Fix test

.gitignore

@@ -0,0 +1,3 @@
+examples/input/gmm/emd_22904.mrc
+examples/runs
+examples/nestor_params_optrep_test.yaml

examples/README.md

@@ -1,5 +1,6 @@
 Here is an example describing the use of NestOR to compare six different coarse-grained representations of the Nucleosome Deacetylase (NuDe) sub-complex of the Nucleosome Remodeling and Deacetylase (NuRD) complex. The `input` and `nude_modeling.py` are adapted from the [Integrative model of the NuRD subcomplexes](https://github.com/isblab/nurd) repository.
 
+**NOTE:** _Prior to running the example, please download EM map from EMD22094, extract it, rename it as `emd_22904.mrc` and place it in `input/gmm/` directory_
 ## Description of the example files
 The `example/input` comprises of the fasta sequences (`example/input/fasta`), PDB structures (`example/input/pdb`), crosslinking mass spectrometry data (`example/input/xlms`) and an EM map along with the corresponding GMM representation (`example/input/gmm`). Each of the target crosslink file from `example/input/xlms/original_xl_data` is split into `sampling_` and `evicalc_` files as described below.
 

examples/input/gmm/HDAC1..1.txt

@@ -0,0 +1,38 @@
+#|num|weight|mean|covariance matrix|
+|0|846.4290789203807|326.19087296691765 273.64532320495846 320.20796043724806|16.618898756189406 -12.4632140212188 -15.862178611728728 -12.4632140212188 15.967544794533337 11.924736594654735 -15.862178611728728 11.924736594654734 22.620573625408888|
+|1|1223.607749185924|331.8887315828804 255.66459434799665 335.0549802072958|32.49295487326958 3.5546130135496585 0.3299877711913849 3.554613013549659 17.729453970433823 -1.6866394893331336 0.329987771191385 -1.6866394893331347 10.447229715290385|
+|2|975.1231975089638|317.14015104919173 250.39995142203065 343.19174965064366|22.436607960048608 3.733151087618844 -4.2425279785035785 3.733151087618844 7.03506951281088 3.741380765804671 -4.242527978503579 3.7413807658046707 11.751400172202066|
+|3|1101.23051448594|343.80834876122674 277.38359884585964 338.1704513188521|27.54142218270641 3.0454407181223977 -1.7001785930152429 3.0454407181223977 13.716613335919718 -2.077271111698442 -1.7001785930152429 -2.077271111698442 5.506231487633157|
+|4|579.7723551622297|338.26936236035704 255.99414231159264 307.4802129063832|7.941102370232631 14.365752372519642 -2.567190324258646 14.365752372519642 44.46245384463081 -12.96910565052082 -2.5671903242586462 -12.96910565052082 7.408767372942739|
+|5|644.4142537211229|320.8265258680368 250.5972489932394 320.2354017630685|6.558038682882418 1.5430277754585402 6.8202997649393815 1.5430277754585404 7.0758317095883685 4.228718666973238 6.820299764939383 4.228718666973238 30.26913505520502|
+|6|1992.7202818451838|338.9721673599664 267.25267488477965 332.3453991043358|35.84777980853885 0.1884400378644629 3.6133727575323897 0.18844003786446206 13.278294317676675 8.623650347229045 3.613372757532389 8.623650347229045 32.060213203783164|
+|7|581.6987046820146|347.5005263349648 254.04038015058373 340.0205380826572|16.677233728491235 3.204882965817402 -0.5911406444818865 3.204882965817403 10.030479461773465 0.5436082145593747 -0.5911406444818866 0.5436082145593748 2.9679659048631266|
+|8|1037.630504215466|333.0924094614285 250.0438099066756 315.33694138347244|23.966977824616336 -7.157319157277169 -13.814876914649986 -7.15731915727717 6.5164205819833825 3.425311706427134 -13.814876914649986 3.4253117064271326 16.10075693470629|
+|9|580.463834180983|306.7286177083292 252.45061278348223 337.51622792315965|2.593302091981078 0.8371938971263899 0.09042807228484828 0.8371938971263897 7.5298216746829425 -6.495976428062201 0.09042807228484828 -6.495976428062201 19.076347541567607|
+|10|832.2813246944233|335.8705821244239 269.7539798128192 308.696137183696|11.552523041067872 -9.446698155332292 -1.2863362698540683 -9.446698155332292 24.72314924989415 -4.1134585313544 -1.2863362698540681 -4.1134585313544 7.314410574952606|
+|11|733.0793634047135|315.37608121132524 267.49930968790665 332.08888669571786|21.952319386448565 -2.6611946050246513 -3.8419283002380875 -2.6611946050246504 6.07895333111428 3.399515584361321 -3.8419283002380875 3.399515584361322 7.424826602066684|
+|12|1465.313035285282|328.3337147802441 273.9182923078831 331.1384824309998|27.559409645448472 6.772706783852777 7.631348811700001 6.772706783852777 14.43625496761014 0.49531072589416425 7.631348811700001 0.49531072589416425 15.141187576682015|
+|13|1138.2783708382563|346.298101980798 250.10316000918323 322.05815965877565|22.906929736356656 15.23521007370873 14.11299218995663 15.235210073708732 23.653207853454337 6.300544958359142 14.11299218995663 6.300544958359141 17.621268428708998|
+|14|894.7729578492914|344.2315225156318 265.4097560088319 317.0293822172632|10.615323698046636 -7.33646513501547 -2.6586190605138507 -7.33646513501547 12.612194782638621 6.718711183785726 -2.6586190605138507 6.718711183785729 11.547559791565488|
+|15|815.8529653333687|316.01767304864956 255.40304548797076 327.7756234248477|9.952062366724116 -4.588335116063467 -6.528069604405071 -4.588335116063467 16.14104810210673 8.346300216603911 -6.528069604405073 8.346300216603915 12.74978071718142|
+|16|1582.3847266003572|324.0303844166216 270.4851029491976 307.42469665426046|20.735932036128965 -15.630103417100194 -7.843878738698315 -15.630103417100194 32.685292189385756 10.479711655621372 -7.843878738698317 10.479711655621372 11.921401907853276|
+|17|884.4632728375699|324.89028678663806 256.3208549093293 311.4214198463057|21.89226484527826 1.7065821583776135 -13.289356125823124 1.7065821583776137 10.491722644704721 -0.007835768913714514 -13.289356125823124 -0.007835768913714292 14.22576012648872|
+|18|388.26004123142366|320.72899982049637 282.7676686186706 316.8672235677957|2.711145159877613 -0.7931478258203238 -2.369737858357799 -0.793147825820324 15.96728064578552 1.2690712602774121 -2.3697378583577984 1.2690712602774121 3.5811719509742814|
+|19|728.2369016647627|333.62612105311354 265.9607115467177 342.0971473581035|10.163175027775011 0.5023531850286099 3.083391637660818 0.5023531850286099 20.223858403692393 9.956167442615655 3.0833916376608177 9.956167442615653 9.51335339015181|
+|20|1405.9120299454923|317.86427771263936 245.900665183505 331.5137889933913|34.43529859305507 -12.571068127369074 -25.741668485607327 -12.571068127369076 12.145534277346142 12.417219953722892 -25.741668485607327 12.417219953722892 31.221528569681695|
+|21|1785.1102960491166|354.50886491248957 265.60487785660365 335.63156114441125|9.222602005393098 -11.861151793529654 -5.232860673990793 -11.861151793529656 48.36142743071168 11.186539309928614 -5.232860673990793 11.186539309928614 14.801735811007388|
+|22|1326.7992317580117|337.6502183397023 257.75127291953885 316.24885607377655|40.40069436785727 -7.829018269586303 20.455174194537648 -7.829018269586303 5.938690128129931 -3.0893265762269504 20.455174194537644 -3.08932657622695 29.255928426495764|
+|23|690.5723815286315|334.5400279290018 284.043086823823 328.96298958723446|5.222221044001453 0.3473679447927298 9.894688654833379 0.3473679447927298 7.406273719239102 4.588065021427054 9.894688654833377 4.588065021427054 33.194844056764836|
+|24|1401.2106090904595|319.6059256010859 259.08607663608717 337.5616461911831|20.36953523224337 1.0433597245419644 -4.135922843555542 1.0433597245419648 12.279936477396706 -0.4400022757611931 -4.135922843555541 -0.4400022757611931 13.331073702839763|
+|25|872.5175666690354|315.3749168665881 275.7400177103618 314.70138176265436|3.683635575306765 6.129145638426353 0.16539568490660583 6.129145638426353 26.509462121948935 -3.8993508691041754 0.16539568490660583 -3.899350869104175 12.133446855553839|
+|26|1821.4030809154297|318.1380629640168 264.5841552804894 319.2892147291548|16.415105327609478 12.071194996225197 -11.689478517193882 12.071194996225197 24.101594324127852 -6.085387358748882 -11.689478517193882 -6.085387358748885 26.86234045172322|
+|27|1128.021145948448|326.43453583385696 245.13111312373877 334.955355095639|14.444768410619513 2.9802801831119137 -9.821991340662148 2.9802801831119146 11.225892588989197 5.654833698665141 -9.821991340662148 5.65483369866514 23.521197470618098|
+|28|1219.2604191048908|348.7914868612317 269.7307243888149 325.7833495846847|11.579484142763476 -20.58456535858376 -2.362111420210975 -20.584565358583756 50.09685074668972 6.1942955264239234 -2.3621114202109745 6.1942955264239234 9.210012251080949|
+|29|724.8213785064039|343.43523560050164 248.89491308500786 334.6495503240096|18.04756951473341 -7.575361003746356 0.8234747898969575 -7.575361003746356 6.0482254058757565 1.899221310725661 0.8234747898969574 1.899221310725661 13.519391479083922|
+|30|1638.5834799063214|338.21853726285093 276.13486907596007 323.22480769065146|17.726911645028263 0.38081141014849695 7.284298355855796 0.38081141014849784 14.560412650967272 15.037263341213283 7.284298355855794 15.037263341213283 48.92197652388017|
+|31|2001.590938048682|329.4915879156559 262.439424956634 322.8651543129507|13.827686854384362 9.34270957242442 0.6699589317663897 9.34270957242442 41.50647668235367 -5.051869418037441 0.6699589317663903 -5.051869418037441 25.11169395421566|
+|32|581.3491394536161|343.0431120672369 262.6001460165424 341.43009528421663|19.46622064982646 2.16669266650207 13.737539865366001 2.1666926665020703 4.525798310377969 2.6427626249760423 13.737539865366003 2.6427626249760423 12.843996453812956|
+|33|1353.064455104617|343.92013778685697 256.50604670611045 330.1846135073666|17.724250368148162 -8.066859809438146 13.334997659029163 -8.066859809438146 23.262651398282422 3.7119267612613154 13.334997659029163 3.7119267612613154 25.175188767020977|
+|34|468.36951946411233|356.4226614598452 257.188409406771 327.1673616462176|25.947216183551095 -13.42790291801061 -0.9063731759706686 -13.42790291801061 16.90547590477306 -4.551991621938771 -0.9063731759706686 -4.551991621938772 4.912247679188692|
+|35|996.6479823192707|335.2867931789084 248.58996858663005 324.65794225493306|14.446705810795281 -8.302450427109264 -7.6920964372363745 -8.302450427109264 15.081557440979163 10.130268050219282 -7.6920964372363745 10.130268050219282 14.280326245664625|
+|36|789.4546125392254|327.81131090232975 281.3171614929279 313.32756396239375|9.111192157077928 -4.146288287072303 -0.27988489480392803 -4.146288287072301 7.576547497002486 -0.2692094776925753 -0.2798848948039279 -0.26920947769257536 14.585075950037492|

examples/input/gmm/HDAC1.1.1.txt

@@ -0,0 +1,38 @@
+#|num|weight|mean|covariance matrix|
+|0|1023.6570466942228|287.74916205707785 252.4278612550699 243.27641638127423|21.668377341817568 -4.4962096732365655 -9.059326282210876 -4.496209673236566 8.011046947131586 6.523040644133771 -9.059326282210876 6.523040644133771 14.118459537501643|
+|1|1315.963702479141|288.25798421198846 268.7026583035889 265.61375198889425|23.855439185155277 -23.713467337150764 -4.768539108282659 -23.713467337150764 35.51541615601099 -0.05610998346903573 -4.76853910828266 -0.05610998346903573 10.275865831131094|
+|2|977.7988371983007|304.20711362438186 289.2447929616727 246.7543804107723|11.490883850914864 -5.681916927453315 -2.765006569722149 -5.681916927453315 14.735617002967125 12.650483279141662 -2.76500656972215 12.650483279141662 19.00680000189082|
+|3|1112.4589882026899|306.23576378668406 263.32224539196545 261.9237759002595|9.780800820362742 -0.2517105679348306 -1.8333011211029149 -0.2517105679348306 26.671631233599687 5.946642871045727 -1.8333011211029149 5.946642871045727 10.956901014416655|
+|4|1308.3663117676588|292.3209380192657 286.6673600674058 246.859478156722|14.463705025743122 -0.3731071343250667 -12.403534850119803 -0.37310713432506626 16.68954029540625 -1.9304333934935827 -12.403534850119804 -1.9304333934935825 23.845616649116547|
+|5|586.3628673560434|301.8909817731585 269.2078998687339 245.33944964779835|7.3483354897909265 -3.3113461501797867 -1.983022570298603 -3.3113461501797867 10.833885566012862 4.769271072089191 -1.9830225702986035 4.769271072089191 7.951772809712339|
+|6|1005.1402540309897|271.45099775218307 266.0994895851724 249.20006087363075|11.066105366636776 0.6221129103226097 -5.434950224088991 0.6221129103226102 9.161177538678217 4.296928107709971 -5.434950224088991 4.296928107709971 18.576814332197678|
+|7|2079.0115801687525|285.01817975321603 270.1295266525047 254.25469543122043|22.46276422041319 0.7454937311149341 4.6858177320063366 0.7454937311149346 17.53625969862798 0.48190386157827547 4.6858177320063366 0.48190386157827536 27.01701840008527|
+|8|1295.0229031675992|294.7531612584513 274.3568250646834 267.5302748078636|17.08349790313458 -9.45115122282355 5.208667103935719 -9.45115122282355 24.151809983533436 -14.056012348828862 5.208667103935719 -14.056012348828864 16.776576165050436|
+|9|748.6098043459882|296.23505935487015 254.1205950633359 265.56618647200645|17.81024593499442 -4.402696922669759 -11.40525713628112 -4.402696922669758 8.803623470937614 -0.5391023977154319 -11.405257136281119 -0.5391023977154319 15.046046672000532|
+|10|1427.537313438484|302.4757239068002 281.7491794713462 260.4379712341315|14.85664231305885 -3.355033071255887 -9.357298083363421 -3.3550330712558876 12.119500400589349 -9.152305517250918 -9.357298083363421 -9.152305517250918 34.406971113503666|
+|11|1191.6513777522391|291.69603673204756 264.7367455531947 232.16796163355073|19.34330871330209 1.7361774952912832 0.21731351829482345 1.7361774952912827 12.922017165352509 2.9036835031391384 0.2173135182948236 2.9036835031391384 7.500523189720995|
+|12|1469.348581894318|297.271253616672 277.6927171033546 250.06165621704238|21.304732726337953 3.5117056720228863 8.066233130092066 3.5117056720228863 28.51894492990739 2.8576678543821394 8.066233130092069 2.857667854382141 21.043483460858443|
+|13|1784.3292057854198|287.4735427430039 257.12178823470913 258.62528350630066|20.81252602492729 -8.962341880364253 -10.759858880086693 -8.962341880364253 16.528959360663578 14.138189191568468 -10.759858880086693 14.13818919156847 31.925902633641364|
+|14|838.0247507317857|298.03717451320057 296.72958802427917 244.82005619230333|14.487212235632265 3.7785405289199394 6.994916680525296 3.7785405289199394 10.71103042332019 7.063913352032185 6.994916680525295 7.063913352032185 11.010237900187283|
+|15|991.4116167688517|277.41954117317874 258.05411993074335 253.52007198958228|13.720255998190236 -7.599507496617633 -7.196833747719264 -7.599507496617634 12.442176747662428 3.459742598171811 -7.196833747719266 3.459742598171811 13.176954468169399|
+|16|972.6754948733843|284.496387219776 264.3814226408338 275.82732362276033|15.429262300685972 -14.107825831575248 -4.998022746560197 -14.107825831575248 22.42124603865399 4.607382738808447 -4.9980227465601965 4.607382738808446 6.872711406525099|
+|17|647.8983151361748|308.12297108174664 262.3723565460511 244.77754104446186|9.351870939676614 -0.05214261360249506 0.45430515809413774 -0.05214261360249506 10.868333730260046 0.06824096976252747 0.45430515809413774 0.06824096976252746 4.386267847336799|
+|18|506.68174247564275|279.88898577833424 265.04202707039417 238.54668338562658|12.101976715642536 4.226960656147213 9.372525619295676 4.226960656147211 6.576142814114243 -2.919725276614166 9.372525619295676 -2.9197252766141664 25.59708770655171|
+|19|1058.1960195994325|284.21124217167943 274.2672849833725 242.9214328167066|18.36227734816411 5.36013578692881 8.902200166544473 5.36013578692881 17.3500159717773 13.789946824879863 8.902200166544475 13.789946824879864 17.90951558666506|
+|20|441.4062646517871|309.984765985884 274.9556342084078 259.0382929293924|7.192153913673777 0.29847801993283474 2.9317831638142433 0.2984780199328345 4.427372367351801 -5.154832128582452 2.9317831638142433 -5.154832128582451 13.594176251857869|
+|21|1822.5010449903814|294.0529654744343 262.5426777834154 248.92156403048082|35.43846898064218 -9.23175067951362 27.868612781978953 -9.23175067951362 10.249393588232344 -2.483222166246894 27.868612781978953 -2.483222166246895 47.8864053703316|
+|22|757.1332846784317|288.4045029554262 285.75130021799254 260.59037985230367|8.916539476476736 -0.029215254588615736 1.5063665453850665 -0.029215254588615736 21.280743626081133 8.024961038402617 1.5063665453850663 8.024961038402617 6.995759930093336|
+|23|742.4674280985564|299.32499079267404 253.40712552884568 252.82695402099404|12.139797345117465 6.0145552531005775 2.1050083490295246 6.014555253100577 9.570054042310339 -5.340680149152181 2.1050083490295246 -5.340680149152181 27.008561041417142|
+|24|539.8765656578238|278.1335518324304 270.1220150340888 245.81805525877243|16.75860690215464 -24.53962668412208 5.101933506922523 -24.539626684122076 44.16117544125187 -4.501469489993391 5.101933506922523 -4.501469489993391 3.8432982662167756|
+|25|1184.9064893282425|307.893973883171 264.6864814557543 253.13668748917942|12.528388041153525 -15.239159099711621 -1.9217028043522975 -15.239159099711621 39.818641983763406 3.8252138359907653 -1.9217028043522977 3.8252138359907653 4.739613795023098|
+|26|920.1686815869632|296.80598484202613 292.0863536225045 255.61363613710026|13.039007612682283 11.889007443033657 2.649309218151629 11.889007443033657 30.594715212229175 -10.754338373666368 2.649309218151628 -10.754338373666368 12.981312460504068|
+|27|1325.1901080058044|297.251224598258 263.96733615707046 273.8044049510956|24.260322636721785 -12.077461248422479 -11.28771319205984 -12.077461248422475 17.22582257950857 9.07280114183339 -11.287713192059838 9.07280114183339 15.312367472182132|
+|28|1077.6527748572219|288.78390393368096 274.4229532831747 277.08431859850884|19.731667298612194 3.8946378300097626 -0.42552759368430265 3.8946378300097626 7.241854066901966 -4.684883001998994 -0.4255275936843028 -4.684883001998994 10.9930560066121|
+|29|604.2986013778957|288.5549738815414 251.13846356802657 233.01346861911898|20.674699651497495 -10.350530570312978 -4.210901476759284 -10.350530570312976 19.195897600162898 0.47875270119738056 -4.210901476759283 0.47875270119738 1.9896271444617892|
+|30|864.3709979403986|298.344767194584 269.38944573193606 259.38071124912756|15.745036988248106 -2.7479346092976287 14.230319980100548 -2.747934609297627 9.961096241165615 -5.843234481320083 14.230319980100548 -5.843234481320084 32.18649085768304|
+|31|623.9287582046194|278.3252789358265 274.71940126118966 257.3563973080313|6.084512031129181 4.44878597241862 6.087127154180094 4.44878597241862 8.728950593809271 0.5531804539922835 6.087127154180095 0.5531804539922831 24.368119283024814|
+|32|1653.9471704247198|276.0089803691432 256.8922260750927 239.95812977779698|37.68370747125502 -7.617860111041622 -21.221346200677672 -7.617860111041622 8.051375394210904 3.723800534639366 -21.221346200677676 3.7238005346393663 24.048758732338477|
+|33|1330.2089575259083|297.234309621661 275.525354103423 240.39362464695617|28.534073253559676 22.69030963391654 0.9820093455964642 22.69030963391654 48.396549475166054 1.7826943080273618 0.9820093455964642 1.7826943080273618 5.017211389317436|
+|34|1209.1627636987616|298.66702309121644 258.21784597410254 239.20204685436366|22.056963056335313 3.076178224559422 3.5732893181254655 3.0761782245594227 11.51917089629996 -2.6544745776607668 3.5732893181254655 -2.6544745776607677 12.8490779068082|
+|35|748.5351776832418|309.05229422693515 277.7039777435413 245.66564769947993|10.023664720911404 -0.4072803268865006 3.9182907932577633 -0.4072803268865002 6.852403564906889 1.9503730989998769 3.9182907932577624 1.9503730989998767 9.510302605517479|
+|36|1044.7999174215468|275.6348527406665 265.7492802214313 262.424740582385|29.316455313026488 -7.075409007798658 11.424786513799383 -7.075409007798658 5.429405240932526 -6.2231241816275755 11.424786513799383 -6.2231241816275755 21.396663024103884|