app.py

import json, time, os, sys, glob

import gradio as gr

sys.path.append("/home/user/app/ProteinMPNN/vanilla_proteinmpnn")

sys.path.append("/home/duerr/phd/08_Code/ProteinMPNN/ProteinMPNN/vanilla_proteinmpnn")

import matplotlib.pyplot as plt
import shutil
import warnings
import numpy as np
import torch
from torch import optim
from torch.utils.data import DataLoader
from torch.utils.data.dataset import random_split, Subset
import copy
import torch.nn as nn
import torch.nn.functional as F
import random
import os
import os.path

import plotly.express as px
import urllib
import jax.numpy as jnp
import tensorflow as tf


from moleculekit.molecule import Molecule

if "/home/user/app/af_backprop" not in sys.path:
    sys.path.append("/home/user/app/af_backprop")

# local only
if "/home/duerr/phd/08_Code/ProteinMPNN/af_backprop" not in sys.path:
    sys.path.append("/home/duerr/phd/08_Code/ProteinMPNN/af_backprop")

from utils import *

# import libraries
import colabfold as cf
from alphafold.common import protein
from alphafold.data import pipeline
from alphafold.model import data, config
from alphafold.model import model as afmodel
from alphafold.common import residue_constants


import plotly.graph_objects as go
import ray

import re

import numpy as np
import jax

tf.config.set_visible_devices([], "GPU")


def chain_break(idx_res, Ls, length=200):
    # Minkyung's code
    # add big enough number to residue index to indicate chain breaks
    L_prev = 0
    for L_i in Ls[:-1]:
        idx_res[L_prev + L_i :] += length
        L_prev += L_i
    return idx_res


def clear_mem():
    backend = jax.lib.xla_bridge.get_backend()
    for buf in backend.live_buffers():
        buf.delete()


def setup_af(seq, model_name="model_5_ptm"):
    clear_mem()
    # setup model
    cfg = config.model_config("model_5_ptm")
    cfg.model.num_recycle = 0
    cfg.data.common.num_recycle = 0
    cfg.data.eval.max_msa_clusters = 1
    cfg.data.common.max_extra_msa = 1
    cfg.data.eval.masked_msa_replace_fraction = 0
    cfg.model.global_config.subbatch_size = None
    if os.path.exists("/home/duerr"):
        datadir = "/home/duerr/phd/08_Code/ProteinMPNN"
    else:
        datadir = "/home/user/app/"
    model_params = data.get_model_haiku_params(model_name=model_name, data_dir=datadir)
    model_runner = afmodel.RunModel(cfg, model_params, is_training=False)
    Ls = [len(s) for s in seq.split("/")]

    seq = re.sub("[^A-Z]", "", seq.upper())
    length = len(seq)
    feature_dict = {
        **pipeline.make_sequence_features(
            sequence=seq, description="none", num_res=length
        ),
        **pipeline.make_msa_features(msas=[[seq]], deletion_matrices=[[[0] * length]]),
    }
    feature_dict["residue_index"] = chain_break(feature_dict["residue_index"], Ls)
    inputs = model_runner.process_features(feature_dict, random_seed=0)

    def runner(seq, opt):
        # update sequence
        inputs = opt["inputs"]
        inputs.update(opt["prev"])
        update_seq(seq, inputs)
        update_aatype(inputs["target_feat"][..., 1:], inputs)

        # mask prediction
        mask = seq.sum(-1)
        inputs["seq_mask"] = inputs["seq_mask"].at[:].set(mask)
        inputs["msa_mask"] = inputs["msa_mask"].at[:].set(mask)
        inputs["residue_index"] = jnp.where(mask == 1, inputs["residue_index"], 0)

        # get prediction
        key = jax.random.PRNGKey(0)
        outputs = model_runner.apply(opt["params"], key, inputs)

        prev = {
            "init_msa_first_row": outputs["representations"]["msa_first_row"][None],
            "init_pair": outputs["representations"]["pair"][None],
            "init_pos": outputs["structure_module"]["final_atom_positions"][None],
        }

        aux = {
            "final_atom_positions": outputs["structure_module"]["final_atom_positions"],
            "final_atom_mask": outputs["structure_module"]["final_atom_mask"],
            "plddt": get_plddt(outputs),
            "pae": get_pae(outputs),
            "inputs": inputs,
            "prev": prev,
        }
        return aux

    return jax.jit(runner), {"inputs": inputs, "params": model_params}


def make_tied_positions_for_homomers(pdb_dict_list):
    my_dict = {}
    for result in pdb_dict_list:
        all_chain_list = sorted(
            [item[-1:] for item in list(result) if item[:9] == "seq_chain"]
        )  # A, B, C, ...
        tied_positions_list = []
        chain_length = len(result[f"seq_chain_{all_chain_list[0]}"])
        for i in range(1, chain_length + 1):
            temp_dict = {}
            for j, chain in enumerate(all_chain_list):
                temp_dict[chain] = [i]  # needs to be a list
            tied_positions_list.append(temp_dict)
        my_dict[result["name"]] = tied_positions_list
    return my_dict


def align_structures(pdb1, pdb2, lenRes):
    """Take two structure and superimpose pdb1 on pdb2"""
    import Bio.PDB
    import subprocess

    pdb_parser = Bio.PDB.PDBParser(QUIET=True)
    # Get the structures
    ref_structure = pdb_parser.get_structure("samle", pdb1)
    sample_structure = pdb_parser.get_structure("reference", pdb2)

    aligner = Bio.PDB.CEAligner()
    aligner.set_reference(ref_structure)
    aligner.align(sample_structure)

    io = Bio.PDB.PDBIO()
    io.set_structure(ref_structure)
    io.save(f"reference.pdb")
    # Doing this to get around biopython CEALIGN bug
    subprocess.call("pymol -c -Q -r cealign.pml", shell=True)

    return aligner.rms, "reference.pdb", "out_aligned.pdb"


def save_pdb(outs, filename, LEN):
    """save pdb coordinates"""
    p = {
        "residue_index": outs["inputs"]["residue_index"][0][:LEN],
        "aatype": outs["inputs"]["aatype"].argmax(-1)[0][:LEN],
        "atom_positions": outs["final_atom_positions"][:LEN],
        "atom_mask": outs["final_atom_mask"][:LEN],
    }
    b_factors = 100.0 * outs["plddt"][:LEN, None] * p["atom_mask"]
    p = protein.Protein(**p, b_factors=b_factors)
    pdb_lines = protein.to_pdb(p)
    with open(filename, "w") as f:
        f.write(pdb_lines)


@ray.remote(num_gpus=1, max_calls=1)
def run_alphafold(sequence, num_recycles):
    recycles = num_recycles
    RUNNER, OPT = setup_af(sequence)

    SEQ = re.sub("[^A-Z]", "", sequence.upper())
    MAX_LEN = len(SEQ)
    LEN = len(SEQ)

    x = np.array([residue_constants.restype_order.get(aa, -1) for aa in SEQ])
    x = np.pad(x, [0, MAX_LEN - LEN], constant_values=-1)
    x = jax.nn.one_hot(x, 20)

    OPT["prev"] = {
        "init_msa_first_row": np.zeros([1, MAX_LEN, 256]),
        "init_pair": np.zeros([1, MAX_LEN, MAX_LEN, 128]),
        "init_pos": np.zeros([1, MAX_LEN, 37, 3]),
    }

    positions = []
    plddts = []
    for r in range(recycles + 1):
        outs = RUNNER(x, OPT)
        outs = jax.tree_map(lambda x: np.asarray(x), outs)
        positions.append(outs["prev"]["init_pos"][0, :LEN])
        plddts.append(outs["plddt"][:LEN])
        OPT["prev"] = outs["prev"]
        if recycles > 0:
            print(r, plddts[-1].mean())
    if os.path.exists("/home/duerr/phd/08_Code/ProteinMPNN"):
        save_pdb(outs, "/home/duerr/phd/08_Code/ProteinMPNN/out.pdb", LEN)
    else:
        save_pdb(outs, "/home/user/app/out.pdb", LEN)
    return plddts, outs["pae"], LEN


if os.path.exists("/home/duerr/phd/08_Code/ProteinMPNN"):
    path_to_model_weights = "/home/duerr/phd/08_Code/ProteinMPNN/ProteinMPNN/vanilla_proteinmpnn/vanilla_model_weights"
else:
    path_to_model_weights = (
        "/home/user/app/ProteinMPNN/vanilla_proteinmpnn/vanilla_model_weights"
    )


def setup_proteinmpnn(model_name="v_48_020", backbone_noise=0.00):
    from protein_mpnn_utils import (
        loss_nll,
        loss_smoothed,
        gather_edges,
        gather_nodes,
        gather_nodes_t,
        cat_neighbors_nodes,
        _scores,
        _S_to_seq,
        tied_featurize,
        parse_PDB,
    )
    from protein_mpnn_utils import StructureDataset, StructureDatasetPDB, ProteinMPNN

    device = torch.device(
        "cpu"
    )  # torch.device("cuda:0" if (torch.cuda.is_available()) else "cpu") #fix for memory issues
    # ProteinMPNN model name: v_48_002, v_48_010, v_48_020, v_48_030, v_32_002, v_32_010; v_32_020, v_32_030; v_48_010=version with 48 edges 0.10A noise
    # Standard deviation of Gaussian noise to add to backbone atoms
    hidden_dim = 128
    num_layers = 3
    model_folder_path = path_to_model_weights
    if model_folder_path[-1] != "/":
        model_folder_path = model_folder_path + "/"
    checkpoint_path = model_folder_path + f"{model_name}.pt"

    checkpoint = torch.load(checkpoint_path, map_location=device)

    noise_level_print = checkpoint["noise_level"]

    model = ProteinMPNN(
        num_letters=21,
        node_features=hidden_dim,
        edge_features=hidden_dim,
        hidden_dim=hidden_dim,
        num_encoder_layers=num_layers,
        num_decoder_layers=num_layers,
        augment_eps=backbone_noise,
        k_neighbors=checkpoint["num_edges"],
    )
    model.to(device)
    model.load_state_dict(checkpoint["model_state_dict"])
    model.eval()
    return model, device


def get_pdb(pdb_code="", filepath=""):
    if pdb_code is None or pdb_code == "":
        try:
            return filepath.name
        except AttributeError as e:
            return None
    else:
        os.system(f"wget -qnc https://files.rcsb.org/view/{pdb_code}.pdb")
        return f"{pdb_code}.pdb"


def preprocess_mol(pdb_code="", filepath=""):
    if pdb_code is None or pdb_code == "":
        try:
            mol = Molecule(filepath.name)
        except AttributeError as e:
            return None
    else:
        mol = Molecule(pdb_code)
    mol.write('original.pdb')
    # clean messy files and only include protein itself
    mol.filter("protein")
    # renumber using moleculekit 0...len(protein)
    df = mol.renumberResidues(returnMapping=True)
    # add proteinMPNN index col which used 1..len(chain), 1...len(chain)
    indexes = []
    for chain, g in df.groupby("chain"):
        j = 1
        for i, row in g.iterrows():
            indexes.append(j)
            j += 1
    df["proteinMPNN_index"] = indexes
    mol.write("cleaned.pdb")
    return "cleaned.pdb", df

def make_fixed_positions_dict(atomsel, residue_index_df):
    # we use the uploaded file for the selection
    mol = Molecule('original.pdb')
    # use index for selection as resids will change
    selected_residues = mol.get("index",atomsel)

    # clean up
    mol.filter("protein")
    mol.renumberResidues()
    # based on selected index now get resids
    selected_residues = [str(i) for i in selected_residues]
    if len(selected_residues)==0:
        return None, []
    selected_residues_str = " ".join(selected_residues)
    selected_residues=set(mol.get('resid', sel=f"index {selected_residues_str}"))

    # use the proteinMPNN index nomenclature to assemble fixed_positions_dict
    fixed_positions_df = residue_index_df[residue_index_df['new_resid'].isin(selected_residues)]

    chains = set(mol.get('chain', sel="all"))
    fixed_position_dict = {'cleaned':{}}
    #store the selected residues in a list for the visualization later with cleaned.pdb
    selected_residues = list(fixed_positions_df['new_resid'])

    for c in chains:
        fixed_position_dict['cleaned'][c]=[]

    for i, row in fixed_positions_df.iterrows():
        fixed_position_dict['cleaned'][row['chain']].append(row['proteinMPNN_index'])
    return fixed_position_dict, selected_residues

def update(
    inp,
    file,
    designed_chain,
    fixed_chain,
    homomer,
    num_seqs,
    sampling_temp,
    model_name,
    backbone_noise,
    atomsel
):
    from protein_mpnn_utils import (
        loss_nll,
        loss_smoothed,
        gather_edges,
        gather_nodes,
        gather_nodes_t,
        cat_neighbors_nodes,
        _scores,
        _S_to_seq,
        tied_featurize,
        parse_PDB,
    )
    from protein_mpnn_utils import StructureDataset, StructureDatasetPDB, ProteinMPNN

    # pdb_path = get_pdb(pdb_code=inp, filepath=file)

    pdb_path, mol_index = preprocess_mol(pdb_code=inp, filepath=file)

    if pdb_path == None:
        return "Error processing PDB"

    model, device = setup_proteinmpnn(
        model_name=model_name, backbone_noise=backbone_noise
    )

    if designed_chain == "":
        designed_chain_list = []
    else:
        designed_chain_list = re.sub("[^A-Za-z]+", ",", designed_chain).split(",")

    if fixed_chain == "":
        fixed_chain_list = []
    else:
        fixed_chain_list = re.sub("[^A-Za-z]+", ",", fixed_chain).split(",")

    chain_list = list(set(designed_chain_list + fixed_chain_list))
    num_seq_per_target = num_seqs
    save_score = 0  # 0 for False, 1 for True; save score=-log_prob to npy files
    save_probs = (
        0  # 0 for False, 1 for True; save MPNN predicted probabilites per position
    )
    score_only = 0  # 0 for False, 1 for True; score input backbone-sequence pairs
    conditional_probs_only = 0  # 0 for False, 1 for True; output conditional probabilities p(s_i given the rest of the sequence and backbone)
    conditional_probs_only_backbone = 0  # 0 for False, 1 for True; if true output conditional probabilities p(s_i given backbone)

    batch_size = 1  # Batch size; can set higher for titan, quadro GPUs, reduce this if running out of GPU memory
    max_length = 20000  # Max sequence length

    out_folder = "."  # Path to a folder to output sequences, e.g. /home/out/
    jsonl_path = ""  # Path to a folder with parsed pdb into jsonl
    omit_AAs = "X"  # Specify which amino acids should be omitted in the generated sequence, e.g. 'AC' would omit alanine and cystine.

    pssm_multi = 0.0  # A value between [0.0, 1.0], 0.0 means do not use pssm, 1.0 ignore MPNN predictions
    pssm_threshold = 0.0  # A value between -inf + inf to restric per position AAs
    pssm_log_odds_flag = 0  # 0 for False, 1 for True
    pssm_bias_flag = 0  # 0 for False, 1 for True

    folder_for_outputs = out_folder

    NUM_BATCHES = num_seq_per_target // batch_size
    BATCH_COPIES = batch_size
    temperatures = [sampling_temp]
    omit_AAs_list = omit_AAs
    alphabet = "ACDEFGHIKLMNPQRSTVWYX"

    omit_AAs_np = np.array([AA in omit_AAs_list for AA in alphabet]).astype(np.float32)

    chain_id_dict = None
    if atomsel == "":
        fixed_positions_dict, selected_residues = None, []
    else:
        fixed_positions_dict, selected_residues=make_fixed_positions_dict(atomsel, mol_index)
    
    pssm_dict = None
    omit_AA_dict = None
    bias_AA_dict = None

    bias_by_res_dict = None
    bias_AAs_np = np.zeros(len(alphabet))

    ###############################################################
    pdb_dict_list = parse_PDB(pdb_path, input_chain_list=chain_list)
    dataset_valid = StructureDatasetPDB(
        pdb_dict_list, truncate=None, max_length=max_length
    )
    if homomer:
        tied_positions_dict = make_tied_positions_for_homomers(pdb_dict_list)
    else:
        tied_positions_dict = None
    
    chain_id_dict = {}
    chain_id_dict[pdb_dict_list[0]["name"]] = (designed_chain_list, fixed_chain_list)
    with torch.no_grad():
        for ix, prot in enumerate(dataset_valid):
            score_list = []
            all_probs_list = []
            all_log_probs_list = []
            S_sample_list = []
            batch_clones = [copy.deepcopy(prot) for i in range(BATCH_COPIES)]
            (
                X,
                S,
                mask,
                lengths,
                chain_M,
                chain_encoding_all,
                chain_list_list,
                visible_list_list,
                masked_list_list,
                masked_chain_length_list_list,
                chain_M_pos,
                omit_AA_mask,
                residue_idx,
                dihedral_mask,
                tied_pos_list_of_lists_list,
                pssm_coef,
                pssm_bias,
                pssm_log_odds_all,
                bias_by_res_all,
                tied_beta,
            ) = tied_featurize(
                batch_clones,
                device,
                chain_id_dict,
                fixed_positions_dict,
                omit_AA_dict,
                tied_positions_dict,
                pssm_dict,
                bias_by_res_dict,
            )
            pssm_log_odds_mask = (
                pssm_log_odds_all > pssm_threshold
            ).float()  # 1.0 for true, 0.0 for false
            name_ = batch_clones[0]["name"]

            randn_1 = torch.randn(chain_M.shape, device=X.device)
            log_probs = model(
                X,
                S,
                mask,
                chain_M * chain_M_pos,
                residue_idx,
                chain_encoding_all,
                randn_1,
            )
            mask_for_loss = mask * chain_M * chain_M_pos
            scores = _scores(S, log_probs, mask_for_loss)
            native_score = scores.cpu().data.numpy()
            message = ""
            seq_list = []
            for temp in temperatures:
                for j in range(NUM_BATCHES):
                    randn_2 = torch.randn(chain_M.shape, device=X.device)
                    if tied_positions_dict == None:
                        sample_dict = model.sample(
                            X,
                            randn_2,
                            S,
                            chain_M,
                            chain_encoding_all,
                            residue_idx,
                            mask=mask,
                            temperature=temp,
                            omit_AAs_np=omit_AAs_np,
                            bias_AAs_np=bias_AAs_np,
                            chain_M_pos=chain_M_pos,
                            omit_AA_mask=omit_AA_mask,
                            pssm_coef=pssm_coef,
                            pssm_bias=pssm_bias,
                            pssm_multi=pssm_multi,
                            pssm_log_odds_flag=bool(pssm_log_odds_flag),
                            pssm_log_odds_mask=pssm_log_odds_mask,
                            pssm_bias_flag=bool(pssm_bias_flag),
                            bias_by_res=bias_by_res_all,
                        )
                        S_sample = sample_dict["S"]
                    else:
                        sample_dict = model.tied_sample(
                            X,
                            randn_2,
                            S,
                            chain_M,
                            chain_encoding_all,
                            residue_idx,
                            mask=mask,
                            temperature=temp,
                            omit_AAs_np=omit_AAs_np,
                            bias_AAs_np=bias_AAs_np,
                            chain_M_pos=chain_M_pos,
                            omit_AA_mask=omit_AA_mask,
                            pssm_coef=pssm_coef,
                            pssm_bias=pssm_bias,
                            pssm_multi=pssm_multi,
                            pssm_log_odds_flag=bool(pssm_log_odds_flag),
                            pssm_log_odds_mask=pssm_log_odds_mask,
                            pssm_bias_flag=bool(pssm_bias_flag),
                            tied_pos=tied_pos_list_of_lists_list[0],
                            tied_beta=tied_beta,
                            bias_by_res=bias_by_res_all,
                        )
                        # Compute scores
                        S_sample = sample_dict["S"]
                    log_probs = model(
                        X,
                        S_sample,
                        mask,
                        chain_M * chain_M_pos,
                        residue_idx,
                        chain_encoding_all,
                        randn_2,
                        use_input_decoding_order=True,
                        decoding_order=sample_dict["decoding_order"],
                    )
                    mask_for_loss = mask * chain_M * chain_M_pos
                    scores = _scores(S_sample, log_probs, mask_for_loss)
                    scores = scores.cpu().data.numpy()
                    all_probs_list.append(sample_dict["probs"].cpu().data.numpy())
                    all_log_probs_list.append(log_probs.cpu().data.numpy())
                    S_sample_list.append(S_sample.cpu().data.numpy())
                    for b_ix in range(BATCH_COPIES):
                        masked_chain_length_list = masked_chain_length_list_list[b_ix]
                        masked_list = masked_list_list[b_ix]
                        seq_recovery_rate = torch.sum(
                            torch.sum(
                                torch.nn.functional.one_hot(S[b_ix], 21)
                                * torch.nn.functional.one_hot(S_sample[b_ix], 21),
                                axis=-1,
                            )
                            * mask_for_loss[b_ix]
                        ) / torch.sum(mask_for_loss[b_ix])
                        seq = _S_to_seq(S_sample[b_ix], chain_M[b_ix])
                        score = scores[b_ix]
                        score_list.append(score)
                        native_seq = _S_to_seq(S[b_ix], chain_M[b_ix])
                        if b_ix == 0 and j == 0 and temp == temperatures[0]:
                            start = 0
                            end = 0
                            list_of_AAs = []
                            for mask_l in masked_chain_length_list:
                                end += mask_l
                                list_of_AAs.append(native_seq[start:end])
                                start = end
                            native_seq = "".join(
                                list(np.array(list_of_AAs)[np.argsort(masked_list)])
                            )
                            l0 = 0
                            for mc_length in list(
                                np.array(masked_chain_length_list)[
                                    np.argsort(masked_list)
                                ]
                            )[:-1]:
                                l0 += mc_length
                                native_seq = native_seq[:l0] + "/" + native_seq[l0:]
                                l0 += 1
                            sorted_masked_chain_letters = np.argsort(
                                masked_list_list[0]
                            )
                            print_masked_chains = [
                                masked_list_list[0][i]
                                for i in sorted_masked_chain_letters
                            ]
                            sorted_visible_chain_letters = np.argsort(
                                visible_list_list[0]
                            )
                            print_visible_chains = [
                                visible_list_list[0][i]
                                for i in sorted_visible_chain_letters
                            ]
                            native_score_print = np.format_float_positional(
                                np.float32(native_score.mean()),
                                unique=False,
                                precision=4,
                            )
                            line = ">{}, score={}, fixed_chains={}, designed_chains={}, model_name={}\n{}\n".format(
                                name_,
                                native_score_print,
                                print_visible_chains,
                                print_masked_chains,
                                model_name,
                                native_seq,
                            )
                            message += f"{line}\n"
                        start = 0
                        end = 0
                        list_of_AAs = []
                        for mask_l in masked_chain_length_list:
                            end += mask_l
                            list_of_AAs.append(seq[start:end])
                            start = end

                        seq = "".join(
                            list(np.array(list_of_AAs)[np.argsort(masked_list)])
                        )
                        # add non designed chains to predicted sequence
                        l0 = 0
                        for mc_length in list(
                            np.array(masked_chain_length_list)[np.argsort(masked_list)]
                        )[:-1]:
                            l0 += mc_length
                            seq = seq[:l0] + "/" + seq[l0:]
                            l0 += 1
                        score_print = np.format_float_positional(
                            np.float32(score), unique=False, precision=4
                        )
                        seq_rec_print = np.format_float_positional(
                            np.float32(seq_recovery_rate.detach().cpu().numpy()),
                            unique=False,
                            precision=4,
                        )
                        chain_s = ""
                        if len(visible_list_list[0]) > 0:
                            chain_M_bool = chain_M.bool()
                            not_designed = _S_to_seq(S[b_ix], ~chain_M_bool[b_ix])

                            labels = (
                                chain_encoding_all[b_ix][~chain_M_bool[b_ix]]
                                .detach()
                                .cpu()
                                .numpy()
                            )

                            for c in set(labels):
                                chain_s += "/"
                                nd_mask = labels == c
                                for i, x in enumerate(not_designed):
                                    if nd_mask[i]:
                                        chain_s += x
                        line = (
                            ">T={}, sample={}, score={}, seq_recovery={}\n{}\n".format(
                                temp, b_ix, score_print, seq_rec_print, seq
                            )
                        )
                        seq_list.append(seq + chain_s)
                        message += f"{line}\n"

    message += f"\nfixed positions:* {fixed_positions_dict['cleaned']} \n\n*uses CHAIN:[1..len(chain)] residue numbering"
    # somehow sequences still contain X, remove again
    for i, x in enumerate(seq_list):
        for aa in omit_AAs:
            seq_list[i] = x.replace(aa, "")
    all_probs_concat = np.concatenate(all_probs_list)
    all_log_probs_concat = np.concatenate(all_log_probs_list)
    np.savetxt("all_probs_concat.csv", all_probs_concat.mean(0).T, delimiter=",")
    np.savetxt(
        "all_log_probs_concat.csv",
        np.exp(all_log_probs_concat).mean(0).T,
        delimiter=",",
    )
    S_sample_concat = np.concatenate(S_sample_list)
    fig = px.imshow(
        np.exp(all_log_probs_concat).mean(0).T,
        labels=dict(x="positions", y="amino acids", color="probability"),
        y=list(alphabet),
        template="simple_white",
    )
    fig.update_xaxes(side="top")

    fig_tadjusted = px.imshow(
        all_probs_concat.mean(0).T,
        labels=dict(x="positions", y="amino acids", color="probability"),
        y=list(alphabet),
        template="simple_white",
    )

    fig_tadjusted.update_xaxes(side="top")

    return (
        message,
        fig,
        fig_tadjusted,
        gr.File.update(value="all_log_probs_concat.csv", visible=True),
        gr.File.update(value="all_probs_concat.csv", visible=True),
        pdb_path,
        gr.Dropdown.update(choices=seq_list),
        selected_residues
    )


def update_AF(startsequence, pdb, num_recycles,selectedResidues):

    # # run alphafold using ray
    # plddts, pae, num_res = run_alphafold(
    #    startsequence, num_recycles
    # )
    if len(startsequence) > 700:
        return (
            """
            <div class="p-4 mb-4 text-sm text-yellow-700 bg-orange-50 rounded-lg" role="alert">
  <span class="font-medium">Sorry!</span> Currently only small proteins can be run in the server in order to reduce wait time. Try a protein <700 aa. Bigger proteins you can run on <a href="https://github.com/sokrypton/colabfold">ColabFold</a>
</div>
""",
            plt.figure(),
            plt.figure(),
        )
    plddts, pae, num_res = ray.get(run_alphafold.remote(startsequence, num_recycles))
    x = np.arange(10)
    plots = []
    for recycle, plddts_val in enumerate(plddts):
        if recycle == 0 or recycle == len(plddts) - 1:
            visible = True
        else:
            visible = "legendonly"
        plots.append(
            go.Scatter(
                x=np.arange(len(plddts_val)),
                y=plddts_val,
                hovertemplate="<i>pLDDT</i>: %{y:.2f} <br><i>Residue index:</i> %{x}<br>Recycle "
                + str(recycle),
                name=f"Recycle {recycle}",
                visible=visible,
            )
        )
    plotAF_plddt = go.Figure(data=plots)
    plotAF_plddt.update_layout(
        title="pLDDT",
        xaxis_title="Residue index",
        yaxis_title="pLDDT",
        height=500,
        template="simple_white",
        legend=dict(yanchor="bottom", y=0.01, xanchor="left", x=0.99),
    )
    plt.figure()
    plt.title("Predicted Aligned Error")
    Ln = pae.shape[0]
    plt.imshow(pae, cmap="bwr", vmin=0, vmax=30, extent=(0, Ln, Ln, 0))
    plt.colorbar()
    plt.xlabel("Scored residue")
    plt.ylabel("Aligned residue")
    plt.savefig("pae_plot.png", dpi=300)
    plt.close()
    # doesnt work (likely because too large)
    # plotAF_pae = px.imshow(
    #     pae,
    #     labels=dict(x="Scored residue", y="Aligned residue", color=""),
    #     template="simple_white",
    #     y=np.arange(len(plddts_val)),
    # )
    # plotAF_pae.write_html("test.html")
    # plotAF_pae.update_layout(title="Predicted Aligned Error", template="simple_white")

    return molecule(pdb, "out.pdb", num_res, selectedResidues), plotAF_plddt, "pae_plot.png"


def read_mol(molpath):
    with open(molpath, "r") as fp:
        lines = fp.readlines()
    mol = ""
    for l in lines:
        mol += l
    return mol


def molecule(pdb, afpdb, num_res, selectedResidues):

    rms, input_pdb, aligned_pdb = align_structures(pdb, afpdb, num_res)
    mol = read_mol(input_pdb)
    pred_mol = read_mol(aligned_pdb)
    x = (
        """<!DOCTYPE html>
        <html>
        <head>    
    <meta http-equiv="content-type" content="text/html; charset=UTF-8" />
     <link rel="stylesheet" href="https://unpkg.com/[email protected]/dist/flowbite.min.css" />
    <style>
    body{
        font-family:sans-serif
    }
.mol-container {
  width: 100%;
  height: 700px;
  position: relative;
}
.space-x-2 > * + *{
    margin-left: 0.5rem;
}
.p-1{
    padding:0.5rem;
}
.w-4{
    width:1rem;
}
.h-4{
    height:1rem;
}
.mt-4{
    margin-top:1rem;
}
select{
    background-image:None;
}
</style>
<script src="https://3Dmol.csb.pitt.edu/build/3Dmol-min.js"></script>
    </head>
    <body>  
   
    <div id="container" class="mol-container"></div>
    <div class="flex">
        <div class="px-4">
        <label for="sidechain" class="relative inline-flex items-center mb-4 cursor-pointer ">
            <input  id="sidechain" type="checkbox" class="sr-only peer">
            <div class="w-11 h-6 bg-gray-200 rounded-full peer peer-focus:ring-4 peer-focus:ring-blue-300 dark:peer-focus:ring-blue-800 dark:bg-gray-700 peer-checked:after:translate-x-full peer-checked:after:border-white after:absolute after:top-0.5 after:left-[2px] after:bg-white after:border-gray-300 after:border after:rounded-full after:h-5 after:w-5 after:transition-all dark:border-gray-600 peer-checked:bg-blue-600"></div>
            <span class="ml-3 text-sm font-medium text-gray-900 dark:text-gray-300">Show side chains</span>
          </label>
        </div>
        <div class="px-4">
        <label for="startstructure" class="relative inline-flex items-center mb-4 cursor-pointer ">
            <input  id="startstructure" type="checkbox" class="sr-only peer" checked>
            <div class="w-11 h-6 bg-gray-200 rounded-full peer peer-focus:ring-4 peer-focus:ring-blue-300 dark:peer-focus:ring-blue-800 dark:bg-gray-700 peer-checked:after:translate-x-full peer-checked:after:border-white after:absolute after:top-0.5 after:left-[2px] after:bg-white after:border-gray-300 after:border after:rounded-full after:h-5 after:w-5 after:transition-all dark:border-gray-600 peer-checked:bg-blue-600"></div>
            <span class="ml-3 text-sm font-medium text-gray-900 dark:text-gray-300">Show input structure</span>
          </label>
        </div>
 <button type="button" class="text-gray-900 bg-white hover:bg-gray-100 border border-gray-200 focus:ring-4 focus:outline-none focus:ring-gray-100 font-medium rounded-lg text-sm px-5 py-2.5 text-center inline-flex items-center dark:focus:ring-gray-600 dark:bg-gray-800 dark:border-gray-700 dark:text-white dark:hover:bg-gray-700 mr-2 mb-2" id="download">
                    <svg class="w-6 h-6 mr-2 -ml-1" fill="none" stroke="currentColor" viewBox="0 0 24 24" xmlns="http://www.w3.org/2000/svg"><path stroke-linecap="round" stroke-linejoin="round" stroke-width="2" d="M4 16v1a3 3 0 003 3h10a3 3 0 003-3v-1m-4-4l-4 4m0 0l-4-4m4 4V4"></path></svg>
                    Download predicted structure
                  </button>
            </div>       
<div class="text-sm">
<div> RMSD AlphaFold vs. native: """
        + f"{rms:.2f}"
        + """Å computed using CEAlign on the aligned fragment</div>
                        </div>
<div class="text-sm flex items-start">
                <div class="w-1/2">
                        
                            <div class="font-medium mt-4 flex items-center space-x-2"><b>AF2 model of redesigned sequence</b></div>
                            <div>AlphaFold model confidence:</div>
                            <div class="flex space-x-2 py-1"><span class="w-4 h-4" style="background-color: rgb(0, 83, 214);">&nbsp;</span><span class="legendlabel">Very high
                                    (pLDDT &gt; 90)</span></div>
                            <div class="flex space-x-2 py-1"><span class="w-4 h-4" style="background-color: rgb(101, 203, 243);">&nbsp;</span><span class="legendlabel">Confident
                                    (90 &gt; pLDDT &gt; 70)</span></div>
                            <div class="flex space-x-2 py-1"><span class="w-4 h-4" style="background-color: rgb(255, 219, 19);">&nbsp;</span><span class="legendlabel">Low (70 &gt;
                                    pLDDT &gt; 50)</span></div>
                            <div class="flex space-x-2 py-1"><span class="w-4 h-4" style="background-color: rgb(255, 125, 69);">&nbsp;</span><span class="legendlabel">Very low
                                    (pLDDT &lt; 50)</span></div>
                            <div class="row column legendDesc"> AlphaFold produces a per-residue confidence
                                score (pLDDT) between 0 and 100. Some regions below 50 pLDDT may be unstructured in isolation.
                            </div>
                        </div>
                        <div class="w-1/2">
                            <div class="font-medium mt-4 flex items-center space-x-2"><b>Input structure </b><span class="w-4 h-4 bg-gray-300 inline-flex" ></span></div>
                            
                            <div class="flex space-x-2 py-1"><span class="w-4 h-4" style="background-color:hotpink" >&nbsp;</span><span class="legendlabel">Fixed positions</span></div>

                        </div>
                    </div>
            <script>
            let viewer = null;
            let voldata = null;
            $(document).ready(function () {
                let element = $("#container");
                let config = { backgroundColor: "white" };
                viewer = $3Dmol.createViewer( element, config );
                viewer.ui.initiateUI();
                let data = `"""
        + pred_mol
        + """`  
                let pdb = `"""
        + mol
        + """`  
                viewer.addModel( data, "pdb" );
                viewer.addModel( pdb, "pdb" );
                //AlphaFold code from https://gist.github.com/piroyon/30d1c1099ad488a7952c3b21a5bebc96
                let colorAlpha = function (atom) {
                    if (atom.b < 50) {
                        return "OrangeRed";
                    } else if (atom.b < 70) {
                        return "Gold";
                    } else if (atom.b < 90) {
                        return "MediumTurquoise";
                    } else {
                        return "Blue";
                    }
                };
                var selectedResidues = """+
                f"{selectedResidues}"
                +"""
                let colors = {}
                for (let i=0; i<"""+str(num_res)+""";i++){
                if (selectedResidues.includes(i)){
                    colors[i]="hotpink"
                }else{
                    colors[i]="lightgray"
                }}

                let colorFixedSidechain = function(atom){
                                if (selectedResidues.includes(atom.resi)){
                                    return "hotpink"
                                }else if (atom.elem == "O"){
                                    return "red"
                                }else if (atom.elem == "N"){
                                    return "blue"
                                }else if (atom.elem == "S"){
                                    return "yellow"
                                }else{
                                    return "lightgray"
                                }
                            }

                viewer.getModel(1).setStyle({},{ cartoon: {colorscheme:{prop:"resi",map:colors} } })
                viewer.getModel(0).setStyle({}, { cartoon: { colorfunc: colorAlpha } });
                viewer.zoomTo();
                viewer.render();
                viewer.zoom(0.8, 2000);
                viewer.getModel(0).setHoverable({}, true,
                    function (atom, viewer, event, container) {
                        if (!atom.label) {
                            atom.label = viewer.addLabel(atom.resn+atom.resi+" pLDDT=" + atom.b, { position: atom, backgroundColor: "mintcream", fontColor: "black" });
                        }
                    },
                    function (atom, viewer) {
                        if (atom.label) {
                            viewer.removeLabel(atom.label);
                            delete atom.label;
                        }
                    }
                );
                $("#sidechain").change(function () {
                    if (this.checked) {
                        BB = ["C", "O", "N"]
                        
                        if ($("#startstructure").prop("checked")) {
                            viewer.getModel(0).setStyle( {"and": [{resn: ["GLY", "PRO"], invert: true},{atom: BB, invert: true},]},{stick: {colorscheme: "WhiteCarbon", radius: 0.3}, cartoon: { colorfunc: colorAlpha }});
                            viewer.getModel(1).setStyle( {"and": [{resn: ["GLY", "PRO"], invert: true},{atom: BB, invert: true},]},{stick: {colorfunc:colorFixedSidechain, radius: 0.3}, cartoon: {colorscheme:{prop:"resi",map:colors} }});
                        }else{
                            viewer.getModel(0).setStyle( {"and": [{resn: ["GLY", "PRO"], invert: true},{atom: BB, invert: true},]},{stick: {colorscheme: "WhiteCarbon", radius: 0.3}, cartoon: { colorfunc: colorAlpha }});
                            viewer.getModel(1).setStyle();                        
                        }
                        
                        viewer.render()
                    } else {
                        if ($("#startstructure").prop("checked")) {
                        viewer.getModel(0).setStyle({cartoon: { colorfunc: colorAlpha }});
                        viewer.getModel(1).setStyle({cartoon: {colorscheme:{prop:"resi",map:colors} }});
                        }else{
                            viewer.getModel(0).setStyle({cartoon: { colorfunc: colorAlpha }});
                            viewer.getModel(1).setStyle();
                            }
                        viewer.render()
                    }
                });

                $("#startstructure").change(function () {
                    if (this.checked) {
                         $("#sidechain").prop( "checked", false );
                       viewer.getModel(1).setStyle({},{cartoon: {colorscheme:{prop:"resi",map:colors} } })
                       viewer.getModel(0).setStyle({}, { cartoon: { colorfunc: colorAlpha } });
                       viewer.render()
                    } else {
                        $("#sidechain").prop( "checked", false );
                       viewer.getModel(1).setStyle({},{})
                       viewer.getModel(0).setStyle({}, { cartoon: { colorfunc: colorAlpha } });
                        viewer.render()
                    }
                });
                $("#download").click(function () {
                    download(\""""
        + aligned_pdb
        + """\", data);
                })
        });
        function download(filename, text) {
            var element = document.createElement("a");
            element.setAttribute("href", "data:text/plain;charset=utf-8," + encodeURIComponent(text));
            element.setAttribute("download", filename);
            element.style.display = "none";
            document.body.appendChild(element);
            element.click();
            document.body.removeChild(element);
        }
        </script>
        </body></html>"""
    )

    return f"""<iframe style="width: 800px; height: 1000px" name="result" allow="midi; geolocation; microphone; camera; 
    display-capture; encrypted-media;" sandbox="allow-modals allow-forms 
    allow-scripts allow-same-origin allow-popups 
    allow-top-navigation-by-user-activation allow-downloads" allowfullscreen="" 
    allowpaymentrequest="" frameborder="0" srcdoc='{x}'></iframe>"""


def set_examples(example):
    label, inp, designed_chain, fixed_chain, homomer, num_seqs, sampling_temp, atomsel = example
    return [
        label,
        inp,
        designed_chain,
        fixed_chain,
        homomer,
        gr.Slider.update(value=num_seqs),
        gr.Radio.update(value=sampling_temp),
        atomsel
    ]


proteinMPNN = gr.Blocks()

with proteinMPNN:
    gr.Markdown("# ProteinMPNN")
    gr.Markdown(
        """This model takes as input a protein structure and based on its backbone predicts new sequences that will fold into that backbone. 
        Optionally, we can run AlphaFold2 on the predicted sequence to check whether the predicted sequences adopt the same backbone (WIP). 
        """
    )
    gr.Markdown("![](https://simonduerr.eu/ProteinMPNN.png)")

    with gr.Tabs():
        with gr.TabItem("Input"):
            inp = gr.Textbox(
                placeholder="PDB Code or upload file below", label="Input structure"
            )
            file = gr.File(file_count="single")

        with gr.TabItem("Settings"):
            with gr.Row():
                designed_chain = gr.Textbox(value="A", label="Designed chain")
                fixed_chain = gr.Textbox(
                    placeholder="Use commas to fix multiple chains", label="Fixed chain"
                )
            with gr.Row():
                num_seqs = gr.Slider(
                    minimum=1, maximum=50, value=1, step=1, label="Number of sequences"
                )
                sampling_temp = gr.Radio(
                    choices=[0.1, 0.15, 0.2, 0.25, 0.3],
                    value=0.1,
                    label="Sampling temperature",
                )
            gr.Markdown(""" Sampling temperature for amino acids, `T=0.0` means taking argmax, `T>>1.0` means sample randomly. Suggested values `0.1, 0.15, 0.2, 0.25, 0.3`. Higher values will lead to more diversity.
            """
            )
            with gr.Row():
                model_name = gr.Dropdown(
                    choices=[
                        "v_48_002",
                        "v_48_010",
                        "v_48_020",
                        "v_48_030",
                    ],
                    label="Model",
                    value="v_48_020",
                )
                backbone_noise = gr.Dropdown(
                    choices=[0, 0.02, 0.10, 0.20, 0.30], label="Backbone noise", value=0
                )
            with gr.Row():
                homomer = gr.Checkbox(value=False, label="Homomer?")
                gr.Markdown(
                    "for correct symmetric tying lenghts of homomer chains should be the same"
                )
            gr.Markdown('## Fixed positions')
            gr.Markdown("""You can fix important positions in the protein. Resid should be specified with the same numbering as in the input pdb file. The fixed residues will be highlighted in the output. 
                The [VMD selection](http://www.ks.uiuc.edu/Research/vmd/vmd-1.9.2/ug/node89.html) synthax is used. You can also select based on ligands or chains in the input structure to specify interfaces to be fixed.

                 - <code>within 5 of resid 94</code> All residues that have >1 atom closer than 5 Å to any atom of residue 94
                 - <code>name CA and within 5 of resid 94</code> All residues that have CA atom closer than 5 Å to any atom of residue 94
                 - <code>resid 94 96 119</code> Residues 94, 94 and 119
                 - <code>within 5 of resname ZN</code> All residues with any atom <5 Å of zinc ion
                 - <code>chain A and within 5 of chain B </code> All residues of chain A that are part of the interface with chain B
                 - <code>protein and within 5 of nucleic </code> All residues that bind to DNA (if present in structure)""")
            atomsel = gr.Textbox(placeholder="Specify atom selection ", label="Fixed positions")

        btn = gr.Button("Run")
    label = gr.Textbox(label="Label", visible=False)
    examples = gr.Dataset(
        components=[
            label,
            inp,
            designed_chain,
            fixed_chain,
            homomer,
            num_seqs,
            sampling_temp,
            atomsel
        ],
        samples=[
            ["Homomer design", "1O91", "A,B,C", "", True, 2, 0.1,""],
            ["Monomer design", "6MRR", "A", "", False, 2, 0.1,""],
            ["Redesign of Homomer to Heteromer", "3HTN", "A,B", "C", False, 2, 0.1, ""],
            ["Redesign of MID1 scaffold keeping binding site fixed", "3V1C", "A,B", "", False, 2, 0.1, "within 5 of resname ZN"],
            ["Redesign of DNA binding protein", "3JRD", "A,B", "", False, 2, 0.1, "within 8 of nucleic"],
        ],
    )


    gr.Markdown("# Output")

    with gr.Tabs():
        with gr.TabItem("Designed sequences"):
            out = gr.Textbox(label="Status")

        with gr.TabItem("Amino acid probabilities"):
            plot = gr.Plot()
            all_log_probs = gr.File(visible=False)
        with gr.TabItem("T adjusted probabilities"):
            gr.Markdown("Sampling temperature adjusted amino acid probabilties")
            plot_tadjusted = gr.Plot()
            all_probs = gr.File(visible=False)
        with gr.TabItem("Structure validation w/ AF2"):
            gr.HTML(
                """
            <div class="flex items-center p-2 bg-gradient-to-r from-yellow-400 via-red-500 to-pink-500 rounded-lg shadow-sm">
                <div class="p-3 mr-4">
                <svg class="w-10 h-10 px-1 text-400" viewBox="0 0 16 16">
                    <path fill-rule="evenodd" d="M1.75 1.5a.25.25 0 00-.25.25v9.5c0 .138.112.25.25.25h2a.75.75 0 01.75.75v2.19l2.72-2.72a.75.75 0 01.53-.22h6.5a.25.25 0 00.25-.25v-9.5a.25.25 0 00-.25-.25H1.75zM0 1.75C0 .784.784 0 1.75 0h12.5C15.216 0 16 .784 16 1.75v9.5A1.75 1.75 0 0114.25 13H8.06l-2.573 2.573A1.457 1.457 0 013 14.543V13H1.75A1.75 1.75 0 010 11.25v-9.5zM9 9a1 1 0 11-2 0 1 1 0 012 0zm-.25-5.25a.75.75 0 00-1.5 0v2.5a.75.75 0 001.5 0v-2.5z"></path>
                </svg>
                </div>
                <div>
                <p class="text-base text-gray-700 dark:text-gray-200">
                    AF2 code is experimental and relies on @sokrypton's trick to speed up compile/module runtime. Results might differ from DeepMind's published results.
                    Predictions are made using <code>model_5_ptm</code> and without MSA based on the selected single sequence (<code>designed_chain</code> + <code>fixed_chain</code>).
                </p>
                </div>
                </div>
            """
            )
            with gr.Row():
                with gr.Row():
                    chosen_seq = gr.Dropdown(
                        choices=[], label="Select a sequence for validation"
                    )
                    num_recycles = gr.Dropdown(
                        choices=[0, 1, 3, 5], value=3, label="num Recycles"
                    )
                btnAF = gr.Button("Run AF2 on sequence")
            with gr.Row():
                mol = gr.HTML()
                with gr.Column():
                    plotAF_plddt = gr.Plot(label="pLDDT")
                    # remove maxh80 class from css
                    plotAF_pae = gr.Image(label="PAE") #gr.Plot(label="PAE")
    tempFile = gr.Variable()
    selectedResidues = gr.Variable()
    btn.click(
        fn=update,
        inputs=[
            inp,
            file,
            designed_chain,
            fixed_chain,
            homomer,
            num_seqs,
            sampling_temp,
            model_name,
            backbone_noise,
            atomsel,
        ],
        outputs=[
            out,
            plot,
            plot_tadjusted,
            all_log_probs,
            all_probs,
            tempFile,
            chosen_seq,
            selectedResidues
        ],
    )
    btnAF.click(
        fn=update_AF,
        inputs=[chosen_seq, tempFile, num_recycles, selectedResidues],
        outputs=[mol, plotAF_plddt, plotAF_pae],
    )
    examples.click(fn=set_examples, inputs=examples, outputs=examples.components)
    gr.Markdown(
        """Citation: **Robust deep learning based protein sequence design using ProteinMPNN** <br>
Justas Dauparas, Ivan Anishchenko, Nathaniel Bennett, Hua Bai, Robert J. Ragotte, Lukas F. Milles, Basile I. M. Wicky, Alexis Courbet, Robbert J. de Haas, Neville Bethel, Philip J. Y. Leung, Timothy F. Huddy, Sam Pellock, Doug Tischer, Frederick Chan, Brian Koepnick, Hannah Nguyen, Alex Kang, Banumathi Sankaran, Asim Bera, Neil P. King, David Baker <br>
bioRxiv 2022.06.03.494563; doi: [10.1101/2022.06.03.494563](https://doi.org/10.1101/2022.06.03.494563) <br><br> Server built by [@simonduerr](https://twitter.com/simonduerr) and hosted by Huggingface"""
    )


ray.init(runtime_env={"working_dir": "./af_backprop"})

proteinMPNN.launch(share=True, debug=True)