Biskit :: Pymoler :: PymolModel :: Class PymolModel

Class PymolModel

Instance Methods

__init__(self, model, modName)

addProperty(self, values, key='temperature_factor')
Add extra value to each atom in Structure.

addResProperty(self, values, key='temperature_factor')
Does the same thing as addProperty but on the residue level, i.e adds extra value to each residue in Structure.

str writeIfNeeded(self)
Create pdb on disc if it's not already there or if it has to be changed.

Method Details

[hide private]

init(self, model, modName)
(Constructor)

source code

Parameters:

model (PDBModel) - model to view
modName (str) - model name, will show up in PyMol

addProperty(self, values, key='temperature_factor')

source code

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 addResProperty.

Parameters:

values ([float]) - list of numbers, len( values ) == number of atoms
key (occupancy|temperature_factor) - key for Atom.properties dictionary ('occupancy' OR 'temperature_factor')

addResProperty(self, values, key='temperature_factor')

source code

Does the same thing as 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'.

Parameters:

values ([float]) - list of numbers, len( values ) == number of residues
key (occupancy|temperature_factor) - key for Atom.properties dictionary ('occupancy' OR 'temperature_factor')

writeIfNeeded(self)

source code

Create pdb on disc if it's not already there or if it has to be changed.

Returns: str: filename of new or existing pdb

Class PymolModel

__init__(self, model, modName) (Constructor)

addProperty(self, values, key='temperature_factor')

addResProperty(self, values, key='temperature_factor')

writeIfNeeded(self)

init(self, model, modName)
(Constructor)