def calc_dg_bar(LPs_map, Es, nfr, T=300):
dg = [0]
ddg2 = []
OIs = []
for temp_Es, temp_nfr in LPs_map.for_neigh_Es_nfr(Es, nfr):
Deltaf_ij, dDeltaf_ij, mbar = calc_dg_mbar(temp_Es, temp_nfr, T=T)
OIs.append(calc_OI_BAR(temp_Es, temp_nfr)[0])
dg.append(dg[-1] + Deltaf_ij[0][1])
ddg2.append(dDeltaf_ij[0][1]**2)
return np.array(dg), np.array(ddg2), OIs
def update_LPs_2(LPs, seg_score_flag, converged_segments, dl_min):
segs2sim = []
W_segs = []
for i in range(len(LPs) - 1):
temp_seg = LPs[i], LPs[i + 1]
if not check_fullseg_in_segs(temp_seg, converged_segments):
W_segs.append(seg_score_flag[temp_seg][0])
segs2sim.append(temp_seg)
W_segs = np.array(W_segs).T
for i in range(len(W_segs)):
W_segs[i] /= float(sum(W_segs[i]))
new_LPs_weights = {}
for i in range(len(segs2sim)):
temp_seg = segs2sim[i]
LPs_2_sim = [temp_seg[0]]
temp_new_lp = Real.fix_float(np.mean(temp_seg))
if dl_min <= Real.fix_float(temp_seg[1] - temp_new_lp):
LPs_2_sim.append(temp_new_lp)
LPs_2_sim.append(temp_seg[1])
temp_w = np.average(W_segs.T[i]) / len(LPs_2_sim)
for temp_l in LPs_2_sim:
if temp_l not in new_LPs_weights:
new_LPs_weights[temp_l] = 0
new_LPs_weights[temp_l] += temp_w
return new_LPs_weights
def calc_dg_exTI_mbar(mbar,
dEs,
LPs_pred,
flag_calc_w=True,
fnc2integrate=integrate.simps):
# calculates dG from exTI in combination with MBAR
dhdl_pred_mbar = _calc_exTI_pred_mbar(mbar,
dEs,
LPs_pred,
flag_calc_w=flag_calc_w)
return _calc_dg_TI(dhdl_pred_mbar, LPs_pred,
fnc2integrate=fnc2integrate), dhdl_pred_mbar
dg = [0]
for i in range(2, len(LPs_pred) + 1):
dg.append(fnc2integrate(dhdl_pred_mbar[:i], LPs_pred[:i]))
return np.array(dg), np.array(dhdl_pred_mbar)
def _parse_header(f_path, dl_max, comments):
f = open(f_path)
c_lines_no_comm, c_lines = 0, 0
sim_l, step, t = None, None, None
for l in f:
if _not_start_with_comm(l, comments):
if c_lines_no_comm==0:
N_LPs = int(l)
elif c_lines_no_comm==1:
LPs = np.array(l.split(), dtype=float)
c_lines_no_comm+=1
else:
if c_lines==0:
temp = l.split()
step, t = int(temp[-2]), float(temp[-1])
elif c_lines==1 and 'lam_s' in l:
sim_l = float(l.split()[-1])
if c_lines_no_comm==3:
break
c_lines+=1
LP_offset = 0
if len(LPs)!=N_LPs:
assert len(LPs) == N_LPs + 1
sim_l = LPs[0]
LP_offset = 1
lp2use, lp2use_pos = _get_LPs2use(LPs, dl_max, sim_l, LP_offset)
return c_lines, lp2use, lp2use_pos, LPs, sim_l, step, t
def get_nfr_mul_from_NFRs(NFRs, LPs, LPs_pred):
nfr_mul = []
for l in LPs_pred:
if l in LPs:
nfr_mul.append(np.array(NFRs[l]))
else:
nfr_mul.append([0])
return nfr_mul
def get_nfr_from_NFRs(NFRs, LPs, LPs_pred):
nfr = []
for l in LPs_pred:
if l in LPs:
nfr.append(sum(NFRs[l]))
else:
nfr.append(0)
return np.array(nfr)
def _calc_exTI_pred_mbar(mbar, dEs, LPs_pred, flag_calc_w=True):
if flag_calc_w:
w = mbar.getWeights().T
else:
w = mbar
dhdl_pred_mbar = []
for i in range(len(LPs_pred)):
dhdl_pred_mbar.append(np.dot(w[i], dEs[i]))
return np.array(dhdl_pred_mbar)
def _calc_singleLP_exTI_pred_mbar(Es, dEs, LPs_pred, nfr, T=300):
assert Es.shape == dEs.shape
kT = kb * T
mbar = MBAR(Es / kT, nfr)
w = mbar.getWeights()
wt = w.T
dgdl_int = []
for i in range(len(LPs_pred)):
dgdl_int.append(np.dot(wt[i], dEs[i]))
return np.array(dgdl_int)
def _get_rot_v(v, n=1, init_pv=None, mrot=210.):
if init_pv is None:
temp = abs(v[0])
pos = 0
for i in range(1, 3):
if abs(v[i]) < temp:
temp = abs(v[i])
pos = i
axis = [0., 0., 0.]
axis[pos] = 1
pv = rot(v, 90, axis)
pv[pos] = 0
else:
pv = np.array(init_pv)
pv /= np.linalg.norm(pv)
rot_vs = np.array(pv)
if n > 1:
rot_angles = np.linspace(0, mrot, n)
for a in rot_angles[1:]:
rot_vs = np.stack([rot_vs, rot(pv, a, v)])
return rot_vs
def rot(v, theta=90, axis=None):
if axis is None:
axis = [0, 0, 1]
axis = np.asarray(axis)
theta = np.radians(theta) / 2.0
axis = axis / np.linalg.norm(axis)
a = np.cos(theta)
b, c, d = -axis * np.sin(theta)
aa, bb, cc, dd = a * a, b * b, c * c, d * d
bc, ad, ac, ab, bd, cd = b * c, a * d, a * c, a * b, b * d, c * d
m = np.array([[aa + bb - cc - dd, 2 * (bc + ad), 2 * (bd - ac)],
[2 * (bc - ad), aa + cc - bb - dd, 2 * (cd + ab)],
[2 * (bd + ac), 2 * (cd - ab), aa + dd - bb - cc]])
return np.dot(m, v)
def calc_exTI_err(exTI_data,
LPs_pred=None,
flag_get_exTI_data_avg=True,
fnc2call_left_right=np.mean):
"""
calculates the difference between predictions from neighbouring points
:param exTI_data:
:param LPs_pred:
:param flag_get_exTI_data_avg:
:param fnc2call_left_right: (np.mean by default); it could also be min, max, lambda x:x[0] (return left)
:return:
exTI_err excluding / including simulated LPs
"""
LPs, LPs_pred = _get_LPs_pred_exTI(exTI_data, LPs_pred)
if flag_get_exTI_data_avg:
exTI_data_avg = _get_exTI_data_avg(exTI_data)
else:
exTI_data_avg = exTI_data
dhdl_err, dhdl_err2 = [], []
for lp in LPs_pred:
pos = bisect_left(LPs, lp)
if lp not in exTI_data:
v1 = exTI_data_avg[LPs[pos - 1]][lp]
v2 = exTI_data_avg[LPs[pos]][lp]
err = abs(v1 - v2)
dhdl_err.append(err)
dhdl_err2.append(err)
else:
dhdl_err.append(0)
temp_err2 = []
v = exTI_data_avg[LPs[pos]][lp]
if pos != 0:
temp_err2.append(abs(v - exTI_data_avg[LPs[pos - 1]][lp]))
if pos + 1 != len(LPs):
temp_err2.append(abs(v - exTI_data_avg[LPs[pos + 1]][lp]))
dhdl_err2.append(fnc2call_left_right(temp_err2))
return np.array(dhdl_err), np.array(dhdl_err2)
def __E(coord_flat, l12, l13, lrest, d_12, d_13, Fk, rest_pow):
E = 0
coord = coord_flat.reshape(coord_flat.shape[0] // 2, 2)
temp_ind_lists = list(zip(*l12))
temp_distances = coord[temp_ind_lists[0], ] - coord[
temp_ind_lists[1], ]
temp_distances = np.linalg.norm(temp_distances, axis=1)
E += 0.5 * Fk[0] * np.linalg.norm(
temp_distances - np.array([d_12] * temp_distances.shape[0]))
if l13:
temp_ind_lists = list(zip(*l13))
temp_distances = coord[temp_ind_lists[0], ] - coord[
temp_ind_lists[1], ]
temp_distances = np.linalg.norm(temp_distances, axis=1)
E += 0.5 * Fk[1] * np.linalg.norm(
temp_distances - np.array([d_13] * temp_distances.shape[0]))
if lrest:
temp_ind_lists = list(zip(*lrest))
temp_distances = coord[temp_ind_lists[0], ] - coord[
temp_ind_lists[1], ]
temp_distances = Fk[2] / np.sum(temp_distances**(2 * rest_pow),
axis=1)
E += np.sum(temp_distances)
return E
def __init__(self, l0, l1, LPs, LPs_pred):
self.l0 = Real(l0).value
self.l1 = Real(l1).value
self.LPs = LPs
self.LPs_pred = LPs_pred
self.LPs_interval = [] # LPs (simulated) in the interval
self.LPs_pred_interval = [] # LPs_pred (predicted) in the interval
self.pos_inLPs_LPs_interval = [
] # position (in LPs) of LPs in the interval (before pos_LPs_interval_inLPs)
self.pos_LPs_interval = [
] # position (in LPs_pred) of LPs in the interval
self.pos_LPs_pred_interval = [
] # position (in LPs_pred) of LPs_pred in the interval
self.pos_LPs = [] # position (in LPs_pred) of LPs (all)
# full interval - for l0 / l1 not in LPs
for i, lp in enumerate(LPs_pred):
if self.l0 <= lp <= self.l1:
self.LPs_pred_interval.append(lp)
self.pos_LPs_pred_interval.append(i)
if lp in LPs:
self.LPs_interval.append(lp)
self.pos_inLPs_LPs_interval.append(LPs.index(lp))
self.pos_LPs_interval.append(i)
self.pos_LPs.append(i)
elif lp in LPs:
self.pos_LPs.append(i)
self.pos_inLPs_pred_interval__LPs_interval = np.array(
self.pos_LPs_interval) - self.pos_LPs_interval[0]
# position (in LPs_pred_interval) of LPs_interval (before pos_LPs_interval_inLPs_pred_interval)
if l0 not in LPs or l1 not in LPs:
self.pos_inLPs_LPs_interval_full = list(
self.pos_inLPs_LPs_interval
) # position (in LPs) of LPs in the interval
if self.LPs_interval[0] != l0:
self.pos_inLPs_LPs_interval_full.insert(
0, self.pos_inLPs_LPs_interval[0] - 1)
if self.LPs_interval[-1] != l1:
self.pos_inLPs_LPs_interval_full.append(
self.pos_inLPs_LPs_interval[-1] + 1)
self.LPs_interval_full = [
LPs[pos] for pos in self.pos_inLPs_LPs_interval_full
] # LPs (simulated) in the interval
def _calc_dg_TI(dhdl, LPs, fnc2integrate=integrate.simps):
"""calculates dG from TI"""
dg = [0]
for i in range(2, len(LPs) + 1):
dg.append(fnc2integrate(dhdl[:i], LPs[:i]))
return np.array(dg)
def rot_2D(v, theta=90):
theta = np.radians(theta)
sin = np.sin(theta)
cos = np.cos(theta)
R = np.array([[cos, -sin], [sin, cos]])
return R.dot(v)
def _add_midpoints(LPs, dl_min):
LPs_mid = get_lset(np.array(LPs)[:-1] + np.diff(LPs) * 0.5)
LPs_mid = set(LPs_mid) & set(get_lset(np.arange(0., 1.0000001, dl_min)))
new_LPs = list(LPs)
new_LPs.extend(LPs_mid)
return get_lset(new_LPs)
def get_nfr_from_nfr_mul(nfr_mul):
return np.array([sum(nfr_list) for nfr_list in nfr_mul])
def get_nfr_LPs(nfr):
nfr_LPs = np.array(nfr)
return nfr_LPs[nfr_LPs > 0]