MMP Molecule Fragment (RDKit)

Options

Molecule & Fragmentation Options

Select Molecule column

Select the column containing the molecules

Select Molecule IDs column

Select the column containing the molecule IDs

Allow HiLiting

If selected, then hiliting between the incoming molecules and fragments is preserved. WARNING - this can result in significant memory use for big tables or large numbers of fragmentations!

Select the Fragmentation Type

Select the required fragmentation option

User SMARTS

The optional user-defined (r)SMARTS (see above for details)

Number of cuts

Select the number of cuts (1-10)

Allow 2 cuts along single bond giving a single bond as 'value'?

If selected, for the 2 cuts case, 1 bond can be cut twice, allowing a 'value' of [*:1]-[*:2] (i.e. a 'bond') to be formed

Explicit Hydrogens

Options for handling explicit hydrogens during fragmentation. Users are strongly advised to retain the recommended default settingsTo understand these options, fragmentation is performed using either a single or two (if explicit H's are added for 1 cut) 'fragmentation factories' for each incoming molecule. The factory with explicit H's added is only used for 1 cut, and only for those cuts of bonds to 'H'. All other bond breaks are performed using the 2nd factory. If you wish to achieve specific effects, using these settings beyond the default then we suggest trialing with with a simple example molecule containing an explicit 'H', e.g. '[H]c1c([Cl])cccc1' or 'C/C([H])=C/C'

Add H's prior to fragmentation

If checked, pairs with -H as a substituent will be included. This is recommended for when the number of cuts is 1, and is unavailable for other values

Remove Added Explicit H's from output

Explicit hydrogens added for a single cut will be removed from the output if selected (Only available when 'Add H's prior to fragmentation' is selected and enabled)

Incoming explicit H's treatment

If incoming molecules contain any explicit H's, how should they be treated? The preferred option is to remove them prior to fragmentation, otherwise seemingly spurious results may follow.

Fragmentation Filtering Settings

Limit by Complexity

If checked, this option will skip molecules likely to have a very large number of fragmentations, based on the number of possible fragmentable bond combinations (different bond combinations leading to identical fragmentations are not discounted)

Maximum Fragmentations

The limit of predicted fragmentations

Treat no undefined chiral centres as chiral

In molecules with explicit chiral centres, newly created stereocentres are given defined chirality. Molecules with only undefined possible stereocentres (e.g. CC(F)Br) will not have explicit stereochemistry assigned to newly created centres. Molecules with neither explicit or undefined stereocentres will have explicit chirality set at newly created centres if this option is selected, otherwise they will not be set.

Filter by maximum number of changing heavy atoms?

If checked, the user can specify a maximum number of heavy atoms which are allowed to change between Matched Pairs

Maximum Number of variable heavy atoms

The maximum number of heavy atoms which are allowed to change between pairs

Filter by fixed heavy atoms?

If checked, the user can specify a minimum number of heavy atoms which are present in the 'Key'

Min Fixed ('Key') Heavy Atoms

The minimum number of heavy atoms which are required in the fixed 'Key' part of the pair

Filter by ratio of changing / unchanging atoms?

If checked, the user can specify a maximum ratio of changing to unchanging heavy atoms during fragmentation

Minimum ratio of changing to unchanging heavy atoms

The minimum ratio of changing to unchanging heavy atoms

Output Settings

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

Add failure reasons to 2nd output table

If checked, the reason the molecule could not be fragmented is added to the second output table

Render Fragmentation

Should the fragmentation be rendered

Show breaking bonds

Should breaking bonds be highlighted in the rendering?

Breaking bond colour

The colour to highlight the breaking bond(s)

Show key

Should the atoms/bonds forming the 'key' be highlighted in the rendering?

Key Colour

The colour to highlight the 'key'

Show value

Should the atoms/bonds forming the 'value' be highlighted in the rendering? If the fragmentation is a double cut to 1 bond, then the breaking bond is also the value, and will be shown as such

Value Colour

The colour to highlight the 'value'

Incoming columns to keep

Select incoming data columns to keep. The ID column will always be present in the output, regardless of the setting here, with the name 'ID'. Fragmentation columns will be left-most in the table, and incoming columns may be renamed by the addition of a suffix, e.g. '(#1)', to avoid duplicate names)

Fingerprints

Show 'Value' attachment point graph distances fingerprint

Include a graph distance fingerprint showing the graph distance between each attachment point in the fragmentation 'value'. The fingeprint is the number of bonds between each pair of attachment points, so '[*:1]-[*:2]' is {1}, '[*:1]c1c([*:2])cc([*:3])cc1' is {3,5,4} etc

Add Attachment Point Fingerprints

If checked, then attachment point fingerprints are added. See above for further details. One column is added for each attachment point

Fingerprint Length

The number of bits in the fingerprints

Morgan Radius

The radius of the Morgan fingerprint

Use Bond Types

Should the bond types be included in the fingerprint generation

Use chirality

Should chirality be included in the fingerprint generation

Views

Fragmentation Progress

The view shows the proportion of the table completely processed, the proportion of the queue currently filled, and the proportion of the allocated threads currently active. The size of the queue and the number of threads can be controlled in the preferences - a bigger queue may use more memory, but is more likely to keep all parallel threads active, resulting in shorter processing times

Workflows

• 00_Setup workflowKNIME Hub
• 00_Setup workflowKNIME Hub
• 03_Simple_MMP_ExampleKNIME Hub
• 04_Matched Molecular PairsKNIME Hub
• 04_Matched Molecular PairsKNIME Hub
• Show all 8 workflows

Links

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Developers