The following index is produced by the "make_index" script.
- 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
- Creates and loads a THOR database from TDT files
- CreateDB
- Creates and loads a THOR database from TDT files
- multifp
- Fingerprint a database on a multiple-CPU machine
- names2smiles
- Find names in available Thor databases
- transfer_data
- Transfer data from one database to another.
- thordbsize
- How big is a database?
- add_mono_smiles
- Add SMILES to definitions in a monomer database
- add_smiles.sh
- Shell script to add SMILES to monomer definitions
- clusterview.c
- View the output of the clustering package
- do_cluster
- A shell script to cluster an example SMILES file
- gadd.c
- main gadd program
- du_mwt.c
- used by gadd.c
- cpfrags.c
- dissects input structures into fragments
- ringsmi.c
- identifies ring systems in input structures
- thorcommonsmi.c
- how many common smiles in N databases
- Makefile
- builds C programs
- datatypes.tdt
- used by gadd.c
- fiddle.pl
- needed for cpfrags.c postprocessing
- fiddle_kek.pl
- needed for cpfrags.c postprocessing
- CreateMinoxenstein
- script to create minoxidil-based library
- DestroyMinoxenstein
- script to destroy minoxidil-based library
- GoMedchem00
- creates gadd-ready fragment files from Medchem00
- minoxidil.cfrags
- minoxidil carbon fragments
- minoxidil.frags
- minoxidil fragments
- minoxidil.rings
- minoxidil ring systems
- minoxidil.smi
- minoxidil
- reject.sma
- sample unfit-smarts file
- usortfreq.pl
- adds frequencies to fragment lists
- ProgOb.perl
- Example Perl program object
- stigmata.c
- Reads SMILES produces TDT's with atom scores
- stigmata.cgi
- stigmata source code (Perl web version)
- stigmata.pl
- stigmata source code (Perl translation)
- thresh.sh
- Example script to run stigmata for several thresholds
- xvstigmata.c
- XView program depicts stigmata output with a 10 colors
- tpsa.c
- calculation of polar surface area based on fragment contributions
- tpsa.pl
- translation of tpsa.c into perl by Eric Allen
- tfmtalk.c
- transform progob talk program
- htpsdemo.c
- Illustrates postscript output for printing from a CGI
- smi_to_2d.c
- Adds 2D coordinates to THOR Datatrees with SMILES
- spewsmi.c
- Illustrates a trivial "drawing library"
- plotsmi.c
- Generates depictions for plot(1) program (Sun only)
- plotsmiv.c
- Like plotsmi, above, but with vector-label library
- 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.c
- Generates vector-label characters
- findsubs.c
- Find/organize substituted parent molecules SMILES file
- addfp.c
- Add fingerprints to TDTs
- chifinger.c
- Program for chiral fingerprinting experiments
- ringfinger.c
- Program for ring fingerprinting experiments
- smi2fp_ascii.c
- Generate fingerprints, write binary in ASCII form
- tdt2fp_ascii.c
- Convert fingerprints to ASCII form
- ascii2bits.c
- Ascii-encoded binary to 1's and 0's
- bits2ascii.c
- 1's and 0's to ascii-encoded binary
- simatrix.c
- Similarity matrix of input SMILES
- simogram.c
- Generate a histogram of frequency of similarity values
- modalfp.c
- Modal fingerprint (Stigmata-like) for a group of smiles.
- namefp.c
- Fingerprint ascii names.
- merq.c
- Merlin query filter
- minimer.c
- Simple Merlin client - read SMILES, produce table output
- testmerlin.c
- Comprehensive "encyclopedia" of Merlin Toolkit calls
- make_parents.c
- standardizes an input smiles into a parent structure
- molalign.c
- aligns depictions according to smarts template
- reroot.c
- standardizes TDT, reroots with parent smiles
- screen.c
- filter input smiles based on hbd's, hba's, rotatable bonds, etc.
- tdtinfo.c
- analyzes a TDT file, reports on datatypes.
- tdt2sql.c
- convert TDT file to SQL inserts based on a control file
- cpfrags.c
- dissects molecules into ClogP fragments and carbon-frags.
- fixarom.c
- modify ringsystems to satisfy aromaticity definition
- spherex.c
- cluster via sphere-exclusion algorithm
- chor2smi.c
- Enumerates SMILES from CHORTLES
- chucktest.c
- CHUCKLES/CHORTLES/CHARTS input; mixture enumeration
- matchtest.c
- Substructure searching at the monomer level
- mono_utils.c
- Defining monomers in a monomer table
- du_pipeio.c
- Functions for "pipetalk" protocol
- du_pipeio_nt.c
- Functions for "pipetalk" protocol, no Daylight Toolkit
- echotalk.c
- Example program object using Daylight Toolkit
- fingertalk.c
- A minimal fingerprint "talk" program
- merlinbintalk.c
- A "talk" program for merlin's binary data
- nt_echotalk.c
- Example program object, no Daylight Toolkit
- nt_verbosetalk.c
- Example program object, no Daylight Toolkit
- pipetalker.c
- Example program that uses a program object
- clogpaccess.c
- Example program that uses CLOGP program object
- stringtalker.c
- Example program, illustrates "string" mode
- shelltalk.c
- Example program object, a bourne-shell script
- verbosetalk.c
- Example program object using Daylight Toolkit
- add_clogp.c
- Runs clogptalk; recovers from ClogP crashes.
- findpath.c
- Find multi-step reaction sequences
- findrxn.c
- Find reactions with common reactants and products
- maprxn.c
- Template-based atom mapper
- rxntest1.c
- Reaction test program
- rxntest2.c
- Reaction test program
- rxntest3.c
- Reaction test program
- react.c
- Apply a transform (SMIRKS) to input molecules (SMILES).
- testatom.c
- Atom map test program
- tests.c
- Reaction toolkit test program
- constrain_distance.c
- Simple rubicon illustration of libdc_rube.a library
- sample_distances.c
- Simple rubicon illustration of libdc_rube.a library
- pma_pharm.c
- Rubicon-based filter, estimates PMA pharmacophore fit
- hbonds.c
- Find potential intramolecular hydrogen bonds
- smarts_filter.c
- Filter SMILES input using SMARTS (like grep(1))
- look4.c
- SMARTS filter with counts
- look4n.c
- SMARTS filter with counts and optimized
- mark.c
- marks string attributes
- minpath.c
- find minimum path between two atoms
- chain.c
- find longest hydrocarbon chain in molecule
- smales.c
- identifies specific SMARTS-targets given generic SMARTS-targets
- smartsmatch.c
- filter w/ explicit-H feature
- cansmi.c
- Generate canonical (unique) SMILES
- chiralify.c
- Generates stereoisomers of molecules
- combine.c
- Produce substitued molecules given parent/substituents
- ct2smi.c
- Convert simple connection table to SMILES
- mol2parts.c
- Split disconnected molecule into several.
- protons.c
- Count protons in a molecule
- protons2.c
- Count protons in a molecule and in each ring
- rings.c
- Recognizes rings and ring-systems
- showmf.c
- Print a molecule's molecular formula
- showparts.c
- Show disconnected parts of molecule
- smiles_ntuple.c
- Reorders atomic-property data
- symmetric.c
- Evaluates symmetry of molecules.
- usual.c
- Adjusts H-count to usual values for atoms in brackets.
- permsmi.c
- Write SMILES in permuted order using dt_arbsmiles().
- addmwt.c
- Calculate average molecular weight, add dataitem to TDT
- bin2tdt.c
- Convert binary data (e.g. GIF file) to TDT
- buildtdt.c
- Illustrates building TDT objects "from scratch"
- showgif.c
- Show pictures (e.g. GIF files) from xvmerlin
- testthor.c
- Comprehensive "encyclopedia" of THOR Toolkit calls
- thordbpath.c
- query/change db search path (thor or merlin)
- thorfdt.c
- Program to demonstrate FDT formatting of datatrees.
- thorget.c
- Program to do a THOR lookup via primary or xref id.
- thorirefs.c
- Find and print all indirect references in a database
- thorload.c
- Load TDTs into a THOR database
- thorloader.c
- Another "unix filter" to load a stream of TDTs into a database.
- thorsearch.c
- Fingerprint-based Thor searcher (slow)
- thorpick.c
- Write selected datatypes from a database to a TDT file
- thorping.c
- Verify that a THOR server is alive
- thorread.c
- Illustrates du_printtdt.c, printing TDT as ASCII text
- tdt2bin.c
- Convert binary data in TDT to a binary file (e.g. GIF)
- thorcommonsmi.c
- Finds the common smiles among multiple databases.
- enumerate.c
- Enumerates all molecules in a mixture
- tranfilter.c
- Filter which applies a given transform to molecules
- transformtest.c
- Formalized transform test program
- trantest1.c
- Simple test program
- trantest2.c
- Simple test program
- tryschemes.c
- Applies sets of transformations exhaustively
- depict_usage_1.c
- Depictions without the Depict Widget
- depict_usage_2.c
- Depictions mixed with other graphics, no Depict Widget
- depict_usage_3.c
- Depict Widget, simple usage
- depict_usage_4.c
- Depict Widget, "autodraw" feature
- depict_usage_5.c
- Depict Widget, non-exclusive selection of molecules
- depict_usage_6.c
- Depict Widget, exclusive selction of a molecule
- depict_smifile.c
- Depict Widget, smifile argument
- depictmol.c
- Depict Widget, MDL molfile input, preserve 2D layout
- smarts_usage.c
- Depict Widget, coloring via SMARTS pattern
- edgar_usage_1.c
- Edgar Widget, controlling depiction colors
- edgar_usage_2.c
- Edgar Widget, controlling non-Daylight-widget colors
- file_usage.c
- File Widget, browsing and selecting a file
- grins_usage.c
- GRINS Widget, fast manual entry of SMILES
- msg_usage.c
- Message Widget, displaying errors and warnings
- status_usage_1.c
- Status Widget, displaying task's progress
- status_usage_2.c
- Status Widget, displaying task's progress
- 3d_usage.c
- 3D Widget, interactive display of conformations
- tdt_usage.c
- TDT Widget, display/edit a THOR Datatree
- MakeACD
- ACD to Daylight database conversion script
- MakeACD_check
- argument and environment checker for MakeACD
- acd2tdt.c
- ACD to TDT conversion program
- acdXYY_datatypes.acd.tdt
- ACD datatypes for Daylight database
- acdXYY_datatypes.dcis.tdt
- DCIS database for Daylight database
- 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
- suppliers
- directory containing script for making ACD HTML header and footer
- units.dat
- ACD to TDT units table
- mol2smi.c
- Convert MDL MOL-file format to SMI/TDT
- smi2mol.c
- Convert SMI/TDT to MOL file; adds 2D via Depict if needed
- rd2tdt.c
- Convert MDL RD-file format to TDT
- rdf2datatdt.perl
- Convert text data from RD files to TDTs
- test.ccr.rdf
- Example dataset from CCR
- tdt2pdbdgeom.c
- Convert TDT to PDBDGEOM format
- pdbdgeom2tdt.c
- Convert PDBDGEOM format to TDT
- ros2tdt.c
- Convert ROSDAL to SMILES, output as TDTs
- du_rosin.c
- Interpret Rosdal into molecule or depiction
- syb2smi.c
- Convert Sybyl MOL2 format to SMILES/TDT
- 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
- CreateWDI
- sh script to convert data and build tables.
- DestroyWDI
- Drop tables created by CreateWDI.
- WDI-DESIGN.sql
- CREATE TABLE sql statements.
- create.sql
- CREATE INDEX sql; invoked after data is loaded.
- queries.sql
- Sample queries.
- wdi.cgi
- demo application written in perl.
- wdi013-unmerged-demo.tdt
- Demo data.
- wdi013.fixed.summary
- Summary written by tdtsummary.pl; used to come up with datatype design.
- wdi2sql.pl
- Converts TDTs to SQL.
- write_destroy.pl
- Creates destroy.sql which drops tables.
- depict.rules
- Rubicon rules for creating 2D depictions
- smarts_examples.html
- Example SMARTS with descriptions
- smi_to_2d.f
- Adds 2D coordinates to THOR Datatrees with SMILES
- fptest.f
- Fingerprint a molecule, print information
- merload.f
- Load Merlin pool
- merrelease.f
- Release Merlin pool
- echotalk.f
- Minimal pipetalking program
- pipetalker.f
- Program which talks to one program via a pipe
- verbosetalk.f
- Demonstration program for writing to/from pipes
- look4.f
- Filter SMILES input using SMARTS
- cansmi.f
- Generate canonical (unique) SMILES
- protons.f
- Count protons in a molecule
- showmf.f
- Print a molecule's molecular formula
- thorirefs.f
- Find and print all indirect references in a database
- thorpick.f
- Write selected datatypes from a database to a TDT file
- thorlist.f
- Write a database to a TDT file
- 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
- du_fp2str.c
- Convert fingerprint object to THOR's ASCII version
- du_str2fp.c
- Convert THOR's ASCII fingerprints to FP object
- du_name2fp.c
- Generate fingerprint for an arbitrary ASCII string
- du_smartin.c
- Like dt_smartin(), but takes NULL-terminated string
- 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_mwt.c
- Functon returning molecular weight.
- 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
- du_printfdt.c
- Print a TDT object in "FDT"format
- du_printtdt.c
- Print a TDT in a formatted ASCII form
- 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_dbopen.c
- Functions for interactive database opening.
- du_fgetline.c
- Read an arbitrarily-long string from input
- du_memory.c
- Memory handling functions.
- du_mergesort.c
- General-purpose sorting algorithm
- du_misc.c
- Miscellaneous
- 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.c
- Convert SMILES file to TDT file
- tdt2smi
- Convert TDT file to SMILES file (shell script)
- tdtcat.c
- Read/write TDT files (illustrates du_tdtfileio.c)
- 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
- clogptalk.sh
- Shell wrapper around clogptalk, for Daycart
- contrib_clean.sql
- SQL to uninstall contrib code from Oracle
- contrib_create.sql
- SQL to install contrib code in Oracle
- echotallk.sh
- Shell wrapper around echotalk, for Daycart
- echo.sql
- Example program object using simple echo of arguments
- muguser.sql
- SQL to create a mug/coffee user with Daycart privileges
- normal_vcs.sql
- SQL example salt and transform normalizations for VCS.
- build_dayperl
- A utility which builds the dayperl package
- dayperl.html
- installation and help
- 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
- kekule.pm
- returns the Kekule form of a smiles
- kekule.pl
- returns the Kekule form of a smiles
- 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
- thorsummary.pl
- db content summarizer; output similar to sthorman's
- tpsa.pl
- translation of Peter Ertl's tpsa.c, by Eric Allen
- PyDaylight-0.8.tar.gz
- PyDaylight version 0.8 archive
- cansmi.py
- Canonicalize SMILES
- match.py
- SMARTS pattern match demo program
- mcl.py
- Converts MCL to PyDaylight code
- pildepict.py
- Create PIL image from a SMILES
- test.py
- PyDaylight test
- thorget.py
- Thor lookup
- CGIPARSE.pm
- Perl package for parsing CGI data
- CGI_Lite.pm
- Perl CPAN package for handling files, etc.
- DU_LIB.pm
- Some Daylight-user non-toolkit utility subroutines
- DU_TLIB.pm
- Some Daylight-user toolkit utility subroutines
- DU_JAVA.pm
- Code to include JavaGRINS
- cansmi.cgi
- Canonicalize SMILES w/ options
- depict.cgi
- Depict SMILES CGI web app (no DayPerl)
- depict-file.cgi
- Depict from file
- daybase.cgi
- Simple Thor/Merlin CGI (no DayPerl)
- daytops.cgi
- Interface to PrintPackage (PS output)
- depictmatch.cgi
- Depict and show SMARTS match
- mol2smi.cgi
- Convert Molfile to SMILES/TDTs
- pcmodels.cgi
- PCModels (Clogp/CMR) interface
- react.cgi
- Apply reaction transforms
- rubicon.cgi
- Rubicon interface
- stigmata
- Stigmata, structural commonalities analyzer
- thor.cgi
- simple read/write Thor interface
- tdt2html.pl
- Converts TDTs to HTML w/ smi2gif depictions
- tdt2smi.pl
- TDTs to SMILES
- tdt2fdt.pl
- Converts TDTs to FDT for daytops.cgi (Treetops)
+==========================================================================+ | This source code is public domain, and may be freely distributed, | | modified, and used for any purpose. IT COMES WITH ABSOLUTELY NO | | WARRANTY OF ANY KIND. | +==========================================================================+
Daylight Chemical Information Systems Inc.