BioBB MODEL Command Line Help

Generic usage:

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

Fix_amides

Fix amide groups from residues.

Get help

Command:

fix_amides -h
/bin/sh: fix_amides: command not found

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:

  • 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
/bin/sh: fix_chirality: command not found

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:

  • 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
/bin/sh: checking_log: command not found

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:

  • 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
/bin/sh: fix_backbone: command not found

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..
  • remove_tmp (boolean): (True) Remove temporal files..
  • restart (boolean): (False) Do not execute if output files exist..

YAML

Common config file

properties:
  add_caps: true
  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": true
  }
}

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

Mutate

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

Get help

Command:

mutate -h
/bin/sh: mutate: command not found

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): (A:Val2Ala) 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..
  • 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
/bin/sh: fix_side_chain: command not found

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..
  • 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