BindCraft

containers/2_ApplicationSpecific/BindCraft/BUILD_with_PyRosetta.md

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+# Build the BindCraft container with PyRosetta
+
+To build and use the PyRosetta version you must have a PyRosetta license.
+You must eaither complete the application for a non commercial license or purchase
+a commercial licenses - see [PyRosetta Licensing](https://els2.comotion.uw.edu/product/pyrosetta) for more info.
+
+## Building the container
+
+1. Start an interactive job
+
+```
+salloc --cluster=ub-hpc --partition=debug --qos=debug --account="[SlurmAccountName]" \
+ --mem=0 --exclusive --time=01:00:00
+```
+
+sample outout:
+
+> ```
+> salloc: Pending job allocation 19781052
+> salloc: job 19781052 queued and waiting for resources
+> salloc: job 19781052 has been allocated resources
+> salloc: Granted job allocation 19781052
+> salloc: Nodes cpn-i14-39 are ready for job
+> CCRusername@cpn-i14-39:~$ 
+> ```
+
+2. Navigate to your build directory and use the Slurm job local temporary directory for cache
+
+You should now be on the compute node allocated to you.  In this example we're using our project directory for our build directory.
+
+Change to your BindCraft directory
+
+```
+cd /projects/academic/[YourGroupName]/BindCraft
+```
+
+Download the BindCraft build files, FreeBindCraft_with_PyRosetta.def and docker-entrypoint.sh to this directory
+
+```
+curl -L -o FreeBindCraft_with_PyRosetta.def https://raw.githubusercontent.com/tonykew/ccr-examples/refs/heads/BindCraft/containers/2_ApplicationSpecific/BindCraft/FreeBindCraft_with_PyRosetta.def
+curl -L -o docker-entrypoint.sh https://raw.githubusercontent.com/tonykew/ccr-examples/refs/heads/BindCraft/containers/2_ApplicationSpecific/BindCraft/docker-entrypoint.sh
+```
+
+Sample output:
+
+> ```
+>   % Total    % Received % Xferd  Average Speed   Time    Time     Time  Current
+>                                  Dload  Upload   Total   Spent    Left  Speed
+> 100  5408  100  5408    0     0  25764      0 --:--:-- --:--:-- --:--:-- 258
+>   % Total    % Received % Xferd  Average Speed   Time    Time     Time  Current
+>                                  Dload  Upload   Total   Spent    Left  Speed
+> 100   404  100   404    0     0   2889      0 --:--:-- --:--:-- --:--:--  2906
+> ```
+
+3. Build your container
+
+Set the apptainer cache dir:
+
+```
+export APPTAINER_CACHEDIR=${SLURMTMPDIR}
+```
+
+Building the BindCraft container takes about half an hour...
+
+```
+apptainer build BindCraft_with_PyRosetta-$(arch).sif FreeBindCraft_with_PyRosetta.def
+```
+
+Sample truncated output:
+
+> ```
+> [....]
+> INFO:    Adding environment to container
+> INFO:    Creating SIF file...
+> INFO:    Build complete: BindCraft-x86_64.sif
+> ```
+
+## Running the container
+
+Start an interactive job with a single GPU e.g.
+NOTE: BindCraft Inference only uses one GPU
+
+```
+salloc --cluster=ub-hpc --partition=general-compute --qos=general-compute \
+ --account="[SlurmAccountName]" --mem=128GB --nodes=1 --cpus-per-task=1 \
+ --tasks-per-node=12 --gpus-per-node=1 --time=05:00:00
+```
+
+Change to your BindCraft directory
+
+```
+cd /projects/academic/[YourGroupName]/BindCraft
+```
+
+Create the input and output directories
+
+```
+mkdir -p ./input ./output
+```
+
+...then start the BindCraft container instance
+
+```
+apptainer shell \
+ -B /projects:/projects,/scratch:/scratch,/util:/util,/vscratch:/vscratch \
+ -B /util/software/data/alphafold/params:/app/params \
+ -B ./input:/work/input,./output:/work/output \
+ --nv \
+ ./BindCraft_with_PyRosetta-$(arch).sif
+```
+
+Sample output:
+
+> ```
+> 
+> GPU info:
+> GPU 0: Tesla T4 (UUID: GPU-fdc92258-5f5b-9ece-ceca-f1545184cd08)
+> 
+> Apptainer> 
+> ```
+
+Verify BindCraft is installed:
+
+The following command is run from the "Apptainer> " prompt
+
+```
+source /singularity
+```
+
+Expected output:
+
+> ```
+> BindCraft> 
+> ```
+
+All the following commands are run from the "BindCraft> " prompt
+
+```
+python3 "/app/bindcraft.py" --help
+```
+
+Sample output:
+
+> ```
+> Open files limits OK (soft=65536, hard=65536)
+> usage: bindcraft.py [-h] [--settings SETTINGS] [--filters FILTERS] [--advanced ADVANCED] [--no-pyrosetta] [--verbose] [--no-plots] [--no-animations]
+>                     [--interactive]
+> 
+> Script to run BindCraft binder design.
+> 
+> options:
+>   -h, --help            show this help message and exit
+>   --settings SETTINGS, -s SETTINGS
+>                         Path to the basic settings.json file. If omitted in a TTY, interactive mode is used.
+>   --filters FILTERS, -f FILTERS
+>                         Path to the filters.json file used to filter design. If not provided, default will be used.
+>   --advanced ADVANCED, -a ADVANCED
+>                         Path to the advanced.json file with additional design settings. If not provided, default will be used.
+>   --no-pyrosetta        Run without PyRosetta (skips relaxation and PyRosetta-based scoring)
+>   --verbose             Enable detailed timing/progress logs
+>   --no-plots            Disable saving design trajectory plots (overrides advanced settings)
+>   --no-animations       Disable saving design animations (overrides advanced settings)
+>   --interactive         Force interactive mode to collect target settings and options
+> ```
+