Molecule Filter (Naomi)

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

Options

Molecule column
Name of the molecule column.
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
Remove duplicates
Unify output, duplicates are discarded.
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

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Library: Input table with molecules in sdf, smiles or mol2 format.

Output Ports

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Passed: The rows of the incoming table that passed the filter defined above.
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Failed: The rows of the incoming table that did not pass the filter defined above.
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Errors: Rows of the incoming table containing molecules which could not be processed for any reason.

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Installation

To use this node in KNIME, install the extension BioSolveIT Naomi for Knime from the below update site following our NodePit Product and Node Installation Guide:

v5.2
Plugin provider: BioSolveIT GmbH
Plugin version: 2.29.3.202309291626
On NodePit since: 2023-12-06
Last update: 2024-11-20
KNIME versions: From v3.6 to v5.2

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