def showResults(self, score, proteinSeqList):
"""
Display the rosetta simulation results in a pop up dialog at the end
of a successful simulation
@param score: Score from the most optimized sequence
@type score: str
@param proteinSeqList: list of size 2, with (protein, sequence) tuple,
containing the input protein and its sequence
and the output protein and its corresponding
sequence
@type proteinSeqList: list
"""
html = "Score of this fixed backbone sequence design using starting"
html = html + " structure " + self.sim_input_file
html = html + " and residue file " + self.resFile
html = html + " is " + "<font face=Courier New color=red>" + score + "</font>"
html = html + "<p>The original protein sequence and the designed sequence"
html = html + " are shown below with differences in designed sequence "
html = html + "shown in red: <br>"
#highlight the differences in sequence between the original protein
#and the new protein
modSeqList, similarity = highlightDifferencesInSequence(proteinSeqList)
for i in range(len(proteinSeqList)):
html = html + "<font face=Courier New>" + proteinSeqList[i][0] + "</font> "+ "<br>"
html = html + "<font face=Courier New>" + modSeqList[i] + "</font>" + "<br>"
html = html + "</p>"
html = html + "<p>Sequence Similarity = " + similarity + "</p>"
w = WikiHelpBrowser(html, parent = self.win, caption = "Rosetta Sequence Design Results", size = 2)
w.show()
return
def showRosettaScore(tmp_file_prefix, scorefile, win):
"""
Show the rosetta score of the current protein sequence
@param tmp_file_prefix: file prefix from which directory of the score file
could be extracted
@type tmp_file_prefix: str
@param scorefile: name of the rosetta score file
@type scorefile: str
@param win: NE-1 window
@type win: L{gl_pane}
"""
dir1 = os.path.dirname(tmp_file_prefix)
scorefile = scorefile + '.sc'
scoreFilePath = os.path.join(dir1, scorefile)
fileObject1 = open(scoreFilePath, 'r')
if fileObject1:
doc = fileObject1.readlines()
copied_lines = []
for line in doc:
#put a comma after each word
i = 0
firstSpace = True
for c in line:
if i > 0 and c == ' ' and firstSpace == True:
line = line[0:i] + ',' + line[i+1:]
firstSpace = False
if c != ' ' and firstSpace == False:
firstSpace = True
i = i + 1
if i == len(line):
copied_lines.append(line)
array_Name = copied_lines[0].split(',')
array_Score = copied_lines[1].split(',')
i = 0
for i in range(len(array_Name)):
array_Name[i] = array_Name[i].strip()
array_Score[i] = array_Score[i].strip()
i = 0
html = ""
for i in range(len(array_Name)):
html = html + "<p><b>" + array_Name[i].upper() + "</b> = "
html = html + "<font color = red> " + array_Score[i] + "</font></p>"
w = WikiHelpBrowser(html, parent = win, caption = "Rosetta Scoring Results", size = 1)
w.show()
return
def showResults(self, score, proteinSeqList):
from foundation.wiki_help import WikiHelpBrowser
html = "Score of this fixed backbone sequence design using starting"
html = html + " structure " + self.sim_input_file
html = html + " and residue file " + self.resFile
html = html + " is " + "<font face=Courier New color=red>" + score + "</font>"
html = html + "<p>The original protein sequence and the designed sequence"
html = html + " are shown below with differences in designed sequence "
html = html + "shown in red: <br>"
modSeqList, similarity = highlightDifferencesInSequence(proteinSeqList)
for i in range(len(proteinSeqList)):
html = html + "<font face=Courier New>" + proteinSeqList[i][0] + "</font> "+ "<br>"
html = html + "<font face=Courier New>" + modSeqList[i] + "</font>" + "<br>"
html = html + "</p>"
html = html + "<p>Sequence Similarity = " + similarity + "</p>"
w = WikiHelpBrowser(html, parent = self.win, caption = "Rosetta Results")
w.show()
return
def wikiHelp(self):
parent = env.mainwindow()
w = WikiHelpBrowser(self.text,parent,caption=self.name)
w.show()
def wikiHelp(self):
parent = env.mainwindow()
w = WikiHelpBrowser(self.text, parent, caption=self.name)
w.show()