WIP: Motif search

.gitignore

@@ -36,6 +36,7 @@ __pycache__
 
 .pypirc
 .gitignore
+.python-version
 
 chauthorinfo.sh
 pre-commit.sh
@@ -48,3 +49,6 @@ Documentation/*
 *log
 *BAK
 *.sublime*
+*.code-workspace
+.vscode/
+data/

docs/conf.py

@@ -2,57 +2,62 @@
 import os
 import sys
 
-
-sys.path.append(os.path.abspath('sphinxext'))
-RTD = os.environ.get('READTHEDOCS', None) == 'True'
+sys.path.append(os.path.abspath("sphinxext"))
+RTD = os.environ.get("READTHEDOCS", None) == "True"
 if RTD:
-    tags.add('rtd')
-
-extensions = ['sphinx.ext.todo',
-              'sphinx.ext.autodoc',
-              'sphinx.ext.doctest',
-              'sphinx.ext.coverage',
-              'sphinx.ext.extlinks',
-              'sphinx.ext.graphviz',
-              'sphinx.ext.ifconfig',
-              'sphinx.ext.viewcode',
-              'sphinx.ext.intersphinx',
-              'sphinx.ext.inheritance_diagram',
-              'matplotlib.sphinxext.mathmpl',
-              'matplotlib.sphinxext.only_directives']
+    tags.add("rtd")
+
+extensions = [
+    "sphinx.ext.todo",
+    "sphinx.ext.autodoc",
+    "sphinx.ext.doctest",
+    "sphinx.ext.coverage",
+    "sphinx.ext.extlinks",
+    "sphinx.ext.graphviz",
+    "sphinx.ext.ifconfig",
+    "sphinx.ext.viewcode",
+    "sphinx.ext.intersphinx",
+    "sphinx.ext.inheritance_diagram",
+    "matplotlib.sphinxext.mathmpl",
+]
 
 # extensions that are included in docs
 extensions.extend(
-             ['IPython.sphinxext.ipython_console_highlighting',
-              'IPython.sphinxext.ipython_directive',
-              'googleanalytics',])
-
-source_suffix = '.rst'
-master_doc = 'index'
-
-project = u'ProDy'
-copyright = u'2010-2014, University of Pittsburgh'
-
-
-__version__ = ''
-for _ in ['../prody/__init__.py', # building docs
-          'ProDy/prody/__init__.py', # building complete website
-          '../../ProDy/prody/__init__.py']: # building tutorial PDFs
+    [
+        "IPython.sphinxext.ipython_console_highlighting",
+        "IPython.sphinxext.ipython_directive",
+        "googleanalytics",
+    ]
+)
+
+source_suffix = ".rst"
+master_doc = "index"
+
+project = u"ProDy"
+copyright = u"2010-2014, University of Pittsburgh"
+
+
+__version__ = ""
+for _ in [
+    "../prody/__init__.py",  # building docs
+    "ProDy/prody/__init__.py",  # building complete website
+    "../../ProDy/prody/__init__.py",
+]:  # building tutorial PDFs
     if os.path.isfile(_):
         with open(_) as inp:
-            statement = ''.join([line for line in inp
-                                 if line[:3] in ('__v', '__r')])
+            statement = "".join([line for line in inp if line[:3] in ("__v", "__r")])
             exec(statement)
 version, release = __version__, __release__
 
 
-if release.endswith('dev'):
+if release.endswith("dev"):
     import shlex
-    from subprocess import Popen, PIPE
-    _ = '../.git'
+    from subprocess import PIPE, Popen
+
+    _ = "../.git"
     if not os.path.isdir(_):
-        _ = 'ProDy/.git'
-    args = shlex.split('git --git-dir {} describe --tags --abbrev=0'.format(_))
+        _ = "ProDy/.git"
+    args = shlex.split("git --git-dir {} describe --tags --abbrev=0".format(_))
     tag = Popen(args, stdout=PIPE, stderr=PIPE)
     rst_prolog = """
 
@@ -64,38 +69,40 @@
         There may be significant differences from the latest stable
         release ({}).
 
-    """.format(tag.communicate()[0].strip())
+    """.format(
+        tag.communicate()[0].strip()
+    )
 
-exclude_patterns = ['_build', '_workdir']
+exclude_patterns = ["_build", "_workdir"]
 
 
 add_module_names = False
 
 show_authors = True
 
-pygments_style = 'sphinx'
+pygments_style = "sphinx"
 
-modindex_common_prefix = ['prody.']
+modindex_common_prefix = ["prody."]
 doctest_global_setup = "from prody import *"
 
 # -- Options for HTML output ---------------------------------------------------
 if RTD:
-    html_theme = 'default'
+    html_theme = "default"
 else:
-    templates_path = ['_theme']
-    html_theme = '_theme'
-    html_theme_path = ['.']
-    html_static_path = ['_static']
+    templates_path = ["_theme"]
+    html_theme = "_theme"
+    html_theme_path = ["."]
+    html_static_path = ["_static"]
 html_theme_options = {}
 
 html_title = "ProDy"
-html_favicon = '_static/favicon.ico'
-html_last_updated_fmt = '%b %d, %Y'
+html_favicon = "_static/favicon.ico"
+html_last_updated_fmt = "%b %d, %Y"
 
-html_index = 'index.html'
+html_index = "index.html"
 
-generic_sidebars = ['toolbox.html', 'releasenotes.html', 'howtocite.html']
-html_sidebars = {'**': generic_sidebars}
+generic_sidebars = ["toolbox.html", "releasenotes.html", "howtocite.html"]
+html_sidebars = {"**": generic_sidebars}
 
 html_copy_source = False
 html_show_sourcelink = False
@@ -104,61 +111,57 @@
 html_show_copyright = True
 
 extlinks = {
-    'issue': ('https://github.com/prody/ProDy/issues/%s', 'issue '),
-    'pdb': ('http://www.pdb.org/pdb/explore/explore.do?structureId=%s', ''),
-    'wiki': ('http://en.wikipedia.org/wiki/%s', ''),
-    'pfam': ('http://pfam.xfam.org/family/%s', ''),
-    'pfamprotein': ('http://pfam.xfam.org/protein/%s', ''),
-    'uniprot': ('http://www.uniprot.org/uniprot/%s', ''),
-    'pdbhet': ('http://www.pdb.org/pdb/ligand/ligandsummary.do?hetId=%s', ''),
+    "issue": ("https://github.com/prody/ProDy/issues/%s", "issue "),
+    "pdb": ("http://www.pdb.org/pdb/explore/explore.do?structureId=%s", ""),
+    "wiki": ("http://en.wikipedia.org/wiki/%s", ""),
+    "pfam": ("http://pfam.xfam.org/family/%s", ""),
+    "pfamprotein": ("http://pfam.xfam.org/protein/%s", ""),
+    "uniprot": ("http://www.uniprot.org/uniprot/%s", ""),
+    "pdbhet": ("http://www.pdb.org/pdb/ligand/ligandsummary.do?hetId=%s", ""),
 }
 
 
 # ipython directive configuration
-ipython_savefig_dir = os.path.join('_static', 'figures')
+ipython_savefig_dir = os.path.join("_static", "figures")
 
 
 # -- Options for LaTeX output --------------------------------------------------
-latex_paper_size = 'letter'
-latex_font_size = '10pt'
+latex_paper_size = "letter"
+latex_font_size = "10pt"
 
-latex_documents = [
-    ('index', 'ProDy.tex',
-     u'ProDy Documentation',
-     u'Ahmet Bakan', 'manual')
-]
+latex_documents = [("index", "ProDy.tex", u"ProDy Documentation", u"Ahmet Bakan", "manual")]
 
-latex_logo = '_static/logo.png'
+latex_logo = "_static/logo.png"
 
 latex_show_pagerefs = True
-latex_show_urls = 'footnote'
+latex_show_urls = "footnote"
 
-latex_preamble = ''
+latex_preamble = ""
 latex_appendices = []
 
 latex_domain_indices = True
 
 latex_elements = {
-    'classoptions': ',openany,oneside',
-    'fontpkg': '\\usepackage{palatino}',
-    'babel': '\\usepackage[english]{babel}'
+    "classoptions": ",openany,oneside",
+    "fontpkg": "\\usepackage{palatino}",
+    "babel": "\\usepackage[english]{babel}",
 }
 
 
-autodoc_member_order = 'groupwise'
+autodoc_member_order = "groupwise"
 autodoc_default_flags = []
-autoclass_content = 'both'
+autoclass_content = "both"
 todo_include_todos = True
 
 googleanalytics_enabled = True
-googleanalytics_id = 'UA-19801227-1'
+googleanalytics_id = "UA-19801227-1"
 
 intersphinx_mapping = {
-    'python': ('http://docs.python.org/', None),
-    'numpy': ('http://docs.scipy.org/doc/numpy/', None),
-    'scipy': ('http://docs.scipy.org/doc/scipy/reference/', None),
-    'matplotlib': ('http://matplotlib.sourceforge.net/', None),
-    'prodywebsite': ('http://prody.csb.pitt.edu/', None),
+    "python": ("http://docs.python.org/", None),
+    "numpy": ("http://docs.scipy.org/doc/numpy/", None),
+    "scipy": ("http://docs.scipy.org/doc/scipy/reference/", None),
+    "matplotlib": ("http://matplotlib.sourceforge.net/", None),
+    "prodywebsite": ("http://prody.csb.pitt.edu/", None),
 }
 
 rst_epilog = u"""

prody/database/__init__.py

@@ -70,31 +70,37 @@
 
 .. _GOA: https://www.ebi.ac.uk/GOA/
 
+Swiss-Prot
+================================
+
+The following classes and functions can be used to search and retrieve data from the Swiss-Prot database:
+
+  * :class:`.SwissProt` - class to handle Swiss-Prot data from Expasy
+  * :func:`.getCurrentRelease` - gets current Swiss-Prot release version
+  * :func:`.downloadRelease` - downloads current Swiss-Prot database files
+  * :func:`.saveRelease` - saves new Swiss-Prot release version
+  * :func:`.updateRelease` - updates Swiss-Prot local database
+  * :func:`.getLocalRelease` - checks local Swiss-Prot release version
+  * :func:`.checkForUpdates` - checks wheather there is newer Swiss-Prot version than current local one
 
+.. _GOA: https://www.ebi.ac.uk/GOA/
 """
 
-__all__ = []
 
-from . import pfam
+from . import cath, dali, goa, pfam, quartataweb, swissprot, uniprot
+from .cath import *
+from .dali import *
+from .goa import *
 from .pfam import *
-__all__.extend(pfam.__all__)
-
-from . import uniprot
+from .quartataweb import *
+from .swissprot import *
 from .uniprot import *
-__all__.extend(uniprot.__all__)
 
-from . import cath
-from .cath import *
+__all__ = []
+__all__.extend(pfam.__all__)
+__all__.extend(uniprot.__all__)
 __all__.extend(cath.__all__)
-
-from . import dali
-from .dali import *
 __all__.extend(dali.__all__)
-
-from . import goa
-from .goa import *
 __all__.extend(goa.__all__)
-
-from . import quartataweb
-from .quartataweb import *
 __all__.extend(quartataweb.__all__)
+__all__.extend(swissprot.__all__)