Bot releases are visible (Hide)
Published by a-r-j about 1 year ago
add_remark
for PandasPdb
by @anton-bushuiev in https://github.com/BioPandas/biopandas/pull/129
Full Changelog: https://github.com/BioPandas/biopandas/compare/v0.4.1...v0.5.0dev
add_remark
for PandasPdb
by @anton-bushuiev in https://github.com/BioPandas/biopandas/pull/129
Full Changelog: https://github.com/BioPandas/biopandas/compare/v0.4.1...v0.5.0dev
Published by rasbt over 2 years ago
Remove walrus operator for Python 3.7 compatibility.
Published by rasbt over 2 years ago
Adds support for extracting structures from PDB files containing multiple models. See the documentation for details. (via Arian Jamasb, PR #101).
Adds support for fetching mmCIF (PandasMmcif().fetch_mmcif(uniprot_id='Q5VSL9', source='alphafold2-v2')
) and PDB structures (e.g., PandasPdb().fetch_pdb(uniprot_id='Q5VSL9', source="alphafold2-v2")
) (via Arian Jamasb, PR #102).
Published by rasbt over 2 years ago
Published by rasbt about 3 years ago
Published by rasbt over 3 years ago
PandasPdb.read_pdb_from_list
method was added analogous to the existing PandasMol2.read_mol2_from_list
(via PR 72 by dominiquesydow)ValueError
raising and improved file format error messages for read_pdb
and read_mol2
functionality. (via PR 73 by dominiquesydow)None
Published by rasbt about 4 years ago
Published by rasbt about 4 years ago
https
queries for the RCSB server via the fetch_pdb
function.Published by rasbt about 4 years ago
PandasPdb.amino3to1
method now also considers insertion codes when converting the amino acid codes; before, inserted amino acides were skipped.Published by rasbt over 5 years ago
Published by rasbt over 6 years ago
PandasMol2.distance_df
was added as a static method that allows distance computations based for external data frames with its behavior otherwise similar to PandasMol2.distance
.PandasPdb.distance_df
was added as a static method that allows distance computations based for external data frames with its behavior otherwise similar to PandasPdb.distance
.PandasPdb.distance
now supports multiple record sections to be considered (e.g., records=('ATOM', 'HETATM')
to include both protein and ligand in a query. Now also defaults to records=('ATOM', 'HETATM')
for concistency with the impute method.PandasPdb.get(...)
now supports external data frames and lets the user specify the record section to be considered (e.g., records=('ATOM', 'HETATM')
to include both protein and ligand in a query. Now also defaults to records=('ATOM', 'HETATM')
for concistency with the impute method.section
parameter of PandasPdb.impute_element(...)
was renamed to records
for API consistency.Published by rasbt over 7 years ago
df
attributes of PandasMol2
and PandasPdb
directly.PandasPdb.pdb_path
and PandasMol2.mol2_path
attributes that store the location of the data file last read.rmsd
methods of PandasMol2
and PandasPdb
don't return a NaN anymore if the array indices of to structures are different.Published by rasbt over 7 years ago
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.distance
method of both PandasPdb
and PandasMol2
(now about 300 percent faster than previously).amino3to1
method of biopandas.pdb.PandasPDB
objects now handles multi-chain proteins correctly.amino3to1
method of biopandas.pdb.PandasPDB
objects now also works as expected if the 'ATOM'
entry DataFrame contains disordered DataFrame indices or duplicate DataFrame index values.Published by rasbt over 7 years ago
amino3to1
method to PandasPdb
data frames to convert 3-amino acid letter codes to 1-letter codes.distance
method to PandasPdb
data frames to compute the Euclidean distance between atoms and a reference point.PandasMol2
class for working with Tripos MOL2 files in pandas DataFrames.PandasPDB
was renamed to PandasPdb
.PandasPdb
is written to PDB and ATOM and HETAM section contains unexpected columns; these columns will now be skipped.Published by rasbt almost 8 years ago
impute_element
method to PandasPDB
objects to infer the Element Symbol from the Atom Name columnPandasPDB
ATOM and HETATM coordinate sections: 'heavy'
and 'carbon'
'hydrogen'
atom selection in PandasPDB
methods is now based on the element type instead of the atom namePublished by rasbt almost 8 years ago
DataFrame.sort
vs DataFrame.sort_values
) incl. DeprecationWarning