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Filter Molecules with Naomi

BioSolveIT Plugins version 2.15.0.0001168 by BioSolveIT GmbH

The Naomi Converter can filter molecules using many different properties, SMARTS expressions and functional groups.

Options

Select the column containing the molecule(s) to be filtered
The molecules provided in this column are filtered according to the settings below. If the input table contains more than one column with a compatible type, you can choose which column should be taken. The column has to be in SDF, Mol2 or SMILES format.
Filter Settings
In this section you can define several filters that are applied to the molecules that are passed through this node.
Add new filter row - You can add another filter by clicking this button. Then you can modify the new filter by directly clicking into the row:
    Negate - tick here to negate the expression in the row
    Property - select the property that should be used for filtering here
    Expression - specify an additional filter expression here
    Min - specify a minimum for the selected property here
    Max - specify a maximum for the selected property here
    Conjunction - obey a logical conjunction of clauses
Remove selected row(s) - You can remove the selected filter by clicking this button.
Tolerance slider - With this slider you can choose how many of the given clauses may be false. NOTE: Using the tolerance disables the logical conjunction of clauses!

Available Properties

MW[min, max]
MW
TPSA[min, max]
TPSA
Atoms[min, max]
Number of Non-hydrogen atoms
Acceptors[min, max]
Number of H-Acceptors
Donors[min, max]
Number of H-Donors
Hetero[min, max]
Number of Hetero atoms
AromAtoms[min, max]
Number of Aromatic atoms
Halogens[min, max]
Number of Halogens
Inorganic[min, max]
Number of Inorganic atoms
NO[min, max]
Number of N + O
Bonds[min, max]
Number of Non-hydrogen bonds
RotB[min, max]
Number of Rot. bonds
CRTB[min, max]
Max CRTB
Ringsystems[min, max]
Number of Ringsystems
AroRingsystems[min, max]
Number of Aromatic ringsystems
Rings[min, max]
Number of Rings (rel. cycles)
RingProto[min, max]
Number of Ring prototypes
AroRings[min, max]
Number of Arom. rings
MaxRing[min, max]
Max atoms in ring
MaxRSsize[min, max]
Max atoms in ringsystem
RS[min, max]
Number of R/S centers
EZ[min, max]
Number of E/Z bonds
Linkers[min, max]
Number of Link atoms
Charge[min, max]
Charge
PLogP[min, max]
PLogP
Volume[min, max]
Volume
Smarts['expression'][min, max]
Smarts
Func['expression'][min, max]
Functional group
LinkName['expression'][min, max]
Occurrence of a link name
Keep debug files and show the log after the run
This setting keeps all temporary files and opens an editor to show the output of the external program. This setting is very helpful for debugging.

Input Ports

Input Molecules: Input table with at least one column containing molecules in SDF, Mol2 or SMILES format to be converted.

Output Ports

Passed: The rows of the incoming table that passed the filter defined above.
Failed: The rows of the incoming table that did not pass the filter defined above.
Errors: The rows of the incoming table where the molecule could not be read by Naomi for any reason.

Best Friends (Incoming)

Best Friends (Outgoing)

Installation

To use this node in KNIME, install BioSolveIT Interfaces from the following update site:

KNIME 4.1
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Developers

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