diff --git a/README.rst b/README.rst index 3bd599fc..ac2be34d 100644 --- a/README.rst +++ b/README.rst @@ -48,7 +48,8 @@ Requirements ~~~~~~~~~~~~ atomium requires the Python library -`geometrica `_ - pip will install this +`points `_ and +`requests `_ - pip will install these automatically when it installs atomium. @@ -85,6 +86,9 @@ from the RCSB over the internet using the PDB code: >>> pdb2.model() +If the PDB has multiple models, these can be accessed using the +``Pdb.models`` method. + The Model ~~~~~~~~~ @@ -239,7 +243,7 @@ Residues are also a kind of Molecule, and have other useful properties: >>> pdb.model().residue("A23").previous() - + Saving ~~~~~~ @@ -266,6 +270,21 @@ The ``Xyz`` or ``Pdb`` object itself can also be saved: Changelog --------- +Release 0.5.0 +~~~~~~~~~~~~~ + +`16 September 2017` + +* Added atom temperature factors. +* Added bond vector production. +* Added parse time tests and reduced parse time by over a half. +* Changed way atoms are stored in structures to make ID lookup orders of \ + magnitude faster. +* Made IDs immutable. +* Added multiple model parsing and saving. +* Added option to fetch PDBs from PDBe rather than RCSB. + + Release 0.4.0 ~~~~~~~~~~~~~ diff --git a/atomium/structures/molecules.py b/atomium/structures/molecules.py index e8922a0f..8f11fc55 100644 --- a/atomium/structures/molecules.py +++ b/atomium/structures/molecules.py @@ -74,10 +74,10 @@ def atom(self, *args, **kwargs): atom matches the criteria you give, it might not be the same atom that is returned each time you call this method. - :param str element: If given, only atoms whose element matches this\ - will be searched. :param int atom_id: If given, only atoms whose atom ID matches this\ will be searched. + :param str element: If given, only atoms whose element matches this\ + will be searched. :param str name: If given, only atoms whose name matches this will be\ searched. :rtype: ``Atom``""" diff --git a/docs/source/api.rst b/docs/source/api.rst index 77c5e93f..f8164079 100644 --- a/docs/source/api.rst +++ b/docs/source/api.rst @@ -31,7 +31,7 @@ Converters api/structure2xyzstring api/string2pdbfile api/pdbfile2pdbdatafile - api/pdbdatafile2model + api/pdbdatafile2models api/pdbdatafile2pdb api/pdb2pdbdatafile api/structure2pdbdatafile diff --git a/docs/source/api/pdbdatafile2model.rst b/docs/source/api/pdbdatafile2model.rst deleted file mode 100644 index 0dea6dda..00000000 --- a/docs/source/api/pdbdatafile2model.rst +++ /dev/null @@ -1,6 +0,0 @@ -``atomium.converters.pdbdatafile2model`` (Pdb datafile to model conversion) -~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ - -.. automodule:: atomium.converters.pdbdatafile2model - :members: - :inherited-members: diff --git a/docs/source/api/pdbdatafile2models.rst b/docs/source/api/pdbdatafile2models.rst new file mode 100644 index 00000000..5c001bfe --- /dev/null +++ b/docs/source/api/pdbdatafile2models.rst @@ -0,0 +1,6 @@ +``atomium.converters.pdbdatafile2models`` (Pdb datafile to models conversion) +~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ + +.. automodule:: atomium.converters.pdbdatafile2models + :members: + :inherited-members: diff --git a/docs/source/changelog.rst b/docs/source/changelog.rst index 865f6115..eae37728 100644 --- a/docs/source/changelog.rst +++ b/docs/source/changelog.rst @@ -9,8 +9,8 @@ Release 0.5.0 * Added atom temperature factors. * Added bond vector production. * Added parse time tests and reduced parse time by over a half. -* Changed way atoms are stored in structures to make ID lookup orders of\ -magnitude faster. +* Changed way atoms are stored in structures to make ID lookup orders of \ + magnitude faster. * Made IDs immutable. * Added multiple model parsing and saving. * Added option to fetch PDBs from PDBe rather than RCSB. diff --git a/docs/source/overview.rst b/docs/source/overview.rst index c75cab01..61bb6b54 100644 --- a/docs/source/overview.rst +++ b/docs/source/overview.rst @@ -31,8 +31,8 @@ from the RCSB over the internet using the PDB code: >>> pdb2.model() -If the PDB has multiple models, these can be accessed using the :py:meth:` -~.Pdb.models` method. +If the PDB has multiple models, these can be accessed using the +:py:meth:`~.Pdb.models` method. The Model ~~~~~~~~~ @@ -188,7 +188,7 @@ Residues are also a kind of Molecule, and have other useful properties: >>> pdb.model().residue("A23").previous() - + Saving ~~~~~~ diff --git a/setup.py b/setup.py index 7748d0ba..62bdde76 100644 --- a/setup.py +++ b/setup.py @@ -24,5 +24,5 @@ ], keywords="chemistry bioinformatics proteins biochemistry molecules PDB XYZ", packages=["atomium", "atomium.files", "atomium.converters", "atomium.structures"], - install_requires=["geometrica"] + install_requires=["geometrica", "points", "requests"] )