API Documentation

This python wrap-up of the GOMoDO webserver

class Modeling.Modeller(**kwargs)

Hommology Modeling with Modeller (https://salilab.org/modeller/).

CreateHMMProfile(**kwargs)

Creates HMM profiles with hhblits (https://github.com/soedinglab/hh-suite).

Parameters:

  • uniprot – optional (str): Uniprot ID (required if sequence not given)

  • filename – optional (str): filename or path+filename (default: “sequence.seq”)

  • sequence – optional (str): sequence of in FASTA format (required if UniprotID not given)

  • ncpus – optional (int): number of cpus (default: 1)

  • rounds – optional (int): number of HHBLITS runs (default: 1)

  • databse – optional (str): dir path of the uniref30 database

MakeModels(**kwargs)

Runs Modeller

Parameters:

  • templates – list of templates

  • nmodels – (int) number of models

  • loop – (boolean) loop refinement (default False)

  • nloop – (int) number of loop models computed (Default 2)

  • ncpus – (int) number of cpus (default 1)

Qmeanbrane(**kwargs)

Submits a job to the Qmean web-service (https://swissmodel.expasy.org/qmean)

Parameters:

  • models – required (list) list of models

  • email – required (str) An email adress is required by the swissmodel webserver.

Note

The e-mail provided is not stored, used or shared with third-parties excepting with swissmodel.org. For details regarding how Sisswmodel uses personal data please visit the Swissmodel website: https://swissmodel.expasy.org

SearchTemplates(**kwargs)

Searches for homologous templates with hhblits (https://github.com/soedinglab/hh-suite). :parameter hmmprofile: optional (str): user profile path+filename (.a3m file) :parameter ncpus: optional (int): number of cpus (default: 1) :parameter rounds: optional (int): number of HHBLITS runs (default: 1) :parameter database optional (str): dir path of the HHblists database

ViewModels(**kwargs)

3D visualization of the models with py3Dmol.

This python wrap-up of the GOMoDO webserver

class Docking.RDOCK(**kwargs)

Molecular docking with rDock (http://rdock.sourceforge.net/).

AnalyseInteractions()

Protein-Ligand interaction analysis with ProLIF (https://prolif.readthedocs.io/en/latest/index.html).

Cavity(**kwargs)

rbcavity – Cavity mapping and preparation of docking site

Parameters:

  • mol (recerence) – Required (kwargs str): reference molecule path

  • REF_MOL – Optional

  • SITE_MAPPER – Optional (str): default ‘RbtLigandSiteMapper’

  • RADIUS – Optional (int): default ‘6.0’

  • SMALL_SPHERE – Optional (int): default ‘1.0’

  • MIN_VOLUME – Optional (int): default ‘100’

  • MAX_CAVITIES – Optional (int): default ‘1’

  • VOL_INCR – Optional (int): default ‘0.0’

  • GRIDSTEP – Optional (int): default ‘0.5’

  • SCORING_FUNCTION – Optional (str): default ‘RbtCavityGridSF’

  • WEIGHT – Optional (int): default ‘1.0’

Note

For a detailed description of the parameters please see rDock documentation http://rdock.sourceforge.net/.

Run(tethered=False, smina_minimize=False, smina_score_only=False, **kwargs)

rbdock – the rDock docking engine itself.

Parameters:

  • target_mol – Required (list or str): path of target molecule

  • nruns – Optional (int): number of docking poses (default 10)

  • output_name – Optional (str): name of the docking files (default ‘docking_poses’)

  • tethered – (False) If true it will run the tethered docking

  • smina_minimize – (False) If true the docking solutions will be minimized with smina (https://sourceforge.net/projects/smina/)

  • smina_score_only – (False) If true the docking solutions will be rescored with smina (https://sourceforge.net/projects/smina/)

Parameters tethered_parameters:

{‘TRANS_MODE’:’TETHERED’, ‘ROT_MODE:’TETHERED’, ‘DIHEDRAL_MODE=’FREE ‘, ‘MAX_TRANS’:1.0 ‘MAX_ROT’:30.0}

Note

For a detailed description of the tethered parameters please see rDock documentation http://rdock.sourceforge.net/.

ViewInteractionsMap(map3D=True, map2D=True, surface=False, fancy=False, **kwargs)

Protein-Ligand interaction visualization.

Parameters:

  • map3D – (True) If true 3D iteraction map is displayed

  • map2D – (True) If true 2D interaction map id displayed

  • opacity – (default 0.65) opacity of protein cartoon (map3D must be True)

  • surface – (default False) add protein surface (map3D must be True)

  • surface_opacity – (default 0.50) opacity of protein surface (map3D and surface must be True)

  • fancy – (default Flase) outline color black (map3D must be True)

ViewPoses(ref_mol=False, surface=False, fancy=False, surface_opacity=0.65, **kwargs)

3D visualization of the docking poses with py3Dmol.

Parameters:

ref_mol – Optional (str) Reference ligand

class Docking.VINA(**kwargs)

Molecular docking with AutoDock Vina (https://vina.scripps.edu/).

AnalyseInteractions()

Protein-Ligand interaction analysis with ProLIF (https://prolif.readthedocs.io/en/latest/index.html).

Grid(**kwargs)

Performs an automatic detection of the binding pocket center coordinates, for specific proteins families (also works for heteromultimer).

Run(**kwargs)

vina docking engine itself.

Parameters:

  • num_modes – exhaustiveness of the global search (roughly proportional to time) (default 20)

  • size_x – size in the X dimension (Angstroms)

  • size_y – size in the Y dimension (Angstroms)

  • size_z – size in the Z dimension (Angstroms)

  • center_x – X coordinate of the center

  • center_Y – Y coordinate of the center

  • center_Z – Z coordinate of the center

  • exhaustiveness – exhaustiveness of the global search (roughly proportional to time) (default 8)

  • energy_range – exhaustiveness of the global search (roughly proportional to time) (default 4)

  • cpus – he number of CPUs to use (default 1)

Note

Size and Center parameters can be automatica aquired by running Vina.Grid() funtion. Those parameters will be passed automatically to the function.

ViewInteractionsMap(map3D=True, map2D=True, surface=False, fancy=False, **kwargs)

Protein-Ligand interaction visualization.

Parameters:

  • map3D – (True) If true 3D iteraction map is displayed

  • map2D – (True) If true 2D interaction map id displayed

  • opacity – (default 0.65) opacity of protein cartoon (map3D must be True)

  • surface – (default False) add protein surface (map3D must be True)

  • surface_opacity – (default 0.50) opacity of protein surface (map3D and surface must be True)

  • fancy – (default Flase) outline color black (map3D must be True)

ViewPoses(surface=False, fancy=False)

3D visualization of the docking poses with py3Dmol.

This python wrap-up of the GOMoDO webserver

class Align.Tethering

Tethered minimization on the MCS of ligands and a reference 3D molecular structure

MolAlignment()
Parameters:

  • reference – (str) reference 3D molecule

  • target_name – (str) name of ligand

  • target_smile – (str) smiles string of ligand

MolsAlignment()
Parameters:

  • reference – (str) reference 3D molecule

  • target_name – (list of str) list of names of ligands

  • target_smile – (list of str) list of smiles strings of ligands

This python wrap-up of the GOMoDO webserver

class Utils.RepOdor(**kwargs)

API access to the RepOdor database

GenereateConformations(**kwargs)

Generates 3D ligand conformations.

Parameters:

mols – optional (list): list of odorant names (case and space sensitive)

search(uniprotID, show3D=False)

Queries the RepOdor database, and returns a list of molecules.

Parameters:

  • uniprotID – required (str): Uniprot ID

  • show2D – optionnal (boolean): Shows 2D structure of molecules (Default False)

Example: RepOdor().search(‘Q8NGJ7’, show2D=True)

class Utils.Upload(**kwargs)

Upload Files

File()

Display Upload widget. It allows to upload one single file. Supports: .pdb, .sd, .sdf, .mol2

Note

To complete the upload process it is necessary to run the FileParser() function.

FileParse()

Saves the upload file in the working directory.

Files()

Display Upload widget. It allows to upload multiple. Supports: .pdb, .sd, .sdf, .mol2

Note

To complete the upload process it is necessary to run the FileParser() function.

FilesParse()

Saves the upload files in the working directory.