Skip to main content

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.

Project details


Release history Release notifications

This version
History Node

0.1.2

History Node

0.1.1

Download files

Download the file for your platform. If you're not sure which to choose, learn more about installing packages.

Filename, size & hash SHA256 hash help File type Python version Upload date
blendpdb-0.1.2.tar.gz (104.3 kB) Copy SHA256 hash SHA256 Source None Jun 8, 2013

Supported by

Elastic Elastic Search Pingdom Pingdom Monitoring Google Google BigQuery Sentry Sentry Error logging CloudAMQP CloudAMQP RabbitMQ AWS AWS Cloud computing Fastly Fastly CDN DigiCert DigiCert EV certificate StatusPage StatusPage Status page