o Zh,@sTdZddlZddlZddlZddlmZmZmZmZm Z m Z m Z m Z ddl ZddlmZe eejfZe eefZdZejddGd d d Zd ed efd dZd#deded eefddZdeded efddZded efddZded ejfddZ     d$dedede ejde ejde ede e ed e e ed efd!d"ZdS)%zProtein data type.N)AnyDictIteratorListMappingOptionalSequenceTuple)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__rrrstrrrrintr r ]/var/www/auris/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).0tagr r r! Is z*from_proteinnet_string..rcSsg|]}|dqS) )split)r'lr r r!r)Jsr )NCACz [PRIMARY]XcSsg|] }tj|tjqSr )r Z restype_orderget restype_num)r'Z res_symbolr r r!r)Wz [TERTIARY]z[MASK])-+).N)rrrrr)rer,zipr&ranger%r restypesrarrayappendlistmapfloatZzerosZ atom_type_numastypeZfloat32 enumerateZ transposeZ atom_orderPICO_TO_ANGSTROMr2r Zarange)r"tag_retagsgroupsZatomsrrrgseqiZtertiaryZaxisZ tertiary_npZatommaskr r r!from_proteinnet_stringGs^(    " &6  (  rKprotchain_idcsg}|j}|dur|d||j}|j}|dur+|dur+fddt||D}|dus5t|dkr8dg}|dd||S)NREMARK csg|] \}}|kr|qSr r )r'rIprMr r!r)r4z#get_pdb_headers..rN/APARENT  )rr=rrr9r%join)rLrMZ pdb_headersrrrr rPr!get_pdb_headersysrUpdb_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+NrNrcSsg|]}t|qSr )r)r'Z chain_idxr r r!r)sz#add_pdb_headers..r rQrOr#cSsdd|S)NrRrS)rT)rOr r r!make_parent_linesz)add_pdb_headers..make_parent_lineZPARENTZREMARKTEREND)r,rr=rr%rr9 setdefaultrmaxr:r2r>rrBrT)rLrVZ out_pdb_lineslinesrZparents_per_chainZ parent_dictrOrIZmax_idxZ chain_parentsrWZ chain_counterr-r r r!add_pdb_headerssB       r]c!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. r1rr#cstj|dS)NZUNK)r Z restype_1to3r2)r^r;r r!res_1to3szto_pdb..res_1to3zInvalid aatypes.rr Ng?ATOMrSg?Az<6z>5z<4z>1z>3z>4z z>8.3fr*z>6.2fz z>2TrXz rYr+)r r;rr atom_typesrrrrrArZint32rranyr3 ValueErrorrUr%extendshapestringascii_uppercaser:r9r=rT)!rLr`reZ pdb_linesrrrrrrheadersnZ atom_indexZprev_chain_indexZ chain_tagsZ chain_tagrIZ res_name_3Z atom_nameposrJZb_factorZ record_typenameZalt_locZinsertion_codeZ occupancyelementZchargeZ atom_lineZshould_terminateZ chain_endZchain_termination_liner r_r!to_pdbs      &       0    rqcCs 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. )r ZSTANDARD_ATOM_MASKr)rLr r r!ideal_atom_masks rrfeaturesresultrrrrrc 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. rZfinal_atom_positionsZfinal_atom_maskrr N) rrrrrrrrr)r rZ zeros_like)rsrtrrrrrr r r!from_prediction+s rur$)NNNNN)r dataclassesr8rjtypingrrrrrrrr numpyrrcr rrZ FeatureDictZ ModelOutputrC dataclassr rKrrUr]rqrrrur r r r!sN(   %22]