ó °™xTc@ sddlmZddlZddlZddlZejjdƒZ ddl Tddl m Z d„Z d„Zd„Zd „Zd „Zd d „Zd efd„ƒYZdefd„ƒYZdefd„ƒYZdefd„ƒYZd„Zd„Zeeddd„ZdS(iÿÿÿÿ(tdivisionNtmmtbx_geometry_asa_ext(t*(taltlocc C sZtjdtd|jd||jjƒjƒ|d|ƒd|jdtjd|ƒƒS(Ntdatatcentretradiustindext coordinatestaltidtatom(Rt Descriptiontspheretxyztelementtstript capitalizet altid_for(RR t radius_fortprobe((s@/public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/mmtbx/geometry/asa.pytcreate_description s    cC sItjd|ƒ}tjd|ƒ}x|D]}|jd|ƒq+W|S(Ntfactorytindexert processor(RtIndexertInsertertaccept(Rt descriptionsRtinsertertd((s@/public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/mmtbx/geometry/asa.pytcreate_and_populate_indexers  cC stdtjd|ƒS(NRR(Rtindexingtlinear_spheres(R((s@/public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/mmtbx/geometry/asa.pytget_linear_indexer_for%s c s+td|ƒ‰td‡fd†d|ƒS(NRRc stjdˆddƒS(Nt voxelizertmargini(Rt hash_spheres((R"(s@/public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/mmtbx/geometry/asa.pyt1s(tget_voxelizer_forR(R((R"s@/public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/mmtbx/geometry/asa.pytget_hash_indexer_for-scC s td|ƒS(NR(R!(R((s@/public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/mmtbx/geometry/asa.pytget_optimal_indexer_for6sicC szg|D]}|jj^q}t|Œ\}}}t|ƒt|ƒt|ƒf}tjjjd|d|||fƒS(Ntbasetstep(Rtlowtziptmintmmtbxtgeometryt shared_typesR"(RR*Rtlowstlow_xstlow_ystlow_zsR+((s@/public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/mmtbx/geometry/asa.pyR&;s !tCompositeCheckerBuildercB seZdZd„ZRS(s# Finds neighbours for a sphere cC sƒtjd|ƒ}|jd|ƒtjƒ|_tjd|jƒ}x6|jD]+}|jj dtj d|d|ƒƒqPWdS(NRRtobjectt neighbourstranget predicate( Rt AggregatorRt accessibilitytpythagorean_checkertcheckertoverlap_equality_predicateRtrangestaddtfilter(tselfRt descriptionRtpredtr((s@/public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/mmtbx/geometry/asa.pyt__init__Ms (t__name__t __module__t__doc__RF(((s@/public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/mmtbx/geometry/asa.pyR5HstSeparateCheckerBuildercB s8eZdZd„Zd„Zd„Zed„ƒZRS(s# Finds neighbours for a sphere cC s5||_tjƒ|_i|_|jd|ƒdS(NR(RR;R<tregulartaltlocsR(RBRRC((s@/public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/mmtbx/geometry/asa.pyRF`s  c C sœ|jd|jjd|d|d|jƒxj|jjjƒD]V\}}tjƒ}|jd|d|d|d|ƒ|jƒr>||j|q>WdS(NRR RR=(tappend_neighboursRRKRLtitemsR;R<R7(RBRRt identifierRR=((s@/public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/mmtbx/geometry/asa.pytprocess_regularhs      c C su|jd|jjd|d|d|jƒtjƒ|j|<|jd|jj|d|d|d|j|ƒdS(NRR RR=(RMRRKR;R<RL(RBRRRO((s@/public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/mmtbx/geometry/asa.pytprocess_altloc~s    c C s>|jdtjd|jd|ƒdtjd|ƒƒƒdS(NR7R8RR9R6(R@R;RAtclose_toR>(RR RR=((s@/public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/mmtbx/geometry/asa.pyRMs  (RGRHRIRFRPRQt staticmethodRM(((s@/public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/mmtbx/geometry/asa.pyRJ[s    tAccessibleSurfaceResultcB s&eZdZd„Zed„ƒZRS(s Result of the calculation cC s||_||_dS(N(tcountt radius_sq(RBRURV((s@/public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/mmtbx/geometry/asa.pyRF s cC s|j|jS(N(RURV(RB((s@/public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/mmtbx/geometry/asa.pytsurface¦s(RGRHRIRFtpropertyRW(((s@/public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/mmtbx/geometry/asa.pyRT›s tAccessibleSurfaceAreascB s5eZdZd„Zed„ƒZed„ƒZRS(s( Result of a series of calculations cC s||_||_dS(N(tvaluestunit(RBRZR[((s@/public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/mmtbx/geometry/asa.pyRF±s cC sg|jD]}|j^q S(N(RZRU(RBtv((s@/public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/mmtbx/geometry/asa.pytpoints·scC s1ddlm}|j|jd„|jDƒƒS(Niÿÿÿÿ(tflexcs s|]}|jVqdS(N(RW(t.0R\((s@/public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/mmtbx/geometry/asa.pys Ás(tscitbx.array_familyR^R[tdoubleRZ(RBR^((s@/public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/mmtbx/geometry/asa.pytareas½s(RGRHRIRFRXR]Rb(((s@/public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/mmtbx/geometry/asa.pyRY¬s c C s‚td|d|ƒ}tjdtjd|jdtjd|jjd|jjƒƒd|j ƒ}t dt |ƒd |jj ƒS( s2 Calculates ASA by not worrying about altlocs RRCR8ttransformationRRR9RURV( R5R;RAt transformR]RcRRRR=RTtlenRV(RtsamplingRCtbuildert overlapped((s@/public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/mmtbx/geometry/asa.pytsimple_surface_calculationÅs       c C sÿtd|d|ƒ}tjdtjd|jdtjd|jjd|jjƒƒd|j ƒ}|j s{t |ƒ}nkg}xL|j j ƒD];}|j t g|D]}|d|ƒr§|^q§ƒƒq‘Wt|ƒt |ƒ}td |d |jjƒS( s² For atoms with altloc identifier, use empty altloc + atom with same altloc. For atoms with empty altloc, run a calculation for each know altloc and average the results. RRCR8RcRRR9tpointRURV(RJR;RARdR]RcRRRRKRLReRZtappendtsumRTRV( RRfRCRgt nonoverlappedRURZR=tp((s@/public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/mmtbx/geometry/asa.pytaltloc_averaged_calculationÜs"       9gffffffö?iÀc C sÑddlm}|jj}gt|ƒD]-\}}td|d|d|d|ƒ^q)} |d| ƒ} ddlm} | jd |ƒ} g| D]!} |d | d | d | ƒ^q”}t d |d| j ƒS(Niÿÿÿÿ(tvan_der_waals_radiiRR RRR(tsphere_surface_samplingRURRfRCRZR[( t cctbx.eltbxRptvdwttablet enumerateRtmmtbx.geometryRqt golden_spiralRYt unit_area(tatomst calculationtindexer_selectorRt precisionRpRtitaRRRqRfRRZ((s@/public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/mmtbx/geometry/asa.pyt calculates =+(t __future__Rtmmtbx.geometry.primitiveR.tmmtbx.geometry.shared_typest boost.pythontboosttpythont import_exttextRRvRRRR!R'R(R&R6R5RJRTRYRiRoR(((s@/public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/mmtbx/geometry/asa.pyts,       @  (