o i,@sPdZddlZddlZddlZddlmZmZmZddlm Z m Z ddl Z ddl mZeee jfZeee fZdZejdd Gd d d Zd ed efddZd$deded eefddZdeded efddZded efddZded e jfddZ     d%dedede e jde e jde ed e eed!e eed efd"d#ZdS)&zProtein data type.N)IteratorMappingSequence)AnyOptional)residue_constantsg{Gz?T)frozenc@seZdZUdZejed<ejed<ejed<ejed<ejed<dZeejed<dZ ee ed <dZ ee e ed <dZ ee eed <dS) Proteinz!Protein structure representation.atom_positionsaatype atom_mask residue_index b_factorsN chain_indexremarkparentsparents_chain_index)__name__ __module__ __qualname____doc__npndarray__annotations__rrrstrrrrintrrb/home/ubuntu/.local/lib/python3.10/site-packages/transformers/models/esm/openfold_utils/protein.pyr "s      r proteinnet_strreturnc Cs&d}ddt||D}t|ddddd|dddD}gd}d}d}d}|D]}d |dkr\|dd} tt| D] } | | tjvrPd | | <qCt d d| D}q-d |dkrg} td D]} | t t t |d| qht | } tt| dd tjd ftj}t|D]\} }t| dd| dd f|ddtj|ddf<q|t9}q-d|dkrt t t dddj|dd}tt|tjftj}t|D]\} }d|ddtj|f<q||d9}q-|dusJt|||tt|ddS)Nz(\[[A-Z]+\]\n)cSs g|] }t|dkr|qSr)lenstrip).0tagrrr Js z*from_proteinnet_string..rcSsg|]}|dqS) )split)r$lrrrr&Ksr)NCACz [PRIMARY]XcSsg|] }tj|tjqSr)r restype_orderget restype_num)r$ res_symbolrrrr&Xz [TERTIARY]z[MASK])-+).N)r r r rr)rer)zipr#ranger"rrestypesrarrayappendlistmapfloatzeros atom_type_numastypefloat32 enumerate transpose atom_orderPICO_TO_ANGSTROMr0r arange)rtag_retagsgroupsatomsr r r gseqitertiaryaxis tertiary_npatommaskrrrfrom_proteinnet_stringHs^(    " &6  (  rUprotchain_idcsg}|j}|dur|d||j}|j}|dur+|dur+fddt||D}|dus5t|dkr8dg}|dd||S)NREMARK csg|] \}}|kr|qSrr)r$rOprWrrr&r3z#get_pdb_headers..rN/APARENT  )rr<rrr8r"join)rVrW pdb_headersrrrrrZrget_pdb_headerszsr`pdb_strcCsg}|d}|j}|dur|d||jdurrt|jdkrrg}|jdurii}t|j|jD]\}}|t|g|t||q2t dd|D} t | dD]}| t|dg} || qWn |t |jndgg}d t td tfd d } || |dd} t|D]6\}} d | vrd| vr|| d| vrd||dvr| d7} | t|ks|| } ndg} || | qd|S)zWAdd pdb headers to an existing PDB string. Useful during multi-chain recycling r(NrXrcss|]}t|VqdS)N)r)r$ chain_idxrrr sz"add_pdb_headers..rr[rYr cSsdd|S)Nr\r])r^)rYrrrmake_parent_linesz)add_pdb_headers..make_parent_linePARENTREMARKTEREND)r)rr<rr"rr8 setdefaultrmaxr9r0r=rrDr^)rVra out_pdb_lineslinesrparents_per_chain parent_dictrYrOmax_idx chain_parentsrd chain_counterr*rrradd_pdb_headerssB       rrc!stjdgdtdtffdd }tj}g}|j}|j}|j}|j t j }|j }|j } t |tjkr8tdt|} t| dkrG|| |jd} d} d} tj}d }t| D]}|||}t|||||||D]v\}}}}|d kryqnd }t|d kr|nd |}d}d}d}|d}d}d}| d ur|| |}|d| dd |d|d|dd |d||d|dd|dd|dd|dd|d|dd|d|d}||| d7} qn|| dk}| d ur|| dkr| |d| krd}| |d} |r>d}|d| dd|||dd |d||d} || | d7} || dkr>|t|| qY|d |dd!|S)"zConverts a `Protein` instance to a PDB string. Args: prot: The protein to convert to PDB. Returns: PDB string. r.rr cstj|dS)NUNK)r restype_1to3r0)rsr:rrres_1to3szto_pdb..res_1to3zInvalid aatypes.rrNg?ATOMr]g?Az<6z>5z<4z>1z>3z>4z z>8.3fr'z>6.2fz z>2Trgz rhr()rr:rr atom_typesr r r rrBrint32rranyr1 ValueErrorr`r"extendshapestringascii_uppercaser9r8r<r^)!rVrwr| pdb_linesr r r rrrheadersn atom_indexprev_chain_index chain_tags chain_tagrO res_name_3 atom_nameposrTb_factor record_typenamealt_locinsertion_code occupancyelementcharge atom_lineshould_terminate chain_endchain_termination_linerrvrto_pdbs      &       0    rcCs tj|jS)aoComputes an ideal atom mask. `Protein.atom_mask` typically is defined according to the atoms that are reported in the PDB. This function computes a mask according to heavy atoms that should be present in the given sequence of amino acids. Args: prot: `Protein` whose fields are `numpy.ndarray` objects. Returns: An ideal atom mask. )rSTANDARD_ATOM_MASKr )rVrrrideal_atom_masks rfeaturesresultrrrrrc CsDt|d|d|d|dd|dur|nt|d||||d S)aAssembles a protein from a prediction. Args: features: Dictionary holding model inputs. result: Dictionary holding model outputs. b_factors: (Optional) B-factors to use for the protein. chain_index: (Optional) Chain indices for multi-chain predictions remark: (Optional) Remark about the prediction parents: (Optional) List of template names Returns: A protein instance. r final_atom_positionsfinal_atom_maskrrN) r r r rrrrrr)r r zeros_like)rrrrrrrrrrfrom_prediction,s rr!)NNNNN)r dataclassesr7rcollections.abcrrrtypingrrnumpyrrzrrr FeatureDict ModelOutputrG dataclassr rUrr=r`rrrrrrrrrsP   %22]