i%(dZddlZddlZddlmZddlmZmZddl m Z m Z m Z m Z mZmZmZmZmZmZddlmZdd lmZddlZGd d eZdS) a MOL2 file format --- :mod:`MDAnalysis.coordinates.MOL2` ======================================================== Classes to read Tripos_ molecule structure format (MOL2_) coordinate and topology files. Used by the DOCK_ docking code. .. _MOL2: http://www.tripos.com/data/support/mol2.pdf .. _Tripos: http://www.tripos.com/ .. _DOCK: http://dock.compbio.ucsf.edu/ Classes ------- .. autoclass:: MOL2Parser :members: :inherited-members: N)openany)TopologyReaderBase squash_by) Atomids Atomnames AtomtypesBondsChargesElementsResidsResnumsResnamesSegids)Topology) SYBYL2SYMBceZdZdZdZdZdS) MOL2Parsera Reads topology from a Tripos_ MOL2_ file. Creates the following Attributes: - Atomids - Atomnames - Atomtypes - Charges - Resids - Resnames - Bonds - Elements .. note:: By default, masses will be guessed on Universe creation. This may change in release 3.0. See :ref:`Guessers` for more information. Notes ----- Elements are obtained directly from the SYBYL atom types. If some atoms have unknown atom types, they will be assigned an empty element record. If all atoms have unknown atom types, the elements attribute will not be set. Dealing with optional fields: 1. ``resid`` will set to 1 when not provided. 2. If no atoms have ``resname`` field, resnames attribute will not be set; If some atoms have ``resname`` while some do not, :exc:`ValueError` will occur. 3. If "NO_CHARGES" shows up in "@MOLECULE" section and no atoms have the ``charge`` field, charges attribute will not be set; If "NO_CHARGES" shows up while ``charge`` field appears, :exc:`ValueError` will occur; If a charge model is specified while some atoms don't have ``charge``, :exc:`ValueError` will occur as well. Raises ------ ValueError If some atoms have the optional field ``resname`` (aka ``subst_name``) while some do not. ValueError If "NO_CHARGES" shows up in "@MOLECULE" section while some atoms have the optional field ``charge``. ValueError If a charge model is specified in "@MOLECULE" section while some atoms do not have the optional field ``charge``. .. versionchanged:: 0.9 Now subclasses TopologyReaderBase .. versionchanged:: 0.20.0 Allows for comments at the top of the file Ignores status bit strings .. versionchanged:: 2.0.0 Bonds attribute is not added if no bonds are present in MOL2 file .. versionchanged:: 2.0.0 Parse elements from atom types. .. versionchanged:: 2.2.0 Read MOL2 files with optional columns omitted. .. versionchanged:: 2.8.0 Removed mass guessing (attributes guessing takes place now through universe.guess_TopologyAttrs() API). 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Returns ------- A MDAnalysis Topology object z@MOLECULE) start_linelinesrNzFThe mol2 file '{0}' needs to have at least one @MOLECULE blockrz @r# atombondz%The mol2 block ({0}:{1}) has no atomsrmolecule NO_CHARGES z%The @ATOM block in mol2 file z} should have at least 6 fields to be unpacked: atom_id atom_name x y z atom_type [subst_id[subst_name [charge [status_bit]]]])rNNzThe mol2 file z indicates a charge modelz", but no charge provided in line: z" indicates no charges, but charge z provided in line: .U3)dtypez'Unknown elements found for some atoms: z0. 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