Installation Instructions

Installation Instructions

These are notes on how to install software, primarily for computational chemistry.

RDKit

Just use conda, it will save you enormous amounts of time:

conda install -c rdkit rdkit

COSMO-RS on Linux

COSMO-RS is a fluid phase thermodynamics program. Usually, you use it from the GUI, COSMOthermX, but sometimes you need to run large numbers of calculations from on a server.

It's not immediately obvious how to install COSMOtherm (i.e., without the GUI) from the command line, so here's a step-by-step guide.

  1. Download COSMOtherm and, optionally, COSMObase (an add-on database with 12k+ extra molecules) from Biovia 3Dpassport download page. You should have a login from when you bought your license. I just installed the highest fidelity COSMObase files (TZVPD-FINE).
    2. image
  2. Copy the zip files for COSMOtherm and COSMObase onto your linux server. For example, replace USER@HOST with the username and address of your server and run the following command (removing the COSMObase file if you don't have it):
    3. scp BIOVIA_2020.AM_BIOVIA_COSMOtherm_2020.zip BIOVIA_2020.COSMObase2020-BP-TZVPD-FINE.zip USER@HOST:/home
  3. Unzip the files on the server and copy the COSMObase files to the correct location if you have them. Replace 2020 with whatever version you have.
    4. unzip BIOVIA_2020.AM_BIOVIA_COSMOtherm_2020.zip
# If you have COSMObase:
unzip BIOVIA_2020.COSMObase2020-BP-TZVPD-FINE.zip
cp COSMObase2020 BIOVIA/COSMOtherm2020/COSMOtherm/DATABASE-COSMOIOVIA/COSMOt
  4. Upload your license file to the server and copy it to the proper location:
    5. mkdir -p BIOVIA/COSMOtherm2020/licensefiles/
cp license.txt BIOVIA/COSMOtherm2020/licensefiles/
  5. If you have any COSMObase files, you need to manually add them to the COSMOtherm XML configuration file:
    6. # Open the configuration file (can do this alternatively with vi, nano, etc.)
vim BIOVIA/COSMOtherm2020/config/settingsLinux.xml

    Scroll down to the <AllDatabases> tag, and add your database. For TZVPD-FINE, you need the following:

    <Database>
     <DatabaseName selected="1">TZVPD-FINE-LARGE</DatabaseName>
     <DatabaseDirectory>../COSMOtherm/DATABASE-COSMO/COSMObase2020/BP-TZVPD-FINE</DatabaseDirectory>
     <parametrisation>TZVPD-FINE</parametrisation>
 </Database>

    Then, under the SQLiteSettings tag, add the database to the correct level, so COSMOtherm knows to look for it:

    <DatabaseList parametrisation="TZVPD-FINE">
      <DatabaseName>Default-TZVPD-FINE</DatabaseName>
      <DatabaseName>TZVPD-FINE-LARGE</DatabaseName>
</DatabaseList>
  6. To use cosmotherm from the command line, make sure to add it to your path. You can modify ~/.bash_profile or ~/.bashrc as follows:
    7. export PATH="~/BIOVIA/COSMOtherm2020/COSMOtherm/BIN-LINUX:$PATH"

    This assumes the BIOVIA directory is in your home directory. Put the reference anywhere you need it.

    As an alternative to using the command line, you can request a copy of BIOVIA's COSMOpy library, which allows you to call COSMOtherm from python.