What is Contrib?
- Public domain source code for use with the Daylight Toolkit.
- Useful applications which might have been supported applications
- Demo applications with useful or illustrative code
Where to find contrib code:
The following index is produced by the "make_index" shell script in the
$DY_ROOT/contrib/src directory.
I N D E X
---------
src/admin:
KILL_DCIS_SERVERS sh script to kill Daylight Thor and Merlin servers
START_DCIS_SERVERS sh script to start Daylight Thor and Merlin servers
convert_indir.sh Convert Daylight 3.6x indirect-data TDT files to 4.x
count_tdts Count SMILES and cross-refs in a TDT file
create_database Createsand load a THOR database from TDT files
multifp Fingerprint a database on a multiple-CPU machine
names2smiles Find names in available Thor databases
thordbsize How big is a database?
thorfix431 Update pre-4.31 databases
thorfixquotes Part of thorfix431; fix mismatched quotes
transfer_data Transfer data from one database to another.
src/data:
depict.rules Rubicon rules for creating 2D depictions
src/applics/clusterview:
clusterview View the output of the clustering package
do_cluster A shell script to cluster an example SMILES file
src/applics/add_mono_smiles:
add_mono_smiles Add SMILES to definitions in a monomer database
add_smiles.sh Shell script to add SMILES to monomer definitions
src/applics/perlob:
ProgOb.perl Example Perl program object
src/applics/stigmata:
stigmata Reads SMILES produces TDT's with atom scores
thresh.sh Example script to run stigmata for several thresholds
xvstigmata XView program depicts stigmata output with a 10 colors
xvstigmata4colors XView program depicts stigmata output with a 4 colors
src/c/depict:
dl_plot.c Example drawing library for plot(1) program (Sun only)
dl_plotlabels.c Example drawing library for plot(1) program (Sun only)
dl_spew.c Minimal drawing library that simply prints requests
dl_stubs.c Dummy drawing library that does no drawing
dl_vectorlab.a Generates vector-label characters
plotsmi Generates depictions for plot(1) program (Sun only)
plotsmi_v Like plotsmi, above, but with vector-label library
smi_to_2d Adds 2D coordinates to THOR Datatrees with SMILES
spewsmi Illustrates a trivial "drawing library"
src/c/findsubs:
findsubs Find/organize substituted parent molecules SMILES file
src/c/fingerprint:
addfp Add fingerprints to TDTs
ascii2bits Ascii-encoded binary to 1's and 0's
bits2ascii 1's and 0's to ascii-encoded binary
chifinger Program for chiral fingerprinting experiments
ringfinger Program for ring fingerprinting experiments
simatrix Similarity matrix of input SMILES
simogram Generate a histogram of frequency of similarity values
smi2fp_ascii Generate fingerprints, write binary in ASCII form
tdt2fp_ascii Convert fingerprints to ASCII form
src/c/merlin:
minimer Simple Merlin client
testmerlin Comprehensive "encyclopedia" of Merlin Toolkit calls
src/c/monomer:
chor2smi Enumerates SMILES from CHORTLES
chucktest CHUCKLES/CHORTLES/CHARTS input; mixture enumeration
matchtest Substructure searching at the monomer level
mono_utils.c Defining monomers in a monomer table
src/c/progob:
clogpaccess Example program that uses CLOGP program object
du_pipeio.c Functions for "pipetalk" protocol
du_pipeio_nt.c Functions for "pipetalk" protocol, no Daylight Toolkit
echotalk Example program object using Daylight Toolkit
fingertalk A minimal fingerprint "talk" program
merlinbintalk A "talk" program for merlin's binary data
nt_echotalk Example program object, no Daylight Toolkit
nt_verbosetalk Example program object, no Daylight Toolkit
pipetalker Example program that uses a program object
shelltalk Example program object, a bourne-shell script
stringtalker Example program, illustrates "string" mode
verbosetalk Example program object using Daylight Toolkit
src/c/reaction:
findpath Find multi-step reaction sequences
findrxn Find reactions with common reactants and products
maprxn Template-based atom mapper
react Apply a transform (SMIRKS) to input molecules (SMILES).
rxntest1 Reaction test program
rxntest2 Reaction test program
rxntest3 Reaction test program
testatom Atom map test program
src/c/rubicon:
constrain_distance Simple rubicon illustration of libdc_rube.a library
pma_pharm Rubicon-based filter, estimates PMA pharmacophore fit
sample_distances Simple rubicon illustration of libdc_rube.a library
src/c/smarts:
chain find longest hydrocarbon chain in molecule
hbonds Find potential intramolecular hydrogen bonds
look4n Look for SMARTS in SMILES up to count N
mark marks string attributes
smales identifies specific SMARTS-targets given generic SMARTS-targets
smarts_filter Filter SMILES input using SMARTS (like grep(1))
src/c/smiles:
cansmi Generate canonical (unique) SMILES
chiralify Generates stereoisomers of molecules
combine Produce substitued molecules given parent/substituents
ct2smi Convert simple connection table to SMILES
protons Count protons in a molecule
protons2 Count protons in a molecule and in each ring
rings Recognizes rings and ring-systems
showmf Print a molecule's molecular formula
showparts Show disconnected parts of molecule
smiles_ntuple Reorders atomic-property data
symmetric Evaluates symmetry of molecules.
src/c/thor:
addmwt Calculate average molecular weight, add dataitem to TDT
bin2tdt Convert binary data (e.g. GIF file) to TDT
buildtdt Illustrates building TDT objects "from scratch"
showgif Show pictures (e.g. GIF files) from xvmerlin
tdt2bin Convert binary data in TDT to a binary file (e.g. GIF)
testthor Comprehensive "encyclopedia" of THOR Toolkit calls
thorfdt Program to demonstrate FDT formatting of datatrees.
thorget Program to do a THOR lookup via primary or xref id.
thorirefs Find and print all indirect references in a database
thorload Load TDTs into a THOR database
thorloader Another "unix filter" to load a stream of TDTs into a database.
thorpick Write selected datatypes from a database to a TDT file
thorping Verify that a THOR server is alive
thorread Illustrates du_printtdt.c, printing TDT as ASCII text
thorsearch Fingerprint-based Thor searcher (slow)
src/c/transform:
enumerate Enumerates all molecules in a mixture
tranfilter Filter which applies a given transform to molecules
transformtest Formalized transform test program
trantest1 Simple test program
trantest2 Simple test program
tryschemes Applies sets of transformations exhaustively
src/c/widgets:
3d_usage 3D Widget, interactive display of conformations
depict_usage_1 Depictions without the Depict Widget
depict_usage_2 Depictions mixed with other graphics, no Depict Widget
depict_usage_3 Depict Widget, simple usage
depict_usage_4 Depict Widget, "autodraw" feature
depict_usage_5 Depict Widget, exclusive selction of a molecule
depict_usage_5 Depict Widget, non-exclusive selection of molecules
edgar_usage_1 Edgar Widget, controlling depiction colors
edgar_usage_2 Edgar Widget, controlling non-Daylight-widget colors
file_usage File Widget, browsing and selecting a file
grins_usage GRINS Widget, fast manual entry of SMILES
msg_usage Message Widget, displaying errors and warnings
smarts_usage Depict Widget, coloring via SMARTS pattern
status_usage_1 Status Widget, displaying task's progress
status_usage_2 Status Widget, displaying task's progress
tdt_usage TDT Widget, display/edit a THOR Datatree
src/c/misc:
make_parents standardizes an input smiles into a parent structure
reroot standardizes TDT, reroots with parent smiles
screen filter input smiles based on hbd's, hba's, rotatable bonds, etc.
tdtinfo analyzes a TDT file, reports on datatypes.
src/fortran/depict:
smi_to_2d Adds 2D coordinates to THOR Datatrees with SMILES
src/fortran/fingerprint:
fptest Fingerprint a molecule, print information
src/fortran/merlin:
merload Load Merlin pool
merrelease Release Merlin pool
src/fortran/progob:
echotalk Minimal pipetalking program
pipetalker Program which talks to one program via a pipe
verbosetalk Demonstration program for writing to/from pipes
src/fortran/smarts:
look4 Filter SMILES input using SMARTS
src/fortran/smiles:
cansmi Generate canonical (unique) SMILES
protons Count protons in a molecule
showmf Print a molecule's molecular formula
src/fortran/thor:
thorirefs Find and print all indirect references in a database
thorlist Write a database to a TDT file
thorpick Write selected datatypes from a database to a TDT file
src/libdu/depict:
dl_stubs.c Do-nothing "Drawing Library" for Depict Toolkit
du_coloratoms.c Coloring atoms in a standard way
du_printconfs.c Print conformation in TDT form
src/libdu/fingerprint:
du_fp2str.c Convert fingerprint object to THOR's ASCII version
du_name2fp Generate fingerprint for an arbitrary ASCII string
du_str2fp.c Convert THOR's ASCII fingerprints to FP object
src/libdu/smarts:
du_smartin.c Like dt_smartin(), but takes NULL-terminated string
src/libdu/smiles:
du_atomicmass.c Return the atomic mass of an atom
du_chiralify.c Returns all possible isomeric SMILES for a molecule
du_eliminate.c Combine ("bond") two molecules into a single one
du_mf.c Generate the molecular formula of a molecule
du_normalmass.c Return the integer mass of atom's most-common isotope
du_part.c Find disconnected parts of a molecule
du_smilin.c Like dt_smilin() but uses null-terminated strings
du_smilinseq.c Convert dot-disconnect SMILES to sequence of molecules
du_symbol.c Like dt_symbol(), but lowercase for aromatic atoms
src/libdu/thor:
du_printfdt.tdt Print a TDT object in "FDT"format
du_printtdt.c Print a TDT in a formatted ASCII form
src/libdu/utils:
du_3d.c Library of 3D functions
du_bin2ascii.c Convert to/from binary to Daylight's ASCII form
du_dbname.c Parse Thor/Merlin database and server names
du_fgetline.c Read an arbitrarily-long string from input
du_mergesort.c General-purpose sorting algorithm
du_noecho.c Input from a terminal with no echoing (for passwords)
du_parse_db.c Parse Daylight db specification.
du_printerrs.c Print errors from Toolkit's error queue
du_props.c Utilties for toolkit object property manipulation
du_quote.c Functions to handle quoted characters in TDTs
du_s3din.c Read 3D data from a TDT
du_strutils.c Miscellaneous utilities for manipulating strings
du_tdtfileio.c Read/write TDTs from/to files
smi2tdt Convert SMILES file to TDT file
tdt2smi Convert TDT file to SMILES file (shell script)
tdtcat Read/write TDT files (illustrates du_tdtfileio.c)
src/mcl:
test1 Illustrates a variety of basic MCL operations
test2 Illustrates a variety of basic MCL operations
test3 Illustrates command-line arguments to MCL programs
test4 Illustrates mixture searching using MCL
test5 Illustrates structures with/without SMILES structure
try5 Shell script to invoke test5 and produce ASCII text
try5h Shell script to invoke test5 and produce HTML text
src/perl:
build_dayperl A utility which builds the dayperl package
build_dayperl-1.1.html The original brief instructions (OBSOLETE)
build_dayperl.html brief instructions (START HERE)
dayperl.html A very brief overview of the system
dayperl.pod Same as above, but in its native pod format
dayperl.test Very simple test to see if DayPerl is working
dayperl_talk.html The html for Alex's talk on DayPerl
src/perl/examples:
CalcMW.pm A sample program which calcs mol weights
DU_LIB.pm non-toolkit utility subroutines
DU_MOLWEIGHT.pm molweight subroutine
DU_TLIB.pm toolkit utility subroutines
add2d.pl adds 2D data to TDTs
add_clogp.pl adds ClogP data via progob
add_mwt.pl add molweight to TDT stream
calcmw_test.pl A sample program which calls CalcMW.pm
cansmi.pl canonicalizes smiles
clogp_bombproof.pl non-toolkit ClogP bomb shelter
cpfrags.pl identifies ClogP fragments in molecules
goforth.pl virtual library GA
mersearch.pl Merlin searches, interactive
minpath.pl find minimum path between two atoms
react.pl transform SMILES with SMIRKS (reaction transforms)
ringsmi.pl find ringsystems, write smiles
smi2cpfrags.pl find ClogP fragments, write smiles
smi2gif.pl write GIFs using dcgi_smi2gif
smi2grf.pl SMILES to GRAPH
smi2tdt.pl SMILES to TDTs
tdt2page.pl TDTs to ascii-formatted pages
tdt2smi.pl TDTs to SMILES
tdt2tab.pl TDTs to TAB files
tdtcat.pl non-toolkit TDT processor
tdtsummary.pl non-toolkit TDT summarizer
tdtwhen.pl filter TDTs based on timestamps
thordbinfo.pl get Thor db info
thorget.pl similar to thorlookup
src/www:
CGIPARSE.pm Perl package for parsing CGI data
CGI_Lite.pm Perl CPAN package for handling files, etc.
DU_JAVA.pm Code to include JavaGRINS
DU_LIB.pm Some Daylight-user non-toolkit utility subroutines
DU_TLIB.pm Some Daylight-user toolkit utility subroutines
cansmi.cgi Canonicalize SMILES w/ options
daybase.cgi Simple Thor/Merlin CGI (no DayPerl)
daytops.cgi Interface to PrintPackage (PS output)
depict-file.cgi Depict from file
depict.cgi Depict SMILES CGI web app (no DayPerl)
depictmatch.cgi Depict and show SMARTS match
mol2smi-file.cgi Convert Molfile to SMILES/TDTs from file
mol2smi.cgi Convert Molfile to SMILES/TDTs
pcmodels.cgi PCModels (Clogp/CMR) interface
react.cgi Apply reaction transforms
rubicon.cgi Rubicon interface
tdt2fdt.pl Converts TDTs to FDT for daytops.cgi (Treetops)
tdt2html.pl Converts TDTs to HTML w/ smi2gif depictions
tdt2smi.pl TDTs to SMILES
thor.cgi simple read/write Thor interface
src/convert/acd2tdt:
MakeACD ACD to Daylight database conversion script
acd2tdt.c ACD to TDT conversion program
acd_units.c ACD to TDT units conversion
ctab2dep.c ACD to TDT mol to depiction conversion
du_acd2tdt_utils.c ACD to TDT utility functions
masses.c ACD to TDT mass conversion
units.dat ACD to TDT units table
src/convert/mdl:
mol2smi Convert MDL MOL-file format to SMI/TDT
rd2tdt Convert MDL RD-file format to TDT
rdf2datatdt.perl Convert text data from RD files to TDTs
smi2mol Convert SMI/TDT to MOL file; adds 2D via Depict if needed
test.ccr.rdf Example dataset from CCR
src/convert/pdb:
pdbdgeom2tdt Convert PDBDGEOM format to TDT
tdt2pdbdgeom Convert TDT to PDBDGEOM format
src/convert/rosdal:
du_rosin Interpret Rosdal into molecule or depiction
ros2tdt Convert ROSDAL to SMILES, output as TDTs
src/convert/sybyl:
syb2smi Convert Sybyl MOL2 format to SMILES/TDT
src/convert/wdi:
MakeWDI Convert World Drug Index (SD files) to Thor database
dtypefix.pl Convert mol2smi output to Daylight-friendly datatypes
reordertdts.pl Reorder dataitems in TDTs
wdi_datatypes.dcis.tdt List of std Daylight datatypes in WDI
wdi_datatypes.wdi.tdt List of special WDI datatypes
wdi_test.sd Sample WDI SD file
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