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Re: [h5md-user] [EXTERNAL] Re: topology

From: Konrad Hinsen
Subject: Re: [h5md-user] [EXTERNAL] Re: topology
Date: Tue, 6 May 2014 17:42:58 +0200

Hi David,

 > The group I work with does a fair amount of analysis on bond
 > lengths, angle distributions and dihedral angle distributions as
 > validation for force field development. So our main use case for a
 > 'topology' module would be to store the pairs, 3- and 4-tuples of
 > atoms that define the bonds, angles and dihedrals.

I can see the need to store the bonds, but why angles and dihedrals?
Once you have the bond network, you can deduce angles and dihedrals
from them.

 > That said, I have use cases for wanting to store lists of
 > non-bonded pairs of atoms such as opposing carbons on a ring or
 > designated 'endpoint' atoms that can be used to represent the
 > overall orientation of a larger molecule, and in this use case a
 > specific 'bond' list would not really be appropriate.

So what you really want is ordered N-tuples of atom indices, right?

 > I am totally guilty of abusing the PDB (and CAR and MDF) formats to
 > sneak in extra information. :-)

Me too! As a way of repenting, I have vowed to avoid using the PDB
format a much as possible in the future ;-)

 > I would definitely agree that a standard storage scheme, would be
 > useful, even if the structure of a 'topology' section varies by
 > module. That way, even if the location of the lists varies, at
 > least the same routines can be used to read/write the data when it
 > is located.


 > As a possible example:
 > <tuple-list>
 >   +-- type:  String
 >   +-- dimension:  Integer[]
 >   \--  values: Integer[n-tuples][D]
 > Where a pair list would be dimension(D) = 2, and the values in list
 > would be the particle IDs.

Looks good to me!

Konrad Hinsen
Centre de Biophysique Moléculaire, CNRS Orléans
Synchrotron Soleil - Division Expériences
Saint Aubin - BP 48
91192 Gif sur Yvette Cedex, France
Tel. +33-1 69 35 97 15
E-Mail: research AT khinsen DOT fastmail DOT net
ORCID: http://orcid.org/0000-0003-0330-9428
Twitter: @khinsen

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