From b3be94b87dedf0c523ab6c8227f4cd9f46236ac2 Mon Sep 17 00:00:00 2001 From: "Vikram K. Mulligan" Date: Tue, 8 Jun 2021 02:01:51 -0400 Subject: [PATCH 1/5] Updating trRosetta application compiliation instructions. --- application_documentation/trRosetta/trRosetta.md | 12 ++++++------ 1 file changed, 6 insertions(+), 6 deletions(-) diff --git a/application_documentation/trRosetta/trRosetta.md b/application_documentation/trRosetta/trRosetta.md index 6e189c5c9..056eb7f79 100644 --- a/application_documentation/trRosetta/trRosetta.md +++ b/application_documentation/trRosetta/trRosetta.md @@ -12,12 +12,12 @@ The trRosetta application uses the trRosetta neural network described in Yang _e The trRosetta application requires that Rosetta be linked against the Tensorflow C-API libraries. To compile with Tensorflow support: -1. Download the Tensorflow 1.15 precompiled libraries for your operating system from one of the following. (Note that GPU versions require CUDA drivers; see https://www.tensorflow.org/install/lang_c for more information.) - * Linux/CPU: https://storage.googleapis.com/tensorflow/libtensorflow/libtensorflow-cpu-linux-x86_64-1.15.0.tar.gz - * Linux/GPU: https://storage.googleapis.com/tensorflow/libtensorflow/libtensorflow-gpu-linux-x86_64-1.15.0.tar.gz - * Windows/CPU: https://storage.googleapis.com/tensorflow/libtensorflow/libtensorflow-cpu-windows-x86_64-1.15.0.zip - * Windows/GPU: https://storage.googleapis.com/tensorflow/libtensorflow/libtensorflow-gpu-windows-x86_64-1.15.0.zip - * MacOS/CPU: https://storage.googleapis.com/tensorflow/libtensorflow/libtensorflow-cpu-darwin-x86_64-1.15.0.tar.gz +1. Download the Tensorflow 2.5.0 precompiled libraries for your operating system from one of the following. (Note that GPU versions require CUDA drivers; see https://www.tensorflow.org/install/lang_c for more information.) + * Linux/CPU: https://storage.googleapis.com/tensorflow/libtensorflow/libtensorflow-cpu-linux-x86_64-2.5.0.tar.gz + * Linux/GPU: https://storage.googleapis.com/tensorflow/libtensorflow/libtensorflow-gpu-linux-x86_64-2.5.0.tar.gz + * Windows/CPU: https://storage.googleapis.com/tensorflow/libtensorflow/libtensorflow-cpu-windows-x86_64-2.5.0.zip + * Windows/GPU: https://storage.googleapis.com/tensorflow/libtensorflow/libtensorflow-gpu-windows-x86_64-2.5.0.zip + * MacOS/CPU: https://storage.googleapis.com/tensorflow/libtensorflow/libtensorflow-cpu-darwin-x86_64-2.5.0.tar.gz * MacOS/GPU: None available. 2. Unzip/untar the archive into a suitable directory (~/mydir/ is used here as an example), and add the following environment variables: From 774684aa0d6eaef9262c7538a17482b611b46a89 Mon Sep 17 00:00:00 2001 From: "Vikram K. Mulligan" Date: Tue, 8 Jun 2021 02:12:36 -0400 Subject: [PATCH 2/5] Updating auto-generated documentation. --- .../RosettaScripts/xsd/filter_FragmentScoreFilter_type.md | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/scripting_documentation/RosettaScripts/xsd/filter_FragmentScoreFilter_type.md b/scripting_documentation/RosettaScripts/xsd/filter_FragmentScoreFilter_type.md index cf17faf3b..c4110da47 100644 --- a/scripting_documentation/RosettaScripts/xsd/filter_FragmentScoreFilter_type.md +++ b/scripting_documentation/RosettaScripts/xsd/filter_FragmentScoreFilter_type.md @@ -13,7 +13,7 @@ Filter based on any score that can be calculated in fragment_picker. outputs_name="(pose &string;)" csblast="(&string;)" blast_pgp="(&string;)" placeholder_seqs="(&string;)" sparks-x="(&string;)" sparks-x_query="(&string;)" psipred="(&string;)" - vall_path="(/scratch/benchmark/W.hojo-1/rosetta.Hojo-1/master/main/database//sampling/vall.jul19.2011.gz &string;)" + vall_path="(/home/vmulligan/rosetta_devcopy_local2/Rosetta/main/database//sampling/vall.jul19.2011.gz &string;)" frags_scoring_config="(&string;)" n_frags="(200 &non_negative_integer;)" n_candidates="(1000 &non_negative_integer;)" print_to_pdb="(false &xs:boolean;)" From 092778fe030e40557c34d764660a17a62193821d Mon Sep 17 00:00:00 2001 From: "Vikram K. Mulligan" Date: Tue, 8 Jun 2021 02:36:42 -0400 Subject: [PATCH 3/5] Updating docs that refer to Tensorflow version. --- ...nt_generator_trRosettaConstraintGenerator_type.md | 12 ++++++------ .../xsd/mover_trRosettaProtocol_type.md | 12 ++++++------ 2 files changed, 12 insertions(+), 12 deletions(-) diff --git a/scripting_documentation/RosettaScripts/xsd/constraint_generator_trRosettaConstraintGenerator_type.md b/scripting_documentation/RosettaScripts/xsd/constraint_generator_trRosettaConstraintGenerator_type.md index 94a961b73..58f780d55 100644 --- a/scripting_documentation/RosettaScripts/xsd/constraint_generator_trRosettaConstraintGenerator_type.md +++ b/scripting_documentation/RosettaScripts/xsd/constraint_generator_trRosettaConstraintGenerator_type.md @@ -7,12 +7,12 @@ The trRosettaConstraintGenerator takes as input a file containing a multiple seq The trRosettaConstraintGenerator requires compilation with Tensorflow support. To compile with Tensorflow support: -1. Download the Tensorflow 1.15 precompiled libraries for your operating system from one of the following. (Note that GPU versions require CUDA drivers; see https://www.tensorflow.org/install/lang_c for more information.) - Linux/CPU: https://storage.googleapis.com/tensorflow/libtensorflow/libtensorflow-cpu-linux-x86_64-1.15.0.tar.gz - Linux/GPU: https://storage.googleapis.com/tensorflow/libtensorflow/libtensorflow-gpu-linux-x86_64-1.15.0.tar.gz - Windows/CPU: https://storage.googleapis.com/tensorflow/libtensorflow/libtensorflow-cpu-windows-x86_64-1.15.0.zip - Windows/GPU: https://storage.googleapis.com/tensorflow/libtensorflow/libtensorflow-gpu-windows-x86_64-1.15.0.zip - MacOS/CPU: https://storage.googleapis.com/tensorflow/libtensorflow/libtensorflow-cpu-darwin-x86_64-1.15.0.tar.gz +1. Download the Tensorflow 2.5.0 precompiled libraries for your operating system from one of the following. (Note that GPU versions require CUDA drivers; see https://www.tensorflow.org/install/lang_c for more information.) + Linux/CPU: https://storage.googleapis.com/tensorflow/libtensorflow/libtensorflow-cpu-linux-x86_64-2.5.0.tar.gz + Linux/GPU: https://storage.googleapis.com/tensorflow/libtensorflow/libtensorflow-gpu-linux-x86_64-2.5.0.tar.gz + Windows/CPU: https://storage.googleapis.com/tensorflow/libtensorflow/libtensorflow-cpu-windows-x86_64-2.5.0.zip + Windows/GPU: https://storage.googleapis.com/tensorflow/libtensorflow/libtensorflow-gpu-windows-x86_64-2.5.0.zip + MacOS/CPU: https://storage.googleapis.com/tensorflow/libtensorflow/libtensorflow-cpu-darwin-x86_64-2.5.0.tar.gz MacOS/GPU: None available. 2. Unzip/untar the archive into a suitable directory (~/mydir/ is used here as an example), and add the following environment variables: diff --git a/scripting_documentation/RosettaScripts/xsd/mover_trRosettaProtocol_type.md b/scripting_documentation/RosettaScripts/xsd/mover_trRosettaProtocol_type.md index febc4e32e..903b32f53 100644 --- a/scripting_documentation/RosettaScripts/xsd/mover_trRosettaProtocol_type.md +++ b/scripting_documentation/RosettaScripts/xsd/mover_trRosettaProtocol_type.md @@ -7,12 +7,12 @@ Implements the full trRosetta protocol, as described in Yang et al. (2020) Impro The trRosettaProtocol mover requires compilation with Tensorflow support. To compile with Tensorflow support: -1. Download the Tensorflow 1.15 precompiled libraries for your operating system from one of the following. (Note that GPU versions require CUDA drivers; see https://www.tensorflow.org/install/lang_c for more information.) - Linux/CPU: https://storage.googleapis.com/tensorflow/libtensorflow/libtensorflow-cpu-linux-x86_64-1.15.0.tar.gz - Linux/GPU: https://storage.googleapis.com/tensorflow/libtensorflow/libtensorflow-gpu-linux-x86_64-1.15.0.tar.gz - Windows/CPU: https://storage.googleapis.com/tensorflow/libtensorflow/libtensorflow-cpu-windows-x86_64-1.15.0.zip - Windows/GPU: https://storage.googleapis.com/tensorflow/libtensorflow/libtensorflow-gpu-windows-x86_64-1.15.0.zip - MacOS/CPU: https://storage.googleapis.com/tensorflow/libtensorflow/libtensorflow-cpu-darwin-x86_64-1.15.0.tar.gz +1. Download the Tensorflow 2.5.0 precompiled libraries for your operating system from one of the following. (Note that GPU versions require CUDA drivers; see https://www.tensorflow.org/install/lang_c for more information.) + Linux/CPU: https://storage.googleapis.com/tensorflow/libtensorflow/libtensorflow-cpu-linux-x86_64-2.5.0.tar.gz + Linux/GPU: https://storage.googleapis.com/tensorflow/libtensorflow/libtensorflow-gpu-linux-x86_64-2.5.0.tar.gz + Windows/CPU: https://storage.googleapis.com/tensorflow/libtensorflow/libtensorflow-cpu-windows-x86_64-2.5.0.zip + Windows/GPU: https://storage.googleapis.com/tensorflow/libtensorflow/libtensorflow-gpu-windows-x86_64-2.5.0.zip + MacOS/CPU: https://storage.googleapis.com/tensorflow/libtensorflow/libtensorflow-cpu-darwin-x86_64-2.5.0.tar.gz MacOS/GPU: None available. 2. Unzip/untar the archive into a suitable directory (~/mydir/ is used here as an example), and add the following environment variables: From 4fbc39e7c78f7b6684847da3df2ad2c1848cd287 Mon Sep 17 00:00:00 2001 From: "Vikram K. Mulligan" Date: Wed, 9 Jun 2021 19:16:58 -0400 Subject: [PATCH 4/5] Adding version information to docs. --- application_documentation/trRosetta/trRosetta.md | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/application_documentation/trRosetta/trRosetta.md b/application_documentation/trRosetta/trRosetta.md index 056eb7f79..c7e866e78 100644 --- a/application_documentation/trRosetta/trRosetta.md +++ b/application_documentation/trRosetta/trRosetta.md @@ -10,7 +10,7 @@ The trRosetta application uses the trRosetta neural network described in Yang _e ### Compilation requirements -The trRosetta application requires that Rosetta be linked against the Tensorflow C-API libraries. To compile with Tensorflow support: +The trRosetta application requires that Rosetta be linked against the Tensorflow 2 C-API libraries, version 2.5.0 or higher. To compile with Tensorflow support: 1. Download the Tensorflow 2.5.0 precompiled libraries for your operating system from one of the following. (Note that GPU versions require CUDA drivers; see https://www.tensorflow.org/install/lang_c for more information.) * Linux/CPU: https://storage.googleapis.com/tensorflow/libtensorflow/libtensorflow-cpu-linux-x86_64-2.5.0.tar.gz From 6eafa5067c57eee07847ede17b1902ed444fb6ac Mon Sep 17 00:00:00 2001 From: "Vikram K. Mulligan" Date: Wed, 9 Jun 2021 19:37:40 -0400 Subject: [PATCH 5/5] Updating messages. --- .../constraint_generator_trRosettaConstraintGenerator_type.md | 2 +- .../RosettaScripts/xsd/mover_trRosettaProtocol_type.md | 2 +- 2 files changed, 2 insertions(+), 2 deletions(-) diff --git a/scripting_documentation/RosettaScripts/xsd/constraint_generator_trRosettaConstraintGenerator_type.md b/scripting_documentation/RosettaScripts/xsd/constraint_generator_trRosettaConstraintGenerator_type.md index 58f780d55..304815257 100644 --- a/scripting_documentation/RosettaScripts/xsd/constraint_generator_trRosettaConstraintGenerator_type.md +++ b/scripting_documentation/RosettaScripts/xsd/constraint_generator_trRosettaConstraintGenerator_type.md @@ -5,7 +5,7 @@ _Autogenerated Tag Syntax Documentation:_ --- The trRosettaConstraintGenerator takes as input a file containing a multiple sequence alignment, feeds this to the trRosetta neural network, and uses the output to generate distance and angle constraints between pairs of residues as described in Yang et al. (2020) Improved protein structure prediction using predicted interresidue orientations. Proc. Natl. Acad. Sci. USA 117(3):1496-503. https://doi.org/10.1073/pnas.1914677117. -The trRosettaConstraintGenerator requires compilation with Tensorflow support. To compile with Tensorflow support: +The trRosettaConstraintGenerator requires compilation with Tensorflow 2 support (version 2.5.0 or higher). To compile with Tensorflow support: 1. Download the Tensorflow 2.5.0 precompiled libraries for your operating system from one of the following. (Note that GPU versions require CUDA drivers; see https://www.tensorflow.org/install/lang_c for more information.) Linux/CPU: https://storage.googleapis.com/tensorflow/libtensorflow/libtensorflow-cpu-linux-x86_64-2.5.0.tar.gz diff --git a/scripting_documentation/RosettaScripts/xsd/mover_trRosettaProtocol_type.md b/scripting_documentation/RosettaScripts/xsd/mover_trRosettaProtocol_type.md index 903b32f53..9e5c44bcb 100644 --- a/scripting_documentation/RosettaScripts/xsd/mover_trRosettaProtocol_type.md +++ b/scripting_documentation/RosettaScripts/xsd/mover_trRosettaProtocol_type.md @@ -5,7 +5,7 @@ _Autogenerated Tag Syntax Documentation:_ --- Implements the full trRosetta protocol, as described in Yang et al. (2020) Improved protein structure prediction using predicted interresidue orientations. Proc. Natl. Acad. Sci. USA 117(3):1496-503. https://doi.org/10.1073/pnas.1914677117. This mover takes as input a multiple sequence alignment, runs the trRosetta neural network, generates distance and angle constraints between pairs of residues, and carries out energy-minimization to produce a structure. Note that this mover deletes and replaces the input structure. If a native structure is provided, the mover tags the output structure with the RMSD to native. -The trRosettaProtocol mover requires compilation with Tensorflow support. To compile with Tensorflow support: +The trRosettaProtocol mover requires compilation with Tensorflow 2 support (version 2.5.0 or higher). To compile with Tensorflow support: 1. Download the Tensorflow 2.5.0 precompiled libraries for your operating system from one of the following. (Note that GPU versions require CUDA drivers; see https://www.tensorflow.org/install/lang_c for more information.) Linux/CPU: https://storage.googleapis.com/tensorflow/libtensorflow/libtensorflow-cpu-linux-x86_64-2.5.0.tar.gz