def exportAtomStructStep(self):
exportAtomStruct = self.exportAtomStruct.get()
originStructPath = exportAtomStruct.getFileName()
dirName = self.filesPath.get()
destinyStructPath = os.path.join(dirName, self.COORDINATEFILENAME)
destinySympleStructPath = os.path.join(dirName, self.SYMPLIFIED_STRUCT)
# save input atom struct with no change
baseName = os.path.basename(originStructPath)
localPath = os.path.abspath(os.path.join(dirName, baseName))
copyFile(originStructPath, localPath)
# call biopython to simplify atom struct and save it
aSH = AtomicStructHandler()
aSH.read(originStructPath)
aSH.write(destinySympleStructPath)
# if pdb convert to mmcif calling maxit twice
if originStructPath.endswith(".pdb"):
# convert pdb to cif using maxit program
log = self._log
fromPDBToCIF(originStructPath, destinyStructPath, log)
try:
# convert cif to mmCIF by using maxit program
fromCIFTommCIF(destinyStructPath, destinyStructPath, log)
except Exception as e:
pass
# if cif convert to mmcif using maxit
elif originStructPath.endswith(".cif"):
# convert cif to mmCIF by using maxit program
log = self._log
try:
fromCIFTommCIF(originStructPath, destinyStructPath, log)
except Exception as e:
pass
def _getDockInMapOutput(self):
outAtomStructName = os.getcwd() + "/" +\
self._getExtraPath("placed_model.pdb")
# convert cif to mmcif by using maxit program
# to get the right number and name of chains
log = self._log
self.outAtomStructName = outAtomStructName.replace("pdb", "cif")
fromPDBToCIF(outAtomStructName, self.outAtomStructName, log)
fromCIFTommCIF(self.outAtomStructName, self.outAtomStructName, log)
def createOutputStep(self, targetSym, targetAtomStructFn):
""" save new atomic structure"""
pdb = AtomStruct()
pdb.setFileName(targetAtomStructFn)
# MM: to get appropriate cif files to be visualize with Chimera
# Transform the output cif file in mmcif
log = self._log
fromCIFTommCIF(pdb.getFileName(), pdb.getFileName(), log)
self._defineOutputs(rotatedAtomStruct=pdb)
self._defineSourceRelation(self.pdbFileToBeRefined, pdb)
def _getRSRefineOutput(self):
inPdbName = os.path.basename(self.inputStructure.get().getFileName())
list_cif = []
for item in os.listdir(self._getExtraPath()):
p = re.compile('\d+')
if p.search(item) is not None and item.endswith(".cif"):
list_cif.append(item)
name = sorted(list_cif)[-1]
outAtomStructName = self._getExtraPath(name)
# convert cif to mmcif by using maxit program
# to get the right number and name of chains
log = self._log
self.outAtomStructName = outAtomStructName
fromCIFTommCIF(outAtomStructName, self.outAtomStructName, log)
def createOutputStep(self, outFileName, twoRelations=False, suffix=''):
outFileName = os.path.abspath(outFileName)
fnCmd = self._getExtraPath("chimera_output.cxc")
f = open(fnCmd, 'a+')
f.write("open %s\n" % outFileName)
f.close()
pdb = AtomStruct()
pdb.setFileName(outFileName)
# MM: to get appropriate cif files to be visualize with Chimera
# Transform the output cif file in mmcif
log = self._log
fromCIFTommCIF(outFileName, outFileName, log)
if suffix == "":
self._defineOutputs(outputPdb=pdb)
else:
outputDict = {'outputPdb_chain%s' % suffix: pdb}
self._defineOutputs(**outputDict)
self._defineSourceRelation(self.pdbFileToBeRefined, pdb)
if twoRelations:
self._defineSourceRelation(self.InputAtomStruct2, pdb)
def _runChangingCifFormatSuperpose(self, list_args):
cwd = os.getcwd() + "/" + self._getExtraPath()
try:
if list_args[0].endswith(".cif") and list_args[1].endswith(".cif"):
try:
# upgrade cifs
list_args1 = []
for i in range(0, 2):
list_args1.append(fromCIFTommCIF(list_args[i], list_args[i]))
args1 = list_args1[0] + " " + list_args1[1]
Plugin.runPhenixProgram(Plugin.getProgram(SUPERPOSE), args1,
extraEnvDict=None, cwd=cwd)
except:
# convert cifs to pdbs
list_args2 = []
for i in range(0, 2):
list_args2.append(fromCIFToPDB(
list_args[i], list_args[i].replace('.cif', '.pdb')))
args2 = list_args2[0] + " " + list_args2[1]
Plugin.runPhenixProgram(Plugin.getProgram(SUPERPOSE), args2,
extraEnvDict=None, cwd=cwd)
elif list_args[0].endswith(".cif") and list_args[1].endswith(".pdb"):
try:
# pdbs: convert cif to pdb
list_args1 = []
list_args1.append(fromCIFToPDB(
list_args[0], list_args[0].replace('.cif', '.pdb')))
args1 = list_args1[0] + " " + list_args[1]
Plugin.runPhenixProgram(Plugin.getProgram(SUPERPOSE), args1,
extraEnvDict=None, cwd=cwd)
except:
try:
# cifs: convert pdb to cif
list_args2 = []
list_args2.append(fromPDBToCIF(
list_args[1], list_args[1].replace('.pdb', '.cif')))
args2 = list_args[0] + " " + list_args2[0]
Plugin.runPhenixProgram(Plugin.getProgram(SUPERPOSE), args2,
extraEnvDict=None, cwd=cwd)
except:
# upgrade cif
list_args3 = []
list_args0 = args2.split()
for i in range(0, 2):
list_args3[i].append(fromCIFTommCIF(
list_args0[i], list_args0[i]))
args3 = list_args3[0] + " " + list_args3[1]
Plugin.runPhenixProgram(Plugin.getProgram(SUPERPOSE),
args3, extraEnvDict=None, cwd=cwd)
elif list_args[0].endswith(".pdb") and list_args[1].endswith(".cif"):
try:
# pdbs: convert cif to pdb
list_args1 = []
list_args1.append(fromCIFToPDB(
list_args[1], list_args[1].replace('.cif', '.pdb')))
args1 = list_args[0] + " " + list_args1[0]
Plugin.runPhenixProgram(Plugin.getProgram(SUPERPOSE), args1,
extraEnvDict=None, cwd=cwd)
except:
try:
# cifs: convert pdb to cif
list_args2 = []
list_args2.append(fromPDBToCIF(
list_args[0], list_args[0].replace('.pdb', '.cif')))
args2 = list_args2[0] + " " + list_args[1]
Plugin.runPhenixProgram(Plugin.getProgram(SUPERPOSE), args2,
extraEnvDict=None, cwd=cwd)
except:
# upgrade cifs
list_args3 = []
list_args0 = args2.split()
for i in range(0, 2):
list_args3.append(fromCIFTommCIF(
list_args0[i], list_args0[i]))
args3 = list_args3[0] + " " + list_args3[1]
Plugin.runPhenixProgram(Plugin.getProgram(SUPERPOSE),
args3, extraEnvDict=None, cwd=cwd)
except:
# biopython conversion
aSH = AtomicStructHandler()
try:
for i in range(0, 2):
aSH.read(list_args[i])
aSH.write(list_args[i])
args = list_args[0] + " " + list_args[1]
Plugin.runPhenixProgram(Plugin.getProgram(SUPERPOSE),
args, extraEnvDict=None, cwd=cwd)
except:
print("CIF file standarization failed.")