biopandas version: 0.2.5

PandasMol2

PandasMol2()

Object for working with Tripos Mol2 structure files.

Attributes

Methods


distance(xyz=(0.0, 0.0, 0.0))

Computes Euclidean distance between atoms in self.df and a 3D point.

Parameters

Returns


distance_df(df, xyz=(0.0, 0.0, 0.0))

Computes Euclidean distance between atoms and a 3D point.

Parameters

Returns


read_mol2(path, columns=None)

Reads Mol2 files (unzipped or gzipped) from local drive

Note that if your mol2 file contains more than one molecule,
only the first molecule is loaded into the DataFrame

Attributes

Returns

self


read_mol2_from_list(mol2_lines, mol2_code, columns=None)

Reads Mol2 file from a list into DataFrames

Attributes

Returns

self


rmsd(df1, df2, heavy_only=True)

Compute the Root Mean Square Deviation between molecules

Parameters

Returns

Properties


df

Acccesses the pandas DataFrame

split_multimol2

split_multimol2(mol2_path)

Splits a multi-mol2 file into individual Mol2 file contents.

Parameters

Returns

A generator object for lists for every extracted mol2-file. Lists contain the molecule ID and the mol2 file contents. e.g., ['ID1234', ['@MOLECULE\n', '...']]. Note that bytestrings are returned (for reasons of efficieny) if the Mol2 content is read from a gzip (.gz) file.