wwpdb.apps.ccmodule 0.32__tar.gz → 0.32.2__tar.gz

{wwpdb_apps_ccmodule-0.32 → wwpdb_apps_ccmodule-0.32.2}/PKG-INFO

@@ -1,6 +1,6 @@
-Metadata-Version: 2.2
+Metadata-Version: 2.4
 Name: wwpdb.apps.ccmodule
-Version: 0.32
+Version: 0.32.2
 Summary: wwPDB workflow engine utils
 Home-page: https://github.com/rcsb/py-wwpdb_apps_wf_engine_utils
 Author: Ezra Peisach

{wwpdb_apps_ccmodule-0.32 → wwpdb_apps_ccmodule-0.32.2}/wwpdb/apps/ccmodule/__init__.py

@@ -3,4 +3,4 @@ __docformat__ = "restructuredtext en"
 __author__ = "Ezra Peisach"
 __email__ = "ezra.peisach@rcsb.org"
 __license__ = "Apache 2.0"
-__version__ = "0.32"
+__version__ = "0.32.2"

{wwpdb_apps_ccmodule-0.32 → wwpdb_apps_ccmodule-0.32.2}/wwpdb/apps/ccmodule/chem/ChemCompAssignDepict.py

@@ -82,6 +82,7 @@
 # 2017-05-03    RPS    Updates so that LOI tracking can succeed even in cases where annotator reruns ligand search and consequently changes value for "author" assigned CCID
 # 2023-06-21    ZF     Added chemical descriptions provided by refinement packages
 # 2024-12-07    ZF     Added extpdbid
+# 2025-05-31    ZF     Added self.__splitCcdList[] and displaying OBS status information for split CCDs
 ##
 """
 Create HTML depiction chemical component assignment files.
@@ -141,7 +142,7 @@ class ChemCompAssignDepict(ChemCompDepict):
         self.__pathAllInstcs = "templates/workflow_ui/instances_view/all_instances"
         self.__pathAllInstncsCmprTmplts = self.__pathAllInstcs + "/comparison_view"
         self.__pathAllInstncsJmolTmplts = self.__pathAllInstncsCmprTmplts + "/jmol"
-
+        #
         self.__dpstrInfoKeyList = ['dpstr_info_name',
                                    'dpstr_info_alt_comp_id',
                                    'dpstr_info_frmla',
@@ -159,6 +160,13 @@ class ChemCompAssignDepict(ChemCompDepict):
                                    'dpstr_restraint_img_pth',
                                    'dpstr_info_type',
                                    'dpstr_info_details']
+        #
+        self.__splitCcdList = [ "1CU", "2OF", "3OF", "543", "CD1", "CD3", "CD5", "CO5", "KO4", "MH3",
+                                "MN5", "MN6", "MO1", "MO2", "MO3", "MO4", "MO5", "MO6", "MW1", "MW2",
+                                "MW3", "NA2", "NA5", "NA6", "NAO", "NAW", "NI1", "NI2", "NI3", "NIK",
+                                "O4M", "OC1", "OC2", "OC3", "OC4", "OC5", "OC6", "OC7", "OC8", "OCL",
+                                "OCM", "OCN", "OCO", "OF1", "OF3", "YH",  "ZH3", "ZN3", "ZNO", "ZO3" ]
+        #
 
     ################################################################################################################
     # ------------------------------------------------------------------------------------------------------------
@@ -314,8 +322,13 @@ class ChemCompAssignDepict(ChemCompDepict):
                     scoreWarnClass = retD['warn_class']
                     scorePrefix = retD['prefix']
                     scoreSuffix = retD['suffix']
+                #
+                status = ''
+                if topHitCcId.upper() in self.__splitCcdList:
+                    status = ' <br/><span style="color: red;">Status: OBS</span>'
+                #
                 # we also apply required html markup to CCID display field when not "None"
-                topHitCcId = '<a href="/ccmodule/cc-view.html?ccid=' + topHitCcId + '" target="_blank" title="Profile in Viewer">' + topHitCcId + '</a>'
+                topHitCcId = '<a href="/ccmodule/cc-view.html?ccid=' + topHitCcId + '" target="_blank" title="Profile in Viewer">' + topHitCcId + '</a>' + status
             #
             cmpstScore = scorePrefix + str(p_ccAssgnDataStr.getBatchBestHitScore(instId)) + scoreSuffix
             #
@@ -861,7 +874,11 @@ class ChemCompAssignDepict(ChemCompDepict):
                 if topHit == 'None':
                     myD['top_hit_ccid'] = topHit
                 else:
-                    myD['top_hit_ccid'] = '<a href="/ccmodule/cc-view.html?ccid=' + topHit + '" target="_blank" title="Profile in Viewer">' + topHit + '</a>'
+                    status = ''
+                    if topHit.upper() in self.__splitCcdList:
+                        status = ' <br/><span style="color: red;">Status: OBS</span>'
+                    #
+                    myD['top_hit_ccid'] = '<a href="/ccmodule/cc-view.html?ccid=' + topHit + '" target="_blank" title="Profile in Viewer">' + topHit + '</a>' + status
                 #
                 hlprD = self.__processWarningMsg(p_ccAssgnDataStr.getCcAssgnWarning(instId))
                 #
@@ -1144,19 +1161,24 @@ class ChemCompAssignDepict(ChemCompDepict):
                 #
                 countr = 0
                 for tupL in p_ccAssgnDataStr.getTopHitsList(instId):
-
+                    candidate_ccid_with_status = tupL[0]
+                    if tupL[0].upper() in self.__splitCcdList:
+                        candidate_ccid_with_status = tupL[0] + ' <br/><span style="color: red;">Status: OBS</span>'
+                    #
+                    myD['candidate_ccid_with_status'] = candidate_ccid_with_status
                     myD['candidate_ccid'] = tupL[0]
                     # template requires "candidate_ccid", "instanceid", and "showstyle" substitution parameters
                     oL.append(self.processTemplate(tmpltPth=p_tmpltPth, fn="cc_all_instncs_assgn_row_tmplt.html", parameterDict=myD))
                     countr += 1
-
+                #
                 if countr == 0:
                     myD['candidate_ccid'] = "None"
                     if self.__verbose:
                         self.__lfh.write("+ChemCompAssignDepict.doRender_InstanceAssgnRows() candidate_ccid for %s set to 'None'\n" % instId)
                     # template requires "candidate_ccid", "instanceid", and "showstyle" substitution parameters
                     oL.append(self.processTemplate(tmpltPth=p_tmpltPth, fn="cc_all_instncs_assgn_row_tmplt.html", parameterDict=myD))
-
+                #
+            #
         # end of iterating through all instanc IDs
 
         return oL
@@ -1639,6 +1661,10 @@ class ChemCompAssignDepict(ChemCompDepict):
             else:
                 assgnChecked = ''
             #
+            status = ''
+            if ccid.upper() in self.__splitCcdList:
+                status = ' <br/><span style="color: red;">Status: OBS</span>'
+            #
             # using lclDict to supply text substitution content for both cc_instnc_match_rslts_tbl_tmplt.html and cc_viz_cmp_li_tmplt.html in this loop
             lclDict['assgn_checked'] = assgnChecked
             #
@@ -1649,6 +1675,7 @@ class ChemCompAssignDepict(ChemCompDepict):
             #
             lclDict['score'] = scorePrefix + cmpstscore + scoreSuffix
             lclDict['ccid'] = ccid
+            lclDict['ccid_status'] = status
             lclDict['cc_name'] = name
             lclDict['cc_name_displ'] = self.truncateForDisplay(name)
             lclDict['cc_formula'] = formula

wwpdb_apps_ccmodule-0.32.2/wwpdb/apps/ccmodule/reports/ChemCompAlignImageGenerator.py

@@ -0,0 +1,154 @@
+##
+# File:  ChemCompAlignImageGenerator.py
+# Date:  31-Oct-2014
+##
+"""
+Utility Class for generating aligned ligand images
+
+This software was developed as part of the World Wide Protein Data Bank
+Common Deposition and Annotation System Project
+
+Copyright (c) 2012 wwPDB
+
+This software is provided under a Creative Commons Attribution 3.0 Unported
+License described at http://creativecommons.org/licenses/by/3.0/.
+
+"""
+__docformat__ = "restructuredtext en"
+__author__ = "Zukang Feng"
+__email__ = "zfeng@rcsb.rutgers.edu"
+__license__ = "Creative Commons Attribution 3.0 Unported"
+__version__ = "V0.01"
+
+import os
+import sys
+import traceback
+
+from wwpdb.utils.config.ConfigInfo import ConfigInfo
+from wwpdb.utils.dp.RcsbDpUtility import RcsbDpUtility
+from wwpdb.io.file.mmCIFUtil import mmCIFUtil
+from wwpdb.io.locator.ChemRefPathInfo import ChemRefPathInfo
+
+
+class ChemCompAlignImageGenerator(object):
+    """Utility Class for generating aligned ligand images
+    """
+    def __init__(self, reqObj=None, verbose=False, log=sys.stderr):
+        self.__reqObj = reqObj
+        self.__verbose = verbose
+        self.__lfh = log
+        #
+        self.__sObj = self.__reqObj.getSessionObj()
+        self.__sessionPath = self.__sObj.getPath()
+        #
+        self.__imagePath = None
+
+        self.__siteId = str(self.__reqObj.getValue("WWPDB_SITE_ID"))
+        self.__cI = ConfigInfo(self.__siteId)
+        #
+        self.__ccRefPathInfo = ChemRefPathInfo(self.__siteId, verbose=self.__verbose, log=self.__lfh)
+
+    def generateImages(self, instId=None, instFile=None, hitList=None):
+        if (not instId) or (not instFile) or (not os.access(instFile, os.F_OK)):
+            return
+        if hitList is None:
+            hitList = []
+        #
+        self.__imagePath = os.path.join(self.__sessionPath, "assign", instId, "image")
+        if not os.access(self.__imagePath, os.F_OK):
+            try:
+                os.makedirs(self.__imagePath)
+            except:  # noqa: E722 pylint: disable=bare-except
+                return
+            #
+        #
+        foundList = []
+        imageFile = os.path.join(self.__imagePath, "image.txt")
+        ofh = open(imageFile, "w")
+        ofh.write(instId + " " + instFile + "\n")
+        for hitId in hitList:  # pylint: disable=redefined-builtin
+            refFile = self.__ccRefPathInfo.getFilePath(str(hitId).upper())
+            if not os.access(refFile, os.F_OK):
+                continue
+            #
+            ofh.write(hitId + " " + refFile + "\n")
+            #
+            alist = []
+            alist.append(hitId)
+            alist.append(refFile)
+            foundList.append(alist)
+        #
+        ofh.close()
+        #
+        if foundList:
+            try:
+                heavyAtomCount = 0
+                cifObj = mmCIFUtil(filePath=instFile)
+                dlist = cifObj.GetValue("chem_comp_atom")
+                for ccDic in dlist:
+                    if ("type_symbol" not in ccDic) or (not ccDic["type_symbol"]):
+                        continue
+                    #
+                    type_symbol = ccDic["type_symbol"].upper().strip()
+                    if (type_symbol == "H") or (type_symbol == "D"):
+                        continue
+                    #
+                    heavyAtomCount += 1
+                #
+                # Only generate aligned images for small ligands - DAOTHER-9883 for D_1292143423: TP3 -> A1IZO
+                #
+                if heavyAtomCount < 100:
+                    self.__lfh.write("+ChemCompAlignImageGenerator.generateImages() - Generating images \n")
+
+                    dp = RcsbDpUtility(tmpPath=self.__imagePath, siteId=self.__cI.get("SITE_PREFIX"), verbose=self.__verbose, log=self.__lfh)
+                    dp.addInput(name="image_file", value=imageFile)
+                    dp.setWorkingDir(self.__imagePath)
+                    returnCode = dp.op("chem-comp-align-img-gen")
+
+                    self.__lfh.write("+ChemCompAlignImageGenerator.generateImages() - remote process returned %d \n" % returnCode)
+
+                    if returnCode == 0:
+                        FounImage = True
+                        imageFile = os.path.join(self.__imagePath, instId + ".svg")
+                        if not os.access(imageFile, os.F_OK):
+                            FounImage = False
+                        #
+                        for hitId in hitList:
+                            imageFile = os.path.join(self.__imagePath, hitId + ".svg")
+                            if not os.access(imageFile, os.F_OK):
+                                FounImage = False
+                            #
+                        #
+                        if FounImage:
+                            return
+                        #
+                    #
+                #
+            except:  # noqa: E722 pylint: disable=bare-except
+                if self.__verbose:
+                    traceback.print_exc(file=self.__lfh)
+                #
+            #
+        #
+
+        self.__generateSingleImage(Id=instId, FileName=instFile)
+        self.__generateSingleImage(Id=instId, FileName=instFile, size=1000, labelAtomName=True, suffix="_Big")
+        if foundList:
+            for flist in foundList:
+                self.__generateSingleImage(Id=flist[0], FileName=flist[1])
+                self.__generateSingleImage(Id=flist[0], FileName=flist[1], size=1000, labelAtomName=True, suffix="_Big")
+            #
+        #
+
+    def __generateSingleImage(self, Id=None, FileName=None, size=300, labelAtomName=False, suffix=""):
+        imgPth = os.path.join(self.__imagePath, Id + suffix + ".svg")
+
+        dp = RcsbDpUtility(tmpPath=self.__imagePath, siteId=self.__cI.get("SITE_PREFIX"), verbose=self.__verbose, log=self.__lfh)
+        dp.addInput(name="title", value=Id)
+        dp.addInput(name="path", value=FileName)
+        dp.addInput(name="image_path", value=imgPth)
+        dp.addInput(name="size", value=size)
+        dp.addInput(name="label", value=labelAtomName)
+
+        return dp.op("chem-comp-gen-images")
+        #

{wwpdb_apps_ccmodule-0.32 → wwpdb_apps_ccmodule-0.32.2}/wwpdb.apps.ccmodule.egg-info/PKG-INFO

@@ -1,6 +1,6 @@
-Metadata-Version: 2.2
+Metadata-Version: 2.4
 Name: wwpdb.apps.ccmodule
-Version: 0.32
+Version: 0.32.2
 Summary: wwPDB workflow engine utils
 Home-page: https://github.com/rcsb/py-wwpdb_apps_wf_engine_utils
 Author: Ezra Peisach

wwpdb_apps_ccmodule-0.32/wwpdb/apps/ccmodule/reports/ChemCompAlignImageGenerator.py

@@ -1,130 +0,0 @@
-##
-# File:  ChemCompAlignImageGenerator.py
-# Date:  31-Oct-2014
-##
-"""
-Utility Class for generating aligned ligand images
-
-This software was developed as part of the World Wide Protein Data Bank
-Common Deposition and Annotation System Project
-
-Copyright (c) 2012 wwPDB
-
-This software is provided under a Creative Commons Attribution 3.0 Unported
-License described at http://creativecommons.org/licenses/by/3.0/.
-
-"""
-__docformat__ = "restructuredtext en"
-__author__ = "Zukang Feng"
-__email__ = "zfeng@rcsb.rutgers.edu"
-__license__ = "Creative Commons Attribution 3.0 Unported"
-__version__ = "V0.01"
-
-import os
-import sys
-
-from wwpdb.utils.config.ConfigInfo import ConfigInfo
-from wwpdb.utils.dp.RcsbDpUtility import RcsbDpUtility
-from wwpdb.io.locator.ChemRefPathInfo import ChemRefPathInfo
-
-
-class ChemCompAlignImageGenerator(object):
-    """Utility Class for generating aligned ligand images
-    """
-    def __init__(self, reqObj=None, verbose=False, log=sys.stderr):
-        self.__reqObj = reqObj
-        self.__verbose = verbose
-        self.__lfh = log
-        #
-        self.__sObj = self.__reqObj.getSessionObj()
-        self.__sessionPath = self.__sObj.getPath()
-        #
-        self.__imagePath = None
-
-        self.__siteId = str(self.__reqObj.getValue("WWPDB_SITE_ID"))
-        self.__cI = ConfigInfo(self.__siteId)
-        #
-        self.__ccRefPathInfo = ChemRefPathInfo(self.__siteId, verbose=self.__verbose, log=self.__lfh)
-
-    def generateImages(self, instId=None, instFile=None, hitList=None):
-        if (not instId) or (not instFile):
-            return
-        if hitList is None:
-            hitList = []
-        #
-        self.__imagePath = os.path.join(self.__sessionPath, 'assign', instId, 'image')
-        if not os.access(self.__imagePath, os.F_OK):
-            try:
-                os.makedirs(self.__imagePath)
-            except:  # noqa: E722 pylint: disable=bare-except
-                return
-            #
-        #
-        foundList = []
-        imageFile = os.path.join(self.__imagePath, 'image.txt')
-        ofh = open(imageFile, 'w')
-        ofh.write(instId + ' ' + instFile + '\n')
-        for id in hitList:  # pylint: disable=redefined-builtin
-            refFile = self.__ccRefPathInfo.getFilePath(str(id).upper())
-            if not os.access(refFile, os.F_OK):
-                continue
-            #
-            ofh.write(id + ' ' + refFile + '\n')
-            #
-            alist = []
-            alist.append(id)
-            alist.append(refFile)
-            foundList.append(alist)
-        #
-        ofh.close()
-        #
-        if foundList:
-            self.__lfh.write('+ChemCompAlignImageGenerator.generateImages() - Generating images \n')
-
-            dp = RcsbDpUtility(tmpPath=self.__imagePath, siteId=self.__cI.get('SITE_PREFIX'), verbose=self.__verbose, log=self.__lfh)
-            dp.addInput(name='image_file', value=imageFile)
-            dp.setWorkingDir(self.__imagePath)
-            returnCode = dp.op('chem-comp-align-img-gen')
-
-            self.__lfh.write('+ChemCompAlignImageGenerator.generateImages() - remote process returned %d \n' % returnCode)
-
-            if returnCode == 0:
-                FounImage = True
-                imageFile = os.path.join(self.__imagePath, instId + '.svg')
-                if not os.access(imageFile, os.F_OK):
-                    FounImage = False
-                #
-                for id in hitList:
-                    imageFile = os.path.join(self.__imagePath, id + '.svg')
-                    if not os.access(imageFile, os.F_OK):
-                        FounImage = False
-                    #
-                #
-                if FounImage:
-                    return
-                #
-            #
-        #
-
-        self.__generateSingleImage(Id=instId, FileName=instFile)
-        self.__generateSingleImage(Id=instId, FileName=instFile, size=1000, labelAtomName=True, suffix='_Big')
-        if foundList:
-            for flist in foundList:
-                self.__generateSingleImage(Id=flist[0], FileName=flist[1])
-                self.__generateSingleImage(Id=flist[0], FileName=flist[1], size=1000, labelAtomName=True, suffix='_Big')
-                #
-            #
-        #
-
-    def __generateSingleImage(self, Id=None, FileName=None, size=300, labelAtomName=False, suffix=''):
-        imgPth = os.path.join(self.__imagePath, Id + suffix + '.svg')
-
-        dp = RcsbDpUtility(tmpPath=self.__imagePath, siteId=self.__cI.get('SITE_PREFIX'), verbose=self.__verbose, log=self.__lfh)
-        dp.addInput(name="title", value=Id)
-        dp.addInput(name="path", value=FileName)
-        dp.addInput(name="image_path", value=imgPth)
-        dp.addInput(name="size", value=size)
-        dp.addInput(name="label", value=labelAtomName)
-
-        return dp.op("chem-comp-gen-images")
-        #