BioBB GODMD Command Line Help
Generic usage:
biobb_command [-h] --config CONFIG --input_file(s) <input_file(s)> --output_file <output_file>
Godmd_run
Wrapper of the GOdMD tool module.
Get help
Command:
godmd_run -h
usage: godmd_run [-h] [--config CONFIG] --input_pdb_orig_path INPUT_PDB_ORIG_PATH --input_pdb_target_path INPUT_PDB_TARGET_PATH --input_aln_orig_path INPUT_ALN_ORIG_PATH --input_aln_target_path INPUT_ALN_TARGET_PATH [--input_config_path INPUT_CONFIG_PATH] --output_log_path OUTPUT_LOG_PATH --output_ene_path OUTPUT_ENE_PATH --output_trj_path OUTPUT_TRJ_PATH --output_pdb_path OUTPUT_PDB_PATH
Computing conformational transition trajectories for proteins using GOdMD tool.
optional arguments:
-h, --help show this help message and exit
--config CONFIG Configuration file
required arguments:
--input_pdb_orig_path INPUT_PDB_ORIG_PATH
Input PDB file to be used as origin in the conformational transition. Accepted formats: pdb.
--input_pdb_target_path INPUT_PDB_TARGET_PATH
Input PDB file to be used as target in the conformational transition. Accepted formats: pdb.
--input_aln_orig_path INPUT_ALN_ORIG_PATH
Input GOdMD alignment file corresponding to the origin structure of the conformational transition. Accepted formats: aln, txt.
--input_aln_target_path INPUT_ALN_TARGET_PATH
Input GOdMD alignment file corresponding to the target structure of the conformational transition. Accepted formats: aln, txt.
--input_config_path INPUT_CONFIG_PATH
Input configuration file (GOdMD run options). Accepted formats: in, txt.
--output_log_path OUTPUT_LOG_PATH
Output log file. Accepted formats: log, out, txt.
--output_ene_path OUTPUT_ENE_PATH
Output energy file. Accepted formats: log, out, txt.
--output_trj_path OUTPUT_TRJ_PATH
Output trajectory file. Accepted formats: mdcrd.
--output_pdb_path OUTPUT_PDB_PATH
Output structure file. Accepted formats: pdb.
I / O Arguments
Syntax: input_argument (datatype) : Definition
Config input / output arguments for this building block:
input_pdb_orig_path (string): Input PDB file to be used as origin in the conformational transition. File type: input. Sample file. Accepted formats: PDB
input_pdb_target_path (string): Input PDB file to be used as target in the conformational transition. File type: input. Sample file. Accepted formats: PDB
input_aln_orig_path (string): Input GOdMD alignment file corresponding to the origin structure of the conformational transition. File type: input. Sample file. Accepted formats: ALN, TXT
input_aln_target_path (string): Input GOdMD alignment file corresponding to the target structure of the conformational transition. File type: input. Sample file. Accepted formats: ALN, TXT
input_config_path (string): Input GOdMD configuration file. File type: input. Sample file. Accepted formats: IN, TXT
output_log_path (string): Output log file. File type: output. Sample file. Accepted formats: LOG, OUT, TXT, O
output_ene_path (string): Output energy file. File type: output. Sample file. Accepted formats: LOG, OUT, TXT, O
output_trj_path (string): Output trajectory file. File type: output. Sample file. Accepted formats: TRJ, CRD, MDCRD, X
output_pdb_path (string): Output structure file. File type: output. Sample file. Accepted formats: PDB
Config
Syntax: input_parameter (datatype) - (default_value) Definition
Config parameters for this building block:
godmdin (object): ({}) GOdMD options specification..
binary_path (string): (discrete) Binary path..
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
godmd_run --config config_godmd_run.yml --input_pdb_orig_path 1ake_A.pdb --input_pdb_target_path 4ake_A.pdb --input_aln_orig_path 1ake_A.aln --input_aln_target_path 4ake_A.aln --input_config_path params.in --output_log_path godmd.log --output_ene_path godmd_ene.out --output_trj_path godmd_trj.mdcrd --output_pdb_path godmd_pdb.pdb
JSON
Common config file
{
"properties": {
"remove_tmp": true
}
}
Command line
godmd_run --config config_godmd_run.json --input_pdb_orig_path 1ake_A.pdb --input_pdb_target_path 4ake_A.pdb --input_aln_orig_path 1ake_A.aln --input_aln_target_path 4ake_A.aln --input_config_path params.in --output_log_path godmd.log --output_ene_path godmd_ene.out --output_trj_path godmd_trj.mdcrd --output_pdb_path godmd_pdb.pdb
Godmd_prep
Helper bb to prepare inputs for the GOdMD tool module.
Get help
Command:
godmd_prep -h
usage: godmd_prep [-h] [--config CONFIG] --input_pdb_orig_path INPUT_PDB_ORIG_PATH --input_pdb_target_path INPUT_PDB_TARGET_PATH --output_aln_orig_path OUTPUT_ALN_ORIG_PATH --output_aln_target_path OUTPUT_ALN_TARGET_PATH
Prepares input files for the GOdMD tool.
optional arguments:
-h, --help show this help message and exit
--config CONFIG Configuration file
required arguments:
--input_pdb_orig_path INPUT_PDB_ORIG_PATH
Input PDB file to be used as origin in the conformational transition. Accepted formats: pdb.
--input_pdb_target_path INPUT_PDB_TARGET_PATH
Input PDB file to be used as target in the conformational transition. Accepted formats: pdb.
--output_aln_orig_path OUTPUT_ALN_ORIG_PATH
Output GOdMD alignment file corresponding to the origin structure of the conformational transition. Accepted formats: aln, txt.
--output_aln_target_path OUTPUT_ALN_TARGET_PATH
Output GOdMD alignment file corresponding to the target structure of the conformational transition. Accepted formats: aln, txt.
I / O Arguments
Syntax: input_argument (datatype) : Definition
Config input / output arguments for this building block:
input_pdb_orig_path (string): Input PDB file to be used as origin in the conformational transition. File type: input. Sample file. Accepted formats: PDB
input_pdb_target_path (string): Input PDB file to be used as target in the conformational transition. File type: input. Sample file. Accepted formats: PDB
output_aln_orig_path (string): Output GOdMD alignment file corresponding to the origin structure of the conformational transition. File type: output. Sample file. Accepted formats: ALN, TXT
output_aln_target_path (string): Output GOdMD alignment file corresponding to the target structure of the conformational transition. File type: output. Sample file. Accepted formats: ALN, TXT
Config
Syntax: input_parameter (datatype) - (default_value) Definition
Config parameters for this building block:
gapopen (number): (12.0) Standard gap penalty: score taken away when a gap is created..
gapextend (number): (2.0) Penalty added to the standard gap penalty for each base or residue in the gap..
datafile (string): (EPAM250) Scoring matrix file used when comparing sequences..
binary_path (string): (water) Binary path..
remove_tmp (boolean): (True) Remove temporal files..
restart (boolean): (False) Do not execute if output files exist..
YAML
Common config file
properties:
gapextend: '2'
gapopen: '12.0'
Command line
godmd_prep --config config_godmd_prep.yml --input_pdb_orig_path 1ake_A.pdb --input_pdb_target_path 4ake_A.pdb --output_aln_orig_path 1ake_A.aln --output_aln_target_path 4ake_A.aln
JSON
Common config file
{
"properties": {
"gapopen": "12.0",
"gapextend": "2"
}
}
Command line
godmd_prep --config config_godmd_prep.json --input_pdb_orig_path 1ake_A.pdb --input_pdb_target_path 4ake_A.pdb --output_aln_orig_path 1ake_A.aln --output_aln_target_path 4ake_A.aln