def restart(self):
log('Restart clicked')
self.gdb.quit()
self.pdb.quit()
self.gdb = gdb.gdb(self.python_file_gdb, self.cpp_file, self.cpp_start_line)
self.pdb = pdb.pdb(self.python_file_pdb, self.python_start_line)
self.button_step_over.setEnabled(True)
self.updateView()
def restart(self):
log('Restart clicked')
self.gdb.quit()
self.pdb.quit()
self.gdb = gdb.gdb(self.python_file_gdb, self.cpp_file,
self.cpp_start_line)
self.pdb = pdb.pdb(self.python_file_pdb, self.python_start_line)
self.button_step_over.setEnabled(True)
self.updateView()
def __init__(self,pdb_folder,modeldir,pdb_file,seq_ali):
self.seq_ali = modeldir + seq_ali
self.pdb_folder = pdb_folder
self.modeldir = modeldir
self.pdb_file = pdb.pdb(modeldir + pdb_file)
self.template = modeldir + pdb_file
self.strname = self.pdb_file.NomedaEstrutura()
# self.hmmresults = None
# self.betterid = None
# self.hmm = None
self.fasta_aligned_file = None
self.template_pir = None
def __init__(self,
mixedText,
python_file_gdb,
cpp_file,
cpp_start_line,
python_file_pdb,
python_start_line,
next_dict,
cpp_offset_lines=0,
python_offset_lines=0,
parent=None,
watches=[],
cpponly=False):
self.python_file_gdb = python_file_gdb
self.cpp_file = cpp_file
self.cpp_start_line = cpp_start_line
self.next_dict = next_dict
self.python_file_pdb = python_file_pdb
self.python_start_line = python_start_line
self.cpp_offset_lines = cpp_offset_lines
self.python_offset_lines = python_offset_lines
self.watches = watches
self.cpponly = cpponly
self.fontFamily = "Courier"
super(Form, self).__init__(parent)
self.setWindowTitle("SEJITS Integrated Debugger")
self.resize(1920, 1024)
self.textedit = QTextEdit()
self.textedit.setReadOnly(True)
self.textedit.setLineWrapMode(QTextEdit.NoWrap)
self.button_step_over = QPushButton("Step over")
self.button_step_over.clicked.connect(self.stepOver)
self.button_restart = QPushButton("Restart")
self.button_restart.clicked.connect(self.restart)
self.button_close = QPushButton("Close")
self.button_close.clicked.connect(self.accept)
self.lang_colors = dict()
self.lang_colors['C++'] = '#ff0000'
self.lang_colors['Python'] = '#0000ff'
if self.cpponly:
self.watches = [x for x in watches if x[0] == 'C++']
self.watch_layout = QGridLayout()
self.watch_values = dict()
self.button_add_watch = QPushButton("Add watch")
self.button_add_watch.clicked.connect(self.add_watch)
self.right_panel = QVBoxLayout()
self.right_panel.addLayout(self.watch_layout)
self.right_panel.addWidget(self.button_add_watch)
self.right_panel.addStretch()
self.button_hlayout = QHBoxLayout()
self.button_hlayout.addWidget(self.button_step_over)
self.button_hlayout.addWidget(self.button_restart)
self.button_hlayout.addWidget(self.button_close)
self.edit_watch_hlayout = QHBoxLayout()
self.edit_watch_hlayout.addWidget(self.textedit)
self.edit_watch_hlayout.addLayout(self.right_panel)
self.edit_watch_hlayout.setStretch(0, 3)
self.edit_watch_hlayout.setStretch(1, 1)
self.vlayout = QVBoxLayout()
self.vlayout.addLayout(self.edit_watch_hlayout)
self.vlayout.addLayout(self.button_hlayout)
self.setLayout(self.vlayout)
self.mixedText = mixedText
self.gdb = gdb.gdb(self.python_file_gdb, self.cpp_file,
self.cpp_start_line)
self.pdb = pdb.pdb(self.python_file_pdb, self.python_start_line)
self.updateView()
self.update_watch_widgets()
# loop over the identifiers.
for ident in ids:
# skip existing directories.
if os.path.exists(ident):
continue
# create the directory.
os.mkdir(ident)
uc = ident.upper()
# download the pdb file.
url = 'https://files.rcsb.org/download/' + uc + '.pdb'
response = urllib2.urlopen(url)
data = response.read()
# write the result to disk.
fpdb = os.path.join(ident, 'input.pdb')
f = open(fpdb, 'w')
f.write(data)
f.close()
# open and parse the pdb file.
struct = pdb.pdb(fpdb)
# write the required input files.
write.runfile(os.path.join(ident, 'run'))
write.fasta(struct, os.path.join(ident, 'input.fa'))
write.params(struct, os.path.join(ident, 'input.par'))
write.restraints(struct, os.path.join(ident, 'input.res'))
# if supplied, get the dihedral expansion value.
eps = 0
if len(sys.argv) >= 2:
eps = float(sys.argv[1])
# if supplied, get the distance restraint limit.
dmax = 10
if len(sys.argv) >= 3:
dmax = float(sys.argv[2])
# build the output filenames.
fres = 'loops-{}-{}.res'.format(eps, dmax)
frun = 'loops-{}-{}.run'.format(eps, dmax)
# parse the target pdb file (from ../talos/talos.dcd).
s = pdb.pdb('loops.pdb')
# get the residue index extents.
(rmin, rmax) = minmax([atom['resSeq'] for atom in s.models[0]])
# initialize the lines of output.
lines = ['', '{{* loops.res: eps = {}, dmax = {} *}}'.format(eps, dmax)]
# add dihedral restraints.
for resid in range(rmin, rmax + 1):
h = resid - rmin
i = resid - rmin + 1
j = resid - rmin + 2
lines.append('')
lines.append('{{* resid {} *}}'.format(i))
def __init__(self, mixedText, python_file_gdb, cpp_file, cpp_start_line, python_file_pdb, python_start_line, next_dict, cpp_offset_lines=0, python_offset_lines=0, parent=None, watches=[], cpponly=False):
self.python_file_gdb = python_file_gdb
self.cpp_file = cpp_file
self.cpp_start_line = cpp_start_line
self.next_dict = next_dict
self.python_file_pdb = python_file_pdb
self.python_start_line = python_start_line
self.cpp_offset_lines = cpp_offset_lines
self.python_offset_lines = python_offset_lines
self.watches = watches
self.cpponly = cpponly
self.fontFamily = "Courier"
super(Form, self).__init__(parent)
self.setWindowTitle("SEJITS Integrated Debugger")
self.resize(1920, 1024)
self.textedit = QTextEdit()
self.textedit.setReadOnly(True)
self.textedit.setLineWrapMode(QTextEdit.NoWrap)
self.button_step_over = QPushButton("Step over")
self.button_step_over.clicked.connect(self.stepOver)
self.button_restart = QPushButton("Restart")
self.button_restart.clicked.connect(self.restart)
self.button_close = QPushButton("Close")
self.button_close.clicked.connect(self.accept)
self.lang_colors = dict()
self.lang_colors['C++'] = '#ff0000'
self.lang_colors['Python'] = '#0000ff'
if self.cpponly:
self.watches = [x for x in watches if x[0] == 'C++']
self.watch_layout = QGridLayout()
self.watch_values = dict()
self.button_add_watch = QPushButton("Add watch")
self.button_add_watch.clicked.connect(self.add_watch)
self.right_panel = QVBoxLayout()
self.right_panel.addLayout(self.watch_layout)
self.right_panel.addWidget(self.button_add_watch)
self.right_panel.addStretch()
self.button_hlayout = QHBoxLayout()
self.button_hlayout.addWidget(self.button_step_over)
self.button_hlayout.addWidget(self.button_restart)
self.button_hlayout.addWidget(self.button_close)
self.edit_watch_hlayout = QHBoxLayout()
self.edit_watch_hlayout.addWidget(self.textedit)
self.edit_watch_hlayout.addLayout(self.right_panel)
self.edit_watch_hlayout.setStretch(0, 3)
self.edit_watch_hlayout.setStretch(1, 1)
self.vlayout = QVBoxLayout()
self.vlayout.addLayout(self.edit_watch_hlayout)
self.vlayout.addLayout(self.button_hlayout)
self.setLayout(self.vlayout)
self.mixedText = mixedText
self.gdb = gdb.gdb(self.python_file_gdb, self.cpp_file, self.cpp_start_line)
self.pdb = pdb.pdb(self.python_file_pdb, self.python_start_line)
self.updateView()
self.update_watch_widgets()