Added additional peaklists and tests for peak list simulator.

nmrstarlib/cli.py

@@ -8,7 +8,7 @@
     nmrstarlib -h | --help
     nmrstarlib --version
     nmrstarlib convert (<from_path> <to_path>) [--from_format=<format>] [--to_format=<format>] [--bmrb_url=<url>] [--nmrstar_version=<version>] [--verbose]
-    nmrstarlib csview <starfile_path> [--aa=<aa>] [--at=<at>] [--aa_at=<aa:at>] [--csview_outfile=<path>] [--csview_format=<format>] [--bmrb_url=<url>] [--nmrstar_version=<version>] [--verbose] [--show]
+    nmrstarlib csview <starfile_path> [--aa=<aa>] [--at=<at>] [--aa_at=<aa-at>] [--csview_outfile=<path>] [--csview_format=<format>] [--bmrb_url=<url>] [--nmrstar_version=<version>] [--verbose] [--show]
     nmrstarlib plsimulate (<from_path> <to_path> <spectrum>) [--from_format=<format>] [--to_format=<format>] [--plsplit=<%>] [--distribution=<func>] [--H=<value>] [--C=<value>] [--N=<value>] [--bmrb_url=<url>] [--nmrstar_version=<version>] [--spectrum_descriptions=<path>] [--verbose]
 
 Options:
@@ -22,7 +22,7 @@
     --bmrb_url=<url>                URL to BMRB REST interface [default: http://rest.bmrb.wisc.edu/bmrb/NMR-STAR3/].
     --aa=<aa>                       Comma-separated amino acid three-letter codes (e.g. --aa=ALA,SER).
     --at=<at>                       Comma-separated BMRB atom codes (e.g. --at=CA,CB).
-    --aa_at=<aa:at>                 Comma-separated amino acid three-letter codes and corresponding atoms (e.g. --aa_at=ALA-CA,CB:LYS-CB,CG,CD).
+    --aa_at=<aa-at>                 Amino acid three-letter codes (keys) and corresponding atoms (values) (e.g. --aa_at=ALA-CA,CB:LYS-CB,CG,CD).
     --csview_outfile=<path>         Where to save chemical shifts table.
     --csview_format=<format>        Format to which save chemical shift table [default: svg].
     --plsplit=<%>                   How to split peak list into chunks by percent [default: 100].
@@ -93,7 +93,7 @@ def cli(cmdargs):
 
             for dim in ("H", "N", "C"):
                 params = cmdargs["--{}".format(dim)]
-                if params is None:
+                if params in (None, ""):
                     for param_name in distribution_parameter_names:
                         parameters["{}_{}".format(dim, param_name)].append(None)
                 else:

tests/example_data/NMRSTAR2/peaklists/single_source_variance/18569_CANCO.txt

@@ -0,0 +1,3 @@
+Assignment		w1		w2		w3
+
+LEU15CA-LEU15N-MET14C		53.70548485599874		121.52559614387339		173.58639115583233

tests/example_data/NMRSTAR2/peaklists/single_source_variance/18569_CANCOCX.txt

@@ -0,0 +1,7 @@
+Assignment		w1		w2		w3		w4
+
+LEU15CA-LEU15N-MET14C-MET14C		53.6916958395461		121.51632117715629		173.6019121545503		173.59068735898833
+LEU15CA-LEU15N-MET14C-MET14CA		53.69590909118096		121.50294878341407		173.58342840660973		53.50840083314913
+LEU15CA-LEU15N-MET14C-MET14CB		53.68625296177268		121.50627498807333		173.5953620212353		36.523852464436416
+LEU15CA-LEU15N-MET14C-MET14CG		53.68132088025588		121.5059075478797		173.60387461991496		32.12531487333262
+LEU15CA-LEU15N-MET14C-MET14CE		53.69565119385473		121.51182834907426		173.6092534610949		17.19704763124244

tests/example_data/NMRSTAR2/peaklists/single_source_variance/18569_HNCO.txt

@@ -0,0 +1,3 @@
+Assignment		w1		w2		w3
+
+LEU15H-LEU15N-MET14C		9.646801383776397		121.51574350966546		173.5952526515115

tests/example_data/NMRSTAR2/peaklists/single_source_variance/18569_HNcaCO.txt

@@ -0,0 +1,4 @@
+Assignment		w1		w2		w3
+
+MET14H-MET14N-MET14C		9.938013493236205		130.06602541153535		173.58273958420546
+LEU15H-LEU15N-MET14C		9.649424137931513		121.49423808322823		173.5937685766946

tests/example_data/NMRSTAR2/peaklists/single_source_variance/18569_HNcoCA.txt

@@ -0,0 +1,111 @@
+Assignment		w1		w2		w3
+
+SER2H-SER2N-MET1CA		8.22376318549179		117.21023635448206		55.486371105702915
+GLU3H-GLU3N-SER2CA		8.00290060964847		119.82711688827708		58.60231566054017
+THR4H-THR4N-GLU3CA		8.956390122939464		117.21561357770315		55.64196315714744
+VAL5H-VAL5N-THR4CA		8.634653197967975		125.97176266712151		60.55462299282811
+ILE6H-ILE6N-VAL5CA		8.9322412061341		124.26392234420987		62.686896279419486
+CYS7H-CYS7N-ILE6CA		7.249414903378847		114.88899387833085		61.04579395616114
+SER8H-SER8N-CYS7CA		8.559752685852482		117.8683721887848		57.200789898143654
+SER9H-SER9N-SER8CA		9.22939914833809		120.24342395637754		57.44228199618614
+ARG10H-ARG10N-SER9CA		8.845817747537707		124.8103336604593		57.84488339726724
+ALA11H-ALA11N-ARG10CA		9.180262798431198		125.91619328141076		54.86081651192519
+THR12H-THR12N-ALA11CA		8.95263221217448		119.33148778476678		51.635801678689774
+VAL13H-VAL13N-THR12CA		8.28287743734231		128.22845170028853		62.601849983395276
+MET14H-MET14N-VAL13CA		9.938582786595136		130.07181069873633		62.82416910764972
+LEU15H-LEU15N-MET14CA		9.649938854926102		121.49763673365293		53.48426796493916
+TYR16H-TYR16N-LEU15CA		8.132826095307989		125.36623767218127		53.67529850770313
+ASP17H-ASP17N-TYR16CA		8.106125881554572		128.66553214655042		58.20284583098533
+ASP18H-ASP18N-ASP17CA		8.332029097009055		124.08166774690172		51.870481897582536
+GLY19H-GLY19N-ASP18CA		8.33866772889993		107.00956537815185		56.4491860781701
+ASN20H-ASN20N-GLY19CA		7.303552784213306		116.00450631941288		46.577796585754314
+LYS21H-LYS21N-ASN20CA		7.676895299960468		118.56763796088563		52.87150363084072
+ARG22H-ARG22N-LYS21CA		6.9837880507858605		114.10295197514695		56.51559488663987
+TRP23H-TRP23N-ARG22CA		8.709107116575318		121.87754162597565		53.89660832189985
+LEU24H-LEU24N-TRP23CA		9.120901780011154		123.52349994824371		56.94196162022527
+ALA26H-ALA26N-PRO25CA		8.410635874782743		126.27632772568411		63.081571479072515
+GLY27H-GLY27N-ALA26CA		8.903814231502079		110.86924132510003		51.96856207215351
+THR28H-THR28N-GLY27CA		8.689474111956788		111.80909021390106		44.329522977727244
+GLY29H-GLY29N-THR28CA		8.52641689417922		109.57730675676913		60.756592191850444
+GLN31H-GLN31N-PRO30CA		8.478761272282672		122.60428882144912		62.90785465091025
+ALA32H-ALA32N-GLN31CA		8.860925392399546		127.23205481721446		56.70826111247097
+PHE33H-PHE33N-ALA32CA		8.569653473102031		118.4135690975297		51.33559740416911
+SER34H-SER34N-PHE33CA		8.828996517868351		115.30134005330866		59.557326579212884
+ARG35H-ARG35N-SER34CA		8.576062472304383		122.59672719813612		59.12287271509644
+VAL36H-VAL36N-ARG35CA		9.423350674183638		129.72587531210834		55.2704892149471
+GLN37H-GLN37N-VAL36CA		9.168997933661117		124.26765363318758		61.39653193465473
+ILE38H-ILE38N-GLN37CA		7.604780664881195		118.44285084145758		53.88897356846709
+TYR39H-TYR39N-ILE38CA		9.486224863309495		127.01110802229006		60.686193851551835
+HIS40H-HIS40N-TYR39CA		9.535590864548075		122.1915470998157		56.729378945410716
+ASN41H-ASN41N-HIS40CA		8.510255348410187		126.05660794271185		52.289284865010835
+THR43H-THR43N-PRO42CA		7.726718003481285		114.13361319238152		63.94828380585132
+ALA44H-ALA44N-THR43CA		6.951901824306961		122.0023006696547		65.46652250947153
+ASN45H-ASN45N-ALA44CA		7.921047347596142		117.25043402902328		51.53887367857515
+SER46H-SER46N-ASN45CA		7.5526105089134505		109.46608709344622		53.70062153029206
+PHE47H-PHE47N-SER46CA		9.373586105460635		120.02209760434425		55.94145055798776
+ARG48H-ARG48N-PHE47CA		8.92266657952718		119.12112445061676		56.71873261051282
+VAL49H-VAL49N-ARG48CA		9.209879992188547		122.81482307229811		54.8991158782754
+VAL50H-VAL50N-VAL49CA		8.880099881699515		125.22389588362306		60.8716406147453
+GLY51H-GLY51N-VAL50CA		9.056804734332502		116.08207907309522		60.443054074924696
+ARG52H-ARG52N-GLY51CA		8.133453607166944		123.66995797273135		44.92274956811166
+LYS53H-LYS53N-ARG52CA		9.185758377262458		125.43351159118811		53.932640285727054
+MET54H-MET54N-LYS53CA		8.933914968530908		122.49834848371161		58.252271247101895
+GLN55H-GLN55N-MET54CA		8.291589903443032		120.5490767402381		55.33771547541558
+ASP57H-ASP57N-PRO56CA		8.25873269698365		113.23767955619623		66.81263825474211
+GLN58H-GLN58N-ASP57CA		8.385782090427318		116.22889729710296		54.31814957921415
+GLN59H-GLN59N-GLN58CA		7.490417608922529		116.33861585830209		55.90775849754876
+VAL60H-VAL60N-GLN59CA		8.790728802762978		127.35133918872944		57.50708815761198
+VAL61H-VAL61N-VAL60CA		8.433803512114684		120.59434738555319		63.33425633623679
+ILE62H-ILE62N-VAL61CA		7.257908726834219		116.89493573706892		61.18397608662929
+ASN63H-ASN63N-ILE62CA		8.177998565684334		125.5675720469047		60.67376850659059
+CYS64H-CYS64N-ASN63CA		8.895838784183532		120.24043053845503		52.7047930037603
+ALA65H-ALA65N-CYS64CA		8.889318118110525		127.37754140036799		56.02258468252736
+ILE66H-ILE66N-ALA65CA		8.216860131880257		123.53268268188982		52.4900936773085
+VAL67H-VAL67N-ILE66CA		6.83467393424423		118.36280211220358		61.09609261297264
+ARG68H-ARG68N-VAL67CA		8.486573969308532		120.0207837411366		59.086811294195485
+GLY69H-GLY69N-ARG68CA		9.049244478959594		113.9112262108358		58.33767393554079
+VAL70H-VAL70N-GLY69CA		7.529716985114993		121.64131883852029		44.95548965071509
+LYS71H-LYS71N-VAL70CA		8.470721506464738		126.51424577046467		63.927456117693936
+TYR72H-TYR72N-LYS71CA		8.76185969483005		128.2808703200781		54.37122220549276
+ASN73H-ASN73N-TYR72CA		9.138894115645115		127.06431007189165		57.62535186231925
+GLN74H-GLN74N-ASN73CA		8.781497665894804		125.73664257658996		52.37080596616353
+ALA75H-ALA75N-GLN74CA		7.75173743776575		129.78477091511954		54.56442208882859
+THR76H-THR76N-ALA75CA		8.78884595188235		109.93618331584142		55.83049447844335
+ASN78H-ASN78N-PRO77CA		7.836163328222702		109.685872381065		65.27334617270027
+PHE79H-PHE79N-ASN78CA		7.908544633125426		123.27792417623402		53.08689979617707
+HIS80H-HIS80N-PHE79CA		8.094273480689447		126.28992931088408		56.7673150218773
+GLN81H-GLN81N-HIS80CA		8.82355110587946		115.64764889602151		51.700513503543014
+TRP82H-TRP82N-GLN81CA		9.101382010054516		119.7840394593519		54.24082543701825
+ARG83H-ARG83N-TRP82CA		8.46993727209603		120.0466480601201		57.80794398852394
+ASP84H-ASP84N-ARG83CA		8.941469973884994		126.65289704675263		54.83978707315547
+ALA85H-ALA85N-ASP84CA		8.517740502047202		121.37783923897211		52.65570355408905
+ARG86H-ARG86N-ALA85CA		8.643784831095191		116.99966816921915		55.02035909143265
+GLN87H-GLN87N-ARG86CA		8.617212379630484		119.87441021653703		56.53799815737029
+VAL88H-VAL88N-GLN87CA		8.191679040638446		121.53138661610927		55.06928384699081
+TRP89H-TRP89N-VAL88CA		8.460501200300516		127.5529886511353		61.72064760407513
+GLY90H-GLY90N-TRP89CA		8.94715118452915		106.59659484085475		55.654022603454386
+LEU91H-LEU91N-GLY90CA		8.483143482310231		121.84634463667362		44.355227796612034
+ASN92H-ASN92N-LEU91CA		8.081167868299378		120.05497746183376		52.65213776396089
+PHE93H-PHE93N-ASN92CA		9.020843910031122		124.38775073600921		50.98769132065394
+GLY94H-GLY94N-PHE93CA		9.178800267108553		107.3590794858294		59.81018760388912
+SER95H-SER95N-GLY94CA		7.620390343515978		110.32141400788635		46.37057465676446
+LYS96H-LYS96N-SER95CA		9.11981949888448		122.94316622727493		57.00051866827631
+GLU97H-GLU97N-LYS96CA		8.86912762022053		122.11102721658358		59.089284420923086
+ASP98H-ASP98N-GLU97CA		7.872838880913205		120.727530941466		60.59518967193375
+ALA99H-ALA99N-ASP98CA		7.179801620261285		122.78769982022253		57.80487016741929
+ALA100H-ALA100N-ALA99CA		8.01060264734608		119.66133549636052		53.83600297093008
+GLN101H-GLN101N-ALA100CA		7.991236834510858		117.5628077512039		54.75827775660038
+PHE102H-PHE102N-GLN101CA		7.779142993275309		122.72035625441457		58.61099170265434
+ALA103H-ALA103N-PHE102CA		8.652276977318124		120.20775731566619		62.07143641112972
+ALA104H-ALA104N-ALA103CA		7.7268147925233155		120.06048116341779		55.17996391985071
+GLY105H-GLY105N-ALA104CA		7.624316104387158		108.78429495730492		54.594517526116576
+MET106H-MET106N-GLY105CA		8.120508843128611		121.93737998310053		46.939237732585646
+ALA107H-ALA107N-MET106CA		7.947720778332565		120.06281695443201		56.15457257102634
+SER108H-SER108N-ALA107CA		7.623432565950824		114.2058419408154		55.0144032823707
+ALA109H-ALA109N-SER108CA		7.57360455268159		126.27365048396568		61.626164831798505
+LEU110H-LEU110N-ALA109CA		8.026300423308893		115.46159260624893		54.31765399471667
+GLU111H-GLU111N-LEU110CA		7.884177872808762		118.77867928105996		57.877184723296
+ALA112H-ALA112N-GLU111CA		7.514624625861584		122.30559128006742		59.08375773739547
+LEU113H-LEU113N-ALA112CA		7.786951374977852		117.46125683088259		54.42794027999957
+GLU114H-GLU114N-LEU113CA		7.617458501508839		118.56643697502102		56.11897294237361
+GLY115H-GLY115N-GLU114CA		7.5913839753190855		113.43888815432871		57.01183317527274