blendpdb

blendpdb is a tool for mixing two different substance to make solvate such as 50% Ethanol.

Install

Use pip or easy_install like

pip install blendpdb

Usage

Usage: blendpdb SUB_A SUB_B PERCENTAGE [options]

Blend PERCENTAGE (v/v) of SUB_B with SUB_A

Options:
-h, --help            show this help message and exit
-c FILE, --config=FILE
                        load configure from FILE (Default '.blendrc')
-v, --verbose         print informations
-n, --dry             do not create blended PDB ('-v' will automatically be
                        set)
-o FILE, --output=FILE
                        output blended PDB into FILE (Default
                        <PERCENTAGE>p_<SUB_B>.pdb)

blendrc

To add different substance, create blendrc file in the working directory like

WAT:                                # Name
  longname: Water                   # Long name
  density: 1                        # Density (g/cm^3)
  molecular_weight: 18.01           # Molecular Weight (g/mol)
  pdb: water.pdb                    # PDB file indicate the substance
TFE:                                # Name
  longname: 2,2,2-Trifluoroethanol  # Long name
  density: 1.393                    # Density (g/cm^3)
  molecular_weight: 100.04          # Molecular Weight (g/mol)
  pdb: tfe.pdb                      # PDB file indicate the substance

blendpdb also try to load .blendrc file in your Home directory.