ADAPT Package For R
R is an environment for statistical analysis and visualization. As a result it is well suited for the development and analysis of QSAR/QSPR models as well as chemical datamining in general. A package is available that provides some utilites for handling ADAPT generated data and file formats. Currently its features include
  • Loading pickle files generated by descmng
  • Writing a data.frame generated from a pickle file to disk in pickle format for use by descmng
  • Generate random descriptor data
  • Read and write tsets.in files
  • Read and write annlin formatted files
  • Splitting dataset (molecule list) into TSET/PSET/CVSET
  • Write descriptor information for selected molecules (TCSET/TSET/PSET/CVSET/all) in annlin or qnetin format for subsequent use by ADAPT programs such as annlin, qnet, gendes etc.
The package does not do any descriptor calculation and so ADAPT must be used to generate the descriptors for the dataset.

Currently, the package does not carry out any Type I, Type II or Type III model development as defined in ADAPT and thus the ADAPT suite of programs is still required. However after the descriptor and set data has been read into R, they may be used as input to the various modeling and statistical functions available in R include linear regression (lm), generalized linear models (glm), neural networks (nnet), random forests (rf), recursive partitioning (rpart) etc.

Future Plans

Future plans for the package are to provide the functionality of genlin, annlin, gendes and qnetin so that Type I, II and III model development can be carried out within the R environment. Long term plans include interfacing the descriptor calculation routines with R - this will probably require a rewrite of the descriptor routines either as C code or R code though the latter would require the development of a full chemical representation subsystem (input of chemical formats, structure representation etc)

Download & Installation

Download the package here

To install the package, from the command line do: R CMD INSTALL ADAPT_1.0.tar.gz. This will install the package in the system wide library directory. If you prefer to install it somewhere else do: R CMD INSTALL adapt_0.8.tar.gz -l /some/other/path