Skip to content

Other

Any Cast

Removes type information for the fronted, so you can artificially combine nodes that have conflicting type information. This is only useful to allow certain edge cases where the types are not correctly inferred.

Example use case: A node generally returns a union and does not dynamically update its output type, but you know for sure that a specific variant will be returned. As long as the node specifies the union as its output type, you cannot pass it into another node requiring that specific variant. In this case, the Any Cast node comes in handy.

Input:

  • Value: The previous node output you want to remove the type information from.

Output: - Value: The input with removed type information.

Batch

Enables batch processing of values, meaning multiple samples can be processed in one run. Provides a list of input values and gets every element from that list one-by-one to process them separately in subsequent nodes.

Input:

  • Batch: A list of any type. These are the values the batch node will be iterating over.

Output: For each element of the input: the item and its index in the list. The index can be important when the analysis pipeline contains branches. It makes sure that the elements are not mixed up.

Range

Creates a range of integer numbers as an array.

Input:

  • Start: Lower bound of the range (included).
  • Stop: Upper bound of the range (excluded).

Output: An array containing the numbers [Start, Stop].

OpenBabel Converter

This tool provides a versatile interface to OpenBabel, a powerful and widely used open-source toolkit for chemical information. It primarily functions as a chemical file format converter, allowing you to transform molecular structures from one file format (like SMILES or PDB) into another (like SDF or PDBQT). Beyond simple conversion, this node can also perform various chemical data manipulations, such as adding molecular properties, generating 2D or 3D atomic coordinates, and adjusting partial charges. This makes it an indispensable tool for preparing and manipulating chemical data for a wide range of bioinformatics and cheminformatics workflows.

Reference:

O'Boyle, N. M., Banck, M., James, C. A., Morley, C., Vandermeersch, T., & Hutchison, G. R. (2011). Open Babel: An Open Chemical Toolbox. Journal of Cheminformatics, 3, 33.https://doi.org/10.1186/1758-2946-3-33

Input

  • Input File: A dropdown list where you select the chemical structure file from your workspace that you want to process with OpenBabel.

Input Parameters

  • Input File Format: A dropdown list to specify the format of your selected input file (e.g., smi for SMILES, pdb for Protein Data Bank). It's crucial to select the correct format for accurate processing.
  • Output File Format: A dropdown list to choose the desired format for the output file (e.g., sdf for Structure-Data File, pdbqt for AutoDock PDBQT).
  • Output File Name: A text field to specify the name of the converted output file. If this field is left empty, the tool will automatically generate a name based on the input file's name, appending "_converted" and the new file extension.

Expert Parameters (available via the menu icon in the node)

This node exposes a range of advanced options for the OpenBabel tool, allowing for fine-grained control over the conversion and manipulation process.

  • --add: Adds properties to the molecule (e.g., for SDF or CML files). You can specify properties like 'MW' (Molecular Weight), 'logP' (Octanol-Water Partition Coefficient), 'TPSA' (Topological Polar Surface Area), 'formula' (Chemical Formula), 'InChI' (International Chemical Identifier), 'InChIKey', 'cansmi' (Canonical SMILES), etc. Provide them as a space-separated list.
  • --addfilename: If enabled, the original input filename will be appended to the molecule's title in the output file.
  • --addinindex: If enabled, the molecule's original index from the input file (before any filtering) will be appended to its title.
  • --addoutindex: If enabled, the molecule's index in the output file (after any filtering) will be appended to its title.
  • --addtotitle: Appends the specified text string to the title of each molecule in the output.
  • --append: Appends values of specific properties or descriptors (e.g., 'MW', 'logP') to the molecule's title.
  • -b: Converts "dative bonds" (special types of chemical bonds often represented differently in various formats) to standard covalent bonds.
  • -c: Centers the atomic coordinates of the molecule at the origin (0,0,0). This only affects the protein structure.
  • --canonical: Ensures that the atom order within the molecule is standardized (canonicalized). This is generally used for internal consistency and not for generating canonical SMILES, for which a specific output format (can) should be used.
  • --delete: Deletes specified properties from the molecule. Provide property names as a space-separated list.
  • -e: Instructs OpenBabel to continue converting molecules even if errors are encountered during the process.
  • --errorlevel: Controls the verbosity of error and warning messages displayed.
    • 1: Citical errors only.
    • 2: Includes warnings (default).
    • 3: Includes informational messages.
    • 4: Includes "audit log" messages detailing data changes.
    • 5: Includes debugging messages.
  • --gen3d: Generates 3D atomic coordinates for the molecule. This primarily affects small molecules (ligands). You can choose the desired speed/quality of the 3D generation: 'fastest', 'fast', 'med' (medium), 'slow', 'slowest', 'better', 'best', 'dist' (distance geometry), 'dg'.
  • -d: Deletes all hydrogen atoms from the molecule, making them "implicit" (not explicitly represented in the structure).
  • --ff: Selects a force field to be used for minimizing the energy of the ligand. A force field is a set of mathematical equations and parameters used to calculate the forces between atoms in a molecule, helping to find stable 3D arrangements. Options include: 'GAFF' (Generalized Amber Force Field, default), 'Ghemical', 'MMFF94', 'MMFF94s', 'UFF'.
  • -n: Specifies the maximum number of steps for the energy minimization process. (Default: 5000)
  • -cut: Enables the use of distance cut-offs for non-bonded interactions (van der Waals and Electrostatic forces) during minimization. By default, no cut-offs are used.
  • -rvdw: Specifies the van der Waals (VDW) cut-off distance in Angstroms. This parameter is only active if '-cut' is enabled. (Default: 6.0 Å)
  • -rele: Specifies the Electrostatic cut-off distance in Angstroms. This parameter is only active if '-cut' is enabled. (Default: 10.0 Å)
  • -pf: Specifies how often (in minimization steps) the list of non-bonded interaction pairs is updated during energy minimization. (Default: 10)
  • -p: Adds hydrogen atoms to the molecule appropriate for a given pH value. This is important for correctly representing the molecule's charge state at a specific physiological pH.
  • --partialcharge: Calculates and assigns partial charges to atoms using a specified method. Partial charges represent the distribution of electron density in a molecule and are crucial for understanding electrostatic interactions. This affects both ligand and receptor molecules. Options include: 'eem', 'eem2015ba', 'eem2015bm', 'eem2015bn', 'eem2015ha', 'eem2015hm', 'eem2015hn', 'eqeq', 'gasteiger', 'mmff94', 'none', 'qeq', 'qtpie'.
  • -r: Removes all disconnected parts of a molecule, keeping only the largest contiguous fragment. This is commonly used to "strip salts" or small solvent molecules attached to a larger compound.
  • --title: Adds or replaces the main title of the molecule in the output file.

Output

  • Output File: The resulting chemical file, converted into the specified output format and incorporating any modifications made by the chosen parameters. The exact type of the output file will match the Output File Format you selected.