# BioBB HADDOCK Command Line Help Generic usage: ```python biobb_command [-h] --config CONFIG --input_file(s) --output_file ``` ----------------- ## Capri_eval Wrapper class for the HADDOCK3 CapriEval module. ### Get help Command: ```python capri_eval -h ``` usage: capri_eval [-h] [-c CONFIG] --input_haddock_wf_data INPUT_HADDOCK_WF_DATA --output_haddock_wf_data OUTPUT_HADDOCK_WF_DATA [--output_evaluation_zip_path OUTPUT_EVALUATION_ZIP_PATH] [--reference_pdb_path REFERENCE_PDB_PATH] [--haddock_config_path HADDOCK_CONFIG_PATH] Wrapper of the HADDOCK3 CapriEval module. options: -h, --help show this help message and exit -c CONFIG, --config CONFIG This file can be a YAML file, JSON file or JSON string required arguments: --input_haddock_wf_data INPUT_HADDOCK_WF_DATA Path to the input directory containing all the current Haddock workflow data. Accepted formats: directory, zip. --output_haddock_wf_data OUTPUT_HADDOCK_WF_DATA Path to the output directory containing all the current Haddock workflow data. Accepted formats: directory, zip. optional arguments: --output_evaluation_zip_path OUTPUT_EVALUATION_ZIP_PATH Path to the output PDB file collection in zip format. Accepted formats: zip. --reference_pdb_path REFERENCE_PDB_PATH Path to the input PDB file containing an structure for reference. Accepted formats: pdb. --haddock_config_path HADDOCK_CONFIG_PATH Haddock configuration CFG file path. Accepted formats: cfg. ### I / O Arguments Syntax: input_argument (datatype) : Definition Config input / output arguments for this building block: * **input_haddock_wf_data** (*dir*): Path to the input directory containing all the current Haddock workflow data. File type: input. [Sample file](https://github.com/bioexcel/biobb_haddock/raw/master/biobb_haddock/test/data/haddock/haddock_wf_data_rigid.zip). Accepted formats: DIRECTORY, ZIP * **output_haddock_wf_data** (*dir*): Path to the output directory containing all the current Haddock workflow data. File type: output. [Sample file](https://github.com/bioexcel/biobb_haddock/raw/master/biobb_haddock/test/data/haddock/haddock_wf_data_caprieval.zip). Accepted formats: DIRECTORY, ZIP * **output_evaluation_zip_path** (*string*): Path to the output PDB file collection in zip format. File type: output. [Sample file](https://raw.githubusercontent.com/bioexcel/biobb_haddock/master/biobb_haddock/test/reference/haddock/ref_caprieval.zip). Accepted formats: ZIP * **reference_pdb_path** (*string*): Path to the input PDB file containing an structure for reference. File type: input. [Sample file](https://raw.githubusercontent.com/bioexcel/biobb_haddock/master/biobb_haddock/test/data/haddock/e2a-hpr_1GGR.pdb). Accepted formats: PDB * **haddock_config_path** (*string*): Haddock configuration CFG file path. File type: input. [Sample file](https://raw.githubusercontent.com/bioexcel/biobb_haddock/master/biobb_haddock/test/data/haddock/run.cfg). Accepted formats: CFG ### Config Syntax: input_parameter (datatype) - (default_value) Definition Config parameters for this building block: * **cfg** (*object*): ({}) Haddock configuration options specification. * **global_cfg** (*object*): ({'postprocess': True}) Global configuration options specification. * **binary_path** (*string*): (haddock) Path to the haddock haddock executable binary. * **remove_tmp** (*boolean*): (True) Remove temporal files. * **restart** (*boolean*): (False) Do not execute if output files exist. * **sandbox_path** (*string*): (./) Parent path to the sandbox directory. * **container_path** (*string*): (None) Path to the binary executable of your container. * **container_image** (*string*): (None) Container Image identifier. * **container_volume_path** (*string*): (/data) Path to an internal directory in the container. * **container_working_dir** (*string*): (None) Path to the internal CWD in the container. * **container_user_id** (*string*): (None) User number id to be mapped inside the container. * **container_shell_path** (*string*): (/bin/bash) Path to the binary executable of the container shell. ### YAML #### [Common config file](https://github.com/bioexcel/biobb_haddock/blob/master/biobb_haddock/test/data/config/config_capri_eval.yml) ```python properties: remove_tmp: false ``` #### Command line ```python capri_eval --config config_capri_eval.yml --input_haddock_wf_data haddock_wf_data_rigid.zip --output_haddock_wf_data haddock_wf_data_caprieval.zip --output_evaluation_zip_path ref_caprieval.zip --reference_pdb_path e2a-hpr_1GGR.pdb --haddock_config_path run.cfg ``` ### JSON #### [Common config file](https://github.com/bioexcel/biobb_haddock/blob/master/biobb_haddock/test/data/config/config_capri_eval.json) ```python { "properties": { "remove_tmp": false } } ``` #### Command line ```python capri_eval --config config_capri_eval.json --input_haddock_wf_data haddock_wf_data_rigid.zip --output_haddock_wf_data haddock_wf_data_caprieval.zip --output_evaluation_zip_path ref_caprieval.zip --reference_pdb_path e2a-hpr_1GGR.pdb --haddock_config_path run.cfg ``` ## Clust_fcc Wrapper class for the HADDOCK3 ClustFCC module. ### Get help Command: ```python clust_fcc -h ``` usage: clust_fcc [-h] [-c CONFIG] --input_haddock_wf_data INPUT_HADDOCK_WF_DATA --output_haddock_wf_data OUTPUT_HADDOCK_WF_DATA [--output_cluster_zip_path OUTPUT_CLUSTER_ZIP_PATH] [--haddock_config_path HADDOCK_CONFIG_PATH] Wrapper of the HADDOCK3 ClustFCC module. options: -h, --help show this help message and exit -c CONFIG, --config CONFIG This file can be a YAML file, JSON file or JSON string required arguments: --input_haddock_wf_data INPUT_HADDOCK_WF_DATA Path to the input directory containing all the current Haddock workflow data. Accepted formats: directory, zip. --output_haddock_wf_data OUTPUT_HADDOCK_WF_DATA Path to the output directory containing all the current Haddock workflow data. Accepted formats: directory, zip. optional arguments: --output_cluster_zip_path OUTPUT_CLUSTER_ZIP_PATH Path to the output PDB file collection in zip format. Accepted formats: zip. --haddock_config_path HADDOCK_CONFIG_PATH Haddock configuration CFG file path. Accepted formats: cfg. ### I / O Arguments Syntax: input_argument (datatype) : Definition Config input / output arguments for this building block: * **input_haddock_wf_data** (*dir*): Path to the input directory containing all the current Haddock workflow data. File type: input. [Sample file](https://github.com/bioexcel/biobb_haddock/raw/master/biobb_haddock/test/data/haddock/haddock_wf_data_rigid.zip). Accepted formats: DIRECTORY, ZIP * **output_haddock_wf_data** (*dir*): Path to the output directory containing all the current Haddock workflow data. File type: output. [Sample file](https://github.com/bioexcel/biobb_haddock/raw/master/biobb_haddock/test/data/haddock/haddock_wf_data_clustfcc.zip). Accepted formats: DIRECTORY, ZIP * **output_cluster_zip_path** (*string*): Path to the output PDB file collection in zip format. File type: output. [Sample file](https://raw.githubusercontent.com/bioexcel/biobb_haddock/master/biobb_haddock/test/reference/haddock/ref_clustfcc.zip). Accepted formats: ZIP * **haddock_config_path** (*string*): Haddock configuration CFG file path. File type: input. [Sample file](https://raw.githubusercontent.com/bioexcel/biobb_haddock/master/biobb_haddock/test/data/haddock/run.cfg). Accepted formats: CFG ### Config Syntax: input_parameter (datatype) - (default_value) Definition Config parameters for this building block: * **cfg** (*object*): ({}) Haddock configuration options specification. * **global_cfg** (*object*): ({'postprocess': False}) Global configuration options specification. * **binary_path** (*string*): (haddock) Path to the haddock haddock executable binary. * **remove_tmp** (*boolean*): (True) Remove temporal files. * **restart** (*boolean*): (False) Do not execute if output files exist. * **sandbox_path** (*string*): (./) Parent path to the sandbox directory. * **container_path** (*string*): (None) Path to the binary executable of your container. * **container_image** (*string*): (None) Container Image identifier. * **container_volume_path** (*string*): (/data) Path to an internal directory in the container. * **container_working_dir** (*string*): (None) Path to the internal CWD in the container. * **container_user_id** (*string*): (None) User number id to be mapped inside the container. * **container_shell_path** (*string*): (/bin/bash) Path to the binary executable of the container shell. ### YAML #### [Common config file](https://github.com/bioexcel/biobb_haddock/blob/master/biobb_haddock/test/data/config/config_clust_fcc.yml) ```python properties: remove_tmp: false ``` #### Command line ```python clust_fcc --config config_clust_fcc.yml --input_haddock_wf_data haddock_wf_data_rigid.zip --output_haddock_wf_data haddock_wf_data_clustfcc.zip --output_cluster_zip_path ref_clustfcc.zip --haddock_config_path run.cfg ``` ### JSON #### [Common config file](https://github.com/bioexcel/biobb_haddock/blob/master/biobb_haddock/test/data/config/config_clust_fcc.json) ```python { "properties": { "remove_tmp": false } } ``` #### Command line ```python clust_fcc --config config_clust_fcc.json --input_haddock_wf_data haddock_wf_data_rigid.zip --output_haddock_wf_data haddock_wf_data_clustfcc.zip --output_cluster_zip_path ref_clustfcc.zip --haddock_config_path run.cfg ``` ## Contact_map Wrapper class for the HADDOCK3 ContactMap module. ### Get help Command: ```python contact_map -h ``` usage: contact_map [-h] [-c CONFIG] --input_haddock_wf_data INPUT_HADDOCK_WF_DATA --output_haddock_wf_data OUTPUT_HADDOCK_WF_DATA [--output_contactmap_zip_path OUTPUT_CONTACTMAP_ZIP_PATH] [--haddock_config_path HADDOCK_CONFIG_PATH] Wrapper of the HADDOCK3 ContactMap module. options: -h, --help show this help message and exit -c CONFIG, --config CONFIG This file can be a YAML file, JSON file or JSON string required arguments: --input_haddock_wf_data INPUT_HADDOCK_WF_DATA Path to the input directory containing all the current Haddock workflow data. Accepted formats: directory, zip. --output_haddock_wf_data OUTPUT_HADDOCK_WF_DATA Path to the output directory containing all the current Haddock workflow data. Accepted formats: directory, zip. optional arguments: --output_contactmap_zip_path OUTPUT_CONTACTMAP_ZIP_PATH Path to the output contact map files in zip format. Accepted formats: zip. --haddock_config_path HADDOCK_CONFIG_PATH Haddock configuration CFG file path. Accepted formats: cfg. ### I / O Arguments Syntax: input_argument (datatype) : Definition Config input / output arguments for this building block: * **input_haddock_wf_data** (*dir*): Path to the input directory containing all the current Haddock workflow data. File type: input. [Sample file](https://github.com/bioexcel/biobb_haddock/raw/master/biobb_haddock/test/data/haddock/haddock_wf_data_rigid.zip). Accepted formats: DIRECTORY, ZIP * **output_haddock_wf_data** (*dir*): Path to the output directory containing all the current Haddock workflow data. File type: output. [Sample file](None). Accepted formats: DIRECTORY, ZIP * **output_contactmap_zip_path** (*string*): Path to the output contact map files in zip format. File type: output. [Sample file](https://github.com/bioexcel/biobb_haddock/raw/master/biobb_haddock/test/reference/haddock/ref_contact_map.zip). Accepted formats: ZIP * **haddock_config_path** (*string*): Haddock configuration CFG file path. File type: input. [Sample file](https://raw.githubusercontent.com/bioexcel/biobb_haddock/master/biobb_haddock/test/data/haddock/run.cfg). Accepted formats: CFG ### Config Syntax: input_parameter (datatype) - (default_value) Definition Config parameters for this building block: * **cfg** (*object*): ({}) Haddock configuration options specification. * **global_cfg** (*object*): ({'postprocess': False}) Global configuration options specification. * **binary_path** (*string*): (haddock) Path to the haddock haddock executable binary. * **remove_tmp** (*boolean*): (True) Remove temporal files. * **restart** (*boolean*): (False) Do not execute if output files exist. * **sandbox_path** (*string*): (./) Parent path to the sandbox directory. * **container_path** (*string*): (None) Path to the binary executable of your container. * **container_image** (*string*): (None) Container Image identifier. * **container_volume_path** (*string*): (/data) Path to an internal directory in the container. * **container_working_dir** (*string*): (None) Path to the internal CWD in the container. * **container_user_id** (*string*): (None) User number id to be mapped inside the container. * **container_shell_path** (*string*): (/bin/bash) Path to the binary executable of the container shell. ### YAML #### [Common config file](https://github.com/bioexcel/biobb_haddock/blob/master/biobb_haddock/test/data/config/config_contact_map.yml) ```python properties: remove_tmp: false ``` #### Command line ```python contact_map --config config_contact_map.yml --input_haddock_wf_data haddock_wf_data_rigid.zip --output_haddock_wf_data output.directory --output_contactmap_zip_path ref_contact_map.zip --haddock_config_path run.cfg ``` ### JSON #### [Common config file](https://github.com/bioexcel/biobb_haddock/blob/master/biobb_haddock/test/data/config/config_contact_map.json) ```python { "properties": { "remove_tmp": false } } ``` #### Command line ```python contact_map --config config_contact_map.json --input_haddock_wf_data haddock_wf_data_rigid.zip --output_haddock_wf_data output.directory --output_contactmap_zip_path ref_contact_map.zip --haddock_config_path run.cfg ``` ## Em_ref Wrapper class for the HADDOCK3 EMRef module. ### Get help Command: ```python em_ref -h ``` usage: em_ref [-h] [-c CONFIG] --input_haddock_wf_data INPUT_HADDOCK_WF_DATA --output_haddock_wf_data OUTPUT_HADDOCK_WF_DATA [--refinement_output_zip_path REFINEMENT_OUTPUT_ZIP_PATH] [--ambig_restraints_table_path AMBIG_RESTRAINTS_TABLE_PATH] [--unambig_restraints_table_path UNAMBIG_RESTRAINTS_TABLE_PATH] [--hb_restraints_table_path HB_RESTRAINTS_TABLE_PATH] [--haddock_config_path HADDOCK_CONFIG_PATH] Wrapper of the HADDOCK3 EMRef module. options: -h, --help show this help message and exit -c CONFIG, --config CONFIG This file can be a YAML file, JSON file or JSON string required arguments: --input_haddock_wf_data INPUT_HADDOCK_WF_DATA Path to the input directory containing all the current Haddock workflow data. Accepted formats: directory, zip. --output_haddock_wf_data OUTPUT_HADDOCK_WF_DATA Path to the output directory containing all the current Haddock workflow data. Accepted formats: directory, zip. optional arguments: --refinement_output_zip_path REFINEMENT_OUTPUT_ZIP_PATH Path to the output PDB file collection in zip format. Accepted formats: zip. --ambig_restraints_table_path AMBIG_RESTRAINTS_TABLE_PATH Path to the input TBL file containing a list of ambiguous restraints for docking. Accepted formats: tbl. --unambig_restraints_table_path UNAMBIG_RESTRAINTS_TABLE_PATH Path to the input TBL file containing a list of unambiguous restraints for docking. Accepted formats: tbl. --hb_restraints_table_path HB_RESTRAINTS_TABLE_PATH Path to the input TBL file containing a list of hydrogen bond restraints for docking. Accepted formats: tbl. --haddock_config_path HADDOCK_CONFIG_PATH Haddock configuration CFG file path. Accepted formats: cfg. ### I / O Arguments Syntax: input_argument (datatype) : Definition Config input / output arguments for this building block: * **input_haddock_wf_data** (*dir*): Path to the input directory containing all the current Haddock workflow data. File type: input. [Sample file](https://github.com/bioexcel/biobb_haddock/raw/master/biobb_haddock/test/data/haddock/haddock_wf_data_topology.zip). Accepted formats: DIRECTORY, ZIP * **output_haddock_wf_data** (*dir*): Path to the output directory containing all the current Haddock workflow data. File type: output. [Sample file](None). Accepted formats: DIRECTORY, ZIP * **refinement_output_zip_path** (*string*): Path to the output PDB file collection in zip format. File type: output. [Sample file](https://raw.githubusercontent.com/bioexcel/biobb_haddock/master/biobb_haddock/test/reference/haddock/ref_rigidbody.zip). Accepted formats: ZIP * **ambig_restraints_table_path** (*string*): Path to the input TBL file containing a list of ambiguous restraints for docking. File type: input. [Sample file](https://raw.githubusercontent.com/bioexcel/biobb_haddock/master/biobb_haddock/test/data/haddock/e2a-hpr_air.tbl). Accepted formats: TBL * **unambig_restraints_table_path** (*string*): Path to the input TBL file containing a list of unambiguous restraints for docking. File type: input. [Sample file](https://raw.githubusercontent.com/bioexcel/biobb_haddock/master/biobb_haddock/test/data/haddock/e2a-hpr_air.tbl). Accepted formats: TBL * **hb_restraints_table_path** (*string*): Path to the input TBL file containing a list of hydrogen bond restraints for docking. File type: input. [Sample file](https://raw.githubusercontent.com/bioexcel/biobb_haddock/master/biobb_haddock/test/data/haddock/e2a-hpr_air.tbl). Accepted formats: TBL * **haddock_config_path** (*string*): Haddock configuration CFG file path. File type: input. [Sample file](https://raw.githubusercontent.com/bioexcel/biobb_haddock/master/biobb_haddock/test/data/haddock/run.cfg). Accepted formats: CFG ### Config Syntax: input_parameter (datatype) - (default_value) Definition Config parameters for this building block: * **cfg** (*object*): ({}) Haddock configuration options specification. * **global_cfg** (*object*): ({'postprocess': False}) Global configuration options specification. * **binary_path** (*string*): (haddock) Path to the haddock haddock executable binary. * **remove_tmp** (*boolean*): (True) Remove temporal files. * **restart** (*boolean*): (False) Do not execute if output files exist. * **sandbox_path** (*string*): (./) Parent path to the sandbox directory. * **container_path** (*string*): (None) Path to the binary executable of your container. * **container_image** (*string*): (None) Container Image identifier. * **container_volume_path** (*string*): (/data) Path to an internal directory in the container. * **container_working_dir** (*string*): (None) Path to the internal CWD in the container. * **container_user_id** (*string*): (None) User number id to be mapped inside the container. * **container_shell_path** (*string*): (/bin/bash) Path to the binary executable of the container shell. ### YAML #### [Common config file](https://github.com/bioexcel/biobb_haddock/blob/master/biobb_haddock/test/data/config/config_em_ref.yml) ```python properties: remove_tmp: false ``` #### Command line ```python em_ref --config config_em_ref.yml --input_haddock_wf_data haddock_wf_data_topology.zip --output_haddock_wf_data output.directory --refinement_output_zip_path ref_rigidbody.zip --ambig_restraints_table_path e2a-hpr_air.tbl --unambig_restraints_table_path e2a-hpr_air.tbl --hb_restraints_table_path e2a-hpr_air.tbl --haddock_config_path run.cfg ``` ### JSON #### [Common config file](https://github.com/bioexcel/biobb_haddock/blob/master/biobb_haddock/test/data/config/config_em_ref.json) ```python { "properties": { "remove_tmp": false } } ``` #### Command line ```python em_ref --config config_em_ref.json --input_haddock_wf_data haddock_wf_data_topology.zip --output_haddock_wf_data output.directory --refinement_output_zip_path ref_rigidbody.zip --ambig_restraints_table_path e2a-hpr_air.tbl --unambig_restraints_table_path e2a-hpr_air.tbl --hb_restraints_table_path e2a-hpr_air.tbl --haddock_config_path run.cfg ``` ## Flex_ref Wrapper class for the HADDOCK3 FlexRef module. ### Get help Command: ```python flex_ref -h ``` usage: flex_ref [-h] [-c CONFIG] --input_haddock_wf_data INPUT_HADDOCK_WF_DATA --output_haddock_wf_data OUTPUT_HADDOCK_WF_DATA [--refinement_output_zip_path REFINEMENT_OUTPUT_ZIP_PATH] [--ambig_restraints_table_path AMBIG_RESTRAINTS_TABLE_PATH] [--unambig_restraints_table_path UNAMBIG_RESTRAINTS_TABLE_PATH] [--hb_restraints_table_path HB_RESTRAINTS_TABLE_PATH] [--haddock_config_path HADDOCK_CONFIG_PATH] Wrapper of the HADDOCK3 FlexRef module. options: -h, --help show this help message and exit -c CONFIG, --config CONFIG This file can be a YAML file, JSON file or JSON string required arguments: --input_haddock_wf_data INPUT_HADDOCK_WF_DATA Path to the input directory containing all the current Haddock workflow data. Accepted formats: directory, zip. --output_haddock_wf_data OUTPUT_HADDOCK_WF_DATA Path to the output directory containing all the current Haddock workflow data. Accepted formats: directory, zip. optional arguments: --refinement_output_zip_path REFINEMENT_OUTPUT_ZIP_PATH Path to the output PDB file collection in zip format. Accepted formats: zip. --ambig_restraints_table_path AMBIG_RESTRAINTS_TABLE_PATH Path to the input TBL file containing a list of ambiguous restraints for docking. Accepted formats: tbl. --unambig_restraints_table_path UNAMBIG_RESTRAINTS_TABLE_PATH Path to the input TBL file containing a list of unambiguous restraints for docking. Accepted formats: tbl. --hb_restraints_table_path HB_RESTRAINTS_TABLE_PATH Path to the input TBL file containing a list of hydrogen bond restraints for docking. Accepted formats: tbl. --haddock_config_path HADDOCK_CONFIG_PATH Haddock configuration CFG file path. Accepted formats: cfg. ### I / O Arguments Syntax: input_argument (datatype) : Definition Config input / output arguments for this building block: * **input_haddock_wf_data** (*dir*): Path to the input directory containing all the current Haddock workflow data. File type: input. [Sample file](https://github.com/bioexcel/biobb_haddock/raw/master/biobb_haddock/test/data/haddock/haddock_wf_data_topology.zip). Accepted formats: DIRECTORY, ZIP * **output_haddock_wf_data** (*dir*): Path to the output directory containing all the current Haddock workflow data. File type: output. [Sample file](None). Accepted formats: DIRECTORY, ZIP * **refinement_output_zip_path** (*string*): Path to the output PDB file collection in zip format. File type: output. [Sample file](https://raw.githubusercontent.com/bioexcel/biobb_haddock/master/biobb_haddock/test/reference/haddock/ref_rigidbody.zip). Accepted formats: ZIP * **ambig_restraints_table_path** (*string*): Path to the input TBL file containing a list of ambiguous restraints for docking. File type: input. [Sample file](https://raw.githubusercontent.com/bioexcel/biobb_haddock/master/biobb_haddock/test/data/haddock/e2a-hpr_air.tbl). Accepted formats: TBL * **unambig_restraints_table_path** (*string*): Path to the input TBL file containing a list of unambiguous restraints for docking. File type: input. [Sample file](https://raw.githubusercontent.com/bioexcel/biobb_haddock/master/biobb_haddock/test/data/haddock/e2a-hpr_air.tbl). Accepted formats: TBL * **hb_restraints_table_path** (*string*): Path to the input TBL file containing a list of hydrogen bond restraints for docking. File type: input. [Sample file](https://raw.githubusercontent.com/bioexcel/biobb_haddock/master/biobb_haddock/test/data/haddock/e2a-hpr_air.tbl). Accepted formats: TBL * **haddock_config_path** (*string*): Haddock configuration CFG file path. File type: input. [Sample file](https://raw.githubusercontent.com/bioexcel/biobb_haddock/master/biobb_haddock/test/data/haddock/run.cfg). Accepted formats: CFG ### Config Syntax: input_parameter (datatype) - (default_value) Definition Config parameters for this building block: * **cfg** (*object*): ({}) Haddock configuration options specification. * **global_cfg** (*object*): ({'postprocess': False}) Global configuration options specification. * **binary_path** (*string*): (haddock) Path to the haddock haddock executable binary. * **remove_tmp** (*boolean*): (True) Remove temporal files. * **restart** (*boolean*): (False) Do not execute if output files exist. * **sandbox_path** (*string*): (./) Parent path to the sandbox directory. * **container_path** (*string*): (None) Path to the binary executable of your container. * **container_image** (*string*): (None) Container Image identifier. * **container_volume_path** (*string*): (/data) Path to an internal directory in the container. * **container_working_dir** (*string*): (None) Path to the internal CWD in the container. * **container_user_id** (*string*): (None) User number id to be mapped inside the container. * **container_shell_path** (*string*): (/bin/bash) Path to the binary executable of the container shell. ### YAML #### [Common config file](https://github.com/bioexcel/biobb_haddock/blob/master/biobb_haddock/test/data/config/config_flex_ref.yml) ```python properties: remove_tmp: false ``` #### Command line ```python flex_ref --config config_flex_ref.yml --input_haddock_wf_data haddock_wf_data_topology.zip --output_haddock_wf_data output.directory --refinement_output_zip_path ref_rigidbody.zip --ambig_restraints_table_path e2a-hpr_air.tbl --unambig_restraints_table_path e2a-hpr_air.tbl --hb_restraints_table_path e2a-hpr_air.tbl --haddock_config_path run.cfg ``` ### JSON #### [Common config file](https://github.com/bioexcel/biobb_haddock/blob/master/biobb_haddock/test/data/config/config_flex_ref.json) ```python { "properties": { "remove_tmp": false } } ``` #### Command line ```python flex_ref --config config_flex_ref.json --input_haddock_wf_data haddock_wf_data_topology.zip --output_haddock_wf_data output.directory --refinement_output_zip_path ref_rigidbody.zip --ambig_restraints_table_path e2a-hpr_air.tbl --unambig_restraints_table_path e2a-hpr_air.tbl --hb_restraints_table_path e2a-hpr_air.tbl --haddock_config_path run.cfg ``` ## Haddock3_accessibility Wrapper class for the Haddock-Restraints Accessibility module. ### Get help Command: ```python haddock3_accessibility -h ``` usage: haddock3_accessibility [-h] [-c CONFIG] -i INPUT_PDB_PATH --output_accessibility_path OUTPUT_ACCESSIBILITY_PATH [--output_actpass_path OUTPUT_ACTPASS_PATH] Wrapper of the Haddock-Restraints Accessibility module. options: -h, --help show this help message and exit -c CONFIG, --config CONFIG This file can be a YAML file, JSON file or JSON string required arguments: -i INPUT_PDB_PATH, --input_pdb_path INPUT_PDB_PATH Path to the input PDB file. Accepted formats: pdb. --output_accessibility_path OUTPUT_ACCESSIBILITY_PATH Path to the output file with accessibility information. Accepted formats: txt, dat, out. optional arguments: --output_actpass_path OUTPUT_ACTPASS_PATH Path to the output file with active/passive residues to be used as haddock3 restraint information. Accepted formats: txt, dat, out. ### I / O Arguments Syntax: input_argument (datatype) : Definition Config input / output arguments for this building block: * **input_pdb_path** (*string*): Path to the input PDB file. File type: input. [Sample file](https://raw.githubusercontent.com/bioexcel/biobb_haddock/master/biobb_haddock/test/data/haddock/e2aP_1F3G_noH.pdb). Accepted formats: PDB * **output_accessibility_path** (*string*): Path to the output file with accessibility information. File type: output. [Sample file](https://raw.githubusercontent.com/bioexcel/biobb_haddock/master/biobb_haddock/test/reference/haddock_restraints/mol1_sasa.txt). Accepted formats: TXT, DAT, OUT * **output_actpass_path** (*string*): Path to the output file with active/passive residues to be used as haddock3 restraint information. File type: output. [Sample file](https://raw.githubusercontent.com/bioexcel/biobb_haddock/master/biobb_haddock/test/reference/haddock_restraints/mol1_haddock_actpass.txt). Accepted formats: TXT, DAT, OUT ### Config Syntax: input_parameter (datatype) - (default_value) Definition Config parameters for this building block: * **chain** (*string*): (A) Chain to be used from the input PDB file. * **cutoff** (*number*): (0.4) Relative cutoff for sidechain accessibility. * **probe_radius** (*number*): (1.4) Probe radius for the accessibility calculation. * **pass_to_act** (*boolean*): (False) If True, the passive residues become active in the actpass file and vice versa. * **binary_path** (*string*): (haddock) Path to the haddock haddock executable binary. * **remove_tmp** (*boolean*): (True) Remove temporal files. * **restart** (*boolean*): (False) Do not execute if output files exist. * **sandbox_path** (*string*): (./) Parent path to the sandbox directory. * **container_path** (*string*): (None) Path to the binary executable of your container. * **container_image** (*string*): (None) Container Image identifier. * **container_volume_path** (*string*): (/data) Path to an internal directory in the container. * **container_working_dir** (*string*): (None) Path to the internal CWD in the container. * **container_user_id** (*string*): (None) User number id to be mapped inside the container. * **container_shell_path** (*string*): (/bin/bash) Path to the binary executable of the container shell. ### YAML #### [Common config file](https://github.com/bioexcel/biobb_haddock/blob/master/biobb_haddock/test/data/config/config_haddock3_accessibility.yml) ```python properties: remove_tmp: false ``` #### Command line ```python haddock3_accessibility --config config_haddock3_accessibility.yml --input_pdb_path e2aP_1F3G_noH.pdb --output_accessibility_path mol1_sasa.txt --output_actpass_path mol1_haddock_actpass.txt ``` ### JSON #### [Common config file](https://github.com/bioexcel/biobb_haddock/blob/master/biobb_haddock/test/data/config/config_haddock3_accessibility.json) ```python { "properties": { "remove_tmp": false } } ``` #### Command line ```python haddock3_accessibility --config config_haddock3_accessibility.json --input_pdb_path e2aP_1F3G_noH.pdb --output_accessibility_path mol1_sasa.txt --output_actpass_path mol1_haddock_actpass.txt ``` ## Haddock3_actpass_to_ambig Wrapper class for the Haddock-Restraints active_passive_to_ambig module. ### Get help Command: ```python haddock3_actpass_to_ambig -h ``` usage: haddock3_actpass_to_ambig [-h] [-c CONFIG] --input_actpass1_path INPUT_ACTPASS1_PATH --input_actpass2_path INPUT_ACTPASS2_PATH -o OUTPUT_TBL_PATH Wrapper of the Haddock-Restraints active_passive_to_ambig module. options: -h, --help show this help message and exit -c CONFIG, --config CONFIG This file can be a YAML file, JSON file or JSON string required arguments: --input_actpass1_path INPUT_ACTPASS1_PATH Path to the first input HADDOCK active-passive file containing active (in the first line) and passive (second line) residues. Accepted formats: txt, dat, in, pass. --input_actpass2_path INPUT_ACTPASS2_PATH Path to the second input HADDOCK active-passive file containing active (in the first line) and passive (second line) residues. Accepted formats: txt, dat, in, pass. -o OUTPUT_TBL_PATH, --output_tbl_path OUTPUT_TBL_PATH Path to the output HADDOCK tbl file with Ambiguous Interaction Restraints (AIR) information. Accepted formats: tbl, txt, out. ### I / O Arguments Syntax: input_argument (datatype) : Definition Config input / output arguments for this building block: * **input_actpass1_path** (*string*): Path to the first input HADDOCK active-passive file containing active (in the first line) and passive (second line) residues. File type: input. [Sample file](https://raw.githubusercontent.com/bioexcel/biobb_haddock/master/biobb_haddock/test/data/haddock_restraints/haddock_actpass1.pass). Accepted formats: TXT, DAT, IN, PASS * **input_actpass2_path** (*string*): Path to the second input HADDOCK active-passive file containing active (in the first line) and passive (second line) residues. File type: input. [Sample file](https://raw.githubusercontent.com/bioexcel/biobb_haddock/master/biobb_haddock/test/data/haddock_restraints/haddock_actpass2.pass). Accepted formats: TXT, DAT, IN, PASS * **output_tbl_path** (*string*): Path to the output HADDOCK tbl file with Ambiguous Interaction Restraints (AIR) information. File type: output. [Sample file](https://raw.githubusercontent.com/bioexcel/biobb_haddock/master/biobb_haddock/test/reference/haddock_restraints/haddock_actpass.tbl). Accepted formats: TBL, TXT, OUT ### Config Syntax: input_parameter (datatype) - (default_value) Definition Config parameters for this building block: * **pass_to_act** (*boolean*): (False) Path to the haddock haddock executable binary. * **segid_one** (*string*): (None) Segid of the first model. * **segid_two** (*string*): (None) Segid of the second model. * **binary_path** (*string*): (haddock) Path to the haddock haddock executable binary. * **remove_tmp** (*boolean*): (True) Remove temporal files. * **restart** (*boolean*): (False) Do not execute if output files exist. * **sandbox_path** (*string*): (./) Parent path to the sandbox directory. * **container_path** (*string*): (None) Path to the binary executable of your container. * **container_image** (*string*): (None) Container Image identifier. * **container_volume_path** (*string*): (/data) Path to an internal directory in the container. * **container_working_dir** (*string*): (None) Path to the internal CWD in the container. * **container_user_id** (*string*): (None) User number id to be mapped inside the container. * **container_shell_path** (*string*): (/bin/bash) Path to the binary executable of the container shell. ### YAML #### [Common config file](https://github.com/bioexcel/biobb_haddock/blob/master/biobb_haddock/test/data/config/config_haddock3_actpass_to_ambig.yml) ```python properties: remove_tmp: false ``` #### Command line ```python haddock3_actpass_to_ambig --config config_haddock3_actpass_to_ambig.yml --input_actpass1_path haddock_actpass1.pass --input_actpass2_path haddock_actpass2.pass --output_tbl_path haddock_actpass.tbl ``` ### JSON #### [Common config file](https://github.com/bioexcel/biobb_haddock/blob/master/biobb_haddock/test/data/config/config_haddock3_actpass_to_ambig.json) ```python { "properties": { "remove_tmp": false } } ``` #### Command line ```python haddock3_actpass_to_ambig --config config_haddock3_actpass_to_ambig.json --input_actpass1_path haddock_actpass1.pass --input_actpass2_path haddock_actpass2.pass --output_tbl_path haddock_actpass.tbl ``` ## Haddock3_extend Wrapper class for the HADDOCK3 extend module. ### Get help Command: ```python haddock3_extend -h ``` usage: haddock3_extend [-h] [-c CONFIG] --input_haddock_wf_data INPUT_HADDOCK_WF_DATA --haddock_config_path HADDOCK_CONFIG_PATH -o OUTPUT_HADDOCK_WF_DATA Wrapper of the HADDOCK3 Haddock3Extend module. options: -h, --help show this help message and exit -c CONFIG, --config CONFIG This file can be a YAML file, JSON file or JSON string required arguments: --input_haddock_wf_data INPUT_HADDOCK_WF_DATA Path to the input zipball containing all the current Haddock workflow data. Accepted formats: zip. --haddock_config_path HADDOCK_CONFIG_PATH Haddock configuration CFG file path. Accepted formats: cfg. -o OUTPUT_HADDOCK_WF_DATA, --output_haddock_wf_data OUTPUT_HADDOCK_WF_DATA Path to the output zipball containing all the current Haddock workflow data. Accepted formats: zip. ### I / O Arguments Syntax: input_argument (datatype) : Definition Config input / output arguments for this building block: * **input_haddock_wf_data** (*dir*): Path to the input zipball containing all the current Haddock workflow data. File type: input. [Sample file](https://github.com/bioexcel/biobb_haddock/raw/master/biobb_haddock/test/data/haddock/haddock_wf_data_caprieval.zip). Accepted formats: ZIP * **haddock_config_path** (*string*): Haddock configuration CFG file path. File type: input. [Sample file](https://raw.githubusercontent.com/bioexcel/biobb_haddock/master/biobb_haddock/test/data/haddock/run.cfg). Accepted formats: CFG * **output_haddock_wf_data** (*dir*): Path to the output zipball containing all the current Haddock workflow data. File type: output. [Sample file](https://github.com/bioexcel/biobb_haddock/raw/master/biobb_haddock/test/reference/haddock/ref_haddock3_extend.zip). Accepted formats: ZIP ### Config Syntax: input_parameter (datatype) - (default_value) Definition Config parameters for this building block: * **cfg** (*object*): ({}) Haddock configuration options specification. * **global_cfg** (*object*): ({'postprocess': True}) Global configuration options specification. * **binary_path** (*string*): (haddock) Path to the haddock haddock executable binary. * **remove_tmp** (*boolean*): (True) Remove temporal files. * **restart** (*boolean*): (False) Do not execute if output files exist. * **sandbox_path** (*string*): (./) Parent path to the sandbox directory. * **container_path** (*string*): (None) Path to the binary executable of your container. * **container_image** (*string*): (None) Container Image identifier. * **container_volume_path** (*string*): (/data) Path to an internal directory in the container. * **container_working_dir** (*string*): (None) Path to the internal CWD in the container. * **container_user_id** (*string*): (None) User number id to be mapped inside the container. * **container_shell_path** (*string*): (/bin/bash) Path to the binary executable of the container shell. ### YAML #### [Common config file](https://github.com/bioexcel/biobb_haddock/blob/master/biobb_haddock/test/data/config/config_haddock3_extend.yml) ```python properties: remove_tmp: false ``` #### Command line ```python haddock3_extend --config config_haddock3_extend.yml --input_haddock_wf_data haddock_wf_data_caprieval.zip --haddock_config_path run.cfg --output_haddock_wf_data ref_haddock3_extend.zip ``` ### JSON #### [Common config file](https://github.com/bioexcel/biobb_haddock/blob/master/biobb_haddock/test/data/config/config_haddock3_extend.json) ```python { "properties": { "remove_tmp": false } } ``` #### Command line ```python haddock3_extend --config config_haddock3_extend.json --input_haddock_wf_data haddock_wf_data_caprieval.zip --haddock_config_path run.cfg --output_haddock_wf_data ref_haddock3_extend.zip ``` ## Haddock3_passive_from_active Wrapper class for the Haddock3-Restraints passive_from_active module. ### Get help Command: ```python haddock3_passive_from_active -h ``` usage: haddock3_passive_from_active [-h] [-c CONFIG] --input_pdb_path INPUT_PDB_PATH -o OUTPUT_ACTPASS_PATH [--input_active_list_path INPUT_ACTIVE_LIST_PATH] Wrapper of the Haddock3-Restraints passive_from_active module. options: -h, --help show this help message and exit -c CONFIG, --config CONFIG This file can be a YAML file, JSON file or JSON string required arguments: --input_pdb_path INPUT_PDB_PATH Path to the input PDB structure file. Accepted formats: pdb. -o OUTPUT_ACTPASS_PATH, --output_actpass_path OUTPUT_ACTPASS_PATH Path to the output file with list of passive residues. Accepted formats: txt, dat, list, out. optional arguments: --input_active_list_path INPUT_ACTIVE_LIST_PATH Path to the input file with list of active residues. Accepted formats: txt, dat, list. ### I / O Arguments Syntax: input_argument (datatype) : Definition Config input / output arguments for this building block: * **input_pdb_path** (*string*): Path to the input PDB structure file. File type: input. [Sample file](https://raw.githubusercontent.com/bioexcel/biobb_haddock/master/biobb_haddock/test/data/haddock_restraints/1A2P_ch.pdb). Accepted formats: PDB * **output_actpass_path** (*string*): Path to the output file with list of passive residues. File type: output. [Sample file](https://raw.githubusercontent.com/bioexcel/biobb_haddock/master/biobb_haddock/test/reference/haddock_restraints/1A2P_manual_actpass.txt). Accepted formats: TXT, DAT, LIST, OUT * **input_active_list_path** (*string*): Path to the input file with list of active residues. File type: input. [Sample file](None). Accepted formats: TXT, DAT, LIST ### Config Syntax: input_parameter (datatype) - (default_value) Definition Config parameters for this building block: * **active_list** (*string*): () List of active residues as a comma-separated string. Required if input_active_list_path is not provided. * **chain_id** (*string*): (None) Chain ID to consider when calculating passive residues. * **surface_list_path** (*string*): () Path to file with list of surface residues to filter. * **radius** (*number*): (6.5) Radius in Angstroms to look for surface residues around active ones. * **binary_path** (*string*): (haddock3-restraints) Path to the haddock3-restraints executable binary. * **remove_tmp** (*boolean*): (True) Remove temporal files. * **restart** (*boolean*): (False) Do not execute if output files exist. * **sandbox_path** (*string*): (./) Parent path to the sandbox directory. * **container_path** (*string*): (None) Path to the binary executable of your container. * **container_image** (*string*): (None) Container Image identifier. * **container_volume_path** (*string*): (/data) Path to an internal directory in the container. * **container_working_dir** (*string*): (None) Path to the internal CWD in the container. * **container_user_id** (*string*): (None) User number id to be mapped inside the container. * **container_shell_path** (*string*): (/bin/bash) Path to the binary executable of the container shell. ### YAML #### [Common config file](https://github.com/bioexcel/biobb_haddock/blob/master/biobb_haddock/test/data/config/config_haddock3_passive_from_active.yml) ```python properties: active_list: 27,73,83,87 remove_tmp: false ``` #### Command line ```python haddock3_passive_from_active --config config_haddock3_passive_from_active.yml --input_pdb_path 1A2P_ch.pdb --output_actpass_path 1A2P_manual_actpass.txt --input_active_list_path input.txt ``` ### JSON #### [Common config file](https://github.com/bioexcel/biobb_haddock/blob/master/biobb_haddock/test/data/config/config_haddock3_passive_from_active.json) ```python { "properties": { "remove_tmp": false, "active_list": "27,73,83,87" } } ``` #### Command line ```python haddock3_passive_from_active --config config_haddock3_passive_from_active.json --input_pdb_path 1A2P_ch.pdb --output_actpass_path 1A2P_manual_actpass.txt --input_active_list_path input.txt ``` ## Haddock3_restrain_bodies Wrapper class for the Haddock-Restraints restrain_bodies module. ### Get help Command: ```python haddock3_restrain_bodies -h ``` usage: haddock3_restrain_bodies [-h] [-c CONFIG] -i INPUT_STRUCTURE_PATH -o OUTPUT_TBL_PATH Wrapper of the HADDOCK3 restrain_bodies module. options: -h, --help show this help message and exit -c CONFIG, --config CONFIG This file can be a YAML file, JSON file or JSON string required arguments: -i INPUT_STRUCTURE_PATH, --input_structure_path INPUT_STRUCTURE_PATH Path to the input PDB structure to be restrained. Accepted formats: pdb. -o OUTPUT_TBL_PATH, --output_tbl_path OUTPUT_TBL_PATH Path to the output HADDOCK tbl file with Ambiguous Interaction Restraints (AIR) information. Accepted formats: tbl, txt, out. ### I / O Arguments Syntax: input_argument (datatype) : Definition Config input / output arguments for this building block: * **input_structure_path** (*string*): Path to the input PDB structure to be restrained. File type: input. [Sample file](https://raw.githubusercontent.com/bioexcel/biobb_haddock/master/biobb_haddock/test/data/haddock_restraints/4G6K_clean.pdb). Accepted formats: PDB * **output_tbl_path** (*string*): Path to the output HADDOCK tbl file with Ambiguous Interaction Restraints (AIR) information. File type: output. [Sample file](https://raw.githubusercontent.com/bioexcel/biobb_haddock/master/biobb_haddock/test/reference/haddock_restraints/antibody-unambig.tbl). Accepted formats: TBL, TXT, OUT ### Config Syntax: input_parameter (datatype) - (default_value) Definition Config parameters for this building block: * **exclude** (*string*): (None) Chains to exclude from the calculation. * **verbose** (*integer*): (0) Tune verbosity of the output. * **binary_path** (*string*): (haddock3-restraints) Path to the HADDOCK3 restraints executable binary. * **remove_tmp** (*boolean*): (True) Remove temporal files. * **restart** (*boolean*): (False) Do not execute if output files exist. * **sandbox_path** (*string*): (./) Parent path to the sandbox directory. * **container_path** (*string*): (None) Path to the binary executable of your container. * **container_image** (*string*): (None) Container Image identifier. * **container_volume_path** (*string*): (/data) Path to an internal directory in the container. * **container_working_dir** (*string*): (None) Path to the internal CWD in the container. * **container_user_id** (*string*): (None) User number id to be mapped inside the container. * **container_shell_path** (*string*): (/bin/bash) Path to the binary executable of the container shell. ### YAML #### [Common config file](https://github.com/bioexcel/biobb_haddock/blob/master/biobb_haddock/test/data/config/config_haddock3_restrain_bodies.yml) ```python properties: remove_tmp: false ``` #### Command line ```python haddock3_restrain_bodies --config config_haddock3_restrain_bodies.yml --input_structure_path 4G6K_clean.pdb --output_tbl_path antibody-unambig.tbl ``` ### JSON #### [Common config file](https://github.com/bioexcel/biobb_haddock/blob/master/biobb_haddock/test/data/config/config_haddock3_restrain_bodies.json) ```python { "properties": { "remove_tmp": false } } ``` #### Command line ```python haddock3_restrain_bodies --config config_haddock3_restrain_bodies.json --input_structure_path 4G6K_clean.pdb --output_tbl_path antibody-unambig.tbl ``` ## Haddock3_run Wrapper class for the HADDOCK3 Run module. ### Get help Command: ```python haddock3_run -h ``` usage: haddock3_run [-h] [-c CONFIG] --input_haddock_wf_data INPUT_HADDOCK_WF_DATA -o OUTPUT_HADDOCK_WF_DATA [--haddock_config_path HADDOCK_CONFIG_PATH] Wrapper of the HADDOCK3 Haddock3Run module. options: -h, --help show this help message and exit -c CONFIG, --config CONFIG This file can be a YAML file, JSON file or JSON string required arguments: --input_haddock_wf_data INPUT_HADDOCK_WF_DATA Input folder containing all the files defined in the config. Accepted formats: directory, zip. -o OUTPUT_HADDOCK_WF_DATA, --output_haddock_wf_data OUTPUT_HADDOCK_WF_DATA Path to the output zipball containing all the current Haddock workflow data. Accepted formats: directory, zip. optional arguments: --haddock_config_path HADDOCK_CONFIG_PATH Haddock configuration CFG file path. Accepted formats: cfg. ### I / O Arguments Syntax: input_argument (datatype) : Definition Config input / output arguments for this building block: * **input_haddock_wf_data** (*dir*): Input folder containing all the files defined in the config. File type: input. [Sample file](https://github.com/bioexcel/biobb_haddock/tree/master/biobb_haddock/test/data/haddock/haddock_wf_data_run.zip). Accepted formats: DIRECTORY, ZIP * **output_haddock_wf_data** (*dir*): Path to the output zipball containing all the current Haddock workflow data. File type: output. [Sample file](None). Accepted formats: DIRECTORY, ZIP * **haddock_config_path** (*string*): Haddock configuration CFG file path. File type: input. [Sample file](https://raw.githubusercontent.com/bioexcel/biobb_haddock/master/biobb_haddock/test/data/haddock/run.cfg). Accepted formats: CFG ### Config Syntax: input_parameter (datatype) - (default_value) Definition Config parameters for this building block: * **cfg** (*object*): ({}) Haddock configuration options specification. * **binary_path** (*string*): (haddock) Path to the haddock haddock executable binary. * **remove_tmp** (*boolean*): (True) Remove temporal files. * **restart** (*boolean*): (False) Do not execute if output files exist. * **sandbox_path** (*string*): (./) Parent path to the sandbox directory. * **container_path** (*string*): (None) Path to the binary executable of your container. * **container_image** (*string*): (None) Container Image identifier. * **container_volume_path** (*string*): (/data) Path to an internal directory in the container. * **container_working_dir** (*string*): (None) Path to the internal CWD in the container. * **container_user_id** (*string*): (None) User number id to be mapped inside the container. * **container_shell_path** (*string*): (/bin/bash) Path to the binary executable of the container shell. ### YAML #### [Common config file](https://github.com/bioexcel/biobb_haddock/blob/master/biobb_haddock/test/data/config/config_haddock3_run.yml) ```python properties: remove_tmp: false ``` #### Command line ```python haddock3_run --config config_haddock3_run.yml --input_haddock_wf_data haddock_wf_data_run.zip --output_haddock_wf_data output.directory --haddock_config_path run.cfg ``` ### JSON #### [Common config file](https://github.com/bioexcel/biobb_haddock/blob/master/biobb_haddock/test/data/config/config_haddock3_run.json) ```python { "properties": { "remove_tmp": false } } ``` #### Command line ```python haddock3_run --config config_haddock3_run.json --input_haddock_wf_data haddock_wf_data_run.zip --output_haddock_wf_data output.directory --haddock_config_path run.cfg ``` ## Rigid_body Wrapper class for the HADDOCK3 RigidBody module. ### Get help Command: ```python rigid_body -h ``` usage: rigid_body [-h] [-c CONFIG] --input_haddock_wf_data INPUT_HADDOCK_WF_DATA --output_haddock_wf_data OUTPUT_HADDOCK_WF_DATA --docking_output_zip_path DOCKING_OUTPUT_ZIP_PATH [--ambig_restraints_table_path AMBIG_RESTRAINTS_TABLE_PATH] [--unambig_restraints_table_path UNAMBIG_RESTRAINTS_TABLE_PATH] [--hb_restraints_table_path HB_RESTRAINTS_TABLE_PATH] [--haddock_config_path HADDOCK_CONFIG_PATH] Wrapper of the HADDOCK3 RigidBody module. options: -h, --help show this help message and exit -c CONFIG, --config CONFIG This file can be a YAML file, JSON file or JSON string required arguments: --input_haddock_wf_data INPUT_HADDOCK_WF_DATA Path to the input directory containing all the current Haddock workflow data. Accepted formats: directory, zip. --output_haddock_wf_data OUTPUT_HADDOCK_WF_DATA Path to the output directory containing all the current Haddock workflow data. Accepted formats: directory, zip. --docking_output_zip_path DOCKING_OUTPUT_ZIP_PATH Path to the output PDB file collection in zip format. Accepted formats: zip. optional arguments: --ambig_restraints_table_path AMBIG_RESTRAINTS_TABLE_PATH Path to the input TBL file containing a list of ambiguous restraints for docking. Accepted formats: tbl. --unambig_restraints_table_path UNAMBIG_RESTRAINTS_TABLE_PATH Path to the input TBL file containing a list of unambiguous restraints for docking. Accepted formats: tbl. --hb_restraints_table_path HB_RESTRAINTS_TABLE_PATH Path to the input TBL file containing a list of hydrogen bond restraints for docking. Accepted formats: tbl. --haddock_config_path HADDOCK_CONFIG_PATH Haddock configuration CFG file path. Accepted formats: cfg. ### I / O Arguments Syntax: input_argument (datatype) : Definition Config input / output arguments for this building block: * **input_haddock_wf_data** (*dir*): Path to the input directory containing all the current Haddock workflow data. File type: input. [Sample file](https://github.com/bioexcel/biobb_haddock/raw/master/biobb_haddock/test/data/haddock/haddock_wf_data_topology.zip). Accepted formats: DIRECTORY, ZIP * **output_haddock_wf_data** (*dir*): Path to the output directory containing all the current Haddock workflow data. File type: output. [Sample file](None). Accepted formats: DIRECTORY, ZIP * **docking_output_zip_path** (*string*): Path to the output PDB file collection in zip format. File type: output. [Sample file](https://raw.githubusercontent.com/bioexcel/biobb_haddock/master/biobb_haddock/test/reference/haddock/ref_rigidbody.zip). Accepted formats: ZIP * **ambig_restraints_table_path** (*string*): Path to the input TBL file containing a list of ambiguous restraints for docking. File type: input. [Sample file](https://raw.githubusercontent.com/bioexcel/biobb_haddock/master/biobb_haddock/test/data/haddock/e2a-hpr_air.tbl). Accepted formats: TBL * **unambig_restraints_table_path** (*string*): Path to the input TBL file containing a list of unambiguous restraints for docking. File type: input. [Sample file](https://raw.githubusercontent.com/bioexcel/biobb_haddock/master/biobb_haddock/test/data/haddock/e2a-hpr_air.tbl). Accepted formats: TBL * **hb_restraints_table_path** (*string*): Path to the input TBL file containing a list of hydrogen bond restraints for docking. File type: input. [Sample file](https://raw.githubusercontent.com/bioexcel/biobb_haddock/master/biobb_haddock/test/data/haddock/e2a-hpr_air.tbl). Accepted formats: TBL * **haddock_config_path** (*string*): Haddock configuration CFG file path. File type: input. [Sample file](https://raw.githubusercontent.com/bioexcel/biobb_haddock/master/biobb_haddock/test/data/haddock/run.cfg). Accepted formats: CFG ### Config Syntax: input_parameter (datatype) - (default_value) Definition Config parameters for this building block: * **cfg** (*object*): ({}) Haddock configuration options specification. * **global_cfg** (*object*): ({'postprocess': False}) Global configuration options specification. * **binary_path** (*string*): (haddock) Path to the haddock haddock executable binary. * **remove_tmp** (*boolean*): (True) Remove temporal files. * **restart** (*boolean*): (False) Do not execute if output files exist. * **sandbox_path** (*string*): (./) Parent path to the sandbox directory. * **container_path** (*string*): (None) Path to the binary executable of your container. * **container_image** (*string*): (None) Container Image identifier. * **container_volume_path** (*string*): (/data) Path to an internal directory in the container. * **container_working_dir** (*string*): (None) Path to the internal CWD in the container. * **container_user_id** (*string*): (None) User number id to be mapped inside the container. * **container_shell_path** (*string*): (/bin/bash) Path to the binary executable of the container shell. ### YAML #### [Common config file](https://github.com/bioexcel/biobb_haddock/blob/master/biobb_haddock/test/data/config/config_rigid_body.yml) ```python properties: remove_tmp: false ``` #### Command line ```python rigid_body --config config_rigid_body.yml --input_haddock_wf_data haddock_wf_data_topology.zip --output_haddock_wf_data output.directory --docking_output_zip_path ref_rigidbody.zip --ambig_restraints_table_path e2a-hpr_air.tbl --unambig_restraints_table_path e2a-hpr_air.tbl --hb_restraints_table_path e2a-hpr_air.tbl --haddock_config_path run.cfg ``` ### JSON #### [Common config file](https://github.com/bioexcel/biobb_haddock/blob/master/biobb_haddock/test/data/config/config_rigid_body.json) ```python { "properties": { "remove_tmp": false } } ``` #### Command line ```python rigid_body --config config_rigid_body.json --input_haddock_wf_data haddock_wf_data_topology.zip --output_haddock_wf_data output.directory --docking_output_zip_path ref_rigidbody.zip --ambig_restraints_table_path e2a-hpr_air.tbl --unambig_restraints_table_path e2a-hpr_air.tbl --hb_restraints_table_path e2a-hpr_air.tbl --haddock_config_path run.cfg ``` ## Sele_top Wrapper class for the HADDOCK3 SeleTop module. ### Get help Command: ```python sele_top -h ``` usage: sele_top [-h] [-c CONFIG] --input_haddock_wf_data INPUT_HADDOCK_WF_DATA --output_haddock_wf_data OUTPUT_HADDOCK_WF_DATA [--output_selection_zip_path OUTPUT_SELECTION_ZIP_PATH] [--haddock_config_path HADDOCK_CONFIG_PATH] Wrapper of the HADDOCK3 SeleTop module. options: -h, --help show this help message and exit -c CONFIG, --config CONFIG This file can be a YAML file, JSON file or JSON string required arguments: --input_haddock_wf_data INPUT_HADDOCK_WF_DATA Path to the input directory containing all the current Haddock workflow data. Accepted formats: directory, zip. --output_haddock_wf_data OUTPUT_HADDOCK_WF_DATA Path to the output directory containing all the current Haddock workflow data. Accepted formats: directory, zip. optional arguments: --output_selection_zip_path OUTPUT_SELECTION_ZIP_PATH Path to the output PDB file collection in zip format. Accepted formats: zip. --haddock_config_path HADDOCK_CONFIG_PATH Haddock configuration CFG file path. Accepted formats: cfg. ### I / O Arguments Syntax: input_argument (datatype) : Definition Config input / output arguments for this building block: * **input_haddock_wf_data** (*dir*): Path to the input directory containing all the current Haddock workflow data. File type: input. [Sample file](https://github.com/bioexcel/biobb_haddock/raw/master/biobb_haddock/test/data/haddock/haddock_wf_data_rigid.zip). Accepted formats: DIRECTORY, ZIP * **output_haddock_wf_data** (*dir*): Path to the output directory containing all the current Haddock workflow data. File type: output. [Sample file](None). Accepted formats: DIRECTORY, ZIP * **output_selection_zip_path** (*string*): Path to the output PDB file collection in zip format. File type: output. [Sample file](https://raw.githubusercontent.com/bioexcel/biobb_haddock/master/biobb_haddock/test/reference/haddock/ref_seletop.zip). Accepted formats: ZIP * **haddock_config_path** (*string*): Haddock configuration CFG file path. File type: input. [Sample file](https://raw.githubusercontent.com/bioexcel/biobb_haddock/master/biobb_haddock/test/data/haddock/run.cfg). Accepted formats: CFG ### Config Syntax: input_parameter (datatype) - (default_value) Definition Config parameters for this building block: * **cfg** (*object*): ({}) Haddock configuration options specification. * **global_cfg** (*object*): ({'postprocess': False}) Global configuration options specification. * **binary_path** (*string*): (haddock) Path to the haddock haddock executable binary. * **remove_tmp** (*boolean*): (True) Remove temporal files. * **restart** (*boolean*): (False) Do not execute if output files exist. * **sandbox_path** (*string*): (./) Parent path to the sandbox directory. * **container_path** (*string*): (None) Path to the binary executable of your container. * **container_image** (*string*): (None) Container Image identifier. * **container_volume_path** (*string*): (/data) Path to an internal directory in the container. * **container_working_dir** (*string*): (None) Path to the internal CWD in the container. * **container_user_id** (*string*): (None) User number id to be mapped inside the container. * **container_shell_path** (*string*): (/bin/bash) Path to the binary executable of the container shell. ### YAML #### [Common config file](https://github.com/bioexcel/biobb_haddock/blob/master/biobb_haddock/test/data/config/config_sele_top.yml) ```python properties: remove_tmp: false ``` #### Command line ```python sele_top --config config_sele_top.yml --input_haddock_wf_data haddock_wf_data_rigid.zip --output_haddock_wf_data output.directory --output_selection_zip_path ref_seletop.zip --haddock_config_path run.cfg ``` ### JSON #### [Common config file](https://github.com/bioexcel/biobb_haddock/blob/master/biobb_haddock/test/data/config/config_sele_top.json) ```python { "properties": { "remove_tmp": false } } ``` #### Command line ```python sele_top --config config_sele_top.json --input_haddock_wf_data haddock_wf_data_rigid.zip --output_haddock_wf_data output.directory --output_selection_zip_path ref_seletop.zip --haddock_config_path run.cfg ``` ## Sele_top_clusts Wrapper class for the HADDOCK3 SeleTopClusts module. ### Get help Command: ```python sele_top_clusts -h ``` usage: sele_top_clusts [-h] [-c CONFIG] --input_haddock_wf_data INPUT_HADDOCK_WF_DATA --output_haddock_wf_data OUTPUT_HADDOCK_WF_DATA [--output_selection_zip_path OUTPUT_SELECTION_ZIP_PATH] [--haddock_config_path HADDOCK_CONFIG_PATH] Wrapper of the HADDOCK3 SeleTopClusts module. options: -h, --help show this help message and exit -c CONFIG, --config CONFIG This file can be a YAML file, JSON file or JSON string required arguments: --input_haddock_wf_data INPUT_HADDOCK_WF_DATA Path to the input directory containing all the current Haddock workflow data. Accepted formats: directory, zip. --output_haddock_wf_data OUTPUT_HADDOCK_WF_DATA Path to the output directory containing all the current Haddock workflow data. Accepted formats: directory, zip. optional arguments: --output_selection_zip_path OUTPUT_SELECTION_ZIP_PATH Path to the output PDB file collection in zip format. Accepted formats: zip. --haddock_config_path HADDOCK_CONFIG_PATH Haddock configuration CFG file path. Accepted formats: cfg. ### I / O Arguments Syntax: input_argument (datatype) : Definition Config input / output arguments for this building block: * **input_haddock_wf_data** (*dir*): Path to the input directory containing all the current Haddock workflow data. File type: input. [Sample file](https://github.com/bioexcel/biobb_haddock/raw/master/biobb_haddock/test/data/haddock/haddock_wf_data_clustfcc.zip). Accepted formats: DIRECTORY, ZIP * **output_haddock_wf_data** (*dir*): Path to the output directory containing all the current Haddock workflow data. File type: output. [Sample file](None). Accepted formats: DIRECTORY, ZIP * **output_selection_zip_path** (*string*): Path to the output PDB file collection in zip format. File type: output. [Sample file](https://raw.githubusercontent.com/bioexcel/biobb_haddock/master/biobb_haddock/test/reference/haddock/ref_seletop.zip). Accepted formats: ZIP * **haddock_config_path** (*string*): Haddock configuration CFG file path. File type: input. [Sample file](https://raw.githubusercontent.com/bioexcel/biobb_haddock/master/biobb_haddock/test/data/haddock/run.cfg). Accepted formats: CFG ### Config Syntax: input_parameter (datatype) - (default_value) Definition Config parameters for this building block: * **cfg** (*object*): ({}) Haddock configuration options specification. * **global_cfg** (*object*): ({'postprocess': False}) Global configuration options specification. * **binary_path** (*string*): (haddock) Path to the haddock haddock executable binary. * **remove_tmp** (*boolean*): (True) Remove temporal files. * **restart** (*boolean*): (False) Do not execute if output files exist. * **sandbox_path** (*string*): (./) Parent path to the sandbox directory. * **container_path** (*string*): (None) Path to the binary executable of your container. * **container_image** (*string*): (None) Container Image identifier. * **container_volume_path** (*string*): (/data) Path to an internal directory in the container. * **container_working_dir** (*string*): (None) Path to the internal CWD in the container. * **container_user_id** (*string*): (None) User number id to be mapped inside the container. * **container_shell_path** (*string*): (/bin/bash) Path to the binary executable of the container shell. ### YAML #### [Common config file](https://github.com/bioexcel/biobb_haddock/blob/master/biobb_haddock/test/data/config/config_sele_top_clusts.yml) ```python properties: remove_tmp: false ``` #### Command line ```python sele_top_clusts --config config_sele_top_clusts.yml --input_haddock_wf_data haddock_wf_data_rigid.zip --output_haddock_wf_data output.directory --output_selection_zip_path ref_seletop.zip --haddock_config_path run.cfg ``` ### JSON #### [Common config file](https://github.com/bioexcel/biobb_haddock/blob/master/biobb_haddock/test/data/config/config_sele_top_clusts.json) ```python { "properties": { "remove_tmp": false } } ``` #### Command line ```python sele_top_clusts --config config_sele_top_clusts.json --input_haddock_wf_data haddock_wf_data_rigid.zip --output_haddock_wf_data output.directory --output_selection_zip_path ref_seletop.zip --haddock_config_path run.cfg ``` ## Topology Wrapper class for the HADDOCK3 Topology module. ### Get help Command: ```python topology -h ``` usage: topology [-h] [-c CONFIG] --mol1_input_pdb_path MOL1_INPUT_PDB_PATH [--mol1_output_top_zip_path MOL1_OUTPUT_TOP_ZIP_PATH] [--mol2_input_pdb_path MOL2_INPUT_PDB_PATH] [--mol2_output_top_zip_path MOL2_OUTPUT_TOP_ZIP_PATH] --output_haddock_wf_data OUTPUT_HADDOCK_WF_DATA [--haddock_config_path HADDOCK_CONFIG_PATH] Wrapper of the HADDOCK3 Topology module. options: -h, --help show this help message and exit -c CONFIG, --config CONFIG This file can be a YAML file, JSON file or JSON string required arguments: --mol1_input_pdb_path MOL1_INPUT_PDB_PATH Path to the input PDB file. Accepted formats: pdb. --output_haddock_wf_data OUTPUT_HADDOCK_WF_DATA Path to the output zipball containing all the current Haddock workflow data. Accepted formats: zip. optional arguments: --mol1_output_top_zip_path MOL1_OUTPUT_TOP_ZIP_PATH Path to the output PDB file collection in zip format. Accepted formats: zip. --mol2_input_pdb_path MOL2_INPUT_PDB_PATH Path to the input PDB file. Accepted formats: pdb. --mol2_output_top_zip_path MOL2_OUTPUT_TOP_ZIP_PATH Path to the output PDB file collection in zip format. Accepted formats: zip. --haddock_config_path HADDOCK_CONFIG_PATH Haddock configuration CFG file path. Accepted formats: cfg. ### I / O Arguments Syntax: input_argument (datatype) : Definition Config input / output arguments for this building block: * **mol1_input_pdb_path** (*string*): Path to the input PDB file. File type: input. [Sample file](https://raw.githubusercontent.com/bioexcel/biobb_haddock/master/biobb_haddock/test/data/haddock/e2aP_1F3G.pdb). Accepted formats: PDB * **mol1_output_top_zip_path** (*string*): Path to the output PDB file collection in zip format. File type: output. [Sample file](https://raw.githubusercontent.com/bioexcel/biobb_haddock/master/biobb_haddock/test/reference/haddock/ref_mol1_top.zip). Accepted formats: ZIP * **mol2_input_pdb_path** (*string*): Path to the input PDB file. File type: input. [Sample file](https://raw.githubusercontent.com/bioexcel/biobb_haddock/master/biobb_haddock/test/data/haddock/hpr_ensemble.pdb). Accepted formats: PDB * **mol2_output_top_zip_path** (*string*): Path to the output PDB file collection in zip format. File type: output. [Sample file](https://raw.githubusercontent.com/bioexcel/biobb_haddock/master/biobb_haddock/test/reference/haddock/ref_mol2_top.zip). Accepted formats: ZIP * **output_haddock_wf_data** (*dir*): Path to the output zipball containing all the current Haddock workflow data. File type: output. [Sample file](None). Accepted formats: ZIP * **haddock_config_path** (*string*): Haddock configuration CFG file path. File type: input. [Sample file](https://raw.githubusercontent.com/bioexcel/biobb_haddock/master/biobb_haddock/test/data/haddock/run.cfg). Accepted formats: CFG ### Config Syntax: input_parameter (datatype) - (default_value) Definition Config parameters for this building block: * **cfg** (*object*): ({}) Haddock configuration options specification. * **global_cfg** (*object*): ({'postprocess': False}) Global configuration options specification. * **binary_path** (*string*): (haddock) Path to the haddock haddock executable binary. * **remove_tmp** (*boolean*): (True) Remove temporal files. * **restart** (*boolean*): (False) Do not execute if output files exist. * **sandbox_path** (*string*): (./) Parent path to the sandbox directory. * **container_path** (*string*): (None) Path to the binary executable of your container. * **container_image** (*string*): (None) Container Image identifier. * **container_volume_path** (*string*): (/data) Path to an internal directory in the container. * **container_working_dir** (*string*): (None) Path to the internal CWD in the container. * **container_user_id** (*string*): (None) User number id to be mapped inside the container. * **container_shell_path** (*string*): (/bin/bash) Path to the binary executable of the container shell. ### YAML #### [Common config file](https://github.com/bioexcel/biobb_haddock/blob/master/biobb_haddock/test/data/config/config_topology.yml) ```python properties: remove_tmp: false ``` #### Command line ```python topology --config config_topology.yml --mol1_input_pdb_path e2aP_1F3G.pdb --mol1_output_top_zip_path ref_mol1_top.zip --mol2_input_pdb_path hpr_ensemble.pdb --mol2_output_top_zip_path ref_mol2_top.zip --output_haddock_wf_data output.zip --haddock_config_path run.cfg ``` ### JSON #### [Common config file](https://github.com/bioexcel/biobb_haddock/blob/master/biobb_haddock/test/data/config/config_topology.json) ```python { "properties": { "remove_tmp": false } } ``` #### Command line ```python topology --config config_topology.json --mol1_input_pdb_path e2aP_1F3G.pdb --mol1_output_top_zip_path ref_mol1_top.zip --mol2_input_pdb_path hpr_ensemble.pdb --mol2_output_top_zip_path ref_mol2_top.zip --output_haddock_wf_data output.zip --haddock_config_path run.cfg ```