def importAco(project, acoFile):
"""Read Cyana acoFile
( 512 THR PSI 116.0 148.0)
convention = CYANA or CYANA2
return a DihedralRestraintList or None on error
"""
maxErrorCount = 50
errorCount = 0
# check the molecule
if not project or not project.molecule:
nTerror("importAco: initialize molecule first")
return None
# end if
molecule = project.molecule
# Sometimes set from other than CYANA coordinate file.
# chainId = molecule.chains[0].name
if not os.path.exists(acoFile):
nTerror('importAco: file "%s" not found\n', acoFile)
return None
# end if
_dir, name, _ext = nTpath(acoFile)
result = project.dihedrals.new(name=name, status="keep")
resNumDict = molecule.getResNumDict()
nTmessage("Now reading: " + acoFile)
for line in AwkLike(acoFile, commentString="#", minNF=5):
resNum = line.int(1)
res = None
if resNum in resNumDict:
res = resNumDict[resNum]
angle = line.dollar[3]
lower = line.float(4)
upper = line.float(5)
if res and angle in res.db:
atoms = translateTopology(res, res.db[angle].atoms)
# print '>', atoms, res, res.db[angle]
if None in atoms:
if errorCount <= maxErrorCount:
nTerror("Failed to decode all atoms from line:" + line.dollar[0])
if errorCount == (maxErrorCount + 1):
nTerror("And so on")
errorCount += 1
continue
else:
r = DihedralRestraint(atoms=atoms, lower=lower, upper=upper, angle=angle, residue=res)
# print r.format()
result.append(r)
# end if
# end if
# end for
if errorCount:
nTerror("Found number of errors importing upl file: %s" % errorCount)
# nTmessage("Imported items: " + repr(len(result)))
nTmessage('==> importAco: new %s from "%s"', result, acoFile)
return result
def importAco( project, acoFile ):
"""Read Cyana acoFile
( 512 THR PSI 116.0 148.0)
convention = CYANA or CYANA2
return a DihedralRestraintList or None on error
"""
maxErrorCount = 50
errorCount = 0
# check the molecule
if (not project or not project.molecule ):
nTerror("importAco: initialize molecule first")
return None
#end if
molecule = project.molecule
# Sometimes set from other than CYANA coordinate file.
# chainId = molecule.chains[0].name
if not os.path.exists( acoFile ):
nTerror('importAco: file "%s" not found\n', acoFile)
return None
#end if
_dir,name,_ext = nTpath( acoFile )
result = project.dihedrals.new( name=name, status='keep')
resNumDict = molecule.getResNumDict()
nTmessage("Now reading: " + acoFile)
for line in AwkLike( acoFile, commentString = '#' , minNF = 5):
resNum = line.int(1)
res = None
if resNum in resNumDict:
res = resNumDict[resNum]
angle = line.dollar[3]
lower = line.float(4)
upper = line.float(5)
if res and angle in res.db:
atoms = translateTopology( res, res.db[angle].atoms )
# print '>', atoms, res, res.db[angle]
if None in atoms:
if errorCount <= maxErrorCount:
nTerror("Failed to decode all atoms from line:"+ line.dollar[0])
if errorCount == (maxErrorCount+1):
nTerror("And so on")
errorCount += 1
continue
else:
r = DihedralRestraint( atoms = atoms, lower=lower, upper=upper,
angle = angle, residue = res
)
#print r.format()
result.append( r )
#end if
#end if
#end for
if errorCount:
nTerror("Found number of errors importing upl file: %s" % errorCount)
# nTmessage("Imported items: " + repr(len(result)))
nTmessage('==> importAco: new %s from "%s"', result, acoFile )
return result
#===========================================================================
# Adjust to generate different output
resonances = [(0, 'HN'), (0, 'N'), (0, 'CA'), (0, 'CB'), (-1, 'CA'),
(-1, 'CB')]
#===========================================================================
# No need to edit below here (I think)
#===========================================================================
nTmessage('%-8s ', ' ')
for index, name in resonances:
nTmessage('%-8s ', name + 'i' + str(index))
#end for
nTmessage('')
# Generate peaks for all residues
for residue in project.molecule.allResidues(): #@UndefinedVariable
atoms = translateTopology(residue, resonances)
nTmessage('%-8s ', residue.name)
for atm in atoms:
if not atm:
nTmessage('%-8s ', '-X-')
elif atm.isAssigned(resonanceListIdx=RESONANCE_LIST_IDX_ANY):
nTmessage('%-8.3f ', atm.shift())
else:
nTmessage('%-8s ', '-?-')
#end if
#end for
nTmessage('')
#end for
def __iter__( self ):
for peak in self.peaks:
atoms = translateTopology( self.residue, peak ).reorder( self.axisOrder )
yield atoms
#===========================================================================
# Adjust to generate different output
resonances =[ (0,'HN'),(0,'N'),( 0,'CA'),(0,'CB'),( -1,'CA'), (-1,'CB')]
#===========================================================================
# No need to edit below here (I think)
#===========================================================================
nTmessage('%-8s ', ' ')
for index,name in resonances:
nTmessage('%-8s ', name+'i'+str(index) )
#end for
nTmessage('')
# Generate peaks for all residues
for residue in project.molecule.allResidues(): #@UndefinedVariable
atoms = translateTopology( residue, resonances )
nTmessage('%-8s ', residue.name)
for atm in atoms:
if not atm:
nTmessage('%-8s ', '-X-')
elif atm.isAssigned(resonanceListIdx=RESONANCE_LIST_IDX_ANY):
nTmessage('%-8.3f ', atm.shift() )
else:
nTmessage('%-8s ', '-?-' )
#end if
#end for
nTmessage('')
#end for