def get_shift_from_rst(self, res1_number, atom1_name, res2_number,
atom2_name, parm, new_rst):
from pyxmol.geometry import distance, angle_deg, translate
from parmed.amber import NetCDFTraj, Rst7, AmberParm
from parmed.geometry import distance2
import numpy as np
for a in parm.atoms:
if a.residue.number == (res1_number - 1) and a.name == atom1_name:
A1 = a
elif a.residue.number == (res2_number -
1) and a.name == atom2_name:
A2 = a
best_dist = np.sqrt(distance2(A1, A2))
#self.log('start get_shift_from_rst')
#self.log('best_dist: {}'.format(best_dist))
A, B, C = self.make_current_lattice_vectors(new_rst.box)
for i in range(-1, 2):
for j in range(-1, 2):
for k in range(-1, 2):
shift = i * A + j * B + k * C
#self.log('shift: {}'.format(shift))
A2.xx += shift[0]
A2.xy += shift[1]
A2.xz += shift[2]
dist = np.sqrt(distance2(A1, A2))
#self.log('dist: {}, best_dist: {}, (best_dist-dist): {}'.format(round(dist, 9), round(best_dist, 9), best_dist-dist))
if round(dist, 9) <= round(best_dist, 9):
best_dist = dist
best_shift = shift
#self.log('best shift: {}'.format(best_shift))
A2.xx -= shift[0]
A2.xy -= shift[1]
A2.xz -= shift[2]
return best_dist, best_shift
def get_shift_from_nc(self, frame_number, res1_number, atom1_name,
res2_number, atom2_name, parm, traj):
from pyxmol.geometry import distance, angle_deg, translate
from parmed.amber import NetCDFTraj, Rst7, AmberParm
from parmed.geometry import distance2
import numpy as np
new_rst7 = Rst7(natom=traj.atom)
new_rst7.coordinates = traj.coordinates[frame_number]
new_rst7.box = traj.box[frame_number]
parm.load_rst7(new_rst7)
for a in parm.atoms:
if a.residue.number == (res1_number - 1) and a.name == atom1_name:
A1 = a
elif a.residue.number == (res2_number -
1) and a.name == atom2_name:
A2 = a
best_dist = np.sqrt(distance2(A1, A2))
A, B, C = self.make_current_lattice_vectors(traj.box[frame_number])
for i in range(-1, 2):
for j in range(-1, 2):
for k in range(-1, 2):
shift = i * A + j * B + k * C
A2.xx += shift[0]
A2.xy += shift[1]
A2.xz += shift[2]
dist = np.sqrt(distance2(A1, A2))
if dist < best_dist:
best_dist = dist
best_shift = shift
A2.xx -= shift[0]
A2.xy -= shift[1]
A2.xz -= shift[2]
return best_dist, best_shift
def test_distance2(self):
""" Tests the distance2 calculation """
a1, a2 = Atom(), Atom()
a1.xx = a1.xy = a1.xz = 0
a2.xx = 3
a2.xy = 4
a2.xz = 0
self.assertEqual(geo.distance2(a1, a2), 25)
# Make sure it also works for tuples and a mixture of both
self.assertEqual(geo.distance2((0, 0, 0), (3, 4, 0)), 25)
self.assertEqual(geo.distance2(a1, (3, 4, 0)), 25)
self.assertEqual(geo.distance2((0, 0, 0), a2), 25)
def test_distance2(self):
""" Tests the distance2 calculation """
a1, a2 = Atom(), Atom()
a1.xx = a1.xy = a1.xz = 0
a2.xx = 3
a2.xy = 4
a2.xz = 0
self.assertEqual(geo.distance2(a1, a2), 25)
# Make sure it also works for tuples and a mixture of both
self.assertEqual(geo.distance2((0, 0, 0), (3, 4, 0)), 25)
self.assertEqual(geo.distance2(a1, (3, 4, 0)), 25)
self.assertEqual(geo.distance2((0, 0, 0), a2), 25)
def getAtomSerialFromAmberMaskHbond(combined_pmd,resnumber,atomname,distance,ligresname="LIG"):
lig_sel=parmed.amber.mask.AmberMask(combined_pmd,"(((:"+resnumber+")&(@"+atomname+"))<@"+distance+") & (:"+ligresname+" & (@N=|@O=))")
lig_idx=[x for x in lig_sel.Selected() ]
rec_sel=parmed.amber.mask.AmberMask(combined_pmd,"((:"+resnumber+")&(@"+atomname+"))")
rec_idx=[x for x in rec_sel.Selected() ]
print(lig_idx,rec_idx)
if len(rec_idx)==1 :
if(len(lig_idx)>1) :
mind=1000
minidx=lig_idx[0]
for idx in lig_idx:
d=g.distance2(combined_pmd[idx],combined_pmd[rec_idx[0]])
if d<mind:
mind=d
minidx=idx
return(rec_idx[0],minidx)
else :
return(rec_idx[0],lig_idx[0])
#sys.exit("The reaction coordinate selection failed here, please consider setting it by hand")
else :
sys.exit("Your receptor atom selection selected more than a single atom. PLease check your atom names or refine your selection")
def find_result(res_atom=None, prot_file=None, combined_pmd=None):
# Find the
distance_atom_1, prot_atom = find_atom(res_atom, prot_file, combined_pmd)
# Now find the one nearest
distance_atom_2 = [(x.idx, distance2(x, prot_atom))
for x in combined_pmd.atoms if is_lig(x)]
distance_atom_2.sort(key=operator.itemgetter(1))
# These are the interactions to find
index_one = distance_atom_1[0][0]
index_two = distance_atom_2[0][0]
out_res = [index_one, index_two, math.sqrt(distance_atom_2[0][1])]
return index_one, index_two, out_res, distance_atom_2[0][1]
def find_disulfides(input_file, threshold=6.2):
structure = parmed.load_file(input_file)
sulfurs = [x for x in structure.atoms if x.residue.name == "CYS" and x.name == "SG"]
disulfides = []
for atom_one in sulfurs:
for atom_two in sulfurs:
if atom_one.idx >= atom_two.idx:
continue
dist = distance2(atom_one, atom_two)
if dist < threshold:
atom_one.residue.name = "CYX"
atom_two.residue.name = "CYX"
disulfides.append((atom_one.residue.number, atom_two.residue.number))
structure.write_pdb(input_file)
return disulfides
def get_dist_and_angle(self, res1_number, atom1_name, res2_number,
atom2_name, res3_number, atom3_name, parm):
from parmed.amber import AmberParm, Rst7
from parmed.geometry import distance2
import numpy as np
rst = Rst7(MD._run_dir + "/run" + MD._pattern % self.current_step +
"mod.rst")
parm.load_rst7(rst)
for a in parm.atoms:
if a.residue.number == (res1_number - 1) and a.name == atom1_name:
A1 = a
elif a.residue.number == (res2_number -
1) and a.name == atom2_name:
A2 = a
elif a.residue.number == (res3_number -
1) and a.name == atom3_name:
A3 = a
A1_A2 = distance2(A1, A2)
A1_A3 = distance2(A1, A3)
A2_A3 = distance2(A2, A3)
cos = (A1_A2 + A2_A3 - A1_A3) / (2 * np.sqrt(A1_A2) * np.sqrt(A2_A3))
A1_A2_A3 = np.degrees(np.arccos(cos))
return np.sqrt(A1_A2), A1_A2_A3
def find_atom(res_atom=None, prot_file=None, combined_pmd=None):
# Parse the input data like this -> "A_LYS_311_N"
chain = res_atom.split("_")[0]
res_name = res_atom.split("_")[1]
res_number = int(res_atom.split("_")[2])
atom_name = res_atom.split("_")[3]
# Read the original PDB File and find the atom coords
protein = parmed.load_file(prot_file)
for atom in protein.atoms:
if check_same(atom, chain, res_name, res_number, atom_name):
prot_atom = atom
break
distance_atom_1 = [(x.idx, distance2(x, prot_atom))
for x in combined_pmd.atoms]
distance_atom_1.sort(key=operator.itemgetter(1))
return distance_atom_1, prot_atom
def find_lig_id(pdb_file, het_pdb, res_name, res_num, atom_name):
print(pdb_file)
protein = parmed.load_file(pdb_file)
atoms = []
for residue in protein.residues:
if residue.name == res_name:
if residue.number == res_num:
for atom in residue.atoms:
if atom.name == atom_name:
atoms.append(atom)
if len(atoms)==0:
print("ISSUE FINDING ATOM: "+" ".join([pdb_file,res_name, str(res_num), atom_name]))
sys.exit()
else:
prot_atom = atoms[0]
ligands = parmed.load_file(het_pdb)["!(:HOH,NA,CL)"]
distance_atom_2 = [(x.residue.name, math.sqrt(distance2(x, prot_atom)),x.name) for x in ligands.atoms]
distance_atom_2.sort(key=operator.itemgetter(1))
print(distance_atom_2[0],distance_atom_2[1],distance_atom_2[2])
return distance_atom_2[0][0]
