R/318-extractDrugChiCluster.R
extractDrugChiCluster.Rd
Evaluates the Kier and Hall Chi cluster indices of orders 3, 4, 5 and 6
extractDrugChiCluster(molecules, silent = TRUE)
molecules | Parsed molucule object. |
---|---|
silent | Logical. Whether the calculating process
should be shown or not, default is |
A data frame, each row represents one of the molecules, each column represents one feature. This function returns 8 columns, the order and names of the columns returned is:
SC.3 - Simple cluster, order 3
SC.4 - Simple cluster, order 4
SC.5 - Simple cluster, order 5
SC.6 - Simple cluster, order 6
VC.3 - Valence cluster, order 3
VC.4 - Valence cluster, order 4
VC.5 - Valence cluster, order 5
VC.6 - Valence cluster, order 6
Evaluates chi cluster descriptors. It utilizes the graph isomorphism code of the CDK to find fragments matching SMILES strings representing the fragments corresponding to each type of chain.
These descriptors are calculated using graph isomorphism to identify the various fragments. As a result calculations may be slow. In addition, recent versions of Molconn-Z use simplified fragment definitions (i.e., rings without branches etc.) whereas these descriptors use the older more complex fragment definitions.
# NOT RUN { smi = system.file('vignettedata/FDAMDD.smi', package = 'Rcpi') # }# NOT RUN { mol = readMolFromSmi(smi, type = 'mol') dat = extractDrugChiCluster(mol) head(dat) # }