Python pick_ray Exemples

Exemple #1

def test_pick_ray(dummy):
    backbone_n = np.array([[-0.334, -0.334], [-0.943, -0.943], [0.000, 0.000],
                           [1.000, 0.000]])

    backbone_c = np.array([[1.251, -0.616], [2.390, 0.788], [0.000, 0.000],
                           [1.000, 0.000]])

    assert_allclose(backbone_n,
                    pick_ray(dummy.residue(1), "1H", "N"),
                    atol=1e-3)
    assert_allclose(backbone_c,
                    pick_ray(dummy.residue(1), "O", "C"),
                    atol=1e-3)

Exemple #2

Fichier : A_CA.py Projet : uw-ipd/privileged_residues

CONECT    1    2
CONECT    2    1    3    4    5
CONECT    3    2
CONECT    4    2
CONECT    5    2
CONECT    6    7
CONECT    7    6    8    9
CONECT    8    7
CONECT    9    7   10   11
CONECT   10    9
CONECT   11    9

"""

pose = Pose()
pose_from_pdbstring(pose, contents)

sc_donor = {
    1: [
        pick_ray(pose.residue(1), "1HZ", "NZ"),
        pick_ray(pose.residue(1), "2HZ", "NZ"),
        pick_ray(pose.residue(1), "3HZ", "NZ")
    ],
    2: [
        pick_ray(pose.residue(2), "1HD2", "ND2"),
        pick_ray(pose.residue(2), "2HD2", "ND2")
    ]
}

sc_acceptor = {2: [pick_ray(pose.residue(2), "OD1", "CG")]}

Exemple #3

Fichier : G_CA.py Projet : uw-ipd/privileged_residues

CONECT    7    4
CONECT    8    4
CONECT    9    5
CONECT   10    5
CONECT   11   12
CONECT   12   11   13   14
CONECT   13   12
CONECT   14   12   15   16
CONECT   15   14
CONECT   16   14
"""

pose = Pose()
pose_from_pdbstring(pose, contents)

sc_donor = {
    1: [
        pick_ray(pose.residue(1), "HE", "NE"),
        pick_ray(pose.residue(1), "1HH1", "NH1"),
        pick_ray(pose.residue(1), "2HH1", "NH1"),
        pick_ray(pose.residue(1), "1HH2", "NH2"),
        pick_ray(pose.residue(1), "2HH2", "NH2")
    ],
    2: [
        pick_ray(pose.residue(2), "1HD2", "ND2"),
        pick_ray(pose.residue(2), "2HD2", "ND2")
    ]
}

sc_acceptor = {2: [pick_ray(pose.residue(2), "OD1", "CG")]}

Exemple #4

Fichier : HIS.py Projet : uw-ipd/privileged_residues

ATOM     33  O   ALA A   3       8.260   5.868   1.023  1.00  0.00           O
ATOM     34  OXT ALA A   3       8.596   5.737  -1.023  1.00  0.00           O
ATOM     35  CB  ALA A   3       8.190   3.050  -1.199  1.00  0.00           C
ATOM     36  H   ALA A   3       5.710   4.705  -0.000  1.00  0.00           H
ATOM     37  HA  ALA A   3       7.999   3.333   0.913  1.00  0.00           H
ATOM     38 1HB  ALA A   3       9.280   3.059  -1.185  1.00  0.00           H
ATOM     39 2HB  ALA A   3       7.835   2.021  -1.154  1.00  0.00           H
ATOM     40 3HB  ALA A   3       7.835   3.516  -2.117  1.00  0.00           H
TER
"""

pose = Pose()
pose_from_pdbstring(pose, contents)

n_rays = {
    1: pick_ray(pose.residue(1), "1H", "N"),
    2: pick_ray(pose.residue(2), "H", "N"),
    3: pick_ray(pose.residue(3), "H", "N")
}

c_rays = {
    1: pick_ray(pose.residue(1), "O", "C"),
    2: pick_ray(pose.residue(2), "O", "C"),
    3: pick_ray(pose.residue(3), "O", "C")
}

sc_donor = {
    2: [
        pick_ray(pose.residue(2), "HE2", "NE2")
    ]
}

Exemple #5

Fichier : TYR.py Projet : uw-ipd/privileged_residues

ATOM     37  O   ALA A   3       8.260   5.868   1.023  1.00  0.00           O
ATOM     38  OXT ALA A   3       8.596   5.737  -1.023  1.00  0.00           O
ATOM     39  CB  ALA A   3       8.190   3.050  -1.199  1.00  0.00           C
ATOM     40  H   ALA A   3       5.710   4.705  -0.000  1.00  0.00           H
ATOM     41  HA  ALA A   3       7.999   3.333   0.913  1.00  0.00           H
ATOM     42 1HB  ALA A   3       9.280   3.059  -1.185  1.00  0.00           H
ATOM     43 2HB  ALA A   3       7.835   2.021  -1.154  1.00  0.00           H
ATOM     44 3HB  ALA A   3       7.835   3.516  -2.117  1.00  0.00           H
TER
"""

pose = Pose()
pose_from_pdbstring(pose, contents)

n_rays = {
    1: pick_ray(pose.residue(1), "1H", "N"),
    2: pick_ray(pose.residue(2), "H", "N"),
    3: pick_ray(pose.residue(3), "H", "N")
}

c_rays = {
    1: pick_ray(pose.residue(1), "O", "C"),
    2: pick_ray(pose.residue(2), "O", "C"),
    3: pick_ray(pose.residue(3), "O", "C")
}

sc_donor = {2: [pick_ray(pose.residue(2), "HH", "OH")]}

sc_acceptor = {2: [pick_ray(pose.residue(2), "OH", "CZ")]}

cat_pi = [(pick_ray(pose.residue(2), "CE1",

Exemple #6

ATOM     36  O   ALA A   3       8.260   5.868   1.023  1.00  0.00           O
ATOM     37  OXT ALA A   3       8.596   5.737  -1.023  1.00  0.00           O
ATOM     38  CB  ALA A   3       8.190   3.050  -1.199  1.00  0.00           C
ATOM     39  H   ALA A   3       5.710   4.705  -0.000  1.00  0.00           H
ATOM     40  HA  ALA A   3       7.999   3.333   0.913  1.00  0.00           H
ATOM     41 1HB  ALA A   3       9.280   3.059  -1.185  1.00  0.00           H
ATOM     42 2HB  ALA A   3       7.835   2.021  -1.154  1.00  0.00           H
ATOM     43 3HB  ALA A   3       7.835   3.516  -2.117  1.00  0.00           H
TER
"""

pose = Pose()
pose_from_pdbstring(pose, contents)

n_rays = {
    1: pick_ray(pose.residue(1), "1H", "N"),
    2: pick_ray(pose.residue(2), "H", "N"),
    3: pick_ray(pose.residue(3), "H", "N")
}

c_rays = {
    1: pick_ray(pose.residue(1), "O", "C"),
    2: pick_ray(pose.residue(2), "O", "C"),
    3: pick_ray(pose.residue(3), "O", "C")
}

sc_donor = { }

sc_acceptor = { }

cat_pi = [

Exemple #7

Fichier : CA_OH.py Projet : uw-ipd/privileged_residues

ATOM     12  OG  SER A   2       4.273  -0.309  -4.595  1.00  0.00           O
ATOM     13  H   SER A   2       1.939  -0.680  -2.908  1.00  0.00           H
ATOM     14  HA  SER A   2       3.320   1.908  -2.627  1.00  0.00           H
ATOM     15 1HB  SER A   2       3.330   1.306  -5.420  1.00  0.00           H
ATOM     16 2HB  SER A   2       4.691   1.679  -4.374  1.00  0.00           H
ATOM     17  HG  SER A   2       3.848  -0.782  -3.875  1.00  0.00           H
TER
CONECT    1    2
CONECT    2    1    3    4
CONECT    3    2
CONECT    4    2    5    6
CONECT    5    4
CONECT    6    4
"""

pose = Pose()
pose_from_pdbstring(pose, contents)

sc_donor = {
    1: [
        pick_ray(pose.residue(1), "1HD2", "ND2"),
        pick_ray(pose.residue(1), "2HD2", "ND2")
    ],
    2: [pick_ray(pose.residue(2), "HG", "OG")]
}

sc_acceptor = {
    1: [pick_ray(pose.residue(1), "OD1", "CG")],
    2: [pick_ray(pose.residue(2), "OG", "CB")]
}

Exemple #8

Fichier : OH_A.py Projet : uw-ipd/privileged_residues

ATOM      8  HA  SER A   1       4.525   0.411  -1.793  1.00  0.00           H
ATOM      9 1HB  SER A   1       4.783   1.209  -4.524  1.00  0.00           H
ATOM     10 2HB  SER A   1       5.814   1.615  -3.161  1.00  0.00           H
ATOM     11  HG  SER A   1       6.258  -0.895  -3.881  1.00  0.00           H
HETATM   12  CV  A__ A   2       3.512  -1.512  -7.034  1.00  0.00           X
HETATM   13  NZ  A__ A   2       4.049  -1.531  -5.683  1.00  0.00           N
HETATM   14 1HZ  A__ A   2       4.411  -0.616  -5.451  1.00  0.00           H
HETATM   15 2HZ  A__ A   2       3.316  -1.777  -5.031  1.00  0.00           H
HETATM   16 3HZ  A__ A   2       4.794  -2.211  -5.622  1.00  0.00           H
TER
CONECT   12   13
CONECT   13   12   14   15   16
CONECT   14   13
CONECT   15   13
CONECT   16   13
"""

pose = Pose()
pose_from_pdbstring(pose, contents)

sc_donor = {
    1: [pick_ray(pose.residue(1), "HG", "OG")],
    2: [
        pick_ray(pose.residue(2), "1HZ", "NZ"),
        pick_ray(pose.residue(2), "2HZ", "NZ"),
        pick_ray(pose.residue(2), "3HZ", "NZ")
    ]
}

sc_acceptor = {1: [pick_ray(pose.residue(1), "OG", "CB")]}

Exemple #9

Fichier : C_OH.py Projet : uw-ipd/privileged_residues

ATOM      5  N   SER A   2       7.756  -0.439  -5.359  1.00  0.00           N
ATOM      6  CA  SER A   2       7.794  -1.267  -4.159  1.00  0.00           C
ATOM      7  C   SER A   2       7.667  -0.419  -2.900  1.00  0.00           C
ATOM      8  O   SER A   2       8.086   0.738  -2.875  1.00  0.00           O
ATOM      9  CB  SER A   2       9.083  -2.064  -4.116  1.00  0.00           C
ATOM     10  OG  SER A   2       9.881  -1.788  -5.234  1.00  0.00           O
ATOM     11  H   SER A   2       8.106   0.507  -5.315  1.00  0.00           H
ATOM     12  HA  SER A   2       6.952  -1.961  -4.191  1.00  0.00           H
ATOM     13 1HB  SER A   2       9.630  -1.821  -3.206  1.00  0.00           H
ATOM     14 2HB  SER A   2       8.852  -3.128  -4.084  1.00  0.00           H
ATOM     15  HG  SER A   2       9.394  -1.147  -5.756  1.00  0.00           H
TER
CONECT    1    2
CONECT    2    1    3    4
CONECT    3    2
CONECT    4    2
"""

pose = Pose()
pose_from_pdbstring(pose, contents)

sc_donor = {2: [pick_ray(pose.residue(2), "HG", "OG")]}

sc_acceptor = {
    1: [
        pick_ray(pose.residue(1), "OE1", "CD"),
        pick_ray(pose.residue(1), "OE2", "CD")
    ],
    2: [pick_ray(pose.residue(2), "OG", "CB")]
}

Exemple #10

ATOM     40  O   ALA A   3       8.260   5.868   1.023  1.00  0.00           O
ATOM     41  OXT ALA A   3       8.596   5.737  -1.023  1.00  0.00           O
ATOM     42  CB  ALA A   3       8.190   3.050  -1.199  1.00  0.00           C
ATOM     43  H   ALA A   3       5.710   4.705  -0.000  1.00  0.00           H
ATOM     44  HA  ALA A   3       7.999   3.333   0.913  1.00  0.00           H
ATOM     45 1HB  ALA A   3       9.280   3.059  -1.185  1.00  0.00           H
ATOM     46 2HB  ALA A   3       7.835   2.021  -1.154  1.00  0.00           H
ATOM     47 3HB  ALA A   3       7.835   3.516  -2.117  1.00  0.00           H
TER
"""

pose = Pose()
pose_from_pdbstring(pose, contents)

n_rays = {
    1: pick_ray(pose.residue(1), "1H", "N"),
    2: pick_ray(pose.residue(2), "H", "N"),
    3: pick_ray(pose.residue(3), "H", "N")
}

c_rays = {
    1: pick_ray(pose.residue(1), "O", "C"),
    2: pick_ray(pose.residue(2), "O", "C"),
    3: pick_ray(pose.residue(3), "O", "C")
}

sc_donor = {
    2: [
        pick_ray(pose.residue(2), "HE", "NE"),
        pick_ray(pose.residue(2), "1HH1", "NH1"),
        pick_ray(pose.residue(2), "2HH1", "NH1"),

Exemple #11

ATOM     30  O   ALA A   3       8.260   5.868   1.023  1.00  0.00           O
ATOM     31  OXT ALA A   3       8.596   5.737  -1.023  1.00  0.00           O
ATOM     32  CB  ALA A   3       8.190   3.050  -1.199  1.00  0.00           C
ATOM     33  H   ALA A   3       5.710   4.705  -0.000  1.00  0.00           H
ATOM     34  HA  ALA A   3       7.999   3.333   0.913  1.00  0.00           H
ATOM     35 1HB  ALA A   3       9.280   3.059  -1.185  1.00  0.00           H
ATOM     36 2HB  ALA A   3       7.835   2.021  -1.154  1.00  0.00           H
ATOM     37 3HB  ALA A   3       7.835   3.516  -2.117  1.00  0.00           H
TER
"""

pose = Pose()
pose_from_pdbstring(pose, contents)

n_rays = {
    1: pick_ray(pose.residue(1), "1H", "N"),
    2: pick_ray(pose.residue(2), "H", "N"),
    3: pick_ray(pose.residue(3), "H", "N")
}

c_rays = {
    1: pick_ray(pose.residue(1), "O", "C"),
    2: pick_ray(pose.residue(2), "O", "C"),
    3: pick_ray(pose.residue(3), "O", "C")
}

sc_donor = {2: [pick_ray(pose.residue(2), "HG1", "OG1")]}

sc_acceptor = {2: [pick_ray(pose.residue(2), "OG1", "CB")]}

cat_pi = []

Exemple #12

Fichier : LYS.py Projet : uw-ipd/privileged_residues

ATOM     38  O   ALA A   3       8.260   5.868   1.023  1.00  0.00           O
ATOM     39  OXT ALA A   3       8.596   5.737  -1.023  1.00  0.00           O
ATOM     40  CB  ALA A   3       8.190   3.050  -1.199  1.00  0.00           C
ATOM     41  H   ALA A   3       5.710   4.705  -0.000  1.00  0.00           H
ATOM     42  HA  ALA A   3       7.999   3.333   0.913  1.00  0.00           H
ATOM     43 1HB  ALA A   3       9.280   3.059  -1.185  1.00  0.00           H
ATOM     44 2HB  ALA A   3       7.835   2.021  -1.154  1.00  0.00           H
ATOM     45 3HB  ALA A   3       7.835   3.516  -2.117  1.00  0.00           H
TER
"""

pose = Pose()
pose_from_pdbstring(pose, contents)

n_rays = {
    1: pick_ray(pose.residue(1), "1H", "N"),
    2: pick_ray(pose.residue(2), "H", "N"),
    3: pick_ray(pose.residue(3), "H", "N")
}

c_rays = {
    1: pick_ray(pose.residue(1), "O", "C"),
    2: pick_ray(pose.residue(2), "O", "C"),
    3: pick_ray(pose.residue(3), "O", "C")
}

sc_donor = {
    2: [
        pick_ray(pose.residue(2), "1HZ", "NZ"),
        pick_ray(pose.residue(2), "2HZ", "NZ"),
        pick_ray(pose.residue(2), "3HZ", "NZ")

Exemple #13

ATOM      8  HA  SER A   1       9.204   0.990   1.080  1.00  0.00           H
ATOM      9 1HB  SER A   1      10.993   0.232  -1.015  1.00  0.00           H
ATOM     10 2HB  SER A   1      11.040  -0.215   0.684  1.00  0.00           H
ATOM     11  HG  SER A   1       9.103  -1.558  -0.523  1.00  0.00           H
ATOM     12  N   SER A   2       9.807  -1.298  -0.973  1.00  0.00           N
ATOM     13  CA  SER A   2       8.484  -1.352  -1.582  1.00  0.00           C
ATOM     14  C   SER A   2       7.533  -2.211  -0.759  1.00  0.00           C
ATOM     15  O   SER A   2       7.953  -3.156  -0.093  1.00  0.00           O
ATOM     16  CB  SER A   2       8.581  -1.899  -2.993  1.00  0.00           C
ATOM     17  OG  SER A   2       9.908  -2.202  -3.324  1.00  0.00           O
ATOM     18  H   SER A   2      10.132  -2.087  -0.431  1.00  0.00           H
ATOM     19  HA  SER A   2       8.081  -0.339  -1.625  1.00  0.00           H
ATOM     20 1HB  SER A   2       7.968  -2.796  -3.078  1.00  0.00           H
ATOM     21 2HB  SER A   2       8.187  -1.166  -3.695  1.00  0.00           H
ATOM     22  HG  SER A   2      10.432  -1.979  -2.550  1.00  0.00           H
TER
"""

pose = Pose()
pose_from_pdbstring(pose, contents)

sc_donor = {
    1: [pick_ray(pose.residue(1), "HG", "OG")],
    2: [pick_ray(pose.residue(2), "HG", "OG")]
}

sc_acceptor = {
    1: [pick_ray(pose.residue(1), "OG", "CB")],
    2: [pick_ray(pose.residue(2), "OG", "CB")]
}

Exemple #14

Fichier : TRP.py Projet : uw-ipd/privileged_residues

ATOM     40  O   ALA A   3       8.260   5.868   1.023  1.00  0.00           O
ATOM     41  OXT ALA A   3       8.596   5.737  -1.023  1.00  0.00           O
ATOM     42  CB  ALA A   3       8.190   3.050  -1.199  1.00  0.00           C
ATOM     43  H   ALA A   3       5.710   4.705  -0.000  1.00  0.00           H
ATOM     44  HA  ALA A   3       7.999   3.333   0.913  1.00  0.00           H
ATOM     45 1HB  ALA A   3       9.280   3.059  -1.185  1.00  0.00           H
ATOM     46 2HB  ALA A   3       7.835   2.021  -1.154  1.00  0.00           H
ATOM     47 3HB  ALA A   3       7.835   3.516  -2.117  1.00  0.00           H
TER
"""

pose = Pose()
pose_from_pdbstring(pose, contents)

n_rays = {
    1: pick_ray(pose.residue(1), "1H", "N"),
    2: pick_ray(pose.residue(2), "H", "N"),
    3: pick_ray(pose.residue(3), "H", "N")
}

c_rays = {
    1: pick_ray(pose.residue(1), "O", "C"),
    2: pick_ray(pose.residue(2), "O", "C"),
    3: pick_ray(pose.residue(3), "O", "C")
}

sc_donor = {2: [pick_ray(pose.residue(2), "HE1", "NE1")]}

sc_acceptor = {}

cat_pi = [(pick_ray(pose.residue(2), "NE1",

Exemple #15

ATOM     30  O   ALA A   3       8.260   5.868   1.023  1.00  0.00           O
ATOM     31  OXT ALA A   3       8.596   5.737  -1.023  1.00  0.00           O
ATOM     32  CB  ALA A   3       8.190   3.050  -1.199  1.00  0.00           C
ATOM     33  H   ALA A   3       5.710   4.705  -0.000  1.00  0.00           H
ATOM     34  HA  ALA A   3       7.999   3.333   0.913  1.00  0.00           H
ATOM     35 1HB  ALA A   3       9.280   3.059  -1.185  1.00  0.00           H
ATOM     36 2HB  ALA A   3       7.835   2.021  -1.154  1.00  0.00           H
ATOM     37 3HB  ALA A   3       7.835   3.516  -2.117  1.00  0.00           H
TER
"""

pose = Pose()
pose_from_pdbstring(pose, contents)

n_rays = {
    1: pick_ray(pose.residue(1), "1H", "N"),
    3: pick_ray(pose.residue(3), "H", "N")
}

c_rays = {
    1: pick_ray(pose.residue(1), "O", "C"),
    2: pick_ray(pose.residue(2), "O", "C"),
    3: pick_ray(pose.residue(3), "O", "C")
}

sc_donor = {}

sc_acceptor = {}

cat_pi = []

Exemple #16

Fichier : ASN.py Projet : uw-ipd/privileged_residues

ATOM     30  O   ALA A   3       8.260   5.868   1.023  1.00  0.00           O
ATOM     31  OXT ALA A   3       8.596   5.737  -1.023  1.00  0.00           O
ATOM     32  CB  ALA A   3       8.190   3.050  -1.199  1.00  0.00           C
ATOM     33  H   ALA A   3       5.710   4.705  -0.000  1.00  0.00           H
ATOM     34  HA  ALA A   3       7.999   3.333   0.913  1.00  0.00           H
ATOM     35 1HB  ALA A   3       9.280   3.059  -1.185  1.00  0.00           H
ATOM     36 2HB  ALA A   3       7.835   2.021  -1.154  1.00  0.00           H
ATOM     37 3HB  ALA A   3       7.835   3.516  -2.117  1.00  0.00           H
TER
"""

pose = Pose()
pose_from_pdbstring(pose, contents)

n_rays = {
    1: pick_ray(pose.residue(1), "1H", "N"),
    2: pick_ray(pose.residue(2), "H", "N"),
    3: pick_ray(pose.residue(3), "H", "N")
}

c_rays = {
    1: pick_ray(pose.residue(1), "O", "C"),
    2: pick_ray(pose.residue(2), "O", "C"),
    3: pick_ray(pose.residue(3), "O", "C")
}

sc_donor = {
    2: [
        pick_ray(pose.residue(2), "1HD2", "ND2"),
        pick_ray(pose.residue(2), "2HD2", "ND2")
    ]

Exemple #17

Fichier : C_CA.py Projet : uw-ipd/privileged_residues

TER
CONECT    1    2
CONECT    2    1    3    4
CONECT    3    2
CONECT    4    2
CONECT    5    6
CONECT    6    5    7    8
CONECT    7    6
CONECT    8    6    9   10
CONECT    9    8
CONECT   10    8
"""

pose = Pose()
pose_from_pdbstring(pose, contents)

sc_donor = {
    2: [
        pick_ray(pose.residue(2), "1HD2", "ND2"),
        pick_ray(pose.residue(2), "2HD2", "ND2")
    ]
}

sc_acceptor = {
    1: [
        pick_ray(pose.residue(1), "OE1", "CD"),
        pick_ray(pose.residue(1), "OE2", "CD")
    ],
    2: [pick_ray(pose.residue(2), "OD1", "CG")]
}

Exemple #18

Fichier : C_A.py Projet : uw-ipd/privileged_residues

HETATM    9 3HZ  A__ A   2       5.292  -0.607  -4.650  1.00  0.00           H
TER
CONECT    1    2
CONECT    2    1    3    4
CONECT    3    2
CONECT    4    2
CONECT    5    6
CONECT    6    5    7    8    9
CONECT    7    6
CONECT    8    6
CONECT    9    6
"""

pose = Pose()
pose_from_pdbstring(pose, contents)

sc_donor = {
    2: [
        pick_ray(pose.residue(2), "1HZ", "NZ"),
        pick_ray(pose.residue(2), "2HZ", "NZ"),
        pick_ray(pose.residue(2), "3HZ", "NZ")
    ]
}

sc_acceptor = {
    1: [
        pick_ray(pose.residue(1), "OE1", "CD"),
        pick_ray(pose.residue(1), "OE2", "CD")
    ]
}

Exemple #19

ATOM     20 2HB  SER A   2       3.626  -3.951  -6.042  1.00  0.00           H
ATOM     21  HG  SER A   2       3.450  -3.695  -3.412  1.00  0.00           H
TER
CONECT    1    2
CONECT    2    1    3    6
CONECT    3    2    4    5
CONECT    4    3    7    8
CONECT    5    3    9   10
CONECT    6    2
CONECT    7    4
CONECT    8    4
CONECT    9    5
CONECT   10    5
"""

pose = Pose()
pose_from_pdbstring(pose, contents)

sc_donor = {
    1: [
        pick_ray(pose.residue(1), "HE", "NE"),
        pick_ray(pose.residue(1), "1HH1", "NH1"),
        pick_ray(pose.residue(1), "2HH1", "NH1"),
        pick_ray(pose.residue(1), "1HH2", "NH2"),
        pick_ray(pose.residue(1), "2HH2", "NH2")
    ],
    2: [pick_ray(pose.residue(2), "HG", "OG")]
}

sc_acceptor = {2: [pick_ray(pose.residue(2), "OG", "CB")]}

Exemple #20

CONECT    6    5    7   10
CONECT    7    6    8    9
CONECT    8    7   11   12
CONECT    9    7   13   14
CONECT   10    6
CONECT   11    8
CONECT   12    8
CONECT   13    9
CONECT   14    9
"""

pose = Pose()
pose_from_pdbstring(pose, contents)

sc_donor = {
    2: [
        pick_ray(pose.residue(2), "HE", "NE"),
        pick_ray(pose.residue(2), "1HH1", "NH1"),
        pick_ray(pose.residue(2), "2HH1", "NH1"),
        pick_ray(pose.residue(2), "1HH2", "NH2"),
        pick_ray(pose.residue(2), "2HH2", "NH2")
    ]
}

sc_acceptor = {
    1: [
        pick_ray(pose.residue(1), "OE1", "CD"),
        pick_ray(pose.residue(1), "OE2", "CD")
    ]
}

Exemple #21

CONECT    9    8   10   11
CONECT   10    9   13   14
CONECT   11    9   15   16
CONECT   12    8
CONECT   13   10
CONECT   14   10
CONECT   15   11
CONECT   16   11
"""

pose = Pose()
pose_from_pdbstring(pose, contents)

sc_donor = {
    1: [
        pick_ray(pose.residue(1), "1HD2", "ND2"),
        pick_ray(pose.residue(1), "2HD2", "ND2")
    ],
    2: [
        pick_ray(pose.residue(2), "HE", "NE"),
        pick_ray(pose.residue(2), "1HH1", "NH1"),
        pick_ray(pose.residue(2), "2HH1", "NH1"),
        pick_ray(pose.residue(2), "1HH2", "NH2"),
        pick_ray(pose.residue(2), "2HH2", "NH2")
    ]
}

sc_acceptor = {
    1: [
        pick_ray(pose.residue(1), "OD1", "CG")
    ]

Exemple #22

Fichier : CA_CA.py Projet : uw-ipd/privileged_residues

CONECT    3    2
CONECT    4    2    5    6
CONECT    5    4
CONECT    6    4
CONECT    7    8
CONECT    8    7    9   10
CONECT    9    8
CONECT   10    8   11   12
CONECT   11   10
CONECT   12   10
"""

pose = Pose()
pose_from_pdbstring(pose, contents)

sc_donor = {
    1: [
        pick_ray(pose.residue(1), "1HD2", "ND2"),
        pick_ray(pose.residue(1), "2HD2", "ND2")
    ],
    2: [
        pick_ray(pose.residue(2), "1HD2", "ND2"),
        pick_ray(pose.residue(2), "2HD2", "ND2")
    ]
}

sc_acceptor = {
    1: [pick_ray(pose.residue(1), "OD1", "CG")],
    2: [pick_ray(pose.residue(2), "OD1", "CG")]
}