def add(self, str):
"""
Add String str and line break to file.
@param str: string to add to pml file
@type str: str
"""
try:
self.fgenerate.write(str + '\n')
except (IOError):
T.errWriteln(
"PymolInput.add(): Error adding string to pymol script file.")
T.errWriteln( T.lastError() )
def dump( self, o ):
"""
Try to pickle an object to the currently valid path.
:return: the absolute path to which o was pickled
:rtype: str
"""
try:
f = self.local()
T.dump( f, o )
return f
except:
T.errWriteln("Couldn't dump to %s (constructed from %s)" %\
self.formatted(), self.local() )
raise
def dump(self, o):
"""
Try to pickle an object to the currently valid path.
:return: the absolute path to which o was pickled
:rtype: str
"""
try:
f = self.local()
T.dump(f, o)
return f
except:
T.errWriteln("Couldn't dump to %s (constructed from %s)" %\
self.formatted(), self.local() )
raise
def test_delphiCharges2(self):
"""
PDB2DelphiCharges test
"""
if self.local:
T.errWrite('loading PDB...')
self.m1 = self.MODEL or PDBModel(T.testRoot('lig/1A19_dry.model'))
Test.MODEL = self.m1
if self.local:
T.errWriteln('Done.')
if self.local:
T.errWrite('Adding hydrogens to model (reduce)...')
self.rmodel = Reduce(self.m1, verbose=self.local).run()
self.rmodel.xplor2amber()
if self.local:
T.errWriteln('Done.')
ac = AtomCharger()
ac.charge(self.rmodel)
self.rmodel.addChainFromSegid()
self.dc = PDB2DelphiCharges(self.rmodel)
self.dc.prepare()
self.assertEqual(len(self.dc.resmap['LYS']), 2) # normal and N'
self.assertEqual(len(self.dc.resmap['SER']), 2) # normal and C'
if self.local:
T.errWriteln('writing delphi charge file to %s' % self.fcrg)
self.dc.tofile(self.fcrg)
self.assertTrue(os.path.exists(self.fcrg))
def setResValues( self, model, values, key='temperature_factor',
lastOnly=0 ):
"""
Add numeric value per residue to all atoms of all Structures
or the last Structure in a model. The values will be written to
either the B- (temperature_factor) or Q-factor 'occupancy' column
in the temporary pdb-file.
These values can then be used to display properties in PyMol
via commands like 'color_b' and 'color_q'. See also
L{setAtomValues}.
@param model: model name
@type model: str
@param values: list of numbers, len( values ) == number of residues
@type values: [float]
@param key: key for Atom.properties dictionary
(default: temperature_factor)
@type key: occupancy|temperature_factor
@param lastOnly: 0 - add to all in model OR
1 - add only to last Structure (default: 0)
@type lastOnly: 1|0
"""
if lastOnly:
self.dic[ model ][-1].addResProperty( values, key )
else:
for m in self.dic[ model ]:
try:
m.addResProperty( values, key )
except:
T.errWriteln( "Warning: error while adding properties.")
T.errWriteln( "Key: "+str( key )+" values: "+str( values ) )
T.errWriteln( T.lastError() )
def test_delphiCharges2( self ):
"""
PDB2DelphiCharges test
"""
if self.local:
T.errWrite( 'loading PDB...' )
self.m1 = self.MODEL or PDBModel( T.testRoot( 'lig/1A19_dry.model' ) )
Test.MODEL = self.m1
if self.local:
T.errWriteln( 'Done.' )
if self.local:
T.errWrite( 'Adding hydrogens to model (reduce)...' )
self.rmodel = Reduce( self.m1, verbose=self.local ).run()
self.rmodel.xplor2amber()
if self.local:
T.errWriteln( 'Done.' )
ac = AtomCharger()
ac.charge(self.rmodel)
self.rmodel.addChainFromSegid()
self.dc = PDB2DelphiCharges( self.rmodel )
self.dc.prepare()
self.assertEqual( len(self.dc.resmap['LYS']), 2 ) # normal and N'
self.assertEqual( len(self.dc.resmap['SER']), 2 ) # normal and C'
if self.local:
T.errWriteln( 'writing delphi charge file to %s' % self.fcrg )
self.dc.tofile( self.fcrg )
self.assertTrue( os.path.exists( self.fcrg ) )
def getFluct_local( self, mask=None, border_res=1,
left_atoms=['C'], right_atoms=['N'], verbose=1 ):
"""
Get mean displacement of each atom from it's average position after
fitting of each residue to the reference backbone coordinates of itself
and selected atoms of neighboring residues to the right and left.
:param mask: N_atoms x 1 array of 0||1, atoms for which fluctuation
should be calculated
:type mask: array
:param border_res: number of neighboring residues to use for fitting
:type border_res: int
:param left_atoms: atoms (names) to use from these neighbore residues
:type left_atoms: [str]
:param right_atoms: atoms (names) to use from these neighbore residues
:type right_atoms: [str]
:return: Numpy array ( N_unmasked x 1 ) of float
:rtype: array
"""
if mask is None:
mask = N0.ones( len( self.frames[0] ), N0.Int32 )
if verbose: T.errWrite( "rmsd fitting per residue..." )
residues = N0.nonzero( self.ref.atom2resMask( mask ) )
## backbone atoms used for fit
fit_atoms_right = N0.nonzero( self.ref.mask( right_atoms ) )
fit_atoms_left = N0.nonzero( self.ref.mask( left_atoms ) )
## chain index of each residue
rchainMap = N0.take( self.ref.chainMap(), self.ref.resIndex() )
result = []
for res in residues:
i_res, i_border = self.__resWindow(res, border_res, rchainMap,
fit_atoms_left, fit_atoms_right)
try:
if not len( i_res ): raise PDBError('empty residue')
t_res = self.takeAtoms( i_res + i_border )
i_center = range( len( i_res ) )
mask_BB = t_res.ref.maskBB() * t_res.ref.maskHeavy()
## fit with border atoms ..
t_res.fit( ref=t_res.ref, mask=mask_BB, verbose=0 )
## .. but calculate only with center residue atoms
frames = N0.take( t_res.frames, i_center, 1 )
avg = N0.average( frames )
rmsd = N0.average(N0.sqrt(N0.sum(N0.power(frames - avg, 2), 2) ))
result.extend( rmsd )
if verbose: T.errWrite('#')
except ZeroDivisionError:
result.extend( N0.zeros( len(i_res), N0.Float32 ) )
T.errWrite('?' + str( res ))
if verbose: T.errWriteln( "done" )
return result