BioBB CHEMISTRY Command Line Help

Generic usage:

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

Babel_minimize

This class is a wrapper of the Open Babel tool.

Get help

Command:

babel_minimize -h

usage: babel_minimize [-h] [--config CONFIG] --input_path INPUT_PATH --output_path OUTPUT_PATH

Energetically minimize small molecules.

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

required arguments:
  --input_path INPUT_PATH
                        Path to the input file. Accepted formats: pdb, mol2.
  --output_path OUTPUT_PATH
                        Path to the output file. Accepted formats: pdb, mol2.

I / O Arguments

Syntax: input_argument (datatype) : Definition

Config input / output arguments for this building block:

input_path (string): Path to the input file. File type: input. Sample file. Accepted formats: PDB, MOL2
output_path (string): Path to the output file. File type: output. Sample file. Accepted formats: PDB, MOL2

Config

Syntax: input_parameter (datatype) - (default_value) Definition

Config parameters for this building block:

criteria (number): (1e-06) Convergence criteria.
method (string): (cg) Method. .
force_field (string): (None) Force field. .
hydrogens (boolean): (False) Add hydrogen atoms..
steps (integer): (2500) Maximum number of steps..
cutoff (boolean): (False) Use cut-off..
rvdw (number): (6.0) VDW cut-off distance..
rele (number): (10.0) Electrostatic cut-off distance..
frequency (integer): (10) Frequency to update the non-bonded pairs..
binary_path (string): (obminimize) Path to the obminimize executable binary..
remove_tmp (boolean): (True) Remove temporal files..
restart (boolean): (False) Do not execute if output files exist..
container_path (string): (None) Container path definition..
container_image (string): (informaticsmatters/obabel: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 config file 

properties:
  criteria: 1e-6
  cutoff: true
  force_field: GAFF
  frequency: 10
  hydrogens: true
  method: cg
  rele: 10.0
  rvdw: 6.0
  steps: 2500

Docker config file 

properties:
  container_image: informaticsmatters/obabel:latest
  container_path: docker
  container_volume_path: /tmp
  criteria: 1e-6
  cutoff: true
  force_field: GAFF
  frequency: 10
  hydrogens: true
  method: cg
  rele: 10.0
  rvdw: 6.0
  steps: 2500

Singularity config file 

properties:
  container_image: shub://bioexcel/obabel_singularity
  container_path: singularity
  container_volume_path: /tmp
  criteria: 1e-6
  cutoff: true
  force_field: GAFF
  frequency: 10
  hydrogens: true
  method: cg
  rele: 10.0
  rvdw: 6.0
  steps: 2500

Command line

babel_minimize --config config_babel_minimize.yml --input_path babel.minimize.pdb --output_path ref_babel.minimize.pdb

JSON

Common config file 

{
  "properties": {
    "criteria": "1e-6",
    "method": "cg",
    "force_field": "GAFF",
    "hydrogens": true,
    "steps": 2500,
    "cutoff": true,
    "rvdw": 6.0,
    "rele": 10.0,
    "frequency": 10
  }
}

Docker config file 

{
  "properties": {
    "criteria": "1e-6",
    "method": "cg",
    "force_field": "GAFF",
    "hydrogens": true,
    "steps": 2500,
    "cutoff": true,
    "rvdw": 6.0,
    "rele": 10.0,
    "frequency": 10,
    "container_path": "docker",
    "container_image": "informaticsmatters/obabel:latest",
    "container_volume_path": "/tmp"
  }
}

Singularity config file 

{
  "properties": {
    "criteria": "1e-6",
    "method": "cg",
    "force_field": "GAFF",
    "hydrogens": true,
    "steps": 2500,
    "cutoff": true,
    "rvdw": 6.0,
    "rele": 10.0,
    "frequency": 10,
    "container_path": "singularity",
    "container_image": "shub://bioexcel/obabel_singularity",
    "container_volume_path": "/tmp"
  }
}

Command line

babel_minimize --config config_babel_minimize.json --input_path babel.minimize.pdb --output_path ref_babel.minimize.pdb

Acpype_params_ac

This class is a wrapper of Acpype tool for small molecule parameterization for AMBER MD package.

Get help

Command:

acpype_params_ac -h

usage: acpype_params_ac [-h] [--config CONFIG] --input_path INPUT_PATH --output_path_frcmod OUTPUT_PATH_FRCMOD --output_path_inpcrd OUTPUT_PATH_INPCRD --output_path_lib OUTPUT_PATH_LIB --output_path_prmtop OUTPUT_PATH_PRMTOP

Small molecule parameterization for AMBER MD package.

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

required arguments:
  --input_path INPUT_PATH
                        Path to the input file. Accepted formats: pdb, mdl, mol2.
  --output_path_frcmod OUTPUT_PATH_FRCMOD
                        Path to the FRCMOD output file. Accepted formats: frcmod.
  --output_path_inpcrd OUTPUT_PATH_INPCRD
                        Path to the INPCRD output file. Accepted formats: inpcrd.
  --output_path_lib OUTPUT_PATH_LIB
                        Path to the LIB output file. Accepted formats: lib.
  --output_path_prmtop OUTPUT_PATH_PRMTOP
                        Path to the PRMTOP output file. Accepted formats: prmtop.

I / O Arguments

Syntax: input_argument (datatype) : Definition

Config input / output arguments for this building block:

input_path (string): Path to the input file. File type: input. Sample file. Accepted formats: PDB, MDL, MOL2
output_path_frcmod (string): Path to the FRCMOD output file. File type: output. Sample file. Accepted formats: FRCMOD
output_path_inpcrd (string): Path to the INPCRD output file. File type: output. Sample file. Accepted formats: INPCRD
output_path_lib (string): Path to the LIB output file. File type: output. Sample file. Accepted formats: LIB
output_path_prmtop (string): Path to the PRMTOP output file. File type: output. Sample file. Accepted formats: PRMTOP

Config

Syntax: input_parameter (datatype) - (default_value) Definition

Config parameters for this building block:

basename (string): (BBB) A basename for the project (folder and output files)..
charge (integer): (0) Net molecular charge, for gas default is 0. If None the charge is guessed by acpype..
binary_path (string): (acpype) Path to the acpype executable binary..
remove_tmp (boolean): (True) Remove temporal files..
restart (boolean): (False) Do not execute if output files exist..
container_path (string): (None) Container path definition..
container_image (string): (acpype/acpype:2022.7.21) 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 

properties:
  basename: BBB
  charge: 0

Docker config file 

properties:
  basename: BBB
  charge: 0
  container_image: acpype/acpype:2022.7.21
  container_path: docker
  container_volume_path: /tmp

Singularity config file 

properties:
  basename: BBB
  charge: 0
  container_image: shub://bioexcel/acpype_container
  container_path: singularity
  container_shell_path: /bin/sh
  container_volume_path: /tmp
  container_working_dir: /tmp

Command line

acpype_params_ac --config config_acpype_params_ac.yml --input_path acpype.params.mol2 --output_path_frcmod ref_acpype.ac.frcmod --output_path_inpcrd ref_acpype.ac.inpcrd --output_path_lib ref_acpype.ac.lib --output_path_prmtop ref_acpype.ac.prmtop

JSON

Common config file 

{
  "properties": {
    "basename": "BBB",
    "charge": 0
  }
}

Docker config file 

{
  "properties": {
    "basename": "BBB",
    "charge": 0,
    "container_path": "docker",
    "container_image": "acpype/acpype:2022.7.21",
    "container_volume_path": "/tmp"
  }
}

Singularity config file 

{
  "properties": {
    "basename": "BBB",
    "charge": 0,
    "container_path": "singularity",
    "container_image": "shub://bioexcel/acpype_container",
    "container_volume_path": "/tmp",
    "container_working_dir": "/tmp",
    "container_shell_path": "/bin/sh"
  }
}

Command line

acpype_params_ac --config config_acpype_params_ac.json --input_path acpype.params.mol2 --output_path_frcmod ref_acpype.ac.frcmod --output_path_inpcrd ref_acpype.ac.inpcrd --output_path_lib ref_acpype.ac.lib --output_path_prmtop ref_acpype.ac.prmtop

Babel_remove_hydrogens

This class is a wrapper of the Open Babel tool.

Get help

Command:

babel_remove_hydrogens -h

usage: babel_remove_hydrogens [-h] [--config CONFIG] --input_path INPUT_PATH --output_path OUTPUT_PATH

Removes hydrogen atoms to small molecules.

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

required arguments:
  --input_path INPUT_PATH
                        Path to the input file. Accepted formats: dat, ent, fa, fasta, gro, inp, log, mcif, mdl, mmcif, mol, mol2, pdb, pdbqt, png, sdf, smi, smiles, txt, xml, xtc.
  --output_path OUTPUT_PATH
                        Path to the output file. Accepted formats: ent, fa, fasta, gro, inp, mcif, mdl, mmcif, mol, mol2, pdb, pdbqt, png, sdf, smi, smiles, txt.

I / O Arguments

Syntax: input_argument (datatype) : Definition

Config input / output arguments for this building block:

input_path (string): Path to the input file. File type: input. Sample file. Accepted formats: DAT, ENT, FA, FASTA, GRO, INP, LOG, MCIF, MDL, MMCIF, MOL, MOL2, PDB, PDBQT, PNG, SDF, SMI, SMILES, TXT, XML, XTC
output_path (string): Path to the output file. File type: output. Sample file. Accepted formats: ENT, FA, FASTA, GRO, INP, MCIF, MDL, MMCIF, MOL, MOL2, PDB, PDBQT, PNG, SDF, SMI, SMILES, TXT

Config

Syntax: input_parameter (datatype) - (default_value) Definition

Config parameters for this building block:

input_format (string): (None) Format of input file. If not provided, input_path extension will be taken. .
output_format (string): (None) Format of output file. If not provided, output_path extension will be taken. .
coordinates (integer): (None) Type of coordinates: 2D or 3D. .
ph (number): (7.4) Add hydrogens appropriate for pH..
binary_path (string): (obabel) Path to the obabel executable binary..
remove_tmp (boolean): (True) Remove temporal files..
restart (boolean): (False) Do not execute if output files exist..
container_path (string): (None) Container path definition..
container_image (string): (informaticsmatters/obabel: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 config file 

properties:
  coordinates: 3
  input_format: pdb
  output_format: pdb
  ph: 7.4

Docker config file 

properties:
  container_image: informaticsmatters/obabel:latest
  container_path: docker
  container_volume_path: /tmp
  coordinates: 3
  input_format: pdb
  output_format: pdb
  ph: 7.4

Singularity config file 

properties:
  container_image: shub://bioexcel/obabel_singularity
  container_path: singularity
  container_volume_path: /tmp
  coordinates: 3
  input_format: pdb
  output_format: pdb
  ph: 7.4

Command line

babel_remove_hydrogens --config config_babel_remove_hydrogens.yml --input_path babel.H.pdb --output_path ref_babel.nohydrogens.pdb

JSON

Common config file 

{
  "properties": {
    "input_format": "pdb",
    "output_format": "pdb",
    "coordinates": 3,
    "ph": 7.4
  }
}

Docker config file 

{
  "properties": {
    "input_format": "pdb",
    "output_format": "pdb",
    "coordinates": 3,
    "ph": 7.4,
    "container_path": "docker",
    "container_image": "informaticsmatters/obabel:latest",
    "container_volume_path": "/tmp"
  }
}

Singularity config file 

{
  "properties": {
    "input_format": "pdb",
    "output_format": "pdb",
    "coordinates": 3,
    "ph": 7.4,
    "container_path": "singularity",
    "container_image": "shub://bioexcel/obabel_singularity",
    "container_volume_path": "/tmp"
  }
}

Command line

babel_remove_hydrogens --config config_babel_remove_hydrogens.json --input_path babel.H.pdb --output_path ref_babel.nohydrogens.pdb

Babel_add_hydrogens

This class is a wrapper of the Open Babel tool.

Get help

Command:

babel_add_hydrogens -h

usage: babel_add_hydrogens [-h] [--config CONFIG] --input_path INPUT_PATH --output_path OUTPUT_PATH

Adds hydrogen atoms to small molecules.

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

required arguments:
  --input_path INPUT_PATH
                        Path to the input file. Accepted formats: dat, ent, fa, fasta, gro, inp, log, mcif, mdl, mmcif, mol, mol2, pdb, pdbqt, png, sdf, smi, smiles, txt, xml, xtc.
  --output_path OUTPUT_PATH
                        Path to the output file. Accepted formats: ent, fa, fasta, gro, inp, mcif, mdl, mmcif, mol, mol2, pdb, pdbqt, png, sdf, smi, smiles, txt.

I / O Arguments

Syntax: input_argument (datatype) : Definition

Config input / output arguments for this building block:

input_path (string): Path to the input file. File type: input. Sample file. Accepted formats: DAT, ENT, FA, FASTA, GRO, INP, LOG, MCIF, MDL, MMCIF, MOL, MOL2, PDB, PDBQT, PNG, SDF, SMI, SMILES, TXT, XML, XTC
output_path (string): Path to the output file. File type: output. Sample file. Accepted formats: ENT, FA, FASTA, GRO, INP, MCIF, MDL, MMCIF, MOL, MOL2, PDB, PDBQT, PNG, SDF, SMI, SMILES, TXT

Config

Syntax: input_parameter (datatype) - (default_value) Definition

Config parameters for this building block:

input_format (string): (None) Format of input file. If not provided, input_path extension will be taken. .
output_format (string): (None) Format of output file. If not provided, output_path extension will be taken. .
coordinates (integer): (None) Type of coordinates: 2D or 3D. .
ph (number): (7.4) Add hydrogens appropriate for pH..
binary_path (string): (obabel) Path to the obabel executable binary..
remove_tmp (boolean): (True) Remove temporal files..
restart (boolean): (False) Do not execute if output files exist..
container_path (string): (None) Container path definition..
container_image (string): (informaticsmatters/obabel: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 config file 

properties:
  coordinates: 3
  input_format: pdb
  output_format: pdb
  ph: 7.4

Docker config file 

properties:
  container_image: informaticsmatters/obabel:latest
  container_path: docker
  container_volume_path: /tmp
  coordinates: 3
  input_format: pdb
  output_format: pdb
  ph: 7.4

Singularity config file 

properties:
  container_image: shub://bioexcel/obabel_singularity
  container_path: singularity
  container_volume_path: /tmp
  coordinates: 3
  input_format: pdb
  output_format: pdb
  ph: 7.4

Command line

babel_add_hydrogens --config config_babel_add_hydrogens.yml --input_path babel.no.H.pdb --output_path ref_babel.hydrogens.pdb

JSON

Common config file 

{
  "properties": {
    "input_format": "pdb",
    "output_format": "pdb",
    "coordinates": 3,
    "ph": 7.4
  }
}

Docker config file 

{
  "properties": {
    "input_format": "pdb",
    "output_format": "pdb",
    "coordinates": 3,
    "ph": 7.4,
    "container_path": "docker",
    "container_image": "informaticsmatters/obabel:latest",
    "container_volume_path": "/tmp"
  }
}

Singularity config file 

{
  "properties": {
    "input_format": "pdb",
    "output_format": "pdb",
    "coordinates": 3,
    "ph": 7.4,
    "container_path": "singularity",
    "container_image": "shub://bioexcel/obabel_singularity",
    "container_volume_path": "/tmp"
  }
}

Command line

babel_add_hydrogens --config config_babel_add_hydrogens.json --input_path babel.no.H.pdb --output_path ref_babel.hydrogens.pdb

Acpype_params_gmx_opls

This class is a wrapper of Acpype tool for generation of topologies for OPLS/AA.

Get help

Command:

acpype_params_gmx_opls -h

usage: acpype_params_gmx_opls [-h] [--config CONFIG] --input_path INPUT_PATH --output_path_itp OUTPUT_PATH_ITP --output_path_top OUTPUT_PATH_TOP

Small molecule parameterization for OPLS/AA MD package.

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

required arguments:
  --input_path INPUT_PATH
                        Path to the input file. Accepted formats: pdb, mdl, mol2.
  --output_path_itp OUTPUT_PATH_ITP
                        Path to the ITP output file. Accepted formats: itp.
  --output_path_top OUTPUT_PATH_TOP
                        Path to the TOP output file. Accepted formats: top.

I / O Arguments

Syntax: input_argument (datatype) : Definition

Config input / output arguments for this building block:

input_path (string): Path to the input file. File type: input. Sample file. Accepted formats: PDB, MDL, MOL2
output_path_itp (string): Path to the ITP output file. File type: output. Sample file. Accepted formats: ITP
output_path_top (string): Path to the TOP output file. File type: output. Sample file. Accepted formats: TOP

Config

Syntax: input_parameter (datatype) - (default_value) Definition

Config parameters for this building block:

basename (string): (BBB) A basename for the project (folder and output files)..
charge (integer): (0) Net molecular charge, for gas default is 0. If None the charge is guessed by acpype..
binary_path (string): (acpype) Path to the acpype executable binary..
remove_tmp (boolean): (True) Remove temporal files..
restart (boolean): (False) Do not execute if output files exist..
container_path (string): (None) Container path definition..
container_image (string): (acpype/acpype:2022.7.21) 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 

properties:
  basename: BBB
  charge: 0

Docker config file 

properties:
  basename: BBB
  charge: 0
  container_image: acpype/acpype:2022.7.21
  container_path: docker
  container_volume_path: /tmp

Singularity config file 

properties:
  basename: BBB
  charge: 0
  container_image: shub://bioexcel/acpype_container
  container_path: singularity
  container_shell_path: /bin/sh
  container_volume_path: /tmp
  container_working_dir: /tmp

Command line

acpype_params_gmx_opls --config config_acpype_params_gmx_opls.yml --input_path acpype.params.mol2 --output_path_itp ref_acpype.gmx.opls.itp --output_path_top ref_acpype.gmx.opls.top

JSON

Common config file 

{
  "properties": {
    "basename": "BBB",
    "charge": 0
  }
}

Docker config file 

{
  "properties": {
    "basename": "BBB",
    "charge": 0,
    "container_path": "docker",
    "container_image": "acpype/acpype:2022.7.21",
    "container_volume_path": "/tmp"
  }
}

Singularity config file 

{
  "properties": {
    "basename": "BBB",
    "charge": 0,
    "container_path": "singularity",
    "container_image": "shub://bioexcel/acpype_container",
    "container_volume_path": "/tmp",
    "container_working_dir": "/tmp",
    "container_shell_path": "/bin/sh"
  }
}

Command line

acpype_params_gmx_opls --config config_acpype_params_gmx_opls.json --input_path acpype.params.mol2 --output_path_itp ref_acpype.gmx.opls.itp --output_path_top ref_acpype.gmx.opls.top

Acpype_params_cns

This class is a wrapper of Acpype tool for small molecule parameterization for CNS/XPLOR MD package.

Get help

Command:

acpype_params_cns -h

usage: acpype_params_cns [-h] [--config CONFIG] --input_path INPUT_PATH --output_path_par OUTPUT_PATH_PAR --output_path_inp OUTPUT_PATH_INP --output_path_top OUTPUT_PATH_TOP

Small molecule parameterization for CNS/XPLOR MD package.

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

required arguments:
  --input_path INPUT_PATH
                        Path to the input file. Accepted formats: pdb, mdl, mol2.
  --output_path_par OUTPUT_PATH_PAR
                        Path to the PAR output file. Accepted formats: par.
  --output_path_inp OUTPUT_PATH_INP
                        Path to the INP output file. Accepted formats: inp.
  --output_path_top OUTPUT_PATH_TOP
                        Path to the TOP output file. Accepted formats: top.

I / O Arguments

Syntax: input_argument (datatype) : Definition

Config input / output arguments for this building block:

input_path (string): Path to the input file. File type: input. Sample file. Accepted formats: PDB, MDL, MOL2
output_path_par (string): Path to the PAR output file. File type: output. Sample file. Accepted formats: PAR
output_path_inp (string): Path to the INP output file. File type: output. Sample file. Accepted formats: INP
output_path_top (string): Path to the TOP output file. File type: output. Sample file. Accepted formats: TOP

Config

Syntax: input_parameter (datatype) - (default_value) Definition

Config parameters for this building block:

basename (string): (BBB) A basename for the project (folder and output files)..
charge (integer): (0) Net molecular charge, for gas default is 0. If None the charge is guessed by acpype..
binary_path (string): (acpype) Path to the acpype executable binary..
remove_tmp (boolean): (True) Remove temporal files..
restart (boolean): (False) Do not execute if output files exist..
container_path (string): (None) Container path definition..
container_image (string): (acpype/acpype:2022.7.21) 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 

properties:
  basename: BBB
  charge: 0

Docker config file 

properties:
  basename: BBB
  charge: 0
  container_image: acpype/acpype:2022.7.21
  container_path: docker
  container_volume_path: /tmp

Singularity config file 

properties:
  basename: BBB
  charge: 0
  container_image: shub://bioexcel/acpype_container
  container_path: singularity
  container_shell_path: /bin/sh
  container_volume_path: /tmp
  container_working_dir: /tmp

Command line

acpype_params_cns --config config_acpype_params_cns.yml --input_path acpype.params.mol2 --output_path_par ref_acpype.cns.par --output_path_inp ref_acpype.cns.inp --output_path_top ref_acpype.cns.top

JSON

Common config file 

{
  "properties": {
    "basename": "BBB",
    "charge": 0
  }
}

Docker config file 

{
  "properties": {
    "basename": "BBB",
    "charge": 0,
    "container_path": "docker",
    "container_image": "acpype/acpype:2022.7.21",
    "container_volume_path": "/tmp"
  }
}

Singularity config file 

{
  "properties": {
    "basename": "BBB",
    "charge": 0,
    "container_path": "singularity",
    "container_image": "shub://bioexcel/acpype_container",
    "container_volume_path": "/tmp",
    "container_working_dir": "/tmp",
    "container_shell_path": "/bin/sh"
  }
}

Command line

acpype_params_cns --config config_acpype_params_cns.json --input_path acpype.params.mol2 --output_path_par ref_acpype.cns.par --output_path_inp ref_acpype.cns.inp --output_path_top ref_acpype.cns.top

Reduce_add_hydrogens

This class is a wrapper of the Ambertools reduce module for adding hydrogens to a given structure.

Get help

Command:

reduce_add_hydrogens -h

usage: reduce_add_hydrogens [-h] [--config CONFIG] --input_path INPUT_PATH --output_path OUTPUT_PATH

Adds hydrogen atoms to small molecules.

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

required arguments:
  --input_path INPUT_PATH
                        Path to the input file. Accepted formats: pdb.
  --output_path OUTPUT_PATH
                        Path to the output file. Accepted formats: pdb.

I / O Arguments

Syntax: input_argument (datatype) : Definition

Config input / output arguments for this building block:

input_path (string): Path to the input file. File type: input. Sample file. Accepted formats: PDB
output_path (string): Path to the output file. File type: output. Sample file. Accepted formats: PDB

Config

Syntax: input_parameter (datatype) - (default_value) Definition

Config parameters for this building block:

flip (boolean): (False) add H and rotate and flip NQH groups.
noflip (boolean): (False) add H and rotate groups with no NQH flips.
nuclear (boolean): (False) use nuclear X-H distances rather than default electron cloud distances.
nooh (boolean): (False) remove hydrogens on OH and SH groups.
oh (boolean): (True) add hydrogens on OH and SH groups (default).
his (boolean): (False) create NH hydrogens on HIS rings (usually used with -HIS).
noheth (boolean): (False) do not attempt to add NH proton on Het groups.
rotnh3 (boolean): (True) allow lysine NH3 to rotate (default).
norotnh3 (boolean): (False) do not allow lysine NH3 to rotate.
rotexist (boolean): (False) allow existing rotatable groups (OH, SH, Met-CH3) to rotate.
rotexoh (boolean): (False) allow existing OH & SH groups to rotate.
allalt (boolean): (True) process adjustments for all conformations (default).
onlya (boolean): (False) only adjust ‘A’ conformations.
charges (boolean): (False) output charge state for appropriate hydrogen records.
dorotmet (boolean): (False) allow methionine methyl groups to rotate (not recommended).
noadjust (boolean): (False) do not process any rot or flip adjustments.
metal_bump (number): (None) H ‘bumps’ metals at radius plus this.
non_metal_bump (number): (None) ‘bumps’ nonmetal at radius plus this.
build (boolean): (False) add H, including His sc NH, then rotate and flip groups (except for pre-existing methionine methyl hydrogens).
binary_path (string): (reduce) Path to the reduce executable binary..
remove_tmp (boolean): (True) Remove temporal files..
restart (boolean): (False) 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 

properties:
  nooh: true

Docker config file 

properties:
  container_image: afandiadib/ambertools:serial
  container_path: docker
  container_volume_path: /tmp
  nooh: true

Singularity config file 

properties:
  container_image: shub://bioexcel/ambertools_singularity
  container_path: singularity
  container_volume_path: /tmp
  nooh: true

Command line

reduce_add_hydrogens --config config_reduce_add_hydrogens.yml --input_path reduce.no.H.pdb --output_path ref_reduce.add.pdb

JSON

Common config file 

{
  "properties": {
    "nooh": true
  }
}

Docker config file 

{
  "properties": {
    "nooh": true,
    "container_path": "docker",
    "container_image": "afandiadib/ambertools:serial",
    "container_volume_path": "/tmp"
  }
}

Singularity config file 

{
  "properties": {
    "nooh": true,
    "container_path": "singularity",
    "container_image": "shub://bioexcel/ambertools_singularity",
    "container_volume_path": "/tmp"
  }
}

Command line

reduce_add_hydrogens --config config_reduce_add_hydrogens.json --input_path reduce.no.H.pdb --output_path ref_reduce.add.pdb

Reduce_remove_hydrogens

This class is a wrapper of the Ambertools reduce module for removing hydrogens from a given structure.

Get help

Command:

reduce_remove_hydrogens -h

usage: reduce_remove_hydrogens [-h] [--config CONFIG] --input_path INPUT_PATH --output_path OUTPUT_PATH

Removes hydrogen atoms to small molecules.

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

required arguments:
  --input_path INPUT_PATH
                        Path to the input file. Accepted formats: pdb.
  --output_path OUTPUT_PATH
                        Path to the output file. Accepted formats: pdb.

I / O Arguments

Syntax: input_argument (datatype) : Definition

Config input / output arguments for this building block:

input_path (string): Path to the input file. File type: input. Sample file. Accepted formats: PDB
output_path (string): Path to the output file. File type: output. Sample file. Accepted formats: PDB

Config

Syntax: input_parameter (datatype) - (default_value) Definition

Config parameters for this building block:

binary_path (string): (reduce) Path to the reduce executable binary..
remove_tmp (boolean): (True) Remove temporal files..
restart (boolean): (False) 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 

properties:
  remove_tmp: false

Docker config file 

properties:
  container_image: afandiadib/ambertools:serial
  container_path: docker
  container_volume_path: /tmp

Singularity config file 

properties:
  container_image: shub://bioexcel/ambertools_singularity
  container_path: singularity
  container_volume_path: /tmp

Command line

reduce_remove_hydrogens --config config_reduce_remove_hydrogens.yml --input_path reduce.H.pdb --output_path ref_reduce.remove.pdb

JSON

Common config file 

{
  "properties": {
    "remove_tmp": false
  }
}

Docker config file 

{
  "properties": {
    "container_path": "docker",
    "container_image": "afandiadib/ambertools:serial",
    "container_volume_path": "/tmp"
  }
}

Singularity config file 

{
  "properties": {
    "container_path": "singularity",
    "container_image": "shub://bioexcel/ambertools_singularity",
    "container_volume_path": "/tmp"
  }
}

Command line

reduce_remove_hydrogens --config config_reduce_remove_hydrogens.json --input_path reduce.H.pdb --output_path ref_reduce.remove.pdb

Acpype_params_gmx

This class is a wrapper of Acpype tool for generation of topologies for GROMACS.

Get help

Command:

acpype_params_gmx -h

usage: acpype_params_gmx [-h] [--config CONFIG] --input_path INPUT_PATH --output_path_gro OUTPUT_PATH_GRO --output_path_itp OUTPUT_PATH_ITP --output_path_top OUTPUT_PATH_TOP

Small molecule parameterization for GROMACS MD package.

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

required arguments:
  --input_path INPUT_PATH
                        Path to the input file. Accepted formats: pdb, mdl, mol2.
  --output_path_gro OUTPUT_PATH_GRO
                        Path to the GRO output file. Accepted formats: gro.
  --output_path_itp OUTPUT_PATH_ITP
                        Path to the ITP output file. Accepted formats: itp.
  --output_path_top OUTPUT_PATH_TOP
                        Path to the TOP output file. Accepted formats: top.

I / O Arguments

Syntax: input_argument (datatype) : Definition

Config input / output arguments for this building block:

input_path (string): Path to the input file. File type: input. Sample file. Accepted formats: PDB, MDL, MOL2
output_path_gro (string): Path to the GRO output file. File type: output. Sample file. Accepted formats: GRO
output_path_itp (string): Path to the ITP output file. File type: output. Sample file. Accepted formats: ITP
output_path_top (string): Path to the TOP output file. File type: output. Sample file. Accepted formats: TOP

Config

Syntax: input_parameter (datatype) - (default_value) Definition

Config parameters for this building block:

basename (string): (BBB) A basename for the project (folder and output files)..
charge (integer): (0) Net molecular charge, for gas default is 0. If None the charge is guessed by acpype..
binary_path (string): (acpype) Path to the acpype executable binary..
remove_tmp (boolean): (True) Remove temporal files..
restart (boolean): (False) Do not execute if output files exist..
container_path (string): (None) Container path definition..
container_image (string): (acpype/acpype:2022.7.21) 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 

properties:
  basename: BBB
  charge: 0

Docker config file 

properties:
  basename: BBB
  charge: 0
  container_image: acpype/acpype:2022.7.21
  container_path: docker
  container_volume_path: /tmp

Singularity config file 

properties:
  basename: BBB
  charge: 0
  container_image: shub://bioexcel/acpype_container
  container_path: singularity
  container_shell_path: /bin/sh
  container_volume_path: /tmp
  container_working_dir: /tmp

Command line

acpype_params_gmx --config config_acpype_params_gmx.yml --input_path acpype.params.mol2 --output_path_gro ref_acpype.gmx.gro --output_path_itp ref_acpype.gmx.itp --output_path_top ref_acpype.gmx.top

JSON

Common config file 

{
  "properties": {
    "basename": "BBB",
    "charge": 0
  }
}

Docker config file 

{
  "properties": {
    "basename": "BBB",
    "charge": 0,
    "container_path": "docker",
    "container_image": "acpype/acpype:2022.7.21",
    "container_volume_path": "/tmp"
  }
}

Singularity config file 

{
  "properties": {
    "basename": "BBB",
    "charge": 0,
    "container_path": "singularity",
    "container_image": "shub://bioexcel/acpype_container",
    "container_volume_path": "/tmp",
    "container_working_dir": "/tmp",
    "container_shell_path": "/bin/sh"
  }
}

Command line

acpype_params_gmx --config config_acpype_params_gmx.json --input_path acpype.params.mol2 --output_path_gro ref_acpype.gmx.gro --output_path_itp ref_acpype.gmx.itp --output_path_top ref_acpype.gmx.top

Babel_convert

This class is a wrapper of the Open Babel tool.

Get help

Command:

babel_convert -h

usage: babel_convert [-h] [--config CONFIG] --input_path INPUT_PATH --output_path OUTPUT_PATH

Small molecule format conversion.

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

required arguments:
  --input_path INPUT_PATH
                        Path to the input file. Accepted formats: dat, ent, fa, fasta, gro, inp, log, mcif, mdl, mmcif, mol, mol2, pdb, pdbqt, png, sdf, smi, smiles, txt, xml, xtc.
  --output_path OUTPUT_PATH
                        Path to the output file. Accepted formats: ent, fa, fasta, gro, inp, mcif, mdl, mmcif, mol, mol2, pdb, pdbqt, png, sdf, smi, smiles, txt.

I / O Arguments

Syntax: input_argument (datatype) : Definition

Config input / output arguments for this building block:

input_path (string): Path to the input file. File type: input. Sample file. Accepted formats: DAT, ENT, FA, FASTA, GRO, INP, LOG, MCIF, MDL, MMCIF, MOL, MOL2, PDB, PDBQT, PNG, SDF, SMI, SMILES, TXT, XML, XTC
output_path (string): Path to the output file. File type: output. Sample file. Accepted formats: ENT, FA, FASTA, GRO, INP, MCIF, MDL, MMCIF, MOL, MOL2, PDB, PDBQT, PNG, SDF, SMI, SMILES, TXT

Config

Syntax: input_parameter (datatype) - (default_value) Definition

Config parameters for this building block:

input_format (string): (None) Format of input file. If not provided, input_path extension will be taken. .
output_format (string): (None) Format of output file. If not provided, output_path extension will be taken. .
coordinates (integer): (None) Type of coordinates: 2D or 3D. .
ph (number): (7.4) Add hydrogens appropriate for pH..
flex (boolean): (False) Remove all but the largest contiguous fragment (strip salts)..
binary_path (string): (obabel) Path to the obabel executable binary..
remove_tmp (boolean): (True) Remove temporal files..
restart (boolean): (False) Do not execute if output files exist..
container_path (string): (None) Container path definition..
container_image (string): (informaticsmatters/obabel: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 config file 

properties:
  coordinates: 2
  input_format: smi
  output_format: mol2
  ph: 7.4

Docker config file 

properties:
  container_image: informaticsmatters/obabel:latest
  container_path: docker
  container_volume_path: /tmp
  coordinates: 2
  input_format: smi
  output_format: mol2
  ph: 7.4

Singularity config file 

properties:
  container_image: shub://bioexcel/obabel_singularity
  container_path: singularity
  container_volume_path: /tmp
  coordinates: 2
  input_format: smi
  output_format: mol2
  ph: 7.4

Command line

babel_convert --config config_babel_convert.yml --input_path babel.smi --output_path ref_babel.convert.mol2

JSON

Common config file 

{
  "properties": {
    "input_format": "smi",
    "output_format": "mol2",
    "coordinates": 2,
    "ph": 7.4
  }
}

Docker config file 

{
  "properties": {
    "input_format": "smi",
    "output_format": "mol2",
    "coordinates": 2,
    "ph": 7.4,
    "container_path": "docker",
    "container_image": "informaticsmatters/obabel:latest",
    "container_volume_path": "/tmp"
  }
}

Singularity config file 

{
  "properties": {
    "input_format": "smi",
    "output_format": "mol2",
    "coordinates": 2,
    "ph": 7.4,
    "container_path": "singularity",
    "container_image": "shub://bioexcel/obabel_singularity",
    "container_volume_path": "/tmp"
  }
}

Command line

babel_convert --config config_babel_convert.json --input_path babel.smi --output_path ref_babel.convert.mol2