def rrtstarsmart(mol,
ligandsel,
step=1,
maxiter=int(1E6),
ligcom=False,
colldist=2,
outdist=8,
radius=2.5):
protcoor, ligcoor = _getCoordinates(mol, ligandsel, ligcom)
viewer = _prepareViewer(mol, ligandsel)
mincoor = np.squeeze(np.min(mol.coords, axis=0) - 10)
maxcoor = np.squeeze(np.max(mol.coords, axis=0) + 10)
print(mincoor, maxcoor)
spherecoor = _pointsOnSphere(maxDistance(mol) + 5)
tree = Tree(ligcoor)
nocol = None
for i in range(maxiter):
print(i)
#p_rand = spherecoor[np.random.randint(spherecoor.shape[0]), :]
p_rand = _randomPoint(mincoor, maxcoor)
parent_idx, p_near = _getNearest(tree.points, p_rand)
p_new = _newPoint(p_rand, p_near, step)
if _collision(protcoor, p_new, buffer=colldist):
continue
print('no collision')
near, neardist = _collisionFreeNeighbours(tree, p_new, radius,
protcoor, colldist, step)
parent_idx, dist = _chooseParent(tree, near, neardist)
tree.addPoint(p_new, parent_idx, dist)
_rewire(tree, near, neardist, len(tree.points) - 1)
if _endCondition(protcoor, p_rand, p_new, outdist, method='exited'):
break
for i in range(len(tree.points)):
if tree.parent[i] is not None:
_drawline(viewer, tree.points[i], tree.points[tree.parent[i]])
print('optimizing')
_pathOptimize(tree, len(tree.points) - 1, protcoor, colldist, step)
print('finished optimization')
# TODO: The algorithm is not finished. Normally you would get beacons and continue sampling around them to optimize
# TODO: the path even more. However, we don't really need this in our case, unless I decide to make a real full impl
# TODO: http://ieeexplore.ieee.org/xpls/icp.jsp?arnumber=6284384
currnode = len(tree.points) - 1
viewer.send('draw color green')
while tree.parent[currnode] is not None:
_drawline(viewer, tree.points[currnode],
tree.points[tree.parent[currnode]])
currnode = tree.parent[currnode]
return
def rrt(mol,
ligandsel,
step=1,
maxiter=int(1e6),
ligcom=False,
colldist=2,
outdist=8):
protcoor, ligcoor = _getCoordinates(mol, ligandsel, ligcom)
viewer = _prepareViewer(mol, ligandsel)
spherecoor = _pointsOnSphere(maxDistance(mol) + 5)
tree = Tree(ligcoor)
nocol = None
for i in range(maxiter):
print(i)
if nocol is None:
p_rand = spherecoor[np.random.randint(
spherecoor.shape[0]
), :] # TODO: Make it clever. Discard failed points
else: # Reusing the same point that caused no collision
p_rand = nocol
parent_idx, p_near = _getNearest(tree.points, p_rand)
p_new = _newPoint(p_rand, p_near, step)
if _collision(protcoor, p_new, buffer=colldist):
nocol = None
continue
nocol = p_rand
print("no collision")
tree.addPoint(p_new, parent_idx, step)
_drawline(viewer, p_near, p_new)
if _dist(p_rand, p_new) < 2:
break
def raytracing(
mol,
ligandsel,
step=1,
colldist=2,
outdist=8,
ligcom=False,
numsamples=2000,
ratioexposed=0,
vmd=True,
):
protcoor, ligcoor = _getCoordinates(mol, ligandsel, ligcom)
spherecoor = _pointsOnSphere(maxDistance(mol) + 5, numsamples=numsamples)
if vmd:
_viewSphere(spherecoor)
viewer = _prepareViewer(mol, ligandsel)
distances = _dist(ligcoor, spherecoor)
from joblib import Parallel, delayed
results = Parallel(n_jobs=-2, verbose=11)(delayed(parallelfunc)(
j,
spherecoor[j, :],
ligcoor,
protcoor,
step,
colldist,
outdist,
distances[:, j],
) for j in range(spherecoor.shape[0]))
points = []
pointdist = []
shortpoints = []
for r in results:
points += r[0]
pointdist += r[1]
shortpoints += r[2]
if len(points) == 0:
raise RuntimeError(
"No ligand atoms can exit the pocket without {}A clashes.".format(
colldist))
points = np.array(points)
numexposed = len(np.unique(points[:, 0]))
percentexposed = (numexposed / ligcoor.shape[0]) * 100
if numexposed < (ratioexposed * ligcoor.shape[0]):
raise RuntimeError(
"Only {:.1f}% ligand atoms can exit the pocket without {}A clashes. "
"This collides with the user-defined required {:.1f}% exposed ligand atoms."
.format(percentexposed, colldist, ratioexposed * 100))
print(
"{:.1f}% ligand atoms can exit the pocket without {}A clashes.".format(
percentexposed, colldist))
from scipy.stats import mode
modesphere = mode(points[:, 1]).mode[0]
idx = points[:, 1] == modesphere
meanlig = np.mean(ligcoor[points[idx, 0], :], axis=0)
if vmd:
viewer.send("draw color green")
_drawline(viewer, meanlig, spherecoor[modesphere, :])
for idx, p in enumerate(points.tolist()):
if p[1] == modesphere:
viewer.send("draw color red")
_drawline(viewer, shortpoints[idx], spherecoor[p[1], :])
viewer.send("draw color green")
_drawline(viewer, ligcoor[p[0], :], shortpoints[idx])
return spherecoor[modesphere, :] - meanlig
from htmd.builder.amber import defaultParam, build
# Test protein ligand building with parametrized ligand
refdir = home(dataDir=join('test-amber-build', 'protLig'))
tmpdir = './protLig'
mol = Molecule(join(refdir, '3ptb_mod.pdb'))
mol.center()
lig = Molecule(join(refdir, 'benzamidine.pdb'),
guess=('bonds', 'angles', 'dihedrals'))
prm, lig = fftype(lig, method='GAFF2')
writeFRCMOD(lig, prm, join(tmpdir, 'mol.frcmod'))
lig.segid[:] = 'L'
lig.center()
from moleculekit.util import maxDistance
D = maxDistance(mol, 'all')
D += 6
lig.moveBy([0, 0, D])
newmol = Molecule()
newmol.append(lig)
newmol.append(mol)
smol = solvate(newmol, posz=3)
params = defaultParam() + [
join(tmpdir, 'mol.frcmod'),
]
_ = build(smol, outdir=tmpdir, param=params, ionize=False)
prot = autoSegment(prot, sel='protein')
prot.set('segid', 'W', sel='water')
prot.set('segid', 'CA', sel='resname CA')
prot.center()
#LIGAND
ligand = Molecule(
'/home/alejandro/covid19/MDrun/melatonin_cov/parameters/GAFF2/mol.mol2')
ligand.center()
ligand.set('segid', 'L')
ligand.set('resname', 'MOL')
ligand.rotateBy(uniformRandomRotation())
from moleculekit.util import maxDistance
D = maxDistance(prot, 'all')
D += 5
ligand.moveBy([D, 0, 0])
mol = Molecule(name='combo')
mol.append(prot)
mol.append(ligand)
mol.reps.add(sel='protein', style='NewCartoon', color='Secondary Structure')
mol.reps.add(sel='resname MOL', style='Licorice')
mol.view()
# We solvate with a larger box to fully solvate the ligand
DW = D + 3
smol = solvate(mol, minmax=[[-DW, -DW, -DW], [DW, DW, DW]])
smol.reps.add(sel='water', style='Lines')
smol.view()