%Tc@sdZddlmZddlmZmZmZmZmZm Z m Z m Z ddlm Z ddlmZddlmZddlmZyddlmZWn!ek rdd lmZnXdd lmZdd lmZdd lmZdd lmZmZdZ dZ!dZ"e#dj$dZ%e#dj$dZ&e#ddddgZ'dZ(dfdYZ)dZ*e*Z+de,fdYZ-dS(s]The pseudoMolecule class for storing atomic coordinate data and updating Coot as appropriate.i(tdeepcopy(tnew_generic_object_numbertset_display_generic_objecttto_generic_object_add_linet graphics_drawtclose_generic_objecttclose_moleculet&get_molecule_bonds_colour_map_rotationt&set_molecule_bonds_colour_map_rotation(tadd_molecule_py(tclear_and_update_molecule_py(tresidue_info_py(t svn_revision(tpython_representation_kk(tpython_representation(tChain(t Nucleotide(tdist(t BOND_LISTtBOND_DIST_CUTOFFtorangesRCrane-molecule-%ig4@s'C2' O2' C3' O3' C4' O4' C5' O5' OP1 OP2t s,N6 O6 N2 N7 N3 C5 C4 N1 C8 C6 O4 O2 N9 N4 C2tPtOP1tOP2tOP3g@tPseudoMoleculecBsEeZdZedOdOdOdOdZdZdZdZdZ dZ dZ dZ d Z d Zd Zd Zd ZdZedZedZdZdZdZdZdZdZdZdZdZedZdOdOdZ dZ!dZ"dZ#dZ$d Z%d!Z&d"Z'd#Z(d$Z)dOdOd%Z*d&Z+d'Z,d(Z-d)Z.d*Z/d+Z0e1d,Z2e1d-Z3d.d/Z4d.d0Z5d1Z6d2Z7d3Z8d4Z9d5Z:d6Z;d7Z<ed8Z=d9Z>iZ?e@eAd:jBd;eCd<e?d=jBd;eCd<e?d?g?s PN(RR'R(RBRAR6R(R7RC((s\/public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/python2.7/site-packages/coot/rcrane/pseudoMolecule.pyt addPhos5ps Lc Cs|jd|jd}|jdkr6t|}n|jd7_|j}|||ddg?s CsC1'iis %ss P s PiN(RR'R(RR@RAtappendtcentertextendRBR!R0R1RR2R3R4R5R6tgetPhosCoordsFromIndexRRt BATONCOLORR( R7tbaseTypet baseCoordst phosCoordsRDR(t baseAtomListtcurAtomRERFtprevPhosCoordstc1coords((s\/public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/python2.7/site-packages/coot/rcrane/pseudoMolecule.pytaddBaseAndPhoss@ ,  H  4 " ==c Cs|jd|jd}|jdkr6d}d}nB||jdd}|dkr`d}n|jd7_|j}ddgdtdg|dd!gd dgdtd g|d dd!gg}xd|D]\}|d krqn|j|jd dgdtd |dd!g||dd!gqW|d||g} |jdkrrx!|D]} | dcd7g?s Pis C1's CsC1'is %siiN(RR'R(RR)RARIRJRBR@R!R0R1RR2R3R4R5R6RLRRRMR(R7RNRORPRDR(t newResNumtatomListRRRFtcurRest new5pResNumRSRT((s\/public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/python2.7/site-packages/coot/rcrane/pseudoMolecule.pytaddBaseAndPhos5psB    ",  H   " ==cCst|tr$|dkr$|}n|j|}xJ|jd|jd|dD](}|ddjdkrT|dSqTWdS(s/Get the coordinates of a specified phosphate. ARGUMENTS: resNum - the residue number RETURNS: the coordinates of the phoshate from residue resNum NOTE: Negative integers can be used to refer to phosphates at the end of the chain (i.e. resNum = -1 will return the coordinates of the last phosphate). If you want to refer to a nucleotide with an actual negative residue number (very uncommon, but they do exist), then pass the number as a string (i.e. "-1") iiiRiN(t isinstancetinttresIndexRR'tstripR(R7tresNumR]RR((s\/public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/python2.7/site-packages/coot/rcrane/pseudoMolecule.pyt getPhosCoordsks  ' cCsQxJ|jd|jdtdD](}|ddjdkr!|dSq!WdS(sGet the coordinates of a specified phosphate. ARGUMENTS: resIndex - the residue index RETURNS: the coordinates of the phoshate from residue resIndex iiiRiN(RR'R]R^R(R7R_RR((s\/public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/python2.7/site-packages/coot/rcrane/pseudoMolecule.pyRLs ' cCsQxJ|jd|jd|dD](}|ddjdkr!|dSq!WdS(sGet the coordinates of a specified C1' atom (NOT the entire sugar). ARGUMENTS: resIndex - the residue index RETURNS: the coordinates of the C1' from the specified residue NOTE: Negative numbers can be used to refer to C1' atoms at the end of the chain (i.e. resNum = -1 will return the coordinates of the last C1') iiisC1'iN(RR'R^(R7R]RR((s\/public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/python2.7/site-packages/coot/rcrane/pseudoMolecule.pytgetSugarCoordsFromIndexs'cCsQxJ|jd|jd|dD](}|ddj|kr!|dSq!WdS(sGet the coordinates of a specified atom ARGUMENTS: atomName - the name of the atom to get coordinates for resIndex - the residue index RETURNS: the coordinates of the specified atom iiiiN(RR'R^R(R7tatomNameR]RR((s\/public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/python2.7/site-packages/coot/rcrane/pseudoMolecule.pytgetAtomCoordsFromIndexs ' cCst|jdS(sclose the Coot generic object for the batons connecting the phosphate and C1' atoms. ARGUMENTS: None RETURNS: None EFFECTS: The batons generic object will be closed N(RR(R7((s\/public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/python2.7/site-packages/coot/rcrane/pseudoMolecule.pytcloseBatonObjects cCst|jd|jdS(sGet the number of nucleotides in the molecule. ARGUMENTS: None RETURNS: the number of nucleotides in the molecule ii(R@RR'(R7((s\/public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/python2.7/site-packages/coot/rcrane/pseudoMolecule.pyt getNumNtss c Cs-|jdkrd S|jd krFt|jd|jd}n |j}|d}|jd|jd|}|jd|jd|}|d}t}x>|ddD].}|ddj}|d} | ||3'. This function provides the equivalent functionality when tracing 3'->5'. This function should *not* be called for pseudoMolecule objects created via the createFromMolecule argument. iiiiisAccepted BatonsiN(NN(ReRR)RR'tpopRfR^R(R!R0R1RRRRRgR@RLRaRRMRR6R(R7tfirstNtRlRCRmRbRnRXRoRSRpRPRqRr((s\/public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/python2.7/site-packages/coot/rcrane/pseudoMolecule.pytremoveFirstBaseAndPhos/s@!   *  +( =Ac Cst}x|jd|jdD]}|d}t|dt|dj}i}x:|dD].}|ddj}|d}|||g?s %siiiN( t iteritemsRIRAR]RR'RKR6R(R7R_t sugarCoordsRWRbRCR]((s\/public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/python2.7/site-packages/coot/rcrane/pseudoMolecule.pytaddSugar s 8'cCs|j|}x\|jd|jd|dD]:}|ddj}|j|r0|||dg?s OiiiN(RRIRARR'RKR6R(R7R]RRWRbRC((s\/public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/python2.7/site-packages/coot/rcrane/pseudoMolecule.pyRKs  ,'cCsi}xr|jd|jd|ddD]L}|dd}|dksW|dkr+|j}nq+|d||Update the Python representation of the specified residues. ARGUMENTS: startingResNum - the first residue to update, using Coot numbering endingResNum - the last residue to update, using Coot numbering RETURNS: newCoordDicts - a list of dictionaries containing the updated atom coordinates EFFECTS: updates the Python representation of the specified residues NOTE: This function must be run whenever atom coordinates are changed in Coot (such as after a minimization run) iiii( R]RgR_t residue_infoRR&RR'R^RI( R7tstartingResNumt endingResNumtstartingResIndextendingResIndext newCoordDictst curResIndext curResNumt curInsCodet newCoordst curResDictRRRb((s\/public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/python2.7/site-packages/coot/rcrane/pseudoMolecule.pyt updateRess  cCst|jdS(sDelete the Coot molecule associated with this object. ARGUMENTS: None RETURNS: None N(RR(R7((s\/public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/python2.7/site-packages/coot/rcrane/pseudoMolecule.pytdeleteMolecules cCsE|j|}|j|}t|jd|jd||d!S(sRetrieve the Coot structure for the specified nucleotides. ARGUMENTS: startingRes - the first residue to retrieve the structure for endingRes - the last residue to retrieve the structure for RETURNS: a copy of the Coot representation of residues startingRes-endingRes NOTE This function is used to cache structure so that it can easily be restored later. ii(R]RRR'(R7t startingRest endingRest startingIndext endingIndex((s\/public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/python2.7/site-packages/coot/rcrane/pseudoMolecule.pyt getCootNucss cCsg|j|}|j|}t||jd|jd||d+|rct|j|jndS(sjSet the structure for the given nucleotides given a Coot-formatted list (typically something that had previously been returned by getCootNucs) ARGUMENTS: startingRes - the first residue to set the structure for endingRes - the last residue to set the structure for cootNucs - a list of the nucleotides to restore, formatted in the Coot internal representation format (typically returned from the getCootNucs function) OPTIONAL ARGUMENTS: updateMol - whether to update the Coot molecule via clear_and_update_molecule defaults to True ONLY use this if you know the Coot molecule will be updated at a later time RETURNS: None EFFECTS: sets the coordinates of the specified nucleotides to cootNucs iiN(R]RRR'R6R(R7RRtcootNucst updateMolRR((s\/public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/python2.7/site-packages/coot/rcrane/pseudoMolecule.pyt setCootNucss )cCs5|j|}|j|}|dk r@||j|}nd}|jd|jd}xt||dD]} | |} xtt|| ddddD]p} || d| ddj} || d| ddj} | dks| tkr|| d| =qqW|dk rC| |krC| dkrC| dkrC|| dk rCxjtt|| dD]N} || d| ddjdkrv|| d|| d| d %5;\%L [\ 5\%L  cCs,|jdk rt|jnd|_dS(sClears any extra bonds drawn by drawExtraBonds ARGUMENTS: None RETURNS: None EFFECTS: Clears all bonds in drawing object self.__extraBondObject N(R RR(R7((s\/public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/python2.7/site-packages/coot/rcrane/pseudoMolecule.pyRs cCs8|j|}|j|d}||_||_dS(sSSet the nucleotides that will have extra bonds drawn during any subsequent drawExtraBonds() call ARGUMENTS startingResNum - the residue number of the first residue to draw bonds for endingResNum - the residue number of the lsat residue to draw bonds for RETURNS: None iN(R]R"R#(R7RRRR((s\/public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/python2.7/site-packages/coot/rcrane/pseudoMolecule.pytsetExtraBondRanges  cCsd|_d|_dS(sMake any subsequent drawExtraBonds() call draw extra bonds for the entire molecule ARGUMENTS None RETURNS: None N(RR"R#(R7((s\/public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/python2.7/site-packages/coot/rcrane/pseudoMolecule.pytclearExtraBondRanges cCs|jt|S(sFind the index (i.e. position in the chain) of a given residue number ARGUMENTS: resNum - the residue number to find (which may include an insertion code) RETURNS: the index of the specified residue number in this chain (R!R0(R7R_((s\/public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/python2.7/site-packages/coot/rcrane/pseudoMolecule.pyR]s cCs.|jd|jd|}|d|dfS(sGiven a residue index, retrieves the residue number and insertion code ARGUMENTS: resIndex - the residue index RETURNS: the residue number (without the insertion code) the insertion code ii(RR'(R7R]tres((s\/public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/python2.7/site-packages/coot/rcrane/pseudoMolecule.pyR_s cCs>|jd|jd|}t|dt|djS(sGiven a residue index, retrieves the full residue number (i.e. including insertion code) ARGUMENTS: resIndex - the residue index RETURNS: the residue number as a string including the insertion code ii(RR'R0R^(R7R]R((s\/public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/python2.7/site-packages/coot/rcrane/pseudoMolecule.pyt resNumFulls cCs{g|jd|jdD]$}t|dt|d^q}tgt|D]\}}||f^qS|_dS(sinitialize the resNum lookup dictionary if this object was created with an initial residue list ARGUMENTS: None RETURNS: None iiN(RR'R0Rft enumerateR!(R7Rt resNumListR]R_((s\/public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/python2.7/site-packages/coot/rcrane/pseudoMolecule.pyt__initializeResNumDicts Cc Cs|j|}|j|}i}xt||dD]t}|j|}i||N(RetFalseRR'R^RtTrue(R7R]tdistanceCutoffRRto3CoordsRP((s\/public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/python2.7/site-packages/coot/rcrane/pseudoMolecule.pyRs" ' + *cCs(|dkrtS|j|d|SdS(sDetermine if a nucleotide is connected to the previous nucleotide ARGUMENTS: resIndex - the residue index OPTIONAL ARGUMENTS: distanceCutoff - how long can the O3'-P bond be before the nucleotides are considered not connected RETURNS: True if the residue is connected to the previous one False otherwise iiN(RR(R7R]R((s\/public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/python2.7/site-packages/coot/rcrane/pseudoMolecule.pyRs g@cCs#|j|}|j||dS(sDetermine if a nucleotide is connected to the next nucleotide ARGUMENTS: resNum - the residue number OPTIONAL ARGUMENTS: distanceCutoff - how long can the O3'-P bond be before the nucleotides are considered not connected RETURNS: True if the residue is connected to the next one False otherwise N(R]R(R7R_RR]((s\/public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/python2.7/site-packages/coot/rcrane/pseudoMolecule.pytconnectedToNexts cCs#|j|}|j||dS(sDetermine if a nucleotide is connected to the next nucleotide ARGUMENTS: resNum - the residue number OPTIONAL ARGUMENTS: distanceCutoff - how long can the O3'-P bond be before the nucleotides are considered not connected RETURNS: True if the residue is connected to the previous one False otherwise N(R]R(R7R_RR]((s\/public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/python2.7/site-packages/coot/rcrane/pseudoMolecule.pytconnectedToPrevs cCs|jd|jd|d}|dks8|dkrAd}n%|dksY|dkrbd }nd Sg|jd|jd|d D]}|ddj^q}t|}x+d d |fD]}||kr|SqWdSdS(s*Make sure that the specified nucleotide contains phosphate and glycosidic bond coordinates ARGUMENTS: resIndex - the residue index RETURNS: None if the nucleotide contains the required atoms atom name of a missing atom otherwise iiitCtUtN1R?RtN9sN1/9iRsC1'N(RR'R^RR(R7R]tresTypetbaseNRRWtatomSetRR((s\/public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/python2.7/site-packages/coot/rcrane/pseudoMolecule.pytcheckPhosAndGlycosidicFromIndexs   A  cCsQxJ|jd|jd|dD]$}|ddjdkr!tSq!WtSdS(sFind out if a given residue using PDB2-style naming ARGUMENTS: resIndex - the residue index to check RETURNS: True if this residue uses PDB2-style naming False otherwise NOTES: Currently, this function simply checks for a C1* atom. If it exists, then the residue is assumed to use PDB2 naming. Otherwise, the residue is assumed to be okay iiisC1*N(RR'R^RR(R7R]RR((s\/public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/python2.7/site-packages/coot/rcrane/pseudoMolecule.pytcheckPDB2FromIndexs 'cCs$t|jd|jd|dS(sReturn the number of atoms within a given residue (useful for deciding if a residue is just a phosphate) ARGUMENTS resIndex - the residue index to check RETURNS: the number of atoms in residue resIndex iii(R@RR'(R7R]((s\/public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/python2.7/site-packages/coot/rcrane/pseudoMolecule.pytnumAtomsFromIndexscCs|j|}|j|S(s<Calculate all torsions for the specified suite. ARGUMENTS: resNum - the suite number to calculate torsions for RETURNS a list containing the seven suite torsions note that missing suite atoms will result in None entries for the undefined torsions (R]tcalcSuiteTorsionsFromIndex(R7R_R]((s\/public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/python2.7/site-packages/coot/rcrane/pseudoMolecule.pytcalcSuiteTorsions$s cCs|dks|j| r dS|j|d|}|jdj|jdj|jdj|jdj|jdj|jdj |jdjgS(s=Calculate all torsions for the specified suite. ARGUMENTS: resIndex - the suite index to calculate torsions for RETURNS a list containing the seven suite torsions note that missing suite atoms will result in None entries for the undefined torsions iiN( RRR~tnucstdeltatepsilontzetatalphatbetatgamma(R7R]Rx((s\/public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/python2.7/site-packages/coot/rcrane/pseudoMolecule.pyR2s cCsx|jdD]}x|dD]}|dd}|dddkr|dddkr|dddkr|dddkr|dddkr|djqqWqWdS( sLWork around a bug in Coot's python_representation function where any TER lines in the PDB file get converted to an unnamed atom with no occupancy at coordinates (0,0,0) ARGUMENTS: None RETURNS: None EFFECTS: Removes any "blank" atoms from self.__molecule iiiiR>giN(RRt(R7tcurChainRXt finalAtom((s\/public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/python2.7/site-packages/coot/rcrane/pseudoMolecule.pyt __fixTerAtomsKs dcCstdkrdSxe|jdD]V}xM|dD]A}x8|dD],}t|ddtrCtdqCqCWq2Wq!WdS(sMake sure that we're not going to have any problems with anisotropic temperature records ARGUMENTS: None RETURNS: None EXCEPTIONS: raises a PseudoMoleculeError if Coot is older than revision 3631 and self.__molecule contains anisotropic temperature records, since clear_and_update_molecule() won't be able to handle reading the molecule back in i/NiiisThis molecule contains anisotropic temperature records. RCrane requires Coot 0.7-pre r3631 or newer to rotamerize molecules with anisotropic temperature records.(R RR[tlistR/(R7RRXRR((s\/public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/python2.7/site-packages/coot/rcrane/pseudoMolecule.pyt __checkAnisohscCsu|j|}g|jd|jd|dD]}|dd^q0}|rmg|D]}|j^qWS|SdS(szGet a list of all the atom names in a specific residue ARGUMENTS: resNum - the residue number to get atom names from OPTIONAL ARGUMENTS: strip - whether to remove leading and trailing spaces from the atom names defaults to True RETURNS: atomNames - a list of atom names iiiN(R]RR'R^(R7R_R^R]RRt atomNames((s\/public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/python2.7/site-packages/coot/rcrane/pseudoMolecule.pyt getAtomNamess ;cCs$t|jd|jd|dS(sGet the residue type (i.e. A, G, C, or U) of the specified residue ARGUMENTS: resIndex - the residue index RETURNS: the residue type of the specified residue iii(R0RR'(R7R]((s\/public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/python2.7/site-packages/coot/rcrane/pseudoMolecule.pytresTypeFromIndexs sKP OP1 OP2 O5' C5' C4' O4' C3' O3' C2' O2' C1' N9 C8 N7 C5 C6 N6 N1 C2 N3 C4Ri(RsNP OP1 OP2 O5' C5' C4' O4' C3' O3' C2' O2' C1' N9 C8 N7 C5 C6 O6 N1 C2 N2 N3 C4R?sEP OP1 OP2 O5' C5' C4' O4' C3' O3' C2' O2' C1' N1 C2 O2 N3 C4 N4 C5 C6RsEP OP1 OP2 O5' C5' C4' O4' C3' O3' C2' O2' C1' N1 C2 O2 N3 C4 O4 C5 C6Rcsd}d}jdk r?jdk r?j}j}nxGjdjd||!D]&djdfdq_Wxojdjd||!D]Ndddd}|dkrx#dD]}||ddsR>N(RR"R#RR'tsortR6R(R7t fixSegidsRRt desiredSegidRR((RXR7s\/public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/python2.7/site-packages/coot/rcrane/pseudoMolecule.pytfinalMoleculeCleanups  &$& cCs|jd|jd|d}t|dkr6tSxP|jd|jd|dD]*}|ddj}|tkrWtSqWWtSdS(sKDetermine if the specified residue contains no more than a phosphate group (i.e. P, OP1, OP2, and/or OP3) ARGUMENTS: resIndex - the residue index RETURNS: True if the specified residue is only a phosphate group (or a subset of a phosphate group) False otherwise iiiiN(RR'R@RR^tPHOS_GROUP_ATOMSR(R7R]RWRRRb((s\/public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/python2.7/site-packages/coot/rcrane/pseudoMolecule.pytisOnlyPhosGroupFromIndexs ' cCs|j|}|j|S(sJDetermine if the specified residue contains no more than a phosphate group (i.e. P, OP1, OP2, and/or OP3) ARGUMENTS: resNum - the residue number RETURNS: True if the specified residue is only a phosphate group (or a subset of a phosphate group) False otherwise (R]R(R7R_R]((s\/public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/python2.7/site-packages/coot/rcrane/pseudoMolecule.pytisOnlyPhosGroups cCsQxJ|jd|jd|dD](}|ddjdkr!|dSq!WdS(sGet the coordinates of a specified phosphate. ARGUMENTS: resIndex - the residue index RETURNS: the coordinates of the phoshate from the specified residue iiiRiN(RR'R^R(R7R]RR((s\/public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/python2.7/site-packages/coot/rcrane/pseudoMolecule.pyRLs ' cCs||_||_dS(sSet the residue insertion point (i.e. where in the chain new nucleotides should be added). This is only necessary when doing an extend chain. ARGUMENTS: resIndex - the residue index to use as the residue insertion point RETURNS: None NOTE: This sets both resInsertionPoint and origResInsertionPoint N(R(R)(R7R]((s\/public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/python2.7/site-packages/coot/rcrane/pseudoMolecule.pytsetResInsertionPoints cCs%t|jd|jd|_dS(sStore the state of the entire molecule (can be restored via restoreMoleculeState) ARGUMENTS: None RETURNS: None iiN(RRR'R*(R7((s\/public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/python2.7/site-packages/coot/rcrane/pseudoMolecule.pytsaveMoleculeState$s cCsI|jdk rA|j|jd|jds@: ^