<jupyter_start><jupyter_text>BioBB Analysis Command Line Help Generic usage:<jupyter_code>biobb_command [-h] --config CONFIG --input_file(s) <input_file(s)> --output_file <output_file><jupyter_output><empty_output><jupyter_text>-----------------  Cpptraj average Calculates a structure average of a given cpptraj compatible trajectory.  Get help Command:<jupyter_code>cpptraj_average -h
usage: cpptraj_average [-h] [--config CONFIG] --input_top_path INPUT_TOP_PATH --input_traj_path INPUT_TRAJ_PATH --output_cpptraj_path OUTPUT_CPPTRAJ_PATH

Calculates a structure average of a given cpptraj compatible trajectory.

optional arguments:
  -h, --help            show this help message and exit
  --config CONFIG       Configuration file

required arguments:
  --input_top_path INPUT_TOP_PATH
                        Path to the input structure or topology file. Accepted formats: top, pdb, prmtop, parmtop, zip.
  --input_traj_path INPUT_TRAJ_PATH
                        Path to the input trajectory to be processed. Accepted formats: crd, cdf, netcdf, restart, ncrestart, restartnc, dcd, charmm, cor, pdb, mol2, trr, gro, binpos, xtc, cif, arc, sqm, sdf, conflib.
  --output_cpptraj_path OUTPUT_CPPTRAJ_PATH
                        Path to the output processed structure.<jupyter_output><empty_output><jupyter_text>I / O Arguments Syntax: input_argument (datatype) : DefinitionConfig input / output arguments for this building block:* **input_top_path** (*str*): Path to the input structure or topology file. File type: input. [Sample file](https://github.com/bioexcel/biobb_analysis/raw/master/biobb_analysis/test/data/ambertools/cpptraj.parm.top). Accepted formats: top, pdb, prmtop, parmtop, zip.* **input_traj_path** (*str*): Path to the input trajectory to be processed. File type: input. [Sample file](https://github.com/bioexcel/biobb_analysis/raw/master/biobb_analysis/test/data/ambertools/cpptraj.traj.dcd). Accepted formats: crd, cdf, netcdf, restart, ncrestart, restartnc, dcd, charmm, cor, pdb, mol2, trr, gro, binpos, xtc, cif, arc, sqm, sdf, conflib.* **output_cpptraj_path** (*str*): Path to the output processed structure. File type: output. [Sample file](https://github.com/bioexcel/biobb_analysis/raw/master/biobb_analysis/test/reference/ambertools/ref_cpptraj.average.pdb). Accepted formats: crd, netcdf, rst7, ncrst, dcd, pdb, mol2, binpos, trr, xtc, sqm.  Config Syntax: input_parameter (datatype) - (default_value) DefinitionConfig parameters for this building block:* **in_parameters** (*dict*) - (None) Parameters for input trajectory. Accepted parameters:    * **start** (*int*) - (1) Starting frame for slicing    * **end** (*int*) - (-1) Ending frame for slicing    * **step** (*int*) - (1) Step for slicing    * **mask** (*string*) - ("all-atoms") Mask definition. Values: c-alpha, backbone, all-atoms, heavy-atoms, side-chain, solute, ions, solvent.* **out_parameters** (*dict*) - (None) Parameters for output trajectory.    * **format** (*str*) - ("netcdf") Output trajectory format. Values: crd, cdf, netcdf, restart, ncrestart, restartnc, dcd, charmm, cor, pdb, mol2, trr, gro, binpos, xtc, cif, arc, sqm, sdf, conflib.* **cpptraj_path** (*str*) - ("cpptraj") Path to the cpptraj executable binary.* **remove_tmp** (*bool*) - (True) [WF property] Remove temporal files.* **restart** (*bool*) - (False) [WF property] Do not execute if output files exist.* **container_path** (*string*) - (None) Container path definition.* **container_image** (*string*) - ('afandiadib/ambertools:serial') Container image definition.* **container_volume_path** (*string*) - ('/tmp') Container volume path definition.* **container_working_dir** (*string*) - (None) Container working directory definition.* **container_user_id** (*string*) - (None) Container user_id definition.* **container_shell_path** (*string*) - ('/bin/bash') Path to default shell inside the container.  YAML  Common config file<jupyter_code>properties:
  in_parameters:
    start: 1
    end: -1
    step: 1
    mask: c-alpha
  out_parameters:
    format: netcdf<jupyter_output><empty_output><jupyter_text>Docker config file<jupyter_code>properties:
  in_parameters:
    start: 1
    end: -1
    step: 1
    mask: c-alpha
  out_parameters:
    format: netcdf
  container_path: docker
  container_image: afandiadib/ambertools:serial
  container_volume_path: /tmp<jupyter_output><empty_output><jupyter_text>Singularity config file<jupyter_code>properties:
  in_parameters:
    start: 1
    end: -1
    step: 1
    mask: c-alpha
  out_parameters:
    format: netcdf
  container_path: singularity
  container_image: shub://bioexcel/ambertools_singularity
  container_volume_path: /tmp<jupyter_output><empty_output><jupyter_text>Command line<jupyter_code>cpptraj_average --config data/conf/average.yml --input_top_path data/input/cpptraj.parm.top --input_traj_path data/input/cpptraj.traj.dcd --output_cpptraj_path data/output/output.average.netcdf<jupyter_output><empty_output><jupyter_text>JSON  Common config file<jupyter_code>{
  "properties": {
    "in_parameters": {
      "start": 1,
      "end": -1,
      "step": 1,
      "mask": "c-alpha"
    },
    "out_parameters": {
       "format": "netcdf"
    }
  }
}<jupyter_output><empty_output><jupyter_text>Docker config file<jupyter_code>{
  "properties": {
    "in_parameters": {
      "start": 1,
      "end": -1,
      "step": 1,
      "mask": "c-alpha"
    },
    "out_parameters": {
       "format": "netcdf"
    },
    "container_path": "docker",
    "container_image": "afandiadib/ambertools:serial",
    "container_volume_path": "/tmp"
  }
}<jupyter_output><empty_output><jupyter_text>Singularity config file<jupyter_code>{
  "properties": {
    "in_parameters": {
      "start": 1,
      "end": -1,
      "step": 1,
      "mask": "c-alpha"
    },
    "out_parameters": {
       "format": "netcdf"
    },
    "container_path": "singularity",
    "container_image": "shub://bioexcel/ambertools_singularity",
    "container_volume_path": "/tmp"
  }
}<jupyter_output><empty_output><jupyter_text>Command line<jupyter_code>cpptraj_average --config data/conf/average.json --input_top_path data/input/cpptraj.parm.top --input_traj_path data/input/cpptraj.traj.dcd --output_cpptraj_path data/output/output.average.netcdf<jupyter_output><empty_output><jupyter_text>Cpptraj bfactor Calculates the Bfactor fluctuations of a given cpptraj compatible trajectory.  Get help Command:<jupyter_code>cpptraj_bfactor -h
usage: cpptraj_bfactor [-h] [--config CONFIG] --input_top_path INPUT_TOP_PATH --input_traj_path INPUT_TRAJ_PATH [--input_exp_path INPUT_EXP_PATH] --output_cpptraj_path OUTPUT_CPPTRAJ_PATH

Calculates the Bfactor fluctuations of a given cpptraj compatible trajectory.

optional arguments:
  -h, --help            show this help message and exit
  --config CONFIG       Configuration file
  --input_exp_path INPUT_EXP_PATH
                        Path to the experimental reference file (required if reference = experimental).

required arguments:
  --input_top_path INPUT_TOP_PATH
                        Path to the input structure or topology file. Accepted formats: top, pdb, prmtop, parmtop, zip.
  --input_traj_path INPUT_TRAJ_PATH
                        Path to the input trajectory to be processed. Accepted formats: crd, cdf, netcdf, restart, ncrestart, restartnc, dcd, charmm, cor, pdb, mol2, trr, gro, binpos, xtc, cif, arc, sqm, sdf, conflib.
  --output_cpptraj_path OUTPUT_CPPTRAJ_PATH
                        Path to the output processed analysis.<jupyter_output><empty_output><jupyter_text>I / O Arguments Syntax: input_argument (datatype) : DefinitionConfig input / output arguments for this building block:* **input_top_path** (*str*): Path to the input structure or topology file. File type: input. [Sample file](https://github.com/bioexcel/biobb_analysis/raw/master/biobb_analysis/test/data/ambertools/cpptraj.parm.top). Accepted formats: top, pdb, prmtop, parmtop, zip.* **input_traj_path** (*str*): Path to the input trajectory to be processed. File type: input. [Sample file](https://github.com/bioexcel/biobb_analysis/raw/master/biobb_analysis/test/data/ambertools/cpptraj.traj.dcd). Accepted formats: crd, cdf, netcdf, restart, ncrestart, restartnc, dcd, charmm, cor, pdb, mol2, trr, gro, binpos, xtc, cif, arc, sqm, sdf, conflib.* **input_exp_path** (*str*) (Optional): Path to the experimental reference file (required if reference = experimental). File type: input. [Sample file](https://github.com/bioexcel/biobb_analysis/raw/master/biobb_analysis/test/data/ambertools/experimental.1e5t.pdb). * **output_cpptraj_path** (*str*): Path to the output processed analysis. File type: output. [Sample file](https://github.com/bioexcel/biobb_analysis/raw/master/biobb_analysis/test/reference/ambertools/ref_cpptraj.bfactor.first.dat). Accepted formats: dat, agr, xmgr, gnu.  Config Syntax: input_parameter (datatype) - (default_value) DefinitionConfig parameters for this building block:* **in_parameters** (*dict*) - (None) Parameters for input trajectory. Accepted parameters:    * **start** (*int*) - (1) Starting frame for slicing    * **end** (*int*) - (-1) Ending frame for slicing    * **step** (*int*) - (1) Step for slicing    * **mask** (*string*) - ("all-atoms") Mask definition. Values: c-alpha, backbone, all-atoms, heavy-atoms, side-chain, solute, ions, solvent.    * **reference** (*string*) - ("first") Reference definition. Values: first, average, experimental.* **cpptraj_path** (*str*) - ("cpptraj") Path to the cpptraj executable binary.* **remove_tmp** (*bool*) - (True) [WF property] Remove temporal files.* **restart** (*bool*) - (False) [WF property] Do not execute if output files exist.* **container_path** (*string*) - (None) Container path definition.* **container_image** (*string*) - ('afandiadib/ambertools:serial') Container image definition.* **container_volume_path** (*string*) - ('/tmp') Container volume path definition.* **container_working_dir** (*string*) - (None) Container working directory definition.* **container_user_id** (*string*) - (None) Container user_id definition.* **container_shell_path** (*string*) - ('/bin/bash') Path to default shell inside the container.  YAML  Common config file<jupyter_code>properties:
  in_parameters:
    start: 1
    end: -1
    step: 1
    mask: c-alpha
    reference: first<jupyter_output><empty_output><jupyter_text>Docker config file<jupyter_code>properties:
  in_parameters:
    start: 1
    end: -1
    step: 1
    mask: c-alpha
    reference: first
  container_path: docker
  container_image: afandiadib/ambertools:serial
  container_volume_path: /tmp<jupyter_output><empty_output><jupyter_text>Singularity config file<jupyter_code>properties:
  in_parameters:
    start: 1
    end: -1
    step: 1
    mask: c-alpha
    reference: first
  container_path: singularity
  container_image: shub://bioexcel/ambertools_singularity
  container_volume_path: /tmp<jupyter_output><empty_output><jupyter_text>Command line<jupyter_code>cpptraj_bfactor --config data/conf/bfactor.yml --input_top_path data/input/cpptraj.parm.top --input_traj_path data/input/cpptraj.traj.dcd --output_cpptraj_path data/output/output.bfactor.dat<jupyter_output><empty_output><jupyter_text>JSON  Common file config<jupyter_code>{
  "properties": {
    "in_parameters": {
      "start": 1,
      "end": -1,
      "step": 1,
      "mask": "c-alpha",
      "reference": "first"
    }
  }
}<jupyter_output><empty_output><jupyter_text>Docker config file<jupyter_code>{
  "properties": {
    "in_parameters": {
      "start": 1,
      "end": -1,
      "step": 1,
      "mask": "c-alpha",
      "reference": "first"
    },
    "container_path": "docker",
    "container_image": "afandiadib/ambertools:serial",
    "container_volume_path": "/tmp"
  }
}<jupyter_output><empty_output><jupyter_text>Singularity config file<jupyter_code>{
  "properties": {
    "in_parameters": {
      "start": 1,
      "end": -1,
      "step": 1,
      "mask": "c-alpha",
      "reference": "first"
    },
    "container_path": "singularity",
    "container_image": "shub://bioexcel/ambertools_singularity",
    "container_volume_path": "/tmp"
  }
}<jupyter_output><empty_output><jupyter_text>Command line<jupyter_code>cpptraj_bfactor --config data/conf/bfactor.json --input_top_path data/input/cpptraj.parm.top --input_traj_path data/input/cpptraj.traj.dcd --output_cpptraj_path data/output/output.average.dat<jupyter_output><empty_output><jupyter_text>Cpptraj convert Converts between cpptraj compatible trajectory file formats and/or extracts a selection of atoms or frames.  Get help Command:<jupyter_code>cpptraj_convert -h
usage: cpptraj_convert [-h] [--config CONFIG] --input_top_path INPUT_TOP_PATH --input_traj_path INPUT_TRAJ_PATH --output_cpptraj_path OUTPUT_CPPTRAJ_PATH

Converts between cpptraj compatible trajectory file formats and/or extracts a selection of atoms or frames.

optional arguments:
  -h, --help            show this help message and exit
  --config CONFIG       Configuration file

required arguments:
  --input_top_path INPUT_TOP_PATH
                        Path to the input structure or topology file. Accepted formats: top, pdb, prmtop, parmtop, zip.
  --input_traj_path INPUT_TRAJ_PATH
                        Path to the input trajectory to be processed. Accepted formats: crd, cdf, netcdf, restart, ncrestart, restartnc, dcd, charmm, cor, pdb, mol2, trr, gro, binpos, xtc, cif, arc, sqm, sdf, conflib.
  --output_cpptraj_path OUTPUT_CPPTRAJ_PATH
                        Path to the output processed structure.<jupyter_output><empty_output><jupyter_text>I / O Arguments Syntax: input_argument (datatype) : DefinitionConfig input / output arguments for this building block:* **input_top_path** (*str*): Path to the input structure or topology file. File type: input. [Sample file](https://github.com/bioexcel/biobb_analysis/raw/master/biobb_analysis/test/data/ambertools/cpptraj.parm.top). Accepted formats: top, pdb, prmtop, parmtop, zip.* **input_traj_path** (*str*): Path to the input trajectory to be processed.  File type: input. [Sample file](https://github.com/bioexcel/biobb_analysis/raw/master/biobb_analysis/test/data/ambertools/cpptraj.traj.dcd). Accepted formats: crd, cdf, netcdf, restart, ncrestart, restartnc, dcd, charmm, cor, pdb, mol2, trr, gro, binpos, xtc, cif, arc, sqm, sdf, conflib.* **output_cpptraj_path** (*str*): Path to the output processed trajectory. File type: output. [Sample file](https://github.com/bioexcel/biobb_analysis/raw/master/biobb_analysis/test/reference/ambertools/ref_cpptraj.convert.netcdf). Accepted formats: crd, netcdf, rst7, ncrst, dcd, pdb, mol2, binpos, trr, xtc, sqm.  Config Syntax: input_parameter (datatype) - (default_value) DefinitionConfig parameters for this building block:* **in_parameters** (*dict*) - (None) Parameters for input trajectory. Accepted parameters:    * **start** (*int*) - (1) Starting frame for slicing    * **end** (*int*) - (-1) Ending frame for slicing    * **step** (*int*) - (1) Step for slicing    * **mask** (*string*) - ("all-atoms") Mask definition. Values: c-alpha, backbone, all-atoms, heavy-atoms, side-chain, solute, ions, solvent.* **out_parameters** (*dict*) - (None) Parameters for output trajectory.    * **format** (*str*) - ("netcdf") Output trajectory format. Values: crd, cdf, netcdf, restart, ncrestart, restartnc, dcd, charmm, cor, pdb, mol2, trr, gro, binpos, xtc, cif, arc, sqm, sdf, conflib.* **cpptraj_path** (*str*) - ("cpptraj") Path to the cpptraj executable binary.* **remove_tmp** (*bool*) - (True) [WF property] Remove temporal files.* **restart** (*bool*) - (False) [WF property] Do not execute if output files exist.* **container_path** (*string*) - (None) Container path definition.* **container_image** (*string*) - ('afandiadib/ambertools:serial') Container image definition.* **container_volume_path** (*string*) - ('/tmp') Container volume path definition.* **container_working_dir** (*string*) - (None) Container working directory definition.* **container_user_id** (*string*) - (None) Container user_id definition.* **container_shell_path** (*string*) - ('/bin/bash') Path to default shell inside the container.  YAML  Common file config<jupyter_code>properties:
  in_parameters:
    start: 1
    end: -1
    step: 1
    mask: c-alpha
  out_parameters:
    format: netcdf<jupyter_output><empty_output><jupyter_text>Docker file config<jupyter_code>properties:
  in_parameters:
    start: 1
    end: -1
    step: 1
    mask: c-alpha
  out_parameters:
    format: netcdf
  container_path: docker
  container_image: afandiadib/ambertools:serial
  container_volume_path: /tmp<jupyter_output><empty_output><jupyter_text>Singularity file config<jupyter_code>properties:
  in_parameters:
    start: 1
    end: -1
    step: 1
    mask: c-alpha
  out_parameters:
    format: netcdf
  container_path: singularity
  container_image: shub://bioexcel/ambertools_singularity
  container_volume_path: /tmp<jupyter_output><empty_output><jupyter_text>Command line<jupyter_code>cpptraj_convert --config data/conf/convert.yml --input_top_path data/input/cpptraj.parm.top --input_traj_path data/input/cpptraj.traj.dcd --output_cpptraj_path data/output/output.convert.netcdf<jupyter_output><empty_output><jupyter_text>JSON file  Common file config<jupyter_code>{
  "properties": {
    "in_parameters": {
      "start": 1,
      "end": -1,
      "step": 1,
      "mask": "c-alpha"
    },
    "out_parameters": {
      "format": "netcdf"
    }
  }
}<jupyter_output><empty_output><jupyter_text>Docker file config<jupyter_code>{
  "properties": {
    "in_parameters": {
      "start": 1,
      "end": -1,
      "step": 1,
      "mask": "c-alpha"
    },
    "out_parameters": {
      "format": "netcdf"
    },
    "container_path": "docker",
    "container_image": "afandiadib/ambertools:serial",
    "container_volume_path": "/tmp"
  }
}<jupyter_output><empty_output><jupyter_text>Singularity file config<jupyter_code>{
  "properties": {
    "in_parameters": {
      "start": 1,
      "end": -1,
      "step": 1,
      "mask": "c-alpha"
    },
    "out_parameters": {
      "format": "netcdf"
    },
    "container_path": "singularity",
    "container_image": "shub://bioexcel/ambertools_singularity",
    "container_volume_path": "/tmp"
  }
}<jupyter_output><empty_output><jupyter_text>Command line<jupyter_code>cpptraj_convert --config data/conf/convert.json --input_top_path data/input/cpptraj.parm.top --input_traj_path data/input/cpptraj.traj.dcd --output_cpptraj_path data/output/output.convert.netcdf<jupyter_output><empty_output><jupyter_text>Cpptraj dry Dehydrates a given cpptraj compatible trajectory stripping out solvent molecules and ions.  Get help Command:<jupyter_code>cpptraj_dry -h
usage: cpptraj_dry [-h] [--config CONFIG] --input_top_path INPUT_TOP_PATH --input_traj_path INPUT_TRAJ_PATH --output_cpptraj_path OUTPUT_CPPTRAJ_PATH

Dehydrates a given cpptraj compatible trajectory stripping out solvent molecules and ions.

optional arguments:
  -h, --help            show this help message and exit
  --config CONFIG       Configuration file

required arguments:
  --input_top_path INPUT_TOP_PATH
                        Path to the input structure or topology file. Accepted formats: top, pdb, prmtop, parmtop, zip.
  --input_traj_path INPUT_TRAJ_PATH
                        Path to the input trajectory to be processed. Accepted formats: crd, cdf, netcdf, restart, ncrestart, restartnc, dcd, charmm, cor, pdb, mol2, trr, gro, binpos, xtc, cif, arc, sqm, sdf, conflib.
  --output_cpptraj_path OUTPUT_CPPTRAJ_PATH
                        Path to the output processed trajectory.<jupyter_output><empty_output><jupyter_text>I / O Arguments Syntax: input_argument (datatype) : DefinitionConfig input / output arguments for this building block:* **input_top_path** (*str*): Path to the input structure or topology file. File type: input. [Sample file](https://github.com/bioexcel/biobb_analysis/raw/master/biobb_analysis/test/data/ambertools/cpptraj.parm.top). Accepted formats: top, pdb, prmtop, parmtop, zip.* **input_traj_path** (*str*): Path to the input trajectory to be processed.  File type: input. [Sample file](https://github.com/bioexcel/biobb_analysis/raw/master/biobb_analysis/test/data/ambertools/cpptraj.traj.dcd). Accepted formats: crd, cdf, netcdf, restart, ncrestart, restartnc, dcd, charmm, cor, pdb, mol2, trr, gro, binpos, xtc, cif, arc, sqm, sdf, conflib.* **output_cpptraj_path** (*str*): Path to the output processed trajectory. File type: output. [Sample file](https://github.com/bioexcel/biobb_analysis/raw/master/biobb_analysis/test/reference/ambertools/ref_cpptraj.dry.netcdf). Accepted formats: crd, netcdf, rst7, ncrst, dcd, pdb, mol2, binpos, trr, xtc, sqm.  Config Syntax: input_parameter (datatype) - (default_value) DefinitionConfig parameters for this building block:* **in_parameters** (*dict*) - (None) Parameters for input trajectory. Accepted parameters:    * **start** (*int*) - (1) Starting frame for slicing    * **end** (*int*) - (-1) Ending frame for slicing    * **step** (*int*) - (1) Step for slicing    * **mask** (*string*) - ("all-atoms") Mask definition. Values: c-alpha, backbone, all-atoms, heavy-atoms, side-chain, solute, ions, solvent.* **out_parameters** (*dict*) - (None) Parameters for output trajectory.    * **format** (*str*) - ("netcdf") Output trajectory format. Values: crd, cdf, netcdf, restart, ncrestart, restartnc, dcd, charmm, cor, pdb, mol2, trr, gro, binpos, xtc, cif, arc, sqm, sdf, conflib.* **cpptraj_path** (*str*) - ("cpptraj") Path to the cpptraj executable binary.* **remove_tmp** (*bool*) - (True) [WF property] Remove temporal files.* **restart** (*bool*) - (False) [WF property] Do not execute if output files exist.* **container_path** (*string*) - (None) Container path definition.* **container_image** (*string*) - ('afandiadib/ambertools:serial') Container image definition.* **container_volume_path** (*string*) - ('/tmp') Container volume path definition.* **container_working_dir** (*string*) - (None) Container working directory definition.* **container_user_id** (*string*) - (None) Container user_id definition.* **container_shell_path** (*string*) - ('/bin/bash') Path to default shell inside the container.  YAML  Common file config<jupyter_code>properties:
  in_parameters:
    start: 1
    end: -1
    step: 1
    mask: c-alpha
  out_parameters:
    format: netcdf<jupyter_output><empty_output><jupyter_text>Docker file config<jupyter_code>properties:
  in_parameters:
    start: 1
    end: -1
    step: 1
    mask: c-alpha
  out_parameters:
    format: netcdf
  container_path: docker
  container_image: afandiadib/ambertools:serial
  container_volume_path: /tmp<jupyter_output><empty_output><jupyter_text>Singularity file config<jupyter_code>properties:
  in_parameters:
    start: 1
    end: -1
    step: 1
    mask: c-alpha
  out_parameters:
    format: netcdf
  container_path: singularity
  container_image: shub://bioexcel/ambertools_singularity
  container_volume_path: /tmp<jupyter_output><empty_output><jupyter_text>Command line<jupyter_code>cpptraj_dry --config data/conf/dry.yml --input_top_path data/input/cpptraj.parm.top --input_traj_path data/input/cpptraj.traj.dcd --output_cpptraj_path data/output/output.dry.netcdf<jupyter_output><empty_output><jupyter_text>JSON  Common file config<jupyter_code>{
  "properties": {
    "in_parameters": {
      "start": 1,
      "end": -1,
      "step": 1,
      "mask": "c-alpha"
    },
    "out_parameters": {
      "format": "netcdf"
    }
  }
}<jupyter_output><empty_output><jupyter_text>Docker file config<jupyter_code>{
  "properties": {
    "in_parameters": {
      "start": 1,
      "end": -1,
      "step": 1,
      "mask": "c-alpha"
    },
    "out_parameters": {
      "format": "netcdf"
    }
  },
  "container_path": "docker",
  "container_image": "afandiadib/ambertools:serial",
  "container_volume_path": "/tmp"
}<jupyter_output><empty_output><jupyter_text>Singularity file config<jupyter_code>{
  "properties": {
    "in_parameters": {
      "start": 1,
      "end": -1,
      "step": 1,
      "mask": "c-alpha"
    },
    "out_parameters": {
      "format": "netcdf"
    },
    "container_path": "singularity",
    "container_image": "shub://bioexcel/ambertools_singularity",
    "container_volume_path": "/tmp"
  }
}<jupyter_output><empty_output><jupyter_text>Command line<jupyter_code>cpptraj_dry --config data/conf/dry.json --input_top_path data/input/cpptraj.parm.top --input_traj_path data/input/cpptraj.traj.dcd --output_cpptraj_path data/output/output.dry.netcdf<jupyter_output><empty_output><jupyter_text>Cpptraj image Corrects periodicity (image) from a given cpptraj trajectory file.  Get help Command:<jupyter_code>cpptraj_image -h
usage: cpptraj_image [-h] [--config CONFIG] --input_top_path INPUT_TOP_PATH --input_traj_path INPUT_TRAJ_PATH --output_cpptraj_path OUTPUT_CPPTRAJ_PATH

Corrects periodicity (image) from a given cpptraj trajectory file.

optional arguments:
  -h, --help            show this help message and exit
  --config CONFIG       Configuration file

required arguments:
  --input_top_path INPUT_TOP_PATH
                        Path to the input structure or topology file. Accepted formats: top, pdb, prmtop, parmtop, zip.
  --input_traj_path INPUT_TRAJ_PATH
                        Path to the input trajectory to be processed. Accepted formats: crd, cdf, netcdf, restart, ncrestart, restartnc, dcd, charmm, cor, pdb, mol2, trr, gro, binpos, xtc, cif, arc, sqm, sdf, conflib.
  --output_cpptraj_path OUTPUT_CPPTRAJ_PATH
                        Path to the output processed trajectory.<jupyter_output><empty_output><jupyter_text>I / O Arguments Syntax: input_argument (datatype) : DefinitionConfig input / output arguments for this building block:* **input_top_path** (*str*): Path to the input structure or topology file. File type: input. [Sample file](https://github.com/bioexcel/biobb_analysis/raw/master/biobb_analysis/test/data/ambertools/cpptraj.parm.top). Accepted formats: top, pdb, prmtop, parmtop, zip.* **input_traj_path** (*str*): Path to the input trajectory to be processed.  File type: input. [Sample file](https://github.com/bioexcel/biobb_analysis/raw/master/biobb_analysis/test/data/ambertools/cpptraj.traj.dcd). Accepted formats: crd, cdf, netcdf, restart, ncrestart, restartnc, dcd, charmm, cor, pdb, mol2, trr, gro, binpos, xtc, cif, arc, sqm, sdf, conflib.* **output_cpptraj_path** (*str*): Path to the output processed trajectory. File type: output. [Sample file](https://github.com/bioexcel/biobb_analysis/raw/master/biobb_analysis/test/reference/ambertools/ref_cpptraj.image.netcdf). Accepted formats: crd, netcdf, rst7, ncrst, dcd, pdb, mol2, binpos, trr, xtc, sqm.  Config Syntax: input_parameter (datatype) - (default_value) DefinitionConfig parameters for this building block:* **in_parameters** (*dict*) - (None) Parameters for input trajectory. Accepted parameters:    * **start** (*int*) - (1) Starting frame for slicing    * **end** (*int*) - (-1) Ending frame for slicing    * **step** (*int*) - (1) Step for slicing    * **mask** (*string*) - ("all-atoms") Mask definition. Values: c-alpha, backbone, all-atoms, heavy-atoms, side-chain, solute, ions, solvent.* **out_parameters** (*dict*) - (None) Parameters for output trajectory.    * **format** (*str*) - ("netcdf") Output trajectory format. Values: crd, cdf, netcdf, restart, ncrestart, restartnc, dcd, charmm, cor, pdb, mol2, trr, gro, binpos, xtc, cif, arc, sqm, sdf, conflib.* **cpptraj_path** (*str*) - ("cpptraj") Path to the cpptraj executable binary.* **remove_tmp** (*bool*) - (True) [WF property] Remove temporal files.* **restart** (*bool*) - (False) [WF property] Do not execute if output files exist.* **container_path** (*string*) - (None) Container path definition.* **container_image** (*string*) - ('afandiadib/ambertools:serial') Container image definition.* **container_volume_path** (*string*) - ('/tmp') Container volume path definition.* **container_working_dir** (*string*) - (None) Container working directory definition.* **container_user_id** (*string*) - (None) Container user_id definition.* **container_shell_path** (*string*) - ('/bin/bash') Path to default shell inside the container.  YAML  Common file config<jupyter_code>properties:
  in_parameters:
    start: 1
    end: -1
    step: 1
    mask: c-alpha
  out_parameters:
    format: netcdf<jupyter_output><empty_output><jupyter_text>Docker file config<jupyter_code>properties:
  in_parameters:
    start: 1
    end: -1
    step: 1
    mask: c-alpha
  out_parameters:
    format: netcdf
  container_path: docker
  container_image: afandiadib/ambertools:serial
  container_volume_path: /tmp<jupyter_output><empty_output><jupyter_text>Common file config<jupyter_code>properties:
  in_parameters:
    start: 1
    end: -1
    step: 1
    mask: c-alpha
  out_parameters:
    format: netcdf
  container_path: singularity
  container_image: shub://bioexcel/ambertools_singularity
  container_volume_path: /tmp<jupyter_output><empty_output><jupyter_text>Command line<jupyter_code>cpptraj_image --config data/conf/image.yml --input_top_path data/input/cpptraj.parm.top --input_traj_path data/input/cpptraj.traj.dcd --output_cpptraj_path data/output/output.image.netcdf<jupyter_output><empty_output><jupyter_text>JSON  Common file config<jupyter_code>{
  "properties": {
    "in_parameters": {
      "start": 1,
      "end": -1,
      "step": 1,
      "mask": "c-alpha"
    },
    "out_parameters": {
      "format": "netcdf"
    }
  }
}<jupyter_output><empty_output><jupyter_text>Docker file config<jupyter_code>{
  "properties": {
    "in_parameters": {
      "start": 1,
      "end": -1,
      "step": 1,
      "mask": "c-alpha"
    },
    "out_parameters": {
      "format": "netcdf"
    }
  },
  "container_path": "docker",
  "container_image": "afandiadib/ambertools:serial",
  "container_volume_path": "/tmp"
}<jupyter_output><empty_output><jupyter_text>Singularity file config<jupyter_code>{
  "properties": {
    "in_parameters": {
      "start": 1,
      "end": -1,
      "step": 1,
      "mask": "c-alpha"
    },
    "out_parameters": {
      "format": "netcdf"
    }
  },
  "container_path": "singularity",
  "container_image": "shub://bioexcel/ambertools_singularity",
  "container_volume_path": "/tmp"
}<jupyter_output><empty_output><jupyter_text>Command line<jupyter_code>cpptraj_image --config data/conf/image.json --input_top_path data/input/cpptraj.parm.top --input_traj_path data/input/cpptraj.traj.dcd --output_cpptraj_path data/output/output.image.netcdf<jupyter_output><empty_output><jupyter_text>Cpptraj input Performs multiple analysis and trajectory operations of a given trajector  Get help Command:<jupyter_code>cpptraj_input -h
usage: cpptraj_input [-h] [--config CONFIG] --input_instructions_path INPUT_INSTRUCTIONS_PATH

Performs multiple analysis and trajectory operations of a given trajectory.

optional arguments:
  -h, --help            show this help message and exit
  --config CONFIG       Configuration file

required arguments:
  --input_instructions_path INPUT_INSTRUCTIONS_PATH
                        Path of the instructions file.<jupyter_output><empty_output><jupyter_text>I / O Arguments Syntax: input_argument (datatype) : DefinitionConfig input / output arguments for this building block:* **input_instructions_path** (*str*): Path of the instructions file. File type: input. [Sample file](https://github.com/bioexcel/biobb_analysis/raw/master/biobb_analysis/test/data/ambertools/cpptraj.in).  Config Syntax: input_parameter (datatype) - (default_value) DefinitionConfig parameters for this building block:* **cpptraj_path** (*str*) - ("cpptraj") Path to the cpptraj executable binary.* **remove_tmp** (*bool*) - (True) [WF property] Remove temporal files.* **restart** (*bool*) - (False) [WF property] Do not execute if output files exist.  Instructions file input.in:<jupyter_code>parm data/input/cpptraj.convert.pdb
trajin data/input/cpptraj.convert.dcd
trajout data/output/output.netcdf netcdf<jupyter_output><empty_output><jupyter_text>YAML  Common file config<jupyter_code>properties:
  cpptraj_path: cpptraj<jupyter_output><empty_output><jupyter_text>Docker file config<jupyter_code>properties:
  cpptraj_path: cpptraj
  container_path: docker
  container_image: afandiadib/ambertools:serial
  container_volume_path: /tmp<jupyter_output><empty_output><jupyter_text>Singularity file config<jupyter_code>properties:
  cpptraj_path: cpptraj
  container_path: singularity
  container_image: shub://bioexcel/ambertools_singularity
  container_volume_path: /tmp<jupyter_output><empty_output><jupyter_text>Command line<jupyter_code>cpptraj_input --config data/conf/input.yml --input_instructions_path data/input/input.in<jupyter_output><empty_output><jupyter_text>JSON  Common file config<jupyter_code>{
  "properties": {
    "cpptraj_path": "cpptraj"
  }
}<jupyter_output><empty_output><jupyter_text>Docker file config<jupyter_code>{
  "properties": {
    "cpptraj_path": "cpptraj",
    "container_path": "docker",
    "container_image": "afandiadib/ambertools:serial",
    "container_volume_path": "/tmp"
  }
}<jupyter_output><empty_output><jupyter_text>Singularity file config<jupyter_code>{
  "properties": {
    "cpptraj_path": "cpptraj",
    "container_path": "singularity",
    "container_image": "shub://bioexcel/ambertools_singularity",
    "container_volume_path": "/tmp"
  }
}<jupyter_output><empty_output><jupyter_text>Command line<jupyter_code>cpptraj_input --config data/conf/input.json --input_instructions_path data/input/input.in<jupyter_output><empty_output><jupyter_text>Cpptraj mask Extracts a selection of atoms from a given cpptraj compatible trajectory.  Get help Command:<jupyter_code>cpptraj_mask -h
usage: cpptraj_mask [-h] [--config CONFIG] --input_top_path INPUT_TOP_PATH --input_traj_path INPUT_TRAJ_PATH --output_cpptraj_path OUTPUT_CPPTRAJ_PATH

Extracts a selection of atoms from a given cpptraj compatible trajectory.

optional arguments:
  -h, --help            show this help message and exit
  --config CONFIG       Configuration file

required arguments:
  --input_top_path INPUT_TOP_PATH
                        Path to the input structure or topology file. Accepted formats: top, pdb, prmtop, parmtop, zip.
  --input_traj_path INPUT_TRAJ_PATH
                        Path to the input trajectory to be processed. Accepted formats: crd, cdf, netcdf, restart, ncrestart, restartnc, dcd, charmm, cor, pdb, mol2, trr, gro, binpos, xtc, cif, arc, sqm, sdf, conflib.
  --output_cpptraj_path OUTPUT_CPPTRAJ_PATH
                        Path to the output processed trajectory.<jupyter_output><empty_output><jupyter_text>I / O Arguments Syntax: input_argument (datatype) : DefinitionConfig input / output arguments for this building block:* **input_top_path** (*str*): Path to the input structure or topology file. File type: input. [Sample file](https://github.com/bioexcel/biobb_analysis/raw/master/biobb_analysis/test/data/ambertools/cpptraj.parm.top). Accepted formats: top, pdb, prmtop, parmtop, zip.* **input_traj_path** (*str*): Path to the input trajectory to be processed.  File type: input. [Sample file](https://github.com/bioexcel/biobb_analysis/raw/master/biobb_analysis/test/data/ambertools/cpptraj.traj.dcd). Accepted formats: crd, cdf, netcdf, restart, ncrestart, restartnc, dcd, charmm, cor, pdb, mol2, trr, gro, binpos, xtc, cif, arc, sqm, sdf, conflib.* **output_cpptraj_path** (*str*): Path to the output processed trajectory. File type: output. [Sample file](https://github.com/bioexcel/biobb_analysis/raw/master/biobb_analysis/test/reference/ambertools/ref_cpptraj.mask.netcdf). Accepted formats: crd, netcdf, rst7, ncrst, dcd, pdb, mol2, binpos, trr, xtc, sqm.  Config Syntax: input_parameter (datatype) - (default_value) DefinitionConfig parameters for this building block:* **in_parameters** (*dict*) - (None) Parameters for input trajectory. Accepted parameters:    * **start** (*int*) - (1) Starting frame for slicing    * **end** (*int*) - (-1) Ending frame for slicing    * **step** (*int*) - (1) Step for slicing    * **mask** (*string*) - ("all-atoms") Mask definition. Values: c-alpha, backbone, all-atoms, heavy-atoms, side-chain, solute, ions, solvent.* **out_parameters** (*dict*) - (None) Parameters for output trajectory.    * **format** (*str*) - ("netcdf") Output trajectory format. Values: crd, cdf, netcdf, restart, ncrestart, restartnc, dcd, charmm, cor, pdb, mol2, trr, gro, binpos, xtc, cif, arc, sqm, sdf, conflib.* **cpptraj_path** (*str*) - ("cpptraj") Path to the cpptraj executable binary.* **remove_tmp** (*bool*) - (True) [WF property] Remove temporal files.* **restart** (*bool*) - (False) [WF property] Do not execute if output files exist.* **container_path** (*string*) - (None) Container path definition.* **container_image** (*string*) - ('afandiadib/ambertools:serial') Container image definition.* **container_volume_path** (*string*) - ('/tmp') Container volume path definition.* **container_working_dir** (*string*) - (None) Container working directory definition.* **container_user_id** (*string*) - (None) Container user_id definition.* **container_shell_path** (*string*) - ('/bin/bash') Path to default shell inside the container.  YAML  Common file config<jupyter_code>properties:
  in_parameters:
    start: 1
    end: -1
    step: 1
    mask: c-alpha
  out_parameters:
    format: netcdf<jupyter_output><empty_output><jupyter_text>Docker file config<jupyter_code>properties:
  in_parameters:
    start: 1
    end: -1
    step: 1
    mask: c-alpha
  out_parameters:
    format: netcdf
  container_path: docker
  container_image: afandiadib/ambertools:serial
  container_volume_path: /tmp<jupyter_output><empty_output><jupyter_text>Singularity file config<jupyter_code>properties:
  in_parameters:
    start: 1
    end: -1
    step: 1
    mask: c-alpha
  out_parameters:
    format: netcdf
  container_path: singularity
  container_image: shub://bioexcel/ambertools_singularity
  container_volume_path: /tmp<jupyter_output><empty_output><jupyter_text>Command line<jupyter_code>cpptraj_mask --config data/conf/mask.yml --input_top_path data/input/cpptraj.parm.top --input_traj_path data/input/cpptraj.traj.dcd --output_cpptraj_path data/output/output.mask.netcdf<jupyter_output><empty_output><jupyter_text>JSON  Common file config<jupyter_code>{
  "properties": {
    "in_parameters": {
      "start": 1,
      "end": -1,
      "step": 1,
      "mask": "c-alpha"
    },
    "out_parameters": {
      "format": "netcdf"
    }
  }
}<jupyter_output><empty_output><jupyter_text>Docker file config<jupyter_code>{
  "properties": {
    "in_parameters": {
      "start": 1,
      "end": -1,
      "step": 1,
      "mask": "c-alpha"
    },
    "out_parameters": {
      "format": "netcdf"
    },
    "container_path": "docker",
    "container_image": "afandiadib/ambertools:serial",
    "container_volume_path": "/tmp"
  }
}<jupyter_output><empty_output><jupyter_text>Singularity file config<jupyter_code>{
  "properties": {
    "in_parameters": {
      "start": 1,
      "end": -1,
      "step": 1,
      "mask": "c-alpha"
    },
    "out_parameters": {
      "format": "netcdf"
    },
    "container_path": "singularity",
    "container_image": "shub://bioexcel/ambertools_singularity",
    "container_volume_path": "/tmp"
  }
}<jupyter_output><empty_output><jupyter_text>Command line<jupyter_code>cpptraj_mask --config data/conf/mask.json --input_top_path data/input/cpptraj.parm.top --input_traj_path data/input/cpptraj.traj.dcd --output_cpptraj_path data/output/output.image.netcdf<jupyter_output><empty_output><jupyter_text>Cpptraj rgyr Computes the radius of gyration (Rgyr) from a given cpptraj compatible trajectory.  Get help Command:<jupyter_code>cpptraj_rgyr -h
usage: cpptraj_rgyr [-h] [--config CONFIG] --input_top_path INPUT_TOP_PATH --input_traj_path INPUT_TRAJ_PATH --output_cpptraj_path OUTPUT_CPPTRAJ_PATH

Computes the radius of gyration (Rgyr) from a given cpptraj compatible trajectory.

optional arguments:
  -h, --help            show this help message and exit
  --config CONFIG       Configuration file

required arguments:
  --input_top_path INPUT_TOP_PATH
                        Path to the input structure or topology file. Accepted formats: top, pdb, prmtop, parmtop, zip.
  --input_traj_path INPUT_TRAJ_PATH
                        Path to the input trajectory to be processed. Accepted formats: crd, cdf, netcdf, restart, ncrestart, restartnc, dcd, charmm, cor, pdb, mol2, trr, gro, binpos, xtc, cif, arc, sqm, sdf, conflib.
  --output_cpptraj_path OUTPUT_CPPTRAJ_PATH
                        Path to the output analysis.<jupyter_output><empty_output><jupyter_text>I / O Arguments Syntax: input_argument (datatype) : DefinitionConfig input / output arguments for this building block:* **input_top_path** (*str*): Path to the input structure or topology file. File type: input. [Sample file](https://github.com/bioexcel/biobb_analysis/raw/master/biobb_analysis/test/data/ambertools/cpptraj.parm.top). Accepted formats: top, pdb, prmtop, parmtop, zip.* **input_traj_path** (*str*): Path to the input trajectory to be processed.  File type: input. [Sample file](https://github.com/bioexcel/biobb_analysis/raw/master/biobb_analysis/test/data/ambertools/cpptraj.traj.dcd). Accepted formats: crd, cdf, netcdf, restart, ncrestart, restartnc, dcd, charmm, cor, pdb, mol2, trr, gro, binpos, xtc, cif, arc, sqm, sdf, conflib.* **output_cpptraj_path** (*str*): Path to the output analysis. File type: output. [Sample file](https://github.com/bioexcel/biobb_analysis/raw/master/biobb_analysis/test/reference/ambertools/ref_cpptraj.rgyr.dat). Accepted formats: dat, agr, xmgr, gnu.  Config Syntax: input_parameter (datatype) - (default_value) DefinitionConfig parameters for this building block:* **in_parameters** (*dict*) - (None) Parameters for input trajectory. Accepted parameters:    * **start** (*int*) - (1) Starting frame for slicing    * **end** (*int*) - (-1) Ending frame for slicing    * **step** (*int*) - (1) Step for slicing    * **mask** (*string*) - ("all-atoms") Mask definition. Values: c-alpha, backbone, all-atoms, heavy-atoms, side-chain, solute, ions, solvent.* **cpptraj_path** (*str*) - ("cpptraj") Path to the cpptraj executable binary.* **remove_tmp** (*bool*) - (True) [WF property] Remove temporal files.* **restart** (*bool*) - (False) [WF property] Do not execute if output files exist.* **container_path** (*string*) - (None) Container path definition.* **container_image** (*string*) - ('afandiadib/ambertools:serial') Container image definition.* **container_volume_path** (*string*) - ('/tmp') Container volume path definition.* **container_working_dir** (*string*) - (None) Container working directory definition.* **container_user_id** (*string*) - (None) Container user_id definition.* **container_shell_path** (*string*) - ('/bin/bash') Path to default shell inside the container.  YAML  Common file config<jupyter_code>properties:
  in_parameters:
    start: 1
    end: -1
    step: 1
    mask: c-alpha<jupyter_output><empty_output><jupyter_text>Docker file config<jupyter_code>properties:
  in_parameters:
    start: 1
    end: -1
    step: 1
    mask: c-alpha
  container_path: docker
  container_image: afandiadib/ambertools:serial
  container_volume_path: /tmp<jupyter_output><empty_output><jupyter_text>Singularity file config<jupyter_code>properties:
  in_parameters:
    start: 1
    end: -1
    step: 1
    mask: c-alpha
  container_path: singularity
  container_image: shub://bioexcel/ambertools_singularity
  container_volume_path: /tmp<jupyter_output><empty_output><jupyter_text>Command line<jupyter_code>cpptraj_rgyr --config data/conf/rgyr.yml --input_top_path data/input/cpptraj.parm.top --input_traj_path data/input/cpptraj.traj.dcd --output_cpptraj_path data/output/output.rgyr.dat<jupyter_output><empty_output><jupyter_text>JSON  Common file config<jupyter_code>{
  "properties": {
    "in_parameters": {
      "start": 1,
      "end": -1,
      "step": 1,
      "mask": "c-alpha"
    }
  }
}<jupyter_output><empty_output><jupyter_text>Docker file config<jupyter_code>{
  "properties": {
    "in_parameters": {
      "start": 1,
      "end": -1,
      "step": 1,
      "mask": "c-alpha"
    },
    "container_path": "docker",
    "container_image": "afandiadib/ambertools:serial",
    "container_volume_path": "/tmp"
  }
}<jupyter_output><empty_output><jupyter_text>Singularity file config<jupyter_code>{
  "properties": {
    "in_parameters": {
      "start": 1,
      "end": -1,
      "step": 1,
      "mask": "c-alpha"
    },
    "container_path": "singularity",
    "container_image": "shub://bioexcel/ambertools_singularity",
    "container_volume_path": "/tmp"
  }
}<jupyter_output><empty_output><jupyter_text>Command line<jupyter_code>cpptraj_rgyr --config data/conf/rgyr.json --input_top_path data/input/cpptraj.parm.top --input_traj_path data/input/cpptraj.traj.dcd --output_cpptraj_path data/output/output.rgyr.dat<jupyter_output><empty_output><jupyter_text>Cpptraj rms Calculates the Root Mean Square deviation (RMSd) of a given cpptraj compatible trajectory.s.  Get help Command:<jupyter_code>cpptraj_rms -h
usage: cpptraj_rms [-h] [--config CONFIG] --input_top_path INPUT_TOP_PATH --input_traj_path INPUT_TRAJ_PATH [--input_exp_path INPUT_EXP_PATH] --output_cpptraj_path OUTPUT_CPPTRAJ_PATH

Calculates the Root Mean Square deviation (RMSd) of a given cpptraj compatible trajectory.

optional arguments:
  -h, --help            show this help message and exit
  --config CONFIG       Configuration file
  --input_exp_path INPUT_EXP_PATH
                        Path to the experimental reference file (required if reference = experimental).

required arguments:
  --input_top_path INPUT_TOP_PATH
                        Path to the input structure or topology file. Accepted formats: top, pdb, prmtop, parmtop, zip.
  --input_traj_path INPUT_TRAJ_PATH
                        Path to the input trajectory to be processed. Accepted formats: crd, cdf, netcdf, restart, ncrestart, restartnc, dcd, charmm, cor, pdb, mol2, trr, gro, binpos, xtc, cif, arc, sqm, sdf, conflib.
  --output_cpptraj_path OUTPUT_CPPTRAJ_PATH
                        Path to the output processed analysis.<jupyter_output><empty_output><jupyter_text>I / O Arguments Syntax: input_argument (datatype) : DefinitionConfig input / output arguments for this building block:* **input_top_path** (*str*): Path to the input structure or topology file. File type: input. [Sample file](https://github.com/bioexcel/biobb_analysis/raw/master/biobb_analysis/test/data/ambertools/cpptraj.parm.top). Accepted formats: top, pdb, prmtop, parmtop, zip.* **input_traj_path** (*str*): Path to the input trajectory to be processed.  File type: input. [Sample file](https://github.com/bioexcel/biobb_analysis/raw/master/biobb_analysis/test/data/ambertools/cpptraj.traj.dcd). Accepted formats: crd, cdf, netcdf, restart, ncrestart, restartnc, dcd, charmm, cor, pdb, mol2, trr, gro, binpos, xtc, cif, arc, sqm, sdf, conflib.* **input_exp_path** (*str*) (Optional): Path to the experimental reference file (required if reference = experimental). File type: input. [Sample file](https://github.com/bioexcel/biobb_analysis/raw/master/biobb_analysis/test/data/ambertools/experimental.1e5t.pdb). * **output_cpptraj_path** (*str*): Path to the output processed analysis. File type: output. [Sample file](https://github.com/bioexcel/biobb_analysis/raw/master/biobb_analysis/test/reference/ambertools/ref_cpptraj.rms.first.dat). Accepted formats: dat, agr, xmgr, gnu.  Config Syntax: input_parameter (datatype) - (default_value) DefinitionConfig parameters for this building block:* **in_parameters** (*dict*) - (None) Parameters for input trajectory. Accepted parameters:    * **start** (*int*) - (1) Starting frame for slicing    * **end** (*int*) - (-1) Ending frame for slicing    * **step** (*int*) - (1) Step for slicing    * **mask** (*string*) - ("all-atoms") Mask definition. Values: c-alpha, backbone, all-atoms, heavy-atoms, side-chain, solute, ions, solvent.    * **reference** (*string*) - ("first") Reference definition. Values: first, average, experimental.* **cpptraj_path** (*str*) - ("cpptraj") Path to the cpptraj executable binary.* **remove_tmp** (*bool*) - (True) [WF property] Remove temporal files.* **restart** (*bool*) - (False) [WF property] Do not execute if output files exist.* **container_path** (*string*) - (None) Container path definition.* **container_image** (*string*) - ('afandiadib/ambertools:serial') Container image definition.* **container_volume_path** (*string*) - ('/tmp') Container volume path definition.* **container_working_dir** (*string*) - (None) Container working directory definition.* **container_user_id** (*string*) - (None) Container user_id definition.* **container_shell_path** (*string*) - ('/bin/bash') Path to default shell inside the container.  YAML  Common file config<jupyter_code>properties:
  in_parameters:
    start: 1
    end: -1
    step: 1
    mask: c-alpha
    reference: first<jupyter_output><empty_output><jupyter_text>Docker file config<jupyter_code>properties:
  in_parameters:
    start: 1
    end: -1
    step: 1
    mask: c-alpha
    reference: first
  container_path: docker
  container_image: afandiadib/ambertools:serial
  container_volume_path: /tmp<jupyter_output><empty_output><jupyter_text>Singularity file config<jupyter_code>properties:
  in_parameters:
    start: 1
    end: -1
    step: 1
    mask: c-alpha
    reference: first
  container_path: singularity
  container_image: shub://bioexcel/ambertools_singularity
  container_volume_path: /tmp<jupyter_output><empty_output><jupyter_text>Command line<jupyter_code>cpptraj_rms --config data/conf/rms.yml --input_top_path data/input/cpptraj.parm.top --input_traj_path data/input/cpptraj.traj.dcd --output_cpptraj_path data/output/output.rms.dat<jupyter_output><empty_output><jupyter_text>JSON  Common file config<jupyter_code>{
  "properties": {
    "in_parameters": {
      "start": 1,
      "end": -1,
      "step": 1,
      "mask": "c-alpha",
      "reference": "first"
    }
  }
}<jupyter_output><empty_output><jupyter_text>Docker file config<jupyter_code>{
  "properties": {
    "in_parameters": {
      "start": 1,
      "end": -1,
      "step": 1,
      "mask": "c-alpha",
      "reference": "first"
    },
    "container_path": "docker",
    "container_image": "afandiadib/ambertools:serial",
    "container_volume_path": "/tmp"
  }
}<jupyter_output><empty_output><jupyter_text>Singularity file config<jupyter_code>{
  "properties": {
    "in_parameters": {
      "start": 1,
      "end": -1,
      "step": 1,
      "mask": "c-alpha",
      "reference": "first"
    },
    "container_path": "singularity",
    "container_image": "shub://bioexcel/ambertools_singularity",
    "container_volume_path": "/tmp"
  }
}<jupyter_output><empty_output><jupyter_text>Command line<jupyter_code>cpptraj_rms --config data/conf/rms.json --input_top_path data/input/cpptraj.parm.top --input_traj_path data/input/cpptraj.traj.dcd --output_cpptraj_path data/output/output.rms.dat<jupyter_output><empty_output><jupyter_text>Cpptraj rmsf Calculates the Root Mean Square fluctuations (RMSf) of a given cpptraj compatible trajectory.  Get help Command:<jupyter_code>cpptraj_rmsf -h
usage: cpptraj_rmsf [-h] [--config CONFIG] --input_top_path INPUT_TOP_PATH --input_traj_path INPUT_TRAJ_PATH [--input_exp_path INPUT_EXP_PATH] --output_cpptraj_path OUTPUT_CPPTRAJ_PATH

Calculates the Root Mean Square fluctuations (RMSf) of a given cpptraj compatible trajectory.

optional arguments:
  -h, --help            show this help message and exit
  --config CONFIG       Configuration file
  --input_exp_path INPUT_EXP_PATH
                        Path to the experimental reference file (required if reference = experimental).

required arguments:
  --input_top_path INPUT_TOP_PATH
                        Path to the input structure or topology file. Accepted formats: top, pdb, prmtop, parmtop, zip.
  --input_traj_path INPUT_TRAJ_PATH
                        Path to the input trajectory to be processed. Accepted formats: crd, cdf, netcdf, restart, ncrestart, restartnc, dcd, charmm, cor, pdb, mol2, trr, gro, binpos, xtc, cif, arc, sqm, sdf, conflib.
  --output_cpptraj_path OUTPUT_CPPTRAJ_PATH
                        Path to the output processed analysis.<jupyter_output><empty_output><jupyter_text>I / O Arguments Syntax: input_argument (datatype) : DefinitionConfig input / output arguments for this building block:* **input_top_path** (*str*): Path to the input structure or topology file. File type: input. [Sample file](https://github.com/bioexcel/biobb_analysis/raw/master/biobb_analysis/test/data/ambertools/cpptraj.parm.top). Accepted formats: top, pdb, prmtop, parmtop, zip.* **input_traj_path** (*str*): Path to the input trajectory to be processed.  File type: input. [Sample file](https://github.com/bioexcel/biobb_analysis/raw/master/biobb_analysis/test/data/ambertools/cpptraj.traj.dcd). Accepted formats: crd, cdf, netcdf, restart, ncrestart, restartnc, dcd, charmm, cor, pdb, mol2, trr, gro, binpos, xtc, cif, arc, sqm, sdf, conflib.* **input_exp_path** (*str*) (Optional): Path to the experimental reference file (required if reference = experimental). File type: input. [Sample file](https://github.com/bioexcel/biobb_analysis/raw/master/biobb_analysis/test/data/ambertools/experimental.1e5t.pdb).* **output_cpptraj_path** (*str*): Path to the output processed analysis. File type: output. [Sample file](https://github.com/bioexcel/biobb_analysis/raw/master/biobb_analysis/test/reference/ambertools/ref_cpptraj.rmsf.first.dat). Accepted formats: dat, agr, xmgr, gnu.  Config Syntax: input_parameter (datatype) - (default_value) DefinitionConfig parameters for this building block:* **in_parameters** (*dict*) - (None) Parameters for input trajectory. Accepted parameters:    * **start** (*int*) - (1) Starting frame for slicing    * **end** (*int*) - (-1) Ending frame for slicing    * **step** (*int*) - (1) Step for slicing    * **mask** (*string*) - ("all-atoms") Mask definition. Values: c-alpha, backbone, all-atoms, heavy-atoms, side-chain, solute, ions, solvent.    * **reference** (*string*) - ("first") Reference definition. Values: first, average, experimental.* **cpptraj_path** (*str*) - ("cpptraj") Path to the cpptraj executable binary.* **remove_tmp** (*bool*) - (True) [WF property] Remove temporal files.* **restart** (*bool*) - (False) [WF property] Do not execute if output files exist.* **container_path** (*string*) - (None) Container path definition.* **container_image** (*string*) - ('afandiadib/ambertools:serial') Container image definition.* **container_volume_path** (*string*) - ('/tmp') Container volume path definition.* **container_working_dir** (*string*) - (None) Container working directory definition.* **container_user_id** (*string*) - (None) Container user_id definition.* **container_shell_path** (*string*) - ('/bin/bash') Path to default shell inside the container.  YAML  Common file config<jupyter_code>properties:
  in_parameters:
    start: 1
    end: -1
    step: 1
    mask: c-alpha
    reference: first<jupyter_output><empty_output><jupyter_text>Docker file config<jupyter_code>properties:
  in_parameters:
    start: 1
    end: -1
    step: 1
    mask: c-alpha
    reference: first
  container_path: docker
  container_image: afandiadib/ambertools:serial
  container_volume_path: /tmp<jupyter_output><empty_output><jupyter_text>Singularity file config<jupyter_code>properties:
  in_parameters:
    start: 1
    end: -1
    step: 1
    mask: c-alpha
    reference: first
  container_path: singularity
  container_image: shub://bioexcel/ambertools_singularity
  container_volume_path: /tmp<jupyter_output><empty_output><jupyter_text>Command line<jupyter_code>cpptraj_rmsf --config data/conf/rmsf.yml --input_top_path data/input/cpptraj.parm.top --input_traj_path data/input/cpptraj.traj.dcd --output_cpptraj_path data/output/output.rmsf.dat<jupyter_output><empty_output><jupyter_text>JSON  Common file config<jupyter_code>{
  "properties": {
    "in_parameters": {
      "start": 1,
      "end": -1,
      "step": 1,
      "mask": "c-alpha",
      "reference": "first"
    }
  }
}<jupyter_output><empty_output><jupyter_text>Docker file config<jupyter_code>{
  "properties": {
    "in_parameters": {
      "start": 1,
      "end": -1,
      "step": 1,
      "mask": "c-alpha",
      "reference": "first"
    },
    "container_path": "docker",
    "container_image": "afandiadib/ambertools:serial",
    "container_volume_path": "/tmp"
  }
}<jupyter_output><empty_output><jupyter_text>Singularity file config<jupyter_code>{
  "properties": {
    "in_parameters": {
      "start": 1,
      "end": -1,
      "step": 1,
      "mask": "c-alpha",
      "reference": "first"
    },
    "container_path": "singularity",
    "container_image": "shub://bioexcel/ambertools_singularity",
    "container_volume_path": "/tmp"
  }
}<jupyter_output><empty_output><jupyter_text>Command line<jupyter_code>cpptraj_rmsf --config data/conf/rmsf.json --input_top_path data/input/cpptraj.parm.top --input_traj_path data/input/cpptraj.traj.dcd --output_cpptraj_path data/output/output.rmsf.dat<jupyter_output><empty_output><jupyter_text>Cpptraj slice Extracts a particular trajectory slice from a given cpptraj compatible trajectory.  Get help Command:<jupyter_code>cpptraj_slice -h
usage: cpptraj_slice [-h] [--config CONFIG] --input_top_path INPUT_TOP_PATH --input_traj_path INPUT_TRAJ_PATH --output_cpptraj_path OUTPUT_CPPTRAJ_PATH

Extracts a particular trajectory slice from a given cpptraj compatible trajectory.

optional arguments:
  -h, --help            show this help message and exit
  --config CONFIG       Configuration file

required arguments:
  --input_top_path INPUT_TOP_PATH
                        Path to the input structure or topology file. Accepted formats: top, pdb, prmtop, parmtop, zip.
  --input_traj_path INPUT_TRAJ_PATH
                        Path to the input trajectory to be processed. Accepted formats: crd, cdf, netcdf, restart, ncrestart, restartnc, dcd, charmm, cor, pdb, mol2, trr, gro, binpos, xtc, cif, arc, sqm, sdf, conflib.
  --output_cpptraj_path OUTPUT_CPPTRAJ_PATH
                        Path to the output processed trajectory.<jupyter_output><empty_output><jupyter_text>I / O Arguments Syntax: input_argument (datatype) : DefinitionConfig input / output arguments for this building block:* **input_top_path** (*str*): Path to the input structure or topology file. File type: input. [Sample file](https://github.com/bioexcel/biobb_analysis/raw/master/biobb_analysis/test/data/ambertools/cpptraj.parm.top). Accepted formats: top, pdb, prmtop, parmtop, zip.* **input_traj_path** (*str*): Path to the input trajectory to be processed.  File type: input. [Sample file](https://github.com/bioexcel/biobb_analysis/raw/master/biobb_analysis/test/data/ambertools/cpptraj.traj.dcd). Accepted formats: crd, cdf, netcdf, restart, ncrestart, restartnc, dcd, charmm, cor, pdb, mol2, trr, gro, binpos, xtc, cif, arc, sqm, sdf, conflib.* **output_cpptraj_path** (*str*): Path to the output processed trajectory. File type: output. [Sample file](https://github.com/bioexcel/biobb_analysis/raw/master/biobb_analysis/test/reference/ambertools/ref_cpptraj.slice.netcdf). Accepted formats: crd, netcdf, rst7, ncrst, dcd, pdb, mol2, binpos, trr, xtc, sqm.  Config Syntax: input_parameter (datatype) - (default_value) DefinitionConfig parameters for this building block:* **in_parameters** (*dict*) - (None) Parameters for input trajectory. Accepted parameters:    * **start** (*int*) - (1) Starting frame for slicing    * **end** (*int*) - (-1) Ending frame for slicing    * **step** (*int*) - (1) Step for slicing    * **mask** (*string*) - ("all-atoms") Mask definition. Values: c-alpha, backbone, all-atoms, heavy-atoms, side-chain, solute, ions, solvent.* **out_parameters** (*dict*) - (None) Parameters for output trajectory.    * **format** (*str*) - ("netcdf") Output trajectory format. Values: crd, cdf, netcdf, restart, ncrestart, restartnc, dcd, charmm, cor, pdb, mol2, trr, gro, binpos, xtc, cif, arc, sqm, sdf, conflib.* **cpptraj_path** (*str*) - ("cpptraj") Path to the cpptraj executable binary.* **remove_tmp** (*bool*) - (True) [WF property] Remove temporal files.* **restart** (*bool*) - (False) [WF property] Do not execute if output files exist.* **container_path** (*string*) - (None) Container path definition.* **container_image** (*string*) - ('afandiadib/ambertools:serial') Container image definition.* **container_volume_path** (*string*) - ('/tmp') Container volume path definition.* **container_working_dir** (*string*) - (None) Container working directory definition.* **container_user_id** (*string*) - (None) Container user_id definition.* **container_shell_path** (*string*) - ('/bin/bash') Path to default shell inside the container.  YAML  Common file config<jupyter_code>properties:
  in_parameters:
    start: 2
    end: 20
    step: 2
    mask: c-alpha
  out_parameters:
    format: netcdf<jupyter_output><empty_output><jupyter_text>Docker file config<jupyter_code>properties:
  in_parameters:
    start: 2
    end: 20
    step: 2
    mask: c-alpha
  out_parameters:
    format: netcdf
  container_path: docker
  container_image: afandiadib/ambertools:serial
  container_volume_path: /tmp<jupyter_output><empty_output><jupyter_text>Singularity file config<jupyter_code>properties:
  in_parameters:
    start: 2
    end: 20
    step: 2
    mask: c-alpha
  out_parameters:
    format: netcdf
  container_path: singularity
  container_image: shub://bioexcel/ambertools_singularity
  container_volume_path: /tmp<jupyter_output><empty_output><jupyter_text>Command line<jupyter_code>cpptraj_slice --config data/conf/slice.yml --input_top_path data/input/cpptraj.parm.top --input_traj_path data/input/cpptraj.traj.dcd --output_cpptraj_path data/output/output.slice.netcdf<jupyter_output><empty_output><jupyter_text>JSON  Common file config<jupyter_code>{
  "properties": {
    "in_parameters": {
      "start": 1,
      "end": -1,
      "step": 1,
      "mask": "c-alpha"
    },
    "out_parameters": {
      "format": "netcdf"
    }
  }
}<jupyter_output><empty_output><jupyter_text>Docker file config<jupyter_code>{
  "properties": {
    "in_parameters": {
      "start": 1,
      "end": -1,
      "step": 1,
      "mask": "c-alpha"
    },
    "out_parameters": {
      "format": "netcdf"
    },
    "container_path": "docker",
    "container_image": "afandiadib/ambertools:serial",
    "container_volume_path": "/tmp"
  }
}<jupyter_output><empty_output><jupyter_text>Singularity file config<jupyter_code>{
  "properties": {
    "in_parameters": {
      "start": 1,
      "end": -1,
      "step": 1,
      "mask": "c-alpha"
    },
    "out_parameters": {
      "format": "netcdf"
    },
    "container_path": "singularity",
    "container_image": "shub://bioexcel/ambertools_singularity",
    "container_volume_path": "/tmp"
  }
}<jupyter_output><empty_output><jupyter_text>Command line<jupyter_code>cpptraj_slice --config data/conf/slice.json --input_top_path data/input/cpptraj.parm.top --input_traj_path data/input/cpptraj.traj.dcd --output_cpptraj_path data/output/output.slice.netcdf<jupyter_output><empty_output><jupyter_text>Cpptraj snapshot Extracts a particular snapshot from a given cpptraj compatible trajectory.  Get help Command:<jupyter_code>cpptraj_snapshot -h
usage: cpptraj_snapshot [-h] --config CONFIG --input_top_path INPUT_TOP_PATH --input_traj_path INPUT_TRAJ_PATH --output_cpptraj_path OUTPUT_CPPTRAJ_PATH

Extracts a particular snapshot from a given cpptraj compatible trajectory.

optional arguments:
  -h, --help            show this help message and exit
  --config CONFIG       Configuration file

required arguments:
  --input_top_path INPUT_TOP_PATH
                        Path to the input structure or topology file. Accepted formats: top, pdb, prmtop, parmtop, zip.
  --input_traj_path INPUT_TRAJ_PATH
                        Path to the input trajectory to be processed. Accepted formats: crd, cdf, netcdf, restart, ncrestart, restartnc, dcd, charmm, cor, pdb, mol2, trr, gro, binpos, xtc, cif, arc, sqm, sdf, conflib.
  --output_cpptraj_path OUTPUT_CPPTRAJ_PATH
                        Path to the output processed structure.<jupyter_output><empty_output><jupyter_text>I / O Arguments Syntax: input_argument (datatype) : DefinitionConfig input / output arguments for this building block:* **input_top_path** (*str*): Path to the input structure or topology file. File type: input. [Sample file](https://github.com/bioexcel/biobb_analysis/raw/master/biobb_analysis/test/data/ambertools/cpptraj.parm.top). Accepted formats: top, pdb, prmtop, parmtop, zip.* **input_traj_path** (*str*): Path to the input trajectory to be processed.  File type: input. [Sample file](https://github.com/bioexcel/biobb_analysis/raw/master/biobb_analysis/test/data/ambertools/cpptraj.traj.dcd). Accepted formats: crd, cdf, netcdf, restart, ncrestart, restartnc, dcd, charmm, cor, pdb, mol2, trr, gro, binpos, xtc, cif, arc, sqm, sdf, conflib.* **output_cpptraj_path** (*str*): Path to the output processed structure. File type: output. [Sample file](https://github.com/bioexcel/biobb_analysis/raw/master/biobb_analysis/test/reference/ambertools/ref_cpptraj.snapshot.pdb). Accepted formats: crd, netcdf, rst7, ncrst, dcd, pdb, mol2, binpos, trr, xtc, sqm.  Config Syntax: input_parameter (datatype) - (default_value) DefinitionConfig parameters for this building block:* **in_parameters** (*dict*) - (None) Parameters for input trajectory. Accepted parameters:    * **snapshot** (*int*) - (1) Frame to be captured for snapshot    * **mask** (*string*) - ("all-atoms") Mask definition. Values: c-alpha, backbone, all-atoms, heavy-atoms, side-chain, solute, ions, solvent.* **out_parameters** (*dict*) - (None) Parameters for output trajectory.    * **format** (*str*) - ("netcdf") Output trajectory format. Values: crd, cdf, netcdf, restart, ncrestart, restartnc, dcd, charmm, cor, pdb, mol2, trr, gro, binpos, xtc, cif, arc, sqm, sdf, conflib.* **cpptraj_path** (*str*) - ("cpptraj") Path to the cpptraj executable binary.* **remove_tmp** (*bool*) - (True) [WF property] Remove temporal files.* **restart** (*bool*) - (False) [WF property] Do not execute if output files exist.* **container_path** (*string*) - (None) Container path definition.* **container_image** (*string*) - ('afandiadib/ambertools:serial') Container image definition.* **container_volume_path** (*string*) - ('/tmp') Container volume path definition.* **container_working_dir** (*string*) - (None) Container working directory definition.* **container_user_id** (*string*) - (None) Container user_id definition.* **container_shell_path** (*string*) - ('/bin/bash') Path to default shell inside the container.  YAML  Common file config<jupyter_code>properties:
  in_parameters:
    snapshot: 12
    mask: c-alpha
  out_parameters:
    format: pdb<jupyter_output><empty_output><jupyter_text>Docker file config<jupyter_code>properties:
  in_parameters:
    snapshot: 12
    mask: c-alpha
  out_parameters:
    format: pdb
  container_path: docker
  container_image: afandiadib/ambertools:serial
  container_volume_path: /tmp<jupyter_output><empty_output><jupyter_text>Singularity file config<jupyter_code>properties:
  in_parameters:
    snapshot: 12
    mask: c-alpha
  out_parameters:
    format: pdb
  container_path: singularity
  container_image: shub://bioexcel/ambertools_singularity
  container_volume_path: /tmp<jupyter_output><empty_output><jupyter_text>Command line<jupyter_code>cpptraj_snapshot --config data/conf/snapshot.yml --input_top_path data/input/cpptraj.parm.top --input_traj_path data/input/cpptraj.traj.dcd --output_cpptraj_path data/output/output.snapshot.pdb<jupyter_output><empty_output><jupyter_text>JSON  Common file config<jupyter_code>{
  "properties": {
    "in_parameters": {
      "snapshot": 12,
      "mask": "c-alpha"
    },
    "out_parameters": {
      "format": "pdb"
    }
  }
}<jupyter_output><empty_output><jupyter_text>Docker file config<jupyter_code>{
  "properties": {
    "in_parameters": {
      "snapshot": 12,
      "mask": "c-alpha"
    },
    "out_parameters": {
      "format": "pdb"
    },
    "container_path": "docker",
    "container_image": "afandiadib/ambertools:serial",
    "container_volume_path": "/tmp"
  }
}<jupyter_output><empty_output><jupyter_text>Singularity file config<jupyter_code>{
  "properties": {
    "in_parameters": {
      "snapshot": 12,
      "mask": "c-alpha"
    },
    "out_parameters": {
      "format": "pdb"
    },
    "container_path": "singularity",
    "container_image": "shub://bioexcel/ambertools_singularity",
    "container_volume_path": "/tmp"
  }
}<jupyter_output><empty_output><jupyter_text>Command line<jupyter_code>cpptraj_snapshot --config data/conf/slice.json --input_top_path data/input/cpptraj.parm.top --input_traj_path data/input/cpptraj.traj.dcd --output_cpptraj_path data/output/output.slice.netcdf<jupyter_output><empty_output><jupyter_text>Cpptraj strip Strips a defined set of atoms (mask) from a given cpptraj compatible trajectory.  Get help Command:<jupyter_code>cpptraj_strip -h
usage: cpptraj_strip [-h] [--config CONFIG] --input_top_path INPUT_TOP_PATH --input_traj_path INPUT_TRAJ_PATH --output_cpptraj_path OUTPUT_CPPTRAJ_PATH

Strips a defined set of atoms (mask) from a given cpptraj compatible trajectory.

optional arguments:
  -h, --help            show this help message and exit
  --config CONFIG       Configuration file

required arguments:
  --input_top_path INPUT_TOP_PATH
                        Path to the input structure or topology file. Accepted formats: top, pdb, prmtop, parmtop, zip.
  --input_traj_path INPUT_TRAJ_PATH
                        Path to the input trajectory to be processed. Accepted formats: crd, cdf, netcdf, restart, ncrestart, restartnc, dcd, charmm, cor, pdb, mol2, trr, gro, binpos, xtc, cif, arc, sqm, sdf, conflib.
  --output_cpptraj_path OUTPUT_CPPTRAJ_PATH
                        Path to the output processed trajectory.<jupyter_output><empty_output><jupyter_text>I / O Arguments Syntax: input_argument (datatype) : DefinitionConfig input / output arguments for this building block:* **input_top_path** (*str*): Path to the input structure or topology file. File type: input. [Sample file](https://github.com/bioexcel/biobb_analysis/raw/master/biobb_analysis/test/data/ambertools/cpptraj.parm.top). Accepted formats: top, pdb, prmtop, parmtop, zip.* **input_traj_path** (*str*): Path to the input trajectory to be processed.  File type: input. [Sample file](https://github.com/bioexcel/biobb_analysis/raw/master/biobb_analysis/test/data/ambertools/cpptraj.traj.dcd). Accepted formats: crd, cdf, netcdf, restart, ncrestart, restartnc, dcd, charmm, cor, pdb, mol2, trr, gro, binpos, xtc, cif, arc, sqm, sdf, conflib.* **output_cpptraj_path** (*str*): Path to the output processed trajectory. File type: output. [Sample file](https://github.com/bioexcel/biobb_analysis/raw/master/biobb_analysis/test/reference/ambertools/ref_cpptraj.strip.netcdf). Accepted formats: crd, netcdf, rst7, ncrst, dcd, pdb, mol2, binpos, trr, xtc, sqm.  Config Syntax: input_parameter (datatype) - (default_value) DefinitionConfig parameters for this building block:* **in_parameters** (*dict*) - (None) Parameters for input trajectory. Accepted parameters:    * **start** (*int*) - (1) Starting frame for slicing    * **end** (*int*) - (-1) Ending frame for slicing    * **step** (*int*) - (1) Step for slicing    * **mask** (*string*) - ("all-atoms") Mask definition. Values: c-alpha, backbone, all-atoms, heavy-atoms, side-chain, solute, ions, solvent.* **out_parameters** (*dict*) - (None) Parameters for output trajectory.    * **format** (*str*) - ("netcdf") Output trajectory format. Values: crd, cdf, netcdf, restart, ncrestart, restartnc, dcd, charmm, cor, pdb, mol2, trr, gro, binpos, xtc, cif, arc, sqm, sdf, conflib.* **cpptraj_path** (*str*) - ("cpptraj") Path to the cpptraj executable binary.* **remove_tmp** (*bool*) - (True) [WF property] Remove temporal files.* **restart** (*bool*) - (False) [WF property] Do not execute if output files exist.* **container_path** (*string*) - (None) Container path definition.* **container_image** (*string*) - ('afandiadib/ambertools:serial') Container image definition.* **container_volume_path** (*string*) - ('/tmp') Container volume path definition.* **container_working_dir** (*string*) - (None) Container working directory definition.* **container_user_id** (*string*) - (None) Container user_id definition.* **container_shell_path** (*string*) - ('/bin/bash') Path to default shell inside the container.  YAML  Common file config<jupyter_code>properties:
  in_parameters:
    start: 2
    end: 20
    step: 2
    mask: c-alpha
  out_parameters:
    format: netcdf<jupyter_output><empty_output><jupyter_text>Docker file config<jupyter_code>properties:
  in_parameters:
    start: 2
    end: 20
    step: 2
    mask: c-alpha
  out_parameters:
    format: netcdf
  container_path: docker
  container_image: afandiadib/ambertools:serial
  container_volume_path: /tmp<jupyter_output><empty_output><jupyter_text>Singularity file config<jupyter_code>properties:
  in_parameters:
    start: 2
    end: 20
    step: 2
    mask: c-alpha
  out_parameters:
    format: netcdf
  container_path: singularity
  container_image: shub://bioexcel/ambertools_singularity
  container_volume_path: /tmp<jupyter_output><empty_output><jupyter_text>Command line<jupyter_code>cpptraj_strip --config data/conf/strip.yml --input_top_path data/input/cpptraj.parm.top --input_traj_path data/input/cpptraj.traj.dcd --output_cpptraj_path data/output/output.strip.netcdf<jupyter_output><empty_output><jupyter_text>JSON  Common file config<jupyter_code>{
  "properties": {
    "in_parameters": {
      "start": 1,
      "end": -1,
      "step": 1,
      "mask": "c-alpha"
    },
    "out_parameters": {
      "format": "netcdf"
    }
  }
}<jupyter_output><empty_output><jupyter_text>Docker file config<jupyter_code>{
  "properties": {
    "in_parameters": {
      "start": 1,
      "end": -1,
      "step": 1,
      "mask": "c-alpha"
    },
    "out_parameters": {
      "format": "netcdf"
    },
    "container_path": "docker",
    "container_image": "afandiadib/ambertools:serial",
    "container_volume_path": "/tmp"
  }
}<jupyter_output><empty_output><jupyter_text>Singularity file config<jupyter_code>{
  "properties": {
    "in_parameters": {
      "start": 1,
      "end": -1,
      "step": 1,
      "mask": "c-alpha"
    },
    "out_parameters": {
      "format": "netcdf"
    },
    "container_path": "singularity",
    "container_image": "shub://bioexcel/ambertools_singularity",
    "container_volume_path": "/tmp"
  }
}<jupyter_output><empty_output><jupyter_text>Command line<jupyter_code>cpptraj_strip --config data/conf/strip.json --input_top_path data/input/cpptraj.parm.top --input_traj_path data/input/cpptraj.traj.dcd --output_cpptraj_path data/output/output.strip.netcdf<jupyter_output><empty_output><jupyter_text>GROMACS cluster Creates cluster structures from a given GROMACS compatible trajectory.  Get help Command:<jupyter_code>gmx_cluster -h
usage: gmx_cluster [-h] [--config CONFIG] --input_structure_path INPUT_STRUCTURE_PATH --input_traj_path INPUT_TRAJ_PATH [--input_index_path INPUT_INDEX_PATH] --output_pdb_path OUTPUT_PDB_PATH

Creates cluster structures from a given GROMACS compatible trajectory.

optional arguments:
  -h, --help            show this help message and exit
  --config CONFIG       Configuration file
  --input_index_path INPUT_INDEX_PATH
                        Path to the GROMACS index file. Accepted formats: ndx.

required arguments:
  --input_structure_path INPUT_STRUCTURE_PATH
                        Path to the input structure file. Accepted formats: tpr, gro, g96, pdb, brk, ent.
  --input_traj_path INPUT_TRAJ_PATH
                        Path to the GROMACS trajectory file. Accepted formats: xtc, trr, cpt, gro, g96, pdb, tng.
  --output_pdb_path OUTPUT_PDB_PATH
                        Path to the output cluster file. Accepted formats: xtc, trr, cpt, gro, g96, pdb, tng.<jupyter_output><empty_output><jupyter_text>I / O Arguments Syntax: input_argument (datatype) : DefinitionConfig input / output arguments for this building block:* **input_structure_path** (*str*): Path to the input structure file. File type: input. [Sample file](https://github.com/bioexcel/biobb_analysis/raw/master/biobb_analysis/test/data/gromacs/topology.tpr). Accepted formats: tpr, gro, g96, pdb, brk, ent.* **input_traj_path** (*str*): Path to the GROMACS trajectory file. File type: input. [Sample file](https://github.com/bioexcel/biobb_analysis/raw/master/biobb_analysis/test/data/gromacs/trajectory.trr). Accepted formats: xtc, trr, cpt, gro, g96, pdb, tng.* **input_index_path** (*str*) (Optional): Path to the GROMACS index file. File type: input. [Sample file](https://github.com/bioexcel/biobb_analysis/raw/master/biobb_analysis/test/data/gromacs/index.ndx). Accepted formats: ndx.* **output_pdb_path** (*str*): Path to the output cluster file. File type: output. [Sample file](https://github.com/bioexcel/biobb_analysis/raw/master/biobb_analysis/test/reference/gromacs/ref_cluster.pdb). Accepted formats: xtc, trr, cpt, gro, g96, pdb, tng.  Config Syntax: input_parameter (datatype) - (default_value) DefinitionConfig parameters for this building block:* **fit_selection** (*str*) - ("System") - Group where the fitting will be performed. If **input_index_path** provided, check the file for the accepted values, if not, values: System, Protein, Protein-H, C-alpha, Backbone, MainChain, MainChain+Cb, MainChain+H, SideChain, SideChain-H, Prot-Masses, non-Protein, Water, SOL, non-Water, Ion, NA, CL, Water_and_ions.* **output_selection** (*str*) - ("System") Group that is going to be written in the output trajectory. If **input_index_path** provided, check the file for the accepted values, if not, values: System, Protein, Protein-H, C-alpha, Backbone, MainChain, MainChain+Cb, MainChain+H, SideChain, SideChain-H, Prot-Masses, non-Protein, Water, SOL, non-Water, Ion, NA, CL, Water_and_ions.* **dista** (*bool*) - (False) Use RMSD of distances instead of RMS deviation.* **method** (*str*) - ("linkage") Method for cluster determination. Values: linkage, jarvis-patrick, monte-carlo, diagonalization, gromos* **cutoff** (*float*) - (0.1) RMSD cut-off (nm) for two structures to be neighbor* **gmx_path** (*str*) - ("gmx") Path to the GROMACS executable binary.* **remove_tmp** (*bool*) - (True) [WF property] Remove temporal files.* **restart** (*bool*) - (False) [WF property] Do not execute if output files exist.* **container_path** (*string*) - (None) Container path definition.* **container_image** (*string*) - ('gromacs/gromacs:latest') Container image definition.* **container_volume_path** (*string*) - ('/tmp') Container volume path definition.* **container_working_dir** (*string*) - (None) Container working directory definition.* **container_user_id** (*string*) - (None) Container user_id definition.* **container_shell_path** (*string*) - ('/bin/bash') Path to default shell inside the container.  YAML  Common file config<jupyter_code>properties:
  fit_selection: System
  output_selection: System
  dista: False
  method: linkage
  cutoff: 0.1<jupyter_output><empty_output><jupyter_text>Docker file config<jupyter_code>properties:
  fit_selection: System
  output_selection: System
  dista: False
  method: linkage
  cutoff: 0.1
  container_path: docker
  container_image: gromacs/gromacs:latest
  container_volume_path: /tmp<jupyter_output><empty_output><jupyter_text>Singularity file config<jupyter_code>properties:
  fit_selection: System
  output_selection: System
  dista: False
  method: linkage
  cutoff: 0.1
  container_path: singularity
  container_image: shub://michael-tn/gromacs
  container_volume_path: /tmp<jupyter_output><empty_output><jupyter_text>Command line<jupyter_code>gmx_cluster --config data/conf/cluster.yml --input_structure_path data/input/cluster.gro --input_traj_path data/input/cluster.trr --output_pdb_path data/output/output.cluster.pdb<jupyter_output><empty_output><jupyter_text>JSON  Common file config<jupyter_code>{
  "properties": {
    "fit_selection": "System",
    "output_selection": "System",
    "dista": false,
    "method": "linkage",
    "cutoff": 0.1
  }
}<jupyter_output><empty_output><jupyter_text>Docker file config<jupyter_code>{
  "properties": {
    "fit_selection": "System",
    "output_selection": "System",
    "dista": false,
    "method": "linkage",
    "cutoff": 0.1,
    "container_path": "docker",
    "container_image": "gromacs/gromacs:latest",
    "container_volume_path": "/tmp"
  }
}<jupyter_output><empty_output><jupyter_text>Singularity file config<jupyter_code>{
  "properties": {
    "fit_selection": "System",
    "output_selection": "System",
    "dista": false,
    "method": "linkage",
    "cutoff": 0.1,
    "container_path": "singularity",
    "container_image": "shub://michael-tn/gromacs",
    "container_volume_path": "/tmp"
  }
}<jupyter_output><empty_output><jupyter_text>Command line<jupyter_code>gmx_cluster --config data/conf/cluster.json --input_structure_path data/input/cluster.gro --input_traj_path data/input/cluster.trr --output_pdb_path data/output/output.cluster.pdb<jupyter_output><empty_output><jupyter_text>GROMACS energy Extracts energy components from a given GROMACS energy file.  Get help Command:<jupyter_code>gmx_energy -h
usage: gmx_energy [-h] [--config CONFIG] --input_energy_path INPUT_ENERGY_PATH --output_xvg_path OUTPUT_XVG_PATH

Extracts energy components from a given GROMACS energy file.

optional arguments:
  -h, --help            show this help message and exit
  --config CONFIG       Configuration file

required arguments:
  --input_energy_path INPUT_ENERGY_PATH
                        Path to the input EDR file. Accepted formats: edr.
  --output_xvg_path OUTPUT_XVG_PATH
                        Path to the XVG output file. Accepted formats: xvg.<jupyter_output><empty_output><jupyter_text>I / O Arguments Syntax: input_argument (datatype) : DefinitionConfig input / output arguments for this building block:* **input_energy_path** (*str*): Path to the input EDR file. File type: input. [Sample file](https://github.com/bioexcel/biobb_analysis/raw/master/biobb_analysis/test/data/gromacs/energy.edr). Accepted formats: edr.* **output_xvg_path** (*str*): Path to the XVG output file. File type: output. [Sample file](https://github.com/bioexcel/biobb_analysis/raw/master/biobb_analysis/test/reference/gromacs/ref_energy.xvg). Accepted formats: xvg.  Config Syntax: input_parameter (datatype) - (default_value) DefinitionConfig parameters for this building block:* **xvg** (*str*) - ("none") XVG plot formatting. Values: xmgrace, xmgr, none.* **terms** (*list*) - (["Potential"]) Energy terms. Select one or more from values: Angle, Proper-Dih., Improper-Dih., LJ-14, Coulomb-14, LJ-(SR), Coulomb-(SR), Coul.-recip., Position-Rest., Potential, Kinetic-En., Total-Energy, Temperature, Pressure,  Constr.-rmsd, Box-X, Box-Y,  Box-Z, Volume, Density, pV, Enthalpy, Vir-XX, Vir-XY, Vir-XZ, Vir-YX, Vir-YY, Vir-YZ, Vir-ZX, Vir-ZY, Vir-ZZ, Pres-XX, Pres-XY, Pres-XZ, Pres-YX, Pres-YY,  Pres-YZ, Pres-ZX, Pres-ZY, Pres-ZZ, Surf*SurfTen, Box-Vel-XX, Box-Vel-YY, Box-Vel-ZZ, Mu-X, Mu-Y, Mu-Z, T-Protein, T-non-Protein, Lamb-Protein, Lamb-non-Protein* **gmx_path** (*str*) - ("gmx") Path to the GROMACS executable binary.* **remove_tmp** (*bool*) - (True) [WF property] Remove temporal files.* **restart** (*bool*) - (False) [WF property] Do not execute if output files exist.* **container_path** (*string*) - (None) Container path definition.* **container_image** (*string*) - ('gromacs/gromacs:latest') Container image definition.* **container_volume_path** (*string*) - ('/tmp') Container volume path definition.* **container_working_dir** (*string*) - (None) Container working directory definition.* **container_user_id** (*string*) - (None) Container user_id definition.* **container_shell_path** (*string*) - ('/bin/bash') Path to default shell inside the container.  YAML  Common file config<jupyter_code>properties:
  terms: [Potential, Pressure]<jupyter_output><empty_output><jupyter_text>Docker file config<jupyter_code>properties:
  terms: [Potential, Pressure]
  container_path: docker
  container_image: gromacs/gromacs:latest
  container_volume_path: /tmp<jupyter_output><empty_output><jupyter_text>Singularity file config<jupyter_code>properties:
  terms: [Potential, Pressure]
  container_path: singularity
  container_image: shub://michael-tn/gromacs
  container_volume_path: /tmp<jupyter_output><empty_output><jupyter_text>Command line<jupyter_code>gmx_energy --config data/conf/energy.yml --input_energy_path data/input/energy.edr --output_xvg_path data/output/output.energy.xvg<jupyter_output><empty_output><jupyter_text>JSON  Common file config<jupyter_code>{
  "properties": {
    "terms": ["Potential", "Pressure"]
  }
}<jupyter_output><empty_output><jupyter_text>Docker file config<jupyter_code>{
  "properties": {
    "terms": ["Potential", "Pressure"],
    "container_path": "docker",
    "container_image": "gromacs/gromacs:latest",
    "container_volume_path": "/tmp"
  }
}<jupyter_output><empty_output><jupyter_text>Singularity file config<jupyter_code>{
  "properties": {
    "terms": ["Potential", "Pressure"],
    "container_path": "singularity",
    "container_image": "shub://michael-tn/gromacs",
    "container_volume_path": "/tmp"
  }
}<jupyter_output><empty_output><jupyter_text>Command line<jupyter_code>gmx_energy --config data/conf/energy.json --input_energy_path data/input/energy.edr --output_xvg_path data/output/output.energy.xvg<jupyter_output><empty_output><jupyter_text>GROMACS image Corrects periodicity (image) from a given GROMACS compatible trajectory file.  Get help Command:<jupyter_code>gmx_image -h
usage: gmx_image [-h] [--config CONFIG] --input_traj_path INPUT_TRAJ_PATH --input_top_path INPUT_TOP_PATH [--input_index_path INPUT_INDEX_PATH] --output_traj_path OUTPUT_TRAJ_PATH

Corrects periodicity (image) from a given GROMACS compatible trajectory file.

optional arguments:
  -h, --help            show this help message and exit
  --config CONFIG       Configuration file
  --input_index_path INPUT_INDEX_PATH
                        Path to the GROMACS index file. Accepted formats: ndx.

required arguments:
  --input_traj_path INPUT_TRAJ_PATH
                        Path to the GROMACS trajectory file. Accepted formats: xtc, trr, cpt, gro, g96, pdb, tng.
  --input_top_path INPUT_TOP_PATH
                        Path to the GROMACS input topology file. Accepted formats: tpr, gro, g96, pdb, brk, ent.
  --output_traj_path OUTPUT_TRAJ_PATH
                        Path to the output file. Accepted formats: xtc, trr, gro, g96, pdb, tng.<jupyter_output><empty_output><jupyter_text>I / O Arguments Syntax: input_argument (datatype) : DefinitionConfig input / output arguments for this building block:* **input_traj_path** (*str*): Path to the GROMACS trajectory file. File type: input. [Sample file](https://github.com/bioexcel/biobb_analysis/raw/master/biobb_analysis/test/data/gromacs/trajectory.trr). Accepted formats: xtc, trr, cpt, gro, g96, pdb, tng.* **input_top_path** (*str*): Path to the GROMACS input topology file. File type: input. [Sample file](https://github.com/bioexcel/biobb_analysis/raw/master/biobb_analysis/test/data/gromacs/topology.tpr). Accepted formats: tpr, gro, g96, pdb, brk, ent.* **input_index_path** (*str*) (Optional): Path to the GROMACS index file. File type: input. [Sample file](https://github.com/bioexcel/biobb_analysis/raw/master/biobb_analysis/test/data/gromacs/index.ndx). Accepted formats: ndx.* **output_traj_path** (*str*): Path to the output file. File type: output. [Sample file](https://github.com/bioexcel/biobb_analysis/raw/master/biobb_analysis/test/reference/gromacs/ref_image.xtc)_. Accepted formats: xtc, trr, gro, g96, pdb, tng.  Config Syntax: input_parameter (datatype) - (default_value) DefinitionConfig parameters for this building block:* **fit_selection** (*str*) - ("System") - Group where the fitting will be performed. If **input_index_path** provided, check the file for the accepted values, if not, values: System, Protein, Protein-H, C-alpha, Backbone, MainChain, MainChain+Cb, MainChain+H, SideChain, SideChain-H, Prot-Masses, non-Protein, Water, SOL, non-Water, Ion, NA, CL, Water_and_ions.* **center_selection** (*str*) - ("System") Group where the trjconv will be performed. If **input_index_path** provided, check the file for the accepted values, if not, values: System, Protein, Protein-H, C-alpha, Backbone, MainChain, MainChain+Cb, MainChain+H, SideChain, SideChain-H, Prot-Masses, non-Protein, Water, SOL, non-Water, Ion, NA, CL, Water_and_ions.* **output_selection** (*str*) - ("System") Group that is going to be written in the output trajectory. If **input_index_path** provided, check the file for the accepted values, if not, values: System, Protein, Protein-H, C-alpha, Backbone, MainChain, MainChain+Cb, MainChain+H, SideChain, SideChain-H, Prot-Masses, non-Protein, Water, SOL, non-Water, Ion, NA, CL, Water_and_ions.* **pbc** (*str*) - ("mol") PBC treatment (see help text for full description). Values: none, mol, res, atom, nojump, cluster, whole.* **center** (*bool*) - (True) Center atoms in box.* **ur** (*str*) - ("compact") Unit-cell representation. Values: rect, tric, compact.* **fit** (*str*) - ("none") Fit molecule to ref structure in the structure file. Values: none, rot+trans, rotxy+transxy, translation, transxy, progressive.* **gmx_path** (*str*) - ("gmx") Path to the GROMACS executable binary.* **remove_tmp** (*bool*) - (True) [WF property] Remove temporal files.* **restart** (*bool*) - (False) [WF property] Do not execute if output files exist.* **container_path** (*string*) - (None) Container path definition.* **container_image** (*string*) - ('gromacs/gromacs:latest') Container image definition.* **container_volume_path** (*string*) - ('/tmp') Container volume path definition.* **container_working_dir** (*string*) - (None) Container working directory definition.* **container_user_id** (*string*) - (None) Container user_id definition.* **container_shell_path** (*string*) - ('/bin/bash') Path to default shell inside the container.  YAML  Common file config<jupyter_code>properties:
  fit_selection: System
  center_selection: System
  output_selection: System
  pbc: mol
  center: True
  fit: rot+trans
  ur: compact<jupyter_output><empty_output><jupyter_text>Docker file config<jupyter_code>properties:
  fit_selection: System
  center_selection: System
  output_selection: System
  pbc: mol
  center: True
  fit: rot+trans
  ur: compact
  container_path: docker
  container_image: gromacs/gromacs:latest
  container_volume_path: /tmp<jupyter_output><empty_output><jupyter_text>Singularity file config<jupyter_code>properties:
  fit_selection: System
  center_selection: System
  output_selection: System
  pbc: mol
  center: True
  fit: rot+trans
  ur: compact
  container_path: singularity
  container_image: shub://michael-tn/gromacs
  container_volume_path: /tmp<jupyter_output><empty_output><jupyter_text>Command line<jupyter_code>gmx_image --config data/conf/gmx_image.yml --input_traj_path data/input/image.trr --input_top_path data/input/image.gro --output_traj_path data/output/output.image.xtc<jupyter_output><empty_output><jupyter_text>JSON  Common file config<jupyter_code>{
  "properties": {
    "fit_selection": "System",
    "center_selection": "System",
    "output_selection": "System",
    "pbc": "mol",
    "center": true,
    "fit": "rot+trans",
    "ur": "compact"
  }
}<jupyter_output><empty_output><jupyter_text>Docker file config<jupyter_code>{
  "properties": {
    "fit_selection": "System",
    "center_selection": "System",
    "output_selection": "System",
    "pbc": "mol",
    "center": true,
    "fit": "rot+trans",
    "ur": "compact",
    "container_path": "docker",
    "container_image": "gromacs/gromacs:latest",
    "container_volume_path": "/tmp"
  }
}<jupyter_output><empty_output><jupyter_text>Singularity file config<jupyter_code>{
  "properties": {
    "fit_selection": "System",
    "center_selection": "System",
    "output_selection": "System",
    "pbc": "mol",
    "center": true,
    "fit": "rot+trans",
    "ur": "compact",
    "container_path": "singularity",
    "container_image": "shub://michael-tn/gromacs",
    "container_volume_path": "/tmp"
  }
}<jupyter_output><empty_output><jupyter_text>Command line<jupyter_code>gmx_image --config data/conf/gmx_image.json --input_traj_path data/input/image.trr --input_top_path data/input/image.gro --output_traj_path data/output/output.image.xtc<jupyter_output><empty_output><jupyter_text>GROMACS rgyr Computes the radius of gyration (Rgyr) of a molecule about the x-, y- and z-axes, as a function of time, from a given GROMACS compatible trajectory.  Get help Command:<jupyter_code>gmx_rgyr -h
usage: gmx_rgyr [-h] [--config CONFIG] --input_structure_path INPUT_STRUCTURE_PATH --input_traj_path INPUT_TRAJ_PATH [--input_index_path INPUT_INDEX_PATH] --output_xvg_path OUTPUT_XVG_PATH

Computes the radius of gyration (Rgyr) of a molecule about the x-, y- and z-axes, as a function of time, from a given GROMACS compatible trajectory.

optional arguments:
  -h, --help            show this help message and exit
  --config CONFIG       Configuration file
  --input_index_path INPUT_INDEX_PATH
                        Path to the GROMACS index file. Accepted formats: ndx.

required arguments:
  --input_structure_path INPUT_STRUCTURE_PATH
                        Path to the input structure file. Accepted formats: tpr, gro, g96, pdb, brk, ent.
  --input_traj_path INPUT_TRAJ_PATH
                        Path to the GROMACS trajectory file. Accepted formats: xtc, trr, cpt, gro, g96, pdb, tng.
  --output_xvg_path OUTPUT_XVG_PATH
                        Path to the XVG output file. Accepted formats: xvg.<jupyter_output><empty_output><jupyter_text>I / O Arguments Syntax: input_argument (datatype) : DefinitionConfig input / output arguments for this building block:* **input_structure_path** (*str*): Path to the input structure file. File type: input. [Sample file](https://github.com/bioexcel/biobb_analysis/raw/master/biobb_analysis/test/data/gromacs/topology.tpr). Accepted formats: tpr, gro, g96, pdb, brk, ent.* **input_traj_path** (*str*): Path to the GROMACS trajectory file. File type: input. [Sample file](https://github.com/bioexcel/biobb_analysis/raw/master/biobb_analysis/test/data/gromacs/trajectory.trr). Accepted formats: xtc, trr, cpt, gro, g96, pdb, tng.* **input_index_path** (*str*) (Optional): Path to the GROMACS index file. File type: input. [Sample file](https://github.com/bioexcel/biobb_analysis/raw/master/biobb_analysis/test/data/gromacs/index.ndx). Accepted formats: ndx.* **output_xvg_path** (*str*): Path to the XVG output file. File type: output. [Sample file](https://github.com/bioexcel/biobb_analysis/raw/master/biobb_analysis/test/reference/gromacs/ref_rgyr.xvg). Accepted formats: xvg.  Config Syntax: input_parameter (datatype) - (default_value) DefinitionConfig parameters for this building block:* **xvg** (*str*) - ("none") XVG plot formatting. Values: xmgrace, xmgr, none.* **selection** (*str*) - ("System") Group where the rgyr will be performed. If **input_index_path** provided, check the file for the accepted values, if not, values: System, Protein, Protein-H, C-alpha, Backbone, MainChain, MainChain+Cb, MainChain+H, SideChain, SideChain-H, Prot-Masses, non-Protein, Water, SOL, non-Water, Ion, NA, CL, Water_and_ions.* **gmx_path** (*str*) - ("gmx") Path to the GROMACS executable binary.* **remove_tmp** (*bool*) - (True) [WF property] Remove temporal files.* **restart** (*bool*) - (False) [WF property] Do not execute if output files exist.* **container_path** (*string*) - (None) Container path definition.* **container_image** (*string*) - ('gromacs/gromacs:latest') Container image definition.* **container_volume_path** (*string*) - ('/tmp') Container volume path definition.* **container_working_dir** (*string*) - (None) Container working directory definition.* **container_user_id** (*string*) - (None) Container user_id definition.* **container_shell_path** (*string*) - ('/bin/bash') Path to default shell inside the container.  YAML  Common file config<jupyter_code>properties:
  selection: System<jupyter_output><empty_output><jupyter_text>Docker file config<jupyter_code>properties:
  selection: System
  container_path: docker
  container_image: gromacs/gromacs:latest
  container_volume_path: /tmp<jupyter_output><empty_output><jupyter_text>Singularity file config<jupyter_code>properties:
  selection: System
  container_path: singularity
  container_image: shub://michael-tn/gromacs
  container_volume_path: /tmp<jupyter_output><empty_output><jupyter_text>Command line<jupyter_code>gmx_rgyr --config data/conf/gmx_rgyr.yml --input_structure_path data/input/rgyr.gro --input_traj_path data/input/rgyr.trr --output_xvg_path data/output/output.rgyr.xvg<jupyter_output><empty_output><jupyter_text>JSON  Common file config<jupyter_code>{
  "properties": {
    "selection": "System"
  }
}<jupyter_output><empty_output><jupyter_text>Docker file config<jupyter_code>{
  "properties": {
    "selection": "System",
    "container_path": "docker",
    "container_image": "gromacs/gromacs:latest",
    "container_volume_path": "/tmp"
  }
}<jupyter_output><empty_output><jupyter_text>Singularity file config<jupyter_code>{
  "properties": {
    "selection": "System",
    "container_path": "singularity",
    "container_image": "shub://michael-tn/gromacs",
    "container_volume_path": "/tmp"
  }
}<jupyter_output><empty_output><jupyter_text>Command line<jupyter_code>gmx_rgyr --config data/conf/gmx_rgyr.json --input_structure_path data/input/rgyr.gro --input_traj_path data/input/rgyr.trr --output_xvg_path data/output/output.rgyr.xvg<jupyter_output><empty_output><jupyter_text>GROMACS rms Performs a Root Mean Square deviation (RMSd) analysis from a given GROMACS compatible trajectory.  Get help Command:<jupyter_code>gmx_rms -h
usage: gmx_rms [-h] [--config CONFIG] --input_structure_path INPUT_STRUCTURE_PATH --input_traj_path INPUT_TRAJ_PATH [--input_index_path INPUT_INDEX_PATH] --output_xvg_path OUTPUT_XVG_PATH

Performs a Root Mean Square deviation (RMSd) analysis from a given GROMACS compatible trajectory.

optional arguments:
  -h, --help            show this help message and exit
  --config CONFIG       Configuration file
  --input_index_path INPUT_INDEX_PATH
                        Path to the GROMACS index file. Accepted formats: ndx.

required arguments:
  --input_structure_path INPUT_STRUCTURE_PATH
                        Path to the input structure file. Accepted formats: tpr, gro, g96, pdb, brk, ent.
  --input_traj_path INPUT_TRAJ_PATH
                        Path to the GROMACS trajectory file. Accepted formats: xtc, trr, cpt, gro, g96, pdb, tng.
  --output_xvg_path OUTPUT_XVG_PATH
                        Path to the XVG output file. Accepted formats: xvg.<jupyter_output><empty_output><jupyter_text>I / O Arguments Syntax: input_argument (datatype) : DefinitionConfig input / output arguments for this building block:* **input_structure_path** (*str*): Path to the input structure file. File type: input. [Sample file](https://github.com/bioexcel/biobb_analysis/raw/master/biobb_analysis/test/data/gromacs/topology.tpr). Accepted formats: tpr, gro, g96, pdb, brk, ent.* **input_traj_path** (*str*): Path to the GROMACS trajectory file. File type: input. [Sample file](https://github.com/bioexcel/biobb_analysis/raw/master/biobb_analysis/test/data/gromacs/trajectory.trr). Accepted formats: xtc, trr, cpt, gro, g96, pdb, tng.* **input_index_path** (*str*) (Optional): Path to the GROMACS index file. File type: input. [Sample file](https://github.com/bioexcel/biobb_analysis/raw/master/biobb_analysis/test/data/gromacs/index.ndx). Accepted formats: ndx.* **output_xvg_path** (*str*): Path to the XVG output file. File type: output. [Sample file](https://github.com/bioexcel/biobb_analysis/raw/master/biobb_analysis/test/reference/gromacs/ref_rms.xvg). Accepted formats: xvg.  Config Syntax: input_parameter (datatype) - (default_value) DefinitionConfig parameters for this building block:* **xvg** (*str*) - ("none") XVG plot formatting. Values: xmgrace, xmgr, none.* **selection** (*str*) - ("System") Group where the rms will be performed. If **input_index_path** provided, check the file for the accepted values, if not, values: System, Protein, Protein-H, C-alpha, Backbone, MainChain, MainChain+Cb, MainChain+H, SideChain, SideChain-H, Prot-Masses, non-Protein, Water, SOL, non-Water, Ion, NA, CL, Water_and_ions.* **gmx_path** (*str*) - ("gmx") Path to the GROMACS executable binary.* **remove_tmp** (*bool*) - (True) [WF property] Remove temporal files.* **restart** (*bool*) - (False) [WF property] Do not execute if output files exist.* **container_path** (*string*) - (None) Container path definition.* **container_image** (*string*) - ('gromacs/gromacs:latest') Container image definition.* **container_volume_path** (*string*) - ('/tmp') Container volume path definition.* **container_working_dir** (*string*) - (None) Container working directory definition.* **container_user_id** (*string*) - (None) Container user_id definition.* **container_shell_path** (*string*) - ('/bin/bash') Path to default shell inside the container.  YAML  Common file config<jupyter_code>properties:
  selection: System<jupyter_output><empty_output><jupyter_text>Docker file config<jupyter_code>properties:
  selection: System
  container_path: docker
  container_image: gromacs/gromacs:latest
  container_volume_path: /tmp<jupyter_output><empty_output><jupyter_text>Singularity file config<jupyter_code>properties:
  selection: System
  container_path: singularity
  container_image: shub://michael-tn/gromacs
  container_volume_path: /tmp<jupyter_output><empty_output><jupyter_text>Command line<jupyter_code>gmx_rms --config data/conf/gmx_rms.yml --input_structure_path data/input/rgyr.gro --input_traj_path data/input/rgyr.trr --output_xvg_path data/output/output.rms.xvg<jupyter_output><empty_output><jupyter_text>JSON  Common file config<jupyter_code>{
  "properties": {
    "selection": "System"
  }
}<jupyter_output><empty_output><jupyter_text>Docker file config<jupyter_code>{
  "properties": {
    "selection": "System",
    "container_path": "docker",
    "container_image": "gromacs/gromacs:latest",
    "container_volume_path": "/tmp"
  }
}<jupyter_output><empty_output><jupyter_text>Singularity file config<jupyter_code>{
  "properties": {
    "selection": "System",
    "container_path": "singularity",
    "container_image": "shub://michael-tn/gromacs",
    "container_volume_path": "/tmp"
  }
}<jupyter_output><empty_output><jupyter_text>Command line<jupyter_code>gmx_rms --config data/conf/gmx_rms.json --input_structure_path data/input/rgyr.gro --input_traj_path data/input/rgyr.trr --output_xvg_path data/output/output.rms.xvg<jupyter_output><empty_output><jupyter_text>GROMACS trjconv structure Converts between GROMACS compatible structure file formats and/or extracts a selection of atoms.  Get help Command:<jupyter_code>gmx_trjconv_str -h
usage: gmx_trjconv_str [-h] [--config CONFIG] --input_structure_path INPUT_STRUCTURE_PATH --input_top_path INPUT_TOP_PATH [--input_index_path INPUT_INDEX_PATH] --output_str_path OUTPUT_STR_PATH

Converts between GROMACS compatible structure file formats and/or extracts a selection of atoms.

optional arguments:
  -h, --help            show this help message and exit
  --config CONFIG       Configuration file
  --input_index_path INPUT_INDEX_PATH
                        Path to the GROMACS index file. Accepted formats: ndx.

required arguments:
  --input_structure_path INPUT_STRUCTURE_PATH
                        Path to the input structure file. Accepted formats: xtc, trr, cpt, gro, g96, pdb, tng.
  --input_top_path INPUT_TOP_PATH
                        Path to the GROMACS input topology file. Accepted formats: tpr, gro, g96, pdb, brk, ent.
  --output_str_path OUTPUT_STR_PATH
                        Path to the output file. Accepted formats: xtc, trr, gro, g96, pdb, tng.<jupyter_output><empty_output><jupyter_text>I / O Arguments Syntax: input_argument (datatype) : DefinitionConfig input / output arguments for this building block:* **input_structure_path** (*str*): Path to the input structure file. File type: input. [Sample file](https://github.com/bioexcel/biobb_analysis/raw/master/biobb_analysis/test/data/gromacs/trajectory.trr). Accepted formats: xtc, trr, cpt, gro, g96, pdb, tng.* **input_top_path** (*str*): Path to the GROMACS input topology file. File type: input. [Sample file](https://github.com/bioexcel/biobb_analysis/raw/master/biobb_analysis/test/data/gromacs/topology.tpr). Accepted formats: tpr, gro, g96, pdb, brk, ent.* **input_index_path** (*str*) (Optional): Path to the GROMACS index file. File type: input. [Sample file](https://github.com/bioexcel/biobb_analysis/raw/master/biobb_analysis/test/data/gromacs/index.ndx). Accepted formats: ndx.* **output_str_path** (*str*): Path to the output file. File type: output. [Sample file](https://github.com/bioexcel/biobb_analysis/raw/master/biobb_analysis/test/reference/gromacs/ref_trjconv.str.pdb). Accepted formats: xtc, trr, gro, g96, pdb, tng.  Config Syntax: input_parameter (datatype) - (default_value) DefinitionConfig parameters for this building block:* **selection** (*str*) - ("System") Group where the trjconv will be performed. If **input_index_path** provided, check the file for the accepted values, if not, values: System, Protein, Protein-H, C-alpha, Backbone, MainChain, MainChain+Cb, MainChain+H, SideChain, SideChain-H, Prot-Masses, non-Protein, Water, SOL, non-Water, Ion, NA, CL, Water_and_ions.* **gmx_path** (*str*) - ("gmx") Path to the GROMACS executable binary.* **remove_tmp** (*bool*) - (True) [WF property] Remove temporal files.* **restart** (*bool*) - (False) [WF property] Do not execute if output files exist.* **container_path** (*string*) - (None) Container path definition.* **container_image** (*string*) - ('gromacs/gromacs:latest') Container image definition.* **container_volume_path** (*string*) - ('/tmp') Container volume path definition.* **container_working_dir** (*string*) - (None) Container working directory definition.* **container_user_id** (*string*) - (None) Container user_id definition.* **container_shell_path** (*string*) - ('/bin/bash') Path to default shell inside the container.  YAML  Common file config<jupyter_code>properties:
  selection: System<jupyter_output><empty_output><jupyter_text>Docker file config<jupyter_code>properties:
  selection: System
  container_path: docker
  container_image: gromacs/gromacs:latest
  container_volume_path: /tmp<jupyter_output><empty_output><jupyter_text>Singularity file config<jupyter_code>properties:
  selection: System
  container_path: singularity
  container_image: shub://michael-tn/gromacs
  container_volume_path: /tmp<jupyter_output><empty_output><jupyter_text>Command line<jupyter_code>gmx_trjconv_str --config data/conf/gmx_trjconv_str.yml --input_structure_path data/input/trjconv.str.gro --input_top_path data/input/trjconv.str.gro --output_str_path data/output/output.trjconv.str.pdb<jupyter_output><empty_output><jupyter_text>JSON  Common file config<jupyter_code>{
  "properties": {
    "selection": "System"
  }
}<jupyter_output><empty_output><jupyter_text>Docker file config<jupyter_code>{
  "properties": {
    "selection": "System",
    "container_path": "docker",
    "container_image": "gromacs/gromacs:latest",
    "container_volume_path": "/tmp"
  }
}<jupyter_output><empty_output><jupyter_text>Singularity file config<jupyter_code>{
  "properties": {
    "selection": "System",
    "container_path": "singularity",
    "container_image": "shub://michael-tn/gromacs",
    "container_volume_path": "/tmp"
  }
}<jupyter_output><empty_output><jupyter_text>Command line<jupyter_code>gmx_trjconv_str --config data/conf/gmx_trjconv_str.json --input_structure_path data/input/trjconv.str.gro --input_top_path data/input/trjconv.str.gro --output_str_path data/output/output.trjconv.str.pdb<jupyter_output><empty_output><jupyter_text>GROMACS trjconv structure ensemble Extracts an ensemble of frames containing a selection of atoms from GROMACS compatible trajectory files.  Get help Command:<jupyter_code>gmx_trjconv_str_ens -h
usage: gmx_trjconv_str_ens [-h] [--config CONFIG] --input_traj_path INPUT_TRAJ_PATH --input_top_path INPUT_TOP_PATH [--input_index_path INPUT_INDEX_PATH] --output_str_ens_path OUTPUT_STR_ENS_PATH

Extracts an ensemble of frames containing a selection of atoms from GROMACS compatible trajectory files.

optional arguments:
  -h, --help            show this help message and exit
  --config CONFIG       Configuration file
  --input_index_path INPUT_INDEX_PATH
                        Path to the GROMACS index file. Accepted formats: ndx.

required arguments:
  --input_traj_path INPUT_TRAJ_PATH
                        Path to the GROMACS trajectory file. Accepted formats: xtc, trr, cpt, gro, g96, pdb, tng.
  --input_top_path INPUT_TOP_PATH
                        Path to the GROMACS input topology file. Accepted formats: tpr, gro, g96, pdb, brk, ent.
  --output_str_ens_path OUTPUT_STR_ENS_PATH
                        Path to the output file. Accepted formats: zip.<jupyter_output><empty_output><jupyter_text>I / O Arguments Syntax: input_argument (datatype) : DefinitionConfig input / output arguments for this building block:* **input_traj_path** (*str*): Path to the GROMACS trajectory file. File type: input. [Sample file](https://github.com/bioexcel/biobb_analysis/raw/master/biobb_analysis/test/data/gromacs/trajectory.trr). Accepted formats: xtc, trr, cpt, gro, g96, pdb, tng.* **input_top_path** (*str*): Path to the GROMACS input topology file. File type: input. [Sample file](https://github.com/bioexcel/biobb_analysis/raw/master/biobb_analysis/test/data/gromacs/topology.tpr). Accepted formats: tpr, gro, g96, pdb, brk, ent.* **input_index_path** (*str*) (Optional): Path to the GROMACS index file. File type: input. [Sample file](https://github.com/bioexcel/biobb_analysis/raw/master/biobb_analysis/test/data/gromacs/index.ndx). Accepted formats: ndx.* **output_str_ens_path** (*str*): Path to the output file. File type: output. [Sample file](https://github.com/bioexcel/biobb_analysis/raw/master/biobb_analysis/test/reference/gromacs/ref_trjconv.str.ens.zip). Accepted formats: zip.  Config Syntax: input_parameter (datatype) - (default_value) DefinitionConfig parameters for this building block:* **selection** (*str*) - ("System") Group where the trjconv will be performed. If **input_index_path** provided, check the file for the accepted values, if not, values: System, Protein, Protein-H, C-alpha, Backbone, MainChain, MainChain+Cb, MainChain+H, SideChain, SideChain-H, Prot-Masses, non-Protein, Water, SOL, non-Water, Ion, NA, CL, Water_and_ions.* **start** (*int*) - (0) Time of first frame to read from trajectory (default unit ps).* **end** (*int*) - (0) Time of last frame to read from trajectory (default unit ps).* **dt** (*int*) - (0) Only write frame when t MOD dt = first time (ps).* **output_name** (*str*) - ("output") File name for ensemble of output files.* **output_type** (*str*) - ("pdb") File type for ensemble of output files. Values: gro, g96, pdb.* **gmx_path** (*str*) - ("gmx") Path to the GROMACS executable binary.* **remove_tmp** (*bool*) - (True) [WF property] Remove temporal files.* **restart** (*bool*) - (False) [WF property] Do not execute if output files exist.* **container_path** (*string*) - (None) Container path definition.* **container_image** (*string*) - ('gromacs/gromacs:latest') Container image definition.* **container_volume_path** (*string*) - ('/tmp') Container volume path definition.* **container_working_dir** (*string*) - (None) Container working directory definition.* **container_user_id** (*string*) - (None) Container user_id definition.* **container_shell_path** (*string*) - ('/bin/bash') Path to default shell inside the container.  YAML  Common file config<jupyter_code>properties:
  selection: System
  start: 0
  end: 10
  dt: 1
  output_name: output
  output_type: pdb<jupyter_output><empty_output><jupyter_text>Docker file config<jupyter_code>properties:
  selection: System
  start: 0
  end: 10
  dt: 1
  output_name: output
  output_type: pdb
  container_path: docker
  container_image: gromacs/gromacs:latest
  container_volume_path: /tmp<jupyter_output><empty_output><jupyter_text>Singularity file config<jupyter_code>properties:
  selection: System
  start: 0
  end: 10
  dt: 1
  output_name: output
  output_type: pdb
  container_path: singularity
  container_image: shub://michael-tn/gromacs
  container_volume_path: /tmp<jupyter_output><empty_output><jupyter_text>Command line<jupyter_code>gmx_trjconv_str_ens --config data/conf/gmx_trjconv_str_ens.yml --input_traj_path data/input/trjconv.str.ens.trr --input_top_path data/input/trjconv.str.ens.gro --output_str_ens_path data/output/output.trjconv.str.ens.zip<jupyter_output><empty_output><jupyter_text>JSON  Common file config<jupyter_code>{
  "properties": {
    "selection": "System",
    "start": 0,
    "end": 10,
    "dt": 1,
    "output_name": "output",
    "output_type": "pdb"
  }
}<jupyter_output><empty_output><jupyter_text>Docker file config<jupyter_code>{
  "properties": {
    "selection": "System",
    "start": 0,
    "end": 10,
    "dt": 1,
    "output_name": "output",
    "output_type": "pdb",
    "container_path": "docker",
    "container_image": "gromacs/gromacs:latest",
    "container_volume_path": "/tmp"
  }
}<jupyter_output><empty_output><jupyter_text>Singularity file config<jupyter_code>{
  "properties": {
    "selection": "System",
    "start": 0,
    "end": 10,
    "dt": 1,
    "output_name": "output",
    "output_type": "pdb",
    "container_path": "singularity",
    "container_image": "shub://michael-tn/gromacs",
    "container_volume_path": "/tmp"
  }
}<jupyter_output><empty_output><jupyter_text>Command line<jupyter_code>gmx_trjconv_str_ens --config data/conf/gmx_trjconv_str_ens.json --input_traj_path data/input/trjconv.str.ens.trr --input_top_path data/input/trjconv.str.ens.gro --output_str_ens_path data/output/output.trjconv.str.ens.zip<jupyter_output><empty_output><jupyter_text>GROMACS trjconv trajectory Converts between GROMACS compatible trajectory file formats and/or extracts a selection of atoms.  Get help Command:<jupyter_code>gmx_trjconv_trj -h
usage: gmx_trjconv_trj [-h] [--config CONFIG] --input_traj_path INPUT_TRAJ_PATH [--input_index_path INPUT_INDEX_PATH] --output_traj_path OUTPUT_TRAJ_PATH

Converts between GROMACS compatible trajectory file formats and/or extracts a selection of atoms.

optional arguments:
  -h, --help            show this help message and exit
  --config CONFIG       Configuration file
  --input_index_path INPUT_INDEX_PATH
                        Path to the GROMACS index file. Accepted formats: ndx.

required arguments:
  --input_traj_path INPUT_TRAJ_PATH
                        Path to the GROMACS trajectory file. Accepted formats: xtc, trr, cpt, gro, g96, pdb, tng.
  --output_traj_path OUTPUT_TRAJ_PATH
                        Path to the output file. Accepted formats: xtc, trr, gro, g96, pdb, tng.<jupyter_output><empty_output><jupyter_text>I / O Arguments Syntax: input_argument (datatype) : DefinitionConfig input / output arguments for this building block:* **input_traj_path** (*str*): Path to the GROMACS trajectory file. File type: input. [Sample file](https://github.com/bioexcel/biobb_analysis/raw/master/biobb_analysis/test/data/gromacs/trajectory.trr). Accepted formats: xtc, trr, cpt, gro, g96, pdb, tng.* **input_index_path** (*str*) (Optional): Path to the GROMACS index file. File type: input. [Sample file](https://github.com/bioexcel/biobb_analysis/raw/master/biobb_analysis/test/data/gromacs/index.ndx). Accepted formats: ndx.* **output_traj_path** (*str*): Path to the output file. File type: output. [Sample file](https://github.com/bioexcel/biobb_analysis/raw/master/biobb_analysis/test/reference/gromacs/ref_trjconv.trj.xtc). Accepted formats: xtc, trr, gro, g96, pdb, tng.  Config Syntax: input_parameter (datatype) - (default_value) DefinitionConfig parameters for this building block:* **selection** (*str*) - ("System") Group where the trjconv will be performed. If **input_index_path** provided, check the file for the accepted values, if not, values: System, Protein, Protein-H, C-alpha, Backbone, MainChain, MainChain+Cb, MainChain+H, SideChain, SideChain-H, Prot-Masses, non-Protein, Water, SOL, non-Water, Ion, NA, CL, Water_and_ions.* **start** (*int*) - (0) Time of first frame to read from trajectory (default unit ps).* **end** (*int*) - (0) Time of last frame to read from trajectory (default unit ps).* **dt** (*int*) - (0) Only write frame when t MOD dt = first time (ps).* **gmx_path** (*str*) - ("gmx") Path to the GROMACS executable binary.* **remove_tmp** (*bool*) - (True) [WF property] Remove temporal files.* **restart** (*bool*) - (False) [WF property] Do not execute if output files exist.* **container_path** (*string*) - (None) Container path definition.* **container_image** (*string*) - ('gromacs/gromacs:latest') Container image definition.* **container_volume_path** (*string*) - ('/tmp') Container volume path definition.* **container_working_dir** (*string*) - (None) Container working directory definition.* **container_user_id** (*string*) - (None) Container user_id definition.* **container_shell_path** (*string*) - ('/bin/bash') Path to default shell inside the container.  YAML  Common file config<jupyter_code>properties:
  selection: System
  start: 0
  end: 0
  dt: 0<jupyter_output><empty_output><jupyter_text>Docker file config<jupyter_code>properties:
  selection: System
  start: 0
  end: 0
  dt: 0
  container_path: docker
  container_image: gromacs/gromacs:latest
  container_volume_path: /tmp<jupyter_output><empty_output><jupyter_text>Singularity file config<jupyter_code>properties:
  selection: System
  start: 0
  end: 0
  dt: 0
  container_path: singularity
  container_image: shub://michael-tn/gromacs
  container_volume_path: /tmp<jupyter_output><empty_output><jupyter_text>Command line<jupyter_code>gmx_trjconv_trj --config data/conf/gmx_trjconv_trj.yml --input_traj_path data/input/trjconv.trj.trr --output_traj_path data/output/output.trjconv.trj.xtc<jupyter_output><empty_output><jupyter_text>JSON  Common file config<jupyter_code>{
  "properties": {
    "selection": "System",
    "start": 0,
    "end": 0,
    "dt": 0
  }
}<jupyter_output><empty_output><jupyter_text>Docker file config<jupyter_code>{
  "properties": {
    "selection": "System",
    "start": 0,
    "end": 0,
    "dt": 0,
    "container_path": "docker",
    "container_image": "gromacs/gromacs:latest",
    "container_volume_path": "/tmp"
  }
}<jupyter_output><empty_output><jupyter_text>Singularity file config<jupyter_code>{
  "properties": {
    "selection": "System",
    "start": 0,
    "end": 0,
    "dt": 0,
    "container_path": "singularity",
    "container_image": "shub://michael-tn/gromacs",
    "container_volume_path": "/tmp"
  }
}<jupyter_output><empty_output><jupyter_text>Command line<jupyter_code>gmx_trjconv_trj --config data/conf/gmx_trjconv_trj.json --input_traj_path data/input/trjconv.trj.trr --output_traj_path data/output/output.trjconv.trj.xtc<jupyter_output><empty_output>
{'fraction_non_alphanumeric': 0.13113551892531541, 'fraction_numerical': 0.0036667277787963133, 'mean_word_length': 4.689853010905643, 'pattern_counts': {'":': 501, '<': 767, '<?xml version=': 0, '>': 767, 'https://': 69, 'lorem ipsum': 0, 'www.': 0, 'xml': 0}, 'pii_count': 0, 'substrings_counts': 0, 'word_list_counts': {'cursed_substrings.json': 0, 'profanity_word_list.json': 0, 'sexual_word_list.json': 0, 'zh_pornsignals.json': 0}}
{'chain_length': '191', 'dir': 'jupyter-structured-clean-dedup', 'id': '527952', 'license': 'Apache-2.0', 'n_tokens_mistral': 40752, 'n_tokens_neox': 39629, 'n_words': 9899, 'path': 'biobb_analysis/docs/jupyter/command_line_template.ipynb', 'repo_name': 'bioexcel/biobb_analysis', 'size': '119998'}