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Placevent solvent placement software

Project Description

Placevent - 3D-RISM-based solvent and ion placement software created by Daniel Sindhikara, sindhikara@gmail.com Placevent This program is designed to automatically place explicit solvent atoms/ions based on 3D-RISM data. Placevent is compatible with AMBER .dx files and MDF .h5 files.

The details of the algorithm are described in: Placevent: An algorithm for prediction of explicit solvent atom distribution – Awpplication to HIV-1 protease and F-ATP synthase Daniel J. Sindhikara, Norio Yoshida, Fumio Hirata http://dansindhikara.com/Software/Entries/2012/6/22_Placevent_New.html

If you have Numpy, this package should work out of the box. Please contact me if you have problems. This package requires Numpy. This package requires grid.py.

EXAMPLE: Please see the tests/1L2Y/ for examples/tests In that directory, run test.sh to see if your local installation matches the reference output.

TUTORIAL: See my website: http://dansindhikara.com/Tutorials/Entries/2012/1/1_Using_3D-RISM_and_PLACEVENT.html for a tutorial.

g(r)_0 is printed in the occupation column g(r)_i is printed in the beta column

Copyright (C) 2012 Daniel J. Sindhikara

This program is free software: you can redistribute it and/or modify it under the terms of the GNU General Public License as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.

This program is distributed in the hope that it will be useful, but WITHOUT ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU General Public License for more details.

You should have received a copy of the GNU General Public License along with this program. If not, see <http://www.gnu.org/licenses/>.

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1.4

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1.3

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1.2.2

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placevent-1.4.tar.gz (2.2 MB) Copy SHA256 hash SHA256 Source None Oct 9, 2013

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