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