֙xTc2@ sHddlmZddlZddlZgZgZgZgZdddddddddddddg Zej egZ dddddddddddddg Zej egZ dd d dd d dddddddg Zej egZ dd d d d d d ddddddg Zej egZ dddddddddd dddg Zej egZdd d dd d dddddddg Zej egZdd d ddd d ddddddg Zej egZddd dddd ddddddg Zej egZdd dddd dddddddg Zej egZddd dddd ddddddg Zej egZdd dddd dddddddg Zej egZddd dd dd ddddddg Zej egZdd dd dd dddddddg Zej egZddd dd dd ddddddg Zej egZdd dd dd ddddddd g Zej egZdd!d!d d"d"d ddddddg Zej egZdd!d!d d#d#d ddddddg Zej egZdd$d$d d%d%d ddddddg Zej egZd&d$d$d d d%d#d#d%ddddg Zej egZd&d$d!d d d%d#d#d"ddddg Zej egZd&d!d$d d d#d%d"d#ddddg Zej egZdd$d!d d d%d"ddd'd(d)d*g Zej egZdd!d$d d d"d%ddd'd(d)d*g Zej egZ d&d$d d dd#d d%d d+d,d-d.g Zej egZ!d&d d$dd d d#d d%d/d0d1d2g Zej egZ"ddd!dd dd"ddd3dd4d5g Zej egZ#dd!dd dd"dddd3dd4d5g Zej egZ$ddd!dd dd#ddd6d7d8d9g Zej egZ%dd!dd dd#dddd6d7d8d9g Zej egZ&dd$d d#dd d ddd:d;d<d=g Zej egZ'dd d$dd#d d ddd:d;d<d=g Zej egZ(ddd!dd"dd ddd>d.d?d@g Zej egZ)dd!dd"dd dddd>d.d?d@g Zej egZ*ddd!dd#dd dddAdBdCdDg Zej egZ+dd!dd#dd dddddEdFdGg Zej egZ,ddd$dd dd%dddHdIdJdKg Zej egZ-dd$dd dd%ddddLdMdNdOg Zej egZ.ddd$dd%dd ddddddg Zej egZ/dd$dd%dd dddddddg Zej egZ0dd d!dd"d d ddddddg Zej egZ1dd!d d"dd d ddddddg Zej egZ2dd d!dd#d d dddPdQdRdSg Zej egZ3dd!d d#dd d dddTdUdVdWg Zej egZ4ddd$dd dd#ddddddg Zej egZ5ddd$d dd#dddddddg Zej egZ6dd d$d d%d d ddddddg Zej egZ7dd$d d%d d d ddddddg Zej egZ8dd d d dd d ddddddg Zej egZ9ddd!dd dd#dddXdYdZdg Zej egZ:dd!dd dd#d[dddXdYdZdg Zej eggggggggggggggggggggggggggggggggggggggggggggggggggg2Zd\d]d^d_d`dadbdcdddedfdgdhdidjdkdldmdndodpdqdrdsdtdudvdwdxdydzd{d|d}d~dddddddddddddddg2Z;ggggggggggggggggggggggggggggggggggggggggggggggggggg2Z<e=dZ>dZ?dZ@dZAdZBdZCdZDdZEdZFdZGdZHdZIdZJdZKdZLdZMdZNdZOe?dejPdZQeQdZRgeQdZdeeko-deeko-deeko-deeko-d eekr-eBeeeeeeend eekr-ej eendeekr.ej eeee^edj endeekrC.ej eeee^edj en~deekr.ej eeee^edj en?d eekr.ej eeee^edj enxee^ekD]ZegeddeekoC/deekoC/deekoC/deekoC/deekoC/d eekrh/ekej eeedZnq.Wq.-WeCed GHdGeGdGHgggZxee^egdD]ZdGegeddGHdGHdGHdGHdGHeUdeedegeddddZeededdeeko>deeko>deeko>deeko>d,eekrI>ej eeddfedZnq=Wegkr?ejeZejedejedddfejedddfejedddfejedddfejedddfejedddfejeddd&fejeddd&fejedddfejedddfejdg eefGeedGd?GeedGd@GeedGd?GeedGHdAGdBGedd Gd1Gedd GdCGedd Gd?Ged&d GdDGedd Gd?Gedd Gd>Gedd Gd?Gedd Gd@Gedd Gd?Gedd GHdEGe;eGdFGeGdGHndZxee^eD]Ze;eeedkrEedkr-EdGGe;eGdHGHnedZeeeee^eedddfeeddfeeeeZnqDWedkrEdIGe;eGdFGeGdGHndZxee^eD]Ze;eeedkrpFedkrFdJGe;eGdHGHnedZeeeee^eedddfeeddfeeeeZnqEWedkrFdKGe;eGdFGeGdGHnqAWdGHd GHgggZeUdeedLddZeeded        ( , , cC s9|d|dkrg|d|dkrg|d|d<|d|d<|d|d<|d d|d High confidence 3-bond basepair formed by residues s and Rs The bases in this basepair may be participating in an interaction with other bases. However, the detection of 3 bonds, makes its assignment as a 3-bond basepair highly probable.RsY----->At least 2 bonds identified out of 3 expected for the base pair formed by residues s4----->2-bond basepair identified formed by residues s/##### END of Initial Basepair Assignment. Run #sm ############################## ##### Searching for additional basepairs by the ELIMINATION criterion. Run # sA##### Number of additional basepairs identified by ELIMINATION = s Run # s############################## sAFTER Bulk Removal: Run # s############################## NO newly identified basepairs to be removed from the list BASES WITH POSSIBLE MULTIPLE CONTACTS. sRun # s############################## NO BASES WITH POSSIBLE MULTIPLE CONTACTS have been identified. Assignement of furhter additional basepairs by the ELIMINATION criterion not possible s~ ############################## ##### SEARCHING FOR ADDITIONAL BASEPAIRS BY USING THE CONTINUITY OF HELICITY CRITERIUM /nRun #s^AFTER SEARCHING FOR ADDITIONAL BASEPAIRS BY USING THE CONTINUITY OF HELICITY CRITERIUM: Run # s ############################## BYPASSING THE SEARCH FOR ADDITIONAL BASEPAIRS BY USING THE CONTINUITY OF HELICITY CRITERIUM /nRun #(RRjRItMASTER_Basepairs_bondsRRtMASTER_Basepairs_schemestMASTER_Basepairs_excludedRRtintRRRRRRRRRR(+t First_ListRRRRRRt run_numberRtFirst_List_smallert First_List_Pt First_List_C1RtC1tMASTER_BasepairsRRRRRRRRHtatomRtfoundRItrt C1_comparetsRRRt first_appendRRRtlength_1RRRt loop_outputR((sA/public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/mmtbx/pdb_distances.pytprogrampsP"( (8dSjZ ! 0HT,&xLx4,<!<,B BV <+7$"" f0B )$   JB )$ 0B )$ &    !   cC st|}t|}t|}t|}d|d|}|GHd|krxd|krx||d|d}ng}g}g} x tt|D]} xtt|| D]} tjd|| | d} | j} tjd|| | d} | j}d|krd || | krd || | kr| |kr`||ksx||kr| |kr||g}| | g} qd|krd || | krd || | kr| |kr||ks| |kr||kr||g}| | g} qd |krd || | krd || | kr| |kr^||ksv||kr| |kr||g}| | g} qqWqW||| gS( Ns> Searching for possible basepairs between residues s and tiiiiiiiiiiiiiiis s\d+iiRRRRR(RRRjRRR(tLISTta0ta1ta2ta3RRt match_found1t match_found2tmatch_positionRR!Rtmatch1tmatch2((sA/public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/mmtbx/pdb_distances.pyR s6      d d d Riis\/+s\.g@g @gg?s ############################################################################################ ############################################################################################ ###### Run # sDISTANCE CUTOFF = s ############################################################################################ ############################################################################################ cC stjd|d}|j}t|}tjd|d}|j}t|}|d|d|d|dg}t|} t||} d| d| dd | d| d} | GHd | d| dd | d| dd | dd | dd | dd | d} | GHd } t|| d| d| d| d| }d}xtddD] }||gkrn|d}t||dt||d|dkrd| d| dd | d| dd||dd ||dd} | GHn|dkryd| d| dd | d| dd||dd ||dd} | GHqyqnqnW|dkrd} | GHn||gS(Ns\d+iiiis= ...using the CONTINUITY OF HELICITY CRITERION criterion for iis and s2 Checking whether the basepair formed by residues sf could be involved in a helical element Searching for the following possible basepair candidates: s or Rs; ##### !!!!Found an adjacent basepair to residues s* This basepair is formed by residues s ##### sA ##### !!!!Found a second adjacent basepair to residues s ##### s4 Neither basepair was found!!!!!( RRRRRRRRR(tMASTER_Basepairs_summary_lineRRRRRRRRRRRRRRRR((sA/public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/mmtbx/pdb_distances.pytCONTINUITY_HELICITY_CRITERIONs>    " *Z+  N N c C sddg} dGHt|t|ddt|t|ddd} t|t|ddt|t|ddd} d||d||d|dd |t|dd ||d|| d |dd |t|d} | | krv| GHd ||d||d |dd||d|| d |dd}|GHddg} n| | kr| GHd ||d|| d |dd||d||d |dd}|GHddg} nd|t|dGH| S(Nis ...using the CUTOFF criterioniii s& The basepair formed by residues Rs and with a s, geometry was assigned at a CUTOFF value of s) whereas the basepair formed by residues s and with a s therefore the s basepair, with a s! geometry, fares better than the s! geometry by the CUTOFF criterionsD Both basepairs have been assigned at the same CUTOFF value of (tfloatRj(RRRRRRtA4tA5tA6tA7tscoretfloat_1tfloat_2RR((sA/public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/mmtbx/pdb_distances.pytCUTOFF_CRITERIONs" >>v N Nc C sIddg} dGH|d|dkrrd||d||d||d|| d} d| dR@RRR iis ################ Basepair, Rs with geometry s and basepair iisI share one base!!!!!! Attempting to deconvolute these two basepairs with s stringency bys5Number of helical elements continuous with basepair, s = sE ################ Two possible geometries for the basepair formed by s, i.e.: s and sCALCULATING SCOREsCALCULATING scoretLOWs$Number of succesful deconvolutions =sTwo base sharings# AFTER DETECTION OF FALSE BASEPAIRSs ########################################################################## ORDERING OUTPUT ########################################################################## Rs\d+cC s(|t|}d}|||}|S(NR(Rj(tSTRINGtNUMtresulttspace((sA/public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/mmtbx/pdb_distances.pyt ADD_SPACES3 sc C st|d|d}t|d|d}t|d|d}|ddkrt|d|d}t|d|d}n0t|d|d }t|d|d }|d |d |d |d |d g} d } xtt| D]} | | d kr d | | Number of BASE-SHARING BASEPAIRS THAT CANNOT BE DECONVOLUTED =s_MISSING-BOND-basepairss LIST OF MISSING-BOND BASEPAIRSs"Number of MISSING-BOND BASEPAIRS =s9############### 'NF' notes Not-found bond ###############tmisssn s0.0s.STATISTICAL VALUES CALCULATED WITHIN STRUCTUREs Bond1: MEAN =sSD =sBond2: MEAN = s Bond3: MEAN =sP-to-P distance =sC1'-to-C1' distance =sNo Basepairs =s(No basepairs of this geometry were founds' LIST OF BASEPAIRS ORDERED BY GEOMETRYs\S+sg=======================================================================================================sg Scheme Resid Base Resid Base Expect. Found ATOM ATOM DIST. DIFF. DIST DIFF. DIST DIFF.sa #1 #1 #2 #2 Bonds Bonds #1 #2 BOND P-P C1'-C1'sPRECALCULATED STATISTICAL DATA:s P-to-P distance =s SD =s C1'-to-C1' distance =s(STATISTICAL DATA FROM CURRENT STRUCTURE:s Bond1: MEAN =s Bond2: MEAN =s Bond3: MEAN =sNUMBER OF BASEPAIRS WITHs geometry =sLIST FALSE BASEPAIRS WITHs geometry:sNUMBER OF FALSE BASEPAIRS WITHs#LIST OF UNDETERMINED BASEPAIRS WITHs%NUMBER OF UNDETERMINED BASEPAIRS WITHs_UNASSIGNABLE-basepairss\w+s color red, /s/*/*/sshow sticks, /s######################################################## #################### END OF PROGRAM #################### ########################################################(t __future__RtsystnumpyRRRRtbondsRIRRRRRRRRRRRRRRRR R!R"R#R$R%R&R'R(R)R*R+R,R-R.R/R0R1R2R3R4R5R6R7R8R9R:R;R<R=R>R?R@RARRtTrueRaRRRRRRRRRRRRRRRR%RtargvRtpdb_filetostgetcwdtdirRtcompiletmatfinditertiteratortaaatmatchtspanRjt directorytFILERtmmtstarttSTARTRRt run_cutoffRRRtrun_cutoff_LISTSt MAX_CUTOFFRt incrementRRRRRR2R;R<RDt$CONTINUITY_HELICITY_CRITERION_outputt while_controlt run_whilet stringencytsingle_base_sharedRCtMODERARRRRRRRRtSCORER8Rt decissionRBRRt new_list_endtmaxt yes_countRRRt compare_toRRKRTRSt count_fortzerostreshapetnew_list_end_floatstmissingtmissing_controlRR+R)R*ta4RtplacetendingtLEGITIMATE_taggedtfalsely_assignedtwrongly_assignedt missing_bondRtpymol0topentline0Rtpymol1Rtbasepair_countRRRtSTATStSUMtcountertetarraytmeantstdtshapeRtgeometry_countertgeometry_counter_realtschemet false_countertundetermined_countertprocessed_controlRt formattedtvtexit(((sA/public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/mmtbx/pdb_distances.pyts  m - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - #  W -  ,      S . , " X =      %          "  7 - & % %  ~  @ @  CC[^mR[^**  cf ccc ,              *                    +(%       @8" # < \ a <,- ?'?$ '$0   ( ( !, , $ 6.Pl   *. 9=+   .-1   .-1   .-1   .-1   .-1 + h 7   @ GLE  Z   Z   . 0