def __init__(self, assy):
QDialog.__init__(self)
self.setupUi(self)
self.connect(self.okPushButton,SIGNAL("clicked()"),self.accept)
self.connect(self.cancelPushButton,SIGNAL("clicked()"),self.reject)
self.nameLineEdit.setText(assy.name)
self.mmpformatLabel.setText("MMP File Format: " + assy.mmpformat)
# Get statistics of part and display them in the statView widget.
from commands.GroupProperties.GroupProp import Statistics
stats = Statistics(assy.tree)
stats.display(self.statsView)
def __init__(self, assy):
QDialog.__init__(self)
self.setupUi(self)
self.connect(self.okPushButton,SIGNAL("clicked()"),self.accept)
self.connect(self.cancelPushButton,SIGNAL("clicked()"),self.reject)
self.nameLineEdit.setText(assy.name)
self.mmpformatLabel.setText("MMP File Format: " + assy.mmpformat)
# Get statistics of part and display them in the statView widget.
from commands.GroupProperties.GroupProp import Statistics
stats = Statistics(assy.tree)
stats.display(self.statsView)
def write_qutemol_files(part, excludeFlags = EXCLUDE_HIDDEN_ATOMS):
"""
Writes a PDB of the current I{part} to the Nanorex temp directory.
@param part: the NE1 part.
@type part: L{assembly}
@param excludeFlags: used to exclude certain atoms from being written
to the QuteMolX PDB file, where:
WRITE_ALL_ATOMS = 0 (even writes hidden and invisble atoms)
EXCLUDE_BONDPOINTS = 1 (excludes bondpoints)
EXCLUDE_HIDDEN_ATOMS = 2 (excludes both hidden and invisible atoms)
EXCLUDE_DNA_ATOMS = 4 (excludes PAM3 and PAM5 pseudo atoms)
EXCLUDE_DNA_AXIS_ATOMS = 8 (excludes PAM3 axis atoms)
EXCLUDE_DNA_AXIS_BONDS = 16 (supresses PAM3 axis bonds)
@type excludeFlags: int
@return: the name of the temp PDB file, or None if no atoms are in I{part}.
@rtype: str
"""
# Is there a better way to get the number of atoms in <part>.?
# Mark 2007-06-02
stats = Statistics(part.tree)
if 0:
stats.num_atoms = stats.natoms - stats.nsinglets
print "write_qutemol_files(): natoms =", stats.natoms, \
"nsinglets =", stats.nsinglets, \
"num_atoms =", stats.num_atoms
if not stats.natoms:
# There are no atoms in the current part.
# writepdb() will create an empty file, which causes
# QuteMolX to crash at launch.
# Mark 2007-06-02
return None
pdb_basename = "QuteMolX.pdb"
# Make full pathnames for the PDB file (in ~/Nanorex/temp/)
tmpdir = find_or_make_Nanorex_subdir('temp')
qutemol_pdb_file = os.path.join(tmpdir, pdb_basename)
# Write the PDB file.
write_qutemol_pdb_file(part, qutemol_pdb_file, excludeFlags)
return qutemol_pdb_file
def write_qutemol_files(part, excludeFlags=EXCLUDE_HIDDEN_ATOMS):
"""
Writes a PDB of the current I{part} to the Nanorex temp directory.
@param part: the NE1 part.
@type part: L{assembly}
@param excludeFlags: used to exclude certain atoms from being written
to the QuteMolX PDB file, where:
WRITE_ALL_ATOMS = 0 (even writes hidden and invisble atoms)
EXCLUDE_BONDPOINTS = 1 (excludes bondpoints)
EXCLUDE_HIDDEN_ATOMS = 2 (excludes both hidden and invisible atoms)
EXCLUDE_DNA_ATOMS = 4 (excludes PAM3 and PAM5 pseudo atoms)
EXCLUDE_DNA_AXIS_ATOMS = 8 (excludes PAM3 axis atoms)
EXCLUDE_DNA_AXIS_BONDS = 16 (supresses PAM3 axis bonds)
@type excludeFlags: int
@return: the name of the temp PDB file, or None if no atoms are in I{part}.
@rtype: str
"""
# Is there a better way to get the number of atoms in <part>.?
# Mark 2007-06-02
stats = Statistics(part.tree)
if 0:
stats.num_atoms = stats.natoms - stats.nsinglets
print "write_qutemol_files(): natoms =", stats.natoms, \
"nsinglets =", stats.nsinglets, \
"num_atoms =", stats.num_atoms
if not stats.natoms:
# There are no atoms in the current part.
# writepdb() will create an empty file, which causes
# QuteMolX to crash at launch.
# Mark 2007-06-02
return None
pdb_basename = "QuteMolX.pdb"
# Make full pathnames for the PDB file (in ~/Nanorex/temp/)
tmpdir = find_or_make_Nanorex_subdir('temp')
qutemol_pdb_file = os.path.join(tmpdir, pdb_basename)
# Write the PDB file.
write_qutemol_pdb_file(part, qutemol_pdb_file, excludeFlags)
return qutemol_pdb_file
