Biskit :: Pymoler :: Pymoler :: Class Pymoler

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Class Pymoler

Run Pymol

Create a pymol script file (.pml) and execule it using Pymol.

Example usage

>>> pm = Pymoler()
>>> pm.addPdb( model )
>>> pm.run()

References

http://pymol.sourceforge.net/

Notes:

the file is only flushed to disc when the object is destructed, or the flush() method is called!
since version 2.6 Pymoler is using Biskit.Executor

Instance Methods

__init__(self, full=0, mode='w', verbose=1, **kw)

__del__(self)

flush(self)
Flush output file (but keep it open).

add(self, str)
Add String str and line break to file.

str addMovie(self, pdb, modName=None)
Add one or several existing pdb files or Structure objects to one model.

addFrame(self, frame, modName)
Add file(s) or Structure(s) to an EXISTING model as movie.

str _getFreeModName(self, base, index)
Return next free model name in dictionary, made up from base + index

str addPdb(self, pdb, modName=None)
Add one or several existing pdbs.

makeSel(self, selDic)
Make a selection.

writeStructures(self)
Write all needed PDB files to disc.

addDeleteScript(self)
Deletes the pymol script file from disc

addDeletePdbs(self)
Deletes the pdb-files in the list from disc

setAtomValues(self, model, values, key='temperature_factor', lastOnly=0)
Add numeric value to all atoms of all Structures or the last Structure in a model..

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.

colorAtoms(self, model, values, lastOnly=0)
Color atoms of this model by list of values.

colorRes(self, model, values, lastOnly=0)
Color residues of this model by list of values.

[str] addColors(self, nColors, firstColor=[1.0,0.0,0.0], lastColor=[0.0,1.0,0.0])
Define a range of colors that can be called in PyMol by name.

initPymol(self)
Do some stuff always first...

prepare(self, cleanUp=1)
Overrides Executor method.

show(self)
Backward compatability with old scripts.

Method Details

init(self, full=0, mode='w', verbose=1, **kw)
(Constructor)

Parameters:

mode (str) - open file with this mode, w=override, a=append

full (0|1|2) - dispaly pymol structures in fill screen mode:

              0 - normal mode
              1 - full screen mode
              2 - full screen and no menues

del(self)
(Destructor)

flush(self)

Flush output file (but keep it open).

add(self, str)

Add String str and line break to file.

Parameters:

str (str) - string to add to pml file

addMovie(self, pdb, modName=None)

Add one or several existing pdb files or Structure objects to one model. Several files will hence end up as single movie (i.e. as frames of a model in PyMol).

Parameters:

pdb (str or [str] OR PDBModel or [PDBModel]) - file name or a list of file names OR PDBModel or list of PDBModels
modName (str OR None) - model name, will show up in PyMol. If 'None' a model name will be created from the source file name and a serial number.

Returns: str: the modName of the added model

addFrame(self, frame, modName)

Add file(s) or Structure(s) to an EXISTING model as movie.

Parameters:

frame (str(s) or PDBModel(s)) - the structure to add to an existing model
modName (str) - model name, must be existing (i.e. an already added model)

_getFreeModName(self, base, index)

Return next free model name in dictionary, made up from base + index

Parameters:

base (str) - name base
index (int) - name suffix

Returns: str: name composed of base+suffix

addPdb(self, pdb, modName=None)

Add one or several existing pdbs. Make sure all go into different models (have different model names).

Parameters:

pdb (str or [str] OR PDBModel or [PDBModel]) - file name or a list of file names OR PDBModel or list of PDBModels
modName (str OR None) - force model name, will change for list of file names. If 'None' a model name will be created from the source file name.

Returns: str: model name of first file

makeSel(self, selDic)

Make a selection.

Parameters:

selDic (dict) - a selection dictionary, that can be of three types:
dictionary with one or more of the keys: 'model' 'segment', 'chain', 'residue', 'atom'
dictionary with key: 'element'
dictionaty with key: 'expression'

writeStructures(self)

Write all needed PDB files to disc.

addDeleteScript(self)

Deletes the pymol script file from disc

addDeletePdbs(self)

Deletes the pdb-files in the list from disc

setAtomValues(self, model, values, key='temperature_factor', lastOnly=0)

Add numeric value 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 setResValues.

Parameters:

model (str) - model name
values ([float]) - list of numbers, len( values ) == number of atoms
key (occupancy|temperature_factor) - key for Atom.properties dictionary (default: temperature_factor)
lastOnly (1|0) - 0 - add to all in model OR 1 - add only to last Structure (default: 0)

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 setAtomValues.

Parameters:

model (str) - model name
values ([float]) - list of numbers, len( values ) == number of residues
key (occupancy|temperature_factor) - key for Atom.properties dictionary (default: temperature_factor)
lastOnly (1|0) - 0 - add to all in model OR 1 - add only to last Structure (default: 0)

colorAtoms(self, model, values, lastOnly=0)

Color atoms of this model by list of values.

Parameters:

model (str) - model name
values ([float]) - len == number of atoms
lastOnly (1|0) - 0 - add to all in model OR 1 - add only to last Structure (default: 0)

colorRes(self, model, values, lastOnly=0)

Color residues of this model by list of values.

Parameters:

model (str) - model name
values (list of numbers) - len == number of residues
lastOnly () - 0 .. add to all in model 1 .. add only to last Structure

addColors(self, nColors, firstColor=[1.0,0.0,0.0], lastColor=[0.0,1.0,0.0])

Define a range of colors that can be called in PyMol by name.

Parameters:

nColors (int) - numbers of colors generated
firstColor ([float]) - first rgb color (default: [1.0, 0.0, 0.0])
lastColor ([float]) - last rgb color (default: [0.0, 1.0, 0.0])

Returns: [str]: a list of the color names

initPymol(self)

Do some stuff always first...

prepare(self, cleanUp=1)

Overrides Executor method.

show(self)

Backward compatability with old scripts.