biointerface 0.3.0__tar.gz → 0.3.2__tar.gz

{biointerface-0.3.0 → biointerface-0.3.2}/HISTORY.rst

@@ -2,28 +2,32 @@
 History
 =======
 
-0.1.0 (2025-02-08)
+0.3.1 (2025-03-05)
 ------------------
 
-* First release on PyPI.
+* Proper tests
 
 
-0.2.0 (2025-02-28)
+0.3.0 (2025-03-05)
 ------------------
 
-* Features: Interface class, with getter methods for atoms, dataframes etc
+* Feature: get all continous protein-bound double-strand nucleic acids;
 
 
-0.2.1 (2025-03-1)
+0.2.3 (2025-03-05)
 ------------------
 
-* Gitlab CI
+* fix: bump-my-version was updating pdbnucleicacids version too
+
+* fix: import classes instead of modules
+
+* chore: remove old tox environments
 
 
 0.2.2 (2025-03-04)
 ------------------
 
-* Interface methods to get residues
+* Interface getter methods to get residues
 
 * Interface raise error condition in case of no protein in the structure
 
@@ -32,16 +36,21 @@ History
 * Full documentation
 
 
-0.2.3 (2025-03-05)
+0.2.1 (2025-03-1)
 ------------------
 
-* fix: bump-my-version was updating pdbnucleicacids version too
+* Gitlab CI
 
-* fix: import classes instead of modules
 
-* chore: remove old tox environments
+0.2.0 (2025-02-28)
+------------------
 
+* Features: Interface class, with getter methods for atoms, dataframes etc
 
-0.3.0 (2025-03-05)
 
-* Feature: get all continous protein-bound double-strand nucleic acids;
+0.1.0 (2025-02-08)
+------------------
+
+* First release on PyPI.
+
+* Feature: interface as pandas dataframe

{biointerface-0.3.0 → biointerface-0.3.2}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.2
 Name: biointerface
-Version: 0.3.0
+Version: 0.3.2
 Summary: BioInterface is a Biopython based package that extracts Protein-DNA interfaces in a PDB structures.
 Author-email: Alessandro Pandolfi <alessandro.pandolfi@protonmail.com>
 Maintainer-email: Alessandro Pandolfi <alessandro.pandolfi@protonmail.com>
@@ -14,12 +14,21 @@ License-File: LICENSE
 License-File: AUTHORS.rst
 Requires-Dist: pandas
 Requires-Dist: biopython
-Requires-Dist: pdbnucleicacids>=0.2.1
+Requires-Dist: pdbnucleicacids>=0.2.2
 Provides-Extra: dev
-Requires-Dist: coverage; extra == "dev"
+Requires-Dist: spyder-kernels; extra == "dev"
+Requires-Dist: flake8; extra == "dev"
+Requires-Dist: ruff; extra == "dev"
 Requires-Dist: mypy; extra == "dev"
 Requires-Dist: pytest; extra == "dev"
-Requires-Dist: ruff; extra == "dev"
+Requires-Dist: tox; extra == "dev"
+Requires-Dist: coverage; extra == "dev"
+Requires-Dist: sphinx; extra == "dev"
+Requires-Dist: watchdog; extra == "dev"
+Requires-Dist: bump-my-version; extra == "dev"
+Requires-Dist: wheel; extra == "dev"
+Requires-Dist: build; extra == "dev"
+Requires-Dist: twine; extra == "dev"
 
 ============
 BioInterface
@@ -107,7 +116,6 @@ Feaures
 TODO
 --------
 
-* Proper tests (WIP)
 
 
 Credits

{biointerface-0.3.0 → biointerface-0.3.2}/README.rst

@@ -84,7 +84,6 @@ Feaures
 TODO
 --------
 
-* Proper tests (WIP)
 
 
 Credits

{biointerface-0.3.0 → biointerface-0.3.2}/docs/usage.rst

@@ -169,7 +169,7 @@ You can get all Protein-DNA interface features as a ``pandas`` DataFrame.
        'prot_atom_coord_z', 'dna_chain_id', 'dna_res_hetfield',
        'dna_res_number', 'dna_res_icode', 'dna_res_name', 'dna_atom_name',
        'dna_atom_altloc', 'dna_atom_element', 'dna_atom_coord_x',
-       'dna_atom_coord_y', 'dna_atom_coord_z', 'euclidian_distance'],
+       'dna_atom_coord_y', 'dna_atom_coord_z', 'euclidean_distance'],
       dtype='object')
 
 .. code-block:: python
@@ -178,7 +178,7 @@ You can get all Protein-DNA interface features as a ``pandas`` DataFrame.
 
 .. code-block:: console
 
-        protein_chain_id prot_res_hetfield  prot_res_number  ... euclidian_distance
+        protein_chain_id prot_res_hetfield  prot_res_number  ... euclidean_distance
     0                  F                                148  ...           4.458498
     1                  F                                148  ...           3.964944
     2                  F                                148  ...           4.066739

{biointerface-0.3.0 → biointerface-0.3.2}/pyproject.toml

@@ -4,7 +4,7 @@ build-backend = "setuptools.build_meta"
 
 [project]
 name = "biointerface"
-version = "0.3.0"
+version = "0.3.2"
 description = "BioInterface is a Biopython based package that extracts Protein-DNA interfaces in a PDB structures."
 readme = "README.rst"
 authors = [
@@ -20,15 +20,24 @@ license = {text = "MIT license"}
 dependencies = [
     "pandas",
     "biopython",
-    "pdbnucleicacids >= 0.2.1",
+    "pdbnucleicacids >= 0.2.2",
 ]
 
 [project.optional-dependencies]
 dev = [
-    "coverage",  # testing
-    "mypy",  # linting
-    "pytest",  # testing
-    "ruff"  # linting
+    "spyder-kernels",
+    "flake8",  # lint
+    "ruff",  # lint & format
+    "mypy",  # type check
+    "pytest",  # test
+    "tox",
+    "coverage",  # test
+    "sphinx",  # docs
+    "watchdog",  # docs
+    "bump-my-version",  # tags & version
+    "wheel",  # build
+    "build",  # build
+    "twine",  # deploy
 ]
 
 [project.urls]
@@ -72,41 +81,6 @@ testpaths = [
 ]
 
 
-# bump-my-version
-# ----
-
-[tool.bumpversion]
-current_version = "0.3.0"
-parse = "(?P<major>\\d+)\\.(?P<minor>\\d+)\\.(?P<patch>\\d+)"
-serialize = ["{major}.{minor}.{patch}"]
-search = "{current_version}"
-replace = "{new_version}"
-regex = false
-ignore_missing_version = false
-ignore_missing_files = false
-tag = true
-sign_tags = false
-tag_name = "v{new_version}"
-tag_message = "Bump version: {current_version} → {new_version}"
-allow_dirty = false
-commit = true
-message = "Bump version: {current_version} → {new_version}"
-commit_args = ""
-setup_hooks = []
-pre_commit_hooks = []
-post_commit_hooks = []
-
-[[tool.bumpversion.files]]
-filename = "src/biointerface/__init__.py"
-search = "{current_version}"
-replace = "{new_version}"
-
-[[tool.bumpversion.files]]
-filename = "pyproject.toml"
-search = 'version = "{current_version}"'
-replace = 'version = "{new_version}"'
-
-
 # ruff
 # ----
 
@@ -134,8 +108,11 @@ envlist = ["py310", "py311", "py312", "py313"]
 [tool.tox.env_run_base]  # Configurazione generale per tutti gli ambienti di test
 description = "Run the tests with pytest"
 deps = [
-    #"pytest-cov",  # Esempio di dipendenza per la coverage dei test
-    "-r requirements-dev.txt"  # Se hai un file requirements per lo sviluppo
+    "flake8",  # lint
+    "ruff",  # lint & format
+    "mypy",  # type check
+    "pytest",  # test
+    #"-r requirements-dev.txt"  # Se hai un file requirements per lo sviluppo
 ]
 commands = [["pytest"]]
 
@@ -162,3 +139,37 @@ description = "Run the tests on Python 3.13"
 #deps = ["flake8"]
 #commands = ["flake8 src tests"]
 
+
+# bump-my-version
+# ----
+
+[tool.bumpversion]
+current_version = "0.3.2"
+parse = "(?P<major>\\d+)\\.(?P<minor>\\d+)\\.(?P<patch>\\d+)"
+serialize = ["{major}.{minor}.{patch}"]
+search = "{current_version}"
+replace = "{new_version}"
+regex = false
+ignore_missing_version = false
+ignore_missing_files = false
+tag = true
+sign_tags = false
+tag_name = "v{new_version}"
+tag_message = "Bump version: {current_version} → {new_version}"
+allow_dirty = false
+commit = true
+message = "Bump version: {current_version} → {new_version}"
+commit_args = ""
+setup_hooks = []
+pre_commit_hooks = []
+post_commit_hooks = []
+
+[[tool.bumpversion.files]]
+filename = "src/biointerface/__init__.py"
+search = "{current_version}"
+replace = "{new_version}"
+
+[[tool.bumpversion.files]]
+filename = "pyproject.toml"
+search = 'version = "{current_version}"'
+replace = 'version = "{new_version}"'

{biointerface-0.3.0 → biointerface-0.3.2}/src/biointerface/__init__.py

@@ -4,6 +4,6 @@ from biointerface.core import Interface, build_interfaces
 
 __author__ = """Alessandro Pandolfi"""
 __email__ = "alessandro.pandolfi@protonmail.com"
-__version__ = "0.3.0"
+__version__ = "0.3.2"
 
 __all__ = ["Interface", "build_interfaces"]

{biointerface-0.3.0 → biointerface-0.3.2}/src/biointerface/core.py

@@ -24,52 +24,6 @@ import copy
 import warnings
 
 
-def build_interfaces(structure, search_radius=5.0) -> list:
-    """
-    Extract all Protein-DNA interfaces found in a structure.
-
-    Parameters
-    ----------
-    structure : Bio.PDB.Structure
-        Biopython Structure entity.
-    search_radius : float | int, optional
-        Search radius, measured in Armstrong, within which Protein-DNA
-        interactions are found. Default is 5.0
-
-    Returns
-    -------
-    list
-        List of all Protein-DNA interfaces found in a structure.
-
-    """
-    # build nucleic acids
-    builder = NABuilder()
-    na_list = builder.build_nucleic_acids(structure)
-    if not na_list:
-        return []
-
-    # dna_chain_ids = list({na.get_chain_id() for na in na_list})
-
-    # build peptides
-    builder = PPBuilder()
-    pp_list = builder.build_peptides(structure)
-    if not pp_list:
-        return []
-
-    prot_chain_ids = list({pp[0].parent.id for pp in pp_list})
-
-    face_list = []
-    for prot_chain_id in prot_chain_ids:
-        face = Interface(
-            structure=structure,
-            protein_chain_id=prot_chain_id,
-            search_radius=search_radius,
-        )
-        face_list.append(face)
-
-    return face_list
-
-
 class Interface:
     """
     Extract Protein-DNA interface.
@@ -98,7 +52,7 @@ class Interface:
             {atom.parent.parent.id for atom in dna_atoms}
         )
 
-    def __repr__(self):
+    def __repr__(self) -> str:
         """Return string representation of the nucleic acid."""
         return f"<Interface chains={self.protein_chain_id}:\
 {''.join(self._dna_chain_ids)} contacts={len(self.contacts)} search_radius=\
@@ -270,7 +224,7 @@ chain id: {self.protein_chain_id}"
             Atom element
             Atomic coordinates (x, y, z)
             From both protein and DNA atoms
-            Euclidean distance
+            Euclidean distance between atom pair in contact
 
         Returns
         -------
@@ -281,7 +235,6 @@ chain id: {self.protein_chain_id}"
         data = []
 
         for na_atom, prot_atom in self.contacts:
-
             prot_res_hetfield = prot_atom.parent.id[0]
             prot_res_number = prot_atom.parent.id[1]
             prot_res_icode = prot_atom.parent.id[2]
@@ -305,7 +258,7 @@ chain id: {self.protein_chain_id}"
             dna_atom_coord_y = na_atom.coord[1]
             dna_atom_coord_z = na_atom.coord[2]
 
-            euclidian_distance = na_atom - prot_atom
+            euclidean_distance = na_atom - prot_atom
 
             row = (
                 self.protein_chain_id,
@@ -330,7 +283,7 @@ chain id: {self.protein_chain_id}"
                 dna_atom_coord_x,
                 dna_atom_coord_y,
                 dna_atom_coord_z,
-                euclidian_distance,
+                euclidean_distance,
             )
 
             data.append(row)
@@ -360,7 +313,7 @@ chain id: {self.protein_chain_id}"
                 "dna_atom_coord_x",
                 "dna_atom_coord_y",
                 "dna_atom_coord_z",
-                "euclidian_distance",
+                "euclidean_distance",
             ],
         )
 
@@ -379,11 +332,11 @@ chain id: {self.protein_chain_id}"
         to being protein-bound or not.
 
         A visual example of "gaps":
-            ```
-            Input full DSNA:            GATATACAAGCCA
-            Protein-bound:                ****  **
-            Output protein-bound DSNA:    TATACAAG
-            ```
+            ``Input full DSNA:            GATATACAAGCCA``
+
+            ``Protein-bound:                ****  **``
+
+            ``Output protein-bound DSNA:    TATACAAG``
 
         Returns
         -------
@@ -399,7 +352,8 @@ chain id: {self.protein_chain_id}"
         for dsna in dsna_list:
             bound_dsna = copy.copy(dsna)
             while (
-                bound_dsna[0].i_res not in bound_nucleotides
+                len(bound_dsna) > 0
+                and bound_dsna[0].i_res not in bound_nucleotides
                 and bound_dsna[0].j_res not in bound_nucleotides
             ):
                 # if the FIRST base pair isn't bound by protein
@@ -407,7 +361,8 @@ chain id: {self.protein_chain_id}"
                 bound_dsna.pop(0)
 
             while (
-                bound_dsna[-1].i_res not in bound_nucleotides
+                len(bound_dsna) > 0
+                and bound_dsna[-1].i_res not in bound_nucleotides
                 and bound_dsna[-1].j_res not in bound_nucleotides
             ):
                 # if the LAST base pair isn't bound by protein
@@ -431,6 +386,56 @@ inside the resulting DoubleStrandNucleicAcid - {bp}"
         return bound_dsna_list
 
 
+def build_interfaces(structure, search_radius=5.0) -> list[Interface]:
+    """
+    Extract all Protein-DNA interfaces found in a structure.
+
+    Parameters
+    ----------
+    structure : Bio.PDB.Structure
+        Biopython Structure entity.
+    search_radius : float | int, optional
+        Search radius, measured in Armstrong, within which Protein-DNA
+        interactions are found. Default is 5.0
+
+    Returns
+    -------
+    list
+        List of all Protein-DNA interfaces found in a structure.
+
+    """
+    # build nucleic acids
+    builder = NABuilder()
+    na_list = builder.build_nucleic_acids(structure)
+    if not na_list:
+        return []
+
+    # dna_chain_ids = list({na.get_chain_id() for na in na_list})
+
+    # build peptides
+    builder = PPBuilder()
+    pp_list = builder.build_peptides(structure)
+    if not pp_list:
+        return []
+
+    prot_chain_ids = list({pp[0].parent.id for pp in pp_list})
+
+    face_list = []
+    for prot_chain_id in prot_chain_ids:
+        # extract interface
+        face = Interface(
+            structure=structure,
+            protein_chain_id=prot_chain_id,
+            search_radius=search_radius,
+        )
+
+        # skip empty interfaces
+        if len(face.get_atomic_contacts()) > 0:
+            face_list.append(face)
+
+    return face_list
+
+
 # def export_atom_list(structure_id, atom_list, out_filepath):
 #     """Export atom list."""
 #     # not in Path but in string

{biointerface-0.3.0 → biointerface-0.3.2}/src/biointerface.egg-info/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.2
 Name: biointerface
-Version: 0.3.0
+Version: 0.3.2
 Summary: BioInterface is a Biopython based package that extracts Protein-DNA interfaces in a PDB structures.
 Author-email: Alessandro Pandolfi <alessandro.pandolfi@protonmail.com>
 Maintainer-email: Alessandro Pandolfi <alessandro.pandolfi@protonmail.com>
@@ -14,12 +14,21 @@ License-File: LICENSE
 License-File: AUTHORS.rst
 Requires-Dist: pandas
 Requires-Dist: biopython
-Requires-Dist: pdbnucleicacids>=0.2.1
+Requires-Dist: pdbnucleicacids>=0.2.2
 Provides-Extra: dev
-Requires-Dist: coverage; extra == "dev"
+Requires-Dist: spyder-kernels; extra == "dev"
+Requires-Dist: flake8; extra == "dev"
+Requires-Dist: ruff; extra == "dev"
 Requires-Dist: mypy; extra == "dev"
 Requires-Dist: pytest; extra == "dev"
-Requires-Dist: ruff; extra == "dev"
+Requires-Dist: tox; extra == "dev"
+Requires-Dist: coverage; extra == "dev"
+Requires-Dist: sphinx; extra == "dev"
+Requires-Dist: watchdog; extra == "dev"
+Requires-Dist: bump-my-version; extra == "dev"
+Requires-Dist: wheel; extra == "dev"
+Requires-Dist: build; extra == "dev"
+Requires-Dist: twine; extra == "dev"
 
 ============
 BioInterface
@@ -107,7 +116,6 @@ Feaures
 TODO
 --------
 
-* Proper tests (WIP)
 
 
 Credits

{biointerface-0.3.0 → biointerface-0.3.2}/src/biointerface.egg-info/SOURCES.txt

@@ -17,9 +17,6 @@ docs/make.bat
 docs/modules.rst
 docs/readme.rst
 docs/usage.rst
-docs/_build/html/_static/file.png
-docs/_build/html/_static/minus.png
-docs/_build/html/_static/plus.png
 src/biointerface/__init__.py
 src/biointerface/core.py
 src/biointerface.egg-info/PKG-INFO
@@ -28,4 +25,6 @@ src/biointerface.egg-info/dependency_links.txt
 src/biointerface.egg-info/requires.txt
 src/biointerface.egg-info/top_level.txt
 tests/__init__.py
-tests/test_biointerface.py
+tests/test_biointerface.py
+tests/test_core.py
+tests/data/gattaca.cif

biointerface-0.3.2/src/biointerface.egg-info/requires.txt

@@ -0,0 +1,18 @@
+pandas
+biopython
+pdbnucleicacids>=0.2.2
+
+[dev]
+spyder-kernels
+flake8
+ruff
+mypy
+pytest
+tox
+coverage
+sphinx
+watchdog
+bump-my-version
+wheel
+build
+twine

biointerface-0.3.2/tests/data/gattaca.cif

@@ -0,0 +1,547 @@
+# generated by PyMOL 3.0.5
+#
+data_gattaca
+_entry.id gattaca
+#
+loop_
+_atom_site.group_PDB
+_atom_site.id
+_atom_site.type_symbol
+_atom_site.label_atom_id
+_atom_site.label_alt_id
+_atom_site.label_comp_id
+_atom_site.label_asym_id
+_atom_site.label_entity_id
+_atom_site.label_seq_id
+_atom_site.pdbx_PDB_ins_code
+_atom_site.Cartn_x
+_atom_site.Cartn_y
+_atom_site.Cartn_z
+_atom_site.occupancy
+_atom_site.B_iso_or_equiv
+_atom_site.pdbx_formal_charge
+_atom_site.auth_asym_id
+_atom_site.pdbx_PDB_model_num
+ATOM   1   N N   . HIS . . 1 ? -0.248  4.140 -11.414 1.00   0.00 0 C 1
+ATOM   2   C CA  . HIS . . 1 ?  0.306  5.459 -11.121 1.00   0.00 0 C 1
+ATOM   3   C C   . HIS . . 1 ?  1.815  5.432 -11.152 1.00   0.00 0 C 1
+ATOM   4   O O   . HIS . . 1 ?  2.449  4.395 -11.399 1.00   0.00 0 C 1
+ATOM   5   C CB  . HIS . . 1 ? -0.195  5.836 -9.717 1.00   0.00 0 C 1
+ATOM   6   C CG  . HIS . . 1 ? -1.027  7.085 -9.725 1.00   0.00 0 C 1
+ATOM   7   C CD2 . HIS . . 1 ? -2.406  7.067 -9.887 1.00   0.00 0 C 1
+ATOM   8   N ND1 . HIS . . 1 ? -0.549  8.385 -9.576 1.00   0.00 0 C 1
+ATOM   9   C CE1 . HIS . . 1 ? -1.705  9.068 -9.667 1.00   0.00 0 C 1
+ATOM   10  N NE2 . HIS . . 1 ? -2.854  8.362 -9.849 1.00   0.00 0 C 1
+ATOM   11  H H   . HIS . . 1 ?  0.383  3.288 -11.619 1.00   0.00 0 C 1
+ATOM   12  H HA  . HIS . . 1 ? -0.014  6.142 -11.926 1.00   0.00 0 C 1
+ATOM   13  H 2HB . HIS . . 1 ?  0.651  5.995 -9.019 1.00   0.00 0 C 1
+ATOM   14  H 3HB . HIS . . 1 ? -0.805  5.029 -9.260 1.00   0.00 0 C 1
+ATOM   15  H 2HD . HIS . . 1 ? -2.998  6.166 -10.019 1.00   0.00 0 C 1
+ATOM   16  H 1HE . HIS . . 1 ? -1.658 10.146 -9.587 1.00   0.00 0 C 1
+ATOM   17  H 2HE . HIS . . 1 ? -3.821  8.706 -9.939 1.00   0.00 0 C 1
+ATOM   18  N N   . VAL . . 2 ?  2.465  6.521 -10.915 1.00   0.00 0 C 1
+ATOM   19  C CA  . VAL . . 2 ?  3.924  6.495 -10.944 1.00   0.00 0 C 1
+ATOM   20  C C   . VAL . . 2 ?  4.495  7.860 -10.643 1.00   0.00 0 C 1
+ATOM   21  O O   . VAL . . 2 ?  3.773  8.837 -10.408 1.00   0.00 0 C 1
+ATOM   22  C CB  . VAL . . 2 ?  4.422  5.976 -12.351 1.00   0.00 0 C 1
+ATOM   23  C CG1 . VAL . . 2 ?  5.951  6.062 -12.616 1.00   0.00 0 C 1
+ATOM   24  C CG2 . VAL . . 2 ?  4.039  4.506 -12.648 1.00   0.00 0 C 1
+ATOM   25  H H   . VAL . . 2 ?  1.971  7.378 -10.711 1.00   0.00 0 C 1
+ATOM   26  H HA  . VAL . . 2 ?  4.285  5.812 -10.154 1.00   0.00 0 C 1
+ATOM   27  H HB  . VAL . . 2 ?  3.932  6.605 -13.125 1.00   0.00 0 C 1
+ATOM   28  H 1HG1 . VAL . . 2 ?  6.541  5.482 -11.882 1.00   0.00 0 C 1
+ATOM   29  H 2HG1 . VAL . . 2 ?  6.224  5.692 -13.623 1.00   0.00 0 C 1
+ATOM   30  H 3HG1 . VAL . . 2 ?  6.327  7.102 -12.585 1.00   0.00 0 C 1
+ATOM   31  H 1HG2 . VAL . . 2 ?  2.951  4.338 -12.556 1.00   0.00 0 C 1
+ATOM   32  H 2HG2 . VAL . . 2 ?  4.306  4.212 -13.682 1.00   0.00 0 C 1
+ATOM   33  H 3HG2 . VAL . . 2 ?  4.539  3.795 -11.965 1.00   0.00 0 C 1
+ATOM   34  N N   . MET . . 3 ?  5.776  8.012 -10.629 1.00   0.00 0 C 1
+ATOM   35  C CA  . MET . . 3 ?  6.330  9.331 -10.337 1.00   0.00 0 C 1
+ATOM   36  C C   . MET . . 3 ?  7.839  9.304 -10.368 1.00   0.00 0 C 1
+ATOM   37  O O   . MET . . 3 ?  8.472  8.267 -10.615 1.00   0.00 0 C 1
+ATOM   38  C CB  . MET . . 3 ?  5.812  9.827 -8.959 1.00   0.00 0 C 1
+ATOM   39  C CG  . MET . . 3 ?  4.286 10.030 -8.845 1.00   0.00 0 C 1
+ATOM   40  S SD  . MET . . 3 ?  3.896 10.874 -7.304 1.00   0.00 0 C 1
+ATOM   41  C CE  . MET . . 3 ?  2.119 10.601 -7.293 1.00   0.00 0 C 1
+ATOM   42  H H   . MET . . 3 ?  6.387  7.230 -10.817 1.00   0.00 0 C 1
+ATOM   43  H HA  . MET . . 3 ?  6.001 10.034 -11.125 1.00   0.00 0 C 1
+ATOM   44  H 2HB . MET . . 3 ?  6.299 10.789 -8.709 1.00   0.00 0 C 1
+ATOM   45  H 3HB . MET . . 3 ?  6.138  9.129 -8.161 1.00   0.00 0 C 1
+ATOM   46  H 2HG . MET . . 3 ?  3.770  9.052 -8.868 1.00   0.00 0 C 1
+ATOM   47  H 3HG . MET . . 3 ?  3.890 10.618 -9.693 1.00   0.00 0 C 1
+ATOM   48  H 1HE . MET . . 3 ?  1.654 10.986 -8.219 1.00   0.00 0 C 1
+ATOM   49  H 2HE . MET . . 3 ?  1.896  9.522 -7.215 1.00   0.00 0 C 1
+ATOM   50  H 3HE . MET . . 3 ?  1.654 11.112 -6.433 1.00   0.00 0 C 1
+ATOM   51  N N   . SER . . 4 ?  8.489 10.393 -10.130 1.00   0.00 0 C 1
+ATOM   52  C CA  . SER . . 4 ?  9.949 10.366 -10.161 1.00   0.00 0 C 1
+ATOM   53  C C   . SER . . 4 ? 10.521 11.731 -9.859 1.00   0.00 0 C 1
+ATOM   54  O O   . SER . . 4 ?  9.802 12.702 -9.625 1.00   0.00 0 C 1
+ATOM   55  C CB  . SER . . 4 ? 10.462  9.820 -11.516 1.00   0.00 0 C 1
+ATOM   56  O OG  . SER . . 4 ? 10.221 10.717 -12.605 1.00   0.00 0 C 1
+ATOM   57  H H   . SER . . 4 ?  7.996 11.251 -9.927 1.00   0.00 0 C 1
+ATOM   58  H HA  . SER . . 4 ? 10.294  9.689 -9.357 1.00   0.00 0 C 1
+ATOM   59  H 2HB . SER . . 4 ? 10.016  8.833 -11.745 1.00   0.00 0 C 1
+ATOM   60  H 3HB . SER . . 4 ? 11.552  9.632 -11.454 1.00   0.00 0 C 1
+ATOM   61  H HG  . SER . . 4 ?  9.270 10.813 -12.694 1.00   0.00 0 C 1
+ATOM   62  P P   . DG  A . 1 ? -1.158  9.255  1.830 1.00   0.00 0 A 1
+ATOM   63  O O1P . DG  A . 1 ? -1.113 10.526  2.587 1.00   0.00 0 A 1
+ATOM   64  O O2P . DG  A . 1 ? -2.136  9.193  0.722 1.00   0.00 -1 A 1
+ATOM   65  C C5' . DG  A . 1 ?  1.219  8.193  2.128 1.00   0.00 0 A 1
+ATOM   66  O O5' . DG  A . 1 ?  0.303  8.906  1.277 1.00   0.00 0 A 1
+ATOM   67  C C4' . DG  A . 1 ?  1.924  7.109  1.337 1.00   0.00 0 A 1
+ATOM   68  O O4' . DG  A . 1 ?  1.184  5.854  1.334 1.00   0.00 0 A 1
+ATOM   69  C C3' . DG  A . 1 ?  2.150  7.407 -0.145 1.00   0.00 0 A 1
+ATOM   70  O O3' . DG  A . 1 ?  3.408  6.869 -0.536 1.00   0.00 0 A 1
+ATOM   71  C C2' . DG  A . 1 ?  1.046  6.635 -0.868 1.00   0.00 0 A 1
+ATOM   72  C C1' . DG  A . 1 ?  1.111  5.381 -0.002 1.00   0.00 0 A 1
+ATOM   73  N N1  . DG  A . 1 ? -0.569  0.570  0.007 1.00   0.00 0 A 1
+ATOM   74  C C2  . DG  A . 1 ?  0.714  1.060  0.154 1.00   0.00 0 A 1
+ATOM   75  N N2  . DG  A . 1 ?  1.674  0.148  0.326 1.00   0.00 0 A 1
+ATOM   76  N N3  . DG  A . 1 ?  1.009  2.358  0.131 1.00   0.00 0 A 1
+ATOM   77  C C4  . DG  A . 1 ? -0.093  3.132 -0.053 1.00   0.00 0 A 1
+ATOM   78  C C5  . DG  A . 1 ? -1.401  2.737 -0.208 1.00   0.00 0 A 1
+ATOM   79  C C6  . DG  A . 1 ? -1.716  1.354 -0.183 1.00   0.00 0 A 1
+ATOM   80  O O6  . DG  A . 1 ? -2.812  0.812 -0.302 1.00   0.00 0 A 1
+ATOM   81  N N7  . DG  A . 1 ? -2.232  3.844 -0.372 1.00   0.00 0 A 1
+ATOM   82  C C8  . DG  A . 1 ? -1.408  4.863 -0.312 1.00   0.00 0 A 1
+ATOM   83  N N9  . DG  A . 1 ? -0.091  4.509 -0.119 1.00   0.00 0 A 1
+ATOM   84  H H01 . DG  A . 1 ? -2.416  8.283  0.592 1.00   0.00 0 A 1
+ATOM   85  H H02 . DG  A . 1 ?  0.664  7.734  2.947 1.00   0.00 0 A 1
+ATOM   86  H H03 . DG  A . 1 ?  1.958  8.888  2.528 1.00   0.00 0 A 1
+ATOM   87  H H04 . DG  A . 1 ?  2.880  7.052  1.858 1.00   0.00 0 A 1
+ATOM   88  H H05 . DG  A . 1 ?  2.136  8.474 -0.364 1.00   0.00 0 A 1
+ATOM   89  H H06 . DG  A . 1 ?  1.166  6.496 -1.942 1.00   0.00 0 A 1
+ATOM   90  H H07 . DG  A . 1 ?  0.079  7.134 -0.810 1.00   0.00 0 A 1
+ATOM   91  H H08 . DG  A . 1 ?  1.960  4.774 -0.316 1.00   0.00 0 A 1
+ATOM   92  H H09 . DG  A . 1 ? -0.691 -0.433  0.039 1.00   0.00 0 A 1
+ATOM   93  H H10 . DG  A . 1 ?  2.634  0.440  0.440 1.00   0.00 0 A 1
+ATOM   94  H H11 . DG  A . 1 ?  1.440 -0.835  0.343 1.00   0.00 0 A 1
+ATOM   95  H H12 . DG  A . 1 ? -1.737  5.898 -0.406 1.00   0.00 0 A 1
+ATOM   96  P P   . DA  A . 2 ?  4.328  7.703 -1.545 1.00   0.00 0 A 1
+ATOM   97  O O1P . DA  A . 2 ?  5.111  8.705 -0.788 1.00   0.00 0 A 1
+ATOM   98  O O2P . DA  A . 2 ?  3.500  8.228 -2.653 1.00   0.00 -1 A 1
+ATOM   99  C C5' . DA  A . 2 ?  5.627  5.447 -1.247 1.00   0.00 0 A 1
+ATOM   100 O O5' . DA  A . 2 ?  5.305  6.562 -2.098 1.00   0.00 0 A 1
+ATOM   101 C C4' . DA  A . 2 ?  5.560  4.156 -2.038 1.00   0.00 0 A 1
+ATOM   102 O O4' . DA  A . 2 ?  4.224  3.575 -2.041 1.00   0.00 0 A 1
+ATOM   103 C C3' . DA  A . 2 ?  5.918  4.264 -3.520 1.00   0.00 0 A 1
+ATOM   104 O O3' . DA  A . 2 ?  6.620  3.089 -3.911 1.00   0.00 0 A 1
+ATOM   105 C C2' . DA  A . 2 ?  4.571  4.288 -4.243 1.00   0.00 0 A 1
+ATOM   106 C C1' . DA  A . 2 ?  3.887  3.236 -3.377 1.00   0.00 0 A 1
+ATOM   107 N N1  . DA  A . 2 ? -0.372  0.360 -3.377 1.00   0.00 0 A 1
+ATOM   108 C C2  . DA  A . 2 ?  0.918  0.056 -3.239 1.00   0.00 0 A 1
+ATOM   109 N N3  . DA  A . 2 ?  1.964  0.853 -3.250 1.00   0.00 0 A 1
+ATOM   110 C C4  . DA  A . 2 ?  1.588  2.135 -3.430 1.00   0.00 0 A 1
+ATOM   111 C C5  . DA  A . 2 ?  0.313  2.599 -3.585 1.00   0.00 0 A 1
+ATOM   112 C C6  . DA  A . 2 ? -0.721  1.647 -3.555 1.00   0.00 0 A 1
+ATOM   113 N N6  . DA  A . 2 ? -2.017  1.959 -3.694 1.00   0.00 0 A 1
+ATOM   114 N N7  . DA  A . 2 ?  0.312  3.977 -3.747 1.00   0.00 0 A 1
+ATOM   115 C C8  . DA  A . 2 ?  1.567  4.299 -3.685 1.00   0.00 0 A 1
+ATOM   116 N N9  . DA  A . 2 ?  2.402  3.237 -3.494 1.00   0.00 0 A 1
+ATOM   117 H H01 . DA  A . 2 ?  4.909  5.403 -0.428 1.00   0.00 0 A 1
+ATOM   118 H H02 . DA  A . 2 ?  6.633  5.575 -0.847 1.00   0.00 0 A 1
+ATOM   119 H H03 . DA  A . 2 ?  6.300  3.548 -1.517 1.00   0.00 0 A 1
+ATOM   120 H H04 . DA  A . 2 ?  6.534  5.136 -3.739 1.00   0.00 0 A 1
+ATOM   121 H H05 . DA  A . 2 ?  4.587  4.105 -5.317 1.00   0.00 0 A 1
+ATOM   122 H H06 . DA  A . 2 ?  4.082  5.261 -4.185 1.00   0.00 0 A 1
+ATOM   123 H H07 . DA  A . 2 ?  4.217  2.245 -3.691 1.00   0.00 0 A 1
+ATOM   124 H H08 . DA  A . 2 ?  1.137 -1.002 -3.096 1.00   0.00 0 A 1
+ATOM   125 H H09 . DA  A . 2 ? -2.717  1.232 -3.664 1.00   0.00 0 A 1
+ATOM   126 H H10 . DA  A . 2 ? -2.294  2.921 -3.828 1.00   0.00 0 A 1
+ATOM   127 H H11 . DA  A . 2 ?  1.922  5.325 -3.777 1.00   0.00 0 A 1
+ATOM   128 H H13 . DA  A . 2 ?  3.246  7.506 -3.232 1.00   0.00 0 A 1
+ATOM   129 P P   . DT  A . 3 ?  7.855  3.224 -4.920 1.00   0.00 0 A 1
+ATOM   130 O O1P . DT  A . 3 ?  9.077  3.574 -4.163 1.00   0.00 0 A 1
+ATOM   131 O O2P . DT  A . 3 ?  7.493  4.135 -6.028 1.00   0.00 -1 A 1
+ATOM   132 C C5' . DT  A . 3 ?  7.579  0.635 -4.622 1.00   0.00 0 A 1
+ATOM   133 O O5' . DT  A . 3 ?  7.974  1.726 -5.473 1.00   0.00 0 A 1
+ATOM   134 C C4' . DT  A . 3 ?  6.766 -0.371 -5.413 1.00   0.00 0 A 1
+ATOM   135 O O4' . DT  A . 3 ?  5.344 -0.055 -5.416 1.00   0.00 0 A 1
+ATOM   136 C C3' . DT  A . 3 ?  7.119 -0.494 -6.895 1.00   0.00 0 A 1
+ATOM   137 O O3' . DT  A . 3 ?  6.996 -1.856 -7.286 1.00   0.00 0 A 1
+ATOM   138 C C2' . DT  A . 3 ?  6.044  0.318 -7.618 1.00   0.00 0 A 1
+ATOM   139 C C1' . DT  A . 3 ?  4.871 -0.131 -6.752 1.00   0.00 0 A 1
+ATOM   140 N N1  . DT  A . 3 ?  3.671  0.742 -6.869 1.00   0.00 0 A 1
+ATOM   141 C C2  . DT  A . 3 ?  2.443  0.133 -6.777 1.00   0.00 0 A 1
+ATOM   142 O O2  . DT  A . 3 ?  2.308 -1.066 -6.607 1.00   0.00 0 A 1
+ATOM   143 N N3  . DT  A . 3 ?  1.352  0.974 -6.891 1.00   0.00 0 A 1
+ATOM   144 C C4  . DT  A . 3 ?  1.390  2.340 -7.084 1.00   0.00 0 A 1
+ATOM   145 O O4  . DT  A . 3 ?  0.345  2.990 -7.171 1.00   0.00 0 A 1
+ATOM   146 C C5  . DT  A . 3 ?  2.723  2.888 -7.168 1.00   0.00 0 A 1
+ATOM   147 C C5M . DT  A . 3 ?  2.854  4.367 -7.378 1.00   0.00 0 A 1
+ATOM   148 C C6  . DT  A . 3 ?  3.801  2.093 -7.061 1.00   0.00 0 A 1
+ATOM   149 H H01 . DT  A . 3 ?  6.972  1.021 -3.803 1.00   0.00 0 A 1
+ATOM   150 H H02 . DT  A . 3 ?  8.468  0.147 -4.222 1.00   0.00 0 A 1
+ATOM   151 H H03 . DT  A . 3 ?  7.008 -1.297 -4.892 1.00   0.00 0 A 1
+ATOM   152 H H04 . DT  A . 3 ?  8.130 -0.150 -7.114 1.00   0.00 0 A 1
+ATOM   153 H H05 . DT  A . 3 ?  5.949  0.160 -8.692 1.00   0.00 0 A 1
+ATOM   154 H H06 . DT  A . 3 ?  6.220  1.392 -7.560 1.00   0.00 0 A 1
+ATOM   155 H H07 . DT  A . 3 ?  4.557 -1.127 -7.066 1.00   0.00 0 A 1
+ATOM   156 H H08 . DT  A . 3 ?  0.439  0.548 -6.826 1.00   0.00 0 A 1
+ATOM   157 H H09 . DT  A . 3 ?  3.813  4.584 -7.849 1.00   0.00 0 A 1
+ATOM   158 H H10 . DT  A . 3 ?  2.047  4.717 -8.021 1.00   0.00 0 A 1
+ATOM   159 H H11 . DT  A . 3 ?  2.800  4.878 -6.416 1.00   0.00 0 A 1
+ATOM   160 H H12 . DT  A . 3 ?  7.269  3.619 -6.806 1.00   0.00 0 A 1
+ATOM   161 H H13 . DT  A . 3 ?  4.797  2.530 -7.128 1.00   0.00 0 A 1
+ATOM   162 P P   . DT  A . 4 ?  8.075 -2.473 -8.295 1.00   0.00 0 A 1
+ATOM   163 O O1P . DT  A . 4 ?  9.270 -2.909 -7.538 1.00   0.00 0 A 1
+ATOM   164 O O2P . DT  A . 4 ?  8.318 -1.524 -9.403 1.00   0.00 -1 A 1
+ATOM   165 C C5' . DT  A . 4 ?  6.330 -4.406 -7.997 1.00   0.00 0 A 1
+ATOM   166 O O5' . DT  A . 4 ?  7.291 -3.755 -8.848 1.00   0.00 0 A 1
+ATOM   167 C C4' . DT  A . 4 ?  5.081 -4.741 -8.788 1.00   0.00 0 A 1
+ATOM   168 O O4' . DT  A . 4 ?  4.116 -3.650 -8.791 1.00   0.00 0 A 1
+ATOM   169 C C3' . DT  A . 4 ?  5.295 -5.048 -10.270 1.00   0.00 0 A 1
+ATOM   170 O O3' . DT  A . 4 ?  4.394 -6.079 -10.661 1.00   0.00 0 A 1
+ATOM   171 C C2' . DT  A . 4 ?  4.902 -3.760 -10.993 1.00   0.00 0 A 1
+ATOM   172 C C1' . DT  A . 4 ?  3.689 -3.434 -10.127 1.00   0.00 0 A 1
+ATOM   173 N N1  . DT  A . 4 ?  3.231 -2.022 -10.244 1.00   0.00 0 A 1
+ATOM   174 C C2  . DT  A . 4 ?  1.880 -1.793 -10.152 1.00   0.00 0 A 1
+ATOM   175 O O2  . DT  A . 4 ?  1.066 -2.684 -9.982 1.00   0.00 0 A 1
+ATOM   176 N N3  . DT  A . 4 ?  1.492 -0.471 -10.266 1.00   0.00 0 A 1
+ATOM   177 C C4  . DT  A . 4 ?  2.325  0.611 -10.459 1.00   0.00 0 A 1
+ATOM   178 O O4  . DT  A . 4 ?  1.862  1.751 -10.546 1.00   0.00 0 A 1
+ATOM   179 C C5  . DT  A . 4 ?  3.726  0.271 -10.543 1.00   0.00 0 A 1
+ATOM   180 C C5M . DT  A . 4 ?  4.702  1.391 -10.753 1.00   0.00 0 A 1
+ATOM   181 C C6  . DT  A . 4 ?  4.130 -1.006 -10.436 1.00   0.00 0 A 1
+ATOM   182 H H01 . DT  A . 4 ?  6.066 -3.736 -7.178 1.00   0.00 0 A 1
+ATOM   183 H H02 . DT  A . 4 ?  6.763 -5.323 -7.597 1.00   0.00 0 A 1
+ATOM   184 H H03 . DT  A . 4 ?  4.732 -5.633 -8.267 1.00   0.00 0 A 1
+ATOM   185 H H04 . DT  A . 4 ?  6.314 -5.365 -10.489 1.00   0.00 0 A 1
+ATOM   186 H H05 . DT  A . 4 ?  4.733 -3.832 -12.067 1.00   0.00 0 A 1
+ATOM   187 H H06 . DT  A . 4 ?  5.676 -2.994 -10.935 1.00   0.00 0 A 1
+ATOM   188 H H07 . DT  A . 4 ?  2.850 -4.055 -10.441 1.00   0.00 0 A 1
+ATOM   189 H H08 . DT  A . 4 ?  0.503 -0.279 -10.201 1.00   0.00 0 A 1
+ATOM   190 H H09 . DT  A . 4 ?  5.622  0.995 -11.182 1.00   0.00 0 A 1
+ATOM   191 H H10 . DT  A . 4 ?  4.271  2.126 -11.432 1.00   0.00 0 A 1
+ATOM   192 H H11 . DT  A . 4 ?  4.923  1.865 -9.796 1.00   0.00 0 A 1
+ATOM   193 H H12 . DT  A . 4 ?  5.193 -1.237 -10.503 1.00   0.00 0 A 1
+ATOM   194 H H14 . DT  A . 4 ?  8.161 -0.628 -9.097 1.00   0.00 0 A 1
+ATOM   195 P P   . DA  A . 5 ?  4.904 -7.212 -11.670 1.00   0.00 0 A 1
+ATOM   196 O O1P . DA  A . 5 ?  5.615 -8.266 -10.913 1.00   0.00 0 A 1
+ATOM   197 O O2P . DA  A . 5 ?  5.659 -6.587 -12.778 1.00   0.00 -1 A 1
+ATOM   198 C C5' . DA  A . 5 ?  2.357 -7.750 -11.372 1.00   0.00 0 A 1
+ATOM   199 O O5' . DA  A . 5 ?  3.517 -7.788 -12.223 1.00   0.00 0 A 1
+ATOM   200 C C4' . DA  A . 5 ?  1.149 -7.287 -12.163 1.00   0.00 0 A 1
+ATOM   201 O O4' . DA  A . 5 ?  1.010 -5.837 -12.166 1.00   0.00 0 A 1
+ATOM   202 C C3' . DA  A . 5 ?  1.142 -7.661 -13.645 1.00   0.00 0 A 1
+ATOM   203 O O3' . DA  A . 5 ? -0.192 -7.965 -14.036 1.00   0.00 0 A 1
+ATOM   204 C C2' . DA  A . 5 ?  1.581 -6.388 -14.368 1.00   0.00 0 A 1
+ATOM   205 C C1' . DA  A . 5 ?  0.791 -5.411 -13.502 1.00   0.00 0 A 1
+ATOM   206 N N1  . DA  A . 5 ? -0.628 -0.472 -13.502 1.00   0.00 0 A 1
+ATOM   207 C C2  . DA  A . 5 ? -1.315 -1.605 -13.364 1.00   0.00 0 A 1
+ATOM   208 N N3  . DA  A . 5 ? -0.881 -2.846 -13.375 1.00   0.00 0 A 1
+ATOM   209 C C4  . DA  A . 5 ?  0.455 -2.885 -13.555 1.00   0.00 0 A 1
+ATOM   210 C C5  . DA  A . 5 ?  1.290 -1.815 -13.710 1.00   0.00 0 A 1
+ATOM   211 C C6  . DA  A . 5 ?  0.705 -0.539 -13.680 1.00   0.00 0 A 1
+ATOM   212 N N6  . DA  A . 5 ?  1.402  0.598 -13.819 1.00   0.00 0 A 1
+ATOM   213 N N7  . DA  A . 5 ?  2.601 -2.241 -13.872 1.00   0.00 0 A 1
+ATOM   214 C C8  . DA  A . 5 ?  2.520 -3.534 -13.810 1.00   0.00 0 A 1
+ATOM   215 N N9  . DA  A . 5 ?  1.251 -3.999 -13.619 1.00   0.00 0 A 1
+ATOM   216 H H01 . DA  A . 5 ?  2.537 -7.053 -10.553 1.00   0.00 0 A 1
+ATOM   217 H H02 . DA  A . 5 ?  2.168 -8.746 -10.972 1.00   0.00 0 A 1
+ATOM   218 H H03 . DA  A . 5 ?  0.343 -7.803 -11.642 1.00   0.00 0 A 1
+ATOM   219 H H04 . DA  A . 5 ?  1.780 -8.516 -13.864 1.00   0.00 0 A 1
+ATOM   220 H H05 . DA  A . 5 ?  1.402 -6.346 -15.442 1.00   0.00 0 A 1
+ATOM   221 H H06 . DA  A . 5 ?  2.657 -6.223 -14.310 1.00   0.00 0 A 1
+ATOM   222 H H07 . DA  A . 5 ? -0.252 -5.420 -13.816 1.00   0.00 0 A 1
+ATOM   223 H H08 . DA  A . 5 ? -2.389 -1.487 -13.221 1.00   0.00 0 A 1
+ATOM   224 H H09 . DA  A . 5 ?  0.926  1.489 -13.789 1.00   0.00 0 A 1
+ATOM   225 H H10 . DA  A . 5 ?  2.402  0.564 -13.953 1.00   0.00 0 A 1
+ATOM   226 H H11 . DA  A . 5 ?  3.386 -4.189 -13.902 1.00   0.00 0 A 1
+ATOM   227 H H13 . DA  A . 5 ?  5.743 -5.644 -12.616 1.00   0.00 0 A 1
+ATOM   228 P P   . DC  A . 6 ? -0.446 -9.181 -15.045 1.00   0.00 0 A 1
+ATOM   229 O O1P . DC  A . 6 ? -0.491 -10.452 -14.288 1.00   0.00 0 A 1
+ATOM   230 O O2P . DC  A . 6 ?  0.532 -9.119 -16.153 1.00   0.00 -1 A 1
+ATOM   231 C C5' . DC  A . 6 ? -2.823 -8.119 -14.747 1.00   0.00 0 A 1
+ATOM   232 O O5' . DC  A . 6 ? -1.907 -8.832 -15.598 1.00   0.00 0 A 1
+ATOM   233 C C4' . DC  A . 6 ? -3.528 -7.035 -15.538 1.00   0.00 0 A 1
+ATOM   234 O O4' . DC  A . 6 ? -2.788 -5.780 -15.541 1.00   0.00 0 A 1
+ATOM   235 C C3' . DC  A . 6 ? -3.754 -7.333 -17.020 1.00   0.00 0 A 1
+ATOM   236 O O3' . DC  A . 6 ? -5.012 -6.795 -17.411 1.00   0.00 0 A 1
+ATOM   237 C C2' . DC  A . 6 ? -2.650 -6.561 -17.743 1.00   0.00 0 A 1
+ATOM   238 C C1' . DC  A . 6 ? -2.715 -5.307 -16.877 1.00   0.00 0 A 1
+ATOM   239 N N1  . DC  A . 6 ? -1.513 -4.435 -16.994 1.00   0.00 0 A 1
+ATOM   240 C C2  . DC  A . 6 ? -1.699 -3.058 -16.903 1.00   0.00 0 A 1
+ATOM   241 O O2  . DC  A . 6 ? -2.842 -2.620 -16.730 1.00   0.00 0 A 1
+ATOM   242 N N3  . DC  A . 6 ? -0.616 -2.245 -17.008 1.00   0.00 0 A 1
+ATOM   243 C C4  . DC  A . 6 ?  0.607 -2.759 -17.195 1.00   0.00 0 A 1
+ATOM   244 N N4  . DC  A . 6 ?  1.631 -1.926 -17.291 1.00   0.00 0 A 1
+ATOM   245 C C5  . DC  A . 6 ?  0.819 -4.173 -17.292 1.00   0.00 0 A 1
+ATOM   246 C C6  . DC  A . 6 ? -0.276 -4.967 -17.185 1.00   0.00 0 A 1
+ATOM   247 H H01 . DC  A . 6 ? -2.268 -7.661 -13.928 1.00   0.00 0 A 1
+ATOM   248 H H02 . DC  A . 6 ? -3.562 -8.815 -14.347 1.00   0.00 0 A 1
+ATOM   249 H H03 . DC  A . 6 ? -4.484 -6.979 -15.017 1.00   0.00 0 A 1
+ATOM   250 H H04 . DC  A . 6 ? -3.740 -8.401 -17.239 1.00   0.00 0 A 1
+ATOM   251 H H05 . DC  A . 6 ? -2.771 -6.423 -18.817 1.00   0.00 0 A 1
+ATOM   252 H H06 . DC  A . 6 ? -1.683 -7.061 -17.685 1.00   0.00 0 A 1
+ATOM   253 H H07 . DC  A . 6 ? -3.565 -4.701 -17.191 1.00   0.00 0 A 1
+ATOM   254 H H08 . DC  A . 6 ?  2.564 -2.287 -17.432 1.00   0.00 0 A 1
+ATOM   255 H H09 . DC  A . 6 ?  1.479 -0.930 -17.222 1.00   0.00 0 A 1
+ATOM   256 H H10 . DC  A . 6 ?  1.814 -4.592 -17.444 1.00   0.00 0 A 1
+ATOM   257 H H11 . DC  A . 6 ? -0.163 -6.049 -17.253 1.00   0.00 0 A 1
+ATOM   258 H H12 . DC  A . 6 ?  0.675 -8.204 -16.402 1.00   0.00 0 A 1
+ATOM   259 P P   . DA  A . 7 ? -5.932 -7.630 -18.420 1.00   0.00 0 A 1
+ATOM   260 O O1P . DA  A . 7 ? -6.716 -8.632 -17.663 1.00   0.00 0 A 1
+ATOM   261 O O2P . DA  A . 7 ? -5.105 -8.155 -19.528 1.00   0.00 -1 A 1
+ATOM   262 C C5' . DA  A . 7 ? -7.231 -5.374 -18.122 1.00   0.00 0 A 1
+ATOM   263 O O5' . DA  A . 7 ? -6.909 -6.489 -18.973 1.00   0.00 0 A 1
+ATOM   264 C C4' . DA  A . 7 ? -7.164 -4.083 -18.913 1.00   0.00 0 A 1
+ATOM   265 O O4' . DA  A . 7 ? -5.828 -3.502 -18.916 1.00   0.00 0 A 1
+ATOM   266 C C3' . DA  A . 7 ? -7.522 -4.191 -20.395 1.00   0.00 0 A 1
+ATOM   267 O O3' . DA  A . 7 ? -8.224 -3.016 -20.786 1.00   0.00 0 A 1
+ATOM   268 C C2' . DA  A . 7 ? -6.175 -4.215 -21.118 1.00   0.00 0 A 1
+ATOM   269 C C1' . DA  A . 7 ? -5.491 -3.162 -20.252 1.00   0.00 0 A 1
+ATOM   270 N N1  . DA  A . 7 ? -1.232 -0.286 -20.252 1.00   0.00 0 A 1
+ATOM   271 C C2  . DA  A . 7 ? -2.522  0.017 -20.114 1.00   0.00 0 A 1
+ATOM   272 N N3  . DA  A . 7 ? -3.568 -0.780 -20.125 1.00   0.00 0 A 1
+ATOM   273 C C4  . DA  A . 7 ? -3.192 -2.062 -20.305 1.00   0.00 0 A 1
+ATOM   274 C C5  . DA  A . 7 ? -1.917 -2.525 -20.460 1.00   0.00 0 A 1
+ATOM   275 C C6  . DA  A . 7 ? -0.884 -1.574 -20.430 1.00   0.00 0 A 1
+ATOM   276 N N6  . DA  A . 7 ?  0.413 -1.886 -20.569 1.00   0.00 0 A 1
+ATOM   277 N N7  . DA  A . 7 ? -1.916 -3.904 -20.622 1.00   0.00 0 A 1
+ATOM   278 C C8  . DA  A . 7 ? -3.171 -4.226 -20.560 1.00   0.00 0 A 1
+ATOM   279 N N9  . DA  A . 7 ? -4.006 -3.163 -20.369 1.00   0.00 0 A 1
+ATOM   280 H H01 . DA  A . 7 ? -6.513 -5.329 -17.303 1.00   0.00 0 A 1
+ATOM   281 H H02 . DA  A . 7 ? -8.237 -5.502 -17.722 1.00   0.00 0 A 1
+ATOM   282 H H03 . DA  A . 7 ? -7.904 -3.475 -18.392 1.00   0.00 0 A 1
+ATOM   283 H H04 . DA  A . 7 ? -8.139 -5.063 -20.614 1.00   0.00 0 A 1
+ATOM   284 H H05 . DA  A . 7 ? -8.413 -3.054 -21.726 1.00   0.00 0 A 1
+ATOM   285 H H06 . DA  A . 7 ? -6.192 -4.032 -22.192 1.00   0.00 0 A 1
+ATOM   286 H H07 . DA  A . 7 ? -5.686 -5.188 -21.060 1.00   0.00 0 A 1
+ATOM   287 H H08 . DA  A . 7 ? -5.822 -2.172 -20.566 1.00   0.00 0 A 1
+ATOM   288 H H09 . DA  A . 7 ? -2.742  1.075 -19.971 1.00   0.00 0 A 1
+ATOM   289 H H10 . DA  A . 7 ?  1.113 -1.158 -20.539 1.00   0.00 0 A 1
+ATOM   290 H H11 . DA  A . 7 ?  0.690 -2.848 -20.703 1.00   0.00 0 A 1
+ATOM   291 H H12 . DA  A . 7 ? -4.996 -7.475 -20.197 1.00   0.00 0 A 1
+ATOM   292 H H13 . DA  A . 7 ? -3.527 -5.252 -20.652 1.00   0.00 0 A 1
+ATOM   293 P P   . DT  B . -7 ?  4.904  7.285 -22.116 1.00   0.00 0 B 1
+ATOM   294 O O1P . DT  B . -7 ?  5.615  8.340 -22.873 1.00   0.00 0 B 1
+ATOM   295 O O2P . DT  B . -7 ?  5.659  6.660 -21.008 1.00   0.00 -1 B 1
+ATOM   296 C C5' . DT  B . -7 ?  2.357  7.823 -22.414 1.00   0.00 0 B 1
+ATOM   297 O O5' . DT  B . -7 ?  3.517  7.861 -21.563 1.00   0.00 0 B 1
+ATOM   298 C C4' . DT  B . -7 ?  1.149  7.360 -21.623 1.00   0.00 0 B 1
+ATOM   299 O O4' . DT  B . -7 ?  1.010  5.910 -21.620 1.00   0.00 0 B 1
+ATOM   300 C C3' . DT  B . -7 ?  1.142  7.734 -20.141 1.00   0.00 0 B 1
+ATOM   301 O O3' . DT  B . -7 ? -0.192  8.038 -19.750 1.00   0.00 0 B 1
+ATOM   302 C C2' . DT  B . -7 ?  1.581  6.461 -19.418 1.00   0.00 0 B 1
+ATOM   303 C C1' . DT  B . -7 ?  0.791  5.484 -20.284 1.00   0.00 0 B 1
+ATOM   304 N N1  . DT  B . -7 ?  1.251  4.072 -20.167 1.00   0.00 0 B 1
+ATOM   305 C C2  . DT  B . -7 ?  0.292  3.093 -20.259 1.00   0.00 0 B 1
+ATOM   306 O O2  . DT  B . -7 ? -0.890  3.335 -20.429 1.00   0.00 0 B 1
+ATOM   307 N N3  . DT  B . -7 ?  0.755  1.796 -20.145 1.00   0.00 0 B 1
+ATOM   308 C C4  . DT  B . -7 ?  2.066  1.410 -19.952 1.00   0.00 0 B 1
+ATOM   309 O O4  . DT  B . -7 ?  2.361  0.215 -19.865 1.00   0.00 0 B 1
+ATOM   310 C C5  . DT  B . -7 ?  2.999  2.509 -19.868 1.00   0.00 0 B 1
+ATOM   311 C C5M . DT  B . -7 ?  4.447  2.176 -19.658 1.00   0.00 0 B 1
+ATOM   312 C C6  . DT  B . -7 ?  2.576  3.779 -19.975 1.00   0.00 0 B 1
+ATOM   313 H H01 . DT  B . -7 ?  2.537  7.126 -23.232 1.00   0.00 0 B 1
+ATOM   314 H H02 . DT  B . -7 ?  2.168  8.819 -22.813 1.00   0.00 0 B 1
+ATOM   315 H H03 . DT  B . -7 ?  0.343  7.876 -22.144 1.00   0.00 0 B 1
+ATOM   316 H H04 . DT  B . -7 ?  1.780  8.590 -19.921 1.00   0.00 0 B 1
+ATOM   317 H H05 . DT  B . -7 ?  1.402  6.419 -18.343 1.00   0.00 0 B 1
+ATOM   318 H H06 . DT  B . -7 ?  2.657  6.296 -19.475 1.00   0.00 0 B 1
+ATOM   319 H H07 . DT  B . -7 ? -0.252  5.493 -19.969 1.00   0.00 0 B 1
+ATOM   320 H H08 . DT  B . -7 ?  0.068  1.059 -20.209 1.00   0.00 0 B 1
+ATOM   321 H H09 . DT  B . -7 ?  5.017  3.097 -19.539 1.00   0.00 0 B 1
+ATOM   322 H H10 . DT  B . -7 ?  4.554  1.565 -18.761 1.00   0.00 0 B 1
+ATOM   323 H H11 . DT  B . -7 ?  4.822  1.625 -20.520 1.00   0.00 0 B 1
+ATOM   324 H H12 . DT  B . -7 ?  3.299  4.591 -19.907 1.00   0.00 0 B 1
+ATOM   325 H H14 . DT  B . -7 ?  5.897  5.762 -21.249 1.00   0.00 0 B 1
+ATOM   326 P P   . DG  B . -6 ? -0.446  9.255 -18.741 1.00   0.00 0 B 1
+ATOM   327 O O1P . DG  B . -6 ? -0.491 10.526 -19.498 1.00   0.00 0 B 1
+ATOM   328 O O2P . DG  B . -6 ?  0.532  9.193 -17.633 1.00   0.00 -1 B 1
+ATOM   329 C C5' . DG  B . -6 ? -2.823  8.193 -19.039 1.00   0.00 0 B 1
+ATOM   330 O O5' . DG  B . -6 ? -1.907  8.906 -18.188 1.00   0.00 0 B 1
+ATOM   331 C C4' . DG  B . -6 ? -3.528  7.109 -18.248 1.00   0.00 0 B 1
+ATOM   332 O O4' . DG  B . -6 ? -2.788  5.854 -18.245 1.00   0.00 0 B 1
+ATOM   333 C C3' . DG  B . -6 ? -3.754  7.407 -16.766 1.00   0.00 0 B 1
+ATOM   334 O O3' . DG  B . -6 ? -5.012  6.869 -16.375 1.00   0.00 0 B 1
+ATOM   335 C C2' . DG  B . -6 ? -2.650  6.635 -16.043 1.00   0.00 0 B 1
+ATOM   336 C C1' . DG  B . -6 ? -2.715  5.381 -16.909 1.00   0.00 0 B 1
+ATOM   337 N N1  . DG  B . -6 ? -1.035  0.570 -16.918 1.00   0.00 0 B 1
+ATOM   338 C C2  . DG  B . -6 ? -2.318  1.060 -17.065 1.00   0.00 0 B 1
+ATOM   339 N N2  . DG  B . -6 ? -3.278  0.148 -17.237 1.00   0.00 0 B 1
+ATOM   340 N N3  . DG  B . -6 ? -2.613  2.358 -17.042 1.00   0.00 0 B 1
+ATOM   341 C C4  . DG  B . -6 ? -1.511  3.132 -16.858 1.00   0.00 0 B 1
+ATOM   342 C C5  . DG  B . -6 ? -0.203  2.737 -16.703 1.00   0.00 0 B 1
+ATOM   343 C C6  . DG  B . -6 ?  0.112  1.354 -16.728 1.00   0.00 0 B 1
+ATOM   344 O O6  . DG  B . -6 ?  1.208  0.812 -16.609 1.00   0.00 0 B 1
+ATOM   345 N N7  . DG  B . -6 ?  0.628  3.844 -16.539 1.00   0.00 0 B 1
+ATOM   346 C C8  . DG  B . -6 ? -0.196  4.863 -16.599 1.00   0.00 0 B 1
+ATOM   347 N N9  . DG  B . -6 ? -1.513  4.509 -16.792 1.00   0.00 0 B 1
+ATOM   348 H H01 . DG  B . -6 ? -2.268  7.734 -19.857 1.00   0.00 0 B 1
+ATOM   349 H H02 . DG  B . -6 ? -3.562  8.888 -19.438 1.00   0.00 0 B 1
+ATOM   350 H H03 . DG  B . -6 ? -4.484  7.052 -18.769 1.00   0.00 0 B 1
+ATOM   351 H H04 . DG  B . -6 ? -3.740  8.474 -16.546 1.00   0.00 0 B 1
+ATOM   352 H H05 . DG  B . -6 ? -2.771  6.496 -14.968 1.00   0.00 0 B 1
+ATOM   353 H H06 . DG  B . -6 ? -1.683  7.134 -16.100 1.00   0.00 0 B 1
+ATOM   354 H H07 . DG  B . -6 ? -3.565  4.774 -16.594 1.00   0.00 0 B 1
+ATOM   355 H H08 . DG  B . -6 ? -0.914 -0.433 -16.949 1.00   0.00 0 B 1
+ATOM   356 H H09 . DG  B . -6 ? -4.238  0.440 -17.350 1.00   0.00 0 B 1
+ATOM   357 H H10 . DG  B . -6 ? -3.044 -0.835 -17.253 1.00   0.00 0 B 1
+ATOM   358 H H11 . DG  B . -6 ?  0.132  5.898 -16.504 1.00   0.00 0 B 1
+ATOM   359 H H13 . DG  B . -6 ?  0.811  8.283 -17.502 1.00   0.00 0 B 1
+ATOM   360 P P   . DT  B . -5 ? -5.932  7.703 -15.366 1.00   0.00 0 B 1
+ATOM   361 O O1P . DT  B . -5 ? -6.716  8.705 -16.123 1.00   0.00 0 B 1
+ATOM   362 O O2P . DT  B . -5 ? -5.105  8.228 -14.258 1.00   0.00 -1 B 1
+ATOM   363 C C5' . DT  B . -5 ? -7.231  5.447 -15.664 1.00   0.00 0 B 1
+ATOM   364 O O5' . DT  B . -5 ? -6.909  6.562 -14.813 1.00   0.00 0 B 1
+ATOM   365 C C4' . DT  B . -5 ? -7.164  4.156 -14.873 1.00   0.00 0 B 1
+ATOM   366 O O4' . DT  B . -5 ? -5.828  3.575 -14.870 1.00   0.00 0 B 1
+ATOM   367 C C3' . DT  B . -5 ? -7.522  4.264 -13.391 1.00   0.00 0 B 1
+ATOM   368 O O3' . DT  B . -5 ? -8.224  3.089 -13.000 1.00   0.00 0 B 1
+ATOM   369 C C2' . DT  B . -5 ? -6.175  4.288 -12.668 1.00   0.00 0 B 1
+ATOM   370 C C1' . DT  B . -5 ? -5.491  3.236 -13.534 1.00   0.00 0 B 1
+ATOM   371 N N1  . DT  B . -5 ? -4.006  3.237 -13.417 1.00   0.00 0 B 1
+ATOM   372 C C2  . DT  B . -5 ? -3.371  2.022 -13.509 1.00   0.00 0 B 1
+ATOM   373 O O2  . DT  B . -5 ? -3.967  0.972 -13.679 1.00   0.00 0 B 1
+ATOM   374 N N3  . DT  B . -5 ? -1.994  2.062 -13.395 1.00   0.00 0 B 1
+ATOM   375 C C4  . DT  B . -5 ? -1.222  3.189 -13.202 1.00   0.00 0 B 1
+ATOM   376 O O4  . DT  B . -5 ?  0.005  3.100 -13.115 1.00   0.00 0 B 1
+ATOM   377 C C5  . DT  B . -5 ? -1.979  4.415 -13.118 1.00   0.00 0 B 1
+ATOM   378 C C5M . DT  B . -5 ? -1.215  5.690 -12.908 1.00   0.00 0 B 1
+ATOM   379 C C6  . DT  B . -5 ? -3.318  4.405 -13.225 1.00   0.00 0 B 1
+ATOM   380 H H01 . DT  B . -5 ? -6.513  5.403 -16.482 1.00   0.00 0 B 1
+ATOM   381 H H02 . DT  B . -5 ? -8.237  5.575 -16.063 1.00   0.00 0 B 1
+ATOM   382 H H03 . DT  B . -5 ? -7.904  3.548 -15.394 1.00   0.00 0 B 1
+ATOM   383 H H04 . DT  B . -5 ? -8.139  5.136 -13.171 1.00   0.00 0 B 1
+ATOM   384 H H05 . DT  B . -5 ? -6.192  4.105 -11.593 1.00   0.00 0 B 1
+ATOM   385 H H06 . DT  B . -5 ? -5.686  5.261 -12.725 1.00   0.00 0 B 1
+ATOM   386 H H07 . DT  B . -5 ? -5.822  2.245 -13.219 1.00   0.00 0 B 1
+ATOM   387 H H08 . DT  B . -5 ? -1.506  1.180 -13.459 1.00   0.00 0 B 1
+ATOM   388 H H09 . DT  B . -5 ? -0.273  5.642 -13.453 1.00   0.00 0 B 1
+ATOM   389 H H10 . DT  B . -5 ? -1.803  6.531 -13.273 1.00   0.00 0 B 1
+ATOM   390 H H11 . DT  B . -5 ? -1.012  5.822 -11.845 1.00   0.00 0 B 1
+ATOM   391 H H12 . DT  B . -5 ? -4.851  7.506 -13.678 1.00   0.00 0 B 1
+ATOM   392 H H13 . DT  B . -5 ? -3.867  5.345 -13.157 1.00   0.00 0 B 1
+ATOM   393 P P   . DA  B . -4 ? -9.459  3.224 -11.991 1.00   0.00 0 B 1
+ATOM   394 O O1P . DA  B . -4 ? -10.682  3.574 -12.748 1.00   0.00 0 B 1
+ATOM   395 O O2P . DA  B . -4 ? -9.098  4.135 -10.883 1.00   0.00 -1 B 1
+ATOM   396 C C5' . DA  B . -4 ? -9.184  0.635 -12.289 1.00   0.00 0 B 1
+ATOM   397 O O5' . DA  B . -4 ? -9.579  1.726 -11.438 1.00   0.00 0 B 1
+ATOM   398 C C4' . DA  B . -4 ? -8.370 -0.371 -11.498 1.00   0.00 0 B 1
+ATOM   399 O O4' . DA  B . -4 ? -6.948 -0.055 -11.495 1.00   0.00 0 B 1
+ATOM   400 C C3' . DA  B . -4 ? -8.724 -0.494 -10.016 1.00   0.00 0 B 1
+ATOM   401 O O3' . DA  B . -4 ? -8.601 -1.856 -9.625 1.00   0.00 0 B 1
+ATOM   402 C C2' . DA  B . -4 ? -7.648  0.318 -9.293 1.00   0.00 0 B 1
+ATOM   403 C C1' . DA  B . -4 ? -6.476 -0.131 -10.159 1.00   0.00 0 B 1
+ATOM   404 N N1  . DA  B . -4 ? -1.340  0.045 -10.159 1.00   0.00 0 B 1
+ATOM   405 C C2  . DA  B . -4 ? -2.205 -0.959 -10.297 1.00   0.00 0 B 1
+ATOM   406 N N3  . DA  B . -4 ? -3.520 -0.929 -10.286 1.00   0.00 0 B 1
+ATOM   407 C C4  . DA  B . -4 ? -3.970  0.330 -10.106 1.00   0.00 0 B 1
+ATOM   408 C C5  . DA  B . -4 ? -3.210  1.454 -9.951 1.00   0.00 0 B 1
+ATOM   409 C C6  . DA  B . -4 ? -1.815  1.292 -9.981 1.00   0.00 0 B 1
+ATOM   410 N N6  . DA  B . -4 ? -0.949  2.306 -9.842 1.00   0.00 0 B 1
+ATOM   411 N N7  . DA  B . -4 ? -4.020  2.570 -9.789 1.00   0.00 0 B 1
+ATOM   412 C C8  . DA  B . -4 ? -5.224  2.093 -9.851 1.00   0.00 0 B 1
+ATOM   413 N N9  . DA  B . -4 ? -5.275  0.742 -10.042 1.00   0.00 0 B 1
+ATOM   414 H H01 . DA  B . -4 ? -8.576  1.021 -13.107 1.00   0.00 0 B 1
+ATOM   415 H H02 . DA  B . -4 ? -10.073  0.147 -12.688 1.00   0.00 0 B 1
+ATOM   416 H H03 . DA  B . -4 ? -8.612 -1.297 -12.019 1.00   0.00 0 B 1
+ATOM   417 H H04 . DA  B . -4 ? -9.735 -0.150 -9.796 1.00   0.00 0 B 1
+ATOM   418 H H05 . DA  B . -4 ? -7.554  0.160 -8.218 1.00   0.00 0 B 1
+ATOM   419 H H06 . DA  B . -4 ? -7.824  1.392 -9.350 1.00   0.00 0 B 1
+ATOM   420 H H07 . DA  B . -4 ? -6.161 -1.127 -9.844 1.00   0.00 0 B 1
+ATOM   421 H H08 . DA  B . -4 ? -1.761 -1.944 -10.439 1.00   0.00 0 B 1
+ATOM   422 H H09 . DA  B . -4 ?  0.045  2.129 -9.871 1.00   0.00 0 B 1
+ATOM   423 H H10 . DA  B . -4 ? -1.291  3.247 -9.707 1.00   0.00 0 B 1
+ATOM   424 H H11 . DA  B . -4 ? -6.115  2.714 -9.758 1.00   0.00 0 B 1
+ATOM   425 H H14 . DA  B . -4 ? -8.874  3.619 -10.104 1.00   0.00 0 B 1
+ATOM   426 P P   . DA  B . -3 ? -9.679 -2.473 -8.616 1.00   0.00 0 B 1
+ATOM   427 O O1P . DA  B . -3 ? -10.874 -2.909 -9.373 1.00   0.00 0 B 1
+ATOM   428 O O2P . DA  B . -3 ? -9.922 -1.524 -7.508 1.00   0.00 -1 B 1
+ATOM   429 C C5' . DA  B . -3 ? -7.934 -4.406 -8.914 1.00   0.00 0 B 1
+ATOM   430 O O5' . DA  B . -3 ? -8.896 -3.755 -8.063 1.00   0.00 0 B 1
+ATOM   431 C C4' . DA  B . -3 ? -6.686 -4.741 -8.123 1.00   0.00 0 B 1
+ATOM   432 O O4' . DA  B . -3 ? -5.721 -3.650 -8.120 1.00   0.00 0 B 1
+ATOM   433 C C3' . DA  B . -3 ? -6.899 -5.048 -6.641 1.00   0.00 0 B 1
+ATOM   434 O O3' . DA  B . -3 ? -5.999 -6.079 -6.250 1.00   0.00 0 B 1
+ATOM   435 C C2' . DA  B . -3 ? -6.506 -3.760 -5.918 1.00   0.00 0 B 1
+ATOM   436 C C1' . DA  B . -3 ? -5.293 -3.434 -6.784 1.00   0.00 0 B 1
+ATOM   437 N N1  . DA  B . -3 ? -1.242 -0.273 -6.784 1.00   0.00 0 B 1
+ATOM   438 C C2  . DA  B . -3 ? -1.352 -1.593 -6.922 1.00   0.00 0 B 1
+ATOM   439 N N3  . DA  B . -3 ? -2.433 -2.342 -6.911 1.00   0.00 0 B 1
+ATOM   440 C C4  . DA  B . -3 ? -3.537 -1.588 -6.731 1.00   0.00 0 B 1
+ATOM   441 C C5  . DA  B . -3 ? -3.583 -0.232 -6.576 1.00   0.00 0 B 1
+ATOM   442 C C6  . DA  B . -3 ? -2.359  0.457 -6.606 1.00   0.00 0 B 1
+ATOM   443 N N6  . DA  B . -3 ? -2.255  1.786 -6.467 1.00   0.00 0 B 1
+ATOM   444 N N7  . DA  B . -3 ? -4.894  0.195 -6.414 1.00   0.00 0 B 1
+ATOM   445 C C8  . DA  B . -3 ? -5.588 -0.899 -6.476 1.00   0.00 0 B 1
+ATOM   446 N N9  . DA  B . -3 ? -4.836 -2.022 -6.667 1.00   0.00 0 B 1
+ATOM   447 H H01 . DA  B . -3 ? -7.670 -3.736 -9.732 1.00   0.00 0 B 1
+ATOM   448 H H02 . DA  B . -3 ? -8.367 -5.323 -9.313 1.00   0.00 0 B 1
+ATOM   449 H H03 . DA  B . -3 ? -6.337 -5.633 -8.644 1.00   0.00 0 B 1
+ATOM   450 H H04 . DA  B . -3 ? -7.919 -5.365 -6.421 1.00   0.00 0 B 1
+ATOM   451 H H05 . DA  B . -3 ? -6.337 -3.832 -4.843 1.00   0.00 0 B 1
+ATOM   452 H H06 . DA  B . -3 ? -7.280 -2.994 -5.975 1.00   0.00 0 B 1
+ATOM   453 H H07 . DA  B . -3 ? -4.454 -4.055 -6.469 1.00   0.00 0 B 1
+ATOM   454 H H08 . DA  B . -3 ? -0.414 -2.129 -7.064 1.00   0.00 0 B 1
+ATOM   455 H H09 . DA  B . -3 ? -1.347  2.227 -6.496 1.00   0.00 0 B 1
+ATOM   456 H H10 . DA  B . -3 ? -3.084  2.347 -6.332 1.00   0.00 0 B 1
+ATOM   457 H H11 . DA  B . -3 ? -6.674 -0.920 -6.383 1.00   0.00 0 B 1
+ATOM   458 H H12 . DA  B . -3 ? -9.765 -0.628 -7.813 1.00   0.00 0 B 1
+ATOM   459 P P   . DT  B . -2 ? -6.508 -7.212 -5.241 1.00   0.00 0 B 1
+ATOM   460 O O1P . DT  B . -2 ? -7.219 -8.266 -5.998 1.00   0.00 0 B 1
+ATOM   461 O O2P . DT  B . -2 ? -7.263 -6.587 -4.133 1.00   0.00 -1 B 1
+ATOM   462 C C5' . DT  B . -2 ? -3.961 -7.750 -5.539 1.00   0.00 0 B 1
+ATOM   463 O O5' . DT  B . -2 ? -5.121 -7.788 -4.688 1.00   0.00 0 B 1
+ATOM   464 C C4' . DT  B . -2 ? -2.754 -7.287 -4.748 1.00   0.00 0 B 1
+ATOM   465 O O4' . DT  B . -2 ? -2.615 -5.837 -4.745 1.00   0.00 0 B 1
+ATOM   466 C C3' . DT  B . -2 ? -2.746 -7.661 -3.266 1.00   0.00 0 B 1
+ATOM   467 O O3' . DT  B . -2 ? -1.412 -7.965 -2.875 1.00   0.00 0 B 1
+ATOM   468 C C2' . DT  B . -2 ? -3.185 -6.388 -2.543 1.00   0.00 0 B 1
+ATOM   469 C C1' . DT  B . -2 ? -2.396 -5.411 -3.409 1.00   0.00 0 B 1
+ATOM   470 N N1  . DT  B . -2 ? -2.856 -3.999 -3.292 1.00   0.00 0 B 1
+ATOM   471 C C2  . DT  B . -2 ? -1.897 -3.020 -3.384 1.00   0.00 0 B 1
+ATOM   472 O O2  . DT  B . -2 ? -0.714 -3.262 -3.554 1.00   0.00 0 B 1
+ATOM   473 N N3  . DT  B . -2 ? -2.360 -1.723 -3.270 1.00   0.00 0 B 1
+ATOM   474 C C4  . DT  B . -2 ? -3.670 -1.337 -3.077 1.00   0.00 0 B 1
+ATOM   475 O O4  . DT  B . -2 ? -3.965 -0.142 -2.990 1.00   0.00 0 B 1
+ATOM   476 C C5  . DT  B . -2 ? -4.603 -2.435 -2.993 1.00   0.00 0 B 1
+ATOM   477 C C5M . DT  B . -2 ? -6.051 -2.103 -2.783 1.00   0.00 0 B 1
+ATOM   478 C C6  . DT  B . -2 ? -4.180 -3.706 -3.100 1.00   0.00 0 B 1
+ATOM   479 H H01 . DT  B . -2 ? -4.141 -7.053 -6.357 1.00   0.00 0 B 1
+ATOM   480 H H02 . DT  B . -2 ? -3.772 -8.746 -5.938 1.00   0.00 0 B 1
+ATOM   481 H H03 . DT  B . -2 ? -1.947 -7.803 -5.269 1.00   0.00 0 B 1
+ATOM   482 H H04 . DT  B . -2 ? -3.385 -8.516 -3.046 1.00   0.00 0 B 1
+ATOM   483 H H05 . DT  B . -2 ? -3.006 -6.346 -1.468 1.00   0.00 0 B 1
+ATOM   484 H H06 . DT  B . -2 ? -4.261 -6.223 -2.600 1.00   0.00 0 B 1
+ATOM   485 H H07 . DT  B . -2 ? -1.352 -5.420 -3.094 1.00   0.00 0 B 1
+ATOM   486 H H08 . DT  B . -2 ? -1.672 -0.986 -3.334 1.00   0.00 0 B 1
+ATOM   487 H H09 . DT  B . -2 ? -6.650 -3.008 -2.883 1.00   0.00 0 B 1
+ATOM   488 H H10 . DT  B . -2 ? -6.188 -1.687 -1.784 1.00   0.00 0 B 1
+ATOM   489 H H11 . DT  B . -2 ? -6.369 -1.373 -3.528 1.00   0.00 0 B 1
+ATOM   490 H H12 . DT  B . -2 ? -7.348 -5.644 -4.294 1.00   0.00 0 B 1
+ATOM   491 H H13 . DT  B . -2 ? -4.904 -4.518 -3.032 1.00   0.00 0 B 1
+ATOM   492 P P   . DC  B . -1 ? -1.158 -9.181 -1.866 1.00   0.00 0 B 1
+ATOM   493 O O1P . DC  B . -1 ? -1.113 -10.452 -2.623 1.00   0.00 0 B 1
+ATOM   494 O O2P . DC  B . -1 ? -2.136 -9.119 -0.758 1.00   0.00 -1 B 1
+ATOM   495 C C5' . DC  B . -1 ?  1.219 -8.119 -2.164 1.00   0.00 0 B 1
+ATOM   496 O O5' . DC  B . -1 ?  0.303 -8.832 -1.313 1.00   0.00 0 B 1
+ATOM   497 C C4' . DC  B . -1 ?  1.924 -7.035 -1.373 1.00   0.00 0 B 1
+ATOM   498 O O4' . DC  B . -1 ?  1.184 -5.780 -1.370 1.00   0.00 0 B 1
+ATOM   499 C C3' . DC  B . -1 ?  2.150 -7.333  0.109 1.00   0.00 0 B 1
+ATOM   500 O O3' . DC  B . -1 ?  3.408 -6.795  0.500 1.00   0.00 0 B 1
+ATOM   501 C C2' . DC  B . -1 ?  1.046 -6.561  0.832 1.00   0.00 0 B 1
+ATOM   502 C C1' . DC  B . -1 ?  1.111 -5.307 -0.034 1.00   0.00 0 B 1
+ATOM   503 N N1  . DC  B . -1 ? -0.091 -4.435  0.083 1.00   0.00 0 B 1
+ATOM   504 C C2  . DC  B . -1 ?  0.095 -3.058 -0.008 1.00   0.00 0 B 1
+ATOM   505 O O2  . DC  B . -1 ?  1.238 -2.620 -0.181 1.00   0.00 0 B 1
+ATOM   506 N N3  . DC  B . -1 ? -0.988 -2.245  0.097 1.00   0.00 0 B 1
+ATOM   507 C C4  . DC  B . -1 ? -2.211 -2.759  0.284 1.00   0.00 0 B 1
+ATOM   508 N N4  . DC  B . -1 ? -3.235 -1.926  0.380 1.00   0.00 0 B 1
+ATOM   509 C C5  . DC  B . -1 ? -2.423 -4.173  0.381 1.00   0.00 0 B 1
+ATOM   510 C C6  . DC  B . -1 ? -1.328 -4.967  0.274 1.00   0.00 0 B 1
+ATOM   511 H H01 . DC  B . -1 ?  0.664 -7.661 -2.982 1.00   0.00 0 B 1
+ATOM   512 H H02 . DC  B . -1 ?  1.958 -8.815 -2.563 1.00   0.00 0 B 1
+ATOM   513 H H03 . DC  B . -1 ?  2.880 -6.979 -1.894 1.00   0.00 0 B 1
+ATOM   514 H H04 . DC  B . -1 ?  2.136 -8.401  0.329 1.00   0.00 0 B 1
+ATOM   515 H H05 . DC  B . -1 ?  3.724 -7.255  1.282 1.00   0.00 0 B 1
+ATOM   516 H H06 . DC  B . -1 ?  1.166 -6.423  1.907 1.00   0.00 0 B 1
+ATOM   517 H H07 . DC  B . -1 ?  0.079 -7.061  0.775 1.00   0.00 0 B 1
+ATOM   518 H H08 . DC  B . -1 ?  1.960 -4.701  0.281 1.00   0.00 0 B 1
+ATOM   519 H H09 . DC  B . -1 ? -4.168 -2.287  0.522 1.00   0.00 0 B 1
+ATOM   520 H H10 . DC  B . -1 ? -3.084 -0.930  0.312 1.00   0.00 0 B 1
+ATOM   521 H H11 . DC  B . -1 ? -3.418 -4.592  0.534 1.00   0.00 0 B 1
+ATOM   522 H H12 . DC  B . -1 ? -1.442 -6.049  0.343 1.00   0.00 0 B 1
+ATOM   523 H H14 . DC  B . -1 ? -2.280 -8.204 -0.508 1.00   0.00 0 B 1

{biointerface-0.3.0 → biointerface-0.3.2}/tests/test_biointerface.py

@@ -21,3 +21,4 @@ def test_content(response):
     """Sample pytest test function with the pytest fixture as an argument."""
     # from bs4 import BeautifulSoup
     # assert 'GitHub' in BeautifulSoup(response.content).title.string
+    assert biointerface.__version__

biointerface-0.3.2/tests/test_core.py

@@ -0,0 +1,105 @@
+"""Test core module of biointerface."""
+
+import pytest
+from Bio.PDB.MMCIFParser import MMCIFParser
+from Bio.PDB.PDBExceptions import PDBConstructionException
+from PDBNucleicAcids.NucleicAcid import DoubleStrandNucleicAcid
+
+# to be tested
+from biointerface import Interface, build_interfaces
+
+
+def get_test_structure():
+    filepath = "tests/data/gattaca.cif"
+    parser = MMCIFParser(QUIET=True)
+    structure = parser.get_structure("gattaca", filepath)
+
+    return structure
+
+
+def test_extract_contacts():
+    structure = get_test_structure()
+    face = Interface(structure=structure, protein_chain_id="C")
+    face.get_atomic_contacts()
+
+    assert isinstance(face.contacts, list)
+    assert all(len(contact) == 2 for contact in face.contacts)
+    assert all(contact[0] != contact[1] for contact in face.contacts)
+
+
+def test_get_atoms():
+    structure = get_test_structure()
+    face = Interface(structure=structure, protein_chain_id="C")
+    atoms = face.get_protein_atoms()
+    assert isinstance(atoms, list)
+    assert all(
+        hasattr(atom, "coord") for atom in atoms
+    )  # Controlla se hanno coordinate
+
+    atoms = face.get_dna_atoms()
+    assert isinstance(atoms, list)
+    assert all(
+        hasattr(atom, "coord") for atom in atoms
+    )  # Controlla se hanno coordinate
+
+
+def test_get_residues():
+    structure = get_test_structure()
+    face = Interface(structure=structure, protein_chain_id="C")
+    residues = face.get_aminoacids()
+    assert isinstance(residues, list)
+    assert all(
+        hasattr(residue, "get_resname") for residue in residues
+    )  # Devono avere nomi di residui
+
+    residues = face.get_nucleotides()
+    assert isinstance(residues, list)
+    assert all(
+        hasattr(residue, "get_resname") for residue in residues
+    )  # Devono avere nomi di residui
+
+
+def test_get_interface_data():
+    structure = get_test_structure()
+    face = Interface(structure=structure, protein_chain_id="C")
+    df = face.get_interface_data()
+    assert df is not None
+    assert not df.empty
+    assert set(
+        ["prot_atom_name", "dna_atom_name", "euclidean_distance"]
+    ).issubset(df.columns)
+
+
+def test_get_bound_double_strands():
+    structure = get_test_structure()
+    face = Interface(structure=structure, protein_chain_id="C")
+    dsna_list = face.get_bound_double_strands()
+    assert isinstance(dsna_list, list)
+    assert isinstance(dsna_list[0], DoubleStrandNucleicAcid)
+
+
+def test_non_protein():
+    structure = get_test_structure()
+
+    # "A" is not a protein but a DNA chain
+    # should raise an error
+    with pytest.raises(PDBConstructionException):
+        Interface(structure=structure, protein_chain_id="A")
+
+
+def test_no_contacts():
+    structure = get_test_structure()
+    face = Interface(
+        structure=structure, protein_chain_id="C", search_radius=1.0
+    )
+
+    assert len(face.contacts) == 0
+
+
+def test_build_interfaces():
+    structure = get_test_structure()
+    face_list = build_interfaces(structure=structure, search_radius=5.0)
+
+    assert isinstance(face_list, list)
+    assert len(face_list) == 1
+    assert isinstance(face_list[0], Interface)

biointerface-0.3.0/src/biointerface.egg-info/requires.txt

@@ -1,9 +0,0 @@
-pandas
-biopython
-pdbnucleicacids>=0.2.1
-
-[dev]
-coverage
-mypy
-pytest
-ruff