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] 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)
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"}))
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 = [] measures.extend(helixTerm.createPhiPsiMeasures([6, 7, 8]))