A python library for converting PDB files into CSV files where XYZ coordinates can be transformed into Hilbert Distances.
A typical PDB file describing a protein consists of hundreds to thousands of lines like the following:
HEADER EXTRACELLULAR MATRIX 22-JAN-98 1A3I
...
ATOM 1 N PRO A 1 8.316 21.206 21.530 1.00 17.44 N
ATOM 2 CA PRO A 1 7.608 20.729 20.336 1.00 17.44 C
ATOM 3 C PRO A 1 8.487 20.707 19.092 1.00 17.44 C
ATOM 4 O PRO A 1 9.466 21.457 19.005 1.00 17.44 O
ATOM 5 CB PRO A 1 6.460 21.723 20.211 1.00 22.26 C
...
The program will create a new CSV file based on the contents of the original PDB file. For example, a call on pdb_to_hilbert_single_frame() would create a CSV file called 1A3I.CSV containing the following rows and columns, based on the official WWPDB Documentation:
FRAME ATOM RESIDUE CHAIN SEQUENCE HILBERT
1 N PRO A 1 12545533786
1 CA PRO A 1 4421809923
1 C PRO A 1 3987905106
1 O PRO A 1 65327816114
1 CB PRO A 1 8015651838
Alternatively, you could chose to compress this data further, having each row represent a frame
and each column represent a specific atom. The data in each cell would be the hilbert position
of that atom at that time. For example, a call on pdb_to_hilbert would create a file called
1A3I.csv containing the folloring rows and columns:
ATOM: 1, 2, 3, ...
FRAME 1: 32015758582631, 32087362750683, 32089387983164, ...
FRAME 2: 32014205098819, 32087325863645, 32086193454873, ...
FRAME 3: 32015888895057, 32087443069683, 32088820506041, ...
... ... ... ... ...
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Demo et al., (2018). PyDMD: Python Dynamic Mode Decomposition. Journal of Open Source Software, 3(22), 530, https://doi.org/10.21105/joss.00530
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This module is based on the C code provided in the 2004 article "Programming the Hilbert Curve" by John Skilling found here: http://adsabs.harvard.edu/abs/2004AIPC..707..381S
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That code was translated from C into python by github user galtay. Their repository can be found here: https://github.com/galtay/hilbertcurve/blob/develop/hilbertcurve/hilbertcurve.py
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There is also an interesting discussion on Stack Overflow about dimension reduction with Hilbert Curves here: http://stackoverflow.com/questions/499166/mapping-n-dimensional-value-to-a-point-on-hilbert-curve
See the LICENSE file for license rights and limitations (MIT).