import sys
from Tailor.Condition import DistanceBoundCondition
from Tailor.Description import StructureDescription, ChainDescription, ResidueDescription, constructSelection
from Tailor.Measure import DistanceMeasure, AngleMeasure
from Tailor.Run import Pipe, Run
# read in the structure
filepath = sys.argv[1]
# create a multichain description
backboneChain = ChainDescription({"chainType" : "Protein", "chainID" : ""})
backboneChain.createResidues(4)
sidechainResidue = ResidueDescription({"position" : 1, "resname" : "ASN" })
sidechainResidue.addAtom("ND2")
sidechainChain = ChainDescription({"chainType" : "Protein"})
sidechainChain.addResidue(sidechainResidue)
description = StructureDescription({}, name="classAStructure")
description.addChain(backboneChain)
description.addChain(sidechainChain)
# create some simple measures and conditions
o1 = constructSelection(chainType="Protein", residuePosition=1, atomName="O")
o3 = constructSelection(chainType="Protein", residuePosition=3, atomName="O")
n = constructSelection(chainType="Protein", residuePosition=1, atomName="ND2")
phi1, psi1 = backboneChain.createPhiPsiMeasure(2)
phi2, psi2 = backboneChain.createPhiPsiMeasure(3)
description.addCondition(DistanceBoundCondition(o1, n, 1.8, 1.8))
description.addCondition(DistanceBoundCondition(o3, n, 1.8, 1.8))
import sys
from Tailor.Condition import DistanceBoundCondition
from Tailor.Description import StructureDescription, ChainDescription, ResidueDescription, constructSelection
from Tailor.Measure import DistanceMeasure, AngleMeasure
from Tailor.Run import Pipe, Run
# read in the structure
filepath = sys.argv[1]
# create a multichain description
proteinChain = ChainDescription({"chainType": "Protein", "chainID": ""})
proteinChain.createResidues(3)
waterResidue = ResidueDescription({"position": 1})
waterResidue.addAtom("O")
waterChain = ChainDescription({"chainType": "Water"})
waterChain.addResidue(waterResidue)
description = StructureDescription({}, name="niche")
description.addChain(proteinChain)
description.addChain(waterChain)
# create some simple measures and conditions
c1 = constructSelection(chainType="Protein", residuePosition=1, atomName="C")
n3 = constructSelection(chainType="Protein", residuePosition=3, atomName="N")
ow = constructSelection(chainType="Water", residuePosition=1, atomName="O")
phi, psi = proteinChain.createPhiPsiMeasure(2)
description.addCondition(DistanceBoundCondition(c1, ow, 1.5, 1.5))
description.addCondition(DistanceBoundCondition(n3, ow, 1.5, 1.5))
# a copy of SimpleExample.java, for comparative testing
import sys
from Tailor.Description import ChainDescription, ResidueDescription, AtomDescription
from Tailor.Condition import PropertyCondition
from Tailor.Measure import DistanceMeasure
from Tailor.Run import Run
motif = ChainDescription({"chainID" : "valmot"})
residueDescription = ResidueDescription({"position" : 1, "resname" : "VAL"})
nAtom = AtomDescription({"name" : "N"})
oAtom = AtomDescription({"name" : "O"})
residueDescription.addSubDescription(nAtom)
residueDescription.addSubDescription(oAtom)
motif.addSubDescription(residueDescription)
atom1 = motif.selectResidue(1).selectAtom("N")
atom2 = motif.selectResidue(1).selectAtom("O")
Run(motif, sys.argv[1], [], [DistanceMeasure(atom1, atom2)]).run()