def idealize_and_relax_pdb_set( PdbCstPairs ):
for PdbName, CstName in PdbCstPairs:
print '(PdbName, CstName) ', (PdbName, CstName)
''' idealize peptide bonds with command line subprocess '''
subprocess.check_output([ 'idealize_jd2.default.linuxgccrelease', '-s', PdbName ])
IdealizedPdbOldName = re.sub( r'(.*).pdb$', r'\1_0001.pdb', PdbName )
IdealizedPdbNewName = re.sub( r'(.*).pdb$', r'\1_Ideal.pdb', PdbName )
subprocess.check_output(['mv', IdealizedPdbOldName, IdealizedPdbNewName])
time.sleep(0.2)
IdealizedCappedPose = rosetta.pose_from_pdb( IdealizedPdbNewName )
# make constraint mover
Constrainer = rosetta.ConstraintSetMover()
# get constraints from file
Constrainer.constraint_file(CstName)
Constrainer.apply(IdealizedCappedPose)
''' SET UP WEIGHTS '''
Talaris = rosetta.getScoreFunction()
TalarisPlusCst = rosetta.getScoreFunction()
TalarisPlusCst.set_weight(rosetta.atom_pair_constraint, 10.0)
TalarisPlusCst.set_weight(rosetta.angle_constraint, 5.0)
TalarisPlusCst.set_weight(rosetta.dihedral_constraint, 2.5)
print 'relaxing %s with %s'%(IdealizedPdbNewName, CstName)
# relax w/ cst
rosetta.relax_pose(IdealizedCappedPose, TalarisPlusCst, 'tag')
# relax w/o cst
rosetta.relax_pose(IdealizedCappedPose, Talaris, 'tag')
RelaxedPdbName = re.sub(r'(.*)_Ideal.pdb$', r'\1_Relax.pdb', IdealizedPdbNewName)
rosetta.dump_pdb(IdealizedCappedPose, RelaxedPdbName)
def optimize_repeat_pdb( (Pdb, CstSets, RepeatLength) ):
''' parallelizable '''
# idealize peptide bonds with command line subprocess
subprocess.check_output(['idealize_jd2.default.linuxgccrelease', '-s', Pdb])
IdealizedPdbOldName = Pdb.replace('.pdb', '_0001.pdb')
IdealizedPdbNewName = Pdb.replace('.pdb', '_ideal.pdb')
subprocess.check_output(['mv', IdealizedPdbOldName, IdealizedPdbNewName])
time.sleep(0.5)
Pose = rosetta.pose_from_pdb(IdealizedPdbNewName)
PoseLength = Pose.n_residue()
assert PoseLength % RepeatLength == 0, 'pdb input into optimize_repeat_pdb must have integer multiple of repeat_length number of residues'
NumberRepeats = PoseLength / RepeatLength
# print 'NumberRepeats', NumberRepeats
# print 'RepeatLength', RepeatLength
Sequence = Pose.sequence()
# print Sequence
RepeatRanges = []
Start = 1
for Repeat in range(NumberRepeats):
End = Start + RepeatLength - 1
RepeatRanges.append((Start, End))
Start += RepeatLength
assert len(RepeatRanges) == NumberRepeats
# print 'RepeatRanges', RepeatRanges
MidRepeat = ( NumberRepeats / 2 ) - 1
ReferenceRange = RepeatRanges[MidRepeat]
# print 'MidRepeat', MidRepeat
# print 'ReferenceRange', ReferenceRange
SetupNCS = symmetry.SetupNCSMover()
for TargetRange in RepeatRanges:
if TargetRange != ReferenceRange:
# print 'OtherRange', TargetRange
# skip first three residue (not enougth atoms for torsion), and amino acid types allowed to vary
if TargetRange[0] == 1:
SetupNCS.add_group( "%dA-%dA"%(ReferenceRange[0]+3, ReferenceRange[1]), "%dA-%dA"%(TargetRange[0]+3, TargetRange[1]) )
# skip last residue (not enougth atoms for torsion)
elif TargetRange[1] == PoseLength:
SetupNCS.add_group( "%dA-%dA"%(ReferenceRange[0], ReferenceRange[1]-3), "%dA-%dA"%(TargetRange[0], TargetRange[1]-3) )
else:
SetupNCS.add_group( "%dA-%dA"%(ReferenceRange[0], ReferenceRange[1]), "%dA-%dA"%(TargetRange[0], TargetRange[1]) )
SetupNCS.apply(Pose)
# default talaris 2013 score function plus dihedral wieght for symmetry ncs mimization
SymmTalaris = rosetta.getScoreFunction()
SymmTalaris.set_weight(rosetta.dihedral_constraint, 1.0)
TalarisPlusCst = rosetta.getScoreFunction()
TalarisPlusCst.set_weight(rosetta.atom_pair_constraint, 10.0)
TalarisPlusCst.set_weight(rosetta.angle_constraint, 5.0)
TalarisPlusCst.set_weight(rosetta.dihedral_constraint, 3.0)
TalarisPlusCstLowerFaRep = rosetta.getScoreFunction()
TalarisPlusCstLowerFaRep.set_weight(rosetta.atom_pair_constraint, 10.0)
TalarisPlusCstLowerFaRep.set_weight(rosetta.angle_constraint, 5.0)
TalarisPlusCstLowerFaRep.set_weight(rosetta.dihedral_constraint, 3.0)
TalarisPlusCstLowerFaRep.set_weight(rosetta.fa_rep, 0.25)
print 'Pdb:', Pdb
OptimizedPoses = []
PoseIDs = []
for Cst in CstSets:
print 'Cst:', Cst
CstPose = Pose.clone()
CstStemName = re.sub(r'^(.*)\.cst$', r'\1', Cst)
# make constraint mover
Constrainer = rosetta.ConstraintSetMover()
# get constraints from file
Constrainer.constraint_file(Cst)
Constrainer.apply(CstPose)
FxnTags = [ 'TalCst', 'LowFaRep' ]
for i, ScoreFunction in enumerate( [ TalarisPlusCst, TalarisPlusCstLowerFaRep ] ):
# for AbsoluteWeight in [1, 5, 10, 100]:
RelaxPose = CstPose.clone()
rosetta.relax_pose(RelaxPose, ScoreFunction, 'tag')
rosetta.dump_pdb( RelaxPose, CstStemName+'_%s.pdb'%FxnTags[i] )
# remove all constraints
RelaxPose.remove_constraints()
# reapply ncs constraints
SetupNCS.apply(RelaxPose)
rosetta.relax_pose(RelaxPose, SymmTalaris, 'tag')
# Trekker.score(RelaxPose)
rosetta.dump_pdb( RelaxPose, CstStemName+'_%s_Relax.pdb'%FxnTags[i] )
JustRelaxPose = Pose.clone()
SetupNCS.apply( JustRelaxPose )
rosetta.relax_pose( JustRelaxPose, SymmTalaris, 'tag' )
rosetta.dump_pdb( JustRelaxPose, CstStemName+'_JustRelax.pdb' )
def main(argv=None):
# if argv is None:
# argv = sys.argv
if argv != None:
sys.argv =[ sys.argv[0] ]+[ arg for arg in argv ]
# print 'sys.argv', sys.argv
# Arg block
ArgParser = argparse.ArgumentParser(description=' expand_cst.py ( -help ) %s'%InfoString)
# Required args
ArgParser.add_argument('-ref_pdb', type=str, help=' reference pdb ', required=True)
ArgParser.add_argument('-ref_cst', type=str, help=' corresponding to reference pdb ', required=True)
ArgParser.add_argument('-repeat_pdb_tag', type=str, help=' input pdb tag ', required=True)
# Optional args
ArgParser.add_argument('-out', type=str, help=' Output directory ', default='./')
Args = ArgParser.parse_args()
if Args.out [-1] != '/':
Args.out = Args.out + '/'
# default talaris 2013 score function
ScoreFunction = rosetta.getScoreFunction()
# turning on constraint weights
ScoreFunction.set_weight(rosetta.atom_pair_constraint, 1.0)
ScoreFunction.set_weight(rosetta.angle_constraint, 1.0)
ScoreFunction.set_weight(rosetta.dihedral_constraint, 1.0)
RefPdb = Args.ref_pdb
# print RefPdb
ReferencePose = rosetta.pose_from_pdb( RefPdb )
print 'ReferencePose', ReferencePose
# modify rosetta cst w/o rosetta
Constrainer = constraint_extrapolator(Args.ref_cst)
# RefCst = Args.ref_cst
# # make constraint mover
# Constrainer = rosetta.ConstraintSetMover()
# # get constraints from file
# Constrainer.constraint_file(RefCst)
# # Apply constraints to pose
# Constrainer.apply(ReferencePose)
# return Constrainer
Pdbs = glob.glob( '*%s*.pdb'%Args.repeat_pdb_tag )
assert len(Pdbs), r"No pdbs found with glob: \n %s \n '* % s *.pdb' % Args.repeat_pdb_tag "%Args.repeat_pdb_tag
for Pdb in Pdbs:
## For debug put pdb of interest here:
# if Pdb == 'src15_38__22_45_rep24_1EZG.pdb':
print 'Pdb:', Pdb
Pose = rosetta.pose_from_pdb(Pdb)
try:
SourceRangeString = re.sub(r'.*src(\d+_\d+__\d+_\d+).*pdb', r'\1', Pdb)
SourceRanges = [ [ int(Number) for Number in Range.split('_') ] for Range in SourceRangeString.split('__') ]
except ValueError:
print 'No src range tag, skipping: %s '%Pdb
continue
print 'SourceRanges:', SourceRanges
RepeatLength = int( re.sub(r'.*rep(\d+).*pdb', r'\1', Pdb) )
print 'RepeatLength', RepeatLength
print
# print [Pdb]
PdbTag = (Pdb+'!').replace('.pdb!', '').replace('!', '')
CstName = PdbTag+'.cst'
ExtrapolatedConstraints = Constrainer.extrapolate_from_repeat_unit(SourceRanges[0][0], SourceRanges[0][1], RepeatLength, Pose, CstName, PdbTag)
def extrapolate_from_repeat_unit(self, ReferenceStart, ReferenceEnd, RepeatUnitLength, NewPose, FinalCstName, PdbTag):
''' renumbers based on repeat unit pose '''
# Loop through positions in range of archetype
# To avoid double counting first only add constraints from archetype residues to
# more C-terminal residues
NewLength = NewPose.n_residue()
self.Range = (1, NewLength)
self.NewPoseStartShift = ReferenceStart - 1 # for 1 indexing
UnitShiftMultiples = (NewLength / RepeatUnitLength)
UnitShiftList = [ RepeatUnitLength * Multiple for Multiple in range( UnitShiftMultiples ) ]
Edge1Cst, Edge2Cst, BothEdgeCst, MiddleCst = self.shift_and_sort_constraints(ReferenceStart, ReferenceEnd, RepeatUnitLength)
# self.output_cst(Edge1Cst, 'Edge1.cst')
# self.output_cst(Edge2Cst, 'Edge2.cst')
# self.output_cst(BothEdgeCst, 'BothEdgeCst.cst')
# self.output_cst(MiddleCst, 'Middle.cst')
# print 'Edge1Cst:', Edge1Cst, '\n'
# print 'Edge2Cst:', Edge2Cst, '\n'
# print 'BothEdgeCst:', BothEdgeCst, '\n'
# print 'MiddleCst:', MiddleCst, '\n'
print 'UnitShiftList:', UnitShiftList
print 'RepeatUnitLength:', RepeatUnitLength
MiddleRepeatCstList = []
MiddleSkippedCst = 0
for Constraint in MiddleCst:
AtomResidueCoords, ConstraintParameters, CstLineNumber, CstType = Constraint
# Loops through all repeat positions corresponding to reference position
for Shift in UnitShiftList:
# print 'Shift:', Shift
# print 'AtomResidueCoords:', AtomResidueCoords
ShiftedAtomResidueCoords = [ (AtomName, ResidueNumber+Shift) for AtomName, ResidueNumber in AtomResidueCoords ]
if pose_has(NewPose, ShiftedAtomResidueCoords):
MiddleRepeatCstList.append( ( ShiftedAtomResidueCoords, ConstraintParameters, CstLineNumber, CstType ) )
else:
MiddleSkippedCst += 1
# print 'Skipping constraint involving:', ShiftedAtomResidueCoords
Edge1RepeatCstList = []
Edge1SkippedCst = 0
for Constraint in Edge1Cst:
AtomResidueCoords, ConstraintParameters, CstLineNumber, CstType = Constraint
for Shift in UnitShiftList[1:]:
ShiftedAtomResidueCoords = [ (AtomName, ResidueNumber+Shift) for AtomName, ResidueNumber in AtomResidueCoords ]
if pose_has(NewPose, ShiftedAtomResidueCoords):
Edge1RepeatCstList.append( ( ShiftedAtomResidueCoords, ConstraintParameters, CstLineNumber, CstType ) )
else:
Edge1SkippedCst += 1
# print 'Skipping constraint involving:', ShiftedAtomResidueCoords
Edge2RepeatCstList = []
Edge2SkippedCst = 0
for Constraint in Edge2Cst:
AtomResidueCoords, ConstraintParameters, CstLineNumber, CstType = Constraint
for Shift in UnitShiftList[:-1]:
ShiftedAtomResidueCoords = [ (AtomName, ResidueNumber+Shift) for AtomName, ResidueNumber in AtomResidueCoords ]
if pose_has(NewPose, ShiftedAtomResidueCoords):
Edge2RepeatCstList.append( ( ShiftedAtomResidueCoords, ConstraintParameters, CstLineNumber, CstType ) )
else:
Edge2SkippedCst += 1
# print 'Skipping constraint involving:', ShiftedAtomResidueCoords
BothEdgeRepeatCstList = []
BothEdgeSkippedCst = 0
for Constraint in BothEdgeCst:
AtomResidueCoords, ConstraintParameters, CstLineNumber, CstType = Constraint
for Shift in UnitShiftList:
ShiftedAtomResidueCoords = [ (AtomName, ResidueNumber+Shift) for AtomName, ResidueNumber in AtomResidueCoords ]
if pose_has(NewPose, ShiftedAtomResidueCoords):
BothEdgeRepeatCstList.append( ( ShiftedAtomResidueCoords, ConstraintParameters, CstLineNumber, CstType ) )
else:
BothEdgeSkippedCst += 1
# print 'Skipping constraint involving:', ShiftedAtomResidueCoords
# RepPose.constraint_set().show_definition(ostream(sys.stdout), RepPose )
self.output_cst(MiddleRepeatCstList, '%s_MidRepTemp.cst'%PdbTag)
self.output_cst(Edge1RepeatCstList, '%s_Edge1RepTemp.cst'%PdbTag)
self.output_cst(Edge2RepeatCstList, '%s_Edge2RepTemp.cst'%PdbTag)
self.output_cst(BothEdgeRepeatCstList, '%s_BothEdgeRepTemp.cst'%PdbTag)
AllRepeatCst = Edge1RepeatCstList[:]
AllRepeatCst.extend(Edge1RepeatCstList)
AllRepeatCst.extend(Edge2RepeatCstList)
AllRepeatCst.extend(BothEdgeRepeatCstList)
self.output_cst(AllRepeatCst, 'AllRepeatCst.cst')
''' trying out constraints to pick between edge 1 and edge 2 (and filter?) '''
# print
# print 'MiddleSkippedCst', MiddleSkippedCst
# print 'Edge1SkippedCst', Edge1SkippedCst
# print 'Edge2SkippedCst', Edge2SkippedCst
# print 'BothEdgeSkippedCst', BothEdgeSkippedCst
# print
# print 'MiddleRepeatCst'
NumberMiddleRepeatCst = len(MiddleRepeatCstList)
# print 'Edge1RepeatCst'
NumberEdge1RepeatCst = len(Edge1RepeatCstList)
# print 'Edge2RepeatCst'
NumberEdge2RepeatCst = len(Edge2RepeatCstList)
# print 'BothEdgeRepeatCst'
NumberBothEdgeRepeatCst = len(BothEdgeRepeatCstList)
NumberAllRepeatCst = len(AllRepeatCst)
# # All default talaris 2013 non zero weights set to zero
CstScoreFunction = set_all_weights_zero( rosetta.getScoreFunction() )
# # turning on constraint weights
CstScoreFunction.set_weight( rosetta.atom_pair_constraint, 1.0 )
CstScoreFunction.set_weight( rosetta.angle_constraint, 1.0 )
CstScoreFunction.set_weight( rosetta.dihedral_constraint, 1.0 )
print 'MiddlePose should have %d constraints !!! '%NumberMiddleRepeatCst
MiddlePose = NewPose.clone()
if NumberEdge1RepeatCst:
ConstraintSetter = rosetta.ConstraintSetMover()
ConstraintSetter.constraint_file('%s_MidRepTemp.cst'%PdbTag)
ConstraintSetter.apply(MiddlePose)
# return ConstraintSetter
# return MiddlePose
CstScoreFunction.show(MiddlePose)
# MiddlePose.constraint_set().show_definition(ostream(sys.stdout), MiddlePose )
print
print 'Edge1Pose should have %d constraints !!! '%NumberEdge1RepeatCst
Edge1Pose = NewPose.clone()
if NumberEdge1RepeatCst:
ConstraintSetter = rosetta.ConstraintSetMover()
ConstraintSetter.constraint_file('%s_Edge1RepTemp.cst'%PdbTag)
ConstraintSetter.apply(Edge1Pose)
CstScoreFunction.show(Edge1Pose)
Edge1Score = CstScoreFunction(Edge1Pose)
Edge1ScoreNorm = Edge1Score / NumberEdge1RepeatCst
# Edge1Pose.constraint_set().show_definition(ostream(sys.stdout), Edge1Pose )
print
print 'Edge2Pose should have %d constraints !!! '%NumberEdge2RepeatCst
Edge2Pose = NewPose.clone()
if NumberEdge2RepeatCst:
ConstraintSetter = rosetta.ConstraintSetMover()
ConstraintSetter.constraint_file('%s_Edge2RepTemp.cst'%PdbTag)
ConstraintSetter.apply(Edge2Pose)
CstScoreFunction.show(Edge2Pose)
Edge2Score = CstScoreFunction(Edge2Pose)
Edge2ScoreNorm = Edge2Score / NumberEdge2RepeatCst
# Edge2Pose.constraint_set().show_definition(ostream(sys.stdout), Edge2Pose )
print
# print 'BothEdgePose should have %d constraints !!! '%NumberBothEdgeRepeatCst
# BothEdgePose = NewPose.clone()
# if NumberBothEdgeRepeatCst:
# ConstraintSetter = rosetta.ConstraintSetMover()
# ConstraintSetter.constraint_file('%s_AllRepeatCstTemp.cst'%PdbTag)
# ConstraintSetter.apply(BothEdgePose)
# CstScoreFunction.show(BothEdgePose)
# BothEdgeScore = CstScoreFunction(BothEdgePose)
# BothEdgeScoreNorm = BothEdgeScore / NumberBothEdgeRepeatCst
# # BothEdgePose.constraint_set().show_definition(ostream(sys.stdout), BothEdgePose )
# print
# print 'AllCstPose should have %d constraints !!! '%NumberAllRepeatCst
# AllCstPose = NewPose.clone()
# ConstraintSetter = rosetta.ConstraintSetMover()
# ConstraintSetter.constraint_file('%s_AllRepeatCstTemp.cst'%PdbTag)
# ConstraintSetter.apply(AllCstPose)
# CstScoreFunction.show(AllCstPose)
# # AllCstPose.constraint_set().show_definition(ostream(sys.stdout), AllCstPose )
# print
CuratedRepeatCst = MiddleRepeatCstList[:]
## whether these should be included or not is up in the air!!
CuratedRepeatCst.extend(BothEdgeRepeatCstList)
if NumberEdge1RepeatCst and NumberEdge2RepeatCst:
if Edge1ScoreNorm <= Edge2ScoreNorm:
CuratedRepeatCst.extend(Edge1RepeatCstList)
else:
CuratedRepeatCst.extend(Edge2RepeatCstList)
elif NumberEdge1RepeatCst:
CuratedRepeatCst.extend(Edge1RepeatCstList)
elif NumberEdge2RepeatCst:
CuratedRepeatCst.extend(Edge2RepeatCstList)
# CuratedRepeatCst
# print 'Edge1ScoreNorm, Edge2ScoreNorm', Edge1ScoreNorm, Edge2ScoreNorm
# self.output_cst(CuratedRepeatCst, FinalCstName)
AllWithEdge1RepeatCst = MiddleRepeatCstList[:]
## whether these should be included or not is up in the air!!
# AllWithEdge1RepeatCst.extend(BothEdgeRepeatCstList)
AllWithEdge1RepeatCst.extend(Edge1RepeatCstList)
AllWithEdge2RepeatCst = MiddleRepeatCstList[:]
## whether these should be included or not is up in the air!!
# AllWithEdge2RepeatCst.extend(BothEdgeRepeatCstList)
AllWithEdge2RepeatCst.extend(Edge2RepeatCstList)
ModFinalCstName = (FinalCstName+'!').replace('.cst!', '')
self.output_cst(AllWithEdge1RepeatCst, ModFinalCstName+'_e1.cst')
self.output_cst(AllWithEdge2RepeatCst, ModFinalCstName+'_e2.cst')
RemainingTempFiles = glob.glob( '%s_*Temp.cst'%PdbTag )
for File in RemainingTempFiles:
subprocess.check_output(['rm', File])
def main(ExtraResidues=0, ipython=0):
### Required args
ArgParser = argparse.ArgumentParser(
description=
" for plotting pdb scores and selecting subsets based on absolute or per residue scores "
)
ArgParser.add_argument('-pdb_glob',
type=str,
help=" pdb stem, start of globs for pdbs and csts ",
required=True)
ArgParser.add_argument('-native',
type=str,
help=" pdb to compare designs against ",
required=True)
### Default args
ArgParser.add_argument(
'-cst',
type=str,
help=" to provide cst manually, will apply to all globed pdbs!!! ",
default=False)
ArgParser.add_argument('-param',
type=str,
nargs='+',
help=" params ",
default=[])
ArgParser.add_argument('-norm',
type=int,
help=" 0|(1) normalize scores by residue ",
default=1)
### following args are for plotly:
### change if you use this script!!!
ArgParser.add_argument('-plotly_id',
type=str,
help=" ",
default="pylesharley") # required=True )
ArgParser.add_argument('-plotly_key',
type=str,
help=" ",
default="cc5z4a8kst") # required=True )
ArgParser.add_argument('-plot',
type=int,
help=" 0|(1) plot scores with plotly ",
default=1)
ArgParser.add_argument('-name', type=str, help=" plot tag ", default='')
ArgParser.add_argument(
'-and_or',
type=str,
help=" And/Or logic for score cutoffs. Default = 'and' ",
default='and')
ArgParser.add_argument(
'-multi',
type=int,
help=" 0|(1) plot different methods together on same plot ",
default=1)
Args = ArgParser.parse_args()
Pdbs = glob.glob(Args.pdb_glob)
print 'globed %d pdbs' % len(Pdbs)
if ExtraResidues == 0 and len(Args.param) > 0:
try:
ExtraParams = rosetta.Vector1(Args.param)
ExtraResidues = rosetta.generate_nonstandard_residue_set(
ExtraParams)
except:
ExtraParams = rosetta.Vector1(Args.param)
ExtraResidues = rosetta.generate_nonstandard_residue_set(
ExtraParams)
### for ipython mode
if ipython:
return ExtraResidues
Args.and_or = Args.and_or.lower()
assert Args.and_or == 'and' or Args.and_or == 'or', " -and_or must equal 'and' or 'or' "
RepeatLengths = []
ProcessTags = {}
TagList = []
TagByPdbName = {}
# better to find out of native pdb is wrong before waiting for pdb scoring
Check = open(Args.native, 'r')
# print ' first loop '
OverlapStarts = []
for Pdb in Pdbs:
Tag = re.sub(r'^.*rep\d+(.*)\.pdb$', r'\1', Pdb)
for OtherPdb in Pdbs:
OtherTag = re.sub(r'^.*rep\d+(.*)\.pdb$', r'\1', Pdb)
i = 0
if Pdb != OtherPdb:
while Pdb[:i] == OtherPdb[:i]:
i += 1
Overlap = OtherPdb[:i - 1]
OverlapStarts.append((len(Overlap), Overlap))
OverlapStarts.sort()
ShortestOverlap = OverlapStarts[0][1]
# print 'OverlapStarts', OverlapStarts
# print 'ShortestOverlap', ShortestOverlap
for Pdb in Pdbs:
try:
RepeatLength = int(re.sub(r'^.*rep(\d+).*pdb$', r'\1', Pdb))
except ValueError:
RepeatLength = 0
# SourceStart = int(re.sub(r'^.*src(\d+).*pdb$', r'\1', Pdb))
assert RepeatLength != Pdb, " regular expression extraction of 'rep' (repeat length) value failed on %s " % Pdb
# assert SourceStart != Pdb and RepeatLength != Pdb, ' regular expression extraction of rep or src value failed on %s '%Pdb
RepeatLengths.append(RepeatLength)
#### re.sub out tag from design process
Tag = re.sub(r'^.*rep\d+(.*)\.pdb$', r'\1', Pdb)
Tag = re.sub(r'^%s(.*)\.pdb$' % (ShortestOverlap), r'\1', Tag)
TagByPdbName[Pdb] = Tag
try:
TagNumber = ProcessTags[Tag]
except:
TagNumber = len(ProcessTags) + 1
ProcessTags[Tag] = TagNumber
TagList.append(TagNumber)
# Scoring is redundant, once for sorting outside plotter, then again in plotter
# making not redundant not a priority.
# Scoring in the plotter object is so multiple score functions can be plotted easily
# Sort by repeat length, then score
if Args.multi:
# Sort by repeat length, then method tag, then score
MultiPoseSortingTuples = []
else:
PoseSortingTuples = []
Talaris = rosetta.getScoreFunction()
for i, Pdb in enumerate(Pdbs):
RepeatLength = RepeatLengths[i]
ProcessNumber = TagList[i]
Pose = rosetta.pose_from_pdb(Pdb)
if Args.norm:
Score = Talaris(Pose) / Pose.n_residue()
else:
Score = Talaris(Pose)
# print 'Pdb', Pdb
if Args.multi:
MultiPoseSortingTuples.append(
(RepeatLength, ProcessNumber, Score, Pose))
else:
PoseSortingTuples.append((RepeatLength, Score, Pose))
if Args.multi:
# Sort by repeat length, then method tag, then score
MultiPoseSortingTuples.sort()
else:
# sorts by repeat length (shortest to longest) then score (best to worst)
PoseSortingTuples.sort()
if Args.multi:
# print 'MultiPoseSortingTuples', MultiPoseSortingTuples
SortedTuples = MultiPoseSortingTuples
else:
# print 'PoseSortingTuples', PoseSortingTuples
SortedTuples = PoseSortingTuples
LastLength = 0
LastTag = 0
AllGroups = []
CurrentGroup = []
for PoseTuple in SortedTuples:
Length = PoseTuple[0]
if Args.multi:
Tag = PoseTuple[1]
if LastLength and Length != LastLength:
AllGroups.append(CurrentGroup)
CurrentGroup = []
if Args.multi:
if LastTag and Tag != LastTag:
AllGroups.append(CurrentGroup)
CurrentGroup = []
CurrentGroup.append(PoseTuple)
LastLength = Length
if Args.multi:
LastTag = Tag
# for last repeat length
AllGroups.append(CurrentGroup)
''' Build score functions here: '''
Talaris = rosetta.getScoreFunction()
# This line returns a talaris function with all default weights set to 0
CstScore = set_all_weights_zero(rosetta.getScoreFunction())
CstScore.set_weight(rosetta.atom_pair_constraint, 10.0)
CstScore.set_weight(rosetta.angle_constraint, 5.0)
CstScore.set_weight(rosetta.dihedral_constraint, 3.0)
HbondScore = set_all_weights_zero(rosetta.getScoreFunction())
HbondScore.set_weight(rosetta.hbond_sr_bb, 1.170)
HbondScore.set_weight(rosetta.hbond_lr_bb, 1.170)
HbondScore.set_weight(rosetta.hbond_bb_sc, 1.170)
HbondScore.set_weight(rosetta.hbond_sc, 1.100)
Disulfide = set_all_weights_zero(rosetta.getScoreFunction())
Disulfide.set_weight(rosetta.dslf_fa13, 1.0)
if Args.plot:
if Args.norm:
PerRes = True
else:
PerRes = False
''' Add and remove score functions here '''
Plotter = plotly_plotter(
Args.plotly_id,
Args.plotly_key,
Args.native,
ScoreFxns=[CstScore, Talaris, HbondScore, Disulfide],
FxnNames=['ConstraintScore', 'Talaris2013', 'H-bond', 'Disulfide'],
PerResidue=PerRes)
XaxisSortingTuples = []
for PoseGroup in AllGroups:
# for PoseGroup in [SortedTuples]:
if len(PoseGroup):
# print
# print 'Group:', PoseGroup
Poses = [PoseTuple[-1] for PoseTuple in PoseGroup]
# print PoseGroup
RepeatLength = PoseGroup[0][0]
# print '\n'.join( [ Pose.pdb_info().name() for Pose in Poses ] )
# print 'Zero index pose tuple:'
# print PoseGroup[0]
if Args.plot:
GroupPdbName = PoseGroup[0][-1].pdb_info().name()
if Args.multi:
Tag = TagByPdbName[GroupPdbName]
if Args.cst:
Plotter.score_poses(Poses, Args.cst, Tag)
else:
Plotter.score_poses(Poses, 1, Tag)
# return Plotter
Plotter.plot_2d_score_combinations()
print 'Plotter.Score2dComboTraces', 3, Plotter.Score2dComboTraces
Plotter.draw_comparisons()
print 'plotting...'
if len(Args.name):
Name = Args.name
else:
Name = '%s based %d res ' % (Args.native, RepeatLength)
Plotter.render_scatter_plot(PlotName=Name)
while 1:
ScoreFunctionScoreCutoffs = []
for i, Name in enumerate(Plotter.FxnNames):
while 1:
try:
Cutoff = float(
raw_input(
'\tEnter cutoff value (maximum) for %s function: '
% Name))
break
except ValueError:
pass
ScoreFunctionScoreCutoffs.append(Cutoff)
print 'Cutoff values set at:'
for i, Name in enumerate(Plotter.FxnNames):
# print Name, ScoreFunctionScoreCutoffs[i]
Plotter.ScoreFunctionScoredPdbs[i].sort()
PassingPdbs = []
for i, Name in enumerate(Plotter.FxnNames):
PassThisFxn = []
Cutoff = ScoreFunctionScoreCutoffs[i]
# print Plotter.ScoreFunctionScoredPdbs[i]
for Score, Pdb in Plotter.ScoreFunctionScoredPdbs[i]:
if Score <= Cutoff:
PassThisFxn.append(Pdb)
else:
break
PassingPdbs.append(PassThisFxn)
PdbsPassingAll = PassingPdbs[0]
if Args.and_or == 'and':
for OtherSet in PassingPdbs[1:]:
PdbsPassingAll = list(set(PdbsPassingAll) & set(OtherSet))
else:
for OtherSet in PassingPdbs[1:]:
PdbsPassingAll = list(set(PdbsPassingAll + OtherSet))
Outdir = raw_input(
'\tEnter folder to copy pdbs that pass these thresholds (%s logic) to: '
% Args.and_or)
if not os.path.isdir(Outdir):
subprocess.check_output(['mkdir', Outdir])
if Outdir[-1] != '/':
Outdir = Outdir + '/'
for Pdb in PdbsPassingAll:
subprocess.check_output(['cp', Pdb, Outdir])
if Plotter.CstDict[Pdb] != None:
subprocess.check_output(['cp', Plotter.CstDict[Pdb], Outdir])
Continue = str(
raw_input(
'\tEnter Y to add another set of selection threshold, or anything else to quit: '
)).upper()
if Continue == 'Y':
pass
else:
break
def main(argv=None):
# if argv is None:
# argv = sys.argv
if argv != None:
sys.argv = [sys.argv[0]] + [arg for arg in argv]
# print 'sys.argv', sys.argv
# Arg block
ArgParser = argparse.ArgumentParser(
description=' expand_cst.py ( -help ) %s' % InfoString)
# Required args
ArgParser.add_argument('-ref_pdb',
type=str,
help=' reference pdb ',
required=True)
ArgParser.add_argument('-ref_cst',
type=str,
help=' corresponding to reference pdb ',
required=True)
ArgParser.add_argument('-repeat_pdb_tag',
type=str,
help=' input pdb tag ',
required=True)
# Optional args
ArgParser.add_argument('-out',
type=str,
help=' Output directory ',
default='./')
Args = ArgParser.parse_args()
if Args.out[-1] != '/':
Args.out = Args.out + '/'
# default talaris 2013 score function
ScoreFunction = rosetta.getScoreFunction()
# turning on constraint weights
ScoreFunction.set_weight(rosetta.atom_pair_constraint, 1.0)
ScoreFunction.set_weight(rosetta.angle_constraint, 1.0)
ScoreFunction.set_weight(rosetta.dihedral_constraint, 1.0)
RefPdb = Args.ref_pdb
# print RefPdb
ReferencePose = rosetta.pose_from_pdb(RefPdb)
print 'ReferencePose', ReferencePose
# modify rosetta cst w/o rosetta
Constrainer = constraint_extrapolator(Args.ref_cst)
# RefCst = Args.ref_cst
# # make constraint mover
# Constrainer = rosetta.ConstraintSetMover()
# # get constraints from file
# Constrainer.constraint_file(RefCst)
# # Apply constraints to pose
# Constrainer.apply(ReferencePose)
# return Constrainer
Pdbs = glob.glob('*%s*.pdb' % Args.repeat_pdb_tag)
assert len(
Pdbs
), r"No pdbs found with glob: \n %s \n '* % s *.pdb' % Args.repeat_pdb_tag " % Args.repeat_pdb_tag
for Pdb in Pdbs:
## For debug put pdb of interest here:
# if Pdb == 'src15_38__22_45_rep24_1EZG.pdb':
print 'Pdb:', Pdb
Pose = rosetta.pose_from_pdb(Pdb)
try:
SourceRangeString = re.sub(r'.*src(\d+_\d+__\d+_\d+).*pdb', r'\1',
Pdb)
SourceRanges = [[int(Number) for Number in Range.split('_')]
for Range in SourceRangeString.split('__')]
except ValueError:
print 'No src range tag, skipping: %s ' % Pdb
continue
print 'SourceRanges:', SourceRanges
RepeatLength = int(re.sub(r'.*rep(\d+).*pdb', r'\1', Pdb))
print 'RepeatLength', RepeatLength
print
# print [Pdb]
PdbTag = (Pdb + '!').replace('.pdb!', '').replace('!', '')
CstName = PdbTag + '.cst'
ExtrapolatedConstraints = Constrainer.extrapolate_from_repeat_unit(
SourceRanges[0][0], SourceRanges[0][1], RepeatLength, Pose,
CstName, PdbTag)
def extrapolate_from_repeat_unit(self, ReferenceStart, ReferenceEnd,
RepeatUnitLength, NewPose, FinalCstName,
PdbTag):
''' renumbers based on repeat unit pose '''
# Loop through positions in range of archetype
# To avoid double counting first only add constraints from archetype residues to
# more C-terminal residues
NewLength = NewPose.n_residue()
self.Range = (1, NewLength)
self.NewPoseStartShift = ReferenceStart - 1 # for 1 indexing
UnitShiftMultiples = (NewLength / RepeatUnitLength)
UnitShiftList = [
RepeatUnitLength * Multiple
for Multiple in range(UnitShiftMultiples)
]
Edge1Cst, Edge2Cst, BothEdgeCst, MiddleCst = self.shift_and_sort_constraints(
ReferenceStart, ReferenceEnd, RepeatUnitLength)
# self.output_cst(Edge1Cst, 'Edge1.cst')
# self.output_cst(Edge2Cst, 'Edge2.cst')
# self.output_cst(BothEdgeCst, 'BothEdgeCst.cst')
# self.output_cst(MiddleCst, 'Middle.cst')
# print 'Edge1Cst:', Edge1Cst, '\n'
# print 'Edge2Cst:', Edge2Cst, '\n'
# print 'BothEdgeCst:', BothEdgeCst, '\n'
# print 'MiddleCst:', MiddleCst, '\n'
print 'UnitShiftList:', UnitShiftList
print 'RepeatUnitLength:', RepeatUnitLength
MiddleRepeatCstList = []
MiddleSkippedCst = 0
for Constraint in MiddleCst:
AtomResidueCoords, ConstraintParameters, CstLineNumber, CstType = Constraint
# Loops through all repeat positions corresponding to reference position
for Shift in UnitShiftList:
# print 'Shift:', Shift
# print 'AtomResidueCoords:', AtomResidueCoords
ShiftedAtomResidueCoords = [
(AtomName, ResidueNumber + Shift)
for AtomName, ResidueNumber in AtomResidueCoords
]
if pose_has(NewPose, ShiftedAtomResidueCoords):
MiddleRepeatCstList.append(
(ShiftedAtomResidueCoords, ConstraintParameters,
CstLineNumber, CstType))
else:
MiddleSkippedCst += 1
# print 'Skipping constraint involving:', ShiftedAtomResidueCoords
Edge1RepeatCstList = []
Edge1SkippedCst = 0
for Constraint in Edge1Cst:
AtomResidueCoords, ConstraintParameters, CstLineNumber, CstType = Constraint
for Shift in UnitShiftList[1:]:
ShiftedAtomResidueCoords = [
(AtomName, ResidueNumber + Shift)
for AtomName, ResidueNumber in AtomResidueCoords
]
if pose_has(NewPose, ShiftedAtomResidueCoords):
Edge1RepeatCstList.append(
(ShiftedAtomResidueCoords, ConstraintParameters,
CstLineNumber, CstType))
else:
Edge1SkippedCst += 1
# print 'Skipping constraint involving:', ShiftedAtomResidueCoords
Edge2RepeatCstList = []
Edge2SkippedCst = 0
for Constraint in Edge2Cst:
AtomResidueCoords, ConstraintParameters, CstLineNumber, CstType = Constraint
for Shift in UnitShiftList[:-1]:
ShiftedAtomResidueCoords = [
(AtomName, ResidueNumber + Shift)
for AtomName, ResidueNumber in AtomResidueCoords
]
if pose_has(NewPose, ShiftedAtomResidueCoords):
Edge2RepeatCstList.append(
(ShiftedAtomResidueCoords, ConstraintParameters,
CstLineNumber, CstType))
else:
Edge2SkippedCst += 1
# print 'Skipping constraint involving:', ShiftedAtomResidueCoords
BothEdgeRepeatCstList = []
BothEdgeSkippedCst = 0
for Constraint in BothEdgeCst:
AtomResidueCoords, ConstraintParameters, CstLineNumber, CstType = Constraint
for Shift in UnitShiftList:
ShiftedAtomResidueCoords = [
(AtomName, ResidueNumber + Shift)
for AtomName, ResidueNumber in AtomResidueCoords
]
if pose_has(NewPose, ShiftedAtomResidueCoords):
BothEdgeRepeatCstList.append(
(ShiftedAtomResidueCoords, ConstraintParameters,
CstLineNumber, CstType))
else:
BothEdgeSkippedCst += 1
# print 'Skipping constraint involving:', ShiftedAtomResidueCoords
# RepPose.constraint_set().show_definition(ostream(sys.stdout), RepPose )
self.output_cst(MiddleRepeatCstList, '%s_MidRepTemp.cst' % PdbTag)
self.output_cst(Edge1RepeatCstList, '%s_Edge1RepTemp.cst' % PdbTag)
self.output_cst(Edge2RepeatCstList, '%s_Edge2RepTemp.cst' % PdbTag)
self.output_cst(BothEdgeRepeatCstList,
'%s_BothEdgeRepTemp.cst' % PdbTag)
AllRepeatCst = Edge1RepeatCstList[:]
AllRepeatCst.extend(Edge1RepeatCstList)
AllRepeatCst.extend(Edge2RepeatCstList)
AllRepeatCst.extend(BothEdgeRepeatCstList)
self.output_cst(AllRepeatCst, 'AllRepeatCst.cst')
''' trying out constraints to pick between edge 1 and edge 2 (and filter?) '''
# print
# print 'MiddleSkippedCst', MiddleSkippedCst
# print 'Edge1SkippedCst', Edge1SkippedCst
# print 'Edge2SkippedCst', Edge2SkippedCst
# print 'BothEdgeSkippedCst', BothEdgeSkippedCst
# print
# print 'MiddleRepeatCst'
NumberMiddleRepeatCst = len(MiddleRepeatCstList)
# print 'Edge1RepeatCst'
NumberEdge1RepeatCst = len(Edge1RepeatCstList)
# print 'Edge2RepeatCst'
NumberEdge2RepeatCst = len(Edge2RepeatCstList)
# print 'BothEdgeRepeatCst'
NumberBothEdgeRepeatCst = len(BothEdgeRepeatCstList)
NumberAllRepeatCst = len(AllRepeatCst)
# # All default talaris 2013 non zero weights set to zero
CstScoreFunction = set_all_weights_zero(rosetta.getScoreFunction())
# # turning on constraint weights
CstScoreFunction.set_weight(rosetta.atom_pair_constraint, 1.0)
CstScoreFunction.set_weight(rosetta.angle_constraint, 1.0)
CstScoreFunction.set_weight(rosetta.dihedral_constraint, 1.0)
print 'MiddlePose should have %d constraints !!! ' % NumberMiddleRepeatCst
MiddlePose = NewPose.clone()
if NumberEdge1RepeatCst:
ConstraintSetter = rosetta.ConstraintSetMover()
ConstraintSetter.constraint_file('%s_MidRepTemp.cst' % PdbTag)
ConstraintSetter.apply(MiddlePose)
# return ConstraintSetter
# return MiddlePose
CstScoreFunction.show(MiddlePose)
# MiddlePose.constraint_set().show_definition(ostream(sys.stdout), MiddlePose )
print
print 'Edge1Pose should have %d constraints !!! ' % NumberEdge1RepeatCst
Edge1Pose = NewPose.clone()
if NumberEdge1RepeatCst:
ConstraintSetter = rosetta.ConstraintSetMover()
ConstraintSetter.constraint_file('%s_Edge1RepTemp.cst' % PdbTag)
ConstraintSetter.apply(Edge1Pose)
CstScoreFunction.show(Edge1Pose)
Edge1Score = CstScoreFunction(Edge1Pose)
Edge1ScoreNorm = Edge1Score / NumberEdge1RepeatCst
# Edge1Pose.constraint_set().show_definition(ostream(sys.stdout), Edge1Pose )
print
print 'Edge2Pose should have %d constraints !!! ' % NumberEdge2RepeatCst
Edge2Pose = NewPose.clone()
if NumberEdge2RepeatCst:
ConstraintSetter = rosetta.ConstraintSetMover()
ConstraintSetter.constraint_file('%s_Edge2RepTemp.cst' % PdbTag)
ConstraintSetter.apply(Edge2Pose)
CstScoreFunction.show(Edge2Pose)
Edge2Score = CstScoreFunction(Edge2Pose)
Edge2ScoreNorm = Edge2Score / NumberEdge2RepeatCst
# Edge2Pose.constraint_set().show_definition(ostream(sys.stdout), Edge2Pose )
print
# print 'BothEdgePose should have %d constraints !!! '%NumberBothEdgeRepeatCst
# BothEdgePose = NewPose.clone()
# if NumberBothEdgeRepeatCst:
# ConstraintSetter = rosetta.ConstraintSetMover()
# ConstraintSetter.constraint_file('%s_AllRepeatCstTemp.cst'%PdbTag)
# ConstraintSetter.apply(BothEdgePose)
# CstScoreFunction.show(BothEdgePose)
# BothEdgeScore = CstScoreFunction(BothEdgePose)
# BothEdgeScoreNorm = BothEdgeScore / NumberBothEdgeRepeatCst
# # BothEdgePose.constraint_set().show_definition(ostream(sys.stdout), BothEdgePose )
# print
# print 'AllCstPose should have %d constraints !!! '%NumberAllRepeatCst
# AllCstPose = NewPose.clone()
# ConstraintSetter = rosetta.ConstraintSetMover()
# ConstraintSetter.constraint_file('%s_AllRepeatCstTemp.cst'%PdbTag)
# ConstraintSetter.apply(AllCstPose)
# CstScoreFunction.show(AllCstPose)
# # AllCstPose.constraint_set().show_definition(ostream(sys.stdout), AllCstPose )
# print
CuratedRepeatCst = MiddleRepeatCstList[:]
## whether these should be included or not is up in the air!!
CuratedRepeatCst.extend(BothEdgeRepeatCstList)
if NumberEdge1RepeatCst and NumberEdge2RepeatCst:
if Edge1ScoreNorm <= Edge2ScoreNorm:
CuratedRepeatCst.extend(Edge1RepeatCstList)
else:
CuratedRepeatCst.extend(Edge2RepeatCstList)
elif NumberEdge1RepeatCst:
CuratedRepeatCst.extend(Edge1RepeatCstList)
elif NumberEdge2RepeatCst:
CuratedRepeatCst.extend(Edge2RepeatCstList)
# CuratedRepeatCst
# print 'Edge1ScoreNorm, Edge2ScoreNorm', Edge1ScoreNorm, Edge2ScoreNorm
# self.output_cst(CuratedRepeatCst, FinalCstName)
AllWithEdge1RepeatCst = MiddleRepeatCstList[:]
## whether these should be included or not is up in the air!!
# AllWithEdge1RepeatCst.extend(BothEdgeRepeatCstList)
AllWithEdge1RepeatCst.extend(Edge1RepeatCstList)
AllWithEdge2RepeatCst = MiddleRepeatCstList[:]
## whether these should be included or not is up in the air!!
# AllWithEdge2RepeatCst.extend(BothEdgeRepeatCstList)
AllWithEdge2RepeatCst.extend(Edge2RepeatCstList)
ModFinalCstName = (FinalCstName + '!').replace('.cst!', '')
self.output_cst(AllWithEdge1RepeatCst, ModFinalCstName + '_e1.cst')
self.output_cst(AllWithEdge2RepeatCst, ModFinalCstName + '_e2.cst')
RemainingTempFiles = glob.glob('%s_*Temp.cst' % PdbTag)
for File in RemainingTempFiles:
subprocess.check_output(['rm', File])
def cap_and_relax_pdb( (RepeatPdb, ReferencePdb, ReferenceCst) ):
RepeatPose = rosetta.pose_from_pdb(RepeatPdb)
TrimmedRepeatPose = grafting.return_region( RepeatPose, 3, RepeatPose.n_residue()-3 )
TrimmedRepeatPose.pdb_info( rosetta.core.pose.PDBInfo( TrimmedRepeatPose ) )
ReferencePose = rosetta.pose_from_pdb( ReferencePdb )
ReferencePose.pdb_info( rosetta.core.pose.PDBInfo( ReferencePose ) )
# rosetta.dump_pdb(TrimmedRepeatPose, 'Trimmed.pdb')
RepeatLength = int(re.sub(r'.*rep(\d+).*pdb', r'\1', RepeatPdb))
SourceRanges = re.sub(r'.*src(\d+_\d+__\d+_\d+).*pdb', r'\1', RepeatPdb)
SourceRanges = SourceRanges.split('__')
SourceRanges = [ [ int(Value) for Value in Range.split('_') ] for Range in SourceRanges ]
SourceStart = SourceRanges[0][0]
SourceEnd = SourceRanges[0][1]
'''
Add N terminal cap
'''
NcapPose = grafting.return_region( ReferencePose, 1, SourceStart+5 )
# rosetta.dump_pdb(NcapPose, 'Ncap.pdb')
NcapLength = NcapPose.n_residue()
NcapOverhangPositions = [ Position for Position in range(NcapLength-3, NcapLength+1) ]
# print NcapOverhangPositions
NcapOverhangArray = get_residue_array( NcapPose, NcapOverhangPositions )
RepStartOverhangPositions = [1,2,3,4]
RepStartOverhangArray = get_residue_array( TrimmedRepeatPose, RepStartOverhangPositions )
# print RepStartOverhangArray
RMSD, rMtx, tVec = solenoid_tools.rmsd_2_np_arrays_rosetta( NcapOverhangArray, RepStartOverhangArray )
rosetta.Pose.apply_transform_Rx_plus_v(TrimmedRepeatPose, rMtx, tVec)
# rosetta.dump_pdb( TrimmedRepeatPose, 'TrimmedShifted.pdb' )
NcapPlusRepeatPose, RMSD, NcapCorrespondingResidues = fuse(NcapPose, TrimmedRepeatPose)
print 'Ncap attachment RMSD %f'%RMSD
# rosetta.dump_pdb( NcapPlusRepeatPose, 'NcapPlusRepeat.pdb' )
NcapPlusRepeatPose.pdb_info( rosetta.core.pose.PDBInfo( NcapPlusRepeatPose ) )
'''
Add C terminal cap
'''
Cshift = SourceEnd-6
CcapPose = grafting.return_region( ReferencePose, Cshift, ReferencePose.n_residue() )
# rosetta.dump_pdb(CcapPose, 'Ccap.pdb')
CcapOverhangPositions = [1,2,3,4]
CcapOverhangArray = get_residue_array( CcapPose, CcapOverhangPositions )
RepEndOverhangPositions = [ Position for Position in range( NcapPlusRepeatPose.n_residue()-3, NcapPlusRepeatPose.n_residue()+1 ) ]
# print 'RepEndOverhangPositions', RepEndOverhangPositions
RepEndOverhangArray = get_residue_array( NcapPlusRepeatPose, RepEndOverhangPositions )
RMSD, rMtx, tVec = solenoid_tools.rmsd_2_np_arrays_rosetta( RepEndOverhangArray, CcapOverhangArray )
rosetta.Pose.apply_transform_Rx_plus_v(CcapPose, rMtx, tVec)
# rosetta.dump_pdb( CcapPose, 'CcapPose.pdb' )
CappedRepeatPose, RMSD, CcapCorrespondingResidues = fuse(NcapPlusRepeatPose, CcapPose)
print 'Ccap attachment RMSD %f'%RMSD
CappedNamePdb = re.sub(r'(.*).pdb$', r'\1_Cap.pdb', RepeatPdb)
assert CappedNamePdb != RepeatPdb, 'regular expression substitution failed!'
rosetta.dump_pdb( CappedRepeatPose, CappedNamePdb )
'''
Generate csts for cap/repeat edges
'''
CstExtrapolator = constraint_extrapolator(ReferenceCst)
ConstraintSet = []
' N cap constraints are easy; no shifts are needed '
# For catching when individual constraints have been considered already
Redundict = {}
for Position in range(1, SourceStart+6):
# print 'Position', Position
# Skip positions w/out constraints
try:
PositionCstDict = CstExtrapolator.Cst[Position]
except KeyError:
continue
for AtomName in PositionCstDict:
for Constraint in PositionCstDict[AtomName]:
# unpack tuple values
AtomResidueCoords, ConstraintParameters, CstLineNumber, CstType = Constraint
# Redundancy check with redundict
try:
Check = Redundict[CstLineNumber]
# if cst considered already, skip it!
continue
except KeyError:
Redundict[CstLineNumber] = 1
if pose_has(CappedRepeatPose, AtomResidueCoords):
ConstraintSet.append(Constraint)
' C cap constraints are harder; need to shift due to pose expansion '
# CstExtrapolator.output_cst(ConstraintSet, 'NcapConstraints.cst')\
Redundict = {}
# print 'CcapCorrespondingResidues', CcapCorrespondingResidues
RepeatCcapPositionStart = CcapCorrespondingResidues[0][0]
# print 'RepeatCcapPositionStart', RepeatCcapPositionStart
ShiftToRepeatPose = RepeatCcapPositionStart - Cshift
# print 'ShiftToRepeatPose', ShiftToRepeatPose
for Position in range( Cshift, ReferencePose.n_residue()+1 ):
# Skip positions w/out constraints
try:
PositionCstDict = CstExtrapolator.Cst[Position]
except KeyError:
continue
for AtomName in PositionCstDict:
for Constraint in PositionCstDict[AtomName]:
# unpack tuple values
AtomResidueCoords, ConstraintParameters, CstLineNumber, CstType = Constraint
# Redundancy check with redundict
try:
Check = Redundict[CstLineNumber]
# if cst considered already, skip it!
continue
except KeyError:
Redundict[CstLineNumber] = 1
ExpandedPoseAtomResidueCoords = []
# iterate through atom residue pairs
for AtomResiduePair in AtomResidueCoords:
# print 'AtomResiduePair', AtomResiduePair
ExpandedPosePosition = (AtomResiduePair[1]) + ShiftToRepeatPose
# print 'ExpandedPosePosition', ExpandedPosePosition
ExpandedPoseAtomResidueCoords.append( ( AtomResiduePair[0], ExpandedPosePosition ) )
ShiftedConstraint = ExpandedPoseAtomResidueCoords, ConstraintParameters, CstLineNumber, CstType
if pose_has(CappedRepeatPose, ExpandedPoseAtomResidueCoords):
ConstraintSet.append(ShiftedConstraint)
CapCstName = re.sub(r'(.*).pdb$', r'\1.cst', CappedNamePdb)
CstExtrapolator.output_cst(ConstraintSet, CapCstName)
'''
idealize peptide bonds with command line subprocess
'''
subprocess.check_output(['idealize_jd2.default.linuxgccrelease', '-s', CappedNamePdb])
IdealizedPdbOldName = re.sub(r'(.*).pdb$', r'\1_0001.pdb', CappedNamePdb)
IdealizedPdbNewName = re.sub(r'(.*).pdb$', r'\1_Ideal.pdb', CappedNamePdb)
subprocess.check_output(['mv', IdealizedPdbOldName, IdealizedPdbNewName])
time.sleep(0.2)
IdealizedCappedPose = rosetta.pose_from_pdb( IdealizedPdbNewName )
# make constraint mover
Constrainer = rosetta.ConstraintSetMover()
# get constraints from file
Constrainer.constraint_file(CapCstName)
Constrainer.apply(IdealizedCappedPose)
''' SET UP WEIGHTS AS decided '''
# RelativeWeight = 0.1
Talaris = rosetta.getScoreFunction()
TalarisPlusCst = rosetta.getScoreFunction()
AtomPairCst = set_all_weights_zero( rosetta.getScoreFunction() )
AtomPairCst.set_weight(rosetta.atom_pair_constraint, 1.0)
# RosettaScore = Talaris(IdealizedCappedPose)
# AtomPairCstScore = AtomPairCst(IdealizedCappedPose)
# Weight = ( RosettaScore * RelativeWeight ) / AtomPairCstScore
Weight = 1.0
TalarisPlusCst.set_weight(rosetta.atom_pair_constraint, Weight)
TalarisPlusCst.set_weight(rosetta.angle_constraint, Weight)
TalarisPlusCst.set_weight(rosetta.dihedral_constraint, Weight)
print 'relaxing %s with %s'%(IdealizedPdbNewName, CapCstName)
print ' Weight %d '%Weight
rosetta.relax_pose(IdealizedCappedPose, TalarisPlusCst, 'tag')
RelaxedPdbName = re.sub(r'(.*)_Ideal.pdb$', r'\1__Relax.pdb', IdealizedPdbNewName)
rosetta.dump_pdb(IdealizedCappedPose, RelaxedPdbName)
rosetta.relax_pose(IdealizedCappedPose, Talaris, 'tag')
RelaxedPdbName = re.sub(r'(.*)_Ideal.pdb$', r'\1__Relax2.pdb', IdealizedPdbNewName)
rosetta.dump_pdb(IdealizedCappedPose, RelaxedPdbName)
def main(argv=None):
if argv is None:
argv = sys.argv
ArgParser = argparse.ArgumentParser(description=" for plotting pdb scores and selecting subsets based on absolute or per residue scores ")
ArgParser.add_argument('-pdb_glob', type=str, help=" pdb stem, start of globs for pdbs and csts ", required=True )
ArgParser.add_argument('-native_pdb', type=str, help=" pdb to compare designs against ", required=True )
ArgParser.add_argument('-out', type=str, help=" folder to move files to ", required=True )
ArgParser.add_argument('-score', type=float, help=" select all structures with less than this REU / residue ", default=None )
ArgParser.add_argument('-plot', type=int, help=" 0|(1) plot scores with plotly ", default=1 )
ArgParser.add_argument('-norm', type=int, help=" 0|(1) normalize scores by residue ", default=1 )
ArgParser.add_argument('-name', type=str, help=" plot tag ", default='' )
Args = ArgParser.parse_args()
print Args
Pdbs = glob.glob( Args.pdb_glob )
print 'globed %d pdbs'%len(Pdbs)
if not os.path.isdir(Args.out):
subprocess.check_output(['mkdir', Args.out])
if Args.out [-1] != '/':
Args.out = Args.out + '/'
if Args.name != '':
Args.out = Args.out + ' '
NativePose = rosetta.pose_from_pdb( Args.native_pdb )
RepeatLengths = []
for Pdb in Pdbs:
RepeatLength = int(re.sub(r'^.*rep(\d+).*pdb$', r'\1', Pdb))
# SourceStart = int(re.sub(r'^.*src(\d+).*pdb$', r'\1', Pdb))
assert RepeatLength != Pdb, " regular expression extraction of 'rep' (repeat length) value failed on %s "%Pdb
# assert SourceStart != Pdb and RepeatLength != Pdb, ' regular expression extraction of rep or src value failed on %s '%Pdb
RepeatLengths.append(RepeatLength)
# RepeatLengths.append(SourceStart)
PoseSortingTuples = []
# Scoring is redundant, once for sorting outside plotter, then again in plotter
# making not redundant not a priority.
# Scoring in the plotter object is so multiple score functions can be plotted easily
Talaris = rosetta.getScoreFunction()
for i, Pdb in enumerate(Pdbs):
RepeatLength = RepeatLengths[i]
Pose = rosetta.pose_from_pdb(Pdb)
if Args.norm:
Score = Talaris(Pose) / Pose.n_residue()
else:
Score = Talaris(Pose)
PoseSortingTuples.append( (RepeatLength, Score, Pose) )
# sorts by repeat length (shortest to longest) then score (best to worst)
PoseSortingTuples.sort()
# print 'PoseSortingTuples', PoseSortingTuples
AllRepeatLengthGroups = []
RepeatRepeatLengthGroup = []
LastLength = 0
for PoseTuple in PoseSortingTuples:
Length = PoseTuple[0]
if LastLength and Length != LastLength:
AllRepeatLengthGroups.append(RepeatRepeatLengthGroup)
RepeatRepeatLengthGroup = []
RepeatRepeatLengthGroup.append(PoseTuple)
LastLength = Length
# for last repeat length
AllRepeatLengthGroups.append(RepeatRepeatLengthGroup)
# print 'AllRepeatLengthGroups', AllRepeatLengthGroups
# Add more score functions as wanted
if Args.plot:
Plotter = plotly_plotter(ScoreFxns=[ Talaris ], FxnNames=[ 'Talaris' ], EnergyPerResidue=True )
for RepeatLengthGroup in AllRepeatLengthGroups:
print 'RepeatLengthGroup', RepeatLengthGroup
Poses = [ PoseTuple[2] for PoseTuple in RepeatLengthGroup ]
RepeatLength = RepeatLengthGroup[0][0]
if Args.plot:
Plotter.clear_traces()
Xaxis = Plotter.score_poses( Poses )
Plotter.add_comparsion_threshold( NativePose, Xaxis )
Plotter.plot_traces( PlotName='%s%s based %d res repeats globed with %s'%(Args.name, Args.native_pdb, RepeatLength, Args.pdb_glob) )
if Args.score != None:
with open('%sScores.log'%Args.out, 'a') as Log:
for RepLen, Score, Pose in RepeatLengthGroup:
if Score > Args.score:
break
PdbName = Pose.pdb_info().name()
subprocess.check_output([ 'cp', PdbName, Args.out ])
print>>Log, '%s\t%.3f'%(PdbName, Score)
def main(ExtraResidues=0, ipython=0):
### Required args
ArgParser = argparse.ArgumentParser(description=" for plotting pdb scores and selecting subsets based on absolute or per residue scores ")
ArgParser.add_argument('-pdb_glob', type=str, help=" pdb stem, start of globs for pdbs and csts ", required=True )
ArgParser.add_argument('-native', type=str, help=" pdb to compare designs against ", required=True )
### Default args
ArgParser.add_argument('-cst', type=str, help=" to provide cst manually, will apply to all globed pdbs!!! ", default=False )
ArgParser.add_argument('-param', type=str, nargs='+', help=" params ", default=[] )
ArgParser.add_argument('-norm', type=int, help=" 0|(1) normalize scores by residue ", default=1 )
### following args are for plotly:
### change if you use this script!!!
ArgParser.add_argument('-plotly_id', type=str, help=" ", default="pylesharley") # required=True )
ArgParser.add_argument('-plotly_key', type=str, help=" ", default="cc5z4a8kst") # required=True )
ArgParser.add_argument('-plot', type=int, help=" 0|(1) plot scores with plotly ", default=1 )
ArgParser.add_argument('-name', type=str, help=" plot tag ", default='' )
ArgParser.add_argument('-and_or', type=str, help=" And/Or logic for score cutoffs. Default = 'and' ", default='and' )
ArgParser.add_argument('-multi', type=int, help=" 0|(1) plot different methods together on same plot ", default=1 )
Args = ArgParser.parse_args()
Pdbs = glob.glob( Args.pdb_glob )
print 'globed %d pdbs'%len(Pdbs)
if ExtraResidues == 0 and len(Args.param) > 0:
try:
ExtraParams = rosetta.Vector1( Args.param )
ExtraResidues = rosetta.generate_nonstandard_residue_set( ExtraParams )
except:
ExtraParams = rosetta.Vector1( Args.param )
ExtraResidues = rosetta.generate_nonstandard_residue_set( ExtraParams )
### for ipython mode
if ipython:
return ExtraResidues
Args.and_or = Args.and_or.lower()
assert Args.and_or == 'and' or Args.and_or == 'or', " -and_or must equal 'and' or 'or' "
RepeatLengths = []
ProcessTags = {}
TagList = []
TagByPdbName = {}
# better to find out of native pdb is wrong before waiting for pdb scoring
Check = open(Args.native, 'r')
# print ' first loop '
OverlapStarts = []
for Pdb in Pdbs:
Tag = re.sub(r'^.*rep\d+(.*)\.pdb$', r'\1', Pdb)
for OtherPdb in Pdbs:
OtherTag = re.sub(r'^.*rep\d+(.*)\.pdb$', r'\1', Pdb)
i = 0
if Pdb != OtherPdb:
while Pdb[:i] == OtherPdb[:i]:
i+=1
Overlap = OtherPdb[:i-1]
OverlapStarts.append( ( len(Overlap), Overlap ) )
OverlapStarts.sort()
ShortestOverlap = OverlapStarts[0][1]
# print 'OverlapStarts', OverlapStarts
# print 'ShortestOverlap', ShortestOverlap
for Pdb in Pdbs:
try:
RepeatLength = int(re.sub(r'^.*rep(\d+).*pdb$', r'\1', Pdb))
except ValueError:
RepeatLength = 0
# SourceStart = int(re.sub(r'^.*src(\d+).*pdb$', r'\1', Pdb))
assert RepeatLength != Pdb, " regular expression extraction of 'rep' (repeat length) value failed on %s "%Pdb
# assert SourceStart != Pdb and RepeatLength != Pdb, ' regular expression extraction of rep or src value failed on %s '%Pdb
RepeatLengths.append(RepeatLength)
#### re.sub out tag from design process
Tag = re.sub(r'^.*rep\d+(.*)\.pdb$', r'\1', Pdb)
Tag = re.sub(r'^%s(.*)\.pdb$'%(ShortestOverlap), r'\1', Tag)
TagByPdbName[Pdb] = Tag
try:
TagNumber = ProcessTags[Tag]
except:
TagNumber = len(ProcessTags) + 1
ProcessTags[Tag] = TagNumber
TagList.append(TagNumber)
# Scoring is redundant, once for sorting outside plotter, then again in plotter
# making not redundant not a priority.
# Scoring in the plotter object is so multiple score functions can be plotted easily
# Sort by repeat length, then score
if Args.multi:
# Sort by repeat length, then method tag, then score
MultiPoseSortingTuples = []
else:
PoseSortingTuples = []
Talaris = rosetta.getScoreFunction()
for i, Pdb in enumerate(Pdbs):
RepeatLength = RepeatLengths[i]
ProcessNumber = TagList[i]
Pose = rosetta.pose_from_pdb(Pdb)
if Args.norm:
Score = Talaris(Pose) / Pose.n_residue()
else:
Score = Talaris(Pose)
# print 'Pdb', Pdb
if Args.multi:
MultiPoseSortingTuples.append( (RepeatLength, ProcessNumber, Score, Pose) )
else:
PoseSortingTuples.append( (RepeatLength, Score, Pose) )
if Args.multi:
# Sort by repeat length, then method tag, then score
MultiPoseSortingTuples.sort()
else:
# sorts by repeat length (shortest to longest) then score (best to worst)
PoseSortingTuples.sort()
if Args.multi:
# print 'MultiPoseSortingTuples', MultiPoseSortingTuples
SortedTuples = MultiPoseSortingTuples
else:
# print 'PoseSortingTuples', PoseSortingTuples
SortedTuples = PoseSortingTuples
LastLength = 0
LastTag = 0
AllGroups = []
CurrentGroup = []
for PoseTuple in SortedTuples:
Length = PoseTuple[0]
if Args.multi:
Tag = PoseTuple[1]
if LastLength and Length != LastLength:
AllGroups.append(CurrentGroup)
CurrentGroup = []
if Args.multi:
if LastTag and Tag != LastTag:
AllGroups.append(CurrentGroup)
CurrentGroup = []
CurrentGroup.append(PoseTuple)
LastLength = Length
if Args.multi:
LastTag = Tag
# for last repeat length
AllGroups.append(CurrentGroup)
''' Build score functions here: '''
Talaris = rosetta.getScoreFunction()
# This line returns a talaris function with all default weights set to 0
CstScore = set_all_weights_zero( rosetta.getScoreFunction() )
CstScore.set_weight(rosetta.atom_pair_constraint, 10.0)
CstScore.set_weight(rosetta.angle_constraint, 5.0)
CstScore.set_weight(rosetta.dihedral_constraint, 3.0)
HbondScore = set_all_weights_zero( rosetta.getScoreFunction() )
HbondScore.set_weight(rosetta.hbond_sr_bb, 1.170)
HbondScore.set_weight(rosetta.hbond_lr_bb, 1.170)
HbondScore.set_weight(rosetta.hbond_bb_sc, 1.170)
HbondScore.set_weight(rosetta.hbond_sc, 1.100)
Disulfide = set_all_weights_zero( rosetta.getScoreFunction() )
Disulfide.set_weight(rosetta.dslf_fa13, 1.0)
if Args.plot:
if Args.norm:
PerRes = True
else:
PerRes = False
''' Add and remove score functions here '''
Plotter = plotly_plotter( Args.plotly_id, Args.plotly_key, Args.native,
ScoreFxns=[ CstScore, Talaris, HbondScore, Disulfide ],
FxnNames=[ 'ConstraintScore', 'Talaris2013', 'H-bond', 'Disulfide' ],
PerResidue=PerRes )
XaxisSortingTuples = []
for PoseGroup in AllGroups:
# for PoseGroup in [SortedTuples]:
if len(PoseGroup):
# print
# print 'Group:', PoseGroup
Poses = [ PoseTuple[-1] for PoseTuple in PoseGroup ]
# print PoseGroup
RepeatLength = PoseGroup[0][0]
# print '\n'.join( [ Pose.pdb_info().name() for Pose in Poses ] )
# print 'Zero index pose tuple:'
# print PoseGroup[0]
if Args.plot:
GroupPdbName = PoseGroup[0][-1].pdb_info().name()
if Args.multi:
Tag = TagByPdbName[GroupPdbName]
if Args.cst:
Plotter.score_poses( Poses, Args.cst, Tag )
else:
Plotter.score_poses( Poses, 1, Tag )
# return Plotter
Plotter.plot_2d_score_combinations()
print 'Plotter.Score2dComboTraces', 3, Plotter.Score2dComboTraces
Plotter.draw_comparisons()
print 'plotting...'
if len(Args.name):
Name = Args.name
else:
Name = '%s based %d res '%( Args.native, RepeatLength )
Plotter.render_scatter_plot( PlotName=Name )
while 1:
ScoreFunctionScoreCutoffs = []
for i, Name in enumerate( Plotter.FxnNames ):
while 1:
try:
Cutoff = float( raw_input('\tEnter cutoff value (maximum) for %s function: '%Name) )
break
except ValueError:
pass
ScoreFunctionScoreCutoffs.append(Cutoff)
print 'Cutoff values set at:'
for i, Name in enumerate( Plotter.FxnNames ):
# print Name, ScoreFunctionScoreCutoffs[i]
Plotter.ScoreFunctionScoredPdbs[i].sort()
PassingPdbs = []
for i, Name in enumerate( Plotter.FxnNames ):
PassThisFxn = []
Cutoff = ScoreFunctionScoreCutoffs[i]
# print Plotter.ScoreFunctionScoredPdbs[i]
for Score, Pdb in Plotter.ScoreFunctionScoredPdbs[i]:
if Score <= Cutoff:
PassThisFxn.append(Pdb)
else:
break
PassingPdbs.append( PassThisFxn )
PdbsPassingAll = PassingPdbs[0]
if Args.and_or == 'and':
for OtherSet in PassingPdbs[1:]:
PdbsPassingAll = list( set(PdbsPassingAll) & set(OtherSet) )
else:
for OtherSet in PassingPdbs[1:]:
PdbsPassingAll = list( set(PdbsPassingAll + OtherSet) )
Outdir = raw_input( '\tEnter folder to copy pdbs that pass these thresholds (%s logic) to: '%Args.and_or )
if not os.path.isdir(Outdir):
subprocess.check_output(['mkdir', Outdir])
if Outdir [-1] != '/':
Outdir = Outdir + '/'
for Pdb in PdbsPassingAll:
subprocess.check_output([ 'cp', Pdb, Outdir ])
if Plotter.CstDict[Pdb] != None:
subprocess.check_output([ 'cp', Plotter.CstDict[Pdb], Outdir ])
Continue = str( raw_input( '\tEnter Y to add another set of selection threshold, or anything else to quit: ') ).upper()
if Continue == 'Y':
pass
else:
break
def optimize_repeat_pdb((Pdb, CstSets, RepeatLength)):
''' parallelizable '''
# idealize peptide bonds with command line subprocess
subprocess.check_output(
['idealize_jd2.default.linuxgccrelease', '-s', Pdb])
IdealizedPdbOldName = Pdb.replace('.pdb', '_0001.pdb')
IdealizedPdbNewName = Pdb.replace('.pdb', '_ideal.pdb')
subprocess.check_output(['mv', IdealizedPdbOldName, IdealizedPdbNewName])
time.sleep(0.5)
Pose = rosetta.pose_from_pdb(IdealizedPdbNewName)
PoseLength = Pose.n_residue()
assert PoseLength % RepeatLength == 0, 'pdb input into optimize_repeat_pdb must have integer multiple of repeat_length number of residues'
NumberRepeats = PoseLength / RepeatLength
# print 'NumberRepeats', NumberRepeats
# print 'RepeatLength', RepeatLength
Sequence = Pose.sequence()
# print Sequence
RepeatRanges = []
Start = 1
for Repeat in range(NumberRepeats):
End = Start + RepeatLength - 1
RepeatRanges.append((Start, End))
Start += RepeatLength
assert len(RepeatRanges) == NumberRepeats
# print 'RepeatRanges', RepeatRanges
MidRepeat = (NumberRepeats / 2) - 1
ReferenceRange = RepeatRanges[MidRepeat]
# print 'MidRepeat', MidRepeat
# print 'ReferenceRange', ReferenceRange
SetupNCS = symmetry.SetupNCSMover()
for TargetRange in RepeatRanges:
if TargetRange != ReferenceRange:
# print 'OtherRange', TargetRange
# skip first three residue (not enougth atoms for torsion), and amino acid types allowed to vary
if TargetRange[0] == 1:
SetupNCS.add_group(
"%dA-%dA" % (ReferenceRange[0] + 3, ReferenceRange[1]),
"%dA-%dA" % (TargetRange[0] + 3, TargetRange[1]))
# skip last residue (not enougth atoms for torsion)
elif TargetRange[1] == PoseLength:
SetupNCS.add_group(
"%dA-%dA" % (ReferenceRange[0], ReferenceRange[1] - 3),
"%dA-%dA" % (TargetRange[0], TargetRange[1] - 3))
else:
SetupNCS.add_group(
"%dA-%dA" % (ReferenceRange[0], ReferenceRange[1]),
"%dA-%dA" % (TargetRange[0], TargetRange[1]))
SetupNCS.apply(Pose)
# default talaris 2013 score function plus dihedral wieght for symmetry ncs mimization
SymmTalaris = rosetta.getScoreFunction()
SymmTalaris.set_weight(rosetta.dihedral_constraint, 1.0)
TalarisPlusCst = rosetta.getScoreFunction()
TalarisPlusCst.set_weight(rosetta.atom_pair_constraint, 10.0)
TalarisPlusCst.set_weight(rosetta.angle_constraint, 5.0)
TalarisPlusCst.set_weight(rosetta.dihedral_constraint, 3.0)
TalarisPlusCstLowerFaRep = rosetta.getScoreFunction()
TalarisPlusCstLowerFaRep.set_weight(rosetta.atom_pair_constraint, 10.0)
TalarisPlusCstLowerFaRep.set_weight(rosetta.angle_constraint, 5.0)
TalarisPlusCstLowerFaRep.set_weight(rosetta.dihedral_constraint, 3.0)
TalarisPlusCstLowerFaRep.set_weight(rosetta.fa_rep, 0.25)
print 'Pdb:', Pdb
OptimizedPoses = []
PoseIDs = []
for Cst in CstSets:
print 'Cst:', Cst
CstPose = Pose.clone()
CstStemName = re.sub(r'^(.*)\.cst$', r'\1', Cst)
# make constraint mover
Constrainer = rosetta.ConstraintSetMover()
# get constraints from file
Constrainer.constraint_file(Cst)
Constrainer.apply(CstPose)
FxnTags = ['TalCst', 'LowFaRep']
for i, ScoreFunction in enumerate(
[TalarisPlusCst, TalarisPlusCstLowerFaRep]):
# for AbsoluteWeight in [1, 5, 10, 100]:
RelaxPose = CstPose.clone()
rosetta.relax_pose(RelaxPose, ScoreFunction, 'tag')
rosetta.dump_pdb(RelaxPose, CstStemName + '_%s.pdb' % FxnTags[i])
# remove all constraints
RelaxPose.remove_constraints()
# reapply ncs constraints
SetupNCS.apply(RelaxPose)
rosetta.relax_pose(RelaxPose, SymmTalaris, 'tag')
# Trekker.score(RelaxPose)
rosetta.dump_pdb(RelaxPose,
CstStemName + '_%s_Relax.pdb' % FxnTags[i])
JustRelaxPose = Pose.clone()
SetupNCS.apply(JustRelaxPose)
rosetta.relax_pose(JustRelaxPose, SymmTalaris, 'tag')
rosetta.dump_pdb(JustRelaxPose, CstStemName + '_JustRelax.pdb')