gemmi-protools 0.1.17__py3-none-any.whl → 1.0.1__py3-none-any.whl

gemmi_protools/utils/ppi.py

@@ -1,74 +0,0 @@
-"""
-@Author: Luo Jiejian
-"""
-import pathlib
-from typing import Union, List
-
-import numpy as np
-from scipy.spatial import cKDTree
-
-from gemmi_protools.io.reader import StructureParser
-
-
-def _ppi_atoms(struct, chains):
-    """
-    Load atoms for N and O of backbone and N, O, P, S of side chains, only for PPI searching
-    :param struct:
-    :param chains:
-    :return:
-    """
-    protein_atoms = ['N', 'ND1', 'ND2', 'NE', 'NE1', 'NE2', 'NH1', 'NH2', 'NZ',
-                     'O', 'OD1', 'OD2', 'OE1', 'OE2', 'OG', 'OG1', 'OH',
-                     'SD', 'SG']
-    xna_atoms = ['N1', 'N2', 'N3', 'N4', 'N6', 'N7', 'N9',
-                 'O2', "O2'", "O3'", 'O4', "O4'", "O5'", 'O6',
-                 'OP1', 'OP2', 'OP3', 'P']
-    pro_chs = []
-    xna_chs = []
-    for c in chains:
-        t = struct.chain_types.get(c, "")
-        if t == "protein":
-            pro_chs.append(c)
-        elif t in ["dna", "rna"]:
-            xna_chs.append(c)
-
-    pro_coord, pro_id = struct.get_atom_coords(pro_chs, protein_atoms)
-    xna_coord, xna_id = struct.get_atom_coords(xna_chs, xna_atoms)
-    return np.concatenate([pro_coord, xna_coord], axis=0), np.concatenate([pro_id, xna_id], axis=0)
-
-
-def ppi_interface_residues(in_file: Union[str, pathlib.Path],
-                           chains_x: List[str],
-                           chains_y: List[str],
-                           threshold: float = 4.0):
-    """
-    identify PPI among protein, DNA, RNA
-    :param in_file:
-    :param chains_x:
-    :param chains_y:
-    :param threshold:
-    :return:
-     PPI residues of chains_x, PPI residues of chains_y
-    """
-
-    st = StructureParser()
-    st.load_from_file(in_file)
-    st.set_default_model()
-    st.STRUCT.remove_alternative_conformations()
-    st.STRUCT.remove_ligands_and_waters()
-    st.STRUCT.remove_hydrogens()
-    st.STRUCT.remove_empty_chains()
-    st.update_entity()
-
-    x_coord, x_id = _ppi_atoms(st, chains_x)
-    y_coord, y_id = _ppi_atoms(st, chains_y)
-
-    kd_tree_x = cKDTree(x_coord)
-    kd_tree_y = cKDTree(y_coord)
-
-    pairs = kd_tree_x.sparse_distance_matrix(kd_tree_y, threshold, output_type='coo_matrix')
-
-    x_res = np.unique(x_id[pairs.row][["ch_name", 'res_num', 'res_icode', 'res_name']])
-    y_res = np.unique(y_id[pairs.col][["ch_name", 'res_num', 'res_icode', 'res_name']])
-
-    return x_res, y_res

gemmi_protools-0.1.17.dist-info/RECORD

@@ -1,27 +0,0 @@
-gemmi_protools/__init__.py,sha256=hwUw-EieCG0kwzHjTjzHF9Bc3D-J5R_l6G8PCcFegkw,331
-gemmi_protools/data/MHC/MHC_combined.hmm,sha256=w0_vzPiEWne_d_kYmqR0OiSsCOpQioItKy3Zq-JMsH4,159451
-gemmi_protools/data/MHC/MHC_combined.hmm.h3f,sha256=QGG4l-v76RYtysJ5rybnz5v6VgJg2RjoQQHUVWL5jmg,45522
-gemmi_protools/data/MHC/MHC_combined.hmm.h3i,sha256=yn-700hoBSJB39Tj8Ia8UhSZWpYiCZFNcbnYAFNjReI,300
-gemmi_protools/data/MHC/MHC_combined.hmm.h3m,sha256=CvNMCsobQiX-wL7iB4CreNcbpnElE31NmmjmMR0iYVI,66174
-gemmi_protools/data/MHC/MHC_combined.hmm.h3p,sha256=-mK278pRedG3-KL-DtuVAQy7La9DgXg5FcP89D6X3Ck,78325
-gemmi_protools/io/__init__.py,sha256=F6e1xNT_7lZAWQgNIneH06o2qtWYrHNr_xPUPTwwx5E,29
-gemmi_protools/io/cif_opts.py,sha256=cYEhubRP2rymbwSlB3ZQPGUFQiXGb2UQ0gdXdTd3c-I,6646
-gemmi_protools/io/convert.py,sha256=780sQcwhslUD4Hj5UZMVlQdbicniJ6jNjncTl_7jaMk,3841
-gemmi_protools/io/parse_pdb_header.py,sha256=UOGMsE3-d3APhO7zaAEE0NT31n-iqt55VpDh_RPOicI,14223
-gemmi_protools/io/parser.py,sha256=HFc4Kovr6rxEpLAEDUtF_e-RnA5OsWMeMFjuVNm7UYY,9507
-gemmi_protools/io/pdb_opts.py,sha256=laUqxlecOe6goax12q8EJGZuZbHyIGsXVucMV3gVrgg,5741
-gemmi_protools/io/peptide.py,sha256=a2wiEutJmvhl6gDCIzzqRCbmyknk2mwgy2FZ53lXclU,750
-gemmi_protools/io/reader.py,sha256=2AXg1JdYT2LxL6jWVsJkLHQREwAoYR7V-g-hQVgSgGg,16237
-gemmi_protools/io/struct_info.py,sha256=9nBj1Zer03S8_Wks7L7uRlc9PlbfCKzoaT32pKR58X8,2769
-gemmi_protools/utils/__init__.py,sha256=F6e1xNT_7lZAWQgNIneH06o2qtWYrHNr_xPUPTwwx5E,29
-gemmi_protools/utils/align.py,sha256=wyJDawxW10kdYWEM1F_LUEc3Qo-3_I7P5hFk-r-yqgY,7432
-gemmi_protools/utils/dockq.py,sha256=XmMwVEy-H4p6sH_HPcDWA3TP77OWdih0fE_BQJDr4pU,4189
-gemmi_protools/utils/fixer.py,sha256=yP9pTJ67n7z56UFfe2-eEsS3jkJfG2lP4KAEpXxlrnE,10142
-gemmi_protools/utils/immune_complex.py,sha256=0ni6j0JpcJrPGDLydlbK5ouF7LsQWvDke3UgTOgKEJM,32213
-gemmi_protools/utils/pdb_annot.py,sha256=nnRlLpjczhCP1ojEgsO3FuVgfsyleDZ34QxqyI8-wr0,11143
-gemmi_protools/utils/ppi.py,sha256=VWYsdxWwQoS1xwEYj5KB96Zz3F8r5Eyuw6NT3ReD-wc,2330
-gemmi_protools-0.1.17.dist-info/licenses/LICENSE,sha256=JuQvKcgj6n11y5y6nXr9rABv3gJSswc4eTCd5WZBtSY,1062
-gemmi_protools-0.1.17.dist-info/METADATA,sha256=sMzScJ0AFMKw9uMWCzxD9vYe6U3nATUX6BflEu6L1Ss,918
-gemmi_protools-0.1.17.dist-info/WHEEL,sha256=_zCd3N1l69ArxyTb8rzEoP9TpbYXkqRFSNOD5OuxnTs,91
-gemmi_protools-0.1.17.dist-info/top_level.txt,sha256=P12mYJi5O5EKIn5u-RFaWxuix431CgLacSRD7rBid_U,15
-gemmi_protools-0.1.17.dist-info/RECORD,,