MUG'01 -- 6-9 March 2001 -- Santa Fe, NM

Jeremy Yang

Contrib Highlights

What is Contrib?

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


  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 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.


  depict.rules         Rubicon rules for creating 2D depictions


  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        Shell script to add SMILES to monomer definitions


  ProgOb.perl          Example Perl program object


  stigmata             Reads SMILES produces TDT's with atom scores            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


  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"


  findsubs             Find/organize substituted parent molecules SMILES file


  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


  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


  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


  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


  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


  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))


  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.


  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)


  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


  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


  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.


  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
  thorlist             Write a database to a TDT file
  thorpick             Write selected datatypes from 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_name2fp           Generate fingerprint for an arbitrary ASCII string
  du_str2fp.c          Convert THOR's ASCII fingerprints to FP object


  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
  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:            A sample program which calcs mol weights            non-toolkit utility subroutines      molweight subroutine           toolkit utility subroutines             adds 2D data to TDTs         adds ClogP data via progob           add molweight to TDT stream       A sample program which calls            canonicalizes smiles   non-toolkit ClogP bomb shelter           identifies ClogP fragments in molecules           virtual library GA         Merlin searches, interactive           find minimum path between two atoms             transform SMILES with SMIRKS (reaction transforms)           find ringsystems, write smiles       find ClogP fragments, write smiles           write GIFs using dcgi_smi2gif           SMILES to GRAPH           SMILES to TDTs          TDTs to ascii-formatted pages           TDTs to SMILES           TDTs to TAB files            non-toolkit TDT processor        non-toolkit TDT summarizer           filter TDTs based on timestamps        get Thor db info           similar to thorlookup

src/www:          Perl package for parsing CGI data          Perl CPAN package for handling files, etc.           Code to include JavaGRINS            Some Daylight-user non-toolkit utility subroutines           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           Converts TDTs to FDT for daytops.cgi (Treetops)          Converts TDTs to HTML w/ smi2gif depictions           TDTs to SMILES
  thor.cgi             simple read/write Thor interface


  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
  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


  pdbdgeom2tdt         Convert PDBDGEOM format to TDT
  tdt2pdbdgeom         Convert TDT to PDBDGEOM format


  du_rosin             Interpret Rosdal into molecule or depiction
  ros2tdt              Convert ROSDAL to SMILES, output as TDTs


  syb2smi              Convert Sybyl MOL2 format to SMILES/TDT 


  MakeWDI              Convert World Drug Index (SD files) to Thor database          Convert mol2smi output to Daylight-friendly datatypes       Reorder dataitems in TDTs
  wdi_datatypes.dcis.tdt List of std Daylight datatypes in WDI
  wdi_datatypes.wdi.tdt List of special WDI datatypes          Sample WDI SD file

Contrib Greatest Hits:


MUG'01 -- 6-9 March 2001 -- Santa Fe, NM

Daylight Chemical Information Systems Inc.