The following node is available in the Open Source KNIME predictive analytics and data mining platform version 2.7.1. Discover over 1000 other nodes, as well as enterprise functionality at
http://knime.com.
MoSS
This node searches for frequent molecular fragments in a set of molecules. The algorithm used is
Christian
Borgelt's MoSS implementation.
Dialog Options
Input options
- Column with molecule structure
-
Select the column in the input table that contains the molecule strings (Smiles, SLN or
SDF).
- Column with class labels
-
Select the column in the input table that contains the class labels (must be a string
column). In the list
below you can choose which values of the class column form the two groups (active or
inactive) used during
the search.
Mining options
- Ignore pure carbon fragments
-
Prevents the search for fragments that only consists of carbon atoms.
- Use ring mining
-
If enabled, ring of the specified sizes are treated as singles entities which makes the
search much faster
and also avoids finding fragments with partial rings.
- Minimum focus support
-
Sets the minimum number of fragments - a fraction of the number of input molecules in
the active class - a
fragment must occur in in order to be frequent and thus reported.
- Maximum complement support
-
Sets the maximum number of fragments - a fraction of the number of input molecules in
the inactive class - a
fragment may occur in in order to be reported.
- Minimum fragment size
-
The minimum size (number of bonds) a fragment must have in order to be reported.
- Maximum fragment size
-
The maximum size (number of bonds) a fragment may have in order to be reported.
MoSS options
- Start with core
-
Provide a Smiles string that is used as a seed for
starting the search. All found
fragments will contain the core.
- Canonical Form pruning
- Turns canonical form pruning on or off.
- Equivalent fragment pruning
- Turns equivalent sibling pruning on or off.
- Perfect extension pruning
- Turns perfect extention pruning on or off.
- Find chains of variable lengths
-
Enables the search for fragments that are equal except the length of their carbon
chains.
- Fragment extension mode
-
Choose between the two possible ways to extend a fragment during the search.
- Maximum embeddings used
-
Sets the upper limit on the number of extension that are stored in memory
Ports
Input Ports
0 |
Datatable with molecules |
Output Ports
0 |
Datatable with frequent fragments |
This node is contained in KNIME MoSS node
provided by KNIME GmbH, Konstanz, Germany.