) means new in 4.71 or significantly
revised.
The following index is produced by the "make_index.pl" script.
NOTE: () means new in 4.71 or significantly
revised.
- 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
- thorfix431
- Update pre-4.31 databases
- thorfixquotes
- Part of thorfix431; fix mismatched quotes
- transfer_data
- Transfer data from one database to another.
- thordbsize
- How big is a database?
- clusterview
- View the output of the clustering package
- do_cluster
- A shell script to cluster an example SMILES file
- add_mono_smiles
- Add SMILES to definitions in a monomer database
- add_smiles.sh
- Shell script to add SMILES to monomer definitions
- 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
- mol2smi
- Convert MDL MOL-file format to SMI/TDT
- smi2mol
- Convert SMI/TDT to MOL file; adds 2D via Depict if needed
- rd2tdt
- 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
- Convert TDT to PDBDGEOM format
- pdbdgeom2tdt
- Convert PDBDGEOM format to TDT
- ros2tdt
- Convert ROSDAL to SMILES, output as TDTs
- du_rosin
- Interpret Rosdal into molecule or depiction
- syb2smi
- 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
- ProgOb.perl
- Example Perl program object
- 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
- smi_to_2d
- Adds 2D coordinates to THOR Datatrees with SMILES
- spewsmi
- Illustrates a trivial "drawing library"
- plotsmi
- Generates depictions for plot(1) program (Sun only)
- plotsmi_v
- 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.a
- Generates vector-label characters
- findsubs
- Find/organize substituted parent molecules SMILES file
- addfp
- Add fingerprints to TDTs
- chifinger
- Program for chiral fingerprinting experiments
- ringfinger
- Program for ring fingerprinting experiments
- smi2fp_ascii
- Generate fingerprints, write binary in ASCII form
- tdt2fp_ascii
- Convert fingerprints to ASCII form
- ascii2bin
- Ascii-encoded binary to 1's and 0's
- bin2ascii
- 1's and 0's to ascii-encoded binary
- simatrix
- Similarity matrix of input SMILES
- simogram
- Similarity histogram of input SMILES
- minimer
- Simple Merlin client
- testmerlin
- Comprehensive "encyclopedia" of Merlin Toolkit calls
- 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
- 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
- clogpaccess
- Example program that uses CLOGP program object
- stringtalker
- Example program, illustrates "string" mode
- shelltalk
- Example program object, a bourne-shell script
- verbosetalk
- Example program object using Daylight Toolkit
- findpath
- Find multi-step reaction sequences
- findrxn
- Find reactions with common reactants and products
- maprxn
- Template-based atom mapper
- rxntest1
- Reaction test program
- rxntest2
- Reaction test program
- rxntest3
- Reaction test program
- react
- Apply a transform (SMIRKS) to input molecules (SMILES).
- testatom
- Atom map test program
- constrain_distance
- Simple rubicon illustration of libdc_rube.a library
- sample_distances
- Simple rubicon illustration of libdc_rube.a library
- pma_pharm
- Rubicon-based filter, estimates PMA pharmacophore fit
- hbonds
- Find potential intramolecular hydrogen bonds
- smarts_filter
- Filter SMILES input using SMARTS (like grep(1))
- look4n
- Look for SMARTS in SMILES up to count N
- mark
- marks string attributes
- chain
- find longest hydrocarbon chain in molecule
- smales
- identifies specific SMARTS-targets given generic SMARTS-targets
- 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
- 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
- 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
- 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)
- tdt2bin
- Convert binary data in TDT to a binary file (e.g. GIF)
- 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
- 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, non-exclusive selection of molecules
- depict_usage_5
- Depict Widget, exclusive selction of a molecule
- smarts_usage
- Depict Widget, coloring via SMARTS pattern
- 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
- status_usage_1
- Status Widget, displaying task's progress
- status_usage_2
- Status Widget, displaying task's progress
- 3d_usage
- 3D Widget, interactive display of conformations
- tdt_usage
- TDT Widget, display/edit a THOR Datatree
- smi_to_2d
- Adds 2D coordinates to THOR Datatrees with SMILES
- fptest
- Fingerprint a molecule, print information
- merload
- Load Merlin pool
- merrelease
- Release Merlin pool
- echotalk
- Minimal pipetalking program
- pipetalker
- Program which talks to one program via a pipe
- verbosetalk
- Demonstration program for writing to/from pipes
- look4
- Filter SMILES input using SMARTS
- cansmi
- Generate canonical (unique) SMILES
- protons
- Count protons in a molecule
- showmf
- Print a molecule's molecular formula
- thorirefs
- Find and print all indirect references in a database
- thorpick
- Write selected datatypes from a database to a TDT file
- thorlist
- 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
- 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_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.tdt
- 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_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)
- 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
- build_dayperl
- A utility which builds the dayperl package
- dayperl.test
- Very simple test to see if DayPerl is working
- dayperl.html
- A very brief overview of the system
- dayperl.pod
- Same as above, but in its native pod format
- dayperl_talk.html
- The html for Alex's talk on DayPerl
- build_dayperl.html
- brief instructions (START HERE)
- build_dayperl-1.1.html
- The original brief instructions (OBSOLETE)
- 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
- 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
- mol2smi-file.cgi
- Convert Molfile to SMILES/TDTs from file
- pcmodels.cgi
- PCModels (Clogp/CMR) interface
- react.cgi
- Apply reaction transforms
- rubicon.cgi
- Rubicon interface
- 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.