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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.
Exactly.
> 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
--
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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
http://dirac.cnrs-orleans.fr/~hinsen/
ORCID: http://orcid.org/0000-0003-0330-9428
Twitter: @khinsen
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