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| # Copyright (C) 2006, Thomas Hamelryck ([email protected]) | |
| # | |
| # This file is part of the Biopython distribution and governed by your | |
| # choice of the "Biopython License Agreement" or the "BSD 3-Clause License". | |
| # Please see the LICENSE file that should have been included as part of this | |
| # package. | |
| """Wrappers for PSEA, a program for secondary structure assignment. | |
| See this citation for P-SEA, PMID: 9183534 | |
| Labesse G, Colloc'h N, Pothier J, Mornon J-P: P-SEA: a new efficient | |
| assignment of secondary structure from C_alpha. | |
| Comput Appl Biosci 1997 , 13:291-295 | |
| ftp://ftp.lmcp.jussieu.fr/pub/sincris/software/protein/p-sea/ | |
| """ | |
| import subprocess | |
| import os | |
| from Bio.PDB.Polypeptide import is_aa | |
| def run_psea(fname, verbose=False): | |
| """Run PSEA and return output filename. | |
| Note that this assumes the P-SEA binary is called "psea" and that it is | |
| on the path. | |
| Note that P-SEA will write an output file in the current directory using | |
| the input filename with extension ".sea". | |
| Note that P-SEA will not write output to the terminal while run unless | |
| verbose is set to True. | |
| """ | |
| last = fname.split("/")[-1] | |
| base = last.split(".")[0] | |
| cmd = ["psea", fname] | |
| p = subprocess.run(cmd, capture_output=True, universal_newlines=True) | |
| if verbose: | |
| print(p.stdout) | |
| if not p.stderr.strip() and os.path.exists(base + ".sea"): | |
| return base + ".sea" | |
| else: | |
| raise RuntimeError(f"Error running p-sea: {p.stderr}") | |
| def psea(pname): | |
| """Parse PSEA output file.""" | |
| fname = run_psea(pname) | |
| start = 0 | |
| ss = "" | |
| with open(fname) as fp: | |
| for line in fp: | |
| if line[0:6] == ">p-sea": | |
| start = 1 | |
| continue | |
| if not start: | |
| continue | |
| if line[0] == "\n": | |
| break | |
| ss = ss + line[0:-1] | |
| return ss | |
| def psea2HEC(pseq): | |
| """Translate PSEA secondary structure string into HEC.""" | |
| seq = [] | |
| for ss in pseq: | |
| if ss == "a": | |
| n = "H" | |
| elif ss == "b": | |
| n = "E" | |
| elif ss == "c": | |
| n = "C" | |
| seq.append(n) | |
| return seq | |
| def annotate(m, ss_seq): | |
| """Apply secondary structure information to residues in model.""" | |
| c = m.get_list()[0] | |
| all = c.get_list() | |
| residues = [] | |
| # Now remove HOH etc. | |
| for res in all: | |
| if is_aa(res): | |
| residues.append(res) | |
| L = len(residues) | |
| if not L == len(ss_seq): | |
| raise ValueError("Length mismatch %i %i" % (L, len(ss_seq))) | |
| for i in range(0, L): | |
| residues[i].xtra["SS_PSEA"] = ss_seq[i] | |
| # subprocess.call(["rm", fname]) | |
| class PSEA: | |
| """Define PSEA class. | |
| PSEA object is a wrapper to PSEA program for secondary structure assignment. | |
| """ | |
| def __init__(self, model, filename): | |
| """Initialize the class.""" | |
| ss_seq = psea(filename) | |
| ss_seq = psea2HEC(ss_seq) | |
| annotate(model, ss_seq) | |
| self.ss_seq = ss_seq | |
| def get_seq(self): | |
| """Return secondary structure string.""" | |
| return self.ss_seq | |