Add support for oxDNA file parsing #536
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pckroon
requested changes
Aug 17, 2023
| from ..molecule import Molecule | ||
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| def read_oxDNA(file_name, exclude=()): |
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I would suggest the actual parser doesn't accept a file name, but rather an iterator of lines. This makes reading e.g. network streams or compressed files easier/possible in the future. A wrapper method can open the file.
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| Returns | ||
| ------- | ||
| vermouth.molecule.Molecule | ||
| The parsed molecules. Will not contain edges. | ||
| """ | ||
| molecule = Molecule() |
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The PDB parser returns a System, and I think that would also make more sense here?
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| has_b= first_line.count(' ') > 2 | ||
| has_n = first_line.count(' ') > 5 |
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| # Start parsing the file in earnest. And let's not forget the first | ||
| # line. | ||
| for line in chain([first_line], oxDNA): |
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| # Start parsing the file in earnest. And let's not forget the first | ||
| # line. | ||
| for line in chain([first_line], oxDNA): |
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Nitpick suggestion
Suggested change
| for line in chain([first_line], oxDNA): | |
| for idx, line in enumerate(chain([first_line], oxDNA)): |
| @@ -0,0 +1,19 @@ | |||
| # -*- coding: utf-8 -*- | |||
| # Copyright 2018 University of Groningen | |||
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Suggested change
| # Copyright 2018 University of Groningen | |
| # Copyright 2023 University of Groningen |
| @@ -0,0 +1,75 @@ | |||
| # -*- coding: utf-8 -*- | |||
| # Copyright 2018 University of Groningen | |||
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Suggested change
| # Copyright 2018 University of Groningen | |
| # Copyright 2023 University of Groningen |
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This PR implements a file parser of oxDNA configuration files to read in rotational frames for residues. The initial goal is to use the file parser to implement a frame-based backmapping processer in Polyply.
Info on the file format can be found here.