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_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)
# 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')