colabfold.py

# fmt: off

############################################
# imports
############################################
import jax
import requests
import hashlib
import tarfile
import time
import pickle
import os
import re

import random
import tqdm.notebook

import numpy as np
import matplotlib.pyplot as plt
import matplotlib
import matplotlib.patheffects
from matplotlib import collections as mcoll

try:
  import py3Dmol
except:
  pass

from string import ascii_uppercase,ascii_lowercase

pymol_color_list = ["#33ff33","#00ffff","#ff33cc","#ffff00","#ff9999","#e5e5e5","#7f7fff","#ff7f00",
                    "#7fff7f","#199999","#ff007f","#ffdd5e","#8c3f99","#b2b2b2","#007fff","#c4b200",
                    "#8cb266","#00bfbf","#b27f7f","#fcd1a5","#ff7f7f","#ffbfdd","#7fffff","#ffff7f",
                    "#00ff7f","#337fcc","#d8337f","#bfff3f","#ff7fff","#d8d8ff","#3fffbf","#b78c4c",
                    "#339933","#66b2b2","#ba8c84","#84bf00","#b24c66","#7f7f7f","#3f3fa5","#a5512b"]

pymol_cmap = matplotlib.colors.ListedColormap(pymol_color_list)
alphabet_list = list(ascii_uppercase+ascii_lowercase)

aatypes = set('ACDEFGHIKLMNPQRSTVWY')


###########################################
# control gpu/cpu memory usage
###########################################
def rm(x):
  '''remove data from device'''
  jax.tree_util.tree_map(lambda y: y.device_buffer.delete(), x)

def to(x,device="cpu"):
  '''move data to device'''
  d = jax.devices(device)[0]
  return jax.tree_util.tree_map(lambda y:jax.device_put(y,d), x)

def clear_mem(device="gpu"):
  '''remove all data from device'''
  backend = jax.lib.xla_bridge.get_backend(device)
  for buf in backend.live_buffers(): buf.delete()
    
##########################################
# call mmseqs2
##########################################

TQDM_BAR_FORMAT = '{l_bar}{bar}| {n_fmt}/{total_fmt} [elapsed: {elapsed} remaining: {remaining}]'

def run_mmseqs2(x, prefix, use_env=True, use_filter=True,
                use_templates=False, filter=None, host_url="https://a3m.mmseqs.com"):
  
  def submit(seqs, mode, N=101):    
    n,query = N,""
    for seq in seqs: 
      query += f">{n}\n{seq}\n"
      n += 1
      
    res = requests.post(f'{host_url}/ticket/msa', data={'q':query,'mode': mode})
    try: out = res.json()
    except ValueError: out = {"status":"UNKNOWN"}
    return out

  def status(ID):
    res = requests.get(f'{host_url}/ticket/{ID}')
    try: out = res.json()
    except ValueError: out = {"status":"UNKNOWN"}
    return out

  def download(ID, path):
    res = requests.get(f'{host_url}/result/download/{ID}')
    with open(path,"wb") as out: out.write(res.content)
  
  # process input x
  seqs = [x] if isinstance(x, str) else x
  
  # compatibility to old option
  if filter is not None:
    use_filter = filter
    
  # setup mode
  if use_filter:
    mode = "env" if use_env else "all"
  else:
    mode = "env-nofilter" if use_env else "nofilter"
  
  # define path
  path = f"{prefix}_{mode}"
  if not os.path.isdir(path): os.mkdir(path)

  # call mmseqs2 api
  tar_gz_file = f'{path}/out.tar.gz'
  N,REDO = 101,True
  
  # deduplicate and keep track of order
  seqs_unique = sorted(list(set(seqs)))
  Ms = [N+seqs_unique.index(seq) for seq in seqs]
  
  # lets do it!
  if not os.path.isfile(tar_gz_file):
    TIME_ESTIMATE = 150 * len(seqs_unique)
    with tqdm.notebook.tqdm(total=TIME_ESTIMATE, bar_format=TQDM_BAR_FORMAT) as pbar:
      while REDO:
        pbar.set_description("SUBMIT")
        
        # Resubmit job until it goes through
        out = submit(seqs_unique, mode, N)
        while out["status"] in ["UNKNOWN","RATELIMIT"]:
          # resubmit
          time.sleep(5 + random.randint(0,5))
          out = submit(seqs_unique, mode, N)

        if out["status"] == "ERROR":
          raise Exception(f'MMseqs2 API is giving errors. Please confirm your input is a valid protein sequence. If error persists, please try again an hour later.')

        if out["status"] == "MAINTENANCE":
          raise Exception(f'MMseqs2 API is undergoing maintenance. Please try again in a few minutes.')

        # wait for job to finish
        ID,TIME = out["id"],0
        pbar.set_description(out["status"])
        while out["status"] in ["UNKNOWN","RUNNING","PENDING"]:
          t = 5 + random.randint(0,5)
          time.sleep(t)
          out = status(ID)    
          pbar.set_description(out["status"])
          if out["status"] == "RUNNING":
            TIME += t
            pbar.update(n=t)
          #if TIME > 900 and out["status"] != "COMPLETE":
          #  # something failed on the server side, need to resubmit
          #  N += 1
          #  break
        
        if out["status"] == "COMPLETE":
          if TIME < TIME_ESTIMATE:
            pbar.update(n=(TIME_ESTIMATE-TIME))
          REDO = False

      # Download results
      download(ID, tar_gz_file)

  # prep list of a3m files
  a3m_files = [f"{path}/uniref.a3m"]
  if use_env: a3m_files.append(f"{path}/bfd.mgnify30.metaeuk30.smag30.a3m")
  
  # extract a3m files
  if not os.path.isfile(a3m_files[0]):
    with tarfile.open(tar_gz_file) as tar_gz:
      tar_gz.extractall(path)  

  # templates
  if use_templates:
    templates = {}
    print("seq\tpdb\tcid\tevalue")
    for line in open(f"{path}/pdb70.m8","r"):
      p = line.rstrip().split()
      M,pdb,qid,e_value = p[0],p[1],p[2],p[10]
      M = int(M)
      if M not in templates: templates[M] = []
      templates[M].append(pdb)
      if len(templates[M]) <= 20:
        print(f"{int(M)-N}\t{pdb}\t{qid}\t{e_value}")
    
    template_paths = {}
    for k,TMPL in templates.items():
      TMPL_PATH = f"{prefix}_{mode}/templates_{k}"
      if not os.path.isdir(TMPL_PATH):
        os.mkdir(TMPL_PATH)
        TMPL_LINE = ",".join(TMPL[:20])
        os.system(f"curl -s https://a3m-templates.mmseqs.com/template/{TMPL_LINE} | tar xzf - -C {TMPL_PATH}/")
        os.system(f"cp {TMPL_PATH}/pdb70_a3m.ffindex {TMPL_PATH}/pdb70_cs219.ffindex")
        os.system(f"touch {TMPL_PATH}/pdb70_cs219.ffdata")
      template_paths[k] = TMPL_PATH

  # gather a3m lines  
  a3m_lines = {}
  for a3m_file in a3m_files:
    update_M,M = True,None
    for line in open(a3m_file,"r"):
      if len(line) > 0:
        if "\x00" in line:
          line = line.replace("\x00","")
          update_M = True
        if line.startswith(">") and update_M:
          M = int(line[1:].rstrip())
          update_M = False
          if M not in a3m_lines: a3m_lines[M] = []
        a3m_lines[M].append(line)
  
  # return results
  a3m_lines = ["".join(a3m_lines[n]) for n in Ms]
  
  if use_templates:
    template_paths_ = [] 
    for n in Ms:
      if n not in template_paths:
        template_paths_.append(None)
        print(f"{n-N}\tno_templates_found")
      else:
        template_paths_.append(template_paths[n])
    template_paths = template_paths_

  if isinstance(x, str):
    return (a3m_lines[0], template_paths[0]) if use_templates else a3m_lines[0]
  else:
    return (a3m_lines, template_paths) if use_templates else a3m_lines


#########################################################################
# utils
#########################################################################
def get_hash(x):
  return hashlib.sha1(x.encode()).hexdigest()
  
def homooligomerize(msas, deletion_matrices, homooligomer=1):
 if homooligomer == 1:
  return msas, deletion_matrices
 else:
  new_msas = []
  new_mtxs = []
  for o in range(homooligomer):
    for msa,mtx in zip(msas, deletion_matrices):
      num_res = len(msa[0])
      L = num_res * o
      R = num_res * (homooligomer-(o+1))
      new_msas.append(["-"*L+s+"-"*R for s in msa])
      new_mtxs.append([[0]*L+m+[0]*R for m in mtx])
  return new_msas, new_mtxs

# keeping typo for cross-compatibility
def homooliomerize(msas, deletion_matrices, homooligomer=1):
  return homooligomerize(msas, deletion_matrices, homooligomer=homooligomer)

def homooligomerize_heterooligomer(msas, deletion_matrices, lengths, homooligomers):
  '''
  ----- inputs -----
  msas: list of msas
  deletion_matrices: list of deletion matrices
  lengths: list of lengths for each component in complex
  homooligomers: list of number of homooligomeric copies for each component
  ----- outputs -----
  (msas, deletion_matrices)
  '''
  if max(homooligomers) == 1:
    return msas, deletion_matrices
  
  elif len(homooligomers) == 1:
    return homooligomerize(msas, deletion_matrices, homooligomers[0])

  else:
    frag_ij = [[0,lengths[0]]]
    for length in lengths[1:]:
      j = frag_ij[-1][-1]
      frag_ij.append([j,j+length])

    # for every msa
    mod_msas, mod_mtxs = [],[]
    for msa, mtx in zip(msas, deletion_matrices):
      mod_msa, mod_mtx = [],[]
      # for every sequence
      for n,(s,m) in enumerate(zip(msa,mtx)):
        # split sequence
        _s,_m,_ok = [],[],[]
        for i,j in frag_ij:
          _s.append(s[i:j]); _m.append(m[i:j])
          _ok.append(max([o != "-" for o in _s[-1]]))

        if n == 0:
          # if first query sequence
          mod_msa.append("".join([x*h for x,h in zip(_s,homooligomers)]))
          mod_mtx.append(sum([x*h for x,h in zip(_m,homooligomers)],[]))

        elif sum(_ok) == 1:
          # elif one fragment: copy each fragment to every homooligomeric copy
          a = _ok.index(True)
          for h_a in range(homooligomers[a]):
            _blank_seq = [["-"*l]*h for l,h in zip(lengths,homooligomers)]
            _blank_mtx = [[[0]*l]*h for l,h in zip(lengths,homooligomers)]
            _blank_seq[a][h_a] = _s[a]
            _blank_mtx[a][h_a] = _m[a]
            mod_msa.append("".join(["".join(x) for x in _blank_seq]))
            mod_mtx.append(sum([sum(x,[]) for x in _blank_mtx],[]))
        else:
          # else: copy fragment pair to every homooligomeric copy pair
          for a in range(len(lengths)-1):
            if _ok[a]:
              for b in range(a+1,len(lengths)):
                if _ok[b]:
                  for h_a in range(homooligomers[a]):
                    for h_b in range(homooligomers[b]):
                      _blank_seq = [["-"*l]*h for l,h in zip(lengths,homooligomers)]
                      _blank_mtx = [[[0]*l]*h for l,h in zip(lengths,homooligomers)]
                      for c,h_c in zip([a,b],[h_a,h_b]):
                        _blank_seq[c][h_c] = _s[c]
                        _blank_mtx[c][h_c] = _m[c]
                      mod_msa.append("".join(["".join(x) for x in _blank_seq]))
                      mod_mtx.append(sum([sum(x,[]) for x in _blank_mtx],[]))
      mod_msas.append(mod_msa)
      mod_mtxs.append(mod_mtx)
    return mod_msas, mod_mtxs

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

##################################################
# plotting
##################################################

def plot_plddt_legend(dpi=100):
  thresh = ['plDDT:','Very low (<50)','Low (60)','OK (70)','Confident (80)','Very high (>90)']
  plt.figure(figsize=(1,0.1),dpi=dpi)
  ########################################
  for c in ["#FFFFFF","#FF0000","#FFFF00","#00FF00","#00FFFF","#0000FF"]:
    plt.bar(0, 0, color=c)
  plt.legend(thresh, frameon=False,
             loc='center', ncol=6,
             handletextpad=1,
             columnspacing=1,
             markerscale=0.5,)
  plt.axis(False)
  return plt

def plot_ticks(Ls):
  Ln = sum(Ls)
  L_prev = 0
  for L_i in Ls[:-1]:
    L = L_prev + L_i
    L_prev += L_i
    plt.plot([0,Ln],[L,L],color="black")
    plt.plot([L,L],[0,Ln],color="black")
  ticks = np.cumsum([0]+Ls)
  ticks = (ticks[1:] + ticks[:-1])/2
  plt.yticks(ticks,alphabet_list[:len(ticks)])

def plot_confidence(plddt, pae=None, Ls=None, dpi=100):
  use_ptm = False if pae is None else True
  if use_ptm:
    plt.figure(figsize=(10,3), dpi=dpi)
    plt.subplot(1,2,1);
  else:
    plt.figure(figsize=(5,3), dpi=dpi)
  plt.title('Predicted lDDT')
  plt.plot(plddt)
  if Ls is not None:
    L_prev = 0
    for L_i in Ls[:-1]:
      L = L_prev + L_i
      L_prev += L_i
      plt.plot([L,L],[0,100],color="black")
  plt.ylim(0,100)
  plt.ylabel('plDDT')
  plt.xlabel('position')
  if use_ptm:
    plt.subplot(1,2,2);plt.title('Predicted Aligned Error')
    Ln = pae.shape[0]
    plt.imshow(pae,cmap="bwr",vmin=0,vmax=30,extent=(0, Ln, Ln, 0))
    if Ls is not None and len(Ls) > 1: plot_ticks(Ls)
    plt.colorbar()
    plt.xlabel('Scored residue')
    plt.ylabel('Aligned residue')
  return plt

def plot_msas(msas, ori_seq=None, sort_by_seqid=True, deduplicate=True, dpi=100, return_plt=True):
  '''
  plot the msas
  '''
  if ori_seq is None: ori_seq = msas[0][0]
  seqs = ori_seq.replace("/","").split(":")
  seqs_dash = ori_seq.replace(":","").split("/")

  Ln = np.cumsum(np.append(0,[len(seq) for seq in seqs]))
  Ln_dash = np.cumsum(np.append(0,[len(seq) for seq in seqs_dash]))
  Nn,lines = [],[]
  for msa in msas:
    msa_ = set(msa) if deduplicate else msa
    if len(msa_) > 0:
      Nn.append(len(msa_))
      msa_ = np.asarray([list(seq) for seq in msa_])
      gap_ = msa_ != "-"
      qid_ = msa_ == np.array(list("".join(seqs)))
      gapid = np.stack([gap_[:,Ln[i]:Ln[i+1]].max(-1) for i in range(len(seqs))],-1)
      seqid = np.stack([qid_[:,Ln[i]:Ln[i+1]].mean(-1) for i in range(len(seqs))],-1).sum(-1) / (gapid.sum(-1) + 1e-8)
      non_gaps = gap_.astype(np.float)
      non_gaps[non_gaps == 0] = np.nan
      if sort_by_seqid:
        lines.append(non_gaps[seqid.argsort()]*seqid[seqid.argsort(),None])
      else:
        lines.append(non_gaps[::-1] * seqid[::-1,None])

  Nn = np.cumsum(np.append(0,Nn))
  lines = np.concatenate(lines,0)

  if return_plt:
    plt.figure(figsize=(8,5),dpi=dpi)
    plt.title("Sequence coverage")
  plt.imshow(lines,
            interpolation='nearest', aspect='auto',
            cmap="rainbow_r", vmin=0, vmax=1, origin='lower',
            extent=(0, lines.shape[1], 0, lines.shape[0]))
  for i in Ln[1:-1]:
    plt.plot([i,i],[0,lines.shape[0]],color="black")
  for i in Ln_dash[1:-1]:
    plt.plot([i,i],[0,lines.shape[0]],"--",color="black")
  for j in Nn[1:-1]:
    plt.plot([0,lines.shape[1]],[j,j],color="black")

  plt.plot((np.isnan(lines) == False).sum(0), color='black')
  plt.xlim(0,lines.shape[1])
  plt.ylim(0,lines.shape[0])
  plt.colorbar(label="Sequence identity to query")
  plt.xlabel("Positions")
  plt.ylabel("Sequences")
  if return_plt: return plt

def read_pdb_renum(pdb_filename, Ls=None):
  if Ls is not None:
    L_init = 0
    new_chain = {}
    for L,c in zip(Ls, alphabet_list):
      new_chain.update({i:c for i in range(L_init,L_init+L)})
      L_init += L  

  n,pdb_out = 1,[]
  resnum_,chain_ = 1,"A"
  for line in open(pdb_filename,"r"):
    if line[:4] == "ATOM":
      chain = line[21:22]
      resnum = int(line[22:22+5])
      if resnum != resnum_ or chain != chain_:
        resnum_,chain_ = resnum,chain
        n += 1
      if Ls is None: pdb_out.append("%s%4i%s" % (line[:22],n,line[26:]))
      else: pdb_out.append("%s%s%4i%s" % (line[:21],new_chain[n-1],n,line[26:]))        
  return "".join(pdb_out)

def show_pdb(pred_output_path, show_sidechains=False, show_mainchains=False,
             color="lDDT", chains=None, Ls=None, vmin=50, vmax=90,
             color_HP=False, size=(800,480)):
  
  if chains is None:
    chains = 1 if Ls is None else len(Ls)

  view = py3Dmol.view(js='https://3dmol.org/build/3Dmol.js', width=size[0], height=size[1])
  view.addModel(read_pdb_renum(pred_output_path, Ls),'pdb')
  if color == "lDDT":
    view.setStyle({'cartoon': {'colorscheme': {'prop':'b','gradient': 'roygb','min':vmin,'max':vmax}}})
  elif color == "rainbow":
    view.setStyle({'cartoon': {'color':'spectrum'}})
  elif color == "chain":
    for n,chain,color in zip(range(chains),alphabet_list,pymol_color_list):
       view.setStyle({'chain':chain},{'cartoon': {'color':color}})
  if show_sidechains:
    BB = ['C','O','N']
    HP = ["ALA","GLY","VAL","ILE","LEU","PHE","MET","PRO","TRP","CYS","TYR"]
    if color_HP:
      view.addStyle({'and':[{'resn':HP},{'atom':BB,'invert':True}]},
                    {'stick':{'colorscheme':"yellowCarbon",'radius':0.3}})
      view.addStyle({'and':[{'resn':HP,'invert':True},{'atom':BB,'invert':True}]},
                    {'stick':{'colorscheme':"whiteCarbon",'radius':0.3}})
      view.addStyle({'and':[{'resn':"GLY"},{'atom':'CA'}]},
                    {'sphere':{'colorscheme':"yellowCarbon",'radius':0.3}})
      view.addStyle({'and':[{'resn':"PRO"},{'atom':['C','O'],'invert':True}]},
                    {'stick':{'colorscheme':"yellowCarbon",'radius':0.3}})
    else:
      view.addStyle({'and':[{'resn':["GLY","PRO"],'invert':True},{'atom':BB,'invert':True}]},
                    {'stick':{'colorscheme':f"WhiteCarbon",'radius':0.3}})
      view.addStyle({'and':[{'resn':"GLY"},{'atom':'CA'}]},
                    {'sphere':{'colorscheme':f"WhiteCarbon",'radius':0.3}})
      view.addStyle({'and':[{'resn':"PRO"},{'atom':['C','O'],'invert':True}]},
                    {'stick':{'colorscheme':f"WhiteCarbon",'radius':0.3}})  
  if show_mainchains:
    BB = ['C','O','N','CA']
    view.addStyle({'atom':BB},{'stick':{'colorscheme':f"WhiteCarbon",'radius':0.3}})
  view.zoomTo()
  return view

def plot_plddts(plddts, Ls=None, dpi=100, fig=True):
  if fig: plt.figure(figsize=(8,5),dpi=100)
  plt.title("Predicted lDDT per position")
  for n,plddt in enumerate(plddts):
    plt.plot(plddt,label=f"rank_{n+1}")
  if Ls is not None:
    L_prev = 0
    for L_i in Ls[:-1]:
      L = L_prev + L_i
      L_prev += L_i
      plt.plot([L,L],[0,100],color="black")
  plt.legend()
  plt.ylim(0,100)
  plt.ylabel("Predicted lDDT")
  plt.xlabel("Positions")
  return plt

def plot_paes(paes, Ls=None, dpi=100, fig=True):
  num_models = len(paes)
  if fig: plt.figure(figsize=(3*num_models,2), dpi=dpi)
  for n,pae in enumerate(paes):
    plt.subplot(1,num_models,n+1)
    plt.title(f"rank_{n+1}")
    Ln = pae.shape[0]
    plt.imshow(pae,cmap="bwr",vmin=0,vmax=30,extent=(0, Ln, Ln, 0))
    if Ls is not None and len(Ls) > 1: plot_ticks(Ls)
    plt.colorbar()
  return plt

def plot_adjs(adjs, Ls=None, dpi=100, fig=True):
  num_models = len(adjs)
  if fig: plt.figure(figsize=(3*num_models,2), dpi=dpi)
  for n,adj in enumerate(adjs):
    plt.subplot(1,num_models,n+1)
    plt.title(f"rank_{n+1}")
    Ln = adj.shape[0]
    plt.imshow(adj,cmap="binary",vmin=0,vmax=1,extent=(0, Ln, Ln, 0))
    if Ls is not None and len(Ls) > 1: plot_ticks(Ls)
    plt.colorbar()
  return plt

def plot_dists(dists, Ls=None, dpi=100, fig=True):
  num_models = len(dists)
  if fig: plt.figure(figsize=(3*num_models,2), dpi=dpi)
  for n,dist in enumerate(dists):
    plt.subplot(1,num_models,n+1)
    plt.title(f"rank_{n+1}")
    Ln = dist.shape[0]
    plt.imshow(dist,extent=(0, Ln, Ln, 0))
    if Ls is not None and len(Ls) > 1: plot_ticks(Ls)
    plt.colorbar()
  return plt

##########################################################################
##########################################################################

def kabsch(a, b, weights=None, return_v=False):
  a = np.asarray(a)
  b = np.asarray(b)
  if weights is None: weights = np.ones(len(b))
  else: weights = np.asarray(weights)
  B = np.einsum('ji,jk->ik', weights[:, None] * a, b)
  u, s, vh = np.linalg.svd(B)
  if np.linalg.det(u @ vh) < 0: u[:, -1] = -u[:, -1]
  if return_v: return u
  else: return u @ vh

def plot_pseudo_3D(xyz, c=None, ax=None, chainbreak=5,
                   cmap="gist_rainbow", line_w=2.0,
                   cmin=None, cmax=None, zmin=None, zmax=None):

  def rescale(a,amin=None,amax=None):
    a = np.copy(a)
    if amin is None: amin = a.min()
    if amax is None: amax = a.max()
    a[a < amin] = amin
    a[a > amax] = amax
    return (a - amin)/(amax - amin)

  # make segments
  xyz = np.asarray(xyz)
  seg = np.concatenate([xyz[:-1,None,:],xyz[1:,None,:]],axis=-2)
  seg_xy = seg[...,:2]
  seg_z = seg[...,2].mean(-1)
  ord = seg_z.argsort()

  # set colors
  if c is None: c = np.arange(len(seg))[::-1]
  else: c = (c[1:] + c[:-1])/2
  c = rescale(c,cmin,cmax)  

  if isinstance(cmap, str):
    if cmap == "gist_rainbow": c *= 0.75
    colors = matplotlib.cm.get_cmap(cmap)(c)
  else:
    colors = cmap(c)
  
  if chainbreak is not None:
    dist = np.linalg.norm(xyz[:-1] - xyz[1:], axis=-1)
    colors[...,3] = (dist < chainbreak).astype(np.float)

  # add shade/tint based on z-dimension
  z = rescale(seg_z,zmin,zmax)[:,None]
  tint, shade = z/3, (z+2)/3
  colors[:,:3] = colors[:,:3] + (1 - colors[:,:3]) * tint
  colors[:,:3] = colors[:,:3] * shade

  set_lim = False
  if ax is None:
    fig, ax = plt.subplots()
    fig.set_figwidth(5)
    fig.set_figheight(5)
    set_lim = True
  else:
    fig = ax.get_figure()
    if ax.get_xlim() == (0,1):
      set_lim = True
      
  if set_lim:
    xy_min = xyz[:,:2].min() - line_w
    xy_max = xyz[:,:2].max() + line_w
    ax.set_xlim(xy_min,xy_max)
    ax.set_ylim(xy_min,xy_max)

  ax.set_aspect('equal')
    
  # determine linewidths
  width = fig.bbox_inches.width * ax.get_position().width
  linewidths = line_w * 72 * width / np.diff(ax.get_xlim())

  lines = mcoll.LineCollection(seg_xy[ord], colors=colors[ord], linewidths=linewidths,
                               path_effects=[matplotlib.patheffects.Stroke(capstyle="round")])
  
  return ax.add_collection(lines)

def add_text(text, ax):
  return plt.text(0.5, 1.01, text, horizontalalignment='center',
                  verticalalignment='bottom', transform=ax.transAxes)

def plot_protein(protein=None, pos=None, plddt=None, Ls=None, dpi=100, best_view=True, line_w=2.0):
  
  if protein is not None:
    pos = np.asarray(protein.atom_positions[:,1,:])
    plddt = np.asarray(protein.b_factors[:,0])

  # get best view
  if best_view:
    if plddt is not None:
      weights = plddt/100
      pos = pos - (pos * weights[:,None]).sum(0,keepdims=True) / weights.sum()
      pos = pos @ kabsch(pos, pos, weights, return_v=True)
    else:
      pos = pos - pos.mean(0,keepdims=True)
      pos = pos @ kabsch(pos, pos, return_v=True)

  if plddt is not None:
    fig, (ax1, ax2) = plt.subplots(1,2)
    fig.set_figwidth(6); fig.set_figheight(3)
    ax = [ax1, ax2]
  else:
    fig, ax1 = plt.subplots(1,1)
    fig.set_figwidth(3); fig.set_figheight(3)
    ax = [ax1]
    
  fig.set_dpi(dpi)
  fig.subplots_adjust(top = 0.9, bottom = 0.1, right = 1, left = 0, hspace = 0, wspace = 0)

  xy_min = pos[...,:2].min() - line_w
  xy_max = pos[...,:2].max() + line_w
  for a in ax:
    a.set_xlim(xy_min, xy_max)
    a.set_ylim(xy_min, xy_max)
    a.axis(False)

  if Ls is None or len(Ls) == 1:
    # color N->C
    c = np.arange(len(pos))[::-1]
    plot_pseudo_3D(pos,  line_w=line_w, ax=ax1)
    add_text("colored by N→C", ax1)
  else:
    # color by chain
    c = np.concatenate([[n]*L for n,L in enumerate(Ls)])
    if len(Ls) > 40:   plot_pseudo_3D(pos, c=c, line_w=line_w, ax=ax1)
    else:              plot_pseudo_3D(pos, c=c, cmap=pymol_cmap, cmin=0, cmax=39, line_w=line_w, ax=ax1)
    add_text("colored by chain", ax1)
    
  if plddt is not None:
    # color by pLDDT
    plot_pseudo_3D(pos, c=plddt, cmin=50, cmax=90, line_w=line_w, ax=ax2)
    add_text("colored by pLDDT", ax2)

  return fig