def rotateCoordinates(coords, rotations, center):
from moleculekit.util import rotationMatrix
def rotate(coords, rotMat, center=(0, 0, 0)):
newcoords = coords - center
return np.dot(newcoords, np.transpose(rotMat)) + center
rotation = list(rotations)
matx = rotationMatrix([1, 0, 0], rotation[0])
maty = rotationMatrix([0, 1, 0], rotation[1])
matz = rotationMatrix([0, 0, 1], rotation[2])
coords = coords.copy()
coords = rotate(coords, matx, center=center)
coords = rotate(coords, maty, center=center)
coords = rotate(coords, matz, center=center)
return coords
def moveLipidToPos(mol, lip):
from moleculekit.util import rotationMatrix
mol = mol.copy()
headpos = mol.coords[mol.name == lip.headname].flatten()[np.newaxis, :]
mol.moveBy(-headpos)
mol.rotateBy(rotationMatrix([0, 0, 1], np.deg2rad(lip.rot)))
mol.moveBy(lip.xyz)
return np.squeeze(mol.coords[:, :, 0])
def test_align(self):
from moleculekit.util import rotationMatrix
import numpy as np
sm = SmallMol(self.benzamidine_mol2)
mol = sm.toMolecule()
mol.rotateBy(rotationMatrix([1, 0, 0], 3.14))
sm.align(mol)
assert (np.abs(sm._coords) - np.abs(mol.coords)).max() # I need to do the abs of the coords since it's a symmetrical molecule
def _loadMolecules(lipids, files):
from moleculekit.util import rotationMatrix
# Create Molecules
for l in lipids:
randidx = np.random.randint(len(files[l.resname]))
mol = Molecule(files[l.resname][randidx])
mol.filter('not water', _logger=False)
if l.xyz[2] < 0:
mol.rotateBy(rotationMatrix([1, 0, 0], np.deg2rad(180))) # Rotate the lower leaflet lipids upside down
l.mol = mol
l.rot = np.random.random() * 360 - 180 # Random starting rotation
def _totalContacts(x, *args):
from moleculekit.util import rotationMatrix
lipids = args[0]
headnames = args[1]
zpos = args[2]
thresh = args[3]
neighbours = args[4]
numlips = args[5]
box = args[6]
newxy = np.array(x[:numlips * 2]).reshape((-1, 2))
rots = x[numlips * 2:]
allcoords = []
for i in range(numlips):
cc = np.squeeze(lipids[i].mol.coords)
headpos = cc[lipids[i].mol.name == headnames[i]].flatten()[
np.newaxis, :]
cc = cc - headpos # Center it on the head position
newloc = np.hstack(
(newxy[i], zpos[i]))[np.newaxis, :] # Calculate new head position
# Doing the rotation
M = rotationMatrix([0, 0, 1], np.deg2rad(rots[i]))
newcoords = np.dot(cc, np.transpose(M))
allcoords.append(newcoords + newloc)
allcoords = np.array(allcoords, dtype=object)
numcontacts = 0
for i in range(len(allcoords)):
if len(neighbours[i]) == 0:
continue
neighcoor = np.vstack(allcoords[neighbours[i]])
dists = _wrapping_dist(allcoords[i], neighcoor,
np.array(box, dtype=float))
numcontacts += np.count_nonzero(dists < thresh)
return numcontacts
def _createMembraneMolecule(lipids):
from moleculekit.util import rotationMatrix
allmols = []
for i, l in enumerate(lipids):
mol = l.mol.copy()
headpos = mol.coords[mol.name == l.headname].flatten()[np.newaxis, :]
mol.moveBy(-headpos)
mol.rotateBy(rotationMatrix([0, 0, 1], np.deg2rad(l.rot)))
mol.moveBy(l.xyz)
mol.resid[:] = i
allmols.append(mol)
def mergeMols(mollist): # Divide and conquer approach for merging molecules
while len(mollist) > 1:
mollist[0].append(mollist[1])
mollist = [mollist[0]] + mergeMols(mollist[2:])
if len(mollist) == 1:
return mollist
return []
return mergeMols(allmols)[0]