def AngleFinder(Atom1,Atom2,Atom3): vector1 = Atom1.get_vector() vector2 = Atom2.get_vector() vector3 = Atom3.get_vector() angle = bp.calc_angle(vector1,vector2,vector3) return math.degrees(angle)
def w_pdb_1(segment1, segment2):
'''Compute writhe contribution from two input line segments. Segments
are pairs of vectors as returned by Biopython.'''
# t1 = time.time()
s1 = segment1
s2 = segment2
#form unit vectors at the segment extremes:
v13 = s2[0] - s1[0]
v23 = s2[0] - s1[1]
v24 = s2[1] - s1[1]
v14 = s2[1] - s1[0]
v = [v13, v23, v24, v14, v13, v23]
e = []
# l13 = np.sqrt(PDB.Vector.__mul__(v13,v13))
# l23 = np.sqrt(PDB.Vector.__mul__(v23,v23))
# l24 = np.sqrt(PDB.Vector.__mul__(v24,v24))
# l14 = np.sqrt(PDB.Vector.__mul__(v14,v14))
l13 = np.sqrt(v13 * v13)
l23 = np.sqrt(v23 * v23)
l24 = np.sqrt(v24 * v24)
l14 = np.sqrt(v14 * v14)
ls = [l13, l23, l24, l14]
for l in ls:
if l == 0.0:
return 0
e13 = v13 / l13
e23 = v23 / l23
e24 = v24 / l24
e14 = v14 / l14
e = [e13, e23, e24, e14, e13, e23]
## n_vect = np.linalg.norm(vect)
## if n_vect == 0: #if one of the vectors is zero the two segments lie in a plane
## return 0
# else:
# n_vect = np.linalg.norm(vect)
# e.append(vect/n_vect)
# t2 = time.time()
#compute the angles
s = 0
for i in range(1, len(e) - 1):
a = e[i - 1]
b = e[i]
c = e[i + 1]
theta = PDB.calc_angle(a, b, c)
# print "angle is %f" % theta
#APPARENTLY THIS ANGLE IS ALWAYS POSITIVE AND BETWEEN O AND PI; PROBABLY THE ANGLE BETWEEN SEGMENT AB, AC (WITHOUT SIGN)
s = s + theta
# print "s is %f " % s
# t3 = time.time
w = np.sign(s) * 2 * np.pi - s
# t4 = time.time()
# print "t2-t1:", 10*(t2-t1)
# print "t3-t2:", 10*(t3-t2)
# print "t4-t3:",10*(t4-t3)
return w
def get_pose_constraints(Pose,
MaxDist,
MinPositionSeperation,
SasaRadius,
SasaScale,
UpstreamGrep,
DownstreamGrep,
NeedHydrogen=True):
''' '''
# AlexsSasaCalculator is from Alex's interface_fragment_matching
# thanks Alex!
#
# This is used to give buried polar contacts more weight. Thanks Alex Ford!
try:
from interface_fragment_matching.utility.analysis import AtomicSasaCalculator
# make instace of Alex's sasa calculator
AlexsSasaCalculator = AtomicSasaCalculator(probe_radius=SasaRadius)
ResidueAtomSasa = AlexsSasaCalculator.calculate_per_atom_sasa(Pose)
except ImportError:
' Error: SASA weighting of contacts requires interface_fragment_matching from Alex Ford '
# for making full atom kd tree
ResAtmCoordLists = []
# for translating from kd tree index to ( residue, atom ) coord
ResAtmRecordLists = []
# loop through all residue numbers
for Res in range(1, Pose.n_residue() + 1):
# remade for each residue
AtmRecordList = []
AtmCoordList = []
# loop through residue's atom numbers
for Atm in range(1, Pose.residue(Res).natoms() + 1):
# add (residue, atom) coord to residue's list
AtmRecordList.append((Res, Atm))
# add atom xyz coord to residue's list
AtmCoordList.append(
np.array(list(Pose.residue(Res).atom(Atm).xyz())))
# add residue's lists to respective global lists
ResAtmCoordLists.extend(AtmCoordList)
ResAtmRecordLists.extend(AtmRecordList)
ResidueAtomArray = np.array(ResAtmCoordLists)
ResidueAtomKDTree = spatial.KDTree(ResidueAtomArray)
ResidueAtomNeighbors = ResidueAtomKDTree.query_ball_point(
ResidueAtomArray, MaxDist)
# ResidueAtomNearNeighbors = ResidueAtomKDTree.query_ball_point( ResidueAtomArray, 2.0 )
ResidueAtomHydrogens = ResidueAtomKDTree.query_ball_point(
ResidueAtomArray, 1.1)
# holds constraints before printing
AllConstraints = []
# holds sorted cst
AllBackboneBackboneCst = []
AllBackboneSidechainCst = []
AllSidechainSidechainCst = []
# All contacts are from upstream to downstream residues to avoid double counting
Upstream = []
for UpIndex, UpXyzCoords in enumerate(ResAtmCoordLists):
UpRes, UpAtm = ResAtmRecordLists[UpIndex]
# # loop through residues storing info on oxygens
# for UpRes in range( 1, Pose.n_residue() + 1 ):
# # loop through atoms
# for UpAtm in range( 1, Pose.residue(UpRes).natoms() + 1 ):
UpName = Pose.residue(UpRes).atom_name(UpAtm).replace(' ', '')
# skip virtual residues
if Pose.residue(UpRes).is_virtual(UpAtm):
continue
# this guy
# /
# checks upstream name V
if re.match(UpstreamGrep, UpName):
# print '\n'*2
# print 'UpRes, UpName', UpRes, UpName
# get neighbors of upstream residues
NeighborsOfUpstream = ResidueAtomNeighbors[UpIndex]
# prep for loop
Downstreams = []
Constraints = []
BackboneBackboneCst = []
BackboneSidechainCst = []
SidechainSidechainCst = []
# ArbitrayOrderOfAtomNames = {}
for DownIndex in NeighborsOfUpstream:
# name presumes downstream, checks with if imediately below
DownRes, DownAtm = ResAtmRecordLists[DownIndex]
# checks that downstream residue is dowstream of upstream and passes min primary sequence spacing
if DownRes - UpRes >= MinPositionSeperation:
DownName = Pose.residue(DownRes).atom_name(
DownAtm).replace(' ', '')
# skip if same atom
if UpRes == DownRes:
if UpName == DownName:
continue
# skip virtual residues
if Pose.residue(DownRes).is_virtual(DownAtm):
continue
# checks downstream name
if re.match(DownstreamGrep, DownName):
# print 'DownRes, DownName', DownRes, DownName
PotentialUpstreamHydrogens = ResidueAtomHydrogens[
UpIndex]
UpstreamHydrogens = []
# print 'PotentialUpstreamHydrogens', PotentialUpstreamHydrogens
for UpH_I in PotentialUpstreamHydrogens:
UpH_Res, UpH_Atm = ResAtmRecordLists[UpH_I]
UpH_Name = Pose.residue(UpH_Res).atom_name(
UpH_Atm).replace(' ', '')
# print 'UpH_Name', UpH_Name
if 'H' in UpH_Name:
UpstreamHydrogens.append(
(UpH_Res, UpH_Atm, UpH_Name))
# print 'UpstreamHydrogens', UpstreamHydrogens
PotentialDownstreamHydrogens = ResidueAtomHydrogens[
DownIndex]
DownstreamHydrogens = []
# print 'PotentialDownstreamHydrogens', PotentialDownstreamHydrogens
for DownH_I in PotentialDownstreamHydrogens:
DownH_Res, DownH_Atm = ResAtmRecordLists[DownH_I]
DownH_Name = Pose.residue(DownH_Res).atom_name(
DownH_Atm).replace(' ', '')
# print 'DownH_Name', DownH_Name
if 'H' in DownH_Name:
DownstreamHydrogens.append(
(DownH_Res, DownH_Atm, DownH_Name))
# print 'DownstreamHydrogens', DownstreamHydrogens
# check their is at least one hydrogen in system before adding constraint
if len(UpstreamHydrogens) or len(
DownstreamHydrogens) or NeedHydrogen == False:
# these trys / excepts seperate
# backbone-backbone from
# backbone-sidechain from
# sidechain-sidechain interactions
#
# in future maybe sort into seperate lists, shouldn't rely on ResidueAtomSasa to know what is in backbone
try:
UpstreamSasa = ResidueAtomSasa[UpRes][UpName]
DownstreamSasa = ResidueAtomSasa[DownRes][
DownName]
AverageSasa = np.mean(
[UpstreamSasa, DownstreamSasa])
BBBB = 1
BBSC = SCSC = 0
except KeyError:
# These lines handle backbone to sidechain interactions
# set weight equal to the most buried
try:
UpstreamSasa = ResidueAtomSasa[UpRes][
UpName]
AverageSasa = SasaScale.FloorSasa
BBSC = 1
BBBB = SCSC = 0
except KeyError:
try:
DownstreamSasa = ResidueAtomSasa[
DownRes][DownName]
AverageSasa = SasaScale.FloorSasa
BBSC = 1
BBBB = SCSC = 0
# set weight of side chain side chain equal to the most buried
except KeyError:
AverageSasa = SasaScale.CeilingSasa
SCSC = 1
BBSC = BBBB = 0
# use instance of sasa_scale to calculate weight based on avg sasa of N and O
SasaBasedWeight = SasaScale.weigh(AverageSasa)
# print
# print 'AverageSasa', AverageSasa
# print 'SasaBasedWeight', SasaBasedWeight
# print 'found downstream neighbor %s'%DownName
DownXyzCoords = np.array(
list(
Pose.residue(DownRes).atom(DownAtm).xyz()))
# print 'DownRes, DownName', DownRes, DownName
# print 'DownXyzCoords', DownXyzCoords
# ## Get neighbors for angles and torsions to use with AtomPairs
SelectUpNeighbors = []
# iterates through upstream atom neighbors for references for angle
for UpNeighborIndex in NeighborsOfUpstream:
UpNeighborRes, UpNeighborAtm = ResAtmRecordLists[
UpNeighborIndex]
UpNeighborName = Pose.residue(
UpNeighborRes).atom_name(
UpNeighborAtm).replace(' ', '')
# keep looking if neighbor is hyrdogen
if 'H' in UpNeighborName:
continue
# skip virtual residues
if Pose.residue(UpNeighborRes).is_virtual(
UpNeighborAtm):
continue
# keep looking if neighbor is self
if UpNeighborName == UpName and UpNeighborRes == UpRes:
continue
# keep looking if neighbor is downstream residue again
if UpNeighborName == DownName and UpNeighborRes == DownRes:
continue
UpNeighborCoords = ResAtmCoordLists[
UpNeighborIndex]
DistanceToNeighbor = solenoid_tools.vector_magnitude(
UpXyzCoords - UpNeighborCoords)
SelectUpNeighbors.append(
(DistanceToNeighbor, UpNeighborName,
UpNeighborRes, UpNeighborCoords))
# sort by distance to atom, nearest first
SelectUpNeighbors.sort()
UpNeighbor1Tuple = SelectUpNeighbors[0]
UpNeighbor2Tuple = SelectUpNeighbors[1]
# print '\n'*2
# print 'UpRes, UpName', UpRes, UpName
# print 'UpstreamHydrogens', UpstreamHydrogens
# print 'SelectUpNeighbors', SelectUpNeighbors
# get neighbors of upstream residues
NeighborsOfDownstream = ResidueAtomNeighbors[
DownIndex]
SelectDownNeighbors = []
# iterates through upstream atom neighbors for references for angle
for DownNeighborIndex in NeighborsOfDownstream:
DownNeighborRes, DownNeighborAtm = ResAtmRecordLists[
DownNeighborIndex]
DownNeighborName = Pose.residue(
DownNeighborRes).atom_name(
DownNeighborAtm).replace(' ', '')
# keep looking if neighbor is hyrdogen
if 'H' in DownNeighborName:
continue
# skip virtual residues
if Pose.residue(DownNeighborRes).is_virtual(
DownNeighborAtm):
continue
# keep looking if neighbor is self
if DownNeighborName == DownName and DownNeighborRes == DownRes:
continue
# keep looking if neighbor is upstream residue
if DownNeighborName == UpName and DownNeighborRes == UpRes:
continue
DownNeighborCoords = ResAtmCoordLists[
DownNeighborIndex]
DistanceToNeighbor = solenoid_tools.vector_magnitude(
DownXyzCoords - DownNeighborCoords)
SelectDownNeighbors.append(
(DistanceToNeighbor, DownNeighborName,
DownNeighborRes, DownNeighborCoords))
# sort by distance to atom, nearest first
SelectDownNeighbors.sort()
DownNeighbor1Tuple = SelectDownNeighbors[0]
DownNeighbor2Tuple = SelectDownNeighbors[1]
# print 'DownRes, DownName', DownRes, DownName
# print 'DownstreamHydrogens', DownstreamHydrogens
# print 'SelectDownNeighbors', SelectDownNeighbors
Distance = solenoid_tools.vector_magnitude(
DownXyzCoords - UpXyzCoords)
DistanceCst = 'AtomPair %s %d %s %d SCALARWEIGHTEDFUNC %f HARMONIC %.2f 1.0' % (
UpName, UpRes, DownName, DownRes,
SasaBasedWeight, Distance)
# Use Biopython for angle and dihedral calculations
# here 'Vec' means PDB.Vector of atom's xyz coord
UpstreamVec = PDB.Vector(UpXyzCoords)
DownstreamVec = PDB.Vector(DownXyzCoords)
UpNeighbor1Vec = PDB.Vector(UpNeighbor1Tuple[3])
UpNeighbor2Vec = PDB.Vector(UpNeighbor2Tuple[3])
DownNeighbor1Vec = PDB.Vector(
DownNeighbor1Tuple[3])
DownNeighbor2Vec = PDB.Vector(
DownNeighbor2Tuple[3])
Angle1 = PDB.calc_angle(UpNeighbor1Vec,
UpstreamVec, DownstreamVec)
AngleCst1 = 'Angle %s %d %s %d %s %d SCALARWEIGHTEDFUNC %f CIRCULARHARMONIC %.2f 0.5' % (
UpNeighbor1Tuple[1], UpNeighbor1Tuple[2],
UpName, UpRes, DownName, DownRes,
SasaBasedWeight, Angle1)
Angle2 = PDB.calc_angle(UpstreamVec, DownstreamVec,
DownNeighbor1Vec)
AngleCst2 = 'Angle %s %d %s %d %s %d SCALARWEIGHTEDFUNC %f CIRCULARHARMONIC %.2f 0.5' % (
UpName, UpRes, DownName, DownRes,
DownNeighbor1Tuple[1], DownNeighbor1Tuple[2],
SasaBasedWeight, Angle2)
Torsion1 = PDB.calc_dihedral(
UpNeighbor2Vec, UpNeighbor1Vec, UpstreamVec,
DownstreamVec)
TorsionCst1 = 'Dihedral %s %d %s %d %s %d %s %d SCALARWEIGHTEDFUNC %f CIRCULARHARMONIC %.2f 0.5' % (
UpNeighbor2Tuple[1], UpNeighbor2Tuple[2],
UpNeighbor1Tuple[1], UpNeighbor1Tuple[2],
UpName, UpRes, DownName, DownRes,
SasaBasedWeight, Torsion1)
Torsion2 = PDB.calc_dihedral(
UpNeighbor1Vec, UpstreamVec, DownstreamVec,
DownNeighbor1Vec)
TorsionCst2 = 'Dihedral %s %d %s %d %s %d %s %d SCALARWEIGHTEDFUNC %f CIRCULARHARMONIC %.2f 0.5' % (
UpNeighbor1Tuple[1], UpNeighbor1Tuple[2],
UpName, UpRes, DownName, DownRes,
DownNeighbor1Tuple[1], DownNeighbor1Tuple[2],
SasaBasedWeight, Torsion2)
Torsion3 = PDB.calc_dihedral(
UpstreamVec, DownstreamVec, DownNeighbor1Vec,
DownNeighbor2Vec)
TorsionCst3 = 'Dihedral %s %d %s %d %s %d %s %d SCALARWEIGHTEDFUNC %f CIRCULARHARMONIC %.2f 0.5' % (
UpName, UpRes, DownName, DownRes,
DownNeighbor1Tuple[1], DownNeighbor1Tuple[2],
DownNeighbor2Tuple[1], DownNeighbor2Tuple[2],
SasaBasedWeight, Torsion3)
# adds constraint to running lists of constraints
Constraints.extend([
DistanceCst, AngleCst1, AngleCst2, TorsionCst1,
TorsionCst2, TorsionCst3
])
if BBBB:
BackboneBackboneCst.extend([
DistanceCst, AngleCst1, AngleCst2,
TorsionCst1, TorsionCst2, TorsionCst3
])
if BBSC:
BackboneSidechainCst.extend([
DistanceCst, AngleCst1, AngleCst2,
TorsionCst1, TorsionCst2, TorsionCst3
])
if SCSC:
SidechainSidechainCst.extend([
DistanceCst, AngleCst1, AngleCst2,
TorsionCst1, TorsionCst2, TorsionCst3
])
# else:
# print 'No hydrogen!'
# sys.exit()
AllConstraints.extend(Constraints)
AllBackboneBackboneCst.extend(BackboneBackboneCst)
AllBackboneSidechainCst.extend(BackboneSidechainCst)
AllSidechainSidechainCst.extend(SidechainSidechainCst)
SortedConstraints = (AllBackboneBackboneCst, AllBackboneSidechainCst,
AllSidechainSidechainCst)
return AllConstraints, SortedConstraints
def get_pose_constraints(Pose, MaxDist, MinPositionSeperation, SasaRadius, SasaScale, UpstreamGrep, DownstreamGrep, NeedHydrogen=True):
''' '''
# AlexsSasaCalculator is from Alex's interface_fragment_matching
# thanks Alex!
#
# This is used to give buried polar contacts more weight. Thanks Alex Ford!
try:
from interface_fragment_matching.utility.analysis import AtomicSasaCalculator
# make instace of Alex's sasa calculator
AlexsSasaCalculator = AtomicSasaCalculator(probe_radius=SasaRadius)
ResidueAtomSasa = AlexsSasaCalculator.calculate_per_atom_sasa(Pose)
except ImportError:
' Error: SASA weighting of contacts requires interface_fragment_matching from Alex Ford '
# for making full atom kd tree
ResAtmCoordLists = []
# for translating from kd tree index to ( residue, atom ) coord
ResAtmRecordLists = []
# loop through all residue numbers
for Res in range(1, Pose.n_residue() + 1):
# remade for each residue
AtmRecordList = []
AtmCoordList = []
# loop through residue's atom numbers
for Atm in range(1, Pose.residue(Res).natoms() + 1):
# add (residue, atom) coord to residue's list
AtmRecordList.append((Res, Atm))
# add atom xyz coord to residue's list
AtmCoordList.append( np.array(list(Pose.residue(Res).atom(Atm).xyz())) )
# add residue's lists to respective global lists
ResAtmCoordLists.extend(AtmCoordList)
ResAtmRecordLists.extend(AtmRecordList)
ResidueAtomArray = np.array( ResAtmCoordLists )
ResidueAtomKDTree = spatial.KDTree( ResidueAtomArray )
ResidueAtomNeighbors = ResidueAtomKDTree.query_ball_point( ResidueAtomArray, MaxDist )
# ResidueAtomNearNeighbors = ResidueAtomKDTree.query_ball_point( ResidueAtomArray, 2.0 )
ResidueAtomHydrogens = ResidueAtomKDTree.query_ball_point( ResidueAtomArray, 1.1 )
# holds constraints before printing
AllConstraints = []
# holds sorted cst
AllBackboneBackboneCst = []
AllBackboneSidechainCst = []
AllSidechainSidechainCst = []
# All contacts are from upstream to downstream residues to avoid double counting
Upstream = []
for UpIndex, UpXyzCoords in enumerate(ResAtmCoordLists):
UpRes, UpAtm = ResAtmRecordLists[UpIndex]
# # loop through residues storing info on oxygens
# for UpRes in range( 1, Pose.n_residue() + 1 ):
# # loop through atoms
# for UpAtm in range( 1, Pose.residue(UpRes).natoms() + 1 ):
UpName = Pose.residue(UpRes).atom_name(UpAtm).replace(' ', '')
# skip virtual residues
if Pose.residue(UpRes).is_virtual(UpAtm):
continue
# this guy
# /
# checks upstream name V
if re.match(UpstreamGrep, UpName ):
# print '\n'*2
# print 'UpRes, UpName', UpRes, UpName
# get neighbors of upstream residues
NeighborsOfUpstream = ResidueAtomNeighbors[UpIndex]
# prep for loop
Downstreams = []
Constraints = []
BackboneBackboneCst = []
BackboneSidechainCst = []
SidechainSidechainCst = []
# ArbitrayOrderOfAtomNames = {}
for DownIndex in NeighborsOfUpstream:
# name presumes downstream, checks with if imediately below
DownRes, DownAtm = ResAtmRecordLists[DownIndex]
# checks that downstream residue is dowstream of upstream and passes min primary sequence spacing
if DownRes - UpRes >= MinPositionSeperation:
DownName = Pose.residue(DownRes).atom_name(DownAtm).replace(' ', '')
# skip if same atom
if UpRes == DownRes:
if UpName == DownName:
continue
# skip virtual residues
if Pose.residue(DownRes).is_virtual(DownAtm):
continue
# checks downstream name
if re.match( DownstreamGrep, DownName ):
# print 'DownRes, DownName', DownRes, DownName
PotentialUpstreamHydrogens = ResidueAtomHydrogens[UpIndex]
UpstreamHydrogens = []
# print 'PotentialUpstreamHydrogens', PotentialUpstreamHydrogens
for UpH_I in PotentialUpstreamHydrogens:
UpH_Res, UpH_Atm = ResAtmRecordLists[UpH_I]
UpH_Name = Pose.residue(UpH_Res).atom_name(UpH_Atm).replace(' ', '')
# print 'UpH_Name', UpH_Name
if 'H' in UpH_Name:
UpstreamHydrogens.append((UpH_Res, UpH_Atm, UpH_Name))
# print 'UpstreamHydrogens', UpstreamHydrogens
PotentialDownstreamHydrogens = ResidueAtomHydrogens[DownIndex]
DownstreamHydrogens = []
# print 'PotentialDownstreamHydrogens', PotentialDownstreamHydrogens
for DownH_I in PotentialDownstreamHydrogens:
DownH_Res, DownH_Atm = ResAtmRecordLists[DownH_I]
DownH_Name = Pose.residue(DownH_Res).atom_name(DownH_Atm).replace(' ', '')
# print 'DownH_Name', DownH_Name
if 'H' in DownH_Name:
DownstreamHydrogens.append((DownH_Res, DownH_Atm, DownH_Name))
# print 'DownstreamHydrogens', DownstreamHydrogens
# check their is at least one hydrogen in system before adding constraint
if len(UpstreamHydrogens) or len(DownstreamHydrogens) or NeedHydrogen == False:
# these trys / excepts seperate
# backbone-backbone from
# backbone-sidechain from
# sidechain-sidechain interactions
#
# in future maybe sort into seperate lists, shouldn't rely on ResidueAtomSasa to know what is in backbone
try:
UpstreamSasa = ResidueAtomSasa[UpRes][UpName]
DownstreamSasa = ResidueAtomSasa[DownRes][DownName]
AverageSasa = np.mean([UpstreamSasa, DownstreamSasa])
BBBB = 1
BBSC = SCSC = 0
except KeyError:
# These lines handle backbone to sidechain interactions
# set weight equal to the most buried
try:
UpstreamSasa = ResidueAtomSasa[UpRes][UpName]
AverageSasa = SasaScale.FloorSasa
BBSC = 1
BBBB = SCSC = 0
except KeyError:
try:
DownstreamSasa = ResidueAtomSasa[DownRes][DownName]
AverageSasa = SasaScale.FloorSasa
BBSC = 1
BBBB = SCSC = 0
# set weight of side chain side chain equal to the most buried
except KeyError:
AverageSasa = SasaScale.CeilingSasa
SCSC = 1
BBSC = BBBB = 0
# use instance of sasa_scale to calculate weight based on avg sasa of N and O
SasaBasedWeight = SasaScale.weigh(AverageSasa)
# print
# print 'AverageSasa', AverageSasa
# print 'SasaBasedWeight', SasaBasedWeight
# print 'found downstream neighbor %s'%DownName
DownXyzCoords = np.array( list(Pose.residue(DownRes).atom(DownAtm).xyz()) )
# print 'DownRes, DownName', DownRes, DownName
# print 'DownXyzCoords', DownXyzCoords
# ## Get neighbors for angles and torsions to use with AtomPairs
SelectUpNeighbors = []
# iterates through upstream atom neighbors for references for angle
for UpNeighborIndex in NeighborsOfUpstream:
UpNeighborRes, UpNeighborAtm = ResAtmRecordLists[UpNeighborIndex]
UpNeighborName = Pose.residue(UpNeighborRes).atom_name(UpNeighborAtm).replace(' ', '')
# keep looking if neighbor is hyrdogen
if 'H' in UpNeighborName:
continue
# skip virtual residues
if Pose.residue(UpNeighborRes).is_virtual(UpNeighborAtm):
continue
# keep looking if neighbor is self
if UpNeighborName == UpName and UpNeighborRes == UpRes:
continue
# keep looking if neighbor is downstream residue again
if UpNeighborName == DownName and UpNeighborRes == DownRes:
continue
UpNeighborCoords = ResAtmCoordLists[UpNeighborIndex]
DistanceToNeighbor = solenoid_tools.vector_magnitude( UpXyzCoords - UpNeighborCoords )
SelectUpNeighbors.append( (DistanceToNeighbor, UpNeighborName, UpNeighborRes, UpNeighborCoords) )
# sort by distance to atom, nearest first
SelectUpNeighbors.sort()
UpNeighbor1Tuple = SelectUpNeighbors[0]
UpNeighbor2Tuple = SelectUpNeighbors[1]
# print '\n'*2
# print 'UpRes, UpName', UpRes, UpName
# print 'UpstreamHydrogens', UpstreamHydrogens
# print 'SelectUpNeighbors', SelectUpNeighbors
# get neighbors of upstream residues
NeighborsOfDownstream = ResidueAtomNeighbors[DownIndex]
SelectDownNeighbors = []
# iterates through upstream atom neighbors for references for angle
for DownNeighborIndex in NeighborsOfDownstream:
DownNeighborRes, DownNeighborAtm = ResAtmRecordLists[DownNeighborIndex]
DownNeighborName = Pose.residue(DownNeighborRes).atom_name(DownNeighborAtm).replace(' ', '')
# keep looking if neighbor is hyrdogen
if 'H' in DownNeighborName:
continue
# skip virtual residues
if Pose.residue(DownNeighborRes).is_virtual(DownNeighborAtm):
continue
# keep looking if neighbor is self
if DownNeighborName == DownName and DownNeighborRes == DownRes:
continue
# keep looking if neighbor is upstream residue
if DownNeighborName == UpName and DownNeighborRes == UpRes:
continue
DownNeighborCoords = ResAtmCoordLists[DownNeighborIndex]
DistanceToNeighbor = solenoid_tools.vector_magnitude( DownXyzCoords - DownNeighborCoords )
SelectDownNeighbors.append( (DistanceToNeighbor, DownNeighborName, DownNeighborRes, DownNeighborCoords) )
# sort by distance to atom, nearest first
SelectDownNeighbors.sort()
DownNeighbor1Tuple = SelectDownNeighbors[0]
DownNeighbor2Tuple = SelectDownNeighbors[1]
# print 'DownRes, DownName', DownRes, DownName
# print 'DownstreamHydrogens', DownstreamHydrogens
# print 'SelectDownNeighbors', SelectDownNeighbors
Distance = solenoid_tools.vector_magnitude(DownXyzCoords - UpXyzCoords)
DistanceCst = 'AtomPair %s %d %s %d SCALARWEIGHTEDFUNC %f HARMONIC %.2f 1.0' %( UpName, UpRes, DownName, DownRes, SasaBasedWeight, Distance )
# Use Biopython for angle and dihedral calculations
# here 'Vec' means PDB.Vector of atom's xyz coord
UpstreamVec = PDB.Vector(UpXyzCoords)
DownstreamVec = PDB.Vector(DownXyzCoords)
UpNeighbor1Vec = PDB.Vector(UpNeighbor1Tuple[3])
UpNeighbor2Vec = PDB.Vector(UpNeighbor2Tuple[3])
DownNeighbor1Vec = PDB.Vector(DownNeighbor1Tuple[3])
DownNeighbor2Vec = PDB.Vector(DownNeighbor2Tuple[3])
Angle1 = PDB.calc_angle(UpNeighbor1Vec, UpstreamVec, DownstreamVec)
AngleCst1 = 'Angle %s %d %s %d %s %d SCALARWEIGHTEDFUNC %f CIRCULARHARMONIC %.2f 0.5' %( UpNeighbor1Tuple[1], UpNeighbor1Tuple[2], UpName, UpRes, DownName, DownRes, SasaBasedWeight, Angle1 )
Angle2 = PDB.calc_angle(UpstreamVec, DownstreamVec, DownNeighbor1Vec)
AngleCst2 = 'Angle %s %d %s %d %s %d SCALARWEIGHTEDFUNC %f CIRCULARHARMONIC %.2f 0.5' %( UpName, UpRes, DownName, DownRes, DownNeighbor1Tuple[1], DownNeighbor1Tuple[2], SasaBasedWeight, Angle2 )
Torsion1 = PDB.calc_dihedral(UpNeighbor2Vec, UpNeighbor1Vec, UpstreamVec, DownstreamVec)
TorsionCst1 = 'Dihedral %s %d %s %d %s %d %s %d SCALARWEIGHTEDFUNC %f CIRCULARHARMONIC %.2f 0.5' %( UpNeighbor2Tuple[1], UpNeighbor2Tuple[2], UpNeighbor1Tuple[1], UpNeighbor1Tuple[2], UpName, UpRes, DownName, DownRes, SasaBasedWeight, Torsion1 )
Torsion2 = PDB.calc_dihedral(UpNeighbor1Vec, UpstreamVec, DownstreamVec, DownNeighbor1Vec)
TorsionCst2 = 'Dihedral %s %d %s %d %s %d %s %d SCALARWEIGHTEDFUNC %f CIRCULARHARMONIC %.2f 0.5' %( UpNeighbor1Tuple[1], UpNeighbor1Tuple[2], UpName, UpRes, DownName, DownRes, DownNeighbor1Tuple[1], DownNeighbor1Tuple[2], SasaBasedWeight, Torsion2 )
Torsion3 = PDB.calc_dihedral(UpstreamVec, DownstreamVec, DownNeighbor1Vec, DownNeighbor2Vec)
TorsionCst3 = 'Dihedral %s %d %s %d %s %d %s %d SCALARWEIGHTEDFUNC %f CIRCULARHARMONIC %.2f 0.5' %( UpName, UpRes, DownName, DownRes, DownNeighbor1Tuple[1], DownNeighbor1Tuple[2], DownNeighbor2Tuple[1], DownNeighbor2Tuple[2], SasaBasedWeight, Torsion3 )
# adds constraint to running lists of constraints
Constraints.extend( [DistanceCst, AngleCst1, AngleCst2, TorsionCst1, TorsionCst2, TorsionCst3] )
if BBBB: BackboneBackboneCst.extend( [DistanceCst, AngleCst1, AngleCst2, TorsionCst1, TorsionCst2, TorsionCst3] )
if BBSC: BackboneSidechainCst.extend( [DistanceCst, AngleCst1, AngleCst2, TorsionCst1, TorsionCst2, TorsionCst3] )
if SCSC: SidechainSidechainCst.extend( [DistanceCst, AngleCst1, AngleCst2, TorsionCst1, TorsionCst2, TorsionCst3] )
# else:
# print 'No hydrogen!'
# sys.exit()
AllConstraints.extend(Constraints)
AllBackboneBackboneCst.extend(BackboneBackboneCst)
AllBackboneSidechainCst.extend(BackboneSidechainCst)
AllSidechainSidechainCst.extend(SidechainSidechainCst)
SortedConstraints = (AllBackboneBackboneCst, AllBackboneSidechainCst, AllSidechainSidechainCst)
return AllConstraints, SortedConstraints
