Usage : Python

This is a quick overview of how to use the python api.

Describe a Motif

The first step is to describe the motif to search for. The description is in two parts; the structure of the motif, and the conditions. The structure can be as simple as a chain of a few residues or could be multiple chains, each with more than one residue.

from Tailor.Description import ChainDescription

my_motif = ChainDescription({"chainID" : "my_motif"})
my_motif.createResidues(3)

The conditions (also known as constraints) are what really makes the motif description. Each condition is attached to part of the motif structure.

my_motif.createPhiBoundCondition(2, -90, 30)
my_motif.createPsiBoundCondition(2, 90, 30)

Define some Measurements

The point of tailor is to measure parts of structure; to do this a list of measures need to be defined. Each measure produces a measurement, in the same order, to produce a list of results.

from Tailor.Measure import DistanceMeasure

firstN = my_motif.selectResidue(1).selectAtom("N")
thirdO = my_motif.selectResidue(3).selectAtom("O")

distanceNOMeasure = DistanceMeasure(firstN, thirdO)

Run on a Data Source

A data source is a database or flat file directory of crystal structures. For example, a single pdb file is a very simple data source. The same motif can be run on several different sources, or several motifs used on one or more sources.

import sys
from Tailor.Run import Run, Pipe

pipe = Pipe(my_motif, [distanceNOMeasure], sys.stdout)
run = Run("/home/pdb_directory", [], [pipe])
run.run()