BioBB STRUCTURE Command Line Help

Generic usage:

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

Cat_pdb

Class to concat two PDB structures in a single PDB file.

Get help

Command:

cat_pdb -h

usage: cat_pdb [-h] [-c CONFIG] -i1 INPUT_STRUCTURE1 -i2 INPUT_STRUCTURE2 -o OUTPUT_STRUCTURE_PATH

Concat two PDB structures in a single PDB file.

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

required arguments:
  -i1 INPUT_STRUCTURE1, --input_structure1 INPUT_STRUCTURE1
                        Input structure 1 file path. Accepted formats: pdb.
  -i2 INPUT_STRUCTURE2, --input_structure2 INPUT_STRUCTURE2
                        Input structure 2 file path. Accepted formats: pdb.
  -o OUTPUT_STRUCTURE_PATH, --output_structure_path OUTPUT_STRUCTURE_PATH
                        Output structure file path. Accepted formats: pdb.

I / O Arguments

Syntax: input_argument (datatype) : Definition

Config input / output arguments for this building block:

input_structure1 (string): Input structure 1 file path. File type: input. Sample file. Accepted formats: PDB, PDBQT
input_structure2 (string): Input structure 2 file path. File type: input. Sample file. Accepted formats: PDB, PDBQT
output_structure_path (string): Output protein file path. File type: output. Sample file. Accepted formats: PDB, PDBQT

Config

Syntax: input_parameter (datatype) - (default_value) Definition

Config parameters for this building block:

remove_tmp (boolean): (True) Remove temporal files..
restart (boolean): (False) Do not execute if output files exist..
sandbox_path (string): (./) Parent path to the sandbox directory..

YAML

Common config file 

properties:
  remove_tmp: true

Command line

cat_pdb --config config_cat_pdb.yml --input_structure1 cat_protein.pdb --input_structure2 cat_ligand.pdb --output_structure_path ref_cat_pdb.pdb

JSON

Common config file 

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

Command line

cat_pdb --config config_cat_pdb.json --input_structure1 cat_protein.pdb --input_structure2 cat_ligand.pdb --output_structure_path ref_cat_pdb.pdb

Extract_molecule

This class is a wrapper of the Structure Checking tool to extract a molecule from a 3D structure.

Get help

Command:

extract_molecule -h

usage: extract_molecule [-h] [-c CONFIG] -i INPUT_STRUCTURE_PATH -o OUTPUT_MOLECULE_PATH

Extract a molecule from a 3D structure.

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

required arguments:
  -i INPUT_STRUCTURE_PATH, --input_structure_path INPUT_STRUCTURE_PATH
                        Input structure file path. Accepted formats: pdb.
  -o OUTPUT_MOLECULE_PATH, --output_molecule_path OUTPUT_MOLECULE_PATH
                        Output heteroatom file path. Accepted formats: pdb.

I / O Arguments

Syntax: input_argument (datatype) : Definition

Config input / output arguments for this building block:

input_structure_path (string): Input structure file path. File type: input. Sample file. Accepted formats: PDB, PDBQT
output_molecule_path (string): Output molecule file path. File type: output. Sample file. Accepted formats: PDB, PDBQT

Config

Syntax: input_parameter (datatype) - (default_value) Definition

Config parameters for this building block:

molecule_type (string): (all) type of molecule to be extracted. If all, only waters and ligands will be removed from the original structure. .
chains (array): (None) if chains selected in molecule_type, specify them here, e.g: [”A”, “C”, “N”]..
binary_path (string): (check_structure) path to the check_structure application.
remove_tmp (boolean): (True) Remove temporal files..
restart (boolean): (False) Do not execute if output files exist..
sandbox_path (string): (./) Parent path to the sandbox directory..

YAML

Common config file 

properties:
  remove_tmp: true

Command line

extract_molecule --config config_extract_molecule.yml --input_structure_path extract_molecule.pdb --output_molecule_path ref_extract_molecule.pdb

JSON

Common config file 

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

Command line

extract_molecule --config config_extract_molecule.json --input_structure_path extract_molecule.pdb --output_molecule_path ref_extract_molecule.pdb

Extract_atoms

Class to extract atoms from a 3D structure.

Get help

Command:

extract_atoms -h

usage: extract_atoms [-h] [-c CONFIG] -i INPUT_STRUCTURE_PATH -o OUTPUT_STRUCTURE_PATH

Remove the selected ligand atoms from a 3D structure.

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

required arguments:
  -i INPUT_STRUCTURE_PATH, --input_structure_path INPUT_STRUCTURE_PATH
                        Input structure file name
  -o OUTPUT_STRUCTURE_PATH, --output_structure_path OUTPUT_STRUCTURE_PATH
                        Output structure file name

I / O Arguments

Syntax: input_argument (datatype) : Definition

Config input / output arguments for this building block:

input_structure_path (string): Input structure file path. File type: input. Sample file. Accepted formats: PDB, GRO
output_structure_path (string): Output structure file path. File type: output. Sample file. Accepted formats: PDB, GRO

Config

Syntax: input_parameter (datatype) - (default_value) Definition

Config parameters for this building block:

regular_expression_pattern (string): (^D) Python style regular expression matching the selected atom names..
remove_tmp (boolean): (True) Remove temporal files..
restart (boolean): (False) Do not execute if output files exist..
sandbox_path (string): (./) Parent path to the sandbox directory..

YAML

Common config file 

properties:
  regular_expression_pattern: OE2

Command line

extract_atoms --config config_extract_atoms.yml --input_structure_path 2vgb.pdb --output_structure_path OE2_atoms.pdb

JSON

Common config file 

{
  "properties": {
    "regular_expression_pattern": "OE2"
  }
}

Command line

extract_atoms --config config_extract_atoms.json --input_structure_path 2vgb.pdb --output_structure_path OE2_atoms.pdb

Str_check_add_hydrogens

This class is a wrapper of the Structure Checking tool to add hydrogens to a 3D structure.

Get help

Command:

str_check_add_hydrogens -h

usage: str_check_add_hydrogens [-h] [-c CONFIG] -i INPUT_STRUCTURE_PATH -o OUTPUT_STRUCTURE_PATH

Class to add hydrogens to a 3D structure.

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

required arguments:
  -i INPUT_STRUCTURE_PATH, --input_structure_path INPUT_STRUCTURE_PATH
                        Input structure file path. Accepted formats: pdb.
  -o OUTPUT_STRUCTURE_PATH, --output_structure_path OUTPUT_STRUCTURE_PATH
                        Output structure file path. Accepted formats: pdb, pdbqt.

I / O Arguments

Syntax: input_argument (datatype) : Definition

Config input / output arguments for this building block:

input_structure_path (string): Input structure file path. File type: input. Sample file. Accepted formats: PDB
output_structure_path (string): Output structure file path. File type: output. Sample file. Accepted formats: PDB, PDBQT

Config

Syntax: input_parameter (datatype) - (default_value) Definition

Config parameters for this building block:

charges (boolean): (False) Whether or not to add charges to the output file. If True the output is in PDBQT format..
mode (string): (auto) Selection mode. .
ph (number): (7.4) Add hydrogens appropriate for pH. Only in case mode ph selected..
list (string): () List of residues to modify separated by commas (i.e HISA234HID,HISB33HIE). Only in case mode list selected..
keep_canonical_resnames (boolean): (False) Whether or not keep canonical residue names.
binary_path (string): (check_structure) path to the check_structure application.
remove_tmp (boolean): (True) Remove temporal files..
restart (boolean): (False) Do not execute if output files exist..
sandbox_path (string): (./) Parent path to the sandbox directory..

YAML

Common config file 

properties:
  charges: true
  keep_canonical_resnames: true
  mode: auto

Command line

str_check_add_hydrogens --config config_str_check_add_hydrogens.yml --input_structure_path str_no_H.pdb --output_structure_path ref_str_H.pdbqt

JSON

Common config file 

{
  "properties": {
    "mode": "auto",
    "charges": true,
    "keep_canonical_resnames": true
  }
}

Command line

str_check_add_hydrogens --config config_str_check_add_hydrogens.json --input_structure_path str_no_H.pdb --output_structure_path ref_str_H.pdbqt

Sort_gro_residues

Class to sort the selected residues from a GRO 3D structure.

Get help

Command:

sort_gro_residues -h

usage: sort_gro_residues [-h] [-c CONFIG] -i INPUT_GRO_PATH -o OUTPUT_GRO_PATH

Renumber atoms and residues from a 3D structure.

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

required arguments:
  -i INPUT_GRO_PATH, --input_gro_path INPUT_GRO_PATH
                        Input GRO file name
  -o OUTPUT_GRO_PATH, --output_gro_path OUTPUT_GRO_PATH
                        Output sorted GRO file name

I / O Arguments

Syntax: input_argument (datatype) : Definition

Config input / output arguments for this building block:

input_gro_path (string): Input GRO file path. File type: input. Sample file. Accepted formats: GRO
output_gro_path (string): Output sorted GRO file path. File type: output. Sample file. Accepted formats: GRO

Config

Syntax: input_parameter (datatype) - (default_value) Definition

Config parameters for this building block:

residue_name_list (array): ([NA, CL, SOL]) Ordered residue name list..
remove_tmp (boolean): (True) Remove temporal files..
restart (boolean): (False) Do not execute if output files exist..
sandbox_path (string): (./) Parent path to the sandbox directory..

YAML

Common config file 

properties:
  residue_name_list:
  - NA
  - CL
  - SOL

Command line

sort_gro_residues --config config_sort_gro_residues.yml --input_gro_path WT_aq4_md_1.gro --output_gro_path WT_aq4_md_sorted.gro

JSON

Common config file 

{
  "properties": {
    "residue_name_list": [
      "NA",
      "CL",
      "SOL"
    ]
  }
}

Command line

sort_gro_residues --config config_sort_gro_residues.json --input_gro_path WT_aq4_md_1.gro --output_gro_path WT_aq4_md_sorted.gro

Extract_chain

This class is a wrapper of the Structure Checking tool to extract a chain from a 3D structure.

Get help

Command:

extract_chain -h

usage: extract_chain [-h] [-c CONFIG] -i INPUT_STRUCTURE_PATH -o OUTPUT_STRUCTURE_PATH

Extract a chain from a 3D structure.

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

required arguments:
  -i INPUT_STRUCTURE_PATH, --input_structure_path INPUT_STRUCTURE_PATH
                        Input structure file path. Accepted formats: pdb.
  -o OUTPUT_STRUCTURE_PATH, --output_structure_path OUTPUT_STRUCTURE_PATH
                        Output structure file path. Accepted formats: pdb.

I / O Arguments

Syntax: input_argument (datatype) : Definition

Config input / output arguments for this building block:

input_structure_path (string): Input structure file path. File type: input. Sample file. Accepted formats: PDB, PDBQT
output_structure_path (string): Output structure file path. File type: output. Sample file. Accepted formats: PDB, PDBQT

Config

Syntax: input_parameter (datatype) - (default_value) Definition

Config parameters for this building block:

chains (array): (None) List of chains to be extracted from the input_structure_path file. If empty, all the chains of the structure will be returned..
permissive (boolean): (False) Use non standard PDB files..
binary_path (string): (check_structure) path to the check_structure application.
remove_tmp (boolean): (True) Remove temporal files..
restart (boolean): (False) Do not execute if output files exist..
sandbox_path (string): (./) Parent path to the sandbox directory..

YAML

Common config file 

properties:
  chains:
  - B
  - C
  permissive: true

Command line

extract_chain --config config_extract_chain.yml --input_structure_path extract_chain.pdb --output_structure_path ref_extract_chain.pdb

JSON

Common config file 

{
  "properties": {
    "permissive": true,
    "chains": [
      "B",
      "C"
    ]
  }
}

Command line

extract_chain --config config_extract_chain.json --input_structure_path extract_chain.pdb --output_structure_path ref_extract_chain.pdb

Remove_molecules

Class to remove molecules from a 3D structure using Biopython.

Get help

Command:

remove_molecules -h

usage: remove_molecules [-h] [-c CONFIG] -i INPUT_STRUCTURE_PATH -o OUTPUT_MOLECULES_PATH

Removes a list of molecules from a 3D structure.

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

required arguments:
  -i INPUT_STRUCTURE_PATH, --input_structure_path INPUT_STRUCTURE_PATH
                        Input structure file path. Accepted formats: pdb.
  -o OUTPUT_MOLECULES_PATH, --output_molecules_path OUTPUT_MOLECULES_PATH
                        Output molecules file path. Accepted formats: pdb.

I / O Arguments

Syntax: input_argument (datatype) : Definition

Config input / output arguments for this building block:

input_structure_path (string): Input structure file path. File type: input. Sample file. Accepted formats: PDB, PDBQT
output_molecules_path (string): Output molcules file path. File type: output. Sample file. Accepted formats: PDB, PDBQT

Config

Syntax: input_parameter (datatype) - (default_value) Definition

Config parameters for this building block:

molecules (array): (None) List of comma separated res_id (will remove all molecules that match the res_id) or list of dictionaries with the name | res_id | chain | model of the molecules to be removed. Format: [{”name”: “HIS”, “res_id”: “72”, “chain”: “A”, “model”: “1”}]..
remove_tmp (boolean): (True) Remove temporal files..
restart (boolean): (False) Do not execute if output files exist..
sandbox_path (string): (./) Parent path to the sandbox directory..

YAML

Common config file 

properties:
  molecules:
  - model: '1'
    name: HIS
  - 61

Command line

remove_molecules --config config_remove_molecules.yml --input_structure_path 2vgb.pdb --output_molecules_path ref_remove_molecules.pdb

JSON

Common config file 

{
  "properties": {
    "molecules": [
      {
        "name": "HIS",
        "model": "1"
      },
      61
    ]
  }
}

Command line

remove_molecules --config config_remove_molecules.json --input_structure_path 2vgb.pdb --output_molecules_path ref_remove_molecules.pdb

Structure_check

This class is a wrapper of the Structure Checking tool to generate summary checking results on a json file.

Get help

Command:

structure_check -h

usage: structure_check [-h] [-c CONFIG] -i INPUT_STRUCTURE_PATH -o OUTPUT_SUMMARY_PATH

This class is a wrapper of the Structure Checking tool to generate summary checking results on a json file.

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

required arguments:
  -i INPUT_STRUCTURE_PATH, --input_structure_path INPUT_STRUCTURE_PATH
                        Input structure file path. Accepted formats: pdb.
  -o OUTPUT_SUMMARY_PATH, --output_summary_path OUTPUT_SUMMARY_PATH
                        Output summary checking results. Accepted formats: json.

I / O Arguments

Syntax: input_argument (datatype) : Definition

Config input / output arguments for this building block:

input_structure_path (string): Input structure file path. File type: input. Sample file. Accepted formats: PDB, PDBQT
output_summary_path (string): Output summary checking results. File type: output. Sample file. Accepted formats: JSON

Config

Syntax: input_parameter (datatype) - (default_value) Definition

Config parameters for this building block:

features (array): (None) Features to summarize. If None, all the features will be computed. .
binary_path (string): (check_structure) path to the check_structure application.
remove_tmp (boolean): (True) Remove temporal files..
restart (boolean): (False) Do not execute if output files exist..
sandbox_path (string): (./) Parent path to the sandbox directory..

YAML

Common config file 

properties:
  features:
  - chains
  - models

Command line

structure_check --config config_structure_check.yml --input_structure_path 2vgb.pdb --output_summary_path summary.json

JSON

Common config file 

{
  "properties": {
    "features": [
      "chains",
      "models"
    ]
  }
}

Command line

structure_check --config config_structure_check.json --input_structure_path 2vgb.pdb --output_summary_path summary.json

Extract_residues

Class to extract residues from a 3D structure using Biopython.

Get help

Command:

extract_residues -h

usage: extract_residues [-h] [-c CONFIG] -i INPUT_STRUCTURE_PATH -o OUTPUT_RESIDUES_PATH

Extract a list of residues from a 3D structure.

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

required arguments:
  -i INPUT_STRUCTURE_PATH, --input_structure_path INPUT_STRUCTURE_PATH
                        Input structure file path. Accepted formats: pdb.
  -o OUTPUT_RESIDUES_PATH, --output_residues_path OUTPUT_RESIDUES_PATH
                        Output residues file path. Accepted formats: pdb.

I / O Arguments

Syntax: input_argument (datatype) : Definition

Config input / output arguments for this building block:

input_structure_path (string): Input structure file path. File type: input. Sample file. Accepted formats: PDB, PDBQT
output_residues_path (string): Output residues file path. File type: output. Sample file. Accepted formats: PDB, PDBQT

Config

Syntax: input_parameter (datatype) - (default_value) Definition

Config parameters for this building block:

residues (array): (None) List of comma separated res_id (will extract all residues that match the res_id) or list of dictionaries with the name | res_id | chain | model of the residues to be extracted. Format: [{”name”: “HIS”, “res_id”: “72”, “chain”: “A”, “model”: “1”}]..
remove_tmp (boolean): (True) Remove temporal files..
restart (boolean): (False) Do not execute if output files exist..
sandbox_path (string): (./) Parent path to the sandbox directory..

YAML

Common config file 

properties:
  residues:
  - model: '1'
    name: HIS
  - 61

Command line

extract_residues --config config_extract_residues.yml --input_structure_path extract_heteroatom.pdb --output_residues_path ref_extract_residues.pdb

JSON

Common config file 

{
  "properties": {
    "residues": [
      {
        "name": "HIS",
        "model": "1"
      },
      61
    ]
  }
}

Command line

extract_residues --config config_extract_residues.json --input_structure_path extract_heteroatom.pdb --output_residues_path ref_extract_residues.pdb

Remove_ligand

Class to remove the selected ligand atoms from a 3D structure.

Get help

Command:

remove_ligand -h

usage: remove_ligand [-h] [-c CONFIG] -i INPUT_STRUCTURE_PATH -o OUTPUT_STRUCTURE_PATH

Remove the selected ligand atoms from a 3D structure.

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

required arguments:
  -i INPUT_STRUCTURE_PATH, --input_structure_path INPUT_STRUCTURE_PATH
                        Input structure file name
  -o OUTPUT_STRUCTURE_PATH, --output_structure_path OUTPUT_STRUCTURE_PATH
                        Output structure file name

I / O Arguments

Syntax: input_argument (datatype) : Definition

Config input / output arguments for this building block:

input_structure_path (string): Input structure file path. File type: input. Sample file. Accepted formats: PDB, GRO
output_structure_path (string): Output structure file path. File type: output. Sample file. Accepted formats: PDB, GRO

Config

Syntax: input_parameter (datatype) - (default_value) Definition

Config parameters for this building block:

ligand (string): (AQ4) Residue code of the ligand to be removed..
remove_tmp (boolean): (True) Remove temporal files..
restart (boolean): (False) Do not execute if output files exist..
sandbox_path (string): (./) Parent path to the sandbox directory..

YAML

Common config file 

properties:
  ligand: AQ4

Command line

remove_ligand --config config_remove_ligand.yml --input_structure_path WT_aq4_md_1.pdb --output_structure_path WT_apo_md_1.pdb

JSON

Common config file 

{
  "properties": {
    "ligand": "AQ4"
  }
}

Command line

remove_ligand --config config_remove_ligand.json --input_structure_path WT_aq4_md_1.pdb --output_structure_path WT_apo_md_1.pdb

Renumber_structure

Class to renumber atomic indexes from a 3D structure.

Get help

Command:

renumber_structure -h

usage: renumber_structure [-h] [-c CONFIG] -i INPUT_STRUCTURE_PATH -o OUTPUT_STRUCTURE_PATH -j OUTPUT_MAPPING_JSON_PATH

Renumber atoms and residues from a 3D structure.

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

required arguments:
  -i INPUT_STRUCTURE_PATH, --input_structure_path INPUT_STRUCTURE_PATH
                        Input structure file name
  -o OUTPUT_STRUCTURE_PATH, --output_structure_path OUTPUT_STRUCTURE_PATH
                        Output structure file name
  -j OUTPUT_MAPPING_JSON_PATH, --output_mapping_json_path OUTPUT_MAPPING_JSON_PATH
                        Output mapping json file name

I / O Arguments

Syntax: input_argument (datatype) : Definition

Config input / output arguments for this building block:

input_structure_path (string): Input structure file path. File type: input. Sample file. Accepted formats: PDB, GRO
output_structure_path (string): Output structure file path. File type: output. Sample file. Accepted formats: PDB, GRO
output_mapping_json_path (string): Output mapping json file path. File type: output. Sample file. Accepted formats: JSON

Config

Syntax: input_parameter (datatype) - (default_value) Definition

Config parameters for this building block:

renumber_residues (boolean): (True) Residue code of the ligand to be removed..
renumber_residues_per_chain (boolean): (True) Restart residue enumeration every time a new chain is detected..
remove_tmp (boolean): (True) Remove temporal files..
restart (boolean): (False) Do not execute if output files exist..
sandbox_path (string): (./) Parent path to the sandbox directory..

YAML

Common config file 

properties:
  renumber_residues: true

Command line

renumber_structure --config config_renumber_structure.yml --input_structure_path cl3.noH.pdb --output_structure_path renum_cl3_noH.pdb --output_mapping_json_path cl3_output_mapping_json_path.json

JSON

Common config file 

{
  "properties": {
    "renumber_residues": true
  }
}

Command line

renumber_structure --config config_renumber_structure.json --input_structure_path cl3.noH.pdb --output_structure_path renum_cl3_noH.pdb --output_mapping_json_path cl3_output_mapping_json_path.json

Remove_pdb_water

This class is a wrapper of the Structure Checking tool to remove water molecules from PDB 3D structures.

Get help

Command:

remove_pdb_water -h

usage: remove_pdb_water [-h] [-c CONFIG] -i INPUT_PDB_PATH -o OUTPUT_PDB_PATH

Remove the water molecules from a PDB 3D structure.

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

required arguments:
  -i INPUT_PDB_PATH, --input_pdb_path INPUT_PDB_PATH
                        Input pdb file name
  -o OUTPUT_PDB_PATH, --output_pdb_path OUTPUT_PDB_PATH
                        Output pdb file name

I / O Arguments

Syntax: input_argument (datatype) : Definition

Config input / output arguments for this building block:

input_pdb_path (string): Input PDB file path. File type: input. Sample file. Accepted formats: PDB
output_pdb_path (string): Output PDB file path. File type: output. Sample file. Accepted formats: PDB

Config

Syntax: input_parameter (datatype) - (default_value) Definition

Config parameters for this building block:

binary_path (string): (check_structure) path to the check_structure application.
remove_tmp (boolean): (True) Remove temporal files..
restart (boolean): (False) Do not execute if output files exist..
sandbox_path (string): (./) Parent path to the sandbox directory..

YAML

Common config file 

properties:
  remove_tmp: true

Command line

remove_pdb_water --config config_remove_pdb_water.yml --input_pdb_path WT_aq4_md_WAT.pdb --output_pdb_path WT_apo_no_wat.pdb

JSON

Common config file 

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

Command line

remove_pdb_water --config config_remove_pdb_water.json --input_pdb_path WT_aq4_md_WAT.pdb --output_pdb_path WT_apo_no_wat.pdb

Extract_heteroatoms

Class to extract hetero-atoms from a 3D structure using Biopython.

Get help

Command:

extract_heteroatoms -h

usage: extract_heteroatoms [-h] [-c CONFIG] -i INPUT_STRUCTURE_PATH -o OUTPUT_HETEROATOM_PATH

Extract a list of heteroatoms from a 3D structure.

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

required arguments:
  -i INPUT_STRUCTURE_PATH, --input_structure_path INPUT_STRUCTURE_PATH
                        Input structure file path. Accepted formats: pdb.
  -o OUTPUT_HETEROATOM_PATH, --output_heteroatom_path OUTPUT_HETEROATOM_PATH
                        Output heteroatom file path. Accepted formats: pdb.

I / O Arguments

Syntax: input_argument (datatype) : Definition

Config input / output arguments for this building block:

input_structure_path (string): Input structure file path. File type: input. Sample file. Accepted formats: PDB, PDBQT
output_heteroatom_path (string): Output heteroatom file path. File type: output. Sample file. Accepted formats: PDB, PDBQT

Config

Syntax: input_parameter (datatype) - (default_value) Definition

Config parameters for this building block:

heteroatoms (array): (None) List of dictionaries with the name | res_id | chain | model of the heteroatoms to be extracted. Format: [{”name”: “ZZ7”, “res_id”: “302”, “chain”: “B”, “model”: “1”}]. If empty, all the heteroatoms of the structure will be returned..
water (boolean): (False) Add or not waters..
remove_tmp (boolean): (True) Remove temporal files..
restart (boolean): (False) Do not execute if output files exist..
sandbox_path (string): (./) Parent path to the sandbox directory..

YAML

Common config file 

properties:
  heteroatoms:
  - model: '1'
    name: TA1
  - name: ADP

Command line

extract_heteroatoms --config config_extract_heteroatoms.yml --input_structure_path extract_heteroatom.pdb --output_heteroatom_path ref_extract_heteroatom.pdb

JSON

Common config file 

{
  "properties": {
    "heteroatoms": [
      {
        "name": "TA1",
        "model": "1"
      },
      {
        "name": "ADP"
      }
    ]
  }
}

Command line

extract_heteroatoms --config config_extract_heteroatoms.json --input_structure_path extract_heteroatom.pdb --output_heteroatom_path ref_extract_heteroatom.pdb

Closest_residues

Class to search closest residues from a 3D structure using Biopython.

Get help

Command:

closest_residues -h

usage: closest_residues [-h] [-c CONFIG] -i INPUT_STRUCTURE_PATH -o OUTPUT_RESIDUES_PATH

Search closest residues to a list of given residues.

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

required arguments:
  -i INPUT_STRUCTURE_PATH, --input_structure_path INPUT_STRUCTURE_PATH
                        Input structure file path. Accepted formats: pdb.
  -o OUTPUT_RESIDUES_PATH, --output_residues_path OUTPUT_RESIDUES_PATH
                        Output residues file path. Accepted formats: pdb.

I / O Arguments

Syntax: input_argument (datatype) : Definition

Config input / output arguments for this building block:

input_structure_path (string): Input structure file path. File type: input. Sample file. Accepted formats: PDB, PDBQT
output_residues_path (string): Output molcules file path. File type: output. Sample file. Accepted formats: PDB, PDBQT

Config

Syntax: input_parameter (datatype) - (default_value) Definition

Config parameters for this building block:

residues (array): (None) List of comma separated res_id or list of dictionaries with the name | res_id | chain | model of the residues to find the closest neighbours. Format: [{”name”: “HIS”, “res_id”: “72”, “chain”: “A”, “model”: “1”}]..
radius (number): (5.0) Distance in Ångströms to neighbours of the given list of residues..
preserve_target (boolean): (True) Whether or not to preserve the target residues in the output structure..
remove_tmp (boolean): (True) Remove temporal files..
restart (boolean): (False) Do not execute if output files exist..
sandbox_path (string): (./) Parent path to the sandbox directory..

YAML

Common config file 

properties:
  radius: 5
  residues:
  - model: '1'
    name: HIS
  - 580
  - 61

Command line

closest_residues --config config_closest_residues.yml --input_structure_path 2vgb.pdb --output_residues_path ref_closest_residues.pdb

JSON

Common config file 

{
  "properties": {
    "residues": [
      {
        "name": "HIS",
        "model": "1"
      },
      580,
      61
    ],
    "radius": 5
  }
}

Command line

closest_residues --config config_closest_residues.json --input_structure_path 2vgb.pdb --output_residues_path ref_closest_residues.pdb

Extract_model

This class is a wrapper of the Structure Checking tool to extract a model from a 3D structure.

Get help

Command:

extract_model -h

usage: extract_model [-h] [-c CONFIG] -i INPUT_STRUCTURE_PATH -o OUTPUT_STRUCTURE_PATH

Extract a model from a 3D structure.

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

required arguments:
  -i INPUT_STRUCTURE_PATH, --input_structure_path INPUT_STRUCTURE_PATH
                        Input structure file path. Accepted formats: pdb.
  -o OUTPUT_STRUCTURE_PATH, --output_structure_path OUTPUT_STRUCTURE_PATH
                        Output structure file path. Accepted formats: pdb.

I / O Arguments

Syntax: input_argument (datatype) : Definition

Config input / output arguments for this building block:

input_structure_path (string): Input structure file path. File type: input. Sample file. Accepted formats: PDB, PDBQT
output_structure_path (string): Output structure file path. File type: output. Sample file. Accepted formats: PDB, PDBQT

Config

Syntax: input_parameter (datatype) - (default_value) Definition

Config parameters for this building block:

models (array): (None) List of models to be extracted from the input_structure_path file. If empty, all the models of the structure will be returned..
binary_path (string): (check_structure) path to the check_structure application.
remove_tmp (boolean): (True) Remove temporal files..
restart (boolean): (False) Do not execute if output files exist..
sandbox_path (string): (./) Parent path to the sandbox directory..

YAML

Common config file 

properties:
  models:
  - 1
  - 4

Command line

extract_model --config config_extract_model.yml --input_structure_path extract_model.pdb --output_structure_path ref_extract_model.pdb

JSON

Common config file 

{
  "properties": {
    "models": [
      1,
      4
    ]
  }
}

Command line

extract_model --config config_extract_model.json --input_structure_path extract_model.pdb --output_structure_path ref_extract_model.pdb