Renaming "Topology"? - Githubissues

ahy3nz commented 5 years ago

Posting random ideas if we choose not to stick with Topology and subtopology

Model/SubModel - in theory, this data structure includes all the information for how you want to model your system. Although dubbing our data structure a "Model" might sound kind of pretentious
MolecularModel/Model
Modelcule/Submodelcule - Less pretentious, but harder to take seriously
System/SubSystem - this is intermol

ahy3nz commented 5 years ago

Without stealing the name from this article We could call this package "OpenSourceMolecularModel" with the topology/subtopolgoy as OSMM and subOSMM (sound them out loud)

ahy3nz commented 5 years ago

TreeTop/TreeBranch

ahy3nz commented 5 years ago

TopoloTree

ahy3nz commented 5 years ago

pyTopology. When we try to mention our Topology in conversation, we always talk about Topology, but it can get mixed up with like the chemical/abstract notion of a "Topology". And to make this clarification, we often say our Topology data structure/core functionality. For ease in conversation for differentiating the conceptual Topology with our package, we could call it a pyTopology

mattwthompson commented 5 years ago

Maybe a dumb play on words like Topyogy

mattwthompson commented 5 years ago

Also there was some confusion from people seeing this for the first time in that the word topology often implies a description of only representation in space, so it's reasonable to think that topology ~= a connectivity graph and nothing more. In other words, it's not clear in just the name that we're including in our scope the force field information, box, etc.

Google says

to·pol·o·gy
/təˈpäləjē/Submit
noun
1.
MATHEMATICS
the study of geometric properties and spatial relations unaffected by the continuous change of shape or size of figures.
2.
the way in which constituent parts are interrelated or arranged.
"the topology of a computer network"

https://www.dictionary.com/browse/topology https://en.wikipedia.org/wiki/Topology

ahy3nz commented 5 years ago

We could move toward things more like "molecularmodel" and not like "topology"

ahy3nz commented 5 years ago

Maye we keep the primary data structure name as Topology but rename the package:

pyTIN (pronounced pie tin, Topological INformation)
pyCPTN (Container for Parametrized Topological iNformation, pronounced pie captain)
pyCRST (Contains rudimentary simulation and topology, pronounced pie crust)
PItSTOP (Parametrized information to Simulation and TOPology)
InterMM (prounounced "interim")
TOPCHFF (Topology Container Has Force Field)
STMMPy/pySTMM (pronounced stim-pie or steam-py Simulation Topology Molecular Model, sidenote: Cornelius Vanderbilt was a steam boat entrepreneur in addition to railroads)
MMSFFT (pronoucned misfit, molecular model simulation forcefield topology)
HerMMeS (hermes greek god of language, acronym still tbd...)
MMercury (mercury the roman counterpart to hermes)
Continuing down the mythology/astronomical route, we could do something with gravity assistance that used mercury as a gravitational slingshot
Polyglot (someone who knows many languages, acronym tbd)
Since cornelius vanderbilt was known for railroads, maybe there's something interesting to be done with "grand central terminal"

ahy3nz commented 5 years ago

C-3PO knew 6 million languages, we could do something like M-3PO (Molecular Model Messenger or something, just to give it some meaning)

ahy3nz commented 5 years ago

HAL - this package will tell you what you can't do for certain packages (FF implementations) SIMBA - simulation builder assistant SIMmY - SIMulation buddY CAMM - computer aid for molecular modeling

mattwthompson commented 5 years ago

MMMMM - Methods for Making Molecular Models for Molecular Mechanics

ahy3nz commented 5 years ago

python? conda? MoMBA - molecular model buildinh assistant

mattwthompson commented 5 years ago

~TopPy~

ahy3nz commented 5 years ago

Flexible wRapper ANd Container [for molecular models] (FRANCmm) Force field Representation ANd Container [for molecular models] (FRANCmm) Simulation Tool for INitialization and Extensibility (STINE) FRANCmm, FRANCmmSTINE?

mattwthompson commented 4 years ago

GTFo - General Topology Format

mattwthompson commented 4 years ago

Kidding aside, I like how GSD was named and wonder if we can think of something that similar denotes our intention of generically storing molecular systems in memory

GMO - General Molecular Object GMSO - General Molecular Simulation Object GMT - General Molecular Topology

mattwthompson commented 4 years ago

MoSS - MoSDeF Simulation Structure

GeMS - General Molecular Structure

GOOSE - General Object-oriented Simulation Environment/Editor

ToMB - Topology Objects for MoSDef Backend

LifeFoRMS - Lossless Internal Formats and Extensions For Reproducible Molecular Simulations

InFoRMS - Internal Format for Reproducible Molecular Simulation

mattwthompson commented 4 years ago

https://www.thefreedictionary.com/words-that-end-in-form

UniFoRMS - Universal Format for Reproducible Molecular Simulations

GOAT - General Objects for Abstract Topology

umesh-timalsina commented 4 years ago

My vote would be for GOAT.

daico007 commented 4 years ago

Another vote for GOAT

mattwthompson commented 4 years ago

We have decided GMSO - available on PyPI and Anaconda Cloud, not too long or cumbersome to type or say, and captures the scope of the package. PR incoming

mosdef-hub / gmso

Renaming "Topology"? #15