Replace CX-MS with crosslinking-MS

ihm_validation/cx.py

@@ -371,7 +371,7 @@ def get_number_of_restraint_groups(self) -> int:
         return nrg
 
     def get_cx_data(self) -> (pd.DataFrame, pd.DataFrame):
-        """Extract CX-MS data from mmcif file"""
+        """Extract crosslinking-MS data from mmcif file"""
 
         output = (None, None)
         raw_restraints = self.get_raw_restraints()

ihm_validation/futures.py

@@ -40,7 +40,7 @@ def __init__(self):
         self.supported_particles = (ihm.model.Atom, ihm.model.Sphere)
 
     def load_restraint(self, restraint: ihm.restraint.CrossLinkRestraint) -> None:
-        """Extract CX-MS data from mmcif file"""
+        """Extract crosslinking-MS data from mmcif file"""
 
         raw_restraints = self._load_restraint_raw(restraint)
 

ihm_validation/report.py

@@ -386,7 +386,7 @@ def run_cx_validation(self, Template_Dict: dict) -> (dict):
         it currently evaluates satisfaction from mmcif files
         and not the enetire ensemble
         '''
-        # if cx-ms dataset was used to build the model, then evaluate satisfaction
+        # if crosslinking-MS dataset was used to build the model, then evaluate satisfaction
         Template_Dict['cx'] = False
         Template_Dict['cx_stats'] = None
         Template_Dict['cx_ertypes'] = None

ihm_validation/utility.py

@@ -429,14 +429,14 @@ def get_rg_data_fits(rg_dict: dict) -> list:
 
 def get_cx_data_fits(cx_dict: dict) -> list:
     '''
-    format cx-ms data for supplementary/summary table
+    format crosslinking-MS data for supplementary/summary table
     '''
 
     fin_cx = []
     count = 0
     for key, val in cx_dict.items():
         count += 1
-        fin_cx.append('CX-MS Fit of medioid: model # ' + str(count) +
+        fin_cx.append('Crosslinking-MS Fit of medioid: model # ' + str(count) +
                       ', percentage satisfied ' + str(round(val, 2))+'%')
     return fin_cx
 

templates/about_validation.html

@@ -16,7 +16,7 @@
           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 style=margin-bottom:0.5cm;> </p>
 
-          <p class=ex2 align='justify' > Validation of models built using Chemical Crosslinking Mass Spectrometry (CX-MS), Förster Resonance Energy Transfer (FRET) and 3D Electron Microscopy (3DEM) data are under development and will be included in subsequent versions of the validation report. </p>
+          <p class=ex2 align='justify' > Validation of models built using Chemical Crosslinking Mass Spectrometry (crosslinking-MS), Förster Resonance Energy Transfer (FRET) and 3D Electron Microscopy (3DEM) data are under development and will be included in subsequent versions of the validation report. </p>
 
           <p style=margin-bottom:0.5cm;> </p>
           <p class=ex2 align='center' ><b><u> <a name='references1'>References</a></u> </b></p>

templates/formodeling.html

@@ -73,7 +73,7 @@ <h5 class= ex2 align= center>
       <div class="card-header" style="background-color: #FFF; height=18rem">
         <div class="row">
           <div class='col-lg-12'>
-            <h4 align=center id="cxms"><u> Fit of model(s) to CX-MS data</u></h4>
+            <h4 align=center id="cxms"><u> Fit of model(s) to crosslinking-MS data</u></h4>
             <h5 align=center id="cxms_ertypes"><u>Restraint types</u></h5>
             {% if cx_ertypes is none %}
               <p>Restraint types in this entry are not supported at the moment.</p>

templates/full_validation_pdf.html

@@ -750,7 +750,7 @@ <h5 align=center>
 
             {% if cx %}
               <h5 align=center id="cxms">
-                <u> Fit of model(s) to CX-MS data</u>
+                <u> Fit of model(s) to crosslinking-MS data</u>
               </h5>
 
               <h5 align=center id="cxms_ertypes">

templates/layout.html

@@ -199,7 +199,7 @@ <h5>
 
 									{% if ('CX-MS DATA' in Data) and enable_cx %}
                     <a class="dropdown-item colorclass" dropdown-toggle href=formodeling.html#cxms>
-                      CX-MS
+                      crosslinking-MS
                     </a>
 
                     <ul class=dropdown-submenu>