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