packmol-memgen-minimal 1.1.16__py3-none-any.whl

packmol_memgen/lib/pdbremix/data.py

@@ -0,0 +1,264 @@
+# encoding: utf-8
+
+__doc__ = """ 
+
+Stores data for PDBREMIX.
+
+- directory of explici data directory
+- mappings of residue names to chars
+- names and locations of binaries used
+- backbone atom types
+- solvent residue types
+- element radii
+- chi dihedral angle topologies
+"""
+
+
+import os
+from . import util
+
+
+module_dir = os.path.dirname(__file__)
+data_dir = os.path.join(module_dir, 'data')
+
+binaries = {
+  "pymol": "",
+  "pymol_batch": "",
+  "chimera": "",
+
+  "theseus": "",
+  "mafft": "",
+
+  "sander": "",
+  "tleap": "",
+
+  "mdrun": "",
+  "pdb2gmx": "",
+  "trjconv": "",
+  "grompp": "",
+  "editconf": "",
+  "genion": "",
+  "genbox": "",
+
+  "vmd": "",
+  "psfgen": "",
+  "namd2": "",
+  "flipdcd": "",
+
+  "mod9v8": ""
+}
+home_dir = os.path.expanduser('~')
+binaries_fname = os.path.join(home_dir, '.pdbremix.config')
+backup_binaries_fname = os.path.join(os.environ['AMBERHOME'], 'dat') if 'AMBERHOME' in os.environ else None
+if not os.path.isfile(binaries_fname):
+  try:
+    util.write_dict(binaries_fname, binaries)
+  except IOError:
+    # May not have permission here, especially in a docker container. If so,
+    # fall back on AMBERHOME
+    if backup_binaries_fname is None:
+      raise
+    binaries_fname = backup_binaries_fname
+else:
+  binaries = util.read_dict(binaries_fname)
+
+
+def binary(bin, arg_str='', out_name=None, in_fname=None):
+  """
+  Runs an external binary, handles arguments, writes out
+  equivalent .sh file, log file, and can pipe in in_fname.
+  """
+  if bin in binaries and binaries[bin]:
+    bin = binaries[bin]
+  else:
+    util.check_program(bin)
+  if arg_str:
+    util.run_with_output_file(
+        '%s %s' % (bin, arg_str), out_name, in_fname)
+  return '"%s"' % bin
+
+
+def invert_dict(d):
+  """
+  Returns dictionaries with swapped key-values.
+  """
+  return dict((v, k) for k,v in list(d.items()))
+
+
+res_name_to_char = {
+    "ALA":"A", "CYS":"C", "ASP":"D",
+    "GLU":"E", "PHE":"F", "GLY":"G",
+    "HIS":"H", "ILE":"I", "LYS":"K",
+    "LEU":"L", "MET":"M", "ASN":"N",
+    "PRO":"P", "GLN":"Q", "ARG":"R",
+    "SER":"S", "THR":"T", "VAL":"V",
+    "TRP":"W", "TYR":"Y", "ACE":">",
+    "NME":"<",
+}
+
+res_char_to_name = invert_dict(res_name_to_char)
+
+res_name_to_char.update({"HID":"H", "HIE":"H", "HIP":"H", "HSE":"H", "LYP":"K", "CYM":"C", "CYX":"C", "CYN":"C"})
+
+# recognized atom types for protein backbone 
+backbone_atoms = [
+    "OXT", # C-terminal carboxyl group
+    "H1", "H2", "H3",  # N-terminal charged group
+    "C", "O", # peptide-bond carbonyl group
+    "H", "HN", "N",  # peptide-bond amide group
+    "CA", "HA" # main-chain C-alpha and alkyl group
+    ]
+    
+solvent_res_types = [
+    'HOH', 'WAT', 'TIP', 'SOL',
+    'CLA', 'SOD', 'NA', 'CL', 
+    'NA+', 'CL-', 'Na', 'Cl',
+    'Na+', 'Cl-']
+
+radii = { 
+ 'H':  1.20,
+ 'N':  1.55,
+ 'NA': 2.27,
+ 'CU': 1.40,
+ 'CL': 1.75,
+ 'C':  1.70,
+ 'O':  1.52,
+ 'I':  1.98,
+ 'P':  1.80,
+ 'B':  1.85,
+ 'BR': 1.85,
+ 'S':  1.80,
+ 'SE': 1.90,
+ 'F':  1.47,
+ 'FE': 1.80,
+ 'K':  2.75,
+ 'MN': 1.73,
+ 'MG': 1.73,
+ 'ZN': 1.39,
+ 'HG': 1.80,
+ 'XE': 1.80,
+ 'AU': 1.80,
+ 'LI': 1.80,
+ '.':  1.80
+}
+
+masses = {'H'  : 1.008,   'HE' : 4.003,   'LI' : 6.941,   'BE' : 9.012,
+          'B'  : 10.811,  'C'  : 12.011,  'N'  : 14.007,  'O'  : 15.999,
+          'F'  : 18.998,  'NE' : 20.180,  'NA' : 22.990,  'MG' : 24.305,
+          'AL' : 26.982,  'SI' : 28.086,  'P'  : 30.974,  'S'  : 32.066,
+          'CL' : 35.453,  'AR' : 39.948,  'K'  : 39.098,  'CA' : 40.078,
+          'SC' : 44.956,  'TI' : 47.867,  'V'  : 50.942,  'CR' : 51.996,
+          'MN' : 54.938,  'FE' : 55.845,  'CO' : 58.933,  'NI' : 58.693,
+          'CU' : 63.546,  'ZN' : 65.38,   'GA' : 69.723,  'GE' : 72.631,
+          'AS' : 74.922,  'SE' : 78.971,  'BR' : 79.904,  'KR' : 84.798,
+          'RB' : 84.468,  'SR' : 87.62,   'Y'  : 88.906,  'ZR' : 91.224,
+          'NB' : 92.906,  'MO' : 95.95,   'TC' : 98.907,  'RU' : 101.07,
+          'RH' : 102.906, 'PD' : 106.42,  'AG' : 107.868, 'CD' : 112.414,
+          'IN' : 114.818, 'SN' : 118.711, 'SB' : 121.760, 'TE' : 126.7,
+          'I'  : 126.904, 'XE' : 131.294, 'CS' : 132.905, 'BA' : 137.328,
+          'LA' : 138.905, 'CE' : 140.116, 'PR' : 140.908, 'ND' : 144.243,
+          'PM' : 144.913, 'SM' : 150.36,  'EU' : 151.964, 'GD' : 157.25,
+          'TB' : 158.925, 'DY' : 162.500, 'HO' : 164.930, 'ER' : 167.259,
+          'TM' : 168.934, 'YB' : 173.055, 'LU' : 174.967, 'HF' : 178.49,
+          'TA' : 180.948, 'W'  : 183.84,  'RE' : 186.207, 'OS' : 190.23,
+          'IR' : 192.217, 'PT' : 195.085, 'AU' : 196.967, 'HG' : 200.592,
+          'TL' : 204.383, 'PB' : 207.2,   'BI' : 208.980, 'PO' : 208.982,
+          'AT' : 209.987, 'RN' : 222.081, 'FR' : 223.020, 'RA' : 226.025,
+          'AC' : 227.028, 'TH' : 232.038, 'PA' : 231.036, 'U'  : 238.029,
+          'NP' : 237,     'PU' : 244,     'AM' : 243,     'CM' : 247, 'BK' : 247,
+          'CT' : 251,     'ES' : 252,     'FM' : 257,     'MD' : 258, 'NO' : 259,
+          'LR' : 262,     'RF' : 261,     'DB' : 262,     'SG' : 266, 'BH' : 264,
+          'HS' : 269,     'MT' : 268,     'DS' : 271,     'RG' : 272, 'CN' : 285,
+          'NH' : 284,     'FL' : 289,     'MC' : 288,     'LV' : 292, 'TS' : 294,
+          'OG' : 294}
+
+two_char_elements = [e for e in list(radii.keys()) if len(e) == 2]
+
+
+def strip_numbers(s):
+  result = ""
+  for c in s:
+    if not c.isdigit() and c != " ":
+      result += c
+  return result
+
+
+def guess_element(res_type, atom_type):
+  """
+  Returns the element type using a dirty heuristic guess.
+  """
+  atom_type = strip_numbers(atom_type)
+  if len(atom_type) == 0:
+    raise Exception("PDB line with no atom name found")
+  if res_type in res_name_to_char:
+    return atom_type[0]
+  if len(atom_type) == 2 and atom_type in two_char_elements:
+    return atom_type
+  return atom_type[0]  
+
+
+chi_topology = {
+  'ARG': [ ['N', 'CA', 'CB', 'CG'],
+           ['CA', 'CB', 'CG', 'CD'],
+           ['CB', 'CG', 'CD', 'NE'],
+           ['CG', 'CD', 'NE', 'CZ']],
+  'ASN': [['N', 'CA', 'CB', 'CG'], ['CA', 'CB', 'CG', 'OD1']],
+  'ASP': [['N', 'CA', 'CB', 'CG'], ['CA', 'CB', 'CG', 'OD1']],
+  'CYS': [['N', 'CA', 'CB', 'SG']],
+  'GLN': [ ['N', 'CA', 'CB', 'CG'],
+           ['CA', 'CB', 'CG', 'CD'],
+           ['CB', 'CG', 'CD', 'OE1']],
+  'GLU': [ ['N', 'CA', 'CB', 'CG'],
+           ['CA', 'CB', 'CG', 'CD'],
+           ['CB', 'CG', 'CD', 'OE1']],
+  'HIS': [['N', 'CA', 'CB', 'CG'], ['CA', 'CB', 'CG', 'ND1']],
+  'ILE': [['N', 'CA', 'CB', 'CG1'], ['CA', 'CB', 'CG1', 'CD1']],
+  'LEU': [['N', 'CA', 'CB', 'CG'], ['CA', 'CB', 'CG', 'CD1']],
+  'LYN': [ ['N', 'CA', 'CB', 'CG'],
+           ['CA', 'CB', 'CG', 'CD'],
+           ['CB', 'CG', 'CD', 'CE'],
+           ['CG', 'CD', 'CE', 'NZ']],
+  'LYP': [ ['N', 'CA', 'CB', 'CG'],
+           ['CA', 'CB', 'CG', 'CD'],
+           ['CB', 'CG', 'CD', 'CE'],
+           ['CG', 'CD', 'CE', 'NZ']],
+  'LYS': [ ['N', 'CA', 'CB', 'CG'],
+           ['CA', 'CB', 'CG', 'CD'],
+           ['CB', 'CG', 'CD', 'CE'],
+           ['CG', 'CD', 'CE', 'NZ']],
+  'MET': [ ['N', 'CA', 'CB', 'CG'],
+           ['CA', 'CB', 'CG', 'SD'],
+           ['CB', 'CG', 'SD', 'CE']],
+  'PHD': [['N', 'CA', 'CB', 'CG'], ['CA', 'CB', 'CG', 'OD1']],
+  'PHE': [['N', 'CA', 'CB', 'CG'], ['CA', 'CB', 'CG', 'CD1']],
+  'PRO': [ ['N', 'CA', 'CB', 'CG'],
+           ['CA', 'CB', 'CG', 'CD'],
+           ['CB', 'CG', 'CD', 'N'],
+           ['CG', 'CD', 'N', 'CA']],
+  'SER': [['N', 'CA', 'CB', 'OG']],
+  'THR': [['N', 'CA', 'CB', 'OG1']],
+  'TRP': [['N', 'CA', 'CB', 'CG'], ['CA', 'CB', 'CG', 'CD1']],
+  'TYR': [['N', 'CA', 'CB', 'CG'], ['CA', 'CB', 'CG', 'CD1']],
+  'VAL': [['N', 'CA', 'CB', 'CG1']]}
+
+
+def get_res_chi_topology(res_type):
+  """
+  Returns the chi topology for a given residue, which is a list of
+  atoms that are affected if one rotates the chi0, chi1... 
+  dihedral angle.
+  """
+  # Some common residue renamings in AMBER and GROMACS
+  if res_type in ["HID", "HIE", "HIP", "HSE"] or "HIS" in res_type:
+    res_type = "HIS"
+  if res_type in ["LYP"]:
+    res_type = "LYS"
+  if res_type in ["CYM", "CYX", "CYN"]:
+    res_type = "CYS"
+  if res_type not in chi_topology:
+    return []
+  else:
+    return chi_topology[res_type]
+
+
+

packmol_memgen/lib/pdbremix/fetch.py

@@ -0,0 +1,102 @@
+# encoding: utf-8
+
+__doc__ = """ 
+
+Fetches PDB files from RCSB web sites.
+
+Simple utility functions to fetch PDB files given a list
+of PDB codes. Several options are available.
+"""
+
+import os
+import urllib.request, urllib.parse, urllib.error
+import gzip
+
+from . import util
+
+
+def expand_pdbs(*pdbs):
+  """
+  Returns a cleaned-up list of PDB codes given a mixed list
+  of pdb codes, pdb filenames, and text files containing such.
+  """
+  results = []
+  for pdb in pdbs:
+    if os.path.isfile(pdb):
+      print("Reading PDB codes from", pdb)
+      new_pdbs = expand_pdbs(*util.words_in_file(pdb))
+      results.extend(new_pdbs)
+    else:
+      pdb = pdb.lower()
+      if pdb.endswith('.pdb'):
+        pdb = pdb[:-4]
+      if len(pdb) != 4:
+        raise Exception("PDB code is not 4 letters long")
+      results.append(pdb)
+  return results
+
+
+def get_pdbs_with_http(*pdbs):
+  """
+  Fetches PDB files using HTTP from a list of pdb-codes/text-files.
+  """
+  for pdb in expand_pdbs(*pdbs):
+    fname = pdb if pdb.endswith('pdb') else '%s.pdb' % pdb 
+    if os.path.isfile(fname):
+      print("Skip: %s exists" % fname)
+    else:
+      try:
+        site = 'http://www.rcsb.org/pdb/files'
+        url = '%s/%s' % (site, fname)
+        sock = urllib.request.urlopen(url)
+        text = sock.read()
+        sock.close()
+        if '<html>' in text:
+          raise Exception
+        open(fname, 'w').write(text)
+        print(fname)
+      except:
+        print("Failed: %s" % fname)
+
+
+template = """#!/bin/bash
+ftp -n %(host)s <<END_SCRIPT
+quote user guest
+quote 
+ls
+cd pub/pdb/data/structures/all/pdb
+binary
+%(mget_str)s
+quit
+END_SCRIPT
+exit 0
+"""
+
+
+def get_pdbs_with_ftp(*pdbs):
+  """
+  Fetches PDB files using FTP from a list of pdb-codes/text-files.
+  """
+  pdbs = expand_pdbs(*pdbs)
+  entries = ['pdb%s.ent.gz' % pdb for pdb in pdbs]
+  mget_scripts = ["get %s" % entry for entry in entries]
+  substitutions = {
+    'host': 'ftp.wwpdb.org',
+    'mget_str': '\n'.join(mget_scripts),
+  }
+  ftp_script = template % substitutions
+  open('ftp.sh', 'w').write(ftp_script)
+  util.run_with_output('chmod +x ftp.sh')
+  util.run_with_output('./ftp.sh')
+  for pdb, entry in zip(pdbs, entries):
+    fname = pdb + '.pdb'
+    if os.path.isfile(entry):
+      out_f = open(fname, 'w')
+      for line in gzip.open(entry):
+        out_f.write(line)
+      util.clean_fname(entry)
+      print(fname)
+    else:
+      print("Failed: %s" % fname)
+  util.clean_fname('ftp.sh')
+