HintLogP 2.35 Manual: Chapter 3 This version of HINT is designed to calculate LogP from Molecular Design Limited's SDF Format, or optionally from SMILES strings in the Daylight .smi file format. The program is intended to be very fast, for processing large quantitites of data, so has few options. If the optional logpD license is purchased, then this version of HINT reads and decodes SMILES files using the Daylight Toolkit. This requires a run-time SMILES Toolkit license from Daylight Chemical Information Systems, Inc. Each record of the Daylight SMILES files, which are generally named with the .smi extension, is simply a SMILES String followed by the Molecule Name (space delimited). There is no file termination code.

Problems, Workarounds, Clarifications (FAQ)

  1. The message: Warning: Adjacent "Fragments" involving Atoms... FPP(0) used to estimate Log P appears when partitioning. This message is simply a warning from the Partition algorithm that your molecule has a functional group or Leo-type fragment that is not in the database. HINT continues the calculation by constructing a new fragment from two (or more) fragments that are present in the database with the application of a polar proximity factor of range zero, FPP(0). FPP(0) represents the polar proximity effect of two groups that have no "insulating carbons" between them. Of course this means that the estimation of LogP that HINT produces is not as valid as one obtained with all of the necessary fragments present in the database, but it is a pragmatic solution to missing data.

Installing the Standalone HINTLOGP (2.35) Program

The HINTLOGP program is included and installed with any interfaced version of HINT. These instructions are for installing HINTLOGP without one of the HINT interface packages.

  1. Unload the HINTLOGP 2.35 tape (or FTP tar set) into the current $EDUSOFT_ROOT directory:
    • cd $EDUSOFT_ROOT
    • tar xov (tar xovf hintlogp235)

  2. Choose the appropriate HINTLOGP login file(s) (see table below). Edit that/those files in /usr/eduSoft/eslc/lib/ to correct the environment for $EDUSOFT_ROOT. If you have a network license and a mixed-platform network, you may have to create some logic to automatically select the appropriate cshrc.

    Product(s) Platform cshrc profile
    HintLogP 2.35 r4000/r5000 cshrc_hintlogp profile_hintlogp
    r8000/r10000/r12000 cshrc_hintlogp_r8 profile_hintlogp_r8
    HintLogP 2.35 &
    Molconn-Z 3.50    		 r4000/r5000 cshrc_hintlogp+molconnz profile_hintlogp+molconnz
    r8000/r10000/r12000 cshrc_hintlogp+molconnz_r8 profile_hintlogp+molconnz_r8

  3. In order to activate HINTLOGP, one of these files must be manually "sourced" with e.g., source /usr/eduSoft/eslc/lib/cshrc_??? which can be placed in the system or each users .cshrc file.

  4. Install the HINT License Keys(s) as described on the included (hardcopy) documentation or on-line.

  5. If you have purchased the Daylight option (logPD) copy your Daylight License Key into /usr/eduSoft/eslc/license/DayLicense.dat or redirect the pointers to DY_LICENSEDATA in the appropriate cshrc_??? or profile_??? file(s).

Running the Standalone HINTLOGP (2.35) Program

  1. To run this version of HINT, use the following syntax to the unix command line:

    $HINT_RUN/hlogp a b datasource c

    where:
    a is either 0, 1 or 2; if a is 0 then the datatype is (Daylight) SMILES; if a is 1 then the datasource is a Molecular Design Limited (MDL) SDF file; if a is 2 then the datasource is a Tripos .mol2 file .

    b is either 0 or 1; if b is 0 then the datasource is a SMILES string (in quotes); if b is 1 then the datasource is a .smi SMILES file; if a is not 0, then b is ignored.

    datasource is either an explicit SMILES string (for a=0, b=0), or a valid file name in .smi format, .sdf format or .mol2 format.

    c is either 0 or 1; if c is 0 then the short output format will be provided; if c is 1 the more verbose output is written.

  2. Notes:
    • each record of the Daylight SMILES files, which are generally named with the .smi extension, is simply a SMILES String followed by the Molecule Name (space delimited). There is no file termination code.

    • the MDL SDFile format is described in an on-line document at the MDL Web site at www.mdli.com/tech/fileformats.html.