# require an hbond between the OD1 atom of residue 2 and the N of residue 4
secondOD1 = rlNestDescription.selectResidue(2).selectAtom("OD1")
secondCG = rlNestDescription.selectResidue(2).selectAtom("CG")
fourthN = rlNestDescription.selectResidue(4).selectAtom("N")
fourthH = rlNestDescription.selectResidue(4).selectAtom("H")
rlNestDescription.addCondition(HBondCondition(fourthN, fourthH, secondOD1, secondCG, 2.5, 120, 90))
# these are not 'real' atoms, but descriptions of those atoms we want in the nest
secondN = rlNestDescription.selectResidue(2).selectAtom("N")
thirdN = rlNestDescription.selectResidue(3).selectAtom("N")
fourthN = rlNestDescription.selectResidue(4).selectAtom("N")
# a 'Measure' is like a ruler or a compass - an instrument for making measurements
nnnAngleMeasure = AngleMeasure(secondN, thirdN, fourthN)
nnDistanceMeasure = DistanceMeasure(secondN, fourthN)
# provide a 'header' for the columns
print("pdbid\tmotif\t%s\t%s" % (nnnAngleMeasure, nnDistanceMeasure))
# this works for 1 or many structures
for structure in structures:
# let the user know what file is being processed now
sys.stderr.write("Processing : %s\n" % structure)
# this structure may have a number of nests, check them all
for nest in structure.listFeaturesThatMatch(rlNestDescription):
# use the measure on this object...
nnnAngle = nnnAngleMeasure.measure(nest)
import sys
from Tailor.Description import ChainDescription
from Tailor.DataSource import structureFromFile
from Tailor.Engine import Matcher
from Tailor.Measure import DistanceMeasure
# read in the structure
filepath = sys.argv[1]
structure = structureFromFile(filepath)
# create a simple description
description = ChainDescription({"chainType" : "Protein"})
description.createResidues(3)
description.createPhiBoundCondition(2, -30, 100)
# create a simple measure
o = description.selectResidue(1).selectAtom("O")
n = description.selectResidue(3).selectAtom("N")
distanceMeasure = DistanceMeasure(o, n)
# match and measure
matcher = Matcher(description)
for fragment in matcher.findAll(structure):
print(fragment.chainID, "".join([str(r) for r in fragment]), distanceMeasure.measure(fragment))
