def Interface_axis(
pose, dist, resmuts, score
): ## return the interface rotation/translation axis and the center
## Compute interface at "dist" of distance and store:
## The contact_list=[i := contact of ith residue ]
## The interface_list= [[interface_1],[interface_2]]
copy_pose = Pose()
copy_pose.assign(pose)
score(copy_pose)
interface = Interface(1)
interface.distance(dist)
interface.calculate(copy_pose)
contact = interface.contact_list()
interface_residue = interface.pair_list()
centroid_interface = []
for interface in interface_residue: ## Compute the axis by taking the whole interfaces.
centroid_interface.append(
centroid([
copy_pose.residue(res).xyz('CA') for res in interface
])) ## store the centroids of the residue in the interfaces.
interface_axis = map(sub, centroid_interface[0], centroid_interface[1])
center = centroid_interface[0]
return (interface_axis, center)
def get_interface_residues(self, chains,
name=None):
# We are going to only change jump 1, so we know which jump to look at
# in the Interface class
movable_jumps = vector1_int(1)
# Now we can alter the fold tree such that the jump is between the
# chains we care about
# chains = left_chains + '_' + right_chains
sfxn = create_score_function('ref2015')
sfxn(self.pose)
print('SETTING UP FOLD TREE FOR INTERFACE {}'.format(chains))
setup_foldtree(self.pose, chains, movable_jumps)
# Set up interface class
interface = Interface(1)
interface.distance(self.dist)
interface.calculate(self.pose)
if not name:
name = self.pdbid
# Logic for filtering out residues not on chains of interest
interface_list = []
# interface_resis = []
for side in interface.pair_list():
for resi in side:
# Find out what chain the residue belongs to
pdbinfo = self.pose.pdb_info().pose2pdb(resi)
# resnum = pdbinfo.split(' ')[0]
chain = pdbinfo.split(' ')[1]
# Find out what chain the resiude is interacting with
closest = interface.closest_interface_residue(self.pose,
resi, self.dist)
interacting_chain = self.pose.pdb_info().pose2pdb(closest).split(' ')[1]
interacting_resi = self.pose.pdb_info().pose2pdb(closest).split(' ')[0]
# If both this chain and its partner are in the chains we care
# about, do something with them (in this case I'm spitting out a
# string that will let me select all the interface residues in
# PyMOL as a sanity check, you'll obviously want to save these
# to a dictionary or something)
if chain in list(chains) and interacting_chain in list(chains):
# interface_resis.append(resi)
row = {'pdb': name,
'interface': chains,
'chain':chain,
'rosetta_resnum': resi,
'closest_chain': interacting_chain,
'closest_rosetta_resnum': closest,
}
# 'closest_pdb_resnum': interacting_resi}
# 'pdb_resnum': resnum,
interface_list.append(row)
return interface_list
def Interface_axis(
pose, dist, resmuts, score
): ## return the interface rotation/translation axis and the center
## Compute interface at "dist" of distance and store:
## The contact_list=[i := contact of ith residue ]
## The interface_list= [[interface_1],[interface_2]]
copy_pose = Pose()
copy_pose.assign(pose)
setup_foldtree(copy_pose, "A_B", Vector1([1]))
score(copy_pose)
interface = Interface(1)
interface.distance(dist)
interface.calculate(copy_pose)
contact = interface.contact_list()
interface_residue = interface.pair_list()
centroid_interface = []
for interface in interface_residue: ## Compute the axis by taking the whole interfaces. (Only for the native)
centroid_interface.append(
centroid([
copy_pose.residue(res).xyz('CA') for res in interface
])) ## store the centroids of the residue in the interfaces.
interface_axis = map(sub, centroid_interface[0], centroid_interface[1])
center = centroid_interface[0]
## If there is mutation. The axis change by moving to the centroid of mutable residue.
if (len(resmuts) != 0 and len(interface_residue[1]) != 0
and len(interface_residue[2]) != 0):
centroid_muts = [] ## array for the mutables centroids
centroid_flexs = [
] ## array for the flexibles centroids i.e centroid of flexible 1, flexible 2 etc...
for res in resmuts: ## Calculate the centroid of flexibles of (of res in resnames)
centroid_flexs.append(
centroid([
copy_pose.residue(i).xyz("CA")
for i in sorted(list(set(contact[int(res)])))
]))
centroid_muts.append(copy_pose.residue(int(res)).xyz("CA"))
centroid_flex = centroid(
centroid_flexs) ## calculate the centroid of flexibles centroids
centroid_mut = centroid(
centroid_muts) ## calculate the centroid of mutables
interface_axis = [
centroid_flex[0] - centroid_mut[0],
centroid_flex[1] - centroid_mut[1],
centroid_flex[2] - centroid_mut[2]
] ## Calculate the axis
center = centroid_mut
return (interface_axis, center)
def Interface_axis(pose, dist, resmuts, score): ## return the interface rotation/translation axis and the center
## Compute interface at "dist" of distance and store:
## The contact_list=[i := contact of ith residue ]
## The interface_list= [[interface_1],[interface_2]]
copy_pose=Pose()
copy_pose.assign(pose)
score(copy_pose)
interface = Interface(1)
interface.distance(dist)
interface.calculate(copy_pose)
contact = interface.contact_list()
interface_residue = interface.pair_list()
centroid_interface=[]
for interface in interface_residue: ## Compute the axis by taking the whole interfaces.
centroid_interface.append(centroid([copy_pose.residue(res).xyz('CA') for res in interface])) ## store the centroids of the residue in the interfaces.
interface_axis= map(sub,centroid_interface[0],centroid_interface[1])
center=centroid_interface[0]
return (interface_axis, center)
from toolbox import *
import StringIO
parser = optparse.OptionParser()
parser.add_option('--pdb',
dest='pdb_file',
default='',
help='Protein comple in PDB format')
parser.add_option('--dist',
dest='dist',
default=10.0,
help='Size of interface')
(options, args) = parser.parse_args()
pdb_file = options.pdb_file
dist = float(options.dist)
init()
pose = pose_from_pdb(pdb_file)
setup_foldtree(pose, "A_B", Vector1([1]))
score = create_score_function("talaris2014")
score(pose)
interface = Interface(1)
interface.distance(dist)
interface.calculate(pose)
contact = interface.contact_list()
interface_residue = interface.pair_list()
print pose.fold_tree()
print interface_residue
from rosetta.core.scoring import *
from rosetta.core.graph import *
from rosetta.protocols.scoring import Interface
from toolbox import *
import StringIO
parser=optparse.OptionParser()
parser.add_option('--pdb', dest = 'pdb_file', default = '', help = 'Protein comple in PDB format' )
parser.add_option( '--dist', dest='dist' ,
default = 10.0,
help = 'Size of interface')
(options,args) = parser.parse_args()
pdb_file=options.pdb_file
dist=float(options.dist)
init()
pose=pose_from_pdb(pdb_file)
setup_foldtree(pose, "A_B", Vector1([1]))
score=create_score_function("talaris2014")
score(pose)
interface = Interface(1)
interface.distance(dist)
interface.calculate(pose)
contact = interface.contact_list()
interface_residue = interface.pair_list()
print pose.fold_tree()
print interface_residue