def parseReference(self, fpdb, dry_out=None ):
flushPrint("parsing "+fpdb+"...")
m = PDBModel( fpdb )
solute_res = m.atom2resMask( N.logical_not( m.maskSolvent() ) )
self.lenres = self.lenres or N.sum( solute_res)
assert isinstance( self.lenres, N.integer )
self.lenatoms = len( m ) - N.sum( m.maskH2O() )
assert isinstance( self.lenatoms, N.integer)
if dry_out:
m.remove( m.maskH2O() )
m.writePdb( dry_out )
flushPrint('done.\n')
def parseReference(self, fpdb, dry_out=None):
flushPrint("parsing " + fpdb + "...")
m = PDBModel(fpdb)
solute_res = m.atom2resMask(N.logical_not(m.maskSolvent()))
self.lenres = self.lenres or N.sum(solute_res)
assert isinstance(self.lenres, N.integer)
self.lenatoms = len(m) - N.sum(m.maskH2O())
assert isinstance(self.lenatoms, N.integer)
if dry_out:
m.remove(m.maskH2O())
m.writePdb(dry_out)
flushPrint('done.\n')
class PymolModel:
def __init__( self, model, modName ):
"""
@param model: model to view
@type model: PDBModel
@param modName: model name, will show up in PyMol
@type modName: str
"""
self.fname = ''
self.temporary = 0
self.struct = None
if type( model ) is str:
self.fname = model
else:
self.struct = model.clone() ## clone atom dicts
self.temporary = 1
self.modName = modName
if self.fname == '':
self.fname = tempfile.mktemp( 'model')
def addProperty( self, values, key='temperature_factor' ):
"""
Add extra value to each atom in Structure. 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{addResProperty}.
@param values: list of numbers, len( values ) == number of atoms
@type values: [float]
@param key: key for Atom.properties dictionary
('occupancy' OR 'temperature_factor')
@type key: occupancy|temperature_factor
"""
if self.struct is None:
self.struct = PDBModel( self.fname )
self.temporary = 1
self.struct[ key ] = values
def addResProperty( self, values, key='temperature_factor'):
"""
Does the same thing as L{addProperty} but on the residue level,
i.e adds extra value to each residue in Structure.
(The same value is added to all atoms of a residue.)
These values can then be used to display properties in PyMol
via commands like 'color_b' and 'color_q'.
@param values: list of numbers, len( values ) == number of residues
@type values: [float]
@param key: key for Atom.properties dictionary
('occupancy' OR 'temperature_factor')
@type key: occupancy|temperature_factor
"""
try:
if self.struct is None:
self.struct = PDBModel( self.fname )
self.temporary = 1
self.struct[ key ] = self.struct.res2atomProfile( values )
except:
print(T.lastError())
def writeIfNeeded( self ):
"""
Create pdb on disc if it's not already there or if it
has to be changed.
@return: filename of new or existing pdb
@rtype: str
"""
if self.temporary:
self.struct.writePdb( self.fname, 2 )
return self.fname
