ó ¤Ic@s´ddlmZddlZddlTddlmZdZdefd„ƒYZdefd „ƒYZd efd „ƒYZd efd „ƒYZ e dkr°ddlZe ƒZ e j dejdƒZedZdZdZeededeƒZxeD] ZeGHqWHeededeƒZxeD] ZeGHq2WHe ededeƒZxeD] ZeGHqaWHx<eD]1Zx(eD] ZyejdGHWq…q…Xq…WqxWndS(iÿÿÿÿ(tpiN(t*(tAbstractPropertyMaps9Half sphere exposure and coordination number calculation.t_AbstractHSExposurecBs#eZdZdd„Zd„ZRS(sî Abstract 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. cCs´|dkst‚g|_tƒ}|j|ƒ}i} g} g} xR|D]J} xAtdt| ƒƒD]*} | dkrƒd}n| | d}| | }| t| ƒdkrºd}n| | d}|j|||ƒ}|dkrïqhn|\}}d}d}|djƒ}xâ|D]Ú}xÑtdt|ƒƒD]º}| |krht | |ƒ|krhq:n||}t |ƒ s:|j dƒ r•q:n|djƒ}||}|j ƒ|kr:|j |ƒtdkrç|d7}qô|d7}q:q:WqW|jƒ}|jƒjƒ}|||f| ||f<| j||||ffƒ| j||fƒ||j|<||j|<|rh||j||j|ƒ} | dkr,d} qD| j| ƒ} nd} | | fS(sM 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} RtCBtGLYN( R R t normalizeRRRRt get_resnameR@( RR&R'R(tca1R-tca3td1td3tbtcbtcb_caR((s…/oak/stanford/groups/akundaje/marinovg/programs/biopython-1.50.tar.gz/biopython-1.50/build/lib.linux-x86_64-2.7/Bio/PDB/HSExposure.pyR –s6           s hs_exp.pycCst|jƒdkr)tjjdƒdSt|dƒ}|jdƒ|jdƒ|jdƒ|jdƒ|jd dƒxu|jD]j\}}|jƒ\}}}|jd |||fƒ|jƒ\}}}|jd |||fƒq‡W|jd ƒ|jd ƒ|jƒdS(sÍ 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 isNothing to draw. Ntwsfrom pymol.cgo import * sfrom pymol import cmd sobj=[ sBEGIN, LINES, sCOLOR, %.2f, %.2f, %.2f, gð?sVERTEX, %.2f, %.2f, %.2f, sEND] scmd.load_cgo(obj, 'HS') (gð?gð?gð?(R Rtsyststderrtwritetopent get_arraytclose(RtfilenametfptcaRQtxtytz((s…/oak/stanford/groups/akundaje/marinovg/programs/biopython-1.50.tar.gz/biopython-1.50/build/lib.linux-x86_64-2.7/Bio/PDB/HSExposure.pytpcb_vectors_pymolÃs"      (RARBRCRR R`(((s…/oak/stanford/groups/akundaje/marinovg/programs/biopython-1.50.tar.gz/biopython-1.50/build/lib.linux-x86_64-2.7/Bio/PDB/HSExposure.pyRDƒs -t HSExposureCBcBs&eZdZddd„Zd„ZRS(sA Class to calculate HSE based on the real CA-CB vectors. i icCs tj||||ddƒdS(s\ @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 t EXP_HSE_B_Ut EXP_HSE_B_DN(RR(RRRR((s…/oak/stanford/groups/akundaje/marinovg/programs/biopython-1.50.tar.gz/biopython-1.50/build/lib.linux-x86_64-2.7/Bio/PDB/HSExposure.pyRâs cCsu|jƒdkr%|j|ƒdfS|jdƒrq|jdƒrq|djƒ}|djƒ}||dfSdS(s¡ Method to calculate CB-CA vector. @param r1, r2, r3: three consecutive residues (only r2 is used) @type r1, r2, r3: L{Residue} RIgRHRN(RKR@RR R (RR&R'R(tvcbtvca((s…/oak/stanford/groups/akundaje/marinovg/programs/biopython-1.50.tar.gz/biopython-1.50/build/lib.linux-x86_64-2.7/Bio/PDB/HSExposure.pyR ðs(RARBRCRR (((s…/oak/stanford/groups/akundaje/marinovg/programs/biopython-1.50.tar.gz/biopython-1.50/build/lib.linux-x86_64-2.7/Bio/PDB/HSExposure.pyRaÞst ExposureCNcBseZddd„ZRS(g(@icCsØ|dkst‚tƒ}|j|ƒ}i}g}g}x|D]w} xntdt| ƒƒD]W} d} | | } t| ƒ s_| jdƒ r˜q_n| d} x°|D]¨}xŸtdt|ƒƒD]ˆ}| |krót| |ƒ|króqÅn||}t|ƒ sÅ|jdƒ r qÅn|d}|| }||krÅ| d7} qÅqÅWq©W| jƒ}| j ƒjƒ}| |||f<|j | | fƒ|j ||fƒ| | j d     "     (RARBR(((s…/oak/stanford/groups/akundaje/marinovg/programs/biopython-1.50.tar.gz/biopython-1.50/build/lib.linux-x86_64-2.7/Bio/PDB/HSExposure.pyRfst__main__tXiig*@RRt PCB_CB_ANGLE(tmathRRTtBio.PDBRRCRRDRaRfRAt PDBParsertpt get_structuretargvtsRtRADIUStOFFSETthsetltctrR(((s…/oak/stanford/groups/akundaje/marinovg/programs/biopython-1.50.tar.gz/biopython-1.50/build/lib.linux-x86_64-2.7/Bio/PDB/HSExposure.pytsB  s[#4