indZddlmZddlZddlZddlZddlZddlmZ ddl Z ddl Z ddl m Z  ddlZddlZdZn #e$rdZYnwxYwddlZdd lmZmZmZmZmZmZdd lmZmZdd lm Z m!Z!d d l"m#Z#d dl$m%Z%d dl&m'Z'm(Z(m)Z)m*Z*m+Z+m,Z,m-Z-m.Z.m/Z/m0Z0ddl$m1Z1m2Z2m3Z3dZ4dZ5dZ6dZ7dZ8dZ9Gdde:Z;GddeGdde=Z?Gd d!e=Z@Gd"d#e=ZAGd$d%eAZBGd&d'ZCGd(d)eCeAZDGd*d+eDZEGd,d-eDZFGd.d/eDZGGd0d1eAZHGd2d3eDZIGd4d5eDZJGd6d7eAZKGd8d9eAZLGd:d;eAZMGd<d=eAZNGd>d?eAZOGd@dAeDZPGdBdCeAZQGdDdEeAZRGdFdGeAZSGdHdIeAZTGdJdKeAZUGdLdMeAZVGdNdOeAZWGdPdQeAZXGdRdSeAZYGdTdUe=ZZGdVdWeCeZZ[GdXdYeZZ\GdZd[e[Z]Gd\d]eZZ^Gd^d_e[Z_Gd`dae[Z`GdbdceZZaGdddee=ZbGdfdgeCebZcGdhdiecZddjZeGdkdle;ZfGdmdneAefZgGdodpegZhGdqdregZiGdsdtegZjGdudvegZkGdwdxegZlGdydzegZmdS){a Topology attribute objects --- :mod:`MDAnalysis.core.topologyattrs` =================================================================== Common :class:`TopologyAttr` instances that are used by most topology parsers. TopologyAttrs are used to contain attributes such as atom names or resids. These are usually read by the TopologyParser. References ---------- .. footbibliography:: ) defaultdictN) signature) MethodTypeTF)cachedconvert_aa_codeiterablewarn_if_not_unique unique_int_1dcheck_atomgroup_not_empty)transformationsmdamath) NoDataErrorSelectionError) TopologyGroup) selection) ComponentBase GroupBaseAtomResidueSegment AtomGroup ResidueGroup SegmentGroupcheck_wrap_and_unwrap _pbc_to_wrap)_TOPOLOGY_ATTRS_TOPOLOGY_TRANSPLANTS_TOPOLOGY_ATTRNAMESc`dddtjfd}|S)aWrapper which checks the length of inputs to set_X Eg: @_check_length def set_X(self, group, values): Will check the length of *values* compared to *group* before proceeding with anything in the *set_X* method. Pseudo code for the check: if group in (Atom, Residue, Segment): values must be single values, ie int, float or string else: values must be single value OR same length as group zoSetting {cls} {attrname} with wrong sized input. Must use single value, length of supplied values: {lenvalues}.zvSetting {group} {attrname} with wrong sized array. Length {group}: {lengroup}, length of supplied values: {lenvalues}.cBt|rt|SdSNr)r lenvaluess g/srv/www/vhosts/g4struct/public_html/venv/lib/python3.11/site-packages/MDAnalysis/core/topologyattrs.py _attr_lenz _check_length.._attr_lenzs% F   v;; 1c |}t|tr;|dks4t|jj|j|n[|dksU|t|ksBt|jj|jt|||||S)Nr)clsattrname lenvalues)groupr,lengroupr-) isinstancer ValueErrorformat __class____name__singularr$r,)attrr.r&val_len_GROUP_VALUE_ERROR_SINGLE_VALUE_ERRORr(funcs r'wrapperz_check_length..wrappers)F## e] + + a<< '..!O4!%")/ qLLGs5zz$9$9 &--#o6!%!$U") .tD%(((r) functoolswraps)r:r;r8r9r(s` @@@r' _check_lengthr?Xsq( I N_T))))))))2 Nr)c*t|ttfrd}n=t|ttfrd}nt|t t frd}t|trd}d}n3t|trd}d}nt|trd}d}t|tr||kr|d}|j }n|d}|j }d}t|||jj| S) aGenerate an error for setting attr at wrong level attr : TopologyAttr that was accessed group : Offending Component/Group Eg: setting mass of residue, gets called with attr=Masses, group=residue raises a NotImplementedError with: 'Cannot set masses from Residue. Use 'Residue.atoms.masses' Mainly used to ensure consistent and helpful error messages rr)atomsatom)residuesresidue)segmentssegmentrz=Cannot set {attr} from {cls}. Use '{cls}.{correct}.{attr} = ')r6r+correct)r0rrrrrrAtomAttr ResidueAttr SegmentAttrrr5r,NotImplementedErrorr2r3r4)r6r. group_level corr_classes attr_levelrHr,err_msgs r'_wronglevel_errorrQs3%$ *++ EG\2 3 3 EG\2 3 3 $!!(  D+ & &.  D+ & &.  %''!Z+-E-Eq/=q/=MG (     r)cfd}tjd}tj|jdz|z|_|_t ||_|S)a Build a stub for a transplanted method. A transplanted stub is a dummy method that gets attached to a core class (usually from :mod:`MDAnalysis.core.groups`) and raises a :exc:`NoDataError`. The stub mimics the original method for everything that has traits with the documentation (docstring, name, signature). It gets overwritten by the actual method when the latter is transplanted at universe creation. Parameters ---------- method_name: str The name of the attribute in the destination class. method: Callable The method to be mimicked. attribute_name: str The name topology attribute that is required for the method to be relevant (e.g. masses, charges, ...) Returns ------- The stub. cfd|jj}t|)NzJ{class_name}.{method_name}() not available; this requires {attribute_name}) class_name method_nameattribute_name)r2r3r4r)selfargskwargsmessagerVrUs r' stub_methodz _build_stub..stub_methods? < &~.#)    '"""r)z .. note:: This requires the underlying topology to have {}. Otherwise, a :exc:`~MDAnalysis.exceptions.NoDataError` is raised. z )textwrapdedentr2__doc__r4inspect_signature __signature__)rUmethodrVr[ annotations` ` r' _build_stubrcs4 # # # # # #       J#/&.99FBZOK&K 1& 9 9K r)c d|j}|D]\}}|dkrddlm}|}|D]}\}}|drd} |j}d}n#t $rYnwxYwt|||} |r!t||t| ddlt||| ~dS)aN Transplant a stub for every method that will be transplanted from a topology attribute. Parameters ---------- attribute_name: str User-facing name of the topology attribute (e.g. masses, charges, ...) topology_attribute_class: Topology attribute class to inspect for transplant methods. Universer)re_FTN) transplantsitemsuniversere startswithfgetAttributeErrorrcsetattrproperty) rVtopology_attribute_classrg dest_classmethodsrerUmethod_callback is_propertystubs r'_attach_transplant_stubsrus+6K*002277 G  # # + * * * * *!J,3 7 7 (K %%c** K "1"6" !    {O^LLD 7 K$d1K1KLLLL K6666' 777s A A&%A&zThe bfactor topology attribute is only provided as an alias to the tempfactor attribute. It will be removed in 3.0. Please use the tempfactor attribute instead.cfd}|S)NcRtjtt|i|S)z, Bfactor alias with warning )warningswarnBFACTOR_WARNINGDeprecationWarning)rXrYr:s r'r;z*deprecate_bfactor_warning..wrapperEs-  o'9:::tT$V$$$r)r:r;s` r'deprecate_bfactor_warningr~Ds#%%%%% Nr)ceZdZdZdZdS)_TopologyAttrMetaaRegister TopologyAttrs on class creation Each topology attribute is added to the top-level dictionaries for various record purposes. The class itself is added to :data:`_TOPOLOGY_ATTRS` and :data:`_TOPOLOGY_ATTRNAMES`. Transplanted methods are also added to :data:`_TOPOLOGY_TRANSPLANTS.` We also attempt to make the topology attribute selectable with atom selection language by automatically generating a relevant selection class with the singular name (``singular``) as the selection token. Only certain ``dtype``\ s are supported; if a selection class cannot be generated, a warning will be raised but no error. See also -------- :func:`MDAnalysis.core.selection.gen_selection_class` c2tt||||d}|d|}||}|r|xt|<t|<|dd}|dd}|t |<|t |<|jD]L\}} | D]D\}} || |gt|<|dd} |t | <EMdD]+} || }t||#t$rY(wxYw|tj jvr|tj j|<|tjjvr|tjj|<|tjvr{|d} | d|d|dj} tj||| |n*#t($rd |d }t+j|YnwxYw|d krZ|xtd <td <tjd d |dd}t/|j|_dSdS)Nr,r5rf)r5r,dtype per_objectrzAA selection keyword could not be automatically generated for the zg attribute. If you need a selection keyword, define it manually by subclassing core.selection.Selection tempfactorsbfactorbfactorsrC)r)type__init__getrlowerreplacer rgrhrruKeyErrorr SameSelection prop_transPropertySelectionprops_SELECTIONDICTrgen_selection_classr1rxryr~apply)r+namebases classdictr,r5 _singular _attrnameclstypergracleanr6rper_objmsgselclss r'rz_TopologyAttrMeta.__init__ds dD%333==,,==X66  H  6DG GOH %(A ((00b99I ((00b99I-5  *-5  *(+(=(=(?(? 6 6$$/66LD&3;VW2M)$/ JJLL00b99E15'..6 - 8 8D 8$T?)37777     92= = =;CI # .x 8 96< < <:BI ' -h 7 93 3 3MM'**E #-- eAh6IJJ '1 (E7"'''B#BBBM#&&&&&' } $ $GJ JOI &)D2 g&&! F 5V\BBFLLL % $s$7E EE5H $H43H4N)r4 __module__ __qualname__r^rr|r)r'rrOs7(ACACACACACr)rceZdZdZdZdZdZdZee Z gZ dZ dZ dZddZedZe ddZd Zd Zd Zd Zed ZdZdZdZdZdZdZdZ edZ!dS) TopologyAttraBase class for Topology attributes. Note ---- This class is intended to be subclassed, and mostly amounts to a skeleton. The methods here should be present in all :class:`TopologyAttr` child classes, but by default they raise appropriate exceptions. Attributes ---------- attrname : str the name used for the attribute when attached to a ``Topology`` object singular : str name for the attribute on a singular object (Atom/Residue/Segment) per_object : str If there is a strict mapping between Component and Attribute dtype : int/float/object Type to coerce this attribute to be. For string use 'object' top : Topology handle for the Topology object TopologyAttr is associated with topologyattrs topologyattrNFcr|j||_n tj||j|_||_dSNr)rr&npasarray_guessed)rWr&guesseds r'rzTopologyAttr.__init__s6 :  DKK*V4:>>>DK r)c td)zPopulate an initial empty data structure for this Attribute The only provided parameters are the "shape" of the Universe Eg for charges, provide np.zeros(n_atoms) zNo default valuesrL)n_atoms n_residues n_segmentss r'_gen_initial_valuesz TopologyAttr._gen_initial_valuess""5666r)c|||||}n"|jtj||j}||S)aCreate a blank version of this TopologyAttribute Parameters ---------- n_atoms : int, optional Size of the TopologyAttribute atoms n_residues: int, optional Size of the TopologyAttribute residues n_segments : int, optional Size of the TopologyAttribute segments values : optional Initial values for the TopologyAttribute Nr)rrrr)r+rrrr&s r' from_blankzTopologyAttr.from_blanksN" >,,Wj*MMFF Y "Zci888Fs6{{r)ch||j|jS)#Return a deepcopy of this attribute)r)r3r&copyrrWs r'rzTopologyAttr.copys(~~dk..00$-~HHHr)c*t|jS)z2Length of the TopologyAttr at its intrinsic level.)r$r&rs r'__len__zTopologyAttr.__len__s4;r)c,t|ttfr||St|tt fr||St|ttfr| |SdS)z2Accepts an AtomGroup, ResidueGroup or SegmentGroupN) r0rr get_atomsrr get_residuesrr get_segments)rWr.s r' __getitem__zTopologyAttr.__getitem__s edI. / / ,>>%(( ( 6 7 7 ,$$U++ + 6 7 7 ,$$U++ + , ,r)c2t|ttfr|||St|tt fr|||St|ttfr| ||SdSN) r0rr set_atomsrr set_residuesrr set_segments)rWr.r&s r' __setitem__zTopologyAttr.__setitem__s edI. / / 4>>%00 0 6 7 7 4$$UF33 3 6 7 7 4$$UF33 3 4 4r)c|jS)z4Bool of if the source of this information is a guessrrs r' is_guessedzTopologyAttr.is_guesseds }r)cltj|jtj|gg|_dS)zkResize TopologyAttr to one larger, with *newval* as the new value .. versionadded:: 2.1.0 N)r concatenater&array)rWnewvals r'_add_newzTopologyAttr._add_news, ndk28VH3E3E%FGG r)ct)z)Get atom attributes for a given AtomGrouprrWags r'rzTopologyAttr.get_atomsr)ct)z)Set atom attributes for a given AtomGrouprrWrr&s r'rzTopologyAttr.set_atoms!!r)ct)z/Get residue attributes for a given ResidueGrouprrWrgs r'rzTopologyAttr.get_residues#rr)ct)z/Set residue attributes for a given ResidueGrouprrWrr&s r'rzTopologyAttr.set_residues'rr)ct)z/Get segment attributes for a given SegmentGrouprrWsgs r'rzTopologyAttr.get_segments+rr)ct)z.Set segmentattributes for a given SegmentGrouprrWrr&s r'rzTopologyAttr.set_segments/rr)ctt|dd}|tjurtj|S||kS)zScheck if an attribute has a missing value .. versionadded:: 2.8.0 missing_value_labelN)getattrrnanisnan)r+r&rs r'are_values_missingzTopologyAttr.are_values_missing3s@ &c+@$GG "& ( (8F## #00 0r)F)NNNN)"r4rrr^r,r5rtoprlistrgtarget_classesgroupdoc singledocrr staticmethodr classmethodrrrrrrnrrrrrrrrrr|r)r'rrs2HHJ C+d##KNHI E    77\7DH[.III   ,,,444XHHH""""""""" 1 1[ 1 1 1r)r) metaclasscHeZdZdZdZdZeeee gZ e Z dZ dZdZdZdZd S) AtomindicesaGlobally unique indices for each atom in the group. If the group is an AtomGroup, then this gives the index for each atom in the group. This is the unambiguous identifier for each atom in the topology, and it is not alterable. If the group is a ResidueGroup or SegmentGroup, then this gives the indices of each atom represented in the group in a 1-D array, in the order of the elements in that group. indicesindexcd|_dSNFrrs r'rzAtomindices.__init__V  r)c td)Nz,Atom indices are fixed; they cannot be resetrlrs r'rzAtomindices.set_atomsYsKLLLr)c|jSrixrs r'rzAtomindices.get_atoms\ u r)cdt|jj|jSr)rrttresidues2atoms_2drrs r'rzAtomindices.get_residues_$DHK11"%88999r)cdt|jj|jSr)rrrsegments2atoms_2drrs r'rzAtomindices.get_segmentsbrr)N)r4rrr^r,r5rrrrrintrrrrrrr|r)r'rrDs  HH|TBN EMMM::::::::r)rcJeZdZdZdZdZeeee e gZ e Z dZdZdZdZdZd S) ResindicesaGlobally unique resindices for each residue in the group. If the group is an AtomGroup, then this gives the resindex for each atom in the group. This unambiguously determines each atom's residue membership. Resetting these values changes the residue membership of the atoms. If the group is a ResidueGroup or SegmentGroup, then this gives the resindices of each residue represented in the group in a 1-D array, in the order of the elements in that group. resindicesresindexcd|_dSrrrs r'rzResindices.__init__xrr)cJ|jj|jSr)rratoms2residuesrrs r'rzResindices.get_atoms{x{))"%000r)c|jSrrrs r'rzResindices.get_residues~rr)c td)Nz/Residue indices are fixed; they cannot be resetrrs r'rzResindices.set_residuesNOOOr)cdt|jj|jSr)rrrsegments2residues_2drrs r'rzResindices.get_segmentss$DHK44RU;;<<z)AtomAttr.get_residues.. 111S C 111r))rrrr)rWraixss` r'rzAtomAttr.get_residues8 x{,,RU331111D1111r)c"t||rrQrs r'rzAtomAttr.set_residuesb)))r)chjj|j}fd|DS)r#c*g|]}j|Sr|r%r%s r'r(z)AtomAttr.get_segments..r)r))rrrr)rWrr*s` r'rzAtomAttr.get_segmentsr+r)c"t||rr-rs r'rzAtomAttr.set_segmentsr.r)N)r4rrr^r,r5rrrrrrr?rrrrrr|r)r'rIrIs))HH|TBN"""$$]$222***222*****r)rIc8eZdZdZdZdZdZeZe dZ dS)AtomidszID for each atom.idsidrCc2tjd|dzSNrrarangenanrnss r'rzAtomids._gen_initial_valuesyBF###r)N r4rrr^r,r5rrrrrr|r)r'r3r3sGHHJ E$$\$$$r)r3c&eZdZdZddZdZdZdS)_StringInternerMixinaString interning pattern Used for faster matching of strings (see _ProtoStringSelection) self.namedict (dict) - maps actual string to string index (str->int) self.namelookup (array dtype object) - maps string index to actual string (int->str) self.nmidx (array dtype int) - maps atom index to string index (int->int) self.values (array dtype object) - the premade per-object string values .. versionadded:: 2.1.0 Mashed together the different implementations to keep it DRY. Fc||_t|_g}tj|t |_t|D]h\}} |j||j|<#t$r@t|j}||j|<| |||j|<YewxYwtj |t|_ |j |j|_dSr)rdictnamedictr zeros_likernmidx enumeraterr$appendrobject name_lookupr&)rWvalsrrJivalnextidxs r'rz_StringInternerMixin.__init__s   ]4s333  oo ( (FAs ( $ c 2 1  ( ( (dm,,%, c"""3''' ' 1  (8Kv>>>&tz2 sA((AB21B2cF |j|}nO#t$rBt|j}||j|<tj|j|gg|_YnwxYwtj|j|gg|_tj|j|gg|_dS)aBAppend new value to the TopologyAttr Parameters ---------- newval : str value to append resizes this attr to size+1 and adds newval as the value of the new entry for string interning this is slightly different hence the override .. versionadded:: 2.1.0 N)rDrr$rrrJrFr&)rWrnewidxs r'rz_StringInternerMixin._add_news L]6*FF L L L''F$*DM& !!~t/?&.JKKD    L ^TZ&$:;; ndkF8%<== s A AAczg}t|trR |j|}n#t$r6t |j}||j|<||YnwxYwt j|t}t|D]^\}} |j|||<#t$r;t |j}||j|<|||||<Y[wxYw||j |j <|r t j |j |g|_ |j |j |_dSr)r0strrDrr$rHrrErrGrFrrrJr&)rWrr&newnamesrPrLrMrNs r'_set_Xz_StringInternerMixin._set_X*sf fc " " ( (v. ( ( (T]++(. f%''''' ( ]6555F#F++ ( (3( $ c 2F1II(((!$-00G)0DM#&OOC((( 'F1III (  25  L!~t/?.JKKD &tz2 s" '=A'&A'B++AC0/C0Nr)r4rrr^rrrTr|r)r'rArAsP"3333.>>>.33333r)rAc:eZdZedZedZdS)AtomStringAttrc.|||SrrTrs r'rzAtomStringAttr.set_atomsK{{2v&&&r)c:tj|dtSNrrrfullrIr:s r'rz"AtomStringAttr._gen_initial_valuesOwr2V,,,,r)N)r4rrr?rrrr|r)r'rVrVJH'']'--\---r)rVceZdZdZdZdZdZeZe e Z ddZ e e d e fdd Ze ed efdd Ze e d efdZe edefdZe edefddZe edefddZe e defddZe edef d dZe e def d dZe edefdS)! AtomnameszName for each atom.namesrrCCNCAc6 jjjdz }jj}jdz }|jj|kr |j|ksNd||} j|jd}n#t$rYdSwxYw|j |j j |k}t|dksdSj j |||g} fd| D} td| DsdS|t| z}|S)aSelect AtomGroup corresponding to the phi protein backbone dihedral C'-N-CA-C. Parameters ---------- c_name: str (optional) name for the backbone C atom n_name: str (optional) name for the backbone N atom ca_name: str (optional) name for the alpha-carbon atom Returns ------- AtomGroup 4-atom selection in the correct order. If no C' found in the previous residue (by resid) then this method returns ``None``. .. versionchanged:: 1.0.0 Added arguments for flexible atom names and refactored code for faster atom matching with boolean arrays. rsegid {} and resid {}rNc2g|]}j|kSr|rBr&natnamesrEs r'r(z+Atomnames.phi_selection..$@@@ gl+@@@r)c3<K|]}t|dkVdSrNr$r&rs r' z*Atomnames.phi_selection..,//B3r77a<//////r))rirDrrGsegidresidr2 select_atoms IndexErrorrBrbr$allsum) rEc_namen_nameca_nameprevsidridselc_ ncac_namesncacrls ` @r' phi_selectionzAtomnames.phi_selection^s>0(a8o#ma "c))djC.?.?)00c::C '44S99B1E   tt  Z (F2 32ww!||4-%gv. @@@@@Z@@@//$///// 43t99n s%%B BBrc|sgS|dj}|j|jdz }|j}|jdz }||gd}t j|j|k|j|kzd} g} t| rt|} t|| || | D]c\} } } | | | | jd| |<?#t$r| |Y`wxYwt| }fd|D}fd|D}t j|t j|z}d|| <t j|t"}d||<||}||}t j|d}|j|jjk}|j|jj|k}|j|jj|k}|j|jjk}d t||||D||<t|S) avSelect list of AtomGroups corresponding to the phi protein backbone dihedral C'-N-CA-C. Parameters ---------- c_name: str (optional) name for the backbone C atom n_name: str (optional) name for the backbone N atom ca_name: str (optional) name for the alpha-carbon atom Returns ------- list of AtomGroups 4-atom selections in the correct order. If no C' found in the previous residue (by resid) then corresponding item in the list is ``None``. .. versionadded:: 1.0.0 rrrgcRg|]#}t|jjkdk$SrryrBrb)r&rrzs r'r(z,Atomnames.phi_selections..s/EEE1S&011Q6EEEr)cHg|]tfdDS)c3ZK|]%}tjj|kdkV&dSrorr&rkrs r'rrz6Atomnames.phi_selections...9AAAGMQ&''1,AAAAAAr)rxr&rrs @r'r(z,Atomnames.phi_selections..G    AAAAjAAA A A   r)FrNc,g|]}t|Sr|ryr&rBs r'r(z,Atomnames.phi_selections..sEEE%3u::EEEr))rirDrsegidsresidsrwherer$rziprvr2rwrHryrrErIrBrb)rDrzr{r|ur}rsidpridrwixinvalidprevlssrrL keep_prevkeep_reskeepresultskeepixrrkcacrs ` @r'phi_selectionszAtomnames.phi_selectionssk. I QK z(+/*"gv. %h t+ t0CDEEaH s88 $ZZFtCy$s)S99 & &1a& !szz!Q/?/? @ @ I! LF1II!&&&NN1%%%%%&v;;DEEEEEEE        x ""RXh%7%77W -777DzD>$" Z (F2 3 N8>/69 : ^HN0G; < N8>/69 :EE3r1b!3D3DEEEG}}s47C,,D Drcj d}jj}jdz} jjjdz}|jj|kr |j|ksd}n#t $rd}YnwxYw|rNd||} j|jd}n#t $rYdSwxYw|j |j j |k} t| dksdSj j |||g} fd| D} td| DsdSt| | z}|S) aSelect AtomGroup corresponding to the psi protein backbone dihedral N-CA-C-N'. Parameters ---------- c_name: str (optional) name for the backbone C atom n_name: str (optional) name for the backbone N atom ca_name: str (optional) name for the alpha-carbon atom Returns ------- AtomGroup 4-atom selection in the correct order. If no N' found in the following residue (by resid) then this method returns ``None``. .. versionchanged:: 1.0.0 Added arguments for flexible atom names and refactored code for faster atom matching with boolean arrays. FrTrgrNc2g|]}j|kSr|rirjs r'r(z+Atomnames.psi_selection..rmr)c3<K|]}t|dkVdSrorprqs r'rrz*Atomnames.psi_selection..rsr))rGrtrurirDrrwr2rvrBrbr$rxry) rErzr{r| _manual_selr~rnxtrn_rrrls ` @r' psi_selectionzAtomnames.psi_selections2 o#ma #"+GJN;CK%,,c1A1A"    KKK   )00c::C &33C88A!D   tt  Ysy&0 12ww!||4-%gv. @@@@@Z@@@//$///// 4$ii"n s#A A#"A#?%B%% B32B3rcF |dj}n#t$r|cYSwxYwtjdgt |zt }tjt |}t|j}|t |j dz kr|j|k}||}||}|j |jdzx||<}|j }|j dz}d} tj |j |k|j |kzd} t | r}t|| || | D]_\} } } || | | j d||| <E#t$rd||| <Y\wxYw|S)aXSelect list of Residues corresponding to the next resid for each residue in `residues`. Returns ------- List of Residues List of the next residues in the Universe, by resid and segid. If not found, the corresponding item in the list is ``None``. .. versionadded:: 1.0.0 rNrrrg)rirwrrr$rIr9maxrrDrrrrrvr2)rDrnxresrlastnotlastrrnridrrrrrLs r'_get_next_residues_by_residz%Atomnames._get_next_residues_by_resid s  $AA   OOO $#h--/v>>> Ys8}} % %8; 3qz??Q& & &kT)GGB(H*X[1_55b C"%h d*szT/ABCCAF s88 (tCy$s)S99 ( (1a(#$>>#**Q2B2B#C#C#LQ#OE"Q%LL!(((#'E"Q%LLL( s  =FFFrcN |dj}n#t$r|cYSwxYwtjdgt |z}|j|jdz x|dd<}|j}|jdz }d}tj |j|k|j|kzd}t |rqt|||||D]S\}} } | | || jd|| <?#t$rd|| <YPwxYw|S)a`Select list of Residues corresponding to the previous resid for each residue in `residues`. Returns ------- List of Residues List of the previous residues in the Universe, by resid and segid. If not found, the corresponding item in the list is ``None``. .. versionadded:: 1.0.0 rNrrg) rirwrrr$rDrrrrrrvr2) rDrpvresr}rrrrrrrLs r'_get_prev_residues_by_residz%Atomnames._get_prev_residues_by_resid6sK  $AA   OOO $#h--/00*X[1_55aaa4"%h t+ t0CDEEaH s88 $tCy$s)S99 $ $1a$ ~~cjjA.>.>??HKE!HH!$$$#E!HHH$ s  7DD"!D"rc$|sgStjdgt|zt}|}tj|d}t ||}||}||gfd|D}fd|D} tj|tj| z} || }|| }tj| d} |j|jjk} |j|jj|k} |j|jj|k}|j|jjk}dt| | ||D||| <t|S)a{Select list of AtomGroups corresponding to the psi protein backbone dihedral N-CA-C-N'. Parameters ---------- c_name: str (optional) name for the backbone C atom n_name: str (optional) name for the backbone N atom ca_name: str (optional) name for the alpha-carbon atom Returns ------- List of AtomGroups 4-atom selections in the correct order. If no N' found in the following residue (by resid) then the corresponding item in the list is ``None``. .. versionadded:: 1.0.0 NrrcRg|]#}t|jjkdk$Srr)r&rr{s r'r(z,Atomnames.psi_selections..{s/CCC!C /00A5CCCr)cHg|]tfdDS)c3ZK|]%}tjj|kdkV&dSrorrs r'rrz6Atomnames.psi_selections...}rr)rrs @r'r(z,Atomnames.psi_selections..|rr)c,g|]}t|Sr|rrs r'r(z,Atomnames.psi_selections..sJJJuE JJJr) rrr$rIrrryrBrbrr)rDrzr{r|rnxtresrixrkeep_nxtrrrrkrrrrs ` @r'psi_selectionszAtomnames.psi_selectionsZs. I(D6CMM1@@@5577hvq!&+C=gv. CCCCsCCC       x!!BHX$6$66$iD>$" N8>/69 : ^HN0G; < N8>/69 : Ysy&0 1JJAr1b8I8IJJJF G}}r)rcd}|jj}|jdz} |jj|jdz}|jj|kr |j|ksd}n#t $rd}YnwxYw|rNd||} |j|jd}n#t $rYdSwxYw|j |j j |k} |j |j j |k} |j |j j |k} |j |j j |k} td| | | | fDsdS| | z| z| zS)aSelect AtomGroup corresponding to the omega protein backbone dihedral CA-C-N'-CA'. omega describes the -C-N- peptide bond. Typically, it is trans (180 degrees) although cis-bonds (0 degrees) are also occasionally observed (especially near Proline). Parameters ---------- c_name: str (optional) name for the backbone C atom n_name: str (optional) name for the backbone N atom ca_name: str (optional) name for the alpha-carbon atom Returns ------- AtomGroup 4-atom selection in the correct order. If no C' found in the previous residue (by resid) then this method returns ``None``. .. versionchanged:: 1.0.0 Added arguments for flexible atom names and refactored code for faster atom matching with boolean arrays. FrTrgrNc3<K|]}t|dkVdSrorprqs r'rrz,Atomnames.omega_selection..s,;;B3r77a<;;;;;;r)) rGrtrurirDrrwr2rvrBrbrx) rErzr{r|rr~rrrrrrca_s r'omega_selectionzAtomnames.omega_selections8 o#ma #"+GJN;CK%,,c1A1A"    KKK   )00c::C &33C88A!D   tt ]7=.'9 : M'--7 8 Ysy&0 1i 723;;3B*:;;;;; 4Av{S  s#A A! A!=%B## B10B1rc*|sgStjdgt|zt}|}tj|d}t ||}||}||g||gfd|D}fd|D} tj|tj| z} || }|| }tj| d} |j|jj|k} |j|jj|k} |j|jj|k}|j|jj|k}dt| | ||D||| <t|S)a=Select list of AtomGroups corresponding to the omega protein backbone dihedral CA-C-N'-CA'. omega describes the -C-N- peptide bond. Typically, it is trans (180 degrees) although cis-bonds (0 degrees) are also occasionally observed (especially near Proline). Parameters ---------- c_name: str (optional) name for the backbone C atom n_name: str (optional) name for the backbone N atom ca_name: str (optional) name for the alpha-carbon atom Returns ------- List of AtomGroups 4-atom selections in the correct order. If no C' found in the previous residue (by resid) then the corresponding item in the list is ``None``. .. versionadded:: 1.0.0 NrrcHg|]tfdDS)c3ZK|]%}tjj|kdkV&dSrorrs r'rrz8Atomnames.omega_selections...9??AGMQ&''1,??????r)r)r&rnxtatomss @r'r(z.Atomnames.omega_selections..sD   DEC????h??? ? ?   r)cHg|]tfdDS)c3ZK|]%}tjj|kdkV&dSrorrs r'rrz8Atomnames.omega_selections...rr)r)r&rresatomss @r'r(z.Atomnames.omega_selections..sG    ????h??? ? ?   r)c,g|]}t|Sr|rrs r'r(z.Atomnames.omega_selections..sLLLuE LLLr)r)rDrzr{r|rrrrrrrrrrrrrrs @@r'omega_selectionszAtomnames.omega_selectionss6 I(D6CMM1@@@5577hvq!&+C=V$V$    IL          x!!BHX$6$66$iD>$" N8>/69 : ^HN0G; < Ysy&0 1i 723LLB2s8K8KLLLF G}}r)rCBCG CG1 OG OG1 SGc||||g}jjfd|D}td|DrdSt|S)azSelect AtomGroup corresponding to the chi1 sidechain dihedral ``N-CA-CB-*G.`` The gamma atom is taken to be the heavy atom in the gamma position. If more than one heavy atom is present (e.g. CG1 and CG2), the one with the lower number is used (CG1). .. warning:: This numbering of chi1 atoms here in following with the IUPAC 1970 rules. However, it should be noted that analyses which use dihedral angles may have different definitions. For example, the :class:`MDAnalysis.analysis.dihedrals.Janin` class does not incorporate amino acids where the gamma atom is not carbon, into its chi1 selections. Parameters ---------- c_name: str (optional) name for the backbone C atom ca_name: str (optional) name for the alpha-carbon atom cb_name: str (optional) name for the beta-carbon atom cg_name: str (optional) name for the gamma-carbon atom Returns ------- AtomGroup 4-atom selection in the correct order. If no CB and/or CG is found then this method returns ``None``. .. versionadded:: 0.7.5 .. versionchanged:: 1.0.0 Added arguments for flexible atom names and refactored code for faster atom matching with boolean arrays. ctg|]4}jtj|5Sr|rBrisinsplitrjs r'r(z,Atomnames.chi1_selection..0s4IIIaw}RWWaggii889IIIr)c3<K|]}t|dkVdSrorprqs r'rrz+Atomnames.chi1_selection..1s,**s2ww!|******r)N)rBrbanyry)rEr{r|cb_namecg_namerbagsrls` @r'chi1_selectionzAtomnames.chi1_selectionsjT'73-%IIIII5III **c*** * * 43xxr)rcF sgStjdgtz}||||g fdD}tj|d}|jj fd D}dt |D||<t|S)aSelect list of AtomGroups corresponding to the chi1 sidechain dihedral N-CA-CB-CG. Parameters ---------- c_name: str (optional) name for the backbone C atom ca_name: str (optional) name for the alpha-carbon atom cb_name: str (optional) name for the beta-carbon atom cg_name: str (optional) name for the gamma-carbon atom Returns ------- List of AtomGroups 4-atom selections in the correct order. If no CB and/or CG is found then the corresponding item in the list is ``None``. .. versionadded:: 1.0.0 NcHg|]tfdDS)c3K|]F}ttjjj|dkVGdSro)ryrrrBrbrrs r'rrz7Atomnames.chi1_selections...[sHKKBGAGM177995566!;KKKKKKr)r)r&rrbs @r'r(z-Atomnames.chi1_selections..ZsG    KKKKUKKK K K   r)rctg|]4}jtj|5Sr|r)r&rkrlrDs r'r(z-Atomnames.chi1_selections..bs4JJJqx~bggqwwyy99:JJJr)c,g|]}t|Sr|rrs r'r(z-Atomnames.chi1_selections..cs===%3u::===r))rrr$rrBrbrr) rDr{r|rrrrrrrlrbs ` @@r'chi1_selectionszAtomnames.chi1_selections7s< I(D6CMM122'73       $"D>.&JJJJJEJJJ==39===G}}r)rN)rcrdre)rdrerr)r4rrr^r,r5rrIrrrrgrrrHrrrrrrrrrrr|r)r'raraUstHHJ E+d##K,,,,\- @AAA????B $$&6%GHHH5555n- @AAA&&&P $$ &(CD@ $$ &(CD0000d $$&6%GHHH6!6!6!6!p!2O DEEE8888t $$&8:J%KLLL" ////b!1> BCCC" ----^ $$&7%IJJJJJr)rac"eZdZdZdZdZdZeZdS) AtomtypeszType for each atomtypesrrCN r4rrr^r,r5rrIrr|r)r'rrjs(HHJ EEEr)rc4eZdZdZdZdZeZedZ dS)ElementszElement for each atomelementselementcftjdt|DtS)Ncg|]}dSrr|r&rfs r'r(z0Elements._gen_initial_values..}//////r)rrrrangerIr:s r'rzElements._gen_initial_values{,x//U2YY///v>>>>r)N) r4rrr^r,r5rIrrrr|r)r'rrtsBHH E??\???r)rc8eZdZdZdZdZdZeZe dZ dS)RadiizRadii for each atomradiiradiusrCc*tj|Srrzerosr:s r'rzRadii._gen_initial_valuesx||r)N r4rrr^r,r5rfloatrrrr|r)r'rrsGHHJ E\r)rc8eZdZdZdZdZdZeZe dZ dS) RecordTypeszFor PDB-like formats, indicates if ATOM or HETATM Defaults to 'ATOM' .. versionchanged:: 0.20.0 Now stores array of dtype object rather than boolean mapping record_types record_typerCc@tjdg|ztS)NATOMr)rrrIr:s r'rzRecordTypes._gen_initial_valuessx2 V4444r)N r4rrr^r,r5rrIrrrr|r)r'rrsMHHJ E55\555r)rc"eZdZdZdZdZdZeZdS)ChainIDszeChainID per atom Note ---- This is an attribute of the Atom, not Residue or Segment chainIDschainIDrCNrr|r)r'rrs.HHJ EEEr)rc reZdZdZdZdZdZeZe e Z e dZ edZedZedZed Ze ed eeed ejfeeeeefD]0Ze ed eeed ejf1d S) TempfactorszTempfactor for atomsr tempfactorrCc*tj|Srrr:s r'rzTempfactors._gen_initial_valuesrr)c:|jj|jjS)aAlias for tempfactor The bfactor topology attribute is only provided as an alias to the tempfactor attribute. It will be removed in 3.0. Please use the tempfactor attribute instead. .. versionadded:: 2.0.0 .. deprecated:: 2.0.0 Will be removed in 3.0.0. Use the ``tempfactor`` attribute instead. rirBrr rs r'rzTempfactors.bfactors }"47+66r)c>||jj|j_dS)zLTempfactor alias property for atom .. versionadded:: 2.0.0 Nr rWvalues r'bfactor_setterzTempfactors.bfactor_setters 38 DG$///r)cD|jj|jjjS)aAlias for tempfactors The bfactor topology attribute is only provided as an alias to the tempfactor attribute. It will be removed in 3.0. Please use the tempfactor attribute instead. .. versionadded:: 2.0.0 .. deprecated:: 2.0.0 Will be removed in 3.0.0. Use the ``tempfactor`` attribute instead. rirBrrrs r'rzTempfactors.bfactorss }"4:=1==r)cH||jj|jj_dS)zWTempfactor alias property for groups of atoms .. versionadded:: 2.0.0 Nrrs r'bfactors_setterzTempfactors.bfactors_setters :? DJM*666r)rNr)r4rrr^r,r5rrrrrrgrrr~rrrrrrHrnrrrrrr.r|r)r'r r s[HHJ E+d##K\777"888>>>"??? HHWndGOLLMWlG\J  E!!?D(:JKK       r)r cveZdZdZdZdZejZe e e e e egZeeZejZdZdZedZdZdZeeeedd Zee !d efeedd Z"ee !de"feeeeddZ#ee !de#feeed dZ$ee !de$feeeddZ%ee !de%feeeddZ&ee !de&feeeeddZ'ee !de'feeed dZ(ee !de(fdZ)ee !de)fdS)!MassesmassesmassrCa-Mass of each component in the Group. If the Group is an AtomGroup, then the masses are for each atom. If the Group is a ResidueGroup or SegmentGroup, the masses are for each residue or segment, respectively. These are obtained by summation of the member atoms for each component. zMass of the component.c*tj|Srrr:s r'rzMasses._gen_initial_valuesrr)c|jj|j}t |jt jr-|jt| }nXtj t|}t|D]'\}}|j| ||<(|Srrrrrr0_ixnumbersIntegralr&tupleryremptyr$rG)rWrrrrLrows r'rzMasses.get_residuess8;0077 bfg. / / 3[x15577FFXc"gg&&F#H-- 3 33 K,0022q  r)c(jj|j}t |jt jr-jt| }n tj fd|D}|S)NcNg|]!}j|"Sr|r&ryr&r"rWs r'r(z'Masses.get_segments..2s,JJJ#t{3/3355JJJr) rrrrr0rrrr&r ryrr)rWrsegatomsrs` r'rzMasses.get_segments*s8;0077 bfg. / / L[x15577FFXJJJJJJJKKF r)Fr.cL|j}||j|||S)a< Center of mass of (compounds of) the group .. math:: \boldsymbol R = \frac{\sum_i m_i \boldsymbol r_i}{\sum m_i} where :math:`m_i` is the mass and :math:`\boldsymbol r_i` the position of atom :math:`i` in the given :class:`MDAnalysis.core.groups.AtomGroup`. Centers of mass per :class:`Residue`, :class:`Segment`, molecule, or fragment can be obtained by setting the `compound` parameter accordingly. If the masses of a compound sum up to zero, the center of mass coordinates of that compound will be ``nan`` (not a number). Parameters ---------- wrap : bool, optional If ``True`` and `compound` is ``'group'``, move all atoms to the primary unit cell before calculation. If ``True`` and `compound` is not ``group``, the centers of mass of each compound will be calculated without moving any atoms to keep the compounds intact. Instead, the resulting center-of-mass position vectors will be moved to the primary unit cell after calculation. unwrap : bool, optional If ``True``, compounds will be unwrapped before computing their centers. compound : {'group', 'segments', 'residues', 'molecules', 'fragments'},\ optional If ``'group'``, the center of mass of all atoms in the group will be returned as a single position vector. Otherwise, the centers of mass of each :class:`Segment`, :class:`Residue`, molecule, or fragment will be returned as an array of position vectors, i.e. a 2d array. Note that, in any case, *only* the positions of :class:`Atoms` *belonging to the group* will be taken into account. Returns ------- center : numpy.ndarray Position vector(s) of the center(s) of mass of the group. If `compound` was set to ``'group'``, the output will be a single position vector. If `compound` was set to ``'segments'`` or ``'residues'``, the output will be a 2d coordinate array of shape ``(n, 3)`` where ``n`` is the number of compounds. Note ---- This method can only be accessed if the underlying topology has information about atomic masses. .. versionchanged:: 0.8 Added `pbc` parameter .. versionchanged:: 0.19.0 Added `compound` parameter .. versionchanged:: 0.20.0 Added ``'molecules'`` and ``'fragments'`` compounds; added `unwrap` parameter .. versionchanged:: 2.1.0 Renamed `pbc` kwarg to `wrap`. `pbc` is still accepted but is deprecated and will be removed in version 3.0. weightswrapcompoundunwrap)rBcenterrr.r,r.r-rBs r'center_of_masszMasses.center_of_mass6s2J ||Lthv   r)r1c0|d|S)aTotal mass of (compounds of) the group. Computes the total mass of :class:`Atoms` in the group. Total masses per :class:`Residue`, :class:`Segment`, molecule, or fragment can be obtained by setting the `compound` parameter accordingly. Parameters ---------- compound : {'group', 'segments', 'residues', 'molecules', 'fragments'},\ optional If ``'group'``, the total mass of all atoms in the group will be returned as a single value. Otherwise, the total masses per :class:`Segment`, :class:`Residue`, molecule, or fragment will be returned as a 1d array. Note that, in any case, *only* the masses of :class:`Atoms` *belonging to the group* will be taken into account. Returns ------- float or numpy.ndarray Total mass of (compounds of) the group. If `compound` was set to ``'group'``, the output will be a single value. Otherwise, the output will be a 1d array of shape ``(n,)`` where ``n`` is the number of compounds. .. versionchanged:: 0.20.0 Added `compound` parameter rr- accumulater.r-s r' total_masszMasses.total_masss@8<<` *belonging to the group* will be taken into account. Returns ------- moment_of_inertia : numpy.ndarray Moment of inertia tensor as a 3 x 3 numpy array. Notes ----- The moment of inertia tensor :math:`\mathsf{I}` is calculated for a group of :math:`N` atoms with coordinates :math:`\mathbf{r}_i,\ 1 \le i \le N` relative to its center of mass from the relative coordinates .. math:: \mathbf{r}'_i = \mathbf{r}_i - \frac{1}{\sum_{i=1}^{N} m_i} \sum_{i=1}^{N} m_i \mathbf{r}_i as .. math:: \mathsf{I} = \sum_{i=1}^{N} m_i \Big[(\mathbf{r}'_i\cdot\mathbf{r}'_i) \sum_{\alpha=1}^{3} \hat{\mathbf{e}}_\alpha \otimes \hat{\mathbf{e}}_\alpha - \mathbf{r}'_i \otimes \mathbf{r}'_i\Big] where :math:`\hat{\mathbf{e}}_\alpha` are Cartesian unit vectors, or in Cartesian coordinates .. math:: I_{\alpha,\beta} = \sum_{k=1}^{N} m_k \Big(\big(\sum_{\gamma=1}^3 (x'^{(k)}_{\gamma})^2 \big)\delta_{\alpha,\beta} - x'^{(k)}_{\alpha} x'^{(k)}_{\beta} \Big). where :math:`x'^{(k)}_{\alpha}` are the Cartesian coordinates of the relative coordinates :math:`\mathbf{r}'_k`. .. versionchanged:: 0.8 Added `pbc` keyword .. versionchanged:: 0.20.0 Added `unwrap` parameter .. versionchanged:: 2.1.0 Renamed `pbc` kwarg to `wrap`. `pbc` is still accepted but is deprecated and will be removed in version 3.0. r,r.r-r.NraxisFinplace)r-r=)rArArrr) rBr1rry pack_into_boxr. positionsrrfloat64) r.r,r.r- atomgroupcomposrtenss r'moment_of_inertiazMasses.moment_of_inertiasBK &&fx'   w  aaag..334   ""#C  ,))%)883>CC  ,""He"DDsJCC%+C!xbj111AAAqD QQQQTa ?@EEGGQ $*SAY$6QQQT$B#G#G#I#I"IIQ T!WQZ$*SAY$6QQQT$B#G#G#I#I"IIQ T!WQZAAAqD QQQQTa ?@EEGGQ $*SAY$6QQQT$B#G#G#I#I"IIQ T!WQZAAAqD QQQQTa ?@EEGGQ  r)rEc <|j}|j}||}|r|d|z }n |j|z }t jd|t jd|||z }t j|S)aRadius of gyration. Parameters ---------- wrap : bool, optional If ``True``, move all atoms within the primary unit cell before calculation. [``False``] .. versionchanged:: 0.8 Added `pbc` keyword .. versionchanged:: 2.1.0 Renamed `pbc` kwarg to `wrap`. `pbc` is still accepted but is deprecated and will be removed in version 3.0. r,Fr<i,i->ij,ij->i) rBrr1r>r?reinsumr7sqrt)r.r,rYrArrB recenteredposrog_sqs r'radius_of_gyrationzMasses.radius_of_gyrations&K !&&D&11  6%33E3BBSHMM%/#5M I *m]CC   ""$$  % wvr)rNcB d |j}|j|||| |dkrQ|r|d z }n(|r|d|d z }n |j z } |}n||\}}} |r||ddn|jtj| d ftj }t||D]+\ } fd t| D| ddf<,|S) u"Moments of the gyration tensor. The moments are defined as the eigenvalues of the gyration tensor. .. math:: \mathsf{T} = \frac{1}{N} \sum_{i=1}^{N} (\mathbf{r}_\mathrm{i} - \mathbf{r}_\mathrm{COM})(\mathbf{r}_\mathrm{i} - \mathbf{r}_\mathrm{COM}) Where :math:`\mathbf{r}_\mathrm{COM}` is the center of mass. See [Dima2004a]_ for background information. Parameters ---------- wrap : bool, optional If ``True``, move all atoms within the primary unit cell before calculation. [``False``] unwrap : bool, optional If ``True``, compounds will be unwrapped before computing their centers. compound : {'group', 'segments', 'residues', 'molecules', 'fragments'}, optional Which type of component to keep together during unwrapping. Returns ------- principle_moments_of_gyration : numpy.ndarray Gyration vector(s) of (compounds of) the group in :math:`Å^2`. If `compound` was set to ``'group'``, the output will be a single vector of length 3. Otherwise, the output will be a 2D array of shape ``(n,3)`` where ``n`` is the number of compounds. .. versionadded:: 2.5.0 c t|jdkrtj|}tjd|tjd||}tj|tj|z S)Nr ki,kj->ijij,i->ij)r$shapersqueezerJlinalgeigvalshry)rLrtensors r' _gyrationz*Masses.gyration_moments.._gyrationess6<  1$$F++Y *mV<<F 9%%frvf~~&=>> >r)r9r.Fr<Nr=r- referencer-rZr=rArcxg|]6\}}||z |dddf7Srr|)r&rLmaskrXrB compound_maskcoordsrs r'r(z+Masses.gyration_moments..se...  4 It s='9!'<<t QQQW-...r)) rBrr1r>r.r?_split_by_compound_indicesrr!r@rrG)r.r,r.r-rArLeig_vals atom_maskscompound_masks n_compounds atom_maskrXrBr^r_rs @@@@@r'gyration_momentszMasses.gyration_moments=sP ? ? ?K !&&fx'   w   : ) 7 7 7 F F L  :$$ %!)"&%   !* 3c 9  y77HH44X>> 6Z -"))%u*#,xa 0 CCCH,/ ,K,K  ( y........ $-Y#7#7 ...)**r)rfc|j}||||}t|jdkr[dt j|t j|dz dzt jt j|ddz }nTdt j|t j|z zt jt j|dz }|S)aShape parameter. See [Dima2004a]_ for background information. Parameters ---------- wrap : bool, optional If ``True``, move all atoms within the primary unit cell before calculation. [``False``] unwrap : bool, optional If ``True``, compounds will be unwrapped before computing their centers. compound : {'group', 'segments', 'residues', 'molecules', 'fragments'}, optional Which type of component to keep together during unwrapping. .. versionadded:: 0.7.7 .. versionchanged:: 0.8 Added `pbc` keyword .. versionchanged:: 2.1.0 Renamed `pbc` kwarg to `wrap`. `pbc` is still accepted but is deprecated and will be removed in version 3.0. Superfluous kwargs were removed. .. versionchanged:: 2.5.0 Added calculation for any `compound` type r9rg;@r:rA) rBrfr$rSrprodmeanpowerryr.r,r.r-rArarSs r'shape_parameterzMasses.shape_parameters:K --fx.   x~   " "'(RWXA%>%>%>>QGGGH(26(333Q778 E'(RWX%6%66778(26(++Q//0   r)rlc|j}||||}t|jdkrNdt j|t j|dz dzdt j|ddzz z}nGdt j|t j|z dzt j|dzz z}|S)aAsphericity. See [Dima2004b]_ for background information. Parameters ---------- wrap : bool, optional If ``True``, move all atoms within the primary unit cell before calculation. [``False``] unwrap : bool, optional If ``True``, compounds will be unwrapped before computing their centers. compound : {'group', 'segments', 'residues', 'molecules', 'fragments'}, optional Which type of component to keep together during unwrapping. .. versionadded:: 0.7.7 .. versionchanged:: 0.8 Added `pbc` keyword .. versionchanged:: 0.20.0 Added *unwrap* and *compound* parameter .. versionchanged:: 2.1.0 Renamed `pbc` kwarg to `wrap`. `pbc` is still accepted but is deprecated and will be removed in version 3.0. .. versionchanged:: 2.5.0 Added calculation for any `compound` type r9rg?r:r)rBrfr$rSrryrirks r' asphericityzMasses.asphericitys>K --fx.   x~   " "278!#<#<#<<BKKK&***a/0EE 278#4#44:;;&""a'(E  r)rncb|j}tj||\}}tj|ddd}|dd|fj}tjtj|d|d|ddkr|dz}|S)aCalculate the principal axes from the moment of inertia. e1,e2,e3 = AtomGroup.principal_axes() The eigenvectors are sorted by eigenvalue, i.e. the first one corresponds to the highest eigenvalue and is thus the first principal axes. The eigenvectors form a right-handed coordinate system. Parameters ---------- wrap : bool, optional If ``True``, move all atoms within the primary unit cell before calculation. [``False``] Returns ------- axis_vectors : array 3 x 3 array with ``v[0]`` as first, ``v[1]`` as second, and ``v[2]`` as third eigenvector. .. versionchanged:: 0.8 Added `pbc` keyword .. versionchanged:: 1.0.0 Always return principal axes in right-hand convention. .. versionchanged:: 2.1.0 Renamed `pbc` kwarg to `wrap`. `pbc` is still accepted but is deprecated and will be removed in version 3.0. rGNrrr) rBrrUeigrEargsortTdotcross)r.r,rAe_vale_vecrs r'principal_axeszMasses.principal_axessFK y}}Y%@%@d%@%K%KLL u*U##DDbD)aaaj!# 6"(58U1X..a 9 9A = = RKE r)rxc||}tjtj||}t j||}|||S)aAlign principal axis with index `axis` with `vector`. Parameters ---------- axis : {0, 1, 2} Index of the principal axis (0, 1, or 2), as produced by :meth:`~principal_axes`. vector : array_like Vector to align principal axis with. Notes ----- To align the long axis of a channel (the first principal axis, i.e. *axis* = 0) with the z-axis:: u.atoms.align_principal_axis(0, [0,0,1]) u.atoms.write("aligned.pdb") )rxrdegreesrangler rotaxisrotateby)r.r;vectorpr{axs r'align_principal_axiszMasses.align_principal_axis6s]&  " "4 ( 7=F3344  $Q / /~~eR(((r)rNFFr.r.r)*r4rrr,r5rrrrrrrrrrrrrrgr@rrrrrrrr rrr r1rrHr7rErNrfrlrnrxrr|r)r'rrsHHJ&  N+d##K JEH-I\      D D D \D L !!#3^"DEEE====@ !!<"<===fff\fP !!#68I"JKKK"""\"H !!#79K"LMMM[[[\[z !!#57G"HIII+++\+Z !!#4o"FGGG***\*X !!=+">???,,,\,\ !!#3^"DEEE)))4 !! !56r)rceZdZdZdZdZeeee e e gZ e eZeZedZdZdZeeeedd Zeed efeedd Zeed efeee ddZeedefdZeedefeee ddZ eede fdZ!eede!fdS)ChargeschargeschargerCc*tj|Srrr:s r'rzCharges._gen_initial_valueserr)c|jj|j}t |jt jr-|jt| }nXtj t|}t|D]'\}}|j| ||<(|Srr)rWrrrrLr"s r'rzCharges.get_residuesis8;0077 bfg. / / 4k%//26688GGhs2ww''G#H-- 4 43![-1133 r)c(jj|j}t |jt jr-jt| }n tj fd|D}|S)NcNg|]!}j|"Sr|r%r&s r'r(z(Charges.get_segments..}s,KKK3 C 0 4 4 6 6KKKr)r')rWrr(rs` r'rzCharges.get_segmentsus8;0077 bfg. / / Mk%//26688GGhKKKK(KKKLLGr)Fr.cp|j}||j|||S)a Center of (absolute) charge of (compounds of) the group .. math:: \boldsymbol R = \frac{\sum_i \vert q_i \vert \boldsymbol r_i} {\sum_i \vert q_i \vert} where :math:`q_i` is the charge and :math:`\boldsymbol r_i` the position of atom :math:`i` in the given :class:`MDAnalysis.core.groups.AtomGroup`. Centers of charge per :class:`Residue`, :class:`Segment`, molecule, or fragment can be obtained by setting the `compound` parameter accordingly. If the charges of a compound sum up to zero, the center of mass coordinates of that compound will be ``nan`` (not a number). Parameters ---------- wrap : bool, optional If ``True`` and `compound` is ``'group'``, move all atoms to the primary unit cell before calculation. If ``True`` and `compound` is not ``group``, the centers of mass of each compound will be calculated without moving any atoms to keep the compounds intact. Instead, the resulting center-of-mass position vectors will be moved to the primary unit cell after calculation. unwrap : bool, optional If ``True``, compounds will be unwrapped before computing their centers. compound : {'group', 'segments', 'residues', 'molecules', \ 'fragments'}, optional If ``'group'``, the center of mass of all atoms in the group will be returned as a single position vector. Otherwise, the centers of mass of each :class:`Segment`, :class:`Residue`, molecule, or fragment will be returned as an array of position vectors, i.e. a 2d array. Note that, in any case, *only* the positions of :class:`Atoms` *belonging to the group* will be taken into account. Returns ------- center : numpy.ndarray Position vector(s) of the center(s) of charge of the group. If `compound` was set to ``'group'``, the output will be a single position vector. If `compound` was set to ``'segments'`` or ``'residues'``, the output will be a 2d coordinate array of shape ``(n, 3)`` where ``n`` is the number of compounds. Note ---- This method can only be accessed if the underlying topology has information about atomic charges. .. versionadded:: 2.2.0 r*)rBr/r__abs__r0s r'center_of_chargezCharges.center_of_chargesAz ||M))++    r)rc0|d|S)aTotal charge of (compounds of) the group. Computes the total charge of :class:`Atoms` in the group. Total charges per :class:`Residue`, :class:`Segment`, molecule, or fragment can be obtained by setting the `compound` parameter accordingly. Parameters ---------- compound : {'group', 'segments', 'residues', 'molecules', 'fragments'},\ optional If 'group', the total charge of all atoms in the group will be returned as a single value. Otherwise, the total charges per :class:`Segment`, :class:`Residue`, molecule, or fragment will be returned as a 1d array. Note that, in any case, *only* the charges of :class:`Atoms` *belonging to the group* will be taken into account. Returns ------- float or numpy.ndarray Total charge of (compounds of) the group. If `compound` was set to ``'group'``, the output will be a single value. Otherwise, the output will be a 1d array of shape ``(n,)`` where ``n`` is the number of compounds. .. versionchanged:: 0.20.0 Added `compound` parameter rr3r4r6s r' total_chargezCharges.total_charges@ H===r)rrc p|}|j}|j}|dkr |j}||||}n6|dkr||||}nddg} t d|d|dkro|r|d|z } n(|r|d|d |z } n |j |z } tj d | |d d tj f} n| |\} } }|r||d d }n|j }|j}tj|d ftj} t!| | D]M\}}tj d||||d d d d d fz ||d d d d d f| |<N| S)u Dipole vector of the group. .. math:: \boldsymbol{\mu} = \sum_{i=1}^{N} q_{i} ( \mathbf{r}_{i} - \mathbf{r}_{COM} ) Computes the dipole vector of :class:`Atoms` in the group. Dipole vector per :class:`Residue`, :class:`Segment`, molecule, or fragment can be obtained by setting the `compound` parameter accordingly. Note that the magnitude of the dipole moment is independent of the ``center`` chosen unless the species has a net charge. In the case of a charged group the dipole moment can be later adjusted with: .. math:: \boldsymbol{\mu}_{COC} = \boldsymbol{\mu}_{COM} + q_{ag}\mathbf{r}_{COM} - q_{ag}\boldsymbol{r}_{COC} Where :math:`\mathbf{r}_{COM}` is the center of mass and :math:`\mathbf{r}_{COC}` is the center of charge. Parameters ---------- wrap : bool, optional If ``True`` and `compound` is ``'group'``, move all atoms to the primary unit cell before calculation. If ``True`` and `compound` is not ``group``, the centers of mass of each compound will be calculated without moving any atoms to keep the compounds intact. unwrap : bool, optional If ``True``, compounds will be unwrapped before computing their centers. compound : {'group', 'segments', 'residues', 'molecules', \ 'fragments'}, optional If ``'group'``, a single dipole vector returns. Otherwise, an array of each :class:`Segment`, :class:`Residue`, molecule, or fragment will be returned as an array of position vectors, i.e. a 2d array. Note that, in any case, *only* the positions of :class:`Atoms` *belonging to the group* will be taken into account. center : {'mass', 'charge'}, optional Choose whether the dipole vector is calculated at the center of "mass" or the center of "charge", default is "mass". Returns ------- numpy.ndarray Dipole vector(s) of (compounds of) the group in :math:`eÅ`. If `compound` was set to ``'group'``, the output will be a single value. Otherwise, the output will be a 1d array of shape ``(n,3)`` where ``n`` is the number of compounds. .. versionadded:: 2.4.0 rr9rzThe dipole center, ,, is not supported. Choose one of: {choices}r.Fr<NrYzij,ij->jr[rArz ijk,ijk->ik)rrBrrr1rr1r>r.r?rrJnewaxisr`r!r@r)r.r,r.r-r/rArrrefchoicesrL dipole_vectorrbrcrdr_chgsr^res r'rzCharges.dipole_vectorsZ@>>##K # V  %F**&8+CCx  ,,&8-CCx(G%f%%%  w   : ) 7 7 7 F F L  :$$ %!)"&%   !* 3c 9 IM7111bj=+AMM 44X>> 6Z -"))%u*#,$DHk1%5RZHHHM,/ ,K,K  ( y/1y!I&]);AAAtQQQJ)GGOAAAqqq$J/00 m,, r)rc |j}|jdi|}t|jdkr)t jt jd||}n(t jt jd||}|S)uDipole moment of the group or compounds in a group. .. math:: \mu = |\boldsymbol{\mu}| = \sqrt{ \sum_{i=1}^{D} \mu^2 } Where :math:`D` is the number of dimensions, in this case 3. Computes the dipole moment of :class:`Atoms` in the group. Dipole per :class:`Residue`, :class:`Segment`, molecule, or fragment can be obtained by setting the `compound` parameter accordingly. Note that when there is a net charge, the magnitude of the dipole moment is dependent on the `center` chosen. See :meth:`~dipole_vector`. Parameters ---------- wrap : bool, optional If ``True`` and `compound` is ``'group'``, move all atoms to the primary unit cell before calculation. If ``True`` and `compound` is not ``group``, the centers of mass of each compound will be calculated without moving any atoms to keep the compounds intact. unwrap : bool, optional If ``True``, compounds will be unwrapped before computing their centers. compound : {'group', 'segments', 'residues', 'molecules', \ 'fragments'}, optional If ``'group'``, a single dipole vector returns. Otherwise, an array of each :class:`Segment`, :class:`Residue`, molecule, or fragment will be returned as an array of position vectors, i.e. a 2d array. Note that, in any case, *only* the positions of :class:`Atoms` *belonging to the group* will be taken into account. center : {'mass', 'charge'}, optional Choose whether the dipole vector is calculated at the center of "mass" or the center of "charge", default is "mass". Returns ------- numpy.ndarray Dipole moment(s) of (compounds of) the group in :math:`eÅ`. If `compound` was set to ``'group'``, the output will be a single value. Otherwise, the output will be a 1d array of shape ``(n,)`` where ``n`` is the number of compounds. .. versionadded:: 2.4.0 rrIrHr|)rBrr$rSrrKrJ)r.rYrAr dipole_moments r'rzCharges.dipole_momentk sjK / /99&99 }" # #a ' 'G *m]CCMMG '=-@@Mr)rcd|}|j}|j}|dkr |j}||||n6|dkr||||nddg}t d|d|dkrQ|r|d z } n(|r|d|d z } n |j z } | |} n| |\} } } |r||d d n|j |jtj | d d ftj } t| | D].\}fdt|D| d d d d f</| S)u Traceless quadrupole tensor of the group or compounds. This tensor is first computed as the outer product of vectors from a reference point to some atom, and multiplied by the atomic charge. The tensor of each atom is then summed to produce the quadrupole tensor of the group: .. math:: \mathsf{Q} = \sum_{i=1}^{N} q_{i} ( \mathbf{r}_{i} - \mathbf{r}_{COM} ) \otimes ( \mathbf{r}_{i} - \mathbf{r}_{COM} ) The traceless quadrupole tensor, :math:`\hat{\mathsf{Q}}`, is then taken from: .. math:: \hat{\mathsf{Q}} = \frac{3}{2} \mathsf{Q} - \frac{1}{2} tr(\mathsf{Q}) Computes the quadrupole tensor of :class:`Atoms` in the group. Tensor per :class:`Residue`, :class:`Segment`, molecule, or fragment can be obtained by setting the `compound` parameter accordingly. Note that when there is an unsymmetrical plane in the molecule or group, the magnitude of the quadrupole tensor is dependent on the ``center`` (e.g., :math:`\mathbf{r}_{COM}`) chosen and cannot be translated. Parameters ---------- wrap : bool, optional If ``True`` and `compound` is ``'group'``, move all atoms to the primary unit cell before calculation. If ``True`` and `compound` is not ``group``, the centers of mass of each compound will be calculated without moving any atoms to keep the compounds intact. unwrap : bool, optional If ``True``, compounds will be unwrapped before computing their centers. compound : {'group', 'segments', 'residues', 'molecules', \ 'fragments'}, optional If ``'group'``, a single quadrupole value returns. Otherwise, an array of each :class:`Segment`, :class:`Residue`, molecule, or fragment will be returned as an array of position vectors, i.e. a 1d array. Note that, in any case, *only* the positions of :class:`Atoms` *belonging to the group* will be taken into account. center : {'mass', 'charge'}, optional Choose whether the dipole vector is calculated at the center of "mass" or the center of "charge", default is "mass". Returns ------- numpy.ndarray Quadrupole tensor(s) of (compounds of) the group in :math:`eÅ^2`. If `compound` was set to ``'group'``, the output will be a single tensor of shape ``(3,3)``. Otherwise, the output will be a 1d array of shape ``(n,3,3)`` where ``n`` is the number of compounds. .. versionadded:: 2.4.0 c t|jdkrtj|}tjd|tjd||}d|zdz tjdtj|zdz z S)z)Calculate the traceless quadrupole tensorrrQrRrAr)r$rSrrTrJidentitytrace)rLrrWs r'__quadrupole_tensorz6Charges.quadrupole_tensor..__quadrupole_tensor s7=!!A%%*W--Y *mW==F v:>BKNNRXf5E5E$E$II Ir)rr9rzThe quadrupole center, rr.Fr<NrYr[rArcxg|]6\}}||z |dddf7Srr|)r&rLr]_Charges__quadrupole_tensorrr^r_rs r'r(z-Charges.quadrupole_tensor..4 sf444  4 ('t s='9!'<<T 111d7+444r))rrBrrr1rr1r>r.r?r`rr!r@rrG)r.r,r.r-r/rArrrrL quad_tensorrbrcrdrerrr^r_rs @@@@@r'quadrupole_tensorzCharges.quadrupole_tensor s`J J J J>>##K # V  %F**&8+CCx  ,,&8-CCx(G%&%%%  w   : ) 7 7 7 F F L  :$$ %!)"&%   !* 3c 9 --mWEEKK44X>> 6Z -"))%u*#,$D(KA#6bjIIIK,/ ,K,K  ( y44444444 $-Y#7#7 444 M111aaa/00r)rc |j}d|jdi|}t|jdkr |}n t jfd|D}|S)uH Quadrupole moment of the group according to :footcite:p:`Gray1984`. .. math:: Q = \sqrt{\frac{2}{3}{\hat{\mathsf{Q}}}:{\hat{\mathsf{Q}}}} where the quadrupole moment is calculated from the tensor double contraction of the traceless quadropole tensor :math:`\hat{\mathsf{Q}}` Computes the quadrupole moment of :class:`Atoms` in the group. Quadrupole per :class:`Residue`, :class:`Segment`, molecule, or fragment can be obtained by setting the `compound` parameter accordingly. Note that when there is an unsymmetrical plane in the molecule or group, the magnitude of the quadrupole moment is dependant on the ``center`` chosen and cannot be translated. Parameters ---------- wrap : bool, optional If ``True`` and `compound` is ``'group'``, move all atoms to the primary unit cell before calculation. If ``True`` and `compound` is not ``group``, the centers of mass of each compound will be calculated without moving any atoms to keep the compounds intact. unwrap : bool, optional If ``True``, compounds will be unwrapped before computing their centers. compound : {'group', 'segments', 'residues', 'molecules', \ 'fragments'}, optional If ``'group'``, a single quadrupole value returns. Otherwise, an array of each :class:`Segment`, :class:`Residue`, molecule, or fragment will be returned as an array of position vectors, i.e. a 1d array. Note that, in any case, *only* the positions of :class:`Atoms` *belonging to the group* will be taken into account. center : {'mass', 'charge'}, optional Choose whether the dipole vector is calculated at the center of "mass" or the center of "charge", default is "mass". Returns ------- numpy.ndarray Quadrupole moment(s) of (compounds of) the group in :math:`eÅ^2`. If `compound` was set to ``'group'``, the output will be a single value. Otherwise, the output will be a 1d array of shape ``(n,)`` where ``n`` is the number of compounds. .. versionadded:: 2.4.0 c\tjdtj||zdz S)NrrA)rrK tensordot)rWs r'__quadrupole_momentz6Charges.quadrupole_moment..__quadrupole_momentx s(71r|FF;;;a?@@ @r)rc&g|] }|Sr|r|)r&x_Charges__quadrupole_moments r'r(z-Charges.quadrupole_moment.. s%===A$$Q''===r)r|)rBrr$rSrr)r.rYrAr quad_momentrs @r'quadrupole_momentzCharges.quadrupole_moment@ slK  A A A2i1;;F;; { ! !Q & &--k::KK(=======Kr)rNrr)FFr.r)"r4rrr,r5rrrrrrrrrrrgrrrrrrr rrr rrrHrrrrrr|r)r'rrVsVHHJ  N+d##K E\      ? ? ? \? B !!#57G"HIII>>>>@ !!><"@AAABHxxx\xt !!?M"BCCCBBBH !!?M"BCCCBHHHH\HT !!#68I"JKKKDDDL !!#68I"JKKKKKr)rc8eZdZdZdZdZdZeZe dZ dS) FormalChargeszFormal charge on each atom formalcharges formalchargerCc*tj|Srrr:s r'rz!FormalCharges._gen_initial_values rr)Nr?r|r)r'rr sG$$HHJ E\r)rc4eZdZdZdZdZeZedZ dS) Occupancies occupancies occupancyrCc*tj|Srrr:s r'rzOccupancies._gen_initial_values rr)N) r4rrr,r5rrrrrr|r)r'rr sAHHJ E\r)rc8eZdZdZdZdZdZeZe dZ dS)AltLocszAltLocs for each atomaltLocsaltLocrCcftjdt|DtS)Ncg|]}dSrr|rs r'r(z/AltLocs._gen_initial_values.. rr)rrr:s r'rzAltLocs._gen_initial_values rr)Nrr|r)r'rr sGHHJ E??\???r)rc8eZdZdZdZdZdZeZe dZ dS) GBScreensz!Generalized Born screening factor gbscreensgbscreenrCc*tj|Srrr:s r'rzGBScreens._gen_initial_values rr)Nrr|r)r'rr sG++HHJ E\r)rc8eZdZdZdZdZdZeZe dZ dS) SolventRadiizIntrinsic solvation radius solventradii solventradiusrCc*tj|Srrr:s r'rz SolventRadii._gen_initial_values rr)Nrr|r)r'rr sG$$HHJ E\r)rc8eZdZdZdZdZdZeZe dZ dS)NonbondedIndiceszNonbonded index (AMBER) nbindicesnbindexrCcBtj|tjSr)rrint32r:s r'rz$NonbondedIndices._gen_initial_values sx"(++++r)Nr?r|r)r'rr sG!!HHJ E,,\,,,r)rc8eZdZdZdZdZdZeZe dZ dS)RMinszThe Rmin/2 LJ parameterrminsrminrCc*tj|Srrr:s r'rzRMins._gen_initial_values rr)Nrr|r)r'rr sG!!HHJ E\r)rc8eZdZdZdZdZdZeZe dZ dS)EpsilonszThe epsilon LJ parameterepsilonsepsilonrCc*tj|Srrr:s r'rzEpsilons._gen_initial_values rr)Nrr|r)r'rr sG""HHJ E\r)rc8eZdZdZdZdZdZeZe dZ dS)RMin14sz,The Rmin/2 LJ parameter for 1-4 interactionsrmin14srmin14rCc*tj|Srrr:s r'rzRMin14s._gen_initial_values rr)Nrr|r)r'rr sG66HHJ E\r)rc8eZdZdZdZdZdZeZe dZ dS) Epsilon14sz-The epsilon LJ parameter for 1-4 interactions epsilon14s epsilon14rCc*tj|Srrr:s r'rzEpsilon14s._gen_initial_values rr)Nrr|r)r'rr sG77HHJ E\r)rc8eZdZdZdZdZdZeZe dZ dS) Aromaticities Aromaticity aromaticities aromaticityrCc8tj|tSr)rrboolr:s r'rz!Aromaticities._gen_initial_values sx$''''r)N) r4rrr^r,r5rrrrrr|r)r'rr sGHHJ E((\(((r)rceZdZdZdZdZdZdS) RSChiralityz R/S chirality chiralities chiralityU1N)r4rrr^r,r5rr|r)r'rr s#HH EEEr)rc\eZdZdZdZeeeee gZ dZ dZ dZ dZedZdZd Zd S) rJ residueattrs residueattrrEcd|jj|j}|j|Sr)rrrrr&)rWrrs r'rzResidueAttr.get_atoms& (hk((//{3r)c"t||rr-rs r'rzResidueAttr.set_atoms* r.r)c&|j|jSrrrs r'rzResidueAttr.get_residues- rr)c$||j|j<dSrrrs r'rzResidueAttr.set_residues0 r!r)chjj|j}fd|DS)zBy default, the values for each residue present in the set of segments are returned in a single array. This behavior can be overriden in child attributes. c*g|]}j|Sr|r%)r&rrWs r'r(z,ResidueAttr.get_segments..; r)r))rrrr)rWrrixss` r'rzResidueAttr.get_segments4 s8 x{//661111D1111r)c"t||rr-rs r'rzResidueAttr.set_segments= r.r)N)r4rrr,r5rrrrrrrrrrr?rrrr|r)r'rJrJ sHH|T7KNJ   ***"""$$]$222*****r)rJc:eZdZedZedZdS)ResidueStringAttrc.|||SrrXrs r'rzResidueStringAttr.set_residuesD rYr)c:tj|dtSr[r\r:s r'rz%ResidueStringAttr._gen_initial_valuesH r^r)N)r4rrr?rrrr|r)r'rrC r_r)rc4eZdZdZdZdZeZedZ dS)Residsz Residue IDrruc2tjd|dzSr7r8r:s r'rzResids._gen_initial_valuesU r>r)N) r4rrr^r,r5rrrrr|r)r'rrN sBHH E$$\$$$r)rceZdZdZdZeeZeZ e dZ dZ ee de fdS)Resnamesresnamesresnamecftjdt|DtS)Ncg|]}dSrr|rs r'r(z0Resnames._gen_initial_values..c rr)rrr:s r'rzResnames._gen_initial_valuesa rr)c tsd}t|d}|dd}||vr6td|d| dd|jjD}n-#t$r }d |j d }t|d d }~wwxYw|d kr|Stj |}|d kr|Stj j |fi|S)a Returns the amino acid sequence. The format of the sequence is selected with the keyword *format*: ============== ============================================ *format* description ============== ============================================ 'SeqRecord' :class:`Bio.SeqRecord.SeqRecord` (default) 'Seq' :class:`Bio.Seq.Seq` 'string' string ============== ============================================ The sequence is returned by default (keyword ``format = 'SeqRecord'``) as a :class:`Bio.SeqRecord.SeqRecord` instance, which can then be further processed. In this case, all keyword arguments (such as the *id* string or the *name* or the *description*) are directly passed to :class:`Bio.SeqRecord.SeqRecord`. If the keyword *format* is set to ``'Seq'``, all *kwargs* are ignored and a :class:`Bio.Seq.Seq` instance is returned. The difference to the record is that the record also contains metadata and can be directly used as an input for other functions in :mod:`Bio`. If the keyword *format* is set to ``'string'``, all *kwargs* are ignored and a Python string is returned. .. rubric:: Example: Write FASTA file Use :func:`Bio.SeqIO.write`, which takes sequence records:: import Bio.SeqIO # get the sequence record of a protein component of a Universe protein = u.select_atoms("protein") record = protein.sequence(id="myseq1", name="myprotein") Bio.SeqIO.write(record, "single.fasta", "fasta") A FASTA file with multiple entries can be written with :: Bio.SeqIO.write([record1, record2, ...], "multi.fasta", "fasta") Parameters ---------- format : string, optional - ``"string"``: return sequence as a string of 1-letter codes - ``"Seq"``: return a :class:`Bio.Seq.Seq` instance - ``"SeqRecord"``: return a :class:`Bio.SeqRecord.SeqRecord` instance Default is ``"SeqRecord"`` id : optional Sequence ID for SeqRecord (should be different for different sequences) name : optional Name of the protein. description : optional Short description of the sequence. kwargs : optional Any other keyword arguments that are understood by class:`Bio.SeqRecord.SeqRecord`. Raises ------ :exc:`ValueError` if a residue name cannot be converted to a 1-letter IUPAC protein amino acid code; make sure to only select protein residues. :exc:`TypeError` if an unknown *format* is selected. :exc:`ImportError` is the Biopython package is not available. .. versionadded:: 0.9.0 .. versionchanged:: 2.7.0 Biopython is now an optional dependency zThe `sequence_alignment` method requires an installation of `Biopython`. Please install `Biopython` to use this method: https://biopython.org/wiki/Download)stringSeq SeqRecordr2rz)Unknown format='{0}': must be one of: {1}, rc,g|]}t|Sr|)r)r&rs r'r(z%Resnames.sequence.. s DDD##DDDr)z#AtomGroup contains a residue name 'z7' that does not have a IUPAC protein 1-letter characterNrr) HAS_BIOPYTHON ImportErrorpop TypeErrorr2joinrDrrrZr1Biorr)rWrYerrmsgformatsr2sequenceerrseqs r'rzResnames.sequencee sR\ &6  f%% %0Hk22  ;BBDIIg..  /wwDDT]-CDDDHH / / /EckEEE V$$$ .  / X  Ogkk(## U??J}&s55f555s,)B C B;;CrN)r4rrr,r5rrrgrIrrrrrrHr|r)r'rr[ szHH+d##K E??\?o6o6o6b $$j(%;<<<<r)N) r4rrr,r5rrrrr|r)r'rr s<HH E$$\$$$r)rceZdZdZdZdZeZdS)ICodeszInsertion code for AtomsicodesicodeNr4rrr^r,r5rIrr|r)r'rr s#""HH EEEr)rceZdZdZdZdZeZdS)MoltypesznName of the molecule type Two molecules that share a molecule type share a common template topology. moltypesmoltypeNrr|r)r'r!r! s) HH EEEr)r!c(eZdZdZdZdZejZdS)MolnumszIndex of molecule from 0molnumsmolnumN) r4rrr^r,r5rintprr|r)r'r%r% s%""HH GEEEr)r%cbeZdZdZdZdZeeee e e gZ dZ dZdZdZdZd Zed Zd S) rKz"Base class for segment attributes. segmentattrs segmentattrrGcd|jj|j}|j|Sr)rrrrr&)rWrsixs r'rzSegmentAttr.get_atoms rr)c"t||rr-rs r'rzSegmentAttr.set_atoms r.r)cd|jj|j}|j|Sr)rrrrr&)rWrr-s r'rzSegmentAttr.get_residues s(hk++BE22{3r)c"t||rr-rs r'rzSegmentAttr.set_residues r.r)c&|j|jSrrrs r'rzSegmentAttr.get_segments rr)c$||j|j<dSrrrs r'rzSegmentAttr.set_segments" r!r)N)r4rrr^r,r5rrrrrrrrrrrrrr?rr|r)r'rKrK s,,HH  NJ   ***   ***"""$$]$$$r)rKc:eZdZedZedZdS)SegmentStringAttrc.|||SrrXrs r'rzSegmentStringAttr.set_segments* rYr)c:tj|dtSr[r\r:s r'rz%SegmentStringAttr._gen_initial_values. r^r)N)r4rrr?rrrr|r)r'r4r4) r_r)r4cFeZdZdZdZeeZeZ e dZ dS)Segidsrrtcftjdt|DtS)Ncg|]}dSrr|rs r'r(z.Segids._gen_initial_values..< rr)rrr:s r'rzSegids._gen_initial_values: rr)N) r4rrr,r5rrrgrIrrrr|r)r'r8r84 sKHH+d##K E??\???r)r8cFtjfd}|S)a Checks values passed to _Connection methods for: - appropriate number of atom indices - coerces them to tuples of ints (for hashing) - ensures that first value is less than last (reversibility & hashing) .. versionadded:: 1.0.0 c<tfd|Ds-tdjjg}|D]A}|d|dkr |ddd}|t |B|g|Ri|S)Nc3zK|]5}t|jkotd|DV6dS)c3XK|]%}t|ttjfV&dSr)r0rrinteger)r&ys r'rrzF_check_connection_values..wrapper...N s3@@Jq3 "344@@@@@@r)N)r$_n_atomsrx)r&rrWs r'rrz<_check_connection_values..wrapper..L sf   FFdm # A@@a@@@@@      r)z5{} must be an iterable of tuples with {} atom indicesrrp)rxr1r2r,rArHr )rWr&rXrYrvr:s` r'r;z)_check_connection_values..wrapperJ s          N& 66   # #Atae||dddG LLq " " " "tD%1$111&111r)r<r}s` r'_check_connection_valuesrC? s:_T22222& Nr)c"eZdZdZfdZxZS)_ConnectionTopologyAttrMetaz Specific metaclass for atom-connectivity topology attributes. This class adds an ``intra_{attrname}`` property to groups to return only the connections within the atoms in the group. c.t||||dXfd}t||}t |dd|j}|jtd|fdSdS)Nr,c2|dS)z*Get connections only within this AtomGroupF)outside)get_connections)rWrr,s r'intra_connectionz>_ConnectionTopologyAttrMeta.__init__..intra_connectionp s))(E)BBBr)intra_) superrrrrnr^rgrrH) r+rrrrJrapropr,r3s @r'rz$_ConnectionTopologyAttrMeta.__init__i s ui000==,,   C C C C C 0#66FFD$??D OI & - -/B/B/BD.I J J J J J r))r4rrr^r __classcell__)r3s@r'rErEa sK K K K K K K K K Kr)rEceZdZdZeddZdZdZee ddZ d Z d Z edd Z ed ZdS) _ConnectionzBase class for connectivity between atoms .. versionchanged:: 1.0.0 Added type checking to atom index values. NFc||_|dgt|z}||_|dvr|gt|z}||_|dgt|z}||_t |_dS)NTF)r&r$rrorderrC_cache)rWr&rrrSs r'rz_Connection.__init__ sz =FS[[(E m # #i#f++-G =FS[[(E ff r)c|tj|jtj|jtj|jtj|jS)r)r3rr&rrrSrs r'rz_Connection.copy sT~~ Idk " " Idj ! ! Idm $ $ Idj ! !    r)c*t|jSr)r$ _bondDictrs r'rz_Connection.__len__ s4>"""r)bdctt}t|j|j|j|jD]+\}}}}|D]!}||||||f",|S)z#Lazily built mapping of atoms:bonds)rrrr&rrrSrH)rWrXbtgoas r'rWz_Connection._bondDict s   KT]DJ   + +JAq!Q + +1 aAq\**** + r)c tdS)NzCannot set bond informationrrs r'rz_Connection.set_atoms s"#@AAAr)ct ttjfd|jD}n"#t$rj|j}YnwxYwt jt|t}t j |d\}}}}t j| t j }| }| }| }t||jjdd|||S)z Get connection values where the atom indices are in the given atomgroup. Parameters ---------- ag : AtomGroup c*g|]}j|Sr|)rW)r&r^rWs r'r(z)_Connection.get_atoms.. s !C!C!C$."3!C!C!Cr)rNrp)set itertoolschainrrrWrrsortedrIhsplitraveltolistrrrir5)rWr unique_bondsbond_idxrrrSs` r'rz_Connection.get_atoms s  1!C!C!C!CRU!C!C!CDLL 1 1 1>"%0LLL 1x| 4 4FCCC *,)L!*D*D'%%8HNN,,3355RXFFF --//  bk4="#5ugu   s,0AATc|tjd}|dvrtj|f}|tjd}t|j}t ||||D]s\}}}} ||vrh|j||j||j||j| t |j d=dS#t$rYdSwxYw)NrrRrX) rdcyclercr&rrHrrrSrTr) rWr&rrrSexistingrBr[r\r]s r' _add_bondsz_Connection._add_bonds s =OG,,E m # #owj11G =OG,,Et{##feWe<< % %JAq!Q   ""1%%% !!!$$$ $$Q''' !!!$$$  D!!!    DD s!C++ C98C9c t| t|j} |sV |z }dt t |}t d|j| fdt|jD}t|dD] }|j|= dD]Y}tj t||d }tj||} t||t!| Z |jd =d S#t$$rYd SwxYw) z) .. versionadded:: 1.0.0 r z@Cannot delete nonexistent {attrname} with atom indices:{indices})r,rc"g|] \}}|v | Sr|r|)r&rLrto_checks r'r(z-_Connection._delete_bonds.. s"EEETQqH}}q}}}r)T)reverse)rrrSrIrrXN)rcr&issubsetrmaprRr1r2r,rGrfrrrdeletermrrTr) rWr& self_valuesmissingridxrLr6arrnewrrs @r' _delete_bondsz_Connection._delete_bonds sc v;;$+&&   -- ,GiiC 1 122G &$-&AA  FEEEYt{33EEET***  A A2 + +D(74..h???C)C%%C D$S * * * *  D!!!    DD s)D33 EE)NFN)NTN)r4rrr^rCrrrrnrrWrrror|r|r)r'rPrPy s        ### VD\\  \X BBB   6(r)rPc eZdZdZdZdZeeZdZ dZ ee  de e dde jfdZedd d Zd Zed d dZdZee  de eddejfee  de eddejfee d e eddejfee de eddejfee de eddejfdS)BondszBonds between two atoms Must be initialised by a list of zero based tuples. These indices refer to the atom indices. E.g., ` [(0, 1), (1, 2), (2, 3)]` Also adds the `bonded_atoms`, `fragment` and `fragments` attributes. bondsrcNfdjD}jj|S)zAn :class:`~MDAnalysis.core.groups.AtomGroup` of all :class:`Atoms` bonded to this :class:`~MDAnalysis.core.groups.Atom`.cDg|]}|jSr|)partnerr)r&rZrWs r'r(z&Bonds.bonded_atoms.. s&999qyy$999r))rrirB)rWrys` r' bonded_atomszBonds.bonded_atoms s0:999dj999}"3''r)rNc:|jj|jjS)zThe index (ID) of the :class:`~MDAnalysis.core.topologyattrs.Bonds.fragment` this :class:`~MDAnalysis.core.groups.Atom` is part of. .. versionadded:: 0.20.0 )ri _fragdictrrs r' fragindexzBonds.fragindex s}&tw/22r) fragindicesT)universe_validationc~|jjtjfd|jDtjS)aThe :class:`fragment indices` of all :class:`Atoms` in this :class:`~MDAnalysis.core.groups.AtomGroup`. A :class:`numpy.ndarray` with :attr:`~numpy.ndarray.shape`\ ``=(``\ :attr:`~AtomGroup.n_atoms`\ ``,)`` and :attr:`~numpy.ndarray.dtype`\ ``=numpy.int64``. .. versionadded:: 0.20.0 c*g|]}|jSr|rr&r'fragdicts r'r(z%Bonds.fragindices..7 s ===c#)===r)r)rirrrrr(rWrs @r'rzBonds.fragindices( s==*x====TW===RWMMMMr)c:|jj|jjS)abAn :class:`~MDAnalysis.core.groups.AtomGroup` representing the fragment this :class:`~MDAnalysis.core.groups.Atom` is part of. A fragment is a :class:`group of atoms` which are interconnected by :class:`~MDAnalysis.core.topologyattrs.Bonds`, i.e., there exists a path along one or more :class:`~MDAnalysis.core.topologyattrs.Bonds` between any pair of :class:`Atoms` within a fragment. Thus, a fragment typically corresponds to a molecule. .. versionadded:: 0.9.0 )rirrfragmentrs r'rzBonds.fragment9 s}&tw/88r) fragmentsc|jjttt fd|jDdS)aRead-only :class:`tuple` of :class:`fragments`. Contains all fragments that any :class:`~MDAnalysis.core.groups.Atom` in this :class:`~MDAnalysis.core.groups.AtomGroup` is part of. A fragment is a :class:`group of atoms` which are interconnected by :class:`~MDAnalysis.core.topologyattrs.Bonds`, i.e., there exists a path along one or more :class:`~MDAnalysis.core.topologyattrs.Bonds` between any pair of :class:`Atoms` within a fragment. Thus, a fragment typically corresponds to a molecule. Note ---- * The contents of the fragments may extend beyond the contents of this :class:`~MDAnalysis.core.groups.AtomGroup`. .. versionadded:: 0.9.0 c32K|]}|jVdSr)rrs r'rrz"Bonds.fragments..f s*>>sHSM*>>>>>>r)c|djSr#r)rs r'z!Bonds.fragments..g s adgr))key)rirr rfrcrrs @r'rzBonds.fragmentsJ s[2=* >>>>dg>>>>>%%      r)cDtt|jS)aThe number of unique :class:`~MDAnalysis.core.topologyattrs.Bonds.fragments` the :class:`Atoms` of this :class:`~MDAnalysis.core.groups.AtomGroup` are part of. .. versionadded:: 0.20.0 )r$r rrs r' n_fragmentszBonds.n_fragmentsk s=!122333r)rrr)r4rrr^r,r5rrrgrArrrHrnrrrrrrrr|r)r'r~r~ s5HH+d##KH(((  H\4|/C D D 333 VMt444NN54N 999" VKT222  32 @ 4 4 4 XXhdH4DEEF hhy$i6GHHI !! hhy$i6GHHI !! dD+:MNNO !! dD+:MNNOr)r~c4eZdZdZdZdZeeZdZ dS) UreyBradleyszAngles between two atoms Initialise with a list of 2 long tuples These indices refer to the atom indices. .. versionadded:: 1.0.0 ureybradleysrN r4rrr^r,r5rrrgrAr|r)r'rr s8HH+d##KHHHr)rc4eZdZdZdZdZeeZdZ dS)AngleszAngles between three atoms Initialise with a list of 3 long tuples E.g., `[(0, 1, 2), (1, 2, 3), (2, 3, 4)]` These indices refer to the atom indices. anglesrANrr|r)r'rr s8HH+d##KHHHr)rc4eZdZdZdZdZeeZdZ dS) Dihedralsz*A connection between four sequential atoms dihedralsrbNrr|r)r'rr s244HH+d##KHHHr)rc4eZdZdZdZdZeeZdZ dS) Impropersz(An imaginary dihedral between four atoms impropersrbNrr|r)r'rr s222HH+d##KHHHr)rc4eZdZdZdZdZeeZdZ dS)CMapszE A connection between five atoms .. versionadded:: 1.0.0 cmapsNrr|r)r'rr s8 HH+d##KHHHr)r)nr^ collectionsrrr=rdrinspectrr_rxr\rrBio.Seqr Bio.SeqRecordr r numpyrlib.utilrrr r r r libr r exceptionsrrtopologyobjectsrrrgroupsrrrrrrrrrrrrr r?rQrcrurzr~rrrIrrrrrIr3rArVrarrrrrr rrrrrrrrrrrrrrrJrrrrrr!r%rKr4r8rCrErPr~rrrrrr|r)r'rs? 0"$##### 222222NNNMMMMM +*******44444444******                        KJJJJJJJJJEEEP222j777t(7(7(7ZVCVCVCVCVCVCVCVCrV1V1V1V1V16%6V1V1V1V1x:::::,:::D========D'P'P'P'P'P'P'P'PZ$*$*$*$*$*|$*$*$*P $ $ $ $ $h $ $ $[3[3[3[3[3[3[3[3@-----)8---QKQKQKQKQKQKQKQKj ? ? ? ? ?~ ? ? ?     H   55555.555&     ~   L L L L L (L L L ^T T T T T XT T T ppLpLpLpLpLhpLpLpLf     H   ( ? ? ? ? ?n ? ? ?             8    , , , , ,x , , ,     H        x        h            ( ( ( ( (H ( ( ((*****,***F-----,k--- $ $ $ $ $[ $ $ ${={={={={= {={={=~$$$$$k$$$  k"$"$"$"$"$,"$"$"$N-----,k---????? ???DKKKKK"3KKK0BBBBB(&ABBBBJJJJJJKJJJZ     ;        [          K     s9AA