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Drop pandas requirement #180

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merged 1 commit into from
Mar 4, 2021
Merged

Drop pandas requirement #180

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10 changes: 4 additions & 6 deletions pdb2pqr/main.py
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Original file line number Diff line number Diff line change
Expand Up @@ -12,7 +12,6 @@
from tempfile import NamedTemporaryFile
from pathlib import Path
from math import isclose
import pandas
import propka.lib
import propka.output as pk_out
import propka.input as pk_in
Expand Down Expand Up @@ -497,8 +496,8 @@ def run_propka(args, biomolecule):
:type args: argparse.Namespace
:param biomolecule: biomolecule object
:type biomolecule: Biomolecule
:return: (DataFrame of assigned pKa values, pKa information from PROPKA)
:rtype: (pandas.DataFrame, str)
:return: (DataFrame-convertible table of assigned pKa values, pKa information from PROPKA)
:rtype: (list, str)
"""
# TODO - eliminate need to write temporary file
lines = io.print_biomolecule_atoms(
Expand Down Expand Up @@ -561,8 +560,7 @@ def run_propka(args, biomolecule):
else:
row_dict["coupled_group"] = None
rows.append(row_dict)
df = pandas.DataFrame(rows)
return df, pka_str
return rows, pka_str


def non_trivial(args, biomolecule, ligand, definition, is_cif):
Expand Down Expand Up @@ -621,7 +619,7 @@ def non_trivial(args, biomolecule, ligand, definition, is_cif):
biomolecule.apply_pka_values(
forcefield_.name,
args.ph,
dict(zip(pka_df.group_label, pka_df.pKa)),
dict((row['group_label'], row['pKa']) for row in pka_df),
)
_LOGGER.info("Adding hydrogens to biomolecule.")
biomolecule.add_hydrogens()
Expand Down
8 changes: 6 additions & 2 deletions setup.py
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Original file line number Diff line number Diff line change
Expand Up @@ -49,8 +49,8 @@
long_description=LONG_DESCRIPTION,
install_requires=[
"propka >= 3.2",
"pandas >= 1.0",
"mmcif_pdbx>=1.1.2",
"numpy",
"requests",
],
url="http://www.poissonboltzmann.org",
Expand All @@ -59,7 +59,11 @@
),
package_data={"pdb2pqr": ["dat/*.xml", "dat/*.DAT", "dat/*.names"]},
python_requires=">=3.5",
tests_require=["pytest", "testfixtures"],
tests_require=[
"pandas >= 1.0",
"pytest",
"testfixtures",
],
test_suite="tests",
license="BSD",
classifiers=[
Expand Down