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

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?

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

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 NEW

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 NEW

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

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 NEW

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

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

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 NEW

Adjusts H-count to usual values for atoms in brackets.

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 NEW

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 NEW

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 NEW

Depict Widget, smifile argument

depictmol.c NEW

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

depict.rules

Rubicon rules for creating 2D depictions

smarts_examples.html NEW

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 NEW

Memory handling functions.

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.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

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 NEW

returns the Kekule form of a smiles

kekule.pl NEW

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 NEW

db content summarizer; output similar to sthorman's

tpsa.pl NEW

translation of Peter Ertl's tpsa.c, by Eric Allen

Thanks to David Nunn of Wyeth-Ayerst for kekule.pm.

PyDaylight-0.8.tar.gz

PyDaylight version 0.8 archive

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)