ó Ñ%Tc@s?dZddlmZmZmZdZddd„ƒYZdS(s=A class for storing information about individual nucleotides.iÿÿÿÿ(ttorsiontdistt distToLinesC1't NucleotidecBs¼eZdZdd„Zd„Zd„Zd„Zd„Zd„Z d„Z d„Z d „Z d „Z d „Zd „Zd „Zd„Zd„Zd„Zd„Zd„Zd„ZRS(scA class for storing information about individual nucleotides (which may be part of a Chain object).cCs1||_||_||_d|_d|_dS(szInitialize a Nucleotide object ARGUMENTS: type - the nucleotide type (i.e. A, C, G, or U) atoms - a hash of atom coordinates (in the form atomName: [x, y, z]) OPTIONAL ARGUMENTS: resNum - the residue number (possibly including an insertion code) RETURNS: an initialized Nucleotide object N(ttypetatomstresNumtNonetchaintseqNum(tselfRRR((sX/public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/python2.7/site-packages/coot/rcrane/nucleotide.pyt__init__s    cCs,|jdkr$|jj|jdSdSdS(sRIf this nucleotide is part of a chain, return the previous nucleotide in the chain ARGUMENTS: None RETURNS: The Nucleotide object of the previous nucleotide if there is one None if this is the first nucleotide of the chain,or if this nucleotide is not part of a chain. iiN(R Rt nucleotidesR(R ((sX/public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/python2.7/site-packages/coot/rcrane/nucleotide.pytprevNuc,s cCs5|j|jjƒkr-|jj|jdSdSdS(sIIf this nucleotide is part of a chain, return the next nucleotide in the chain ARGUMENTS: None RETURNS: The Nucleotide object of the next nucleotide if there is one None if this is the last nucleotide of the chain or if this nucleotide is not part of a chain. iN(R RtlenR R(R ((sX/public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/python2.7/site-packages/coot/rcrane/nucleotide.pytnextNuc<s cCs |jdkS(söIs this nucleotide connected to the previous nucleotide of the chain? ARGUMENTS: None RETURNS: True if this nucleotide is connected to the previous nucleotide of the chain False if it isn't or if this nucleotide is not part of a chain. NOTE: Because the chain module does not currently support unconnected nucleotides, this function only tells you if this is the first nucleotide of the chain or not. i(R (R ((sX/public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/python2.7/site-packages/coot/rcrane/nucleotide.pytconnectedToPrevLs cCs|j|jjƒdkS(s†Is this nucleotide connected to the next nucleotide of the chain? ARGUMENTS: None RETURNS: True if this nucleotide is connected to the previous nucleotide of the chain False if it isn't Note that the behavior of this function (unlike that of connectedToPrev()) is not defined if this nucleotide is not part of a chain. (Currently, it raises an error.) NOTE: Because the chain module does not currently support unconnected nucleotides, this function only tells you if this is the last nucleotide of the chain or not. i(R RR(R ((sX/public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/python2.7/site-packages/coot/rcrane/nucleotide.pytconnectedToNext\scCs|jj|ƒS(sæDoes this nucleotide contain the specified atom? ARGUMENTS: atomName - the name of the atom to check for RETURNS: True if this nucleotide contains atomName, False otherwise (Rthas_key(R tatomName((sX/public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/python2.7/site-packages/coot/rcrane/nucleotide.pythasAtomns cCs£|jƒr›|jƒr›|jƒjtƒr›|jdƒr›|jtƒr›|jƒjdƒr›t|jƒjt|jd|jt|jƒjdƒSdSdS(sçCalculate the eta pseudotorsion for the current nucleotide ARGUMENTS: None RETURNS: The value of eta if it is defined, None otherwise. NOTE: Calculating eta requires the sugar atom of the previous nucleotide and the phosphate atom of the next nucleotide. As a result, behaviour of this function is undefined if this nucleotide is not part of a chain. (Currently, it raises an error.) tPN( RRR Rt SUGARATOMRRRR(R ((sX/public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/python2.7/site-packages/coot/rcrane/nucleotide.pytetays   cCs—|jƒr|jdƒr|jtƒr|jƒjdƒr|jƒjtƒrt|jd|jt|jƒjd|jƒjtƒSdSdS(sÈCalculate the theta pseudotorsion for the current nucleotide ARGUMENTS: None RETURNS: The value of theta if it is defined, None otherwise. NOTE: Calculating theta requires the phosphate and sugar atom of the next nucleotide. As a result, behaviour of this function is undefined if this nucleotide is not part of a chain. (Currently, it raises an error.) RN(RRRRRRR(R ((sX/public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/python2.7/site-packages/coot/rcrane/nucleotide.pyttheta”s   cCs¬|jdƒr|jd}n%|jdƒr>|jd}nd}|dk r¤|jtƒr¤|jƒr¤|jƒjdƒr¤t|jƒjd|jt|ƒSdSdS(sÓCalculate the base-phosphate perpendicular distance (P-perp distance) for the current nucleotide ARGUMENTS: None RETURNS: The P-perp distance if it is defined, None otherwise NOTE: Calculating P-perp requires the phosphate of the next nucleotide. As a result, behaviour of this function is undefined if this nucleotide is not part of a chain. (Currently, it raises an error.) tN9tN1RN(RRRRRRR(R tbaseN((sX/public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/python2.7/site-packages/coot/rcrane/nucleotide.pytpperp¯s< cCsY|jƒrQ|jdƒrQ|jƒjdƒrQt|jd|jƒjdƒSdSdS(s¢Calculate the phosphate-phosphate distance ARGUMENTS: None RETURNS: The distance from the phosphate of this nucleotide to the phosphate of the next nucleotide None if no next phosphate if present NOTE: Behavior of this function is undefined if this nucleotide is not part of a chain. (Currently, it raises an error.) RN(RRRRRR(R ((sX/public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/python2.7/site-packages/coot/rcrane/nucleotide.pytphosDistÌs 0!cCsY|jƒrQ|jtƒrQ|jƒjtƒrQt|jt|jƒjtƒSdSdS(sÛCalculate the sugar-sugar distance for the starting suite of this nucleotide ARGUMENTS: None RETURNS: the distance from the sugar atom (i.e. C1') of the previous nucleotide to the sugar atom (C1') of this nucleotide None if there is no previous nucleotide NOTE: Behavior of this function is undefined if this nucleotide is not part of a chain. (Currently, it returns None.) N(RRRR RRR(R ((sX/public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/python2.7/site-packages/coot/rcrane/nucleotide.pytstartingSugarDistßs 0!cCs$|jƒr|jƒjƒSdSdS(sØCalculate the sugar-sugar distance for the ending suite of this nucleotide ARGUMENTS: None RETURNS: the distance from the sugar atom (i.e. C1') of this nucleotide to the sugar atom (C1') of the next nucleotide None if there is no previous nucleotide NOTE: Behavior of this function is undefined if this nucleotide is not part of a chain. (Currently, it raises an error.) N(RRRR(R ((sX/public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/python2.7/site-packages/coot/rcrane/nucleotide.pytendingSugarDistòs cCs›dt|jƒd}|dt|jƒd7}|dt|jƒd7}|d7}x=|jjƒD],\}}|d|dt|ƒd7}qgW|S(s,Create a string representation of the objects Nuc Num: s s Seq Num: s Nuc type: sAtoms: s s: (tstrRR RRt iteritems(R tretValtnametcoords((sX/public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/python2.7/site-packages/coot/rcrane/nucleotide.pyt__str__s $cCs‹|jƒrƒ|jƒjdƒrƒ|jdƒrƒ|jdƒrƒ|jdƒrƒt|jd|jd|jd|jƒjdƒSdSdS(s£Calculate the alpha torsion ARGUMENTS: None RETURNS: The value of alpha if it is defined, None otherwise. sO3'RsO5'sC5'N(RR RRRR(R ((sX/public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/python2.7/site-packages/coot/rcrane/nucleotide.pytalphas    cCss|jdƒrk|jdƒrk|jdƒrk|jdƒrkt|jd|jd|jd|jdƒSdSdS(s¡Calculate the beta torsion ARGUMENTS: None RETURNS: The value of beta if it is defined, None otherwise. RsO5'sC5'sC4'N(RRRR(R ((sX/public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/python2.7/site-packages/coot/rcrane/nucleotide.pytbeta's    cCss|jdƒrk|jdƒrk|jdƒrk|jdƒrkt|jd|jd|jd|jdƒSdSdS(s£Calculate the gamma torsion ARGUMENTS: None RETURNS: The value of gamma if it is defined, None otherwise. sO5'sC5'sC4'sC3'N(RRRR(R ((sX/public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/python2.7/site-packages/coot/rcrane/nucleotide.pytgamma=s    cCss|jdƒrk|jdƒrk|jdƒrk|jdƒrkt|jd|jd|jd|jdƒSdSdS(s£Calculate the delta torsion ARGUMENTS: None RETURNS: The value of delta if it is defined, None otherwise. sC5'sC4'sC3'sO3'N(RRRR(R ((sX/public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/python2.7/site-packages/coot/rcrane/nucleotide.pytdeltaSs    cCs‹|jƒrƒ|jdƒrƒ|jdƒrƒ|jdƒrƒ|jƒjdƒrƒt|jd|jd|jd|jƒjdƒSdSdS(s§Calculate the epsilon torsion ARGUMENTS: None RETURNS: The value of epsilon if it is defined, None otherwise. sC4'sC3'sO3'RN(RRRRRR(R ((sX/public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/python2.7/site-packages/coot/rcrane/nucleotide.pytepsilonis    cCs—|jƒr|jdƒr|jdƒr|jƒjdƒr|jƒjdƒrt|jd|jd|jƒjd|jƒjdƒSdSdS(s¡Calculate the zeta torsion ARGUMENTS: None RETURNS: The value of zeta if it is defined, None otherwise. sC3'sO3'RsO5'N(RRRRRR(R ((sX/public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/python2.7/site-packages/coot/rcrane/nucleotide.pytzetas   N(t__name__t __module__t__doc__RR R RRRRRRRRRRR%R&R'R(R)R*R+(((sX/public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/python2.7/site-packages/coot/rcrane/nucleotide.pyRs(                N((R.t strucCalcRRRRR(((sX/public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/python2.7/site-packages/coot/rcrane/nucleotide.pyts