import sys
from Tailor.Condition import HBondCondition, NoneCombiner
from Tailor.Description import ChainDescription, AtomDescription
from Tailor.Measure import PropertyMeasure, DistanceMeasure
from Tailor.Run import Run, Pipe
path = sys.argv[1]
maxHO = 3.5
minHOC = 90.0
minNHO = 90.0
helixTerm = ChainDescription({"chainID" : "h"})
helixTerm.createResidues(9)
helixTerm.createBackboneHBondCondition(6, 2, maxHO, minHOC, minNHO)
helixTerm.createBackboneHBondCondition(7, 3, maxHO, minHOC, minNHO)
helixTerm.getResidue(8).addPropertyCondition("resname", "PRO")
helixTerm.getResidue(8).children.pop()
helixTerm.getResidue(8).children.append(AtomDescription({"name" : "2HD"}))
measures = []
measures.extend(helixTerm.createPhiPsiMeasures([6, 7, 8]))
o = helixTerm.selectResidue(5).selectAtom("O")
h = helixTerm.selectResidue(8).selectAtom("2HD")
measures.append(DistanceMeasure(o, h))
pipes = [Pipe(helixTerm, measures, sys.stdout)]
run = Run(pipes, path)
run.run()
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.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)
path = sys.argv[1]
maxHO = 3.5
minHOC = 90.0
minNHO = 90.0
helixTerm = ChainDescription({"chainID" : "h"})
helixTerm.createResidues(12)
helixTerm.createBackboneHBondCondition(6, 2, maxHO, minHOC, minNHO)
helixTerm.createBackboneHBondCondition(7, 3, maxHO, minHOC, minNHO)
helixTerm.createBackboneHBondCondition(8, 4, maxHO, minHOC, minNHO)
helixTerm.createBackboneHBondCondition(9, 5, maxHO, minHOC, minNHO)
helixTerm.createBackboneHBondCondition(10, 6, maxHO, minHOC, minNHO)
helixTerm.getResidue(11).addPropertyCondition("resname", "PRO")
helixTerm.getResidue(11).children.pop()
#antiBond = helixTerm.createBackboneHBondCondition(11, 7, maxHO, minHOC, minNHO)
#antiBond.negate()
#antiPhiBound9 = helixTerm.createPhiBoundCondition(11, -90, 90)
#antiPsiBound9 = helixTerm.createPsiBoundCondition(11, -30, 60)
#helixTerm.conditions.remove(antiPhiBound9)
#helixTerm.conditions.remove(antiPsiBound9)
#antiPhiPsiBound9 = NoneCombiner([antiPhiBound9, antiPsiBound9])
#helixTerm.addCondition(antiPhiPsiBound9)
measures = []
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)
