added PCM/PTM checking

wwPDB · Aug 28, 2024 · 19396f7 · 19396f7
1 parent cb2e40f
commit 19396f7
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Showing 4 changed files with 35 additions and 7 deletions.
diff --git a/wwpdb/apps/entity_transform/__init__.py b/wwpdb/apps/entity_transform/__init__.py
@@ -2,4 +2,4 @@
 __author__ = "Ezra Peisach"
 __email__ = "[email protected]"
 __license__ = "Apache 2.0"
-__version__ = "0.20"
+__version__ = "0.21"
diff --git a/wwpdb/apps/entity_transform/depict/PrdSummaryDepict.py b/wwpdb/apps/entity_transform/depict/PrdSummaryDepict.py
@@ -2,6 +2,10 @@
 # File:  PrdSummaryDepict.py
 # Date:  09-Oct-2012
 # Updates:
+# 25-Aug-2024  zf   add following warning message:
+#                       Unknown CCD ID covalently linked to a polymer residue, or in the polymer sequence
+#                       Existing CCD ID without PCM data covalently linked to a polymer residue, or in the polymer sequence
+#                       CCD ID that should be not used as PCM/PTM observed  covalently linked to a polymer residue, or in the polymer sequence
 ##
 """
 Create HTML depiction for PRD search summary.
@@ -50,6 +54,7 @@ def DoRenderSummaryPage(self, imageFlag=True):
         self.__graphmatchResultFlag = prdUtil.getGraphmatchResultFlag()
         self.__combResidueFlag = prdUtil.getCombResidueFlag()
         self.__splitPolymerResidueFlag = prdUtil.getSplitPolymerResidueFlag()
+        self.__pcmLabelList = prdUtil.getPcmLabelList()
         #
         input_data = 'sessionid=' + self._sessionId + '&identifier=' + self._identifier + '&pdbid=' + self._pdbId
         #
@@ -85,6 +90,15 @@ def DoRenderSummaryPage(self, imageFlag=True):
         #
         text += '<li><a class="fltlft" href="https://rcsbpdb.atlassian.net/wiki/spaces/WT/pages/2375385215/Protein+Modifications+Annotation+Documentation" target="_blank"> View PCM/PTM Documentation </a></li>\n'  # noqa: E501
         #
+        if "1" in self.__pcmLabelList:
+            text += '<li><span style="color:orange" class="fltlft">Unknown CCD ID covalently linked to a polymer residue, or in the polymer sequence</span></li>\n'
+        #
+        if "2" in self.__pcmLabelList:
+            text += '<li><span style="color:orange" class="fltlft">Existing CCD ID without PCM data covalently linked to a polymer residue, or in the polymer sequence</span></li>\n'
+        #
+        if "3" in self.__pcmLabelList:
+            text += '<li><span style="color:red" class="fltlft">CCD ID that should be not used as PCM/PTM observed  covalently linked to a polymer residue, or in the polymer sequence</span></li>\n'
+        #
         text += '</ul>\n'
         #
         return text

diff --git a/wwpdb/apps/entity_transform/depict/ProcessPrdSummary.py b/wwpdb/apps/entity_transform/depict/ProcessPrdSummary.py
@@ -2,6 +2,8 @@
 # File:  ProcessPrdSummary.py
 # Date:  15-Feb-2019
 # Updates:
+#  25-Aug-2024  zf   add getPcmLabelList()
+#                    change the default 'red' color code to different color codes read from '_pdbx_non_polymer_info.highlight_with_color' item
 ##
 """
 Process PRD search results and generate images.
@@ -55,6 +57,7 @@ def __init__(self, reqObj=None, summaryCifObj=None, verbose=False, log=sys.stder
         self.__graphmatchResultFlag = False
         self.__combResidueFlag = False
         self.__splitPolymerResidueFlag = False
+        self.__pcmLabelList = []
 
     def setTopDirPath(self, topPath):
         self.__topDirPath = topPath
@@ -74,6 +77,10 @@ def run(self, imageFlag=True):
         if imageFlag:
             self.__generateImage()
         #
+        val = self.__cifObj.getPcmLabel() 
+        if val:
+            self.__pcmLabelList = val.split(",")
+        #
         if self.__action_required_data:
             dic = {}
             dic["id"] = "action"
@@ -112,6 +119,9 @@ def getCombResidueFlag(self):
     def getSplitPolymerResidueFlag(self):
         return self.__splitPolymerResidueFlag
 
+    def getPcmLabelList(self):
+        return self.__pcmLabelList
+
     def __readEntityData(self):
         elist = self.__cifObj.getValueList("pdbx_entity_info")
         if not elist:
@@ -273,14 +283,14 @@ def __readNonPolymerData(self):
             return
         #
         nonpolymermap = {}
-        colorList = []
+        colorMap = {}
         for d in elist:
             if ('instance_id' not in d) or ('residue_id' not in d) or ('linkage_info' not in d):
                 continue
             #
-            if ("highlight_with_color" in d) and (d["highlight_with_color"] == "Y"):
-                if d['residue_id'] not in colorList:
-                    colorList.append(d['residue_id'])
+            if ("highlight_with_color" in d) and d["highlight_with_color"]:
+                if d['residue_id'] not in colorMap:
+                    colorMap[d['residue_id']] = d["highlight_with_color"]
                 #
             #
             if d['linkage_info'] == 'linked':
@@ -308,8 +318,8 @@ def __readNonPolymerData(self):
         for k in keylist:
             v = nonpolymermap[k]
             count = len(v)
-            if k in colorList:
-                text = '<span style="color:red;">' + k + "</span> (" + str(count) + " "
+            if k in colorMap:
+                text = '<span style="color:' + colorMap[k] + ';">' + k + "</span> (" + str(count) + " "
             else:
                 text = k + ' (' + str(count) + ' '
             #

diff --git a/wwpdb/apps/entity_transform/utils/SummaryCifUtil.py b/wwpdb/apps/entity_transform/utils/SummaryCifUtil.py
@@ -2,6 +2,7 @@
 # File:  SummaryCifUtil.py
 # Date:  17-Oct-2012
 # Updates:
+#  25-Aug-2024  zf   add getPcmLabel() method to read PCM information from '_entry.pcm_label' item
 ##
 """
 Read and handle search summary cif file.
@@ -70,6 +71,9 @@ def getEntryIds(self):
     def getFileId(self):
         return self.__cifObj.GetSingleValue('entry', 'file')
 
+    def getPcmLabel(self):
+        return self.__cifObj.GetSingleValue('entry', 'pcm_label')
+
     def getTitle(self):
         return self.__cifObj.GetSingleValue('struct', 'title')