iMdZddlZddlZddlZddlmZmZmZddl m Z dZ Gdd e Z Gd d e ZdS) aCore Topology object --- :mod:`MDAnalysis.core.topology` ======================================================== .. versionadded:: 0.16.0 :class:`Topology` is the core object that holds all topology information. TODO: Add in-depth discussion. Notes ----- For developers: In MDAnalysis 0.16.0 this new topology system was introduced and discussed as issue `#363`_; this issue contains key information and discussions on the new system. The issue number *363* is also being used as a short-hand in discussions to refer to the new topology system. .. _`#363`: https://github.com/MDAnalysis/mdanalysis/issues/363 Classes ------- .. autoclass:: Topology :members: .. autoclass:: TransTable :members: Helper functions ---------------- .. autofunction:: make_downshift_arrays N) Atomindices Resindices Segindices) NoDataErrorct|stjgtStj|d}||}tj|d\}}tj||dzg}tj|t}tj tj tj ||}tj ||j d}|dd||<|D]}|dkrd||<||dz ||<tj||dd } | dtj| tS) a From an upwards translation table, create the opposite direction Turns a many to one mapping (eg atoms to residues) to a one to many mapping (residues to atoms) Parameters ---------- upshift : array_like Array of integers describing which parent each item belongs to nparents : integer Total number of parents that exist. Returns ------- downshift : array_like (dtype object) An array of arrays, each containing the indices of the children of each parent. Length `nparents` + 1 Examples -------- To find the residue to atom mappings for a given atom to residue mapping: >>> import numpy as np >>> import MDAnalysis as mda >>> from MDAnalysis.core.topology import make_downshift_arrays >>> atom2res = np.array([0, 1, 0, 2, 2, 0, 2]) >>> make_downshift_arrays(atom2res, 3) array([array([0, 2, 5]), array([1]), array([3, 4, 6]), None], dtype=object) Entry 0 corresponds to residue 0 and says that this contains atoms 0, 2 & 5 Notes ----- The final entry in the return array will be ``None`` to ensure that the dtype of the array is :class:`object`. .. warning:: This means negative indexing should **never** be used with these arrays. dtype mergesort)kindT) return_indexrrN)lennparrayobjectargsortuniquemaxzerosintsort setdiff1darangeappendshapesplit) upshiftnparentsorderupshift_sortedu_valuesindicesresidue_indicesmissing_resids missing_resid downshifts b/srv/www/vhosts/g4struct/public_html/venv/lib/python3.11/site-packages/MDAnalysis/core/topology.pymake_downshift_arraysr*DslR w<<*x&)))) Jw[ 1 1 1EU^N .tDDDHgvx!!3455Hhxs333OWR\")H*=*=xHHIINi!5a!899G ' OH'PP A  -.OM * *-<]Q=N-OOM * * 455IT 8IV , , ,,ceZdZdZ ddZdZedZedZedZ dZ d Z d Z d Z d Zd ZdZdZdZdZdZdZdZdZdS) TransTablea;Membership tables with methods to translate indices across levels. There are three levels; Atom, Residue and Segment. Each Atom **must** belong in a Residue, each Residue **must** belong to a Segment. When translating upwards, eg finding which Segment a Residue belongs in, a single numpy array is returned. When translating downwards, two options are available; a concatenated result (suffix `_1`) or a list for each parent object (suffix `_2d`). Parameters ---------- n_atoms : int number of atoms in topology n_residues : int number of residues in topology n_segments : int number of segments in topology atom_resindex : 1-D array resindex for each atom in the topology; the number of unique values in this array must be <= `n_residues`, and the array must be length `n_atoms`; giving None defaults to placing all atoms in residue 0 residue_segindex : 1-D array segindex for each residue in the topology; the number of unique values in this array must be <= `n_segments`, and the array must be length `n_residues`; giving None defaults to placing all residues in segment 0 Attributes ---------- n_atoms : int number of atoms in topology n_residues : int number of residues in topology n_segments : int number of segments in topology size : tuple tuple ``(n_atoms, n_residues, n_segments)`` describing the shape of the TransTable .. versionchanged:: 2.3.0 Lazy building RA and SR. Ncd||_||_||_|&tj|tj|_n^tj|tj|_t|j|kstdd|_ |&tj|tj|_ n^tj|tj|_ t|j |kstdd|_ dS)Nr z!atom_resindex must be len n_atomsz'residue_segindex must be len n_residues)n_atoms n_residues n_segmentsrrintp_ARasarraycopyr ValueError_RA_RS_SR)selfr/r0r1 atom_resindexresidue_segindexs r)__init__zTransTable.__init__s $$  xrw777DHHz-rw???DDFFDHtx==G++ !DEEE  #x "':::DHHz"2"'BBBGGIIDHtx==J.. !JKKKr+ch||j|j|j|j|jS)z$Return a deepcopy of this Transtabler;r<) __class__r/r0r1r3r8r:s r)r5zTransTable.copys6~~ L O O(!X    r+c\|jt|j|j|_|jSN)r7r*r3r0rAs r)RAz TransTable.RA& 8 ,TXtGGDHxr+c\|jt|j|j|_|jSrC)r9r*r8r1rAs r)SRz TransTable.SRrEr+c*|j|j|jfS)z_The shape of the table, ``(n_atoms, n_residues, n_segments)``. :meta private: )r/r0r1rAs r)sizezTransTable.sizes  dot??r+c|j|S)zGet residue indices for each atom. Parameters ---------- aix : array atom indices Returns ------- rix : array residue index for each atom )r3)r:aixs r)atoms2residueszTransTable.atoms2residuesx}r+c|j} tj||S#t$r*||tjdcYSwxYw)aGet atom indices collectively represented by given residue indices. Parameters ---------- rix : array residue indices Returns ------- aix : array indices of atoms present in residues, collectively Tr5)rDr concatenater6astyper2r:rixrDs r)residues2atoms_1dzTransTable.residues2atoms_1daW 6>"S'** * 6 6 6c7>>"'>55 5 5 5 6#1AAc|j fd|DS#t$r|gcYSwxYw)aGet atom indices represented by each residue index. Parameters ---------- rix : array residue indices Returns ------- raix : list each element corresponds to a residue index, in order given in `rix`, with each element being an array of the atom indices present in that residue cDg|]}|SrO).0rrDs r) z0TransTable.residues2atoms_2d..,%...QBqEJJLL...r+)rD TypeErrorr5rRs @r)residues2atoms_2dzTransTable.residues2atoms_2da W $....#... . $ $ $sGLLNN# # # # $ %AAc|j|S)zGet segment indices for each residue. Parameters ---------- rix : array residue indices Returns ------- six : array segment index for each residue )r8)r:rSs r)residues2segmentszTransTable.residues2segments0rMr+c|j} tj||S#t$r*||tjdcYSwxYw)a$Get residue indices collectively represented by given segment indices Parameters ---------- six : array segment indices Returns ------- rix : array sorted indices of residues present in segments, collectively TrO)rGrrPr6rQr2r:sixrGs r)segments2residues_1dzTransTable.segments2residues_1d@rUrVc|j fd|DS#t$r|gcYSwxYw)aGet residue indices represented by each segment index. Parameters ---------- six : array residue indices Returns ------- srix : list each element corresponds to a segment index, in order given in `six`, with each element being an array of the residue indices present in that segment cDg|]}|SrYrO)rZsrGs r)r\z3TransTable.segments2residues_2d..gr]r+)rGr^r5res @r)segments2residues_2dzTransTable.segments2residues_2dUr`racV||}||S)zGet segment indices for each atom. Parameters ---------- aix : array atom indices Returns ------- rix : array segment index for each atom )rLrcr:rKrSs r)atoms2segmentszTransTable.atoms2segmentsls+!!#&&%%c***r+cV||}||S)aGet atom indices collectively represented by given segment indices. Parameters ---------- six : array segment indices Returns ------- aix : array sorted indices of atoms present in segments, collectively )rgrT)r:rfrSs r)segments2atoms_1dzTransTable.segments2atoms_1d}s+'',,%%c***r+cJ|}fd|DS)aGet atom indices represented by each segment index. Parameters ---------- six : array residue indices Returns ------- saix : list each element corresponds to a segment index, in order given in `six`, with each element being an array of the atom indices present in that segment c:g|]}|SrY)rT)rZrSr:s r)r\z0TransTable.segments2atoms_2d..s'<<<&&s++<<48RXvh-?-?"@AA""r+cD|xjdz c_d|_|jdz Sr{)r1r9rAs r) add_SegmentzTransTable.add_Segments& 1""r+c(|j}d|d<d|d<|S)Nr7r9)__dict__)r:attrss r) __getstate__zTransTable.__getstate__s  e e  r+)NN)__name__ __module__ __qualname____doc__r=r5propertyrDrGrIrLrTr_rcrgrkrnrprtrvryr}rrrYr+r)r-r-sp**b <   X X @@X@ 666*$$$, 666*$$$.+++"+++"===*  ###### r+r-ceZdZdZ ddZdZedZedZedZ d Z d Z ed Z ed Z d ZdZdS)TopologyatIn-memory, array-based topology database. The topology model of MDanalysis features atoms, which must each be a member of one residue. Each residue, in turn, must be a member of one segment. The details of maintaining this heirarchy, and mappings of atoms to residues, residues to segments, and vice-versa, are handled internally by this object. rNct||||||_|g}|tt t fg|_|D]}||dS)a Parameters ---------- n_atoms : int number of atoms in topology. Must be larger then 1 at each level n_residues : int number of residues in topology. Must be larger then 1 at each level n_segments : int number of segments in topology. Must be larger then 1 at each level attrs : TopologyAttr objects components of the topology to be included atom_resindex : array 1-D array giving the resindex of each atom in the system residue_segindex : array 1-D array giving the segindex of each residue in the system r?N)r-ttextendrrrradd_TopologyAttr)r:r/n_resn_segrr;r< topologyattrs r)r=zTopology.__init__s4   '-     =E kmmZ\\:<<@AAA ! 0 0L  ! !, / / / / 0 0r+c|ddd}|j|_|jD]L}t |t t tfr%||M|S)z"Return a deepcopy of this Topologyr) r@rr5r isinstancerrrr)r:newattrs r)r5z Topology.copysynnQ1%%J . .D$j* EFF    - - - - r+c|jjSrC)rr/rAs r)r/zTopology.n_atomss wr+c|jjSrC)rr0rAs r)r0zTopology.n_residues  w!!r+c|jjSrC)rr1rAs r)r1zTopology.n_segmentsrr+c~|j|||_||j|dS)z|Add a new TopologyAttr to the Topology. Parameters ---------- topologyattr : TopologyAttr N)rrtop __setattr__attrnamer:rs r)rzTopology.add_TopologyAttrsA ,'''  . =====r+cn||j|j|dS)zRemove a TopologyAttr from the Topology. If it is not present, nothing happens. Parameters ---------- topologyattr : TopologyAttr .. versionadded:: 2.0.0 N) __delattr__rrremovers r)del_TopologyAttrzTopology.del_TopologyAttrs7 ./// ,'''''r+c.td|jS)z1A list of the guessed attributes in this topologyc`t|jtjs|jnd|jvS)NTr is_guessedtyping Containerxs r)z-Topology.guessed_attributes..1s."1<1ABB* Q\)r+filterrrAs r)guessed_attributeszTopology.guessed_attributes-'   J    r+c.td|jS)z/A list of the attributes read from the topologycbt|jtjs|j nd|jvS)NFrrs r)rz*Topology.read_attributes..=s2"1<1ABB+AL  al*r+rrAs r)read_attributeszTopology.read_attributes9rr+c |jD]_}|jdks|jvrHfd|jD}tdd|`|j|j}|jD]0}|jdks|j}| |1|S)a+ Returns ------- residx of the new Residue Raises ------ NoDataError If not all data was provided. This error is raised before any changes .. versionchanged:: 2.1.0 Added use of _add_new to TopologyAttr resize residuec3NK|]}|jdkr|jv|jV dS)rN per_objectsingularrZr new_attrss r) z'Topology.add_Residue..YsM944 M:: M;::: r+z8Missing the following attributes for the new Residue: {}, ) rrrrformatjoinrr}segindex_add_new)r:segmentrrmissingresidxnewvals ` r)r}zTopology.add_ResidueEs J  D?i//}I-- $ "##)6$))G*<*<#=#=.$$W%566J " "D?i//t}-F MM& ! ! ! ! r+c v|jD]^}|jdkrQ|jvrHfd|jD}tdd|_|j}|jD]0}|jdks|j}||1|S)aAdds a new Segment to the Topology Parameters ---------- new_attrs : dict the new attributes for the new segment, eg {'segid': 'B'} Raises ------- NoDataError if an attribute wasn't specified. Returns ------- ix : int the idx of the new segment .. versionchanged:: 2.1.0 Added use of _add_new to resize topology attrs rc3NK|]}|jdkr|jv|jV dS)rNrrs r)rz'Topology.add_Segment..sM  Oy88 $ Y > >  !? > > > r+z8Missing the following attributes for the new Segment: {}r) rrrrrrrrr)r:rrrr|rs ` r)rzTopology.add_Segmentrs,J  D)++= 11$(JG&!6$))G"4"455 $$&&J " "D?i//t}-F MM& ! ! ! ! r+)rrrNNN)rrrrr=r5rr/r0r1rrrrr}rrYr+r)rrs*0*0*0*0X   X""X"""X" > > > ( ( (   X     X  +++Z/////r+r)r contextlibnumpyrr topologyattrsrrr exceptionsrr*rr-rrYr+r)rs0""F >>>>>>>>>>$$$$$$E-E-E-Pttttttttn ^^^^^v^^^^^r+