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paramost/pdb_crawler

By paramost

•Updated almost 7 years ago

Gather information of pdbs.

Image
1

279

paramost/pdb_crawler repository overview

⁠What this does

  1. Scrape information of each pdb from RCSB into a tab delimited text file and an excel (xlsx) file, using a list of an inputted excel
  2. Download pdb files.
  3. Parse each entity into separate files.

⁠Usage

docker run --rm -v <path_of_where_your_input_file_belongs>:/mnt -it paramost/pdb_crawler:<tag> --input_excel_name <input_excel_file_name> --sheet_name <sheet_name_of_the_excel_file> [--process <number_of_process>]

⁠Issues

⁠version 1.3.1

  1. Still got glitch on locking file when multiprocessing is on. Therefore sometimes it might have a problem when converting txt file to excel file. In this case you can simply delete the line which has no pdb title from txt file and rerun.
    --> fixed
  2. when the names of the molecules are same, it overrides previous one.
    --> fixed

⁠version 1.3.2

  1. It doesn't distinguish upper and lower case letters for chains.
    --> fixed

⁠version 1.3.3

  1. Redirected pdbs are overwritten, while txt file is being checked out.

⁠Github

Check codes at:
https://github.com/satchellhong/pdb_crawler⁠

⁠PDB FORMAT

column            1         2         3         4         5         6         7         8
number   12345678901234567890123456789012345678901234567890123456789012345678901234567890

         ATOM      1  N   GLY A   3      17.119   0.186  36.320  1.00 64.10           N  
         ATOM      2  CA  GLY A   3      16.944  -0.800  35.208  1.00 63.46           C  
         ATOM      3  C   GLY A   3      16.818  -0.087  33.851  1.00 61.22           C  
         ATOM      4  O   GLY A   3      15.721   0.337  33.463  1.00 62.81           O  
         ATOM      5  N   PRO A   4      17.944   0.077  33.129  1.00 57.39           N  
         ATOM      6  CA  PRO A   4      17.950   0.742  31.815  1.00 53.27           C  
         ATOM      7  C   PRO A   4      18.005  -0.247  30.629  1.00 49.78           C  
         ATOM      8  O   PRO A   4      19.086  -0.678  30.218  1.00 48.17           O  
         ATOM      9  CB  PRO A   4      19.191   1.613  31.898  1.00 54.33           C  
         ATOM     10  CG  PRO A   4      20.161   0.686  32.625  1.00 55.45           C  
         ATOM     11  CD  PRO A   4      19.305   0.019  33.701  1.00 55.83           C  

field id   1     2     3 4 5  6  7 8       9      10      11     12    13            1415
field iddefinitionlengthformatrangestring slicing (Python)
1"ATOM " or "HETATM"6{:6s}01-06[0:6]
2atom serial number5{:5d}07-11[6:11]
3atom name4{:^4s}13-16[12:16]
4alternate location indicator1{:1s}17[16:17]
5residue name3{:3s}18-20[17:20]
6chain identifier1{:1s}22[21:22]
7residue sequence number4{:4d}23-26[22:26]
8code for insertion of residues1{:1s}27[26:27]
9orthogonal coordinates for X (in Angstroms)8{:8.3f}31-38[30:38]
10orthogonal coordinates for Y (in Angstroms)8{:8.3f}39-46[38:46]
11orthogonal coordinates for Z (in Angstroms)8{:8.3f}47-54[46:54]
12occupancy6{:6.2f}55-60[54:60]
13temperature factor6{:6.2f}61-66[60:66]
14element symbol2{:>2s}77-78[76:78]
15charge on the atom2{:2s}79-80[78:80]

Tag summary

Content type

Image

Digest

Size

828.4 MB

Last updated

almost 7 years ago

docker pull paramost/pdb_crawler:1.3.3