diff --git a/biopandas/__init__.py b/biopandas/__init__.py index 2431007..5aeb1ea 100644 --- a/biopandas/__init__.py +++ b/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 " diff --git a/docs/sources/CHANGELOG.md b/docs/sources/CHANGELOG.md index 72cecb2..62ecbc0 100755 --- a/docs/sources/CHANGELOG.md +++ b/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 diff --git a/files.txt b/files.txt deleted file mode 100644 index b88beeb..0000000 --- a/files.txt +++ /dev/null @@ -1 +0,0 @@ -/Users/Sebastian/miniconda3/lib/python3.5/site-packages/biopandas-0.1.5-py3.5.egg diff --git a/paper.md b/paper.md new file mode 100644 index 0000000..267fa4e --- /dev/null +++ b/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.*