BioBB CMIP Command Line Help

Generic usage:

biobb_command [-h] --config CONFIG --input_file(s) <input_file(s)> --output_file <output_file>

Cmip_prepare_pdb

Class to add CMIP charges and atom types.

Get help

Command:

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.

optional arguments:
  -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 name
  -o OUTPUT_CMIP_PDB_PATH, --output_cmip_pdb_path OUTPUT_CMIP_PDB_PATH
                        Output PDB file name

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. Accepted formats: PDB
output_cmip_pdb_path (string): Output PDB file path. File type: output. Sample file. 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..

YAML

Common config file 

properties:
  remove_tmp: true

Command line

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 

{
  "properties": {
    "remove_tmp": true
  }
}

Command line

cmip_prepare_pdb --config config_cmip_prepare_pdb.json --input_pdb_path 1aki.pdb --output_cmip_pdb_path egfr_cmip.pdb

Cmip_ignore_residues

Class to ignore residues in CMIP potential calculations.

Get help

Command:

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.

optional arguments:
  -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 name
  -o OUTPUT_CMIP_PDB_PATH, --output_cmip_pdb_path OUTPUT_CMIP_PDB_PATH
                        Output PDB file name

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. Accepted formats: PDB
output_cmip_pdb_path (string): Output PDB file path. File type: output. Sample file. 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..

YAML

Common config file 

properties:
  remove_tmp: true
  residue_list: 3

Command line

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 

{
  "properties": {
    "residue_list": 3,
    "remove_tmp": true
  }
}

Command line

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_titration

Wrapper class for the CMIP titration module.

Get help

Command:

cmip_titration -h

usage: cmip_titration [-h] [-c CONFIG] --input_pdb_path INPUT_PDB_PATH --output_pdb_path OUTPUT_PDB_PATH [--input_vdw_params_path INPUT_VDW_PARAMS_PATH] [--input_params_path INPUT_PARAMS_PATH]

Wrapper of the CMIP Titration module.

optional arguments:
  -h, --help            show this help message and exit
  -c CONFIG, --config CONFIG
                        This file can be a YAML file, JSON file or JSON string
  --input_vdw_params_path INPUT_VDW_PARAMS_PATH
  --input_params_path INPUT_PARAMS_PATH

required arguments:
  --input_pdb_path INPUT_PDB_PATH
  --output_pdb_path OUTPUT_PDB_PATH

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. Accepted formats: PDB
output_pdb_path (string): Path to the output PDB file. File type: output. Sample file. 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. Accepted formats: TXT
input_params_path (string): Path to the CMIP input parameters file. File type: input. Sample file. 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..
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 

properties:
  neutral: true
  remove_tmp: false

Docker config file 

properties:
  container_image: quay.io/biocontainers/cmip:2.7.0--h8c3ec31_0
  container_path: docker
  container_volume_path: /inout
  neutral: true

Singularity config file 

properties:
  container_image: cmip.simg
  container_path: singularity
  container_volume_path: /inout
  neutral: true

Command line

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 

{
  "properties": {
    "remove_tmp": false,
    "neutral": true
  }
}

Docker config file 

{
  "properties": {
    "neutral": true,
    "container_path": "docker",
    "container_image": "quay.io/biocontainers/cmip:2.7.0--h8c3ec31_0",
    "container_volume_path": "/inout"
  }
}

Singularity config file 

{
  "properties": {
    "neutral": true,
    "container_path": "singularity",
    "container_image": "cmip.simg",
    "container_volume_path": "/inout"
  }
}

Command line

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

Cmip_run

Wrapper class for the CMIP cmip module.

Get help

Command:

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] [--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.

optional arguments:
  -h, --help            show this help message and exit
  -c CONFIG, --config CONFIG
                        This file can be a YAML file, JSON file or JSON string
  --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
  --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

required arguments:
  --input_pdb_path INPUT_PDB_PATH

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. Accepted formats: PDB
input_probe_pdb_path (string): Path to the input probe file in PDB format. File type: input. Sample file. Accepted formats: PDB
output_pdb_path (string): Path to the output PDB file. File type: output. Sample file. Accepted formats: PDB
output_grd_path (string): Path to the output grid file in GRD format. File type: output. Sample file. Accepted formats: GRD
output_cube_path (string): Path to the output grid file in cube format. File type: output. Sample file. Accepted formats: CUBE
output_rst_path (string): Path to the output restart file. File type: output. Sample file. Accepted formats: TXT
input_rst_path (string): Path to the input restart file. File type: output. Sample file. Accepted formats: TXT
output_byat_path (string): Path to the output atom by atom energy file. File type: output. Sample file. Accepted formats: TXT, OUT
output_log_path (string): Path to the output CMIP log file LOG. File type: output. Sample file. 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. Accepted formats: TXT
input_params_path (string): Path to the CMIP input parameters file. File type: input. Sample file. Accepted formats: TXT
output_json_box_path (string): Path to the output CMIP box in JSON format. File type: output. Sample file. Accepted formats: JSON
output_json_external_box_path (string): Path to the output external CMIP box in JSON format. File type: output. Sample file. Accepted formats: JSON
input_json_box_path (string): Path to the input CMIP box in JSON format. File type: input. Sample file. Accepted formats: JSON
input_json_external_box_path (string): Path to the input CMIP box in JSON format. File type: input. Sample file. 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..
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 

properties:
  execution_type: pb_interaction_energy

Docker config file 

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 

properties:
  container_image: cmip.simg
  container_path: singularity
  container_volume_path: /inout
  execution_type: mip_pos
  remove_tmp: true

Command line

cmip_run --config config_cmip_run.yml --input_pdb_path 1kim_h.pdb --input_probe_pdb_path input.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 output.txt --output_byat_path output.txt --output_log_path ref_cmip.log --input_vdw_params_path input.txt --input_params_path input.txt --output_json_box_path ref_box.json --output_json_external_box_path ref_box.json --input_json_box_path ref_box.json --input_json_external_box_path ref_box.json

JSON

Common config file 

{
  "properties": {
    "execution_type": "pb_interaction_energy"
  }
}

Docker config file 

{
  "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 

{
  "properties": {
    "remove_tmp": true,
    "execution_type": "mip_pos",
    "container_path": "singularity",
    "container_image": "cmip.simg",
    "container_volume_path": "/inout"
  }
}

Command line

cmip_run --config config_cmip_run.json --input_pdb_path 1kim_h.pdb --input_probe_pdb_path input.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 output.txt --output_byat_path output.txt --output_log_path ref_cmip.log --input_vdw_params_path input.txt --input_params_path input.txt --output_json_box_path ref_box.json --output_json_external_box_path ref_box.json --input_json_box_path ref_box.json --input_json_external_box_path ref_box.json

Cmip_prepare_structure

Generate a CMIP suitable PDB input.

Get help

Command:

cmip_prepare_structure -h

usage: cmip_prepare_structure [-h] [-c CONFIG] --input_pdb_path INPUT_PDB_PATH --output_cmip_pdb_path OUTPUT_CMIP_PDB_PATH [--input_topology_path INPUT_TOPOLOGY_PATH]

Wrapper of the cmip prepare_structure module.

optional arguments:
  -h, --help            show this help message and exit
  -c CONFIG, --config CONFIG
                        This file can be a YAML file, JSON file or JSON string
  --input_topology_path INPUT_TOPOLOGY_PATH

required arguments:
  --input_pdb_path INPUT_PDB_PATH
  --output_cmip_pdb_path OUTPUT_CMIP_PDB_PATH

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. Accepted formats: PDB
input_topology_path (string): Path to the input topology path. File type: input. Sample file. Accepted formats: ZIP, TOP, PSF, PRMTOP
output_cmip_pdb_path (string): Path to the output PDB file. File type: output. Sample file. 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..
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 

properties:
  remove_tmp: true

Command line

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 

{
  "properties": {
    "remove_tmp": true
  }
}

Command line

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