eiR: Accelerated similarity searching of small molecules

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The eiR package provides utilities for accelerated structure similarity searching of very large small molecule data sets using an embedding and indexing approach.

Author
Kevin Horan, Yiqun Cao and Tyler Backman
Date of publication
None
Maintainer
Thomas Girke <thomas.girke@ucr.edu>
License
Artistic-2.0
Version
1.14.1
URLs

View on Bioconductor

Man pages

addTransform
Add Transform
eiAdd
Add new compounds
eiCluster
Cluster compounds
eiInit
Initialize a compound database
eiMakeDb
Create an embedded database
eiPerformanceTest
Test the performance of LSH search
eiQuery
Perform a query on an embedded database
example_compounds
Example Compounds
freeLSHData
Free LSH Data
loadLSHData
Load LSH Data
setDefaultDistance
Set the default distance function for a descriptor type

Files in this package

eiR/.BBSoptions
eiR/DESCRIPTION
eiR/INSTALL
eiR/LICENSE
eiR/NAMESPACE
eiR/R
eiR/R/core.R
eiR/R/db.R
eiR/R/eiR.R
eiR/R/evaluations.R
eiR/R/measures.R
eiR/README.md
eiR/build
eiR/build/vignette.rds
eiR/cleanup
eiR/data
eiR/data/example_compounds.RData
eiR/inst
eiR/inst/CITATION
eiR/inst/NEWS.Rd
eiR/inst/doc
eiR/inst/doc/eiR.R
eiR/inst/doc/eiR.Rmd
eiR/inst/doc/eiR.html
eiR/inst/schema
eiR/inst/schema/data.RPostgreSQL
eiR/inst/schema/data.SQLite
eiR/inst/unitTests
eiR/inst/unitTests/test_main.R
eiR/man
eiR/man/addTransform.Rd
eiR/man/eiAdd.Rd
eiR/man/eiCluster.Rd
eiR/man/eiInit.Rd
eiR/man/eiMakeDb.Rd
eiR/man/eiPerformanceTest.Rd
eiR/man/eiQuery.Rd
eiR/man/example_compounds.Rd
eiR/man/freeLSHData.Rd
eiR/man/loadLSHData.Rd
eiR/man/setDefaultDistance.Rd
eiR/src
eiR/src/Makevars
eiR/src/Makevars.win
eiR/src/apost.cpp
eiR/src/char_bit_cnt.cpp
eiR/src/config.h
eiR/src/embedCoords.cc
eiR/src/eucsearch.cc
eiR/src/eucsearch.h
eiR/src/f2c
eiR/src/f2c.h
eiR/src/f2c/Makefile
eiR/src/f2c/Notice
eiR/src/f2c/README
eiR/src/f2c/a.out.dSYM
eiR/src/f2c/a.out.dSYM/Contents
eiR/src/f2c/a.out.dSYM/Contents/Resources
eiR/src/f2c/a.out.dSYM/Contents/Resources/DWARF
eiR/src/f2c/abort_.c
eiR/src/f2c/arithchk.c
eiR/src/f2c/backspac.c
eiR/src/f2c/c_abs.c
eiR/src/f2c/c_cos.c
eiR/src/f2c/c_div.c
eiR/src/f2c/c_exp.c
eiR/src/f2c/c_log.c
eiR/src/f2c/c_sin.c
eiR/src/f2c/c_sqrt.c
eiR/src/f2c/cabs.c
eiR/src/f2c/close.c
eiR/src/f2c/comptry.bat
eiR/src/f2c/ctype.c
eiR/src/f2c/ctype.h
eiR/src/f2c/d_abs.c
eiR/src/f2c/d_acos.c
eiR/src/f2c/d_asin.c
eiR/src/f2c/d_atan.c
eiR/src/f2c/d_atn2.c
eiR/src/f2c/d_cnjg.c
eiR/src/f2c/d_cos.c
eiR/src/f2c/d_cosh.c
eiR/src/f2c/d_dim.c
eiR/src/f2c/d_exp.c
eiR/src/f2c/d_imag.c
eiR/src/f2c/d_int.c
eiR/src/f2c/d_lg10.c
eiR/src/f2c/d_log.c
eiR/src/f2c/d_mod.c
eiR/src/f2c/d_nint.c
eiR/src/f2c/d_prod.c
eiR/src/f2c/d_sign.c
eiR/src/f2c/d_sin.c
eiR/src/f2c/d_sinh.c
eiR/src/f2c/d_sqrt.c
eiR/src/f2c/d_tan.c
eiR/src/f2c/d_tanh.c
eiR/src/f2c/derf_.c
eiR/src/f2c/derfc_.c
eiR/src/f2c/dfe.c
eiR/src/f2c/dolio.c
eiR/src/f2c/dtime_.c
eiR/src/f2c/due.c
eiR/src/f2c/ef1asc_.c
eiR/src/f2c/ef1cmc_.c
eiR/src/f2c/endfile.c
eiR/src/f2c/erf_.c
eiR/src/f2c/erfc_.c
eiR/src/f2c/err.c
eiR/src/f2c/etime_.c
eiR/src/f2c/exit_.c
eiR/src/f2c/f2c.h
eiR/src/f2c/f2c.h0
eiR/src/f2c/f2ch.add
eiR/src/f2c/f77_aloc.c
eiR/src/f2c/f77vers.c
eiR/src/f2c/fio.h
eiR/src/f2c/fmt.c
eiR/src/f2c/fmt.h
eiR/src/f2c/fmtlib.c
eiR/src/f2c/fp.h
eiR/src/f2c/ftell64_.c
eiR/src/f2c/ftell_.c
eiR/src/f2c/getarg_.c
eiR/src/f2c/getenv_.c
eiR/src/f2c/h_abs.c
eiR/src/f2c/h_dim.c
eiR/src/f2c/h_dnnt.c
eiR/src/f2c/h_indx.c
eiR/src/f2c/h_len.c
eiR/src/f2c/h_mod.c
eiR/src/f2c/h_nint.c
eiR/src/f2c/h_sign.c
eiR/src/f2c/hl_ge.c
eiR/src/f2c/hl_gt.c
eiR/src/f2c/hl_le.c
eiR/src/f2c/hl_lt.c
eiR/src/f2c/i77vers.c
eiR/src/f2c/i_abs.c
eiR/src/f2c/i_dim.c
eiR/src/f2c/i_dnnt.c
eiR/src/f2c/i_indx.c
eiR/src/f2c/i_len.c
eiR/src/f2c/i_mod.c
eiR/src/f2c/i_nint.c
eiR/src/f2c/i_sign.c
eiR/src/f2c/iargc_.c
eiR/src/f2c/iio.c
eiR/src/f2c/ilnw.c
eiR/src/f2c/inquire.c
eiR/src/f2c/l_ge.c
eiR/src/f2c/l_gt.c
eiR/src/f2c/l_le.c
eiR/src/f2c/l_lt.c
eiR/src/f2c/lbitbits.c
eiR/src/f2c/lbitshft.c
eiR/src/f2c/lio.h
eiR/src/f2c/lread.c
eiR/src/f2c/lwrite.c
eiR/src/f2c/main.c
eiR/src/f2c/makefile.sy
eiR/src/f2c/makefile.u
eiR/src/f2c/makefile.vc
eiR/src/f2c/makefile.wat
eiR/src/f2c/math.hvc
eiR/src/f2c/mkfile.plan9
eiR/src/f2c/open.c
eiR/src/f2c/pow_ci.c
eiR/src/f2c/pow_dd.c
eiR/src/f2c/pow_di.c
eiR/src/f2c/pow_hh.c
eiR/src/f2c/pow_ii.c
eiR/src/f2c/pow_qq.c
eiR/src/f2c/pow_ri.c
eiR/src/f2c/pow_zi.c
eiR/src/f2c/pow_zz.c
eiR/src/f2c/qbitbits.c
eiR/src/f2c/qbitshft.c
eiR/src/f2c/r_abs.c
eiR/src/f2c/r_acos.c
eiR/src/f2c/r_asin.c
eiR/src/f2c/r_atan.c
eiR/src/f2c/r_atn2.c
eiR/src/f2c/r_cnjg.c
eiR/src/f2c/r_cos.c
eiR/src/f2c/r_cosh.c
eiR/src/f2c/r_dim.c
eiR/src/f2c/r_exp.c
eiR/src/f2c/r_imag.c
eiR/src/f2c/r_int.c
eiR/src/f2c/r_lg10.c
eiR/src/f2c/r_log.c
eiR/src/f2c/r_mod.c
eiR/src/f2c/r_nint.c
eiR/src/f2c/r_sign.c
eiR/src/f2c/r_sin.c
eiR/src/f2c/r_sinh.c
eiR/src/f2c/r_sqrt.c
eiR/src/f2c/r_tan.c
eiR/src/f2c/r_tanh.c
eiR/src/f2c/rawio.h
eiR/src/f2c/rdfmt.c
eiR/src/f2c/rewind.c
eiR/src/f2c/rsfe.c
eiR/src/f2c/rsli.c
eiR/src/f2c/rsne.c
eiR/src/f2c/s_cat.c
eiR/src/f2c/s_cmp.c
eiR/src/f2c/s_copy.c
eiR/src/f2c/s_paus.c
eiR/src/f2c/s_rnge.c
eiR/src/f2c/s_stop.c
eiR/src/f2c/scomptry.bat
eiR/src/f2c/sfe.c
eiR/src/f2c/sig_die.c
eiR/src/f2c/signal1.h0
eiR/src/f2c/signal_.c
eiR/src/f2c/signbit.c
eiR/src/f2c/sue.c
eiR/src/f2c/sysdep1.h0
eiR/src/f2c/system_.c
eiR/src/f2c/typesize.c
eiR/src/f2c/uio.c
eiR/src/f2c/uninit.c
eiR/src/f2c/util.c
eiR/src/f2c/wref.c
eiR/src/f2c/wrtfmt.c
eiR/src/f2c/wsfe.c
eiR/src/f2c/wsle.c
eiR/src/f2c/wsne.c
eiR/src/f2c/xsum0.out
eiR/src/f2c/xwsne.c
eiR/src/f2c/z_abs.c
eiR/src/f2c/z_cos.c
eiR/src/f2c/z_div.c
eiR/src/f2c/z_exp.c
eiR/src/f2c/z_log.c
eiR/src/f2c/z_sin.c
eiR/src/f2c/z_sqrt.c
eiR/src/format.cc
eiR/src/include
eiR/src/include/lshkit
eiR/src/include/lshkit.h
eiR/src/include/lshkit/adaptor.h
eiR/src/include/lshkit/apost.h
eiR/src/include/lshkit/archive.h
eiR/src/include/lshkit/common.h
eiR/src/include/lshkit/composite.h
eiR/src/include/lshkit/concept.h
eiR/src/include/lshkit/eval.h
eiR/src/include/lshkit/forest.h
eiR/src/include/lshkit/histogram.h
eiR/src/include/lshkit/kernel.h
eiR/src/include/lshkit/lsh-file.h
eiR/src/include/lshkit/lsh-index.h
eiR/src/include/lshkit/lsh.h
eiR/src/include/lshkit/matrix-io.h
eiR/src/include/lshkit/matrix.h
eiR/src/include/lshkit/metric.h
eiR/src/include/lshkit/mplsh-file.h
eiR/src/include/lshkit/mplsh-model.h
eiR/src/include/lshkit/mplsh.h
eiR/src/include/lshkit/sketch.h
eiR/src/include/lshkit/spectral-hash.h
eiR/src/include/lshkit/storage.h
eiR/src/include/lshkit/topk.h
eiR/src/include/lshkit/tune.h
eiR/src/include/lshkit/vq.h
eiR/src/mplsh-model.cpp
eiR/src/mplsh.cpp
eiR/src/profiling.cc
eiR/src/profiling.h
eiR/src/r_wrap.cpp
eiR/src/recordfile.cc
eiR/src/routines.c
eiR/src/scan.cc
eiR/src/search_r.cpp
eiR/src/solver.cc
eiR/src/solver.h
eiR/tests
eiR/tests/runTests.R
eiR/tmp
eiR/tmp/data
eiR/tmp/fp_test
eiR/tmp/fp_test/data
eiR/tmp/run-50-40
eiR/vignettes
eiR/vignettes/Makefile_bootstrap
eiR/vignettes/eiR.Rmd
eiR/vignettes/eiR.Rmd_bootstrap
eiR/vignettes/header.html
eiR/vignettes/html.template_bootstrap
eiR/vignettes/references.bib