0.8.0; based on AlphaFold 2.1.0

PombertLab · Dec 23, 2021 · 66dfd32 · 66dfd32
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diff --git a/Notes/Installation_notes.sh b/Notes/Installation_notes.sh
@@ -1,6 +1,8 @@
 ## On Fedora 34
 ##### Installing Aria2, Conda and Docker #####
 sudo dnf install aria2 conda docker
+sudo dnf install python-docker
+sudo dnf install python-absl ## absl is required for alphafold
 
 ## Starting Docker / enabling at boot
 sudo systemctl start docker

diff --git a/Prediction/AlphaFold2/alphafold.pl b/Prediction/AlphaFold2/alphafold.pl
@@ -1,8 +1,8 @@
 #!/usr/bin/perl
 ## Pombert Lab, Illinois Tech, 2021
 my $name = 'alphafold.pl';
-my $version = '0.5'; ## to test with alphafold fork
-my $updated = '2021-09-18';
+my $version = '0.5a'; ## Update to match Alphafold 2.1 cmd line switches
+my $updated = '2021-12-23';
 
 use strict;
 use warnings;
@@ -34,7 +34,8 @@
 -o (--outdir)		Output directory
 -d (--docker)		Docker image name [Default: alphafold_3dfi]
 -m (--max_date)		--max_template_date option (YYYY-MM-DD) from AlphaFold2 [Default: current date]
--p (--preset)		Alphafold preset: full_dbs, reduced_dbs or casp14 [Default: full_dbs]
+-p (--preset)		Alphafold --db_preset: full_dbs or reduced_dbs [Default: full_dbs]
+-u (--use_msas)		Use precomputed MSAs
 -g (--gpu_dev)		List of GPU devices to use: e.g. all; 0,1; 0,1,2,3 [Default: all]
 -n (--no_gpu)		Turns off GPU acceleration
 -ah (--alpha_home)	AlphaFold2 installation directory [Default: \$ALPHAFOLD_HOME]
@@ -48,6 +49,7 @@
 my $docker_image_name = 'alphafold_3dfi';
 my $max_date = strftime("%F", localtime);
 my $preset = 'full_dbs';
+my $precomputed_msas;
 my $gpus = 'all';
 my $no_gpu;
 my $alpha_home;
@@ -58,6 +60,7 @@
 	'd|docker=s' => $docker_image_name,
 	'm|max_date=s' => \$max_date,
 	'p|preset=s' => \$preset,
+	'u|use_msas' => \$precomputed_msas,
 	'g|gpu_dev=s' => $gpus,
 	'n|no_gpu' => \$no_gpu,
 	'ah|alpha_home=s' => \$alpha_home,
@@ -103,7 +106,7 @@
 	casp14 => ''
 );
 unless (exists $presets{$preset}){
-	die "Unrecognized AlphaFold2 preset. Please use full_dbs, reduced_dbs, or casp14\n";
+	die "Unrecognized AlphaFold2 preset. Please use full_dbs or reduced_dbs\n";
 }
 
 ### Checking output directory + creating log file
@@ -115,7 +118,7 @@
 print LOG "\nCOMMAND = $name @command\n";
 print LOG "\nFolding started on $timestamp\n";
 print LOG "\nSetting AlphaFold2 --max_template_date option to: $max_date\n\n";
-print "\nSetting AlphaFold2 options --preset to $preset and --max_template_date to $max_date\n";
+print "\nSetting AlphaFold2 options --db_preset to $preset, --max_template_date to $max_date, and --docker_image_name to $docker_image_name\n";
 
 ### Running AlphaFold2 docker image
 my $prefix;
@@ -135,23 +138,28 @@
 		print "\n$time: working on $fasta\n";
 		my $start = time;
 
+		## Gpu check
 		my $gpu_devices = "--gpu_devices=$gpus";
-
 		my $gpu_check = '';
 		if ($no_gpu){
 			$gpu_check = '--use_gpu=False';
 			$gpu_devices = '';
 		}
 
+		## MSA
+		my $msa = 'False';
+		if ($precomputed_msas){ $msa = 'True'; }
+
 		# Folding
 		system "python3 \\
 			$alpha_home/docker/run_docker.py \\
 			--fasta_paths=$fasta \\
 			--docker_image_name=$docker_image_name \\
-			--download_dir=$alpha_db \\
+			--data_dir=$alpha_db \\
 			--output_dir=$outdir \\
 			--max_template_date=$max_date \\
-			--preset=$preset \\
+			--db_preset=$preset \\
+			--use_precomputed_msas=$msa \\
 			$gpu_devices \\
 			$gpu_check
 		";

diff --git a/README.md b/README.md
@@ -194,6 +194,9 @@ cd 3DFI/
 -pyr (--pyrosetta)	PyRosetta4 [Python-3.7.Release] .tar.bz2 archive to install
 			# Download - https://www.pyrosetta.org/downloads#h.xe4c0yjfkl19
 			# License - https://els2.comotion.uw.edu/product/pyrosetta
+
+## Docker
+-name (--docker_image) Name of the AlphaFold docker image to build [Default: alphafold_3dfi]
 ```
 </details>
 
@@ -336,12 +339,16 @@ run_3DFI.pl \
 
 ## 3D Folding options
 -n (--nogpu)		ALPHAFOLD/ROSETTAFOLD: Turn off GPU acceleration / use CPU only
+-g (--gpu_dev)		ALPHAFOLD: list of GPU devices to use: e.g. all; 0,1; 0,1,2,3 [Default: all]
 -m (--maxdate)		ALPHAFOLD: --max_template_date option (YYYY-MM-DD) [Default: current date]
--k (--ranks)		RAPTORX: Number of top ranks to model [Default: 5]
+-s (--preset)		ALPHAFOLD: full_dbs or reduced_dbs [Default: full_dbs]
+-i (--docker_image)	ALPHAFOLD: docker image name [Default: alphafold_3dfi]
+-u (--use_msas)		ALPHAFOLD: Use precomputed MSAs
+-k (--ranks)		RAPTORX: \# Number of top ranks to model [Default: 5]
 --modeller		RAPTORX: Modeller version [Default: mod10.1]
 
 ## Structural homology / alignment
--d (--db)		3DFI database location containing the RCSB PDB files / GESAMT archive [Default: $TDFI_DB]
+-d (--db)		3DFI database location containing the RCSB PDB files / GESAMT archive [Default: \$TDFI_DB]
 -q (--qscore)		Mininum Q-score to keep [Default: 0.3]
 -b (--best)		Keep the best match(es) only (top X hits) [Default: 5]
 --query			Models to query per protein and predictor: all or best [Default: all]
@@ -712,11 +719,12 @@ alphafold.pl \
 -o (--outdir)		Output directory
 -d (--docker)		Docker image name [Default: alphafold_3dfi]
 -m (--max_date)		--max_template_date option (YYYY-MM-DD) from AlphaFold2 [Default: current date]
--p (--preset)		Alphafold preset: full_dbs, reduced_dbs or casp14 [Default: full_dbs]
+-p (--preset)		Alphafold --db_preset: full_dbs or reduced_dbs [Default: full_dbs]
+-u (--use_msas)		Use precomputed MSAs
 -g (--gpu_dev)		List of GPU devices to use: e.g. all; 0,1; 0,1,2,3 [Default: all]
 -n (--no_gpu)		Turns off GPU acceleration
--ah (--alpha_home)	AlphaFold2 installation directory [Default: $ALPHAFOLD_HOME]
--ad (--alpha_db)	AlphaFold2 databases location [Default: $TDFI_DB/ALPHAFOLD]
+-ah (--alpha_home)	AlphaFold2 installation directory [Default: \$ALPHAFOLD_HOME]
+-ad (--alpha_db)	AlphaFold2 databases location [Default: \$TDFI_DB/ALPHAFOLD]
 ```
 </details>
 

diff --git a/run_3DFI.pl b/run_3DFI.pl
@@ -1,8 +1,8 @@
 #!/usr/bin/perl
 ## Pombert Lab, Illinois Tech, 2021
 my $name = 'run_3DFI.pl';
-my $version = '0.4b';
-my $updated = '2021-12-21';
+my $version = '0.5';
+my $updated = '2021-12-23';
 
 use strict;
 use warnings;
@@ -46,7 +46,9 @@
 -n (--nogpu)		ALPHAFOLD/ROSETTAFOLD: Turn off GPU acceleration / use CPU only
 -g (--gpu_dev)		ALPHAFOLD: list of GPU devices to use: e.g. all; 0,1; 0,1,2,3 [Default: all]
 -m (--maxdate)		ALPHAFOLD: --max_template_date option (YYYY-MM-DD) [Default: current date]
---preset		ALPHAFOLD:  full_dbs, reduced_dbs or casp14 [Default: full_dbs]
+-s (--preset)		ALPHAFOLD: full_dbs or reduced_dbs [Default: full_dbs]
+-i (--docker_image)	ALPHAFOLD: docker image name [Default: alphafold_3dfi]
+-u (--use_msas)		ALPHAFOLD: Use precomputed MSAs
 -k (--ranks)		RAPTORX: # Number of top ranks to model [Default: 5]
 --modeller		RAPTORX: Modeller version [Default: mod10.1]
 
@@ -77,6 +79,8 @@
 my $gpus = 'all';
 my $maxdate;
 my $preset = 'full_dbs';
+my $docker_image = 'alphafold_3dfi';
+my $precomputed_msas;
 my $ranks = 5;
 my $modeller = 'mod10.1';
 
@@ -107,8 +111,11 @@
 	# 3D folding
 	'n|nogpu' => \$nogpu,
 	'g|gpu_dev=s' => $gpus,
-	'k|ranks=i' => \$ranks,
 	'm|maxdate=s' => \$maxdate,
+	's|preset=s' => \$preset,
+	'i|docker_image=s' => \$docker_image,
+	'u|use_msas' => \$precomputed_msas,
+	'k|ranks=i' => \$ranks,
 	'modeller=s' => \$modeller,
 
 	# Structural homology 
@@ -364,19 +371,28 @@
 		$pred_scripts_home = "$home_3DFI".'/Prediction/AlphaFold2/';
 
 		## Checking options
+		# GPU
 		my $gpu_devices = "--gpu_dev $gpus";
 		if ($nogpu) { $gpu_devices = '--no_gpu'; }
+
+		# Maxdate
 		my $maxdate_flag = '';
 		if ($maxdate) { $maxdate_flag = "--max_date $maxdate"; }
 
+		# Use precomputed MSAs
+		my $msas_flag = '';
+		if ($precomputed_msas){ $msas_flag = "--use_msas"; }
+
 		## Running alphafold
 		$time = localtime;
 		print "\n# $time: Running AlphaFold protein structure prediction\n";
 		system "$pred_scripts_home"."alphafold.pl \\
 			--fasta $fasta_dir/*.fasta \\
 			--preset $preset \\
+			--docker $docker_image \\
 			$gpu_devices \\
 			$maxdate_flag \\
+			$msas_flag \\
 			-o $af_dir";
 
 		## Parsing AlphaFold output folders

diff --git a/setup_3DFI.pl b/setup_3DFI.pl
@@ -35,7 +35,11 @@
 -i (--install)		3D structure predictor(s) to install (alphafold raptorx and/or rosettafold)
 -pyr (--pyrosetta)	PyRosetta4 [Python-3.7.Release] .tar.bz2 archive to install
 			# Download - https://www.pyrosetta.org/downloads#h.xe4c0yjfkl19
-			# License - https://els2.comotion.uw.edu/product/pyrosetta 
+			# License - https://els2.comotion.uw.edu/product/pyrosetta
+
+## Docker
+-name (--docker_image) Name of the AlphaFold docker image to build [Default: alphafold_3dfi]
+
 OPTIONS
 die "\n$usage\n" unless @ARGV;
 
@@ -45,13 +49,15 @@
 my $database;
 my @predictors;
 my $pyrosetta;
+my $docker_image = 'alphafold_3dfi';
 GetOptions(
 	'c|config=s' => \$config_file,
 	'w|write=s' => \$write,
 	'p|path=s' => \$path_3DFI,
 	'd|dbdir=s' => \$database,
 	'i|install=s@{1,}' => \@predictors,
-	'pyr|pyrosetta=s' => \$pyrosetta
+	'pyr|pyrosetta=s' => \$pyrosetta,
+	'name|docker_image=s' => \$docker_image
 );
 
 ######################################################
@@ -212,9 +218,9 @@
 		else { system "git clone $alphafold_git"; }
 
 		# Creating Docker image + pip install of reqs
-		print "\nCreating AlphaFold docker image named alphafold_3dfi\n";
+		print "\nCreating AlphaFold docker image named $docker_image\n";
 		chdir "$root_3D/alphafold/";
-		system "docker build -f $root_3D/alphafold/docker/Dockerfile -t alphafold_3dfi .";
+		system "docker build -f $root_3D/alphafold/docker/Dockerfile -t $docker_image .";
 
 		# Creating a pip location for AlphaFold requirements
 		unless (-d $pip_location){