:>"^ÛKã-@sfdZddlmZddlZddlmZddlZddlZddlm Z ddl m Z ddl m Z ddlmZejd ƒZd d d d ddddddddddddddddddd d!d"d#d$d%d&d'd(d)d*d+d,d-d.d/d0d1d2id3d d4d d5dd6dd7dd8dd9dd:dd;dd<dd=dd>d!d?d#d<d%d@d'dAd)dBd+dCd-dDd/dEd1dFidGd dHd dIddJddKddLddMddddNddOddPddQd!dRd#dSd%d=d'dTd)dUd+dVd-dWd/dXd1dViiZdYdZ„Zd[d\d]„Zd^d_„Zd`da„ZGdbdc„dce ƒZdS)daS 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 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 ============ === é)Úprint_functionN)ÚStringIO)ÚAbstractResiduePropertyMap)Ú PDBException)Ú PDBParser)Ú three_to_onez[a-z]ZMillerZALAg@\@ZARGg n@ZASNgÀc@ZASPgàb@ZCYSg€a@ZGLNg g@ZGLUgàf@ZGLYg@U@ZHISg@h@ZILEgÀf@ZLEUg€f@ZLYSg`j@ZMETg€i@ZPHEg@k@ZPROgàa@ZSERg€^@ZTHRg@b@ZTRPg0p@ZTYRg l@ZVALgd@ZWilkeg `@g q@g`h@g h@gàd@g l@gàk@gZ@gl@g h@g i@g€m@gn@gàc@g`c@g€e@gÐq@gpp@gÀe@ÚSanderg€Z@go@g c@g`d@gà`@gÀh@gU@gg@g e@g€d@g i@g€g@ga@g@`@gÀa@g`l@gÀk@cCs@|dkrdS|dkr dS|dkr0dSds<t‚dS)zBSecondary structure symbol to index. H=0 E=1 C=2 ÚHrÚEéÚCéN)ÚAssertionError)Úss©rú1/tmp/pip-build-ww9dw3qa/biopython/Bio/PDB/DSSP.pyÚ ss_to_index¶s   rÚdsspcCsçy1tj||gdddtjdtjƒ}WnNtk r|dkrP‚tjd|gdddtjdtjƒ}YnX|jƒ\}}|jƒrÅtj|ƒ|jƒsÅtdƒ‚t t |ƒƒ\}}||fS)aƒCreate a DSSP dictionary from a PDB file. Parameters ---------- in_file : string pdb file DSSP : string DSSP executable (argument to os.system) 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, ' ')]) Úuniversal_newlinesTÚstdoutÚstderrÚmkdsspz DSSP failed to produce an output) Ú subprocessÚPopenÚPIPEÚOSErrorÚ communicateÚstripÚwarningsÚwarnÚ ExceptionÚ_make_dssp_dictr)Úin_fileÚDSSPÚpÚoutÚerrZout_dictÚkeysrrrÚdssp_dict_from_pdb_fileÆs*!          r(c Cs't|dƒ}t|ƒSWdQRXdS)zöDSSP 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 ÚrN)Úopenr!)ÚfilenameÚhandlerrrÚmake_dssp_dicts r-cCsëi}d}g}xÌ|jƒD]¾}|jƒ}t|ƒdkrFq|ddkr_d}q|shq|ddkr{qt|dd…ƒ}t|dd …ƒ}|d }|d } |d } |d } | dkrád } yöt|dd…ƒ} t|dd…ƒ} t|dd…ƒ}t|dd…ƒ}t|dd…ƒ}t|dd…ƒ}t|dd…ƒ}t|dd…ƒ}t|dd…ƒ}t|dd…ƒ}t|dd…ƒ}Wn§tk r€}z‡|ddkrb|dd…jdƒ}t|d|d|…ƒ} t|d|d|…ƒ} t|d|d|…ƒ}t|d|d|…ƒ}t|d|d|…ƒ}t|d|d|…ƒ}t|d|d|…ƒ}t|d|d|…ƒ}t|d|d|…ƒ}t|d|d|…ƒ}t|d|d|…ƒ}n t|ƒ‚WYdd}~XnXd||f}| | ||||| | ||||||f|| |f<|j| |fƒqW||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 ZRESIDUEé ú Néé é é éú-é&é-é.é2é8é9é=éCéDéHéNéOéSé"égémés)Ú readlinesÚsplitÚlenÚintÚfloatÚ ValueErrorÚfindÚappend)r,rÚstartr'ÚlÚslÚ dssp_indexZresseqZicodeZchainidÚaarÚ NH_O_1_relidxÚ NH_O_1_energyÚ O_NH_1_relidxÚ O_NH_1_energyÚ NH_O_2_relidxÚ NH_O_2_energyÚ O_NH_2_relidxÚ O_NH_2_energyÚaccÚphiÚpsiÚexcZshiftÚres_idrrrr!s„      !r!c@s+eZdZdZddddd„ZdS)r#a]Run DSSP and parse secondary structure and accessibility. Run DSSP on a pdb 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] rrÚPDBc&/CsÊt||_|jƒ}|d#ks+t‚|dkrªyt||ƒ\}}Wn?tk r‘|dkrud}n|dkrŠd}n‚YnXt||ƒ\}}n|dkrÈt|ƒ\}}i}g} dd„} xÍ|D]Å} | \} } || }y|| }Wnjtk r}| | ƒ}xI|D]5}|jdd$kr4| |jƒ|kr4|}Pq4Wt| ƒ‚YnX|jƒd krþx|j ƒD]C}|j |j ƒdj ƒ}|t d ƒkr|j|ƒPqW|j|j ƒdƒn¨|jƒd kr¦d d„|jƒDƒ}|jd ƒr¦| | ƒ}x_|D]W}|jdd%krK| |jƒ|krK|j ƒdj ƒt d ƒkrK|}PqKW|| \}}}}}}}}}}}} }!}"||jd<||jd<||jd<||jd<||jd<||jd<||jd<||jd<||jd<||jd<| |jd<|!|jd<|"|jd<|jƒ}#y||j|#}$Wntk r¾d}$YnX|$dkrÑd}$|$|jd.resid2coderr/ÚWr zA1 r cSsh|]}|jƒ’qSr)Ú get_altloc)Ú.0Úarrrú ùs z DSSP.__init__..ZSS_DSSPZ EXP_DSSP_ASAZPHI_DSSPZPSI_DSSPZ DSSP_INDEXZNH_O_1_RELIDX_DSSPZNH_O_1_ENERGY_DSSPZO_NH_1_RELIDX_DSSPZO_NH_1_ENERGY_DSSPZNH_O_2_RELIDX_DSSPZNH_O_2_ENERGY_DSSPZO_NH_2_RELIDX_DSSPZO_NH_2_ENERGY_DSSPZNAgð?Z EXP_DSSP_RASAÚXr zStructure/DSSP mismatch at %sN)razDSSP)r/rc)r/rc)Úresidue_max_accÚupperrr(rr-ÚKeyErrorÚidZ is_disorderedZdisordered_get_id_listZ child_dictZget_listrdÚtupleZdisordered_selectZget_unpacked_listÚ isdisjointZxtraZ get_resnamerÚ _dssp_cysÚmatchrrNrÚ__init__)&ÚselfÚmodelr"rZ acc_arrayÚ file_typeZ dssp_dictZ dssp_keysZdssp_mapZ dssp_listrbÚkeyZchain_idr`ÚchainÚresZ res_seq_icoder)ZrkZaltlocZaltlocsrSrr\r]r^rRrTrUrVrWrXrYrZr[ÚresnameZrel_accZ dssp_valsrrrrqŽs                     4                     +  z DSSP.__init__N)Ú__name__Ú __module__Ú __qualname__Ú__doc__rqrrrrr#ss r#)r|Ú __future__rÚreZ Bio._py3krrrZBio.PDB.AbstractPropertyMaprZBio.PDB.PDBExceptionsrZBio.PDB.PDBParserrZBio.PDB.PolypeptiderÚcompilerorirr(r-r!r#rrrrÚYsœ       =  `