Design

The WWW (world wide web) philosophy allows HTMLs and CGIs to reference each other via URLs (uniform resource locations) without restriction. This "footloose" approach works well for a fundamentally disorganized collection of resources (what else can you do?) but is not adequate to achieve Daylight's goals.

To keep things supportable, we have adopted a strict organization of our HTMLs and CGIs (called components) which includes some rather severe restrictions on the way URL references are used:

• All system components system appear under two aliases (or "logical directories"):
  • "/daycgi/" (CGI programs and scripts),
  • "/dayhtml/" (HTML documents and supporting files) and
• All components exist as part of a named "package", which appear as one or more subdirectories of the aliased logical directories and are named after the package. E.g., the HTMLs for the "database" package are found under the directory "/dayhtml/databases"
• Each package publishes a set of URLs which start with one of the above three aliases. In fact, the set of published URLs for a package is the definition of that package's interface. As long as that package is supported, the published URLs will exist and remain valid. Conversely, the URLs of unpublished components are expressly not supported (they may disappear or change function in future releases).
• Package components may reference only:
  • local URLs (files in the package directory or its subdirectories)
  • published URLs of other packages

Published URLs, by package

/daycgi/coord2cex

Produce a CEX molecule from Daylight CGI context variables "smiles" and "coords", send it as a CEX object on standard output with mime type "x-cex-3d". No arguments are accepted.

/daycgi/dcgi_env.sh

Establish Daylight CGI environment in /bin/sh, e.g., define DY_ROOT, CX_ROOT, standard image sizes, etc.

/daycgi/depict

Invoke page providing interactive depiction of SMILES. A hex-encoded SMILES is accepted as an optional argument.

/daycgi/depictform

Invoke /daycgi/depict from a form entry containing INPUT field "smiles".

/daycgi/hyperthor [dbname [idtag [idval]]]

Thor database browser with hyperactive tendencies. All three arguments are optional. If dbname is not specified, tries to connect to thorserver on the local host; if unsuccessful, allows interactive specification of the server. The entry point /daycgi/hyperthorall offers all databases (i.e., including normally invisible databases).

/daycgi/hypertree dbname idtag idval [hints]

Display HTML Thor datatree(s) for idtag-idval in given database. Optional argument `hints' may be "*ALL" or a membership class name the form "*class", e.g., "*Common". Data tuple summaries are produced for items per the bar-delimited list in environment variable "DY_TUPLESUM_TAGS". This (currently) uses the external utilities depict (for items per DY_DEPICT_TAGS), smi2gif (per DY_DRAW2D_TAGS and DY_SCHEMA_TAGS) and coord2cex (per DY_DRAW3D_TAGS). External utilities are provided as per "DY_DCGI_HOST" (if not defined, the local host).

/daycgi/post4eval

Convert FORM/POST output stream to DCGI_ environment variables.

/daycgi/postfilter

Convert FORM/POST output stream to simpler DCGI context (pairs of name/value lines).

/daycgi/shortdbname

Simplify string in standard database name syntax (base%pw@host:service:user%upw) for display; options are [-a(ll) | -b(ase) | -h(ost) | -s(s) | -u(ser)] [ -x defaultservice ]. Default settings are "-h -x thor".

/daycgi/smi2gif

Produces an automatically-generated depiction from a hex-encoded smiles argument. Colormode is color-on-black, geometry is set from DY_WIDE_WIDTH and DY_WIDE_HEIGHT (set to 200x400 in dcgi_env.sh).

/daycgi/smi2gif-bop

Like /daycgi/smi2gif, but produces a black-on-paper image. This is generally used to draw depictions in an HTML document which is to be printed on a monochrome printer.

/daycgi/smi2gif-small

Like /daycgi/smi2gif, but produces a DY_SMALL_WIDTH x DY_SMALL_HEIGHT image (set to 96x64 in dcgi_env.sh). This is generally used to draw molecular icons.

/daycgi/acd

A simplified interface to the Available Chemicals Directory. Accepts a single optional argument, a hex-encoded identifier value.

/daycgi/savant

A simplified interface to the Spresi database providing a survey of the synthetic literature. Accepts a single optional argument, a hex-encoded SMILES.

/daycgi/wdi

A simplified interface to the World Drug Index. Accepts a single optional argument, a hex-encoded identifier value.

/daycgi/wizard [@host:service:user]

An MCL-based hypertext interface to the Merlin search engine. The initial merlinserver connection is defined by the optional argument with defaults as per the environment variables DY_WIZ_HOST (localhost), DY_WIZ_SERVICE ("merlin"), and DY_WIZ_INFOUSER ("thorinfo").

/dayhtml/doc/index.html

Index to "documentation" package, includes Daylight Theory Manual, Daylight Adminstration Manual, Daylight Programmer's Tutorial, Daylight Reference Manual, and more.

/dayhtml/doc/release_notes/index.html

Index to the release notes specific to a particular version of Daylight Software.

/dayhtml/help/shortnames.html

Short chemical names in demo databases.

/dayhtml/index.html

Index to everything, "home page" for Daylight Software.