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()
["c4_6r", 10, [(1, 10), (10, 1), (3, 8)], [(8, 3)], [4, 5, 6, 7]],
["c4_8r", 10, [(1, 10), (10, 1)], [(3, 8), (8, 3)], [4, 5, 6, 7]],
["c4_10r", 10, [(1, 10)], [(10, 1), (3, 8), (8, 3)], [4, 5, 6, 7]],
]
pipes = []
for name, resnum, hBondNumberList, antiHBondNumberList, phipsiNums in hairpin_data:
# description
hairpin = ChainDescription({"chainID" : name})
hairpin.createResidues(resnum)
hairpin.createBackboneHBondConditions(hBondNumberList, maxHO, minHOC, minNHO)
# antibonds
for i, j in antiHBondNumberList:
bond = hairpin.createBackboneHBondCondition(i, j, maxHO, minHOC, minNHO)
bond.negate()
# measures
measures = []
measures.extend(hairpin.createPhiPsiMeasures(phipsiNums))
# either this line or the other 3 would do...
#measures.extend(hairpin.createBackboneHBondMeasures(hBondNumberList))
# ...but this latter is arguably more efficient, since it means less calculations
for i, j in hBondNumberList:
measures.append(PropertyMeasure(hairpin, "NH(%i)->CO(%i):H_A" % (i, j), float))
measures.append(PropertyMeasure(hairpin, "NH(%i)->CO(%i):DHA" % (i, j), float))
measures.append(PropertyMeasure(hairpin, "NH(%i)->CO(%i):HAA" % (i, j), float))
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 = 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
