr_plidflow.xml Tue Jan 14 07:52:48 2020 -0500 @@ -0,0 +1,18 @@ + + Converts a pdb to pqr + + + + ${pdb_processed} ; + + rm ${pdb_processed}.pqr + + ]]> + + + + diff -r eda62adfc858 -r afd5b5ffc38f PLIDflow/scripts/cluster_to_vina_cluster.R --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/PLIDflow/scripts/cluster_to_vina_cluster.R Tue Jan 14 07:52:48 2020 -0500 @@ -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 ") + #stop("USE: Rscript cluster_to_vina_clusters.R ") +} + +#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] + + + # + 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 + + + diff -r eda62adfc858 -r afd5b5ffc38f PLIDflow/scripts/clusterfilemaker.R --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/PLIDflow/scripts/clusterfilemaker.R Tue Jan 14 07:52:48 2020 -0500 @@ -0,0 +1,101 @@ +#clusterfilemaker.R makes a file containg geometric center coordenates for FILL_Xout1.pdb files. X represents envelopes size from 10 to 100 + +#!/usr/bin/env Rscript +args = commandArgs(trailingOnly=TRUE) + +if(length(args) < 1){ + stop("USE: Rscript clusterfilemaker.R ") +} + +#Select the directory where all files are being stored + +session_id <- args[1] + +print(session_id) + +setwd(session_id) + +#Scan dataset containig FILL_out1.pdb with point from 10 to 500 +fill_outs_1 <- scan("templatefillouts1.txt", what = character(), quiet = TRUE) + +#Write the head for the file later created which contains the middle point from FILL_out1.pdb with point from 10 to 500 +cabecera_fillfile <- paste("npts", sep = ";") +cabecera <- c("x","y","z") + +for(i in 1:3){ + cabecera_fillfile <- paste(cabecera_fillfile, cabecera[i], sep=";") +} +write(cabecera_fillfile, file="fillouts1file.txt", append= TRUE) + +#Loop to read the files FILL_out1.pdb and calculate the middle point +num_points <- 0 +start_env <- 10 # to fit the first envelope size. In case to change envelope size, only modify this parameter +jp <- 10 #jump between envelopes size. In case modify jump between envelopes size, only modify this parameter +#In case modify start envelope size and jump, only modify start_env and jp parameters in the script nothing in following steps + + + + + +num_points <- (start_env - jp) +for(f in 1:length(fill_outs_1)){ +# print(paste("Testing file ", fill_outs_1[f])) + if(file_test("-f", fill_outs_1[f])){ + archivo <- scan(fill_outs_1[f], what = character(), quiet = TRUE) + }else{ + next + } + +#Make a table with only x, y, z coordenates for C atoms only +salto <- 0 +for(i in 1:(length(archivo)-2)){ + if(archivo[i] == "ATOM" && ( archivo[i+2] == "C" || archivo[i+2] == "O" || archivo[i+2] == "H" )){ + salto <- salto + 1 + } +} +tablaC <- matrix(1, nrow = salto, ncol = 4) + +#Names for columns +##First column correspond to position for atoms C. This column will be created when the C atom positions will be know +###Write the name for columns and rows +colnames(tablaC) <- c("C Position","X", "Y", "z") +rownames(tablaC) <- 1:salto + +#Calculate the number of C atoms and to write theirs coordenates x,y,z in the tablaC +salto <- 0 +posicionC <- c() +for(i in 1:(length(archivo)-2)){ + if(archivo[i] == "ATOM" && ( archivo[i+2] == "C" || archivo[i+2] == "O" || archivo[i+2] == "H" )){ + salto <- salto + 1 + posicionC <- c(posicionC, archivo[i+1]) + tablaC[salto,2] <- as.numeric(archivo[i+5]) + tablaC[salto,3] <- as.numeric(archivo[i+6]) + tablaC[salto,4] <- as.numeric(archivo[i+7]) + } +} + +#Write the C atoms positions in column 1 of the table tablaC +for(i in 1:salto){ +tablaC[i,1] <- as.numeric(posicionC[i]) +} + +#Calculate middle point for the FILL_out1.pdb given +pto_x_medio <- (max(tablaC[,2]) + min(tablaC[,2]))/2 +pto_y_medio <- (max(tablaC[,3]) + min(tablaC[,3]))/2 +pto_z_medio <- (max(tablaC[,4]) + min(tablaC[,4]))/2 + +#Write a plain text called fillouts1file.txt which contain in the first column number of point +#for the envelope according to AutoLigand program. Columns 2,3,4 for coordenates x, y ,z +#for the middle points for FILL_out1.pdb from 10 to 500 points +num_points <- num_points + jp +write(paste(num_points,pto_x_medio, pto_y_medio, pto_z_medio, sep=";"),file="fillouts1file.txt", append= TRUE) +} + + + + + + + + + diff -r eda62adfc858 -r afd5b5ffc38f PLIDflow/scripts/clusterfinder_Auto.R --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/PLIDflow/scripts/clusterfinder_Auto.R Tue Jan 14 07:52:48 2020 -0500 @@ -0,0 +1,170 @@ +# #clusterfinder_Auto.R makes a file containig the coordenates of the identified cluster/-s by Silhouette criterion +# +#!/usr/bin/env Rscript +args = commandArgs(trailingOnly=TRUE) + +if(length(args) < 1){ + stop("USE: Rscript clusterfinder_Auto.R ") +} + +#Arguments definition + +session_id <- args[1] + +print(session_id) + +setwd(session_id) + +options(error=traceback) +options(warn=-1) + +#Load required library +library(cluster) + +#Load required libraries +library(clValid) + +#Loading required package: cluster +library(fpc) + +#Install NbClust package +#install.packages("NbClust",dependencies = TRUE) + +#Loading required package: NbClust +library(NbClust) + + +#Read the dataset +data_centers <- read.table("fillouts1file.txt", header=TRUE, sep=";", na.strings="") +#data_centers <- read.table("fillouts1file.txt", header=TRUE, sep=";", na.strings="") + + +#Run the XXX for selection of the number of clusters + +clustersdata <- NbClust(data_centers, diss=NULL, distance = "euclidean", min.nc=2, max.nc=15, method = "kmeans", index = "all", alphaBeale = 0.1) + +#capture.output(clustersdata$Best.nc[1,], file = "bestnumberclusters.txt") + +#capture.output(NbClust(data_centers, diss=NULL, distance = "euclidean", min.nc=2, max.nc=15, method = "kmeans", index = "all", alphaBeale = 0.1), file = "proofclusters.txt") + +#capture.output(NbClust(data_centers, diss=NULL, distance = "euclidean", min.nc=2, max.nc=15, method = "kmeans", index = "all", alphaBeale = 0.1), file = "numclusters.txt") + +#best_num_cluster <- scan("proofclusters.txt", what = character(), quiet = TRUE) + +k.max <- as.integer(rownames(table(clustersdata$Best.nc[1,]))[which.max(apply(table(clustersdata$Best.nc[1,]),MARGIN=1,max))]) + +km.res <- kmeans(as.matrix(data_centers), centers = k.max, nstart = 25) + +best_position <- as.integer(rownames(table(clustersdata$Best.nc[1,]))[which.max(apply(table(clustersdata$Best.nc[1,]),MARGIN=1,max))]) + +# Make clustercoordenates table +#X Coordenate +start_x <- best_position + 1 +end_x <- start_x + (best_position - 1) + +cluster_pos_x <- 1 +x_pos <- c() +for (c in start_x:end_x){ + x_pos[cluster_pos_x] <- km.res$centers[c] + cluster_pos_x <- cluster_pos_x + 1 +} +#print(x_pos) + +#Y Coordenate +start_y <- end_x + 1 +end_y <- start_y + (best_position - 1) + +cluster_pos_y <- 1 +y_pos <- c() +for(cc in start_y:end_y){ + y_pos[cluster_pos_y] <- km.res$centers[cc] + cluster_pos_y <- cluster_pos_y + 1 +} +#print(y_pos) + +#Z Coordenate +start_z <- end_y + 1 +end_z <- start_z + (best_position - 1) + +cluster_pos_z <- 1 +z_pos <- c() +for(ccc in start_z:end_z){ + z_pos[cluster_pos_z] <- km.res$centers[ccc] + cluster_pos_z <- cluster_pos_z + 1 +} +#print(z_pos) + +#Create a file with clusters coordenates. Cluster coordenates are vectors x_pos, y_pos, z_pos +num_filas <- length(x_pos) +clusters_tabla <- matrix(1, nrow = num_filas, ncol = 4) #columns are column 1 number of ccluster, column 2 x-coordenates, colum 3 y-coordenates, column 4 z-coordenates + +##Add number of cluster located in column 1 +for(i in 1:num_filas){ + clusters_tabla[i,1] <- i +} + +##Add cluster x,y,z-coordenates in clusters_tabla +#x-coordenates +v_pos_x <- 1 +for(f in 1:num_filas){ + clusters_tabla[f,2] <- x_pos[v_pos_x] + v_pos_x <- v_pos_x + 1 +} + +#y-coordenates +v_pos_y <- 1 +for(ff in 1:num_filas){ + clusters_tabla[ff,3] <- y_pos[v_pos_y] + v_pos_y <- v_pos_y + 1 +} + +#z-coordenates +v_pos_z <- 1 +for(fff in 1:num_filas){ + clusters_tabla[fff,4] <- z_pos[v_pos_z] + v_pos_z <- v_pos_z + 1 +} + +#Write the head for the file which contains the number of clusters annd their coordenates +cabecera_clusterscoordenates <- paste("cluster", sep = " ") +cabecera <- c("x","y","z") + +for(i in 1:3){ + cabecera_clusterscoordenates <- paste(cabecera_clusterscoordenates, cabecera[i], sep=" ") +} +#write(cabecera_clusterscoordenates, file="/home/galaxy/galaxy/tools/proteindocking/scripts/clusterscoordenates.txt", append= TRUE) +write(cabecera_clusterscoordenates, file="clusterscoordenates.txt", append= TRUE) + +#Write rows containing number of cluster and coordenates +for(i in 1:nrow(clusters_tabla)){ + fila_completa <- paste(clusters_tabla[i,1], sep = " ") + for(j in 2:ncol(clusters_tabla)){ + fila_completa <- paste(fila_completa, clusters_tabla[i,j], sep=" ") + } + write(fila_completa, file="clusterscoordenates.txt", append= TRUE) + #write(fila_completa, file="/home/galaxy/galaxy/tools/proteindocking/scripts/clusterscoordenates.txt", append= TRUE) +} + + +#Table to see Binding Sited finded in Galaxy screen +#BS_screen <- scan("/home/galaxy/galaxy/tools/proteindocking/scripts/clusterscoordenates.txt", what = character(), quiet = TRUE) +BS_screen <- scan("clusterscoordenates.txt", what = character(), quiet = TRUE) + +BS_table <- matrix(1, nrow = nrow(clusters_tabla), ncol = ncol(clusters_tabla)) + +bs_count <- 5 +for(i in 1:nrow(clusters_tabla)){ + for(j in 1:ncol(clusters_tabla)){ + BS_table[i,j] <- BS_screen[bs_count] + bs_count <- bs_count +1 + } +} + +colnames(BS_table) <- c("Binding Site", "X", "Y", "Z") +print(BS_table) + + + + + + diff -r eda62adfc858 -r afd5b5ffc38f PLIDflow/scripts/envelopesmaker.R --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/PLIDflow/scripts/envelopesmaker.R Tue Jan 14 07:52:48 2020 -0500 @@ -0,0 +1,57 @@ +#envelopesmaker.R makes FILL_Xout.pdb files where X represents values for envelopes from 10 to 100 + +#!/usr/bin/env Rscript +args = commandArgs(trailingOnly=TRUE) + +if(length(args) < 1){ + stop("USE: Rscript envelopesmaker.R ") +} + +#Arguments definition +receptor_name <- args[1] +session_dir <- args[2] +pathLigand <- args[3] + +#recopy <- paste("/home/galaxy/galaxy/tools/proteindocking/scripts/", basename(args[1]), ".txt", sep="") +#command <- paste("cp ", args[1], " ", recopy, sep="") #18jun2018 +#system(command) #18jun2018 + +# + +recopy_2 <- scan(paste(basename(args[1]), ".txt", sep=""), what = character(), quiet = TRUE) + + +#print(paste("es lo que va a salir",recopy_2[1])) + +#Ejecute from R a python script for Running Autoligand +sizes_file <- scan("templateenvelopsizes.txt", what = character(), quiet = TRUE) + +path_cajonDesastre <- recopy_2[1] + +segment_paste <- paste("python", pathLigand, "-r", path_cajonDesastre, "-p", sep = " ") +#segment_paste <- paste("python /home/eugenia/workflowsoftware/mgltools_x86_64Linux2_1.5.6/MGLToolsPckgs/AutoDockTools/AutoLigand.py -r", path_cajonDesastre, "-p", sep = " ") + +#print(segment_paste) + +#print(paste("es lo que va a salir",recopy_2[1])) + +for(i in 1:length(sizes_file)){ +size <- sizes_file[i] + +##porcentaje <- (i/length(sizes_file))*100 + +##print(paste(paste(porcentaje, "%", sep = ""),"completed", sep = " ")) + + +# HEMOS TACHADO ESTE SYSTEM +print(paste(segment_paste,size, sep = " ")) + +# ENABLE THIS SYSTEM +#system(paste(segment_paste,size, sep = " "), intern = TRUE) +write(paste(segment_paste,size, sep = " "), file = "commands", append = TRUE) +} + +system("tac commands > rev_commands") +system("./parallel_launch.sh rev_commands 2") + + diff -r eda62adfc858 -r afd5b5ffc38f PLIDflow/scripts/glgfilemaker.R --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/PLIDflow/scripts/glgfilemaker.R Tue Jan 14 07:52:48 2020 -0500 @@ -0,0 +1,35 @@ +#glgfilemarker.R makes GLG file and map files + +#!/usr/bin/env Rscript +args = commandArgs(trailingOnly=TRUE) + +if(length(args) < 1){ + stop("USE: Rscript glgfilemaker.R ") +} + +#Arguments definition +receptor_name <- args[1] +session_dir <- args[2] + +#Running AutiGrid4 +##autogrid4 -p .gpf -l .glg & + + +recopy <- paste( basename(args[1]),".pdbqt" ,sep="") +command <- paste("cp ", args[1], " ", recopy, sep="") +#print(paste("ESTOY IMPRIMIENDO ", command)) +system(command) + +#print(recopy) + +receptor_name_gpf <- paste( basename(args[1]), ".gpf", sep="") +receptor_name_glg <- paste( basename(args[1]), ".glg", sep="") +#print(receptor_name_gpf) +elemento_concetenar <- paste( "autogrid4 -p", sep = " ") +elemento_concetenar <- paste(elemento_concetenar, receptor_name_gpf, sep = " ") +elemento_concetenar <- paste(elemento_concetenar, "-l ", receptor_name_glg, sep = " ") + +#print(elemento_concetenar) + + +system(elemento_concetenar) diff -r eda62adfc858 -r afd5b5ffc38f PLIDflow/scripts/gpffilemaker.R --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/PLIDflow/scripts/gpffilemaker.R Tue Jan 14 07:52:48 2020 -0500 @@ -0,0 +1,116 @@ +#gpffilemaker makes the GPF file + +#!/usr/bin/env Rscript +args = commandArgs(trailingOnly=TRUE) + +if(length(args) < 1){ + stop("USE: Rscript gpffilemaker.R ") +} + +#Read file containing PDB geometric center and number of points x, y ,z +#archivo_center_npts <- scan("/home/galaxy/galaxy/tools/proteindocking/scripts/pdbcenter_npts.txt", what = character(), quiet = TRUE) +archivo_center_npts <- scan("pdbcenter_npts.txt", what = character(), quiet = TRUE) + +#Read file containing receptor atom types +ver <- scan("receptor_atm_types.txt", what = character(), quiet = TRUE, na.strings = "NULLAJSKAJSFL") + + +#Arguments definition +receptor_name <- args[1] +session_dir <- args[2] +aux_receptor_name <- basename(args[1]) +#aux_receptor_name <- paste("/home/galaxy/galaxy/tools/proteindocking/scripts/", basename(args[1]), sep="") +npts_x <- archivo_center_npts[4] +npts_y <- archivo_center_npts[5] +npts_z <- archivo_center_npts[6] +gridcenter_x <- archivo_center_npts[1] +gridcenter_y <- archivo_center_npts[2] +gridcenter_z <- archivo_center_npts[3] + +#Creation of the GPF file +#Row 1 +fila_1_e1 <- paste("npts", npts_x, sep = " ") +fila_1_e2 <- paste(fila_1_e1, npts_y, sep = " ") +fila_1_e3 <- paste(fila_1_e2, npts_z, sep = " ") +fila_1 <- paste(fila_1_e3, "# num.grid points in xyz", sep = " ") + +#Row 2 +fila_2_e2 <- paste(aux_receptor_name, ".maps.fld", sep = "") +fila_2_e1 <- paste("gridfld", fila_2_e2, sep = " " ) +fila_2 <- paste(fila_2_e1, "# grid_data_file", sep = " ") + +#Row 3 +fila_3 <- paste("spacing 1.0", "# spacing(A)", sep = " ") + +#Row 4 +#fila_4 <- paste("receptor_types A C HD N NA OA S SA", "# receptor atom types", sep = " ") +cabecera_f4 <- ver[1] +vector_f4 <- c() +for(f4 in 2:length(ver)){ + cabecera_f4 <- paste(cabecera_f4, ver[f4], sep = " ") +} + +fila_4 <- paste("receptor_types", cabecera_f4, "# receptor atom types", sep = " ") +#print(fila_4) + +#Row 5 +fila_5 <- paste("ligand_types C HD OA", "# ligand atom types", sep = " ") + +#Row 6 +fila_6_e2 <- paste(aux_receptor_name, ".pdbqt", sep = "") +fila_6_e1 <- paste("receptor", fila_6_e2, sep = " ") +fila_6 <- paste(fila_6_e1, "# macromolecule", sep = " ") + +#Row 7 +fila_7_e1 <- paste("gridcenter",gridcenter_x, sep = " ") +fila_7_e2 <- paste(fila_7_e1, gridcenter_y, sep = " ") +fila_7_e3 <- paste(fila_7_e2, gridcenter_z, sep = " ") +fila_7 <- paste(fila_7_e3, "# xyz-coordinates or auto", sep = " ") + +#Row 8 +fila_8 <- paste("smooth 0.5", "# store minimum energy w/in rad(A)", sep = " ") + +#Row 9 +fila_9_e2 <- paste(aux_receptor_name, ".C.map", sep = "") +fila_9_e1 <- paste("map", fila_9_e2, sep = " ") +fila_9 <- paste(fila_9_e1, "# atom-specific affinity map", sep = " ") + +#Row 10 +fila_10_e2 <- paste(aux_receptor_name, ".HD.map", sep = "") +fila_10_e1 <- paste("map",fila_10_e2, sep = " ") +fila_10 <- paste(fila_10_e1, "# atom-specific affinity map", sep = " ") + +#Row 11 +fila_11_e2 <- paste(aux_receptor_name, ".OA.map", sep = "") +fila_11_e1 <- paste("map", fila_11_e2, sep = " ") +fila_11 <- paste(fila_11_e1, "# atom-specific affinity map", sep = " ") + +#Row 12 +fila_12_e2 <- paste(aux_receptor_name, ".e.map", sep = "") +fila_12_e1 <- paste("elecmap", fila_12_e2, sep = " ") +fila_12 <- paste(fila_12_e1, "# electrostatic potential map", sep = " ") + +#Row 13 +fila_13_e2 <- paste(aux_receptor_name, ".d.map", sep = "") +fila_13_e1 <- paste("dsolvmap", fila_13_e2, sep = " ") +fila_13 <- paste(fila_13_e1, "# desolvation potential map", sep = " ") + +#Row 14 +fila_14 <- paste("dielectric -0.1465", "# <0, AD4 distance-dep.diel;>0, constant", sep = " ") + +#Paste all rows with a line jump for separation +filas <- c(fila_1, fila_2, fila_3, fila_4, fila_5, fila_6, fila_7, fila_8, fila_9, fila_10, fila_11, fila_12, fila_13, fila_14) + +datos<- c() +for(i in 1:14){ +datos <- paste(c(datos, filas[i])) +} + +#nombre_final <- paste("/home/galaxy/galaxy/tools/proteindocking/scripts/", basename(args[1]), ".gpf", sep="") +nombre_final <- paste(basename(args[1]), ".gpf", sep="") + +write(datos, file=nombre_final, append = FALSE) + +#write(basename(args[1]), file= paste("/home/galaxy/galaxy/tools/proteindocking/scripts/", basename(args[1]), ".txt", sep="")) #parte añadida 18jun2018 +write(basename(args[1]), file= paste(basename(args[1]), ".txt", sep="")) #parte añadida 18jun2018 + diff -r eda62adfc858 -r afd5b5ffc38f PLIDflow/scripts/includeAtom3.sh --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/PLIDflow/scripts/includeAtom3.sh Tue Jan 14 07:52:48 2020 -0500 @@ -0,0 +1,139 @@ + +if [ $# != 2 ]; then + echo "***ERROR*** Use: $0 " + exit -1 +fi + + +PQR=$2 +TABLE=$1 + +grep -v "REMARK" $PQR > $PQR.temp + +#awk ' +#{ +# if(length($5 > 1)) print $5 +#} ' $PQR.temp + + + + +awk ' + + +FNR==NR{ + equivalence[$1] = $2 + next +} + +FNR!=NR{ + if(substr($3,1,1) == "H"){ + + if(length($3) > 1){ + + + print $0, "H" + } + }else{ + + print $0, equivalence[$3]; + + + + } + +} +' $TABLE $PQR.temp | sed 's/ \+/ /g' > $PQR.temp.bad + +awk ' +{ + x=$10; + y=$11; + z=$12; + $10=""; + $11=""; + $12=""; + if(substr($0,1,3) != "TER" && substr($0,1,3) != "END") + printf("%s %.2f %.2f %s\n", $0, x, y, z) + else + print $0 +} +' $PQR.temp.bad > $PQR.temp.format + + +awk ' + +NR==1{ x1=0; x2=0; x3=0; x4=0; x5=0; x6=0; x7=0; x8=0; x9=0; x10=0; x11=0; x12=0; x13=0; } + +FNR==NR{ + if($1 == "ATOM" || $1 == "HETATM"){ + if(length($1) > x1) x1 = length($1); + if(length($2) > x2) x2 = length($2); + if(length($3) > x3) x3 = length($3); + if(length($4) > x4) x4 = length($4); + if(length($5) > x5) x5 = length($5); + if(length($6) > x6) x6 = length($6); + if(length($7) > x7) x7 = length($7); + if(length($8) > x8) x8 = length($8); + if(length($9) > x9) x9 = length($9); + if(length($10) > x10) x10 = length($10); + if(length($11) > x11) x11 = length($11); + if(length($12) > x12) x12 = length($12); + } + +} + + +FNR!=NR{ + + + #total=length($1)+3+x1+2+x3+1+x4+1+x5+6+x7+1+x8+1+x9+1+x10+1+x11+2+x11; + total=0; + + printf("%s", $1); total+=length($1); + if($1=="ATOM") for(i=0; i<7-length($2); i++) { printf(" "); total+=1; } + if($1=="HETATM") for(i=0; i<5-length($2); i++) { printf(" "); total+=1; } + printf("%s", $2); total+=length($2); + for(i=0; i<2; i++){ printf(" "); total+=1} + printf("%s", $3); total+=length($3); + for(i=0; i<4-length($3); i++){ printf(" "); total+=1;} + printf("%s", $4); total+=length($4); + for(i=0; i<1+x4-length($4); i++){ printf(" ");total+=1;} + printf("%s", $5); total+=length($5); + for(i=0; i<3-length($5); i++){ printf(" ");total+=1;} + printf("%s", $6); total+=length($6); + for(i=0; i<(13-length($7)-length($6)); i++){ printf(" "); total+=1;} + printf("%s", $7); total+=length($7); + for(i=0; i<8-length($8); i++){ printf(" ");total+=1;} + printf("%s", $8); total+=length($8); + for(i=0; i<8-length($9); i++){ printf(" ");total+=1;} + printf("%s", $9); total+=length($9); + for(i=0; i<6-length($10); i++){ printf(" ");total+=1;} + printf("%s", $10); total+=length($10); + for(i=0; i<5-length($11); i++){ printf(" ");total+=1;} + printf("%s", $11); total+=length($11); + for(i=0; i<79-total; i++) printf(" "); + printf("%s", $12); total+=length($12); + if(length($12) < x12){ + for(i=0; i [max cores]" + echo "" + echo " MANDATORY : a text file containing one command per line" + echo " OPTIONAL [max cores] : number of cores to use. Default is available cores minus one" + echo "" + exit -1 +fi + +input=$1 +cores=$(grep -c ^processor /proc/cpuinfo) +cores=`expr $cores - 1` +current_jobs=0 +pidArray=() +jobsArray=() +totalJobs=0 +executedJobs=0 +finishedJobs=0 + +if [ $# -eq 2 ]; then + cores=$2 +fi + +echo "Using $cores cores" + + +#initialize +for ((i=0 ; i < $cores ; i++)) +do + pidArray[$i]=-1 +done + +# read execution guide and launch jobs +while IFS= read -r var +do + + jobsArray[$totalJobs]=$var + #echo "${jobsArray[$totalJobs]}" + totalJobs=`expr $totalJobs + 1` + +done < "$input" + + +# control them and only launch as many as specified +while [[ $executedJobs -lt $totalJobs || $finishedJobs -lt $totalJobs ]]; do + + # Execute job + + if [[ $current_jobs -lt $cores ]]; then + + ${jobsArray[$executedJobs]} & + pid=$! + for ((i=0 ; i < $cores ; i++)) + do + + + if [[ ${pidArray[$i]} -eq -1 && $executedJobs -lt $totalJobs ]]; then + pidArray[$i]=$pid + current_jobs=`expr $current_jobs + 1` + echo "PID: $pid JOBS: $current_jobs LAUNCHING: ${jobsArray[$executedJobs]}" + executedJobs=`expr $executedJobs + 1` + break + fi + done + + + fi + + for ((i=0 ; i < $cores ; i++)) + do + pid=${pidArray[$i]} + if [[ $pid -ne -1 ]]; then + + ps -p $pid > /dev/null + if [[ $? == 1 ]]; then + current_jobs=`expr $current_jobs - 1` + finishedJobs=`expr $finishedJobs + 1` + echo "PID: $pid finished! Completed: $finishedJobs from total: $totalJobs" + pidArray[$i]=-1 + fi + + fi + done + + sleep .01 + +done + + +#deactivate + + +#for job in `jobs -p` +#do + #echo $job +# wait $job +#done diff -r eda62adfc858 -r afd5b5ffc38f PLIDflow/scripts/pdbcenter_npts_finder.R --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/PLIDflow/scripts/pdbcenter_npts_finder.R Tue Jan 14 07:52:48 2020 -0500 @@ -0,0 +1,84 @@ +#pdbcenter_npts_finder.R calculates the geometric center of a PDB file + +#!/usr/bin/env Rscript +args = commandArgs(trailingOnly=TRUE) + +if(length(args) < 1){ + stop("USE: Rscript pdbcenter_npts_finder.R ") +} + +#Arguments definition +receptor_name <- args[1] +session_dir <- args[2] + +#Read PDB file +archivo <- scan(args[1], what = character(), quiet = TRUE) + +#Make a table where positions of carbon (C) atoms and their x, y, z coordenates will be placed +salto <- 0 +for(i in 1:(length(archivo)-2)){ + if(archivo[i] == "ATOM" && archivo[i+2] == "C"){ + salto <- salto + 1 + } +} +tablaC <- matrix(1, nrow = salto, ncol = 4) + +#Header. Note: first column: C atom position (will be filled in when the number of C will be known) +#Row labels +colnames(tablaC) <- c("C Position","X", "Y", "z") +rownames(tablaC) <- 1:salto + +#Fill in tablaC with x, y,z coordenates of the C atoms as numeric +salto <- 0 +posicionC <- c() +for(i in 1:(length(archivo)-2)){ + if(archivo[i] == "ATOM" && archivo[i+2] == "C"){ + salto <- salto + 1 + posicionC <- c(posicionC, archivo[i+1]) + + tablaC[salto,2] <- as.numeric(archivo[i+6]) + tablaC[salto,3] <- as.numeric(archivo[i+7]) + tablaC[salto,4] <- as.numeric(archivo[i+8]) + } +} + +#Add C atom positions in the column 1 +for(i in 1:salto){ + tablaC[i,1] <- as.numeric(posicionC[i]) +} + +#Geometric center calculation as grid center x, y, z to be introduced in the GPF file +pto_x_medio <- (max(tablaC[,2]) + min(tablaC[,2]))/2 +pto_y_medio <- (max(tablaC[,3]) + min(tablaC[,3]))/2 +pto_z_medio <- (max(tablaC[,4]) + min(tablaC[,4]))/2 + +pto_x_medio_r <- round(pto_x_medio,digits=3) +pto_y_medio_r <- round(pto_y_medio,digits=3) +pto_z_medio_r <- round(pto_z_medio,digits=3) + +#print(paste(pto_x_medio_r, pto_y_medio_r, pto_z_medio_r, sep = ";")) + +#Calculate distances in each coordenate to have de number of points (npts) x, y, z to be introduced in the GPF file +eu_x <- max(tablaC[,2])-min(tablaC[,2]) +eu_y <- max(tablaC[,3])-min(tablaC[,3]) +eu_z <- max(tablaC[,4])-min(tablaC[,4]) + +eu_x_r <- round(eu_x,digits=0) +eu_y_r <- round(eu_y,digits=0) +eu_z_r <- round(eu_z,digits=0) + +#print(paste(eu_x, eu_y, eu_z, sep = ";")) +#print(paste(eu_x_r, eu_y_r, eu_z_r, sep = ";")) + +if(eu_x > 126 || eu_y > 126 || eu_x > 126){ + print("At least one dimension in number of points is out of range (>126) according AutoDock software") + break +} + +#Write PDB geometric center and eu_x_r, eu_y_r, eu_z_r in a file +#write(paste(pto_x_medio_r, pto_y_medio_r, pto_z_medio_r, eu_x_r, eu_y_r, eu_z_r,sep= "\n"), file = "/home/galaxy/galaxy/tools/proteindocking/scripts/pdbcenter_npts.txt") +write(paste(pto_x_medio_r, pto_y_medio_r, pto_z_medio_r, eu_x_r, eu_y_r, eu_z_r,sep= "\n"), file = "pdbcenter_npts.txt") + + + + diff -r eda62adfc858 -r afd5b5ffc38f PLIDflow/scripts/pdbqtcorrector.R --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/PLIDflow/scripts/pdbqtcorrector.R Tue Jan 14 07:52:48 2020 -0500 @@ -0,0 +1,128 @@ +#pdbqtcorrector.R corrests the out PDBQT file from AutoDockTools prepare receptor + +#!/usr/bin/env Rscript +args = commandArgs(trailingOnly=TRUE) + +if(length(args) < 1){ + stop("USE: Rscript pdbqtcorrector.R ") +} + +#Argument definition +receptor_name <- args[1] + +#Scan file +original_file <- scan(args[1], what = character(), quiet = TRUE, na.strings = "NULLAJSKAJSFL") + +#Calculate first root word and "TER" +for(e in 1:length(original_file)){ + if(original_file[e] == "ATOM" || original_file[e] == "HETATM" || original_file[e] == "TER"){ + k <- e + break + } +} + +#Calculate the row number for table which conteins aligned x,y,z coordenates +counter <- 0 +for(c in e:length(original_file)){ + if(original_file[c] == "ATOM" || original_file[c] == "HETATM" || original_file[c] == "TER"){ + counter <- counter + 1 + } +} + +#Table to be fills in named tabla_ordenados +tabla_ordenados <- matrix(1, nrow = (counter), ncol = 13) + +#Calculate TER times and make a vector +ele_ter_vector <- 1 +ter_vector <- c() +k_position <- c() +for(o in 1:(length(original_file))){ + if(original_file[o] =="TER"){ + k_position <- c(k_position, o) + for(g in o:(o+4)){ + ter_vector <- c(ter_vector,original_file[g] ) + } + + } +} + +#Fill in the tabla_ordenados with values scaned until counter-1 since last row (ter) has diferent length and this could give you back an error +for(i in 1:(counter-1)){ + for(j in 1:13){ + tabla_ordenados[i,j] <- original_file[k] + if(tabla_ordenados[i,13]=="ATOM" || tabla_ordenados[i,13]== "HETATM"|| tabla_ordenados[i,13]=="TER"){ + corte <- c() + for(v in 4:12){ + corte <- c(corte,tabla_ordenados[i,v]) + } + coo_corte <- 1 + tabla_ordenados[i,4] <- "" + for(m in 5:13){ + tabla_ordenados[i,m] <- corte[coo_corte] + coo_corte <- coo_corte + 1 + } + k <- k-1 + } + k <- k + 1 + } + if(tabla_ordenados[i,1]=="TER"){ + k <- k - 8 + } +} + + +#Fill in TER row until last one +star_ter <- 2 +mmm <- 1 +for(ii in 1:counter){ + if(tabla_ordenados[ii,1]=="TER"){ + k <- k_position[mmm] + 4 + mmm <- mmm + 1 + y <- 2 + for(l in star_ter:(star_ter+3)){ + if(y%%3==0 && y!=6){ + tabla_ordenados[ii,y] <- "" + y <- y + 1 + tabla_ordenados[ii,y] <- ter_vector[l] + } + tabla_ordenados[ii,y] <- ter_vector[l] + y <- y +1 + } + star_ter <- star_ter + 5 + for(b in 7:13){ + tabla_ordenados[ii,b] <- "" + } + } +} + +#Fill in last row with TER row values +last_ter <- length(ter_vector)-4 +for(jj in 1:6){ + tabla_ordenados[counter,jj] <- ter_vector[last_ter] + if(jj%%3==0 && jj !=6){ + tabla_ordenados[counter, jj] <- "" + last_ter <- last_ter - 1 + } + last_ter <- last_ter + 1 +} +for(jj in 7:13){ + tabla_ordenados[counter, jj] <- "" +} + +#View(tabla_ordenados) + +#Write oredered table in a PDBQT file +for(xi in 1:nrow(tabla_ordenados)){ + cabecera <- tabla_ordenados[xi,1] + for(xj in 2:13){ + cabecera <- paste(cabecera, tabla_ordenados[xi,xj], sep = " ") + } + write(cabecera, file = args[2], append = TRUE) +} + + + + + + + diff -r eda62adfc858 -r afd5b5ffc38f PLIDflow/scripts/pdbqtcorrector2step.R --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/PLIDflow/scripts/pdbqtcorrector2step.R Tue Jan 14 07:52:48 2020 -0500 @@ -0,0 +1,1127 @@ +#pdbqtcorrector2step.R prepare the out PDBQT file from pdbqtcorrector.R to run Vina + +#!/usr/bin/env Rscript +args = commandArgs(trailingOnly=TRUE) + +if(length(args) < 2){ + stop("USE: Rscript pdbqtcorrector.R ") +} + +#Argument definition +receptor_name <- args[1] +receptor_types_file_out <- args[3] + +#Scan file +original_file <- scan(args[1], what = character(), quiet = TRUE, na.strings = "NULLAJSKAJSFL") + +#13FEB2019 +#In order to avoid col 1 and col 2 fussion, split by characters all words. Then paste characters fron col 1 in a word, and those for col 2, rest columns change by " " + +buscador <- c() +for(of in 1:length(original_file)){ + buscador <- c(buscador,strsplit(original_file[of], "")) +} + +fix_row_1 <- 0 +for(off in 1:length(buscador)){ + if(buscador[[off]][1] == "A"){ + if(length(buscador[[off]]) >= 3){ + if(buscador[[off]][2] == "T"){ + if(buscador[[off]][3] == "O"){ + if(buscador[[off]][4] == "M"){ + fix_row_1 <- fix_row_1 + 1 + buscador[[off]][1] <- paste(buscador[[off]][1], buscador[[off]][2], buscador[[off]][3], buscador[[off]][4], sep = "") + if(length(buscador[[off]]) == 4){ + for(off1 in 2:length(buscador[[off]])){ + buscador[[off]][off1] <- "" + } + for(qu in 1:(length(buscador[[off]])-1)){ + buscador[[off]] <- buscador[[off]][-length(buscador[[off]])] + + + } + } + if(length(buscador[[off]]) > 4){ + var_aux <- c() + for(off1 in 5:length(buscador[[off]])){ + var_aux <- c(var_aux, paste(buscador[[off]][off1])) + } + termino <- var_aux[1] + for(ofu in 2:length(var_aux)){ + termino <- paste(termino, var_aux[ofu], sep = "") + } + + buscador[[off]][2] <- termino + + for(off1 in 3:length(buscador[[off]])){ + buscador[[off]][off1] <- "" + } + for(qu in 2:(length(buscador[[off]])-1)){ + buscador[[off]] <- buscador[[off]][-length(buscador[[off]])] + + + } + } + } + } + } + } + } +} +#print(fix_row_1) + + +fix_row_2 <- 0 +for(off in 1:length(buscador)){ + if(buscador[[off]][1] == "H"){ + if(length(buscador[[off]]) >= 3){ + if(buscador[[off]][2] == "E"){ + if(buscador[[off]][3] == "T"){ + if(buscador[[off]][4] == "A"){ + if(buscador[[off]][5] == "T"){ + if(buscador[[off]][6] == "M"){ + fix_row_2 <- fix_row_2 + 1 + buscador[[off]][1] <- paste(buscador[[off]][1], buscador[[off]][2], buscador[[off]][3], buscador[[off]][4], buscador[[off]][5], buscador[[off]][6], sep = "") + if(length(buscador[[off]]) == 6){ + for(off1 in 2:length(buscador[[off]])){ + buscador[[off]][off1] <- "" + } + for(qu in 1:(length(buscador[[off]])-1)){ + buscador[[off]] <- buscador[[off]][-length(buscador[[off]])] + + + } + } + if(length(buscador[[off]]) > 6){ + var_aux <- c() + for(off1 in 7:length(buscador[[off]])){ + var_aux <- c(var_aux, paste(buscador[[off]][off1])) + } + termino <- var_aux[1] + for(ofu in 2:length(var_aux)){ + termino <- paste(termino, var_aux[ofu], sep = "") + } + + buscador[[off]][2] <- termino + + for(off1 in 3:length(buscador[[off]])){ + buscador[[off]][off1] <- "" + } + + for(qu in 2:(length(buscador[[off]])-1)){ + buscador[[off]] <- buscador[[off]][-length(buscador[[off]])] + } + } + } + } + } + } + } + } + } +} +#print(fix_row_2) + +fix_row_3 <- 0 +for(off in 1:length(buscador)){ + if(buscador[[off]][1] == "T"){ + if(length(buscador[[off]]) >= 3){ + if(buscador[[off]][2] == "E"){ + if(buscador[[off]][3] == "R"){ + fix_row_3 <- fix_row_3 + 1 + } + } + } + } +} +#print(fix_row_3) + +final_row <- fix_row_1 + fix_row_2 + fix_row_3 + +#counter <- final_row +#print(counter) + +# At this point roots "ATOM", "HETATM" and "TER" are isolated in case fusion. This step component differrent for those are pasted +for(off in 1:length(buscador)){ + if(as.character(buscador[[off]][1]) != "ATOM" && buscador[[off]][1] != "HETATM"){ + #print(off) + pegado <- buscador[[off]][1] + for(fus in 2:length(buscador[[off]])){ + if(length(buscador[[off]]) > 1){ + pegado <- paste(pegado, buscador[[off]][fus], sep = "") + buscador[[off]][1] <- pegado + } + } + if(length(buscador[[off]]) > 1){ + for(qu in 1:(length(buscador[[off]])-1)){ + buscador[[off]] <- buscador[[off]][-length(buscador[[off]])] + } + } + } +} + + +# strsplit applied to the original_file return a list format. In this steps it is for changing list for vector format for buscador varible + +total_original_file <- c() +for(si in 1:length(buscador)){ + total_original_file <- c(total_original_file, buscador[[si]]) +} +#13feb2019 + +original_file <- total_original_file + +#Starts pdbqtcorrector + +#Calculate first root word and "TER" +for(e in 1:length(original_file)){ + if(original_file[e] == "ATOM" || original_file[e] == "HETATM" || original_file[e] == "TER"){ + k <- e + break + } +} + +#Calculate the row number for table which conteins aligned x,y,z coordenates +counter <- 0 +for(c in e:length(original_file)){ + if(original_file[c] == "ATOM" || original_file[c] == "HETATM" || original_file[c] == "TER"){ + counter <- counter + 1 + } +} + +#Table to be fills in named tabla_ordenados +tabla_ordenados <- matrix(1, nrow = (counter), ncol = 13) + +#Calculate TER times and make a vector +ele_ter_vector <- 1 +ter_vector <- c() +k_position <- c() +#ter_pos <- 0 #21sep2018 +for(o in 1:(length(original_file))){ + if(original_file[o] =="TER"){ + k_position <- c(k_position, o) + ter_pos <- o #21sep + for(g in o:(o+4)){ + ter_vector <- c(ter_vector,original_file[g] ) + } + + } +} + + +#Fill in the tabla_ordenados with values scaned until counter-1 since last row (ter) has diferent length and this could give you back an error +for(i in 1:(counter-1)){ + for(j in 1:13){ + tabla_ordenados[i,j] <- original_file[k] + if(tabla_ordenados[i,13]=="ATOM" || tabla_ordenados[i,13]== "HETATM"|| tabla_ordenados[i,13]=="TER"){ + corte <- c() + for(v in 4:12){ + corte <- c(corte,tabla_ordenados[i,v]) + } + coo_corte <- 1 + tabla_ordenados[i,4] <- "" + for(m in 5:13){ + tabla_ordenados[i,m] <- corte[coo_corte] + coo_corte <- coo_corte + 1 + } + k <- k-1 + } + # #################02julio2019################################ + + if(tabla_ordenados[i,12]=="ATOM" || tabla_ordenados[i,12]== "HETATM"|| tabla_ordenados[i,12]=="TER"){ + + + #print("ENTERING") + #stop() + + corte_2 <- c() + for(iv in 5:11){ + corte_2 <- c(corte_2,tabla_ordenados[i,iv]) + } + + #print(corte_2) + + first_number <- substr(corte_2[5], 1, 4) + second_number <- substr(corte_2[5], 5, 1000) + + + + coo_corte_2 <- 1 + tabla_ordenados[i,5] <- "" + tabla_ordenados[i,12] <- "" + tabla_ordenados[i,13] <- "" + for(im in 6:13){ + tabla_ordenados[i,im] <- corte_2[coo_corte_2] + coo_corte_2 <- coo_corte_2 + 1 + } + k <- k-2 + + tabla_ordenados[i,12] <- corte_2[6] + tabla_ordenados[i,10] <- first_number + tabla_ordenados[i,11] <- second_number + + + + + } + + + + #################02julio2019################################ + + + k <- k + 1 + } + if(tabla_ordenados[i,1]=="TER"){ + k <- k - 8 + } +} + +#Fill in TER row until last one +star_ter <- 2 +mmm <- 1 +for(ii in 1:counter){ + if(tabla_ordenados[ii,1]=="TER"){ + k <- k_position[mmm] + 4 + mmm <- mmm + 1 + y <- 2 + for(l in star_ter:(star_ter+3)){ + if(y%%3==0 && y!=6){ + tabla_ordenados[ii,y] <- "" + y <- y + 1 + tabla_ordenados[ii,y] <- ter_vector[l] + } + tabla_ordenados[ii,y] <- ter_vector[l] + y <- y +1 + } + star_ter <- star_ter + 5 + for(b in 7:13){ + tabla_ordenados[ii,b] <- "" + } + } +} + +##Fill if last row is not TER root +if(ter_pos < (length(original_file)-14)){ + tpnt <- 0 + ntn <- length(original_file) - 12 + for(jnt in 1:13){ + tabla_ordenados[nrow(tabla_ordenados),jnt] <- original_file[ntn] + + ntn <- ntn + 1 + } +} + +##Fill in last row with TER row values ## +#ajustcel4 <-0 +if(ter_pos > (length(original_file)-14)){ + for(rtv in 1:length(ter_vector)){ + ajustcel4 <- rtv #14nov2018 + if(is.na(ter_vector[rtv])){ + ajustcel4 <- rtv - 1 + } + } + + ter_vector_numeric <- strsplit(ter_vector[ajustcel4], "") + + last_ter <- length(ter_vector)-4 + if(length(ter_vector_numeric[[1]]) != 1){ + if(length(ter_vector) < 5){ + + for(jj in 1:6){ + tabla_ordenados[counter,jj] <- ter_vector[last_ter] + + if(jj%%3==0 && jj !=6 || jj == 4){ #he incluido el jj == 4 + tabla_ordenados[counter, jj] <- "" + last_ter <- last_ter - 1 + } + last_ter <- last_ter + 1 + } + for(jj in 7:13){ + tabla_ordenados[counter, jj] <- "" + } + } + + if(length(ter_vector) >= 5){ + for(jj in 1:7){ + tabla_ordenados[counter,jj] <- ter_vector[last_ter] + if(jj%%3==0 && jj !=6){ #he incluido el jj == 4 + tabla_ordenados[counter, jj] <- "" + last_ter <- last_ter -1 + } + last_ter <- last_ter + 1 + } + for(jj in 8:13){ + tabla_ordenados[counter, jj] <- "" + } + } + } + + if(length(ter_vector_numeric[[1]]) == 1){ + if(length(ter_vector) <= 5){ + + for(jj in 1:6){ + tabla_ordenados[counter,jj] <- ter_vector[last_ter] + + if(jj%%3==0 && jj !=6 ){ #he incluido el jj == 4 + tabla_ordenados[counter, jj] <- "" + last_ter <- last_ter - 1 + } + last_ter <- last_ter + 1 + } + for(jj in 7:13){ + tabla_ordenados[counter, jj] <- "" + } + } + + if(length(ter_vector) > 5){ + for(jj in 1:7){ + tabla_ordenados[counter,jj] <- ter_vector[last_ter] + if(jj%%3==0 && jj !=6){ #he incluido el jj == 4 + tabla_ordenados[counter, jj] <- "" + last_ter <- last_ter -1 + } + last_ter <- last_ter + 1 + } + for(jj in 8:13){ + tabla_ordenados[counter, jj] <- "" + } + } + } + +} + + +#View(tabla_ordenados) + +#19octubre2018 + +#listacol11 <- matrix(0, nrow = nrow(tabla_ordenados), ncol = 1) +twopoint <- c() +for(dc11 in 1:nrow(tabla_ordenados)){ + listacol11 <-strsplit(tabla_ordenados[dc11,11], "") + + if(length(listacol11[[1]]) != 0){ + num_poin <- 0 + for(findpoint in 1:length(listacol11[[1]])){ + if(listacol11[[1]][findpoint] == "."){ + num_poin <- num_poin + 1 + } + } + if(num_poin == 2){ + twopoint <- c(twopoint, dc11) + unopto0 <- listacol11[[1]][1] + dospto0 <- listacol11[[1]][5] + for(div1pto in 2:4){ + unopto0 <- paste(unopto0, listacol11[[1]][div1pto], sep = "") + } + for(div2pto in 6:length(listacol11[[1]])){ + dospto0 <- paste(dospto0, listacol11[[1]][div2pto], sep = "") + } + #19oct2018 Voy a guardar cada fila en un vector para luego pegarlo + vec_guarfilas <- c() + for(vgf in 1:10){ + + if(tabla_ordenados[dc11,vgf] != ""){ + vec_guarfilas <- c(vec_guarfilas, tabla_ordenados[dc11,vgf]) + } + } + vec_guarfilas[10] <- unopto0 + vec_guarfilas[11] <- dospto0 + vec_guarfilas[12] <- tabla_ordenados[dc11,12] + vec_guarfilas[13] <- tabla_ordenados[dc11,13] + + #print(vec_guarfilas) + for(mvc in 1:13){ + tabla_ordenados[dc11,mvc] <- vec_guarfilas[mvc] + } + + } + } +} + +#View(tabla_ordenados) +#acaba 19octubre2018 + + + +#Make a table containing for each cell the number of characters for each for the tabla_ordenados +tabla_ordenados_numcarac <- matrix(1, nrow = nrow(tabla_ordenados), ncol = ncol(tabla_ordenados)) + +for(i in 1:nrow(tabla_ordenados)){ + for(j in 1:ncol(tabla_ordenados)){ + caracteres <- strsplit(tabla_ordenados[i,j], "") + num_carac <- 0 + # if(tabla_ordenados[i,j] == ""){ + # num_carac <- "" + # } + #if(tabla_ordenados[i,j] != ""){ + for(k in 1:length(caracteres[[1]])){ + num_carac <- num_carac + 1 + } + tabla_ordenados_numcarac[i,j] <- num_carac + #} + } +} +#View(tabla_ordenados_numcarac) #27mar2019 + +#################03julio2019###################3 ## + +for(i in 1:nrow(tabla_ordenados)){ + + if(tabla_ordenados_numcarac[i,4] == 2 && tabla_ordenados_numcarac[i,5] == 3){ + cambio_posicion5 <- tabla_ordenados[i,5] + tabla_ordenados[i,5] <- "" + tabla_ordenados_numcarac[i,5] <- 2 + tabla_ordenados[i,4] <- cambio_posicion5 + tabla_ordenados_numcarac[i,4] <- 3 + } + } + +for(i in 1:nrow(tabla_ordenados)){ + if(tabla_ordenados_numcarac[i,5] == 2 && tabla_ordenados_numcarac[i,6] == 5){ + Aaposicion5 <- substr(tabla_ordenados[i,6], 1, 1) + cambio_posicion5 <- substr(tabla_ordenados[i,6], 2, 5) + tabla_ordenados[i,5] <- Aaposicion5 + tabla_ordenados_numcarac[i,5] <- 1 + tabla_ordenados[i,6] <- cambio_posicion5 + tabla_ordenados_numcarac[i,6] <- 4 + } +} + +for(i in 1:nrow(tabla_ordenados)){ + if(tabla_ordenados[i, 3] < 6 && tabla_ordenados[i, 4] == ""){ + tabla_ordenados[i, 4] <- "XX" + } +} + +#################03julio2019###################3 ## + +# &&&&& 03sep2019 &&&&&&&&&&&& +if(tabla_ordenados_numcarac[counter,5] >= 5){ + ter_5_col <- substr(tabla_ordenados[counter, 5], 1, 1) + ter_6_col <- substr(tabla_ordenados[counter, 5], 2, 1000) + + + tabla_ordenados[counter, 5] <- ter_5_col + tabla_ordenados[counter, 6] <- ter_6_col +} + +# &&&&& 03sep2019 &&&&&&&&&&&& + + +####····̣# &&&&& 30oct2019 &&&&&&&&&&&& +for(ac3 in 1:counter){ + if(tabla_ordenados_numcarac[ac3,3] >= 7){ + ter_3_col <- substr(tabla_ordenados[ac3, 3], 1, 4) + ter_4_col <- substr(tabla_ordenados[ac3, 3], 5, 1000) + + + tabla_ordenados[ac3, 3] <- ter_3_col + tabla_ordenados[ac3, 4] <- ter_4_col + tabla_ordenados_numcarac[ac3, 3] <- 4 + tabla_ordenados_numcarac[ac3, 4] <- 3 +} + +} + +####····̣# &&&&& 30oct2019 &&&&&&&&&&&& + + + + + +#:;:;:;:;:;:;:;:;________09septiembre2019. Remove line with "Na" in column 13 in tabla_ordenados and tabla_ordenados_numcarac + +# quitar_fila <- 0 +# for(ena in 1:counter){ +# if(tabla_ordenados[ena,13] == "Na"){ +# print(ena) +# tabla_ordenados_numcarac <- tabla_ordenados_numcarac[-ena,] +# ena <- ena - 1 +# quitar_fila <- quitar_fila + 1 +# counter <- counter - quitar_fila +# +# } +# } +# +# tabla_ordenados <- subset(tabla_ordenados, tabla_ordenados[,13] != "Na") + +#:;:;:;:;:;:;:;:;________09septiembre2019 + +#View(tabla_ordenados) +#View(tabla_ordenados_numcarac) + + + + +#Fit spaces for write() +#Fit spaces for write() +#Pairwise 1col-2col con 1col == "ATOM" + +for(i in 1:nrow(tabla_ordenados)){ + linea <- c() + if(tabla_ordenados_numcarac[i,1] == 4){ + num_espacios <- 6 + ajuste <- 0 + for(a in 1:(tabla_ordenados_numcarac[i,2])){ + if(a != tabla_ordenados_numcarac[i,2]){ + ajuste <- ajuste + 1 + } + if(a == tabla_ordenados_numcarac[i,2]){ + espacios <- rep(" ", num_espacios-ajuste) + linea <- c(espacios, tabla_ordenados[i,2]) + break + } + } + } + + #1col == HETATM INI + if(tabla_ordenados_numcarac[i,1] == 6){ + num_espacios <- 4 + ajuste <- 0 + for(a in 1:(tabla_ordenados_numcarac[i,2])){ + if(a != tabla_ordenados_numcarac[i,2]){ + ajuste <- ajuste + 1 + } + if(a == tabla_ordenados_numcarac[i,2]){ + espacios <- rep(" ", num_espacios-ajuste) + linea <- c(espacios, tabla_ordenados[i,2]) + + ###21feb2019 + if(tabla_ordenados_numcarac[i,2] == 5){ + espacios <- rep(" ", (num_espacios-ajuste) + 1) + linea <- c(espacios, tabla_ordenados[i,2]) + } + ###21feb2019 + + break + } + } + } + #1col == HETATM FIN + + ##1col == TER INICIO + if(tabla_ordenados_numcarac[i,1] == 3){ + num_espacios <- 7 + ajuste <- 0 + for(a in 1:(tabla_ordenados_numcarac[i,2])){ + if(a != tabla_ordenados_numcarac[i,2]){ + ajuste <- ajuste + 1 + espacios <- rep(" ", num_espacios-ajuste) + } + if(a == tabla_ordenados_numcarac[i,2]){ + espacios <- rep(" ", num_espacios-ajuste) + linea <- c(espacios, tabla_ordenados[i,2]) + break + } + } + } + ##1col == TER FIN + + ##Pairwise 2col-3col + linea2 <- c() + for(b in 1:(tabla_ordenados_numcarac[i,3])){ + if(b < 4){ + espacios2 <- rep(" ", 2) + } + if(b >= 4){ + if(tabla_ordenados[i,4] == ""){ + espacios2 <- rep(" ", 2) + } + + if(tabla_ordenados[i,4]!= ""){ + espacios2 <- rep(" ", 1) + } + } + } + + if(tabla_ordenados_numcarac[i,3] >= 8){ + e_espacios2 <- length(espacios2)-1 + espacios2 <- rep(" ",e_espacios2) + + + } + + linea2 <- c(linea, espacios2, tabla_ordenados[i,3]) + + ###21feb2019 + if(tabla_ordenados_numcarac[i,1] == 6 && tabla_ordenados_numcarac[i,2] == 5){ + espacios2 <- espacios2[-length(espacios2)] + linea2 <- c(linea, espacios2, tabla_ordenados[i,3]) + } + ###21feb2019 + + ###Pairwise 3col-4col + linea3 <- c() + + for(c in 1:(tabla_ordenados_numcarac[i,4])){ + + #28nov + if(c == 2){ + if(tabla_ordenados_numcarac[i,1] == 6 && tabla_ordenados_numcarac[i,3] == 1){ + espacios3 <- rep(" ", 2) + } + if(tabla_ordenados_numcarac[i,1] == 6 && tabla_ordenados_numcarac[i,3] == 2){ + espacios3 <- rep(" ", 1) + } + if(tabla_ordenados_numcarac[i,1] == 6 && tabla_ordenados_numcarac[i,3] == 2 && tabla_ordenados_numcarac[i,5] == 1){ + espacios3 <- rep(" ", 3) + } + + #########21junio2019 + + if(tabla_ordenados_numcarac[i,1] == 4 && tabla_ordenados_numcarac[i,3] == 1 && tabla_ordenados_numcarac[i,6] == 5){ + espacios3 <- rep(" ", 2) + } + if(tabla_ordenados_numcarac[i,1] == 4 && tabla_ordenados_numcarac[i,3] == 2 && tabla_ordenados_numcarac[i,6] == 5){ + espacios3 <- rep(" ", 1) + } + + ########21junio2019 + + + + + } + #28nov. Hace falta corregir para el resto de HETATM + + + if(c == 3){ + if(b == 1){ + espacios3 <- rep(" ", 3) + } + if(b == 2){ + espacios3 <- rep(" ", 2) + } + if(b >= 3){ + espacios3 <- rep(" ", 1) + } + } + if(c == 4){ + if(b == 1){ + espacios3 <- rep(" ", 2) + } + if(b >= 2){ + espacios3 <- rep(" ", 1) + } + } + #27mar2019 ###################################### + if(c == 5){ + if(b >= 2){ + espacios3 <- rep("", 1) + } + } + #27mar2019 ###################################### + } + + linea3 <- c(linea2, espacios3, tabla_ordenados[i,4]) + ####03julio2019####################### ##################### +# if(tabla_ordenados_numcarac[i,3] == 3 && tabla_ordenados_numcarac[i,4] == 3 && tabla_ordenados_numcarac[i,5] == 2 && tabla_ordenados_numcarac[i,6] == 5){ +# linea3 <- c(linea2, " ", tabla_ordenados[i,4]) +# } + ####03julio2019####################### ##################### + + #TER + if(tabla_ordenados_numcarac[i,1] == 3){ + num_espacios4 <- 8 + ajuste_t1 <- 0 + for(l in 1:tabla_ordenados_numcarac[i,4]){ + if(l != tabla_ordenados_numcarac[i,4]){ + ajuste_t1 <-ajuste_t1 + 1 + num_espacios4 <- 8 - ajuste_t1 + } + if(l == tabla_ordenados_numcarac[i,4]){ + num_espacios4 <- 8 - ajuste_t1 + } + } + linea3 <- c(linea, rep(" ", num_espacios4), tabla_ordenados[i,4]) + + } + + ####Pairwise 4col-5col + linea4 <- c() + if(tabla_ordenados_numcarac[i,1] != 3){ + if(tabla_ordenados_numcarac[i,3] >= 7){ + linea4 <- c(linea3, tabla_ordenados[i,5]) + } + if(tabla_ordenados_numcarac[i,3] < 7){ + linea4 <- c(linea3, " ", tabla_ordenados[i,5]) + ###18oct2018 + if(tabla_ordenados_numcarac[i,3] >= 3 && tabla_ordenados[i,4] == ""){ + linea4 <- c(linea2, " ", tabla_ordenados[i,5]) + } + ###18oct2018 + } + #------------29julio2019--------------------# + + if(isTRUE(tabla_ordenados[i,3] == "NA") && tabla_ordenados[i,4] == ""){ + linea4 <- c(linea2, rep(" ", 6), tabla_ordenados[i,5]) + } + + + #------------29julio2019--------------------# + } + + + + + if(tabla_ordenados_numcarac[i,1] == 3){ + + linea4 <- c(linea3, " ", tabla_ordenados[i,5]) + ## + if(tabla_ordenados[i,4] == ""){ + linea4 <- c(linea2,rep(" ", 4),tabla_ordenados[i,5]) + } + + ## + + + } + + #####Pairwise 5col-6col. NO espacios4 + if(tabla_ordenados_numcarac[i,1] != 3){ + linea5 <-c() + for(d in 1:(tabla_ordenados_numcarac[i,6])){ + if(d == 1){ + espacios5 <- rep(" ", 3) + } + if(d == 2){ + espacios5 <- rep(" ", 2) + } + if(d >= 3){ + espacios5 <- rep(" ", 1) + } + + ##################21junio2109############# + + if(tabla_ordenados_numcarac[i,3] == 2 && tabla_ordenados_numcarac[i,5] == 2 && tabla_ordenados_numcarac[i,6] == 5){ + espacios5 <- rep(" ", 2) + } + + ##################21junio2109############# + ###########03julio################ ############ + # if(tabla_ordenados_numcarac[i,3] == 1 && tabla_ordenados_numcarac[i,4] == 3 && tabla_ordenados_numcarac[i,5] == 2 && tabla_ordenados_numcarac[i,6] == 5){ + # + # espacios5 <- "" + # } + + ###########03julio################ ############ + + + } + linea5 <- c(linea4, espacios5, tabla_ordenados[i,6]) + + + } + if(tabla_ordenados_numcarac[i,1] == 3){ + for(dd in 1:(tabla_ordenados_numcarac[i,6])){ + if(dd == 1){ + espacios55 <- rep(" ", 3) + } + + #14nov + if(dd == 1 && tabla_ordenados_numcarac[i,5] == 3){ + espacios55 <- rep(" ", 1) + } + #14nov + + if(dd == 2){ + espacios55 <- rep(" ", 2) + } + if(dd >= 3){ + espacios55 <- rep(" ", 1) + } + + + } + linea5 <- c(linea4, espacios55, tabla_ordenados[i,6]) + + #------------------05sep2019------------# + + if(tabla_ordenados_numcarac[i,6] == 1 && tabla_ordenados_numcarac[i,5] >= 5){ + espacios55 <- rep(" ", 1) + linea5 <- c(linea4, espacios55, tabla_ordenados[i,6]) + } + + #------------------05sep2019------------# + + } + + + + + ######Pairwise 6col-7col + linea6 <- c() + if(tabla_ordenados_numcarac[i,7] == 5){ + espacios6 <- rep(" ", 7) + linea6 <-c(linea5, espacios6, tabla_ordenados[i,7]) + + ###################21junio2109################# + if(tabla_ordenados_numcarac[i,3] == 4 && tabla_ordenados_numcarac[i,6] == 5){ + espacios6 <- rep(" ", 6) + linea6 <-c(linea5, espacios6, tabla_ordenados[i,7]) + } + + ###################21junio2109################# + + ## 03julio2019 ######### + + if(tabla_ordenados_numcarac[i,6] == 4 && tabla_ordenados_numcarac[i,6] == 4){ + espacios6 <- rep(" ", 6) + linea6 <-c(linea5, espacios6, tabla_ordenados[i,7]) + } + + ## 03julio2019 ######### + + + } + + if(tabla_ordenados_numcarac[i,7] > 5){ + out_spaces <- tabla_ordenados_numcarac[i,7] - 5 + espacios6 <- rep(" ", (7-out_spaces)) + linea6 <-c(linea5, espacios6, tabla_ordenados[i,7]) + + ###################21junio2109################# + if(tabla_ordenados_numcarac[i,3] == 4 && tabla_ordenados_numcarac[i,6] == 5){ + out_spaces <- tabla_ordenados_numcarac[i,7] - 4 + espacios6 <- rep(" ", (7-out_spaces)) + linea6 <-c(linea5, espacios6, tabla_ordenados[i,7]) + } + + ###################21junio2109################# + ## 03julio2019 ######### + + if(tabla_ordenados_numcarac[i,6] == 4 && tabla_ordenados_numcarac[i,6] == 4){ + out_spaces_2 <- tabla_ordenados_numcarac[i,7] - 4 + espacios6 <- rep(" ", (7-out_spaces_2)) + linea6 <-c(linea5, espacios6, tabla_ordenados[i,7]) + } + + ## 03julio2019 ######### + + + } + + ######################################27mar2019 + # + # if(tabla_ordenados_numcarac[i,4] == 5){ + # espacios6 <- rep(" ",5) + # linea6 <-c(linea5, espacios6, tabla_ordenados[i,7]) + # } + # + # if(tabla_ordenados_numcarac[i,4] > 5){ + # espacios6 <- rep(" ",4) + # linea6 <-c(linea5, espacios6, tabla_ordenados[i,7]) + # } + + ######################################27mar2019 + + + #######Pairwise 7col-8col + linea7 <- c() + ajuste3 <- 0 + if(tabla_ordenados_numcarac[i,8] == 5){ + espacios7 <- rep(" ", 3) + linea7 <-c(linea6, espacios7, tabla_ordenados[i,8]) + } + if(tabla_ordenados_numcarac[i,8] == 6){ + espacios7 <- rep(" ", 2) + linea7 <-c(linea6, espacios7, tabla_ordenados[i,8]) + } + if(tabla_ordenados_numcarac[i,8] > 6){ + espacios7 <- rep(" ", 1) + linea7 <-c(linea6, espacios7, tabla_ordenados[i,8]) + } + + ########Pairwise 8col-9col + linea8 <- c() + ajuste4 <- 0 + if(tabla_ordenados_numcarac[i,9] == 5){ + espacios8 <- rep(" ", 3) + linea8 <-c(linea7, espacios8, tabla_ordenados[i,9]) + } + if(tabla_ordenados_numcarac[i,9] == 6){ + espacios8 <- rep(" ", 2) + linea8 <-c(linea7, espacios8, tabla_ordenados[i,9]) + } + if(tabla_ordenados_numcarac[i,9] > 6){ + espacios8 <- rep(" ", 1) + linea8 <-c(linea7, espacios8, tabla_ordenados[i,9]) + } + + #########Pairwise 9col-10col + linea9 <- c() + if(tabla_ordenados_numcarac[i,10] == 4){ + espacios9 <- rep(" ", 2) + linea9 <- c(linea8, espacios9, tabla_ordenados[i,10]) + } + if(tabla_ordenados_numcarac[i,10] > 4){ + espacios9 <- rep(" ", 1) + linea9 <- c(linea8, espacios9, tabla_ordenados[i,10]) + } + + ##########Pairwise 10col-11col + # linea10 <- c() + # if(tabla_ordenados_numcarac[i,11] == 4){ + # espacios10 <- rep(" ", 2) + # linea10 <- c(linea9, espacios10, tabla_ordenados[i,11]) + # } + # if(tabla_ordenados_numcarac[i,11] > 4){ + # espacios10 <- rep(" ", 1) + # linea10 <- c(linea9, espacios10, tabla_ordenados[i,11]) + # } + #22oct2018 + ##########Pairwise 10col-11col + linea10 <- c() + if(tabla_ordenados_numcarac[i,11] == 4){ + espacios10 <- rep(" ", 3) + linea10 <- c(linea9, espacios10, tabla_ordenados[i,11]) + } + if(tabla_ordenados_numcarac[i,11] == 5){ + espacios10 <- rep(" ", 2) + linea10 <- c(linea9, espacios10, tabla_ordenados[i,11]) + } + + if(tabla_ordenados_numcarac[i,11] > 5){ + espacios10 <- rep(" ", 1) + linea10 <- c(linea9, espacios10, tabla_ordenados[i,11]) + } + #22oct2018 + + + ###########Pairwise 11col-12col + linea11 <- c() + if(tabla_ordenados_numcarac[i,12] == 5){ + espacios11 <- rep(" ", 5) + linea11 <-c(linea10, espacios11, tabla_ordenados[i,12]) + } + ajuste5 <- 0 + for(h in 6:tabla_ordenados_numcarac[i,12]){ + if(tabla_ordenados_numcarac[i,12] > 5){ + ajuste5 <- ajuste5 + 1 + espacios11 <- rep(" ", (5-ajuste5)) + ##espacios11 <- rep(" ", (5-ajuste5)) + linea11 <-c(linea10, espacios11, tabla_ordenados[i,12]) + } + } + + ############Pairwise 12col-13col + linea12 <- c(linea11," ", tabla_ordenados[i,13]) + + #TER + if(tabla_ordenados_numcarac[i,1] == 3){ + cabecera <- tabla_ordenados[i,1] + for(w in 1:length(linea5)){ + cabecera <- paste(cabecera,linea5[w], sep = "") + } + #write(cabecera, file = "1z95_wo_198andwater_ph7_MOD.pdbqt", append = TRUE) + write(cabecera, file = args[2], append = TRUE) + } + + #!= TER + if(tabla_ordenados_numcarac[i,1] != 3){ + cabecera <- tabla_ordenados[i,1] + for(w in 1:length(linea12)){ + cabecera <- paste(cabecera,linea12[w], sep = "") + } + #write(cabecera, file = "1z95_wo_198andwater_ph7_MOD.pdbqt", append = TRUE) + write(cabecera, file = args[2], append = TRUE) + } +} + +#21junio2019 +# #### Make file receptor_atm_types.txt to be paste in the GPF file ### + +prereceptor_atmtypes <- c() +for(i in 1:nrow(tabla_ordenados)){ + if(tabla_ordenados[i,13] != ""){ + prereceptor_atmtypes <- c(prereceptor_atmtypes, tabla_ordenados[i,13]) + } +} +# + receptor_atmtypes <- unique(prereceptor_atmtypes) +# + +filtered_receptor <- c() +for(i in 1:length(receptor_atmtypes)){ + + #print(receptor_atmtypes[i]) + #print(is.na(as.numeric(receptor_atmtypes[i]))) + + if(suppressWarnings(is.na(as.numeric(receptor_atmtypes[i])))){ + filtered_receptor <- c(filtered_receptor, receptor_atmtypes[i]) + } + +} + +receptor_atmtypes <- filtered_receptor + +cabeceratm <- receptor_atmtypes[1] +for(rat in 2:length(receptor_atmtypes)){ + + cabeceratm <- paste(cabeceratm, receptor_atmtypes[rat], sep = " ") +} + +write(cabeceratm, file = receptor_types_file_out, append = FALSE) + + +#21junio2019 + + + + +# #::::::::06sep2019:::::::::::::::::# +# +# #Make the file receptor_types_file_out.txt removing duplicates and Na +# #21junio2019 +# +# # +# prereceptor_atmtypes <- c() +# for(i in 1:nrow(tabla_ordenados)){ +# if(tabla_ordenados[i,13] != ""){ +# prereceptor_atmtypes <- c(prereceptor_atmtypes, tabla_ordenados[i,13]) +# } +# } +# # +# # #print(prereceptor_atmtypes) +# # +# receptor_atmtypes <- unique(prereceptor_atmtypes) +# #21junio2019 +# +# quitar <- 0 +# for(i in 1:length(receptor_atmtypes)){ +# if(isTRUE(receptor_atmtypes[i] == "Na")){ +# quitar <- i +# break +# } +# } +# +# if(quitar == 0){ +# cabeceratm <- receptor_atmtypes[1] +# for(rat in 2:length(receptor_atmtypes)){ +# cabeceratm <- paste(cabeceratm, receptor_atmtypes[rat], sep = " ") +# } +# +# write(cabeceratm, file = "receptor_types_file_out.txt", append = FALSE) +# } +# +# if(quitar != 0){ +# receptor_atmtypes <- receptor_atmtypes[-quitar] +# cabeceratm_types <- receptor_atmtypes[1] +# for(at_t in 2:length(receptor_atmtypes)){ +# cabeceratm_types <- paste(cabeceratm_types, receptor_atmtypes[at_t], sep = " ") +# } +# write(cabeceratm_types, file = "receptor_types_file_out.txt", append = FALSE) +# } + + + + + + + + + + + diff -r eda62adfc858 -r afd5b5ffc38f PLIDflow/scripts/receptor_atm_types.txt --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/PLIDflow/scripts/receptor_atm_types.txt Tue Jan 14 07:52:48 2020 -0500 @@ -0,0 +1,2 @@ +N HD C OA A SA NA +N HD C OA A SA NA diff -r eda62adfc858 -r afd5b5ffc38f PLIDflow/scripts/requirements.txt --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/PLIDflow/scripts/requirements.txt Tue Jan 14 07:52:48 2020 -0500 @@ -0,0 +1,77 @@ +amqp==1.4.8 +anyjson==0.3.3 +asn1crypto==0.24.0 +Babel==2.5.1 +bcrypt==3.1.4 +Beaker==1.7.0 +bioblend==0.7.0 +boltons==17.1.0 +boto==2.38.0 +boto3==1.6.21 +botocore==1.9.21 +bx-python==0.7.3 +bz2file==0.98 +certifi==2017.7.27.1 +cffi==1.11.5 +chardet==3.0.4 +Cheetah==2.4.4 +cryptography==2.2.2 +decorator==4.0.2 +dictobj==0.3.1 +docopt==0.6.2 +docutils==0.14 +ecdsa==0.13 +enum34==1.1.6 +Fabric==1.13.2 +futures==3.2.0 +galaxy-sequence-utils==1.0.2 +h5py==2.7.1 +idna==2.6 +ipaddress==1.0.18 +jmespath==0.9.3 +kombu==3.0.30 +Mako==1.0.2 +Markdown==2.6.3 +MarkupSafe==1.0 +mercurial==3.7.3 +nose==1.3.7 +numpy==1.8.0 +packaging==16.8 +paramiko==2.2.1 +Parsley==1.3 +Paste==2.0.2 +PasteDeploy==1.5.2 +PasteScript==2.0.2 +pbr==3.1.1 +pkg-resources==0.0.0 +psutil==4.1.0 +pulsar-galaxy-lib==0.8.0 +pyasn1==0.4.2 +pycparser==2.18 +pycrypto==2.6.1 +pykwalify==1.6.0 +PyNaCl==1.2.1 +pyparsing==2.1.1 +pysam==0.14 +python-dateutil==2.5.3 +python-genomespaceclient==0.1.8 +python-swiftclient==3.5.0 +pytz==2017.3 +PyYAML==3.12 +repoze.lru==0.6 +requests==2.18.4 +requests-toolbelt==0.8.0 +Routes==2.4.1 +s3transfer==0.1.13 +six==1.11.0 +SQLAlchemy==1.0.15 +sqlalchemy-migrate==0.11.0 +SQLAlchemy-Utils==0.32.19 +sqlparse==0.1.16 +svgwrite==1.1.6 +Tempita==0.5.3.dev0 +urllib3==1.22 +uWSGI==2.0.15 +WebHelpers==1.3 +WebOb==1.4.1 +Whoosh==2.7.4 diff -r eda62adfc858 -r afd5b5ffc38f PLIDflow/scripts/separateChain.sh --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/PLIDflow/scripts/separateChain.sh Tue Jan 14 07:52:48 2020 -0500 @@ -0,0 +1,7 @@ +#!/bin/bash + +# Arguments +# $1 = pdb + +grep "ATOM\|HETATM" $1 | awk '{ if(length($5)==1) updateName=$5; if($1 == "ATOM" || $1 == "HETATM"){ print $0 > "chain"updateName".pdb"; }}' ; +for i in chain* ; do echo "TER" >> $i ; echo "END" >> $i ; done diff -r eda62adfc858 -r afd5b5ffc38f PLIDflow/scripts/table --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/PLIDflow/scripts/table Tue Jan 14 07:52:48 2020 -0500 @@ -0,0 +1,74 @@ +H* H +HN H +HG1 H +HE H +HE1 H +HZ1 H +HZ2 H +HZ3 H +HH H +HD2 H +HD3 H +HD13 H +HB H +HA H +C C +CA C +CB C +CG C +CG1 C +CG2 C +CD C +CD1 C +CD2 C +CE C +CE1 C +CE2 C +CE3 C +CZ C +CZ2 C +CZ3 C +CH2 C +N N +NH2 N +ND1 N +ND2 N +NE N +NE1 N +NE2 N +SD S +SG S +NZ N1+ +NH1 N1+ +OH O +O O +OE1 O +OG O +OG1 O +OD1 O +OE2 O1- +OD2 O1- +OXT O1- +NA NA +Na Na +F F +Mg Mg +MG MG +P P +CL CL +Cl Cl +Ca Ca +Mn Mn +MN MN +Fe Fe +FE FE +Zn Zn +ZN ZN +Br Br +BR BR +I I +Z Z +G G +GA GA +J J +Q Q diff -r eda62adfc858 -r afd5b5ffc38f PLIDflow/scripts/templateenvelopsizes.txt --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/PLIDflow/scripts/templateenvelopsizes.txt Tue Jan 14 07:52:48 2020 -0500 @@ -0,0 +1,63 @@ +10 +20 +30 +40 +50 +60 +70 +80 +90 +100 +110 +120 +130 +140 +150 +160 +170 +180 +190 +200 +210 +220 +230 +240 +250 +260 +270 +280 +290 +300 +310 +320 +330 +340 +350 +360 +370 +380 +390 +400 +410 +420 +430 +440 +450 +460 +470 +480 +490 +500 +510 +520 +530 +540 +550 +560 +570 +580 +590 +600 + + + diff -r eda62adfc858 -r afd5b5ffc38f PLIDflow/scripts/templatefillouts1.txt --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/PLIDflow/scripts/templatefillouts1.txt Tue Jan 14 07:52:48 2020 -0500 @@ -0,0 +1,61 @@ +FILL_10out1.pdb +FILL_20out1.pdb +FILL_30out1.pdb +FILL_40out1.pdb +FILL_50out1.pdb +FILL_60out1.pdb +FILL_70out1.pdb +FILL_80out1.pdb +FILL_90out1.pdb +FILL_100out1.pdb +FILL_110out1.pdb +FILL_120out1.pdb +FILL_130out1.pdb +FILL_140out1.pdb +FILL_150out1.pdb +FILL_160out1.pdb +FILL_170out1.pdb +FILL_180out1.pdb +FILL_190out1.pdb +FILL_200out1.pdb +FILL_210out1.pdb +FILL_220out1.pdb +FILL_230out1.pdb +FILL_240out1.pdb +FILL_250out1.pdb +FILL_260out1.pdb +FILL_270out1.pdb +FILL_280out1.pdb +FILL_290out1.pdb +FILL_300out1.pdb +FILL_310out1.pdb +FILL_320out1.pdb +FILL_330out1.pdb +FILL_340out1.pdb +FILL_350out1.pdb +FILL_360out1.pdb +FILL_370out1.pdb +FILL_380out1.pdb +FILL_390out1.pdb +FILL_400out1.pdb +FILL_410out1.pdb +FILL_420out1.pdb +FILL_430out1.pdb +FILL_440out1.pdb +FILL_450out1.pdb +FILL_460out1.pdb +FILL_470out1.pdb +FILL_480out1.pdb +FILL_490out1.pdb +FILL_500out1.pdb +FILL_510out1.pdb +FILL_520out1.pdb +FILL_530out1.pdb +FILL_540out1.pdb +FILL_550out1.pdb +FILL_560out1.pdb +FILL_570out1.pdb +FILL_580out1.pdb +FILL_590out1.pdb +FILL_600out1.pdb + diff -r eda62adfc858 -r afd5b5ffc38f PLIDflow/scripts/templatefillouts1_1_8.txt --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/PLIDflow/scripts/templatefillouts1_1_8.txt Tue Jan 14 07:52:48 2020 -0500 @@ -0,0 +1,480 @@ +FILL_10out1.pdb +FILL_10out2.pdb +FILL_10out3.pdb +FILL_10out4.pdb +FILL_10out5.pdb +FILL_10out6.pdb +FILL_10out7.pdb +FILL_10out8.pdb +FILL_20out1.pdb +FILL_20out2.pdb +FILL_20out3.pdb +FILL_20out4.pdb +FILL_20out5.pdb +FILL_20out6.pdb +FILL_20out7.pdb +FILL_20out8.pdb +FILL_30out1.pdb +FILL_30out2.pdb +FILL_30out3.pdb +FILL_30out4.pdb +FILL_30out5.pdb +FILL_30out6.pdb +FILL_30out7.pdb +FILL_30out8.pdb +FILL_40out1.pdb +FILL_40out2.pdb +FILL_40out3.pdb +FILL_40out4.pdb +FILL_40out5.pdb +FILL_40out6.pdb +FILL_40out7.pdb +FILL_40out8.pdb +FILL_50out1.pdb +FILL_50out2.pdb +FILL_50out3.pdb +FILL_50out4.pdb +FILL_50out5.pdb +FILL_50out6.pdb +FILL_50out7.pdb +FILL_50out8.pdb +FILL_60out1.pdb +FILL_60out2.pdb +FILL_60out3.pdb +FILL_60out4.pdb +FILL_60out5.pdb +FILL_60out6.pdb +FILL_60out7.pdb +FILL_60out8.pdb +FILL_70out1.pdb +FILL_70out2.pdb +FILL_70out3.pdb +FILL_70out4.pdb +FILL_70out5.pdb +FILL_70out6.pdb +FILL_70out7.pdb +FILL_70out8.pdb +FILL_80out1.pdb +FILL_80out2.pdb +FILL_80out3.pdb +FILL_80out4.pdb +FILL_80out5.pdb +FILL_80out6.pdb +FILL_80out7.pdb +FILL_80out8.pdb +FILL_90out1.pdb +FILL_90out2.pdb +FILL_90out3.pdb +FILL_90out4.pdb +FILL_90out5.pdb +FILL_90out6.pdb +FILL_90out7.pdb +FILL_90out8.pdb +FILL_100out1.pdb +FILL_100out2.pdb +FILL_100out3.pdb +FILL_100out4.pdb +FILL_100out5.pdb +FILL_100out6.pdb +FILL_100out7.pdb +FILL_100out8.pdb +FILL_110out1.pdb +FILL_110out2.pdb +FILL_110out3.pdb +FILL_110out4.pdb +FILL_110out5.pdb +FILL_110out6.pdb +FILL_110out7.pdb +FILL_110out8.pdb +FILL_120out1.pdb +FILL_120out2.pdb +FILL_120out3.pdb +FILL_120out4.pdb +FILL_120out5.pdb +FILL_120out6.pdb +FILL_120out7.pdb +FILL_120out8.pdb +FILL_130out1.pdb +FILL_130out2.pdb +FILL_130out3.pdb +FILL_130out4.pdb +FILL_130out5.pdb +FILL_130out6.pdb +FILL_130out7.pdb +FILL_130out8.pdb +FILL_140out1.pdb +FILL_140out2.pdb +FILL_140out3.pdb +FILL_140out4.pdb +FILL_140out5.pdb +FILL_140out6.pdb +FILL_140out7.pdb +FILL_140out8.pdb +FILL_150out1.pdb +FILL_150out2.pdb +FILL_150out3.pdb +FILL_150out4.pdb +FILL_150out5.pdb +FILL_150out6.pdb +FILL_150out7.pdb +FILL_150out8.pdb +FILL_160out1.pdb +FILL_160out2.pdb +FILL_160out3.pdb +FILL_160out4.pdb +FILL_160out5.pdb +FILL_160out6.pdb +FILL_160out7.pdb +FILL_160out8.pdb +FILL_170out1.pdb +FILL_170out2.pdb +FILL_170out3.pdb +FILL_170out4.pdb +FILL_170out5.pdb +FILL_170out6.pdb +FILL_170out7.pdb +FILL_170out8.pdb +FILL_180out1.pdb +FILL_180out2.pdb +FILL_180out3.pdb +FILL_180out4.pdb +FILL_180out5.pdb +FILL_180out6.pdb +FILL_180out7.pdb +FILL_180out8.pdb +FILL_190out1.pdb +FILL_190out2.pdb +FILL_190out3.pdb +FILL_190out4.pdb +FILL_190out5.pdb +FILL_190out6.pdb +FILL_190out7.pdb +FILL_190out8.pdb +FILL_200out1.pdb +FILL_200out2.pdb +FILL_200out3.pdb +FILL_200out4.pdb +FILL_200out5.pdb +FILL_200out6.pdb +FILL_200out7.pdb +FILL_200out8.pdb +FILL_210out1.pdb +FILL_210out2.pdb +FILL_210out3.pdb +FILL_210out4.pdb +FILL_210out5.pdb +FILL_210out6.pdb +FILL_210out7.pdb +FILL_210out8.pdb +FILL_220out1.pdb +FILL_220out2.pdb +FILL_220out3.pdb +FILL_220out4.pdb +FILL_220out5.pdb +FILL_220out6.pdb +FILL_220out7.pdb +FILL_220out8.pdb +FILL_230out1.pdb +FILL_230out2.pdb +FILL_230out3.pdb +FILL_230out4.pdb +FILL_230out5.pdb +FILL_230out6.pdb +FILL_230out7.pdb +FILL_230out8.pdb +FILL_240out1.pdb +FILL_240out2.pdb +FILL_240out3.pdb +FILL_240out4.pdb +FILL_240out5.pdb +FILL_240out6.pdb +FILL_240out7.pdb +FILL_240out8.pdb +FILL_250out1.pdb +FILL_250out2.pdb +FILL_250out3.pdb +FILL_250out4.pdb +FILL_250out5.pdb +FILL_250out6.pdb +FILL_250out7.pdb +FILL_250out8.pdb +FILL_260out1.pdb +FILL_260out2.pdb +FILL_260out3.pdb +FILL_260out4.pdb +FILL_260out5.pdb +FILL_260out6.pdb +FILL_260out7.pdb +FILL_260out8.pdb +FILL_270out1.pdb +FILL_270out2.pdb +FILL_270out3.pdb +FILL_270out4.pdb +FILL_270out5.pdb +FILL_270out6.pdb +FILL_270out7.pdb +FILL_270out8.pdb +FILL_280out1.pdb +FILL_280out2.pdb +FILL_280out3.pdb +FILL_280out4.pdb +FILL_280out5.pdb +FILL_280out6.pdb +FILL_280out7.pdb +FILL_280out8.pdb +FILL_290out1.pdb +FILL_290out2.pdb +FILL_290out3.pdb +FILL_290out4.pdb +FILL_290out5.pdb +FILL_290out6.pdb +FILL_290out7.pdb +FILL_290out8.pdb +FILL_300out1.pdb +FILL_300out2.pdb +FILL_300out3.pdb +FILL_300out4.pdb +FILL_300out5.pdb +FILL_300out6.pdb +FILL_300out7.pdb +FILL_300out8.pdb +FILL_310out1.pdb +FILL_310out2.pdb +FILL_310out3.pdb +FILL_310out4.pdb +FILL_310out5.pdb +FILL_310out6.pdb +FILL_310out7.pdb +FILL_310out8.pdb +FILL_320out1.pdb +FILL_320out2.pdb +FILL_320out3.pdb +FILL_320out4.pdb +FILL_320out5.pdb +FILL_320out6.pdb +FILL_320out7.pdb +FILL_320out8.pdb +FILL_330out1.pdb +FILL_330out2.pdb +FILL_330out3.pdb +FILL_330out4.pdb +FILL_330out5.pdb +FILL_330out6.pdb +FILL_330out7.pdb +FILL_330out8.pdb +FILL_340out1.pdb +FILL_340out2.pdb +FILL_340out3.pdb +FILL_340out4.pdb +FILL_340out5.pdb +FILL_340out6.pdb +FILL_340out7.pdb +FILL_340out8.pdb +FILL_350out1.pdb +FILL_350out2.pdb +FILL_350out3.pdb +FILL_350out4.pdb +FILL_350out5.pdb +FILL_350out6.pdb +FILL_350out7.pdb +FILL_350out8.pdb +FILL_360out1.pdb +FILL_360out2.pdb +FILL_360out3.pdb +FILL_360out4.pdb +FILL_360out5.pdb +FILL_360out6.pdb +FILL_360out7.pdb +FILL_360out8.pdb +FILL_370out1.pdb +FILL_370out2.pdb +FILL_370out3.pdb +FILL_370out4.pdb +FILL_370out5.pdb +FILL_370out6.pdb +FILL_370out7.pdb +FILL_370out8.pdb +FILL_380out1.pdb +FILL_380out2.pdb +FILL_380out3.pdb +FILL_380out4.pdb +FILL_380out5.pdb +FILL_380out6.pdb +FILL_380out7.pdb +FILL_380out8.pdb +FILL_390out1.pdb +FILL_390out2.pdb +FILL_390out3.pdb +FILL_390out4.pdb +FILL_390out5.pdb +FILL_390out6.pdb +FILL_390out7.pdb +FILL_390out8.pdb +FILL_400out1.pdb +FILL_400out2.pdb +FILL_400out3.pdb +FILL_400out4.pdb +FILL_400out5.pdb +FILL_400out6.pdb +FILL_400out7.pdb +FILL_400out8.pdb +FILL_410out1.pdb +FILL_410out2.pdb +FILL_410out3.pdb +FILL_410out4.pdb +FILL_410out5.pdb +FILL_410out6.pdb +FILL_410out7.pdb +FILL_410out8.pdb +FILL_420out1.pdb +FILL_420out2.pdb +FILL_420out3.pdb +FILL_420out4.pdb +FILL_420out5.pdb +FILL_420out6.pdb +FILL_420out7.pdb +FILL_420out8.pdb +FILL_430out1.pdb +FILL_430out2.pdb +FILL_430out3.pdb +FILL_430out4.pdb +FILL_430out5.pdb +FILL_430out6.pdb +FILL_430out7.pdb +FILL_430out8.pdb +FILL_440out1.pdb +FILL_440out2.pdb +FILL_440out3.pdb +FILL_440out4.pdb +FILL_440out5.pdb +FILL_440out6.pdb +FILL_440out7.pdb +FILL_440out8.pdb +FILL_450out1.pdb +FILL_450out2.pdb +FILL_450out3.pdb +FILL_450out4.pdb +FILL_450out5.pdb +FILL_450out6.pdb +FILL_450out7.pdb +FILL_450out8.pdb +FILL_460out1.pdb +FILL_460out2.pdb +FILL_460out3.pdb +FILL_460out4.pdb +FILL_460out5.pdb +FILL_460out6.pdb +FILL_460out7.pdb +FILL_460out8.pdb +FILL_470out1.pdb +FILL_470out2.pdb +FILL_470out3.pdb +FILL_470out4.pdb +FILL_470out5.pdb +FILL_470out6.pdb +FILL_470out7.pdb +FILL_470out8.pdb +FILL_480out1.pdb +FILL_480out2.pdb +FILL_480out3.pdb +FILL_480out4.pdb +FILL_480out5.pdb +FILL_480out6.pdb +FILL_480out7.pdb +FILL_480out8.pdb +FILL_490out1.pdb +FILL_490out2.pdb +FILL_490out3.pdb +FILL_490out4.pdb +FILL_490out5.pdb +FILL_490out6.pdb +FILL_490out7.pdb +FILL_490out8.pdb +FILL_500out1.pdb +FILL_500out2.pdb +FILL_500out3.pdb +FILL_500out4.pdb +FILL_500out5.pdb +FILL_500out6.pdb +FILL_500out7.pdb +FILL_500out8.pdb +FILL_510out1.pdb +FILL_510out2.pdb +FILL_510out3.pdb +FILL_510out4.pdb +FILL_510out5.pdb +FILL_510out6.pdb +FILL_510out7.pdb +FILL_510out8.pdb +FILL_520out1.pdb +FILL_520out2.pdb +FILL_520out3.pdb +FILL_520out4.pdb +FILL_520out5.pdb +FILL_520out6.pdb +FILL_520out7.pdb +FILL_520out8.pdb +FILL_530out1.pdb +FILL_530out2.pdb +FILL_530out3.pdb +FILL_530out4.pdb +FILL_530out5.pdb +FILL_530out6.pdb +FILL_530out7.pdb +FILL_530out8.pdb +FILL_540out1.pdb +FILL_540out2.pdb +FILL_540out3.pdb +FILL_540out4.pdb +FILL_540out5.pdb +FILL_540out6.pdb +FILL_540out7.pdb +FILL_540out8.pdb +FILL_550out1.pdb +FILL_550out2.pdb +FILL_550out3.pdb +FILL_550out4.pdb +FILL_550out5.pdb +FILL_550out6.pdb +FILL_550out7.pdb +FILL_550out8.pdb +FILL_560out1.pdb +FILL_560out2.pdb +FILL_560out3.pdb +FILL_560out4.pdb +FILL_560out5.pdb +FILL_560out6.pdb +FILL_560out7.pdb +FILL_560out8.pdb +FILL_570out1.pdb +FILL_570out2.pdb +FILL_570out3.pdb +FILL_570out4.pdb +FILL_570out5.pdb +FILL_570out6.pdb +FILL_570out7.pdb +FILL_570out8.pdb +FILL_580out1.pdb +FILL_580out2.pdb +FILL_580out3.pdb +FILL_580out4.pdb +FILL_580out5.pdb +FILL_580out6.pdb +FILL_580out7.pdb +FILL_580out8.pdb +FILL_590out1.pdb +FILL_590out2.pdb +FILL_590out3.pdb +FILL_590out4.pdb +FILL_590out5.pdb +FILL_590out6.pdb +FILL_590out7.pdb +FILL_590out8.pdb +FILL_600out1.pdb +FILL_600out2.pdb +FILL_600out3.pdb +FILL_600out4.pdb +FILL_600out5.pdb +FILL_600out6.pdb +FILL_600out7.pdb +FILL_600out8.pdb diff -r eda62adfc858 -r afd5b5ffc38f PLIDflow/scripts/templatefillouts1_ALLFILLS.txt --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/PLIDflow/scripts/templatefillouts1_ALLFILLS.txt Tue Jan 14 07:52:48 2020 -0500 @@ -0,0 +1,600 @@ +FILL_10out1.pdb +FILL_10out2.pdb +FILL_10out3.pdb +FILL_10out4.pdb +FILL_10out5.pdb +FILL_10out6.pdb +FILL_10out7.pdb +FILL_10out8.pdb +FILL_10out9.pdb +FILL_10out10.pdb +FILL_20out1.pdb +FILL_20out2.pdb +FILL_20out3.pdb +FILL_20out4.pdb +FILL_20out5.pdb +FILL_20out6.pdb +FILL_20out7.pdb +FILL_20out8.pdb +FILL_20out9.pdb +FILL_20out10.pdb +FILL_30out1.pdb +FILL_30out2.pdb +FILL_30out3.pdb 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+FILL_470out7.pdb +FILL_470out8.pdb +FILL_470out9.pdb +FILL_470out10.pdb +FILL_480out1.pdb +FILL_480out2.pdb +FILL_480out3.pdb +FILL_480out4.pdb +FILL_480out5.pdb +FILL_480out6.pdb +FILL_480out7.pdb +FILL_480out8.pdb +FILL_480out9.pdb +FILL_480out10.pdb +FILL_490out1.pdb +FILL_490out2.pdb +FILL_490out3.pdb +FILL_490out4.pdb +FILL_490out5.pdb +FILL_490out6.pdb +FILL_490out7.pdb +FILL_490out8.pdb +FILL_490out9.pdb +FILL_490out10.pdb +FILL_500out1.pdb +FILL_500out2.pdb +FILL_500out3.pdb +FILL_500out4.pdb +FILL_500out5.pdb +FILL_500out6.pdb +FILL_500out7.pdb +FILL_500out8.pdb +FILL_500out9.pdb +FILL_500out10.pdb +FILL_510out1.pdb +FILL_510out2.pdb +FILL_510out3.pdb +FILL_510out4.pdb +FILL_510out5.pdb +FILL_510out6.pdb +FILL_510out7.pdb +FILL_510out8.pdb +FILL_510out9.pdb +FILL_510out10.pdb +FILL_520out1.pdb +FILL_520out2.pdb +FILL_520out3.pdb +FILL_520out4.pdb +FILL_520out5.pdb +FILL_520out6.pdb +FILL_520out7.pdb +FILL_520out8.pdb +FILL_520out9.pdb +FILL_520out10.pdb +FILL_530out1.pdb +FILL_530out2.pdb +FILL_530out3.pdb +FILL_530out4.pdb +FILL_530out5.pdb +FILL_530out6.pdb +FILL_530out7.pdb +FILL_530out8.pdb +FILL_530out9.pdb +FILL_530out10.pdb +FILL_540out1.pdb +FILL_540out2.pdb +FILL_540out3.pdb +FILL_540out4.pdb +FILL_540out5.pdb +FILL_540out6.pdb +FILL_540out7.pdb +FILL_540out8.pdb +FILL_540out9.pdb +FILL_540out10.pdb +FILL_550out1.pdb +FILL_550out2.pdb +FILL_550out3.pdb +FILL_550out4.pdb +FILL_550out5.pdb +FILL_550out6.pdb +FILL_550out7.pdb +FILL_550out8.pdb +FILL_550out9.pdb +FILL_550out10.pdb +FILL_560out1.pdb +FILL_560out2.pdb +FILL_560out3.pdb +FILL_560out4.pdb +FILL_560out5.pdb +FILL_560out6.pdb +FILL_560out7.pdb +FILL_560out8.pdb +FILL_560out9.pdb +FILL_560out10.pdb +FILL_570out1.pdb +FILL_570out2.pdb +FILL_570out3.pdb +FILL_570out4.pdb +FILL_570out5.pdb +FILL_570out6.pdb +FILL_570out7.pdb +FILL_570out8.pdb +FILL_570out9.pdb +FILL_570out10.pdb +FILL_580out1.pdb +FILL_580out2.pdb +FILL_580out3.pdb +FILL_580out4.pdb +FILL_580out5.pdb +FILL_580out6.pdb +FILL_580out7.pdb +FILL_580out8.pdb +FILL_580out9.pdb +FILL_580out10.pdb +FILL_590out1.pdb +FILL_590out2.pdb +FILL_590out3.pdb +FILL_590out4.pdb +FILL_590out5.pdb +FILL_590out6.pdb +FILL_590out7.pdb +FILL_590out8.pdb +FILL_590out9.pdb +FILL_590out10.pdb +FILL_600out1.pdb +FILL_600out2.pdb +FILL_600out3.pdb +FILL_600out4.pdb +FILL_600out5.pdb +FILL_600out6.pdb +FILL_600out7.pdb +FILL_600out8.pdb +FILL_600out9.pdb +FILL_600out10.pdb diff -r eda62adfc858 -r afd5b5ffc38f PLIDflow/scripts/templatefillouts1_OKsoloout1.txt --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/PLIDflow/scripts/templatefillouts1_OKsoloout1.txt Tue Jan 14 07:52:48 2020 -0500 @@ -0,0 +1,61 @@ +FILL_10out1.pdb +FILL_20out1.pdb +FILL_30out1.pdb +FILL_40out1.pdb +FILL_50out1.pdb +FILL_60out1.pdb +FILL_70out1.pdb +FILL_80out1.pdb +FILL_90out1.pdb +FILL_100out1.pdb +FILL_110out1.pdb +FILL_120out1.pdb +FILL_130out1.pdb +FILL_140out1.pdb +FILL_150out1.pdb +FILL_160out1.pdb +FILL_170out1.pdb +FILL_180out1.pdb +FILL_190out1.pdb +FILL_200out1.pdb +FILL_210out1.pdb +FILL_220out1.pdb +FILL_230out1.pdb +FILL_240out1.pdb +FILL_250out1.pdb +FILL_260out1.pdb +FILL_270out1.pdb +FILL_280out1.pdb +FILL_290out1.pdb +FILL_300out1.pdb +FILL_310out1.pdb +FILL_320out1.pdb +FILL_330out1.pdb +FILL_340out1.pdb +FILL_350out1.pdb +FILL_360out1.pdb +FILL_370out1.pdb +FILL_380out1.pdb +FILL_390out1.pdb +FILL_400out1.pdb +FILL_410out1.pdb +FILL_420out1.pdb +FILL_430out1.pdb +FILL_440out1.pdb +FILL_450out1.pdb +FILL_460out1.pdb +FILL_470out1.pdb +FILL_480out1.pdb +FILL_490out1.pdb +FILL_500out1.pdb +FILL_510out1.pdb +FILL_520out1.pdb +FILL_530out1.pdb +FILL_540out1.pdb +FILL_550out1.pdb +FILL_560out1.pdb +FILL_570out1.pdb +FILL_580out1.pdb +FILL_590out1.pdb +FILL_600out1.pdb + diff -r eda62adfc858 -r afd5b5ffc38f PLIDflow/scripts/vinafilemaker.R --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/PLIDflow/scripts/vinafilemaker.R Tue Jan 14 07:52:48 2020 -0500 @@ -0,0 +1,38 @@ + +#!/usr/bin/env Rscript # siempre va comentado, la consola lo interpreta asi. +args = commandArgs(trailingOnly=TRUE) # siempre es asi, no cambia. + +if(length(args) < 9){ + stop("USE: Rscript.exe walker.R ") + } + +receptor_PDBQT <- args[1] +ligand_PDBQT <- args[2] +out_PDBQT <- args[3] +log_file <- args[4] +coo_x <- args[5] +coo_y <- args[6] +coo_z <- args[7] +eboxsizedata <- args[8] + +receptor_data <- paste("receptor =", args[1], sep = " ") +ligando_data <- paste("ligand =" , args[2], sep = " ") +out_data <- paste("out =" , args[3], sep = " ") +log_file <- paste("log =", args[4], sep = " ") +center_x_data <- paste("center_x =", args[5], sep = " ") +center_y_data <- paste("center_y =", args[6], sep = " ") +center_z_data <- paste("center_z =", args[7], sep = " ") +aux <- as.numeric(scan(args[8], what="character", quiet=TRUE), quiet = TRUE) +size_x_data <- paste("size_x =", aux, sep = " ") +size_y_data <- paste("size_y =", aux, sep = " ") +size_z_data <- paste("size_z =", aux, sep = " ") + +campos <- c(receptor_data,ligando_data, out_data, log_file, center_x_data, center_y_data, center_z_data, size_x_data, size_y_data, size_z_data) + +datos <- c() +for(i in 1:length(campos)){ + datos <-paste(c(datos, campos[i], sep="\n")) +} + +write(datos, file=args[9], append=FALSE) + diff -r eda62adfc858 -r afd5b5ffc38f PLIDflow/scripts/vinafilemarkerclusters.R --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/PLIDflow/scripts/vinafilemarkerclusters.R Tue Jan 14 07:52:48 2020 -0500 @@ -0,0 +1,40 @@ +#!/usr/bin/env Rscript # siempre va comentado, la consola lo interpreta asi. +args = commandArgs(trailingOnly=TRUE) # siempre es asi, no cambia. + +if(length(args) < 10){ + # stop("USE: Rscript.exe vinafilemarkerclusters.R ") + stop("USE: Rscript vinafilemarkerclusters.R ") + } + + +receptor_PDBQT <- args[1] +ligand_PDBQT <- args[2] +out_PDBQT <- args[3] +log_file <- args[4] +eboxsizedata <- args[8] +v <- args[9] +session_dir <- args[10] + +setwd(session_dir) + +receptor_data <- paste("receptor =", args[1], sep = " ") +ligando_data <- paste("ligand =" , args[2], sep = " ") +out_data <- paste("out =" , args[3], sep = " ") +log_file <- paste("log =", args[4], sep = " ") +center_x_data <- paste("center_x =", args[5], sep =" ") +center_y_data <- paste("center_y =", args[6], sep =" ") +center_z_data <- paste("center_z =", args[7], sep =" ") +aux <- as.numeric(scan(args[8], what="character", quiet=TRUE), quiet=TRUE) +size_x_data <- paste("size_x =", aux, sep = " ") +size_y_data <- paste("size_y =", aux, sep = " ") +size_z_data <- paste("size_z =", aux, sep = " ") + +campos <- c(receptor_data,ligando_data, out_data, log_file, center_x_data, center_y_data, center_z_data, size_x_data, size_y_data, size_z_data) + +datos <- c() +for(i in 1:length(campos)){ + datos <-paste(c(datos, campos[i], sep="\n")) +} + +write(datos, file=paste(v, "_vinaconfig", sep = ""), append=FALSE) + diff -r eda62adfc858 -r afd5b5ffc38f PLIDflow/scripts/vinaoutpututility.sh --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/PLIDflow/scripts/vinaoutpututility.sh Tue Jan 14 07:52:48 2020 -0500 @@ -0,0 +1,12 @@ +#!/bin/bash +OUT=$1 +LOG=$2 +FILE=$3 + + +sed -i "s|out = NULL|out = ${OUT}|g" $FILE + +sed -i "s|log = NULL|log = ${LOG}|g" $FILE + + + diff -r eda62adfc858 -r afd5b5ffc38f PLIDflow/separate_chain_plidflow.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/PLIDflow/separate_chain_plidflow.xml Tue Jan 14 07:52:48 2020 -0500 @@ -0,0 +1,18 @@ + + Separates chains from a PDB into multiple files + + + + + + + + + + + diff -r eda62adfc858 -r afd5b5ffc38f PLIDflow/vina_plidflow.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/PLIDflow/vina_plidflow.xml Tue Jan 14 07:52:48 2020 -0500 @@ -0,0 +1,11 @@ + + is an open-source program for doing molecular docking. + + + + ${__tool_directory__}/scripts/vinaoutpututility.sh $outfile $outlog $configvina ; vina --config $configvina + + + + +