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Introduction

This is an initial attempt at a Java software implementation of the SSIP method as described in the paper "Footprinting molecular electrostatic potential surfaces for calculation of solvation energies".

Specifically, the footprinting aspect of the calculation will be initially worked upon here since a Java QM solution does not exist at the moment. For the moment, the QM aspects will be dealt with by NWChem.

Compiling from Source

This will compile and install the SSIP tools to the Debian based OS.

Debian Stretch / Ubuntu Trusty / Ubuntu Xenial Debian package

  1. Install the needed packages and configure Java.

    sudo apt-get install git maven openjdk-8-jdk

    Ensure java8 is selected

    sudo update-alternatives --config java sudo update-alternatives --config javac

  2. Clone, build and install.

    git clone https://bitbucket.org/mjw99/ssip.git cd ssip ; mvn clean package ; sudo dpkg -i ./ssip-/target/.deb

  3. Check command line output.

SSIP Code:

 ssip - A tool for footprinting molecular electrostatic potential surfaces
        http://dx.doi.org/10.1039/C3CP53158A
 
        Git version: develop e608f92
 
    Option                Description                                                   
    ------                -----------                                                   
    -?, -h, --help        display this output                                           
    -c, --cml <String>    the CML file of the corresponding molecule in the cube        
                            file.                                                       
    -i, --isout <String>  the isout file that has been generated using the QM tool      
    --legacy              this switches to the legacy mode, allowing the use of an      
                            isout file and pdb.                                         
    -m, --cube <String>   the cube file for the MEPS corresponding to the molecule,     
                            generated by the QM tool.                                   
    -n                    Function in a non-interactive mode.                           
    -p, --pdb <String>    the PDB file of the corresponding molecule in the isout       
                            file                                                        
    -v                    Visualise SSIP surface.                                       
    -w <String>           write the files to file.                                      
 Example usage:
   ssip --legacy -i /usr/share/ssip-repo/ExampleData/benzene_001_0.002_0.00003.isout -p /usr/share/ssip-repo/ExampleData/benzene_001_new.pdb 
   ssip -m /usr/share/ssip-repo/ExampleData/XLYOFNOQVPJJNP-UHFFFAOYSA-N_0.0020_merged.cube -c /usr/share/ssip-repo/ExampleData/XLYOFNOQVPJJNP-UHFFFAOYSA-N.cml 

Phase transfer code:

 phasetransfer - A tool for calculating free and bound concentations and free energies of transfer
        Git version: phasetransfer e8bbd7b
 
 Option                        Description
 ------                        -----------
 -?, -h, --help                display this output
 --calc                        option sets it to calculate new concentrations
                                 for the phases, otherwise they are read in.    
 --concentrationUnit <String>  concentrationUnit (default: MOLAR)
 -e, --energies [String]       output the free energies (default: all)
 -o, --outputfile <String>     output file name, required
 -p, --phaseOut                output the phase states from the calculation to a
                                 PhaseCollectionList                            
 --phaseCollection             phase collection in input file
 --phaseCollectionList         phase collection list in input file.
 --phaseFile <String>          phase input file name
 --solute <String>             solute file name
 --solvent <String>            solvent file name
 -t, --temperature <Double>    temperature value (default: 298.0)
 --temperatureUnit <String>    temperatureUnit (default: KELVIN)
 
 Example usage:
   phasetransfer -p -o phaseOutFile.xml --solute /usr/share/ssip-repo/phasetransfer/ExampleData/watersolute.xml --solvent /usr/share/ssip-repo/phasetransfer/ExampleData/waterphasesolvent.xml
 phasetransfer -e -o energyOutFile.xml --solute /usr/share/ssip-repo/phasetransfer/ExampleData/watersolute.xml --solvent /usr/share/ssip-repo/phasetransfer/ExampleData/waterphasesolvent.xml

Debian Stretch / Ubuntu Trusty / Ubuntu Xenial standalone jar

  1. Repeat the steps above, but build using

    mvn clean compile assembly:single

  2. Execute using

    java -jar ./ssip-footprint/target/ssip-foorprint-2.2.0-SNAPSHOT-jar-with-dependencies.jar java -jar ./ssip-phasetransfer/target/ssip-phasetransfer-2.2.0-SNAPSHOT-jar-with-dependencies.jar