def sim_input_filename(self, part):
#write the pdb for the part that is in the NE-1 window now and set the
#filename to that pdb
pdbId, chunk = self.getPDBIDFromChunk(part)
if pdbId is None:
return None
fileName = pdbId + '.pdb'
dir = os.path.dirname(self.tmp_file_prefix)
fileLocation = os.path.join(dir, fileName)
writepdb(part, str(fileLocation))
return fileName
def sim_input_filename(self, args):
"""
write the pdb for the part that is in the NE-1 window now and set the
filename to that pdb
@param part: NE-1 part
@type part: L{Part}
@param args: name of the protein for which simulation should be run
@type args: str
@return: name of the pdb file which is going to be the starting structure
for the current rosetta simulation
"""
# if we run rosetta from within build protein mode, then we can run
# rosetta for the current protein which is args
#if we are outside this mode, we can run rosetta for a selected protein
#chunk, if there's one
if args != "":
pdbId = args
for mol in self.win.assy.molecules:
if mol.name == args:
chunk = mol
break
else:
#run it for the first available protein in chunklist
pdbId, chunk = self.getPDBIDFromChunk()
if pdbId is None:
return None
#input filename
fileName = pdbId + '.pdb'
dir = os.path.dirname(self.tmp_file_prefix)
fileLocation = os.path.join(dir, fileName)
#since the starting structure could be in arbitrary location in users
#hard disk, we write a pdb file for the imported/inserted/fetched protein
#chunk in RosettaDesignFiles directory under Nanorex
writepdb(self.part, str(fileLocation), singleChunk = chunk)
return fileName
def write_qutemol_pdb_file(part, filename, excludeFlags):
"""
Writes an NE1-QuteMolX PDB file of I{part} to I{filename}.
@param part: the NE1 part.
@type part: L{assembly}
@param filename: the PDB filename to write
@type filename: string
@param excludeFlags: used to exclude certain atoms from being written
to the QuteMolX PDB file.
@type excludeFlags: int
@see L{writepdb()} for more information about I{excludeFlags}.
"""
f = open(filename, "w")
skyBlue = env.prefs[ backgroundGradient_prefs_key ]
bgcolor = env.prefs[ backgroundColor_prefs_key ]
r = int (bgcolor[0] * 255 + 0.5)
g = int (bgcolor[1] * 255 + 0.5)
b = int (bgcolor[2] * 255 + 0.5)
TubBond1Radius = TubeRadius
BASBond1Radius = \
diBALL_SigmaBondRadius * \
env.prefs[diBALL_BondCylinderRadius_prefs_key]
writePDB_Header(f) # Writes our generic PDB header
# Write the QuteMolX REMARKS "header".
# See the following wiki page for more information about
# the format of all NE1-QuteMolX REMARK records:
# http://www.nanoengineer-1.net/mediawiki/index.php?title=NE1_PDB_REMARK_Records_Display_Data_Format
#
f.write("""\
REMARK 6 - The ";" character is used to denote non-data (explanatory) records
REMARK 6 in the REMARK 7 and REMARK 8 blocks.
REMARK 6
REMARK 7
REMARK 7 ;Display Data (format version 0.1.0) nanoengineer-1.com/PDB_REMARK_7
REMARK 7\n""")
f.write("REMARK 7 ORIENTATION: %1.6f %1.6f %1.6f %1.6f\n"
% (part.o.quat.w, part.o.quat.x, part.o.quat.y, part.o.quat.z))
f.write("REMARK 7 SCALE: %4.6f\n"
% part.o.scale)
f.write("REMARK 7 POINT_OF_VIEW: %6.6f %6.6f %6.6f\n"
% (part.o.pov[0], part.o.pov[1], part.o.pov[2]))
f.write("REMARK 7 ZOOM=%6.6f\n"
% part.o.zoomFactor)
if skyBlue:
f.write("REMARK 7 BACKGROUND_COLOR: SkyBlue\n")
else:
f.write("REMARK 7 BACKGROUND_COLOR: %3d %3d %3d\n"
% (r, g, b))
f.write("REMARK 7 DISPLAY_STYLE: %s\n"
% properDisplayNames[part.o.displayMode])
f.write("REMARK 7 TUBES_BOND_RADIUS: %1.3f\n"
% TubBond1Radius)
f.write("REMARK 7 BALL_AND_STICK_BOND_RADIUS: %1.3f\n"
% BASBond1Radius)
# Now write the REMARK records for each chunk (chain) in the part.
molNum = 1
for mol in part.molecules:
if mol.hidden:
# Skip hidden chunks. See docstring in writepdb() for details.
# Mark 2008-02-13.
continue
f.write("REMARK 7 CHAIN: %s " % (molNum))
f.write(" DISPLAY_STYLE: %s " % properDisplayNames[mol.display])
if mol.color:
r = int (mol.color[0] * 255 + 0.5)
g = int (mol.color[1] * 255 + 0.5)
b = int (mol.color[2] * 255 + 0.5)
f.write(" COLOR: %3d %3d %3d " % (r, g, b))
f.write(" NAME: \"%s\"\n" % mol.name)
molNum+=1
f.write("REMARK 7\n")
write_art_data(f)
f.close()
# Write the "body" of PDB file (appending it to what we just wrote).
writepdb(part, filename, mode = 'a', excludeFlags = excludeFlags)
def write_qutemol_pdb_file(part, filename, excludeFlags):
"""
Writes an NE1-QuteMolX PDB file of I{part} to I{filename}.
@param part: the NE1 part.
@type part: L{assembly}
@param filename: the PDB filename to write
@type filename: string
@param excludeFlags: used to exclude certain atoms from being written
to the QuteMolX PDB file.
@type excludeFlags: int
@see L{writepdb()} for more information about I{excludeFlags}.
"""
f = open(filename, "w")
skyBlue = env.prefs[backgroundGradient_prefs_key]
bgcolor = env.prefs[backgroundColor_prefs_key]
r = int(bgcolor[0] * 255 + 0.5)
g = int(bgcolor[1] * 255 + 0.5)
b = int(bgcolor[2] * 255 + 0.5)
TubBond1Radius = TubeRadius
BASBond1Radius = \
diBALL_SigmaBondRadius * \
env.prefs[diBALL_BondCylinderRadius_prefs_key]
writePDB_Header(f) # Writes our generic PDB header
# Write the QuteMolX REMARKS "header".
# See the following wiki page for more information about
# the format of all NE1-QuteMolX REMARK records:
# http://www.nanoengineer-1.net/mediawiki/index.php?title=NE1_PDB_REMARK_Records_Display_Data_Format
#
f.write("""\
REMARK 6 - The ";" character is used to denote non-data (explanatory) records
REMARK 6 in the REMARK 7 and REMARK 8 blocks.
REMARK 6
REMARK 7
REMARK 7 ;Display Data (format version 0.1.0) nanoengineer-1.com/PDB_REMARK_7
REMARK 7\n""")
f.write("REMARK 7 ORIENTATION: %1.6f %1.6f %1.6f %1.6f\n" %
(part.o.quat.w, part.o.quat.x, part.o.quat.y, part.o.quat.z))
f.write("REMARK 7 SCALE: %4.6f\n" % part.o.scale)
f.write("REMARK 7 POINT_OF_VIEW: %6.6f %6.6f %6.6f\n" %
(part.o.pov[0], part.o.pov[1], part.o.pov[2]))
f.write("REMARK 7 ZOOM=%6.6f\n" % part.o.zoomFactor)
if skyBlue:
f.write("REMARK 7 BACKGROUND_COLOR: SkyBlue\n")
else:
f.write("REMARK 7 BACKGROUND_COLOR: %3d %3d %3d\n" % (r, g, b))
f.write("REMARK 7 DISPLAY_STYLE: %s\n" %
properDisplayNames[part.o.displayMode])
f.write("REMARK 7 TUBES_BOND_RADIUS: %1.3f\n" % TubBond1Radius)
f.write("REMARK 7 BALL_AND_STICK_BOND_RADIUS: %1.3f\n" % BASBond1Radius)
# Now write the REMARK records for each chunk (chain) in the part.
molNum = 1
for mol in part.molecules:
if mol.hidden:
# Skip hidden chunks. See docstring in writepdb() for details.
# Mark 2008-02-13.
continue
f.write("REMARK 7 CHAIN: %s " % (molNum))
f.write(" DISPLAY_STYLE: %s " % properDisplayNames[mol.display])
if mol.color:
r = int(mol.color[0] * 255 + 0.5)
g = int(mol.color[1] * 255 + 0.5)
b = int(mol.color[2] * 255 + 0.5)
f.write(" COLOR: %3d %3d %3d " % (r, g, b))
f.write(" NAME: \"%s\"\n" % mol.name)
molNum += 1
f.write("REMARK 7\n")
write_art_data(f)
f.close()
# Write the "body" of PDB file (appending it to what we just wrote).
writepdb(part, filename, mode='a', excludeFlags=excludeFlags)