# BioBB CMIP Command Line Help Generic usage: ```python biobb_command [-h] --config CONFIG --input_file(s) --output_file ``` ----------------- ## Cmip_ignore_residues Class to ignore residues in CMIP potential calculations. ### Get help Command: ```python cmip_ignore_residues -h ``` usage: cmip_ignore_residues [-h] [-c CONFIG] -i INPUT_CMIP_PDB_PATH -o OUTPUT_CMIP_PDB_PATH Mark residues which charges will be ignored in the CMIP potential calculations. 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_CMIP_PDB_PATH, --input_cmip_pdb_path INPUT_CMIP_PDB_PATH Input PDB file path. Accepted formats: pdb. -o OUTPUT_CMIP_PDB_PATH, --output_cmip_pdb_path OUTPUT_CMIP_PDB_PATH Output PDB file path. Accepted formats: pdb. ### I / O Arguments Syntax: input_argument (datatype) : Definition Config input / output arguments for this building block: * **input_cmip_pdb_path** (*string*): Input PDB file path. File type: input. [Sample file](https://github.com/bioexcel/biobb_cmip/raw/master/biobb_cmip/test/data/cmip/input_ignore_res.pdb). Accepted formats: PDB * **output_cmip_pdb_path** (*string*): Output PDB file path. File type: output. [Sample file](https://github.com/bioexcel/biobb_cmip/raw/master/biobb_cmip/test/reference/cmip/ignore_res_gln3.pdb). Accepted formats: PDB ### Config Syntax: input_parameter (datatype) - (default_value) Definition Config parameters for this building block: * **residue_list** (*string*): (None) Residue list in the format "Chain:Resnum" (no spaces between the elements) separated by commas. If no chain is provided all the residues in the pdb file will be market. ie: "A:3".. * **ignore_all** (*boolean*): (False) Mark all the residues in the PDB file.. * **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.. ### YAML #### [Common config file](https://github.com/bioexcel/biobb_cmip/blob/master/biobb_cmip/test/data/config/config_cmip_ignore_residues.yml) ```python properties: remove_tmp: true residue_list: 3 ``` #### Command line ```python cmip_ignore_residues --config config_cmip_ignore_residues.yml --input_cmip_pdb_path input_ignore_res.pdb --output_cmip_pdb_path ignore_res_gln3.pdb ``` ### JSON #### [Common config file](https://github.com/bioexcel/biobb_cmip/blob/master/biobb_cmip/test/data/config/config_cmip_ignore_residues.json) ```python { "properties": { "residue_list": 3, "remove_tmp": true } } ``` #### Command line ```python cmip_ignore_residues --config config_cmip_ignore_residues.json --input_cmip_pdb_path input_ignore_res.pdb --output_cmip_pdb_path ignore_res_gln3.pdb ``` ## Cmip_prepare_pdb Class to add CMIP charges and atom types. ### Get help Command: ```python cmip_prepare_pdb -h ``` usage: cmip_prepare_pdb [-h] [-c CONFIG] -i INPUT_PDB_PATH -o OUTPUT_CMIP_PDB_PATH Model the missing atoms in the backbone of a PDB structure. 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 Input PDB file path. Accepted formats: pdb. -o OUTPUT_CMIP_PDB_PATH, --output_cmip_pdb_path OUTPUT_CMIP_PDB_PATH Output PDB file path. Accepted formats: pdb. ### I / O Arguments Syntax: input_argument (datatype) : Definition Config input / output arguments for this building block: * **input_pdb_path** (*string*): Input PDB file path. File type: input. [Sample file](https://github.com/bioexcel/biobb_cmip/raw/master/biobb_cmip/test/data/cmip/1aki.pdb). Accepted formats: PDB * **output_cmip_pdb_path** (*string*): Output PDB file path. File type: output. [Sample file](https://github.com/bioexcel/biobb_cmip/raw/master/biobb_cmip/test/reference/cmip/egfr_cmip.pdb). Accepted formats: PDB ### Config Syntax: input_parameter (datatype) - (default_value) Definition Config parameters for this building block: * **remove_water** (*boolean*): (True) Remove Water molecules.. * **add_hydrogen** (*boolean*): (True) Add Hydrogen atoms to the structure.. * **keep_hydrogen** (*boolean*): (False) If **add_hydrogen** is True. All hydrogen atoms will be removed before adding the new ones unless this option is set True.. * **fix_sidechains** (*boolean*): (True) Complete side chains (heavy atoms, protein only).. * **fix_backbone_atoms** (*boolean*): (True) Add missing O, OXT backbone atoms.. * **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.. ### YAML #### [Common config file](https://github.com/bioexcel/biobb_cmip/blob/master/biobb_cmip/test/data/config/config_cmip_prepare_pdb.yml) ```python properties: remove_tmp: true ``` #### Command line ```python cmip_prepare_pdb --config config_cmip_prepare_pdb.yml --input_pdb_path 1aki.pdb --output_cmip_pdb_path egfr_cmip.pdb ``` ### JSON #### [Common config file](https://github.com/bioexcel/biobb_cmip/blob/master/biobb_cmip/test/data/config/config_cmip_prepare_pdb.json) ```python { "properties": { "remove_tmp": true } } ``` #### Command line ```python cmip_prepare_pdb --config config_cmip_prepare_pdb.json --input_pdb_path 1aki.pdb --output_cmip_pdb_path egfr_cmip.pdb ``` ## Cmip_prepare_structure Generate a CMIP suitable PDB input. ### Get help Command: ```python cmip_prepare_structure -h ``` usage: cmip_prepare_structure [-h] [-c CONFIG] --input_pdb_path INPUT_PDB_PATH [--input_topology_path INPUT_TOPOLOGY_PATH] -o OUTPUT_CMIP_PDB_PATH Wrapper of the cmip prepare_structure 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 file. Accepted formats: pdb. -o OUTPUT_CMIP_PDB_PATH, --output_cmip_pdb_path OUTPUT_CMIP_PDB_PATH Path to the output PDB file. Accepted formats: pdb. optional arguments: --input_topology_path INPUT_TOPOLOGY_PATH Path to the input topology path. Accepted formats: zip, top, psf, prmtop. ### 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://github.com/bioexcel/biobb_cmip/raw/master/biobb_cmip/test/data/cmip/egfr.pdb). Accepted formats: PDB * **input_topology_path** (*string*): Path to the input topology path. File type: input. [Sample file](https://github.com/bioexcel/biobb_cmip/raw/master/biobb_cmip/test/data/cmip/egfr_topology.zip). Accepted formats: ZIP, TOP, PSF, PRMTOP * **output_cmip_pdb_path** (*string*): Path to the output PDB file. File type: output. [Sample file](https://github.com/bioexcel/biobb_cmip/raw/master/biobb_cmip/test/reference/cmip/egfr_cmip.pdb). Accepted formats: PDB ### Config Syntax: input_parameter (datatype) - (default_value) Definition Config parameters for this building block: * **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*): (cmip/cmip:latest) 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_cmip/blob/master/biobb_cmip/test/data/config/config_cmip_prepare_structure.yml) ```python properties: remove_tmp: true ``` #### Command line ```python cmip_prepare_structure --config config_cmip_prepare_structure.yml --input_pdb_path egfr.pdb --input_topology_path egfr_topology.zip --output_cmip_pdb_path egfr_cmip.pdb ``` ### JSON #### [Common config file](https://github.com/bioexcel/biobb_cmip/blob/master/biobb_cmip/test/data/config/config_cmip_prepare_structure.json) ```python { "properties": { "remove_tmp": true } } ``` #### Command line ```python cmip_prepare_structure --config config_cmip_prepare_structure.json --input_pdb_path egfr.pdb --input_topology_path egfr_topology.zip --output_cmip_pdb_path egfr_cmip.pdb ``` ## Cmip_run Wrapper class for the CMIP cmip module. ### Get help Command: ```python cmip_run -h ``` usage: cmip_run [-h] [-c CONFIG] --input_pdb_path INPUT_PDB_PATH --input_probe_pdb_path INPUT_PROBE_PDB_PATH [--output_pdb_path OUTPUT_PDB_PATH] [--output_grd_path OUTPUT_GRD_PATH] [--output_cube_path OUTPUT_CUBE_PATH] [--output_rst_path OUTPUT_RST_PATH] [--input_rst_path INPUT_RST_PATH] [--output_byat_path OUTPUT_BYAT_PATH] [--output_log_path OUTPUT_LOG_PATH] [--input_vdw_params_path INPUT_VDW_PARAMS_PATH] [--input_params_path INPUT_PARAMS_PATH] [--output_json_box_path OUTPUT_JSON_BOX_PATH] [--output_json_external_box_path OUTPUT_JSON_EXTERNAL_BOX_PATH] [--input_json_box_path INPUT_JSON_BOX_PATH] [--input_json_external_box_path INPUT_JSON_EXTERNAL_BOX_PATH] Wrapper of the CMIP cmip 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 file. Accepted formats: pdb. --input_probe_pdb_path INPUT_PROBE_PDB_PATH Path to the input probe file in PDB format. Accepted formats: pdb. optional arguments: --output_pdb_path OUTPUT_PDB_PATH Path to the output PDB file. Accepted formats: pdb. --output_grd_path OUTPUT_GRD_PATH Path to the output grid file in GRD format. Accepted formats: grd. --output_cube_path OUTPUT_CUBE_PATH Path to the output grid file in cube format. Accepted formats: cube. --output_rst_path OUTPUT_RST_PATH Path to the output restart file. Accepted formats: txt. --input_rst_path INPUT_RST_PATH Path to the input restart file. Accepted formats: txt. --output_byat_path OUTPUT_BYAT_PATH Path to the output atom by atom energy file. Accepted formats: txt, out. --output_log_path OUTPUT_LOG_PATH Path to the output CMIP log file LOG. Accepted formats: log. --input_vdw_params_path INPUT_VDW_PARAMS_PATH Path to the CMIP input Van der Waals force parameters, if not provided the CMIP conda installation one is used ("$CONDA_PREFIX/share/cmip/dat/vdwprm"). Accepted formats: txt. --input_params_path INPUT_PARAMS_PATH Path to the CMIP input parameters file. Accepted formats: txt. --output_json_box_path OUTPUT_JSON_BOX_PATH Path to the output CMIP box in JSON format. Accepted formats: json. --output_json_external_box_path OUTPUT_JSON_EXTERNAL_BOX_PATH Path to the output external CMIP box in JSON format. Accepted formats: json. --input_json_box_path INPUT_JSON_BOX_PATH Path to the input CMIP box in JSON format. Accepted formats: json. --input_json_external_box_path INPUT_JSON_EXTERNAL_BOX_PATH Path to the input CMIP box in JSON format. Accepted formats: json. ### 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_cmip/master/biobb_cmip/test/data/cmip/1kim_h.pdb). Accepted formats: PDB * **input_probe_pdb_path** (*string*): Path to the input probe file in PDB format. File type: input. [Sample file](https://raw.githubusercontent.com/bioexcel/biobb_cmip/master/biobb_cmip/test/data/cmip/RBD-hACE2.RBD.cmip.pdb). Accepted formats: PDB * **output_pdb_path** (*string*): Path to the output PDB file. File type: output. [Sample file](https://raw.githubusercontent.com/bioexcel/biobb_cmip/master/biobb_cmip/test/reference/cmip/1kim_neutral.pdb). Accepted formats: PDB * **output_grd_path** (*string*): Path to the output grid file in GRD format. File type: output. [Sample file](None). Accepted formats: GRD * **output_cube_path** (*string*): Path to the output grid file in cube format. File type: output. [Sample file](None). Accepted formats: CUBE * **output_rst_path** (*string*): Path to the output restart file. File type: output. [Sample file](None). Accepted formats: TXT * **input_rst_path** (*string*): Path to the input restart file. File type: input. [Sample file](None). Accepted formats: TXT * **output_byat_path** (*string*): Path to the output atom by atom energy file. File type: output. [Sample file](None). Accepted formats: TXT, OUT * **output_log_path** (*string*): Path to the output CMIP log file LOG. File type: output. [Sample file](None). Accepted formats: LOG * **input_vdw_params_path** (*string*): Path to the CMIP input Van der Waals force parameters, if not provided the CMIP conda installation one is used ("$CONDA_PREFIX/share/cmip/dat/vdwprm"). File type: input. [Sample file](None). Accepted formats: TXT * **input_params_path** (*string*): Path to the CMIP input parameters file. File type: input. [Sample file](None). Accepted formats: TXT * **output_json_box_path** (*string*): Path to the output CMIP box in JSON format. File type: output. [Sample file](None). Accepted formats: JSON * **output_json_external_box_path** (*string*): Path to the output external CMIP box in JSON format. File type: output. [Sample file](None). Accepted formats: JSON * **input_json_box_path** (*string*): Path to the input CMIP box in JSON format. File type: input. [Sample file](None). Accepted formats: JSON * **input_json_external_box_path** (*string*): Path to the input CMIP box in JSON format. File type: input. [Sample file](None). Accepted formats: JSON ### Config Syntax: input_parameter (datatype) - (default_value) Definition Config parameters for this building block: * **execution_type** (*string*): (mip_pos) Default options for the params file, each one creates a different params file. . * **params** (*object*): ({}) CMIP options specification.. * **binary_path** (*string*): (cmip) Path to the CMIP cmip 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*): (cmip/cmip:latest) 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_cmip/blob/master/biobb_cmip/test/data/config/config_cmip_run.yml) ```python properties: execution_type: pb_interaction_energy ``` #### [Docker config file](https://github.com/bioexcel/biobb_cmip/blob/master/biobb_cmip/test/data/config/config_cmip_run_docker.yml) ```python properties: container_image: quay.io/biocontainers/cmip:2.7.0--h8c3ec31_0 container_path: docker container_volume_path: /inout execution_type: pb_interaction_energy remove_tmp: true ``` #### [Singularity config file](https://github.com/bioexcel/biobb_cmip/blob/master/biobb_cmip/test/data/config/config_cmip_run_singularity.yml) ```python properties: container_image: cmip.simg container_path: singularity container_volume_path: /inout execution_type: mip_pos remove_tmp: true ``` #### Command line ```python cmip_run --config config_cmip_run.yml --input_pdb_path 1kim_h.pdb --input_probe_pdb_path RBD-hACE2.RBD.cmip.pdb --output_pdb_path 1kim_neutral.pdb --output_grd_path output.grd --output_cube_path output.cube --output_rst_path output.txt --input_rst_path input.txt --output_byat_path output.txt --output_log_path output.log --input_vdw_params_path input.txt --input_params_path input.txt --output_json_box_path output.json --output_json_external_box_path output.json --input_json_box_path input.json --input_json_external_box_path input.json ``` ### JSON #### [Common config file](https://github.com/bioexcel/biobb_cmip/blob/master/biobb_cmip/test/data/config/config_cmip_run.json) ```python { "properties": { "execution_type": "pb_interaction_energy" } } ``` #### [Docker config file](https://github.com/bioexcel/biobb_cmip/blob/master/biobb_cmip/test/data/config/config_cmip_run_docker.json) ```python { "properties": { "remove_tmp": true, "execution_type": "pb_interaction_energy", "container_path": "docker", "container_image": "quay.io/biocontainers/cmip:2.7.0--h8c3ec31_0", "container_volume_path": "/inout" } } ``` #### [Singularity config file](https://github.com/bioexcel/biobb_cmip/blob/master/biobb_cmip/test/data/config/config_cmip_run_singularity.json) ```python { "properties": { "remove_tmp": true, "execution_type": "mip_pos", "container_path": "singularity", "container_image": "cmip.simg", "container_volume_path": "/inout" } } ``` #### Command line ```python cmip_run --config config_cmip_run.json --input_pdb_path 1kim_h.pdb --input_probe_pdb_path RBD-hACE2.RBD.cmip.pdb --output_pdb_path 1kim_neutral.pdb --output_grd_path output.grd --output_cube_path output.cube --output_rst_path output.txt --input_rst_path input.txt --output_byat_path output.txt --output_log_path output.log --input_vdw_params_path input.txt --input_params_path input.txt --output_json_box_path output.json --output_json_external_box_path output.json --input_json_box_path input.json --input_json_external_box_path input.json ``` ## Cmip_titration Wrapper class for the CMIP titration module. ### Get help Command: ```python cmip_titration -h ``` usage: cmip_titration [-h] [-c CONFIG] --input_pdb_path INPUT_PDB_PATH -o OUTPUT_PDB_PATH [--input_vdw_params_path INPUT_VDW_PARAMS_PATH] [--input_params_path INPUT_PARAMS_PATH] Wrapper of the CMIP Titration 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 file. Accepted formats: pdb. -o OUTPUT_PDB_PATH, --output_pdb_path OUTPUT_PDB_PATH Path to the output PDB file. Accepted formats: pdb. optional arguments: --input_vdw_params_path INPUT_VDW_PARAMS_PATH Path to the CMIP input Van der Waals force parameters, if not provided the CMIP conda installation one is used ("$CONDA_PREFIX/share/cmip/dat/vdwprm"). Accepted formats: txt. --input_params_path INPUT_PARAMS_PATH Path to the CMIP input parameters file. Accepted formats: txt. ### I / O Arguments Syntax: input_argument (datatype) : Definition Config input / output arguments for this building block: * **input_pdb_path** (*string*): Path to the input PDB file. File type: input. [Sample file](https://raw.githubusercontent.com/bioexcel/biobb_cmip/master/biobb_cmip/test/data/cmip/1kim_h.pdb). Accepted formats: PDB * **output_pdb_path** (*string*): Path to the output PDB file. File type: output. [Sample file](https://raw.githubusercontent.com/bioexcel/biobb_cmip/master/biobb_cmip/test/reference/cmip/1kim_neutral.pdb). Accepted formats: PDB * **input_vdw_params_path** (*string*): Path to the CMIP input Van der Waals force parameters, if not provided the CMIP conda installation one is used ("$CONDA_PREFIX/share/cmip/dat/vdwprm"). File type: input. [Sample file](None). Accepted formats: TXT * **input_params_path** (*string*): Path to the CMIP input parameters file. File type: input. [Sample file](None). Accepted formats: TXT ### Config Syntax: input_parameter (datatype) - (default_value) Definition Config parameters for this building block: * **params** (*object*): ({}) CMIP options specification.. * **energy_cutoff** (*number*): (9999.9) Energy cutoff, extremely hight value to enable the addition of all the ions and waters before reaching the cutoff.. * **num_wats** (*integer*): (10) Number of water molecules to be added.. * **neutral** (*boolean*): (False) Neutralize the charge of the system. If selected *num_positive_ions* and *num_negative_ions* values will not be taken into account.. * **num_positive_ions** (*integer*): (10) Number of positive ions to be added (Tipatom IP=Na+).. * **num_negative_ions** (*integer*): (10) Number of negative ions to be added (Tipatom IM=Cl-).. * **binary_path** (*string*): (titration) Path to the CMIP Titration 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*): (cmip/cmip:latest) 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_cmip/blob/master/biobb_cmip/test/data/config/config_cmip_titration.yml) ```python properties: neutral: true remove_tmp: false ``` #### [Docker config file](https://github.com/bioexcel/biobb_cmip/blob/master/biobb_cmip/test/data/config/config_cmip_titration_docker.yml) ```python properties: container_image: quay.io/biocontainers/cmip:2.7.0--h8c3ec31_0 container_path: docker container_volume_path: /inout neutral: true ``` #### [Singularity config file](https://github.com/bioexcel/biobb_cmip/blob/master/biobb_cmip/test/data/config/config_cmip_titration_singularity.yml) ```python properties: container_image: cmip.simg container_path: singularity container_volume_path: /inout neutral: true ``` #### Command line ```python cmip_titration --config config_cmip_titration.yml --input_pdb_path 1kim_h.pdb --output_pdb_path 1kim_neutral.pdb --input_vdw_params_path input.txt --input_params_path input.txt ``` ### JSON #### [Common config file](https://github.com/bioexcel/biobb_cmip/blob/master/biobb_cmip/test/data/config/config_cmip_titration.json) ```python { "properties": { "remove_tmp": false, "neutral": true } } ``` #### [Docker config file](https://github.com/bioexcel/biobb_cmip/blob/master/biobb_cmip/test/data/config/config_cmip_titration_docker.json) ```python { "properties": { "neutral": true, "container_path": "docker", "container_image": "quay.io/biocontainers/cmip:2.7.0--h8c3ec31_0", "container_volume_path": "/inout" } } ``` #### [Singularity config file](https://github.com/bioexcel/biobb_cmip/blob/master/biobb_cmip/test/data/config/config_cmip_titration_singularity.json) ```python { "properties": { "neutral": true, "container_path": "singularity", "container_image": "cmip.simg", "container_volume_path": "/inout" } } ``` #### Command line ```python cmip_titration --config config_cmip_titration.json --input_pdb_path 1kim_h.pdb --output_pdb_path 1kim_neutral.pdb --input_vdw_params_path input.txt --input_params_path input.txt ```