From 81a8ddb4e23350ed35e531d6370439faa181e721 Mon Sep 17 00:00:00 2001 From: Marcin Wojdyr Date: Thu, 11 Jul 2024 18:21:33 +0200 Subject: [PATCH] calendar.html: update and add choice of period one of 2011-2014, 2015-2018 or 2019-2022 --- README.md | 19 ++++----- calendar.html | 39 ++++++++++++++++--- calendar.json | 98 ----------------------------------------------- calendar2011.json | 98 +++++++++++++++++++++++++++++++++++++++++++++++ calendar2015.json | 98 +++++++++++++++++++++++++++++++++++++++++++++++ calendar2019.json | 98 +++++++++++++++++++++++++++++++++++++++++++++++ coldates.py | 4 +- extract.sh | 9 +++-- process.py | 3 ++ 9 files changed, 350 insertions(+), 116 deletions(-) delete mode 100644 calendar.json create mode 100644 calendar2011.json create mode 100644 calendar2015.json create mode 100644 calendar2019.json diff --git a/README.md b/README.md index ec00027..56b6845 100644 --- a/README.md +++ b/README.md @@ -1,15 +1,16 @@ These statistics serve as an example how to use `gemmi-grep` - (one of the utilities provided by the [project gemmi][1]) - to quickly extract data from mmCIF files. +(one of the utilities provided by the [project gemmi][1]) +to quickly extract data from mmCIF files. -The data is extracted from a local copy of the PDB archive in mmCIF format -(we rsync it once a week). +The data of interest is extracted from a local copy of the PDB archive +(mmCIF coordinate files) to a file `grep.out`: -We use `gemmi-grep` in the `extract.sh` script to extract all the needed -metadata (and some more). -Reading all the archive (34GB of compressed files) takes 20-30min. -The output is redirected to a file (`grep.out`) that is later used + $ ./extract.sh --auto + +This script uses `gemmi-grep` to extract metadata to a file `grep.out`. +Reading all the archive (69GB of compressed files) takes about 30min. +The output is redirected to a file (`grep.out`) that is then used to prepare JSON files used in our web pages. ### Filter-able statistics @@ -30,7 +31,7 @@ https://project-gemmi.github.io/pdb-stats/ ### Synchrotron work patterns -`./coldates.py >calendar.json` writes the data used in calendar.html: +`./coldates.py` prepares json files for calendar.html, see `extract.sh`. https://project-gemmi.github.io/pdb-stats/calendar.html diff --git a/calendar.html b/calendar.html index 0638f33..d0925f3 100644 --- a/calendar.html +++ b/calendar.html @@ -12,6 +12,8 @@ body { font: 14px sans-serif; margin: 0; shape-rendering: crispEdges; } h1 { text-align: center; font-size: 30px; font-weight: normal; } h4 { text-align: center; font-size: 15px; font-weight: normal; } +h5 { text-align: center; font-size: 14px; font-weight: normal; } +h5 a { margin: 0 50px 0 50px; } h2 { text-align: center; font-size: 18px; margin: 30px 0 0 0; } .cal { min-height: 280px; padding-left: 50px; } @media only screen and (max-width: 600px) { .cal { padding-left: 0; } } @@ -42,7 +44,13 @@

Synchrotron Work Patterns

Data collection -dates from PDB entries released before 2021-01-21.

+dates from PDB entries released before 2024-07-09. + +
+2011-2014 +2015-2018 +2019-2022 +

APS

@@ -111,7 +119,7 @@

all home sources

This is part of the project GEMMI. - Uses this dc.js example, + Uses this d3.js example, SVG flags and wwPDB data.

@@ -122,6 +130,13 @@

all home sources