RiI,dZddlZddlmZddlmZddlmZddlmZddl m Z Gdd eZ Gd d e Z Gd d e Z GddeZy)z9Half-sphere exposure and coordination number calculation.N)pi)AbstractPropertyMap) CaPPBuilder)is_aa)rotaxisc$eZdZdZddZdZdZy)_AbstractHSExposurezAbstract class to calculate Half-Sphere Exposure (HSE). The HSE can be calculated based on the CA-CB vector, or the pseudo CB-CA vector based on three consecutive CA atoms. This is done by two separate subclasses. Nc|dk\sJg|_t}|j|}i} g} g} |D]} tt | D]} | dk(rd}n| | dz }| | }| t | dz k(rd}n| | dz}|j |||}|K|\}}d}d}|dj }|D]}tt |D]}| |urt| |z |kr||}t|r|jds;|dj }||z }|j|ksg|j|tdz kr|dz }|dz }|j}|jj}|||f| ||f<| j||||ff| j||f||j |<||j |<|s||j |<t#j$|| | | y)aInitialize class. :param model: model :type model: L{Model} :param radius: HSE radius :type radius: float :param offset: number of flanking residues that are ignored in the calculation of the number of neighbors :type offset: int :param hse_up_key: key used to store HSEup in the entity.xtra attribute :type hse_up_key: string :param hse_down_key: key used to store HSEdown in the entity.xtra attribute :type hse_down_key: string :param angle_key: key used to store the angle between CA-CB and CA-pCB in the entity.xtra attribute :type angle_key: string rNCA) ca_cb_listrbuild_peptidesrangelen_get_cb get_vectorabsrhas_idnormanglerget_id get_parentappendxtrar__init__)selfmodelradiusoffset hse_up_key hse_down_key angle_keyppbpplhse_maphse_listhse_keyspp1ir1r2r3resultpcbrhse_uhse_dca2pp2jrocaodres_idchain_ids J/home/agent/.friday_env/lib/python3.12/site-packages/Bio/PDB/HSExposure.pyrz_AbstractHSExposure.__init__s6.{{m  '- /C3s8_, /6BQUBVC1 $BQUBb"b1># Uh))++C"3s8_ +#:#a!e**>$ V$Ry $$ h113#I668f, wws|rAv6 %  %  ++==?113/4eU.C6*+eUE%: ;<6 23&+ #(- %).BGGI&Y, /- /\ $$T7HhGctSN)NotImplemented)rr+r,r-s r:rz_AbstractHSExposure._get_cbjsr;c@ |dj}|dj}|dj}||z }||z }tt dzdz |}|j |}||z}|j j ||f|S#t$rYywxYw)zReturn a pseudo CB vector for a Gly residue (PRIVATE). The pseudoCB vector is centered at the origin. CB coord=N coord rotated over -120 degrees along the CA-C axis. NCr Ng^@gf@)r Exceptionrr left_multiplyrr)rresiduen_vc_vca_vrotcb_at_origin_vcb_vs r:_get_gly_cb_vectorz&_AbstractHSExposure._get_gly_cb_vectorms #,))+C#,))+C4=++-DDjDjrcEkE)3/**3/$ d|,  s9B BBr=)__name__ __module__ __qualname____doc__rrrKr;r:r r sMH^r;r c&eZdZdZddZdZddZy) HSExposureCAzmClass to calculate HSE based on the approximate CA-CB vectors. Uses three consecutive CA positions. c :tj||||dddy)zInitialize class. :param model: the model that contains the residues :type model: L{Model} :param radius: radius of the sphere (centred at the CA atom) :type radius: float :param offset: number of flanking residues that are ignored in the calculation of the number of neighbors :type offset: int EXP_HSE_A_U EXP_HSE_A_DEXP_CB_PCB_ANGLENr rrrrr s r:rzHSExposureCA.__init__s' $$        r;c||y |dj}|dj}|dj}||z }||z }|j|j||z} | j|jj || |zf|j dr=|dj} | |z } | j| j | } | | fS|jdk(r.|j|} | d} | | fS| j | } | | fSd} | | fS#t$rYywxYw)apCalculate approx CA-CB direction (PRIVATE). Calculate the approximate CA-CB direction for a central CA atom based on the two flanking CA positions, and the angle with the real CA-CB vector. The CA-CB vector is centered at the origin. :param r1, r2, r3: three consecutive residues :type r1, r2, r3: L{Residue} Nr CBGLY) rrB normalizerrrr get_resnamerK) rr+r,r-ca1r2ca3d1d3bcbcb_cars r:rzHSExposureCA._get_cbsY : T(%%'CT(%%'CT(%%'C3Y 3Y   G  QW~. 99T?D$$&BHE OO KKNE%x^^  &++B/E} %x  A%xE%x5  s9D44 E?Ec |jstjdtyt |d5}|j d|j d|j d|j d|j dd d d d d d d d d |jD]i\}}|j \}}}|j d |d d |d d |d d |j \}}}|j d |d d |d d |d d k|j d|j ddddy#1swYyxYw)zWrite PyMol script for visualization. Write a PyMol script that visualizes the pseudo CB-CA directions at the CA coordinates. :param filename: the name of the pymol script file :type filename: string zNothing to draw.Nwzfrom pymol.cgo import * zfrom pymol import cmd zobj=[ zBEGIN, LINES, zCOLOR, g?z.2fz, z, zVERTEX, zEND] zcmd.load_cgo(obj, 'HS') )rwarningswarnRuntimeWarningopenwrite get_array)rfilenamefpcardxyzs r:pcb_vectors_pymolzHSExposureCA.pcb_vectors_pymols< MM,n =  (C 2B HH0 1 HH. / HHY  HH& ' HHws3ir#c"SISA B// BB,,.1a8Ac7"QsG2aWC@A,,.1a8Ac7"QsG2aWC@A  B HHX  HH0 1 2 2 2s C=D::EN r)z hs_exp.py)rLrMrNrOrrrtrPr;r:rRrRs  .,\2r;rRceZdZdZddZdZy) HSExposureCBz7Class to calculate HSE based on the real CA-CB vectors.c8tj||||ddy)rT EXP_HSE_B_U EXP_HSE_B_DNrXrYs r:rzHSExposureCB.__init__s $$ %  r;c|jdk(r|j|dfS|jdr>|jdr-|dj}|dj}||z dfSy)zCalculate CB-CA vector (PRIVATE). :param r1, r2, r3: three consecutive residues (only r2 is used) :type r1, r2, r3: L{Residue} r\gr[r N)r^rKrr)rr+r,r-vcbvcas r:rzHSExposureCB._get_cbst >> u $**2.3 3yy299T?h))+h))+c C''r;Nru)rLrMrNrOrrrPr;r:rxrxsA " r;rxceZdZdZddZy) ExposureCNz:Residue exposure as number of CA atoms around its CA atom.c|dk\sJt}|j|}i}g}g}|D]} tt| D]} d} | | } t | r| j ds(| d} |D]h}tt|D]O}| |urt | |z |kr||}t |r|j ds;|d}|| z }||ksK| dz } Qj| j}| jj}| |||f<|j| | f|j||f| | jd<!tj||||y)a]Initialize class. A residue's exposure is defined as the number of CA atoms around that residue's CA atom. A dictionary is returned that uses a L{Residue} object as key, and the residue exposure as corresponding value. :param model: the model that contains the residues :type model: L{Model} :param radius: radius of the sphere (centred at the CA atom) :type radius: float :param offset: number of flanking residues that are ignored in the calculation of the number of neighbors :type offset: int rr r EXP_CNN) rrrrrrrrrrrrr)rrrr r$r%fs_mapfs_listfs_keysr)r*fsr+r_r3r4r,r2r7r8r9s r:rzExposureCN.__init__sz${{m  ' 'C3s8_ 'VRy $h $C"3s8_ $#:#a!e**>$ V$Ry $$ h#Iv:!GB $ $==?113-/&)*Bx(&12$&!1 ' '4 $$T67GDr;N)g(@r)rLrMrNrOrrPr;r:rrs D2Er;r)rOrhmathrBio.PDB.AbstractPropertyMaprBio.PDB.PolypeptiderrBio.PDB.vectorsrr rRrxrrPr;r:rsZ@;+%#r-rjc2&c2L!&!H5E$5Er;