Fragments to MMPs

Options

Select the Fragment Key column

Select the column containing the fragment 'keys'

Select the Fragment Value column

Select the column containing the fragment 'values'

Incoming table is sorted by Keys and Values?

Use this option if the input table is pre-sorted by 'keys', then by 'values'. See above for details

Select the ID column

Select the column containing the parent molecule IDs

Allow self-transforms

Allows two regioisomeric fragmentations of an input molecule resulting in identical keys but differing values to provide a 'self-transform' between the fragmentations

Filter by HAC Change

Should the transform be filtered by delta HAC? NB This is asymmetric so the 'Show reverse-direction transforms' option will not show pairs in some cases, e.g. if the range is set from -2 to +4 then a transform losing 3 heavy atoms in the forwards direction will only show in the reverse direction

HAC Change Range

The range of acceptable HAC changes

Show HAC change in output table

Should the HAC change be shown in the output table

Graph Distance Similarity

If a fragmentation value attachment point graph distance fingerprint was calculated during fragmentation, than that can be used to restrict the transforms generated according to various similarity or disance cut-off functions (see above)

Cutoff (Double)

The cutoff threshold for doubles

Cutoff (Integer)

The cutoff threshold for integers

Graph Distance fingerint column

The column containing the counts fingerprint for the graph distances between attachment points

Include distance/similarity in output

Should the calculated graph distance or similarity be included in the output table

Pass-through columns

Left Columns to pass through unchanged

The columns from the left molecule of the transform to pass through unchanged

Right Columns to pass through unchanged

The columns from the right molecule of the transform to pass through unchanged

Difference columns

Left - Right

Those numeric (int, double, long, complex number) columns for which the L-R difference should be calculated

Right - Left

Those numeric (int, double, long, complex number) columns for which the R-L difference should be calculated

Ratio columns

Left / Right

Those numeric double columns for which the L/R ratio should be calculated

Right - Left

Those numeric double columns for which the R/L ratio should be calculated

Output Settings

Remove Explicit H's from output

Explicit hydrogens will be removed from the output if selected

Show unchanging portion

A SMILES cell will be included showing the 'key' resulting in the fragmentation pattern

Show number of changing atoms

The number of heavy atoms (not including 'A', the attachment point) will be included for Left and Right fragments

Show ratio of constant / changing heavy atoms

The ratio of constant / changing heavy atoms (not including 'A', the attachment point) will be included for Left and Right fragments

Show reverse-direction transforms

The transformations will be duplicated in the 'reverse' direction, e.g. A-->B and B-->A

Include Reactions SMARTS

In addition to the SMIRKS representation of the transformation, the transform is shown in an rSMARTS representation with atom mappings

Require single acyclicly bonded attachment points

Should the reaction SMARTS explicitly require that the bonds to attachment point dummy atoms are all single, acyclic bonds ('-!@'), as this is what is allowed to break

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Workflows

• 03_Simple_MMP_ExampleKNIME Hub
• 04_Databased_MMP_ExampleKNIME Hub
• 04_Matched Molecular PairsKNIME Hub
• 04_Matched Molecular PairsKNIME Hub
• Matched Molecular PairsKNIME Hub
• Show all 6 workflows

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