fixed docs for PDBParser "conect" keyword (#1329)

- fixes #1246
- supercedes and closes PR #1279 by @Shtkddud123
- added @Shtkddud123 to AUTHORS
- updated CHANGELOG

package/AUTHORS

@@ -87,6 +87,7 @@ Chronological list of authors
   - Akshay Gupta
   - Juan Eiros Zamora
   - Jon Kapla
+  - Sang Young Noh
 
 External code
 -------------

package/CHANGELOG

@@ -15,7 +15,7 @@ The rules for this file:
 ------------------------------------------------------------------------------
 
 mm/dd/17 utkbansal, kain88-de, xiki-tempula, kaplajon, wouterboomsma,
-         richardjgowers
+         richardjgowers, Shtkddud123
 
   * 0.16.1
 
@@ -36,6 +36,7 @@ Fixes
     module.
   * Fix hbond_analysis cannot deal with Universe where no two atoms are with 3A.
     (PR #1325)
+  * Fix PDBParser docs for conect (issue #1246)
 
 Changes
   * Enable various pylint warnings to increase python 3 compatibility

package/MDAnalysis/coordinates/PDB.py

@@ -505,31 +505,32 @@ def __init__(self, filename, bonds="conect", n_atoms=None, start=0, step=1,
                  convert_units=None, multiframe=None):
         """Create a new PDBWriter
 
-        :Arguments:
-         *filename*
+        Parameters
+        ----------
+        filename: str
            name of output file
-         *start*
+        start: int (optional)
            starting timestep
-         *step*
+        step: int (optional)
            skip between subsequent timesteps
-         *remarks*
-           comments to annotate pdb file (added to the TITLE record); note that
+        remarks: str (optional)
+           comments to annotate pdb file (added to the *TITLE* record); note that
            any remarks from the trajectory that serves as input are
            written to REMARK records with lines longer than :attr:`remark_max_length` (66
            characters) being wrapped.
-         *convert_units*
+        convert_units: str (optional)
            units are converted to the MDAnalysis base format; ``None`` selects
            the value of :data:`MDAnalysis.core.flags` ['convert_lengths']
-         *bonds*
-           write bonds to the PDB file as CONECT_ records [``False``]
-         *multiframe*
+        bonds : {"conect", "all", None} (optional)
+           If set to "conect", then only write those bonds that were already
+           defined in an input PDB file as PDB CONECT_ record. If set to "all",
+           write all bonds (including guessed ones) to the file. ``None`` does
+           not write any bonds. The default is "conect".
+        multiframe: bool (optional)
            ``False``: write a single frame to the file; ``True``: create a
            multi frame PDB file in which frames are written as MODEL_ ... ENDMDL_
            records. If ``None``, then the class default is chosen.    [``None``]
 
-        .. _CONECT: http://www.wwpdb.org/documentation/format32/sect10.html#CONECT
-        .. _MODEL: http://www.wwpdb.org/documentation/format32/sect9.html#MODEL
-        .. _ENDMDL: http://www.wwpdb.org/documentation/format32/sect9.html#ENDMDL
 
         Note
         ----
@@ -540,6 +541,11 @@ def __init__(self, filename, bonds="conect", n_atoms=None, start=0, step=1,
         atoms in the new PDB file and therefore a :exc:`NotImplementedError` is
         raised.)
 
+
+        .. _CONECT: http://www.wwpdb.org/documentation/format32/sect10.html#CONECT
+        .. _MODEL: http://www.wwpdb.org/documentation/format32/sect9.html#MODEL
+        .. _ENDMDL: http://www.wwpdb.org/documentation/format32/sect9.html#ENDMDL
+
         """
         # n_atoms = None : dummy keyword argument
         # (not used, but Writer() always provides n_atoms as the second argument)