pyjess 0.7.0__pp39-pypy39_pp73-win_amd64.whl → 0.8.0__pp39-pypy39_pp73-win_amd64.whl

pyjess/_jess.pyi

@@ -181,6 +181,8 @@ class TemplateAtom:
     @property
     def distance_weight(self) -> float: ...
     def copy(self: _SELF) -> _SELF: ...
+    def dump(self, file: TextIO) -> None: ...
+    def dumps(self) -> str: ...
 
 class Template(Sequence[TemplateAtom]):
     @classmethod
@@ -204,6 +206,8 @@ class Template(Sequence[TemplateAtom]):
     @property
     def dimension(self) -> int: ...
     def copy(self) -> Template: ...
+    def dump(self, file: TextIO) -> None: ...
+    def dumps(self) -> str: ...
 
 _T = TypeVar("_T", bound=Template)
 

pyjess/_jess.pyx

@@ -4,20 +4,20 @@
 
 Jess is an algorithm for constraint-based structural template matching
 proposed by Jonathan Barker *et al.*. It can be used to identify
-catalytic residues from a known template inside a protein structure. 
+catalytic residues from a known template inside a protein structure.
 Jess is an evolution of TESS, a geometric hashing algorithm developed by
 Andrew Wallace *et al.*, removing some pre-computation and
-structural requirements from the original algorithm. 
+structural requirements from the original algorithm.
 
 PyJess is a Python module that provides bindings to Jess using
-`Cython <https://cython.org/>`_. It allows creating templates, querying 
-them with protein structures, and retrieving the hits using a Python API 
-without performing any external I/O. It's also more than 10x faster than 
-Jess thanks to algorithmic optimizations added to improve the original Jess 
+`Cython <https://cython.org/>`_. It allows creating templates, querying
+them with protein structures, and retrieving the hits using a Python API
+without performing any external I/O. It's also more than 10x faster than
+Jess thanks to algorithmic optimizations added to improve the original Jess
 code while producing consistent results.
 
 Example:
-    Load templates from a file, either as a file-like object or 
+    Load templates from a file, either as a file-like object or
     given a filename::
 
         >>> t1 = pyjess.Template.load("1.3.3.tpl")  # load from filename
@@ -31,15 +31,15 @@ Example:
         >>> mol[0]
         Atom(serial=1, name='N', altloc=' ', residue_name='GLN', ...)
 
-    Create a `Jess` object storing the templates to support running 
-    queries on them. The individual templates can still be accessed by 
+    Create a `Jess` object storing the templates to support running
+    queries on them. The individual templates can still be accessed by
     index::
 
         >>> jess = pyjess.Jess([t1, t2])
         >>> jess[0].id
         '3r6v'
 
-    Run a query on the Jess object to retrieve all templates matching 
+    Run a query on the Jess object to retrieve all templates matching
     a `Molecule`, *in no particular order*::
 
         >>> hits = jess.query(mol, 2, 2, 2)
@@ -59,7 +59,7 @@ Example:
         2om2 1.0711...
         2om2 1.1494...
 
-    By default, a template can match a molecule in more than one way, 
+    By default, a template can match a molecule in more than one way,
     if several sets of atoms match the geometric constraints. Use the
     ``best_match`` argument of `~Jess.query` to only retrieve the
     best match per template::
@@ -86,6 +86,7 @@ References:
 
 cimport cython
 from cpython.exc cimport PyErr_WarnEx
+from cpython.bytes cimport PyBytes_FromStringAndSize
 from cpython.unicode cimport (
     PyUnicode_FromStringAndSize,
     PyUnicode_FromFormat,
@@ -119,6 +120,8 @@ from jess.tess_atom cimport TessAtom as _TessAtom
 import functools
 import io
 
+from ._peekable import PeekableFile
+
 __version__ = PROJECT_VERSION
 
 # --- Utils ------------------------------------------------------------------
@@ -149,6 +152,30 @@ class nullcontext:
     def __exit__(self, exc_type, exc_value, traceback):
         return False
 
+cdef extern from * nogil:
+    """
+    const char AA3[21][3] = {
+        "ALA", "CYS", "ASP", "GLU", "PHE", "GLY", "HIS",
+        "ILE", "LYS", "LEU", "MET", "ASN", "PRO", "GLN",
+        "ARG", "SER", "THR", "VAL", "TRP", "TYR", "XXX"
+    };
+
+    const char AA1[21] = {
+        'A', 'C', 'D', 'E', 'F', 'G', 'H',
+        'I', 'K', 'L', 'M', 'N', 'P', 'Q',
+        'R', 'S', 'T', 'V', 'W', 'Y', 'X'
+    };
+    """
+    const char[21][3] AA3
+    const char[21] AA1
+
+cdef inline char encode_resname(const char* src) noexcept nogil:
+    cdef size_t i
+    for i in range(21):
+        if AA3[i][0] == src[0] and AA3[i][1] == src[1] and AA3[i][2] == src[2]:
+            return AA1[i]
+    return ord('X')
+
 # --- Classes ----------------------------------------------------------------
 
 cdef class _MoleculeParser:
@@ -198,26 +225,34 @@ cdef class _CIFMoleculeParser(_MoleculeParser):
     cdef object gemmi
     cdef bint use_author
     cdef bint skip_hetatm
+    cdef bint ignore_endmdl
 
     _PRIMARY_COLUMNS = [
         'id', 'type_symbol', 'label_atom_id', 'label_alt_id', 'label_comp_id',
         'label_asym_id', 'label_seq_id', '?pdbx_PDB_ins_code', 'Cartn_x',
         'Cartn_y', 'Cartn_z', 'occupancy', 'B_iso_or_equiv',
-        '?pdbx_formal_charge', '?group_PDB',
+        '?pdbx_formal_charge', '?group_PDB', 'pdbx_PDB_model_num',
     ]
 
     _AUTH_COLUMNS = [
         'id', 'type_symbol', 'auth_atom_id', 'label_alt_id', 'auth_comp_id',
         'auth_asym_id', 'auth_seq_id', '?pdbx_PDB_ins_code', 'Cartn_x',
         'Cartn_y', 'Cartn_z', 'occupancy', 'B_iso_or_equiv',
-        '?pdbx_formal_charge', '?group_PDB',
+        '?pdbx_formal_charge', '?group_PDB', 'pdbx_PDB_model_num',
     ]
 
-    def __init__(self, str id = None, bint use_author = False, bint skip_hetatm = False):
+    def __init__(
+        self,
+        str id = None,
+        bint use_author = False,
+        bint skip_hetatm = False,
+        bint ignore_endmdl = False,
+    ):
         super().__init__(id=id)
         self.gemmi = __import__('gemmi')
         self.use_author = use_author
         self.skip_hetatm = skip_hetatm
+        self.ignore_endmdl = ignore_endmdl
 
     def _load_block(self, document, molecule_type):
         block = document.sole_block()
@@ -230,6 +265,12 @@ cdef class _CIFMoleculeParser(_MoleculeParser):
 
         atoms = []
         for row in table:
+
+            # row[15] contains _atom_site.pdbx_PDB_model_num
+            # by default (if ignore_endmdl is False) we break on model number
+            if not self.ignore_endmdl and row[15] != '1':
+                break
+
             if row[14] != "ATOM" and (row[14] != "HETATM" or self.skip_hetatm):
                 continue
 
@@ -251,7 +292,7 @@ cdef class _CIFMoleculeParser(_MoleculeParser):
             atom = Atom(
                 serial=int(row[0]),
                 element=row[1],
-                name=row[2],
+                name=row[2].strip('"'),
                 altloc=' ' if row[3] == "." else row[3], # FIXME: replace with None?
                 residue_name=row[4],
                 chain_id=row[5],
@@ -261,7 +302,7 @@ cdef class _CIFMoleculeParser(_MoleculeParser):
                 y=float(row[9]),
                 z=float(row[10]),
                 occupancy=0.0 if row[11] == '.' else float(row[11]),
-                temperature_factor=float(row[12]),
+                temperature_factor=0.0 if row[12] == '.' else float(row[12]),
                 charge=0 if not row.has(13) or row[13] == "?" else int(row[13]),
             )
             atoms.append(atom)
@@ -324,7 +365,7 @@ cdef class Molecule:
             ignore_endmdl (`bool`): Pass `True` to make the parser read all
                 the atoms from the PDB file. By default, the parser only
                 reads the atoms of the first model, and stops at the first
-                ``ENDMDL`` line. *Ignored for CIF files*.
+                ``ENDMDL`` line - or for CIF files stops if the PDB model > 1.
             use_author (`bool`): Pass `True` to use the author-defined
                 labels while parsing CIF files, e.g. read the chain name
                 from ``_atom_site.auth_asym_id`` rather than
@@ -348,8 +389,6 @@ cdef class Molecule:
             The ``format`` argument, and support for CIF parsing.
 
         """
-        if format == "detect":
-            format = "cif" if text.lstrip().startswith(("data_", "loop_")) else "pdb"
         return cls.load(
             io.StringIO(text),
             format=format,
@@ -389,7 +428,7 @@ cdef class Molecule:
             ignore_endmdl (`bool`): Pass `True` to make the parser read all
                 the atoms from the PDB file. By default, the parser only
                 reads the atoms of the first model, and stops at the first
-                ``ENDMDL`` line. *Ignored for CIF files*.
+                ``ENDMDL`` line - or for CIF files stops if the PDB model > 1.
             use_author (`bool`): Pass `True` to use the author-defined
                 labels while parsing CIF files, e.g. read the chain name
                 from ``_atom_site.auth_asym_id`` rather than
@@ -423,17 +462,17 @@ cdef class Molecule:
             except TypeError:
                 handle = nullcontext(file)
             with handle as f:
-                if f.seekable():
-                    peek = f.read(5)
-                    f.seek(0)
-                else:
-                    f = f.read()
-                    peek = f[5:]
+                f = PeekableFile(f)
+                peek = f.peek(10)
+                while peek.startswith("#"):
+                    f.readline()
+                    peek = f.peek(5)
                 if peek.startswith(("data_", "loop_")):
                     parser = _CIFMoleculeParser(
                         id=id,
                         use_author=use_author,
                         skip_hetatm=skip_hetatm,
+                        ignore_endmdl=ignore_endmdl,
                     )
                 else:
                     parser = _PDBMoleculeParser(
@@ -441,10 +480,8 @@ cdef class Molecule:
                         ignore_endmdl=ignore_endmdl,
                         skip_hetatm=skip_hetatm,
                     )
-                if isinstance(f, str):
-                    return parser.loads(f, molecule_type=cls)
                 return parser.load(f, molecule_type=cls)
-        if format == "pdb":
+        elif format == "pdb":
             parser = _PDBMoleculeParser(
                 id=id,
                 ignore_endmdl=ignore_endmdl,
@@ -455,6 +492,7 @@ cdef class Molecule:
                 id=id,
                 use_author=use_author,
                 skip_hetatm=skip_hetatm,
+                ignore_endmdl=ignore_endmdl,
             )
         else:
             raise ValueError(f"invalid value for `format` argument: {format!r}")
@@ -1193,11 +1231,21 @@ cdef class TemplateAtom:
         self._atom.pos[0] = x
         self._atom.pos[1] = y
         self._atom.pos[2] = z
-        self._atom.chainID1, self._atom.chainID2 = map(ord, chain_id.ljust(2))
         self._atom.nameCount = ac
         self._atom.resNameCount = rc
         self._atom.distWeight = distance_weight
 
+        # copy chain ID
+        if len(chain_id) == 2:
+            self._atom.chainID1 = ord(chain_id[0])
+            self._atom.chainID2 = ord(chain_id[1])
+        elif len(chain_id) == 1:
+            self._atom.chainID1 = ord(' ')
+            self._atom.chainID2 = ord(chain_id[0])
+        else:
+            self._atom.chainID1 = ord(' ')
+            self._atom.chainID2 = ord('0')
+
         # setup string pointers
         p = <char*> &self._atom[1]
         self._atom.name = <char**> p
@@ -1303,6 +1351,8 @@ cdef class TemplateAtom:
         assert self._atom is not NULL
         cdef char c1 = jess.tess_atom.TessAtom_chainID1(self._atom)
         cdef char c2 = jess.tess_atom.TessAtom_chainID2(self._atom)
+        if c1 == ord(' '):
+            return chr(c2)
         return PyUnicode_FromFormat("%c%c", c1, c2).strip()
 
     @property
@@ -1382,6 +1432,63 @@ cdef class TemplateAtom:
             atom._atom = jess.tess_atom.TessAtom_copy(self._atom)
         return atom
 
+    cpdef str dumps(self):
+        """Write the template atom to a string.
+
+        Returns:
+            `str`: The serialized template atom.
+
+        .. versionadded:: 0.8.0
+
+        """
+        file = io.StringIO()
+        self.dump(file)
+        return file.getvalue()
+
+    cpdef void dump(self, object file):
+        """Write the template atom to a file.
+
+        Arguments:
+            file (file-like object): A file opened in *text* mode where the
+                template atom will be written.
+
+        .. versionadded:: 0.8.0
+
+        """
+        assert self._atom is not NULL
+
+        cdef size_t    k
+        cdef char[80]  buffer
+        cdef char[5]   name
+        cdef char[5]   resname
+        cdef _TessAtom* atom   = self._atom
+
+        decode_token(name, atom.name[0], 4)
+        decode_token(resname, atom.resName[0], 3)
+
+        n = sprintf(
+            buffer,
+            "ATOM  %5i %4s %3s%c%c%4i    %8.3f%8.3f%8.3f",
+            atom.code,
+            name,
+            resname,
+            jess.tess_atom.TessAtom_chainID1(self._atom),
+            jess.tess_atom.TessAtom_chainID2(self._atom),
+            atom.resSeq,
+            atom.pos[0],
+            atom.pos[1],
+            atom.pos[2],
+        )
+
+        memset(&buffer[n], ord(' '), 7*sizeof(char))
+        for k in range(1, atom.resNameCount):
+            buffer[n + k] = encode_resname(atom.resName[k])
+
+        n += 7
+        n += sprintf(&buffer[n], "%4.2f", atom.distWeight)
+
+        file.write(PyUnicode_FromStringAndSize(buffer, n))
+
 
 cdef class Template:
     """A template, as a sequence of `TemplateAtom` objects.
@@ -1656,6 +1763,40 @@ cdef class Template:
             tpl._tess = <_TessTemplate*> &tpl._tpl[1]
         return tpl
 
+    cpdef str dumps(self):
+        """Write the template to a string.
+
+        Returns:
+            `str`: The serialized template atom.
+
+        .. versionadded:: 0.8.0
+
+        """
+        file = io.StringIO()
+        self.dump(file)
+        return file.getvalue()
+
+    cpdef void dump(self, object file, bint write_id=True):
+        """Write the template to a file.
+
+        Arguments:
+            file (file-like object): A file opened in *text* mode where the
+                template will be written.
+            write_id (`bool`): Whether to write the identifier of the
+                template as a ``REMARK`` line.
+
+        .. versionadded:: 0.8.0
+
+        """
+        cdef str id_ = self.id
+        if write_id and id_ is not None:
+            file.write(f"REMARK PDB_ID {id_}\n")
+        for template_atom in self:
+            template_atom.dump(file)
+            file.write("\n")
+        file.write("END\n")
+
+
 cdef class Query:
     """A query over templates with a given molecule.
 
@@ -1860,7 +2001,6 @@ cdef class Hit:
         rmsd (`float`): The RMSD between the aligned structures.
         template (`~pyjess.Template`): The template that matched the
             query molecule.
-        molecule (`~pyjess.Molecule`): The query molecule.
 
     """
     cdef double[9]       _rotation

pyjess/_peekable.py

@@ -0,0 +1,53 @@
+import typing
+
+
+class PeekableFile(typing.TextIO):
+    """A buffered file that supports peeking.
+    """
+
+    def __init__(self, file):
+        self.file = file
+        self._buffer = ""
+
+    def __iter__(self):
+        return self
+
+    def __next__(self):
+        line = self.readline()
+        if not line:
+            raise StopIteration
+        return line
+
+    def read(self, n=-1):
+        l = len(self._buffer)
+        if l == 0:
+            output = self.file.read(n)
+        elif n is None or n == -1:
+            output = self._buffer + self.file.read()
+            self._buffer = ""
+        elif n < l:
+            output = self._buffer[:n]
+            self._buffer = self._buffer[n:]
+        else:
+            output = self._buffer + self.file.read(n - l)
+            self._buffer = ""
+        return output
+
+    def readline(self):
+        i = self._buffer.find("\n")
+        if i == -1:
+            line = self._buffer + self.file.readline()
+            self._buffer = ""
+        else:
+            line = self._buffer[:i+1]
+            self._buffer = self._buffer[i+1:]
+        return line
+
+    def peek(self, n):
+        l = len(self._buffer)
+        if l < n:
+            self._buffer += self.file.read(n - l)
+        return self._buffer[:n]
+
+    def close(self):
+        self.file.close()

pyjess/tests/test_molecule.py

@@ -1,10 +1,12 @@
 import itertools
+import io
 import os
 import pickle
 import unittest
 import tempfile
 import textwrap
 import sys
+import shutil
 import warnings
 
 from .utils import files
@@ -191,6 +193,47 @@ class TestMolecule(unittest.TestCase):
         self.assertEqual(mol1.id, mol2.id)
         self.assertEqual(mol1, mol2)
 
+    @unittest.skipUnless(files, "importlib.resources not available")
+    @unittest.skipUnless(gemmi, "gemmi not available")
+    def test_load_mmcif_comment(self):
+        # load mmCIF file into a buffer and add a comment at the top
+        buffer = io.StringIO()
+        buffer.write("# this is a comment line \n")
+        buffer.write("# and a second comment line \n")
+        with files(data).joinpath("1AMY.cif").open() as f:
+            shutil.copyfileobj(f, buffer)
+            
+        with warnings.catch_warnings():
+            warnings.simplefilter('ignore')
+            # should work when explicitly given "CIF" formula
+            buffer.seek(0)
+            cif_molecule = Molecule.load(buffer, format="cif")
+            self.assertEqual(len(cif_molecule), 3339)
+            # should work when not given format
+            buffer.seek(0)
+            cif_molecule = Molecule.load(buffer, format="detect")
+            self.assertEqual(len(cif_molecule), 3339)
+
+    @unittest.skipUnless(files, "importlib.resources not available")
+    @unittest.skipUnless(gemmi, "gemmi not available")
+    def test_loads_mmcif_comment(self):
+        # load mmCIF file into a buffer and add a comment at the top
+        buffer = io.StringIO()
+        buffer.write("# this is a comment line \n")
+        buffer.write("# and a second comment line \n")
+        with files(data).joinpath("1AMY.cif").open() as f:
+            shutil.copyfileobj(f, buffer)
+        text = buffer.getvalue()
+            
+        with warnings.catch_warnings():
+            warnings.simplefilter('ignore')
+            # should work when explicitly given "CIF" formula
+            cif_molecule = Molecule.loads(text, format="cif")
+            self.assertEqual(len(cif_molecule), 3339)
+            # should work when not given format
+            cif_molecule = Molecule.loads(text, format="detect")
+            self.assertEqual(len(cif_molecule), 3339)
+
     @unittest.skipUnless(files, "importlib.resources not available")
     @unittest.skipUnless(gemmi, "gemmi not available")
     def test_load_consistency_no_skip_hetatm(self):

pyjess/tests/test_template.py

@@ -119,6 +119,12 @@ class TestTemplate(unittest.TestCase):
         self.assertEqual(len(tpl1), len(tpl2))
         self.assertEqual(tpl1, tpl2)
 
+    def test_dumps_roundtrip(self):
+        tpl1 = Template.loads(TEMPLATE, id="tpl1")
+        tpl2 = Template.loads(tpl1.dumps())
+        self.assertEqual(len(tpl1), len(tpl2))
+        self.assertEqual(tpl1, tpl2)
+
     @unittest.skipUnless(files, "importlib.resources not available")
     def test_dimension_multiple_chains(self):
         with files(data).joinpath("1sur.qry").open() as f:

pyjess/tests/test_template_atom.py

@@ -2,7 +2,7 @@ import unittest
 import sys
 import pickle
 
-from .._jess import TemplateAtom
+from .._jess import TemplateAtom, Atom
 
 
 class TestTemplateAtom(unittest.TestCase):
@@ -89,4 +89,32 @@ class TestTemplateAtom(unittest.TestCase):
         copy = pickle.loads(pickle.dumps(atom))
         for attribute in ("atom_names", "residue_names", "chain_id", "x", "y", "z", "match_mode"):
             self.assertEqual(getattr(copy, attribute), getattr(atom, attribute))
+        self.assertEqual(atom, copy)
+
+    def test_dumps(self):
+        atom = TemplateAtom(
+            chain_id="A",
+            residue_number=1136,
+            x=3.953,
+            y=0.597,
+            z=-1.721,
+            residue_names=["ARG", "LYS"],
+            atom_names=["NE"],
+            distance_weight=0.00,
+            match_mode=1,
+        )
+        t = atom.dumps()
+        self.assertEqual(
+            t,
+            "ATOM      1  NE  ARG A1136       3.953   0.597  -1.721 K     0.00"
+        )
+
+    def test_dumps_roundtrip(self):
+        atom = self._create_atom()
+        self.assertEqual(atom.chain_id, 'A')
+        t = atom.dumps()
+        self.assertEqual(t[20:22], ' A')
+        copy = TemplateAtom.loads(atom.dumps())
+        for attribute in ("atom_names", "residue_names", "chain_id", "x", "y", "z", "match_mode"):
+            self.assertEqual(getattr(copy, attribute), getattr(atom, attribute), attribute)
         self.assertEqual(atom, copy)

{pyjess-0.7.0.dist-info → pyjess-0.8.0.dist-info}/METADATA

@@ -1,6 +1,6 @@
 Metadata-Version: 2.2
 Name: pyjess
-Version: 0.7.0
+Version: 0.8.0
 Summary: Cython bindings and Python interface to JESS, a 3D template matching software.
 Keywords: bioinformatics,structure,template,matching
 Author-Email: Martin Larralde <martin.larralde@embl.de>
@@ -40,6 +40,7 @@ Classifier: Programming Language :: Python :: 3.10
 Classifier: Programming Language :: Python :: 3.11
 Classifier: Programming Language :: Python :: 3.12
 Classifier: Programming Language :: Python :: 3.13
+Classifier: Programming Language :: Python :: 3.14
 Classifier: Programming Language :: Python :: Implementation :: CPython
 Classifier: Programming Language :: Python :: Implementation :: PyPy
 Classifier: Topic :: Scientific/Engineering :: Bio-Informatics
@@ -190,7 +191,7 @@ computed on-the-fly when requested:
 
 ```python
 for hit in query:
-    print(hit.molecule.id, hit.template.id, hit.rmsd, hit.log_evalue)
+    print(hit.molecule().id, hit.template.id, hit.rmsd, hit.log_evalue)
     for atom in hit.atoms():
         print(atom.name, atom.x, atom.y, atom.z)
 ```

{pyjess-0.7.0.dist-info → pyjess-0.8.0.dist-info}/RECORD

@@ -1,9 +1,10 @@
 pyjess/.gitignore,sha256=u14v4OOy8U50Kp9SUKU8DupCG-mQIuel47gdbNDmAwg,21
 pyjess/__init__.py,sha256=Xe9GBQUBm9ik-ty5tcE3UQ9Ip1p-C_IGvTPuGULolng,766
 pyjess/__main__.py,sha256=Kc823UjDqgAMU6YJdDwfNlEPWjpX_94QXgCBlLMnUMo,53
-pyjess/_jess.pyi,sha256=jLNw73JPngD1fxSZeIUzf1kTEBLr89kncqoUilnZYXQ,8588
-pyjess/_jess.pypy39-pp73-win_amd64.pyd,sha256=eDzwmQUVBnicPxNzh58p8WPaNOdSabrggMdGJ_MHM6M,361984
-pyjess/_jess.pyx,sha256=XprzJKRlaEjtXCW7dODOYRjPy5DELKd-TB1DluNfKXM,82944
+pyjess/_jess.pyi,sha256=soIsXPg2INGEqZ7AXQ3aZWKsr-piSzVXY-FSfOFXURQ,8748
+pyjess/_jess.pypy39-pp73-win_amd64.pyd,sha256=-ES2-Zm4HVnonjfzKN23w-tY353iY9IEUsx0wJlWBns,349696
+pyjess/_jess.pyx,sha256=PSr3lGPKQ6est9bZJZWq0Z_dPw-hIAYkbxOpC6XIpqo,86976
+pyjess/_peekable.py,sha256=Blu35yPXFp85gMxLRGl5qmZfuUybM1ttM448o1LUlsc,1357
 pyjess/cli.py,sha256=82qa2vDMWVqmAScPYxGS3-5bEFuqBDAmuQ6M-9WQsLA,9211
 pyjess/CMakeLists.txt,sha256=H9eXbrFcGF2OLP8muQctb4cOb27Qp2uZj5KRjoDAROg,36
 pyjess/py.typed,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
@@ -23,12 +24,12 @@ pyjess/tests/test_atom.py,sha256=clLN9IVuivadztGtagDhdPBDGoMkUgs41lEWuTCCmFA,474
 pyjess/tests/test_doctest.py,sha256=Z46WI6d2rvRoShOGQFZM_9zAzzgBqPlOaozpFu8bvDM,2632
 pyjess/tests/test_hit.py,sha256=3z1JgGI87w_77Rdk_zrG2zA9M1n8u9L-XtTU3HtpSaY,2468
 pyjess/tests/test_jess.py,sha256=E6j27Y3N9Da19YL30QFVCwREUO9fID2HH75zWMn2V5Y,17669
-pyjess/tests/test_molecule.py,sha256=vn2539meiT1khDRp-_pDUAute9C7alrQ9SOqFLpb3Js,12833
-pyjess/tests/test_template.py,sha256=jnFTegP6_llNvp8f965yXt_v55JSrIh6-tNpE6UbHe8,5026
-pyjess/tests/test_template_atom.py,sha256=oK8cfKe4_k3Pm1PqoTTxTzAoeUVLiCFsg6QmiTQ-RCQ,3496
+pyjess/tests/test_molecule.py,sha256=MPDHFGbcw83E1vm4Z1_3PuPADW0qT7qzBoehaJyMURE,14818
+pyjess/tests/test_template.py,sha256=3lbN_jzWjsEcw00r0Y4PxYBuiWlq47Wh1bba189jjiM,5248
+pyjess/tests/test_template_atom.py,sha256=vHT1I2nmaP34LUg-7SuqbpUYAJnL2iyRGd3k3yDNQdU,4467
 pyjess/tests/utils.py,sha256=Z7rUPC-D8dZlRfHAnLaXHUg6M10D3zFvNiwDvvHA3xc,202
-pyjess-0.7.0.dist-info/METADATA,sha256=5dzLVyfgSMsKIpC5os1TXVIGZIAw7yAKGLurBegAC3M,14276
-pyjess-0.7.0.dist-info/WHEEL,sha256=k0WUL95hfPxp-oNxWWxpwaSfyWqqHRsPPz7teFk1VMg,111
-pyjess-0.7.0.dist-info/entry_points.txt,sha256=5dgYfglg8P5hPTIyrKAnOBmYqs2GRR0kb6x0BncaHbA,44
-pyjess-0.7.0.dist-info/licenses/COPYING,sha256=Iyx2bRDPnLgoEzW2KVanb61cjhW8lnhJNU-mjS-KhIY,1124
-pyjess-0.7.0.dist-info/RECORD,,
+pyjess-0.8.0.dist-info/METADATA,sha256=Zxnk5McI0xVW_Y_WIYKRLIVTioGlNE7LGtre5KnzWvo,14329
+pyjess-0.8.0.dist-info/WHEEL,sha256=k0WUL95hfPxp-oNxWWxpwaSfyWqqHRsPPz7teFk1VMg,111
+pyjess-0.8.0.dist-info/entry_points.txt,sha256=5dgYfglg8P5hPTIyrKAnOBmYqs2GRR0kb6x0BncaHbA,44
+pyjess-0.8.0.dist-info/licenses/COPYING,sha256=Iyx2bRDPnLgoEzW2KVanb61cjhW8lnhJNU-mjS-KhIY,1124
+pyjess-0.8.0.dist-info/RECORD,,