EntDetect 1.2.0__py3-none-any.whl

EntDetect/Jwalk/__init__.py

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+# ===============================================================================
+#     This file is part of Jwalk (Python 3).
+#     
+#     Jwalk - A tool to calculate the solvent accessible surface distance (SASD) 
+#     between crosslinked residues.
+#     
+#     Copyright 2016 Josh Bullock and Birkbeck College University of London.
+# 
+#     Jwalk is available under Public Licence.
+#     This software is made available under GPL V3
+#
+#     Please cite your use of Jwalk in published work:
+#     
+#     J.Bullock, J. Schwab, K. Thalassinos, M. Topf (2016)
+#     The importance of non-accessible crosslinks and solvent accessible surface distance
+#     in modelling proteins with restraints from crosslinking mass spectrometry. 
+#     Molecular and Cellular Proteomics (15) pp.2491-2500
+#
+# ===============================================================================

EntDetect/Jwalk/naccess.config.txt

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+# Contributed by João Rodrigues
+
+name: NACCESS
+
+types:
+C_ALI 1.87 apolar
+C_CAR 1.76 apolar
+C_NUC 1.80 apolar
+N_AMN 1.50 polar
+N_AMD 1.65 polar
+N_NUC 1.60 polar
+O 1.40 polar
+S 1.85 apolar
+SE 1.80 apolar
+P 1.90 apolar
+
+atoms:
+ANY C   C_CAR
+ANY O   O
+ANY CA  C_ALI
+ANY N   N_AMD
+ANY CB  C_ALI
+ANY OXT O
+# nucleic acid
+ANY P   P
+ANY OP1 O
+ANY OP2 O
+ANY OP3 O
+ANY O5' O
+ANY O4' O
+ANY O3' O
+ANY O2' O
+ANY C5' C_NUC
+ANY C4' C_NUC
+ANY C3' C_NUC
+ANY C2' C_NUC
+ANY C1' C_NUC
+
+ALA CB C_ALI # included so that RSA values will be generated
+
+ARG CG C_ALI
+ARG CD C_ALI
+ARG NE N_AMD
+ARG CZ C_CAR
+ARG NH1 N_AMD
+ARG NH2 N_AMD
+
+ASN CG  C_CAR
+ASN OD1 O
+ASN ND2 N_AMD
+
+ASP CG  C_CAR
+ASP OD1 O
+ASP OD2 O
+
+CYS SG  S
+
+GLN CG  C_ALI
+GLN CD  C_CAR
+GLN OE1 O
+GLN NE2 N_AMD
+
+GLU CG  C_ALI
+GLU CD  C_CAR
+GLU OE1 O
+GLU OE2 O
+
+GLY CA C_ALI # included so that RSA values will be generated
+
+HIS CG  C_CAR
+HIS ND1 N_AMD
+HIS CD2 C_CAR
+HIS NE2 N_AMD
+HIS CE1 C_CAR
+
+ILE CG1 C_ALI
+ILE CG2 C_ALI
+ILE CD1 C_ALI
+
+LEU CG  C_ALI
+LEU CD1 C_ALI
+LEU CD2 C_ALI
+
+LYS CG  C_ALI
+LYS CD  C_ALI
+LYS CE  C_ALI
+LYS NZ  N_AMN
+
+MET CG  C_ALI
+MET SD  S
+MET CE  C_ALI
+
+PHE CG  C_CAR
+PHE CD1 C_CAR
+PHE CD2 C_CAR
+PHE CE1 C_CAR
+PHE CE2 C_CAR
+PHE CZ  C_CAR
+
+PRO CG  C_ALI
+PRO CD  C_ALI
+
+SEC SE  SE
+
+MSE SE  SE
+
+SER OG  O
+
+THR OG1 O
+THR CG2 C_ALI
+
+TRP CG  C_CAR
+TRP CD1 C_CAR
+TRP CD2 C_CAR
+TRP NE1 N_AMD
+TRP CE2 C_CAR
+TRP CE3 C_CAR
+TRP CZ2 C_CAR
+TRP CZ3 C_CAR
+TRP CH2 C_CAR
+
+TYR CG  C_CAR
+TYR CD1 C_CAR
+TYR CD2 C_CAR
+TYR CE1 C_CAR
+TYR CE2 C_CAR
+TYR CZ  C_CAR
+TYR OH  O
+
+VAL CG1 C_ALI
+VAL CG2 C_ALI
+
+A N9 N_NUC
+A C8 C_NUC
+A N7 N_NUC
+A C5 C_NUC
+A C6 C_NUC
+A N6 N_NUC
+A N1 N_NUC
+A C2 C_NUC
+A N3 N_NUC
+A C4 C_NUC
+
+C N1 N_NUC
+C C2 C_NUC
+C O2 O
+C N3 N_NUC
+C C4 C_NUC
+C N4 N_NUC
+C C5 C_NUC
+C C6 C_NUC
+
+G N9 N_NUC
+G C8 C_NUC
+G N7 N_NUC
+G C5 C_NUC
+G C6 C_NUC
+G O6 O
+G N1 N_NUC
+G C2 C_NUC
+G N2 N_NUC
+G N3 N_NUC
+G C4 C_NUC
+
+I N9 N_NUC
+I C8 C_NUC
+I N7 N_NUC
+I C5 C_NUC
+I C6 C_NUC
+I O6 O
+I N1 N_NUC
+I C2 C_NUC
+I N3 N_NUC
+I C4 C_NUC
+
+T N1 N_NUC
+T C2 C_NUC
+T O2 O
+T N3 N_NUC
+T C4 C_NUC
+T O4 O
+T C5 C_NUC
+T C7 C_NUC
+T C6 C_NUC
+
+U N1 N_NUC
+U C2 C_NUC
+U O2 O
+U N3 N_NUC
+U C4 C_NUC
+U O4 O
+U C5 C_NUC
+U C6 C_NUC
+
+DA N9 N_NUC
+DA C8 C_NUC
+DA N7 N_NUC
+DA C5 C_NUC
+DA C6 C_NUC
+DA N6 N_NUC
+DA N1 N_NUC
+DA C2 C_NUC
+DA N3 N_NUC
+DA C4 C_NUC
+
+DC N1 N_NUC
+DC C2 C_NUC
+DC O2 O
+DC N3 N_NUC
+DC C4 C_NUC
+DC N4 N_NUC
+DC C5 C_NUC
+DC C6 C_NUC
+
+DG N9 N_NUC
+DG C8 C_NUC
+DG N7 N_NUC
+DG C5 C_NUC
+DG C6 C_NUC
+DG O6 O
+DG N1 N_NUC
+DG C2 C_NUC
+DG N2 N_NUC
+DG N3 N_NUC
+DG C4 C_NUC
+
+DI N9 N_NUC
+DI C8 C_NUC
+DI N7 N_NUC
+DI C5 C_NUC
+DI C6 C_NUC
+DI O6 O
+DI N1 N_NUC
+DI C2 C_NUC
+DI N3 N_NUC
+DI C4 C_NUC
+
+DT N1 N_NUC
+DT C2 C_NUC
+DT O2 O
+DT N3 N_NUC
+DT C4 C_NUC
+DT O4 O
+DT C5 C_NUC
+DT C7 C_NUC
+DT C6 C_NUC
+
+DU N1 N_NUC
+DU C2 C_NUC
+DU O2 O
+DU N3 N_NUC
+DU C4 C_NUC
+DU O4 O
+DU C5 C_NUC
+DU C6 C_NUC

EntDetect/__init__.py

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+"""EntDetect - Entanglement Detection in Protein Structures
+
+A package for identifying and analyzing non-covalent lasso-like entanglements
+in protein structures using Gaussian linking numbers and topological analysis.
+"""
+
+__version__ = "1.1.6"
+__author__ = "O'Brien Lab"
+__email__ = "contact@example.com"
+

EntDetect/_logging.py

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+"""
+Internal logging helper for EntDetect.
+
+Usage within a class ``__init__``::
+
+    from EntDetect._logging import setup_logger
+    self.logger = setup_logger('ClassName', outdir=self.outdir, ID=self.ID, log_level=log_level)
+
+Users of the package can control verbosity at the top-level ``EntDetect`` logger::
+
+    import logging
+    logging.getLogger('EntDetect').setLevel(logging.WARNING)   # suppress INFO
+    logging.getLogger('EntDetect').setLevel(logging.DEBUG)     # enable DEBUG
+
+"""
+import logging
+import os
+
+
+def setup_logger(
+    name: str,
+    outdir: str = None,
+    ID: str = '',
+    log_level: int = logging.INFO,
+) -> logging.Logger:
+    """
+    Create and return a named logger for an EntDetect class.
+
+    Parameters
+    ----------
+    name : str
+        Short class name used as the logger suffix (e.g. ``'GaussianEntanglement'``).
+    outdir : str, optional
+        If provided, a ``FileHandler`` writing to ``<outdir>/<ID>.log`` (or
+        ``<outdir>/<name>.log`` when *ID* is empty) is added alongside the
+        stream handler.
+    ID : str, optional
+        Identifier used as the log file stem when *outdir* is given.
+    log_level : int, optional
+        Logging level for this logger, by default ``logging.INFO``.
+
+    Returns
+    -------
+    logging.Logger
+        Configured logger under the ``EntDetect.<name>`` hierarchy.
+    """
+    logger = logging.getLogger(f'EntDetect.{name}')
+    logger.setLevel(log_level)
+
+    # Avoid adding duplicate handlers when the class is re-instantiated
+    if not logger.handlers:
+        fmt = logging.Formatter(
+            '%(asctime)s [%(name)s] %(levelname)s: %(message)s',
+            datefmt='%Y-%m-%d %H:%M:%S',
+        )
+
+        sh = logging.StreamHandler()
+        sh.setFormatter(fmt)
+        logger.addHandler(sh)
+
+        if outdir:
+            os.makedirs(outdir, exist_ok=True)
+            logfilename = f'{ID}.log' if ID else f'{name}.log'
+            fh = logging.FileHandler(os.path.join(outdir, logfilename))
+            fh.setFormatter(fmt)
+            logger.addHandler(fh)
+
+        # Prevent double output if the user has also configured the root logger
+        logger.propagate = False
+
+    return logger