Merge pull request #50 from fsimkovic/master

Update docs primarily
rigdenlab · Jul 30, 2018 · 6a6bc7c · 6a6bc7c
2 parents 2e8b7a9 + 8487874
commit 6a6bc7c
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diff --git a/CHANGELOG.rst b/CHANGELOG.rst
@@ -35,6 +35,7 @@ Changed
 - ``Contact.is_match`` and ``Contact.define_match`` renamed to attribute ``Contact.true_positive``
 - ``Contact.is_mismatch`` and ``Contact.define_mismatch`` renamed to attribute ``Contact.false_positive``
 - ``Contact.is_unknown`` and ``Contact.define_unknown`` renamed to attribute ``Contact.status_unknown``
+- ``Entity``, ``Gap`` and ``Residue`` classes made public
 Fixed
 ~~~~~
 - Bug fix in ``SequenceFile.filter`` to remove ``Sequence`` entries reliably

diff --git a/conkit/__init__.py b/conkit/__init__.py
@@ -27,7 +27,6 @@
 # CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY,
 # OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE
 # OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
-
 """
 ConKit is a Python interface for handling and manipulating
 contact predictions obtained from a variety of different 
@@ -37,6 +36,6 @@
 import conkit.version
 
 __author__ = "Felix Simkovic"
-__contributing_authors__ = "Jens Thomas"
+__contributing_authors__ = "Jens Thomas & Adam Simpkin"
 __credits__ = "Stefan Seemayer"
 __version__ = conkit.version.__version__
diff --git a/conkit/applications/bbcontacts.py b/conkit/applications/bbcontacts.py
@@ -71,13 +71,12 @@ class BbcontactsCommandline(AbstractCommandline):
     bbcontacts
 
     You would typically run the command line with :func:`bbcontacts_cline` or via
-    the Python subprocess module.
+    the :mod:`~subprocess` module.
 
-    Notes
-    -----
-    In order to use bbcontacts, head over to the `GitHub repository
-    <https://github.com/soedinglab/bbcontacts>`_, download the latest version
-    and install it using python setup.py install.
+    Note
+    ----
+    Installation instructions are available via the `GitHub repository 
+    <https://github.com/soedinglab/bbcontacts>`_.
 
     """
 
@@ -92,46 +91,32 @@ def __init__(self, cmd="bbcontacts", **kwargs):
             raise RuntimeError(msg)
 
         self.parameters = [
-            _Option(['-c', 'config_file'],
-                    'bbcontacts configuration file',
-                    filename=True,
-                    equate=False),
-            _Option(['-s', 'smoothing_size'],
-                    'Perform local background correction of the coupling matrix '
-                    'before decoding: from each coupling, subtract the average '
-                    'coupling (smoothed background) over an area extending by '
-                    'SMOOTHINGSIZE in each direction [default=10, use 0 for no '
-                    'local background correction]',
-                    equate=False),
-            _Switch(['-l', 'long_predictions'],
-                    'Turn off (slow) prediction-shortening mode (this mode is on '
+            _Option(['-c', 'config_file'], 'bbcontacts configuration file', filename=True, equate=False),
+            _Option(
+                ['-s', 'smoothing_size'],
+                'Perform local background correction of the coupling matrix '
+                'before decoding: from each coupling, subtract the average '
+                'coupling (smoothed background) over an area extending by '
+                'SMOOTHINGSIZE in each direction [default=10, use 0 for no '
+                'local background correction]',
+                equate=False),
+            _Switch(['-l', 'long_predictions'], 'Turn off (slow) prediction-shortening mode (this mode is on '
                     'by default but will only get triggered when long predictions occur)'),
-            _Option(['-n', 'pdb_name'],
-                    'Provide a PDB identifier (when also using -e, this will be the '
-                    'PDB name to look for in EVALUATIONFILE)',
-                    equate=False),
-            _Option(['-e', 'evaluation_file'],
-                    'Provide a file containing the true contacts (BetaSheet916.dat, '
-                    'BetaSheet1452.dat or same format) for evaluation',
-                    filename=True,
-                    equate=False),
-            _Argument(['matfile'],
-                      'CCMpred-like coupling matrix',
-                      filename=True,
-                      is_required=True),
-            _Argument(['diversity_score'],
-                       'sequence-dependent diversity score',
-                       is_required=True),
-            _Argument(['prefix'],
-                       'output prefix',
-                       is_required=True),
-            _Option(['-d', 'dssp_file'],
-                    'DSSP secondary structure prediction file',
-                    filename=True,
-                    equate=False),
-            _Option(['-p', 'psipred_file'],
-                    'PSIPRED secondary structure prediction file',
-                    filename=True,
-                    equate=False),
+            _Option(
+                ['-n', 'pdb_name'],
+                'Provide a PDB identifier (when also using -e, this will be the '
+                'PDB name to look for in EVALUATIONFILE)',
+                equate=False),
+            _Option(
+                ['-e', 'evaluation_file'],
+                'Provide a file containing the true contacts (BetaSheet916.dat, '
+                'BetaSheet1452.dat or same format) for evaluation',
+                filename=True,
+                equate=False),
+            _Argument(['matfile'], 'CCMpred-like coupling matrix', filename=True, is_required=True),
+            _Argument(['diversity_score'], 'sequence-dependent diversity score', is_required=True),
+            _Argument(['prefix'], 'output prefix', is_required=True),
+            _Option(['-d', 'dssp_file'], 'DSSP secondary structure prediction file', filename=True, equate=False),
+            _Option(['-p', 'psipred_file'], 'PSIPRED secondary structure prediction file', filename=True, equate=False),
         ]
         AbstractCommandline.__init__(self, cmd, **kwargs)
diff --git a/conkit/applications/ccmpred.py b/conkit/applications/ccmpred.py
@@ -70,54 +70,36 @@ class CCMpredCommandline(AbstractCommandline):
     ccmpred test.aln output.mat
 
     You would typically run the command line with :func:`ccmpred_cline` or via
-    the Python subprocess module.
+    the :mod:`~subprocess` module.
 
     """
-    
+
     def __init__(self, cmd="ccmpred", **kwargs):
         self.parameters = [
-            _Option(['-n', "numiter"],
-                    'Compute a maximum of NUMITER operations [default: 50]',
-                    equate=False),
-            _Option(['-e', 'epsilon'],
-                    "Set convergence criterion for minimum decrease in the "
-                    "last K iterations to EPSILON [default: 0.01]",
-                    equate=False),
-            _Option(['-k', 'lastk'],
-                    "Set K parameter for convergence criterion to LASTK [default: 5]",
-                    equate=False),
-
-            _Option(['-i', 'inifile'],
-                    "Read initial weights from INIFILE",
-                    filename=True,
-                    equate=False),
-            _Option(['-r', 'rawfile'],
-                    "Store raw prediction matrix in RAWFILE",
-                    filename=True,
-                    equate=False),
-            _Option(['-t', 'threads'],
-                    'Calculate using THREADS threads on the CPU (automatically disables CUDA if available) [default: 1]',
-                    equate=False),
-
-            _Option(['-w', 'idthres'],
-                     "Set sequence reweighting identity threshold to IDTHRES [default: 0.8]",
-                     equate=False),
-            _Option(['-l', 'lfactor'],
-                     "Set pairwise regularization coefficients to LFACTOR * (L-1) [default: 0.2]",
-                     equate=False),
-
-            _Switch(['-A', 'apc'],
-                    "Disable average product correction (APC)"),
-            _Switch(['-R', 'renormalize'],
-                     "Re-normalize output matrix to [0,1]"),
-
-            _Argument(['alnfile'],
-                      "Input alignment file [JONES format]",
-                      filename=True,
-                      is_required=True),
-            _Argument(['matfile'],
-                       "Output matrix file",
-                       filename=True,
-                       is_required=True),
+            _Option(['-n', "numiter"], 'Compute a maximum of NUMITER operations [default: 50]', equate=False),
+            _Option(
+                ['-e', 'epsilon'],
+                "Set convergence criterion for minimum decrease in the "
+                "last K iterations to EPSILON [default: 0.01]",
+                equate=False),
+            _Option(['-k', 'lastk'], "Set K parameter for convergence criterion to LASTK [default: 5]", equate=False),
+            _Option(['-i', 'inifile'], "Read initial weights from INIFILE", filename=True, equate=False),
+            _Option(['-r', 'rawfile'], "Store raw prediction matrix in RAWFILE", filename=True, equate=False),
+            _Option(
+                ['-t', 'threads'],
+                'Calculate using THREADS threads on the CPU (automatically disables CUDA if available) [default: 1]',
+                equate=False),
+            _Option(
+                ['-w', 'idthres'],
+                "Set sequence reweighting identity threshold to IDTHRES [default: 0.8]",
+                equate=False),
+            _Option(
+                ['-l', 'lfactor'],
+                "Set pairwise regularization coefficients to LFACTOR * (L-1) [default: 0.2]",
+                equate=False),
+            _Switch(['-A', 'apc'], "Disable average product correction (APC)"),
+            _Switch(['-R', 'renormalize'], "Re-normalize output matrix to [0,1]"),
+            _Argument(['alnfile'], "Input alignment file [JONES format]", filename=True, is_required=True),
+            _Argument(['matfile'], "Output matrix file", filename=True, is_required=True),
         ]
         AbstractCommandline.__init__(self, cmd, **kwargs)