def getdata(self):
ext_prog = find_progs(self.parent.app.INPUT)
self.ntraj = Trajectory(self.parent.app.FILES.complex_prmtop, self.parent.app.FILES.complex_trajs,
ext_prog['cpptraj'].full_path)
self.ntraj.Setup(1, 999999, 1)
last = self.parent.app.INPUT['startframe'] + (self.ntraj.processed_frames - 1) * self.parent.app.INPUT[
'interval']
self.current_frame_s.setRange(self.parent.app.INPUT['startframe'], last)
self.current_frame_s.setSingleStep(self.parent.app.INPUT['interval'])
self.current_frame_s.setValue(self.parent.app.INPUT['startframe'])
class ExportDialog(QDialog):
def __init__(self, parent=None):
super(ExportDialog, self).__init__(parent)
self.parent = parent
self.setWindowTitle('Save Energy to b-factor')
self.current_frame_s = QSpinBox()
self.current_frame_l = QLabel('Frame:')
self.output_label = QLabel('Output:')
self.output_text = QLineEdit('complex_e2bfactor')
self.output_text.setPlaceholderText('complex_e2bfactor')
self.save_btn = QPushButton('Save')
self.save_btn.clicked.connect(self.save)
self.close_btn = QPushButton('Close')
self.close_btn.clicked.connect(self.close)
self.out_layout = QHBoxLayout()
self.out_layout.addWidget(self.output_label)
self.out_layout.addWidget(self.output_text)
self.frame_layout = QHBoxLayout()
self.frame_layout.addWidget(self.current_frame_l)
self.frame_layout.addWidget(self.current_frame_s)
# self.frame_layout.addWidget(self.interval_l, alignment=Qt.AlignRight)
# self.frame_layout.addWidget(self.interval_s)
self.btn_layout = QHBoxLayout()
self.btn_layout.addStretch(1)
self.btn_layout.addWidget(self.save_btn, alignment=Qt.AlignRight)
self.btn_layout.addWidget(self.close_btn, alignment=Qt.AlignRight)
self.layout = QVBoxLayout(self)
self.layout.addLayout(self.out_layout)
# self.layout.addWidget(self.location_btn)
self.layout.addLayout(self.frame_layout)
self.layout.addLayout(self.btn_layout)
self.getdata()
def getdata(self):
ext_prog = find_progs(self.parent.app.INPUT)
self.ntraj = Trajectory(self.parent.app.FILES.complex_prmtop, self.parent.app.FILES.complex_trajs,
ext_prog['cpptraj'].full_path)
self.ntraj.Setup(1, 999999, 1)
last = self.parent.app.INPUT['startframe'] + (self.ntraj.processed_frames - 1) * self.parent.app.INPUT[
'interval']
self.current_frame_s.setRange(self.parent.app.INPUT['startframe'], last)
self.current_frame_s.setSingleStep(self.parent.app.INPUT['interval'])
self.current_frame_s.setValue(self.parent.app.INPUT['startframe'])
@pyqtSlot()
def save(self):
self.ntraj.Outtraj('_temp_.pdb', frames=str(self.current_frame_s.value()),
filetype='pdb')
self.ntraj.Run('cpptraj.out')
pdb = PDB()
pdb.parse('_temp_.pdb')
with open(str(self.output_text.text()) + '.pdb', 'w') as pdbout:
for atm in pdb.allAtoms:
if atm['id'] == 'TER':
pdbout.write(pdb.getOutLine(atm, ter=True))
else:
if atm['resnum'] in self.parent.decomp and atm['resname'] in std_aa:
atm['b_factor'] = self.parent.decomp[atm['resnum']]
else:
atm['b_factor'] = 0.0
pdbout.write(pdb.getOutLine(atm, ter=False))
# os.remove('_temp_.pdb')
self.parent.statusbar.showMessage('Saving {} file... Done'.format(self.output_text.text() + '.pdb'))
self.close()