iFdZddlZddlZddlZddlmZddlmZddl m Z dZ e dd e d Z e dd e d Z e dd e d Ze dd e dZejdZejdZe dd e dZe dd e ddZe dd e dZe dd e dZe dd e dZe dd e dZe dd e dZe dd e dZe dd e dZe dd e dZdS)aY Guessing unknown Topology information --- :mod:`MDAnalysis.topology.guessers` ============================================================================= .. deprecated:: 2.8.0 The :mod:`MDAnalysis.topology.guessers` module will be removed in release 3.0.0. It is deprecated in favor of the new Guessers API. See :mod:`MDAnalysis.guesser.default_guesser` for more details. In general `guess_atom_X` returns the guessed value for a single value, while `guess_Xs` will work on an array of many atoms. Example uses of guessers ------------------------ Guessing elements from atom names ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ Currently, it is possible to guess elements from atom names using :func:`guess_atom_element` (or the synonymous :func:`guess_atom_type`). This can be done in the following manner:: import MDAnalysis as mda from MDAnalysis.topology.guessers import guess_atom_element from MDAnalysisTests.datafiles import PRM7 u = mda.Universe(PRM7) print(u.atoms.names[1]) # returns the atom name H1 element = guess_atom_element(u.atoms.names[1]) print(element) # returns element H In the above example, we take an atom named H1 and use :func:`guess_atom_element` to guess the element hydrogen (i.e. H). It is important to note that element guessing is not always accurate. Indeed in cases where the atom type is not recognised, we may end up with the wrong element. For example:: import MDAnalysis as mda from MDAnalysis.topology.guessers import guess_atom_element from MDAnalysisTests.datafiles import PRM19SBOPC u = mda.Universe(PRM19SBOPC) print(u.atoms.names[-1]) # returns the atom name EPW element = guess_atom_element(u.atoms.names[-1]) print(element) # returns element P Here we find that virtual site atom 'EPW' was given the element P, which would not be an expected result. We therefore always recommend that users carefully check the outcomes of any guessers. In some cases, one may want to guess elements for an entire universe and add this guess as a topology attribute. This can be done using :func:`guess_types` in the following manner:: import MDAnalysis as mda from MDAnalysis.topology.guessers import guess_types from MDAnalysisTests.datafiles import PRM7 u = mda.Universe(PRM7) guessed_elements = guess_types(u.atoms.names) u.add_TopologyAttr('elements', guessed_elements) print(u.atoms.elements) # returns an array of guessed elements More information on adding topology attributes can found in the `user guide`_. .. Links .. _user guide: https://www.mdanalysis.org/UserGuide/examples/constructing_universe.html#Adding-topology-attributes N) distances)tables) deprecatezMDAnalysis.topology.guessers is deprecated in favour of the new Guessers API. See MDAnalysis.guesser.default_guesser for more details.z2.8.0z3.0.0)releaseremovemessagecxt|tjd|Dtj}|S)zGuess the mass of many atoms based upon their type Parameters ---------- atom_types Type of each atom Returns ------- atom_masses : np.ndarray dtype float64 c,g|]}t|S) get_atom_mass).0atom_ts f/srv/www/vhosts/g4struct/public_html/venv/lib/python3.11/site-packages/MDAnalysis/topology/guessers.py z guess_masses..s 8886v  888dtype)validate_atom_typesnparrayfloat64) atom_typesmassess r guess_massesrxsD ### X88Z888 F Mrc4tj|D]} tj|#t$r` tj|n7#t$r*t jd|YnwxYwYwxYwdS)aVaildates the atom types based on whether they are available in our tables Parameters ---------- atom_types Type of each atom Returns ------- None .. versionchanged:: 0.20.0 Try uppercase atom type name as well z9Failed to guess the mass for the following atom types: {}N) runiquerrKeyErrorupperwarningswarnformat)r atom_types rrrs Yz**     M) $ $ $     ioo//000    OVV!    s2+ B$AB1B BBBBcLtjd|DtS)zGuess the atom type of many atoms based on atom name Parameters ---------- atom_names Name of each atom Returns ------- atom_types : np.ndarray dtype object c,g|]}t|Sr guess_atom_element)rnames rrzguess_types..s!999d D ! !999rr)rrobject) atom_namess r guess_typesr+s0 899j999   rc t|S)zGuess atom type from the name. At the moment, this function simply returns the element, as guessed by :func:`guess_atom_element`. See Also -------- :func:`guess_atom_element` :mod:`MDAnalysis.topology.tables` r&atomnames rguess_atom_typer/s h ' ''rz[0-9]z[*+-]c|dkrdS tj|S#t$rt jt d|}t jt|}ttd|}|r|dnd}|tjvrtj|cYS|r|tj vr|cYS|ddtj vr |ddcYS|ddtj vr |ddcYSt|dkr |dcYS|dd}||cYSwxYw)a5Guess the element of the atom from the name. Looks in dict to see if element is found, otherwise it uses the first character in the atomname. The table comes from CHARMM and AMBER atom types, where the first character is not sufficient to determine the atom type. Some GROMOS ions have also been added. .. Warning: The translation table is incomplete. This will probably result in some mistakes, but it still better than nothing! See Also -------- :func:`guess_atom_type` :mod:`MDAnalysis.topology.tables` Nrr) r atomelementsrrresubSYMBOLSsplitNUMBERSlistfilterelementslen)r. no_symbols no_numbersr(s rr'r'sx"2~~r"8>>#3#344 VGR22 Xgz22 &z2233 (2:z!}""$$$ 6& & &&t, , , , v&& CRCyFO++CRCy   ABBx6?**ABBx4yyA~~Aw9D 5s.#.BE E E E#EEEc t|t|krtd|dd}tj|dd}|r||j}tfdt|DsDtdd fd t|Dzd zd z|d d }|tj |}tfd|D}g} tj|d|z||\} } t!| D]a\} \} }|| ||z|z}| | |kr-| || j||jfbt'| S)ac Guess if bonds exist between two atoms based on their distance. Bond between two atoms is created, if the two atoms are within .. math:: d < f \cdot (R_1 + R_2) of each other, where :math:`R_1` and :math:`R_2` are the VdW radii of the atoms and :math:`f` is an ad-hoc *fudge_factor*. This is the `same algorithm that VMD uses`_. Parameters ---------- atoms : AtomGroup atoms for which bonds should be guessed coords : array coordinates of the atoms (i.e., `AtomGroup.positions)`) fudge_factor : float, optional The factor by which atoms must overlap eachother to be considered a bond. Larger values will increase the number of bonds found. [0.55] vdwradii : dict, optional To supply custom vdwradii for atoms in the algorithm. Must be a dict of format {type:radii}. The default table of van der Waals radii is hard-coded as :data:`MDAnalysis.topology.tables.vdwradii`. Any user defined vdwradii passed as an argument will supercede the table values. [``None``] lower_bound : float, optional The minimum bond length. All bonds found shorter than this length will be ignored. This is useful for parsing PDB with altloc records where atoms with altloc A and B maybe very close together and there should be no chemical bond between them. [0.1] box : array_like, optional Bonds are found using a distance search, if unit cell information is given, periodic boundary conditions will be considered in the distance search. [``None``] Returns ------- list List of tuples suitable for use in Universe topology building. Warnings -------- No check is done after the bonds are guessed to see if Lewis structure is correct. This is wrong and will burn somebody. Raises ------ :exc:`ValueError` if inputs are malformed or `vdwradii` data is missing. .. _`same algorithm that VMD uses`: http://www.ks.uiuc.edu/Research/vmd/vmd-1.9.1/ug/node26.html .. versionadded:: 0.7.7 .. versionchanged:: 0.9.0 Updated method internally to use more :mod:`numpy`, should work faster. Should also use less memory, previously scaled as :math:`O(n^2)`. *vdwradii* argument now augments table list rather than replacing entirely. z+'atoms' and 'coord' must be the same length fudge_factorg?vdwradiiNc3 K|]}|vV dSNr )rvalrBs r zguess_bonds..Ss'993sh999999rzvdw radii for types: z, cg|]}|v| Sr r rtrBs rrzguess_bonds..WsLLL1a8mmQmmmrz). These can be defined manually using thez keyword 'vdwradii' lower_boundg?c g|] }| Sr r rHs rrzguess_bonds..es22218A;222rg@) max_cutoff min_cutoffbox)r= ValueErrorgetrrBcopyupdatetypesallsetjoinrasarraymaxrself_capped_distance enumerateappendindextuple)atomscoordsrNkwargsrA user_vdwradii atomtypesrJmax_vdwbondspairsdistidxijdrBs @r guess_bondsrksB 5zzS[[  FGGG::nd33L##%%HJJz400M' &&& I 9999#i..999 9 9 '))LLLLILLLMMN=>((   **]C00K joo 2222 22233G E03=[cKE4!'';; Va il #hy|&< < L 9q== LL%(.%(.9 : : : <<rcjt}|D]}|D]}||}|jD]p}||krh||}t|j|j|jg}|d|dkr |ddd}||qt|S)aGiven a list of Bonds, find all angles that exist between atoms. Works by assuming that if atoms 1 & 2 are bonded, and 2 & 3 are bonded, then (1,2,3) must be an angle. Returns ------- list of tuples List of tuples defining the angles. Suitable for use in u._topology See Also -------- :meth:`guess_bonds` .. versionadded 0.9.0 rr2N)rUpartnerrdr]r\add)rd angles_foundbatomother_aother_bthird_adescs r guess_anglesrvss*55L  + + + +DiiooG: + +a<<%ood33G '-W]!KLLDAwb))#DDbDz $$T***  + +   rct}|D]}td|D}t|jd|jdg|ddd|gD]x\}}|jD]k}|||vrR||}||jfz}|d|dkr |ddd}||lyt|S)aXGiven a list of Angles, find all dihedrals that exist between atoms. Works by assuming that if (1,2,3) is an angle, and 3 & 4 are bonded, then (1,2,3,4) must be a dihedral. Returns ------- list of tuples List of tuples defining the dihedrals. Suitable for use in u._topology .. versionadded 0.9.0 cg|] }|j Sr r\)ras rrz#guess_dihedrals..s***1qw***rrr2N)rUr]zipr^rdrmr\rn) anglesdihedrals_foundrpa_tuprqprefixrsrtrus rguess_dihedralsrseeO  . .*****++ WQZ %ddd U';  . .LD& : . .t,,11%ood33G!W]$44DAwb))#DDbDz#''---  . .  ! !!rcNt}|D]d}tfddD}|jD]X}||}|vr=||jfz}|d|dkr |ddd}||Yt|S)aGiven a list of Angles, find all improper dihedrals that exist between atoms. Works by assuming that if (1,2,3) is an angle, and 2 & 4 are bonded, then (2, 1, 3, 4) must be an improper dihedral. ie the improper dihedral is the angle between the planes formed by (1, 2, 3) and (1, 3, 4) Returns ------- List of tuples defining the improper dihedrals. Suitable for use in u._topology .. versionadded 0.9.0 r3c*g|]}|jSr ry)rrzrps rrz,guess_improper_dihedrals..s555aqtz555r)r3rrrr2N)rUr]rdrmr\rn)r|r}rqr~rs other_atomrurps @rguess_improper_dihedralsrs"eeO  * *t5555955566z * *G ..J?? 0227T"X%%":D##D))) *  ! !!rc tj|S#t$r: tj|cYS#t$rYYdSwxYwwxYw)zReturn the atomic mass in u for *element*. Masses are looked up in :data:`MDAnalysis.topology.tables.masses`. .. Warning:: Unknown masses are set to 0.0 .. versionchanged:: 0.20.0 Try uppercase atom type name as well )rrrr)elements rr r ss}W%%  =1 1 1 1   333 s, A#AA AAAAc:tt|S)zGuess a mass based on the atom name. :func:`guess_atom_element` is used to determine the kind of atom. .. warning:: Anything not recognized is simply set to 0; if you rely on the masses you might want to double check. )r r'r-s rguess_atom_massrs +H55 6 66rcdS)zZGuess atom charge from the name. .. Warning:: Not implemented; simply returns 0. rr r-s rguess_atom_chargers  3rc|d}tjd|DS)aFGuess aromaticity of atoms using RDKit Parameters ---------- atomgroup : mda.core.groups.AtomGroup Atoms for which the aromaticity will be guessed Returns ------- aromaticities : numpy.ndarray Array of boolean values for the aromaticity of each atom .. versionadded:: 2.0.0 RDKITc6g|]}|Sr ) GetIsAromaticrrqs rrz'guess_aromaticities..s$EEEdT''))EEEr) convert_torrGetAtoms) atomgroupmols rguess_aromaticitiesr s>"   w ' 'C 8EEcllnnEEE F FFrc|d}ddlm}||dtjd|DtjS)aCGuess Gasteiger partial charges using RDKit Parameters ---------- atomgroup : mda.core.groups.AtomGroup Atoms for which the charges will be guessed Returns ------- charges : numpy.ndarray Array of float values representing the charge of each atom .. versionadded:: 2.0.0 rr)ComputeGasteigerChargesT)throwOnParamFailurec8g|]}|dS)_GasteigerCharge) GetDoubleProprs rrz+guess_gasteiger_charges..5s'KKKD  . / /KKKrr)rrdkit.Chem.rdPartialChargesrrrrfloat32)rrrs rguess_gasteiger_chargesrsv"   w ' 'CCCCCCCCT:::: 8KKCLLNNKKKj   rrD)__doc__numpyrr r5librMDAnalysis.guesserrMDAnalysis.lib.utilrdeprecation_msgrrr+r/compiler9r7r'rkrvrrr rrrrr rrrs5.PPb %%%%%%))))))? 77ODDDED& 77ODDDED: 77ODDDED" 77ODDD((ED(" "*X   "*X   77ODDD..ED.b 77ODDDkkkEDk\ 77ODDD!!ED!H 77ODDD""ED"D 77ODDD!"!"ED!"H 77ODDDED& 77ODDD77ED7 77ODDDED 77ODDDGGEDG( 77ODDDEDr