PCmodels Manual

Copyright notice

This document and the xvpcmodels program discussed herein are copyrighted © 1991-2011 by Daylight Chemical Information Systems, Inc. Daylight explicitly grants permission to reproduce this document under the condition that it is reproduced in its entirety, including this notice. All other rights are reserved.

Table of Contents

3.1 Defining an input structure
3.2 Selecting Model CLOGP or CMR
3.3 Selecting Output Level
3.4 Text Operations
3.5 DEPICT, Help, Etc.

6. Modifying or adding CLOGP fragment data

1. About PCmodels; Scope of this manual

• This "User Guide", intended to provide a working knowledge of interactive and batch interfaces to the PCmodels algorithms.
• The "CLOGP Reference Manual" which describes the theory and methodology of the CLOGP algorithm for hydrophobicity estimation, including examples.
• The "CMR Reference Manual" which describes the theory and methodology of the CMR algorithm for polarizability estimation, including examples.

2. Getting Started

• The PCmodels module has been installed (see installation instructions)
• Local environment variables have been defined.
• The Daylight software license is valid for "xvpcmodels", "clogp", and "cmr".
• To start the program enter "xvpcmodels" (on IRIX/SGI, enter "xvpcmodels4d").

3. Interactive PCmodels usage: xvpcmodels

3.1. Defining an input structure

GRINS provides graphical structure specification. To use GRINS, press the Grins button and the GRINS window should appear, as shown below:

The GRINS widget is described in the Daylight Widgets User Guide. Refer to that document for detailed instructions. GRINS allows the user to graphically edit a structure from atoms, bonds, templates, and parent molecules. When the structure has been selected in GRINS, the SMILES for the structure will appear in xvpcmodels' input text pane.

A third way to define the input structure is to load a SMILES file into the input text pane, locate the cursor on the desired SMILES, and then press the Compute button. Note that the triangular cursor in the input text pane may be placed anywhere on the SMILES line; the syntax of a SMILES line is a SMILES string followed by an optional space and name.

Refer to the section "Text operations" in the following pages for details of loading text files, writing text files, and handling text files using the text pane windows and popup menus.

3.2. Selecting Model CLOGP or CMR

3.3. Selecting Output Level

Changing the output level invokes model computation.

3.4 Text Operations

To load a file into the input text pane, select "Load file"/"Open" from the Text-File submenu. To save the contents of the output text pane, select "Store as New File"/"Save As" from the Text-File submenu.

To find a selected string, select "Find Selection" from the Text-Find submenu. To find the same string again, select "Again" from the Text-Edit submenu.

3.5. Depict, Help, etc.

The Help widget is invoked by selection the Help button on the main xvpcmodels window.

4. Using PCmodels batch filters

These programs read in a TDT(THOR Data Tree) file and write out a TDT file with CLOGP or CMR data added. The program clogp is used in the following examples; cmr has identical commands.

To add CLOGP data to a TDT file, enter:

        % clogp < infile.tdt > outfile.tdt

or
        % clogp infile.tdt outfile.tdt

        % clogp -HELP 


+----------------------------------------------------------+
| CLOGP -- Add CLOGP results from/to .TDT files            |
+----------------------------------------------------------+
| Copyright  1990-2011 (c) Daylight CIS, Inc.              |
| Copyright  1985-2011 (c) Pomona College                  |
+----------------------------------------------------------+
| $ clogp [options] [infile.tdt [outfile.tdt]]             |
|     Copy .TDT input file to output file, adding CLOGP    |
|     polarizability estimate as a CLOGP datum.  The CLOGP |
|     datatype has 3 fields:  CP.   |
|     Output to standard output if second argument is      |
|     missing. Input from standard input if no arguments   |
|     are given.  Exit w/ warning if CLOGP is inaccessible;|
|     copy unchanged input tree to output on other errors, |
|     e.g., invalid input, CLOGP can't make valid estimate.|
|                                                          |
| $ clogp -HELP [TRUE|FALSE]                               |
|     Write this help message to standard output and exit. |
|                                                          |
| $ clogp -PCMODELS_VERSION [TRUE|FALSE]                   |
|     If true, writes the version numbers of the program,  |
|     Biobyte algorithm, and database to standard output.  |
|                                                          |
| $ clogp -PCMODELS_ERRORTEXT [TRUE|FALSE]                 |
|     Write a list of English translations of all possible |
|     CLOGP error levels to standard output and exit.      |
|     Format is: $I<-{errorlevel}P;{translation}>|.        |
|                                                          |
| $ clogp -PCMODELS_ERRORWORST [ERROR_LEVEL]               |
|     For TDT output, suppresses any output above the      |
|     given ERROR_LEVEL threshold.  The default is '999',  |
|     eg. all results are shown.                           |
|                                                          |
| $ clogp -PCMODELS_TABLEOUTPUT [TRUE|FALSE]               |
|     Set output format to verbose tables.                 |
|                                                          |
| $ clogp -PCMODELS_DUMPFRAGDB [TRUE|FALSE]                |
|     Dump fragment database to standard output and exit.  |
+----------------------------------------------------------+



Note that these command line options are Daylight options which must be
defined.
5. Using PCmodels with other Daylight Software
The fundamental connecting thread of all Daylight software is the chemical
nomenclature SMILES. In a window environment, SMILES may be copied from
other Daylight programs and pasted to the xvpcmodels window. SMILES
and TDT files written by other programs can be read into the input text
pane of xvpcmodels, or processed by batch programs clogp
and cmr. Output TDT files can be loaded into Daylight databases.
6. PCmodels Management
PCmodels includes a facility for adding and modifying CLOGP fragment data.
This "algorithm manager" does not include a user-friendly interface, but
provides full access to CLOGP fragment constants.
6.1 Modifying or adding CLOGP fragment data
Temporarily modifying or adding fragment data is achieved by editing fragdb.del
to include the new data. The new data will be available the next time clogp
(or xvpcmodels or clogptalk) is started. To make such changes
permanent, delete the file fradb(relno).bin, (e.g. fradb461.bin), then
run clogp (or xvpcmodels or clogptalk) which will
automatically recreate fradb(relno).bin from fradb(relno).dat and fradb.del.
Finally, create an empty fradb.del fro subsequent changes.

Methods for determining the values to be added is beyond the scope of
this help text. However, briefly speaking, the best way to obtain a fragment
value is to compare two high-confidence LOGP values for compounds differing
only in that one possesses the given fragment.

Once the values are determined, it is fairly straightforward to add
them to the data files. The first step should be to assure that the fragment
is not already defined. Note that if a fragment is reported missing in
a CLOGP calculation, this is only relevant to a particular atom environment
(e.g. two aliphatic-atom and one aromatic-atom connection). Two ways of
searching for an existing fragment are (1) by inspecting the data files
(tricky) and (2) running CLOGP for test compounds to try each case.

If the fragment does not exist in the data files, a name must be assigned
in an "ENGLISH" line. To add a fragment value, an "FVALUE" line must be
added. Also, optionally, the following parameters may be defined for the
fragment: BRANCH, PROXTYPE, OHCONT, NEVERAGE, ZWITTER, OCLASS, SIGMA, and
RHO. For descriptions of these parameters, refer to the CLOGP Reference
Manual.

It is also possible, but not recommended, to modify "CLOGP constants"
(CONSTANTs and OVALUEs).

Contact Daylight Technical Support for more information on CLOGP customization.
7. PCmodels Programming "Toolkit": clogptalk and cmrtalk
In order to support users who wish to run CLOGP or CMR from their own programs,
the current version of Daylight includes the programs "clogptalk" and "cmrtalk",
which are designed to be accessed as "program objects" by a calling program.
This program-object method is much faster than using the C function "system()".
For details, see the source files in the $DY_ROOT/contrib/src/c/progob.