eduSoft LC Toolkits Programmers' Guide

eduSoft LC Toolkits Programmers' Guide

Toolkit Installation, Guidelines and Background

Introduction to eduSoft LC Toolkits

For a number of years the functionality of two of our programs, HINT and Molconn-Z, has been available in pre-packaged executables where the usage was severely restricted by menu systems that were either mandated by a host program (such as Sybyl) or otherwise necessary to operate the programs. This restrictive architecture did not even allow us, as we developed new algorithms and applications, sufficient flexibility to incorporate our ideas into the programs. Thus, we have been developing these toolkit packages for three purposes: 1) to make it easier for us to keep our HINT and Molconn-Z programs current; 2) to provide a mechanism for end-user programmers to incorporate our algorithms into their programs, for both internal and (potentially) distributed use; and 3) to broaden the platform availability of HINT and Molconn-Z in a manner that is very flexible as we respond to new innovations in computer hardware and software.

Introduction to the Molconn-Z Toolkit

The Molconn-Z Toolkit is a new collection of functions designed to be simply and efficiently incorporated into proprietery code in applications of drug discovery, database analysis and mining, and other places where the non-empirical Molconn-Z paramater set can be useful.

This toolkit is a complete re-write of the venerable Molconn code of Lowell Hall (Eastern Nazarene College). The toolkit is now more modular and in the "C" programming language. It has been developed under the SGI Irix 6.5.11 operating system, but compiles under Linux and will very likely port to other platforms as needed.

Inspiration for the Molconn-Z toolkit comes from our friends and colleagues at Daylight Chemical Information System, Inc. (Dave Weininger) and at OpenEye Scientific Software, Inc. (Ant Nicholls, Matt Stahl and Roger Sayle). As do Daylight and OpenEye tools, the molconnz toolkit communicates through the use of "handles", that are persistent identifiers to blocks of data that may be atoms, molecules, or molconnz parameters. A handle is created at the time that a data structure is created, e.g., a new molecule or molconnz parameter set. With the handle, specific data values or groups of data can be obtained from the toolkit and used as desired in the main program. In effect the handle is a "key". In the eduSoft implementation of toolkit programming the handles are identified with variable type ehandle. Using this toolkit/program structure it is possible to construct programs that maintain molconnz parameters for many molecules simultaneously, in such a way that patterns and similarities can be exploited as the data is created, rather than by later analysis of a dump file.

Installation of Molconn-Z Toolkit

SGI platforms (IRIX)
The molconnz toolkit is distributed as a gzipped tar that you probably got as a download from our FTP server. The libraries were compiled for this version using SGI cc/CC (version 7.2.1) compilers under IRIX 6.5. Installation is simple;

  1. Create an eduSoft directory in a convenient location like /usr/.
  2. cp mcztk410_irix.tar.gz /usr/eduSoft/
  3. gunzip mcztk410_irix.tar.gz
  4. tar xovf mcztk410_irix.tar
  5. Edit /usr/eduSoft/mcztoolkit4.10_irix/cshrc so that EDUSOFT_ROOT is correct. If you are using the Daylight toolkit, fix DY_ROOT. If you have your own release of OELib, fix the definition for OE_ROOT.
  6. Install the molconnz toolkit license as described in the key installation instructions. The license locks the executable(s) created to a single node. Additional "run-time" node licenses are available at a nominal cost.
  7. The current version of the html toolkit programmer's guide is included in the distribution in the /usr/eduSoft/mcztoolkit4.10_irix/toolkit_docs directory. You may wish to link it or copy it to a more convenient location for your browser.
  8. Note that the make files described below are designed to work with a standard installation, but we can't anticipate the names of subdirectories, etc., so it may be necessary to edit these files for your installation.
  9. For this platform two versions of the eduSoft library are provided (libESLC.a and libESLC_nosyb.a). The latter is for use if you do not have access to the Sybyl libraries that are only used for creation of 3D contour files within Sybyl.

Sun platforms (SOLARIS)
The molconnz toolkit is distributed as a gzipped tar that you probably got as a download from our FTP server. The libraries were compiled for this version using GNU compiler version 2.95.2 19991024, on a sparc-sun-solaris2.7 machine. Installation is simple;

  1. Create an eduSoft directory in a convenient location like /usr/.
  2. cp mcztk410_solaris.tar.gz /usr/eduSoft/
  3. gunzip mcztk410_solaris.tar.gz
  4. tar xovf mcztk410_solaris.tar
  5. Edit /usr/eduSoft/mcztoolkit4.10_solaris/cshrc so that EDUSOFT_ROOT is correct. If you are using the Daylight toolkit, fix DY_ROOT. If you have your own release of OELib, fix the definition for OE_ROOT.
  6. Install the molconnz toolkit license as described in the key installation instructions. The license locks the executable(s) created to a single node. Additional "run-time" node licenses are available at a nominal cost.
  7. The current version of the html toolkit programmer's guide is included in the distribution in the /usr/eduSoft/mcztoolkit4.10_solaris/toolkit_docs directory. You may wish to link it or copy it to a more convenient location for your browser.
  8. Note that the make files described below are designed to work with a standard installation, but we can't anticipate the names of subdirectories, etc., so it may be necessary to edit these files for your installation.

Intel platforms (LINUX)
The molconnz toolkit is distributed as a gzipped tar that you probably got as a download from our FTP server. The libraries were compiled for this version using GNU compiler version 2.96 under Red Hat Linux 7.1 (Linux 2.4 kernel). Installation is simple;

  1. Create an eduSoft directory in a convenient location like /usr/.
  2. cp mcztk410_linux.tar.gz /usr/eduSoft/
  3. gunzip mcztk410_linux.tar.gz
  4. tar xovf mcztk410_linux.tar
  5. Edit /usr/eduSoft/mcztoolkit4.10_linux/cshrc so that EDUSOFT_ROOT is correct. If you are using the Daylight toolkit, fix DY_ROOT. If you have your own release of OELib, fix the definition for OE_ROOT.
  6. Install the molconnz toolkit license as described in the key installation instructions. The license locks the executable(s) created to a single node. Additional "run-time" node licenses are available at a nominal cost.
  7. The current version of the html toolkit programmer's guide is included in the distribution in the /usr/eduSoft/mcztoolkit4.10_linux/toolkit_docs directory. You may wish to link it or copy it to a more convenient location for your browser.
  8. Note that the make files described below are designed to work with a standard installation, but we can't anticipate the names of subdirectories, etc., so it may be necessary to edit these files for your installation.
  9. For this platform two versions of the eduSoft library are provided (libESLC.a and libESLC_nosyb.a). The latter is for use if you do not have access to the Sybyl libraries that are only used for creation of 3D contour files within Sybyl.

Macintosh platforms (OS X)
The molconnz toolkit is distributed as a gzipped tar that you probably got as a download from our FTP server. The libraries were compiled for this version using the native compilers in Mac OS X.1. Installation is simple;

  1. Create an eduSoft directory in a convenient location like /usr/.
  2. cp mcztk410_macosx.tar.gz /usr/eduSoft/
  3. gunzip mcztk410_macosx.tar.gz
  4. tar xovf mcztk410_macosx.tar
  5. Edit /usr/eduSoft/mcztoolkit4.10_macosx/cshrc so that EDUSOFT_ROOT is correct. If you have your own release of OELib, fix the definition for OE_ROOT.
  6. Install the molconnz toolkit license as described in the key installation instructions. The license locks the executable(s) created to a single node. Additional "run-time" node licenses are available at a nominal cost.
  7. The current version of the html toolkit programmer's guide is included in the distribution in the /usr/eduSoft/mcztoolkit4.10_macosx/toolkit_docs directory. You may wish to link it or copy it to a more convenient location for your browser.
  8. Note that the make files described below are designed to work with a standard installation, but we can't anticipate the names of subdirectories, etc., so it may be necessary to edit these files for your installation.

Intel platforms (Win2k)
The molconnz toolkit is distributed as a PKZipped archive that you probably got as a download from our FTP server. In this case the package includes both a Microsoft Visual Studio® "workspace" that has been created for production of a simple executable linking OElib and the molconnz toolkit and an analogous CYGWIN (GNU) distribution. Also it should be pointed out, that inasmuch as there is interoperability between Windows programs among the various Windows OS releases, programs developed with this toolkit may work under Windows versions other than Windows2000®, but we have only lightly tested it.

Installation is simple;

  1. Create an eduSoft directory in a convenient location like C:\eduSoft\.
  2. PKunZip the file mcztk410_win2k.ZIP into the C:\eduSoft directory.
  3. Install the molconnz toolkit license as described in the key installation instructions into the C:\eduSoft\mcztoolkit4.10_win2k\license directory. The license locks the executable(s) created to a single node. Additional "run-time" node licenses are available at a nominal cost.
  4. Define the location of the Molconn-Z license using Windows environmental variables: MCONN_LICENSE=C:\eduSoft\mcztoolkit4.10_win2k\license\MolconnzToolkitLicense.dat.
    • For Windows2000® or WindowsXP®: use the Environment tab in the System monitor in the Control panel to set this value.
    • For Windows98 or WindowsME®: add a line set MCONN_LICENSE=C:\eduSoft\mcztoolkit4.10_win2k\license\MolconnzToolkitLicense.dat to the AUTOEXEC.BAT file.
  5. The current version of the html toolkit programmer's guide is included in the distribution in the C:\eduSoft\mcztoolkit4.10_win2k\toolkit_docs directory. You may wish to link it or copy it to a more convenient location for your browser.
  6. Note that the files included with the release are designed to work with a standard installation, but we can't anticipate the names of subdirectories, etc., so it may be necessary to edit these files for your installation.

Sample Molconn-Z Program Code

Using Daylight Toolkit (C)
A sample program, written in C, has been provided as part of the molconnz toolkit distribution to demonstrate linking with the Daylight Toolkit. This sample program is called DaylightTKMolconnZ.c and can be found in the distribution source directory. It is structured to highlight the use(s) of the molconnz toolkit and the Daylight (smiles in particular) toolkit rather than to produce elegant output. As such, there are three parts to the program: 1) Reading molecule data using Daylight smiles input functionality; 2) collecting the important molecular and atomic data for each molecule from Daylight data structures (i.e., elements, bonds, bond orders, formal charges) and passing that data to the molconnz toolkit to create molecule and molconnz data objects; and 3) retrieving and reporting specific molconnz parameters for each molecule.

There are simple make files for producing the DaylightTKMolconnZ executable in the distribution source directory. Note, however, that licenses for the Daylight smiles toolkit must be obtained from Daylight in order to produce a functional DaylightTKMolconnZ executable. Once created, the DaylightTKMolconnZ executable is simply run as follows:

./DaylightTKMolconnZ n smiles,

where n is 0 if smiles is a smiles string, and n is 1 if smiles is a smiles file.

You may need to properly install the license for the molconnz toolkit; if so, see the key installation instructions.

Using OpenEye's OELib (C++)
A sample program, written in C++, has been provided as part of the molconnz toolkit distribution to demonstrate linking with the OELib open source chemical data manipulation library of OpenEye Scientific Software. This sample program is called OElibMolconnZ.cpp and can be found in the distribution source directory. It is structured to highlight the use(s) of the molconnz toolkit and OELib rather than to produce elegant output. As such, there are three parts to the program: 1) Reading molecule data using OELib from a variety of data formats (e.g., smiles, sdf, mol2, etc.); 2) collecting the important molecular and atomic data for each molecule from OELib (elements, bonds, bond orders, formal charges) and passing that data to the molconnz toolkit to create molecule and molconnz data objects; and 3) retrieving and reporting specific molconnz parameters for each molecule.

For convenience and with the permission of OpenEye, we have provided OELib archives with the molconnz toolkit distribution. (The source code for OELib is available for free download at the OpenEye website: www.eyesopen.com/links.html and is to be considered the authoritative version.) Also in the distribution source directory are simplified make files for creating the OElibMolconnZ executable with unix operating systems and a workspace (Microsoft Virtual Studio) for Windows2000®.

Once created, the OElibMolconnZ executable, is simply run as follows:

./OElibMolconnZ -iformat filename, [unix]

OElibMolconnZ -iformat filename, [win2k, in a "console" or MS-DOS window]

where format is one of the currently supported input types, and filename is the name of a molecular data file.

You may need to properly install the license for the molconnz toolkit; if so, see the key installation instructions.

The Distributed Standalone Molconn-Z (C++)
We also include molconnz410_day.cpp (include daylight options) and molconnz410_noday.cpp, the source code for the standalone molconnz executable (see http://www.edusoft-lc.com/molconn/manuals/400/) for more information on using this program. Makefile.molconnz410 is also included in the source directory of the distribution. Note that for platforms where Daylight tools are available, this program/makefile is written to link with the Daylight libraries. If you do not have access to these libraries, then you will need to use the molconnz410_noday.cpp and edit the Makefile for that option. Likewise, the OpenEye (OElib) references should be removed if you are not using OElib.

Introduction to the HINT Toolkit

The HINT Toolkit provides a convenient access mechanism for the unique HINT free energy scoring function(s) as well as access to the HINT 3D grid map objects. The toolkit is designed for end-user programmers to simply and efficiently incorporate these data objects into proprietery code in applications of drug discovery and biomolecular structure analysis.

This toolkit is a re-write of the core code that has been present in the HINT tools for a number of years. The code has been carefully re-constructed, with particular attention to speed and modularity. The underlying data structures (databse and dictionary) have been reevaluated and validated. Virtually all* of the toolkit is in the "C" programming language. It has been developed under the SGI Irix 6.5.11 operating system, but compiles under Linux and will very likely port to other platforms as needed.

*The "biosym" and "grasp" 3D map formats require "formatted binary" output which is written by FORTRAN. All other code in teh toolkit is "C".

Inspiration for the HINT toolkit comes from our friends and colleagues at Daylight Chemical Information System, Inc. (Dave Weininger) and at OpenEye Scientific Software, Inc. (Ant Nicholls, Matt Stahl and Roger Sayle). As do Daylight and OpenEye tools, the hint toolkit communicates through the use of "handles", that are persistent identifiers to blocks of data that may be atoms, molecules, or hint parameters. A handle is created at the time that a data structure is created, e.g., a new molecule or hint parameter set. With the handle, specific data values or groups of data can be obtained from the toolkit and used as desired in the main program. In effect the handle is a "key". In the eduSoft implementation of toolkit programming the handles are identified with variable type ehandle.

Installation of HINT Toolkit

SGI platforms (IRIX)
The hint toolkit is distributed as a gzipped tar that you probably got as a download from our FTP server. The libraries were compiled for this version using SGI cc/CC (version 7.2.1) compilers under IRIX 6.5. Installation is simple;

  1. Create an eduSoft directory in a convenient location like /usr/.
  2. cp hinttk306irix.gz /usr/eduSoft/
  3. gunzip hinttk306irix.gz
  4. tar xovf hinttk306irix
  5. Edit /usr/eduSoft/hinttoolkit3.06_irix/cshrc so that EDUSOFT_ROOT is correct. If you are using the Daylight toolkit, fix DY_ROOT. If you have your own release of OELib, fix the definition for OE_ROOT.
  6. Install the hint toolkit license as described in the key installation instructions. The license locks the executable(s) created to a single node. Additional "run-time" node licenses are available at a nominal cost.
  7. The current version of the html toolkit programmer's guide is included in the distribution in the /usr/eduSoft/hinttoolkit3.06_irix/toolkit_docs directory. You may wish to link it or copy it to a more convenient location for your browser.
  8. Note that the make files described below are designed to work with a standard installation, but we can't anticipate the names of subdirectories, etc., so it may be necessary to edit these files for your installation.

Sun platforms (SOLARIS)
The hint toolkit is distributed as a gzipped tar that you probably got as a download from our FTP server. The libraries were compiled for this version using GNU compiler version 2.95.2 19991024, on a sparc-sun-solaris2.7 machine. Installation is simple;

  1. Create an eduSoft directory in a convenient location like /usr/.
  2. cp hinttk306solaris.gz /usr/eduSoft/
  3. gunzip hinttk306solaris.gz
  4. tar xovf hinttk306solaris
  5. Edit /usr/eduSoft/hinttoolkit3.06_solaris/cshrc so that EDUSOFT_ROOT is correct. If you are using the Daylight toolkit, fix DY_ROOT. If you have your own release of OELib, fix the definition for OE_ROOT.
  6. Install the molconnz toolkit license as described in the key installation instructions. The license locks the executable(s) created to a single node. Additional "run-time" node licenses are available at a nominal cost.
  7. The current version of the html toolkit programmer's guide is included in the distribution in the /usr/eduSoft/hinttoolkit3.06_solaris/toolkit_docs directory. You may wish to link it or copy it to a more convenient location for your browser.
  8. Note that the make files described below are designed to work with a standard installation, but we can't anticipate the names of subdirectories, etc., so it may be necessary to edit these files for your installation.

Intel platforms (LINUX)
The hint toolkit is distributed as a gzipped tar that you probably got as a download from our FTP server. The libraries were compiled for this version using GNU compiler version 2.96 under Red Hat Linux 7.1 (Linux 2.4 kernel). Installation is simple;

  1. Create an eduSoft directory in a convenient location like /usr/.
  2. cp hinttk306linux.gz /usr/eduSoft/
  3. gunzip hinttk306linux.gz
  4. tar xovf hinttk306linux
  5. Edit /usr/eduSoft/hinttoolkit3.06_linux/cshrc so that EDUSOFT_ROOT is correct. If you are using the Daylight toolkit, fix DY_ROOT. If you have your own release of OELib, fix the definition for OE_ROOT.
  6. Install the hint toolkit license as described in the key installation instructions. The license locks the executable(s) created to a single node. Additional "run-time" node licenses are available at a nominal cost.
  7. The current version of the html toolkit programmer's guide is included in the distribution in the /usr/eduSoft/hinttoolkit3.06_linux/toolkit_docs directory. You may wish to link it or copy it to a more convenient location for your browser.
  8. Note that the make files described below are designed to work with a standard installation, but we can't anticipate the names of subdirectories, etc., so it may be necessary to edit these files for your installation.

Macintosh platforms (OS X)
The hint toolkit is distributed as a gzipped tar that you probably got as a download from our FTP server. The libraries were compiled for this version using the native compilers in Mac OS X.1. Installation is simple;

  1. Create an eduSoft directory in a convenient location like /usr/.
  2. cp hinttk306macosx.gz /usr/eduSoft/
  3. gunzip hinttk306macosx.gz
  4. tar xovf hinttk306macosx
  5. Edit /usr/eduSoft/hinttoolkit3.06_macosx/cshrc so that EDUSOFT_ROOT is correct. If you have your own release of OELib, fix the definition for OE_ROOT.
  6. Install the hint toolkit license as described in the key installation instructions. The license locks the executable(s) created to a single node. Additional "run-time" node licenses are available at a nominal cost.
  7. The current version of the html toolkit programmer's guide is included in the distribution in the /usr/eduSoft/hinttoolkit3.06_macosx/toolkit_docs directory. You may wish to link it or copy it to a more convenient location for your browser.
  8. Note that the make files described below are designed to work with a standard installation, but we can't anticipate the names of subdirectories, etc., so it may be necessary to edit these files for your installation.

Intel platforms (Win2k)
The hint toolkit is distributed as a PKZipped archive that you probably got as a download from our FTP server. In this case the package includes a Microsoft Visual Studio® "workspace" that has been created for production of a simple executable linking OElib and the hint toolkit. Other compiler packages such as those available from GNU should also work in creating hint executables for the Win2k environment. Also it should be pointed out, that inasmuch as there is interoperability between Windows programs among the various Windows OS releases, programs developed with this toolkit may work under Windows versions other than Windows2000®, but we have only lightly tested it.

Installation is simple;

  1. Create an eduSoft directory in a convenient location like C:\eduSoft\.
  2. PKunZip the file hinttk306win2k.ZIP into the C:\eduSoft directory.
  3. Install the hint toolkit license as described in the key installation instructions into the C:\eduSoft\hinttoolkit3.06_win2k\license directory. The license locks the executable(s) created to a single node. Additional "run-time" node licenses are available at a nominal cost.
  4. Define the location of the HINT license using Windows environmental variables: MCONN_LICENSE=C:\eduSoft\hinttoolkit3.06_win2k\license\HintToolkitLicense.dat.
    • For Windows2000® or WindowsXP®: use the Environment tab in the System monitor in the Control panel to set this value.
    • For Windows98 or WindowsME®: add a line set HINT_LICENSE=C:\eduSoft\hinttoolkit3.06_win2k\license\HintToolkitLicense.dat to the AUTOEXEC.BAT file.
  5. The current version of the html toolkit programmer's guide is included in the distribution in the C:\eduSoft\hinttoolkit3.06_win2k\toolkit_docs directory. You may wish to link it or copy it to a more convenient location for your browser.
  6. Note that the files included with the release are designed to work with a standard installation, but we can't anticipate the names of subdirectories, etc., so it may be necessary to edit these files for your installation.

Sample HINT Program Code

The Distributed Standalone HintLogP (C++)
We include hintlogp306.cpp, the source code for the standalone hintlogp executable (see http://www.edusoft-lc.com/hint/manuals/300/ for more information on using this program. makefile.hintlogp is also included in the source directory of the distribution. Note that for platforms where Daylight tools are available, this program/makefile is written to link with the Daylight libraries. If you do not have access to these libraries, then you will have to appropriately edit the source and makefile to remove these references. Likewise, the OpenEye (OElib) references should be removed if you are not using OElib.

HINT/PDB Ligand Scoring Tool
This example uses the HINT toolkit, the PDB toolkit (see below) and OElib to produce a generalized tool for calculating a HINT free energy score for a small molecule ligand bound to a biomacromolecule. The small molecule ligand is interpreted by tools in the OpenEye Scientific Software OElib library, and the biomacromolecule is manipulated with the eduSoft LC PDB Crystallographers' Toolkit. makefile.hintpdb is also included in the source directory.

HINT 3D Map Creation Utility
This program is designed as a standalone program for calculating HINT 3D map objects in background calculations. As such, it reads the appropriate input data for a previously "partitioned" molecule as an input ASCII file. The program is simply linked to the HINT Programmers' Toolkit for all platforms, but the availability of specific output map formats is dictated by the hardware platform, and specific software installations on your system. For example, the Sybyl® contour library is only available for the SGI/Irix platform at present, but will be availbale for Linux in early 2003. Because the "Biosym" and "Grasp" formats presently use FORTRAN subroutines, these are currently unavailable for the Windows 2000 and Macintosh OS-X platforms.

platformavailable map formats
SGI/IrixList
ASCII
Sybyl
Biosym
GRASP
Sun/SolarisList
ASCII
Biosym
GRASP
LinuxList
ASCII
Biosym
GRASP
Windows 2000List
ASCII
Macintosh OS-XList
ASCII

The hintmap executable is created with makefile.hintmap. In addition to the hintmap.c source, this program also requires hint_macros.c, which is a useful set of designed purpose subroutines applying multiple toolkit calls.

The expected input for hintmap can be ascertained from the code, but in general first two lines list a number of calculational parameters for the map, the third line describes the dimensions of the grid box, and the fourth line lists the map format and output file name. Then the molecular partition data is listed, including LogP for the molecule, molecule name and some partition parameters on lines 5, 6 and 7, followed by the number of atoms in the molecule on line 8. The next batch of records has the atomic data on three lines per atom if direction vectors are not being used and four lines if they are. If the HINT map calculation is InterMolecular then the second molecule is included in the file, in exactly the same way, starting with the second molecules' LogP.

While this program is designed to read data from a previously partitioned molecule, because of its purpose as a background map engine, it could be, rather simply, modified to start with an unpartitioned molecule.

HINT for insightII (SGI only)
Also included as a HINT toolkit example is an open source version of a HINT program that can be compiled and linked into the insightII environment for those who are using this Accelrys product. Note that you must have an Accelrys insightII license for execution. However, much of the HINT toolkit code in this example is fairly general and may be applicable to other platforms. You will also need to compile and link the hintmap executable described above.

This example is in a gzipped archive (hint307i.tgz) within the toolkit source directory. To unpack it use the command gzip -dc hint307i.tgz | tar xvf -. The files included, and their purpose are as below:

filedescription
makefile.i2hintmakefile for hint/insightII dynamic shared object
cshrcsample csh resource to define environmental variables
hint307i.csource (C)
hint307i.hheader (C)
hint_grid_runsh script to run hint_bkg
hint_macros.csource (C): useful toolkit hint macros
hint_macros.hheader (C): useful toolkit hint macros
oi_customize.csource (C) for insightII/hint module creation
tutor/a directory of insightII sample molecule files
manual/a directory listing the hint3.0I html manual

To create this program, which is actually a dynamic shared object (DSO) called libuser.so, follow the steps below:

  1. Modify the "cshrc" file to point to your locations for the HINT toolkit, HINT toolkit license, and insightII. Other HINT environmentals are set to the current working directory for testing purposes, but would be more appropriately defined elsewhere when the program is installed.
  2. Because the insightII and hint toolkits use similar names for some of the header files (e.g., the amazingly creative name atom.h), you have to adjust their names in the hint toolkit "include" directory:
    cd $HINTTOOLS_ROOT/include
    ln -s atom.h e_atom.h
    ln -s core.h e_core.h
    ln -s gridm.h e_gridm.h
    ln -s molecule.h e_molecule.h
    ln -s molconnz.h e_molconnz.h
    ln -s monomer.h e_monomer.h
    You will note that there already is an "e_hint.h" header. This is because there was a conflict between the Open Interface and hint toolkit headers. For a reason that totally escapes us, one of the Open Interface headers has a #define statement which replaces all "S" with the atomic number for sulfur, while we had previously chosen to use S as the variable name for hint Solvent Accessible Surface Area. You will note that e_hint.h (and the source code) use Sx instead of S when referring to this quantity.
  3. Return to your working directory and source the cshrc file to define the enviromentals:
    source cshrc
  4. Create the insightII dynamic shared object for hint:
    make -f makefile.i2hint
    Note that there can be a few reported warnings upon compilation of the hint307i.c object. One of these concerns a re-definition of "TRUE" and/or "FALSE". This doesn't seem to have any effect in our hands, so it appears safe to disregard these warnings.
  5. You will need to make the hintmap executable as described in the section above. This program needs to be moved to the location pointed to by $HINT_EXE (see cshrc). Ultimately libuser.so should be placed in $HINT_SO and hint_grid_run should be placed in $HINT_RUN.
  6. invoke insightII with hint! option:
    DEFINE_HINT
    insightII
  7. If the hint! module is properly linked and installed, insightII will halt loading and display a warning that it has been modified by inclusion of hint! and wait for you to authorize it to continue loading.
  8. The hint! "module" should be listed in the modules list (under Accelrys logo) in the insightII menus.
  9. Refer to the hint! 3.0I manual for further instructions, including tutorials, on the applications of hint!