ABCFold

[root@rockylinux9 ~]# source /apps/pyenv/versions/anaconda3-2024.10-1/etc/profile.d/conda.sh
[root@rockylinux9 ~]# conda create -n abcfold python=3.11
 
[root@rockylinux9 ~]# conda activate abcfold
(abcfold) [root@rockylinux9 ~]#
(abcfold) [root@rockylinux9 ~]# cd /apps/src/
(abcfold) [root@rockylinux9 src]# git clone https://github.com/rigdenlab/ABCFold
(abcfold) [root@rockylinux9 src]# cd ABCFold/
(abcfold) [root@rockylinux9 ABCFold]# python -m pip install .
(abcfold) [root@rockylinux9 ABCFold]# conda deactivate
[root@rockylinux9 ABCFold]#

#%Module
prepend-path PATH /apps/pyenv/versions/anaconda3-2024.10-1/envs/abcfold/bin

[illya@rockylinux9 ~]$ module use /apps/modulefiles/
[illya@rockylinux9 ~]$ module load ABCFold
 
[illya@rockylinux9 ~]$ abcfold -h
usage: abcfold [-h] [--override] [--output_json OUTPUT_JSON] [--database DATABASE_DIR] [--model_params MODEL_PARAMS] [--sif_path SIF_PATH] [-a]
               [--use_af3_template_search] [-b] [--save_input] [-c] [--mmseqs2] [--mmseqs_database MMSEQS_DATABASE] [--templates]
               [--num_templates NUM_TEMPLATES] [--target_id TARGET_ID [TARGET_ID ...]] [--custom_template CUSTOM_TEMPLATE [CUSTOM_TEMPLATE ...]]
               [--custom_template_chain CUSTOM_TEMPLATE_CHAIN [CUSTOM_TEMPLATE_CHAIN ...]] [--number_of_models NUMBER_OF_MODELS] [--num_recycles NUM_RECYCLES]
               [--no_visuals] [--no_server]
               input_json output_dir
 
Run AlphaFold3 / Boltz1 / Chai-1
 
positional arguments:
  input_json            Path to the input JSON in AlphaFold3 format
  output_dir            Path to the output directory
 
options:
  -h, --help            show this help message and exit
  --override            [optional] Override the existing output directory, if it exists
  --output_json OUTPUT_JSON
                        [optional] Specify the path of the output ABCFold json file, this can be used to run subsequent runs of ABCFold with the same input
                        features (e.g. MSA)
  --database DATABASE_DIR
                        [optional] The database directory for the generation of the MSA. This is only required if using the built in AlphaFold3 MSA generation
  --model_params MODEL_PARAMS
                        [required] The directory containing the AlphaFold3 model parameters
  --sif_path SIF_PATH   [conditionally required] The path to the sif image of AlphaFold3 if using Singularity
  -a, --alphafold3      Run Alphafold3
  --use_af3_template_search
                        If providing your own custom MSA or if you've run `--mmseqs2`, allow Alphafold3 to search for templates
  -b, --boltz1          Run Boltz1
  --save_input          Save the input json file
  -c, --chai1           Run Chai-1
  --mmseqs2             [optional] Use MMseqs2 for MSA generation and template searching (if used with --templates flag)
  --mmseqs_database MMSEQS_DATABASE
                        [optional] The database directory for the generation of the MSA. This is only required if using a local installation of MMseqs2
  --templates           [optional] Enable template search
  --num_templates NUM_TEMPLATES
                        [optional] The number of templates to use (default: 20)
  --target_id TARGET_ID [TARGET_ID ...]
                        [conditionally required] The ID of the sequence that the custom template relates to. This is only required if modelling a complex. If
                        providing a list of custom templates, the target_id must be a list of the same length as the custom template list
  --custom_template CUSTOM_TEMPLATE [CUSTOM_TEMPLATE ...]
                        [optional] Path to a custom template file in mmCif format or a list of paths to custom template files in mmCif format. If providing a
                        list of custom templates, you must also provide a list of custom template chains.
  --custom_template_chain CUSTOM_TEMPLATE_CHAIN [CUSTOM_TEMPLATE_CHAIN ...]
                        [conditionally required] The chain ID of the chain to use in your custom template. This is only required if using a multi-chain
                        template. If providing a list of custom templates, you must also provide a list of custom template chains of the same length as the
                        custom template list
  --number_of_models NUMBER_OF_MODELS
                        [optional] The number of models to generate with each method (default: 5)
  --num_recycles NUM_RECYCLES
                        [optional] Number of recycles to use during inference (default: 10)
  --no_visuals          [optional] Do not generate the output pages, best for running on a cluster without a display
  --no_server           [optional] Do not start a local server to view the results, the output page is still generated and is accessible in the output
                        directory
[illya@rockylinux9 ~]$