B ‰°b?,ã@s„dZddlZddlmZddlmZddlmZmZddl m Z Gdd„deƒZ Gd d „d e ƒZ Gd d „d e ƒZ Gd d„deƒZdS)z9Half-sphere exposure and coordination number calculation.éN)Úpi)ÚAbstractPropertyMap)Ú CaPPBuilderÚis_aa)Úrotaxisc@s*eZdZdZd dd„Zdd„Zdd„ZdS) Ú_AbstractHSExposurezçAbstract 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. NcCsú|dks t‚g|_tƒ}| |¡}i} g} g} x´|D]ª} x¢tdt| ƒƒD]Ž} | dkrbd}n | | d}| | }| t| ƒdkrŒd}n | | d}| |||¡}|dkr°qN|\}}d}d}|d ¡}x¦|D]ž}x˜tdt|ƒƒD]†}| |krt| |ƒ|krqæ||}t |ƒræ|  d¡s&qæ|d ¡}||}|  ¡|kræ|  |¡t dkrd|d7}qæ|d7}qæWqÒW| ¡}| ¡ ¡}|||f| ||f<|  ||||ff¡|  ||f¡||j|<||j|<|rN||j|<qNWq6Wt || | | ¡dS)aÉInitialize 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 rNéÚCAé)ÚAssertionErrorÚ ca_cb_listrÚbuild_peptidesÚrangeÚlenÚ_get_cbÚ get_vectorÚabsrÚhas_idZnormÚanglerÚget_idÚ get_parentÚappendÚxtrarÚ__init__)ÚselfÚmodelÚradiusÚoffsetZ hse_up_keyZ hse_down_keyZ angle_keyÚppbÚpplZhse_mapZhse_listZhse_keysÚpp1ÚiÚr1Úr2Úr3ÚresultZpcbrZhse_uZhse_dÚca2Úpp2ÚjZroZcaoÚdÚres_idÚchain_id©r,ú1lib/python3.7/site-packages/Bio/PDB/HSExposure.pyrs\            z_AbstractHSExposure.__init__cCstS)N)ÚNotImplemented)rr"r#r$r,r,r-rjsz_AbstractHSExposure._get_cbcCsˆy(|d ¡}|d ¡}|d ¡}Wntk r<dSX||}||}tt dd|ƒ}| |¡}||}|j ||f¡|S)zÈReturn a pseudo CB vector for a Gly residue (PRIVATE). The pseudoCB vector is centered at the origin. CB coord=N coord rotated over -120 degrees along the CA-C axis. ÚNÚCr Ng^@g€f@)rÚ ExceptionrrZ left_multiplyr r)rZresidueZn_vZc_vZca_vZrotZcb_at_origin_vZcb_vr,r,r-Ú_get_gly_cb_vectorms   z&_AbstractHSExposure._get_gly_cb_vector)N)Ú__name__Ú __module__Ú __qualname__Ú__doc__rrr2r,r,r,r-rs Orc@s,eZdZdZd dd„Zdd„Zd d d „Zd S)Ú HSExposureCAzmClass to calculate HSE based on the approximate CA-CB vectors. Uses three consecutive CA positions. é rc Cst ||||ddd¡dS)azInitialize class. :param model: the model that contains the residues :type model: L{Model} :param radius: radius of the sphere (centred at the CA atom) :type radius: float :param offset: number of flanking residues that are ignored in the calculation of the number of neighbors :type offset: int Z EXP_HSE_A_UZ EXP_HSE_A_DZEXP_CB_PCB_ANGLEN)rr)rrrrr,r,r-rŽs zHSExposureCA.__init__c Cs|dks|dkrdSy(|d ¡}|d ¡}|d ¡}Wntk rPdSX||}||}| ¡| ¡||} |  ¡|j || |f¡| d¡rÈ|d ¡} | |} |  ¡|  | ¡} n4| ¡dkrø| |¡} | dkrìd} n |  | ¡} nd} | | fS)apCalculate approx CA-CB direction (PRIVATE). Calculate the approximate CA-CB direction for a central CA atom based on the two flanking CA positions, and the angle with the real CA-CB vector. The CA-CB vector is centered at the origin. :param r1, r2, r3: three consecutive residues :type r1, r2, r3: L{Residue} Nr ÚCBÚGLY) rr1Z normalizer rrrÚ get_resnamer2) rr"r#r$Úca1r&Zca3Zd1Zd3ÚbÚcbZcb_carr,r,r-r¥s6         zHSExposureCA._get_cbú hs_exp.pyc CsÒ|jst dt¡dSt|dƒ¨}| d¡| d¡| d¡| d¡| dd ¡xV|jD]L\}}| ¡\}}}| d |||f¡| ¡\}}}| d |||f¡q`W| d ¡| d ¡WdQRXdS) zòWrite 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.NÚwzfrom pymol.cgo import * zfrom pymol import cmd zobj=[ zBEGIN, LINES, zCOLOR, %.2f, %.2f, %.2f, )gð?gð?gð?zVERTEX, %.2f, %.2f, %.2f, zEND] zcmd.load_cgo(obj, 'HS') )r ÚwarningsÚwarnÚRuntimeWarningÚopenÚwriteZ get_array)rÚfilenameÚfpZcar>ÚxÚyÚzr,r,r-Úpcb_vectors_pymolÓs        zHSExposureCA.pcb_vectors_pymolN)r8r)r?)r3r4r5r6rrrKr,r,r,r-r7ˆs .r7c@s"eZdZdZd dd„Zdd„ZdS) Ú HSExposureCBz7Class to calculate HSE based on the real CA-CB vectors.r8rcCst ||||dd¡dS)azInitialize 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 Z EXP_HSE_B_UZ EXP_HSE_B_DN)rr)rrrrr,r,r-rñs zHSExposureCB.__init__cCsV| ¡dkr| |¡dfS| d¡rR| d¡rR|d ¡}|d ¡}||dfSdS)z˜Calculate CB-CA vector (PRIVATE). :param r1, r2, r3: three consecutive residues (only r2 is used) :type r1, r2, r3: L{Residue} r:gr9r N)r;r2rr)rr"r#r$ZvcbZvcar,r,r-rs    zHSExposureCB._get_cbN)r8r)r3r4r5r6rrr,r,r,r-rLîs rLc@seZdZdZddd„ZdS)Ú ExposureCNz:Residue exposure as number of CA atoms around its CA atom.ç(@rcCsR|dks t‚tƒ}| |¡}i}g}g}x|D]} xtdt| ƒƒD]î} d} | | } t| ƒrH|  d¡slqH| d} xz|D]r}xltdt|ƒƒD]Z}| |kr¬t| |ƒ|kr¬qŽ||}t|ƒrŽ| d¡sÈqŽ|d}|| }||krŽ| d7} qŽWqzW|  ¡}|   ¡ ¡}| |||f<|  | | f¡|  ||f¡| | j d<qHWq0Wt   ||||¡dS)a]Initialize class. A residue's exposure is defined as the number of CA atoms around that residue's CA atom. A dictionary is returned that uses a L{Residue} object as key, and the residue exposure as corresponding value. :param model: the model that contains the residues :type model: L{Model} :param radius: radius of the sphere (centred at the CA atom) :type radius: float :param offset: number of flanking residues that are ignored in the calculation of the number of neighbors :type offset: int rr rZEXP_CNN)r rr rrrrrrrrrrr)rrrrrrZfs_mapZfs_listZfs_keysr r!Zfsr"r<r'r(r#r&r)r*r+r,r,r-rs>     zExposureCN.__init__N)rNr)r3r4r5r6rr,r,r,r-rMsrM)r6rAZmathrZBio.PDB.AbstractPropertyMaprZBio.PDB.PolypeptiderrZBio.PDB.vectorsrrr7rLrMr,r,r,r-Ús   uf$