def xyzr_to_vertices(xyzr_filename, gts_filename, probe_radius=1.4):
master_vlist, master_tlist = get_spherical_mesh(2)
spheres = open(xyzr_filename,'r').readlines()
vlist = []
tlist = []
nlist = []
for sph in spheres:
offset = len(vlist)
x,y,z,r = [float(xx) for xx in sph.split()]
r += probe_radius
for vv in master_vlist:
n = Vector(vv)
nlist.append(n)
xx = (vv.x * r) + x
yy = (vv.y * r) + y
zz = (vv.z * r) + z
vlist.append(Vector(xx,yy,zz))
for v1_idx, v2_idx, v3_idx in master_tlist:
tlist.append( (v1_idx+offset, v2_idx+offset, v3_idx+offset) )
write_gts(gts_filename, vlist, tlist)
return
def clean_gts(filename):
vertices, triangles = get_vertices_triangles_from_gts(filename)
# get centre of set of points
centre = Vector(0,0,0)
for v in vertices:
centre += v
centre = centre / len(vertices)
# get maximum xyz extent of set of points
maxdim = max([ (v - centre).length() for v in vertices ])
# insert vertices into an Octree
max_neighbours = 27
adaptive_tree = Octree(max_neighbours, Vector(centre.x, centre.y, centre.z), maxdim*2)
duplicates = []
ctr = 0
mappingA = {}
mappingB = {}
for i,v in enumerate(vertices):
# check for duplicate already in tree
pre_existing = adaptive_tree.check_for_duplicate(v)
if (pre_existing == -1):
mappingA[i] = ctr
mappingB[ctr] = i
adaptive_tree.insert(v)
ctr += 1
else:
pre_existing_idx = mappingB[pre_existing]
print("Clash between %d %s and %d %s" %(i, v, pre_existing_idx, vertices[pre_existing_idx]))
duplicates.append(i)
mappingA[i] = pre_existing
vertices = [v for i,v in enumerate(vertices) if i not in duplicates]
print("Number of vertices: ", len(vertices))
new_tri = []
for i,t in enumerate(triangles):
#print t[0]
new_v1 = mappingA[t[0]]
new_v2 = mappingA[t[1]]
new_v3 = mappingA[t[2]]
if (new_v1 in (new_v2, new_v3) or
new_v2 in (new_v1, new_v3) or
new_v3 in (new_v1, new_v2)
):
print("skipped a dud triangle (%d) " %(i), t)
continue
new_tri.append([new_v1, new_v2, new_v3])
# write the gts file
write_gts(filename, vertices, new_tri)
def gts2off(gts_filename, off_filename):
vertices, triangles = get_vertices_triangles_from_gts(gts_filename)
vnormals = [Vector(0,0,0) for ii in range(len(vertices))]
for tri in triangles:
v1,v2,v3 = tri
v1v = vertices[v1]
v2v = vertices[v2]
v3v = vertices[v3]
vnormals[v1] += tnormal(v1v, v2v, v3v) * tarea(v1v,v2v,v3v)
vnormals[v2] += tnormal(v1v, v2v, v3v) * tarea(v1v,v2v,v3v)
vnormals[v3] += tnormal(v1v, v2v, v3v) * tarea(v1v,v2v,v3v)
vnormals = [v.normalised() for v in vnormals]
fout = open(off_filename,'w')
print("nOFF", file=fout)
print("3", file=fout)
# last number is number of edges; unused by OFF format, but must be present
print("%9d%9d%9d" %(len(vertices),len(triangles),0), file=fout)
for v,vn in zip(vertices, vnormals):
print("%9.3f%9.3f%9.3f%9.3f%9.3f%9.3f" %(v.x, v.y, v.z, vn.x, vn.y, vn.z), file=fout)
for t in triangles:
print(" 3 %8d%8d%8d" %(t[0],t[1],t[2]), file=fout)
fout.close()
return
def gts2msms(gts_filename, msms_filename):
vertices, triangles = get_vertices_triangles_from_gts(gts_filename)
vnormals = [Vector(0,0,0) for ii in range(len(vertices))]
for tri in triangles:
v1,v2,v3 = tri
v1v = vertices[v1]
v2v = vertices[v2]
v3v = vertices[v3]
vnormals[v1] += tnormal(v1v, v2v, v3v) * tarea(v1v,v2v,v3v)
vnormals[v2] += tnormal(v1v, v2v, v3v) * tarea(v1v,v2v,v3v)
vnormals[v3] += tnormal(v1v, v2v, v3v) * tarea(v1v,v2v,v3v)
vnormals = [v.normalised() for v in vnormals]
fout = open(msms_filename,'w')
print("%d %d" %(len(vertices),len(triangles)), file=fout)
for ii,(v,vn) in enumerate(zip(vertices, vnormals)):
print("%9.3f %9.3f %9.3f %9.3f %9.3f %9.3f %7d %7d 2" %(v.x, v.y, v.z, vn.x, vn.y, vn.z, 0, 0), file=fout)
for t in triangles:
print("%8d%8d%8d" %(t[0]+1,t[1]+1,t[2]+1), file=fout)
fout.close()
return
def off2gts(off_filename, gts_filename):
off_file = open(off_filename,'r')
first_line = off_file.readline()
num_verts, num_tris = [float(xx) for xx in first_line.split()]
vertex_lines = [off_file.readline() for ii in range(num_verts)]
tri_lines = [off_file.readline() for ii in range(num_tris)]
vertices = [[float(xx) for xx in line.split()]
for line in vertex_lines]
triangles = [[int(xx) for xx in line.split()[1:4]]
for line in tri_lines]
vnormals = [Vector(0,0,0) for ii in range(num_verts)]
for tri in triangles:
v1,v2,v3 = tri
v1v = vertices[v1]
v2v = vertices[v2]
v3v = vertices[v3]
vnormals[v1] += tnormal(v1v, v2v, v3v) * tarea(v1v,v2v,v3v)
vnormals[v2] += tnormal(v1v, v2v, v3v) * tarea(v1v,v2v,v3v)
vnormals[v3] += tnormal(v1v, v2v, v3v) * tarea(v1v,v2v,v3v)
vnormals = [v.normalised() for v in vnormals]
write_gts(gts_filename, vertices, triangles)
return
def get_clean_msms_vertices(msms_vertex_filename):
vfloat = [line.split() for line in open(msms_vertex_filename,'r') if line[0] != '#']
# delete the first lines of each list, which are column totals
vfloat.remove(vfloat[0])
vertices = []
normals = []
for vertex_descriptor in vfloat:
x,y,z,xn,yn,zn = [float(v) for v in vertex_descriptor[:6]]
vertices.append( Vector(x,y,z) )
normals.append( Vector(xn,yn,zn) )
# get centre of set of points
centre = Vector(0,0,0)
for v in vertices:
centre += v
centre = centre / len(vertices)
# get maximum xyz extent of set of points
maxdim = max([ (v - centre).length() for v in vertices ])
# insert vertices into an Octree
max_neighbours = 27
adaptive_tree = Octree(max_neighbours, Vector(centre.x, centre.y, centre.z), maxdim*2)
remap = {}
for i,(v,n) in enumerate(zip(vertices,normals)):
# check for duplicate already in tree
pre_existing = adaptive_tree.check_for_duplicate(v)
if (pre_existing == -1):
adaptive_tree.insert(v)
else:
pre_existing = new_vertex_map[pre_existing]
print("Clash between %d %s %s and %d %s %s" %(i, v, n, pre_existing, vertices[pre_existing], normals[pre_existing]))
remap[i] = pre_existing
normals[pre_existing] += n
vertices = [v for i,v in enumerate(vertices) if i not in remap.keys()]
normals = [v.normalised() for i,v in enumerate(normals) if i not in remap.keys()]
print("done cleaning duplicate vertices")
return vertices, normals
def __init__(self, a: float, size: float, centre: Vector):
""" Constructor with packed sphere radius a, arena radius size """
# Set the arena size
if size <= a:
size = a
self.radius = size
self.centre = centre
# Packed sphere radius, half row height and half layer height
(self._rx, self._ry, self._rz) = (a, sqrt(3) * a / 2,
sqrt(2 / 3.0) * a)
log.debug(f"Packed sphere radius {self._rx}, centre {self.centre}")
# Arena dimensions in packed spheres, rows and layers
self._psx = int((self._rx + size - 1e-3) / (2 * self._rx))
self._psy = int((self._ry + size - 1e-3) / (2 * self._ry))
self._psz = int((self._rz + size - 1e-3) / (2 * self._rz))
# Build the arena: x,y,z at least 1, and 1 means only 1 sphere/row/layer
self._psa = dict()
for layer in range(-self._psz + 1, self._psz):
for row in range(-self._psy + 1, self._psy):
start = centre + Vector(
((layer + row) % 2) * a,
sqrt(3) *
(row +
(layer % 2) / 3.0) * a, 2 * sqrt(2 / 3.0) * layer * a)
for sphere in range(self._psx): # Reflection captured below
# Intention is that arena is spherical (roughly)
pv = start + Vector(2 * a, 0, 0) * sphere
if (pv - self.centre).length() > self.radius:
continue
# As plus is in sphere, so is minus...
self._psa[(sphere, row, layer)] = pv
log.debug(f"init ({sphere},{row},{layer}) = %s" % \
(_asString(self._psa[(sphere,row,layer)])))
self._psa[(-sphere,row,layer)] = \
start-Vector(2*a,0,0)*sphere
log.debug(f"init (-{sphere},{row},{layer}) = %s" % \
(_asString(self._psa[(-sphere,row,layer)])))
# Initialise sphere occupancy
self._pso = dict()
self.clear()
# Calculate the volume of the arena
self._psvoleq = 4 * (a**3) * sqrt(
2) # Volume equivalent of packed sphere
self.volume = len(self._psa) * self._psvoleq
def normalised(vector):
"""Return normalised (length=1.0) Vector version of the input.
This function is here to remove some ambiguity in the term 'normal' where
I sometimes mean perpendicular to a plane, and sometimes I mean,
normalised to length=1.0 (i.e. a unit vector)."""
return Vector(vector).normal()
def _makeVectorRange(m: re.match, sx: int) -> List[Vector]:
vr = [
Scenario._makeRange(m, n, n + 3, n + 6) for n in range(sx, sx + 3)
]
vl = max([len(r) for r in vr]) # Length of longest coordinate list
# Extend each coordinate list to the length of the longest one
vr = [vr[n] + [vr[n][-1]] * (vl - len(vr[n])) for n in range(3)]
return [Vector(vr[0][n], vr[1][n], vr[2][n]) for n in range(vl)]
def getLocation(self, ref: PSARef) -> Vector:
if ref in self._psa:
return self._psa[ref]
a = self._rx
(sphere, row, layer) = ref
return self.centre + Vector(
(2 * sphere + (layer + row) % 2) * a,
sqrt(3) * (row +
(layer % 2) / 3.0) * a, 2 * sqrt(2 / 3.0) * layer * a)
def calculate_mass(pdb: str) -> Tuple[float, Vector]:
mass = 0.0
com = Vector(0, 0, 0)
atom = "none"
try:
with open(pdb) as f:
for line in f:
if line[0:6] != "ATOM ":
continue
pos = Vector(float(line[31:39]), float(line[39:47]),
float(line[47:55]))
atom = line[77] if line[76] == " " else line[76:78]
matom = MolMass[atom]
mass += matom
com -= (com - pos) * matom / mass
except Exception as e:
log.warning(f"Zero mass assumed for {pdb} atom {atom} because {e}")
return (mass, com)
def getResidueCharges(filename):
"""Returns a list of residues and total charge located at Calpha from PQR file."""
pqr_file = open(filename, 'r')
pqr_data = []
pqr_atoms, err_lines = readPQR(pqr_file)
atom_set = []
residue = []
last_seq = -1
for pqr in pqr_atoms:
if (pqr.resSeq == 0):
raise Exception # can't identify residues by sequence number
if (pqr.resSeq != last_seq):
if (last_seq != -1):
atom_set.append(residue)
residue = [pqr]
last_seq = pqr.resSeq
else:
residue.append(pqr)
if (last_seq != -1 and len(residue) > 0):
atom_set.append(residue)
for residue in atom_set:
backbone = [xx for xx in residue if xx.name in ["O", "N", "C"]]
assert (len(backbone) == 3)
sidechain = [
xx for xx in residue if xx.name not in ["CA", "O", "N", "C"]
]
alpha = [pqr for pqr in residue if pqr.name == "CA"]
assert (len(alpha) == 1)
for pqr in backbone:
pqr_data.append(Charge(Vector(pqr.x, pqr.y, pqr.z), pqr.q, pqr.r))
calpha_xyz = Vector(alpha[0].x, alpha[0].y, alpha[0].z)
total_sidechain_charge = sum([pqr.q for pqr in sidechain])
pqr_data.append(
Charge(calpha_xyz, total_sidechain_charge + alpha[0].q,
alpha[0].r))
return pqr_data
def reflect(gts_filename, output_filename):
vertices, triangles = get_vertices_triangles_from_gts(gts_filename)
vertices = [Vector(-v.x, v.y, v.z) for v in vertices]
tnormals = [tnormal(vertices[t[0]],vertices[t[1]],vertices[t[2]])
for t in triangles]
write_gts(output_filename, vertices, triangles)
return;
def getCharges(filename):
"""Returns a list of charges and corresponding lines from PQR file."""
pqr_file = open(filename, 'r')
pqr_data = []
pqr_atoms, err_lines = readPQR(pqr_file)
for pqr in pqr_atoms:
xyz = Vector(pqr.x, pqr.y, pqr.z)
pqr_data.append(Charge(xyz, pqr.q, pqr.r))
return pqr_data
def msms2xyzn(msms_vertex_filename, xyzn_filename):
"""Convert msms files to xyz-with-normal format"""
vfloat = [line.split() for line in open(msms_vertex_filename,'r') if line[0] != '#']
# delete the first lines of each list, which are column totals
vfloat.remove(vfloat[0])
vertices = []
normals = []
for vertex_descriptor in vfloat:
x,y,z,xn,yn,zn = [float(v) for v in vertex_descriptor[:6]]
vertices.append( Vector(x,y,z) )
normals.append( Vector(xn,yn,zn) )
fout = open(xyzn_filename,'w')
for v,n in zip(vertices, normals):
print(v.x, v.y, v.z, n.x, n.y, n.z, file=fout)
fout.close()
return
def test_rand_rot():
xx = Vector(1.0, 0.0, 0.0)
from geometry import apply_quaternion_to_vector
f = open("random_rotation_test.kin", "w")
print("@kinemage", file=f)
print("@dotlist", file=f)
for ii in range(10000):
rand_pt_on_surface_of_sphere = apply_quaternion_to_vector(
_rand_rot(), xx)
print("%f %f %f" %
(rand_pt_on_surface_of_sphere.x, rand_pt_on_surface_of_sphere.y,
rand_pt_on_surface_of_sphere.z),
file=f)
f.close()
def get_vertices_triangles_from_gts(filename):
# first get the number of vertices, edges, faces
(nv, ne, nf), f = get_gts_info(filename, return_handle=True)
vertices, triangles = [], []
try:
while (len(vertices) < nv):
# convert to Vertex object
vx, vy, vz = [float(xx) for xx in get_next_line_not_comment(f).split()]
vertices.append(Vector(vx, vy, vz))
# edges are defined as an ordered pair of vertices
edges = []
while (len(edges) < ne):
edge_verts = get_next_line_not_comment(f).split()
edges.append( set([int(edge_verts[0])-1, int(edge_verts[1])-1]) )
# triangle defs come after the edge defs
while (len(triangles) < nf):
e1, e2, e3 = [edges[int(xx)-1] for xx in get_next_line_not_comment(f).split()]
# get the 3 vertices, in order
v1_idx = e1.intersection(e2).pop()
v2_idx = e2.intersection(e3).pop()
v3_idx = e3.intersection(e1).pop()
new_t = (v1_idx,v2_idx,v3_idx)
triangles.append(new_t)
except IOError:
print("Bad GTS file.")
vertices, triangles = [], []
finally:
f.close()
return vertices, triangles
def get_vertices_from_gts(filename):
"""returns a list of vertices and the number of faces from a gts file."""
# first get the number of vertices, edges, faces
(nv, ne, nf), f = get_gts_info(filename, return_handle=True)
vertices = []
try:
while (len(vertices) < nv):
# convert to Vertex object
vx, vy, vz = [float(xx) for xx in get_next_line_not_comment(f).split()]
vertices.append(Vector(vx, vy, vz))
except IOError:
print("Bad GTS file.")
vertices = []
finally:
f.close()
return vertices
from pybeep import BEEP, Mesh, Vector, Quaternion
from geometry import _rand_rot
from constants import calculate_kappa
import sys
#running_output = open("ache-fas-pair.txt",'w')
#running_output.close()
Dsolvent = 80.0
Dprotein = 2.0
kappa = float(sys.argv[1])
GMRES_tolerance = 1e-6
GMRES_max_iterations = 100
no_rotation = Quaternion(1, 0, 0, 0)
centre_crystal_ache = Vector(35.3081, 17.9041, 169.832)
centre_crystal_fas = Vector(6.91911, 25.184, 168.836)
axis = (centre_crystal_fas - centre_crystal_ache)
crystal_separation = axis.length()
print(crystal_separation)
axis.normalise()
minimum_separation = 10.165
ache_location = Vector(0, 0, 0)
ache = "ache-fas-png1/1MAH-ache.7.mtz"
fas = "ache-fas-png1/1MAH-fas.10.mtz"
qual_pts = 0
quad_pts = 0
nbsize = 2200
for dummy in [0]:
def gts_overmesh(filename_in, filename_out):
"""Overmesh the mesh by subividing all triangles into 6 new triangles."""
# first get the number of vertices, edges, faces
(nv, ne, nf), f = get_gts_info(filename_in, return_handle=True)
vertices, triangles = [], []
mid_edge_vertices = {}
tri_norms = []
try:
while (len(vertices) < nv):
# convert to Vertex object
vx, vy, vz = [float(xx) for xx in get_next_line_not_comment(f).split()]
vertices.append(Vector(vx, vy, vz))
edges = []
# edges are defined as an ordered pair of vertices
while (len(edges) < ne):
edge_verts = get_next_line_not_comment(f).split()
edges.append( set([int(edge_verts[0])-1, int(edge_verts[1])-1]) )
# triangle defs come after the edge defs
while (len(triangles) < nf*6):
next_line = get_next_line_not_comment(f).split()
e1_idx, e2_idx, e3_idx = [int(xx)-1 for xx in next_line]
e1, e2, e3 = [edges[int(xx)-1] for xx in next_line]
# get the 3 vertices, in order
v1_idx = e1.intersection(e2).pop()
v2_idx = e2.intersection(e3).pop()
v3_idx = e3.intersection(e1).pop()
#new_t = (v1_idx,v2_idx,v3_idx)
t_centre = (vertices[v1_idx] + vertices[v2_idx] + vertices[v3_idx]) / 3.0
t_centre_idx = len(vertices)
vertices.append(t_centre)
# add new vertices to vertex list if necessary
def get_mid_edge_vertex(edge_idx):
try:
e_mid = mid_edge_vertices[edge_idx]
except KeyError:
e_mid = len(vertices)
v1_idx, v2_idx = edges[edge_idx]
vertices.append( (vertices[v1_idx] + vertices[v2_idx]) / 2.0)
mid_edge_vertices[edge_idx] = e_mid
return e_mid
def add_triangle(v1,v2,v3):
triangles.append( (v1,v2,v3) )
tri_norms.append( tnormal(vertices[v1],vertices[v2],vertices[v3]) )
add_triangle(v1_idx, t_centre_idx, get_mid_edge_vertex(e1_idx))
add_triangle(get_mid_edge_vertex(e1_idx), t_centre_idx, v3_idx)
add_triangle(v3_idx, t_centre_idx, get_mid_edge_vertex(e3_idx))
add_triangle(get_mid_edge_vertex(e3_idx), t_centre_idx, v2_idx)
add_triangle(v2_idx, t_centre_idx, get_mid_edge_vertex(e2_idx))
add_triangle(get_mid_edge_vertex(e2_idx), t_centre_idx, v1_idx)
except IOError:
print("Bad GTS file.")
finally:
f.close()
write_gts(filename_out,vertices, triangles)
return
#for n in range(cbase, cbase+len(scenario.crwdlist)):
# m = beep.get_library_mesh(n);
# r = m.get_radius()
# a = max(a, r)
a = maxcr # packed sphere radius
if a == 0.0:
a = scenario.parameters['ArenaGrainSize']
if a == 0.0 or a > scenario.radius: # Having no crowders is ok, use arena size
a = scenario.radius
# Build the arena
psa = PackedSphereArena(a, scenario.radius, scenario.centre)
log.info(f"Arena initialised with {psa.capacity()} packed spheres")
# Load BEEP with subject mesh instances as these persist
origin = Vector(0, 0, 0)
no_rotation = Quaternion(1, 0, 0, 0)
for s in range(cbase):
log.debug(f"Insert mesh instance {s}")
m = beep.insert_mesh_instance(s, scenario.locnlist[s][0], no_rotation,
scenario.parameters['Dprotein'])
log.info("Subject instances created, "
f"Dprotein={scenario.parameters['Dprotein']}")
# Outline of the rest of the program:
# For each subject-location
# Clear crowder instances
# Move the subjects to new locations
# For each crowder count
# Load the crowder instances
# MCMC loop: BEEP, propose crowder instance moves
def __init__(self, spec: TextIOWrapper):
# Public object attributes
self.centre = Vector(0.0, 0.0, 0.0)
self.radius = 0.0
self.subjlist = list()
self.crwdlist = list()
self.proplist = list()
self.locnlist = list()
self.rotnlist = list()
self.parameters = {
'ArenaRadius': -1,
'ArenaGrainSize': 0.0,
'ArenaCentre': None,
'CrowderRotate': True,
'RhoProtein': 1.35,
'RhoSolvent': 1.02,
'MCwarmup': -1,
'MCiter': -1,
'Dsolvent': 80.0,
'Dprotein': 2.0,
'Kappa': 0.102,
'GMREStol': 1e-6,
'GMRESmaxit': 100,
'QualPts': 4,
'QuadPts': 0,
'NbSize': 2200,
'Planar': False
}
self._paramTypes = {
'ArenaRadius': float,
'ArenaGrainSize': float,
'ArenaCentre': Vector,
'CrowderRotate': strtobool,
'RhoProtein': float,
'RhoSolvent': float,
'MCwarmup': int,
'MCiter': int,
'Dsolvent': float,
'Dprotein': float,
'Kappa': float,
'GMREStol': float,
'GMRESmaxit': int,
'QualPts': int,
'QuadPts': int,
'NbSize': int,
'Planar': bool
}
# Read scenario specification file
lastmatch = 0 # Type of active configuration line last matched
n = 0
for line in spec:
n += 1
if len(line.split()) == 0 or line.split()[0][0] == '#':
continue
ml = self._subjre.match(line)
if ml:
lastmatch = 1 # Subject code
self.subjlist += [ml.group(1)]
self.locnlist += [Scenario._makeVectorRange(ml, 2)]
self.rotnlist += [Scenario._makeQuaternionRange(ml, 11)]
continue
ml = self._contre.match(line)
if ml:
if lastmatch != 1:
log.warning(f"Continuation line out of order, "
f"line {n} -- ignored")
continue
self.locnlist[-1] += Scenario._makeVectorRange(ml, 1)
self.rotnlist[-1] += Scenario._makeQuaternionRange(ml, 10)
continue
mc = self._crwdre.match(line)
if mc:
lastmatch = 2 # Crowder code
self.crwdlist += [mc.group(1)]
self.proplist += [Scenario._makeRange(mc, 2, 3, 4)]
continue
mp = self._parmre.match(line)
if mp:
lastmatch = 3 # Parameter code
if mp.group(1) in self.parameters:
self.parameters[mp.group(1)] = \
self._paramTypes[mp.group(1)](mp.group(2))
else:
log.warning(f"Unrecognised parameter {mp.group(1)}, "
f"line {n} -- ignored")
log.debug(f"parameter {mp.group(1)}="
f"{self.parameters[mp.group(1)]}, line {n}")
else:
log.warning(f"Invalid line [{n}] in scenario specification: "
f"{line} -- ignored")
# Extend the shorter lists so all are the same length
llen = Scenario._makeSameLength(self.locnlist + self.rotnlist)
plen = Scenario._makeSameLength(self.proplist)
# Scenario specification checks
# There has to be at least one subject protein
if len(self.subjlist) == 0:
log.error("No subject proteins in specification")
exit(1)
# Ensure crowder proportions are in [0,1]
# Divide by the largest sum of proportions if outside this
maxsum = max([0] + \
[sum([x[n] for x in self.proplist]) for n in range(plen)])
if maxsum > 1:
log.warning(f"Maximum proportions {maxsum} greater than one "
"- corrected")
self.proplist = [[y / maxsum for y in x] for x in self.proplist]
# Calculate the arena radius and the centre if not provided
n = sum([len(locn) for locn in self.locnlist])
maxsep = 0.0
for i in range(len(self.locnlist)):
for u in self.locnlist[i]:
self.centre += u
for j in range(i + 1, len(self.locnlist)):
for v in self.locnlist[j]:
maxsep = max(maxsep, (u - v).length())
if maxsep == 0.0:
maxsep = 2 / 3 # to get a default of 1.0 below
self.centre /= n
if self.parameters['ArenaCentre'] != None:
self.centre = self.parameters['ArenaCentre']
if self.parameters['ArenaRadius'] <= 0:
self.radius = 3 * maxsep / 2 # Default value
else:
self.radius = self.parameters['ArenaRadius']
log.debug(f"Arena radius {self.radius}, centre {self.centre}")
def pack(crowdant_radius, volume_fraction, distance_limit, forbidden, minimum_separation):
"""pack a load of spherical crowders around a set of existing spherical objects, to a
specified distance_limit with specified total volume_fraction occluded (approx.)"""
# centroid of the forbidden set
centroid = Vector(0,0,0)
for xx,rad in forbidden:
centroid += xx
centroid /= len(forbidden)
# semi-axis limits -- centroid to furthest point in forbidden set
dists = [(xx-centroid).length()+radx for (xx,radx) in forbidden]
edge_length = max(dists)*2 + distance_limit*2 + crowdant_radius*4
volume = edge_length ** 3
# calculate number required to reach specified volume fraction
individual_vol = (4. / 3.) * pi * crowdant_radius ** 3
target_vol = volume * volume_fraction
n = int(ceil(target_vol / individual_vol))
# now loop
centres = forbidden[:]
num_added = 0
iterations_since_successful_addition = 0
while (num_added < n and iterations_since_successful_addition < 10000):
new_pt = _rand_xyz(edge_length) + centroid
ok = True
for xx,r in centres:
if ((new_pt - xx).length() < (minimum_separation+crowdant_radius+r)):
ok = False
break
if ok:
iterations_since_successful_addition = 0
num_added += 1
centres.append((new_pt,crowdant_radius))
else:
iterations_since_successful_addition += 1
##rot = Quaternion(0,0,0,0)
#for ctr,(pt,d) in enumerate(centres):
##rot = _rand_rot()
#rot = Quaternion(0,0,0,0)
#print "<instance instance_id=%d mesh_id=0 conformation=0 x=%f y=%f z=%f a=%f b=%f c=%f d=%f/>" %(ctr, pt.x, pt.y, pt.z, rot.x, rot.y, rot.z, rot.w)
##print "%f %f %f" %(pt.x, pt.y, pt.z)
#print
final_vol_fraction = num_added * individual_vol / volume
print("Added %d crowders, reached volume fraction of %f" %(num_added, final_vol_fraction))
centres = centres[len(forbidden):]
print("Culling anything further than %f from the forbidden range" %(distance_limit))
# utility function- returns true if the point/radius is further than
# distance_limit from any object in forbidden (NB: could use lambda
# function here)
def cull_function(x,r):
dists = [(x - fx).length()-fr-r for fx,fr in forbidden]
return (min(dists) < distance_limit)
# cull using list comprehension
centres = [x for x,r in centres if cull_function(x,r)]
print("%d crowders remain" %(len(centres)))
return centres
log.error(f"Integer not found for face count, line {n}")
exit(1)
if fn % 2 != 0:
log.error(f"Weird face count {fn}, line {n}")
exit(1)
elif line[0:10] == "end_header":
en = int(3 * fn / 2)
print(f"{vn} {en} {fn} GtsSurface GtsFace GtsEdge GtsVertex",
file=out)
state = 1
# Vertices
elif state == 1:
ll = line.split()
print(f"{ll[0]} {ll[1]} {ll[2]}", file=out)
try:
vertex.append(Vector(*[float(ll[i]) for i in range(3)]))
except:
log.error(f"Bad vertex {ll[0:3]}, line {n}")
exit(1)
vn -= 1
if vn == 0:
state = 2
# Faces, er, edges
elif state == 2:
ll = line.split()
if ll[0] != "3":
log.error(f"Weird face vertex count {ll[0]}, line {n}")
exit(1)
# define and store unique edges and define faces in terms of these
try:
vix = [int(ll[i]) for i in range(1, 4)]
loglevel = args['loglevel']
logstream = args['log']
ifs = args['in']
ofs = args['out']
if args['fmt'] == 'pdb':
fmt = 0
ofmt = str().join(["{:8.3f}" for i in range(3)]) # [-999.999,9999.999]
elif args['fmt'] == 'xyz':
fmt = 1
ofmt = " ".join(["{:.6f}" for i in range(3)])
else:
print(f"This should not have happened - bad format {args['fmt']}")
exit(1)
beg = args['beg']
end = args['end']
ax = [Vector(*args['axis'][i]) for i in range(2)]
qa = ax[0].cross(ax[1]) # a for axis
qd = ax[0].dot(ax[1]) # d for dot
# To get half-way, add (1,0,0,0) but ql not normalised yet, so adjust unit
unit = sqrt(qd * qd + qa.length2())
ql = Quaternion(unit + qd, qa.x, qa.y, qa.z)
ql.normalise()
# Set up logging - if to stdout, assume caller handles time and module name
if logstream == stdout:
lfmt = "%(levelname)s:%(message)s"
else:
lfmt = "%(asctime)s %(module)s %(levelname)s:%(message)s"
log.basicConfig(stream=logstream,
format=lfmt,
level=getattr(log, loglevel.upper()))
def msms_remesh(msms_vertex_filename, gts_filename):
"""Triangulate an MSMS vertex list to GTS format."""
vertices, normals = get_clean_msms_vertices(msms_vertex_filename)
# get centre of set of points
centre = Vector(0,0,0)
for v in vertices:
centre += v
centre = centre / len(vertices)
# get maximum xyz extent of set of points
maxdim = max([ (v - centre).length() for v in vertices ])
patch_vertex_list = [ [] for v in vertices ]
# insert vertices into an Octree
max_neighbours = 100
adaptive_tree = Octree(max_neighbours, Vector(centre.x, centre.y, centre.z), maxdim*2)
for i,(v,n) in enumerate(zip(vertices,normals)):
adaptive_tree.insert(Vector(v.x, v.y, v.z))
def get_neighbourlist(idx):
near_pts = [0]*(max_neighbours)
try:
num = adaptive_tree.get(idx,near_pts)
except IndexError:
print("IndexError: %d (%d vertices)" %(idx, len(vertices)))
raise IndexError
#print near_pts
near_pts = [pt for pt in near_pts[:num] if pt != idx]
return near_pts
for working_idx,(v,vn) in enumerate(zip(vertices, normals)):
near_pts = get_neighbourlist(working_idx)
# select set of working points which define this patch
proximity_scores = []
for pt_idx in near_pts:
pt = vertices[pt_idx]
r = (pt - v)
score = (r.length()**2) / (1.0 - r.normalised().dot(vn))
proximity_scores.append( (score, pt_idx) )
proximity_scores.sort()
closest = proximity_scores[0][1]
points = [closest]
near_pts.remove(closest)
while True:
if len(points) == 3:
near_pts.append(points[0])
# now find the next point which best forms a triangle
for pt_idx in near_pts:
pt = vertices[pt_idx]
r = (pt - v)
score = (r.length()**2) / (1.0 - r.normalised().dot(vn))
proximity_scores.append( (score, pt_idx) )
proximity_scores.sort()
closest = proximity_scores[0][1]
return
def upsample_fh_vals(low_res_mesh, high_res_mesh, low_res_results, high_res_results):
"""Forces all vertices in the mesh_to_realign to lie on the surface defined by reference_mesh."""
low_res_results = [(float(x.split()[0]), float(x.split()[1])) for x in open(low_res_results,'r').readlines()]
high_res_out = open(high_res_results, 'w')
low_res_vertices, low_res_triangles = get_vertices_triangles_from_gts(low_res_mesh)
high_res_vertices, high_res_triangles = get_vertices_triangles_from_gts(high_res_mesh)
# get centre of set of points
centre = Vector(0,0,0)
for v in low_res_vertices:
centre += v
centre = centre / len(low_res_vertices)
# get maximum xyz extent of set of points
maxdim = max(max([ (v - centre).length() for v in high_res_vertices ]),
max([ (v - centre).length() for v in low_res_vertices ])
)
# insert reference vertices into an Octree
max_neighbours = 27
adaptive_tree = Octree(max_neighbours, Vector(centre.x, centre.y, centre.z), maxdim*2)
for i,v in enumerate(low_res_vertices):
v.uid = i # Vector is python object so can add an attribute
adaptive_tree.insert(v)
new_vertices = []
for i,v in enumerate(high_res_vertices):
closest_vertex = adaptive_tree.nearest(v)
closest_original_vertex = -1
for ii,vv in enumerate(low_res_vertices):
if ((closest_vertex - vv).length() < 1e-6):
closest_original_vertex = ii
break
if (closest_original_vertex == -1):
print("Failed to find closest vertex.")
raise Exception
#print "dist to closest vertex: ", (low_res_vertices[closest_original_vertex] - v).length()
possible_triangles = [t for t in low_res_triangles if closest_original_vertex in t]
if len(possible_triangles) == 0:
print(v, centre, maxdim*2)
print(v, closest_original_vertex, low_res_vertices[closest_original_vertex], (low_res_vertices[closest_original_vertex] - v).length())
raise Exception
vert_checklist = []
for t in possible_triangles:
for v_idx in t:
if v_idx == closest_original_vertex: continue
if v_idx not in vert_checklist:
vert_checklist.append(v_idx)
def get_closest_vertex_from_list(v, vlist):
vert_dists = [ ( (v - low_res_vertices[vert_chk]).length(), vert_chk)
for vert_chk in vlist]
vert_dists.sort()
#print "sorted list: ", vert_dists
return vert_dists[0][1]
second_closest_vertex = get_closest_vertex_from_list(v, vert_checklist)
possible_triangles = [t for t in possible_triangles
if second_closest_vertex in t]
vert_checklist = []
for t in possible_triangles:
for v_idx in t:
if v_idx == closest_original_vertex: continue
if v_idx == second_closest_vertex: continue
if v_idx not in vert_checklist:
vert_checklist.append(v_idx)
third_closest_vertex = get_closest_vertex_from_list(v, vert_checklist)
closest_triangles = [t for t in possible_triangles
if third_closest_vertex in t]
ct = closest_triangles[0]
#print ct
# at this point we have a vertex v which needs projecting onto a point
# within the triangle defined by "ct"
v1 = low_res_vertices[ct[0]]
v2 = low_res_vertices[ct[1]]
v3 = low_res_vertices[ct[2]]
v1f = low_res_results[ct[0]][0]
v1h = low_res_results[ct[0]][1]
v2f = low_res_results[ct[1]][0]
v2h = low_res_results[ct[1]][1]
v3f = low_res_results[ct[2]][0]
v3h = low_res_results[ct[2]][1]
new_x_axis = (v2-v1).normalised()
new_y_axis = (v3-v1).normalised()
pt_from_v1 = v - v1
new_f = v1f + pt_from_v1.dot(new_x_axis)*(v2f-v1f) + pt_from_v1.dot(new_y_axis)*(v3f-v1f);
new_h = v1h + pt_from_v1.dot(new_x_axis)*(v2h-v1h) + pt_from_v1.dot(new_y_axis)*(v3h-v1h);
print(new_f, new_h, file=high_res_out)
high_res_out.close();
return
def msms2gts(msms_vertex_filename, msms_face_filename, gts_filename):
"""Convert msms files to gts format (Gnu Triangulated Surface)"""
vfloat = [line.split() for line in open(msms_vertex_filename,'r') if line[0] != '#']
# delete the first lines of each list, which are column totals
vfloat.remove(vfloat[0])
vertices = []
normals = []
for vertex_descriptor in vfloat:
x,y,z,xn,yn,zn = [float(v) for v in vertex_descriptor[:6]]
vertices.append( Vector(x,y,z) )
normals.append( Vector(xn,yn,zn) )
# get centre of set of points
centre = Vector(0,0,0)
for v in vertices:
centre += v
centre /= len(vertices)
# get maximum xyz extent of set of points
maxdim = max([ (v - centre).length() for v in vertices ])
# insert vertices into an Octree
max_neighbours = 27
adaptive_tree = Octree(max_neighbours, Vector(centre.x, centre.y, centre.z), maxdim*2)
duplicates = []
ctr = 0
mappingA = {}
mappingB = {}
for i,(v,n) in enumerate(zip(vertices,normals)):
# check for duplicate already in tree
pre_existing = adaptive_tree.check_for_duplicate(v)
if (pre_existing == -1):
mappingA[i] = ctr
mappingB[ctr] = i
adaptive_tree.insert(v)
ctr += 1
else:
pre_existing_idx = mappingB[pre_existing]
print("Clash between %d %s %s and %d %s %s" %(i, v, n, pre_existing_idx, vertices[pre_existing_idx], normals[pre_existing_idx]))
duplicates.append(i)
mappingA[i] = pre_existing
vertices = [v for i,v in enumerate(vertices) if i not in duplicates]
normals = [n for i,n in enumerate(normals) if i not in duplicates]
tri = [line.split() for line in open(msms_face_filename,'r') if line[0] != '#']
tri = [[int(float(t))-1 for t in tri_def] for tri_def in tri]
tri.remove(tri[0])
print("Number of vertices: ", len(vertices))
print("Number of normals: ", len(normals))
#new_tri = tri[:]
new_tri = []
for i,t in enumerate(tri):
#print t[0]
new_v1 = mappingA[t[0]]
new_v2 = mappingA[t[1]]
new_v3 = mappingA[t[2]]
if (new_v1 in (new_v2, new_v3) or
new_v2 in (new_v1, new_v3) or
new_v3 in (new_v1, new_v2)
):
print("skipped a dud triangle (%d) " %(i), t)
continue
new_tri.append([new_v1, new_v2, new_v3])
# write the gts file
write_gts(gts_filename, vertices, new_tri)
return
# Module utilities
def _asString(v: Vector) -> str:
return "(%f, %f, %f)" % (v.x, v.y, v.z)
def intRef(coord: float, radius: float):
return int((coord + radius) // (2 * radius))
# Declare the subclass status
#PackedSphereArena.register(Arena)
# No main program, so used for testing
if __name__ == "__main__":
log.basicConfig(level=getattr(log, "DEBUG"))
psa = PackedSphereArena(1, 10, Vector(0, 0, 0))
print("Capacity starting at ", psa.capacity())
(v, ref) = psa._occupy(0, 1, 0)
print("Occupied at ", v, ref)
(v, ref2) = psa.move(ref, vacant=2)
print("Moved to ", v, ref2)
(v, ref3) = psa.move(ref2, to=ref)
print("Moved back to ", v, ref3)
print("isOccupied=", psa.isOccupied(v))
print("Capacity is now ", psa.capacity())
print(f"Ref for {v} is ", psa._getRef(v))
try:
psa.occupy(ref, 1, 0)
print("No collision")
except:
print("Error: collision detected")
def align_mesh_to_reference(reference_mesh, mesh_to_realign):
"""Forces all vertices in the mesh_to_realign to lie on the surface defined by reference_mesh."""
ref_vertices, ref_triangles = get_vertices_triangles_from_gts(reference_mesh)
vertices, triangles = get_vertices_triangles_from_gts(mesh_to_realign)
# get centre of set of points
centre = Vector(0,0,0)
for v in ref_vertices:
centre += v
centre = centre / len(ref_vertices)
# get maximum xyz extent of set of points
maxdim = max(max([ (v - centre).length() for v in vertices ]),
max([ (v - centre).length() for v in ref_vertices ])
)
# insert reference vertices into an Octree
max_neighbours = 27
adaptive_tree = Octree(max_neighbours, Vector(centre.x, centre.y, centre.z), maxdim*2)
for i,v in enumerate(ref_vertices):
adaptive_tree.insert(Vector(v.x, v.y, v.z))
new_vertices = []
for i,v in enumerate(vertices):
closest_original_vertex = adaptive_tree.get_uid_closest_to(v)
#print "dist to closest vertex: ", (ref_vertices[closest_original_vertex] - v).length()
possible_triangles = [t for t in ref_triangles if closest_original_vertex in t]
if len(possible_triangles) == 0:
print(v, centre, maxdim*2)
print(v, closest_original_vertex, ref_vertices[closest_original_vertex], (ref_vertices[closest_original_vertex] - v).length())
raise Exception
vert_checklist = []
for t in possible_triangles:
for v_idx in t:
if v_idx == closest_original_vertex: continue
if v_idx not in vert_checklist:
vert_checklist.append(v_idx)
def get_closest_vertex_from_list(v, vlist):
vert_dists = [ ( (v - ref_vertices[vert_chk]).length(), vert_chk)
for vert_chk in vlist]
vert_dists.sort()
#print "sorted list: ", vert_dists
return vert_dists[0][1]
second_closest_vertex = get_closest_vertex_from_list(v, vert_checklist)
possible_triangles = [t for t in possible_triangles
if second_closest_vertex in t]
vert_checklist = []
for t in possible_triangles:
for v_idx in t:
if v_idx == closest_original_vertex: continue
if v_idx == second_closest_vertex: continue
if v_idx not in vert_checklist:
vert_checklist.append(v_idx)
third_closest_vertex = get_closest_vertex_from_list(v, vert_checklist)
closest_triangles = [t for t in possible_triangles
if third_closest_vertex in t]
ct = closest_triangles[0]
#print ct
# at this point we have a vertex v which needs projecting onto a point
# within the triangle defined by "ct"
v1 = ref_vertices[ct[0]]
v2 = ref_vertices[ct[1]]
v3 = ref_vertices[ct[2]]
norm = tnormal(v1,v2,v3)
new_z_axis = norm
new_x_axis = (v2-v1).normalised()
new_y_axis = new_z_axis.cross(new_x_axis).normalised()
pt_from_v1 = v - v1
projected_pt = v1 + (new_x_axis * pt_from_v1.dot(new_x_axis)) + \
(new_y_axis * pt_from_v1.dot(new_y_axis))
assert( (projected_pt - v1).dot(norm) < 1e-3 )
assert( (projected_pt - v2).dot(norm) < 1e-3 )
assert( (projected_pt - v3).dot(norm) < 1e-3 )
new_vertices.append(projected_pt)
#vertices[i] = projected_pt
# if ((projected_pt - v).length() > 1e-3):
# print "moved vertex by: ", (projected_pt - v).length()
tnormals = [tnormal(new_vertices[t[0]],new_vertices[t[1]], new_vertices[t[2]])
for t in triangles]
write_gts(mesh_to_realign, new_vertices, triangles)
return
