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nextflow_schema.json
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{
"$schema": "https://json-schema.org/draft/2020-12/schema",
"$id": "https://raw.githubusercontent.com/nf-core/proteinfold/master/nextflow_schema.json",
"title": "nf-core/proteinfold pipeline parameters",
"description": "Protein 3D structure prediction pipeline",
"type": "object",
"$defs": {
"input_output_options": {
"title": "Global options",
"type": "object",
"fa_icon": "fas fa-coins",
"description": "Define where the pipeline should find input data and save output data.",
"required": ["input", "outdir"],
"properties": {
"input": {
"type": "string",
"format": "file-path",
"exists": true,
"schema": "assets/schema_input.json",
"mimetype": "text/csv",
"pattern": "^\\S+\\.csv$",
"description": "Path to comma-separated file containing information about the samples in the experiment.",
"help_text": "You will need to create a design file with information about the samples in your experiment before running the pipeline. Use this parameter to specify its location. It has to be a comma-separated file with 3 columns, and a header row. See [usage docs](https://nf-co.re/proteinfold/usage#samplesheet-input).",
"fa_icon": "fas fa-file-csv"
},
"outdir": {
"type": "string",
"format": "directory-path",
"description": "The output directory where the results will be saved. You have to use absolute paths to storage on Cloud infrastructure.",
"fa_icon": "fas fa-folder-open"
},
"mode": {
"type": "string",
"default": "alphafold2",
"description": "Specifies the mode in which the pipeline will be run. mode can be any combination of ['alphafold2', 'colabfold', 'esmfold'] separated by a comma (',') with no spaces.",
"fa_icon": "fas fa-cogs"
},
"use_gpu": {
"type": "boolean",
"description": "Run on CPUs (default) or GPUs",
"fa_icon": "fas fa-microchip"
},
"split_fasta": {
"type": "boolean",
"description": "Split input multi-fasta file in separated fasta files each of them containing one sequence to be folded",
"fa_icon": "fas fa-microchip"
},
"email": {
"type": "string",
"description": "Email address for completion summary.",
"fa_icon": "fas fa-envelope",
"help_text": "Set this parameter to your e-mail address to get a summary e-mail with details of the run sent to you when the workflow exits. If set in your user config file (`~/.nextflow/config`) then you don't need to specify this on the command line for every run.",
"pattern": "^([a-zA-Z0-9_\\-\\.]+)@([a-zA-Z0-9_\\-\\.]+)\\.([a-zA-Z]{2,5})$"
},
"multiqc_title": {
"type": "string",
"description": "MultiQC report title. Printed as page header, used for filename if not otherwise specified.",
"fa_icon": "fas fa-file-signature"
}
}
},
"alphafold2_options": {
"title": "Alphafold2 options",
"type": "object",
"fa_icon": "fas fa-dna",
"description": "Alphafold2 options.",
"properties": {
"max_template_date": {
"type": "string",
"default": "2020-05-14",
"description": "Maximum date of the PDB templates used by 'AlphaFold2' mode",
"fa_icon": "fas fa-calendar-check"
},
"alphafold2_db": {
"type": "string",
"format": "path",
"exists": true,
"description": "Specifies the DB and PARAMS path used by 'AlphaFold2' mode",
"fa_icon": "fas fa-database"
},
"full_dbs": {
"type": "boolean",
"description": "If true uses the full version of the BFD database otherwise, otherwise it uses its reduced version, small bfd",
"fa_icon": "fas fa-battery-full"
},
"alphafold2_mode": {
"type": "string",
"default": "standard",
"description": "Specifies the mode in which Alphafold2 will be run",
"enum": ["standard", "split_msa_prediction"],
"fa_icon": "fas fa-exchange-alt"
},
"alphafold2_model_preset": {
"type": "string",
"default": "monomer",
"description": "Model preset for 'AlphaFold2' mode",
"enum": ["monomer", "monomer_casp14", "monomer_ptm", "multimer"],
"fa_icon": "fas fa-stream"
}
}
},
"colabfold_options": {
"title": "Colabfold options",
"type": "object",
"fa_icon": "fas fa-coins",
"description": "Colabfold options.",
"properties": {
"colabfold_db": {
"type": "string",
"format": "path",
"exists": true,
"description": "Specifies the PARAMS and DB path used by 'colabfold' mode",
"fa_icon": "fas fa-folder-open"
},
"colabfold_server": {
"type": "string",
"default": "webserver",
"description": "Specifies the MSA server used by Colabfold",
"enum": ["webserver", "local"],
"fa_icon": "fas fa-server"
},
"colabfold_model_preset": {
"type": "string",
"default": "alphafold2_ptm",
"description": "Model preset for 'colabfold' mode",
"enum": [
"auto",
"alphafold2",
"alphafold2_ptm",
"alphafold2_multimer_v1",
"alphafold2_multimer_v2",
"alphafold2_multimer_v3"
],
"fa_icon": "fas fa-stream"
},
"num_recycles_colabfold": {
"type": "integer",
"default": 3,
"description": "Number of recycles for Colabfold",
"fa_icon": "fas fa-recycle"
},
"use_amber": {
"type": "boolean",
"default": true,
"description": "Use Amber minimization to refine the predicted structures",
"fa_icon": "fas fa-compress-alt"
},
"db_load_mode": {
"type": "integer",
"default": 0,
"description": "Specify the way that MMSeqs2 will load the required databases in memory",
"fa_icon": "fas fa-download",
"enum": [0, 1, 2, 3]
},
"host_url": {
"type": "string",
"description": "Specify your custom MMSeqs2 API server url",
"fa_icon": "fas fa-link"
},
"use_templates": {
"type": "boolean",
"default": true,
"description": "Use PDB templates",
"fa_icon": "fas fa-paste"
},
"create_colabfold_index": {
"type": "boolean",
"description": "Create databases indexes when running colabfold_local mode",
"fa_icon": "fas fa-bezier-curve"
}
}
},
"esmfold_options": {
"title": "Esmfold options",
"type": "object",
"fa_icon": "fas fa-coins",
"description": "Esmfold options.",
"properties": {
"esmfold_db": {
"type": "string",
"format": "path",
"exists": true,
"description": "Specifies the PARAMS path used by 'esmfold' mode",
"fa_icon": "fas fa-folder-open"
},
"num_recycles_esmfold": {
"type": "integer",
"default": 4,
"description": "Specifies the number of recycles used by Esmfold",
"fa_icon": "fas fa-server"
},
"esmfold_model_preset": {
"type": "string",
"description": "Specifies whether is a 'monomer' or 'multimer' prediction",
"enum": ["monomer", "multimer"],
"fa_icon": "fas fa-stream",
"default": "monomer"
}
}
},
"foldseek_options": {
"title": "Foldseek options",
"type": "object",
"fa_icon": "fas fa-coins",
"description": "Foldseek options.",
"properties": {
"foldseek_search": {
"type": "string",
"enum": [null, "easysearch"],
"default": null,
"description": "Specifies the mode of foldseek search.",
"fa_icon": "fas fa-search"
},
"foldseek_db": {
"type": "string",
"description": "The ID of Foldseek databases",
"fa_icon": "fas fa-server"
},
"foldseek_db_path": {
"type": "string",
"format": "path",
"exists": true,
"description": "Specifies the path to foldseek databases used by 'foldseek'.",
"fa_icon": "fas fa-folder-open"
},
"foldseek_easysearch_arg": {
"type": "string",
"description": "Specifies the arguments to be passed to foldseek easysearch command",
"fa_icon": "fas fa-server"
}
}
},
"process_skipping_options": {
"title": "Process skipping options",
"type": "object",
"fa_icon": "fas fa-fast-forward",
"description": "Options to skip various steps within the workflow.",
"properties": {
"skip_multiqc": {
"type": "boolean",
"description": "Skip MultiQC.",
"fa_icon": "fas fa-fast-forward"
},
"skip_visualisation": {
"type": "boolean",
"description": "Skip visualisation reports.",
"fa_icon": "fas fa-fast-forward"
}
}
},
"institutional_config_options": {
"title": "Institutional config options",
"type": "object",
"fa_icon": "fas fa-university",
"description": "Parameters used to describe centralised config profiles. These should not be edited.",
"help_text": "The centralised nf-core configuration profiles use a handful of pipeline parameters to describe themselves. This information is then printed to the Nextflow log when you run a pipeline. You should not need to change these values when you run a pipeline.",
"properties": {
"custom_config_version": {
"type": "string",
"description": "Git commit id for Institutional configs.",
"default": "master",
"hidden": true,
"fa_icon": "fas fa-users-cog"
},
"custom_config_base": {
"type": "string",
"description": "Base directory for Institutional configs.",
"default": "https://raw.githubusercontent.com/nf-core/configs/master",
"hidden": true,
"help_text": "If you're running offline, Nextflow will not be able to fetch the institutional config files from the internet. If you don't need them, then this is not a problem. If you do need them, you should download the files from the repo and tell Nextflow where to find them with this parameter.",
"fa_icon": "fas fa-users-cog"
},
"config_profile_name": {
"type": "string",
"description": "Institutional config name.",
"hidden": true,
"fa_icon": "fas fa-users-cog"
},
"config_profile_description": {
"type": "string",
"description": "Institutional config description.",
"hidden": true,
"fa_icon": "fas fa-users-cog"
},
"config_profile_contact": {
"type": "string",
"description": "Institutional config contact information.",
"hidden": true,
"fa_icon": "fas fa-users-cog"
},
"config_profile_url": {
"type": "string",
"description": "Institutional config URL link.",
"hidden": true,
"fa_icon": "fas fa-users-cog"
}
}
},
"alphafold2_dbs_and_parameters_link_options": {
"title": "Alphafold2 DBs and parameters links options",
"type": "object",
"fa_icon": "fas fa-database",
"description": "Parameters used to provide the links to the DBs and parameters public resources to Alphafold2.",
"properties": {
"bfd_link": {
"type": "string",
"default": "https://storage.googleapis.com/alphafold-databases/casp14_versions/bfd_metaclust_clu_complete_id30_c90_final_seq.sorted_opt.tar.gz",
"description": "Link to BFD dababase",
"fa_icon": "fas fa-link"
},
"small_bfd_link": {
"type": "string",
"default": "https://storage.googleapis.com/alphafold-databases/reduced_dbs/bfd-first_non_consensus_sequences.fasta.gz",
"description": "Link to a reduced version of the BFD dababase",
"fa_icon": "fas fa-link"
},
"alphafold2_params_link": {
"type": "string",
"default": "https://storage.googleapis.com/alphafold/alphafold_params_2022-12-06.tar",
"description": "Link to the Alphafold2 parameters",
"fa_icon": "fas fa-link"
},
"mgnify_link": {
"type": "string",
"default": "https://storage.googleapis.com/alphafold-databases/v2.3/mgy_clusters_2022_05.fa.gz",
"description": "Link to the MGnify database",
"fa_icon": "fas fa-link"
},
"pdb70_link": {
"type": "string",
"default": "http://wwwuser.gwdg.de/~compbiol/data/hhsuite/databases/hhsuite_dbs/old-releases/pdb70_from_mmcif_200916.tar.gz",
"description": "Link to the PDB70 database",
"fa_icon": "fas fa-link"
},
"pdb_mmcif_link": {
"type": "string",
"default": "rsync.rcsb.org::ftp_data/structures/divided/mmCIF/",
"description": "Link to the PDB mmCIF database",
"fa_icon": "fas fa-link"
},
"pdb_obsolete_link": {
"type": "string",
"default": "https://files.wwpdb.org/pub/pdb/data/status/obsolete.dat",
"description": "Link to the PDB obsolete database",
"fa_icon": "fas fa-link"
},
"uniref30_alphafold2_link": {
"type": "string",
"default": "https://storage.googleapis.com/alphafold-databases/v2.3/UniRef30_2021_03.tar.gz",
"description": "Link to the Uniclust30 database",
"fa_icon": "fas fa-link"
},
"uniref90_link": {
"type": "string",
"default": "https://ftp.ebi.ac.uk/pub/databases/uniprot/uniref/uniref90/uniref90.fasta.gz",
"description": "Link to the UniRef90 database",
"fa_icon": "fas fa-link"
},
"pdb_seqres_link": {
"type": "string",
"default": "https://files.wwpdb.org/pub/pdb/derived_data/pdb_seqres.txt",
"description": "Link to the PDB SEQRES database",
"fa_icon": "fas fa-link"
},
"uniprot_sprot_link": {
"type": "string",
"default": "https://ftp.ebi.ac.uk/pub/databases/uniprot/current_release/knowledgebase/complete/uniprot_sprot.fasta.gz",
"description": "Link to the SwissProt UniProt database",
"fa_icon": "fas fa-link"
},
"uniprot_trembl_link": {
"type": "string",
"default": "https://ftp.ebi.ac.uk/pub/databases/uniprot/current_release/knowledgebase/complete/uniprot_trembl.fasta.gz",
"description": "Link to the TrEMBL UniProt database",
"fa_icon": "fas fa-link"
}
}
},
"alphafold2_dbs_and_parameters_path_options": {
"title": "Alphafold2 DBs and parameters links options",
"type": "object",
"fa_icon": "fas fa-database",
"description": "Parameters used to provide the paths to the DBs and parameters for Alphafold2.",
"properties": {
"bfd_path": {
"type": "string",
"description": "Path to BFD dababase",
"fa_icon": "fas fa-folder-open",
"default": "null/bfd/*"
},
"small_bfd_path": {
"type": "string",
"description": "Path to a reduced version of the BFD database",
"fa_icon": "fas fa-folder-open",
"default": "null/small_bfd/*"
},
"alphafold2_params_path": {
"type": "string",
"description": "Path to the Alphafold2 parameters",
"fa_icon": "fas fa-folder-open",
"default": "null/alphafold_params_*/*"
},
"mgnify_path": {
"type": "string",
"description": "Path to the MGnify database",
"fa_icon": "fas fa-folder-open",
"default": "null/mgnify/*"
},
"pdb70_path": {
"type": "string",
"description": "Path to the PDB70 database",
"fa_icon": "fas fa-folder-open",
"default": "null/pdb70/**"
},
"pdb_mmcif_path": {
"type": "string",
"description": "Path to the PDB mmCIF database",
"fa_icon": "fas fa-folder-open",
"default": "null/pdb_mmcif/*"
},
"uniref30_alphafold2_path": {
"type": "string",
"description": "Path to the Uniref30 database",
"fa_icon": "fas fa-folder-open",
"default": "null/uniref30/*"
},
"uniref90_path": {
"type": "string",
"description": "Path to the UniRef90 database",
"fa_icon": "fas fa-folder-open",
"default": "null/uniref90/*"
},
"pdb_seqres_path": {
"type": "string",
"description": "Path to the PDB SEQRES database",
"fa_icon": "fas fa-folder-open",
"default": "null/pdb_seqres/*"
},
"uniprot_path": {
"type": "string",
"description": "Path to UniProt database containing the SwissProt and the TrEMBL databases",
"fa_icon": "fas fa-folder-open",
"default": "null/uniprot/*"
}
}
},
"colabfold_dbs_and_parameters_link_options": {
"title": "Colabfold DBs and parameters links options",
"type": "object",
"description": "Parameters used to provide the links to the DBs and parameters public resources to Colabfold.",
"fa_icon": "fas fa-database",
"properties": {
"colabfold_db_link": {
"type": "string",
"default": "http://wwwuser.gwdg.de/~compbiol/colabfold/colabfold_envdb_202108.tar.gz",
"description": "Link to the Colabfold database",
"fa_icon": "fas fa-link"
},
"uniref30_colabfold_link": {
"type": "string",
"default": "https://wwwuser.gwdg.de/~compbiol/colabfold/uniref30_2302.tar.gz",
"description": "Link to the UniRef30 database",
"fa_icon": "fas fa-link"
},
"colabfold_alphafold2_params_link": {
"type": "string",
"description": "Link to the Alphafold2 parameters for Colabfold",
"fa_icon": "fas fa-link"
}
}
},
"colabfold_dbs_and_parameters_path_options": {
"title": "Colabfold DBs and parameters links options",
"type": "object",
"description": "Parameters used to provide the links to the DBs and parameters public resources to Colabfold.",
"fa_icon": "fas fa-database",
"properties": {
"colabfold_db_path": {
"type": "string",
"description": "Link to the Colabfold database",
"fa_icon": "fas fa-folder-open",
"default": "null/colabfold_envdb_202108"
},
"uniref30_colabfold_path": {
"type": "string",
"description": "Link to the UniRef30 database",
"fa_icon": "fas fa-folder-open",
"default": "null/uniref30_2302"
},
"colabfold_alphafold2_params_path": {
"type": "string",
"description": "Link to the Alphafold2 parameters for Colabfold",
"fa_icon": "fas fa-folder-open"
},
"colabfold_alphafold2_params_tags": {
"type": "object",
"description": "Dictionary with Alphafold2 parameters tags",
"fa_icon": "fas fa-stream"
}
}
},
"esmfold_parameters_link_options": {
"title": "Esmfold parameters links options",
"type": "object",
"description": "Parameters used to provide the links to the parameters public resources to Esmfold.",
"fa_icon": "fas fa-database",
"properties": {
"esmfold_3B_v1": {
"type": "string",
"default": "https://dl.fbaipublicfiles.com/fair-esm/models/esmfold_3B_v1.pt",
"description": "Link to the Esmfold 3B-v1 model",
"fa_icon": "fas fa-link"
},
"esm2_t36_3B_UR50D": {
"type": "string",
"default": "https://dl.fbaipublicfiles.com/fair-esm/models/esm2_t36_3B_UR50D.pt",
"description": "Link to the Esmfold t36-3B-UR50D model",
"fa_icon": "fas fa-link"
},
"esm2_t36_3B_UR50D_contact_regression": {
"type": "string",
"default": "https://dl.fbaipublicfiles.com/fair-esm/regression/esm2_t36_3B_UR50D-contact-regression.pt",
"description": "Link to the Esmfold t36-3B-UR50D-contact-regression model",
"fa_icon": "fas fa-link"
}
}
},
"esmfold_parameters_path_options": {
"title": "Esmfold parameters links options",
"type": "object",
"description": "Parameters used to provide the links to the parameters public resources to Esmfold.",
"fa_icon": "fas fa-database",
"properties": {
"esmfold_params_path": {
"type": "string",
"description": "Link to the Esmfold parameters",
"fa_icon": "fas fa-folder-open",
"default": "null/*"
}
}
},
"generic_options": {
"title": "Generic options",
"type": "object",
"fa_icon": "fas fa-file-import",
"description": "Less common options for the pipeline, typically set in a config file.",
"help_text": "These options are common to all nf-core pipelines and allow you to customise some of the core preferences for how the pipeline runs.\n\nTypically these options would be set in a Nextflow config file loaded for all pipeline runs, such as `~/.nextflow/config`.",
"properties": {
"version": {
"type": "boolean",
"description": "Display version and exit.",
"fa_icon": "fas fa-question-circle",
"hidden": true
},
"publish_dir_mode": {
"type": "string",
"default": "copy",
"description": "Method used to save pipeline results to output directory.",
"help_text": "The Nextflow `publishDir` option specifies which intermediate files should be saved to the output directory. This option tells the pipeline what method should be used to move these files. See [Nextflow docs](https://www.nextflow.io/docs/latest/process.html#publishdir) for details.",
"fa_icon": "fas fa-copy",
"enum": ["symlink", "rellink", "link", "copy", "copyNoFollow", "move"],
"hidden": true
},
"email_on_fail": {
"type": "string",
"description": "Email address for completion summary, only when pipeline fails.",
"fa_icon": "fas fa-exclamation-triangle",
"pattern": "^([a-zA-Z0-9_\\-\\.]+)@([a-zA-Z0-9_\\-\\.]+)\\.([a-zA-Z]{2,5})$",
"help_text": "An email address to send a summary email to when the pipeline is completed - ONLY sent if the pipeline does not exit successfully.",
"hidden": true
},
"plaintext_email": {
"type": "boolean",
"description": "Send plain-text email instead of HTML.",
"fa_icon": "fas fa-remove-format",
"hidden": true
},
"max_multiqc_email_size": {
"type": "string",
"description": "File size limit when attaching MultiQC reports to summary emails.",
"pattern": "^\\d+(\\.\\d+)?\\.?\\s*(K|M|G|T)?B$",
"default": "25.MB",
"fa_icon": "fas fa-file-upload",
"hidden": true
},
"monochrome_logs": {
"type": "boolean",
"description": "Do not use coloured log outputs.",
"fa_icon": "fas fa-palette",
"hidden": true
},
"hook_url": {
"type": "string",
"description": "Incoming hook URL for messaging service",
"fa_icon": "fas fa-people-group",
"help_text": "Incoming hook URL for messaging service. Currently, MS Teams and Slack are supported.",
"hidden": true
},
"multiqc_config": {
"type": "string",
"format": "file-path",
"exists": true,
"mimetype": "text/plain",
"description": "Custom config file to supply to MultiQC.",
"fa_icon": "fas fa-cog",
"hidden": true
},
"multiqc_logo": {
"type": "string",
"format": "file-path",
"exists": true,
"mimetype": "text/plain",
"description": "Custom logo file to supply to MultiQC. File name must also be set in the MultiQC config file",
"fa_icon": "fas fa-image",
"hidden": true
},
"multiqc_methods_description": {
"type": "string",
"format": "file-path",
"exists": true,
"mimetype": "text/plain",
"description": "Custom MultiQC yaml file containing HTML including a methods description.",
"fa_icon": "fas fa-cog"
},
"validate_params": {
"type": "boolean",
"description": "Boolean whether to validate parameters against the schema at runtime",
"default": true,
"fa_icon": "fas fa-check-square",
"hidden": true
},
"pipelines_testdata_base_path": {
"type": "string",
"fa_icon": "far fa-check-circle",
"description": "Base URL or local path to location of pipeline test dataset files",
"default": "https://raw.githubusercontent.com/nf-core/test-datasets/",
"hidden": true
}
}
}
},
"allOf": [
{
"$ref": "#/$defs/input_output_options"
},
{
"$ref": "#/$defs/alphafold2_options"
},
{
"$ref": "#/$defs/colabfold_options"
},
{
"$ref": "#/$defs/esmfold_options"
},
{
"$ref": "#/$defs/foldseek_options"
},
{
"$ref": "#/$defs/process_skipping_options"
},
{
"$ref": "#/$defs/institutional_config_options"
},
{
"$ref": "#/$defs/alphafold2_dbs_and_parameters_link_options"
},
{
"$ref": "#/$defs/alphafold2_dbs_and_parameters_path_options"
},
{
"$ref": "#/$defs/colabfold_dbs_and_parameters_link_options"
},
{
"$ref": "#/$defs/colabfold_dbs_and_parameters_path_options"
},
{
"$ref": "#/$defs/esmfold_parameters_link_options"
},
{
"$ref": "#/$defs/esmfold_parameters_path_options"
},
{
"$ref": "#/$defs/generic_options"
}
],
"properties": {
"helixfold3_init_models_link": {
"type": "string",
"default": "https://paddlehelix.bd.bcebos.com/HelixFold3/params/HelixFold3-params-240814.zip"
},
"helixfold3_init_models_path": {
"type": "string",
"default": "null/HelixFold3-240814.pdparams"
},
"helixfold3_db": {
"type": "string"
},
"helixfold3_uniclust30_link": {
"type": "string",
"default": "https://storage.googleapis.com/alphafold-databases/casp14_versions/uniclust30_2018_08_hhsuite.tar.gz"
},
"helixfold3_ccd_preprocessed_link": {
"type": "string",
"default": "https://paddlehelix.bd.bcebos.com/HelixFold3/CCD/ccd_preprocessed_etkdg.pkl.gz"
},
"helixfold3_rfam_link": {
"type": "string",
"default": "https://paddlehelix.bd.bcebos.com/HelixFold3/MSA/Rfam-14.9_rep_seq.fasta"
},
"helixfold3_bfd_link": {
"type": "string",
"default": "https://storage.googleapis.com/alphafold-databases/casp14_versions/bfd_metaclust_clu_complete_id30_c90_final_seq.sorted_opt.tar.gz"
},
"helixfold3_small_bfd_link": {
"type": "string",
"default": "https://storage.googleapis.com/alphafold-databases/reduced_dbs/bfd-first_non_consensus_sequences.fasta.gz"
},
"helixfold3_pdb_seqres_link": {
"type": "string",
"default": "https://files.wwpdb.org/pub/pdb/derived_data/pdb_seqres.txt"
},
"helixfold3_uniref90_link": {
"type": "string",
"default": "ftp://ftp.uniprot.org/pub/databases/uniprot/uniref/uniref90/uniref90.fasta.gz"
},
"helixfold3_mgnify_link": {
"type": "string",
"default": "https://storage.googleapis.com/alphafold-databases/casp14_versions/mgy_clusters_2018_12.fa.gz"
},
"helixfold3_pdb_mmcif_link": {
"type": "string",
"default": "rsync.rcsb.org::ftp_data/structures/divided/mmCIF/"
},
"helixfold3_uniclust30_path": {
"type": "string",
"default": "null/uniclust30/*"
},
"helixfold3_ccd_preprocessed_path": {
"type": "string",
"default": "null/ccd_preprocessed_etkdg.pkl.gz"
},
"helixfold3_rfam_path": {
"type": "string",
"default": "null/Rfam-14.9_rep_seq.fasta"
},
"helixfold3_bfd_path": {
"type": "string",
"default": "null/bfd/*"
},
"helixfold3_small_bfd_path": {
"type": "string",
"default": "null/small_bfd/*"
},
"helixfold3_uniprot_path": {
"type": "string",
"default": "null/uniprot/*"
},
"helixfold3_pdb_seqres_path": {
"type": "string",
"default": "null/pdb_seqres/*"
},
"helixfold3_uniref90_path": {
"type": "string",
"default": "null/uniref90/*"
},
"helixfold3_mgnify_path": {
"type": "string",
"default": "null/mgnify/*"
},
"helixfold3_pdb_mmcif_path": {
"type": "string",
"default": "null/pdb_mmcif/*"
},
"helixfold3_uniprot_sprot_link": {
"type": "string",
"default": "ftp://ftp.ebi.ac.uk/pub/databases/uniprot/current_release/knowledgebase/complete/uniprot_sprot.fasta.gz"
},
"helixfold3_uniprot_trembl_link": {
"type": "string",
"default": "ftp://ftp.ebi.ac.uk/pub/databases/uniprot/current_release/knowledgebase/complete/uniprot_trembl.fasta.gz"
},
"helixfold3_pdb_obsolete_link": {
"type": "string",
"default": "ftp://ftp.wwpdb.org/pub/pdb/data/status/obsolete.dat"
},
"helixfold3_maxit_src_path": {
"type": "string",
"default": "null/maxit-v11.200-prod-src"
},
"rosettafold_all_atom_db": {
"type": "string"
},
"uniref30_rosettafold_all_atom_link": {
"type": "string",
"default": "http://wwwuser.gwdg.de/~compbiol/uniclust/2020_06/UniRef30_2020_06_hhsuite.tar.gz"
},
"pdb100_rosettafold_all_atom_link": {
"type": "string",
"default": "https://files.ipd.uw.edu/pub/RoseTTAFold/pdb100_2021Mar03.tar.gz"
},
"bfd_rosettafold_all_atom_path": {
"type": "string",
"default": "null/bfd/*"
},
"rfaa_paper_weights_link": {
"type": "string",
"default": "http://files.ipd.uw.edu/pub/RF-All-Atom/weights/RFAA_paper_weights.pt"
},
"uniref30_rosettafold_all_atom_path": {
"type": "string",
"default": "null/uniref30/UniRef30_2020_06/*"
},
"pdb100_rosettafold_all_atom_path": {
"type": "string",
"default": "null/pdb100_2021Mar03/*"
},
"rfaa_paper_weights_path": {
"type": "string",
"default": "null/RFAA_paper_weights.pt"
},
"bfd_rosettafold_all_atom_link": {
"type": "string",
"default": "https://bfd.mmseqs.com/bfd_metaclust_clu_complete_id30_c90_final_seq.sorted_opt.tar.gz"
}
}
}