iEdZddlZddlZddlZddlZddlZddlZddlZddl Z ddl Z ddl Z ddl Z ddl mZmZddlmZddlmZddlmZddlmZmZmZdd lmZd d l mZd d lmZmZd d lm Z m!Z!m"Z"m#Z#m$Z$m%Z%m&Z&m'Z'd dl(m)Z)d dl*m+Z+m,Z,m-Z-m.Z.m/Z/m0Z0m1Z1m2Z2m3Z3m4Z4d dl5m6Z6ddl7m8Z8ej9dZ:dZ;dZddddZ?dZ@GddeAZBdZCdS) a========================================================= Core object: Universe --- :mod:`MDAnalysis.core.universe` ========================================================= The :class:`~MDAnalysis.core.universe.Universe` class ties a topology and a trajectory together. Almost all code in MDAnalysis starts with a ``Universe``. Normally, a ``Universe`` is created from files:: import MDAnalysis as mda u = mda.Universe("topology.psf", "trajectory.dcd") In order to construct new simulation system it is also convenient to construct a ``Universe`` from existing :class:`~MDAnalysis.core.group.AtomGroup` instances with the :func:`Merge` function. Classes ======= .. autoclass:: Universe :members: Functions ========= .. autofunction:: Merge N)_TOPOLOGY_ATTRS_PARSERS) NoDataError)util) ProgressBar)cached NamedStreamisstream)find_fragments)groups)get_reader_forget_parser_for) ComponentBase GroupBaseAtomResidueSegment AtomGroup ResidueGroup SegmentGroup)Topology) AtomAttr ResidueAttr SegmentAttr SegindicesSegids ResindicesResids AtomindicesBFACTOR_WARNING _Connection)TopologyObject) get_guesserzMDAnalysis.core.universecNddlm}jdtjD}fd|D}dtjD}||gfd|Dz}||gfd|Dz}|||\} } | d} | d } t | } | dd t | gfd t|Dz}|||| f| f\}\}t |}|t|d jD}tj j | ||| | t |dkr|D]} |_d S)a>Update the topology of a Universe with new atomwise resids and segids. Parameters ---------- universe : Universe The universe to update. atomwise_resids : numpy.ndarray The new atomwise residue indices. atomwise_segids : numpy.ndarray The new atomwise segment indices. r) change_squashc^g|]*\}}t|jvt|t(|+S)rtarget_classes isinstancer!.0idx each_attrs b/srv/www/vhosts/g4struct/public_html/venv/lib/python3.11/site-packages/MDAnalysis/core/universe.py z+_update_topology_by_ids..sF C 93 3 3I{33 4 3 3 3c*g|]}j|Sr)attrs)r-r/tops r0r1z+_update_topology_by_ids..s D D DiSYy ! D D Dr2cg|]M\}}t|jvr:t|jv!t|t6t|t K|NSr))rr*rr+r rr,s r0r1z+_update_topology_by_ids..sh    C  0 0 0 888 6229 :669 988r2cg|]=}j|jdktjj|j>S)resnums)r5attrnamegetattratomsr-r/r6universes r0r1z+_update_topology_by_ids..sN999  9Y  (I 5 5  ) 4 =>> 5 5 5r2cZg|]'}tjj|j(Sr))r;r<r5r:r=s r0r1z+_update_topology_by_ids..s?:::   ) 4 =>>:::r2rr Ncbg|]+\}}j||,Sr))r5 __class__)r-r.r/res_squashed_res_attrsr6s r0r1z+_update_topology_by_ids..sJ$$$ C )&&'=c'BCC$$$r2cg|]f}t|jvt|t%t|t:t|t Ot|t d|gSr))rr*r+rr!rr)r-r/s r0r1z+_update_topology_by_ids..s~      0 0 0 6221 ;771 :661 :66 1 1 0 0r2r5 atom_resindexresidue_segindex) topology.baser' _topology enumerater5lenr extendappendrrr<n_atomsadd_TopologyAttr)r>atomwise_residsatomwise_segidsr'atom_attrindicesr5residue_attrindices res_criteria res_to_squashresidx res_squashedresidsres_squashed_segids n_residues res_attrssegidxsegids n_segments other_attrseach_otherattrrBr6s` @@r0_update_topology_by_idsr`ps.-----  C' 22 E D D D3C D D DE  ' 22   $_599999,999L %o6:::::,:::M )=}EEFL !_F&q/VJ)!""- $$$$$((;<<$$$I  LL& !4 6FIVVJ LL        K     C ;!) 1 1N   0 0 0 0Hr2cxt|r*t|dr|j}nd}t||S|S)Nname)r hasattrrbr )topology_names r0_check_file_likerfsG, 8V $ $ MEEE8U+++ Or2c t||} ||5}|jdi|}dddn #1swxYwYn#ttf$rc}|j3tj|jdvrt jd|td|||d}~wttf$r)}td|||d}~wwxYw|S)Nformat)ENOENTEACCESr zEFailed to load from the topology file {0} with parser {1}. Error: {2}zFFailed to construct topology from file {0} with parser {1}. Error: {2}r)) rparseIOErrorOSErrorerrno errorcodesysexc_infori ValueErrorNotImplementedError) topology_filetopology_formatkwargsparserprderrs r0_topology_from_file_liker{sh M/ B B BF VM " " )aqw((((H ) ) ) ) ) ) ) ) ) ) ) ) ) ) ) W  9 U_SY%?D & & ,..# ,#VM63??  + ,     vs;;    Os@ A8 A<A<AC0AB33C0$C++C0rirvc |s ||}n||}||fSNr))rirv coordinatess r0_resolve_formatsrs, % >$FF  $$O ? ""r2Friall_coordinatesc|s|sY|W t|||f|z}n>#ttf$r*tjd|YnwxYw|S)Nrhz6No coordinate reader found for {}. Skipping this file.)rrs TypeErrorwarningswarnri)filenamerirrs r0_resolve_coordinatesr s 4k 4h.B 4 8F 3 3 3 3$+ 3KK I&    M#VH--       s 8AActj\|_|_|jjD]}||ttj |jj ||_ ttj |jj ||_ttj |jj||_dSr~)r make_classes _class_bases_classesrHr5 _process_attrrnparangerMr<rrYresiduesrr]segments)r>attrs r0_generate_from_topologyrs06/B/D/D,H8,"(%%t$$$$ry);)CDDhOOHN$ ($/00(H% ($/00(Hr2ceZdZdZ d6ddddddddddddd d d Zd Ze d7d ZedZ d8dZ d9dZ dZ edZ edZedZedZdZedZdZedZejdZedZedZedZejdZd6dZd Zd!Zd"Zd6d#Zd$Z d:d%Zd:d&Z d'Z!d;d(Z"d;d)Z#d;d*Z$d+Z%d,Z&d-Z'd.Z(d/Z)ee*d0d1Z+e dd5Z.dS)?Universea*The MDAnalysis Universe contains all the information describing the system. The system always requires a *topology file* --- in the simplest case just a list of atoms. This can be a CHARMM/NAMD PSF file or a simple coordinate file with atom informations such as XYZ, PDB, GROMACS GRO or TPR, or CHARMM CRD. See :ref:`Supported topology formats` for what kind of topologies can be read. A *trajectory file* provides coordinates; the coordinates have to be ordered in the same way as the list of atoms in the topology. A trajectory can be a single frame such as a PDB, CRD, or GRO file, or it can be a MD trajectory (in CHARMM/NAMD/LAMMPS DCD, GROMACS XTC/TRR, AMBER nc, generic XYZ format, ...). See :ref:`Supported coordinate formats` for what can be read as a "trajectory". As a special case, when the topology is a file that contains atom information *and* coordinates (such as XYZ, PDB, GRO or CRD, see :ref:`Supported coordinate formats`) then the coordinates are immediately loaded from the "topology" file unless a trajectory is supplied. Parameters ---------- topology: str, stream, Topology, numpy.ndarray, None A CHARMM/XPLOR PSF topology file, PDB file or Gromacs GRO file; used to define the list of atoms. If the file includes bond information, partial charges, atom masses, ... then these data will be available to MDAnalysis. Alternatively, an existing :class:`MDAnalysis.core.topology.Topology` instance may be given, numpy coordinates, or ``None`` for an empty universe. coordinates: str, stream, list of str, list of stream (optional) Coordinates can be provided as files of a single frame (eg a PDB, CRD, or GRO file); a list of single frames; or a trajectory file (in CHARMM/NAMD/LAMMPS DCD, Gromacs XTC/TRR, or generic XYZ format). The coordinates must be ordered in the same way as the list of atoms in the topology. See :ref:`Supported coordinate formats` for what can be read as coordinates. Alternatively, streams can be given. topology_format: str, ``None``, default ``None`` Provide the file format of the topology file; ``None`` guesses it from the file extension. Can also pass a subclass of :class:`MDAnalysis.topology.base.TopologyReaderBase` to define a custom reader to be used on the topology file. format: str, ``None``, default ``None`` Provide the file format of the coordinate or trajectory file; ``None`` guesses it from the file extension. Note that this keyword has no effect if a list of file names is supplied because the "chained" reader has to guess the file format for each individual list member. Can also pass a subclass of :class:`MDAnalysis.coordinates.base.ProtoReader` to define a custom reader to be used on the trajectory file. all_coordinates: bool, default ``False`` If set to ``True`` specifies that if more than one filename is passed they are all to be used, if possible, as coordinate files (employing a :class:`MDAnalysis.coordinates.chain.ChainReader`). The default behavior is to take the first file as a topology and the remaining as coordinates. The first argument will always always be used to infer a topology regardless of *all_coordinates*. guess_bonds: bool, default ``False`` Once Universe has been loaded, attempt to guess the connectivity between atoms. This will populate the .bonds, .angles, and .dihedrals attributes of the Universe. .. deprecated:: 2.8.0 This keyword is deprecated and will be removed in MDAnalysis 3.0. Please pass ("bonds", "angles", "dihedrals") into `to_guess` or `force_guess` instead to guess bonds, angles, and dihedrals respectively. vdwradii: dict, ``None``, default ``None`` For use with *guess_bonds*. Supply a dict giving a vdwradii for each atom type which are used in guessing bonds. .. deprecated:: 2.8.0 This keyword is deprecated and will be removed in MDAnalysis 3.0. Please pass it into Guesser creation (:mod:`~MDAnalysis.guesser`), or to :meth:`~MDAnalysis.core.universe.Universe.guess_TopologyAttrs` method instead. If passed into `guess_TopologyAttrs`, it will override the values set during Guesser creation. context: str or :mod:`Guesser`, default ``'default'`` Type of the Guesser to be used in guessing TopologyAttrs to_guess: list[str] (optional, default ``['types', 'masses']``) TopologyAttrs to be guessed. These TopologyAttrs will be wholly guessed if they don't exist in the Universe. If they already exist in the Universe, only empty or missing values will be guessed. .. warning:: In MDAnalysis 2.x, types and masses are being automatically guessed if they are missing (``to_guess=('types, 'masses')``). However, starting with release 3.0 **no guessing will be done by default** and it will be up to the user to request guessing using ``to_guess`` and ``force_guess``. force_guess: list[str], (optional) TopologyAttrs in this list will be force guessed. If the TopologyAttr does not already exist in the Universe, this has no effect. If the TopologyAttr does already exist, all values will be overwritten by guessed values. fudge_factor: float, default [0.55] For use with *guess_bonds*. Supply the factor by which atoms must overlap each other to be considered a bond. .. deprecated:: 2.8.0 This keyword is deprecated and will be removed in MDAnalysis 3.0. Please pass it into Guesser creation (:mod:`~MDAnalysis.guesser`), or to :meth:`~MDAnalysis.core.universe.Universe.guess_TopologyAttrs` method instead. If passed into `guess_TopologyAttrs`, it will override the values set during Guesser creation. lower_bound: float, default [0.1] For use with *guess_bonds*. Supply the minimum bond length. .. deprecated:: 2.8.0 This keyword is deprecated and will be removed in MDAnalysis 3.0. Please pass it into Guesser creation (:mod:`~MDAnalysis.guesser`), or to :meth:`~MDAnalysis.core.universe.Universe.guess_TopologyAttrs` method instead. If passed into `guess_TopologyAttrs`, it will override the values set during Guesser creation. transformations: function or list, ``None``, default ``None`` Provide a list of transformations that you wish to apply to the trajectory upon reading. Transformations can be found in :mod:`MDAnalysis.transformations`, or can be user-created. in_memory: bool, default ``False`` After reading in the trajectory, transfer it to an in-memory representations, which allow for manipulation of coordinates. in_memory_step: int, default 1 Only read every nth frame into in-memory representation. continuous: bool, default ``False`` The `continuous` option is used by the :mod:`ChainReader`, which contains the functionality to treat independent trajectory files as a single virtual trajectory. **kwargs: extra arguments are passed to the topology parser. For instance, when reading a PDB file (:class:`PDBReader`, :class:`PDBParser`), set ``force_chainids_to_segids=True`` to make the universe use the chainIDs (column 22) instead of the segmentIDs (column 73-76) as the `segids` in the universe and select the corresponding SegmentGroup. Attributes ---------- trajectory : base.ReaderBase or base.SingleFrameReaderBase currently loaded trajectory reader; readers are described in :ref:`Coordinates` dimensions : numpy.ndarray system dimensions (simulation unit cell, if set in the trajectory) at the *current time step* (see :attr:`MDAnalysis.coordinates.base.Timestep.dimensions`). The unit cell can be set for the current time step (but the change is not permanent unless written to a file). atoms : AtomGroup all particles (:class:`~MDAnalysis.core.groups.Atom`) in the system, as read from the `topology` file residues : ResidueGroup all residues (:class:`~MDAnalysis.core.groups.Residue`) in the system segments : SegmentGroup all segments (:class:`~MDAnalysis.core.groups.Segment`) in the system bonds : topologyattrs.Bonds all bonds (if defined in the `topology`) as provided by :attr:`Universe.atoms.bonds` angles : topologyattrs.Angles all angles (if defined in the `topology`), same as :attr:`Universe.atoms.angles` dihedrals : topologyattrs.Dihedrals all dihedral angles (if defined in the `topology`), same as :attr:`Universe.atoms.dihedrals` impropers : topologyattrs.Impropers all improper dihedral angles (if defined in the `topology`), same as :attr:`Universe.atoms.impropers` Examples -------- Examples for setting up a :class:`Universe`:: u = Universe(topology, trajectory) # read system from file(s) u = Universe(pdbfile) # read atoms and coordinates from PDB or GRO u = Universe(topology, [traj1, traj2, ...]) # read from a list of trajectories u = Universe(topology, traj1, traj2, ...) # read from multiple trajectories Load new data into a universe (replaces old trajectory and does *not* append):: u.load_new(trajectory) # read from a new trajectory file Selecting atoms with :meth:`~Universe.select_atoms` :: ag = u.select_atoms(...) returns an :class:`~MDAnalysis.core.groups.AtomGroup`. .. versionchanged:: 1.0.0 Universe() now raises an error. Use Universe(None) or :func:`Universe.empty()` instead. Removed instant selectors. .. versionchanged:: 2.0.0 Universe now can be (un)pickled. ``topology`` and ``trajectory`` are reserved upon unpickle. .. versionchanged:: 2.5.0 Added fudge_factor and lower_bound parameters for use with *guess_bonds*. .. versionchanged:: 2.8.0 Added :meth:`~MDAnalysis.core.universe.Universe.guess_TopologyAttrs` API guessing masses and atom types after topology is read from a registered parser. .. versionchanged:: 2.10.0 Added :meth: `~MDAnalysis.core.universe.Universe.set_groups` API to set residues/segments based on the atomwise resids/segids. NFg?g?default)typesmassesr)r ) rrirvtransformations guess_bondsvdwradii fudge_factor lower_bound in_memorycontextto_guess force_guessin_memory_stepc d|_dii|_d|_d|_d|_d|_t | |_||||| | ||||d |_|j |t|||d\}}t|ts*|(t||_t|jfd|i|}|||_nt!dt#|t%|jg|R||d}|r|j|f|| |d||r!t)|r|g}|jj||r.t-jdt0t3| gd z} || | | d dS) N_valid) rrrrrrrrirvrr|rvzmTopology argument required to make Universe. Try Universe.empty(n_atoms, ...) to construct your own Universe.r)rirraBond guessing through the `guess_bonds` keyword is deprecated and will be removed in MDAnalysis 3.0. Instead, pass 'bonds', 'angles', and 'dihedrals' to the `to_guess` keyword in Universe for guessing these if they are not present, or `force_guess` if they are and you wish to replace these bonds with guessed values. The kwargs `fudge_factor`, `vdwradii`, and `lower_bound` are also deprecated and will be removed in MDAnalysis 3.0, where they should be passed into the Context for guessing on Universe instantiation. If using guess_TopologyAttrs, pass these kwargs to the method instead, as they will override the previous Context values.)bondsangles dihedralsF)error_if_missing) _trajectory_cacher<rrrr%_context_kwargsupdaterr+rrfr{rHrrrload_newcallableadd_transformationsrrDeprecationWarninglistguess_TopologyAttrs)selfrdrrirvrrrrrrrrrrrrws r0__init__zUniverse.__init__ sJ( n     #G,, .& (&",..     F###"2 # # # (H-- h6F,X66DM/ />BHH  %DNN%  %%%* M   +       DM #-          C(( 4#2"3 0D  0/ B B  I M /#   $H~~(H(H(HHH   X{U !     r2c|j}||jd|}|j|_|S)z+Return an independent copy of this Universer)rr)rcopyrArH trajectory)rrnews r0rz Universe.copyws^-$$&&nn N   ! !B  --// r2c |sd}d}| |dkrtjdt| |dkrtjdtt|||||} || d} |dks|rut j||d ftj } |rt j| nd} | rt j| nd} t| | d || | | _ | S) aCreate a blank Universe Useful for building a Universe without requiring existing files, for example for system building. If `trajectory` is set to ``True``, a :class:`MDAnalysis.coordinates.memory.MemoryReader` will be attached to the Universe. Parameters ---------- n_atoms: int number of Atoms in the Universe n_residues: int, default 1 number of Residues in the Universe, defaults to 1 n_segments: int, default 1 number of Segments in the Universe, defaults to 1 n_frames: int, default 1 number of Frames in the Universe, defaults to 1 atom_resindex: array like, optional mapping of atoms to residues, e.g. with 6 atoms, `atom_resindex=[0, 0, 1, 1, 2, 2]` would put 2 atoms into each of 3 residues. residue_segindex: array like, optional mapping of residues to segments trajectory: bool, optional if ``True``, attaches a :class:`MDAnalysis.coordinates.memory.MemoryReader` allowing coordinates to be set and written. velocities: bool, optional include velocities in the :class:`MDAnalysis.coordinates.memory.MemoryReader` forces: bool, optional include forces in the :class:`MDAnalysis.coordinates.memory.MemoryReader` Returns ------- Universe :class:`~MDAnalysis.core.universe.Universe` instance with dummy values for atoms and undefined coordinates/velocities/forces Examples -------- For example to create a new Universe with 6 atoms in 2 residues, with positions for the atoms and a mass attribute:: u = mda.Universe.empty(6, 2, atom_resindex=np.array([0, 0, 0, 1, 1, 1]), trajectory=True, ) u.add_TopologyAttr('masses') .. versionadded:: 0.17.0 .. versionchanged:: 0.19.0 The attached Reader when trajectory=True is now a MemoryReader .. versionchanged:: 1.0.0 Universes can now be created with 0 atoms rNr zZResidues specified but no atom_resindex given. All atoms will be placed in first Residue.z_Segments specified but no segment_resindex given. All residues will be placed in first Segment)rErFr))rdtypefac)orderrM velocitiesforces) rr UserWarningrrzerosfloat32 zeros_likerr)clsrMrYr]n_framesrErFrrrr6ucoordsvelss r0emptyzUniverse.emptys<R JJ  Z!^^ M=     # Q M?       '-     Cb ! ! ! a<<:<Xx!4BJGGGF,6@2=(((DD.4>R]6***$F2>&11 ALr2c|Sr~r)rs r0r>zUniverse.universes  r2c ||Sttj|dkrtj|d}td| t ||}n5#t$r(}td||d}~wwxYw|j j |d<||fd|i||_ |j j t|j krLtd |j jt|j ||j j |r|j d d |i||S) a Load coordinates from `filename`. The file format of `filename` is autodetected from the file name suffix or can be explicitly set with the `format` keyword. A sequence of files can be read as a single virtual trajectory by providing a list of filenames. Parameters ---------- filename: str or list the coordinate file (single frame or trajectory) *or* a list of filenames, which are read one after another. format: str or list or object (optional) provide the file format of the coordinate or trajectory file; ``None`` guesses it from the file extension. Note that this keyword has no effect if a list of file names is supplied because the "chained" reader has to guess the file format for each individual list member [``None``]. Can also pass a subclass of :class:`MDAnalysis.coordinates.base.ProtoReader` to define a custom reader to be used on the trajectory file. in_memory: bool (optional) Directly load trajectory into memory with the :class:`~MDAnalysis.coordinates.memory.MemoryReader` .. versionadded:: 0.16.0 **kwargs: dict Other kwargs are passed to the trajectory reader (only for advanced use) Returns ------- universe: Universe Raises ------ TypeError if trajectory format can not be determined or no appropriate trajectory reader found .. versionchanged:: 0.8 If a list or sequence that is provided for `filename` only contains a single entry then it is treated as single coordinate file. This has the consequence that it is not read by the :class:`~MDAnalysis.coordinates.chain.ChainReader` but directly by its specialized file format reader, which typically has more features than the :class:`~MDAnalysis.coordinates.chain.ChainReader`. .. versionchanged:: 0.17.0 Now returns a :class:`Universe` instead of the tuple of file/array and detected file type. .. versionchanged:: 2.4.0 Passes through kwargs if `in_memory=True`. Nr rz#Universe.load_new(): loading {0}...rhzKCannot find an appropriate coordinate reader for file '{0}'. {1}rMrizThe topology and {form} trajectory files don't have the same number of atoms! Topology number of atoms {top_n_atoms} Trajectory: {fname} Number of atoms {trj_n_atoms})form top_n_atomsfname trj_n_atomsstepr)) rJr asiterableloggerdebugrirrsrr<rMrtransfer_to_memory)rrrirrrwreaderrzs r0rzUniverse.load_newsF  K tx(( ) )Q . .x003H :AA(KKLLL #HV<<)rM)rirJr<rs r0__repr__zUniverse.__repr__s, 177 OO8   r2c0||d|}||_|S)z;Special method used by __reduce__ to deserialise a Universer)r)r)rr6trajrrs r0 _unpickle_UzUniverse._unpickle_Us& Cb' 2 2 2 r2c\|j|j|j|jffSr~)rrHrrrrs r0 __reduce__zUniverse.__reduce__s1   ^T-t}/A/A/C/C D  r2c|jjS)zDCurrent dimensions of the unitcell. :meta private: coordrrs r0rzUniverse.dimensionss z$$r2c||j_dS)zTSet dimensions if the Timestep allows this .. versionadded:: 0.9.0 Nr)rboxs r0rzUniverse.dimensionss!$ r2c|jjS)a|Reference to current timestep and coordinates of universe. The raw trajectory coordinates are :attr:`Universe.coord.positions`, represented as a :class:`numpy.float32` array. Because :attr:`coord` is a reference to a :class:`~MDAnalysis.coordinates.timestep.Timestep`, it changes its contents while one is stepping through the trajectory. .. Note:: In order to access the coordinates it is better to use the :meth:`AtomGroup.positions` method; for instance, all coordinates of the Universe as a numpy array: :meth:`Universe.atoms.positions`. )rrrs r0rzUniverse.coord s$!!r2c4tj|jS)z2keyword arguments used to initialize this universe)rdeepcopyrrs r0rwzUniverse.kwargs s}T\***r2c<|j|jStd)zbReference to trajectory reader object containing trajectory data. :meta private: Nz"No trajectory loaded into Universe)rAttributeErrorrs r0rzUniverse.trajectory%s%   '# # !EFF Fr2c|`||_dSr~)r)rvalues r0rzUniverse.trajectory0s   r2c *t|tr|dvrtjtt  t |}||jj |jj |jj |}ne#t$rXd |dtt j}t#|dwxYw|j|||dS)aAdd a new topology attribute to the Universe Adding a TopologyAttribute to the Universe makes it available to all AtomGroups etc throughout the Universe. Parameters ---------- topologyattr: TopologyAttr or string Either a MDAnalysis TopologyAttr object or the name of a possible topology attribute. values: np.ndarray, optional If initiating an attribute from a string, the initial values to use. If not supplied, the new TopologyAttribute will have empty or zero values. Example ------- For example to add bfactors to a Universe: >>> import MDAnalysis as mda >>> from MDAnalysis.tests.datafiles import PSF, DCD >>> u = mda.Universe(PSF, DCD) >>> u.add_TopologyAttr('tempfactors') >>> u.atoms.tempfactors array([0., 0., 0., ..., 0., 0., 0.]) .. versionchanged:: 0.17.0 Can now also add TopologyAttrs with a string of the name of the attribute to add (eg 'charges'), can also supply initial values using values keyword. .. versionchanged:: 1.1.0 Now warns when adding bfactors to a Universe with existing tempfactors, or adding tempfactors to a Universe with existing bfactors. In version 2.0, MDAnalysis will stop treating tempfactors and bfactors as separate attributes. Instead, they will be aliases of the same attribute. )bfactorbfactors)rMrYr]valueszUnrecognised topology attribute name: '{}'. Possible values: '{}' To raise an issue go to: https://github.com/MDAnalysis/mdanalysis/issues, N)r+strrrr"rr from_blankrHrMrYr]KeyErrorrijoinsortedkeysrsrNr)r topologyattrrtclserrmsgs r0rNzUniverse.add_TopologyAttr5sP lC ( ( 666 o/ABBB &|4 $ N2#~8#~8! /    3 3 3v$dii7K7M7M0N0N&O&O !((d2 3$ '' 555 <(((((s A??A"C!cjt|tsS |j}nJ#t$r= |jdz}n.#t$r!t dt |dwxYwYnwxYw t|j}nN#t$rAd tt}d|d|d}t |dwxYw t|j |}n"#t$rt d|d dwxYw|j |||dS) a]Remove a topology attribute from the Universe Removing a TopologyAttribute from the Universe makes it unavailable to all AtomGroups etc throughout the Universe. Parameters ---------- topologyattr: TopologyAttr or string Either a MDAnalysis TopologyAttr object or the name of a possible topology attribute. Example ------- For example to remove bfactors to a Universe: >>> import MDAnalysis as mda >>> from MDAnalysis.tests.datafiles import PSF, DCD >>> u = mda.Universe(PSF, DCD) >>> u.add_TopologyAttr('tempfactors') >>> hasattr(u.atoms[:3], 'tempfactors') True >>> >>> u.del_TopologyAttr('tempfactors') >>> hasattr(u.atoms[:3], 'tempfactors') False .. versionadded:: 2.0.0 szGTopology attribute must be str or TopologyAttr object or class. Given: Nrz"Unrecognised topology attribute: 'z'. Possible values: 'zJ' To raise an issue go to: https://github.com/MDAnalysis/mdanalysis/issueszTopology attribute z not in Universe.)r+rr:rbtyperstyperrrrr;rHdel_TopologyAttr_unprocess_attr)rrr5rtopattrs r0rzUniverse.del_TopologyAttrws>,,,  +4 !   $0#5#;LL%   $7"&|"4"477   !L  /*<8ALL / / /IIf_5566EB\BB',BBB  V$$$ . / dnl;;GG   HlHHH   ''000 W%%%%%s< A& 5A&+A  A&%A&*A==A C C""Dc |jj|jj|jjd}td||jft|||jkrHtd|j |j||jt||j D]"}|j | |#ttt t"t$t&t(fD]1}|j|D]!\}}t-|j |||"2|jdD]\}}t-|j||dS)zSqueeze a topologyattr for its information Grabs: - Group properties (attribute access) - Component properties - Transplant methods )atomresiduesegmentz%_process_attr: Adding {0} to topologyNzKLength of {attr} does not match number of {obj}s. Expect: {n:d} Have: {m:d})robjnmr)rHrMrYr]rrri per_objectrJrsr:r*r _add_proprrrrrrr transplantssetattrrA)rrn_dictrfuncnamemeths r0rzUniverse._process_attrsN*~0~0    <CCDIIJJJ O 'D VDO444,,2FT_-$ii -3--   & 3 3C  c " , ,T 2 2 2 2        @ @C#'"23"7 @ @$)#.$???? @#.z: 4 4NHd DNHd 3 3 3 3 4 4r2cJ|jD]"}|j||#|jdgD]\}}t |j||jD](\}}|D] \}}t |j||!)dS)z Undo all the stuff in _process_attr. If the topology attribute is not present, nothing happens (silent fail). rN)r*r _del_propr)popdelattrrAitems)rrrr,_r)s r0rzUniverse._unprocess_attrs& 3 3C  c " , ,T 2 2 2 2 +// B?? . .KHa DNH - - - - $ 0 6 6 8 8 : : C* : : !)#.9999 : : :r2c t|jdkr |jd}|td|jj|fi|}t t j|jj||_ |j |S)aAdd a new Residue to this Universe New Residues will not contain any Atoms, but can be assigned to Atoms as per usual. If the Universe contains multiple segments, this must be specified as a keyword. Parameters ---------- segment: MDAnalysis.Segment If there are multiple segments, then the Segment that the new Residue will belong in must be specified. attrs: dict For each Residue attribute, the value for the new Residue must be specified Returns ------- A reference to the new Residue Raises ------ NoDataError If any information was missing. This happens before any changes have been made, ie the change is rolled back. Example ------- Adding a new GLY residue, then placing atoms within it: >>> import MDAnalysis as mda >>> from MDAnalysis.tests.datafiles import PSF, DCD >>> u = mda.Universe(PSF, DCD) >>> newres = u.add_Residue(segment=u.segments[0], resid=42, resname='GLY', resnum=0) >>> u.atoms[[1, 2, 3]].residues = newres >>> u.select_atoms('resname GLY and resid 42 and resnum 0') r rN) rJrrrH add_ResiduerrrrYr)rr#r5rUs r0r6zUniverse.add_ResiduesR t}   " "mA&G ?b// !++G==u==$ Idn/ 0 0$   }V$$r2c |jjdi|}ttj|jj||_|j|S)aAdd a new Segment to this Universe Parameters ---------- attrs: dict For each Segment attribute as a key, give the value in the new Segment Returns ------- A reference to the new Segment Raises ------ NoDataError If any attributes were not specified as a keyword. r))rH add_Segmentrrrr]r)rr5r[s r0r8zUniverse.add_Segment5sR(,+44e44$ Idn/ 0 0$   }V$$r2ctd|Dr8 d|D}n#t$rd}YnwxYwd|D}d|D}g}|D]{}t|ttfrH|j|ur$d}t ||||j f|||td|D} | t|j j z } | rMd tt| } d }t |||  t|j|} n;#t$r.||gt|j|} YnwxYw| |||| dS) aAdd new TopologyObjects to this Universe Parameters ---------- object_type : {'bonds', 'angles', 'dihedrals', 'impropers'} The type of TopologyObject to add. values : TopologyGroup or iterable of tuples, AtomGroups, or TopologyObjects An iterable of: tuples of atom indices, or AtomGroups, or TopologyObjects. If every value is a TopologyObject, all keywords are ignored. If AtomGroups or TopologyObjects are passed, they *must* be from the same Universe. types : iterable (optional, default None) None, or an iterable of hashable values with the same length as ``values`` guessed : bool or iterable (optional, default False) bool, or an iterable of hashable values with the same length as ``values`` order : iterable (optional, default None) None, or an iterable of hashable values with the same length as ``values`` .. versionadded:: 1.0.0 c3@K|]}t|tVdSr~)r+r$)r-xs r0 z1Universe._add_topology_objects..js,==z!^,,======r2cg|] }|j Sr))rr-ts r0r1z2Universe._add_topology_objects..ls000A000r2Ncg|] }|j Sr)) is_guessedr>s r0r1z2Universe._add_topology_objects..os444q|444r2cg|] }|j Sr))rr>s r0r1z2Universe._add_topology_objects..ps---QW---r2z'Cannot add {} from different Universes.cg|] }|D]}| Sr)r))r-r$rs r0r1z2Universe._add_topology_objects..|s%=====A1====r2rz.Cannot add {} for nonexistent atom indices: {}rguessedr)allrr+rr$r>rsrirLindicessetr<rmaprr;rHrN _add_bonds) r object_typerrrErrGr;err_msg all_indices nonexistentistrrs r0_add_topology_objectszUniverse._add_topology_objectsQs2 ==f=== = = . 00000!    44V444G--f---E " "A!i899 ":T))GG$W^^K%@%@AAAqy))))q!!!!=====>> !C (:$;$;;  @99Sk2233DFGW^^K>>?? ? 84>;77DD 8 8 8  ! !+r 2 2 24>;77DDD 8 ugUKKKKKs ( 77E--5F%$F%cb|d|||||dS)a0Add new Bonds to this Universe. Parameters ---------- values : iterable of tuples, AtomGroups, or Bonds; or TopologyGroup An iterable of: tuples of 2 atom indices, or AtomGroups with 2 atoms, or Bonds. If every value is a Bond, all keywords are ignored. If AtomGroups, Bonds, or a TopologyGroup are passed, they *must* be from the same Universe. types : iterable (optional, default None) None, or an iterable of hashable values with the same length as ``values`` guessed : bool or iterable (optional, default False) bool, or an iterable of hashable values with the same length as ``values`` order : iterable (optional, default None) None, or an iterable of hashable values with the same length as ``values`` Example ------- Adding TIP4P water bonds with a list of AtomGroups:: import MDAnalysis as mda from MDAnalysis.tests.datafiles import GRO u = mda.Universe(GRO) sol = u.select_atoms('resname SOL') ow_hw1 = sol.select_atoms('name OW or name HW1').split('residue') ow_hw2 = sol.select_atoms('name OW or name HW2').split('residue') ow_mw = sol.select_atoms('name OW or name MW').split('residue') u.add_bonds(ow_hw1 + ow_hw2 + ow_mw) You can only add bonds from the same Universe. If you would like to add AtomGroups, Bonds, or a TopologyGroup from a different Universe, convert them to indices first. :: from MDAnalysis.tests.datafiles import PSF u2 = mda.Universe(PSF) # assuming you have already added bonds to u u2.add_bonds(u.bonds.to_indices()) .. versionadded:: 1.0.0 rrDN)rP_invalidate_bond_related_caches)rrrrErs r0 add_bondszUniverse.add_bondssG\ "" V5' #    ,,.....r2c|jdd|jddd|jddddS)z Invalidate caches related to bonds and fragments. This should be called whenever the Universe's bonds are modified. .. versionadded: 2.8.0 fragmentsNr fragindices)rr0rs r0rRz(Universe._invalidate_bond_related_cachessZ  T*** H!!+t444 H!!-66666r2c8|d|||dS)aAdd new Angles to this Universe. Parameters ---------- values : iterable of tuples, AtomGroups, or Angles; or TopologyGroup An iterable of: tuples of 3 atom indices, or AtomGroups with 3 atoms, or Angles. If every value is a Angle, all keywords are ignored. If AtomGroups, Angles, or a TopologyGroup are passed, they *must* be from the same Universe. types : iterable (optional, default None) None, or an iterable of hashable values with the same length as ``values`` guessed : bool or iterable (optional, default False) bool, or an iterable of hashable values with the same length as ``values`` .. versionadded:: 1.0.0 rrrENrPrrrrEs r0 add_angleszUniverse.add_angless4$ "" fE7 #     r2c8|d|||dS)a Add new Dihedrals to this Universe. Parameters ---------- values : iterable of tuples, AtomGroups, or Dihedrals; or TopologyGroup An iterable of: tuples of 4 atom indices, or AtomGroups with 4 atoms, or Dihedrals. If every value is a Dihedral, all keywords are ignored. If AtomGroups, Dihedrals, or a TopologyGroup are passed, they *must* be from the same Universe. types : iterable (optional, default None) None, or an iterable of hashable values with the same length as ``values`` guessed : bool or iterable (optional, default False) bool, or an iterable of hashable values with the same length as ``values`` .. versionadded:: 1.0.0 rrXNrYrZs r0 add_dihedralszUniverse.add_dihedrals4& "" ug #     r2c8|d|||dS)a Add new Impropers to this Universe. Parameters ---------- values : iterable of tuples, AtomGroups, or Impropers; or TopologyGroup An iterable of: tuples of 4 atom indices, or AtomGroups with 4 atoms, or Impropers. If every value is an Improper, all keywords are ignored. If AtomGroups, Impropers, or a TopologyGroup are passed, they *must* be from the same Universe. types : iterable (optional, default None) None, or an iterable of hashable values with the same length as ``values`` guessed : bool or iterable (optional, default False) bool, or an iterable of hashable values with the same length as ``values`` .. versionadded:: 1.0.0 rrXNrYrZs r0 add_improperszUniverse.add_impropersr^r2cg}|D]{}t|ttfrH|j|ur$d}t ||||jf||| t|j |}n0#t$r#t d|wxYw| |dS)a'Delete TopologyObjects from this Universe Parameters ---------- object_type : {'bonds', 'angles', 'dihedrals', 'impropers'} The type of TopologyObject to delete. values : iterable of tuples, AtomGroups, or TopologyObjects; or TopologyGroup An iterable of: tuples of atom indices, or AtomGroups, or TopologyObjects. If AtomGroups, TopologyObjects, or a TopologyGroup are passed, they *must* be from the same Universe. .. versionadded:: 1.0.0 z*Cannot delete {} from different Universes.zThere are no {} to deleteN) r+rr$r>rsrirLrGr;rHr _delete_bonds)rrKrrGr;rLrs r0_delete_topology_objectsz!Universe._delete_topology_objectss " "A!i899 ":T))JG$W^^K%@%@AAAqy))))q!!!! N4>;77DD N N N8?? LLMM M N 7#####s B-CcZ|d||dS)a&Delete Bonds from this Universe. Parameters ---------- values : iterable of tuples, AtomGroups, or Bonds; or TopologyGroup An iterable of: tuples of 2 atom indices, or AtomGroups with 2 atoms, or Bonds. If AtomGroups, Bonds, or a TopologyGroup are passed, they *must* be from the same Universe. Example ------- Deleting bonds from a Universe:: import MDAnalysis as mda from MDAnalysis.tests.datafiles import PSF u = mda.Universe(PSF) # delete first 5 bonds u.delete_bonds(u.bonds[:5]) If you are deleting bonds in the form of AtomGroups, Bonds, or a TopologyGroup, they must come from the same Universe. If you want to delete bonds from another Universe, convert them to indices first. :: from MDAnalysis.tests.datafiles import PDB u2 = mda.Universe(PDB) u.delete_bonds(u2.bonds.to_indices()) .. versionadded:: 1.0.0 rN)rcrRrrs r0 delete_bondszUniverse.delete_bonds.s3J %%gv666 ,,.....r2c2|d|dS)aDelete Angles from this Universe. Parameters ---------- values : iterable of tuples, AtomGroups, or Angles; or TopologyGroup An iterable of: tuples of 3 atom indices, or AtomGroups with 3 atoms, or Angles. If AtomGroups, Angles, or a TopologyGroup are passed, they *must* be from the same Universe. .. versionadded:: 1.0.0 rNrcres r0 delete_angleszUniverse.delete_anglesVs  %%h77777r2c2|d|dS)aDelete Dihedrals from this Universe. Parameters ---------- values : iterable of tuples, AtomGroups, or Dihedrals; or TopologyGroup An iterable of: tuples of 4 atom indices, or AtomGroups with 4 atoms, or Dihedrals. If AtomGroups, Dihedrals, or a TopologyGroup are passed, they *must* be from the same Universe. .. versionadded:: 1.0.0 rNrhres r0delete_dihedralszUniverse.delete_dihedralsf  %%k6:::::r2c2|d|dS)aDelete Impropers from this Universe. Parameters ---------- values : iterable of tuples, AtomGroups, or Impropers; or TopologyGroup An iterable of: tuples of 4 atom indices, or AtomGroups with 4 atoms, or Impropers. If AtomGroups, Angles, or a TopologyGroup are passed, they *must* be from the same Universe. .. versionadded:: 1.0.0 rNrhres r0delete_improperszUniverse.delete_impropersvrlr2rUc<jj}jj}t ||}t fd|D}i}t jdd}t|D]\}}|D]} ||||| j<|S)a  .. versionadded:: 0.9.0 .. versionchanged:: 0.16.0 Fragment atoms are sorted by their index, and framgents are sorted by their first atom index so their order is predictable. .. versionchanged:: 0.19.0 Uses faster C++ implementation .. versionchanged:: 0.20.0 * _fragdict keys are now atom indices instead of Atoms * _fragdict items are now a namedtuple ``fraginfo(ix, fragment)`` storing the fragindex ``ix`` along with the fragment. cTg|]$}ttj|%Sr))rrsort)r-ixrs r0r1z&Universe._fragdict..s+KKKyd33KKKr2fraginfoz ix, fragment) r<rrr to_indicesr tuple collections namedtuplerI) rr<r frag_indicesfragsfragdictrsrfas ` r0 _fragdictzUniverse._fragdicts   ++--%eU33 KKKKlKKKLL)*nEEe$$ 0 0DAq 0 0!)!Q 0r2Tc |i} ddlm}ddlm} n"#t$r} t d| d} ~ wwxYw|||} | "t d||r|| } |rs|std| d |}t|tr|dks"t d || j | |fi||| fi|S) aCreate a Universe from a SMILES string with rdkit Parameters ---------- smiles : str SMILES string sanitize : bool (optional, default True) Toggle the sanitization of the molecule addHs : bool (optional, default True) Add all necessary hydrogens to the molecule generate_coordinates : bool (optional, default True) Generate 3D coordinates using RDKit's :func:`AllChem.EmbedMultipleConfs` function. Requires adding hydrogens with the `addHs` parameter numConfs : int (optional, default 1) Number of frames to generate coordinates for. Ignored if ``generate_coordinates=False`` rdkit_kwargs : dict (optional) Other arguments passed to the RDKit :func:`EmbedMultipleConfs` function kwargs : dict Parameters passed on Universe creation Returns ------- universe : Universe contains atom names and topology information (bonds) derived from the input SMILES string; coordinates are included if `generate_coordinates` was set to ``True`` Examples -------- To create a Universe with 10 conformers of ethanol: >>> from rdkit.Chem import AllChem >>> u = mda.Universe.from_smiles('CCO', numConfs=10) >>> u >>> u.trajectory To use a different conformer generation algorithm, like ETKDGv3: >>> u = mda.Universe.from_smiles('CCO', rdkit_kwargs=dict( ... params=AllChem.ETKDGv3())) >>> u.trajectory .. versionadded:: 2.0.0 Nr)Chem)AllChemz^Creating a Universe from a SMILES string requires RDKit but it does not appear to be installed)sanitizezError while parsing SMILES {0}zBGenerating coordinates requires adding hydrogens with `addHs=True`numConfsz;numConfs must be a non-zero positive integer instead of {0})rdkitr rdkit.Chemr ImportError MolFromSmiles SyntaxErrorriAddHsrsr0r+intEmbedMultipleConfs) rsmilesraddHsgenerate_coordinatesr rdkit_kwargsrwrremols r0 from_smileszUniverse.from_smiless~@  L  " " " " " " * * * * * * *   5     ( ;; ;>EEfMMNN N  "**S//C  F  2 $'' H==Hx-- (Q,,!--3VH-=-= 'G &sH E E E E Es3!!&!!!s  2-2c |s|j}i}||j||t||jfi|}||_|g}|g}t |t |z}t t |}tdtj D} |j j dkrd|j j D} t|t| z} dd| D} t| dkrt d| d|D]L} || r!| |v} || | }n>#t($r1}|s| r|t+jt/|Yd}~kd}~wwxYw|v| | vru| r@t1|j| r+t5|j| }|| ||| |d | d kr|n+t| |d }||t d | d :t?|d| dSt+jddS)ai Guess and add attributes through a specific context-aware guesser. Parameters ---------- context: str or :mod:`Guesser` class For calling a matching guesser class for this specific context to_guess: Optional[list[str]] TopologyAttrs to be guessed. These TopologyAttrs will be wholly guessed if they don't exist in the Universe. If they already exist in the Universe, only empty or missing values will be guessed. .. warning:: In MDAnalysis 2.x, types and masses are being automatically guessed if they are missing (``to_guess=('types, 'masses')``). However, starting with release 3.0 **no guessing will be done by default** and it will be up to the user to request guessing using ``to_guess`` and ``force_guess``. force_guess: Optional[list[str]] TopologyAttrs in this list will be force guessed. If the TopologyAttr does not already exist in the Universe, this has no effect. If the TopologyAttr does already exist, all values will be overwritten by guessed values. error_if_missing: bool If `True`, raise an error if the guesser cannot guess the attribute due to missing TopologyAttrs used as the inputs for guessing. If `False`, a warning will be raised instead. Errors will always be raised if an attribute is in the ``force_guess`` list, even if this parameter is set to False. **kwargs: extra arguments to be passed to the guesser class Examples -------- To guess ``masses`` and ``types`` attributes:: u.guess_TopologyAttrs(context='default', to_guess=['masses', 'types']) .. versionadded:: 2.8.0 Nc3NK|] }t|t|jV!dSr~) issubclassr#r:)r-rs r0r<z/Universe.guess_TopologyAttrs..WsI  ';//        r2rcg|] }|j Sr))r:)r-atts r0r1z0Universe.guess_TopologyAttrs..as'!$ r2rc3K|]}|VdSr~r))r-rs r0r<z/Universe.guess_TopologyAttrs..fs"$C$CdT$C$C$C$C$C$Cr2zThe attribute(s) z have already been read from the topology file. The guesser will only guess empty values for this attribute, if any exists. To overwrite it by completely guessed values, you can pass the attribute to the force_guess parameter instead of the to_guess oneT)rErz attribute z has been guessed successfully.z0 guesser can not guess the following attribute: z2Can not guess attributes for universe with 0 atoms) rrrr%r>rdictfromkeysrHrrrHrMread_attributesrrJrinfo is_guessable guess_attrrrrrrcr<r;rcrPrRrNrs)rrrrrrwguesser_kwargsguesser total_guessobjectstopology_attrs common_attrsrfgrrgroup guessed_attrs r0rzUniverse.guess_TopologyAttrs sod $mGdl+++f%%%gt}GGGG  H  K8nntK'8'88 4==5566   *133      > !A % %(,(FNx==3~+>+>>L99$C$Cl$C$C$CCCL<  1$$ ' '''$# # ''--",B%!(!3!3D"!=!=&%%%+%r%"#G$M#a&&111$HHHH %~ wG'$*d";";G$+DJ$=$=E 99$FFF2242NNN7?? @@BBB'6t'>> .. versionadded:: 2.10.0 NzFNot setting groups. Please provide atomwise_resids or atomwise_segids.zXThe length of atomwise_resids should be the same as the number of atoms in the universe.z_The new resids replaces the current one. The original resids is stored in atomwise_resids_orig.zXThe length of atomwise_segids should be the same as the number of atoms in the universe.z_The new resids replaces the current one. The original segids is stored in atomwise_segids_orig.r)rOrP)rrr<rWrJrMrsatomwise_resids_origrrr\atomwise_segids_origrarrayrobjectr`r)rrOrPs r0 set_groupszUniverse.set_groupssnj  #/*A M#    F  ""j/OO?##tz'999 ; )- (9D % KK(     ""j/OO?##tz'999 ; )- (9D % KK(    (?#>>>(?&AAA ++    %%%%%r2r~)r r r NNFFF)NFr )NNNF)NFN)NF)TTTr N)NNNT)NN)/__name__ __module__ __qualname____doc__rr classmethodrpropertyr>rrrrrrrrrrrsetterrrwrrNrrrr6r8rPrSrRr[r]r`rcrfrirkrnr r}rrrr)r2r0rr3sbTTpk $!k k k k k Zrrr[rhX ggggT9>IIII^888  X !!X!$$X$$$X$   [   %%X%$$$""X"&++X+GGXG!!!@)@)@)@)DB&B&B&H/4/4/4b:::$5%5%5%5%n%%%:EI8L8L8L8Lt1/1/1/1/f 7 7 7    ,    .    .$$$>&/&/&/P888 ;;; ;;;2 VKX6!^"^"^"[^"D NNNN`j&j&j&j&j&j&r2rc   !ddlm}t|dkrtd|D];}t |t jstt|dz<|D]$}t|dkrtd%tttg}tj d|D}tgd }g}||z |z }|D]v}|D]7} t| |} tt| jj|} t#| t$rnet#| t&rt| j|} n:t#| t*rt| j|} nt/d t| t0jkr/td t|  | | #t8$rt;| } Y5wxYw|| t1j| | j ~ x||zD]p} d}g}g}|D]} d tC| |D|t| z }t| | }tt| jj| }|"| d}fd|j#D}||tI|dr||j%|dgt|ztMd|Dr |||;t1j|d }||||rtOd|D}g}g}d}d}|D]} dtC| j|D dtC| j|D!|t| jz }|t| jz }| fd| j(D|!fd| j)Dt1j|t0j* }t1j|t0j* }|||\}}\}tt|}tt|}t||||||} t1j+d|D}tY||dddddftZj.j/j0}n#tb$rtY|}YnwxYw|S)aCreate a new new :class:`Universe` from one or more :class:`~MDAnalysis.core.groups.AtomGroup` instances. Parameters ---------- *args: :class:`~MDAnalysis.core.groups.AtomGroup` One or more AtomGroups. Returns ------- universe: :class:`Universe` Raises ------ ValueError Too few arguments or an AtomGroup is empty and TypeError Arguments are not :class:`AtomGroup` instances. Notes ----- The resulting :class:`Universe` will only inherit the common topology attributes that all merged universes share. :class:`AtomGroup` instances can come from different Universes, or can come directly from a :meth:`~Universe.select_atoms` call. :class:`Merge` can also be used with a single :class:`AtomGroup` if the user wants to, for example, re-order the atoms in the :class:`Universe`. If multiple :class:`AtomGroup` instances from the same :class:`Universe` are given, the merge will first simply "add" together the :class:`AtomGroup` instances. Merging does not create a full trajectory but only a single structure even if the input consists of one or more trajectories. However, one can use the :class:`~MDAnalysis.coordinates.memory.MemoryReader` to construct a trajectory for the new Universe as described under :ref:`creating-in-memory-trajectory-label`. Example ------- In this example, protein, ligand, and solvent were externally prepared in three different PDB files. They are loaded into separate :class:`Universe` objects (where they could be further manipulated, e.g. renumbered, relabeled, rotated, ...) The :func:`Merge` command is used to combine all of them together:: u1 = Universe("protein.pdb") u2 = Universe("ligand.pdb") u3 = Universe("solvent.pdb") u = Merge(u1.select_atoms("protein"), u2.atoms, u3.atoms) u.atoms.write("system.pdb") The complete system is then written out to a new PDB file. .. versionchanged:: 0.9.0 Raises exceptions instead of assertion errors. .. versionchanged:: 0.16.0 The trajectory is now a :class:`~MDAnalysis.coordinates.memory.MemoryReader`. r) squash_byrz'Need at least one AtomGroup for mergingz is not an AtomGroupzcannot merge empty AtomGroupr4cZg|](}tt|jj)Sr))rHdirr>rHr-ags r0r1zMerge..[s- 9 9 9b#c"+'(( ) ) 9 9 9r2)rrrrz`Don't know how to handle TopologyAttr not subclassed from AtomAttr, ResidueAttr, or SegmentAttr.z4Encountered unexpected topology attribute of type {}rc$i|] \}}|j|Sr))index)r-rr|s r0 zMerge..s JJJdaqwJJJr2)rT)strictcFg|]}tfd|DS)c g|] }| Sr)r))r-r;mappings r0r1z$Merge...s111awqz111r2)ru)r-entryrs r0r1zMerge..sC7<1111511122r2 _bondtypesNc3K|]}|duV dSr~r)r>s r0r<zMerge..s&((QqDy((((((r2z|S8c,g|]}t|Sr))rJrs r0r1zMerge..s***r3r77***r2c$i|] \}}|j|Sr))resindexr-rrs r0rzMerge..-   "aAJ   r2c$i|] \}}|j|Sr))segindexrs r0rzMerge..rr2c g|] }| Sr)r))r-r; res_mappings r0r1zMerge..===!{1~===r2c g|] }| Sr)r))r-r; seg_mappings r0r1zMerge..rr2rDcg|] }|j Sr))r)r-r|s r0r1zMerge..s666AAK666r2rh)2rGrrJrsr+rrrreprrHrr intersectionr;rr>rHrrrrrrrtrndarrayrirK NameErrorrrLrrrIatomgroup_intersectionrGrcranysum resindices segindicesint32vstackr MDAnalysisrmemoryrr)"rrr|blank_topology_attrsrtopsr5common_array_attrsr:rr attr_class attr_arrayr?offsetbondidxrtg bonds_classnew_idxrMrUr[ res_offset seg_offsetr3rYr]r6rrrrrs" @@@r0Merger suD*))))) 4yyA~~BCCC >>!V-.. >DGG&<<== = > == q66Q;;;<< < s8"#5#5#56677# 9 9D 9 9 9L <<< = =D E&(<>> ====r}===>>>> XfBH - - -F XfBH - - -FYvv..NAq(6S[[!!JS[[!!J     C 6666677   4AAA: )0=     SMM Hs%7HH+*H+AV11W  W r~)Drronumpyrloggingrr contextlibrvrrqosuuidr5rr exceptionsrlibrlib.logrlib.utilr r r lib.mdamathr r _get_readersrrrrrrrrrrrdr topologyattrsrrrrrrr r!r"r#topologyobjectsr$ guesser.baser% getLoggerrr`rfr{rrrrrrr)r2r0rs+0@    (((((((($$$$$$!!!!!!4444444444((((((88888888                                            ,+++++&&&&&&  5 6 6cccL@+/#####$(      4T&T&T&T&T&vT&T&T&n6L L L L L r2