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.

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