blendpdb 0.1.2

Blending two PDB files to create solvate

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

System Message: ERROR/3 (<string>, line 23)

Unexpected indentation.

load configure from FILE (Default '.blendrc')

System Message: WARNING/2 (<string>, line 24)

Block quote ends without a blank line; unexpected unindent.

-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.