import sys
from Tailor.Description import ChainDescription
from Tailor.Measure import DistanceMeasure
from Tailor.Run import Run, Pipe
path = sys.argv[1]
catmat3 = ChainDescription({"chainID" : "c3"})
catmat3.createResidues(4)
for i in range(1, 5):
print(catmat3.getResidue(i).children.pop())
catmat3.createPhiBoundCondition(2, -85, 45)
catmat3.createPsiBoundCondition(2, -5, 45)
catmat3.createPhiBoundCondition(3, -70, 40)
catmat3.createPsiBoundCondition(3, 135, 45)
measures3 = []
measures3.extend(catmat3.createPhiPsiMeasures([2, 3]))
catmat4 = ChainDescription({"chainID" : "c4"})
catmat4.createResidues(5)
for i in range(1, 6):
print(catmat4.getResidue(i).children.pop())
catmat4.createPhiBoundCondition(2, -75, 45)
catmat4.createPsiBoundCondition(2, -15, 45)
catmat4.createPhiBoundCondition(3, -95, 45)
import sys
from Tailor.Description import ChainDescription
from Tailor.Measure import DistanceMeasure
from Tailor.Run import Run, Pipe
path = sys.argv[1]
rlNest = ChainDescription({"chainID" : "RL"})
rlNest.createResidues(4)
for i in range(1, 5):
print(rlNest.getResidue(i).children.pop())
rlNest.createPhiBoundCondition(2, -90, 45)
rlNest.createPsiBoundCondition(2, 0, 45)
rlNest.createPhiBoundCondition(3, 80, 45)
rlNest.createPsiBoundCondition(3, 10, 45)
measuresRL = []
measuresRL.extend(rlNest.createPhiPsiMeasures([2, 3]))
lrNest = ChainDescription({"chainID" : "LR"})
lrNest.createResidues(4)
for i in range(1, 5):
print(lrNest.getResidue(i).children.pop())
lrNest.createPhiBoundCondition(2, 80, 45)
lrNest.createPsiBoundCondition(2, 10, 45)
lrNest.createPhiBoundCondition(3, -90, 45)
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))
from Tailor.Description import ChainDescription, AtomDescription
from Tailor.Measure import PropertyMeasure, DistanceMeasure
from Tailor.Run import Run, Pipe
path = sys.argv[1]
maxHO = 2.5
minHOC = 90.0
minNHO = 120.0
helixTerm = ChainDescription({"chainID" : "h"})
helixTerm.createResidues(7)
helixTerm.createBackboneHBondCondition(4, 1, maxHO, minHOC, minNHO)
helixTerm.createBackboneHBondCondition(5, 2, maxHO, minHOC, minNHO)
helixTerm.createPhiBoundCondition(2, -90, 60)
helixTerm.createPsiBoundCondition(2, 0, 60)
helixTerm.createPhiBoundCondition(3, -90, 60)
helixTerm.createPsiBoundCondition(3, 0, 60)
helixTerm.createPhiBoundCondition(4, -90, 60)
helixTerm.createPsiBoundCondition(4, 0, 60)
hbond = helixTerm.createBackboneHBondCondition(6, 3, maxHO, minHOC, minNHO)
hbond.negate()
# for proline searches
#helixTerm.getResidue(6).addPropertyCondition("resname", "PRO")
#helixTerm.getResidue(6).children.pop()
#helixTerm.getResidue(6).children.append(AtomDescription({"name" : "2HD"}))
import sys
from Tailor.Description import ChainDescription
from Tailor.Measure import DistanceMeasure
from Tailor.Run import Run, Pipe
path = sys.argv[1]
rlCatgrip = ChainDescription({"chainID": "RL"})
rlCatgrip.createResidues(4)
for i in range(1, 5):
print rlCatgrip.getResidue(i).children.pop()
rlCatgrip.createPhiBoundCondition(2, -90, 45)
rlCatgrip.createPsiBoundCondition(2, 135, 45)
rlCatgrip.createPhiBoundCondition(3, 90, 45)
rlCatgrip.createPsiBoundCondition(3, -135, 45)
measuresRL = []
measuresRL.extend(rlCatgrip.createPhiPsiMeasures([2, 3]))
lrCatgrip = ChainDescription({"chainID": "LR"})
lrCatgrip.createResidues(4)
for i in range(1, 5):
print lrCatgrip.getResidue(i).children.pop()
lrCatgrip.createPhiBoundCondition(2, 90, 45)
lrCatgrip.createPsiBoundCondition(2, -135, 45)
lrCatgrip.createPhiBoundCondition(3, -90, 45)
path = sys.argv[1]
maxHO = 3.5
minHOC = 90.0
minNHO = 90.0
helixTerm = ChainDescription({"chainID" : "helix_terminus"})
helixTerm.createResidues(9)
helixTerm.createBackboneHBondCondition(6, 2, maxHO, minHOC, minNHO)
helixTerm.createBackboneHBondCondition(7, 3, maxHO, minHOC, minNHO)
antiBond = helixTerm.createBackboneHBondCondition(8, 4, maxHO, minHOC, minNHO)
antiBond.negate()
helixTerm.createPhiBoundCondition(7, 75, 50)
helixTerm.createPsiBoundCondition(7, 30, 50)
#antiPhiBound8 = helixTerm.createPhiBoundCondition(8, -50, 50)
#antiPhiBound8.negate()
#antiPsiBound8 = helixTerm.createPsiBoundCondition(8, -50, 50)
#antiPsiBound8.negate()
#helixTerm.conditions.remove(antiPhiBound8)
#helixTerm.conditions.remove(antiPsiBound8)
#antiPhiPsiBound8 = NoneCombiner([antiPhiBound8, antiPsiBound8])
#helixTerm.addCondition(antiPhiPsiBound8)
measures = []
