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element parsing and channels #41

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10 changes: 6 additions & 4 deletions protein_holography/coordinates/get_holograms.py
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Original file line number Diff line number Diff line change
Expand Up @@ -11,10 +11,10 @@
from progress.bar import Bar
import traceback

def c(np_nh,L_max,ks,num_combi_channels,r_max):
def c(np_nh,L_max,ks,num_combi_channels,r_max,element_channels):

#try:
hgm = get_hologram(np_nh,L_max,ks,num_combi_channels,r_max)
hgm = get_hologram(np_nh,L_max,ks,num_combi_channels,r_max,element_channels)
#except Exception as e:
# print(e)
# print('Error with',np_nh[0])
Expand Down Expand Up @@ -50,7 +50,8 @@ def c(np_nh,L_max,ks,num_combi_channels,r_max):
ds = PDBPreprocessor(args.hdf5_in,args.neighborhood_list)
bad_neighborhoods = []
n = 0
channels = ['C','N','O','S','H','SASA','charge']
element_channels = [b'C',b'N',b'O',b'S',b'H',b"P",b"F",b"Cl",]
channels = np.concatenate((element_channels, [b"Unk", b'SASA',b'charge']))
num_combi_channels = len(channels) * len(args.ks)

dt = np.dtype([(str(l),'complex64',(num_combi_channels,2*l+1)) for l in range(args.Lmax + 1)])
Expand All @@ -77,7 +78,8 @@ def c(np_nh,L_max,ks,num_combi_channels,r_max):
params = {'L_max': args.Lmax,
'ks':args.ks,
'num_combi_channels': num_combi_channels,
'r_max': args.r_max},
'r_max': args.r_max,
"element_channels":element_channels},
parallelism = args.parallelism)):
if hgm is None:
bar.next()
Expand Down
10 changes: 6 additions & 4 deletions protein_holography/coordinates/get_holograms_zach.py
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Original file line number Diff line number Diff line change
Expand Up @@ -10,10 +10,10 @@
from progress.bar import Bar
import traceback

def c(np_nh,L_max,ks,num_combi_channels,r_max):
def c(np_nh,L_max,ks,num_combi_channels,r_max,element_channels):

#try:
hgm = get_hologram(np_nh,L_max,ks,num_combi_channels,r_max)
hgm = get_hologram(np_nh,L_max,ks,num_combi_channels,r_max,element_channels)

#except Exception as e:
# print(e)
Expand Down Expand Up @@ -50,7 +50,8 @@ def c(np_nh,L_max,ks,num_combi_channels,r_max):
ds = PDBPreprocessor(args.hdf5_in,args.neighborhood_list)
bad_neighborhoods = []
n = 0
channels = ['C','N','O','S','H','SASA','charge']
element_channels = [b'C',b'N',b'O',b'S',b'H',b"P",b"F",b"Cl",]
channels = np.concatenate((element_channels, [b"Unk", b'SASA',b'charge']))
num_combi_channels = len(channels) * len(args.ks)

dt = np.dtype([(str(l),'complex64',(num_combi_channels,2*l+1)) for l in range(args.Lmax + 1)])
Expand All @@ -77,7 +78,8 @@ def c(np_nh,L_max,ks,num_combi_channels,r_max):
params = {'L_max': args.Lmax,
'ks':args.ks,
'num_combi_channels': num_combi_channels,
'r_max': args.r_max},
'r_max': args.r_max,
"element_channels":element_channels},
parallelism = args.parallelism)):
if hgm is None:
bar.next()
Expand Down
2 changes: 1 addition & 1 deletion protein_holography/coordinates/get_neighborhoods.py
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Original file line number Diff line number Diff line change
Expand Up @@ -65,7 +65,7 @@ def get_neighborhoods(
dt = np.dtype([
('res_id','S5',(6)),
('atom_names', 'S4', (max_atoms)),
('elements', 'S1', (max_atoms)),
('elements', 'S3', (max_atoms)),
('res_ids', 'S5', (max_atoms,6)),
('coords', 'f8', (max_atoms,3)),
('SASAs', 'f8', (max_atoms)),
Expand Down
2 changes: 1 addition & 1 deletion protein_holography/coordinates/get_structural_info.py
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Original file line number Diff line number Diff line change
Expand Up @@ -66,7 +66,7 @@ def c(pose,padded_length=200000):
dt = np.dtype([
('pdb','S4',()),
('atom_names', 'S4', (max_atoms)),
('elements', 'S1', (max_atoms)),
('elements', 'S3', (max_atoms)),
('res_ids', 'S5', (max_atoms,6)),
('coords', 'f8', (max_atoms,3)),
('SASAs', 'f8', (max_atoms)),
Expand Down
10 changes: 6 additions & 4 deletions protein_holography/coordinates/get_zernikegrams.py
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Original file line number Diff line number Diff line change
Expand Up @@ -10,10 +10,10 @@
from progress.bar import Bar
import traceback

def c(np_nh,L_max,ks,num_combi_channels,r_max):
def c(np_nh,L_max,ks,num_combi_channels,r_max,element_channels):

#try:
hgm = get_hologram(np_nh,L_max,ks,num_combi_channels,r_max)
hgm = get_hologram(np_nh,L_max,ks,num_combi_channels,r_max,element_channels)

#except Exception as e:
# print(e)
Expand Down Expand Up @@ -45,7 +45,8 @@ def get_zernikegrams(
ds = PDBPreprocessor(hdf5_in,neighborhood_list)
bad_neighborhoods = []
n = 0
channels = ['C','N','O','S','H','SASA','charge']
element_channels = [b'C',b'N',b'O',b'S',b'H',b"P",b"F",b"Cl",]
channels = np.concatenate((element_channels, [b"Unk", b'SASA',b'charge']))
num_combi_channels = len(channels) * len(ks)

dt = np.dtype([(str(l),'complex64',(num_combi_channels,2*l+1)) for l in range(Lmax + 1)])
Expand Down Expand Up @@ -77,7 +78,8 @@ def get_zernikegrams(
params = {'L_max': Lmax,
'ks':ks,
'num_combi_channels': num_combi_channels,
'r_max': r_max},
'r_max': r_max,
"element_channels":element_channels},
parallelism = parallelism)):
if hgm is None or hgm[0] is None:
bar.next()
Expand Down
40 changes: 13 additions & 27 deletions protein_holography/coordinates/pyrosetta_hdf5_holograms.py
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Original file line number Diff line number Diff line change
Expand Up @@ -66,12 +66,13 @@ def zernike_coeff_lm_new(r, t, p, n, r_max, l, m, weights):

return coeffs

def get_hologram(nh,L_max,ks,num_combi_channels,r_max):
def get_hologram(nh,L_max,ks,num_combi_channels,r_max,
element_channels=[b'C',b'N',b'O',b'S',b'H',b"P",b"F",b"Cl",]):
dt = np.dtype([(str(l),'complex64',(num_combi_channels,2*l+1)) for l in range(L_max + 1)])
arr = np.zeros(shape=(1,),dtype=dt)

# get info from nh
channels = ['C','N','O','S','H','SASA','charge']
channels = np.concatenate((element_channels, [b"Unk", b'SASA',b'charge']))
num_channels = len(channels)
atom_names = nh['atom_names']
real_locs = np.logical_and(atom_names != b'',nh['coords'][:,0] <= r_max)
Expand Down Expand Up @@ -104,31 +105,16 @@ def get_hologram(nh,L_max,ks,num_combi_channels,r_max):
nonzero_len = np.count_nonzero(nonzero_idxs)
nmax = len(ks)


for i_ch,ch in enumerate(channels):

if ch == 'C':
r,t,p = *atom_coords[elements == b'C'].T,
weights=np.ones(shape=(r.shape[-1],))
if ch == 'N':
r,t,p = *atom_coords[elements == b'N'].T,
weights=np.ones(shape=(r.shape[-1],))
if ch == 'O':
r,t,p = *atom_coords[elements == b'O'].T,
weights=np.ones(shape=(r.shape[-1],))
if ch == 'S':
r,t,p = *atom_coords[elements == b'S'].T,
weights=np.ones(shape=(r.shape[-1],))
if ch == 'H':
r,t,p = *atom_coords[elements == b'H'].T,
weights=np.ones(shape=(r.shape[-1],))
if ch == 'SASA':
weights = curr_SASA
r,t,p = np.einsum('ij->ji',atom_coords)
#print(weights)
if ch == 'charge':
r,t,p = np.einsum('ij->ji',atom_coords)
weights = curr_charge
arr_weights = np.empty(shape=(num_channels,r.shape[-1],))
which_channel = np.array( elements[:,None] == element_channels, dtype=float)
r,t,p = np.einsum('ij->ji',atom_coords)

arr_weights[:len(element_channels)] = which_channel
arr_weights[-3] = np.logical_not( np.any( which_channel,axis=1))
arr_weights[-2] = curr_SASA
arr_weights[-1] = curr_charge

out_z = np.zeros(shape=(num_channels,ns.shape[0]), dtype=np.complex64)

out_z = np.zeros(shape=ns.shape[0], dtype=np.complex64)

Expand Down
32 changes: 13 additions & 19 deletions protein_holography/coordinates/pyrosetta_hdf5_holograms_zach.py
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Original file line number Diff line number Diff line change
Expand Up @@ -66,12 +66,13 @@ def zernike_coeff_lm_new(r, t, p, n, r_max, l, m, weights):

return coeffs

def get_hologram(nh,L_max,ks,num_combi_channels,r_max):
def get_hologram(nh,L_max,ks,num_combi_channels,r_max,
element_channels = [b'C',b'N',b'O',b'S',b'H',b"P",b"F",b"Cl",]):
dt = np.dtype([(str(l),'complex64',(num_combi_channels,2*l+1)) for l in range(L_max + 1)])
arr = np.zeros(shape=(1,),dtype=dt)

# get info from nh
channels = ['C','N','O','S','H','SASA','charge']
channels = np.concatenate((element_channels, [b"Unk", b'SASA',b'charge']))
num_channels = len(channels)
atom_names = nh['atom_names']
real_locs = np.logical_and(atom_names != b'',nh['coords'][:,0] <= r_max)
Expand Down Expand Up @@ -105,28 +106,21 @@ def get_hologram(nh,L_max,ks,num_combi_channels,r_max):
nmax = len(ks)


which_channel = elements[:,None] == element_channels)
for i_ch,ch in enumerate(channels):

if ch == 'C':
r,t,p = *atom_coords[elements == b'C'].T,
weights=np.ones(shape=(r.shape[-1],))
if ch == 'N':
r,t,p = *atom_coords[elements == b'N'].T,
weights=np.ones(shape=(r.shape[-1],))
if ch == 'O':
r,t,p = *atom_coords[elements == b'O'].T,
weights=np.ones(shape=(r.shape[-1],))
if ch == 'S':
r,t,p = *atom_coords[elements == b'S'].T,

if ch in element_channels:
r,t,p = *atom_coords[np.where(which_channel[:,i_ch])].T,
weights=np.ones(shape=(r.shape[-1],))
if ch == 'H':
r,t,p = *atom_coords[elements == b'H'].T,

elif ch == b'Unk':
r,t,p = *atom_coords[np.where(np.logical_not( np.any( which_channel,axis=1)))].T,
weights=np.ones(shape=(r.shape[-1],))
if ch == 'SASA':

elif ch == b'SASA':
weights = curr_SASA
r,t,p = np.einsum('ij->ji',atom_coords)
#print(weights)
if ch == 'charge':
elif ch == b'charge':
r,t,p = np.einsum('ij->ji',atom_coords)
weights = curr_charge

Expand Down
60 changes: 20 additions & 40 deletions protein_holography/coordinates/pyrosetta_hdf5_zernikegrams.py
View file
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Original file line number Diff line number Diff line change
Expand Up @@ -86,12 +86,13 @@ def zernike_coeff_lm_new(r: np.ndarray, t: np.ndarray, p: np.ndarray, n: np.ndar

return coeffs

def get_hologram(nh, L_max: int, ks, num_combi_channels, r_max: np.float64):
def get_hologram(nh, L_max: int, ks, num_combi_channels, r_max: np.float64,
element_channels=[b'C',b'N',b'O',b'S',b'H',b"P",b"F",b"Cl",]):
dt = np.dtype([(str(l),'complex64',(num_combi_channels,2*l+1)) for l in range(L_max + 1)])
arr = np.zeros(shape=(1,),dtype=dt)

# get info from nh
channels = ['C','N','O','S','H','SASA','charge']
channels = np.concatenate((element_channels, [b"Unk", b'SASA',b'charge']))
num_channels = len(channels)
atom_names = nh['atom_names']
real_locs = np.logical_and(atom_names != b'',nh['coords'][:,0] <= r_max)
Expand Down Expand Up @@ -123,38 +124,17 @@ def get_hologram(nh, L_max: int, ks, num_combi_channels, r_max: np.float64):
nonzero_idxs = ~(l_greater_n | odds)
nonzero_len = np.count_nonzero(nonzero_idxs)
nmax = len(ks)

arr_weights = np.empty(shape=(num_channels,r.shape[-1],))
which_channel = np.array( elements[:,None] == element_channels, dtype=float)
r,t,p = np.einsum('ij->ji',atom_coords)

arr_weights[:len(element_channels)] = which_channel
arr_weights[-3] = np.logical_not( np.any( which_channel,axis=1))
arr_weights[-2] = curr_SASA
arr_weights[-1] = curr_charge

arr_weights = np.empty(shape=(7,r.shape[-1],))
# for i_ch,ch in enumerate(channels):


# r,t,p = np.einsum('ij->ji',atom_coords)
# if ch == 'C':
# weights=np.array(elements == b'C',dtype=float)
# if ch == 'N':
# weights=np.array(elements == b'N',dtype=float)
# if ch == 'O':
# weights=np.array(elements == b'O',dtype=float)
# if ch == 'S':
# weights=np.array(elements == b'S',dtype=float)
# if ch == 'H':
# weights=np.array(elements == b'H',dtype=float)
# if ch == 'SASA':
# weights = curr_SASA
# if ch == 'charge':
# weights = curr_charge

# arr_weights[i_ch] = weights
arr_weights[0] = np.array(elements == b'C', dtype=float)
arr_weights[1] = np.array(elements == b'N', dtype=float)
arr_weights[2] = np.array(elements == b'O', dtype=float)
arr_weights[3] = np.array(elements == b'S', dtype=float)
arr_weights[4] = np.array(elements == b'H', dtype=float)
arr_weights[5] = curr_SASA
arr_weights[6] = curr_charge

ch_num = len(channels)
out_z = np.zeros(shape=(ch_num,ns.shape[0]), dtype=np.complex64)
out_z = np.zeros(shape=(num_channels,ns.shape[0]), dtype=np.complex64)

rs = np.tile(r, (nonzero_len, 1))
ts = np.tile(t, (nonzero_len, 1))
Expand All @@ -168,7 +148,7 @@ def get_hologram(nh, L_max: int, ks, num_combi_channels, r_max: np.float64):
for l in range(L_max + 1):
num_m = (2 * l + 1)
high_idx = (nmax) * num_m + low_idx
arr[0][l][:,:] = out_z[:,low_idx:high_idx].reshape(nmax*ch_num, num_m, )
arr[0][l][:,:] = out_z[:,low_idx:high_idx].reshape(nmax*num_channels, num_m, )
low_idx = high_idx

return arr[0]
Expand Down Expand Up @@ -240,8 +220,8 @@ def get_sparse_hologram(nh,L_max,ks,num_combi_channels,r_max):
arr_weights[4] = np.array(atom_names == b'CB',dtype=float)


ch_num = len(channels)
out_z = np.zeros(shape=(ch_num,ns.shape[0]), dtype=np.complex64)
num_channels = len(channels)
out_z = np.zeros(shape=(num_channels,ns.shape[0]), dtype=np.complex64)

rs = np.tile(r, (nonzero_len, 1))
ts = np.tile(t, (nonzero_len, 1))
Expand All @@ -258,7 +238,7 @@ def get_sparse_hologram(nh,L_max,ks,num_combi_channels,r_max):
for l in range(L_max + 1):
num_m = (2 * l + 1)
high_idx = (nmax) * num_m + low_idx
arr[0][l][:,:] = out_z[:,low_idx:high_idx].reshape(nmax*ch_num, num_m, )
arr[0][l][:,:] = out_z[:,low_idx:high_idx].reshape(nmax*num_channels, num_m, )
low_idx = high_idx


Expand Down Expand Up @@ -343,8 +323,8 @@ def get_backbone_hologram(nh,L_max,ks,num_combi_channels,r_max):
]),dtype=float)


ch_num = len(channels)
out_z = np.zeros(shape=(ch_num,ns.shape[0]), dtype=np.complex64)
num_channels = len(channels)
out_z = np.zeros(shape=(num_channels,ns.shape[0]), dtype=np.complex64)

rs = np.tile(r, (nonzero_len, 1))
ts = np.tile(t, (nonzero_len, 1))
Expand All @@ -361,7 +341,7 @@ def get_backbone_hologram(nh,L_max,ks,num_combi_channels,r_max):
for l in range(L_max + 1):
num_m = (2 * l + 1)
high_idx = (nmax) * num_m + low_idx
arr[0][l][:,:] = out_z[:,low_idx:high_idx].reshape(nmax*ch_num, num_m, )
arr[0][l][:,:] = out_z[:,low_idx:high_idx].reshape(nmax*num_channels, num_m, )
low_idx = high_idx


Expand Down