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

packmol_memgen/lib/pdbremix/asa.py

@@ -0,0 +1,227 @@
+# encoding: utf-8
+
+__doc__ = """ 
+
+Calculate the accessible-surface area of atoms.
+
+Uses the simple Shrake-Rupley algorithm, that generates a
+relatively uniform density of dots over every atoms and
+eliminates those within the sphere of another atom. The remaining
+dots is used to calculate the area.
+
+Reference: A. Shrake & J. A. Rupley. "Environment and Exposure to
+Solvent of Protein Atoms. Lysozyme and Insulin." J Mol Biol. 79
+(1973) 351- 371. """
+
+import math
+
+from . import v3
+from . import pdbatoms
+from collections import defaultdict
+
+
+def generate_sphere_points(n):
+  """
+  Returns list of coordinates on a sphere using the Golden-
+  Section Spiral algorithm.
+  """
+  points = []
+  inc = math.pi * (3 - math.sqrt(5))
+  offset = 2 / float(n)
+  for k in range(int(n)):
+    y = k * offset - 1 + (offset / 2)
+    r = math.sqrt(1 - y*y)
+    phi = k * inc
+    points.append(v3.vector(math.cos(phi)*r, y, math.sin(phi)*r))
+  return points
+
+
+def find_neighbor_indices(atoms, probe, k):
+  """
+  Returns list of indices of atoms within probe distance to atom k. 
+  """
+  neighbor_indices = []
+  atom_k = atoms[k]
+  radius = atom_k.radius + probe + probe
+  indices = list(range(k))
+  indices.extend(list(range(k+1, len(atoms))))
+  for i in indices:
+    atom_i = atoms[i]
+    dist = v3.distance(atom_k.pos, atom_i.pos)
+    if dist < radius + atom_i.radius:
+      neighbor_indices.append(i)
+  return neighbor_indices
+
+
+def calculate_asa(atoms, probe, n_sphere_point=960):
+  """
+  Returns the accessible-surface areas of the atoms, by rolling a
+  ball with probe radius over the atoms with their radius
+  defined.
+  """
+  sphere_points = generate_sphere_points(n_sphere_point)
+ 
+  const = 4.0 * math.pi / len(sphere_points)
+  areas = []
+  for i, atom_i in enumerate(atoms):
+    
+    neighbor_indices = find_neighbor_indices(atoms, probe, i)
+    n_neighbor = len(neighbor_indices)
+    j_closest_neighbor = 0
+    radius = probe + atom_i.radius
+    
+    n_accessible_point = 0
+    for point in sphere_points:
+      is_accessible = True
+      test_point = v3.scale(point, radius) + atom_i.pos
+      cycled_indices = list(range(j_closest_neighbor, n_neighbor))
+      cycled_indices.extend(list(range(j_closest_neighbor)))
+      
+      for j in cycled_indices:
+        atom_j = atoms[neighbor_indices[j]]
+        r = atom_j.radius + probe
+        diff = v3.distance(atom_j.pos, test_point)
+        if diff*diff < r*r:
+          j_closest_neighbor = j
+          is_accessible = False
+          break
+      if is_accessible:
+        n_accessible_point += 1
+    
+    area = const*n_accessible_point*radius*radius 
+    areas.append(area)
+
+  return areas
+
+
+def make_boxes(a, d_max):
+    '''
+    Returns dictionary which keys are indecies of boxes (regions)
+    with d_max length side and values
+    are indicies of atoms belonging to these boxes
+    '''
+    b = defaultdict(list) # space divided into boxes
+    for i in range(len(a)):
+        atom = a[i]
+        box_coor = tuple(int(math.floor(x / d_max)) for x in atom.pos)
+        b[box_coor].append(i)
+    return b
+
+
+def add_bond(a, a1, a2, conn, d_max):
+    '''
+    If distance between atoms a1 and a2 is less than d_max (neighboring atoms),
+    add atoms a1 and a2 in adjacency list conn to each other
+    '''
+    atom1 = a[a1]
+    atom2 = a[a2]
+    if v3.mag2(atom1.pos - atom2.pos) <= d_max * d_max:  # connected
+        conn[a1].append(a2)
+        conn[a2].append(a1)
+
+
+def neighbor_atoms(b, box):
+    '''
+    Returns list of atoms from half of neighbouring boxes of the box
+    another half is accounted when symmetric (opposite) boxes considered
+    '''
+    na = [] # list for neighboring atoms
+    x, y, z = box # coordinates of the box
+    # top layer consisting of 9 boxes
+    if (x + 1, y + 1, z +1) in b: na.extend(b[(x + 1, y + 1, z +1)])
+    if (x, y + 1, z +1) in b: na.extend(b[(x, y + 1, z +1)])
+    if (x + 1, y, z +1) in b: na.extend(b[(x + 1, y, z +1)])
+    if (x, y, z +1) in b: na.extend(b[(x, y, z +1)])
+    if (x - 1, y + 1, z +1) in b: na.extend(b[(x - 1, y + 1, z +1)])
+    if (x + 1, y - 1, z +1) in b: na.extend(b[(x + 1, y - 1, z +1)])
+    if (x, y - 1, z +1) in b: na.extend(b[(x, y - 1, z +1)])
+    if (x - 1, y, z +1) in b: na.extend(b[(x - 1, y, z +1)])
+    if (x - 1, y - 1, z +1) in b: na.extend(b[(x - 1, y - 1, z +1)])
+    # half of the middle layer excluding the box itself (4 boxes)
+    if (x + 1, y + 1, z) in b: na.extend(b[(x + 1, y + 1, z)])
+    if (x, y + 1, z) in b: na.extend(b[(x, y + 1, z)])
+    if (x + 1, y, z) in b: na.extend(b[(x + 1, y, z)])
+    if (x + 1, y - 1, z) in b: na.extend(b[(x + 1, y - 1, z)])
+    return na
+
+
+def adjacency_list(a, d_max):
+    '''
+    Returns adjacency list from coordinate file
+    in O(len(a)) time
+    '''
+    b = make_boxes(a, d_max) # put atoms into the boxes with dmax length side
+    # now go on boxes and check connections inside 3x3 superboxes
+    conn = [[] for i in range(len(a))] # list of bond lengths each atom implicated
+    for box in b:
+        lb = len(b[box])
+        for i in range(lb):
+            a1 = b[box][i]
+            # check possible connections inside the box
+            for j in range(i+1, lb):
+                a2 = b[box][j]
+                add_bond(a, a1, a2, conn, d_max)
+            # check connections with atoms from neighbouring boxes
+            na = neighbor_atoms(b, box) # list of such atoms
+            for a2 in na:
+                add_bond(a, a1, a2, conn, d_max)
+    return conn
+
+
+def find_neighbor_indices_modified(atoms, indices, probe, k):
+  """
+  Returns list of indices of atoms within probe distance to atom k. 
+  """
+  neighbor_indices = []
+  atom_k = atoms[k]
+  radius = atom_k.radius + probe + probe
+  for i in indices:
+    if i == k: continue
+    atom_i = atoms[i]
+    dist2 = v3.mag2(atom_k.pos - atom_i.pos) # ToAn
+    if dist2 < (radius + atom_i.radius) ** 2: # ToAn
+      neighbor_indices.append(i)
+  return neighbor_indices
+
+
+def calculate_asa_optimized(atoms, probe, n_sphere_point=960):
+  """
+  Returns the accessible-surface areas of the atoms, by rolling a
+  ball with probe radius over the atoms with their radius
+  defined.
+  """
+  sphere_points = generate_sphere_points(n_sphere_point)
+ 
+  const = 4.0 * math.pi / len(sphere_points)
+  areas = []
+  neighbor_list = adjacency_list(atoms, 2 * (probe + max(atoms, key=lambda p: p.radius).radius))
+  for i, atom_i in enumerate(atoms):
+    
+    neighbor_indices = [neig for neig in neighbor_list[i]]
+    neighbor_indices = find_neighbor_indices_modified(atoms, neighbor_indices, probe, i) # even further narrow diapazon
+    n_neighbor = len(neighbor_indices)
+    j_closest_neighbor = 0
+    radius = probe + atom_i.radius
+    
+    n_accessible_point = 0
+    for point in sphere_points:
+      is_accessible = True
+      test_point = v3.scale(point, radius) + atom_i.pos
+      cycled_indices = list(range(j_closest_neighbor, n_neighbor))
+      cycled_indices.extend(list(range(j_closest_neighbor)))
+      
+      for j in cycled_indices:
+        atom_j = atoms[neighbor_indices[j]]
+        r = atom_j.radius + probe
+        diff2 = v3.mag2(atom_j.pos - test_point)
+        if diff2 < r*r:
+          j_closest_neighbor = j
+          is_accessible = False
+          break
+      if is_accessible:
+        n_accessible_point += 1
+    
+    area = const*n_accessible_point*radius*radius 
+    areas.append(area)
+
+  return areas

packmol_memgen/lib/pdbremix/data/aminoacid.pdb

@@ -0,0 +1,334 @@
+ATOM      1  CH3 ACE     1      37.701 -10.284  -3.831  1.00  0.00
+ATOM      2  C   ACE     1      37.141 -11.445  -3.006  1.00  0.00
+ATOM      3  O   ACE     1      36.543 -12.369  -3.554  1.00  0.00
+ATOM      4 1HH3 ACE     1      36.874  -9.789  -4.360  1.00  0.00
+ATOM      5 2HH3 ACE     1      38.195  -9.571  -3.155  1.00  0.00
+ATOM      6 3HH3 ACE     1      38.428 -10.679  -4.557  1.00  0.00
+ATOM      7  N   ALA     2      37.356 -11.359  -1.701  1.00  0.00
+ATOM      8  CA  ALA     2      36.876 -12.399  -0.788  1.00  0.00
+ATOM      9  C   ALA     2      36.570 -11.774   0.575  1.00  0.00
+ATOM     10  O   ALA     2      37.454 -11.206   1.214  1.00  0.00
+ATOM     11  CB  ALA     2      37.949 -13.478  -0.628  1.00  0.00
+ATOM     12  H   ALA     2      37.843 -10.604  -1.263  1.00  0.00
+ATOM     13  HA  ALA     2      35.964 -12.859  -1.197  1.00  0.00
+ATOM     14 1HB  ALA     2      38.861 -13.019  -0.219  1.00  0.00
+ATOM     15 2HB  ALA     2      37.579 -14.253   0.059  1.00  0.00
+ATOM     16 3HB  ALA     2      38.161 -13.920  -1.613  1.00  0.00
+ATOM     17  N   CYS     3      35.314 -11.899   0.978  1.00  0.00
+ATOM     18  CA  CYS     3      34.876 -11.349   2.264  1.00  0.00
+ATOM     19  C   CYS     3      33.733 -12.202   2.817  1.00  0.00
+ATOM     20  O   CYS     3      32.688 -12.333   2.182  1.00  0.00
+ATOM     21  CB  CYS     3      34.395  -9.909   2.069  1.00  0.00
+ATOM     22  SG  CYS     3      33.846  -9.212   3.670  1.00  0.00
+ATOM     23  H   CYS     3      34.601 -12.362   0.452  1.00  0.00
+ATOM     24  HA  CYS     3      35.717 -11.353   2.973  1.00  0.00
+ATOM     25 1HB  CYS     3      35.224  -9.305   1.672  1.00  0.00
+ATOM     26 2HB  CYS     3      33.555  -9.905   1.360  1.00  0.00
+ATOM     27  N   ASP     4      33.971 -12.762   3.994  1.00  0.00
+ATOM     28  CA  ASP     4      32.966 -13.606   4.645  1.00  0.00
+ATOM     29  C   ASP     4      33.123 -13.500   6.163  1.00  0.00
+ATOM     30  O   ASP     4      34.177 -13.826   6.706  1.00  0.00
+ATOM     31  CB  ASP     4      33.157 -15.060   4.209  1.00  0.00
+ATOM     32  CG  ASP     4      32.121 -15.971   4.871  1.00  0.00
+ATOM     33  OD1 ASP     4      32.124 -17.169   4.638  1.00  0.00
+ATOM     34  OD2 ASP     4      31.293 -15.500   5.634  1.00  0.00
+ATOM     35  H   ASP     4      34.824 -12.651   4.504  1.00  0.00
+ATOM     36  HA  ASP     4      31.959 -13.274   4.353  1.00  0.00
+ATOM     37 1HB  ASP     4      33.042 -15.125   3.117  1.00  0.00
+ATOM     38 2HB  ASP     4      34.164 -15.393   4.501  1.00  0.00
+ATOM     39  N   GLU     5      32.058 -13.042   6.805  1.00  0.00
+ATOM     40  CA  GLU     5      32.064 -12.888   8.262  1.00  0.00
+ATOM     41  C   GLU     5      30.645 -13.085   8.797  1.00  0.00
+ATOM     42  O   GLU     5      29.731 -12.349   8.428  1.00  0.00
+ATOM     43  CB  GLU     5      32.563 -11.488   8.628  1.00  0.00
+ATOM     44  CG  GLU     5      32.582 -11.293  10.146  1.00  0.00
+ATOM     45  CD  GLU     5      33.080  -9.893  10.512  1.00  0.00
+ATOM     46  OE1 GLU     5      33.162  -9.556  11.703  1.00  0.00
+ATOM     47  OE2 GLU     5      33.402  -9.096   9.618  1.00  0.00
+ATOM     48  H   GLU     5      31.205 -12.779   6.356  1.00  0.00
+ATOM     49  HA  GLU     5      32.735 -13.635   8.710  1.00  0.00
+ATOM     50 1HB  GLU     5      33.583 -11.358   8.239  1.00  0.00
+ATOM     51 2HB  GLU     5      31.892 -10.741   8.180  1.00  0.00
+ATOM     52 1HG  GLU     5      31.562 -11.422  10.536  1.00  0.00
+ATOM     53 2HG  GLU     5      33.253 -12.040  10.595  1.00  0.00
+ATOM     54  N   PHE     6      30.505 -14.081   9.660  1.00  0.00
+ATOM     55  CA  PHE     6      29.201 -14.386  10.255  1.00  0.00
+ATOM     56  C   PHE     6      29.408 -14.980  11.649  1.00  0.00
+ATOM     57  O   PHE     6      30.049 -16.020  11.796  1.00  0.00
+ATOM     58  CB  PHE     6      28.456 -15.391   9.373  1.00  0.00
+ATOM     59  CG  PHE     6      27.088 -15.732   9.967  1.00  0.00
+ATOM     60  CD1 PHE     6      26.270 -16.612   9.328  1.00  0.00
+ATOM     61  CD2 PHE     6      26.690 -15.156  11.133  1.00  0.00
+ATOM     62  CE1 PHE     6      25.001 -16.929   9.879  1.00  0.00
+ATOM     63  CE2 PHE     6      25.420 -15.473  11.683  1.00  0.00
+ATOM     64  CZ  PHE     6      24.602 -16.353  11.045  1.00  0.00
+ATOM     65  H   PHE     6      31.253 -14.674   9.955  1.00  0.00
+ATOM     66  HA  PHE     6      28.605 -13.465  10.330  1.00  0.00
+ATOM     67 1HB  PHE     6      28.313 -14.954   8.374  1.00  0.00
+ATOM     68 2HB  PHE     6      29.053 -16.312   9.298  1.00  0.00
+ATOM     69  HD1 PHE     6      26.593 -17.077   8.385  1.00  0.00
+ATOM     70  HE1 PHE     6      24.339 -17.640   9.363  1.00  0.00
+ATOM     71  HZ  PHE     6      23.618 -16.598  11.472  1.00  0.00
+ATOM     72  HE2 PHE     6      25.098 -15.008  12.626  1.00  0.00
+ATOM     73  HD2 PHE     6      27.351 -14.445  11.649  1.00  0.00
+ATOM     74  N   GLY     7      28.854 -14.294  12.638  1.00  0.00
+ATOM     75  CA  GLY     7      28.971 -14.745  14.027  1.00  0.00
+ATOM     76  C   GLY     7      27.734 -14.298  14.810  1.00  0.00
+ATOM     77  O   GLY     7      27.457 -13.104  14.910  1.00  0.00
+ATOM     78  H   GLY     7      28.335 -13.449  12.510  1.00  0.00
+ATOM     79 1HA  GLY     7      29.050 -15.842  14.055  1.00  0.00
+ATOM     80 2HA  GLY     7      29.873 -14.310  14.482  1.00  0.00
+ATOM     81  N   HIS     8      27.024 -15.281  15.343  1.00  0.00
+ATOM     82  CA  HIS     8      25.814 -15.002  16.120  1.00  0.00
+ATOM     83  C   HIS     8      25.631 -16.090  17.180  1.00  0.00
+ATOM     84  O   HIS     8      25.503 -17.268  16.849  1.00  0.00
+ATOM     85  CB  HIS     8      24.599 -14.982  15.189  1.00  0.00
+ATOM     86  CG  HIS     8      23.316 -14.692  15.970  1.00  0.00
+ATOM     87  ND1 HIS     8      22.072 -14.618  15.366  1.00  0.00
+ATOM     88  CD2 HIS     8      23.303 -14.493  17.274  1.00  0.00
+ATOM     89  CE1 HIS     8      21.169 -14.356  16.300  1.00  0.00
+ATOM     90  NE2 HIS     8      21.808 -14.259  17.501  1.00  0.00
+ATOM     91  H   HIS     8      27.257 -16.250  15.257  1.00  0.00
+ATOM     92  HA  HIS     8      25.907 -14.022  16.609  1.00  0.00
+ATOM     93 1HB  HIS     8      24.742 -14.197  14.432  1.00  0.00
+ATOM     94 2HB  HIS     8      24.507 -15.962  14.700  1.00  0.00
+ATOM     95  HE1 HIS     8      20.187 -14.248  16.150  1.00  0.00
+ATOM     96  HD2 HIS     8      24.181 -14.509  17.936  1.00  0.00
+ATOM     97  N   ILE     9      25.624 -15.657  18.432  1.00  0.00
+ATOM     98  CA  ILE     9      25.458 -16.587  19.551  1.00  0.00
+ATOM     99  C   ILE     9      24.762 -15.867  20.708  1.00  0.00
+ATOM    100  O   ILE     9      25.275 -14.875  21.224  1.00  0.00
+ATOM    101  CB  ILE     9      26.828 -17.092  20.009  1.00  0.00
+ATOM    102  CG1 ILE     9      26.690 -18.067  21.179  1.00  0.00
+ATOM    103  CG2 ILE     9      27.715 -15.931  20.466  1.00  0.00
+ATOM    104  CD1 ILE     9      28.060 -18.571  21.637  1.00  0.00
+ATOM    105  H   ILE     9      25.729 -14.697  18.692  1.00  0.00
+ATOM    106  HA  ILE     9      24.849 -17.446  19.231  1.00  0.00
+ATOM    107  HB  ILE     9      27.318 -17.607  19.170  1.00  0.00
+ATOM    108 1HG2 ILE     9      27.225 -15.416  21.305  1.00  0.00
+ATOM    109 2HG2 ILE     9      28.688 -16.330  20.787  1.00  0.00
+ATOM    110 3HG2 ILE     9      27.853 -15.234  19.626  1.00  0.00
+ATOM    111 1HG1 ILE     9      26.200 -17.552  22.019  1.00  0.00
+ATOM    112 2HG1 ILE     9      26.082 -18.926  20.860  1.00  0.00
+ATOM    113 1HD1 ILE     9      28.669 -17.713  21.957  1.00  0.00
+ATOM    114 2HD1 ILE     9      27.923 -19.268  22.477  1.00  0.00
+ATOM    115 3HD1 ILE     9      28.551 -19.087  20.798  1.00  0.00
+ATOM    116  N   LYS    10      23.606 -16.394  21.082  1.00  0.00
+ATOM    117  CA  LYS    10      22.828 -15.809  22.177  1.00  0.00
+ATOM    118  C   LYS    10      22.031 -16.912  22.876  1.00  0.00
+ATOM    119  O   LYS    10      21.205 -17.576  22.252  1.00  0.00
+ATOM    120  CB  LYS    10      21.870 -14.755  21.621  1.00  0.00
+ATOM    121  CG  LYS    10      21.041 -14.122  22.741  1.00  0.00
+ATOM    122  CD  LYS    10      20.082 -13.067  22.185  1.00  0.00
+ATOM    123  CE  LYS    10      19.278 -12.466  23.340  1.00  0.00
+ATOM    124  NZ  LYS    10      18.302 -11.403  22.833  1.00  0.00
+ATOM    125  H   LYS    10      23.196 -17.201  20.657  1.00  0.00
+ATOM    126 1HZ  LYS    10      17.607 -11.867  22.118  1.00  0.00
+ATOM    127 2HZ  LYS    10      17.743 -10.994  23.688  1.00  0.00
+ATOM    128 3HZ  LYS    10      18.870 -10.602  22.338  1.00  0.00
+ATOM    129  HA  LYS    10      23.508 -15.331  22.898  1.00  0.00
+ATOM    130 1HB  LYS    10      22.453 -13.968  21.121  1.00  0.00
+ATOM    131 2HB  LYS    10      21.190 -15.233  20.900  1.00  0.00
+ATOM    132 1HG  LYS    10      20.456 -14.908  23.241  1.00  0.00
+ATOM    133 2HG  LYS    10      21.719 -13.643  23.462  1.00  0.00
+ATOM    134 1HD  LYS    10      20.666 -12.281  21.685  1.00  0.00
+ATOM    135 2HD  LYS    10      19.402 -13.546  21.464  1.00  0.00
+ATOM    136  HE1 LYS    10      18.709 -13.267  23.835  1.00  0.00
+ATOM    137 2HE  LYS    10      19.973 -12.002  24.055  1.00  0.00
+ATOM    138  N   LEU    11      22.306 -17.072  24.163  1.00  0.00
+ATOM    139  CA  LEU    11      21.618 -18.091  24.960  1.00  0.00
+ATOM    140  C   LEU    11      21.523 -17.618  26.412  1.00  0.00
+ATOM    141  O   LEU    11      22.542 -17.377  27.058  1.00  0.00
+ATOM    142  CB  LEU    11      22.399 -19.405  24.898  1.00  0.00
+ATOM    143  CG  LEU    11      21.707 -20.493  25.721  1.00  0.00
+ATOM    144  CD1 LEU    11      22.487 -21.808  25.659  1.00  0.00
+ATOM    145  CD2 LEU    11      21.596 -20.081  27.191  1.00  0.00
+ATOM    146  H   LEU    11      22.979 -16.527  24.663  1.00  0.00
+ATOM    147  HA  LEU    11      20.608 -18.255  24.558  1.00  0.00
+ATOM    148 1HB  LEU    11      22.461 -19.736  23.850  1.00  0.00
+ATOM    149 2HB  LEU    11      23.409 -19.241  25.300  1.00  0.00
+ATOM    150  HG  LEU    11      20.696 -20.659  25.319  1.00  0.00
+ATOM    151 1HD1 LEU    11      23.498 -21.644  26.061  1.00  0.00
+ATOM    152 2HD1 LEU    11      21.963 -22.565  26.260  1.00  0.00
+ATOM    153 3HD1 LEU    11      22.550 -22.138  24.612  1.00  0.00
+ATOM    154 1HD2 LEU    11      21.008 -19.154  27.259  1.00  0.00
+ATOM    155 2HD2 LEU    11      21.095 -20.885  27.751  1.00  0.00
+ATOM    156 3HD2 LEU    11      22.606 -19.916  27.594  1.00  0.00
+ATOM    157  N   MET    12      20.290 -17.499  26.882  1.00  0.00
+ATOM    158  CA  MET    12      20.047 -17.055  28.257  1.00  0.00
+ATOM    159  C   MET    12      18.750 -17.684  28.769  1.00  0.00
+ATOM    160  O   MET    12      17.682 -17.467  28.197  1.00  0.00
+ATOM    161  CB  MET    12      19.927 -15.530  28.292  1.00  0.00
+ATOM    162  CG  MET    12      19.672 -15.032  29.716  1.00  0.00
+ATOM    163  SD  MET    12      19.560 -13.506  29.697  1.00  0.00
+ATOM    164  CE  MET    12      19.305 -13.008  31.121  1.00  0.00
+ATOM    165  H   MET    12      19.467 -17.696  26.350  1.00  0.00
+ATOM    166  HA  MET    12      20.885 -17.363  28.899  1.00  0.00
+ATOM    167 1HB  MET    12      20.864 -15.089  27.921  1.00  0.00
+ATOM    168 2HB  MET    12      19.088 -15.222  27.650  1.00  0.00
+ATOM    169 1HG  MET    12      18.735 -15.472  30.087  1.00  0.00
+ATOM    170 2HG  MET    12      20.511 -15.339  30.358  1.00  0.00
+ATOM    171 1HE  MET    12      20.144 -13.315  31.764  1.00  0.00
+ATOM    172 2HE  MET    12      19.225 -11.911  31.108  1.00  0.00
+ATOM    173 3HE  MET    12      18.368 -13.449  31.492  1.00  0.00
+ATOM    174  N   ASN    13      18.884 -18.451  29.842  1.00  0.00
+ATOM    175  CA  ASN    13      17.727 -19.118  30.442  1.00  0.00
+ATOM    176  C   ASN    13      17.958 -19.277  31.946  1.00  0.00
+ATOM    177  O   ASN    13      18.919 -19.920  32.366  1.00  0.00
+ATOM    178  CB  ASN    13      17.539 -20.496  29.803  1.00  0.00
+ATOM    179  CG  ASN    13      16.336 -21.221  30.409  1.00  0.00
+ATOM    180  OD1 ASN    13      16.036 -22.337  30.017  1.00  0.00
+ATOM    181  ND2 ASN    13      15.617 -20.636  31.362  1.00  0.00
+ATOM    182  H   ASN    13      19.756 -18.622  30.301  1.00  0.00
+ATOM    183 1HD2 ASN    13      15.862 -19.721  31.683  1.00  0.00
+ATOM    184 2HD2 ASN    13      14.830 -21.110  31.758  1.00  0.00
+ATOM    185  HA  ASN    13      16.822 -18.517  30.269  1.00  0.00
+ATOM    186 1HB  ASN    13      17.373 -20.370  28.723  1.00  0.00
+ATOM    187 2HB  ASN    13      18.443 -21.097  29.977  1.00  0.00
+ATOM    188  N   PRO    14      17.062 -18.678  32.717  1.00  0.00
+ATOM    189  CA  PRO    14      17.158 -18.745  34.177  1.00  0.00
+ATOM    190  C   PRO    14      17.093 -20.208  34.622  1.00  0.00
+ATOM    191  O   PRO    14      16.109 -20.897  34.360  1.00  0.00
+ATOM    192  CB  PRO    14      15.952 -17.934  34.656  1.00  0.00
+ATOM    193  CG  PRO    14      14.991 -18.013  33.506  1.00  0.00
+ATOM    194  CD  PRO    14      15.892 -17.889  32.286  1.00  0.00
+ATOM    195 2HD  PRO    14      16.161 -16.841  32.084  1.00  0.00
+ATOM    196 1HD  PRO    14      15.421 -18.317  31.388  1.00  0.00
+ATOM    197 2HG  PRO    14      14.260 -17.191  33.544  1.00  0.00
+ATOM    198 1HG  PRO    14      14.452 -18.972  33.505  1.00  0.00
+ATOM    199 1HB  PRO    14      15.516 -18.374  35.565  1.00  0.00
+ATOM    200 2HB  PRO    14      16.235 -16.891  34.863  1.00  0.00
+ATOM    201  HA  PRO    14      18.108 -18.301  34.506  1.00  0.00
+ATOM    202  N   GLN    15      18.155 -20.639  35.286  1.00  0.00
+ATOM    203  CA  GLN    15      18.233 -22.018  35.774  1.00  0.00
+ATOM    204  C   GLN    15      19.082 -22.059  37.045  1.00  0.00
+ATOM    205  O   GLN    15      20.255 -21.688  37.025  1.00  0.00
+ATOM    206  CB  GLN    15      18.868 -22.907  34.702  1.00  0.00
+ATOM    207  CG  GLN    15      18.964 -24.357  35.179  1.00  0.00
+ATOM    208  CD  GLN    15      19.600 -25.246  34.108  1.00  0.00
+ATOM    209  OE1 GLN    15      19.755 -26.438  34.318  1.00  0.00
+ATOM    210  NE2 GLN    15      19.982 -24.719  32.948  1.00  0.00
+ATOM    211  H   GLN    15      18.952 -20.072  35.495  1.00  0.00
+ATOM    212 1HE2 GLN    15      19.854 -23.742  32.776  1.00  0.00
+ATOM    213 2HE2 GLN    15      20.397 -25.300  32.248  1.00  0.00
+ATOM    214  HA  GLN    15      17.221 -22.390  35.993  1.00  0.00
+ATOM    215 1HB  GLN    15      18.250 -22.870  33.793  1.00  0.00
+ATOM    216 2HB  GLN    15      19.880 -22.535  34.483  1.00  0.00
+ATOM    217 1HG  GLN    15      19.583 -24.395  36.088  1.00  0.00
+ATOM    218 2HG  GLN    15      17.953 -24.730  35.399  1.00  0.00
+ATOM    219  N   ARG    16      18.457 -22.512  38.122  1.00  0.00
+ATOM    220  CA  ARG    16      19.147 -22.606  39.411  1.00  0.00
+ATOM    221  C   ARG    16      18.552 -23.761  40.220  1.00  0.00
+ATOM    222  O   ARG    16      17.360 -23.762  40.523  1.00  0.00
+ATOM    223  CB  ARG    16      18.975 -21.296  40.183  1.00  0.00
+ATOM    224  CG  ARG    16      19.685 -21.361  41.537  1.00  0.00
+ATOM    225  CD  ARG    16      19.513 -20.051  42.309  1.00  0.00
+ATOM    226  NE  ARG    16      20.238 -20.166  43.652  1.00  0.00
+ATOM    227  CZ  ARG    16      20.227 -18.989  44.630  1.00  0.00
+ATOM    228  NH1 ARG    16      19.491 -17.698  44.265  1.00  0.00
+ATOM    229  NH2 ARG    16      20.952 -19.103  45.972  1.00  0.00
+ATOM    230  H   ARG    16      17.503 -22.811  38.130  1.00  0.00
+ATOM    231 1HH1 ARG    16      19.017 -17.624  43.388  1.00  0.00
+ATOM    232 1HH2 ARG    16      21.433 -19.947  46.210  1.00  0.00
+ATOM    233  HE  ARG    16      20.767 -21.094  43.914  1.00  0.00
+ATOM    234  HA  ARG    16      20.219 -22.785  39.244  1.00  0.00
+ATOM    235 1HB  ARG    16      19.405 -20.474  39.593  1.00  0.00
+ATOM    236 2HB  ARG    16      17.903 -21.117  40.350  1.00  0.00
+ATOM    237 1HG  ARG    16      19.254 -22.183  42.128  1.00  0.00
+ATOM    238 2HG  ARG    16      20.757 -21.540  41.371  1.00  0.00
+ATOM    239 1HD  ARG    16      19.943 -19.229  41.719  1.00  0.00
+ATOM    240 2HD  ARG    16      18.440 -19.872  42.476  1.00  0.00
+ATOM    241 2HH1 ARG    16      19.483 -16.929  44.905  1.00  0.00
+ATOM    242 2HH2 ARG    16      20.945 -18.334  46.611  1.00  0.00
+ATOM    243  N   SER    17      19.410 -24.717  40.545  1.00  0.00
+ATOM    244  CA  SER    17      18.981 -25.885  41.318  1.00  0.00
+ATOM    245  C   SER    17      20.154 -26.393  42.160  1.00  0.00
+ATOM    246  O   SER    17      21.195 -26.764  41.620  1.00  0.00
+ATOM    247  CB  SER    17      18.515 -26.989  40.367  1.00  0.00
+ATOM    248  OG  SER    17      18.085 -28.152  41.069  1.00  0.00
+ATOM    249  H   SER    17      20.378 -24.709  40.294  1.00  0.00
+ATOM    250  HG  SER    17      17.787 -28.852  40.420  1.00  0.00
+ATOM    251  HA  SER    17      18.147 -25.605  41.978  1.00  0.00
+ATOM    252 1HB  SER    17      17.673 -26.612  39.767  1.00  0.00
+ATOM    253 2HB  SER    17      19.349 -27.269  39.707  1.00  0.00
+ATOM    254  N   THR    18      19.946 -26.393  43.468  1.00  0.00
+ATOM    255  CA  THR    18      20.981 -26.853  44.397  1.00  0.00
+ATOM    256  C   THR    18      20.317 -27.447  45.640  1.00  0.00
+ATOM    257  O   THR    18      19.577 -26.760  46.342  1.00  0.00
+ATOM    258  CB  THR    18      21.869 -25.674  44.802  1.00  0.00
+ATOM    259  OG1 THR    18      22.820 -26.250  45.693  1.00  0.00
+ATOM    260  CG2 THR    18      21.048 -24.580  45.488  1.00  0.00
+ATOM    261  H   THR    18      19.096 -26.089  43.899  1.00  0.00
+ATOM    262  HG1 THR    18      23.454 -25.547  46.017  1.00  0.00
+ATOM    263  HA  THR    18      21.602 -27.618  43.908  1.00  0.00
+ATOM    264  HB  THR    18      22.340 -25.255  43.901  1.00  0.00
+ATOM    265 1HG2 THR    18      20.577 -24.999  46.389  1.00  0.00
+ATOM    266 2HG2 THR    18      21.717 -23.752  45.765  1.00  0.00
+ATOM    267 3HG2 THR    18      20.275 -24.223  44.792  1.00  0.00
+ATOM    268  N   VAL    19      20.605 -28.719  45.875  1.00  0.00
+ATOM    269  CA  VAL    19      20.040 -29.420  47.031  1.00  0.00
+ATOM    270  C   VAL    19      21.019 -30.501  47.495  1.00  0.00
+ATOM    271  O   VAL    19      21.352 -31.409  46.735  1.00  0.00
+ATOM    272  CB  VAL    19      18.709 -30.065  46.641  1.00  0.00
+ATOM    273  CG1 VAL    19      18.091 -30.807  47.828  1.00  0.00
+ATOM    274  CG2 VAL    19      17.705 -29.010  46.171  1.00  0.00
+ATOM    275  H   VAL    19      21.208 -29.272  45.299  1.00  0.00
+ATOM    276  HA  VAL    19      19.866 -28.704  47.848  1.00  0.00
+ATOM    277  HB  VAL    19      18.883 -30.781  45.824  1.00  0.00
+ATOM    278 1HG1 VAL    19      17.915 -30.091  48.645  1.00  0.00
+ATOM    279 2HG1 VAL    19      17.138 -31.256  47.512  1.00  0.00
+ATOM    280 3HG1 VAL    19      18.785 -31.593  48.160  1.00  0.00
+ATOM    281 1HG2 VAL    19      18.119 -28.487  45.296  1.00  0.00
+ATOM    282 2HG2 VAL    19      16.763 -29.508  45.900  1.00  0.00
+ATOM    283 3HG2 VAL    19      17.530 -28.294  46.988  1.00  0.00
+ATOM    284  N   TRP    20      21.452 -30.367  48.740  1.00  0.00
+ATOM    285  CA  TRP    20      22.393 -31.329  49.319  1.00  0.00
+ATOM    286  C   TRP    20      22.159 -31.421  50.828  1.00  0.00
+ATOM    287  O   TRP    20      22.281 -30.425  51.540  1.00  0.00
+ATOM    288  CB  TRP    20      23.828 -30.871  49.048  1.00  0.00
+ATOM    289  CG  TRP    20      24.839 -31.855  49.640  1.00  0.00
+ATOM    290  CD1 TRP    20      26.176 -31.786  49.602  1.00  0.00
+ATOM    291  CD2 TRP    20      24.538 -33.066  50.365  1.00  0.00
+ATOM    292  NE1 TRP    20      26.756 -32.860  50.247  1.00  0.00
+ATOM    293  CE2 TRP    20      25.728 -33.663  50.725  1.00  0.00
+ATOM    294  CE3 TRP    20      23.287 -33.627  50.698  1.00  0.00
+ATOM    295  CZ2 TRP    20      25.792 -34.862  51.444  1.00  0.00
+ATOM    296  CZ3 TRP    20      23.340 -34.827  51.417  1.00  0.00
+ATOM    297  CH2 TRP    20      24.513 -35.465  51.802  1.00  0.00
+ATOM    298  H   TRP    20      21.176 -29.626  49.351  1.00  0.00
+ATOM    299  HE1 TRP    20      27.735 -33.036  50.355  1.00  0.00
+ATOM    300  HA  TRP    20      22.241 -32.317  48.860  1.00  0.00
+ATOM    301 1HB  TRP    20      23.985 -30.809  47.961  1.00  0.00
+ATOM    302 2HB  TRP    20      23.981 -29.883  49.506  1.00  0.00
+ATOM    303  HD1 TRP    20      26.742 -30.976  49.119  1.00  0.00
+ATOM    304  HZ2 TRP    20      26.713 -35.377  51.755  1.00  0.00
+ATOM    305  HH2 TRP    20      24.378 -36.402  52.363  1.00  0.00
+ATOM    306  HZ3 TRP    20      22.473 -35.408  51.763  1.00  0.00
+ATOM    307  HE3 TRP    20      22.304 -33.205  50.442  1.00  0.00
+ATOM    308  N   TYR    21      21.827 -32.624  51.271  1.00  0.00
+ATOM    309  CA  TYR    21      21.572 -32.861  52.694  1.00  0.00
+ATOM    310  C   TYR    21      21.947 -34.303  53.042  1.00  0.00
+ATOM    311  O   TYR    21      21.388 -35.245  52.483  1.00  0.00
+ATOM    312  CB  TYR    21      20.091 -32.627  52.997  1.00  0.00
+ATOM    313  CG  TYR    21      19.790 -32.866  54.478  1.00  0.00
+ATOM    314  CD1 TYR    21      18.523 -32.709  54.949  1.00  0.00
+ATOM    315  CD2 TYR    21      20.789 -33.235  55.324  1.00  0.00
+ATOM    316  CE1 TYR    21      18.244 -32.930  56.323  1.00  0.00
+ATOM    317  CE2 TYR    21      20.509 -33.457  56.699  1.00  0.00
+ATOM    318  CZ  TYR    21      19.243 -33.300  57.169  1.00  0.00
+ATOM    319  OH  TYR    21      18.975 -33.512  58.485  1.00  0.00
+ATOM    320  H   TYR    21      21.730 -33.429  50.685  1.00  0.00
+ATOM    321  HH  TYR    21      19.895 -33.801  59.014  1.00  0.00
+ATOM    322  HA  TYR    21      22.175 -32.166  53.298  1.00  0.00
+ATOM    323 1HB  TYR    21      19.833 -31.588  52.743  1.00  0.00
+ATOM    324 2HB  TYR    21      19.488 -33.322  52.394  1.00  0.00
+ATOM    325  HD1 TYR    21      17.716 -32.410  54.264  1.00  0.00
+ATOM    326  HE1 TYR    21      17.220 -32.803  56.703  1.00  0.00
+ATOM    327  HE2 TYR    21      21.317 -33.755  57.383  1.00  0.00
+ATOM    328  HD2 TYR    21      21.813 -33.362  54.944  1.00  0.00
+ATOM    329  CH3 NME    22      23.350 -35.751  54.397  1.00  0.00
+ATOM    330  N   NME    22      22.891 -34.429  53.964  1.00  0.00
+ATOM    331  H   NME    22      23.340 -33.657  54.413  1.00  0.00
+ATOM    332 1HH3 NME    22      22.499 -36.307  54.816  1.00  0.00
+ATOM    333 2HH3 NME    22      23.758 -36.290  53.529  1.00  0.00
+ATOM    334 3HH3 NME    22      24.131 -35.626  55.162  1.00  0.00

packmol_memgen/lib/pdbremix/data/binaries.json

@@ -0,0 +1,26 @@
+{
+  "pymol": "/Applications/MacPyMOL.app/Contents/MacOS/MacPyMOL",
+  "pymol_batch": "/opt/local/bin/pymol",
+  "chimera": "/Applications/Chimera.app/Contents/MacOS/chimera",
+
+  "theseus": "",
+  "mafft": "",
+
+  "sander": "",
+  "tleap": "",
+
+  "mdrun": "",
+  "pdb2gmx": "",
+  "trjconv": "",
+  "grompp": "",
+  "editconf": "",
+  "genion": "",
+  "genbox": "",
+
+  "vmd": "/Applications/VMD\ 1.8.7.app/Contents/Resources/VMD.app/Contents/MacOS/VMD",
+  "psfgen": "",
+  "namd2": "",
+  "flipdcd": "",
+
+  "mod9v8": ""
+}