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()