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Blending two PDB files to create solvate

Project Description


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

Use pip or easy_install like

pip install blendpdb


Usage: blendpdb SUB_A SUB_B PERCENTAGE [options]

Blend PERCENTAGE (v/v) of SUB_B with SUB_A

-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
-o FILE, --output=FILE
output blended PDB into FILE (Default

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.

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Source None Jun 8, 2013

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