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How to use do_select method in localstack

Best Python code snippet using localstack_python

mutation_one_by_one.py

Source:mutation_one_by_one.py

...31# prot_list = [['1shr', 'B']] # example [['1nzp', 'A'], ['4oxn', 'B']] # how many proteins do you want32residues_list = [int(z) for x,y,z in second_shell_residues]33aminoacid = ['ALA','GLY' ] # only two34def mutate_this(prot, res ,num ):35    cmd.get_wizard().do_select("/obj_%s//%s/%d" % (num,prot[1], res))36    cmd.frame(1)37    cmd.get_wizard().apply()38    cmd.save(f"../files/mutant_{res}_{prot[1]}.pdb","obj_%s"%(num))39def mutate_all(prot, res ,num ):40    if res != "ALA":41        cmd.get_wizard().set_mode(aminoacid[0])42        cmd.get_wizard().do_select("/obj_%s//%s/%d" % (num,prot[1], res))43        cmd.frame(1)44        cmd.get_wizard().apply()45        cmd.save(f"../files/mutant_{res}_{prot[1]}_ALA.pdb","obj_%s"%(num))46     #   cmd.save("../files/mutant_all_residues.pdb","obj_%s"%(num))47    else:48        cmd.get_wizard().set_mode(aminoacid[1])49        cmd.get_wizard().do_select("/obj_%s//%s/%d" % (num,prot[1], res))50        cmd.frame(1)51        cmd.get_wizard().apply()52        cmd.save(f"../files/mutant_{res}_{prot[1]}_GLY.pdb","obj_%s"%(num))53    #    cmd.save("../files/mutant_all_residues.pdb","obj_%s"%(num)) 54for prot in prot_list:55    #Initialize56    # fetch protein by PDB code57    cmd.fetch(prot[0], async_=0)58    # mutagenesis mode59    cmd.wizard("mutagenesis")60    cmd.do("refresh_wizard")61    62    # create 7 object 63    for obj in range(len(second_shell_residues)):64        cmd.create('obj_%s' % obj, prot[0])65    # Mutate66    # cmd.get_wizard().set_mode(aminoacid)67    #for obj_1 (mutation in all residues) 68    for num,res in enumerate ( residues_list ) :69        num +=170        if num == choice:   71            mutate_all(prot, res, num=num)72        73            74    # cmd.get_wizard().do_select("/obj_1//%s/%d" % (prot[1], residues_list[1]))75    # cmd.frame(1)76    # cmd.get_wizard().apply()77    # cmd.get_wizard().do_select("/obj_1//%s/%d" % (prot[1], residues_list[2]))78    # cmd.frame(1)79    # cmd.get_wizard().apply()80    # cmd.save("%s_%s_%s_%s_%s_x_%s.pdb" % (prot[0], prot[1], residues_list[0], residues_list[1], residues_list[2], aminoacid),'obj_1')81    82#    #for obj_2 (mutation in residue # 1 and 2)83#    cmd.get_wizard().do_select("/obj_2//%s/%d" % (prot[1], residues_list[0]))84#    cmd.frame(1)85#    cmd.get_wizard().apply()86#    cmd.get_wizard().do_select("/obj_2//%s/%d" % (prot[1], residues_list[1]))87#    cmd.frame(1)88#    cmd.get_wizard().apply()89#    cmd.save("%s_%s_%s_%s_x_%s.pdb" % (prot[0], prot[1], residues_list[0], residues_list[2], aminoacid),'obj_2')90#    91#    #for obj_3 (mutation in residue # 1 and 3)92#    cmd.get_wizard().do_select("/obj_3//%s/%d" % (prot[1], residues_list[0]))93#    cmd.frame(1)94#    cmd.get_wizard().apply()95#    cmd.get_wizard().do_select("/obj_3//%s/%d" % (prot[1], residues_list[2]))96#    cmd.frame(1)97#    cmd.get_wizard().apply()98#    cmd.save("%s_%s_%s_%s_x_%s.pdb" % (prot[0], prot[1], residues_list[0], residues_list[2], aminoacid),'obj_3')99#    100#    #for obj_4 (mutation in residue # 2 and 3)101#    cmd.get_wizard().do_select("/obj_4//%s/%d" % (prot[1], residues_list[1]))102#    cmd.frame(1)103#    cmd.get_wizard().apply()104#    cmd.get_wizard().do_select("/obj_4//%s/%d" % (prot[1], residues_list[2]))105#    cmd.frame(1)106#    cmd.get_wizard().apply()107#    cmd.save("%s_%s_%s_%s_x_%s.pdb" % (prot[0], prot[1], residues_list[1], residues_list[2], aminoacid),'obj_4')108#    109#    #for obj_5 (mutation in residue # 1)110#    cmd.get_wizard().do_select("/obj_5//%s/%d" % (prot[1], residues_list[0]))111#    cmd.frame(1)112#    cmd.get_wizard().apply()113#    cmd.save("%s_%s_%s_x_%s.pdb" % (prot[0], prot[1], residues_list[0], aminoacid),'obj_5')114#    #for obj_6 (mutation in residue # 2)115#    cmd.get_wizard().do_select("/obj_6//%s/%d" % (prot[1], residues_list[1]))116#    cmd.frame(1)117#    cmd.get_wizard().apply()118#    cmd.save("%s_%s_%s_x_%s.pdb" % (prot[0], prot[1], residues_list[1], aminoacid),'obj_6')119#    #for obj_7 (mutation in residue # 3)120#    cmd.get_wizard().do_select("/obj_7//%s/%d" % (prot[1], residues_list[2]))121#    cmd.frame(1)122#    cmd.get_wizard().apply()123#    cmd.save("%s_%s_%s_x_%s.pdb" % (prot[0], prot[1], residues_list[2], aminoacid),'obj_7')124#125#    # Done126#    cmd.set_wizard()127#    if len(prot_list) == 1:128#        continue129#    else:130#        cmd.reinitialize()  131#   ...

mutation.py

Source:mutation.py

...29# prot_list = [['1shr', 'B']] # example [['1nzp', 'A'], ['4oxn', 'B']] # how many proteins do you want30residues_list = [int(z) for x,y,z in second_shell_residues]31aminoacid = ['ALA','GLY' ] # only two32def mutate_this(prot, res ,num ):33    cmd.get_wizard().do_select("/obj_%s//%s/%d" % (num,prot[1], res))34    cmd.frame(1)35    cmd.get_wizard().apply()36    cmd.save(f"../files/mutant_{res}_{prot[1]}.pdb","obj_%s"%(num))37def mutate_all(prot, res ,num ):38    if res != "ALA":39        cmd.get_wizard().set_mode(aminoacid[0])40        cmd.get_wizard().do_select("/obj_%s//%s/%d" % (num,prot[1], res))41        cmd.frame(1)42        cmd.get_wizard().apply()43        cmd.save("../files/mutant_all_residues.pdb","obj_%s"%(num))44    else:45        cmd.get_wizard().set_mode(aminoacid[1])46        cmd.get_wizard().do_select("/obj_%s//%s/%d" % (num,prot[1], res))47        cmd.frame(1)48        cmd.get_wizard().apply()49        cmd.save("../files/mutant_all_residues.pdb","obj_%s"%(num)) 50for prot in prot_list:51    #Initialize52    # fetch protein by PDB code53    cmd.fetch(prot[0], async_=0)54    # mutagenesis mode55    cmd.wizard("mutagenesis")56    cmd.do("refresh_wizard")57    58    # create 7 object 59    for obj in range(len(second_shell_residues)):60        cmd.create('obj_%s' % obj, prot[0])61    # Mutate62    # cmd.get_wizard().set_mode(aminoacid)63    #for obj_1 (mutation in all residues) 64    for res in residues_list:  65        mutate_all(prot, res, num=1)66    # cmd.get_wizard().do_select("/obj_1//%s/%d" % (prot[1], residues_list[1]))67    # cmd.frame(1)68    # cmd.get_wizard().apply()69    # cmd.get_wizard().do_select("/obj_1//%s/%d" % (prot[1], residues_list[2]))70    # cmd.frame(1)71    # cmd.get_wizard().apply()72    # cmd.save("%s_%s_%s_%s_%s_x_%s.pdb" % (prot[0], prot[1], residues_list[0], residues_list[1], residues_list[2], aminoacid),'obj_1')73    74#    #for obj_2 (mutation in residue # 1 and 2)75#    cmd.get_wizard().do_select("/obj_2//%s/%d" % (prot[1], residues_list[0]))76#    cmd.frame(1)77#    cmd.get_wizard().apply()78#    cmd.get_wizard().do_select("/obj_2//%s/%d" % (prot[1], residues_list[1]))79#    cmd.frame(1)80#    cmd.get_wizard().apply()81#    cmd.save("%s_%s_%s_%s_x_%s.pdb" % (prot[0], prot[1], residues_list[0], residues_list[2], aminoacid),'obj_2')82#    83#    #for obj_3 (mutation in residue # 1 and 3)84#    cmd.get_wizard().do_select("/obj_3//%s/%d" % (prot[1], residues_list[0]))85#    cmd.frame(1)86#    cmd.get_wizard().apply()87#    cmd.get_wizard().do_select("/obj_3//%s/%d" % (prot[1], residues_list[2]))88#    cmd.frame(1)89#    cmd.get_wizard().apply()90#    cmd.save("%s_%s_%s_%s_x_%s.pdb" % (prot[0], prot[1], residues_list[0], residues_list[2], aminoacid),'obj_3')91#    92#    #for obj_4 (mutation in residue # 2 and 3)93#    cmd.get_wizard().do_select("/obj_4//%s/%d" % (prot[1], residues_list[1]))94#    cmd.frame(1)95#    cmd.get_wizard().apply()96#    cmd.get_wizard().do_select("/obj_4//%s/%d" % (prot[1], residues_list[2]))97#    cmd.frame(1)98#    cmd.get_wizard().apply()99#    cmd.save("%s_%s_%s_%s_x_%s.pdb" % (prot[0], prot[1], residues_list[1], residues_list[2], aminoacid),'obj_4')100#    101#    #for obj_5 (mutation in residue # 1)102#    cmd.get_wizard().do_select("/obj_5//%s/%d" % (prot[1], residues_list[0]))103#    cmd.frame(1)104#    cmd.get_wizard().apply()105#    cmd.save("%s_%s_%s_x_%s.pdb" % (prot[0], prot[1], residues_list[0], aminoacid),'obj_5')106#    #for obj_6 (mutation in residue # 2)107#    cmd.get_wizard().do_select("/obj_6//%s/%d" % (prot[1], residues_list[1]))108#    cmd.frame(1)109#    cmd.get_wizard().apply()110#    cmd.save("%s_%s_%s_x_%s.pdb" % (prot[0], prot[1], residues_list[1], aminoacid),'obj_6')111#    #for obj_7 (mutation in residue # 3)112#    cmd.get_wizard().do_select("/obj_7//%s/%d" % (prot[1], residues_list[2]))113#    cmd.frame(1)114#    cmd.get_wizard().apply()115#    cmd.save("%s_%s_%s_x_%s.pdb" % (prot[0], prot[1], residues_list[2], aminoacid),'obj_7')116#117#    # Done118#    cmd.set_wizard()119#    if len(prot_list) == 1:120#        continue121#    else:122#        cmd.reinitialize()  123#   ...

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