0.2 release

BioPandas · Apr 2, 2017 · 4216adf · 4216adf
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diff --git a/docs/mkdocs.yml b/docs/mkdocs.yml
@@ -31,6 +31,7 @@ pages:
 - Home: index.md
 - Tutorials:
   - tutorials/Working_with_PDB_Structures_in_DataFrames.md
+  - tutorials/Working_with_MOL2_Structures_in_DataFrames.md
 - API:
   - api_subpackages/biopandas.pdb.md
   - api_subpackages/biopandas.mol2.md

diff --git a/docs/sources/CHANGELOG.md b/docs/sources/CHANGELOG.md
@@ -1,20 +1,25 @@
 # Release Notes ![](img/logos/3eiy_120.png)
 
-### 0.2.0dev
+The CHANGELOG for the current development version is available at
+[https://github.com/rasbt/biopandas/blob/master/docs/sources/CHANGELOG.md](https://github.com/rasbt/biopandas/blob/master/docs/sources/CHANGELOG.md).
+
+### 0.2.0 (2017-04-02)
 
 ##### Downloads
 
-- -
+- [Source code (zip)](https://github.com/rasbt/biopandas/releases/tag/v0.2.0)
+- [Source code (tar.gz)](https://github.com/rasbt/biopandas/releases/tag/v0.2.0.tar.gz)
 
 ##### New Features
 
 - Added an `amino3to1` method to `PandasPdb` data frames to convert 3-amino acid letter codes to 1-letter codes.
 - Added a `distance` method to `PandasPdb` data frames to compute the Euclidean distance between atoms and a reference point.
-- Added the `PandasMol2` class for working with Tripos MOL2 files in pandas DataFrames
+- Added the `PandasMol2` class for working with Tripos MOL2 files in pandas DataFrames.
 
 
 ##### Changes
 
+- `PandasPDB` was renamed to `PandasPdb`.
 - Raises a warning if `PandasPdb` is written to PDB and ATOM and HETAM section contains unexpected columns; these columns will now be skipped.
 
 ##### Bug Fixes
@@ -31,13 +36,13 @@
 
 ##### New Features
 
-- Added an `impute_element` method to `PandasPdb` objects to infer the Element Symbol from the Atom Name column.
-- Added two new selection types for `PandasPdb` ATOM and HETATM coordinate sections: `'heavy'` and `'carbon'`.
+- Added an `impute_element` method to `PandasPDB` objects to infer the Element Symbol from the Atom Name column.
+- Added two new selection types for `PandasPDB` ATOM and HETATM coordinate sections: `'heavy'` and `'carbon'`.
 
 ##### Changes
 
 - Include test data in the PyPI package; add install_requires for pandas.
-- The `'hydrogen'` atom selection in `PandasPdb` methods is now based on the element type instead of the atom name.
+- The `'hydrogen'` atom selection in `PandasPDB` methods is now based on the element type instead of the atom name.
 - By default, the RMSD is now computed on all atoms unless a specific selection is defined.
 
 ##### Bug Fixes

diff --git a/docs/sources/api_subpackages/biopandas.mol2.md b/docs/sources/api_subpackages/biopandas.mol2.md
@@ -1,4 +1,4 @@
-biopandas version: 0.2.0.dev0
+biopandas version: 0.2.0
 ## PandasMol2
 
 *PandasMol2()*
@@ -21,9 +21,26 @@ Object for working with Tripos Mol2 structure files.
 
     ID, code, or name of the molecule stored
 
+### Methods
+
+<hr>
 
+*distance(xyz=(0.0, 0.0, 0.0))*
 
-### Methods
+Computes Euclidean distance between atoms and a 3D point.
+
+**Parameters**
+
+- `xyz` : tuple (0.00, 0.00, 0.00)
+
+    X, Y, and Z coordinate of the reference center for the distance
+    computation
+
+**Returns**
+
+- `pandas.Series` : Pandas Series object containing the Euclidean
+
+    distance between the atoms in the atom section and `xyz`.
 
 <hr>
 
@@ -71,24 +88,15 @@ Reads Mol2 file from a list into DataFrames
 - `mol2_lines` : list
 
     A list of lines containing the mol2 file contents. For example,
-    ['@<TRIPOS>MOLECULE
-    ',
-    'ZINC38611810
-    ',
-    '   65    68     0     0     0
-    ',
-    'SMALL
-    ',
-    'NO_CHARGES
-    ',
-    '
-    ',
-    '@<TRIPOS>ATOM
-    ',
-    '      1 C1  -1.1786  2.7011  -4.0323 C.3  1 <0>   -0.1537
-    ',
-    '      2 C2  -1.2950  1.2442  -3.5798 C.3  1 <0>   -0.1156
-    ',
+    ['@<TRIPOS>MOLECULE\n',
+    'ZINC38611810\n',
+    '   65    68     0     0     0\n',
+    'SMALL\n',
+    'NO_CHARGES\n',
+    '\n',
+    '@<TRIPOS>ATOM\n',
+    '      1 C1  -1.1786  2.7011  -4.0323 C.3  1 <0>   -0.1537\n',
+    '      2 C2  -1.2950  1.2442  -3.5798 C.3  1 <0>   -0.1156\n',
     ...]
 
 
@@ -114,8 +122,6 @@ Reads Mol2 file from a list into DataFrames
 
 self
 
-
-
 <hr>
 
 *rmsd(df1, df2, heavy_only=True)*
@@ -169,10 +175,7 @@ Splits a multi-mol2 file into individual Mol2 file contents.
 
 A generator object for lists for every extracted mol2-file. Lists contain
     the molecule ID and the mol2 file contents.
-    e.g., ['ID1234', ['@<TRIPOS>MOLECULE
-    ', '...']]. Note that bytestrings
+    e.g., ['ID1234', ['@<TRIPOS>MOLECULE\n', '...']]. Note that bytestrings
     are returned (for reasons of efficieny) if the Mol2 content is read
     from a gzip (.gz) file.
 
-
-
diff --git a/docs/sources/api_subpackages/biopandas.pdb.md b/docs/sources/api_subpackages/biopandas.pdb.md
@@ -1,4 +1,4 @@
-biopandas version: 0.2.0.dev0
+biopandas version: 0.2.0
 ## PandasPdb
 
 *PandasPdb()*
@@ -137,13 +137,13 @@ Filter PDB DataFrames by properties
 
 <hr>
 
-*impute_element(sections=['ATOM', 'HETATM'], inplace=False)*
+*impute_element(sections=('ATOM', 'HETATM'), inplace=False)*
 
 Impute element_symbol from atom_name section.
 
 **Parameters**
 
-- `sections` : iterable (default: ['ATOM', 'HETATM'])
+- `sections` : iterable (default: ('ATOM', 'HETATM'))
 
     Coordinate sections for which the element symbols should be
     imputed.

diff --git a/docs/sources/api_subpackages/biopandas.testutils.md b/docs/sources/api_subpackages/biopandas.testutils.md
@@ -1 +1 @@
-biopandas version: 0.2.0.dev0
+biopandas version: 0.2.0