i[d2dZddlmZddlZddlZddlZddlZddlm Z ddl m Z ddl m Z dd lmZmZmZdd lmZmZmZmZmZmZmZmZmZmZmZmZmZm Z m!Z!m"Z"m#Z#dd l$m%Z%Gd d e"Z&GddZ'GddZ(GddeZ)dS)a4 ITP topology parser =================== Reads a GROMACS ITP_ or TOP_ file to build the system. The topology will contain atom IDs, segids, residue IDs, residue names, atom names, atom types, charges, chargegroups, masses, moltypes, and molnums. Any masses that are in the file will be read; any missing values will be guessed. Bonds, angles, dihedrals and impropers are also read from the file. If an ITP file is passed without a ``[ molecules ]`` directive, passing ``infer_system=True`` (the default option) will create a Universe with 1 molecule of each defined ``moleculetype``. If a ``[ molecules ]`` section is present, ``infer_system`` is ignored. If files are included with the `#include` directive, they will also be read. If they are not in the working directory, ITPParser will look for them in the ``include_dir`` directory. By default, this is set to ``include_dir="/usr/local/gromacs/share/gromacs/top/"``. Variables can be defined with the `#define` directive in files, or by passing in :ref:`keyword arguments `. Examples -------- .. code-block:: python import MDAnalysis as mda from MDAnalysis.tests.datafiles import ITP_tip5p # override charge of HW2 atom (defined in file as HW2_CHARGE) u = mda.Universe(ITP_tip5p, HW2_CHARGE=2, infer_system=True) .. note:: AMBER also uses topology files with the .top extension. To use ITPParser to read GROMACS top files, pass ``topology_format='ITP'``. :: import MDAnalysis as mda u = mda.Universe('topol.top', topology_format='ITP') .. _itp-define-kwargs: Preprocessor variables ---------------------- ITP files are often defined with lines that depend on whether a keyword flag is given. For example, this modified TIP5P water file: .. code-block:: none [ moleculetype ] ; molname nrexcl SOL 2 #ifndef HW1_CHARGE #define HW1_CHARGE 0.241 #endif #define HW2_CHARGE 0.241 [ atoms ] ; id at type res nr residu name at name cg nr charge 1 opls_118 1 SOL OW 1 0 2 opls_119 1 SOL HW1 1 HW1_CHARGE 3 opls_119 1 SOL HW2 1 HW2_CHARGE 4 opls_120 1 SOL LP1 1 -0.241 5 opls_120 1 SOL LP2 1 -0.241 #ifdef EXTRA_ATOMS ; added for keyword tests 6 opls_120 1 SOL LP3 1 -0.241 7 opls_120 1 SOL LP4 1 0.241 #endif Define these preprocessor variables by passing keyword arguments. Any arguments that you pass in *override* any variables defined in the file. For example, the universe below will have charges of 3 for the HW1 and HW2 atoms:: import MDAnalysis as mda from MDAnalysis.tests.datafiles import ITP_tip5p u = mda.Universe(ITP_tip5p, EXTRA_ATOMS=True, HW1_CHARGE=3, HW2_CHARGE=3) These keyword variables are **case-sensitive**. Note that if you set keywords to ``False`` or ``None``, they will be treated as if they are not defined in #ifdef conditions. For example, the universe below will only have 5 atoms. :: u = mda.Universe(ITP_tip5p, EXTRA_ATOMS=False) .. _ITP: http://manual.gromacs.org/current/reference-manual/topologies/topology-file-formats.html#molecule-itp-file .. _TOP: http://manual.gromacs.org/current/reference-manual/file-formats.html#top Classes ------- .. autoclass:: ITPParser :members: :inherited-members: ) defaultdictN)openany)SYMB2Z)DefaultGuesser)TopologyReaderBase change_squashreduce_singular)Atomids Atomnames AtomtypesMassesMoltypesMolnumsChargesResidsResnumsResnamesSegidsBondsAngles Dihedrals ImpropersAtomAttrElements)TopologyceZdZdZdZdZdS) ChargegroupszThe charge group for each Atom chargegroups chargegroupN)__name__ __module__ __qualname____doc__attrnamesingularg/srv/www/vhosts/g4struct/public_html/venv/lib/python3.11/site-packages/MDAnalysis/topology/ITPParser.pyrrs((HHHHr)rcdeZdZdZdZedZdZdZdZ dZ dZ d Z d Z d Zd Zd S)GmxTopIteratora Iterate over the lines of a TOP/ITP file and its included files The iterator strips comments, deals with #ifdef and #ifndef conditions, and substitutes defined variables. Defined variables passed into ``__init__`` *override* anything defined in the file. cb||_tdi||_||_|g|_||_dS)Nr()_original_definesdictdefines include_dir file_stack starting_file)selfpathr1r0s r*__init__zGmxTopIterator.__init__s:!(g &&!r)c|jdS)N)r2r4s r* current_filezGmxTopIterator.current_filesr""r)c#LK||jD]}|VdSN)iter_from_filer3r4lines r*__iter__zGmxTopIterator.__iter__s;''(:;;  DJJJJ  r)c#0K||}t|5}|j|||D] }|drA|ddddd}||D]}|VY|dr|||dr| |||dr| ||dr|r| |}|V|j ddddS#1swxYwYdS)Nz#includerr8z#define#if#else#) find_pathrr2appendclean_file_lines startswithsplitr=definedo_ifskip_until_endifsubstitute_definedpop)r4r5 found_pathinfiler?incs r*r=zGmxTopIterator.iter_from_files^^D)) Z  "F O " "6 * * *--f55  ??:..**T1--a026C $ 3 3C 8 8##" #__Y// KK%%%%__U++JJtV,,,,__W--))&1111__S))22488DJJJ O   ! ! !' " " " " " " " " " " " " " " " " " "sEF  FFc |dd\}}}n)#t$r|\}}d}YnwxYw||jvr ||j|<dSdS)NrT)rI ValueErrorr.r0)r4r?_variablevalues r*rJzGmxTopIterator.defines !%D!!4!4 Ax   **,,KAxEEE  41 1 1%*DL " " " 2 1s#AAc|}|jD].\}}||vr%t||||</d|}|S)N )rIr0itemsstrindexjoin)r4r?rIkvs r*rMz!GmxTopIterator.substitute_definedsh L&&(( / /DAqEzz(+Aekk!nn%xx r)c#vK|D]3}|dd}|V4dS)N;r)rIstripr4rPr?s r*rGzGmxTopIterator.clean_file_linessJ  D::c??1%++--DJJJJ  r)c |\}}|dkr5|j|dvr||dSdS|dkr3|j|dvr||dSdSdS)Nz#ifdef)FNz#ifndef)rIr0getskip_until_else)r4r?rPifdefrUs r*rKzGmxTopIterator.do_ifs**,,x H  |))]::$$V,,,,,;: i  |))>>$$V,,,,, >>r)c0||D]Z}|dr||-|ds|drdS[td|j)z#Skip lines until #if condition endsrB#endifrCMissing #endif in {}NrGrHrLIOErrorformatr:rbs r*rezGmxTopIterator.skip_until_elses))&11 L LDu%% %%f----** doog.F.F  0778IJJKK Kr)c||D]E}|dr||-|drdSFtd|j)zSkip lines until #endifrBrhriNrjrbs r*rLzGmxTopIterator.skip_until_endifs))&11 L LDu%% %%f----**  0778IJJKK Kr)cH |jj}n#t$r |j}YnwxYw tj|j}n#t$rYnwxYwtj|}tj||}tj|r|Stj|j |}tj|r|Std |)NzCould not find {}) r:nameAttributeErrorosr5abspathdirnamer\existsr1rkrl)r4r5r: current_dirdir_path include_paths r*rEzGmxTopIterator.find_paths  -,1LL - - -,LLL - 7??49--DD    D gool33 7<< T22 7>>( # # Ow||D$4d;; 7>>, ' '  )0066777s ##$A AAN)r"r#r$r%r6propertyr:r@r=rJrMrGrKrerLrEr(r)r*r,r,s"""##X#""". + + + ---LLLLLL88888r)r,ceZdZdZdZedZedZdZdZ dZ dZ d Z d Z d Z dd ZddZdZdS)Moleculez&Store moleculetype-specific attributesc||_g|_g|_g|_g|_g|_g|_g|_g|_tt|_ tt|_ tt|_ tt|_|j|j|j|j|j|jd|_d|_dS)N)atomsbondsangles dihedrals constraintssettlesF)roidstypesresidsresnamesnamesr chargesmassesrlistr}r~r impropers parse_atoms parse_bonds parse_anglesparse_dihedralsparse_constraints parse_settlesparsersresolved_residue_attrs)r4ros r*r6zMolecule.__init__'s        && !$'' $T**$T**%%'-1)    ',###r)cf|j|j|j|j|j|j|j|jgSr<)rrrrrr rrr9s r* atom_orderzMolecule.atom_orderBs7 H J K M J   L K  r)c6|j|j|j|jgSr<)r}r~rrr9s r*paramszMolecule.paramsOs DKHHr)c|}|jD]P} ||d,#t$r|dYMwxYwdS)Nr)rIrrFrN IndexError)r4r?valueslsts r*rzMolecule.parse_atomsSs|?  C  6::a==))))    2   s(AA*)A*cB|||jdddS)Nr) rr n_funct funct_values add_paramr}r>s r*rzMolecule.parse_bonds[s5   J8      r)cB|||jdddS)Nr)rrrrrrrrr)rr~r>s r*rzMolecule.parse_anglescs5   K2      r)c|||jdd}|s |||jdddSdS)Nr)rrrrrr r)rr)rrr)r4r?dihs r*rzMolecule.parse_dihedralskslnn  N0      NNdnaf        r)cB|||jdddS)Nr)rrrrr>s r*rzMolecule.parse_constraintsws$ tTZHHHHHr)c(|\}}}} ||gd}|j||dzfd|j||dzfddS#t$rYdSwxYw)Nrrrr)rI index_idsr}rFrS)r4r?oxygenfunctdohdhhbases r*rzMolecule.parse_settleszs#'**,,sC ;>>6(++A.D JdQh' ( / / : : : JdQh' ( / / : : : : :     DD sB BBctj|jtj}tj|jt }t |f||f\|_\|_}t||_|j gt|jz|_ tjdgt|jz|_ d|_ dS)z:Figure out residue borders and assign moltypes and molnumsdtyperTN)nparrayrint32robjectr residxrrolenmoltypesmolnumsr)r4rrs r*resolve_residue_attrszMolecule.resolve_residue_attrss$+RX6668DM888/< I)0 0 , ,dk8X  c$+&6&66 xc$+&6&6 677 &*###r)rc |js|ttj|j|z}ttj|j|z}ttj|j|z} ttj|jt|z} tj|j t} n:#t$r-tj dt|j dz} YnwxYwt| |z} | |j||j|j| |j|jg} g}|jD]Z}i}|D],\}}||t+tj||z<-||[| || |j|fS)a Get attributes ready for adding onto a larger topology. Shifts atom indices, residue indices, molnums, and chargegroup numbers. Returns ------- atom_attrs: list of lists attributes in the [ atoms ] section new_params: list of dicts Bonds, angles, dihedrals, impropers as dicts of shape {indices: parameters} molnums: list moltypes: list residx: list rr)rrrrrrrrrintr rSarangerrrrrrrrYtuplerFr)r4atomidresidmolnumcgnrn_resn_atomsrrrrcgr r new_paramspnewindicesrs r* shift_indiceszMolecule.shift_indicess(* )  & & ( ( (bht{++e344bht{++e344rx --67728DHC00069:: :$+3777BB : : :1c$"344q899BBB :BI   J  M J  L K    # #AC#$7799 A A:@E"(7++g56677   c " " " ":w vEEs C))4D D rNc|g}|}t||}||vrL ||d|}|||n#t$rYnwxYwdSdS)zMAdd defined GROMACS directive lines, only if the funct is in ``funct_values``NTF)rIrrrFrS)r4r? containerrrrrrs r*rzMolecule.add_params  LF7O$$ L  nnVHWH%566#%%e,,,,    45s8A,, A98A9cPtt|jj|S)z; Get indices of atom ids (list of strings) )rmaprr[)r4rs r*rzMolecule.index_idss S00111r))rrrrrr)rN)r"r#r$r%r6rxrrrrrrrrrrrrr(r)r*rzrz$s00,,,6   X  IIXI         III;;;& + + +EF4F4F4F4Fl 22222r)rzc@eZdZdZdZ d dZdZdZdZd Z d Z d S) ITPParsera`Read topology information from a GROMACS ITP_ or TOP_ file. Creates a Topology with the following Attributes: - ids - names - types - masses - charges - chargegroups - resids - resnames - segids - moltypes - molnums - bonds - angles - dihedrals - impropers .. _ITP: http://manual.gromacs.org/current/reference-manual/topologies/topology-file-formats.html#molecule-itp-file .. _TOP: http://manual.gromacs.org/current/reference-manual/file-formats.html#top .. note:: By default, atomtypes and masses will be guessed on Universe creation if they are not read from the input file. This may change in release 3.0. See :ref:`Guessers` for more information. .. versionchanged:: 2.2.0 no longer adds angles for water molecules with SETTLE constraint .. versionchanged:: 2.8.0 Removed mass guessing (attributes guessing takes place now through universe.guess_TopologyAttrs() API). Added guessed elements if all elements are valid to preserve partial mass guessing behavior ITP%/usr/local/gromacs/share/gromacs/top/Tc i_i_g_d_j_g_tj5}t|||_ j D]}d|vrd|vr| dd dd }|dkr j _c|dkr j_v|dkr j_jr+jj|j_j_ȉ| dddn #1swxYwYjs|rd jD_t'jj_t'jjt. _t'jjt. _t3js,jd k}fd j|Dj|<t3js,jd k}fd j|Dj|<g}jt6t&jfjt:t.fjt>t.fj tBt&jfjtDt&j#ffD]G\} } } t3| r2|$| t'j| | Ht3jsjd k}tJj&j|<|$tKt'jjt&j' dtQd)j_*t3dj*Dr]|$tWt'jj*t. dtYj-dt\ntYj-dt'jj/t&j } t'jj0t. } t'jj1t&j }|$te| |$tg| 4|$tk| |$tmt'jj7t. |$tq|tsj}tsj/}tsj}|$tut'jjt. |dz }tw||||j<|}j=t|dfj?tdfjAtdfjCtdffD]f\}} }|r,tt|G\}}ngg}}d|D}| ||}|H|g|S)aParse ITP file into Topology Parameters ---------- include_dir: str, optional A directory in which to look for other files included from the original file, if the files are not first found in the current directory. Default: "/usr/local/gromacs/share/gromacs/top/" infer_system: bool, optional (default True) If a ``[ molecules ]`` directive is not found within the the topology file, create a Topology with one of every ``[ moleculetype ]`` defined. If a ``[ molecules ]`` directive is found, this keyword is ignored. Returns ------- MDAnalysis *Topology* object N[]rr atomtypes moleculetype moleculescg|] }|j Sr()ro).0xs r* z#ITPParser.parse..Os$E$E$EQV$E$E$Er)rrcg|]?}|jvr j|dnd@S)chargerrkeysrdrrr4s r*rz#ITPParser.parse..Ysa### DN//1111N&&q))(33 ###r)cg|]?}|jvr j|dnd@S)massrrrs r*rz#ITPParser.parse..dsa""" DN//1111N&&q))&11 """r)F)guessedc3LK|]}|tvV dSr<) capitalizer)res r* z"ITPParser.parse..s/??Aq||~~'??????r)TaThe elements attribute has been populated by guessing elements from atom types. This behaviour has been temporarily added to the ITPParser as we transition to the new guessing API. This behavior will be removed in release 3.0. Please see issue #4698 for more information. zElement information is missing, elements attribute will not be populated. If needed these can be guessed using universe.guess_TopologyAttrs(to_guess=['elements']).)attrs atom_resindexresidue_segindexr}r~rrc,g|]}t|Sr()r )rts r*rz#ITPParser.parse..s 777A_Q''777r))r)Irr _molecules current_mol_passparsersystem_moleculesrfilenamer,linesrIraparse_atomtypesparse_moleculetypeparse_moleculesrrd build_systemrrrrrrallrr rrrr r rrfloat32rFrmissing_value_labelfloat64r guess_typeselementsrwarningswarnDeprecationWarningrrrrrcopyrrrrrrrrr}rr~rrrrrziprrYadd_TopologyAttr)r4r1 infer_systemkwargsitpfiler?sectionemptyrvalsAttrrrrrr n_residues n_segmentssegidxtopdctr&rrtattrs` r*parsezITPParser.parses6j "T] # # &w'fEEDJ  & &$;;3$;;"jjooa066s;;A>DDFFG+--&*&:  N22&*&=  K//&*&: )1&*&6&>&B&B#TZ'' '+j KK%%%%- & & & & & & & & & & & & & & & &4$ F F$E$ET_$E$E$ED ! Xdj)) x F;;; ht{&999 4<  LB&E#### E* ###DL 4; K2%E"""" E* """DK Xw ) ZF + ZF +   bh 7 \7BJ / "  @ @ D$4yy @ TT"(4u"="="=>>???4; <K2%E!'!;DK  28DKrz:::E J J J   't,,88DD ????? ? ?  LL$-v>>>MMM    M@ #     M*   $+RX6668DM888(4s r*rzITPParser._passs r)cgd}|}t|ddkr%|dr |dd}nt|ddkr4|drdd|d|d|df}nt|ddkry|dr_|dd r |dd|d|d|df}nd|d|d|d|df}tt |||j|d <dS) N) type_bonded atomic_numberrrp_typerrrrrrrr)rIrisalphar/r r)r4r?rfieldsrs r*rzITPParser.parse_atomtypessLKKK vay>>Q  6!9#4#4#6#6 AaC[FF ^^q VAY%6%6%8%8 VAYq 6!9$/ t/00000r)c|\}}|j|gt|zdSr<)rIrextendr)r4r?ron_mols r*rzITPParser.parse_moleculess=jjll e $$dVc%jj%899999r)c g|_g|_g|_g|_g|_g|_g|_g|_g|_g|_ g|_ |j|j|j|j|j|j|j|jg|_ tt|_tt|_tt|_tt|_|j|j|j|jg|_t'|jD]N\}}|j|}|jr |jdnd}|jr |jdnd}|jr |jdnd}t-|j}t-|j}|||||||} | \} } } } }t1|j | D]\}}|||j| |j | |j |t1|j| D]\}}||PdS)Nr8r)rrrrrr)rrrrrr rrrrrrrrr}r~rrr enumeraterrrrr r#update)r4imoltypemolrrrrrshiftedrrrrr system_attrmol_attr system_param mol_params r*rzITPParser.build_systemsd          H J K M J   L K  !&& !$'' $T**$T**z4;O #D$9:: / /JAw.)C%)X4TXb\\1F'+{9DKOOE,0,=D4$R((1D $$E$(mmG'' (G=D 9J6),T_j)I)I - -% X""8,,,, M  * * * L   ( ( ( K  v & & &+.t{F+C+C / /' i##I.... /5 / /r)N)rT) r"r#r$r%rlrrrrrrr(r)r*rrs%%NF<ppppd    < < <111 ::::/:/:/:/:/r)r)*r% collectionsrrqloggingnumpyrrlib.utilrguesser.tablesrguesser.default_guesserrrr r r core.topologyattrsr r rrrrrrrrrrrrrrr core.topologyrrr,rzrr(r)r*r8s>0iiT$##### ######444444DDDDDDDDDD&%$$$$$8w8w8w8w8w8w8w8w8t@2@2@2@2@2@2@2@2Fp/p/p/p/p/"p/p/p/p/p/r)