new dev version

biopandas/__init__.py

@@ -4,5 +4,5 @@
 # Project Website: http://rasbt.github.io/biopandas/
 # Code Repository: https://github.com/rasbt/biopandas
 
-__version__ = '0.2.1'
+__version__ = '0.2.2dev'
 __author__ = "Sebastian Raschka <mail@sebastianraschka.com>"

docs/sources/CHANGELOG.md

@@ -3,6 +3,24 @@
 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).
 
+### 0.2.2dev (TBD)
+
+##### Downloads
+
+- [Source code (zip)](https://github.com/rasbt/biopandas/archive/v0.2.2.zip)
+- [Source code (tar.gz)](https://github.com/rasbt/biopandas/archive/v0.2.2.tar.gz)
+
+##### New Features
+
+- -
+
+##### Changes
+
+-  Add meaningful error message if attempting to overwrite the `df` attributes of `PandasMol2` and `PandasPdb` directly.
+
+##### Bug Fixes
+
+
 ### 0.2.1  (2017-05-11)
 
 ##### Downloads
@@ -18,7 +36,7 @@ The CHANGELOG for the current development version is available at
 
 - The `amino3to1` method of `biopandas.pdb.PandasPDB` objects now returns a pandas `DataFrame` instead of a pandas `Series` object. The returned data frame has two columns, `'chain_id'` and `'residue_name'`, where the former contains the chain ID of the amino acid and the latter contains the 1-letter amino acid code, respectively.
 -  Significant speed improvements of the `distance` method of both `PandasPdb` and `PandasMol2` (now about 300 percent faster than previously).
--  Add meaningful error message if attempting to overwrite the `df` attributes of `PandasMol2` and `PandasPdb` directly.
+
 
 ##### Bug Fixes
 

paper.md

@@ -0,0 +1,37 @@
+---
+title: 'BioPandas: Working with molecular structures in pandas DataFrames'
+tags:
+  - bioinformatics
+  - computational biology
+  - protein structure analysis
+  - protein-ligand docking
+  - virtual screening
+authors:
+ - name: Sebastian Raschka
+   orcid: 0000-0001-6989-4493
+   affiliation: 1
+affiliations:
+ - name: Michigan State University, East-Lansing, USA
+   index: 1
+date: 31 May 2017
+---
+
+
+
+# Summary
+
+BioPandas is a Python library that reads molecular structures from 3D-coordinate files, such as PDB (Bernstein *and others* 1977) and MOL2, into pandas DataFrames (McKinney 2010) for convenient data analysis and data mining related tasks.
+
+In addition to parsing protein and small molecule data into a data frame format, BioPandas provides additional utility functions for structure analysis. These functions include common computations such as computing the root-mean-squared-deviation between structures and converting protein structures into primary amino acid sequence formats. 
+
+Furthermore, useful small-molecule related functions are provided for reading and parsing millions of small molecule structures (from multi-MOL2 files) fast and efficiently in virtual screening applications. Inbuilt functions for filtering molecules by the presence of functional groups and their pair-wise distances to each other make BioPandas a particularly attractive utility library for virtual screening and protein-ligand docking applications.
+
+
+# References
+
+**McKinney, Wes** (2010). Data structures for statistical computing in Pyt
+hon. *Proceedings of the 9th Python in Science Conference. Vol. 445.* 
+
+**Bernstein, Frances C., Thomas F. Koetzle, Graheme JB Williams, Edgar F. Meyer, Michael D. Brice, John R. Rodgers, Olga Kennard, Takehiko Shimanouchi, and Mitsuo Tasumi** (1977). The Protein Data Bank. *European Journal of Biochemistry 80, no. 2: 319-324.*
+
+**Tripos, L.** (2007). Tripos Mol2 File Format. *St. Louis, MO: Tripos.*