def rama_rescale(results):
res1 = []
res2 = []
for (r1_id_str, diff2, r1_phi, r1_psi, r2_phi, r2_psi, v, r2_res_type,
r1_score, r2_score) in results:
for phi, psi, score, res in [(r1_phi, r1_psi, r1_score, res1),
(r2_phi, r2_psi, r2_score, res2)]:
max_value = find_region_max_value(r2_res_type, phi, psi)
if max_value is None:
res.append(score)
else:
res.append(score / max_value[1])
return res1, res2
def __init__(self, models, params, log):
self.models = models
self.log = log
self.params = params
self.total_rama = []
rama_res = easy_mp.pool_map(
processes=self.params.nproc,
fixed_func=ramalyze_parallel,
args=[m.get_hierarchy() for m in self.models])
for r in rama_res:
for res in r.results:
self.total_rama.append(res)
self.results = {}
for rama_type in range(5):
print "Working with", res_types[rama_type], "plot"
for peak in get_favored_peaks(rama_type):
print " Working with peak:", peak
start_point = peak[0] if self.params.grid_center_on_peak else (
0, 0)
gof = grid_over_favored(
rama_type=rama_type,
rama_region=peak[0],
start_point=start_point,
grid_size=self.params.grid_size,
corners_inside=self.params.corners_inside)
points = []
for r in self.total_rama:
if (r.res_type == rama_type and
(r.rama_type == RAMALYZE_FAVORED
or self.params.use_allowed) and find_region_max_value(
rama_type,
r.phi,
r.psi,
allow_outside=self.params.use_allowed) == peak):
points.append((r.phi, r.psi))
gof.add_points(points,
stop_on_outsiders=self.params.use_allowed)
c = gof.get_corr(), gof.grid.get_total_points()
if c.count(None) > 0:
c = None
self.results[(rama_type, peak)] = c
def __init__(self,
rama_type,
rama_region,
start_point,
grid_size,
corners_inside,
use_allowed=False):
self.rama_type = rama_type
self.rama_region = rama_region
self.start_point = start_point
self.grid_size = grid_size
self.corners_inside = corners_inside
self.r = ramachandran_eval.RamachandranEval()
self.grid = grid() # list of square objects
points_x = grid_over_favored._get_grid_points(start_point[0],
grid_size)
points_y = grid_over_favored._get_grid_points(start_point[1],
grid_size)
for x in points_x:
for y in points_y:
n_inside = 0
for dx in [0, 1]:
for dy in [0, 1]:
reg = find_region_max_value(rama_type,
x + grid_size * dx,
y + grid_size * dy)
if reg is not None and reg[0] == rama_region:
n_inside += 1
if n_inside >= corners_inside:
v = self.r.evaluate(
rama_type, [x + 0.5 * grid_size, y + 0.5 * grid_size])
self.grid.append(
square((x, y), (x + grid_size, y + grid_size), v))
print " Number of grid cells", len(self.grid)
self.grid.scale_to_1()
def exercise_1():
# ((-63.0, -43.0), 1.0)
print(find_region_max_value(RAMA_GENERAL, -100, 0))
assert find_region_max_value(RAMA_GENERAL, -100,
0) == ((-63.0, -43.0), 1.0)
assert find_region_max_value(RAMA_GENERAL, -120,
40) == ((-63.0, -43.0), 1.0)
assert find_region_max_value(RAMA_GENERAL, -45,
-55) == ((-63.0, -43.0), 1.0)
assert find_region_max_value(RAMA_GENERAL, 0, 0) == None
# ((-115.0, 131.0), 0.57068)
assert find_region_max_value(RAMA_GENERAL, -80,
100) == ((-115.0, 131.0), 0.57068)
assert find_region_max_value(RAMA_GENERAL, -160,
179) == ((-115.0, 131.0), 0.57068)
assert find_region_max_value(RAMA_GENERAL, -80,
60) == ((-115.0, 131.0), 0.57068)
assert find_region_max_value(RAMA_GENERAL, -120,
-179) == ((-115.0, 131.0), 0.57068)
# ((53.0, 43.0), 0.323004)
assert find_region_max_value(RAMA_GENERAL, 60,
40) == ((53.0, 43.0), 0.323004)
assert find_region_max_value(RAMA_GENERAL, 75,
0) == ((53.0, 43.0), 0.323004)
assert find_region_max_value(RAMA_GENERAL, 60,
60) == ((53.0, 43.0), 0.323004)
# ((53.0, -127.0), 0.0246619)
assert find_region_max_value(RAMA_GENERAL, 53,
-127) == ((53.0, -127.0), 0.0246619)
assert find_region_max_value(RAMA_GENERAL, 54,
-128) == ((53.0, -127.0), 0.0246619)
assert find_region_max_value(RAMA_GENERAL, 53,
-130) == ((53.0, -127.0), 0.0246619)
print("==================================================")
# ((-63.0, -41.0), 1.0)
assert find_region_max_value(RAMA_GLYCINE, -80,
-20) == ((-63.0, -41.0), 1.0)
assert find_region_max_value(RAMA_GLYCINE, -80,
60) == ((-63.0, -41.0), 1.0)
assert find_region_max_value(RAMA_GLYCINE, -80,
65) == ((-63.0, -41.0), 1.0)
# ((63.0, 41.0), 1.0)
assert find_region_max_value(RAMA_GLYCINE, 80, 0) == ((63.0, 41.0), 1.0)
assert find_region_max_value(RAMA_GLYCINE, 80, -60) == ((63.0, 41.0), 1.0)
# ((79.0, -173.0), 0.553852)
assert find_region_max_value(RAMA_GLYCINE, 100,
-160) == ((79.0, -173.0), 0.553852)
assert find_region_max_value(RAMA_GLYCINE, 120,
160) == ((79.0, -173.0), 0.553852)
assert find_region_max_value(RAMA_GLYCINE, -100,
140) == ((79.0, -173.0), 0.553852)
assert find_region_max_value(RAMA_GLYCINE, -100,
-160) == ((79.0, -173.0), 0.553852)
print("==================================================")
# ((-89.0, 5.0), 0.701149)
assert find_region_max_value(RAMA_CISPRO, -80,
0) == ((-89.0, 5.0), 0.701149)
assert find_region_max_value(RAMA_CISPRO, -60,
-20) == ((-89.0, 5.0), 0.701149)
assert find_region_max_value(RAMA_CISPRO, -100,
40) == ((-89.0, 5.0), 0.701149)
# ((-75.0, 155.0), 1.0)
assert find_region_max_value(RAMA_CISPRO, -80,
140) == ((-75.0, 155.0), 1.0)
assert find_region_max_value(RAMA_CISPRO, -80,
-178) == ((-75.0, 155.0), 1.0)
print("==================================================")
# ((-57.0, -37.0), 0.99566)
assert find_region_max_value(RAMA_TRANSPRO, -60,
-20) == ((-57.0, -37.0), 0.99566)
assert find_region_max_value(RAMA_TRANSPRO, -80,
0) == ((-57.0, -37.0), 0.99566)
assert find_region_max_value(RAMA_TRANSPRO, -40,
-40) == ((-57.0, -37.0), 0.99566)
# ((-81.0, 65.0), 0.0896269)
assert find_region_max_value(RAMA_TRANSPRO, -80,
60) == ((-81.0, 65.0), 0.0896269)
# ((-59.0, 143.0), 1.0)
assert find_region_max_value(RAMA_TRANSPRO, -60,
140) == ((-59.0, 143.0), 1.0)
assert find_region_max_value(RAMA_TRANSPRO, -80,
-179) == ((-59.0, 143.0), 1.0)
print("==================================================")
# ((-70.1, 149.0), 0.9619998)
assert find_region_max_value(RAMA_PREPRO, -120,
140) == ((-67.0, 147.0), 0.992025)
assert find_region_max_value(RAMA_PREPRO, -120,
60) == ((-67.0, 147.0), 0.992025)
assert find_region_max_value(RAMA_PREPRO, -160,
80) == ((-67.0, 147.0), 0.992025)
assert find_region_max_value(RAMA_PREPRO, -160,
160) == ((-67.0, 147.0), 0.992025)
# ((-57.0, -45.0), 1.0)
assert find_region_max_value(RAMA_PREPRO, -60,
-40) == ((-57.0, -45.0), 1.0)
assert find_region_max_value(RAMA_PREPRO, -45,
-55) == ((-57.0, -45.0), 1.0)
# ((49.0, 57.0), 0.185259)
assert find_region_max_value(RAMA_PREPRO, 49,
57) == ((49.0, 57.0), 0.185259)
assert find_region_max_value(RAMA_PREPRO, 60,
60) == ((49.0, 57.0), 0.185259)
assert find_region_max_value(RAMA_PREPRO, 55,
55) == ((49.0, 57.0), 0.185259)
print("==================================================")
# ((-63.0, -45.0), 1.0)
assert find_region_max_value(RAMA_ILE_VAL, -60,
-40) == ((-63.0, -45.0), 1.0)
assert find_region_max_value(RAMA_ILE_VAL, -120,
-60) == ((-63.0, -45.0), 1.0)
assert find_region_max_value(RAMA_ILE_VAL, -120,
20) == ((-63.0, -45.0), 1.0)
assert find_region_max_value(RAMA_ILE_VAL, -80, 0) == ((-63.0, -45.0), 1.0)
# ((-121.0, 129.0), 0.76163)
assert find_region_max_value(RAMA_ILE_VAL, -100,
140) == ((-121.0, 129.0), 0.76163)
assert find_region_max_value(RAMA_ILE_VAL, -160,
140) == ((-121.0, 129.0), 0.76163)
assert find_region_max_value(RAMA_ILE_VAL, -60,
140) == ((-121.0, 129.0), 0.76163)
assert find_region_max_value(RAMA_ILE_VAL, -130,
-179) == ((-121.0, 129.0), 0.76163)