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added _getCovalentBondContentOp() and _updateCovalentBondContentOp()
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Ezra Peisach
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Jan 23, 2024
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| __author__ = "Ezra Peisach" | ||
| __email__ = "[email protected]" | ||
| __license__ = "Apache 2.0" | ||
| __version__ = "0.36" | ||
| __version__ = "0.37" | ||
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| Original file line number | Diff line number | Diff line change |
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| @@ -0,0 +1,166 @@ | ||
| ## | ||
| # File: GetCovalentBond.py | ||
| # Date: 28-Sep-2020 Zukang Feng | ||
| # | ||
| # Update: | ||
| ## | ||
| """ | ||
| Manage utility to correct covalent bond problems | ||
| """ | ||
| __docformat__ = "restructuredtext en" | ||
| __author__ = "Zukang Feng" | ||
| __email__ = "[email protected]" | ||
| __license__ = "Creative Commons Attribution 3.0 Unported" | ||
| __version__ = "V0.07" | ||
|
|
||
| import json | ||
| import os | ||
| import sys | ||
| import traceback | ||
|
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||
| from wwpdb.utils.dp.RcsbDpUtility import RcsbDpUtility | ||
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| class GetCovalentBond(object): | ||
| """ | ||
| GetCovalentBond class encapsulates correcting covalent bond problems. | ||
| """ | ||
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| def __init__(self, reqObj=None, verbose=False, log=sys.stderr): | ||
| self.__reqObj = reqObj | ||
| self.__verbose = verbose | ||
| self.__lfh = log | ||
| # | ||
| self.__setup() | ||
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| def __setup(self): | ||
| self.__siteId = self.__reqObj.getValue("WWPDB_SITE_ID") | ||
| self.__sObj = self.__reqObj.getSessionObj() | ||
| self.__sessionPath = self.__sObj.getPath() | ||
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| def run(self, entryId, inpFile): | ||
| """Run the calculation""" | ||
| retD = {} | ||
| retD["found"] = "no" | ||
| try: | ||
| inpPath = os.path.join(self.__sessionPath, inpFile) | ||
| logPath = os.path.join(self.__sessionPath, entryId + "-get-covalent-bond.log") | ||
| retPath = os.path.join(self.__sessionPath, entryId + "-covalent-bond.json") | ||
| for filePath in (logPath, retPath): | ||
| if os.access(filePath, os.R_OK): | ||
| os.remove(filePath) | ||
| # | ||
| # | ||
| dp = RcsbDpUtility(tmpPath=self.__sessionPath, siteId=self.__siteId, verbose=self.__verbose, log=self.__lfh) | ||
| # | ||
| dp.imp(inpPath) | ||
| dp.op("annot-get-covalent-bond") | ||
| dp.expLog(dstPath=logPath, appendMode=False) | ||
| dp.exp(retPath) | ||
| # | ||
| if os.access(retPath, os.R_OK): | ||
| with open(retPath) as ifh: | ||
| jsonObj = json.load(ifh) | ||
| htmlcontent = self.__processCloseContactContent(jsonObj) | ||
| if htmlcontent: | ||
| retD["htmlcontent"] = htmlcontent | ||
| retD["found"] = "yes" | ||
| # | ||
| # | ||
| # | ||
| dp.cleanup() | ||
| except: # noqa: E722 pylint: disable=bare-except | ||
| traceback.print_exc(file=self.__lfh) | ||
| # | ||
| return retD | ||
|
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| def __processCloseContactContent(self, jsonObj): | ||
| """ """ | ||
| if (not jsonObj) or ("covalent_bond" not in jsonObj) or (not jsonObj["covalent_bond"]): | ||
| return "" | ||
| # | ||
| htmlTemplate = """ | ||
| <input type="hidden" name="total_covalent_bond_num" value="%s" /> | ||
| <table class="table table-borderedless width80"> | ||
| <tr> | ||
| <th><input id="covalent_bond_select_all" class="btn btn-primary my-task-form-submit" value="Select All" type="button" | ||
| onClick="select_close_contact_covalent_bond('update-covalent-bond-form', 'covalent_bond_', 'covalent_bond_select_all', '');" /></th> | ||
| <th><input id="covalent_bond_submit" class="btn btn-primary my-task-form-submit" value="Submit" type="submit" /></th> | ||
| <th><input id="covalent_bond_exit" class="btn btn-primary my-task-form-submit" value="Exit" type="button" | ||
| onClick="exit_close_contact_covalent_bond_page();" /></th> | ||
| </tr> | ||
| </table> | ||
| <br/> | ||
| <table class="table table-bordered table-striped width100"> | ||
| <tr> | ||
| <th colspan="5">Atom1</th> | ||
| <th colspan="5">Atom2</th> | ||
| <th rowspan="2">Distance</th> | ||
| </tr> | ||
| <tr> | ||
| <th>Chain ID</th> | ||
| <th>Residue</th> | ||
| <th>Number</th> | ||
| <th>Atom</th> | ||
| <th>Symmetry</th> | ||
| <th>Chain ID</th> | ||
| <th>Residue</th> | ||
| <th>Number</th> | ||
| <th>Atom</th> | ||
| <th>Symmetry</th> | ||
| </tr> | ||
| %s | ||
| </table> | ||
| """ | ||
| # | ||
| tablerow = "" | ||
| count = 0 | ||
| for tupL in jsonObj["covalent_bond"]: | ||
| tablerow += "<tr>" | ||
| # | ||
| atom = tupL[4] | ||
| if tupL[5]: | ||
| atom += "(" + tupL[5] + ")" | ||
| # | ||
| tablerow += "<td>" + tupL[0] + "</td>" + "<td>" + tupL[1] + "</td>" + "<td>" + tupL[2] + tupL[3] + "</td>" + "<td>" + atom + "</td>" + "<td>" + tupL[6] + "</td>" | ||
| atom = tupL[11] | ||
| if tupL[12]: | ||
| atom += "(" + tupL[12] + ")" | ||
| # | ||
| tablerow += "<td>" + tupL[7] + "</td>" + "<td>" + tupL[8] + "</td>" + "<td>" + tupL[9] + tupL[10] + "</td>" + "<td>" + atom + "</td>" + "<td>" + tupL[13] + "</td>" | ||
| # | ||
| tupL[6] = tupL[6].replace("_", "-"); | ||
| tupL[13] = tupL[13].replace("_", "-"); | ||
| bond_id = "covalent_bond_" + str(count) | ||
| # | ||
| tablerow += "<td>" + tupL[14] + ' <input type="checkbox" id="' + bond_id + '" name="' + bond_id + '" value="' + "_".join(tupL) + '"/></td>' | ||
| # | ||
| tablerow += "</tr>\n" | ||
| count += 1 | ||
| # | ||
| return htmlTemplate % (str(count), tablerow) | ||
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| def main(): | ||
| from wwpdb.utils.config.ConfigInfo import ConfigInfo | ||
| from wwpdb.utils.session.WebRequest import InputRequest | ||
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| # | ||
| siteId = os.getenv("WWPDB_SITE_ID") | ||
| cI = ConfigInfo(siteId) | ||
| # | ||
| myReqObj = InputRequest({}, verbose=True, log=sys.stderr) | ||
| myReqObj.setValue("TopSessionPath", cI.get("SITE_WEB_APPS_TOP_SESSIONS_PATH")) | ||
| myReqObj.setValue("TopPath", cI.get("SITE_WEB_APPS_TOP_PATH")) | ||
| myReqObj.setValue("WWPDB_SITE_ID", siteId) | ||
| myReqObj.setValue("sessionid", "d581f7aa63cc8feba7d96fb9fd103866fca45a7d") | ||
| # | ||
| calc = GetCovalentBond(reqObj=myReqObj, verbose=True, log=sys.stderr) | ||
| retD = calc.run("D_1000001900", "D_1000001900_model_P1.cif") | ||
| for k, v in retD.items(): | ||
| print(k + "=" + v) | ||
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| if __name__ == "__main__": | ||
| main() |
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,95 @@ | ||
| ## | ||
| # File: UpdateCovalentBond.py | ||
| # Date: 22-Jan-2024 Zukang Feng | ||
| # | ||
| # Update: | ||
| ## | ||
| """ | ||
| Manage utility to correct covalent bond problems | ||
| """ | ||
| __docformat__ = "restructuredtext en" | ||
| __author__ = "Zukang Feng" | ||
| __email__ = "[email protected]" | ||
| __license__ = "Creative Commons Attribution 3.0 Unported" | ||
| __version__ = "V0.07" | ||
|
|
||
| import sys | ||
| import os.path | ||
| import os | ||
| import traceback | ||
|
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| from wwpdb.utils.dp.RcsbDpUtility import RcsbDpUtility | ||
| from wwpdb.apps.ann_tasks_v2.utils.SessionWebDownloadUtils import SessionWebDownloadUtils | ||
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| class UpdateCovalentBond(SessionWebDownloadUtils): | ||
| """ | ||
| UpdateCovalentBond class encapsulates correcting covalent bond problems. | ||
| """ | ||
|
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| def __init__(self, reqObj=None, verbose=False, log=sys.stderr): | ||
| super(UpdateCovalentBond, self).__init__(reqObj=reqObj, verbose=verbose, log=log) | ||
| self.__verbose = verbose | ||
| self.__lfh = log | ||
| self.__reqObj = reqObj | ||
| # | ||
| self.__setup() | ||
|
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| def __setup(self): | ||
| self.__siteId = self.__reqObj.getValue("WWPDB_SITE_ID") | ||
| self.__sObj = self.__reqObj.getSessionObj() | ||
| self.__sessionPath = self.__sObj.getPath() | ||
|
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| def __checkStatus(self, logFilePath): | ||
| status = "error" | ||
| if os.access(logFilePath, os.R_OK): | ||
| ifh = open(logFilePath, "r") | ||
| for line in ifh: | ||
| if str(line).startswith("Finished!"): | ||
| status = "ok" | ||
| break | ||
| # | ||
| # | ||
| # | ||
| return status | ||
|
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| def run(self, entryId, inpFile, closeContactList): | ||
| """Run the calculation""" | ||
| try: | ||
| inpPath = os.path.join(self.__sessionPath, inpFile) | ||
| logPath = os.path.join(self.__sessionPath, entryId + "-update-covalent-bond.log") | ||
| dataPath = os.path.join(self.__sessionPath, entryId + "-covalent-bond.txt") | ||
| for filePath in (logPath, dataPath): | ||
| if os.access(filePath, os.R_OK): | ||
| os.remove(filePath) | ||
| # | ||
| # | ||
| ofh = open(dataPath, "w") | ||
| for closeContact in closeContactList: | ||
| ofh.write("%s\n" % closeContact) | ||
| # | ||
| ofh.close() | ||
| # | ||
| status = False | ||
| dp = RcsbDpUtility(tmpPath=self.__sessionPath, siteId=self.__siteId, verbose=self.__verbose, log=self.__lfh) | ||
| # | ||
| dp.imp(inpPath) | ||
| dp.addInput(name="datafile", value=dataPath) | ||
| dp.op("annot-remove-covalent-bond") | ||
| dp.expLog(dstPath=logPath, appendMode=False) | ||
| if os.access(logPath, os.R_OK): | ||
| self.addDownloadPath(logPath) | ||
| if self.__checkStatus(logPath) == "ok": | ||
| dp.exp(inpPath) | ||
| self.addDownloadPath(inpPath) | ||
| status = True | ||
| # | ||
| # | ||
| dp.cleanup() | ||
| return status | ||
| except: # noqa: E722 pylint: disable=bare-except | ||
| traceback.print_exc(file=self.__lfh) | ||
| return False | ||
| # |
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