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RoseTTAFold-All-Atom/rf2aa/util_module.py

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initial commit
2024-03-05 06:38:17 +00:00
import numpy as np
import torch
import torch.nn as nn
import torch.nn.functional as F
from opt_einsum import contract as einsum
import copy
import dgl
import networkx as nx
from rf2aa.util import *
from rf2aa.chemical import ChemicalData as ChemData
from rf2aa.chemical import th_dih, th_ang_v
def init_lecun_normal(module, scale=1.0):
def truncated_normal(uniform, mu=0.0, sigma=1.0, a=-2, b=2):
normal = torch.distributions.normal.Normal(0, 1)
alpha = (a - mu) / sigma
beta = (b - mu) / sigma
alpha_normal_cdf = normal.cdf(torch.tensor(alpha))
p = alpha_normal_cdf + (normal.cdf(torch.tensor(beta)) - alpha_normal_cdf) * uniform
v = torch.clamp(2 * p - 1, -1 + 1e-8, 1 - 1e-8)
x = mu + sigma * np.sqrt(2) * torch.erfinv(v)
x = torch.clamp(x, a, b)
return x
def sample_truncated_normal(shape, scale=1.0):
stddev = np.sqrt(scale/shape[-1])/.87962566103423978 # shape[-1] = fan_in
return stddev * truncated_normal(torch.rand(shape))
module.weight = torch.nn.Parameter( (sample_truncated_normal(module.weight.shape)) )
return module
def init_lecun_normal_param(weight, scale=1.0):
def truncated_normal(uniform, mu=0.0, sigma=1.0, a=-2, b=2):
normal = torch.distributions.normal.Normal(0, 1)
alpha = (a - mu) / sigma
beta = (b - mu) / sigma
alpha_normal_cdf = normal.cdf(torch.tensor(alpha))
p = alpha_normal_cdf + (normal.cdf(torch.tensor(beta)) - alpha_normal_cdf) * uniform
v = torch.clamp(2 * p - 1, -1 + 1e-8, 1 - 1e-8)
x = mu + sigma * np.sqrt(2) * torch.erfinv(v)
x = torch.clamp(x, a, b)
return x
def sample_truncated_normal(shape, scale=1.0):
stddev = np.sqrt(scale/shape[-1])/.87962566103423978 # shape[-1] = fan_in
return stddev * truncated_normal(torch.rand(shape))
weight = torch.nn.Parameter( (sample_truncated_normal(weight.shape)) )
return weight
# for gradient checkpointing
def create_custom_forward(module, **kwargs):
def custom_forward(*inputs):
return module(*inputs, **kwargs)
return custom_forward
def get_clones(module, N):
return nn.ModuleList([copy.deepcopy(module) for i in range(N)])
class Dropout(nn.Module):
# Dropout entire row or column
def __init__(self, broadcast_dim=None, p_drop=0.15):
super(Dropout, self).__init__()
# give ones with probability of 1-p_drop / zeros with p_drop
self.sampler = torch.distributions.bernoulli.Bernoulli(torch.tensor([1-p_drop]))
self.broadcast_dim=broadcast_dim
self.p_drop=p_drop
def forward(self, x):
if not self.training: # no drophead during evaluation mode
return x
shape = list(x.shape)
if not self.broadcast_dim == None:
shape[self.broadcast_dim] = 1
mask = self.sampler.sample(shape).to(x.device).view(shape)
x = mask * x / (1.0 - self.p_drop)
return x
def rbf(D, D_min=0.0, D_count=64, D_sigma=0.5):
# Distance radial basis function
D_max = D_min + (D_count-1) * D_sigma
D_mu = torch.linspace(D_min, D_max, D_count).to(D.device)
D_mu = D_mu[None,:]
D_expand = torch.unsqueeze(D, -1)
RBF = torch.exp(-((D_expand - D_mu) / D_sigma)**2)
return RBF
def get_seqsep(idx):
'''
Sequence separation feature for structure module. Protein-only.
Input:
- idx: residue indices of given sequence (B,L)
Output:
- seqsep: sequence separation feature with sign (B, L, L, 1)
Sergey found that having sign in seqsep features helps a little
'''
seqsep = idx[:,None,:] - idx[:,:,None]
sign = torch.sign(seqsep)
neigh = torch.abs(seqsep)
neigh[neigh > 1] = 0.0 # if bonded -- 1.0 / else 0.0
neigh = sign * neigh
return neigh.unsqueeze(-1)
def get_seqsep_protein_sm(idx, bond_feats, dist_matrix, sm_mask):
'''
Sequence separation features for protein-SM complex
Input:
- idx: residue indices of given sequence (B,L)
- bond_feats: bond features (B, L, L)
- dist_matrix: precomputed bond distances (B, L, L) NOTE: need to run nan_to_num to remove infinities
- sm_mask: boolean feature True if a position represents atom, False if residue (B, L)
Output:
- seqsep: sequence separation feature with sign (B, L, L, 1)
-1 or 1 for bonded protein residues
1 for bonded SM atoms or residue-atom bonds
0 elsewhere
'''
sm_mask = sm_mask[0] # assume batch = 1
res_dist, atom_dist = get_res_atom_dist(idx, bond_feats, dist_matrix, sm_mask)
sm_mask_2d = sm_mask[None,:]*sm_mask[:,None]
prot_mask_2d = (~sm_mask[None,:]) * (~sm_mask[:,None])
inter_mask_2d = (~sm_mask[None,:]) * (sm_mask[:,None]) + (sm_mask[None,:]) * (~sm_mask[:,None])
res_dist[(res_dist > 1) | (res_dist < -1)] = 0.0
atom_dist[(atom_dist > 1)] = 0.0
seqsep = sm_mask_2d*atom_dist + prot_mask_2d*res_dist + inter_mask_2d*(bond_feats==6)
return seqsep.unsqueeze(-1)
def get_res_atom_dist(idx, bond_feats, dist_matrix, sm_mask, minpos_res=-32, maxpos_res=32, maxpos_atom=8):
'''
Calculates residue and atom bond distances of protein/SM complex. Used for positional
embedding and structure module. 2nd version (2022-9-19); handles atomized proteins.
Input:
- idx: residue index (B, L)
- bond_feats: bond features (B, L, L)
- dist_matrix: precomputed bond distances (B, L, L) NOTE: need to run nan_to_num to remove infinities
- sm_mask: boolean feature (L). True if a position represents atom, False otherwise
- minpos_res: minimum value of residue distances
- maxpos_res: maximum value of residue distances
- maxpos_atom: maximum value of atom bond distances
Output:
- res_dist: residue distance (B, L, L)
- atom_dist: atom bond distance (B, L, L)
'''
bond_feats = bond_feats[0] # assume batch = 1
L = bond_feats.shape[0]
device = bond_feats.device
sm_mask_2d = sm_mask[None,:]*sm_mask[:,None]
prot_mask_2d = (~sm_mask[None,:]) * (~sm_mask[:,None])
inter_mask_2d = (~sm_mask[None,:]) * (sm_mask[:,None]) + (sm_mask[None,:]) * (~sm_mask[:,None])
# protein residue distances
res_dist_prot = torch.clamp(idx[0,None,:] - idx[0,:,None],
min=minpos_res, max=maxpos_res) # (L, L) intra-protein
res_dist_sm = torch.full((L,L), maxpos_res+1, device=device) # (L, L) with "unknown" res. dist. token
# small molecule atom bond graph
atom_dist_sm = torch.nan_to_num(dist_matrix, posinf=maxpos_atom)[0].long() # this comes through the dataloader so it is batched
atom_dist_prot = torch.full((L,L), maxpos_atom+1, device=device)
#fd new impl
i_s, j_s = torch.where(bond_feats==6)
i_sm = i_s[sm_mask[i_s]]
i_prot = j_s[sm_mask[i_s]]
res_dist_inter = torch.full((L,L), maxpos_res, device=device)
atom_dist_inter = torch.full((L,L), maxpos_atom, device=device)
if i_prot.shape[0] > 0:
closest_prot_res = i_prot[torch.argmin(atom_dist_sm[sm_mask,:][:,i_sm], dim=-1)]
res_dist_inter[sm_mask,:] = res_dist_prot[closest_prot_res,:]
res_dist_inter[:,sm_mask] = res_dist_prot[:,closest_prot_res]
closest_atom = i_sm[torch.argmin(torch.abs(res_dist_prot[~sm_mask,:][:,i_prot]), dim=-1)]
atom_dist_inter[~sm_mask,:] = atom_dist_sm[closest_atom,:] + 1
atom_dist_inter[:,~sm_mask] = atom_dist_sm[:,closest_atom] + 1
res_dist = res_dist_prot * prot_mask_2d + res_dist_inter * inter_mask_2d + res_dist_sm * sm_mask_2d
atom_dist = atom_dist_prot * prot_mask_2d + atom_dist_inter * inter_mask_2d + atom_dist_sm * sm_mask_2d
return res_dist[None], atom_dist[None] # add batch dim.
def get_relpos(idx, bond_feats, sm_mask, inter_pos=32, maxpath=32):
'''
Relative position matrix of protein/SM complex. Used for positional
embedding and structure module. Simple version from 9/2/2022 that doesn't
handle atomized proteins.
Input:
- idx: residue index (B, L)
- bond_feats: bond features (B, L, L)
- sm_mask: boolean feature True if a position represents atom, False if residue (B, L)
- inter_pos: value to assign as the protein-SM residue index differences
- maxpath: bond distances greater than this are clipped to this value
Output:
- relpos: relative position feature (B, L, L)
for intra-protein this is the residue index difference
for intra-SM this is the bond distance
for protein-SM this is user-defined value inter_pos
'''
bond_feats = bond_feats[0]
sm_mask_2d = sm_mask[None,:]*sm_mask[:,None]
prot_mask_2d = (~sm_mask[None,:]) * (~sm_mask[:,None])
inter_mask_2d = (~sm_mask[None,:]) * (sm_mask[:,None]) + (sm_mask[None,:]) * (~sm_mask[:,None])
# intra-protein: residue # differences
seqsep = idx[:,None,:] - idx[:,:,None] # (B, L, L)
# intra-small molecule: bond distances
sm_bond_feats = torch.zeros_like(bond_feats) + sm_mask*bond_feats
G = nx.from_numpy_matrix(sm_bond_feats.detach().cpu().numpy())
paths = dict(nx.all_pairs_shortest_path_length(G,cutoff=maxpath))
paths = [(i,j,vij) for i,vi in paths.items() for j,vij in vi.items()]
i,j,v = torch.tensor(paths).T
bond_separation = torch.full_like(bond_feats, maxpath) \
- maxpath*torch.eye(bond_feats.shape[0]).to(bond_feats.device).long()
bond_separation[i,j] = v.to(bond_feats.device)
# combine: protein-s.m. are always positive maximum distance apart
# assumes one small molecule per example
relpos = prot_mask_2d * seqsep + sm_mask_2d * bond_separation + inter_mask_2d * inter_pos # (B, L, L)
relpos = relpos.to(bond_feats.device)
return relpos
def make_full_graph(xyz, pair, idx):
'''
Input:
- xyz: current backbone cooordinates (B, L, 3, 3)
- pair: pair features from Trunk (B, L, L, E)
- idx: residue index from ground truth pdb
Output:
- G: defined graph
'''
B, L = xyz.shape[:2]
device = xyz.device
# seq sep
sep = idx[:,None,:] - idx[:,:,None]
b,i,j = torch.where(sep.abs() > 0)
src = b*L+i
tgt = b*L+j
G = dgl.graph((src, tgt), num_nodes=B*L).to(device)
G.edata['rel_pos'] = (xyz[b,j,:] - xyz[b,i,:]) #.detach() # no gradient through basis function
return G, pair[b,i,j][...,None]
def make_topk_graph(xyz, pair, idx, top_k=128, nlocal=33, topk_incl_local=True, eps=1e-6):
'''
Input:
- xyz: current backbone cooordinates (B, L, 3, 3)
- pair: pair features from Trunk (B, L, L, E)
- idx: residue index from ground truth pdb
Output:
- G: defined graph
'''
B, L = xyz.shape[:2]
device = xyz.device
# distance map from current CA coordinates
D = torch.cdist(xyz, xyz) + torch.eye(L, device=device).unsqueeze(0)*9999.9 # (B, L, L)
# seq sep
sep = idx[:,None,:] - idx[:,:,None]
sep = sep.abs() + torch.eye(L, device=device).unsqueeze(0)*9999.9
if (topk_incl_local):
D = D + sep*eps
D[sep<nlocal] = 0.0
# get top_k neighbors
D_neigh, E_idx = torch.topk(D, min(top_k, L-1), largest=False) # shape of E_idx: (B, L, top_k)
topk_matrix = torch.zeros((B, L, L), device=device)
topk_matrix.scatter_(2, E_idx, 1.0)
cond = topk_matrix > 0.0
else:
D = D + sep*eps
# get top_k neighbors
D_neigh, E_idx = torch.topk(D, min(top_k, L-1), largest=False) # shape of E_idx: (B, L, top_k)
topk_matrix = torch.zeros((B, L, L), device=device)
topk_matrix.scatter_(2, E_idx, 1.0)
# put an edge if any of the 3 conditions are met:
# 1) |i-j| <= kmin (connect sequentially adjacent residues)
# 2) top_k neighbors
cond = torch.logical_or(topk_matrix > 0.0, sep < nlocal)
b,i,j = torch.where(cond)
src = b*L+i
tgt = b*L+j
G = dgl.graph((src, tgt), num_nodes=B*L).to(device)
G.edata['rel_pos'] = (xyz[b,j,:] - xyz[b,i,:]).detach() # no gradient through basis function
return G, pair[b,i,j][...,None]
def make_atom_graph( xyz, mask, num_bonds, top_k=16, maxbonds=4 ):
B,L,A = xyz.shape[:3]
device = xyz.device
D = torch.norm(
xyz[:,None,None,:,:] - xyz[:,:,:,None,None], dim=-1
)
mask2d = mask[:,:,:,None,None]*mask[:,None,None,:,:]
D[~mask2d] = 9999.
D[D==0] = 9999.
# select top K neighbors for each atom
# keep indices as batch/res/atm indices
D_neigh, E_idx = torch.topk(D.reshape(B,L,A,-1), top_k, largest=False) # shape of E_idx: (B, L, top_k)
Eres, Eatm = torch.div(E_idx,A,rounding_mode='trunc'), E_idx%A
bi,ri,ai = mask.nonzero(as_tuple=True)
bi = bi[:,None].repeat(1,top_k).reshape(-1)
ri = ri[:,None].repeat(1,top_k).reshape(-1)
ai = ai[:,None].repeat(1,top_k).reshape(-1)
rj,aj = Eres[mask].reshape(-1), Eatm[mask].reshape(-1)
# on each edge, 1-hot encode the number of bonds (up to maxbonds) seperating each atom
edge = torch.full(ri.shape, maxbonds, device=device)
resmask = ri==rj
edge[resmask] = num_bonds[bi[resmask],ri[resmask],ai[resmask],aj[resmask]]-1
resmask = ri+1==rj
edge[resmask] = num_bonds[bi[resmask],ri[resmask],ai[resmask],2]+num_bonds[bi[resmask],rj[resmask],0,aj[resmask]]
resmask = ri-1==rj
edge[resmask] = num_bonds[bi[resmask],ri[resmask],ai[resmask],0]+num_bonds[bi[resmask],rj[resmask],2,aj[resmask]]
edge = edge.clamp(0,maxbonds-1)
edge = F.one_hot(edge)[...,None]
natm = torch.sum(mask)
index = torch.zeros_like(mask, dtype=torch.long, device=device)
index[mask] = torch.arange(natm, device=device)
src=index[bi,ri,ai]
tgt=index[bi,rj,aj]
G = dgl.graph((src, tgt), num_nodes=natm).to(device)
G.edata['rel_pos'] = (xyz[bi,ri,ai] - xyz[bi,rj,aj]).detach() # no gradient through basis function
return G, edge
# rotate about the x axis
def make_rotX(angs, eps=1e-6):
B,L = angs.shape[:2]
NORM = torch.linalg.norm(angs, dim=-1) + eps
RTs = torch.eye(4, device=angs.device).repeat(B,L,1,1)
RTs[:,:,1,1] = angs[:,:,0]/NORM
RTs[:,:,1,2] = -angs[:,:,1]/NORM
RTs[:,:,2,1] = angs[:,:,1]/NORM
RTs[:,:,2,2] = angs[:,:,0]/NORM
return RTs
# rotate about the x axis
def make_rotZ(angs, eps=1e-6):
B,L = angs.shape[:2]
NORM = torch.linalg.norm(angs, dim=-1) + eps
RTs = torch.eye(4, device=angs.device).repeat(B,L,1,1)
RTs[:,:,0,0] = angs[:,:,0]/NORM
RTs[:,:,0,1] = -angs[:,:,1]/NORM
RTs[:,:,1,0] = angs[:,:,1]/NORM
RTs[:,:,1,1] = angs[:,:,0]/NORM
return RTs
# rotate about an arbitrary axis
def make_rot_axis(angs, u, eps=1e-6):
B,L = angs.shape[:2]
NORM = torch.linalg.norm(angs, dim=-1) + eps
RTs = torch.eye(4, device=angs.device).repeat(B,L,1,1)
ct = angs[:,:,0]/NORM
st = angs[:,:,1]/NORM
u0 = u[:,:,0]
u1 = u[:,:,1]
u2 = u[:,:,2]
RTs[:,:,0,0] = ct+u0*u0*(1-ct)
RTs[:,:,0,1] = u0*u1*(1-ct)-u2*st
RTs[:,:,0,2] = u0*u2*(1-ct)+u1*st
RTs[:,:,1,0] = u0*u1*(1-ct)+u2*st
RTs[:,:,1,1] = ct+u1*u1*(1-ct)
RTs[:,:,1,2] = u1*u2*(1-ct)-u0*st
RTs[:,:,2,0] = u0*u2*(1-ct)-u1*st
RTs[:,:,2,1] = u1*u2*(1-ct)+u0*st
RTs[:,:,2,2] = ct+u2*u2*(1-ct)
return RTs
# compute allatom structure from backbone frames and torsions
#
# alphas:
# omega/phi/psi: 0-2
# chi_1-4(prot): 3-6
# cb/cg bend: 7-9
# eps(p)/zeta(p): 10-11
# alpha/beta/gamma/delta: 12-15
# nu2/nu1/nu0: 16-18
# chi_1(na): 19
#
# RTs_in_base_frame:
# omega/phi/psi: 0-2
# chi_1-4(prot): 3-6
# eps(p)/zeta(p): 7-8
# alpha/beta/gamma/delta: 9-12
# nu2/nu1/nu0: 13-15
# chi_1(na): 16
#
# RT frames (output):
# origin: 0
# omega/phi/psi: 1-3
# chi_1-4(prot): 4-7
# cb bend: 8
# alpha/beta/gamma/delta: 9-12
# nu2/nu1/nu0: 13-15
# chi_1(na): 16
#
class XYZConverter(nn.Module):
def __init__(self):
super(XYZConverter, self).__init__()
self.register_buffer("torsion_indices", ChemData().torsion_indices, persistent=False)
self.register_buffer("torsion_can_flip", ChemData().torsion_can_flip.to(torch.int32), persistent=False)
self.register_buffer("ref_angles", ChemData().reference_angles, persistent=False)
self.register_buffer("base_indices", ChemData().base_indices, persistent=False)
self.register_buffer("RTs_in_base_frame", ChemData().RTs_by_torsion, persistent=False)
self.register_buffer("xyzs_in_base_frame", ChemData().xyzs_in_base_frame, persistent=False)
def compute_all_atom(self, seq, xyz, alphas):
B,L = xyz.shape[:2]
is_NA = is_nucleic(seq)
Rs, Ts = rigid_from_3_points(xyz[...,0,:],xyz[...,1,:],xyz[...,2,:], is_NA)
RTF0 = torch.eye(4).repeat(B,L,1,1).to(device=Rs.device)
# bb
RTF0[:,:,:3,:3] = Rs
RTF0[:,:,:3,3] = Ts
# omega
RTF1 = torch.einsum(
'brij,brjk,brkl->bril',
RTF0, self.RTs_in_base_frame[seq,0,:], make_rotX(alphas[:,:,0,:]))
# phi
RTF2 = torch.einsum(
'brij,brjk,brkl->bril',
RTF0, self.RTs_in_base_frame[seq,1,:], make_rotX(alphas[:,:,1,:]))
# psi
RTF3 = torch.einsum(
'brij,brjk,brkl->bril',
RTF0, self.RTs_in_base_frame[seq,2,:], make_rotX(alphas[:,:,2,:]))
# CB bend
basexyzs = self.xyzs_in_base_frame[seq]
NCr = 0.5*(basexyzs[:,:,2,:3]+basexyzs[:,:,0,:3])
CAr = (basexyzs[:,:,1,:3])
CBr = (basexyzs[:,:,4,:3])
CBrotaxis1 = (CBr-CAr).cross(NCr-CAr)
CBrotaxis1 /= torch.linalg.norm(CBrotaxis1, dim=-1, keepdim=True)+1e-8
# CB twist
NCp = basexyzs[:,:,2,:3] - basexyzs[:,:,0,:3]
NCpp = NCp - torch.sum(NCp*NCr, dim=-1, keepdim=True)/ torch.sum(NCr*NCr, dim=-1, keepdim=True) * NCr
CBrotaxis2 = (CBr-CAr).cross(NCpp)
CBrotaxis2 /= torch.linalg.norm(CBrotaxis2, dim=-1, keepdim=True)+1e-8
CBrot1 = make_rot_axis(alphas[:,:,7,:], CBrotaxis1 )
CBrot2 = make_rot_axis(alphas[:,:,8,:], CBrotaxis2 )
RTF8 = torch.einsum(
'brij,brjk,brkl->bril',
RTF0, CBrot1,CBrot2)
# chi1 + CG bend
RTF4 = torch.einsum(
'brij,brjk,brkl,brlm->brim',
RTF8,
self.RTs_in_base_frame[seq,3,:],
make_rotX(alphas[:,:,3,:]),
make_rotZ(alphas[:,:,9,:]))
# chi2
RTF5 = torch.einsum(
'brij,brjk,brkl->bril',
RTF4, self.RTs_in_base_frame[seq,4,:],make_rotX(alphas[:,:,4,:]))
# chi3
RTF6 = torch.einsum(
'brij,brjk,brkl->bril',
RTF5,self.RTs_in_base_frame[seq,5,:],make_rotX(alphas[:,:,5,:]))
# chi4
RTF7 = torch.einsum(
'brij,brjk,brkl->bril',
RTF6,self.RTs_in_base_frame[seq,6,:],make_rotX(alphas[:,:,6,:]))
# ignore RTs_in_base_frame[seq,7:9,:] and alphas[:,:,10:12,:]
# which mode are we running in
if (not ChemData().params.use_phospate_frames_for_NA):
# NA nu1 --> from base frame
RTF14 = torch.einsum(
'brij,brjk,brkl->bril',
RTF0, self.RTs_in_base_frame[seq,14,:], make_rotX(alphas[:,:,17,:]))
# NA nu0 --> from base frame
RTF15 = torch.einsum(
'brij,brjk,brkl->bril',
RTF0, self.RTs_in_base_frame[seq,15,:], make_rotX(alphas[:,:,18,:]))
# NA chi --> from base frame
RTF16= torch.einsum(
'brij,brjk,brkl->bril',
RTF0, self.RTs_in_base_frame[seq,16,:], make_rotX(alphas[:,:,19,:]))
# NA nu2 --> from nu1 frame
RTF13 = torch.einsum(
'brij,brjk,brkl->bril',
RTF14, self.RTs_in_base_frame[seq,13,:], make_rotX(alphas[:,:,16,:]))
# NA delta --> from nu2 frame
RTF12 = torch.einsum(
'brij,brjk,brkl->bril',
RTF13, self.RTs_in_base_frame[seq,12,:], make_rotX(alphas[:,:,15,:]))
# NA gamma --> from delta frame
RTF11 = torch.einsum(
'brij,brjk,brkl->bril',
RTF12, self.RTs_in_base_frame[seq,11,:], make_rotX(alphas[:,:,14,:]))
# NA beta --> from gamma frame
RTF10 = torch.einsum(
'brij,brjk,brkl->bril',
RTF11, self.RTs_in_base_frame[seq,10,:], make_rotX(alphas[:,:,13,:]))
# NA alpha --> from beta frame
RTF9 = torch.einsum(
'brij,brjk,brkl->bril',
RTF10, self.RTs_in_base_frame[seq,9,:], make_rotX(alphas[:,:,12,:]))
else:
# NA alpha
RTF9 = torch.einsum(
'brij,brjk,brkl->bril',
RTF0, self.RTs_in_base_frame[seq,9,:], make_rotX(alphas[:,:,12,:]))
# NA beta
RTF10 = torch.einsum(
'brij,brjk,brkl->bril',
RTF9, self.RTs_in_base_frame[seq,10,:], make_rotX(alphas[:,:,13,:]))
# NA gamma
RTF11 = torch.einsum(
'brij,brjk,brkl->bril',
RTF10, self.RTs_in_base_frame[seq,11,:], make_rotX(alphas[:,:,14,:]))
# NA delta
RTF12 = torch.einsum(
'brij,brjk,brkl->bril',
RTF11, self.RTs_in_base_frame[seq,12,:], make_rotX(alphas[:,:,15,:]))
# NA nu2 - from gamma frame
RTF13 = torch.einsum(
'brij,brjk,brkl->bril',
RTF11, self.RTs_in_base_frame[seq,13,:], make_rotX(alphas[:,:,16,:]))
# NA nu1
RTF14 = torch.einsum(
'brij,brjk,brkl->bril',
RTF13, self.RTs_in_base_frame[seq,14,:], make_rotX(alphas[:,:,17,:]))
# NA nu0
RTF15 = torch.einsum(
'brij,brjk,brkl->bril',
RTF14, self.RTs_in_base_frame[seq,15,:], make_rotX(alphas[:,:,18,:]))
# NA chi - from nu1 frame
RTF16= torch.einsum(
'brij,brjk,brkl->bril',
RTF14, self.RTs_in_base_frame[seq,16,:], make_rotX(alphas[:,:,19,:]))
RTframes = torch.stack((
RTF0,RTF1,RTF2,RTF3,RTF4,RTF5,RTF6,RTF7,RTF8,
RTF9,RTF10,RTF11,RTF12,RTF13,RTF14,RTF15,RTF16
),dim=2)
xyzs = torch.einsum(
'brtij,brtj->brti',
RTframes.gather(2,self.base_indices[seq][...,None,None].repeat(1,1,1,4,4)), basexyzs
)
return RTframes, xyzs[...,:3]
def get_tor_mask(self, seq, mask_in=None):
B,L = seq.shape[:2]
dna_mask = is_nucleic(seq)
prot_mask = ~dna_mask
tors_mask = self.torsion_indices[seq,:,-1] > 0
if mask_in != None:
N = mask_in.shape[2]
ts = self.torsion_indices[seq]
bs = torch.arange(B, device=seq.device)[:,None,None,None]
rs = torch.arange(L, device=seq.device)[None,:,None,None] - (ts<0)*1 # ts<-1 ==> prev res
ts = torch.abs(ts)
tors_mask *= mask_in[bs,rs,ts].all(dim=-1)
return tors_mask
def get_torsions(self, xyz_in, seq, mask_in=None):
B,L = xyz_in.shape[:2]
tors_mask = self.get_tor_mask(seq, mask_in)
# idealize given xyz coordinates before computing torsion angles
xyz = idealize_reference_frame(seq, xyz_in)
ts = self.torsion_indices[seq]
bs = torch.arange(B, device=xyz_in.device)[:,None,None,None]
xs = torch.arange(L, device=xyz_in.device)[None,:,None,None] - (ts<0)*1 # ts<-1 ==> prev res
ys = torch.abs(ts)
xyzs_bytor = xyz[bs,xs,ys,:]
torsions = torch.zeros( (B,L,ChemData().NTOTALDOFS,2), device=xyz_in.device )
# protein torsion
torsions[...,:7,:] = th_dih(
xyzs_bytor[...,:7,0,:],xyzs_bytor[...,:7,1,:],xyzs_bytor[...,:7,2,:],xyzs_bytor[...,:7,3,:]
)
torsions[:,:,2,:] = -1 * torsions[:,:,2,:] # shift psi by pi
# NA
torsions[...,10:,:] = th_dih(
xyzs_bytor[...,10:,0,:],xyzs_bytor[...,10:,1,:],xyzs_bytor[...,10:,2,:],xyzs_bytor[...,10:,3,:]
)
# protein angles
# CB bend
NC = 0.5*( xyz[:,:,0,:3] + xyz[:,:,2,:3] )
CA = xyz[:,:,1,:3]
CB = xyz[:,:,4,:3]
t = th_ang_v(CB-CA,NC-CA)
t0 = self.ref_angles[seq][...,0,:]
torsions[:,:,7,:] = torch.stack(
(torch.sum(t*t0,dim=-1),t[...,0]*t0[...,1]-t[...,1]*t0[...,0]),
dim=-1 )
# CB twist
NCCA = NC-CA
NCp = xyz[:,:,2,:3] - xyz[:,:,0,:3]
NCpp = NCp - torch.sum(NCp*NCCA, dim=-1, keepdim=True)/ torch.sum(NCCA*NCCA, dim=-1, keepdim=True) * NCCA
t = th_ang_v(CB-CA,NCpp)
t0 = self.ref_angles[seq][...,1,:]
torsions[:,:,8,:] = torch.stack(
(torch.sum(t*t0,dim=-1),t[...,0]*t0[...,1]-t[...,1]*t0[...,0]),
dim=-1 )
# CG bend
CG = xyz[:,:,5,:3]
t = th_ang_v(CG-CB,CA-CB)
t0 = self.ref_angles[seq][...,2,:]
torsions[:,:,9,:] = torch.stack(
(torch.sum(t*t0,dim=-1),t[...,0]*t0[...,1]-t[...,1]*t0[...,0]),
dim=-1 )
mask0 = (torch.isnan(torsions[...,0])).nonzero()
mask1 = (torch.isnan(torsions[...,1])).nonzero()
torsions[mask0[:,0],mask0[:,1],mask0[:,2],0] = 1.0
torsions[mask1[:,0],mask1[:,1],mask1[:,2],1] = 0.0
# alt chis
torsions_alt = torsions.clone()
torsions_alt[self.torsion_can_flip[seq,:].to(torch.bool)] *= -1
# torsions to restrain to 0 or 180 degree
# (this should be specified in chemical?)
tors_planar = torch.zeros((B, L, ChemData().NTOTALDOFS), dtype=torch.bool, device=xyz_in.device)
tors_planar[:,:,5] = seq == ChemData().aa2num['TYR'] # TYR chi 3 should be planar
return torsions, torsions_alt, tors_mask, tors_planar
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