o RŀgN@sdZddlZddlZddlZddlZddlmZddlmZddlm Z ddl m Z ddl m Z ddlmZdd lmZed Ze Zd d Zd dZdddZddZddZGddde ZdS)a 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 https://swift.cmbi.umcn.nl/gv/dssp/. The following Accessible surface area (ASA) values can be used, defaulting to the Sander and Rost values: Ahmad Ahmad et al. 2003 https://doi.org/10.1002/prot.10328 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)protein_letters_3to1)residue_sasa_scales)AbstractResiduePropertyMap) MMCIF2Dict) PDBException) PDBParserz[a-z]cCsttt|dS)z2Parse semantic version scheme for easy comparison..)tuplemapintsplit)version_stringr@/var/www/html/myenv/lib/python3.10/site-packages/Bio/PDB/DSSP.pyversionrrcCs(|dkrdS|dkr dS|dkrdSJ)zBSecondary structure symbol to index. H=0 E=1 C=2 HrECr)ssrrr ss_to_indexwsrdssp3.9.9c Cszt|tdkr||g}n|d|g}tj|dtjtjd}Wn+tyJ|dkr+t|tdkr8d|g}ndd|g}tj|dtjtjd}Ynw|\}}|rbt||sbt dt t |\}}||fS)aCreate a DSSP dictionary from a PDB file. Parameters ---------- in_file : string pdb file DSSP : string DSSP executable (argument to subprocess) dssp_version : string Version of DSSP executable Returns ------- (out_dict, keys) : tuple a dictionary that maps (chainid, resid) to amino acid type, secondary structure code and accessibility. Examples -------- How dssp_dict_from_pdb_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, ' ')]) 4.0.0z--output-format=dsspT)universal_newlinesstdoutstderrmkdsspz DSSP failed to produce an output) r subprocessPopenPIPEFileNotFoundError communicatestripwarningswarn Exception_make_dssp_dictr) in_fileDSSP dssp_versionDSSP_cmdpouterrout_dictkeysrrrdssp_dict_from_pdb_files<$        r4cCs4t| }t|WdS1swYdS)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 $r8cCsi}d}g}|D]n}|}t|dkrq|ddkrd}q|s"q|ddkr)qt|dd}t|dd }|d }|d } |d } |d } | dkrOd } zZt|dd} t|dd} t|dd}t|dd}t|dd}t|dd}t|dd}t|dd}t|dd}t|dd}t|dd}WntyV}z|ddkrG|ddd}t|d|d|} t|d|d|} t|d|d|}t|d|d|}t|d|d|}t|d|d|}t|d|d|}t|d|d|}t|d|d|}t|d|d|}t|d|d|}nt|dWYd}~nd}~wwd||f}| | ||||| | ||||||f|| |f<|| |fq||fS)aReturn a DSSP dictionary, used by mask_dssp_dict (PRIVATE). DSSP dictionary maps (chainid, resid) to an amino acid, secondary structure symbol, solvent accessibility value, and hydrogen bond information (relative dssp indices and hydrogen bond energies) from an open DSSP file object. Parameters ---------- handle : file the open DSSP output file handle rrrRESIDUE  N -&-.289=CDHNOS"gms)r lenr float ValueErrorfindappend)r7rstartr3linesl dssp_indexresseqicodechainidaar NH_O_1_relidx NH_O_1_energy O_NH_1_relidx O_NH_1_energy NH_O_2_relidx NH_O_2_energy O_NH_2_relidx O_NH_2_energyaccphipsiexcshiftres_idrrrr*s        r*c@seZdZdZdddZdS) r,acRun DSSP and parse secondary structure and accessibility. Run DSSP on a PDB/mmCIF file, and provide a handle to the DSSP secondary structure and accessibility. **Note** that DSSP can only handle one model. Examples -------- How DSSP could be used:: from Bio.PDB import PDBParser from Bio.PDB.DSSP import DSSP p = PDBParser() structure = p.get_structure("1MOT", "/local-pdb/1mot.pdb") model = structure[0] dssp = DSSP(model, "/local-pdb/1mot.pdb") # DSSP data is accessed by a tuple (chain_id, res_id) a_key = list(dssp.keys())[2] # (dssp index, amino acid, secondary structure, relative ASA, phi, psi, # NH_O_1_relidx, NH_O_1_energy, O_NH_1_relidx, O_NH_1_energy, # NH_O_2_relidx, NH_O_2_energy, O_NH_2_relidx, O_NH_2_energy) dssp[a_key] rSanderc-Cst||_|dkrtj|ddd}|}|dkrd}|dvs'Jd|dks/|dkr~ztj|d gd d }td | d}t |||\}} Wn<t y}|d krYd}n|dkr`d }ntj|d gd d }td | d}t |||\}} Yn w|dkrt |\}} i} g} dd} |dkrt |t dkrt|} i}t| dD]\}}||vr| d|||<qg}| D]}|\}}|dkrt |t dkr||}|||f||}z||}Wn,ty| |}|D]}|jddvr | |j|kr |}nqt|dYnw|dkrD|D]}|j|d}|tdvr8||n q||dnA|dkrdd|D}|dr| |}|D]$}|jddvr| |j|kr|dtdvr|}nq`||\}}}}} }!}"}#}$}%}&}'}(})||jd<||jd<||jd<| |jd<|!|jd<|"|jd <|#|jd!<|$|jd"<|%|jd#<|&|jd$<|'|jd%<|(|jd&<|)|jd'<|}*z ||j|*}+Wn tyd(}+Ynw|+d)krd)}+|+|jd*<t|*d+}*|*d,krt !|rd,}|*|kr*|jdd-ks#|d+kr*t"d.||!|||+|| |"|#|$|%|&|'|(|)f},|,| ||f<| |,q|dkrVt |t dkrV|} t#$|| | | dS)/aCreate a DSSP object. Parameters ---------- model : Model The first model of the structure in_file : string Either a PDB file or a DSSP file. dssp : string The dssp executable (ie. the argument to subprocess) acc_array : string Accessible surface area (ASA) from either Miller et al. (1987), Sander & Rost (1994), Wilke: Tien et al. 2013, or Ahmad et al. (2003) as string Sander/Wilke/Miller/Ahmad. Defaults to Sander. file_type: string File type switch: either PDB, MMCIF or DSSP. Inferred from the file extension by default. rorNCIFMMCIF)PDBrqr,z$File type must be PDB, mmCIF or DSSPrrz --versionT)textz \s*([\d.]+)rr r,cSs|d|dS)z;Serialize a residue's resseq and icode for easy comparison.rrr)rmrrr resid2coderz!DSSP.__init__..resid2coderz_atom_site.label_asym_idz_atom_site.auth_asym_idr)r;WrzA1 cSsh|]}|qSr) get_altloc).0arrr sz DSSP.__init__..SS_DSSP EXP_DSSP_ASAPHI_DSSPPSI_DSSP DSSP_INDEXNH_O_1_RELIDX_DSSPNH_O_1_ENERGY_DSSPO_NH_1_RELIDX_DSSPO_NH_1_ENERGY_DSSPNH_O_2_RELIDX_DSSPNH_O_2_ENERGY_DSSPO_NH_2_RELIDX_DSSPO_NH_2_ENERGY_DSSPNAg? EXP_DSSP_RASAXrr;zStructure/DSSP mismatch at )%residue_max_accospathsplitextupperr! check_outputresearchgroupr4r$r8rr enumeraterWKeyErrorid is_disordereddisordered_get_id_list child_dictget_listrvr disordered_selectget_unpacked_list isdisjointxtra get_resnamerget _dssp_cysmatchrr__init__)-selfmodelr+r acc_array file_typerr- dssp_dict dssp_keysdssp_map dssp_listrt mmcif_dictmmcif_chain_dicticdssp_mapped_keyskeychain_idrmchainres res_seq_icoderrkaltlocaltlocsr_rrhrirjr[r`rarbrcrdrerfrgresnamerel_acc dssp_valsrrrrZs&                               $  z DSSP.__init__N)rrnro)__name__ __module__ __qualname____doc__rrrrrr,?sr,)rr)rrrr!r'iorBio.Data.PDBDatarrBio.PDB.AbstractPropertyMaprBio.PDB.MMCIF2DictrBio.PDB.PDBExceptionsrBio.PDB.PDBParserrcompilerrrrr4r8r*r,rrrrs(U         H`