def hook6(lattice):
global nwateratoms
lattice.logger.info("Hook6: Output water molecules in Yaplot format.")
lattice.logger.info(" Total number of atoms: {0}".format(
len(lattice.atoms)))
# prepare the reverse dict
waters = defaultdict(dict)
for atom in lattice.atoms:
resno, resname, atomname, position, order = atom
if "O" in atomname:
waters[order]["O"] = position
elif "H" in atomname:
if "H0" not in waters[order]:
waters[order]["H0"] = position
else:
waters[order]["H1"] = position
s = ""
s += yp.Color(3)
for order, water in waters.items():
O = water["O"]
H0 = water["H0"]
H1 = water["H1"]
s += yp.Layer(4)
s += yp.Color(3)
s += yp.Size(0.03)
s += yp.Circle(O)
s += yp.Line(O, H0)
s += yp.Line(O, H1)
s += yp.Size(lattice.yaplot_size_H)
s += yp.Circle(H0)
s += yp.Circle(H1)
s += yp.Color(2)
s += yp.Layer(1)
s += yp.Text(O, "{0}".format(order))
s += yp.Layer(3)
s += yp.Color(4)
s += yp.ArrowType(1)
s += yp.Size(0.03)
for i, j in lattice.spacegraph.edges(data=False):
if i in waters and j in waters: # edge may connect to the dopant
O = waters[j]["O"]
H0 = waters[i]["H0"]
H1 = waters[i]["H1"]
d0 = H0 - O
d1 = H1 - O
rr0 = np.dot(d0, d0)
rr1 = np.dot(d1, d1)
if rr0 < rr1 and rr0 < 0.245**2:
s += yp.Arrow(H0, O)
if rr1 < rr0 and rr1 < 0.245**2:
s += yp.Arrow(H1, O)
print(s, end="")
nwateratoms = len(lattice.atoms)
lattice.logger.info("Hook6: end.")
def main():
import sys
groname, twiname = sys.argv[1:3]
with open(twiname) as twifile:
with open(groname) as grofile:
while True:
if groname[-4:] == ".pdb":
gr = pdb.PDB(grofile, "O", "H", resname="WAT")
else:
# assume it is gromacs
gr = gro.Gromacs(grofile, "Ow", "Hw", "Mw")
btw = btwc.load_BTWC(twifile)
if btw is None or gr is None:
break
celli = np.linalg.inv(gr.cell)
# relative coord
rs = np.array([np.dot(x, celli) for x in gr.solutes])
ro = np.array([np.dot(x, celli) for x in gr.waters])
print(len(rs))
print(len(ro))
grid = pl.determine_grid(gr.cell, 0.245)
shell1 = np.vstack(
pl.pairs_fine_hetero(rs,
ro,
0.4,
gr.cell,
grid,
distance=False))
# some solute atoms are isolated from water.
shell1s = set(shell1[:, 0])
shell1w = set(shell1[:, 1])
#show all bonds in yaplot
s = ""
for i in range(-10, 0):
s += yap.SetPalette(i + 10 + 3, 255 * (-i) // 10, 0, 0)
for i in range(11):
s += yap.SetPalette(i + 10 + 3, 0, 0, 255 * i // 10)
for b in btw:
i, j = b[0]
if i in shell1w or j in shell1w:
s += yap.Layer(1)
else:
s += yap.Layer(2)
r = abs(b[2])
sine = b[2].imag
s += yap.Size(r)
s += yap.Color(int(sine * 10) + 10 + 3)
s += yap.Circle(b[1])
print(s)
def hook2(lattice):
logger = getLogger()
logger.info("Hook2: Show rings in Yaplot format.")
# copied from svg_poly
graph = nx.Graph(lattice.graph) #undirected
cellmat = lattice.repcell.mat
s = ""
s += yp.Layer(2)
s += yp.Color(0)
for i, j in graph.edges():
pi, pj = lattice.reppositions[i], lattice.reppositions[j]
d = pj - pi
d -= np.floor(d + 0.5)
s += yp.Line(pi @ cellmat, (pi + d) @ cellmat)
for ring in cr.CountRings(graph, pos=lattice.reppositions).rings_iter(
lattice.largestring):
deltas = np.zeros((len(ring), 3))
d2 = np.zeros(3)
for k, i in enumerate(ring):
d = lattice.reppositions[i] - lattice.reppositions[ring[0]]
d -= np.floor(d + 0.5)
deltas[k] = d
comofs = np.sum(deltas, axis=0) / len(ring)
deltas -= comofs
com = lattice.reppositions[ring[0]] + comofs
com -= np.floor(com)
# rel to abs
com = np.dot(com, cellmat)
deltas = np.dot(deltas, cellmat)
s += face(com, deltas)
print(s)
logger.info("Hook2: end.")
def face(center, rpos):
pos = rpos + center
n = rpos.shape[0]
s = yp.Color(n)
s += yp.Layer(n)
s += yp.Polygon(pos)
return s
def hook1(lattice):
lattice.logger.info("Hook1: Diffraction.")
lattice.logger.info(" 3D FFT.")
cellmat = lattice.repcell.mat
atoms = lattice.reppositions - np.floor(lattice.reppositions)
grid = [32, 32, 32]
distrib = np.zeros(grid)
grid = np.array(grid)
iatoms = np.array(np.floor(atoms * grid), dtype=int)
for x, y, z in iatoms:
distrib[x, y, z] += 1
diffr = np.fft.fftn(distrib, axes=(0, 1, 2))
power = np.real(diffr * np.conj(diffr)) / len(atoms)
lattice.logger.info(" Rendering in Yaplot format.")
cnt = contour3d.Contour(power, pbc=True, center=True)
cnt.double()
s = ""
for layer, threshold in enumerate(lattice.thresholds):
s += yp.Color(layer + 3)
s += yp.Layer(layer + 1)
nfacet = 0
#for face in cnt.facets(threshold):
for face in cnt.contour_flakes(threshold):
s += yp.Polygon(face)
nfacet += 1
lattice.logger.info(
" {0} facets rendered for threshold {1}.".format(
nfacet, threshold))
print(s)
lattice.logger.info("Hook1: end.")
def hook7(lattice):
global nwateratoms
lattice.logger.info("Hook7: Output water molecules in Yaplot format.")
lattice.logger.info(" Total number of atoms: {0}".format(
len(lattice.atoms)))
gatoms = lattice.atoms[nwateratoms:]
palettes = dict()
s = ""
s += yp.Layer(4)
s += yp.ArrowType(1)
H = []
O = ""
for atom in gatoms:
resno, resname, atomname, position, order = atom
if atomname in palettes:
pal = palettes[atomname]
else:
pal = 4 + len(palettes)
palettes[atomname] = pal
s += yp.Color(pal)
s += yp.Size(0.04)
s += yp.Circle(position)
s = '#' + "\n#".join(lattice.doc) + "\n" + s
print(s)
lattice.logger.info("Hook7: end.")
def hook1(lattice):
lattice.logger.info("Hook1: Draw the cell in Yaplot format.")
s = yp.Layer(2)
x, y, z = lattice.repcell.mat
for p, q, r in ((x, y, z), (y, z, x), (z, x, y)):
for a in (np.zeros(3), p, q, p + q):
s += yp.Line(a, a + r)
print(s, end="")
lattice.logger.info("Hook1: end.")
def hook2(lattice):
global options
logger = getLogger()
logger.info("Hook2: Petal statistics.")
database = options.database
if database is None:
logger.info(" Using temporary database. (volatile)")
gc = graphstat.GraphStat()
elif database[:4] == "http":
logger.info(" Using MySQL: {0}".format(database))
gc = graphstat_mysql.GraphStat(database)
else:
logger.info(" Using local Sqlite3: {0}".format(database))
import os.path
create = not os.path.isfile(database)
if create:
logger.info(" Create new DB.")
gc = graphstat_sqlite3.GraphStat(database, create=create)
cell = lattice.repcell.mat
positions = lattice.reppositions
graph = nx.Graph(lattice.graph) #undirected
rings, subgraphs, rings_at = prepare(graph, positions)
gids = collect(subgraphs, gc)
if options.json:
# In JSON, a key must be a string.
ids = {str(i): gids[i] for i in gids}
print(json.dumps(ids, indent=2, sort_keys=True))
elif options.yaplot:
# Draw top 10 most popular petal types with Yaplot.
count = defaultdict(int)
typical = dict()
for node in gids:
count[gids[node]] += 1
typical[gids[node]] = node
top10 = sorted(count, key=lambda gid: -count[gid])[:30]
ranks = {gid: i for i, gid in enumerate(top10)}
for i, gid in enumerate(ranks):
node = typical[gid]
logger.info(" Ranking {0}: {2} x {1} (id {3})".format(
i, [len(rings[ringid]) for ringid in rings_at[node]],
count[gid], gid))
s = ""
for node in gids:
gid = gids[node]
if gid in ranks:
rank = ranks[gid]
s += yp.Color(rank + 3)
s += yp.Layer(rank + 1)
for ringid in rings_at[node]:
s += draw_ring(rings[ringid],
positions,
cell=cell,
center=positions[node])
print(s)
logger.info("Hook2: end.")
def draw_water(water, povray=False):
s = ""
if povray:
s += pov.Sphere(water[0], r="RH", material="MATH")
s += pov.Sphere(water[1], r="RH", material="MATH")
s += pov.Sphere(water[2], r="RO", material="MATO")
s += pov.Cylinder(water[0], water[2], r="ROH", material="MATOH")
s += pov.Cylinder(water[1], water[2], r="ROH", material="MATOH")
else:
s += yp.Layer(1)
s += yp.Color(5)
s += yp.Size(0.2)
s += yp.Circle(water[0])
s += yp.Circle(water[1])
s += yp.Color(4)
s += yp.Size(0.4)
s += yp.Circle(water[2])
s += yp.Color(2)
d0 = water[0] - water[2]
L0 = np.linalg.norm(d0)
s += yp.Line(water[2] + d0 / L0 * 0.4, water[0] - d0 / L0 * 0.2)
d1 = water[1] - water[2]
L1 = np.linalg.norm(d1)
s += yp.Line(water[2] + d1 / L1 * 0.4, water[1] - d1 / L1 * 0.2)
# draw a tetrahedron
y = water[1] - water[0]
z = (water[1] + water[0]) / 2 - water[2]
x = np.cross(y, z)
x /= np.linalg.norm(x)
y /= np.linalg.norm(y)
z /= np.linalg.norm(z)
com = (water[1] + water[0] + water[2] * 16) / 18
R = 2.76 / 2
a = y * (2 / 3)**0.5 + z * (1 / 3)**0.5
b = -y * (2 / 3)**0.5 + z * (1 / 3)**0.5
c = x * (2 / 3)**0.5 - z * (1 / 3)**0.5
d = -x * (2 / 3)**0.5 - z * (1 / 3)**0.5
s += yp.Layer(2)
for e, f in it.combinations((a, b, c, d), 2):
s += yp.Line(com + e * R, com + f * R)
return s
def to_yaplot(cellmat, rpos, anions, cations, G, cation="N", anion="F"):
"""
cellmat: セル行列(後置記法)
rpos: 分子のセル内相対位置
anions: アニオン番号
cations: カチオン番号
G: 水素結合ネットワーク
"""
# 水分子の原子位置
water = tip4picesites()
s = ""
for mol in G:
if mol not in anions and mol not in cations:
# genuine water molecule.
rO = rpos[mol]
H1, H2 = G[mol]
rH1 = rpos[H1] - rO
rH1 -= np.floor(rH1 + 0.5)
rH2 = rpos[H2] - rO
rH2 -= np.floor(rH2 + 0.5)
# 実座標 (angstrom)
pO = rO @ cellmat
pH1 = rH1 @ cellmat
pH2 = rH2 @ cellmat
ey = pH1 - pH2
ez = pH1 + pH2
ex = np.cross(ey, ez)
# 分子内座標方向の単位ベクトル
ex /= np.linalg.norm(ex)
ey /= np.linalg.norm(ey)
ez /= np.linalg.norm(ez)
# 回転行列
R = np.array([ex, ey, ez])
# 水分子の原子位置
intra = water @ R + pO
s += draw_water(intra)
s += yp.Layer(3)
s += yp.Size(0.5)
s += yp.Color(6)
for mol in G:
if mol in anions:
pos = rpos[mol] @ cellmat
s += yp.Circle(pos)
s += yp.Size(0.3)
s += yp.Color(7)
for mol in G:
if mol in cations:
pos = rpos[mol] @ cellmat
s += yp.Circle(pos)
s += yp.NewPage()
return s
def hook2(lattice):
global nwateratoms
if lattice.yaplot_size_H > 0:
return
lattice.logger.info(
"Hook2: Output CoM of water molecules in Yaplot format.")
# prepare the reverse dict
waters = defaultdict(dict)
pos = lattice.reppositions @ lattice.repcell.mat
s = ""
for p in pos:
s += yp.Layer(4)
s += yp.Color(3)
s += yp.Size(0.03)
s += yp.Circle(p)
print(s, end="")
lattice.logger.info("Hook2: end.")
return True
def draw_cell(voro_cell, box, kind=0):
layer = kind + 2
if layer > 30:
layer = 30
# draw frame
s = yp.Layer(layer)
s += yp.Color(0)
origin = voro_cell['original']
voro_vertices = voro_cell['vertices']
voro_faces = voro_cell['faces']
g = voro_cell['graph']
for i, j in g.edges():
di = voro_vertices[i] - origin
dj = voro_vertices[j] - origin
s += yp.Line(origin + di * 0.9, origin + dj * 0.9)
# draw faces
s += yp.Color(kind + 10)
for face in voro_faces:
points = []
for point in face['vertices']:
d = voro_vertices[point] - origin
points.append(d * 0.89 + origin)
s += yp.Polygon(points)
return s
def main():
basicConfig(level=INFO, format="%(levelname)s %(message)s")
logger = getLogger()
every = 1
maxval = 1.0
adjdens = False
while sys.argv[1][0] == "-":
if sys.argv[1] == "-e":
sys.argv.pop(1)
every = int(sys.argv[2])
sys.argv.pop(1)
elif sys.argv[1] == "-v":
maxval = float(sys.argv[2])
sys.argv.pop(1)
sys.argv.pop(1)
elif sys.argv[1] == "-a":
adjdens = True
sys.argv.pop(1)
else:
usage()
gcell, gatoms = LoadGRO(open(sys.argv[1])) # in AA, in AA
ucell, uatoms = LoadGRO(open(sys.argv[2])) # in AA
dens0 = gatoms.shape[0] / np.linalg.det(gcell)
dens1 = uatoms.shape[0] / np.linalg.det(ucell)
ratio = (dens1 / dens0)**(1. / 3.)
if adjdens:
logger.info(f"Scaling ratio: {ratio}")
ucell *= ratio
uatoms *= ratio
gcelli = np.linalg.inv(gcell)
ucelli = np.linalg.inv(ucell)
mode = ""
if len(sys.argv) > 3:
mode = sys.argv[3]
s = ""
s += yp.Color(2)
s += yp.Layer(1)
origin = np.zeros(3)
s += drawbox(origin, gcell, halfshift=False)
#in absolute coord
# unitatoms = np.dot(unitatoms, ucell)
#s += unitatoms)
#s = ""
nline = 0
matched = set()
palette = dict()
while True:
line = sys.stdin.readline()
if len(line) == 0:
break
nline += 1
#parse the line
cols = line.split()
if len(cols) < 13:
break
# 2018-4-9 New output format of matcher.c
msd = float(cols[0])
gcenter = gatoms[int(cols[1])].copy() #atom at the matching center
gcenter -= np.floor(gcenter @ gcelli) @ gcell
ucenter = int(cols[2])
rotmat = np.array([float(x) for x in cols[3:12]]).reshape((3, 3))
N = int(cols[12])
if len(cols) < 13 + N:
break
irot = np.linalg.inv(rotmat)
members = [int(x) for x in cols[13:N + 13]]
#draw matched box
# roll the unit cell to center (abs)
rel = uatoms - uatoms[ucenter]
rel -= np.floor(rel @ ucelli + 0.5) @ ucell
# rel to abs
Slid = rel
# rotate box
Rotucell = ucell @ rotmat
#
Boxslide = -uatoms[ucenter] @ rotmat + gcenter
# rotate atoms in the unit cell
Slidunit = (Slid @ rotmat) + gcenter
#s += yp.Color(3)
if mode == "R":
color = direction2color(rotmat[0] + rotmat[1] + rotmat[2])
elif mode == "T":
color = direction2color(rotmat[2])
else:
color = (0, 3, 0) #green
if color not in palette:
palette[color] = len(palette) + 6
s += yp.SetPalette(palette[color], color[0] * 255 // 3,
color[1] * 255 // 3, color[2] * 255 // 3)
if msd < maxval:
matched |= set(members)
if every != 0 and nline % every == 0 and msd < maxval:
s += yp.Color(palette[color])
# matched box
s += yp.Layer(4)
s += drawbox(gcenter, Rotucell, halfshift=True, diag=(mode == "R"))
# s += yp.Layer(2)
# # unit cell
# s += drawbox(Boxslide,Rotucell,halfshift=True)
s += yp.Layer(2)
#s += drawbox2(Boxslide,Rotucell)
s += yp.Layer(5)
s += yp.Size(0.3)
s += yp.Color(5)
s += drawatoms(Slidunit)
for i in range(len(Slidunit)):
g = gatoms[members[i]]
d = Slidunit[i] - gatoms[members[i]]
d -= np.floor(d @ gcelli + 0.5) @ gcell
s += yp.Line(g, g + d)
# 変位ベクトルはどうやってもうまくいかないので、やめる。
s += yp.Size(0.3)
s += yp.Color(4)
s += yp.Layer(3)
s += drawatoms(gatoms, members=matched)
print(s) # end of frame
def main():
gro = open(sys.argv[1])
box, atoms = LoadGRO(gro)
ratoms = atoms/box
cellmat = np.diag(box)
page1 = ""
page2 = ""
page3 = ""
page4 = ""
page1 += yp.Size(0.05)
grid = None
while True:
line = sys.stdin.readline() #expect *.smatch result of slide-matcher2
if len(line) == 0:
break
cols = line.split()
if len(cols)<7:
break # broken line; maybe end of the file.
i,j = [int(x) for x in cols[:2]]
rad, dx,dy,dz, rmsd = [float(x) for x in cols[2:]]
if grid is None:
grid = pairlist.determine_grid(cellmat, rad)
lastrad = rad
p,q,r = pairlist.pairs_fine(ratoms, rad, cellmat, grid, distance=True, raw=True)
g = nx.Graph()
for k,pq in enumerate(zip(p,q)):
p,q = pq
g.add_edge(p,q,length=r[k])
else:
assert lastrad == rad
d = np.array([dx,dy,dz])
if rmsd < 0.09: # 0.09 for hyper ice T
# page 1: displacement vectors
page1 += yp.Line(atoms[i], atoms[i]+d)
page1 += yp.Circle(atoms[j])
# pages 2: displacement vectors (centered)
page2 += yp.Size(0.05)
page2 += yp.Line(np.zeros(3), d)
page2 += yp.Circle(d)
page2 += yp.Text(d, "{0} {1}".format(i,j))
# page 3..: matching
s = ""
s += yp.Size(0.05)
s += yp.Layer(1)
s += yp.Color(3)
for ni in g[i]:
s += yp.Circle(atoms[ni])
s += yp.Layer(2)
s += yp.Color(4)
for nj in g[j]:
s += yp.Circle(atoms[nj]-atoms[j]+atoms[i])
page3 += s
s = ""
s += yp.Size(0.05)
s += yp.Layer(1)
s += yp.Color(3)
for ni in g[i]:
s += yp.Circle(atoms[ni]-atoms[i])
s += yp.Layer(2)
s += yp.Color(4)
for nj in g[j]:
s += yp.Circle(atoms[nj]-atoms[j])
page4 += s
page4 += yp.NewPage()
print(page1)
print(page2)
print(page3)
print(page4)
def hook2(lattice):
global options
logger = getLogger()
logger.info("Hook2: Cages and vitrites")
cell = lattice.repcell.mat
positions = lattice.reppositions
graph = nx.Graph(lattice.graph) #undirected
ringsize = options.ring
ringlist = [[
int(x) for x in ring
] for ring in cr.CountRings(graph, pos=positions).rings_iter(max(ringsize))
]
ringpos = [centerOfMass(ringnodes, positions) for ringnodes in ringlist]
logger.info(" Rings: {0}".format(len(ringlist)))
maxcagesize = max(options.sizes)
cages = []
for cage in Polyhed(ringlist, maxcagesize):
if len(cage) in options.sizes:
valid = True
for ringid in cage:
if len(ringlist[ringid]) not in ringsize:
valid = False
if valid:
cages.append(list(cage))
logger.info(" Cages: {0}".format(len(cages)))
cagepos = np.array([centerOfMass(cage, ringpos) for cage in cages])
if options.gromacs:
options.rings = ringlist
options.cages = cages
logger.debug("##2 {0}".format(cages))
logger.info("Hook2: end.")
return
if options.quad:
oncage = defaultdict(list)
for cage in cages:
nodes = set()
for ringid in cage:
nodes |= set(ringlist[ringid])
for node in nodes:
oncage[node].append(len(cage))
op = dict()
for node in oncage:
count = [0 for i in range(17)]
for v in oncage[node]:
count[v] += 1
v = "{0}{1}{2}{3}".format(count[12], count[14], count[15],
count[16])
op[node] = v
stat = defaultdict(int)
for node in sorted(op):
v = op[node]
stat[v] += 1
if options.json:
output = dict()
N = positions.shape[0]
output["op"] = {str(k): v for k, v in op.items()}
output["stat"] = {k: v / N for k, v in stat.items()}
print(json.dumps(output, indent=2, sort_keys=True))
else:
for node in sorted(op):
print(node, op[node])
print("# Statistics")
for v in sorted(stat):
print("{0} {1} {2}/{3}".format(v, stat[v] / positions.shape[0],
stat[v], positions.shape[0]))
#ideal = {"CS2": {"2002": 0.7058823529411765,
# "3001": 0.23529411764705882,
# "4000": 0.058823529411764705},
# "CS1": {"0400": 0.13043478260869565,
# "1300": 0.8695652173913043},
#}
#for ref in ideal:
# dKL = 0
# for v in sorted(stat):
# if v in ideal[ref]:
# dKL += ideal[ref][v]*(log2(ideal[ref][v]) - log2(stat[v]/positions.shape[0]))
# print("{0} dKL={1}".format(ref, dKL))
elif options.json:
output = dict()
output["rings"] = ringlist
output["cages"] = cages
output["ringpos"] = [[x, y, z] for x, y, z in ringpos]
output["cagepos"] = [[x, y, z] for x, y, z in cagepos]
print(json.dumps(output, indent=2, sort_keys=True))
elif options.yaplot:
s = ""
for c, cage in enumerate(cages):
nodes = dict()
cagesize = len(cage)
for ringid in cage:
ns = ringlist[ringid]
for node in ns:
if node not in nodes:
# relative pos of the node
nodepos = positions[node] - cagepos[c]
nodepos -= np.floor(nodepos + 0.5)
# shrink a little
nodes[node] = nodepos * 0.9
s += yp.Color(len(ns))
s += yp.Layer(cagesize)
polygon = (np.array([nodes[node]
for node in ns]) + cagepos[c]) @ cell
s += yp.Polygon(polygon)
print(s + "\n")
elif options.python:
import graphstat as gs
db = gs.GraphStat()
labels = set()
g_id2label = dict()
print('cages="""')
for c, cage in enumerate(cages):
g = cage_to_graph(cage, ringlist)
cagesize = len(cage)
g_id = db.query_id(g)
if g_id < 0:
g_id = db.register()
enum = 0
label = "{0}".format(cagesize, enum)
while label in labels:
enum += 1
label = "{0}_{1}".format(cagesize, enum)
g_id2label[g_id] = label
labels.add(label)
else:
label = g_id2label[g_id]
print("{0:10s} {1:.4f} {2:.4f} {3:.4f}".format(label, *cagepos[c]))
print('"""')
else:
# human-friendly redundant format
for cageid, cage in enumerate(cages):
print("Cage {0}: ({1}, {2}, {3}) {4} hedron".format(
cageid, *cagepos[cageid], len(cage)))
for ringid in sorted(cage):
print(" Ring {0}: ({1}, {2}, {3}) {4} gon".format(
ringid, *ringpos[ringid], len(ringlist[ringid])))
print(" Nodes: {0}".format(ringlist[ringid]))
logger.info("Hook2: end.")
return True # terminate