v0.7.5

MolDf v0.7.5

To install this version

pip install moldf -U

New features

• Added write_jcsv function. Any dict of Pandas Frames can be writen to the JCSV format.
• Added read_jcsv function. The JCSV files written by the above write_jcsv function can be read into dicts of DataFrames.
• The above two close #20.

Fixes

• get_residue_template now returns both (A, B) and (B, A) for A-B bonding information.
• For mmcif, columns of the _atom_site category but not in the provided file are skipped in building PDBDataFrame.
• label_entity_id is char in mmcif specification.
• The newline character in windows os is respected like in CSV and Pandas.

v0.7.4

PyPI wheel

v0.7.3

To install this version

pip install moldf

Fixes

• The covalent_bonds folder is now included in the PyPI dist so that the get_bonds_by_distance method is usable if the package is pip-installed.

• Covalent bonds between hetero ligands and normal residues are included as well.

Break changes

• The internal helper function get_covalent_radii is replaced by the get_covalent_bond_cutoffs function so that the code is cleaner and more maintainable.

v0.7.2

Fixes

v0.7.1

MolDf v0.7.1

To install this version

pip install moldf

New features

• Added covalent bonding information through get_bonds_by_distance and get_bonds_by_template methods, and bonds property to the PDBDataFrame class. The first method simply uses distance cutoffs to identify bonds, similar to many methods to build molecular graphs. The second method takes advantage of the fact that all residues and ligands in RCSB PDB files have template files, so that we can use those template files to accurately identify covalent bonds intra- residue/ligand atom. However, for covalent bonds between residues/ligands, we still have to use the distance cutoff method.

v0.6.7

pdbx2df v0.6.7

Last version under the name pdbx2df. Now it is renamed as MolDF.

Future installation by pip install pdbx2df will install moldf as well.

Fixes

• Fixed the problem that PDBDataFrame .atoms failed for PDBx DataFrame.

v0.6.6

pdbx2df v0.6.6

From this version on, changelog is kept for each new version, compared to the previous version.

New features

• Parsing mol2 file header lines starting with # in read_mol2.
• radius_of_gyration can be accessed as a property in PDBDataFrame.
• rmsd method added in PDBDataFrame.
• Can feed PDBDataFrame with the PDBx _atom_site DataFrame now.

Fixes

• Corrected center_of_mass calculation in PDBDataFrame.

Docs

• Cleaned up empty lines in all function and method's docstrings.
• Added a quick start section for calculating RMSD, radius of gyration, and distance matrix.

v0.6.4

Improved docs; API documentation works on RTD now; minor bug fixed fo…

…r read_mol2

v0.6.3

Bug fixes for PDBDataFrame; docs in RTD now.