replaced all mentions of PDB-Dev with PDB-IHM; pdb-dev.wwpdb.org link…

…s with pdb-ihm.org; bumped version to 1.2.1

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)

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

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 = ['']

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,

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)

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):

templates/about_validation.html

@@ -7,7 +7,7 @@
   <nav class="navbar navbar-expand-xl navbar-dark">
     <div class="dropdown">
       <a class="navbar-brand" href="/Validation/about.html">
-        <h5>About the PDB-Dev validation reports for integrative structures</h5>
+        <h5>About the PDB-IHM validation reports for integrative structures</h5>
       </a>
       <button class="navbar-toggler" type="button" data-toggle="collapse" data-target="#navbarSupportedContent" aria-controls="navbarSupportedContent" aria-expanded="false" aria-label="Toggle navigation">
         <span class="navbar-toggler-icon"></span>
@@ -25,11 +25,11 @@ <h5>About the PDB-Dev validation reports for integrative structures</h5>
       <div class="col-lg-12">
         <div class="card-header" style="background-color: #E4E4E4;">
           <p class=ex2 align='center'>
-            <b><u><a name='overview'>PDB-Dev Validation Report</a></u></b>
+            <b><u><a name='overview'>PDB-IHM Validation Report</a></u></b>
           </p>
 
           <p class=ex2 align='justify'>
-            This validation report was created based on guidelines and recommendations from IHM TaskForce <a href='https://pubmed.ncbi.nlm.nih.gov/31780431/'>(Berman et al. 2019)</a>. The first version of the PDB-Dev validation report consists of four categories, (i) model composition, (ii) data quality assessments, (iii) model quality assessments, and (iv) fit to data used to build the model. A fifth category, fit to data used to validate the model is under development. 
+            This validation report was created based on guidelines and recommendations from IHM TaskForce <a href='https://pubmed.ncbi.nlm.nih.gov/31780431/'>(Berman et al. 2019)</a>. The first version of the PDB-IHM validation report consists of four categories, (i) model composition, (ii) data quality assessments, (iii) model quality assessments, and (iv) fit to data used to build the model. A fifth category, fit to data used to validate the model is under development. 
 
           Data quality assessments and fit to data used for modeling categories are dependent on the different types of experimental data used in integrative modeling. We are breaking down this section based on experimental data type and addressing each method separately. The first version of the validation report is focused on validating models built using Small Angle Scattering (SAS) data and is based on the model and data validation guidelines published by the <a href='https://www.wwpdb.org/task/sas'>wwPDB SAS validation task force</a> <a href='https://pubmed.ncbi.nlm.nih.gov/28876235/'>(Trewhella et al. 2017)</a>.
           </p>