update outdated examples

examples/code_fragments/entity/gfx_symmetry.py

@@ -6,9 +6,9 @@ if len(sys.argv)>1:
   filename=sys.argv[1]
 ent=io.LoadEntity(filename)
 
-edi=ent.RequestXCSEditor()
+edi=ent.EditXCS()
 m=geom.Mat4()
-m.PasteTranslation(-ent.GetGeometricStart())
+m.PasteTranslation(-ent.bounds.min)
 edi.ApplyTransform(m)
 edi.UpdateICS()
 frag=gfx.Entity('frag', ent)

examples/code_fragments/entity/superpose.py

@@ -20,7 +20,7 @@ g=gfx.Entity("second", ev_b)
 scene.Add(g)
 h=gfx.Entity("first",ev_a)
 scene.Add(h)
-h.SetColor(gfx.Color(0x0000ff), '')
-g.SetColor(gfx.Color(0xff0000), '')
+h.SetColor(gfx.RED)
+g.SetColor(gfx.BLUE)
 scene.CenterOn(g)
 

examples/code_fragments/misc/roll_helix.py

@@ -3,7 +3,7 @@ import math
 e=io.LoadEntity('../entity/sdh.pdb')
 c=e.FindChain('A')
 
-edi=e.RequestICSEditor(mol.EditMode.BUFFERED_EDIT)
+edi=e.EditXCS(mol.EditMode.BUFFERED_EDIT)
 for r in c.GetResidueList():
   phi=r.GetPhiTorsion()
   psi=r.GetPsiTorsion()

examples/code_fragments/misc/strip_sidechains.py

@@ -9,7 +9,7 @@ def StripSidechain(edi, residue):
       edi.DeleteAtom(atom)
 
 def StripSidechains(entity):
-  edi=entity.RequestXCSEditor(mol.EditMode.BUFFERED_EDIT)
+  edi=entity.EditXCS(mol.EditMode.BUFFERED_EDIT)
   for c in e.GetChainList():
     residues=c.GetResidueList()
     for residue in residues:

examples/code_fragments/seq/sh2.aln

+CLUSTAL 2.0.12 multiple sequence alignment
+
+
+SH2                         -------------------------KP-HPWFFGKIPRAKAEEMLSKQR- 23
+UniRef90_UPI0000EB201F      KAELNGKDGFIPKN-------YIEMKP-HPWFFGKIPRAKAEEMLSKQR- 45
+UniRef90_P62993             KAELNGKDGFIPKN-------YIEMKP-HPWFFGKIPRAKAEEMLSKQR- 78
+UniRef90_P87379             KAELNGKDGFIPKN-------YIEMKA-HPWFFGKIPRAKAEEMLGKQR- 78
+UniRef90_UPI00016E653C      KAELRGKDGFIPKN-------YIEMKA-HPWFYGKIPRAKAEEILNKQR- 78
+UniRef90_UPI00016E653B      KAELRGKDGFIPKN-------YIEMKA-HPWFYGKIPRAKAEEILNKQR- 78
+UniRef90_Q4T656             DQALS-FASLLPVS-------FSAC---CRWFYGKIPRAKAEEILNKQR- 75
+UniRef90_UPI0001555716      KAELNGKDGFIPKN-------YIEMKP-HLWFFGKIPRAYAEEMLGKQL- 388
+UniRef90_UPI000180AF26      KAEQDGKEGLVPMN-------YIQMKP-CEWFARNMTRANAELRL-KNA- 52
+UniRef90_UPI000180AF37      KAEQDGKEGLVPMN-------YIEIKE-CEWFARNMTRANAELRL-KNT- 77
+UniRef90_A8XPY6             KAELDGTEGFIPSN-------YIRMGD-CSWYLGKITRNDAEVLLKKSNV 79
+UniRef90_P29355             KAELDGNEGFIPSN-------YIRMTE-CNWYLGKITRNDAEVLLKKPTV 79
+UniRef90_UPI000186E6C5      RAELDSKEGLIPSN-------YIEMKN-HDWYYGRITRADAEKLLMNK-- 77
+UniRef90_Q08012             RAELDGKEGLIPSN-------YIEMKN-HDWYYGRITRADAEKLLSNK-- 77
+UniRef90_B7P0R2             RAELDSKEGLIPSN-------YIEMKK-HDWYYGRITRADAEKLLSNK-- 77
+UniRef90_D3PIQ8             RAESGGKEGLIPSN-------YIDMKP-HDWYYSRMTRATAEKLLSNK-- 77
+UniRef90_C4WWT7             RAEFEGKEGLIPSN-------YIEMKN-HDWYYGKITRADAEKLLDQQ-- 77
+UniRef90_UPI0000586DB6      -------------------------------------RDGAEELLKND-- 40
+UniRef90_UPI0001CBA623      KAELDGREGFIPKN-------YITMRP-HDWFHGKISRAKAEELLQLQP- 78
+UniRef90_UPI0001CBA624      NAELDGREGLIPKN-------YIEMKP-HEWFHGKISREKAEELLQLQS- 77
+UniRef90_UPI000192619C      KAEQNGKEGFVPKN-------YIQMKP-HSWYYGKIRRSEAEQLLLQEP- 52
+UniRef90_UPI0000521DDC      RAEIDGRMGLVPKN-------YIELKA-HDWYHGKISRVKAEQSLNKPHY 79
+UniRef90_C1LZF7             LAEQEGRTGLIPCN-------YITMRP-HPWYIRHCSRMEAEERLQEIDQ 79
+UniRef90_UPI0000E478D2      LAHQGAKQGLVPEN-------YLKIEKSHPWYVGKISRKVAEEYLMSMP- 80
+UniRef90_UPI0000E49A1C      ----------MGPK-------HTYPEIAMAWFFPTITRKNAELLLMQE-- 31
+UniRef90_A8E5T1             KAELFGREGYIPKN-------YIKVKP-HPWYAGRISRQVAEEILLKRNF 79
+UniRef90_C1C3T6             KAELKGQEGYIPKN-------YIKVKP-HPWYAGRISRQVAEEILLKKRF 79
+UniRef90_Q13588             KAELRGVEGFIPKN-------YIRVKP-HPWYSGRISRQLAEEILMKRNH 79
+UniRef90_UPI0001C606E3      KAELRGAEGFVPKN-------YIHIKP-HPWYSGRISRQLAEEILMKRNQ 79
+UniRef90_Q9CX99             KAELRGAEGFVPKN-------YIRVKP-HPWYSGRISRQLAEETLMKRNH 79
+UniRef90_UPI0000DA3575      GVGLKPIEGMRPTNRTXRIPADIVPSP-HRWYSGRISRQLAEETLMKRNH 86
+UniRef90_UPI0000D9440A      KAELRGAEGFIPKN-------YIQVKP-HPWFAGRISRQFAEEILLRRNH 79
+UniRef90_UPI000155C0E1      RTSLLGGESFFYKN-------IQKLSP-SPWYAGRISRQLAEEVLLKRNH 79
+UniRef90_UPI0000E80FCB      KAELYGCEGFVPKN-------YIKVKP-HPWYAGRISRHVAEELLLKRRY 79
+UniRef90_UPI00016E4BE7      TAELHNRKGFVPKN-------YINLRP-HAWFAGRISRSVAESRLRQRE- 78
+UniRef90_Q503S8             TAEFVNRKGYVPKN-------YISLRP-HAWFAGRISRHVAENRLHQRD- 78
+UniRef90_Q4V9Q1             TAELLGRRGYVPKN-------YINVRP-HTWFVGGISRQAAENRLRPLE- 78
+UniRef90_UPI00017B202F      TAEIQGKRGYIPQN-------YISLLP-YPWFVGRVSRLEAEKRLRWQD- 78
+UniRef90_UPI0000E25B42      KAELGSQEGYVPKN-------FIDIQF-PEWFHEGLSRHQAENLLMGKE- 149
+UniRef90_O75791             KAELGSQEGYVPKN-------FIDIQF-PKWFHEGLSRHQAENLLMGKE- 76
+UniRef90_B7Z8F8             RHKLNP---FSSK----------------RWFHEGLSRHQAENLLMGKE- 50
+UniRef90_UPI00005BC6B6      KAELGSQEGYVPKN-------FIEIEF-PEWFHEGLSRHQAESLLMGKE- 76
+UniRef90_O89100             KAELGSQEGYVPKN-------FIDIEF-PEWFHEGLSRHQAENLLMGKD- 76
+UniRef90_UPI0000EDE7DF      KAELKSHEGYVPKN-------FIDIHI-PGWFHEGISRHEAESLLMGKE- 76
+UniRef90_UPI0000F2E19C      KAELGSQEGYVPKN-------FIDIQF-PSWFHEDISRHDAESLLMGKD- 241
+UniRef90_UPI0000E7F8B9      KAELRSQEGYVPKN-------FIDFHV-PPWFDEKISRHEAESILMNKG- 76
+UniRef90_UPI0000ECD2B7      KAELRSQEGYVPKN-------FIDFHV-PPWFDEKISRHEAESILMNKG- 76
+UniRef90_UPI000194E163      KAELRSHEGYVPKN-------FIDFHV-PHWFDEKISRHEAENLLMSKG- 91
+UniRef90_B5X487             KAELHGQEGFVPQN-------YIERQT-PSWFKETASRSSAEELLMSRE- 76
+UniRef90_Q567F1             KAELHGHEGYVPKN-------YVDRQI-PSWFKESASRGSAEETLMSRE- 76
+
+
+SH2                         -------HDGAFLIRESESA--PGDFSL----SVKFGNDVQHFKVLR--D 58
+UniRef90_UPI0000EB201F      -------HDGAFLIRESESA--PGDFSL----SVKFGNDVQHFKVLR--D 80
+UniRef90_P62993             -------HDGAFLIRESESA--PGDFSL----SVKFGNDVQHFKVLR--D 113
+UniRef90_P87379             -------HDGAFLIRESESA--PGDFSL----SVKFGNDVQHFKVLR--D 113
+UniRef90_UPI00016E653C      -------RDGAFLIRESESA--PGDFSL----SVKYGNDVQHFKVLR--D 113
+UniRef90_UPI00016E653B      -------RDGAFLIRESESA--PGDFSL----SVKYGNDVQHFKVLR--D 113
+UniRef90_Q4T656             -------RDGAFLIRESESA--PGDFSL----SVKYGNDVQHFKVLR--D 110
+UniRef90_UPI0001555716      -------NYGSFFILXXXXP--PGDALTGARSTPRFGNDVQHFKVLR--D 427
+UniRef90_UPI000180AF26      -------LDESFLVRESEST--PGDFSL----SVKTNSGVQHFKVLR--D 87
+UniRef90_UPI000180AF37      -------LDGSFLVRESEST--PGEFSV----SVKTNSGVQHFKVLR--D 112
+UniRef90_A8XPY6             -------RDGHFLVRQCESS--PGEFSI----SVRFQDSVQHFKVLR--D 114
+UniRef90_P29355             -------RDGHFLVRQCESS--PGEFSI----SVRFQDSVQHFKVLR--D 114
+UniRef90_UPI000186E6C5      -------HEGAFLIRVSESS--PGDFSL----SVKCSDGVQHFKVLR--D 112
+UniRef90_Q08012             -------HEGAFLIRISESS--PGDFSL----SVKCPDGVQHFKVLR--D 112
+UniRef90_B7P0R2             -------HEGAFLIRVSESS--PGDFSL----SVRCGDGVQHFKVLR--D 112
+UniRef90_D3PIQ8             -------HEGAFVIRVSESS--PGDFSL----SVKCGDGVQHFKVLR--D 112
+UniRef90_C4WWT7             -------PEGCFLVRISESS--PGDFSL----SVKCGDGVQHFKVLR--D 112
+UniRef90_UPI0000586DB6      -------GDGAFLIRESEGT--PGDYSL----SVKFVDGVQHFKVLR--D 75
+UniRef90_UPI0001CBA623      -------HDGAFLIRESESA--PGDFSL----SVKFKDEVQHFKVLR--D 113
+UniRef90_UPI0001CBA624      -------YDGAFLIRESEST--PGDFSL----SVKFKDGVQNFKILR--D 112
+UniRef90_UPI000192619C      -------HDGAYLIRDSEST--AGDFSL----SVKFNNQVQHFKVLR--D 87
+UniRef90_UPI0000521DDC      -------PDGAFLIRESESS--PGDFSL----SVKYGSAVQHFKVLR--D 114
+UniRef90_C1LZF7             ETAQHLQPDGAFILRQSEAD--GKGFSL----SVKQGCEVLHFKVLQ--D 121
+UniRef90_UPI0000E478D2      -------SDGAFMIRDSESNPDSGNFSL----SVKFRDQVQHFKILT--D 117
+UniRef90_UPI0000E49A1C      -------RNGAFLVRRSESS--EGLYSL----SVKYNESVQHFRILQ--D 66
+UniRef90_A8E5T1             --------VGAFLIRDSESS--PGDFSI----SVNYGHHVQHFKVLRDTE 115
+UniRef90_C1C3T6             --------LGAFLIRDSESS--PGEFSI----SVNYGHHVQHFKVLR--E 113
+UniRef90_Q13588             --------LGAFLIRESESS--PGEFSV----SVNYGDQVQHFKVLR--E 113
+UniRef90_UPI0001C606E3      --------LGAFLIRESESS--PGEFSV----SVNYGDQVQHFKVLR--E 113
+UniRef90_Q9CX99             --------LGAFLIRESESS--PGEFSV----SVNYGDQVQHFKVLR--E 113
+UniRef90_UPI0000DA3575      --------LGAFLIRESESS--PGEFSV----SVNYGDQVQHFKVLR--E 120
+UniRef90_UPI0000D9440A      --------LGAFLIRESESS--PGEFSV----SVNYGNQVQHFKVLR--E 113
+UniRef90_UPI000155C0E1      --------LGAFLIRESESS--PGEFSV----SVNYGDQVQHFKVLR--E 113
+UniRef90_UPI0000E80FCB      --------VGAFLIRESESA--PGEFSI----SVNYGQHVQHFKVLR--E 113
+UniRef90_UPI00016E4BE7      --------CGAFLVRESESA--PGEFSM----SVSYGDHVQHFKVLQD-- 112
+UniRef90_Q503S8             --------CGSFLVRESESA--PGEFSM----SVSYGDHVQHFKVLKD-- 112
+UniRef90_Q4V9Q1             --------CGAFLIRESEST--PGEFSV----SVSYGDHVQHFKVLKD-- 112
+UniRef90_UPI00017B202F      --------PGVFLVRESESA--PGEFSV----SVSYGNRVEHFRVLE--- 111
+UniRef90_UPI0000E25B42      --------VGFFIIRASQSS--PGDFSI----SVRHEDDVQHFKVMR--D 183
+UniRef90_O75791             --------VGFFIIRASQSS--PGDFSI----SVRHEDDVQHFKVMR--D 110
+UniRef90_B7Z8F8             --------VGFFIIRASQSS--PGDFSI----SVRHEDDVQHFKVMR--D 84
+UniRef90_UPI00005BC6B6      --------LGCFIIRASQSS--PGDFSI----SVRHEDDVQHFKVMR--D 110
+UniRef90_O89100             --------IGFFIIRASQSS--PGDFSI----SVRHEDDVQHFKVMR--D 110
+UniRef90_UPI0000EDE7DF      --------VGSFIIRASQSS--PGDFSI----SVRHEDDVQHFKVMR--D 110
+UniRef90_UPI0000F2E19C      --------VGSFIIRASQSS--PGDFSI----SVRHEDDVQHFKVMR--D 275
+UniRef90_UPI0000E7F8B9      --------VGSFIVRASQNS--HGDFSI----SVRHEDDVQHFKVMR--D 110
+UniRef90_UPI0000ECD2B7      --------VGSFIVRASQNS--HGDFSI----SVRHEDDVQHFKVMR--D 110
+UniRef90_UPI000194E163      --------VGCFVVRASQNS--HGDFSI----SVRHEDDVQHFKVMR--D 125
+UniRef90_B5X487             --------VGGFLIRGSQSS--PGEFSI----SVRHEFDVQHFKVMK--D 110
+UniRef90_Q567F1             --------VGAFLIRGSQSS--PGDFSI----SVRHDYDVQHFKVMK--D 110
+                                                                   * :*:::
+
+SH2                         GAGKYFLWVVKFNSLNELVDYHRSTSVSR---------------NQQIFL 93
+UniRef90_UPI0000EB201F      GAGKYFLWVVKFNSLNELVDYHRSTSVSR---------------NQQIFL 115
+UniRef90_P62993             GAGKYFLWVVKFNSLNELVDYHRSTSVSR---------------NQQIFL 148
+UniRef90_P87379             GAGKYFLWVVKFNSLNELVDYHRSTSVSR---------------NQQIFL 148
+UniRef90_UPI00016E653C      GAGKYFLWVVKFNSLNELVEYHRTTSVSR---------------NQQIFL 148
+UniRef90_UPI00016E653B      GAGKYFLWVVKFNSLNELVEYHRTTSVSR---------------NQQIFL 148
+UniRef90_Q4T656             GAGKYFLWVVKFTSLNELVEYHRTTSVSR---------------NQQIFL 145
+UniRef90_UPI0001555716      GAGKYFLWVVKFNSLNELVDYHRSTSVSR---------------NQQIFL 462
+UniRef90_UPI000180AF26      GAGKYFIWLVKFKSLNQLVDYHRTSSVSR---------------SEQILL 122
+UniRef90_UPI000180AF37      GAGKYFIWVVKFSSLNELVVYHRVMTVSG---------------SERIFL 147
+UniRef90_A8XPY6             QNGKYYLWAVKFNSLNELVAYHRTASVSR---------------THTILL 149
+UniRef90_P29355             QNGKYYLWAVKFNSLNELVAYHRTASVSR---------------THTILL 149
+UniRef90_UPI000186E6C5      AQGKFFLWVVKFSSLNELVEYHRTSSVSR---------------SQHVKL 147
+UniRef90_Q08012             AQSKFFLWVVKFNSLNELVEYHRTASVSR---------------SQDVKL 147
+UniRef90_B7P0R2             TLGKFFLWVVKFASLNELVEYHRSASVSR---------------SQDIKL 147
+UniRef90_D3PIQ8             GQGKFFLWVVKFNSLNELVEYHHSASVSR---------------SQDIKL 147
+UniRef90_C4WWT7             AQAKFFLWVVKFDSLNELVDYHRESSVSR---------------SQDVRL 147
+UniRef90_UPI0000586DB6      GAGKYFLWVVKFNSLNQLVEYHRTSSVSR---------------SQTIYL 110
+UniRef90_UPI0001CBA623      GAGKYFLWVVKFNSLNELVEYHRSSSVSR---------------TQTIYL 148
+UniRef90_UPI0001CBA624      GAGKYFLWVVKFNSLNQLVDYHRTSSVSR---------------SEQIFL 147
+UniRef90_UPI000192619C      GAGKYFLWVVKFNSLNQLVEYHRAASVSR---------------SQTIYL 122
+UniRef90_UPI0000521DDC      GAGKYFLWVVKFSSLNELIKYHREQSISR---------------TQQIML 149
+UniRef90_C1LZF7             EAGKYFFWLSKFDSINQLIDHHRKTSISR---------------NRLLTL 156
+UniRef90_UPI0000E478D2      LAGKYFLWVVKFTSINDLVDYHKDNSVSRTQEIVLNEPCVPIEDANQRPQ 167
+UniRef90_UPI0000E49A1C      TAGKFHLWIVKFPSLDALVDYYRTTSVTR---------------ENQVST 101
+UniRef90_A8E5T1             SNGKYYLWEAKFNSLNELVDYYRRHSIAK---------------FHEVFL 150
+UniRef90_C1C3T6             KSGTYFLWETKFGSLNELVEFYRSSSIAK---------------THPVLL 148
+UniRef90_Q13588             ASGKYFLWEEKFNSLNELVDFYRTTTIAK---------------KRQIFL 148
+UniRef90_UPI0001C606E3      ASGKYFLWEEKFNSLNELVDFYRTTTIAK---------------KRQIFL 148
+UniRef90_Q9CX99             ASGKYFLWEEKFNSLNELVDFYRTTTIAK---------------RRQIFL 148
+UniRef90_UPI0000DA3575      ASGKYFLWEEKFNSLNELVDFYRTTTIAK---------------RRQIFL 155
+UniRef90_UPI0000D9440A      NMGKYFLWEEKFNSLNELVDFYRTTTIAK---------------KKQIFL 148
+UniRef90_UPI000155C0E1      RIGKYYLWEEKFNSLNELVDFYRTTTIAK---------------KKQIFL 148
+UniRef90_UPI0000E80FCB      RNGKYFLWEEKFNSLNELVDFYRTTTIAK---------------KQQIFL 148
+UniRef90_UPI00016E4BE7      RGGQYYVWDELFPSLNELVEFYHCNSIAR---------------ERTVLL 147
+UniRef90_Q503S8             REGYYFVWEEIFPSLNQLVDFYKTNSIAK---------------ERTVFL 147
+UniRef90_Q4V9Q1             GLGQYFIWDEVFSSLNQLVDFYRINSIAK---------------ERTVFL 147
+UniRef90_UPI00017B202F      GGGQYCIWEESFCSLNRLVDFYRTHSIAM---------------DKVVCL 146
+UniRef90_UPI0000E25B42      NKGNYFLWTEKFPSLNKLVDYYRTNSISR---------------QKQIFL 218
+UniRef90_O75791             NKGNYFLWTEKFPSLNKLVDYYRTNSISR---------------QKQIFL 145
+UniRef90_B7Z8F8             NKGNYFLWTEKFPSLNKLVDYYRTNSISR---------------QKQIFL 119
+UniRef90_UPI00005BC6B6      NKGNYFLWTEKFPSLNKLVDYYRKNSISK---------------QKQIFL 145
+UniRef90_O89100             TKGNYFLWTEKFPSLNKLVDYYRTTSISK---------------QKQVFL 145
+UniRef90_UPI0000EDE7DF      AKGHYFLWTEKFQSLNRLVEFYKTSSISR---------------QKQIFL 145
+UniRef90_UPI0000F2E19C      AKGHYFLWTEKFQSLNQLVNFYRTSSISK---------------QKQIYL 310
+UniRef90_UPI0000E7F8B9      SKGNYYLWTEKFYSLNKLVDYYRTSTISR---------------QKQILL 145
+UniRef90_UPI0000ECD2B7      SKGNYYLWTEKFYSLNKLVDYYRTSTISR---------------QKQILL 145
+UniRef90_UPI000194E163      SKGSYYLWTEKFHSLNKLVDYYKTSSISR---------------QKQIFL 160
+UniRef90_B5X487             SKGHYFLWSEKFTSLNKLVDFYKNTSISK---------------QRDIYL 145
+UniRef90_Q567F1             KSGHYYLWTEKFTSLNKLVDFYKTTSISK---------------QKEIFL 145
+                              . : .*   * *:: *: .::  :::                 .
+
+SH2                         RDIEQVP------------------------------------------- 100
+UniRef90_UPI0000EB201F      RDIEQVPQQNSIFSLCQR----TSLTLCSIVSLEASEEENPVVREWSPHS 161
+UniRef90_P62993             RDIEQVP------------------------------------------- 155
+UniRef90_P87379             RDIEQVPQVHGGDRATS--------------------------------- 165
+UniRef90_UPI00016E653C      REIEQ--------------------------------------------- 153
+UniRef90_UPI00016E653B      REIEQVTQVNVGTHYIN--------------------------------- 165
+UniRef90_Q4T656             RDIEQVTQV----------------------------------------- 154
+UniRef90_UPI0001555716      RDIEQMPQQKSPVCDRLS----FLFCAVNCRACSDGVFHG---------- 498
+UniRef90_UPI000180AF26      RHPIIS-------------------------------------------- 128
+UniRef90_UPI000180AF37      LHPIS--------------------------------------------- 152
+UniRef90_A8XPY6             ADMNV--------------------------------------------- 154
+UniRef90_P29355             SDMNV--------------------------------------------- 154
+UniRef90_UPI000186E6C5      RDMVP--------------------------------------------- 152
+UniRef90_Q08012             RDMIP--------------------------------------------- 152
+UniRef90_B7P0R2             RDMHP--------------------------------------------- 152
+UniRef90_D3PIQ8             KEIIC--------------------------------------------- 152
+UniRef90_C4WWT7             RDMPAATQNG---------------------------------------- 157
+UniRef90_UPI0000586DB6      KDRKS--------------------------------------------- 115
+UniRef90_UPI0001CBA623      LKMHV--------------------------------------------- 153
+UniRef90_UPI0001CBA624      KDKQ---------------------------------------------- 151
+UniRef90_UPI000192619C      KDMTN--------------------------------------------- 127
+UniRef90_UPI0000521DDC      VDLPV--------------------------------------------- 154
+UniRef90_C1LZF7             VDLVPSKRFPTN-------------------------------------- 168
+UniRef90_UPI0000E478D2      PAMQQSR------------------------------------------- 174
+UniRef90_UPI0000E49A1C      QSVEQWS------------------------------------------- 108
+UniRef90_A8E5T1             CDEEQ--------------------------------------------- 155
+UniRef90_C1C3T6             RDEEE--------------------------------------------- 153
+UniRef90_Q13588             RDEEP--------------------------------------------- 153
+UniRef90_UPI0001C606E3      RDEEP--------------------------------------------- 153
+UniRef90_Q9CX99             CDEQP--------------------------------------------- 153
+UniRef90_UPI0000DA3575      CDEQP--------------------------------------------- 160
+UniRef90_UPI0000D9440A      RDEEP--------------------------------------------- 153
+UniRef90_UPI000155C0E1      RDEEQ--------------------------------------------- 153
+UniRef90_UPI0000E80FCB      RDDEQ--------------------------------------------- 153
+UniRef90_UPI00016E4BE7      RDPEQ--------------------------------------------- 152
+UniRef90_Q503S8             RDLDH--------------------------------------------- 152
+UniRef90_Q4V9Q1             RDPEG--------------------------------------------- 152
+UniRef90_UPI00017B202F      RDPPS--------------------------------------------- 151
+UniRef90_UPI0000E25B42      RDRTREDQGHRGNSLDR---RSQGGPHLSGAVGEEIRPSMNRKLSDHPPT 265
+UniRef90_O75791             RDRTREDQGHRGNSLDR---RSQGGPHLSGAVGEEIRPSMNRKLSDHPPT 192
+UniRef90_B7Z8F8             RDRTREDQGHRGNSLDR---RSQGGPHLSGAVGEEIRPSMNRKLSDHPPT 166
+UniRef90_UPI00005BC6B6      RDRTREEQGQRGNSLDR---RSQGGHPLSGAVGEEIRPSMNRKPSDHP-L 191
+UniRef90_O89100             RDGTQ-DQGHRGNSLDR---RSQGGPHPSGTVGEEIRPSVNRKLSDHLPL 191
+UniRef90_UPI0000EDE7DF      RDGTREDQERRGGSLDR---RAQEGLGLGGACGEEIRVPMNRKMSDLHPP 192
+UniRef90_UPI0000F2E19C      RDGGREEQDRWGGSLER---RLQEGLHISGGVGEETRPSTNRKQSDHPPA 357
+UniRef90_UPI0000E7F8B9      RDDSREEKERRGGSLER---MSRDGLHVGGAAAEAHS-SMSKRYVDHP-- 189
+UniRef90_UPI0000ECD2B7      RDDSREEKERRGGSLER---MSRDGLHVGGAAAEAHS-SMSKRYVDHPVP 191
+UniRef90_UPI000194E163      RDNSQEEKERHGGSLER---IGREGFHMGGAAGEDHS-SISKRYVEYPIP 206
+UniRef90_B5X487             RDGSRDDQSPSTPQPLKRGSLPEERS-----YGAPTAATSHRRASDLP-- 188
+UniRef90_Q567F1             RDGSGDE--PRAPPPIK--SQPEVRPPPGGGYGSPQTSSQNRSTTDPT-- 189

examples/code_fragments/trj/test_trj.py

@@ -17,8 +17,8 @@ class Anim(QtCore.QTimer):
 
 
 # old-style CHARMM format, requires flag bit 0 set
-cg = io.LoadCHARMMTraj("mpor_trj.crd","mpor_trj_short.trj",1)
-eh=cg.GetEntity()
+eh = io.LoadCRD("mpor_trj.crd")
+cg = io.LoadCHARMMTraj(eh,"mpor_trj_short.trj")
 go=gfx.Entity("test",eh.CreateFullView())
 
 scene.Add(go)