Python Tools for Computational Molecular Biology
Python Tools for Computational Molecular Biology
This is a draft page for the PDBParser class.
A performance benchmark of the parser was carried out to evaluate wether the development of new features degraded the overall parsing speed.
CATH Domain Collection - 11330 Structures containing only coordinate information (no Element assigned).
Protein Data Bank Collection - 72836 Structures containing both headers and coordinate information.
Biopython 1.49 (Nov. 2008)
Biopython 1.57+ (May 2011) | Element column auto-assignment.
Biopython PDB branch (May 2011 @ Github) | Warnings module replaced _handle_pdb_exception() && Other minor changes
The following script was used to benchmark the parser. The garbage collection module - gc - was necessary to avoid dead objects still in memory causing the machine to start swapping.
#!/usr/bin/env python
""" Script to Benchmark Bio.PDB PDBParser """
import sys, os, warnings
# Parsing Function
def parse_structure(path):
"""Parses a PDB file"""
s = P.get_structure("test", path)
return 0
def fancy_output(tps):
"""Outputs the results in a nicer way"""
print("# Bio.PDB PDBParser Benchmark")
print()
print("Structure \tLenght \tTime Spent (ms)")
for i, s in enumerate(tps):
print(
" %s\t (%s) \t%3.3f" % (os.path.basename(pdb_library[i]), pdb_length[i], s)
)
print()
print("Total time spent: %5.3fs" % (sum(tps) / 1000))
print("Average time per structure: %5.3fms" % (sum(tps) / len(tps)))
if __name__ == "__main__":
import time, gc
from Bio.PDB import PDBParser
P = PDBParser(
PERMISSIVE=1
) # For the pdb_enhancements branch benchmarking, PERMISSIVE was set to 2 (silence warnings).
library_path = sys.argv[1]
pdb_library = [os.path.join(library_path, f) for f in os.listdir(library_path)]
pdb_length = [
len(set([l[17:26] for l in open(f) if l.startswith("ATOM")]))
for f in pdb_library
] # Unique counting of residues
sys.stderr.write(
"Loaded %s structures (Average Length: %4.3f residues)\n"
% (len(pdb_length), (sum(pdb_length) / float(len(pdb_length))))
)
tps = []
# Run the Test
for i, pdb_file in enumerate(pdb_library):
sys.stderr.write(
"[%s] %i Structure(s) Parsed \n" % (os.path.basename(pdb_file), i + 1)
)
a = time.time()
parse_structure(pdb_file)
b = time.time() - a
tps.append(b * 1000)
gc.collect()
# Output Results
fancy_output(tps)
Average Structure Length: 146 residues
Total Time Spent: 530.686s
Average Time per Structure: 46.84ms/structure
Average Structures per Second: 21.38 structures/s
Failed to parse 0 structures due to errors.
Length N. Structures Average Time Spent ms
< 100 3660 25.09
100 =< x < 200 5296 44.67
200 =< x < 500 2330 83.40
500 =< x < 1000 43 177.10
>= 1000 1 320.10
TOTAL 11330 46.84
Link to full results | Plot of the full results
Total Time Spent: 686.176s
Average Time per Structure: 60.56ms/structure
Average Structures per Second: 16.51 structures/s
Failed to parse 0 structures due to errors.
Length N. Structures Average Time Spent ms
< 100 3660 32.55
100 =< x < 200 5296 57.75
200 =< x < 500 2330 107.54
500 =< x < 1000 43 236.62
>= 1000 1 486.602
TOTAL 11330 60.56
Link to full results | Plot of the full results
Total Time Spent: 695.405s
Average Time per Structure: 61.37ms/structure
Average Structures per Second: 16.29 structures/s
Failed to parse 0 structures due to errors.
Length N. Structures Average Time Spent ms
< 100 3660 33.21
100 =< x < 200 5296 58.45
200 =< x < 500 2330 108.76
500 =< x < 1000 43 234.37
>= 1000 1 797.583
TOTAL 11330 61.38
Link to full results | Plot of the full results
Average Structure Length: 589 residues
Failed to parse 2 structures due to errors:
1. 3NH3 (negative occupancy) - fix: http://bit.ly/ks6PDN (still being discussed) 2. 2WMW (invalid ANISOU field) - fix: http://bit.ly/ld9BWs
Total Time Spent: 27801.934s (7.72h)
Average Time per Structure: 381.706ms/structure
Average Structures per Second: 2.62 structures/s
Length N. Structures Average Time Spent (ms)
< 100 8402 410.270
100 =< x < 200 12226 461.744
200 =< x < 500 26493 182.027
500 =< x < 1000 15878 290.693
>= 1000 9837 942.513
TOTAL 72836 381.706
Total Time Spent: 29516.480s (~8.20h)
Average Time per Structure: 405.246 ms/structure
Average Structures per Second: 2.47 structures/s
Length N. Structures Average Time Spent (ms)
< 100 8402 451.819
100 =< x < 200 12226 505.933
200 =< x < 500 26493 190.991
500 =< x < 1000 15878 304.453
>= 1000 9837 980.047
TOTAL 72836 405.246
In progress