Blending two PDB files to create solvate
Project description
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.
===============================================================================
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.
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