o RŀgI,@sdZddlZddlmZddlmZddlmZddlmZddl m Z Gdd d eZ Gd d d e Z Gd d d e Z GdddeZdS)z9Half-sphere exposure and coordination number calculation.N)pi)AbstractPropertyMap) CaPPBuilder)is_aa)rotaxisc@s*eZdZdZd ddZddZddZdS) _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. NcCs|dksJg|_t}||}i} g} g} |D]} tt| D]} | dkr*d}n| | d}| | }| t| dkr?d}n| | d}||||}|durQq!|\}}d}d}|d}|D]H}tt|D]?}| |urxt| ||krxqi||}t|r| dsqi|d}||}| |kr| |t dkr|d7}qi|d7}qiqa| }| }|||f| ||f<| ||||ff| ||f||j|<||j|<|r||j|<q!qt|| | | dS)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_idr7F/var/www/html/myenv/lib/python3.10/site-packages/Bio/PDB/HSExposure.pyrsd            -z_AbstractHSExposure.__init__cCstSN)NotImplemented)rr(r)r*r7r7r8rjsz_AbstractHSExposure._get_cbcCsz|d}|d}|d}Wn tyYdSw||}||}tt dd|}||}||}|j||f|S)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_multiplyr r)rresiduen_vc_vca_vrotcb_at_origin_vcb_vr7r7r8_get_gly_cb_vectorms    z&_AbstractHSExposure._get_gly_cb_vectorr9)__name__ __module__ __qualname____doc__rrrFr7r7r7r8rs  O rc@s,eZdZdZd ddZddZd d d Zd S) HSExposureCAzmClass to calculate HSE based on the approximate CA-CB vectors. Uses three consecutive CA positions. rc Cst||||ddddS)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_ANGLENrrrrrrr7r7r8rs zHSExposureCA.__init__c Cs|dus|dur dSz|d}|d}|d}Wn ty(YdSw||}||}||||} | |j|| |f|drg|d} | |} | | | } | | fS|dkr||} | dur|d} | | fS| | } | | fSd} | | fS)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) rr= normalizer rrr get_resnamerF) rr(r)r*ca1r/ca3d1d3bcbcb_carr7r7r8rs>         zHSExposureCA._get_cb hs_exp.pyc Cs|js tdtdSt|ds}|d|d|d|d|dd d d d d d d d d |jD]6\}}|\}}}|d |d d |d d |d d |\}}}|d |d d |d d |d d q:|d|dWddS1swYdS)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') )r warningswarnRuntimeWarningopenwrite get_array)rfilenamefpcar\xyzr7r7r8pcb_vectors_pymols"      $$&  "zHSExposureCA.pcb_vectors_pymolNrLr)r^)rGrHrIrJrrrlr7r7r7r8rKs  .rKc@s"eZdZdZd ddZddZdS) HSExposureCBz7Class to calculate HSE based on the real CA-CB vectors.rLrcCst||||dddS)rM EXP_HSE_B_U EXP_HSE_B_DNrQrRr7r7r8rs zHSExposureCB.__init__cCsV|dkr ||dfS|dr)|dr)|d}|d}||dfSdS)zCalculate CB-CA vector (PRIVATE). :param r1, r2, r3: three consecutive residues (only r2 is used) :type r1, r2, r3: L{Residue} rTgrSr N)rVrFrr)rr(r)r*vcbvcar7r7r8rs    zHSExposureCB._get_cbNrm)rGrHrIrJrrr7r7r7r8rns  rnc@seZdZdZdddZdS) ExposureCNz:Residue exposure as number of CA atoms around its CA atom.(@rcCs8|dksJt}||}i}g}g}|D]{} tt| D]r} d} | | } t| r/| ds0q| d} |D]6}tt|D]-}| |urMt| ||krMq>||}t|rZ|ds[q>|d}|| }||krk| d7} q>q6| }| }| |||f<| | | f| ||f| | j d<qqt ||||dS)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 rEXP_CNN) rr r rrrrrrrrrr)rrrrr!r"fs_mapfs_listfs_keysr&r'fsr(rWr0r1r)r/r4r5r6r7r7r8rsD     zExposureCN.__init__N)rtr)rGrHrIrJrr7r7r7r8rssrs)rJr`mathrBio.PDB.AbstractPropertyMaprBio.PDB.PolypeptiderrBio.PDB.vectorsrrrKrnrsr7r7r7r8s     uf$