10 minutes to pdb2sql¶
This is a short introduction to pdb2sql.
Download PDB files¶
A handy tool fetch is provided to download PDB files from PDB website.
In [1]: from pdb2sql import fetch
In [2]: fetch('3CRO', './pdb/')
In [3]: ls ./pdb
1AK4_10w.pdb 3CRO.pdb dummy.pdb ref.pdb
1AK4_5w.pdb decoy.pdb dummy_transform.pdb test.pdb
For clear illustration, some dummy PDB files are used in the following examples.
Get and set data¶
First, we import as follows:
In [4]: from pdb2sql import pdb2sql
Create a SQL database instance:
In [5]: db = pdb2sql("./pdb/dummy.pdb")
The db is a SQL instance that contains one table named ATOM.
In this table, each row represents one atom, and columns are atom properties:
In [6]: db.print()
serial name altLoc resName chainID resSeq iCode x y z occ temp element model
1 N MET A 1 -20.948 -13.418 28.32 1.0 46.93 N 0
2 CA MET A 1 -21.093 -12.112 28.939 1.0 52.5 C 0
3 C MET A 1 -22.482 -11.566 28.846 1.0 52.55 C 0
4 O MET A 1 -22.816 -10.393 28.618 1.0 52.75 O 0
5 CB MET A 1 -19.916 -11.178 28.789 1.0 59.92 C 0
6 CG MET A 1 -18.839 -11.701 29.713 1.0 80.88 C 0
7 SD MET A 1 -17.178 -11.517 29.038 1.0 95.94 S 0
8 CE MET A 1 -16.527 -13.173 29.365 1.0 90.58 C 0
9 N GLN A 2 -23.243 -12.593 29.074 1.0 51.78 N 0
10 CA GLN A 2 -24.639 -12.681 29.076 1.0 52.49 C 0
11 C GLN A 2 -25.268 -12.252 30.349 1.0 42.74 C 0
12 O GLN A 2 -24.688 -12.207 31.435 1.0 47.12 O 0
13 CB GLN A 2 -24.971 -14.147 28.858 1.0 45.95 C 0
14 CG GLN A 2 -24.141 -14.712 27.71 1.0 53.26 C 0
15 CD GLN A 2 -24.923 -15.776 27.001 1.0 68.74 C 0
16 OE1 GLN A 2 -25.159 -16.851 27.563 1.0 82.61 O 0
17 NE2 GLN A 2 -25.382 -15.458 25.797 1.0 76.83 N 0
18 N THR A 3 -26.513 -11.973 30.116 1.0 21.94 N 0
19 CA THR A 3 -27.44 -11.567 31.088 1.0 15.55 C 0
20 C THR A 3 -28.2 -12.824 31.459 1.0 5.55 C 0
21 O THR A 3 -27.96 -13.91 30.947 1.0 13.48 O 0
22 CB THR A 3 -28.318 -10.497 30.412 1.0 14.6 C 0
23 OG1 THR A 3 -27.55 -9.329 30.158 1.0 7.6 O 0
24 CG2 THR A 3 -29.542 -10.173 31.249 1.0 14.52 C 0
25 N LEU A 4 -29.107 -12.704 32.36 1.0 2.0 N 0
26 CA LEU A 4 -29.866 -13.85 32.734 1.0 2.0 C 0
27 C LEU A 4 -31.054 -13.904 31.795 1.0 23.22 C 0
28 O LEU A 4 -31.605 -14.952 31.468 1.0 22.54 O 0
29 CB LEU A 4 -30.361 -13.645 34.167 1.0 2.0 C 0
30 CG LEU A 4 -31.598 -14.458 34.413 1.0 2.0 C 0
31 CD1 LEU A 4 -31.138 -15.884 34.58 1.0 10.7 C 0
32 CD2 LEU A 4 -32.285 -13.993 35.678 1.0 2.0 C 0
33 N ILE B 5 -24.269 -24.311 62.813 1.0 9.48 N 0
34 CA ILE B 5 -23.843 -24.77 64.102 1.0 26.84 C 0
35 C ILE B 5 -22.871 -25.894 64.054 1.0 25.15 C 0
36 O ILE B 5 -21.848 -25.947 64.74 1.0 26.7 O 0
37 CB ILE B 5 -25.073 -25.455 64.56 1.0 2.0 C 0
38 CG1 ILE B 5 -26.132 -24.381 64.698 1.0 8.15 C 0
39 CG2 ILE B 5 -24.748 -26.175 65.844 1.0 15.39 C 0
40 CD1 ILE B 5 -27.169 -24.675 65.763 1.0 4.14 C 0
41 N ALA B 6 -23.314 -26.842 63.273 1.0 5.6 N 0
42 CA ALA B 6 -22.569 -28.021 63.037 1.0 6.15 C 0
43 C ALA B 6 -21.334 -27.605 62.3 1.0 2.0 C 0
44 O ALA B 6 -20.346 -28.31 62.26 1.0 19.27 O 0
45 CB ALA B 6 -23.39 -28.992 62.204 1.0 28.29 C 0
46 N LYS B 7 -20.313 -24.801 63.054 1.0 42.89 N 0
47 CA LYS B 7 -19.947 -23.992 64.206 1.0 35.06 C 0
48 C LYS B 7 -19.63 -22.543 63.931 1.0 28.97 C 0
49 O LYS B 7 -18.474 -22.128 63.903 1.0 23.79 O 0
50 CB LYS B 7 -19.233 -24.631 65.379 1.0 29.85 C 0
51 CG LYS B 7 -18.891 -26.083 65.15 1.0 33.26 C 0
52 CD LYS B 7 -17.459 -26.383 65.536 1.0 40.19 C 0
53 CE LYS B 7 -17.355 -27.043 66.897 1.0 63.4 C 0
54 NZ LYS B 7 -17.415 -28.509 66.822 1.0 66.95 N 0
Get data¶
Get chainID, residue number, residue name and atom name of all atoms:
In [7]: p = db.get('chainID, resSeq, resName, name')
In [8]: p
Out[8]:
[['A', 1, 'MET', 'N'],
['A', 1, 'MET', 'CA'],
['A', 1, 'MET', 'C'],
['A', 1, 'MET', 'O'],
['A', 1, 'MET', 'CB'],
['A', 1, 'MET', 'CG'],
['A', 1, 'MET', 'SD'],
['A', 1, 'MET', 'CE'],
['A', 2, 'GLN', 'N'],
['A', 2, 'GLN', 'CA'],
['A', 2, 'GLN', 'C'],
['A', 2, 'GLN', 'O'],
['A', 2, 'GLN', 'CB'],
['A', 2, 'GLN', 'CG'],
['A', 2, 'GLN', 'CD'],
['A', 2, 'GLN', 'OE1'],
['A', 2, 'GLN', 'NE2'],
['A', 3, 'THR', 'N'],
['A', 3, 'THR', 'CA'],
['A', 3, 'THR', 'C'],
['A', 3, 'THR', 'O'],
['A', 3, 'THR', 'CB'],
['A', 3, 'THR', 'OG1'],
['A', 3, 'THR', 'CG2'],
['A', 4, 'LEU', 'N'],
['A', 4, 'LEU', 'CA'],
['A', 4, 'LEU', 'C'],
['A', 4, 'LEU', 'O'],
['A', 4, 'LEU', 'CB'],
['A', 4, 'LEU', 'CG'],
['A', 4, 'LEU', 'CD1'],
['A', 4, 'LEU', 'CD2'],
['B', 5, 'ILE', 'N'],
['B', 5, 'ILE', 'CA'],
['B', 5, 'ILE', 'C'],
['B', 5, 'ILE', 'O'],
['B', 5, 'ILE', 'CB'],
['B', 5, 'ILE', 'CG1'],
['B', 5, 'ILE', 'CG2'],
['B', 5, 'ILE', 'CD1'],
['B', 6, 'ALA', 'N'],
['B', 6, 'ALA', 'CA'],
['B', 6, 'ALA', 'C'],
['B', 6, 'ALA', 'O'],
['B', 6, 'ALA', 'CB'],
['B', 7, 'LYS', 'N'],
['B', 7, 'LYS', 'CA'],
['B', 7, 'LYS', 'C'],
['B', 7, 'LYS', 'O'],
['B', 7, 'LYS', 'CB'],
['B', 7, 'LYS', 'CG'],
['B', 7, 'LYS', 'CD'],
['B', 7, 'LYS', 'CE'],
['B', 7, 'LYS', 'NZ']]
Get x,y,z coordinates of all atoms:
In [9]: p = db.get('x,y,z')
In [10]: p
Out[10]:
[[-20.948, -13.418, 28.32],
[-21.093, -12.112, 28.939],
[-22.482, -11.566, 28.846],
[-22.816, -10.393, 28.618],
[-19.916, -11.178, 28.789],
[-18.839, -11.701, 29.713],
[-17.178, -11.517, 29.038],
[-16.527, -13.173, 29.365],
[-23.243, -12.593, 29.074],
[-24.639, -12.681, 29.076],
[-25.268, -12.252, 30.349],
[-24.688, -12.207, 31.435],
[-24.971, -14.147, 28.858],
[-24.141, -14.712, 27.71],
[-24.923, -15.776, 27.001],
[-25.159, -16.851, 27.563],
[-25.382, -15.458, 25.797],
[-26.513, -11.973, 30.116],
[-27.44, -11.567, 31.088],
[-28.2, -12.824, 31.459],
[-27.96, -13.91, 30.947],
[-28.318, -10.497, 30.412],
[-27.55, -9.329, 30.158],
[-29.542, -10.173, 31.249],
[-29.107, -12.704, 32.36],
[-29.866, -13.85, 32.734],
[-31.054, -13.904, 31.795],
[-31.605, -14.952, 31.468],
[-30.361, -13.645, 34.167],
[-31.598, -14.458, 34.413],
[-31.138, -15.884, 34.58],
[-32.285, -13.993, 35.678],
[-24.269, -24.311, 62.813],
[-23.843, -24.77, 64.102],
[-22.871, -25.894, 64.054],
[-21.848, -25.947, 64.74],
[-25.073, -25.455, 64.56],
[-26.132, -24.381, 64.698],
[-24.748, -26.175, 65.844],
[-27.169, -24.675, 65.763],
[-23.314, -26.842, 63.273],
[-22.569, -28.021, 63.037],
[-21.334, -27.605, 62.3],
[-20.346, -28.31, 62.26],
[-23.39, -28.992, 62.204],
[-20.313, -24.801, 63.054],
[-19.947, -23.992, 64.206],
[-19.63, -22.543, 63.931],
[-18.474, -22.128, 63.903],
[-19.233, -24.631, 65.379],
[-18.891, -26.083, 65.15],
[-17.459, -26.383, 65.536],
[-17.355, -27.043, 66.897],
[-17.415, -28.509, 66.822]]
Get x,y,z coordinates of chain A atoms:
In [11]: p = db.get('chainID, x,y,z', chainID=['A'])
In [12]: p
Out[12]:
[['A', -20.948, -13.418, 28.32],
['A', -21.093, -12.112, 28.939],
['A', -22.482, -11.566, 28.846],
['A', -22.816, -10.393, 28.618],
['A', -19.916, -11.178, 28.789],
['A', -18.839, -11.701, 29.713],
['A', -17.178, -11.517, 29.038],
['A', -16.527, -13.173, 29.365],
['A', -23.243, -12.593, 29.074],
['A', -24.639, -12.681, 29.076],
['A', -25.268, -12.252, 30.349],
['A', -24.688, -12.207, 31.435],
['A', -24.971, -14.147, 28.858],
['A', -24.141, -14.712, 27.71],
['A', -24.923, -15.776, 27.001],
['A', -25.159, -16.851, 27.563],
['A', -25.382, -15.458, 25.797],
['A', -26.513, -11.973, 30.116],
['A', -27.44, -11.567, 31.088],
['A', -28.2, -12.824, 31.459],
['A', -27.96, -13.91, 30.947],
['A', -28.318, -10.497, 30.412],
['A', -27.55, -9.329, 30.158],
['A', -29.542, -10.173, 31.249],
['A', -29.107, -12.704, 32.36],
['A', -29.866, -13.85, 32.734],
['A', -31.054, -13.904, 31.795],
['A', -31.605, -14.952, 31.468],
['A', -30.361, -13.645, 34.167],
['A', -31.598, -14.458, 34.413],
['A', -31.138, -15.884, 34.58],
['A', -32.285, -13.993, 35.678]]
Get x,y,z coordinates of atoms on residue 1 and 4 of Chain A
In [13]: p = db.get('chainID,resSeq,x,y,z', chainID=['A'], resSeq=['1', '4'])
In [14]: p
Out[14]:
[['A', 1, -20.948, -13.418, 28.32],
['A', 1, -21.093, -12.112, 28.939],
['A', 1, -22.482, -11.566, 28.846],
['A', 1, -22.816, -10.393, 28.618],
['A', 1, -19.916, -11.178, 28.789],
['A', 1, -18.839, -11.701, 29.713],
['A', 1, -17.178, -11.517, 29.038],
['A', 1, -16.527, -13.173, 29.365],
['A', 4, -29.107, -12.704, 32.36],
['A', 4, -29.866, -13.85, 32.734],
['A', 4, -31.054, -13.904, 31.795],
['A', 4, -31.605, -14.952, 31.468],
['A', 4, -30.361, -13.645, 34.167],
['A', 4, -31.598, -14.458, 34.413],
['A', 4, -31.138, -15.884, 34.58],
['A', 4, -32.285, -13.993, 35.678]]
Get data of all atoms except residue MET and GLN atoms
In [15]: p = db.get('chainID, resSeq, resName, name', no_resName = ['MET', 'GLN'])
In [16]: p
Out[16]:
[['A', 3, 'THR', 'N'],
['A', 3, 'THR', 'CA'],
['A', 3, 'THR', 'C'],
['A', 3, 'THR', 'O'],
['A', 3, 'THR', 'CB'],
['A', 3, 'THR', 'OG1'],
['A', 3, 'THR', 'CG2'],
['A', 4, 'LEU', 'N'],
['A', 4, 'LEU', 'CA'],
['A', 4, 'LEU', 'C'],
['A', 4, 'LEU', 'O'],
['A', 4, 'LEU', 'CB'],
['A', 4, 'LEU', 'CG'],
['A', 4, 'LEU', 'CD1'],
['A', 4, 'LEU', 'CD2'],
['B', 5, 'ILE', 'N'],
['B', 5, 'ILE', 'CA'],
['B', 5, 'ILE', 'C'],
['B', 5, 'ILE', 'O'],
['B', 5, 'ILE', 'CB'],
['B', 5, 'ILE', 'CG1'],
['B', 5, 'ILE', 'CG2'],
['B', 5, 'ILE', 'CD1'],
['B', 6, 'ALA', 'N'],
['B', 6, 'ALA', 'CA'],
['B', 6, 'ALA', 'C'],
['B', 6, 'ALA', 'O'],
['B', 6, 'ALA', 'CB'],
['B', 7, 'LYS', 'N'],
['B', 7, 'LYS', 'CA'],
['B', 7, 'LYS', 'C'],
['B', 7, 'LYS', 'O'],
['B', 7, 'LYS', 'CB'],
['B', 7, 'LYS', 'CG'],
['B', 7, 'LYS', 'CD'],
['B', 7, 'LYS', 'CE'],
['B', 7, 'LYS', 'NZ']]
Get data of all atoms except residue MET and GLN atoms or CA (carbon alpha) atoms
In [17]: p = db.get('chainID, resSeq, resName, name', no_resName = ['MET', 'GLN'], no_name = ['CA'])
In [18]: p
Out[18]:
[['A', 3, 'THR', 'N'],
['A', 3, 'THR', 'C'],
['A', 3, 'THR', 'O'],
['A', 3, 'THR', 'CB'],
['A', 3, 'THR', 'OG1'],
['A', 3, 'THR', 'CG2'],
['A', 4, 'LEU', 'N'],
['A', 4, 'LEU', 'C'],
['A', 4, 'LEU', 'O'],
['A', 4, 'LEU', 'CB'],
['A', 4, 'LEU', 'CG'],
['A', 4, 'LEU', 'CD1'],
['A', 4, 'LEU', 'CD2'],
['B', 5, 'ILE', 'N'],
['B', 5, 'ILE', 'C'],
['B', 5, 'ILE', 'O'],
['B', 5, 'ILE', 'CB'],
['B', 5, 'ILE', 'CG1'],
['B', 5, 'ILE', 'CG2'],
['B', 5, 'ILE', 'CD1'],
['B', 6, 'ALA', 'N'],
['B', 6, 'ALA', 'C'],
['B', 6, 'ALA', 'O'],
['B', 6, 'ALA', 'CB'],
['B', 7, 'LYS', 'N'],
['B', 7, 'LYS', 'C'],
['B', 7, 'LYS', 'O'],
['B', 7, 'LYS', 'CB'],
['B', 7, 'LYS', 'CG'],
['B', 7, 'LYS', 'CD'],
['B', 7, 'LYS', 'CE'],
['B', 7, 'LYS', 'NZ']]
Get all data, a simple way is db.get('*').
A shortcut to get x,y,z coordinates:
In [19]: p = db.get_xyz()
In [20]: p
Out[20]:
[[-20.948, -13.418, 28.32],
[-21.093, -12.112, 28.939],
[-22.482, -11.566, 28.846],
[-22.816, -10.393, 28.618],
[-19.916, -11.178, 28.789],
[-18.839, -11.701, 29.713],
[-17.178, -11.517, 29.038],
[-16.527, -13.173, 29.365],
[-23.243, -12.593, 29.074],
[-24.639, -12.681, 29.076],
[-25.268, -12.252, 30.349],
[-24.688, -12.207, 31.435],
[-24.971, -14.147, 28.858],
[-24.141, -14.712, 27.71],
[-24.923, -15.776, 27.001],
[-25.159, -16.851, 27.563],
[-25.382, -15.458, 25.797],
[-26.513, -11.973, 30.116],
[-27.44, -11.567, 31.088],
[-28.2, -12.824, 31.459],
[-27.96, -13.91, 30.947],
[-28.318, -10.497, 30.412],
[-27.55, -9.329, 30.158],
[-29.542, -10.173, 31.249],
[-29.107, -12.704, 32.36],
[-29.866, -13.85, 32.734],
[-31.054, -13.904, 31.795],
[-31.605, -14.952, 31.468],
[-30.361, -13.645, 34.167],
[-31.598, -14.458, 34.413],
[-31.138, -15.884, 34.58],
[-32.285, -13.993, 35.678],
[-24.269, -24.311, 62.813],
[-23.843, -24.77, 64.102],
[-22.871, -25.894, 64.054],
[-21.848, -25.947, 64.74],
[-25.073, -25.455, 64.56],
[-26.132, -24.381, 64.698],
[-24.748, -26.175, 65.844],
[-27.169, -24.675, 65.763],
[-23.314, -26.842, 63.273],
[-22.569, -28.021, 63.037],
[-21.334, -27.605, 62.3],
[-20.346, -28.31, 62.26],
[-23.39, -28.992, 62.204],
[-20.313, -24.801, 63.054],
[-19.947, -23.992, 64.206],
[-19.63, -22.543, 63.931],
[-18.474, -22.128, 63.903],
[-19.233, -24.631, 65.379],
[-18.891, -26.083, 65.15],
[-17.459, -26.383, 65.536],
[-17.355, -27.043, 66.897],
[-17.415, -28.509, 66.822]]
Get chain IDs:
In [21]: p = db.get_chains()
In [22]: p
Out[22]: ['A', 'B']
Get residue list:
In [23]: p = db.get_residues()
In [24]: p
Out[24]:
[('A', 'MET', 1),
('A', 'GLN', 2),
('A', 'THR', 3),
('A', 'LEU', 4),
('B', 'ILE', 5),
('B', 'ALA', 6),
('B', 'LYS', 7)]
Filter the data base¶
pdb2sql allows to create a new database by filtering the one we jut created
In [25]: db_chainA = db(chainID='A')
In [26]: db_chainA.print()
serial name altLoc resName chainID resSeq iCode x y z occ temp element model
1 N MET A 1 -20.948 -13.418 28.32 1.0 46.93 N 0
2 CA MET A 1 -21.093 -12.112 28.939 1.0 52.5 C 0
3 C MET A 1 -22.482 -11.566 28.846 1.0 52.55 C 0
4 O MET A 1 -22.816 -10.393 28.618 1.0 52.75 O 0
5 CB MET A 1 -19.916 -11.178 28.789 1.0 59.92 C 0
6 CG MET A 1 -18.839 -11.701 29.713 1.0 80.88 C 0
7 SD MET A 1 -17.178 -11.517 29.038 1.0 95.94 S 0
8 CE MET A 1 -16.527 -13.173 29.365 1.0 90.58 C 0
9 N GLN A 2 -23.243 -12.593 29.074 1.0 51.78 N 0
10 CA GLN A 2 -24.639 -12.681 29.076 1.0 52.49 C 0
11 C GLN A 2 -25.268 -12.252 30.349 1.0 42.74 C 0
12 O GLN A 2 -24.688 -12.207 31.435 1.0 47.12 O 0
13 CB GLN A 2 -24.971 -14.147 28.858 1.0 45.95 C 0
14 CG GLN A 2 -24.141 -14.712 27.71 1.0 53.26 C 0
15 CD GLN A 2 -24.923 -15.776 27.001 1.0 68.74 C 0
16 OE1 GLN A 2 -25.159 -16.851 27.563 1.0 82.61 O 0
17 NE2 GLN A 2 -25.382 -15.458 25.797 1.0 76.83 N 0
18 N THR A 3 -26.513 -11.973 30.116 1.0 21.94 N 0
19 CA THR A 3 -27.44 -11.567 31.088 1.0 15.55 C 0
20 C THR A 3 -28.2 -12.824 31.459 1.0 5.55 C 0
21 O THR A 3 -27.96 -13.91 30.947 1.0 13.48 O 0
22 CB THR A 3 -28.318 -10.497 30.412 1.0 14.6 C 0
23 OG1 THR A 3 -27.55 -9.329 30.158 1.0 7.6 O 0
24 CG2 THR A 3 -29.542 -10.173 31.249 1.0 14.52 C 0
25 N LEU A 4 -29.107 -12.704 32.36 1.0 2.0 N 0
26 CA LEU A 4 -29.866 -13.85 32.734 1.0 2.0 C 0
27 C LEU A 4 -31.054 -13.904 31.795 1.0 23.22 C 0
28 O LEU A 4 -31.605 -14.952 31.468 1.0 22.54 O 0
29 CB LEU A 4 -30.361 -13.645 34.167 1.0 2.0 C 0
30 CG LEU A 4 -31.598 -14.458 34.413 1.0 2.0 C 0
31 CD1 LEU A 4 -31.138 -15.884 34.58 1.0 10.7 C 0
32 CD2 LEU A 4 -32.285 -13.993 35.678 1.0 2.0 C 0
In that example dp_chainA is a sql database that only includes the atoms from chain A. All the selection keywords (chainID, resSeq, resName, name) and their negations (no_chainID, no_resSeq, no_resName, no_name) can be used and combined to obtain the new database.
Set data¶
Rename chain B to C:
In [27]: num_B_atoms = len(db.get('chainID', chainID=['B']))
In [28]: chainC = ['C'] * num_B_atoms
In [29]: db.get_chains()
Out[29]: ['A', 'B']
In [30]: db.update('chainID', chainC, chainID = ['B'])
In [31]: db.get_chains()
Out[31]: ['A', 'C']
Update x,y,z coordinates for structure translatation of [10,10,10]
In [32]: xyz_old = db.get_xyz()
In [33]: xyz = np.array(xyz_old) + 10.0
In [34]: db.update('x,y,z', xyz)
In [35]: xyz_new = db.get_xyz()
In [36]: print("old:\n", xyz_old)
old:
[[-20.948, -13.418, 28.32], [-21.093, -12.112, 28.939], [-22.482, -11.566, 28.846], [-22.816, -10.393, 28.618], [-19.916, -11.178, 28.789], [-18.839, -11.701, 29.713], [-17.178, -11.517, 29.038], [-16.527, -13.173, 29.365], [-23.243, -12.593, 29.074], [-24.639, -12.681, 29.076], [-25.268, -12.252, 30.349], [-24.688, -12.207, 31.435], [-24.971, -14.147, 28.858], [-24.141, -14.712, 27.71], [-24.923, -15.776, 27.001], [-25.159, -16.851, 27.563], [-25.382, -15.458, 25.797], [-26.513, -11.973, 30.116], [-27.44, -11.567, 31.088], [-28.2, -12.824, 31.459], [-27.96, -13.91, 30.947], [-28.318, -10.497, 30.412], [-27.55, -9.329, 30.158], [-29.542, -10.173, 31.249], [-29.107, -12.704, 32.36], [-29.866, -13.85, 32.734], [-31.054, -13.904, 31.795], [-31.605, -14.952, 31.468], [-30.361, -13.645, 34.167], [-31.598, -14.458, 34.413], [-31.138, -15.884, 34.58], [-32.285, -13.993, 35.678], [-24.269, -24.311, 62.813], [-23.843, -24.77, 64.102], [-22.871, -25.894, 64.054], [-21.848, -25.947, 64.74], [-25.073, -25.455, 64.56], [-26.132, -24.381, 64.698], [-24.748, -26.175, 65.844], [-27.169, -24.675, 65.763], [-23.314, -26.842, 63.273], [-22.569, -28.021, 63.037], [-21.334, -27.605, 62.3], [-20.346, -28.31, 62.26], [-23.39, -28.992, 62.204], [-20.313, -24.801, 63.054], [-19.947, -23.992, 64.206], [-19.63, -22.543, 63.931], [-18.474, -22.128, 63.903], [-19.233, -24.631, 65.379], [-18.891, -26.083, 65.15], [-17.459, -26.383, 65.536], [-17.355, -27.043, 66.897], [-17.415, -28.509, 66.822]]
In [37]: print("new:\n", xyz_new)
new:
[[-10.948, -3.4179999999999993, 38.32], [-11.093, -2.112, 38.939], [-12.482, -1.5660000000000007, 38.846000000000004], [-12.815999999999999, -0.3930000000000007, 38.617999999999995], [-9.916, -1.1780000000000008, 38.789], [-8.838999999999999, -1.7010000000000005, 39.713], [-7.178000000000001, -1.5169999999999995, 39.038], [-6.527000000000001, -3.173, 39.364999999999995], [-13.242999999999999, -2.593, 39.074], [-14.639, -2.680999999999999, 39.076], [-15.268, -2.2520000000000007, 40.349000000000004], [-14.687999999999999, -2.2070000000000007, 41.435], [-14.971, -4.147, 38.858000000000004], [-14.140999999999998, -4.712, 37.71], [-14.922999999999998, -5.776, 37.001000000000005], [-15.158999999999999, -6.850999999999999, 37.563], [-15.382000000000001, -5.458, 35.797], [-16.513, -1.9730000000000008, 40.116], [-17.44, -1.5670000000000002, 41.088], [-18.2, -2.824, 41.459], [-17.96, -3.91, 40.947], [-18.318, -0.4969999999999999, 40.412], [-17.55, 0.6709999999999994, 40.158], [-19.542, -0.17300000000000004, 41.248999999999995], [-19.107, -2.7040000000000006, 42.36], [-19.866, -3.8499999999999996, 42.734], [-21.054, -3.904, 41.795], [-21.605, -4.952, 41.468], [-20.361, -3.6449999999999996, 44.167], [-21.598, -4.458, 44.413], [-21.138, -5.884, 44.58], [-22.284999999999997, -3.9930000000000003, 45.678], [-14.268999999999998, -14.311, 72.813], [-13.843, -14.77, 74.102], [-12.870999999999999, -15.893999999999998, 74.054], [-11.847999999999999, -15.947, 74.74], [-15.073, -15.454999999999998, 74.56], [-16.132, -14.381, 74.698], [-14.748000000000001, -16.175, 75.844], [-17.169, -14.675, 75.763], [-13.314, -16.842, 73.273], [-12.568999999999999, -18.021, 73.037], [-11.334, -17.605, 72.3], [-10.346, -18.31, 72.25999999999999], [-13.39, -18.992, 72.20400000000001], [-10.312999999999999, -14.800999999999998, 73.054], [-9.947, -13.992, 74.206], [-9.629999999999999, -12.543, 73.931], [-8.474, -12.128, 73.90299999999999], [-9.233, -14.631, 75.379], [-8.890999999999998, -16.083, 75.15], [-7.459, -16.383, 75.536], [-7.355, -17.043, 76.897], [-7.414999999999999, -18.509, 76.822]]
Update a column using index, e.g. change the x coordinates of the first 10 atoms to 2:
In [38]: x = np.ones(10) + 1
In [39]: db.update_column('x', values=x, index=list(range(10)))
In [40]: db.print('serial, name, x')
serial name x
1 N 2.0
2 CA 2.0
3 C 2.0
4 O 2.0
5 CB 2.0
6 CG 2.0
7 SD 2.0
8 CE 2.0
9 N 2.0
10 CA 2.0
11 C -15.268
12 O -14.687999999999999
13 CB -14.971
14 CG -14.140999999999998
15 CD -14.922999999999998
16 OE1 -15.158999999999999
17 NE2 -15.382000000000001
18 N -16.513
19 CA -17.44
20 C -18.2
21 O -17.96
22 CB -18.318
23 OG1 -17.55
24 CG2 -19.542
25 N -19.107
26 CA -19.866
27 C -21.054
28 O -21.605
29 CB -20.361
30 CG -21.598
31 CD1 -21.138
32 CD2 -22.284999999999997
33 N -14.268999999999998
34 CA -13.843
35 C -12.870999999999999
36 O -11.847999999999999
37 CB -15.073
38 CG1 -16.132
39 CG2 -14.748000000000001
40 CD1 -17.169
41 N -13.314
42 CA -12.568999999999999
43 C -11.334
44 O -10.346
45 CB -13.39
46 N -10.312999999999999
47 CA -9.947
48 C -9.629999999999999
49 O -8.474
50 CB -9.233
51 CG -8.890999999999998
52 CD -7.459
53 CE -7.355
54 NZ -7.414999999999999
Add a new column type with value high:
In [41]: db.add_column('type', value = 'high', coltype = 'str')
In [42]: db.print('serial, name, type')
serial name type
1 N high
2 CA high
3 C high
4 O high
5 CB high
6 CG high
7 SD high
8 CE high
9 N high
10 CA high
11 C high
12 O high
13 CB high
14 CG high
15 CD high
16 OE1 high
17 NE2 high
18 N high
19 CA high
20 C high
21 O high
22 CB high
23 OG1 high
24 CG2 high
25 N high
26 CA high
27 C high
28 O high
29 CB high
30 CG high
31 CD1 high
32 CD2 high
33 N high
34 CA high
35 C high
36 O high
37 CB high
38 CG1 high
39 CG2 high
40 CD1 high
41 N high
42 CA high
43 C high
44 O high
45 CB high
46 N high
47 CA high
48 C high
49 O high
50 CB high
51 CG high
52 CD high
53 CE high
54 NZ high
PDB I/O¶
Read PDB file or data to a list:
In [43]: pdb = pdb2sql.read_pdb('./pdb/dummy.pdb')
In [44]: pdb
Out[44]:
['ATOM 1 N MET A 1 -20.948 -13.418 28.320 1.00 46.93 N \n',
'ATOM 2 CA MET A 1 -21.093 -12.112 28.939 1.00 52.50 C \n',
'ATOM 3 C MET A 1 -22.482 -11.566 28.846 1.00 52.55 C \n',
'ATOM 4 O MET A 1 -22.816 -10.393 28.618 1.00 52.75 O \n',
'ATOM 5 CB MET A 1 -19.916 -11.178 28.789 1.00 59.92 C \n',
'ATOM 6 CG MET A 1 -18.839 -11.701 29.713 1.00 80.88 C \n',
'ATOM 7 SD MET A 1 -17.178 -11.517 29.038 1.00 95.94 S \n',
'ATOM 8 CE MET A 1 -16.527 -13.173 29.365 1.00 90.58 C \n',
'ATOM 9 N GLN A 2 -23.243 -12.593 29.074 1.00 51.78 N \n',
'ATOM 10 CA GLN A 2 -24.639 -12.681 29.076 1.00 52.49 C \n',
'ATOM 11 C GLN A 2 -25.268 -12.252 30.349 1.00 42.74 C \n',
'ATOM 12 O GLN A 2 -24.688 -12.207 31.435 1.00 47.12 O \n',
'ATOM 13 CB GLN A 2 -24.971 -14.147 28.858 1.00 45.95 C \n',
'ATOM 14 CG GLN A 2 -24.141 -14.712 27.710 1.00 53.26 C \n',
'ATOM 15 CD GLN A 2 -24.923 -15.776 27.001 1.00 68.74 C \n',
'ATOM 16 OE1 GLN A 2 -25.159 -16.851 27.563 1.00 82.61 O \n',
'ATOM 17 NE2 GLN A 2 -25.382 -15.458 25.797 1.00 76.83 N \n',
'ATOM 18 N THR A 3 -26.513 -11.973 30.116 1.00 21.94 N \n',
'ATOM 19 CA THR A 3 -27.440 -11.567 31.088 1.00 15.55 C \n',
'ATOM 20 C THR A 3 -28.200 -12.824 31.459 1.00 5.55 C \n',
'ATOM 21 O THR A 3 -27.960 -13.910 30.947 1.00 13.48 O \n',
'ATOM 22 CB THR A 3 -28.318 -10.497 30.412 1.00 14.60 C \n',
'ATOM 23 OG1 THR A 3 -27.550 -9.329 30.158 1.00 7.60 O \n',
'ATOM 24 CG2 THR A 3 -29.542 -10.173 31.249 1.00 14.52 C \n',
'ATOM 25 N LEU A 4 -29.107 -12.704 32.360 1.00 2.00 N \n',
'ATOM 26 CA LEU A 4 -29.866 -13.850 32.734 1.00 2.00 C \n',
'ATOM 27 C LEU A 4 -31.054 -13.904 31.795 1.00 23.22 C \n',
'ATOM 28 O LEU A 4 -31.605 -14.952 31.468 1.00 22.54 O \n',
'ATOM 29 CB LEU A 4 -30.361 -13.645 34.167 1.00 2.00 C \n',
'ATOM 30 CG LEU A 4 -31.598 -14.458 34.413 1.00 2.00 C \n',
'ATOM 31 CD1 LEU A 4 -31.138 -15.884 34.580 1.00 10.70 C \n',
'ATOM 32 CD2 LEU A 4 -32.285 -13.993 35.678 1.00 2.00 C \n',
'TER 32 LEU A\n',
'ATOM 33 N ILE B 5 -24.269 -24.311 62.813 1.00 9.48 N \n',
'ATOM 34 CA ILE B 5 -23.843 -24.770 64.102 1.00 26.84 C \n',
'ATOM 35 C ILE B 5 -22.871 -25.894 64.054 1.00 25.15 C \n',
'ATOM 36 O ILE B 5 -21.848 -25.947 64.740 1.00 26.70 O \n',
'ATOM 37 CB ILE B 5 -25.073 -25.455 64.560 1.00 2.00 C \n',
'ATOM 38 CG1 ILE B 5 -26.132 -24.381 64.698 1.00 8.15 C \n',
'ATOM 39 CG2 ILE B 5 -24.748 -26.175 65.844 1.00 15.39 C \n',
'ATOM 40 CD1 ILE B 5 -27.169 -24.675 65.763 1.00 4.14 C \n',
'ATOM 41 N ALA B 6 -23.314 -26.842 63.273 1.00 5.60 N \n',
'ATOM 42 CA ALA B 6 -22.569 -28.021 63.037 1.00 6.15 C \n',
'ATOM 43 C ALA B 6 -21.334 -27.605 62.300 1.00 2.00 C \n',
'ATOM 44 O ALA B 6 -20.346 -28.310 62.260 1.00 19.27 O \n',
'ATOM 45 CB ALA B 6 -23.390 -28.992 62.204 1.00 28.29 C \n',
'ATOM 46 N LYS B 7 -20.313 -24.801 63.054 1.00 42.89 N \n',
'ATOM 47 CA LYS B 7 -19.947 -23.992 64.206 1.00 35.06 C \n',
'ATOM 48 C LYS B 7 -19.630 -22.543 63.931 1.00 28.97 C \n',
'ATOM 49 O LYS B 7 -18.474 -22.128 63.903 1.00 23.79 O \n',
'ATOM 50 CB LYS B 7 -19.233 -24.631 65.379 1.00 29.85 C \n',
'ATOM 51 CG LYS B 7 -18.891 -26.083 65.150 1.00 33.26 C \n',
'ATOM 52 CD LYS B 7 -17.459 -26.383 65.536 1.00 40.19 C \n',
'ATOM 53 CE LYS B 7 -17.355 -27.043 66.897 1.00 63.40 C \n',
'ATOM 54 NZ LYS B 7 -17.415 -28.509 66.822 1.00 66.95 N \n',
'END\n']
Convert SQL data to PDB-formated data:
In [45]: pdb = db.sql2pdb()
In [46]: pdb
Out[46]:
['ATOM 1 N MET A 1 2.000 -3.418 38.320 1.00 46.93 N ',
'ATOM 2 CA MET A 1 2.000 -2.112 38.939 1.00 52.50 C ',
'ATOM 3 C MET A 1 2.000 -1.566 38.846 1.00 52.55 C ',
'ATOM 4 O MET A 1 2.000 -0.393 38.618 1.00 52.75 O ',
'ATOM 5 CB MET A 1 2.000 -1.178 38.789 1.00 59.92 C ',
'ATOM 6 CG MET A 1 2.000 -1.701 39.713 1.00 80.88 C ',
'ATOM 7 SD MET A 1 2.000 -1.517 39.038 1.00 95.94 S ',
'ATOM 8 CE MET A 1 2.000 -3.173 39.365 1.00 90.58 C ',
'ATOM 9 N GLN A 2 2.000 -2.593 39.074 1.00 51.78 N ',
'ATOM 10 CA GLN A 2 2.000 -2.681 39.076 1.00 52.49 C ',
'ATOM 11 C GLN A 2 -15.268 -2.252 40.349 1.00 42.74 C ',
'ATOM 12 O GLN A 2 -14.688 -2.207 41.435 1.00 47.12 O ',
'ATOM 13 CB GLN A 2 -14.971 -4.147 38.858 1.00 45.95 C ',
'ATOM 14 CG GLN A 2 -14.141 -4.712 37.710 1.00 53.26 C ',
'ATOM 15 CD GLN A 2 -14.923 -5.776 37.001 1.00 68.74 C ',
'ATOM 16 OE1 GLN A 2 -15.159 -6.851 37.563 1.00 82.61 O ',
'ATOM 17 NE2 GLN A 2 -15.382 -5.458 35.797 1.00 76.83 N ',
'ATOM 18 N THR A 3 -16.513 -1.973 40.116 1.00 21.94 N ',
'ATOM 19 CA THR A 3 -17.440 -1.567 41.088 1.00 15.55 C ',
'ATOM 20 C THR A 3 -18.200 -2.824 41.459 1.00 5.55 C ',
'ATOM 21 O THR A 3 -17.960 -3.910 40.947 1.00 13.48 O ',
'ATOM 22 CB THR A 3 -18.318 -0.497 40.412 1.00 14.60 C ',
'ATOM 23 OG1 THR A 3 -17.550 0.671 40.158 1.00 7.60 O ',
'ATOM 24 CG2 THR A 3 -19.542 -0.173 41.249 1.00 14.52 C ',
'ATOM 25 N LEU A 4 -19.107 -2.704 42.360 1.00 2.00 N ',
'ATOM 26 CA LEU A 4 -19.866 -3.850 42.734 1.00 2.00 C ',
'ATOM 27 C LEU A 4 -21.054 -3.904 41.795 1.00 23.22 C ',
'ATOM 28 O LEU A 4 -21.605 -4.952 41.468 1.00 22.54 O ',
'ATOM 29 CB LEU A 4 -20.361 -3.645 44.167 1.00 2.00 C ',
'ATOM 30 CG LEU A 4 -21.598 -4.458 44.413 1.00 2.00 C ',
'ATOM 31 CD1 LEU A 4 -21.138 -5.884 44.580 1.00 10.70 C ',
'ATOM 32 CD2 LEU A 4 -22.285 -3.993 45.678 1.00 2.00 C ',
'ATOM 33 N ILE C 5 -14.269 -14.311 72.813 1.00 9.48 N ',
'ATOM 34 CA ILE C 5 -13.843 -14.770 74.102 1.00 26.84 C ',
'ATOM 35 C ILE C 5 -12.871 -15.894 74.054 1.00 25.15 C ',
'ATOM 36 O ILE C 5 -11.848 -15.947 74.740 1.00 26.70 O ',
'ATOM 37 CB ILE C 5 -15.073 -15.455 74.560 1.00 2.00 C ',
'ATOM 38 CG1 ILE C 5 -16.132 -14.381 74.698 1.00 8.15 C ',
'ATOM 39 CG2 ILE C 5 -14.748 -16.175 75.844 1.00 15.39 C ',
'ATOM 40 CD1 ILE C 5 -17.169 -14.675 75.763 1.00 4.14 C ',
'ATOM 41 N ALA C 6 -13.314 -16.842 73.273 1.00 5.60 N ',
'ATOM 42 CA ALA C 6 -12.569 -18.021 73.037 1.00 6.15 C ',
'ATOM 43 C ALA C 6 -11.334 -17.605 72.300 1.00 2.00 C ',
'ATOM 44 O ALA C 6 -10.346 -18.310 72.260 1.00 19.27 O ',
'ATOM 45 CB ALA C 6 -13.390 -18.992 72.204 1.00 28.29 C ',
'ATOM 46 N LYS C 7 -10.313 -14.801 73.054 1.00 42.89 N ',
'ATOM 47 CA LYS C 7 -9.947 -13.992 74.206 1.00 35.06 C ',
'ATOM 48 C LYS C 7 -9.630 -12.543 73.931 1.00 28.97 C ',
'ATOM 49 O LYS C 7 -8.474 -12.128 73.903 1.00 23.79 O ',
'ATOM 50 CB LYS C 7 -9.233 -14.631 75.379 1.00 29.85 C ',
'ATOM 51 CG LYS C 7 -8.891 -16.083 75.150 1.00 33.26 C ',
'ATOM 52 CD LYS C 7 -7.459 -16.383 75.536 1.00 40.19 C ',
'ATOM 53 CE LYS C 7 -7.355 -17.043 76.897 1.00 63.40 C ',
'ATOM 54 NZ LYS C 7 -7.415 -18.509 76.822 1.00 66.95 N ']
Write PDB file from SQL database:
In [47]: db.exportpdb('./pdb/test.pdb')
# show the test.pdb file
In [48]: ls ./pdb
1AK4_10w.pdb 3CRO.pdb dummy.pdb ref.pdb
1AK4_5w.pdb decoy.pdb dummy_transform.pdb test.pdb
Interface calculation¶
Create an interface SQL database instance:
In [49]: from pdb2sql import interface
# use pdb2sql instance as input
In [50]: from pdb2sql import pdb2sql
In [51]: pdb_db = pdb2sql('./pdb/3CRO.pdb')
In [52]: db = interface(pdb_db)
# or use pdb file as input
In [53]: db = interface('./pdb/3CRO.pdb')
Interface atoms¶
In [54]: itf_atom = db.get_contact_atoms(cutoff = 3)
In [55]: itf_atom_pair = db.get_contact_atoms(cutoff = 3, return_contact_pairs=True)
In [56]: print("interface atom:\n", itf_atom)
interface atom:
{'A': [13, 33, 34, 35, 55, 56, 58, 75, 97, 98, 116, 118, 137, 138, 158, 179, 180, 200, 215, 216, 219, 239, 256, 257, 258, 259, 276, 277, 279, 294, 295, 298, 316, 318, 338, 358, 360, 380, 401], 'B': [438, 459, 479, 480, 500, 519, 520, 540, 561, 562, 564, 583, 584, 585, 604, 606, 625, 646, 648, 649, 666, 668, 688, 706, 708, 728, 729, 748, 750, 770, 771, 788, 789, 791, 808, 810]}
In [57]: print("interface atom pairs:\n", itf_atom_pair)
interface atom pairs:
{13: [810], 33: [810], 34: [791, 810], 35: [808, 810], 55: [770, 791], 56: [789], 58: [788], 75: [771], 97: [750], 98: [748], 116: [728, 729], 118: [728], 137: [708], 138: [706], 158: [688], 179: [668], 180: [666], 200: [646], 215: [649], 216: [648, 649], 219: [625], 239: [604], 256: [606], 257: [583, 584], 258: [583], 259: [583], 276: [585], 277: [562], 279: [561], 294: [564], 295: [564], 298: [519, 540], 316: [520], 318: [519, 520], 338: [500], 358: [480], 360: [479, 480], 380: [459], 401: [438]}
Interface residues¶
In [58]: itf_residue = db.get_contact_residues(cutoff = 3)
In [59]: itf_residue_pair = db.get_contact_residues(cutoff = 3, return_contact_pairs=True)
In [60]: itf_residue
Out[60]:
{'A': [('A', 1, 'DA'),
('A', 2, 'DA'),
('A', 3, 'DG'),
('A', 4, 'DT'),
('A', 5, 'DA'),
('A', 6, 'DC'),
('A', 7, 'DA'),
('A', 8, 'DA'),
('A', 9, 'DA'),
('A', 10, 'DC'),
('A', 11, 'DT'),
('A', 12, 'DT'),
('A', 13, 'DT'),
('A', 14, 'DC'),
('A', 15, 'DT'),
('A', 16, 'DT'),
('A', 17, 'DG'),
('A', 18, 'DT'),
('A', 19, 'DA'),
('A', 20, 'DT')],
'B': [('B', 2, 'DA'),
('B', 3, 'DT'),
('B', 4, 'DA'),
('B', 5, 'DC'),
('B', 6, 'DA'),
('B', 7, 'DA'),
('B', 8, 'DG'),
('B', 9, 'DA'),
('B', 10, 'DA'),
('B', 11, 'DA'),
('B', 12, 'DG'),
('B', 13, 'DT'),
('B', 14, 'DT'),
('B', 15, 'DT'),
('B', 16, 'DG'),
('B', 17, 'DT'),
('B', 18, 'DA'),
('B', 19, 'DC'),
('B', 20, 'DT')]}
In [61]: itf_residue_pair
Out[61]:
{('A', 1, 'DA'): [('B', 20, 'DT')],
('A', 2, 'DA'): [('B', 19, 'DC'), ('B', 20, 'DT')],
('A', 3, 'DG'): [('B', 18, 'DA'), ('B', 19, 'DC')],
('A', 4, 'DT'): [('B', 18, 'DA')],
('A', 5, 'DA'): [('B', 17, 'DT')],
('A', 6, 'DC'): [('B', 16, 'DG')],
('A', 7, 'DA'): [('B', 15, 'DT')],
('A', 8, 'DA'): [('B', 14, 'DT')],
('A', 9, 'DA'): [('B', 13, 'DT')],
('A', 10, 'DC'): [('B', 12, 'DG')],
('A', 11, 'DT'): [('B', 11, 'DA'), ('B', 12, 'DG')],
('A', 12, 'DT'): [('B', 10, 'DA')],
('A', 13, 'DT'): [('B', 9, 'DA'), ('B', 10, 'DA')],
('A', 14, 'DC'): [('B', 8, 'DG'), ('B', 9, 'DA')],
('A', 15, 'DT'): [('B', 6, 'DA'), ('B', 7, 'DA'), ('B', 8, 'DG')],
('A', 16, 'DT'): [('B', 6, 'DA')],
('A', 17, 'DG'): [('B', 5, 'DC')],
('A', 18, 'DT'): [('B', 4, 'DA')],
('A', 19, 'DA'): [('B', 3, 'DT')],
('A', 20, 'DT'): [('B', 2, 'DA')]}
Structure superposition¶
pdb2sql allows to superpose two structure on top of each other either using the full structure or with selection keywords. For example to superpose the chain A of two PDB one can use :
In [62]: from pdb2sql import superpose
In [63]: ref = pdb2sql('./pdb/1AK4_5w.pdb')
In [64]: decoy = pdb2sql('./pdb/1AK4_10w.pdb')
In [65]: superposed_decoy = superpose(decoy, ref, chainID='A', export=True)
This will export a new PDB file containining the structure of the decoy superposed onto the reference.
Structure alignement¶
pdb2sql allows to align structure along a specific axis
In [66]: from pdb2sql import align
In [67]: db = pdb2sql('./pdb/1AK4_10w.pdb')
In [68]: aligned_db = align(db, axis='z', export=True)
The alignement can also consider only a subpart of the complex using the selection keywords:
In [69]: aligned_db = align(db, axis='z', chainID='A')
There the chain A will be aligned along the z-axis
This will create a new PDB file containing the structure aligned along the z-axis. It is also possible aligning an interface in a given plane
In [70]: from pdb2sql import align_interface
In [71]: db = pdb2sql('./pdb/3CRO.pdb')
In [72]: aligned_db = align_interface(db, plane='xy', export=True)
By default the interface formed by chain A and B will be considered. In case multiple chains are present in the structure it is possible to specify wich interface to consider:
In [73]: aligned_db = align_interface(db, plane='xy', chain1='L', chain2='R')
There the interface between chain L and R will be considered. Note that any other selection keyword can be used to specify which interface to account for.
Structure similarity calculation¶
Create a StructureSimilarity instance:
In [74]: from pdb2sql.StructureSimilarity import StructureSimilarity
In [75]: sim = StructureSimilarity('./pdb/decoy.pdb', './pdb/ref.pdb')
interface RMSD¶
In [76]: irmsd_fast = sim.compute_irmsd_fast()
---------------------------------------------------------------------------
ValueError Traceback (most recent call last)
<ipython-input-76-0ffc09c59f8a> in <module>
----> 1 irmsd_fast = sim.compute_irmsd_fast()
~/checkouts/readthedocs.org/user_builds/pdb2sql/envs/latest/lib/python3.7/site-packages/pdb2sql/StructureSimilarity.py in compute_irmsd_fast(self, izone, method, cutoff, check)
307 if check or self.enforce_residue_matching:
308
--> 309 self.check_residues()
310
311 data_decoy = self.get_data_zone_backbone(
~/checkouts/readthedocs.org/user_builds/pdb2sql/envs/latest/lib/python3.7/site-packages/pdb2sql/StructureSimilarity.py in check_residues(self, **kwargs)
100 if self.enforce_residue_matching == True:
101 raise ValueError(
--> 102 'Atoms not identical in ref and decoy.\n Set enforce_residue_matching=False to bypass this error.')
103 else:
104 warnings.warn('Atoms not identical in ref and decoy.')
ValueError: Atoms not identical in ref and decoy.
Set enforce_residue_matching=False to bypass this error.
In [77]: irmsd_pdb2sql = sim.compute_irmsd_pdb2sql()
In [78]: irmsd_fast
---------------------------------------------------------------------------
NameError Traceback (most recent call last)
<ipython-input-78-d58ceea2462b> in <module>
----> 1 irmsd_fast
NameError: name 'irmsd_fast' is not defined
In [79]: irmsd_pdb2sql
Out[79]: 1.135
ligand RMSD¶
In [80]: lrmsd_fast = sim.compute_lrmsd_fast()
In [81]: lrmsd_pdb2sql = sim.compute_lrmsd_pdb2sql()
In [82]: lrmsd_fast
Out[82]: 6.655
In [83]: lrmsd_pdb2sql
Out[83]: 6.655
FNAT¶
Calculate the fraction of native contacts:
In [84]: fnat_fast = sim.compute_fnat_fast()
In [85]: fnat_pdb2sql = sim.compute_fnat_pdb2sql()
In [86]: fnat_fast
Out[86]: 0.790698
In [87]: fnat_pdb2sql
Out[87]: 0.790698
DockQ score¶
In [88]: dockQ = sim.compute_DockQScore(fnat_fast, lrmsd_fast, irmsd_fast)
---------------------------------------------------------------------------
NameError Traceback (most recent call last)
<ipython-input-88-a18b2f03db3a> in <module>
----> 1 dockQ = sim.compute_DockQScore(fnat_fast, lrmsd_fast, irmsd_fast)
NameError: name 'irmsd_fast' is not defined
In [89]: dockQ
---------------------------------------------------------------------------
NameError Traceback (most recent call last)
<ipython-input-89-2012a35270fa> in <module>
----> 1 dockQ
NameError: name 'dockQ' is not defined
Structure transformation¶
Create SQL instance:
In [90]: from pdb2sql import transform
In [91]: db = pdb2sql('./pdb/dummy_transform.pdb')
The atom coordinates are:
In [92]: db.get_xyz()
Out[92]:
[[1.0, 0.0, 0.0],
[-1.0, 0.0, 0.0],
[0.0, 1.0, 0.0],
[0.0, -1.0, 0.0],
[0.0, 0.0, 1.0],
[0.0, 0.0, -1.0]]
Rotations¶
Rotate structures 180 degrees along the x-axis:
In [93]: angle = np.pi
In [94]: axis = (1., 0., 0.)
In [95]: transform.rot_axis(db, axis, angle)
In [96]: db.get_xyz()
Out[96]:
[[1.0, 0.0, 0.0],
[-1.0, 0.0, 0.0],
[0.0, -1.0, 1.2246467991473532e-16],
[0.0, 1.0, -1.2246467991473532e-16],
[0.0, -1.2246467991473532e-16, -1.0],
[0.0, 1.2246467991473532e-16, 1.0]]
Get random rotation axis and angle:
In [97]: axis, angle = transform.get_rot_axis_angle()
In [98]: axis
Out[98]: [-0.06788982155971889, 0.7589085252919632, -0.6476486874593103]
In [99]: angle
Out[99]: 0.06654169272612691
Translations¶
Translate structure 5Å along y-axis:
In [100]: trans_vec = np.array([0,5,0])
In [101]: transform.translation(db, trans_vec)
In [102]: db.get_xyz()
Out[102]:
[[1.0, 5.0, 0.0],
[-1.0, 5.0, 0.0],
[0.0, 4.0, 1.2246467991473532e-16],
[0.0, 6.0, -1.2246467991473532e-16],
[0.0, 5.0, -1.0],
[0.0, 5.0, 1.0]]