godmd package

Submodules

godmd.godmd_prep module

Module containing the GOdMDPrep class and the command line interface.

class godmd.godmd_prep.GOdMDPrep(input_pdb_orig_path: str, input_pdb_target_path: str, output_aln_orig_path: str, output_aln_target_path: str, properties: dict | None = None, **kwargs)[source]

Bases: BiobbObject

biobb_godmd GOdMDPrep
Helper bb to prepare inputs for the GOdMD tool module.
Prepares input files for the GOdMD tool.
Parameters:

  • input_pdb_orig_path (str) – Input PDB file to be used as origin in the conformational transition. File type: input. Sample file. Accepted formats: pdb (edam:format_1476).

  • input_pdb_target_path (str) –

    Input PDB file to be used as target in the conformational transition. File type: input. Sample file. Accepted formats: pdb (edam:format_1476).

  • output_aln_orig_path (str) –

    Output GOdMD alignment file corresponding to the origin structure of the conformational transition. File type: output. Sample file. Accepted formats: aln (edam:format_2330), txt (edam:format_2330).

  • output_aln_target_path (str) –

    Output GOdMD alignment file corresponding to the target structure of the conformational transition. File type: output. Sample file. Accepted formats: aln (edam:format_2330), txt (edam:format_2330).

  • properties (dict - Python dictionary object containing the tool parameters, not input/output files) –

    • gapopen (float) - (12.0) Standard gap penalty: score taken away when a gap is created.

    • gapextend (float) - (2.0) Penalty added to the standard gap penalty for each base or residue in the gap.

    • datafile (str) - (“EPAM250”) Scoring matrix file used when comparing sequences.

    • binary_path (str) - (“water”) Binary path.

    • remove_tmp (bool) - (True) [WF property] Remove temporal files.

    • restart (bool) - (False) [WF property] Do not execute if output files exist.

Examples

This is a use example of how to use the building block from Python:

from biobb_godmd.godmd.godmd_prep import godmd_prep
prop = {
    'gapopen': 10.0,
    'gapextend': 2.0
}
godmd_prep( input_pdb_orig_path='/path/to/input_orig.pdb',
            input_pdb_target_path='/path/to/input_target.pdb',
            output_aln_orig_path='/path/to/orig.aln',
            output_aln_target_path='/path/to/target.aln',
            properties=prop)
Info:
check_data_params(out_log, out_err)[source]

Checks input/output paths correctness

extract_sequence(pdb)[source]

Parses a PDB file to retrieve the sequence of a certain chain.

launch()[source]

Launches the execution of the GOdMDPrep module.

retrieve_alignment(waterFile, resids1, resids2)[source]

Gets the FASTA sequence of two PDB structures and a list of their residues in Biopython residue format. Opens a file containing a local sequence alignment (Water program of EMBOSS package) between those two PDB structures. Returns the sequence identity and the pairs of residues of the alignment.

godmd.godmd_prep.godmd_prep(input_pdb_orig_path: str, input_pdb_target_path: str, output_aln_orig_path: str, output_aln_target_path: str, properties: dict | None = None, **kwargs) → int[source]

Create GOdMDPrep method

godmd.godmd_prep.main()[source]

godmd.godmd_run module

Module containing the GOdMDRun class and the command line interface.

class godmd.godmd_run.GOdMDRun(input_pdb_orig_path: str, input_pdb_target_path: str, input_aln_orig_path: str, input_aln_target_path: str, input_config_path: str, output_log_path: str, output_ene_path: str, output_trj_path: str, output_pdb_path: str, properties: dict | None = None, **kwargs)[source]

Bases: BiobbObject

biobb_godmd GOdMDRun
Wrapper of the GOdMD tool module.
Computes conformational transition trajectories for proteins using GOdMD tool.
Parameters:

  • input_pdb_orig_path (str) –

    Input PDB file to be used as origin in the conformational transition. File type: input. Sample file. Accepted formats: pdb (edam:format_1476).

  • input_pdb_target_path (str) –

    Input PDB file to be used as target in the conformational transition. File type: input. Sample file. Accepted formats: pdb (edam:format_1476).

  • input_aln_orig_path (str) –

    Input GOdMD alignment file corresponding to the origin structure of the conformational transition. File type: input. Sample file. Accepted formats: aln (edam:format_2330), txt (edam:format_2330).

  • input_aln_target_path (str) –

    Input GOdMD alignment file corresponding to the target structure of the conformational transition. File type: input. Sample file. Accepted formats: aln (edam:format_2330), txt (edam:format_2330).

  • input_config_path (str) (Optional) –

    Input GOdMD configuration file. File type: input. Sample file. Accepted formats: in (edam:format_2330), txt (edam:format_2330).

  • output_log_path (str) –

    Output log file. File type: output. Sample file. Accepted formats: log (edam:format_2330), out (edam:format_2330), txt (edam:format_2330), o (edam:format_2330).

  • output_ene_path (str) –

    Output energy file. File type: output. Sample file. Accepted formats: log (edam:format_2330), out (edam:format_2330), txt (edam:format_2330), o (edam:format_2330).

  • output_trj_path (str) –

    Output trajectory file. File type: output. Sample file. Accepted formats: trj (edam:format_3878), crd (edam:format_3878), mdcrd (edam:format_3878), x (edam:format_3878).

  • output_pdb_path (str) –

    Output structure file. File type: output. Sample file. Accepted formats: pdb (edam:format_1476).

  • properties (dict - Python dictionary object containing the tool parameters, not input/output files) –

    • godmdin (dict) - ({}) GOdMD options specification.

    • binary_path (str) - (“discrete”) Binary path.

    • remove_tmp (bool) - (True) [WF property] Remove temporal files.

    • restart (bool) - (False) [WF property] Do not execute if output files exist.

Examples

This is a use example of how to use the building block from Python:

from biobb_godmd.godmd.godmd_run import godmd_run
prop = {
    'remove_tmp': True
}
godmd_run(   input_pdb_orig_path='/path/to/pdb_orig.pdb',
             input_pdb_target_path='/path/to/pdb_target.pdb',
             input_aln_orig_path='/path/to/aln_orig.aln',
             input_aln_target_path='/path/to/aln_target.aln',
             output_log_path='/path/to/godmd_log.log',
             output_ene_path='/path/to/godmd_ene.txt',
             output_trj_path='/path/to/godmd_trj.mdcrd',
             output_pdb_path='/path/to/godmd_pdb.pdb',
             properties=prop)
Info:
check_data_params(out_log, out_err)[source]

Checks input/output paths correctness

create_godmdin(path: str | None = None) → str[source]

Creates a GOdMD configuration file (godmdin) using the properties file settings

launch()[source]

Launches the execution of the GOdMDRun module.

godmd.godmd_run.godmd_run(input_pdb_orig_path: str, input_pdb_target_path: str, input_aln_orig_path: str, input_aln_target_path: str, output_log_path: str, output_ene_path: str, output_trj_path: str, output_pdb_path: str, input_config_path: str | None = None, properties: dict | None = None, **kwargs) → int[source]

Create GOdMDRun method

godmd.godmd_run.main()[source]