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..
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..
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..
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..
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..
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..
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..
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..
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..
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..
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..
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..
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..
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..
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..
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