def test_anisou():
"""Test writing ANISOU entries."""
ppdb = PandasPDB()
ppdb.read_pdb(TESTDATA_FILENAME2)
ppdb.to_pdb(path=OUTFILE, records=None)
with open(OUTFILE, 'r') as f:
f1 = f.read()
# os.remove(OUTFILE)
assert f1 == four_eiy
def test_records():
"""Test private _read_pdb."""
ppdb = PandasPDB()
ppdb.read_pdb(TESTDATA_FILENAME)
ppdb.to_pdb(path=OUTFILE, records=["HETATM"])
with open(OUTFILE, "r") as f:
f1 = f.read()
os.remove(OUTFILE)
assert f1 == hetatm
def test_records():
"""Test private _read_pdb."""
ppdb = PandasPDB()
ppdb.read_pdb(TESTDATA_FILENAME)
ppdb.to_pdb(path=OUTFILE, records=['HETATM'])
with open(OUTFILE, 'r') as f:
f1 = f.read()
os.remove(OUTFILE)
assert f1 == hetatm
def test_anisou():
"""Test writing ANISOU entries."""
ppdb = PandasPDB()
ppdb.read_pdb(TESTDATA_FILENAME2)
ppdb.to_pdb(path=OUTFILE, records=None)
with open(OUTFILE, "r") as f:
f1 = f.read()
# os.remove(OUTFILE)
assert f1 == four_eiy
def test_defaults():
ppdb = PandasPDB()
ppdb.read_pdb(TESTDATA_FILENAME)
ppdb.to_pdb(path=OUTFILE, records=None)
with open(TESTDATA_FILENAME, 'r') as f:
f1 = f.read()
with open(OUTFILE, 'r') as f:
f2 = f.read()
assert f1 == f2
os.remove(OUTFILE)
def test_defaults():
ppdb = PandasPDB()
ppdb.read_pdb(TESTDATA_FILENAME)
ppdb.to_pdb(path=OUTFILE, records=None)
with open(TESTDATA_FILENAME, "r") as f:
f1 = f.read()
with open(OUTFILE, "r") as f:
f2 = f.read()
assert f1 == f2
os.remove(OUTFILE)
def test_get_df():
ppdb = PandasPDB()
ppdb.read_pdb(TESTDATA_FILENAME)
shape = ppdb.get('c-alpha').shape
assert shape == (174, 21), shape
shape = ppdb.get('hydrogen', invert=True).shape
assert shape == (1330, 21), shape
shape = ppdb.get('hydrogen').shape
assert shape == (0, 21), shape
shape = ppdb.get('main chain').shape
assert shape == (696, 21), shape
def test_get_df():
ppdb = PandasPDB()
ppdb.read_pdb(TESTDATA_FILENAME)
shape = ppdb.get('c-alpha').shape
assert shape == (174, 21), shape
shape = ppdb.get('hydrogen', invert=True).shape
assert shape == (1330, 21), shape
shape = ppdb.get('hydrogen').shape
assert shape == (0, 21), shape
shape = ppdb.get('main chain').shape
assert shape == (696, 21), shape
def test_read_pdb():
"""Test public read_pdb"""
ppdb = PandasPDB()
ppdb.read_pdb(TESTDATA_FILENAME)
assert ppdb.pdb_text == three_eiy
assert ppdb.code == '3eiy', ppdb.code
def test_anisou_input_handling():
"""Test public read_pdb"""
ppdb = PandasPDB()
ppdb.read_pdb(TESTDATA_FILENAME2)
assert ppdb.pdb_text == four_eiy
assert ppdb.code == '4eiy', ppdb.code
def test_get_exceptions():
ppdb = PandasPDB()
ppdb.read_pdb(TESTDATA_FILENAME)
ppdb.get('main-chai')
# License: BSD 3 clause
# Project Website: http://rasbt.github.io/biopandas/
# Code Repository: https://github.com/rasbt/biopandas
from biopandas.pdb import PandasPDB
import os
import numpy as np
import pandas as pd
from nose.tools import raises
TESTDATA_FILENAME = os.path.join(os.path.dirname(__file__), 'data',
'3eiy_stripped_no_ele.pdb')
ppdb = PandasPDB()
ppdb.read_pdb(TESTDATA_FILENAME)
def test_impute_hetatm():
new = ppdb.impute_element(sections=['HETATM'])
assert new['HETATM']['element_symbol'][1] == 'N'
assert new['HETATM']['element_symbol'][10] == 'O'
assert new['ATOM']['element_symbol'][1] == ''
assert new['ATOM']['element_symbol'][10] == ''
def test_impute_atom():
new = ppdb.impute_element(sections=['ATOM'])
assert new['ATOM']['element_symbol'][1] == 'C'
assert new['ATOM']['element_symbol'][10] == 'C'
assert new['HETATM']['element_symbol'][1] == ''
def test_get_all():
ppdb = PandasPDB()
ppdb.read_pdb(TESTDATA_FILENAME)
for i in ['c-alpha', 'hydrogen', 'main chain']:
ppdb.get(i)
def test_get_exceptions():
ppdb = PandasPDB()
ppdb.read_pdb(TESTDATA_FILENAME)
ppdb.get('main-chai')
def test_anisou_input_handling():
"""Test public read_pdb"""
ppdb = PandasPDB()
ppdb.read_pdb(TESTDATA_FILENAME2)
assert ppdb.pdb_text == four_eiy
assert ppdb.code == '4eiy', ppdb.code
def test_read_pdb():
"""Test public read_pdb"""
ppdb = PandasPDB()
ppdb.read_pdb(TESTDATA_FILENAME)
assert ppdb.pdb_text == three_eiy
assert ppdb.code == '3eiy', ppdb.code
# Code Repository: https://github.com/rasbt/biopandas
from biopandas.pdb import PandasPDB
import os
import numpy as np
import pandas as pd
from nose.tools import raises
TESTDATA_1t48 = os.path.join(os.path.dirname(__file__), 'data', '1t48_995.pdb')
TESTDATA_1t49 = os.path.join(os.path.dirname(__file__), 'data', '1t49_995.pdb')
TESTDATA_lig1 = os.path.join(os.path.dirname(__file__), 'data', 'lig_conf_1.pdb')
TESTDATA_lig2 = os.path.join(os.path.dirname(__file__), 'data', 'lig_conf_2.pdb')
p1t48 = PandasPDB()
p1t48.read_pdb(TESTDATA_1t48)
p1t49 = PandasPDB()
p1t49.read_pdb(TESTDATA_1t49)
pl1 = PandasPDB()
pl1.read_pdb(TESTDATA_lig1)
pl2 = PandasPDB()
pl2.read_pdb(TESTDATA_lig2)
def test_equal():
r = PandasPDB.rmsd(p1t48.df['ATOM'], p1t48.df['ATOM'], s=None)
assert r == 0.000, r
@raises(AttributeError)
def test_wrong_arg():
r = PandasPDB.rmsd(p1t48.df['ATOM'].loc[1:, :], p1t48.df['ATOM'], s='bla')
def test_get_all():
ppdb = PandasPDB()
ppdb.read_pdb(TESTDATA_FILENAME)
for i in ['c-alpha', 'hydrogen', 'main chain']:
ppdb.get(i)
