# HG changeset patch # User bitlab # Date 1587550233 14400 # Node ID 97f12f7cc852fc599db43b8e1aa2ca7bcde3dda3 # Parent b9e7ec4e3cdefbcf8b8992bfe7791f80ef2844f2 Deleted selected files diff -r b9e7ec4e3cde -r 97f12f7cc852 PLIDflow/autodocktools_lig_plidflow.xml --- a/PLIDflow/autodocktools_lig_plidflow.xml Mon Jan 27 07:12:19 2020 -0500 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,17 +0,0 @@ - - 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 b9e7ec4e3cde -r 97f12f7cc852 PLIDflow/autodocktools_rec_plidflow.xml --- a/PLIDflow/autodocktools_rec_plidflow.xml Mon Jan 27 07:12:19 2020 -0500 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,22 +0,0 @@ - - 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 b9e7ec4e3cde -r 97f12f7cc852 PLIDflow/confmaker_multiple_plidflow.xml --- a/PLIDflow/confmaker_multiple_plidflow.xml Mon Jan 27 07:12:19 2020 -0500 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,33 +0,0 @@ - - is a tool to select optimal Vina mode 1 energy. - - - - - - - - - - - - - - - - - - - - diff -r b9e7ec4e3cde -r 97f12f7cc852 PLIDflow/eboxsize_plidflow.xml --- a/PLIDflow/eboxsize_plidflow.xml Mon Jan 27 07:12:19 2020 -0500 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,15 +0,0 @@ - - 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 b9e7ec4e3cde -r 97f12f7cc852 PLIDflow/launch_confmaker_multiple.sh --- a/PLIDflow/launch_confmaker_multiple.sh Mon Jan 27 07:12:19 2020 -0500 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,76 +0,0 @@ -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) 2>&1 - -#echo "[RUNNING] - (Rscript gpffilemaker.R $receptor_pdbqt $RANDDIR) " -(Rscript gpffilemaker.R $receptor_pdbqt_modified2 $MYPWD/$RANDDIR) 2>&1 - -#echo "[RUNNING] - (Rscript glgfilemaker.R $receptor_pdbqt $RANDDIR) " -(Rscript glgfilemaker.R $receptor_pdbqt_modified2 $MYPWD/$RANDDIR) 2>&1 - -#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) 2>&1 - -#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) 2>&1 - - -#echo "[RUNNING] - (Rscript clusterfinder_Auto.R $RANDDIR) " -(Rscript clusterfinder_Auto.R $MYPWD/$RANDDIR) 2>&1 - - -#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) 2>&1 - - -cd $MYPWD - - -deactivate diff -r b9e7ec4e3cde -r 97f12f7cc852 PLIDflow/openbabel_SDF_plidflow.xml --- a/PLIDflow/openbabel_SDF_plidflow.xml Mon Jan 27 07:12:19 2020 -0500 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,10 +0,0 @@ - - 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 b9e7ec4e3cde -r 97f12f7cc852 PLIDflow/openbabel_SMI_plidflow.xml --- a/PLIDflow/openbabel_SMI_plidflow.xml Mon Jan 27 07:12:19 2020 -0500 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,10 +0,0 @@ - - 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 b9e7ec4e3cde -r 97f12f7cc852 PLIDflow/pdb2pqr_plidflow.xml --- a/PLIDflow/pdb2pqr_plidflow.xml Mon Jan 27 07:12:19 2020 -0500 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,18 +0,0 @@ - - Converts a pdb to pqr - - - - ${pdb_processed} ; - - rm ${pdb_processed}.pqr - - ]]> - - - - diff -r b9e7ec4e3cde -r 97f12f7cc852 PLIDflow/scripts/ADT_VENV/requirements.txt --- a/PLIDflow/scripts/ADT_VENV/requirements.txt Mon Jan 27 07:12:19 2020 -0500 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,77 +0,0 @@ -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 b9e7ec4e3cde -r 97f12f7cc852 PLIDflow/scripts/cluster_to_vina_cluster.R --- a/PLIDflow/scripts/cluster_to_vina_cluster.R Mon Jan 27 07:12:19 2020 -0500 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,100 +0,0 @@ -#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 b9e7ec4e3cde -r 97f12f7cc852 PLIDflow/scripts/clusterfilemaker.R --- a/PLIDflow/scripts/clusterfilemaker.R Mon Jan 27 07:12:19 2020 -0500 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,101 +0,0 @@ -#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 b9e7ec4e3cde -r 97f12f7cc852 PLIDflow/scripts/clusterfinder_Auto.R --- a/PLIDflow/scripts/clusterfinder_Auto.R Mon Jan 27 07:12:19 2020 -0500 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,170 +0,0 @@ -# #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 b9e7ec4e3cde -r 97f12f7cc852 PLIDflow/scripts/envelopesmaker.R --- a/PLIDflow/scripts/envelopesmaker.R Mon Jan 27 07:12:19 2020 -0500 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,57 +0,0 @@ -#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 b9e7ec4e3cde -r 97f12f7cc852 PLIDflow/scripts/glgfilemaker.R --- a/PLIDflow/scripts/glgfilemaker.R Mon Jan 27 07:12:19 2020 -0500 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,35 +0,0 @@ -#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 b9e7ec4e3cde -r 97f12f7cc852 PLIDflow/scripts/gpffilemaker.R --- a/PLIDflow/scripts/gpffilemaker.R Mon Jan 27 07:12:19 2020 -0500 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,116 +0,0 @@ -#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 b9e7ec4e3cde -r 97f12f7cc852 PLIDflow/scripts/includeAtom3.sh --- a/PLIDflow/scripts/includeAtom3.sh Mon Jan 27 07:12:19 2020 -0500 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,139 +0,0 @@ - -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 b9e7ec4e3cde -r 97f12f7cc852 PLIDflow/scripts/pdbcenter_npts_finder.R --- a/PLIDflow/scripts/pdbcenter_npts_finder.R Mon Jan 27 07:12:19 2020 -0500 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,84 +0,0 @@ -#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 b9e7ec4e3cde -r 97f12f7cc852 PLIDflow/scripts/pdbqtcorrector.R --- a/PLIDflow/scripts/pdbqtcorrector.R Mon Jan 27 07:12:19 2020 -0500 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,128 +0,0 @@ -#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 b9e7ec4e3cde -r 97f12f7cc852 PLIDflow/scripts/pdbqtcorrector2step.R --- a/PLIDflow/scripts/pdbqtcorrector2step.R Mon Jan 27 07:12:19 2020 -0500 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,1127 +0,0 @@ -#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 b9e7ec4e3cde -r 97f12f7cc852 PLIDflow/scripts/receptor_atm_types.txt --- a/PLIDflow/scripts/receptor_atm_types.txt Mon Jan 27 07:12:19 2020 -0500 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,2 +0,0 @@ -N HD C OA A SA NA -N HD C OA A SA NA diff -r b9e7ec4e3cde -r 97f12f7cc852 PLIDflow/scripts/requirements.txt --- a/PLIDflow/scripts/requirements.txt Mon Jan 27 07:12:19 2020 -0500 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,77 +0,0 @@ -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 b9e7ec4e3cde -r 97f12f7cc852 PLIDflow/scripts/separateChain.sh --- a/PLIDflow/scripts/separateChain.sh Mon Jan 27 07:12:19 2020 -0500 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,7 +0,0 @@ -#!/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 b9e7ec4e3cde -r 97f12f7cc852 PLIDflow/scripts/table --- a/PLIDflow/scripts/table Mon Jan 27 07:12:19 2020 -0500 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,74 +0,0 @@ -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 b9e7ec4e3cde -r 97f12f7cc852 PLIDflow/scripts/templateenvelopsizes.txt --- a/PLIDflow/scripts/templateenvelopsizes.txt Mon Jan 27 07:12:19 2020 -0500 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,63 +0,0 @@ -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 b9e7ec4e3cde -r 97f12f7cc852 PLIDflow/scripts/templatefillouts1.txt --- a/PLIDflow/scripts/templatefillouts1.txt Mon Jan 27 07:12:19 2020 -0500 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,61 +0,0 @@ -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 b9e7ec4e3cde -r 97f12f7cc852 PLIDflow/scripts/templatefillouts1_1_8.txt --- a/PLIDflow/scripts/templatefillouts1_1_8.txt Mon Jan 27 07:12:19 2020 -0500 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,480 +0,0 @@ -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 b9e7ec4e3cde -r 97f12f7cc852 PLIDflow/scripts/templatefillouts1_ALLFILLS.txt --- a/PLIDflow/scripts/templatefillouts1_ALLFILLS.txt Mon Jan 27 07:12:19 2020 -0500 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,600 +0,0 @@ -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 -FILL_30out4.pdb -FILL_30out5.pdb -FILL_30out6.pdb -FILL_30out7.pdb -FILL_30out8.pdb -FILL_30out9.pdb -FILL_30out10.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_40out9.pdb -FILL_40out10.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_50out9.pdb -FILL_50out10.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_60out9.pdb -FILL_60out10.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_70out9.pdb -FILL_70out10.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_80out9.pdb -FILL_80out10.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_90out9.pdb -FILL_90out10.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_100out9.pdb -FILL_100out10.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_110out9.pdb -FILL_110out10.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_120out9.pdb -FILL_120out10.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_130out9.pdb -FILL_130out10.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_140out9.pdb -FILL_140out10.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_150out9.pdb -FILL_150out10.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_160out9.pdb -FILL_160out10.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_170out9.pdb -FILL_170out10.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_180out9.pdb -FILL_180out10.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_190out9.pdb -FILL_190out10.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_200out9.pdb -FILL_200out10.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_210out9.pdb -FILL_210out10.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_220out9.pdb -FILL_220out10.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_230out9.pdb -FILL_230out10.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_240out9.pdb -FILL_240out10.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_250out9.pdb -FILL_250out10.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_260out9.pdb -FILL_260out10.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_270out9.pdb -FILL_270out10.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_280out9.pdb -FILL_280out10.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_290out9.pdb -FILL_290out10.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_300out9.pdb -FILL_300out10.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_310out9.pdb -FILL_310out10.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_320out9.pdb -FILL_320out10.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_330out9.pdb -FILL_330out10.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_340out9.pdb -FILL_340out10.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_350out9.pdb -FILL_350out10.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_360out9.pdb -FILL_360out10.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_370out9.pdb -FILL_370out10.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_380out9.pdb -FILL_380out10.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_390out9.pdb -FILL_390out10.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_400out9.pdb -FILL_400out10.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_410out9.pdb -FILL_410out10.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_420out9.pdb -FILL_420out10.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_430out9.pdb -FILL_430out10.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_440out9.pdb -FILL_440out10.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_450out9.pdb -FILL_450out10.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_460out9.pdb -FILL_460out10.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_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 b9e7ec4e3cde -r 97f12f7cc852 PLIDflow/scripts/templatefillouts1_OKsoloout1.txt --- a/PLIDflow/scripts/templatefillouts1_OKsoloout1.txt Mon Jan 27 07:12:19 2020 -0500 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,61 +0,0 @@ -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 b9e7ec4e3cde -r 97f12f7cc852 PLIDflow/scripts/vinafilemaker.R --- a/PLIDflow/scripts/vinafilemaker.R Mon Jan 27 07:12:19 2020 -0500 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,38 +0,0 @@ - -#!/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 b9e7ec4e3cde -r 97f12f7cc852 PLIDflow/scripts/vinafilemarkerclusters.R --- a/PLIDflow/scripts/vinafilemarkerclusters.R Mon Jan 27 07:12:19 2020 -0500 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,40 +0,0 @@ -#!/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 b9e7ec4e3cde -r 97f12f7cc852 PLIDflow/scripts/vinaoutpututility.sh --- a/PLIDflow/scripts/vinaoutpututility.sh Mon Jan 27 07:12:19 2020 -0500 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,12 +0,0 @@ -#!/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 b9e7ec4e3cde -r 97f12f7cc852 PLIDflow/separate_chain_plidflow.xml --- a/PLIDflow/separate_chain_plidflow.xml Mon Jan 27 07:12:19 2020 -0500 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,18 +0,0 @@ - - Separates chains from a PDB into multiple files - - - - - - - - - - - diff -r b9e7ec4e3cde -r 97f12f7cc852 PLIDflow/vina_plidflow.xml --- a/PLIDflow/vina_plidflow.xml Mon Jan 27 07:12:19 2020 -0500 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,11 +0,0 @@ - - is an open-source program for doing molecular docking. - - - - ${__tool_directory__}/scripts/vinaoutpututility.sh $outfile $outlog $configvina ; vina --config $configvina - - - - -