added chopping modification off of resiude in polymer sequence functi…

…onality

wwpdb/apps/entity_transform/__init__.py

@@ -2,4 +2,4 @@
 __author__ = "Ezra Peisach"
 __email__ = "[email protected]"
 __license__ = "Apache 2.0"
-__version__ = "0.18"
+__version__ = "0.19"

wwpdb/apps/entity_transform/depict/PrdSummaryDepict.py

@@ -61,22 +61,25 @@ def DoRenderSummaryPage(self, imageFlag=True):
         #
         if self.__splitPolymerResidueFlag:
             text += '<li><a class="fltlft" href="/service/entity/result_view?' + input_data + '&type=split" target="_blank"> ' \
-                + '<span style="color:red;">Split modified residue to standard residue + modification in polymer</span> </a></li>\n'
+                  + '<span style="color:red;">Split modified residue to standard residue + modification in polymer</span> </a></li>\n'
         #
         if self.__combResidueFlag:
             text += '<li><a class="fltlft" href="/service/entity/result_view?' + input_data + '&type=merge" target="_blank"> ' \
-                + '<span style="color:red;">Merge standard amino acid residue + modification to modified amino acid residue in polymer</span> </a></li>\n'
+                  + '<span style="color:red;">Merge standard amino acid residue + modification to modified amino acid residue in polymer</span> </a></li>\n'
         #
         if self.__matchResultFlag:
             text += '<li><a class="fltlft" href="/service/entity/result_view?' + input_data \
-                + '" target="_blank"> <span style="color:red;">View All Search Result(s)</span> </a></li>\n'
+                  + '" target="_blank"> <span style="color:red;">View All Search Result(s)</span> </a></li>\n'
         #
         if self.__graphmatchResultFlag:
             text += '<li><a class="fltlft" href="/service/entity/result_view?' + input_data \
-                + '&type=match" target="_blank"> Update Coordinate File with Match Result(s) </a></li>\n'
+                  + '&type=match" target="_blank"> Update Coordinate File with Match Result(s) </a></li>\n'
         #
         text += '<li><a class="fltlft" href="/service/entity/result_view?' + input_data \
-            + '&type=input" target="_blank"> Update Coordinate File with Input IDs </a></li>\n'
+              + '&type=input" target="_blank"> Update Coordinate File with Input IDs </a></li>\n'
+        #
+        text += '<li><a class="fltlft" href="/service/entity/result_view?' + input_data + '&type=split_with_input" target="_blank"> ' \
+              + 'Split non standard residue in polymer </a></li>\n'
         #
         text += '<li><a class="fltlft" href="/service/entity/download_file?' + input_data + '" target="_blank"> Download Files </a></li>\n'
         #

wwpdb/apps/entity_transform/depict/StrFormDepict.py

@@ -106,9 +106,13 @@ def LaunchEditor(self):
 
     def __processSplitWithChopper(self, myD):
         ciffile = self._identifier + '_model_P1.cif'
-        combObj = CombineCoord(reqObj=self._reqObj, instList=[str(self._reqObj.getValue('split_polymer_residue'))], cifFile=ciffile,
-                               verbose=self._verbose, log=self._lfh)
-        combObj.processWithCopy()
+        residueId = str(self._reqObj.getValue('split_polymer_residue'))
+        if not residueId:
+            residueId = '_'.join([str(self._reqObj.getValue('chain_id')), str(self._reqObj.getValue('res_name')), \
+                                  str(self._reqObj.getValue('res_num')), str(self._reqObj.getValue('ins_code'))])
+        #
+        combObj = CombineCoord(reqObj=self._reqObj, instList=[residueId], cifFile=ciffile, verbose=self._verbose, log=self._lfh)
+        combObj.processWithCopy(submitValue=self.__submitValue)
         message = combObj.getMessage()
         #
         if message:

wwpdb/apps/entity_transform/depict/StrSummaryDepict.py

@@ -227,7 +227,8 @@ def __depictionChain(self):
     def __depictionLigand(self):
         text = '<table>\n'
         text += '<tr>\n'
-        text += '<th>Selection/<br/>User Defined Group ID</th>\n'
+        text += '<th>Selection/<br/>User Defined Group ID<br/><input id="ligand_select_all" value="Select All" type="button" onClick="select_ligand(' \
+              + "'ligand_select_all'" + ');" /></th>\n'
         text += '<th>3 Letter Code</th>\n'
         text += '<th>Chain ID</th>\n'
         text += '<th>ResNum</th>\n'

wwpdb/apps/entity_transform/update/ChopperHandler.py

@@ -21,6 +21,12 @@
 __license__ = "Creative Commons Attribution 3.0 Unported"
 __version__ = "V0.07"
 
+try:
+    import cPickle as pickle
+except ImportError:
+    import pickle as pickle
+#
+
 import os
 import sys
 
@@ -104,10 +110,29 @@ def __runMappingScript(self):
     def __searchOtherInstances(self):
         """ Get other instances list
         """
+        residue_id = ''
+        if self.__option == 'split_residue':
+            pickleFilePath = os.path.join(self.__instancePath, self.__instId + ".pkl")
+            if os.access(pickleFilePath, os.F_OK):
+                fb = open(pickleFilePath, "rb")
+                pickleD = pickle.load(fb)
+                fb.close()
+                #
+                if ('residue' in pickleD) and pickleD['residue']:
+                    residue_id = pickleD['residue']
+                #
+            #
+        #
+        self.__lfh.write("residue_id=%s\n" % residue_id)
         searchPath = os.path.join(self.__sessionPath, 'search')
         extraOptions = ' -summaryfile ' + self.__summaryFile + ' -searchpath ' + searchPath + ' -merge_cif ' + self.__instId \
             + '.merge.cif -chopper_cif ' + os.path.join(self.__instancePath, 'chopper_output.cif') + ' '
         #
+        if residue_id != '':
+            identifier = str(self.__reqObj.getValue("identifier"))
+            ciffile = os.path.join(self.__sessionPath, identifier + '_model_P1.cif')
+            extraOptions += ' -residue_id ' + residue_id + ' -model_cif ' + ciffile
+        #
         self.__cmdUtil.setSessionPath(self.__instancePath)
         self.__cmdUtil.runAnnotCmd('SearchAllInstances', '', self.__instId + '.all_instance_search.list',
                                    'search-instances.log', 'search-instances.clog', extraOptions)

wwpdb/apps/entity_transform/update/CombineCoord.py

@@ -21,6 +21,12 @@
 __license__ = "Creative Commons Attribution 3.0 Unported"
 __version__ = "V0.07"
 
+try:
+    import cPickle as pickle
+except ImportError:
+    import pickle as pickle
+#
+
 import os
 import shutil
 import sys
@@ -45,6 +51,7 @@ def __init__(self, reqObj=None, instList=None, cifFile=None, verbose=False, log=
         self.__sessionPath = None
         self.__instId = ''
         self.__message = ''
+        self.__submitValue = ''
         #
         self.__getSession()
         self.__getInstId()
@@ -62,7 +69,22 @@ def processWithCombine(self):
         #
         self.__runUpdateScript()
 
-    def processWithCopy(self):
+    def processWithCopy(self, submitValue=''):
+        #
+        self.__submitValue = submitValue
+        #
+        if self.__submitValue and (len(self.__instList) == 1) and self.__instList[0]:
+            pickleFilePath = os.path.join(self.__instancePath, self.__instId + ".pkl")
+            if os.access(pickleFilePath, os.F_OK):
+                 os.remove(pickleFilePath)
+            #
+            pickleD = {}
+            pickleD['residue'] = self.__instList[0]
+            pickleD['submit'] = self.__submitValue
+            #
+            fb = open(pickleFilePath, "wb")
+            pickle.dump(pickleD, fb)
+            fb.close()
         #
         if not self.__runCopyScript():
             self.__runCombineScript()
@@ -122,7 +144,6 @@ def __runCopyScript(self):
             if not os.access(source, os.F_OK):
                 return False
             #
-            #
             shutil.copyfile(source, os.path.join(self.__instancePath, self.__instId + ext))
         #
         return True

wwpdb/apps/entity_transform/webapp/EntityWebApp.py

@@ -793,7 +793,7 @@ def _resultView(self):
         rC = ResponseContent(reqObj=self.__reqObj, verbose=self.__verbose, log=self.__lfh)
         #
         instId = str(self.__reqObj.getValue("instanceid"))
-        type = str(self.__reqObj.getValue("type"))  # pylint: disable=redefined-builtin
+        viewType = str(self.__reqObj.getValue("type"))  # pylint: disable=redefined-builtin
         resultObj = None
         if self.__summaryCifObj:
             resultObj = ResultDepict(reqObj=self.__reqObj, summaryCifObj=self.__summaryCifObj, verbose=self.__verbose, log=self.__lfh)
@@ -804,28 +804,30 @@ def _resultView(self):
         myD['title'] = self.__title
         myD['pdbid'] = self.__reqObj.getValue('pdbid')
         myD['label'] = self.__reqObj.getValue('label')
-        if type == 'match':
+        if viewType == 'match':
             if resultObj:
                 myD['form_data'] = resultObj.DoRenderUpdatePage()
             else:
                 myD['form_data'] = 'Can not find summary result file.'
             #
             rC.setHtmlText(self.__processTemplate('update_form/update_match_tmplt.html', myD))
-        elif type == 'input':
+        elif viewType == 'input':
             if resultObj:
                 myD['form_data'] = resultObj.DoRenderInputPage()
             else:
                 myD['form_data'] = 'Can not find summary result file.'
             #
             rC.setHtmlText(self.__processTemplate('update_form/update_user_input_tmplt.html', myD))
-        elif type == 'split':
+        elif viewType == 'split':
             if resultObj:
                 myD['form_data'] = resultObj.DoRenderSplitPage()
             else:
                 myD['form_data'] = '<tr><td colspan="6">Can not find summary result file.</td></tr>'
             #
             rC.setHtmlText(self.__processTemplate('summary_view/split_polymer_residue_tmplt.html', myD))
-        elif type == 'merge':
+        elif viewType == 'split_with_input':
+            rC.setHtmlText(self.__processTemplate('summary_view/split_polymer_residue_input_tmplt.html', myD))
+        elif viewType == 'merge':
             if resultObj:
                 myD['form_data'] = resultObj.DoRenderMergePage()
             else:

wwpdb/apps/entity_transform/webapp/FormPreProcess.py

@@ -38,6 +38,9 @@ def __init__(self, reqObj=None, verbose=False, log=sys.stderr):  # pylint: disab
         self.__ligandList = self.__reqObj.getValueList('ligand')
         self.__groupList = self.__reqObj.getValueList('group')
         self.__splitPolymerResidue = str(self.__reqObj.getValue('split_polymer_residue'))
+        self.__chainID = str(self.__reqObj.getValue('chain_id'))
+        self.__resName = str(self.__reqObj.getValue('res_name'))
+        self.__resNum = str(self.__reqObj.getValue('res_num'))
         #
         self.__errorMessage = ''
         #
@@ -51,8 +54,13 @@ def __preProcessForm(self):
         # Check for non standard residue
         #
         if self.__submitValue == 'Split with chopper':
-            if not self.__splitPolymerResidue:
+            hasResidueSelected = False
+            if self.__splitPolymerResidue or (self.__chainID and self.__resName and self.__resNum):
+                hasResidueSelected = True
+            #
+            if not hasResidueSelected:
                 self.__errorMessage = 'No residue selected'
+            #
             return
         #
         # Check no values