ó Žï Ic@sddlZddlZddlZddlZddlTddlmZdZd„Zddd„Zd „Z d „Z d „Z d efd „ƒYZ e dkr ddlZeƒZejdejdƒZedZe eejdƒZxeD] ZeGHqúWndS(iÿÿÿÿN(t*(tAbstractPropertyMapsß Calculation of residue depth (using Michel Sanner's MSMS program for the surface calculation). Residue depth is the average distance of the atoms of a residue from the solvent accessible surface. Residue Depth: rd=ResidueDepth(model, pdb_file) print rd[(chain_id, res_id)] Direct MSMS interface: Typical use: surface=get_surface("1FAT.pdb") Surface is a Numeric array with all the surface vertices. Distance to surface: dist=min_dist(coord, surface) where coord is the coord of an atom within the volume bound by the surface (ie. atom depth). To calculate the residue depth (average atom depth of the atoms in a residue): rd=residue_depth(residue, surface) cCsŠt|dƒ}g}x[|jƒD]M}|jƒ}t|ƒdksLq"ntt|dd!ƒ}|j|ƒq"W|jƒtj |ƒS(s4 Read the vertex list into a Numeric array. tri ii( topent readlinestsplittlentmaptfloattappendtclosetnumpytarray(tfilenametfpt vertex_listtltsltvl((s‡/oak/stanford/groups/akundaje/marinovg/programs/biopython-1.50.tar.gz/biopython-1.50/build/lib.linux-x86_64-2.7/Bio/PDB/ResidueDepth.pyt_read_vertex_array1s  t pdb_to_xyzrtmsmsc CsŠtjƒ}|d}|||f}tj|ƒtjƒ}|dtjƒ}|||f}tj|ƒ|d}t|ƒ}|S(sÐ Return a Numeric array that represents the vertex list of the molecular surface. PDB_TO_XYZR --- pdb_to_xyzr executable (arg. to os.system) MSMS --- msms executable (arg. to os.system) s %s > %ss# -probe_radius 1.5 -if %s -of %s > s.vert(ttempfiletmktemptostsystemR( tpdb_filet PDB_TO_XYZRtMSMStxyz_tmptmake_xyzt surface_tmpt make_surfacet surface_filetsurface((s‡/oak/stanford/groups/akundaje/marinovg/programs/biopython-1.50.tar.gz/biopython-1.50/build/lib.linux-x86_64-2.7/Bio/PDB/ResidueDepth.pyt get_surfaceAs       cCs0||}t||dƒ}tjt|ƒƒS(s@ Return minimum distance between coord and surface. i(tsumR tsqrttmin(tcoordR"tdtd2((s‡/oak/stanford/groups/akundaje/marinovg/programs/biopython-1.50.tar.gz/biopython-1.50/build/lib.linux-x86_64-2.7/Bio/PDB/ResidueDepth.pytmin_dist^s cCsV|jƒ}t|ƒ}d}x-|D]%}|jƒ}|t||ƒ}q%W||S(sc Return average distance to surface for all atoms in a residue, ie. the residue depth. i(tget_unpacked_listRt get_coordR*(tresidueR"t atom_listtlengthR(tatomR'((s‡/oak/stanford/groups/akundaje/marinovg/programs/biopython-1.50.tar.gz/biopython-1.50/build/lib.linux-x86_64-2.7/Bio/PDB/ResidueDepth.pyt residue_depthgs    cCs6|jdƒsdS|d}|jƒ}t||ƒS(NtCA(thas_idtNoneR,R*(R-R"tcaR'((s‡/oak/stanford/groups/akundaje/marinovg/programs/biopython-1.50.tar.gz/biopython-1.50/build/lib.linux-x86_64-2.7/Bio/PDB/ResidueDepth.pytca_depthts   t ResidueDepthcBseZdZd„ZRS(s: Calculate residue and CA depth for all residues. c Csi}g}g}tj|dƒ}t|ƒ}x¸|D]°}t|ƒsOq7nt||ƒ} t||ƒ} |jƒ} |jƒjƒ} | | f|| | f<|j|| | ffƒ|j| | fƒ| |j d<| |j ds(     #