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Scripts | - | Use YASARA as a Python module |
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If you are a Linux or MacOSX user, the versatile scripting language Python is already present. If you are running Windows,
it depends on your installation. Try to click Help > Install program > Python. If this option is not available,
Python is already installed. If you are new to Python,
you can find a tutorial here.
THE YASARA PYTHON MODULE IS IN BETA-TESTING PHASE, PLEASE REPORT PROBLEMS EARLIER THAN LATER
There are currently three ways of running YASARA automatically:
To use YASARA from your Python scripts, perform the following installation steps:
from yasara import *
LoadPDB("1crn")
You can also resort to the following alternative, which requires more typing and is therefore not used here
(if you choose this option, you have to prepend 'yasara.' to all variable names and function calls shown throughout the rest of this chapter).
import yasara
yasara.LoadPDB("1crn")
The syntax of YASARA commands is optimized for a minimum number of key-strokes,
which conflicts with Python's own syntax. The YASARA Python module therefore contains Python function wrappers for most YASARA commands.
Example: The YASARA command to choose a new font..
Font Arial,Height=2,Spacing=1.5,Color=Yellow,Depth=5,DepthCol=Red..has the following equivalent in the Python module:
Font("Arial",height=2,spacing=1.5,color="Yellow",depth=5,depthcol="Red")
The documentation page of each YASARA command lists the prototype of the corresponding Python function,
e.g. the Font command (look at the 'Python:' row in the table at the top of each page).
In the Yanaconda macro language
you can choose between a single return value and a list by appending parentheses to the variable name
. This is obviously not possible in Python. Instead those functions that are guaranteed to never return more than one value simply return this value,
while functions possibly returning more than one value always return a list.
Examples:
# This function never returns a result:
Clear()
# This function always returns a single result, the number of the object loaded:
obj = LoadYOb("crambin")
# This function may return many results (if the PDB file contains an NMR bundle with many MODELs)
objlist = LoadPDB("3gb1")
# Or if you know that the PDB file contains only a single MODEL/object (note the slice [0]):
obj = LoadPDB("1crn")[0]
To find out what exactly a function returns, simply check the prototype on the documentation page,
e.g. LoadPDB and LoadYOb
Assuming you used 'from yasara import *', the following variables are defined:
Since Yanaconda is a reinterpreted language
, YASARA commands can accept arguments in a rather flexible way. In Python on the other hand,
the number and order of function arguments must not change. If a YASARA command supports more than one format,
it thus has to be wrapped by different Python functions. The names of these Python functions differ at the end,
using either an increasing number or the name of the first argument. Example for an increasing number: # In Yanaconda: # Format 1: Show an arrow between atoms 123 and 456 ShowArrow Start=AtAtom,123,End=AtAtom,456,Radius=0.5,Color=Red # Format 2: Show an arrow between points 1/2/3 and 4/5/6 ShowArrow Start=Point,X=1,Y=2,Z=3,End=Point,X=4,Y=5,Y=6,Radius=0.5,Color=Red # In Python: ShowArrow(start="AtAtom",selection1=123,end="AtAtom",selection2=456,radius=0.5,color="Red") ShowArrow2(start="Point",x=1,y=2,z=3,end="Point",x2=4,y2=5,z2=6,radius=0.5,color="Red") Note above that argument names in Python are case-sensitive and expected to be all lowercase. They may also not be repeated,
that's why the coordinates of the second point are x2/y2/z2. Example for using the name of the first argument:
# In Yanaconda:
# Format 1: Define a 20x30x40 A cell with angles 80/90/70 degrees:
Cell X=20,Y=30,Z=40,Alpha=80,Beta=90,Gamma=70
# Format 2: Define cell automatically to enclose everything with a 10 A extension:
Cell Auto,Extension=10
# Format 3: Define cell like the crystallographic cell of object 1crn:
Cell Crystal,1crn
# In Python:
Cell(x=20,y=30,z=40,alpha=80,beta=90,gamma=70)
CellAuto(extension=10)
CellCrystal("1crn")
Again, to find out details about the function variants available in Python,
check out the Python prototypes on the documentation page, e.g. ShowArrow
and Cell.
YASARA comes with a Python PDB file interface that can be found at yasara/plg/pdb_file.py. In addition,
you can easily obtain any part of the YASARA soup
as an instance of such a PDB file interface. This means that you can use the same piece of Python code to analyze a PDB file loaded from disk and the YASARA
soup. The following examples list all Calpha atoms in the PDB file
1crn.pdb:
import pdb_file
pdb=pdb_file.interface("1crn.pdb")
for i in range(pdb.atoms):
if (pdb.atom[i].name=="CA"): print pdb.atom[i]
from yasara import *
LoadPDB("1crn")
pdb=Atom("CA")
print pdb
The instance 'pdb' stores the data in the following way:
The following data are currently only available if you use pdb_file.interface to create the instance:
The YASARA Python module provides five commands to extract selected portions of the YASARA
soup as a PDB file instance: Atom, Residue
, Molecule, Object and All. The first four take a selection
as the only argument:
from yasara import *
# Load PDB file 5tim
LoadPDB("5tim")
# Get all atoms in molecule A that contact molecule B
contact=Atom("Mol A with distance<5 from Mol B")
print "There are %d contacts:"%contact.atoms
print contact
# Get all Arg residues that form a salt-bridge with Asp or Glu
bridge=Residue("Arg Atom NH? with distance<3.5 from Asp Glu Atom OD? OE?")
print "There are %d salt-bridged arginines"%bridge.residues
for i in range(bridge.residues):
print bridge.residue[i].name,bridge.residue[i].num
# Get the protein molecules
protein=Molecule("Protein")
print "There are %d protein molecules containing %d atoms"%(protein.molecules,protein.atoms)
# Clear the YASARA soup and load an NMR structure bundle
Clear()
LoadPDB("3gb1")
# Get the first model (each model is stored in a separate object)
first=Object(1)
print "The first model contains %d atoms, %d residues and %d molecules"%(first.atoms,first.residues,first.molecules)
# Get the entire soup
soup=All()
print "The bundle contains %d models"%soup.objects
By default, the Python module runs YASARA in interactive graphical mode. This means that the YASARA window is permanently updated
(at least after each YASARA Python function you call), and that you can even work with YASARA interactively while your Python script is doing something else.
If your Python script needs to call thousands of YASARA functions in a loop,
this approach soon becomes too slow. The solution is the same as used by Yanaconda macros and Python plugins
, switching off the console:
Console("Off")
Your Python script is then responsible for updating the screen by
calling the Wait() function.
In YASARA Dynamics and YASARA Structure, several
experiments are available that perform complex tasks at the touch of a button. In Yanaconda,
experiments expect their parameters in a separate, indented section: # Prepare neutralization experiment Experiment Neutralization # Fill the cell with water at a density of 1.0 g/cm^3 WaterDensity 1.0 # And NaCl counter ions with 0.9% NaCl 0.9 # Protonate ionizable groups according to pH 7.0 pH 7.0 # Save pKa predictions as dat/1crn_mutant.pka pKaFile 1crn_mutant # Finish quickly (final water density will be OK, but not exact) Speed Fast # Start experiment Experiment On # Wait till end of experiment Wait ExpEnd In Python, each experiment is wrapped by its own function instead:
ExperimentNeutralization(waterdensity=1.0,nacl=0.9,ph=7.0,pkafile="1crn_mutant",speed="fast")
Experiment("On")
Wait("ExpEnd")
Normally the Python module runs YASARA in graphics mode,
so that you can follow its work visually on screen. To choose text-only output instead,
set info.mode to 'txt' before you call the first YASARA Python function:
from yasara import *
# Choose text mode before the first function call
info.mode='txt'
# First function call, load a PDB file
LoadPDB("1crn")
# List all arginine residues
ListRes("Arg")
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