Clever

A software for 3D molecular fields calculations. 3D molecular fields are the scalar fields that represents some physical functions.

An example of 3D molecular fields is a density distribution function of hydrogens and oxygens atoms of water molecules surrounding the solute.

Hydrogens	Oxygens

Requirements

• General requirements
  • python3 (python2.7 support coming soon)
  • AmberTools 16
  • python-rdkit
  • h5py
  • pyyaml
  • six
  • numpy
  • progressbar2
  • future
• MPI support
  • mpi4py
• Parallel processing
  • pebble

Description

This program is a framework for calculation 3D molecular descriptors from molecular structures.

Initially, you have to prepare the database. Clever can read sdf files and saves the results in HDF5 files.

Database generation

To do it, use createdb command

python3 clever.py createdb --file <path to sdf file> --properties <list of comma separated properties> --output <output directory>

This script will create a new directory, and place each structure from sdf file to separate hdf file with names: <database>_<sequential number in sdf file - 1 >_zzz.hdf i.e. LD50_0_zzz.hdf denontes the file with first structure from original sdf file

Conformers generation

To do it, use geometry command

python3 clever.py geometry --database <path to database directory> --number_of_conformers <the maximal number of conformers for generation>

If the calculation succeeds, the files will be renamed from zzz prefix to gzz, otherwise troubled molecules will be marked as gfailed.

We recommend to do all heavy calculations on a cluster with MPI support

python3 mpiclever.py geometry --database <path to database directory> --number_of_conformers <the maximal number of conformers to generate>

Charges calculations

After conformers generation one can calculate charges.

mpirun -n <num of procs> python3 mpiclever.py charges --database <path to database directory>

If the calculation succeeds, the files will be renamed from gzz prefix to gcz, otherwise troubled molecules will be marked as cfailed.

3D-RISM calculations

Once you have a database with charges calculated, it is possible to calculate 3D-RISM scalar fileds.

mpirun -n <num of procs> python3 mpiclever.py rism --database <path to database directory> --xvvfile <path to amber file with solute susceptibility function>

If the calculation succeeds, the files will be renamed from gcz prefix to gcr, otherwise troubled molecules will be marked as rfailed.