From 42d37ecda618274d462c43fed84de5b2df196b56 Mon Sep 17 00:00:00 2001 From: Arthur Zalevsky Date: Wed, 13 Nov 2024 21:16:21 -0800 Subject: [PATCH] replaced all mentions of PDB-Dev with PDB-IHM; pdb-dev.wwpdb.org links with pdb-ihm.org; bumped version to 1.2.1 --- README.md | 2 +- ihm_validation/generate_static_html_pages.py | 6 +- ihm_validation/get_plots.py | 2 +- ihm_validation/ihm_validator.py | 4 +- ihm_validation/molprobity.py | 2 +- ihm_validation/report.py | 2 +- templates/about_validation.html | 6 +- templates/full_validation_pdf.html | 66 ++++++++++---------- templates/layout.html | 4 +- templates/main.html | 2 +- templates/static_navbar.j2 | 2 +- templates/summary_validation_pdf.html | 48 +++++++------- templates/validation_help.html | 8 +-- 13 files changed, 77 insertions(+), 77 deletions(-) diff --git a/README.md b/README.md index 4670ef85..704c33cf 100644 --- a/README.md +++ b/README.md @@ -1,7 +1,7 @@ # Validation pipeline for integrative and hybrid models ## Project objective -- `1.` Develop a validation pipeline (including data validation, model validation, fit of input to model, fit of data not used for modeling and uncertainty of the model) for assessing IHM structures deposited to [PDB-Dev](https://pdb-dev.wwpdb.org/index.html) +- `1.` Develop a validation pipeline (including data validation, model validation, fit of input to model, fit of data not used for modeling and uncertainty of the model) for assessing IHM structures deposited to [PDB-IHM](https://pdb-ihm.org/index.html) ## List of files and directories: - `docs` documentation for all classes and functions (sphinx) diff --git a/ihm_validation/generate_static_html_pages.py b/ihm_validation/generate_static_html_pages.py index 477a1c35..cbb88c72 100755 --- a/ihm_validation/generate_static_html_pages.py +++ b/ihm_validation/generate_static_html_pages.py @@ -25,8 +25,8 @@ help="Generate validation help page") parser.add_argument('--output-root', type=str, default=str(Path(Path(__file__).parent.resolve(), 'Validation')), help="Path to a directory where the output will be written") -# parser.add_argument('--html-mode', type=str, default='pdb-dev', -# choices=['local', 'pdb-dev'], +# parser.add_argument('--html-mode', type=str, default='pdb-ihm', +# choices=['local', 'pdb-ihm'], # help="HTML mode affects paths to various statis resources") # parser.add_argument('--html-resources', # type=str, @@ -66,7 +66,7 @@ templateEnv = jinja2.Environment(loader=templateLoader) Template_Dict = {} Template_Dict['version'] = REPORT_VERSION -Template_Dict['html_mode'] = 'pdb-dev' +Template_Dict['html_mode'] = 'pdb-ihm' ############################################################################################################################# # Jinja scripts diff --git a/ihm_validation/get_plots.py b/ihm_validation/get_plots.py index 8599a232..0992f55b 100644 --- a/ihm_validation/get_plots.py +++ b/ihm_validation/get_plots.py @@ -185,7 +185,7 @@ def plot_quality_at_glance(self, molprobity_data: dict, exv_data: dict, fullplot = column(title, grid) # if neither exc vol nor molp data exists, we create a blank plot - # pdb-dev visuals keep changing, so this plot might or might not make sense + # pdb-ihm visuals keep changing, so this plot might or might not make sense # we are keeping it, just in case the visuals change again else: Scores = [''] diff --git a/ihm_validation/ihm_validator.py b/ihm_validation/ihm_validator.py index 00cb0942..f56ff181 100755 --- a/ihm_validation/ihm_validator.py +++ b/ihm_validation/ihm_validator.py @@ -48,8 +48,8 @@ help="Path to a directory where the output will be written") parser.add_argument('--output-prefix', type=str, default=None, help="Prefix of the output directory. Default is a stem of the mmCIF file") -parser.add_argument('--html-mode', type=str, default='pdb-dev', - choices=['local', 'pdb-dev'], +parser.add_argument('--html-mode', type=str, default='pdb-ihm', + choices=['local', 'pdb-ihm'], help="HTML mode affects paths to various statis resources") parser.add_argument('--html-resources', type=str, diff --git a/ihm_validation/molprobity.py b/ihm_validation/molprobity.py index dbd7b55d..5496a129 100644 --- a/ihm_validation/molprobity.py +++ b/ihm_validation/molprobity.py @@ -257,7 +257,7 @@ def run_molprobity(self, d: dict): # "disable_uc_volume_vs_n_atoms_check=True", # This is a legacy option and causes extremely # large memory consumption with recent - # molprobity versions on PDB-Dev entries + # molprobity versions on PDB-IHM entries "coot=False"], stdout=f, cwd=self.cache) diff --git a/ihm_validation/report.py b/ihm_validation/report.py index 38600f59..24ebc573 100644 --- a/ihm_validation/report.py +++ b/ihm_validation/report.py @@ -24,7 +24,7 @@ import numpy as np from selenium import webdriver -REPORT_VERSION = '1.2' +REPORT_VERSION = '1.2.1' class WriteReport(object): def __init__(self, mmcif_file, db, cache, nocache=False): diff --git a/templates/about_validation.html b/templates/about_validation.html index 5349e3a3..429d0d6c 100644 --- a/templates/about_validation.html +++ b/templates/about_validation.html @@ -7,7 +7,7 @@