BioBB MODEL Command Line Help

Generic usage:

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

Fix_altlocs

Fix alternate locations from residues.

Get help

Command:

fix_altlocs -h

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

Fix alternate locations from 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_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:

altlocs (array): (None) List of alternate locations to fix. Format: [”A339:A”, “A171:B”, “A768:A”]; where for each residue the format is as follows: “:”. If empty, no action will be executed..
modeller_key (string): (None) Modeller license key..
binary_path (string): (check_structure) Path to the check_structure executable binary..
remove_tmp (boolean): (True) Remove temporal files..
restart (boolean): (False) Do not execute if output files exist..

YAML

Common config file 

properties:
  altlocs:
  - A339:A
  - A171:B
  - A768:A

Command line

fix_altlocs --config config_fix_altlocs.yml --input_pdb_path 3ebp.pdb --output_pdb_path output_altloc.pdb

JSON

Common config file 

{
  "properties": {
    "altlocs": [
      "A339:A",
      "A171:B",
      "A768:A"
    ]
  }
}

Command line

fix_altlocs --config config_fix_altlocs.json --input_pdb_path 3ebp.pdb --output_pdb_path output_altloc.pdb

Fix_amides

Fix amide groups from residues.

Get help

Command:

fix_amides -h

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

Flip the clashing amide groups to avoid clashes.

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:

modeller_key (string): (None) Modeller license key..
binary_path (string): (check_structure) Path to the check_structure executable binary..
remove_tmp (boolean): (True) Remove temporal files..
restart (boolean): (False) Do not execute if output files exist..

YAML

Common config file 

properties:
  restart: false

Command line

fix_amides --config config_fix_amides.yml --input_pdb_path 5s2z.pdb --output_pdb_path output_amide_pdb_path.pdb

JSON

Common config file 

{
  "properties": {
    "restart": false
  }
}

Command line

fix_amides --config config_fix_amides.json --input_pdb_path 5s2z.pdb --output_pdb_path output_amide_pdb_path.pdb

Fix_chirality

Fix chirality errors of residues.

Get help

Command:

fix_chirality -h

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

Fix stereochemical errors in residues changing It's chirality.

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:

modeller_key (string): (None) Modeller license key..
binary_path (string): (check_structure) Path to the check_structure executable binary..
remove_tmp (boolean): (True) Remove temporal files..
restart (boolean): (False) Do not execute if output files exist..

YAML

Common config file 

properties:
  restart: false

Command line

fix_chirality --config config_fix_chirality.yml --input_pdb_path 5s2z.pdb --output_pdb_path output_amide_pdb_path.pdb

JSON

Common config file 

{
  "properties": {
    "restart": false
  }
}

Command line

fix_chirality --config config_fix_chirality.json --input_pdb_path 5s2z.pdb --output_pdb_path output_amide_pdb_path.pdb

Checking_log

Class to check the errors of a PDB structure.

Get help

Command:

checking_log -h

usage: checking_log [-h] [-c CONFIG] -i INPUT_PDB_PATH -o OUTPUT_LOG_PATH

Check the errors of a PDB structure and create a report log 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_PDB_PATH, --input_pdb_path INPUT_PDB_PATH
                        Input PDB file name
  -o OUTPUT_LOG_PATH, --output_log_path OUTPUT_LOG_PATH
                        Output log 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_log_path (string): Output report log file path. File type: output. Sample file. Accepted formats: LOG

Config

Syntax: input_parameter (datatype) - (default_value) Definition

Config parameters for this building block:

modeller_key (string): (None) Modeller license key..
binary_path (string): (check_structure) Path to the check_structure executable binary..
remove_tmp (boolean): (True) Remove temporal files..
restart (boolean): (False) Do not execute if output files exist..

YAML

Common config file 

properties:
  restart: false

Command line

checking_log --config config_checking_log.yml --input_pdb_path 2ki5.pdb --output_log_path checking.log

JSON

Common config file 

{
  "properties": {
    "restart": false
  }
}

Command line

checking_log --config config_checking_log.json --input_pdb_path 2ki5.pdb --output_log_path checking.log

Fix_backbone

Class to model the missing atoms in the backbone of a PDB structure.

Get help

Command:

fix_backbone -h

usage: fix_backbone [-h] [-c CONFIG] -i INPUT_PDB_PATH -f INPUT_FASTA_CANONICAL_SEQUENCE_PATH -o OUTPUT_PDB_PATH

Model the missing atoms in the backbone of a PDB structure.

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

required arguments:
  -i INPUT_PDB_PATH, --input_pdb_path INPUT_PDB_PATH
                        Input PDB file name
  -f INPUT_FASTA_CANONICAL_SEQUENCE_PATH, --input_fasta_canonical_sequence_path INPUT_FASTA_CANONICAL_SEQUENCE_PATH
                        Input FASTA 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
input_fasta_canonical_sequence_path (string): Input FASTA file path. File type: input. Sample file. Accepted formats: FASTA
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:

add_caps (boolean): (False) Add caps to terminal residues..
modeller_key (string): (None) Modeller license key..
binary_path (string): (check_structure) Path to the check_structure executable binary..
remove_tmp (boolean): (True) Remove temporal files..
restart (boolean): (False) Do not execute if output files exist..

YAML

Common config file 

properties:
  add_caps: false
  modeller_key: MODELIRANJE
  restart: false

Command line

fix_backbone --config config_fix_backbone.yml --input_pdb_path 2ki5.pdb --input_fasta_canonical_sequence_path 2ki5.fasta --output_pdb_path output_pdb_path.pdb

JSON

Common config file 

{
  "properties": {
    "restart": false,
    "add_caps": false,
    "modeller_key": "MODELIRANJE"
  }
}

Command line

fix_backbone --config config_fix_backbone.json --input_pdb_path 2ki5.pdb --input_fasta_canonical_sequence_path 2ki5.fasta --output_pdb_path output_pdb_path.pdb

Fix_pdb

Class to renumerate residues in a PDB structure according to a reference sequence from UniProt.

Get help

Command:

fix_pdb -h

/bin/sh: /Users/pau/mambaforge/envs/dev38/bin/fix_pdb: Permission denied

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:

forced_uniprot_references (string): (None) Set the UniProt accessions for sequences to be used as reference..
remove_tmp (boolean): (True) Remove temporal files..
restart (boolean): (False) Do not execute if output files exist..

YAML

Common config file 

properties:
  forced_uniprot_references:
  - P0DTC2
  - Q9BYF1
  restart: false

Command line

fix_pdb --config config_fix_pdb.yml --input_pdb_path 2ki5.pdb --output_pdb_path output_pdb_path.pdb

JSON

Common config file 

{
  "properties": {
    "restart": false,
    "forced_uniprot_references": [
      "P0DTC2",
      "Q9BYF1"
    ]
  }
}

Command line

fix_pdb --config config_fix_pdb.json --input_pdb_path 2ki5.pdb --output_pdb_path output_pdb_path.pdb

Fix_ssbonds

Fix SS bonds from residues.

Get help

Command:

fix_ssbonds -h

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

Fix SS bonds from 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_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:

modeller_key (string): (None) Modeller license key..
binary_path (string): (check_structure) Path to the check_structure executable binary..
remove_tmp (boolean): (True) Remove temporal files..
restart (boolean): (False) Do not execute if output files exist..

YAML

Common config file 

properties:
  restart: false

Command line

fix_ssbonds --config config_fix_ssbonds.yml --input_pdb_path 1aki.pdb --output_pdb_path output_ssbonds.pdb

JSON

Common config file 

{
  "properties": {
    "restart": false
  }
}

Command line

fix_ssbonds --config config_fix_ssbonds.json --input_pdb_path 1aki.pdb --output_pdb_path output_ssbonds.pdb

Mutate

Class to mutate one amino acid by another in a 3d structure.

Get help

Command:

mutate -h

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

Model the missing atoms in aminoacid side chains of a PDB.

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:

mutation_list (string): (None) Mutation list in the format “Chain:WT_AA_ThreeLeterCode Resnum MUT_AA_ThreeLeterCode” (no spaces between the elements) separated by commas. If no chain is provided as chain code all the chains in the pdb file will be mutated. ie: “A:ALA15CYS”.
use_modeller (boolean): (False) Use Modeller suite to optimize the side chains..
modeller_key (string): (None) Modeller license key..
binary_path (string): (check_structure) Path to the check_structure executable binary..
remove_tmp (boolean): (True) Remove temporal files..
restart (boolean): (False) Do not execute if output files exist..

YAML

Common config file 

properties:
  mutation_list: Leu49Ile, B:arg51Lys

Command line

mutate --config config_mutate.yml --input_pdb_path 2ki5.pdb --output_pdb_path output_mutated_pdb_path.pdb

JSON

Common config file 

{
  "properties": {
    "mutation_list": "Leu49Ile, B:arg51Lys"
  }
}

Command line

mutate --config config_mutate.json --input_pdb_path 2ki5.pdb --output_pdb_path output_mutated_pdb_path.pdb

Fix_side_chain

Class to model the missing atoms in amino acid side chains of a PDB.

Get help

Command:

fix_side_chain -h

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

Model the missing atoms in amino acid side chains of a PDB.

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:

use_modeller (boolean): (False) Use Modeller suite to rebuild the missing side chain atoms..
modeller_key (string): (None) Modeller license key..
binary_path (string): (check_structure) Path to the check_structure executable binary..
remove_tmp (boolean): (True) Remove temporal files..
restart (boolean): (False) Do not execute if output files exist..

YAML

Common config file 

properties:
  restart: false

Command line

fix_side_chain --config config_fix_side_chain.yml --input_pdb_path 2ki5.pdb --output_pdb_path output_pdb_path.pdb

JSON

Common config file 

{
  "properties": {
    "restart": false
  }
}

Command line

fix_side_chain --config config_fix_side_chain.json --input_pdb_path 2ki5.pdb --output_pdb_path output_pdb_path.pdb