<html><head><meta http-equiv="Content-Type" content="text/html charset=utf-8"></head><body style="word-wrap: break-word; -webkit-nbsp-mode: space; -webkit-line-break: after-white-space;" class="">Hi,<div class=""><br class=""></div><div class=""><div><blockquote type="cite" class=""><div class="">On 25 May 2016, at 16:40, David van der Spoel <<a href="mailto:spoel@xray.bmc.uu.se" class="">spoel@xray.bmc.uu.se</a>> wrote:</div><div class=""><blockquote type="cite" style="font-family: Helvetica; font-size: 12px; font-style: normal; font-variant: normal; font-weight: normal; letter-spacing: normal; orphans: auto; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; widows: auto; word-spacing: 0px; -webkit-text-stroke-width: 0px;" class=""><br class=""></blockquote><span style="font-family: Helvetica; font-size: 12px; font-style: normal; font-variant: normal; font-weight: normal; letter-spacing: normal; orphans: auto; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; widows: auto; word-spacing: 0px; -webkit-text-stroke-width: 0px; float: none; display: inline !important;" class="">You are absolutely right that my "approach" does not give us more than independence from the underlying library. However my concern has been for a while that waiting for one monster file format does not get us further either. Fitting force field files, topologies and lots of random data all in one structure is not the way forward either.</span><br style="font-family: Helvetica; font-size: 12px; font-style: normal; font-variant: normal; font-weight: normal; letter-spacing: normal; orphans: auto; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; widows: auto; word-spacing: 0px; -webkit-text-stroke-width: 0px;" class=""><br style="font-family: Helvetica; font-size: 12px; font-style: normal; font-variant: normal; font-weight: normal; letter-spacing: normal; orphans: auto; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; widows: auto; word-spacing: 0px; -webkit-text-stroke-width: 0px;" class=""><span style="font-family: Helvetica; font-size: 12px; font-style: normal; font-variant: normal; font-weight: normal; letter-spacing: normal; orphans: auto; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; widows: auto; word-spacing: 0px; -webkit-text-stroke-width: 0px; float: none; display: inline !important;" class="">But rather than whining I will propose a JSON schema for the WAXS patch that is in gerrit, then we can take the discussion from there.</span><br style="font-family: Helvetica; font-size: 12px; font-style: normal; font-variant: normal; font-weight: normal; letter-spacing: normal; orphans: auto; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; widows: auto; word-spacing: 0px; -webkit-text-stroke-width: 0px;" class=""><br style="font-family: Helvetica; font-size: 12px; font-style: normal; font-variant: normal; font-weight: normal; letter-spacing: normal; orphans: auto; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; widows: auto; word-spacing: 0px; -webkit-text-stroke-width: 0px;" class=""></div></blockquote></div><br class=""></div><div class="">A couple of things we could probably decide on relatively easy (and these are probably all needed for the WAXS stuff):</div><div class=""><br class=""></div><div class=""><br class=""></div><div class="">1) What grouping/nomenclature should we use for all stuff like this (physical data) on the very highest level? </div><div class=""><br class=""></div><div class="">2) How should we handle/classify (nota bene: not implement) different scattering factors? They should likely go into separate objects, but somebody should likely spend a little time making a list of the ones we expect to implement, and then we can have a quick discussion in redmine that it makes sense.</div><div class=""><br class=""></div><div class="">3) How do we handle the mapping of particles (in particular for different force fields) to physical properties? I would guess that we might want to use elements when we can (to make things FF independent), but we also need ways to create arbitrary mappings, including wildcards. How do we handle cases with multiple alternative names for a residue? Some setups might use residue-like groups, but not all of them. </div><div class=""><br class=""></div><div class="">4) How will we handle units and possibly conversions?</div><div class=""><br class=""></div><div class="">5) How do we handle literature references?</div><div class=""><br class=""></div><div class="">Cheers,</div><div class=""><br class=""></div><div class="">Erik</div><div class=""><br class=""></div><div class="">PS: As both Teemu & I commented about year ago, the old WAXS patch in gerrit suffers from a very large number concepts in a single change. I added some ~120 comments a year ago that I think nobody got back about. I can kind of understand that given the complexity, but given the patch’s age and that we now are all C++, I would strongly recommend trying to break it up into smaller parts rather than extending it!</div><div class=""><br class=""></div><div class=""><br class=""></div><div class=""><br class=""></div></body></html>