def save(self, filename): # WIP
self.filename = filename
exception = None
open_file = None
try:
if not self.filename:
raise IOError("no filename specified for saving")
open_file = open(self.filename, 'w')
dataExtra = self.extractInitData()
GRO_parse.write_extraData_to_GRO(open_file, dataExtra[0])
GRO_parse.write_extraData_to_GRO(open_file, [str(self.rowCount())])
for row in self.GRO_rows:
residNum = row.residNum
residName = row.residName # (residNum, residName, atomName, atomNum, X,Y,Z ) = range(7)
atomName = row.atomName
atomNum = row.atomNum
x = row.X
y = row.Y
z = row.Z
line = [residNum, residName, atomName, atomNum, x, y, z]
# print('line is ',line)
GRO_parse.write_SingleLine_to_GRO(open_file, line)
GRO_parse.write_vectorBox_to_GRO(open_file, dataExtra[2])
self.dirty = False
except IOError as e:
exception = e
finally:
if open_file is not None:
open_file.close()
if exception is not None:
raise exception
def load(self):
exception = None
fh = None
try:
if not self.filename:
raise IOError("no filename specified for loading")
self.mol = GRO_parse.groParse(self.filename)
for row in self.mol:
ATOM = row[0]
serial = row[1]
name = row[2]
resName = row[3]
ChainID = row[4]
resNum = row[5]
X = row[6]
Y = row[7]
Z = row[8]
occupancy = row[9]
charge = row[10]
element = row[11]
GROrow = GRO_rowInfo(ATOM, serial, name, resName, ChainID, resNum, X, Y, Z, occupancy, charge, element)
self.PDB_ROWS[id(GROrow)] = GROrow
self.dirty = False
except IOError as e:
exception = e
def load(self, fname): # This parts need modification
self.filename = fname
exception = None
fh = None
try:
if self.filename != '':
if not self.filename:
raise IOError("no filename specified for loading")
self.GRO_rows = []
self.molTotal = GRO_parse.groParse(self.filename)
self.mol = self.molTotal[2:-1]
# print('self.mol is ',self.mol)
self.flag_color = True
self.val = int(self.mol[2][0])
for row in self.mol:
residNum = row[0]
if self.val != int(residNum):
if self.flag_color == True:
self.flag_color = False
# self.val = int(resNum)
residNum_color = QColor(Qt.green)
elif self.flag_color == False:
self.flag_color = True
# self.val = int(GRO_row.resNum)
residNum_color = QColor(Qt.yellow)
self.val = int(residNum)
elif self.flag_color == True and self.val == int(residNum):
residNum_color = QColor(Qt.yellow)
elif self.flag_color == False and self.val == int(residNum):
residNum_color = QColor(Qt.green)
residName = row[1]
if residName in RESID_COLORS_RGB:
Col = RESID_COLORS_RGB[residName]
residName_color = QColor(Col[0], Col[1], Col[2])
else:
Col = RESID_COLORS_RGB['other']
residName_color = QColor(Col[0], Col[1], Col[2])
atomName = row[2]
atomNum = row[3]
X = row[4]
Y = row[5]
Z = row[6]
GROrow = GRO_rowInfo(residNum, residNum_color, residName, residName_color, atomName, atomNum, X, Y,
Z)
self.GRO_rows.append(GROrow)
self.dirty = False
# self.extractInitData() #For test Purpose
except IOError as e:
exception = e
finally:
if fh is not None:
fh.close()
if exception is not None:
raise exception