barrOs now also can deal with OMBBs that are formed by multiple chains

BARRoS_results.csv

+	PDBs	TMsegm	BB_diameter	BB_diameter_mad	Shear	Membrane_thickness	a	a_mad	b	b_mad	h	CAi-CAi+1	CAi-CAi+1_mad	CAi-CAi+1-CAi+2	CAi-CAi+1-CAi+2_mad	CAi+2-CAi-CAi+1	CAi+2-CAi-CAi+1_mad

barrOs.py

@@ -52,7 +52,8 @@ if __name__ ==  '__main__':
             if len(pdbIDs) > 1:
                 for param in data.columns:
                     if 'mad' not in param and param != 'PDBs' and param != 'TMsegm':
-                        barros.plot_parameter('TMsegm', param, data, fit_line = True, saveto = '{}_{}.pdf'.format(outf.split('.')[-1], param))
+                        barros.plot_parameter('TMsegm', param, data.loc[data.N_chains == 1], fit_line = True, saveto = '{}_{}_monomers.pdf'.format(outf.split('.')[-2], param))
+                        barros.plot_parameter('TMsegm', param, data.loc[data.N_chains > 1], fit_line = True, saveto = '{}_{}_multimers.pdf'.format(outf.split('.')[-2], param))
                         
 
             

examples_multimers/hhpred_MSPA_MYCS2.hhr

+Query         sp A0QR29 MSPA_MYCS2 Porin MspA OS=Mycolicibacterium smegmatis (strain ATCC 700084 / mc(2)155) OX=246196 GN=mspA PE=1 SV=1
+Match_columns 211
+No_of_seqs    108 out of 951
+Neff          6.85499
+Searched_HMMs 61622
+Date          Sun Apr  2 11:57:34 2023
+Command       hhsearch -cpu 8 -i ../results/full.a3m -d /cluster/toolkit/production/databases/hh-suite/mmcif70/pdb70 -o ../results/MSPA_MYCS2.hhr -oa3m ../results/MSPA_MYCS2.a3m -p 20 -Z 10000 -loc -z 1 -b 1 -B 10000 -ssm 2 -sc 1 -seq 1 -dbstrlen 10000 -norealign -maxres 32000 -contxt /cluster/toolkit/production/bioprogs/tools/hh-suite-build-new/data/context_data.crf 
+
+ No Hit                             Prob E-value P-value  Score    SS Cols Query HMM  Template HMM
+  1 1UUN_A MSPA; PORIN, MYCOBACTER 100.0 1.6E-44 2.6E-49  298.3  25.9  182   30-211     3-184 (184)
+  2 2V9U_E MSPA; PORI, PORIN, MYCO 100.0   1E-36 1.7E-41  239.6  20.3  130   30-211     3-132 (132)
+  3 6ADQ_W LpqE protein; Respirato  25.1 4.6E+02  0.0075   21.4   7.6   74    1-74      2-78  (186)
+
+No 1
+>1UUN_A MSPA; PORIN, MYCOBACTERIA; 2.5A {MYCOBACTERIUM SMEGMATIS} SCOP: f.6.1.2
+Probab=100.00  E-value=1.6e-44  Score=298.27  Aligned_cols=182  Identities=99%  Similarity=1.548  Sum_probs=160.5  Template_Neff=7.100
+
+Q ss_pred             CceeEEEcCCCcEEEEEEeceEEEeeCCCCcCCCCccEEEeeEEEEEEECCCccceeEEEEEEEEEEccccccCCccccc
+Q sp               30 DNELSLVDGQDRTLTVQQWDTFLNGVFPLDRNRLTREWFHSGRAKYIVAGPGADEFEGTLELGYQIGFPWSLGVGINFSY  109 (211)
+Q Consensus        30 ~~~~t~~~~dG~~v~v~~~~e~~~~vppl~~~p~sRea~vsg~~~~~v~g~~~~~~~gtl~~GY~VGC~vdv~~g~~~g~  109 (211)
+                      |++++.+++|||++++.+.+|+++.+|||+.+|++||+|++++++++|+|++.+..+|+|++|||||||+|++++++++.
+T Consensus         3 d~~~t~~t~DG~~v~v~~~~e~~~~vppl~~~p~sRe~~vsg~~~~~i~g~~~~~~~g~l~~GY~VGC~vd~~~g~~~g~   82 (184)
+T 1UUN_A            3 DNELSLVDGQDRTLTVQQWDTFLNGVFPLDRNRLTREWFHSGRAKYIVAGPGADEFEGTLELGYQIGFPWSLGVGINFSY   82 (184)
+T ss_dssp             EEEEEEECTTSCEEEEEEEEEEEEEECCTTCCTTCEEEEEEEEEEEEEESTTGGGCEEEEEEEEEEECSEEEEEEEEEEE
+T ss_pred             ccceEEEcCCCcEEEEEEEccEEEeeCCCCCCCCccceEeeeEEEEEEECCCcccceEEEEEEEEEEccceecCCccccc
+Confidence            68899999999999999999999999999999999999999999999999765456799999999999999986777765
+
+
+Q ss_pred             cCcceEecCCCCCCCCCcccccccCccCCcceEEEEcccCCceEEEEEEEEEEecceEEEEEEcEEEEEeeeeecCEEEE
+Q sp              110 TTPNILIDDGDITAPPFGLNSVITPNLFPGVSISADLGNGPGIQEVATFSVDVSGAEGGVAVSNAHGTVTGAAGGVLLRP  189 (211)
+Q Consensus       110 ~tp~~~~~~~~~~~~~~~~~~~~~~~~~p~~~~~i~~~l~PGi~~v~v~~~~l~g~~~~v~~~~~~i~VdgC~G~a~~R~  189 (211)
+                      .+|+++++.+...++..+++++.+.++.|+....+.+.++||++++++.+|+|++.+++++++|+||+||||+||+++|+
+T Consensus        83 ~~p~~~~~~~~~~~~~~~~~~~~~~~l~Pg~~~~~~~~~~p~~~~v~v~~~~~~g~~~~v~~~~~~i~VdgC~G~a~~R~  162 (184)
+T 1UUN_A           83 TTPNILIDDGDITRPPFGLNSVITPNLFPGVSISADLGNGPGIQEVATFSVDVSGAEGGVAVSNAHGTVTGAAGGVLLRP  162 (184)
+T ss_dssp             ECCCCEEEEECTTSTTTTTTSEECCCSSCEEEEEEEEEECCCCEEEEEEEEEEESSEEEEEEEEEEEEECSEESCCEEEE
+T ss_pred             cccceEecCCCCCCCCCcccccccccccCceEEEEEcccCCceeEEEEEEEEEecCeeEEEEecEEEEEeeeccccEEEE
+Confidence            57888775221112333444556678889998888888889999999999999999999999999999999999999999
+
+
+Q ss_pred             EEEEEEeeCCeEEEEeccEecC
+Q sp              190 FARLIASTGDSVTTYGEPWNMN  211 (211)
+Q Consensus       190 y~~v~~~t~~~~t~YG~p~~l~  211 (211)
+                      |+++++++|+++++||+||+|+
+T Consensus       163 y~~v~~~td~~~t~YG~p~~l~  184 (184)
+T 1UUN_A          163 FARLIASTGDSVTTYGEPWNMN  184 (184)
+T ss_dssp             EEEEEETTSCEEEEECCCEECC
+T ss_pred             EEEEEEeeCCeEEEEeccEECC
+Confidence            9999999999999999999996
+
+
+No 2
+>2V9U_E MSPA; PORI, PORIN, MYCOBACTERIA, TRANSPORT PROTEIN; 2.59A {MYCOBACTERIUM SMEGMATIS}
+Probab=100.00  E-value=1e-36  Score=239.58  Aligned_cols=130  Identities=99%  Similarity=1.497  Sum_probs=121.1  Template_Neff=6.600
+
+Q ss_pred             CceeEEEcCCCcEEEEEEeceEEEeeCCCCcCCCCccEEEeeEEEEEEECCCccceeEEEEEEEEEEccccccCCccccc
+Q sp               30 DNELSLVDGQDRTLTVQQWDTFLNGVFPLDRNRLTREWFHSGRAKYIVAGPGADEFEGTLELGYQIGFPWSLGVGINFSY  109 (211)
+Q Consensus        30 ~~~~t~~~~dG~~v~v~~~~e~~~~vppl~~~p~sRea~vsg~~~~~v~g~~~~~~~gtl~~GY~VGC~vdv~~g~~~g~  109 (211)
+                      |++++.+++|||++++.+++|+++.+|||+++|++||+|++++++++|+|++.+..+|+|++|||||||           
+T Consensus         3 d~~~t~~t~DG~~v~v~~~~e~~~~vp~l~~~p~sRe~~vsg~~~~~v~g~~~~~~~g~l~~GY~vGCp-----------   71 (132)
+T 2V9U_E            3 DNELSLVDGQDRTLTVQQWDTFLNGVFPLDRNRLTREWFHSGRAKYIVAGPGADEFEGTLELGYQIGGP-----------   71 (132)
+T ss_dssp             EEEEEEECTTSCEEEEEEEEEEEEEECCTTCCTTCEEEEEEEEEEEEEESTTGGGCEEEEEEEEEEESS-----------
+T ss_pred             CcceEEEcCCCcEEEEEEeccEEEeeCCCCCCCCCccEEEeeEEEEEEECCCcccceEEEEEEEEeecC-----------
+Confidence            678999999999999999999999999999999999999999999999997654567999999999992           
+
+
+Q ss_pred             cCcceEecCCCCCCCCCcccccccCccCCcceEEEEcccCCceEEEEEEEEEEecceEEEEEEcEEEEEeeeeecCEEEE
+Q sp              110 TTPNILIDDGDITAPPFGLNSVITPNLFPGVSISADLGNGPGIQEVATFSVDVSGAEGGVAVSNAHGTVTGAAGGVLLRP  189 (211)
+Q Consensus       110 ~tp~~~~~~~~~~~~~~~~~~~~~~~~~p~~~~~i~~~l~PGi~~v~v~~~~l~g~~~~v~~~~~~i~VdgC~G~a~~R~  189 (211)
+                                                               ||+++++.+++|++..+.++|+|+||+||||+||+++|+
+T Consensus        72 -----------------------------------------Gi~~v~~~~~~~~g~~~~v~~~~~~~~v~gC~G~a~~R~  110 (132)
+T 2V9U_E           72 -----------------------------------------GIQEVATFSVDVSGAEGGVAVSNAHGTVTGAAGGVLLRP  110 (132)
+T ss_dssp             -----------------------------------------SEEEEEEEEEEEESSEECCEECCCCEEECCCCSCEEEEC
+T ss_pred             -----------------------------------------ccceEEEEEEEEcCCeeEEEEeCeEEEEecceecCEEEE
+Confidence                                                     344566788999999999999999999999999999999
+
+
+Q ss_pred             EEEEEEeeCCeEEEEeccEecC
+Q sp              190 FARLIASTGDSVTTYGEPWNMN  211 (211)
+Q Consensus       190 y~~v~~~t~~~~t~YG~p~~l~  211 (211)
+                      |+++++++|+++++||+||+|+
+T Consensus       111 ya~v~~~t~~~vt~YG~p~~l~  132 (132)
+T 2V9U_E          111 FARLIASTGDSVTTYGEPWNMN  132 (132)
+T ss_dssp             EEEEEETTSCEEEEECCCEEEC
+T ss_pred             EEEEEEccCCEEEEEecCEecC
+Confidence            9999999999999999999986
+
+
+No 3
+>6ADQ_W LpqE protein; Respiratory, Supercomplex, SOD, Mycobacterium, ETC, Lipoprotein, ELECTRON TRANSPORT; HET: HEC, HEA, MQ9, 9Y0, 9XX, HEM, PLM, 9YF, CDL; 3.5A {Mycobacterium smegmatis MC2 51}
+Probab=25.07  E-value=4.6e+02  Score=21.39  Aligned_cols=74  Identities=11%  Similarity=-0.118  Sum_probs=0.0  Template_Neff=8.500
+
+Q ss_pred             ChhHHHHHHHHHHHHHHHHhcccccccCCCceeEEEcCCCcEEE---EEEeceEEEeeCCCCcCCCCccEEEeeEEE
+Q sp                1 MKAISRVLIAMVAAIAALFTSTGTSHAGLDNELSLVDGQDRTLT---VQQWDTFLNGVFPLDRNRLTREWFHSGRAK   74 (211)
+Q Consensus         1 ~~~~~~~~~~~~~~~~~~~~~~g~A~A~~~~~~t~~~~dG~~v~---v~~~~e~~~~vppl~~~p~sRea~vsg~~~   74 (211)
+                      +|+.||+.++++++++++++....+.............+|....   +...+-.+....+-...+-...+-+.+...
+T Consensus         2 ~r~~~r~~~~~~~~~~~l~l~gC~~~~~~~t~~~~~~~~g~~~~~~~v~i~~~~v~~~~~g~~~~~g~~a~~~~ti~   78 (186)
+T 6ADQ_W            2 NRFSSRAGLAVCGLATAVALTACSAGQISQTTTQEPAVNGVNAQAGQVSLRNVHLRAPQQTDYVEPGTTVELLFVAA   78 (186)
+T ss_dssp             ----------------------CCSSSSCTTTSCCCSSSSEEECCSSEEEEEEEEECCCCSSSBCTTCEEEEEEEEE
+T ss_pred             chhHHHHHHHHHHHHHHHHHHcccCCCccCCCCCCCCCCCcccccceEEEEEEEEeCCCCCCCCCCCCeEEEEEEEE
+
+