import os,sys
# install environment goods
#os.system("pip -q install dgl -f https://data.dgl.ai/wheels/cu113/repo.html")
os.system('pip install dgl==1.0.2+cu116 -f https://data.dgl.ai/wheels/cu116/repo.html')
#os.system('pip install gradio')
os.environ["DGLBACKEND"] = "pytorch"
#os.system(f'pip install -r ./PROTEIN_GENERATOR/requirements.txt')
print('Modules installed')
#os.system('pip install --force gradio==3.36.1')
#os.system('pip install gradio_client==0.2.7')
#os.system('pip install \"numpy<2\"')
#os.system('pip install numpy --upgrade')
#os.system('pip install --force numpy==1.24.1')
if not os.path.exists('./SEQDIFF_230205_dssp_hotspots_25mask_EQtasks_mod30.pt'):
print('Downloading model weights 1')
os.system('wget http://files.ipd.uw.edu/pub/sequence_diffusion/checkpoints/SEQDIFF_230205_dssp_hotspots_25mask_EQtasks_mod30.pt')
print('Successfully Downloaded')
if not os.path.exists('./SEQDIFF_221219_equalTASKS_nostrSELFCOND_mod30.pt'):
print('Downloading model weights 2')
os.system('wget http://files.ipd.uw.edu/pub/sequence_diffusion/checkpoints/SEQDIFF_221219_equalTASKS_nostrSELFCOND_mod30.pt')
print('Successfully Downloaded')
import numpy as np
import gradio as gr
import py3Dmol
from io import StringIO
import json
import secrets
import copy
import matplotlib.pyplot as plt
from utils.sampler import HuggingFace_sampler
from utils.parsers_inference import parse_pdb
from model.util import writepdb
from utils.inpainting_util import *
plt.rcParams.update({'font.size': 13})
with open('./tmp/args.json','r') as f:
args = json.load(f)
# manually set checkpoint to load
args['checkpoint'] = None
args['dump_trb'] = False
args['dump_args'] = True
args['save_best_plddt'] = True
args['T'] = 25
args['strand_bias'] = 0.0
args['loop_bias'] = 0.0
args['helix_bias'] = 0.0
def protein_diffusion_model(sequence, seq_len, helix_bias, strand_bias, loop_bias,
secondary_structure, aa_bias, aa_bias_potential,
#target_charge, target_ph, charge_potential,
num_steps, noise, hydrophobic_target_score, hydrophobic_potential,
contigs, pssm, seq_mask, str_mask, rewrite_pdb):
dssp_checkpoint = './SEQDIFF_230205_dssp_hotspots_25mask_EQtasks_mod30.pt'
og_checkpoint = './SEQDIFF_221219_equalTASKS_nostrSELFCOND_mod30.pt'
model_args = copy.deepcopy(args)
# make sampler
S = HuggingFace_sampler(args=model_args)
# get random prefix
S.out_prefix = './tmp/'+secrets.token_hex(nbytes=10).upper()
# set args
S.args['checkpoint'] = None
S.args['dump_trb'] = False
S.args['dump_args'] = True
S.args['save_best_plddt'] = True
S.args['T'] = 20
S.args['strand_bias'] = 0.0
S.args['loop_bias'] = 0.0
S.args['helix_bias'] = 0.0
S.args['potentials'] = None
S.args['potential_scale'] = None
S.args['aa_composition'] = None
# get sequence if entered and make sure all chars are valid
alt_aa_dict = {'B':['D','N'],'J':['I','L'],'U':['C'],'Z':['E','Q'],'O':['K']}
if sequence not in ['',None]:
L = len(sequence)
aa_seq = []
for aa in sequence.upper():
if aa in alt_aa_dict.keys():
aa_seq.append(np.random.choice(alt_aa_dict[aa]))
else:
aa_seq.append(aa)
S.args['sequence'] = aa_seq
elif contigs not in ['',None]:
S.args['contigs'] = [contigs]
else:
S.args['contigs'] = [f'{seq_len}']
L = int(seq_len)
print('DEBUG: ',rewrite_pdb)
if rewrite_pdb not in ['',None]:
S.args['pdb'] = rewrite_pdb.name
if seq_mask not in ['',None]:
S.args['inpaint_seq'] = [seq_mask]
if str_mask not in ['',None]:
S.args['inpaint_str'] = [str_mask]
if secondary_structure in ['',None]:
secondary_structure = None
else:
secondary_structure = ''.join(['E' if x == 'S' else x for x in secondary_structure])
if L < len(secondary_structure):
secondary_structure = secondary_structure[:len(sequence)]
elif L == len(secondary_structure):
pass
else:
dseq = L - len(secondary_structure)
secondary_structure += secondary_structure[-1]*dseq
# potentials
potential_list = []
potential_bias_list = []
if aa_bias not in ['',None]:
potential_list.append('aa_bias')
S.args['aa_composition'] = aa_bias
if aa_bias_potential in ['',None]:
aa_bias_potential = 3
potential_bias_list.append(str(aa_bias_potential))
'''
if target_charge not in ['',None]:
potential_list.append('charge')
if charge_potential in ['',None]:
charge_potential = 1
potential_bias_list.append(str(charge_potential))
S.args['target_charge'] = float(target_charge)
if target_ph in ['',None]:
target_ph = 7.4
S.args['target_pH'] = float(target_ph)
'''
if hydrophobic_target_score not in ['',None]:
potential_list.append('hydrophobic')
S.args['hydrophobic_score'] = float(hydrophobic_target_score)
if hydrophobic_potential in ['',None]:
hydrophobic_potential = 3
potential_bias_list.append(str(hydrophobic_potential))
if pssm not in ['',None]:
potential_list.append('PSSM')
potential_bias_list.append('5')
S.args['PSSM'] = pssm.name
if len(potential_list) > 0:
S.args['potentials'] = ','.join(potential_list)
S.args['potential_scale'] = ','.join(potential_bias_list)
# normalise secondary_structure bias from range 0-0.3
S.args['secondary_structure'] = secondary_structure
S.args['helix_bias'] = helix_bias
S.args['strand_bias'] = strand_bias
S.args['loop_bias'] = loop_bias
# set T
if num_steps in ['',None]:
S.args['T'] = 20
else:
S.args['T'] = int(num_steps)
# noise
if 'normal' in noise:
S.args['sample_distribution'] = noise
S.args['sample_distribution_gmm_means'] = [0]
S.args['sample_distribution_gmm_variances'] = [1]
elif 'gmm2' in noise:
S.args['sample_distribution'] = noise
S.args['sample_distribution_gmm_means'] = [-1,1]
S.args['sample_distribution_gmm_variances'] = [1,1]
elif 'gmm3' in noise:
S.args['sample_distribution'] = noise
S.args['sample_distribution_gmm_means'] = [-1,0,1]
S.args['sample_distribution_gmm_variances'] = [1,1,1]
if secondary_structure not in ['',None] or helix_bias+strand_bias+loop_bias > 0:
S.args['checkpoint'] = dssp_checkpoint
S.args['d_t1d'] = 29
print('using dssp checkpoint')
else:
S.args['checkpoint'] = og_checkpoint
S.args['d_t1d'] = 24
print('using og checkpoint')
for k,v in S.args.items():
print(f"{k} --> {v}")
# init S
S.model_init()
S.diffuser_init()
S.setup()
# sampling loop
plddt_data = []
for j in range(S.max_t):
print(f'on step {j}')
output_seq, output_pdb, plddt = S.take_step_get_outputs(j)
plddt_data.append(plddt)
yield output_seq, output_pdb, display_pdb(output_pdb), get_plddt_plot(plddt_data, S.max_t)
output_seq, output_pdb, plddt = S.get_outputs()
yield output_seq, output_pdb, display_pdb(output_pdb), get_plddt_plot(plddt_data, S.max_t)
def get_plddt_plot(plddt_data, max_t):
x = [i+1 for i in range(len(plddt_data))]
fig, ax = plt.subplots(figsize=(15,6))
ax.plot(x,plddt_data,color='#661dbf', linewidth=3,marker='o')
ax.set_xticks([i+1 for i in range(max_t)])
ax.set_yticks([(i+1)/10 for i in range(10)])
ax.set_ylim([0,1])
ax.set_ylabel('model confidence (plddt)')
ax.set_xlabel('diffusion steps (t)')
return fig
def display_pdb(path_to_pdb):
'''
#function to display pdb in py3dmol
'''
pdb = open(path_to_pdb, "r").read()
view = py3Dmol.view(width=500, height=500)
view.addModel(pdb, "pdb")
view.setStyle({'model': -1}, {"cartoon": {'colorscheme':{'prop':'b','gradient':'roygb','min':0,'max':1}}})#'linear', 'min': 0, 'max': 1, 'colors': ["#ff9ef0","#a903fc",]}}})
view.zoomTo()
output = view._make_html().replace("'", '"')
print(view._make_html())
x = f""" {output} """ # do not use ' in this input
return f""""""
'''
return f""""""
'''
# MOTIF SCAFFOLDING
def get_motif_preview(pdb_id, contigs):
'''
#function to display selected motif in py3dmol
'''
input_pdb = fetch_pdb(pdb_id=pdb_id.lower())
# rewrite pdb
parse = parse_pdb(input_pdb)
#output_name = './rewrite_'+input_pdb.split('/')[-1]
#writepdb(output_name, torch.tensor(parse_og['xyz']),torch.tensor(parse_og['seq']))
#parse = parse_pdb(output_name)
output_name = input_pdb
pdb = open(output_name, "r").read()
view = py3Dmol.view(width=500, height=500)
view.addModel(pdb, "pdb")
if contigs in ['',0]:
contigs = ['0']
else:
contigs = [contigs]
print('DEBUG: ',contigs)
pdb_map = get_mappings(ContigMap(parse,contigs))
print('DEBUG: ',pdb_map)
print('DEBUG: ',pdb_map['con_ref_idx0'])
roi = [x[1]-1 for x in pdb_map['con_ref_pdb_idx']]
colormap = {0:'#D3D3D3', 1:'#F74CFF'}
colors = {i+1: colormap[1] if i in roi else colormap[0] for i in range(parse['xyz'].shape[0])}
view.setStyle({"cartoon": {"colorscheme": {"prop": "resi", "map": colors}}})
view.zoomTo()
output = view._make_html().replace("'", '"')
print(view._make_html())
x = f""" {output} """ # do not use ' in this input
return f"""""", output_name
def fetch_pdb(pdb_id=None):
if pdb_id is None or pdb_id == "":
return None
else:
os.system(f"wget -qnc https://files.rcsb.org/view/{pdb_id}.pdb")
return f"{pdb_id}.pdb"
# MSA AND PSSM GUIDANCE
def save_pssm(file_upload):
filename = file_upload.name
orig_name = file_upload.orig_name
if filename.split('.')[-1] in ['fasta', 'a3m']:
return msa_to_pssm(file_upload)
return filename
def msa_to_pssm(msa_file):
# Define the lookup table for converting amino acids to indices
aa_to_index = {'A': 0, 'R': 1, 'N': 2, 'D': 3, 'C': 4, 'Q': 5, 'E': 6, 'G': 7, 'H': 8, 'I': 9, 'L': 10,
'K': 11, 'M': 12, 'F': 13, 'P': 14, 'S': 15, 'T': 16, 'W': 17, 'Y': 18, 'V': 19, 'X': 20, '-': 21}
# Open the FASTA file and read the sequences
records = list(SeqIO.parse(msa_file.name, "fasta"))
assert len(records) >= 1, "MSA must contain more than one protein sequecne."
first_seq = str(records[0].seq)
aligned_seqs = [first_seq]
# print(aligned_seqs)
# Perform sequence alignment using the Needleman-Wunsch algorithm
aligner = Align.PairwiseAligner()
aligner.open_gap_score = -0.7
aligner.extend_gap_score = -0.3
for record in records[1:]:
alignment = aligner.align(first_seq, str(record.seq))[0]
alignment = alignment.format().split("\n")
al1 = alignment[0]
al2 = alignment[2]
al1_fin = ""
al2_fin = ""
percent_gap = al2.count('-')/ len(al2)
if percent_gap > 0.4:
continue
for i in range(len(al1)):
if al1[i] != '-':
al1_fin += al1[i]
al2_fin += al2[i]
aligned_seqs.append(str(al2_fin))
# Get the length of the aligned sequences
aligned_seq_length = len(first_seq)
# Initialize the position scoring matrix
matrix = np.zeros((22, aligned_seq_length))
# Iterate through the aligned sequences and count the amino acids at each position
for seq in aligned_seqs:
#print(seq)
for i in range(aligned_seq_length):
if i == len(seq):
break
amino_acid = seq[i]
if amino_acid.upper() not in aa_to_index.keys():
continue
else:
aa_index = aa_to_index[amino_acid.upper()]
matrix[aa_index, i] += 1
# Normalize the counts to get the frequency of each amino acid at each position
matrix /= len(aligned_seqs)
print(len(aligned_seqs))
matrix[20:,]=0
outdir = ".".join(msa_file.name.split('.')[:-1]) + ".csv"
np.savetxt(outdir, matrix[:21,:].T, delimiter=",")
return outdir
def get_pssm(fasta_msa, input_pssm):
if input_pssm not in ['',None]:
outdir = input_pssm.name
else:
outdir = save_pssm(fasta_msa)
pssm = np.loadtxt(outdir, delimiter=",", dtype=float)
fig, ax = plt.subplots(figsize=(15,6))
plt.imshow(torch.permute(torch.tensor(pssm),(1,0)))
return fig, outdir
#toggle options
def toggle_seq_input(choice):
if choice == "protein length":
return gr.update(visible=True, value=None), gr.update(visible=False, value=None)
elif choice == "custom sequence":
return gr.update(visible=False, value=None), gr.update(visible=True, value=None)
def toggle_secondary_structure(choice):
if choice == "sliders":
return gr.update(visible=True, value=None),gr.update(visible=True, value=None),gr.update(visible=True, value=None),gr.update(visible=False, value=None)
elif choice == "explicit":
return gr.update(visible=False, value=None),gr.update(visible=False, value=None),gr.update(visible=False, value=None),gr.update(visible=True, value=None)
# Define the Gradio interface
with gr.Blocks(theme='ParityError/Interstellar') as demo:
gr.Markdown(f"""# Protein Generation via Diffusion in Sequence Space""")
with gr.Row():
with gr.Column(min_width=500):
gr.Markdown("""
## Model in Action
""")
#with gr.Row().style(equal_height=False):
with gr.Row():
with gr.Column():
with gr.Tabs():
with gr.TabItem("Inputs"):
gr.Markdown("""## INPUTS""")
gr.Markdown("""#### Start Sequence
Specify the protein length for complete unconditional generation, or scaffold a motif (or your name) using the custom sequence input""")
seq_opt = gr.Radio(["protein length","custom sequence"], label="How would you like to specify the starting sequence?", value='protein length')
sequence = gr.Textbox(label="custom sequence", lines=1, placeholder='AMINO ACIDS: A,C,D,E,F,G,H,I,K,L,M,N,P,Q,R,S,T,V,W,Y\n MASK TOKEN: X', visible=False)
seq_len = gr.Slider(minimum=5.0, maximum=250.0, label="protein length", value=100, visible=True)
seq_opt.change(fn=toggle_seq_input,
inputs=[seq_opt],
outputs=[seq_len, sequence],
queue=False)
gr.Markdown("""### Optional Parameters""")
with gr.Accordion(label='Secondary Structure',open=True):
gr.Markdown("""Try changing the sliders or inputing explicit secondary structure conditioning for each residue""")
sec_str_opt = gr.Radio(["sliders","explicit"], label="How would you like to specify secondary structure?", value='sliders')
secondary_structure = gr.Textbox(label="secondary structure", lines=1, placeholder='HELIX = H STRAND = S LOOP = L MASK = X(must be the same length as input sequence)', visible=False)
with gr.Column():
helix_bias = gr.Slider(minimum=0.0, maximum=0.05, label="helix bias", visible=True)
strand_bias = gr.Slider(minimum=0.0, maximum=0.05, label="strand bias", visible=True)
loop_bias = gr.Slider(minimum=0.0, maximum=0.20, label="loop bias", visible=True)
sec_str_opt.change(fn=toggle_secondary_structure,
inputs=[sec_str_opt],
outputs=[helix_bias,strand_bias,loop_bias,secondary_structure],
queue=False)
with gr.Accordion(label='Amino Acid Compositional Bias',open=False):
gr.Markdown("""Bias sequence composition for particular amino acids by specifying the one letter code followed by the fraction to bias. This can be input as a list for example: W0.2,E0.1""")
with gr.Row():
aa_bias = gr.Textbox(label="aa bias", lines=1, placeholder='specify one letter AA and fraction to bias, for example W0.1 or M0.1,K0.1' )
aa_bias_potential = gr.Textbox(label="aa bias scale", lines=1, placeholder='AA Bias potential scale (recomended range 1.0-5.0)')
'''
with gr.Accordion(label='Charge Bias',open=False):
gr.Markdown("""Bias for a specified net charge at a particular pH using the boxes below""")
with gr.Row():
target_charge = gr.Textbox(label="net charge", lines=1, placeholder='net charge to target')
target_ph = gr.Textbox(label="pH", lines=1, placeholder='pH at which net charge is desired')
charge_potential = gr.Textbox(label="charge potential scale", lines=1, placeholder='charge potential scale (recomended range 1.0-5.0)')
'''
with gr.Accordion(label='Hydrophobic Bias',open=False):
gr.Markdown("""Bias for or against hydrophobic composition, to get more soluble proteins, bias away with a negative target score (ex. -5)""")
with gr.Row():
hydrophobic_target_score = gr.Textbox(label="hydrophobic score", lines=1, placeholder='hydrophobic score to target (negative score is good for solublility)')
hydrophobic_potential = gr.Textbox(label="hydrophobic potential scale", lines=1, placeholder='hydrophobic potential scale (recomended range 1.0-2.0)')
with gr.Accordion(label='Diffusion Params',open=False):
gr.Markdown("""Increasing T to more steps can be helpful for harder design challenges, sampling from different distributions can change the sequence and structural composition""")
with gr.Row():
num_steps = gr.Textbox(label="T", lines=1, placeholder='number of diffusion steps (25 or less will speed things up)')
noise = gr.Dropdown(['normal','gmm2 [-1,1]','gmm3 [-1,0,1]'], label='noise type', value='normal')
with gr.TabItem("Motif Selection"):
gr.Markdown("""### Motif Selection Preview""")
gr.Markdown('Contigs explained: to grab residues (seq and str) on a pdb chain you will provide the chain letter followed by a range of residues as indexed in the pdb file for example (A3-10) is the syntax to select residues 3-10 on chain A (the chain always needs to be specified). To add diffused residues to either side of this motif you can specify a range or discrete value without a chain letter infront. To add 15 residues before the motif and 20-30 residues (randomly sampled) after use the following syntax: 15,A3-10,20-30 commas are used to separate regions selected from the pdb and designed (diffused) resiudes which will be added. ')
pdb_id_code = gr.Textbox(label="PDB ID", lines=1, placeholder='INPUT PDB ID TO FETCH (ex. 1DPX)', visible=True)
contigs = gr.Textbox(label="contigs", lines=1, placeholder='specify contigs to grab particular residues from pdb ()', visible=True)
gr.Markdown('Using the same contig syntax, seq or str of input motif residues can be masked, allowing the model to hold strucutre fixed and design sequence or vice-versa')
with gr.Row():
seq_mask = gr.Textbox(label='seq mask',lines=1,placeholder='input residues to mask sequence')
str_mask = gr.Textbox(label='str mask',lines=1,placeholder='input residues to mask structure')
preview_viewer = gr.HTML()
rewrite_pdb = gr.File(label='PDB file')
preview_btn = gr.Button("Preview Motif")
with gr.TabItem("MSA to PSSM"):
gr.Markdown("""### MSA to PSSM Generation""")
gr.Markdown('input either an MSA or PSSM to guide the model toward generating samples within your family of interest')
with gr.Row():
fasta_msa = gr.File(label='MSA')
input_pssm = gr.File(label='PSSM (.csv)')
pssm = gr.File(label='Generated PSSM')
pssm_view = gr.Plot(label='PSSM Viewer')
pssm_gen_btn = gr.Button("Generate PSSM")
btn = gr.Button("GENERATE")
#with gr.Row():
with gr.Column():
gr.Markdown("""## OUTPUTS""")
gr.Markdown("""#### Confidence score for generated structure at each timestep""")
plddt_plot = gr.Plot(label='plddt at step t')
gr.Markdown("""#### Output protein sequnece""")
output_seq = gr.Textbox(label="sequence")
gr.Markdown("""#### Download PDB file""")
output_pdb = gr.File(label="PDB file")
gr.Markdown("""#### Structure viewer""")
output_viewer = gr.HTML()
'''
gr.Markdown("""### Don't know where to get started? Click on an example below to try it out!""")
gr.Examples(
[["","125",0.0,0.0,0.2,"","","","20","normal",'','','',None,'','',None],
["","100",0.0,0.0,0.0,"","W0.2","2","20","normal",'','','',None,'','',None],
# ["","100",0.0,0.0,0.0,
# "XXHHHHHHHHHXXXXXXXHHHHHHHHHXXXXXXXHHHHHHHHXXXXSSSSSSSSSSSXXXXXXXXSSSSSSSSSSSSXXXXXXXSSSSSSSSSXXXXXXX",
# "","","25","normal",'','','',None,'','',None],
# ["XXXXXXXXXXXXXXXXXXXXXXXXXIPDXXXXXXXXXXXXXXXXXXXXXXPEPSEQXXXXXXXXXXXXXXXXXXXXXXXXXXIPDXXXXXXXXXXXXXXXXXXX",
# "",0.0,0.0,0.0,"","","","25","normal",'','','',None,'','',None],
# ["","",0.0,0.0,0.0,"","","","25","normal",'','',
# '9,D10-11,8,D20-20,4,D25-35,65,D101-101,2,D104-105,8,D114-116,15,D132-138,6,D145-145,2,D148-148,12,D161-161,3',
# './tmp/PSSM_lysozyme.csv',
# 'D25-25,D27-31,D33-35,D132-137',
# 'D26-26','./tmp/150l.pdb']
],
inputs=[sequence,
seq_len,
helix_bias,
strand_bias,
loop_bias,
secondary_structure,
aa_bias,
aa_bias_potential,
#target_charge,
#target_ph,
#charge_potential,
num_steps,
noise,
hydrophobic_target_score,
hydrophobic_potential,
contigs,
pssm,
seq_mask,
str_mask,
rewrite_pdb],
outputs=[output_seq,
output_pdb,
output_viewer,
plddt_plot],
fn=protein_diffusion_model,
)
'''
preview_btn.click(get_motif_preview,[pdb_id_code, contigs],[preview_viewer, rewrite_pdb])
pssm_gen_btn.click(get_pssm,[fasta_msa,input_pssm],[pssm_view, pssm])
btn.click(protein_diffusion_model,
[sequence,
seq_len,
helix_bias,
strand_bias,
loop_bias,
secondary_structure,
aa_bias,
aa_bias_potential,
#target_charge,
#target_ph,
#charge_potential,
num_steps,
noise,
hydrophobic_target_score,
hydrophobic_potential,
contigs,
pssm,
seq_mask,
str_mask,
rewrite_pdb],
[output_seq,
output_pdb,
output_viewer,
plddt_plot])
demo.queue()
demo.launch(debug=True)