B b (%@sdZddddddddd d d d d ddddddddddddddddddd d!d"d#d$d%g%ZGd&d'd'eZGd(ddeZed)ddZed*dd+Zed,dd-Zed.dd/d0d1gZed2dd d3d4gZ ed5d d6d7d8gZ ed9d d:Z ed;d dZ edd?d@gZ edAd dBZedCddDZedEddFZedGddHdIgZedJddKZedLddMZedNddOZedPddQZedRddSZedTddUZedVddWZedXddYZGdZddeZGd[ddeZed\dd]d^d_d`gZedaddbdcdddedfgZedgddhdidjdkdlgZedmddndodpgZed\dd]dqdrdsdtdudvdwgZ edad dbdxdydzd{d|d}d~dg Z!edgddhdddddddgZ"eddddddddddgZ#edmdSdndddddddgZ$dddddddhZ%e%dhBZ&ddhZ'dddddddddddddddddHdhZ(ddddddddhZ)e(e)BZ*dBS)zq This module contains basic information and functionality related to individual residues in typical biopolymers. AminoAcidResidue RNAResidue DNAResidueALAARGASNASPCYSGLUGLNGLYHISHYPILELEULYSMETPHEPROSERTHRTRPTYRVALDADTDGDCAUGC SOLVENT_NAMESEXTRA_POINT_NAMES CATION_NAMES ANION_NAMES ALLION_NAMESc@sNeZdZdZeZeZeZgZddZ e ddZ ddZ e dd Z d S) BiomolecularResiduez9 Base class for different classes of biopolymer residues cOs tddS)Nz&BiomolecularResidue must be subclassed)NotImplementedError)selfargskwargsr+-lib/python3.7/site-packages/parmed/residue.pyZ__init_szBiomolecularResidue.__init_cCs tddS)Nz&BiomolecularResidue must be subclassed)r')clskeyr+r+r,getszBiomolecularResidue.getcCs|jS)N)name)r(r+r+r,__str__szBiomolecularResidue.__str__cCs@t|tr||jkSy||Wntk r6dSXdSdS)a Determines if a particular BiomolecularResidue or residue name is present in this classification of biomolecular residues Parameters ---------- thing : str or :class:`BiomolecularResidue` Returns ------- contains : bool If the residue or residue name *is* of this type, True. Otherwise, False. FTN) isinstancer& all_residuesr/KeyError)r-thingr+r+r,hass  zBiomolecularResidue.hasN)__name__ __module__ __qualname____doc__dict_all_residues_by_name_all_residues_by_abbr_all_residues_by_symbolr3Z_BiomolecularResidue__init_ classmethodr/r1r6r+r+r+r,r&s r&c@sFeZdZdZeZeZeZgZd ddZ ddZ e d dd Z dS) ra An individual amino acid residue. Parameters ---------- name : str The name of the residue abbr : str The 3-letter abbreviation of the amino acid residue symbol : str The 1-letter symbol of the amino acid aliases : list of str, optional A list of other abbreviations that *also* refer to this residue Raises ------ ValueError If any aliases have the same abbreviation as *other* NcCs||_||_||_|t|j|<|t|j|<|dk rP|t|j|<t|j ||dk rx<|D]4}|}|t|jkrt d||t|j|<qnWdS)Nz%s is already an abbreviation) r0abbrsymboltyper<upperr=r>r3append ValueError)r(r0r@rAaliasesaliasr+r+r,__init__Ss  zAminoAcidResidue.__init__cCsd|j|j|jfS)Nz )r0r@rA)r(r+r+r,__repr__cs zAminoAcidResidue.__repr__FcCsxt|dkr|s|j|St|dkr8|j|St|dkrj|ddkrj|j|ddS|j|S)a Gets the amino acid corresponding to either the residue name, 3-letter abbreviation or 1-letter symbol. It is case-insensitive. Parameters ---------- key : str 1-letter symbol, 3-letter abbreviation, or residue name abbronly : bool If True, only look for the 3-letter abbreviation (not the 1-letter symbol) Returns ------- residue : :class:`AminoAcidResidue` The residue corresponding to the given key Raises ------ KeyError if ``key`` is not a symbol, abbreviation, or case-insensitive name of an amino acid residue, or any of its abbreviations. CNN)lenr>rCr=r<)r-r.Zabbronlyr+r+r,r/gs zAminoAcidResidue.get)N)F) r7r8r9r:r;r<r=r>r3rHrIr?r/r+r+r+r,r:s ZAlanineZArginineRZ AsparagineNZ AspartateDZASHZAS4ZCysteineZCYMZCYXZ GlutamateEZGLHZGL4Z GlutamineQZGlycineZ HistidineHZHIPZHIEZHIDZHydroxyprolineNZ IsoleucineIZLeucineLZLysineKZLYNZ MethionineMZ PhenylalanineFZProlinePZSerineSZ ThreonineTZ TryptophanWZTyrosineYZValineVc@sDeZdZdZeZeZeZgZd ddZ ddZ e ddZ dS) ra An individual DNA residue Parameters ---------- name : str The name of the residue abbr : str The abbreviation of the nucleic acid residue aliases : list of str, optional A list of other abbreviations that *also* refer to this residue NcCs||_||_|t|j|<|t|j|<t|j||dk rx<|D]4}|}|t|jkrttd||t|j|<qNWdS)Nz%s is already an abbreviation) r0r@rBr<rCr=r3rDrE)r(r0r@rFrGr+r+r,rHs  zDNAResidue.__init__cCsd|j|jfS)Nz)r0r@)r(r+r+r,rIszDNAResidue.__repr__cCsTy0|ddkr$|j|ddS|j|Stk rN|j|SXdS)a Gets the nucleic acid corresponding to either the residue name or abbreviation. It is case-insensitive. Parameters ---------- key : str abbreviation or residue name Returns ------- residue : :class:`DNAResidue` The residue corresponding to the given key Raises ------ KeyError if ``key`` is not a recognized residue name or abbreviation for an DNA residue. 35N)r=rCr4r<)r-r.r+r+r,r/s  zDNAResidue.get)N) r7r8r9r:r;r<r=r>r3rHrIr?r/r+r+r+r,rs  c@s:eZdZdZeZeZeZgZddZ e ddZ dS)ra An individual RNA residue Parameters ---------- name : str The name of the residue abbr : str The abbreviation of the nucleic acid residue aliases : list of str, optional A list of other abbreviations that *also* refer to this residue cCsd|j|jfS)Nz)r0r@)r(r+r+r,rIszRNAResidue.__repr__cCsTy0|ddkr$|j|ddS|j|Stk rN|j|SXdS)a Gets the nucleic acid corresponding to either the residue name or abbreviation. It is case-insensitive. Parameters ---------- key : str abbreviation or residue name Returns ------- residue : :class:`RNAResidue` The residue corresponding to the given key Raises ------ KeyError if ``key`` is not a recognized residue name or abbreviation for an RNA residue. rarbN)r=rCr4r<)r-r.r+r+r,r/s  zRNAResidue.getN) r7r8r9r:r;r<r=r>r3rIr?r/r+r+r+r,rs ZGuanineZGUAZDG5ZDG3ZDGNZCytosineZCYTZDC5ZDC3ZDCNZDCPZAdenineZADEZDA5ZDA3ZDANZDAPZThymineZTHYZDT5ZDT3ZG5ZG3ZGNZRGZRG3ZRG5ZRGNZCPZC5ZC3rNZRCZRC5ZRC3ZRCNZAPZA5ZA3ZANZRAZRA3ZRA5ZUracilZURAZU3ZU5ZUNZRUZRU3ZRU5ZRUNZT3ZT5ZTNZRTZRT3ZRT5ZRTNZWATZHOHZTIP3ZTIP4ZTIP5ZSPCEZSPCZSOLZEPZLPzNa+zLi+zMg+zRb+ZMGzCs+ZPOTZSODZMG2ZCALZRUBZLITZZN2ZCD2ZNAzK+zNA+zCl-zBr-zF-zI-ZCLAZCLZBRzCL-)+r:__all__objectr&rrrrrrr r r r r rrrrrrrrrrrrrrrrrrr rrr]Z WATER_NAMESr!r"r#r$r%r+r+r+r,sf  ,N                =0