OpenMM
 All Classes Namespaces Functions Variables Pages
simtk.openmm.app.charmmpsffile Namespace Reference

Classes

class  CharmmPsfFile
 A chemical structure instantiated from CHARMM files. More...
 

Functions

def set_molecules
 Correctly sets the molecularity of the system based on connectivity. More...
 

Variables

int TINY = 1
 
tuple WATNAMES = ('WAT', 'HOH', 'TIP3', 'TIP4', 'TIP5', 'SPCE', 'SPC')
 
tuple _resre = re.compile(r'(\d+)([a-zA-Z]*)')
 

Detailed Description

Provides a Python class for parsing a PSF file and setting up a system

structure for it within the OpenMM framework.



This file is part of the OpenMM molecular simulation toolkit originating from

Simbios, the NIH National Center for Physics-Based Simulation of Biological

Structures at Stanford, funded under the NIH Roadmap for Medical Research,

grant U54 GM072970. See https://simtk.org.  This code was originally part of

the ParmEd program and was ported for use with OpenMM.



Copyright (c) 2014-2015 the Authors



Author: Jason M. Swails

Contributors:

Date: August 19, 2014



Permission is hereby granted, free of charge, to any person obtaining a

copy of this software and associated documentation files (the "Software"),

to deal in the Software without restriction, including without limitation

the rights to use, copy, modify, merge, publish, distribute, sublicense,

and/or sell copies of the Software, and to permit persons to whom the

Software is furnished to do so, subject to the following conditions:



The above copyright notice and this permission notice shall be included in

all copies or substantial portions of the Software.



THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR

IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,

FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL

THE AUTHORS, CONTRIBUTORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM,

DAMAGES OR OTHER LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR

OTHERWISE, ARISING FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE

USE OR OTHER DEALINGS IN THE SOFTWARE.

Function Documentation

def simtk.openmm.app.charmmpsffile.set_molecules (   atom_list)

Correctly sets the molecularity of the system based on connectivity.

Referenced by CharmmPsfFile.__init__().

Variable Documentation

tuple _resre = re.compile(r'(\d+)([a-zA-Z]*)')
int TINY = 1
tuple WATNAMES = ('WAT', 'HOH', 'TIP3', 'TIP4', 'TIP5', 'SPCE', 'SPC')