o *j'@sdZddlZddlZddlZddlmZmZmZddlZ ddl m Z dZ idgdgdgd gd gd gd gdgd gdgdgd gdgdgdgdgd gdgdgdgd gdgdgdgdgdgdgdgdgdgdgdgdgdgd gdgdgdgdgd gd!gd"gdgdgd#gdgd gd$gd%gd&gd'ggdgdggdgdggdgd(Z gd)gd*gd+gd+gd,gd-gd-gd)gd+gd+gd+gd*gd-gd+gd+gd,gd,gd+gd+gd,gZgd)gd)gd)gd.gd)gd)gd/gd)gd)gd)gd)gd)gd)gd.gd)gd)gd)gd)gd.gd)gd)gZidgd0gd1gd2gd3gd4gdgd5gd1gd6gd7gd8gd9gd:gd;gd<gd=gd>g d gd?gd1gd2gd@gdAgdBgdCgdDgdgdEgd1gdFgdGgdHgdIgdJgdKgdgdLgd1gdMgdNgdOgdPgdgdQgd1gdRgdSgdHgdTgdUgdVgdWg dgdXgd1gd2gdYgd8gdZgd[gd\gd]g dgd^gd1gd_gdHgdgd`gd1gdagdbgdcgddgdegdfgdggdhg dgdigd1gdjgdkgdlgdmgdngdogdgdpgd1gd6gdqgdrgdsgdtgdugdgdvgd1gdRgdwgdHgdxgdygdzgd{g dgd|gd1gdagd}gdOgd~gdgdgd"gdgd1gdgdgdHgdgdgdgdgdgdg d#gdgd1gdgdgdgdgdgd$gdgd1gd6gdgdHgdgd&gdgd1gdgdgd8gdgdggdgd1gdgdgd4gdgdgdgdgdgdgdgdgdggdgd1gdgdgdlgdgdgdgdgdgdgdg gdgd1gdjgdgdlgdgdgd(Zidgddgddgdd gddgddgddgddgddgddgddgddgddgdd"gdd#gdd$gdd&gd¢gdâgdĢgdŢd(Zddiddiddd̜ddd̜d͜ZdddddҜZedgdԢZedgd֢Zejdd׍ddلZddgZddgZddgZddgZgdZddeeDZe eZ!idgddgdd gddgddgddgddgddgddgddgddgddgddgdd"gdd#gdd$gdd&gdgdgdgdgddZ"gdZ#ddee#DZ$e e#Z%e%Z&e#dgZ'ddee'DZ( d^de)dee)e*fde+de j,fddZ-idddddd d dd dd dd dd ddddddddddddd"dd#dd$dd&ddddZ.dde./DZ0dZ1dde#De1gZ2ddee2DZ3iddd d!d d"d d!d d#dd$d d%dd&dd'd(d)dd*dd+dd,dd-d.d)dd/d d0d1d2d3d"d4d5d)d6d#d7d8 Z4iddd"d d!d d#d d$dd%d d&dd'dd*dd+dd,dd-dd/dd0d d1dd2dd3dd9d:d;dd<d=Z5e#ddd?e8e e6DZ9de j,fd@dAZ:e:Z;dBe*de j,fdCdDZdEde#DZ?e dFdGe?e)dHZ?e @dIde?DZ?eAeBZCe /D]$\ZDZEeeED]\ZFZGeeGD]\ZHZIeCeDeIfJeFeHfqqqeKeCZCdJdKZLe jMd7dLge jNdMZOe jMd7dLge jPdMZQe jMgdNe jPdMZRe jMd7d1ge jNdMZSe jMd7d1ge jPdMZTe jMgdOe jPdMZUe jMgdPe jPdMZVdQdRZWeW S 2d_dTdUZXdVdWZYeY\ZZZ[ZTdXdYZ\e\Z]dZd[Z^e^Z_d\d]Z`e`ZadS(`zConstants used in AlphaFold.N)ListMappingTuple)tree_mapgj@ZALAZARG)NCACBCG)rrr CD)rr r NE)r r r CZZASN)rrr OD1ASPZCYS)rrrSGZGLN)rr r OE1GLUZGLYZHIS)rrr ND1ZILE)rrrCG1)rrrCD1ZLEU)rrr rZLYS)rr r CE)r r rNZZMET)rrr SD)rr rrPHEZPROZSER)rrrOGZTHR)rrrOG1)TRPTYRVAL)rrr)?rrr)rrrr)rrrr)rrrr)rrrr)rrrr)rr)+?r)rr)rrr)Cr)"~j?r$)rr)!rhS㥛gHzG)O)Mb?ˡE?r)rr)S㥛n?r$)r"r)ffffff?r$r$)rr)r+L7A`gMbX)r'r()x&1?r*r)r )gʡE?= ףp=?r$)r )g?5^I ?g9v?r)r )gsh|??ʡE?r$)NH1)g|?5^?g rh@r)NH2r6)g9v@gK?r$)r r6)gK7A?grh|?r$)rr)x&r4r)rr)gˡEgv/g333333)r'r()?r*r)r r0)g㥛 ?Mb?r)ND2r2)`"?g5^I gMbP?)r r2)gK7A?gl?r)rr)r r,r$)r"r);On?rr$)rr)Er.S)r'r()r/r*r$)r r0)r<g|?5^?r$)r r2)gQ?~jt?r)OD2r2)gl?gV-~jth)rr)NbX9r,r$)r"r)Mb?rr)rr)gS㥛#~j1Zd)r'r()r9r*r$)rr0)gK?g r?r)rr)r>-?r$)r"r)r#rr)rr)r g!rhZd;O)r r0)Gz?g}?5^I?r)r r2)gbX9?r:r$)NE2r3)r<g/$MbP)rr3)g}?5^I?g(\?r)rr)gL7A`rGr)rr)r>gˡErH)r r0)rIgʡE?r)r r2)333333?g'1Z?r)rr3)Cl?gQ?r$)OE2r3)g +?gDlrK)rr)gMg1Zd?r)r"r)gʡE?r$r$)rr)gw/(\?r)r"r)r-rr)rr)r r.r?)r'r()r95^I ?r)r r0)rLQ?r$)CD2r2)g r?gtVg~jth?)rr2)g+?g(\?r$)CE1r2)g= ףp=@gZd;?gMb`?)rJr2)g)\(@gmݿgMbp?)rr)gZd;O߿+?r$)r"r)r=r$r$)rr)r8K7A` rh)r'r()r)r*r$)rr0)gJ +?gˡE?r$)CG2r0)HzG?gQgv/)rr2)+?K7A?r)rr)gp= ףr!r)rr)rCrEgCl)r'r()r9rPr$)r r0)gV-?gV-?r)rr2)g(\?gzG?r$)rRr2)gQ?r&333333?)rr)r>r,r$)rr)r+r.r?)r r0)rYr1r)r r2)gS?gy&1?r)rr3)gQ?g-?r)rr6)g|?5^?gx&1?r)rr)y&1m?r$)rr)#~jEg\(\)r r0)gV-?rZr$)rr2)g"~?gQ?r)rr3)g{Gz?g~jt?r$)rr)~jtr!r)r"r)rDrr$)rr)r r_rF)r r0)rMgx&1?r)rr2)g㥛 ?Q?r$)rRr2)gd;O?gA`"r)rSr2)g7A`@g^I +?r$)CE2r2)gbX9@K7r$)r r2)g'1Z@rBrK)rr)g&1gV-?r$)r"r)r=r$r)rr)gFxgZd;Og㥛 )r'r()gZd;?guV?r)r r0)g r?gQ?r)r r2)gI +?gbX9?r)rr)r%rOr$)rr)r`gw/gK7A`)rr0)gjt?g333333?r)rr)g%Cr]r)r"r)r#rr$)rr)gPnrUgq= ףp)rWr0)g?g`"gS)rr0)gh|?5?gS?r)rr)r\r!r)r"r)r-r$r)rr)r^r_rF)r r0)grh|?rQr$)rr2)g|?5^?r@r)rRr2)gS?g|?5^{Gzt)rbr2)grh|@gV-y&1|)CE3r2)gCl?g= ףp=re)NE1r2)gQ@gGz?gMbp)CH2r2)gMbX9@gQg9v)CZ2r2)g$C @g㥛 I +)CZ3r2)gq= ףp?g&1 rj)rr)rCr,r)r"r)rDr$r$)rr)rCr_rV)r r0)rMg&1?r$)rr2)gx?rar$)rRr2)g7A`?gvrK)rSr2)gB`"@r[Mb`)rbr2)gE@rcrB)OHr2)gy&1@rlrd)r r2)gS@rKrB)rr)gV-߿rTr$)rr)guVgq= ףprV)rr0)rXgw/?r$)rWr0)guV?r_gsh|??)r"rrrr') r"rrr r r rr r'r5r7)r"rrr rr'r rA)r"rrr rr;r'r )r"rrrr'r) r"rrr r rr'rrN) r"rrr r rrJr'r)r"rrr') r"rrr rRrSrrrJr')r"rrrrWrrr')r"rrr rrRrr') r"rrr r rrrr')r"rrr rrr'r) r"rrr rrRrSrbr rr')r"rrr r rr')r"rrrr'r)r"rrrWrr'r)r"rrr rrRrbrfrirkrhrrgr') r"rrr rrRrSrbr rr'rm)r"rrrrWrr'r rArrNrRrb)rrS)rrrrg333333?g?gRQ?g?)r"rr'SBond) atom1_name atom2_namelengthstddev BondAngle)rprq atom3name angle_radrs)maxsizec Cstjtjtjtd}t|ddd }|}Wdn1s%wYt| }i}t ||D]1}| dkrBn(| \}}}} | d\} } ||vrYg||<|| t| | t|t| q8g|d<i} t |t ||D]=}| dkrn4| \}}} }| d\} } }|| vrg| |<| | t| | |t| dtjt|dtjqzg| d<d d }i}| D]\}}i}||D] }||||j|j<qg||<|D]}|||j|j}|||j|j}|j}t|jd |jd d |j|jt|}d |}d |j|jt||}d |jd |jt||}d |jd |jt||}t||jd ||jd ||jd } || t|j|j|| qq||| fS) aLoad stereo_chemical_props.txt into a nice structure. Load literature values for bond lengths and bond angles and translate bond angles into the length of the opposite edge of the triangle ("residue_virtual_bonds"). Returns: residue_bonds: Dict that maps resname -> list of Bond tuples. residue_virtual_bonds: Dict that maps resname -> list of Bond tuples. residue_bond_angles: Dict that maps resname -> list of BondAngle tuples. zstereo_chemical_props.txtrtzutf-8)encodingN-UNKgf@cSsdt||gS)zUnique key to lookup bonds.rz)joinsorted)rprqr~y/var/www/html/Deteccion_Ine/venv/lib/python3.10/site-packages/modelscope/models/science/unifold/data/residue_constants.py make_bond_keysz1load_stereo_chemical_props..make_bond_keyg?)ospathr|dirnameabspath__file__openreaditer splitlinesnextstripsplitappendrofloatrtnppiitemsrprqrurvsqrtrrcossinrs)Zstereo_chemical_props_pathfZstereo_chemical_propsZ lines_iter residue_bondslineZbondresnamerrrsZatom1Zatom2Zresidue_bond_anglesZ angle_degreeZ stddev_degreeZatom3rresidue_virtual_bondsZ bond_anglesZ bond_cachebbaZbond1Zbond2gammaZdl_outerZ dl_dgammaZdl_db1Zdl_db2r~r~rload_stereo_chemical_propss        rg$C?g~jt?gy&1?gMb?gJ{/LgPs?g -ܿgU؟?)%rrr"rr'r rrWrrrr rrRrr;r rArrrSrbrfr rgrJrrNrhr5r7rmr rirkrZOXTcCi|]\}}||qSr~r~).0i atom_typer~r~r =r)rrr"r'rrrrrrrrr)rrr"r'rr r r r r5r7rrr)rrr"r'rr r r;rrrrrr)rrr"r'rr r rArrrrrr)rrr"r'rrrrrrrrrr)rrr"r'rr r rrJrrrrr)rrr"r'rr r rrNrrrrr)rrr"r'rrrrrrrrrr)rrr"r'rr rrRrSrJrrrr)rrr"r'rrrWrrrrrrr)rrr"r'rr rrRrrrrrr)rrr"r'rr r rrrrrrr)rrr"r'rr rrrrrrrr)rrr"r'rr rrRrSrbr rrr)rrr"r'rr r rrrrrrr)rrr"r'rrrrrrrrrr)rrr"r'rrrWrrrrrrr)rrr"r'rr rrRrgrbrfrirkrh)rrr"r'rr rrRrSrbr rmrr)rrr"r'rrrWrrrrrrr)rrrrrrrrrrrrrr)rrrr{)ARrDr"QEGHILKMFPrnTWYVcCrr~r~rrrestyper~r~rrrXcCrr~r~rr~r~rrsFsequencemappingmap_unknown_to_xreturncCst|d}tt|tt|kr tdt|tjt ||ftj d}t |D](\}}|rN| rG| rG|||d}n td|||}d|||f<q0|S)aMaps the given sequence into a one-hot encoded matrix. Args: sequence: An amino acid sequence. mapping: A dictionary mapping amino acids to integers. map_unknown_to_x: If True, any amino acid that is not in the mapping will be mapped to the unknown amino acid 'X'. If the mapping doesn't contain amino acid 'X', an error will be thrown. If False, any amino acid not in the mapping will throw an error. Returns: A numpy array of shape (seq_len, num_unique_aas) with one-hot encoding of the sequence. Raises: ValueError: If the mapping doesn't contain values from 0 to num_unique_aas - 1 without any gaps. zQThe mapping must have values from 0 to num_unique_aas-1 without any gaps. Got: %sZdtyperz#Invalid character in the sequence: )maxvaluesr}setlistrange ValueErrorrzeroslenint32 enumerateisalphaisupperget)rrrZ num_entriesZ one_hot_arrZaa_indexZaa_typeZaa_idr~r~rsequence_to_onehots$ rrrrrr"rrrrrrrrrrrnrrrr)rrrcCrr~r~)rkvr~r~rrrr{cCg|]}t|qSr~ restype_1to3rrr~r~r !rcCrr~r~)rrrr~r~rr"rBrrr(r0r2r3r6J r' ) rrnrUrrrrZrzrrrrz)rrrrrccs|] }tt|VqdSN)restypes_with_x_and_gapindexID_TO_HHBLITS_AA)rrr~r~r ds  rcCs\tjtdtgtjd}ttD]\}}t|}t|}|D] }t |}d|||f<qq|S)z3Returns [num_res_types, num_atom_types] mask array.rr) rr restype_num atom_type_numrrrestypesr residue_atoms atom_order)maskrrestype_letterZ restype_name atom_namesZ atom_namerr~r~r_make_standard_atom_maskisr atom_indexc si}g}tD]\}}fdd|D}|dgdt||||<qtD]}t|}tt||}| |q(| t dtgtj |dd}t |gd}|S)z:Define chi-angle rigid groups via one-hot representations.csg|] }t|qSr~) atom_typesr)rsrr~rrsz"chi_angle_atom..r0rZaxis)rrr) chi_angles_atomsrextendrrrreyerrrstack transpose) rZchi_angles_indexZone_hotsrrindicesrZres3Zone_hotr~rrchi_angle_atom{s  rcCsg|]}tt|qSr~)rrrr~r~rrcCst|Srr)nr~r~rsr)Z leaf_typecCs&g|]}|gdgdt|qS)rrrrr0)r)rZ chi_atomsr~r~rrscCsr|tj|}|t|||}|tj|}t||}t||||g}tj|gdggdd}|S)zBCreate a rigid 4x4 transformation matrix from two axes and transl.)rrrrrr)rZlinalgZnormdotcrossrrZ concatenate)exey translationZ ex_normalizedZ ey_normalizedZeznormmr~r~r_make_rigid_transformation_4x4s  r%r)rrr()rrr()rrr0r0c s\ttD]G\}}t|}t|D]:\}}}t|}|t||f<dt||f<|t||ddf<t| |}|t ||f<dt ||f<|t ||ddf<qqttD]\}}t|}ddt|Dt dt|dddddf<t dt|dddddf<tddt gd dd }|t|d ddddf<td dddd d }|t|d ddddf<t|drt|d} fdd| D} t| d | d| d| d| d d }|t|dddddf<tddD]/} t|| r*t|| d } | } t| t gd| d }|t|d| ddddf<qqPdS)zFill the arrays above.rNcSsi|] \}}}|t|qSr~)rarray)rname_posr~r~rrs z/_make_rigid_group_constants..r0rrr)rrr)r r r rr"r(cg|]}|qSr~r~rrZatom_positionsr~rrsz/_make_rigid_group_constants..)grr)rrrrigid_group_atom_positionsrrestype_atom37_to_rigid_grouprestype_atom37_mask$restype_atom37_rigid_group_positionsrestype_name_to_atom14_namesrrestype_atom14_to_rigid_grouprestype_atom14_mask$restype_atom14_rigid_group_positionsrr!restype_rigid_group_default_framerrchi_angles_maskrr)rrrZatomnameZ group_idxZ atom_positionZatomtypeZ atom14idxZmatZbase_atom_namesZbase_atom_positionsZchi_idxZaxis_end_atom_nameZaxis_end_atom_positionr~rr_make_rigid_group_constantss         r"?cCstgdtj}tgdtj}tgdtj}t\}}}ttD]\}} t| } t| } t| D]G\} } | scompute upper and lower bounds for bonds to assess violations.)rrrrg _B) lower_bound upper_boundrs)rrfloat32rrrrrvan_der_waals_radiusrrprqrrrs)Zoverlap_toleranceZbond_length_tolerance_factorZrestype_atom14_bond_lower_boundZrestype_atom14_bond_upper_boundZrestype_atom14_bond_stddevrrrrrrZ atom_listZ atom1_idxrpZ atom1_radiusZ atom2_idxrqZ atom2_radiuslowerupperrr~r~rmake_atom14_dists_boundss       r*csg}g}g}tD]1}tt|}|dd|Dddt|D|fddtD|dd|Dq|dgd|dgd |d gdtj|tjd }tj|tjd }tj|tj d }|||fS) NcSsg|] }|r t|ndqSrrrr~r~rrUsz5_make_atom14_and_atom37_constants..cSrr~r~)rrrr~r~rrWrz5_make_atom14_and_atom37_constants..cs g|] }|vr |ndqSr+r~rZatom_name_to_idx14r~rrXscSsg|]}|rdndqS)rrr~rr~r~rr]srrrrr) rrrrrrrrrr&)restype_atom14_to_atom37restype_atom37_to_atom14rrxrr~r,r!_make_atom14_and_atom37_constantsNs4     r/c sddtD}|dg7}dd|DtD]@\}}td}|D].\}}t||}t||}|||<|||<td}t|D] \} } d|| | f<qGq$||<qt fd d|D} | S) NcSrr~rrresr~r~rrxrz+_make_renaming_matrices..r{cSsi|]}|tdqS)r)rrr0r~r~rr|rz+_make_renaming_matrices..r)rrrcrr~r~)rrZ all_matricesr~rrr) rresidue_atom_renaming_swapsrrZarangerrrrr) Z restype_3rswapZcorrespondencesZsource_atom_swapZtarget_atom_swapZ source_indexZ target_indexZrenaming_matrixrZcorrespondencerenaming_matricesr~r2r_make_renaming_matricesus.    r6cCsrtd}tD]-\}}|D]$\}}tt|}t||}t||}d|||f<d|||f<qq |S)N)rrr)rrr3r restype_order restype_3to1rr)restype_atom14_is_ambiguousrr4Z atom_name1Z atom_name2rZ atom_idx1Z atom_idx2r~r~r_make_atom14_is_ambiguouss   r:cCsg}tD]2}t|}t|}g}|D] }|dd|Dqtdt|D] }|gdq'||q|gdgd|S)ajReturns atom indices needed to compute chi angles for all residue types. Returns: A tensor of shape [residue_types=21, chis=4, atoms=4]. The residue types are in the order specified in restypes + unknown residue type at the end. For chi angles which are not defined on the residue, the positions indices are by default set to 0. cSrr~r)ratomr~r~rrrz(get_chi_atom_indices..r0r)rrrrrr)chi_atom_indicesZ residue_nameZresidue_chi_anglesZ atom_indicesZ chi_anglerr~r~rget_chi_atom_indicess  r=)F)r#r)b__doc__ collections functoolsrtypingrrrnumpyrZ unicore.utilsrZca_carr!Zchi_pi_periodicrrr3r' namedtuplerort lru_cacherZbetween_res_bond_length_c_nZ"between_res_bond_length_stddev_c_nZbetween_res_cos_angles_c_n_caZbetween_res_cos_angles_ca_c_nrrrrrrrr7rZunk_restype_indexZrestypes_with_xZrestype_order_with_xstrintboolZndarrayrrrr8Z unk_restypeZresnamesZresname_to_idxZHHBLITS_AA_TO_IDrrtuplerZ MAP_HHBLITS_AATYPE_TO_OUR_AATYPErZSTANDARD_ATOM_MASKrZchi_atom_1_one_hotZchi_atom_2_one_hotZchi_angles_atom_indicesr defaultdictrZchi_groups_for_atomZres_nameZchi_angle_atoms_for_resZ chi_group_iZ chi_groupZatom_ir;rdictrrint_rr&rrrrrr r"r*r/r-r.r6r5r:r9r=r<r~r~r~rs*       %& ' ()1$)1<GMYcmx",U     /  ^',.024DEFHq  ,                           N 8$