B bP@s6dZddlZddlZddlmZddlZddlZddlmZddl m Z ddl m Z ddl mZddlmZed Zd d d d ddddddddddddddddddd d!d"d#d$d%d&d'd(d)d*d'd+d,d-d.d/d0d1dd2d3d4d5d6d7dd8d9d:d;dd?d@dAdBd@ddCZdDdEZdOdGdHZdIdJZdKdLZGdMdNdNeZdS)Pa\ Use the DSSP program to calculate secondary structure and accessibility. You need to have a working version of DSSP (and a license, free for academic use) in order to use this. For DSSP, see http://swift.cmbi.ru.nl/gv/dssp/. The following Accessible surface area (ASA) values can be used, defaulting to the Sander and Rost values: Miller Miller et al. 1987 https://doi.org/10.1016/0022-2836(87)90038-6 Sander Sander and Rost 1994 https://doi.org/10.1002/prot.340200303 Wilke Tien et al. 2013 https://doi.org/10.1371/journal.pone.0080635 The DSSP codes for secondary structure used here are: ===== ==== Code Structure ===== ==== H Alpha helix (4-12) B Isolated beta-bridge residue E Strand G 3-10 helix I Pi helix T Turn S Bend \- None ===== ==== Usage ----- The DSSP class can be used to run DSSP on a PDB or mmCIF file, and provides a handle to the DSSP secondary structure and accessibility. **Note** that DSSP can only handle one model, and will only run calculations on the first model in the provided PDB file. Examples -------- Typical use:: from Bio.PDB import PDBParser from Bio.PDB.DSSP import DSSP p = PDBParser() structure = p.get_structure("1MOT", "/local-pdb/1mot.pdb") model = structure[0] dssp = DSSP(model, "/local-pdb/1mot.pdb") Note that the recent DSSP executable from the DSSP-2 package was renamed from ``dssp`` to ``mkdssp``. If using a recent DSSP release, you may need to provide the name of your DSSP executable:: dssp = DSSP(model, '/local-pdb/1mot.pdb', dssp='mkdssp') DSSP data is accessed by a tuple - (chain id, residue id):: a_key = list(dssp.keys())[2] dssp[a_key] The dssp data returned for a single residue is a tuple in the form: ============ === Tuple Index Value ============ === 0 DSSP index 1 Amino acid 2 Secondary structure 3 Relative ASA 4 Phi 5 Psi 6 NH-->O_1_relidx 7 NH-->O_1_energy 8 O-->NH_1_relidx 9 O-->NH_1_energy 10 NH-->O_2_relidx 11 NH-->O_2_energy 12 O-->NH_2_relidx 13 O-->NH_2_energy ============ === N)StringIO)AbstractResiduePropertyMap) PDBException) PDBParser) three_to_one) MMCIF2Dictz[a-z]g@\@g n@gc@gb@ga@gg@gf@g@U@g@h@gf@gf@g`j@gi@g@k@ga@g^@g@b@g0p@gl@gd@)ZALAZARGZASNZASPZCYSZGLNZGLUZGLYZHISZILEZLEUZLYSZMETZPHEZPROZSERZTHRZTRPZTYRZVALg `@g q@g`h@g h@gd@g l@gk@gZ@gl@gh@g i@gm@gn@gc@g`c@ge@gq@gpp@ge@gZ@go@gc@g`d@g`@gh@gU@gg@g e@gd@gi@gg@ga@g@`@ga@g`l@gk@)ZMillerZWilkeSandercCs0|dkr dS|dkrdS|dkr$dSds,tdS)zBSecondary structure symbol to index. H=0 E=1 C=2 HrECN)AssertionError)ssr+lib/python3.7/site-packages/Bio/PDB/DSSP.py ss_to_indexsrdsspc Csytj||gdtjtjd}Wn8tk rV|dkr8tjd|gdtjtjd}YnX|\}}|rt||stdt t |\}}||fS)aCreate a DSSP dictionary from a PDB file. Parameters ---------- in_file : string pdb file DSSP : string DSSP executable (argument to subprocess) Returns ------- (out_dict, keys) : tuple a dictionary that maps (chainid, resid) to amino acid type, secondary structure code and accessibility. Examples -------- How dssp_dict_frompdb_file could be used:: from Bio.PDB.DSSP import dssp_dict_from_pdb_file dssp_tuple = dssp_dict_from_pdb_file("/local-pdb/1fat.pdb") dssp_dict = dssp_tuple[0] print(dssp_dict['A',(' ', 1, ' ')]) T)Zuniversal_newlinesstdoutstderrmkdsspz DSSP failed to produce an output) subprocessPopenPIPEFileNotFoundErrorZ communicatestripwarningswarn Exception_make_dssp_dictr)in_fileDSSPpouterrZout_dictkeysrrrdssp_dict_from_pdb_files*!  r&c Cst| }t|SQRXdS)zDSSP dictionary mapping identifiers to properties. Return a DSSP dictionary that maps (chainid, resid) to aa, ss and accessibility, from a DSSP file. Parameters ---------- filename : string the DSSP output file N)openr)filenamehandlerrrmake_dssp_dicts r*cCsi}d}g}x|D]}|}t|dkr0q|ddkrBd}q|sHq|ddkrVqt|dd}t|dd }|d }|d } |d } |d } | dkrd } yt|dd} t|dd} t|dd}t|dd}t|dd}t|dd}t|dd}t|dd}t|dd}t|dd}t|dd}WnZtk r}z8|ddkr|ddd}t|d|d|} t|d|d|} t|d|d|}t|d|d|}t|d|d|}t|d|d|}t|d|d|}t|d|d|}t|d|d|}t|d|d|}t|d|d|}n t|dWdd}~XYnXd||f}| | ||||| | ||||||f|| |f<|| |fqW||fS)aReturn a DSSP dictionary, used by mask_dssp_dict (PRIVATE). DSSP dictionary maps (chainid, resid) to an amino acid, secondary structure symbol, solvent accessibility value, and hydrogen bond information (relative dssp indices and hydrogen bond energies) from an open DSSP file object. Parameters ---------- handle : file the open DSSP output file handle rr r ZRESIDUE  N -&-.289=CDHNOS"gms)splitlenintfloat ValueErrorfindappend)r)rstartr%lZsl dssp_indexZresseqZicodeZchainidaar NH_O_1_relidx NH_O_1_energy O_NH_1_relidx O_NH_1_energy NH_O_2_relidx NH_O_2_energy O_NH_2_relidx O_NH_2_energyaccphipsiexcshiftres_idrrrrs    rc@seZdZdZdddZdS) r!acRun DSSP and parse secondary structure and accessibility. Run DSSP on a PDB/mmCIF file, and provide a handle to the DSSP secondary structure and accessibility. **Note** that DSSP can only handle one model. Examples -------- How DSSP could be used:: from Bio.PDB import PDBParser from Bio.PDB.DSSP import DSSP p = PDBParser() structure = p.get_structure("1MOT", "/local-pdb/1mot.pdb") model = structure[0] dssp = DSSP(model, "/local-pdb/1mot.pdb") # DSSP data is accessed by a tuple (chain_id, res_id) a_key = list(dssp.keys())[2] # (dssp index, amino acid, secondary structure, relative ASA, phi, psi, # NH_O_1_relidx, NH_O_1_energy, O_NH_1_relidx, O_NH_1_energy, # NH_O_2_relidx, NH_O_2_energy, O_NH_2_relidx, O_NH_2_energy) dssp[a_key] rrc+Cs|t||_|dkr*tj|ddd}|}|dkr>d}|dksNtd|dks^|dkryt||\}}Wn2tk r|d krd }n|d krd }nYnXt||\}}n|d krt|\}}i}g} d d } |dkr$t |} i} x0t | dD] \} }|| kr| d| | |<qWg}x2|D](}|\}}|dkrZ| |}| ||f||}y ||}Wn^t k r| |}x>|D],}|j ddkr| |j |kr|}PqWt |dYnX|dkr4x|D]6}|j|d}|tdkr||PqW||dn|dkrdd|D}|dr| |}xN|D]F}|j ddkrn| |j |krn|dtdkrn|}PqnW||\}}}}}}} }!}"}#}$}%}&}'||jd<||jd<||jd<||jd<||jd<| |jd<|!|jd<|"|jd<|#|jd<|$|jd<|%|jd <|&|jd!<|'|jd"<|}(y||j|(})Wnt k rd#})YnX|)d$krd$})|)|jd%<y t|(}(Wnt k rd&}(YnX|(d'krt|rd'}|(|kr|j dd(ks|d&krtd)|||||)||| |!|"|#|$|%|&|'f}*|*|||f<| |*q,W|dkrh|}t|||| dS)*aCreate a DSSP object. Parameters ---------- model : Model The first model of the structure in_file : string Either a PDB file or a DSSP file. dssp : string The dssp executable (ie. the argument to subprocess) acc_array : string Accessible surface area (ASA) from either Miller et al. (1987), Sander & Rost (1994), or Wilke: Tien et al. 2013, as string Sander/Wilke/Miller. Defaults to Sander. file_type: string File type switch: either PDB, MMCIF or DSSP. 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