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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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