def align_1kx5(): ''' align the 1kx5 to the dimer then save pdbs for psfgen ''' mono_file = '1KX5tailfold_fx_CG.pdb' # goal_file = 'new_c11_tetramer.pdb' goal_file = 'c11_folded_tails.pdb' in_vars = inputs() in_vars.goal = goal_file in_vars.ref = in_vars.move = mono_file in_vars.path = './' in_vars.move_filter = '((chain[i] == "I") and (name[i] == "C1\'"))' # NCP 1 in_vars.out = '4mer_ncp1/1KX5_4mer_ncp1.pdb' in_vars.goal_filter = '((segname[i] == "DNA1") and (name[i] == "C1\'") and (resid[i] > 22) and (resid[i] < 170))' align.align(in_vars) # NCP 2 in_vars.out = '4mer_ncp2/1KX5_4mer_ncp2.pdb' in_vars.goal_filter = '((segname[i] == "DNA1") and (name[i] == "C1\'") and (resid[i] > 189) and (resid[i] < 337))' align.align(in_vars) # NCP 3 in_vars.out = '4mer_ncp3/1KX5_4mer_ncp3.pdb' in_vars.goal_filter = '((segname[i] == "DNA1") and (name[i] == "C1\'") and (resid[i] > 356) and (resid[i] < 504))' align.align(in_vars) # NCP 4 in_vars.out = '4mer_ncp4/1KX5_4mer_ncp4.pdb' in_vars.goal_filter = '((segname[i] == "DNA1") and (name[i] == "C1\'") and (resid[i] > 523) and (resid[i] < 671))' align.align(in_vars)
def main(): ''' this did not work well, there histones to not match well in the NCP so there was overlap btwn the aligned versions ''' in_vars = inputs() goals = [ 'histone_A0.pdb', 'histone_B0.pdb', 'histone_C0.pdb', 'histone_D0.pdb', 'histone_E0.pdb', 'histone_F0.pdb', 'histone_G0.pdb', 'histone_H0.pdb', 'histone_A1.pdb', 'histone_B1.pdb', 'histone_C1.pdb', 'histone_D1.pdb', 'histone_E1.pdb', 'histone_F1.pdb', 'histone_G1.pdb', 'histone_H1.pdb' ] move = [ '1KX5tailfold_167bp_chain_A1.pdb', '1KX5tailfold_167bp_chain_B1.pdb', '1KX5tailfold_167bp_chain_C1_trun.pdb', '1KX5tailfold_167bp_chain_D1.pdb', '1KX5tailfold_167bp_chain_A1.pdb', '1KX5tailfold_167bp_chain_F1.pdb', '1KX5tailfold_167bp_chain_G1_trun.pdb', '1KX5tailfold_167bp_chain_H1.pdb' ] out = [ '1H3.pdb', '1H4.pdb', '1H2A.pdb', '1H2B.pdb', '2H3.pdb', '2H4.pdb', '2H2A.pdb', '2H2B.pdb', '3H3.pdb', '3H4.pdb', '3H2A.pdb', '3H2B.pdb', '4H3.pdb', '4H4.pdb', '4H2A.pdb', '4H2B.pdb' ] move_seg = ['A', 'B', 'C', 'D', 'A', 'F', 'G', 'H'] goal_seg = [ 'A0', 'B0', 'C0', 'D0', 'E0', 'F0', 'G0', 'H0', 'A1', 'B1', 'C1', 'D1', 'E1', 'F1', 'G1', 'H1' ] in_vars.move_seg_or_ch = 'segname' in_vars.goal_seg_or_ch = 'segname' in_vars.path = './' match_res_min = [50, 20, 01, 50] match_res_max = [70, 40, 50, 124] for i in xrange(len(goals)): in_vars.goal = goals[i] in_vars.move = in_vars.ref = move[i % 8] in_vars.out = out[i] in_vars.move_seg_chain = move_seg[i % 8] in_vars.goal_seg_chain = goal_seg[i] in_vars.min = match_res_min[i % 4] in_vars.max = match_res_max[i % 4] align.align(in_vars)
def align_1kx5(): ''' align the 1kx5 to the dimer then save pdbs for psfgen ''' mono_file = '1KX5tailfold_fx_CG.pdb' goal_file = 'gH5_NCP.pdb' in_vars = inputs() in_vars.goal = goal_file in_vars.ref = in_vars.move = mono_file in_vars.path = './' in_vars.move_filter = '((chain[i] == "I") and (name[i] == "C1\'"))' # NCP 1 in_vars.out = '4mer_ncp1/1KX5_4mer_ncp1.pdb' in_vars.goal_filter = '((segname[i] == "I") and (name[i] == "C1\'") and (resid[i] >= 11) and (resid[i] <= 157))' align.align(in_vars)
def mv_A_to_E(): ''' this worked well to move A to E (no apparent overlap) ''' in_vars = inputs() in_vars.goal = '1KX5tailfold_167bp_chain_E1.pdb' in_vars.ref = '1KX5tailfold_167bp_chain_A1.pdb' in_vars.move = '1KX5tailfold_167bp_chain_A1.pdb' in_vars.out = '1KX5tailfold_A2E_2.pdb' in_vars.move_seg_chain = 'A' in_vars.goal_seg_chain = 'E' in_vars.path = './' in_vars.move_seg_or_ch = 'segname' in_vars.goal_seg_or_ch = 'segname' in_vars.min = 38 in_vars.max = 50 align.align(in_vars)
def main(): ''' this did not work well, there histones to not match well in the NCP so there was overlap btwn the aligned versions ''' in_vars = inputs() goals = ['histone_A0.pdb', 'histone_B0.pdb', 'histone_C0.pdb', 'histone_D0.pdb', 'histone_E0.pdb', 'histone_F0.pdb', 'histone_G0.pdb', 'histone_H0.pdb', 'histone_A1.pdb', 'histone_B1.pdb', 'histone_C1.pdb', 'histone_D1.pdb', 'histone_E1.pdb', 'histone_F1.pdb', 'histone_G1.pdb', 'histone_H1.pdb'] move = ['1KX5tailfold_167bp_chain_A1.pdb', '1KX5tailfold_167bp_chain_B1.pdb', '1KX5tailfold_167bp_chain_C1_trun.pdb', '1KX5tailfold_167bp_chain_D1.pdb', '1KX5tailfold_167bp_chain_A1.pdb', '1KX5tailfold_167bp_chain_F1.pdb', '1KX5tailfold_167bp_chain_G1_trun.pdb', '1KX5tailfold_167bp_chain_H1.pdb'] out = ['1H3.pdb', '1H4.pdb', '1H2A.pdb', '1H2B.pdb', '2H3.pdb', '2H4.pdb', '2H2A.pdb', '2H2B.pdb', '3H3.pdb', '3H4.pdb', '3H2A.pdb', '3H2B.pdb', '4H3.pdb', '4H4.pdb', '4H2A.pdb', '4H2B.pdb'] move_seg = ['A', 'B', 'C', 'D', 'A', 'F', 'G', 'H'] goal_seg = ['A0', 'B0', 'C0', 'D0', 'E0', 'F0', 'G0', 'H0', 'A1', 'B1', 'C1', 'D1', 'E1', 'F1', 'G1', 'H1'] in_vars.move_seg_or_ch = 'segname' in_vars.goal_seg_or_ch = 'segname' in_vars.path = './' match_res_min = [50, 20, 01, 50] match_res_max = [70, 40, 50, 124] for i in xrange(len(goals)): in_vars.goal = goals[i] in_vars.move = in_vars.ref = move[i % 8] in_vars.out = out[i] in_vars.move_seg_chain = move_seg[i % 8] in_vars.goal_seg_chain = goal_seg[i] in_vars.min = match_res_min[i % 4] in_vars.max = match_res_max[i % 4] align.align(in_vars)
def align_1kx5(): ''' align the 1kx5 to the dimer then save pdbs for psfgen ''' mono_file = '1KX5tailfold_fxd.pdb' dimer_file = '../150205dimer.pdb' in_vars = inputs() in_vars.goal = dimer_file in_vars.ref = in_vars.move = mono_file in_vars.path = './' in_vars.move_filter = '((chain[i] == "I") and (name[i] == "C1\'"))' # NCP 1 in_vars.out = '1KX5tailfold_dimer_ncp1.pdb' in_vars.goal_filter = '((segname[i] == "DNA1") and (name[i] == "C1\'") and (resid[i] > 14) and (resid[i] < 162))' align.align(in_vars) # NCP 2 in_vars.out = '1KX5tailfold_dimer_ncp2.pdb' in_vars.goal_filter = '((segname[i] == "DNA1") and (name[i] == "C1\'") and (resid[i] > 181) and (resid[i] < 329))' align.align(in_vars)
'4x167/run7/monte_carlo/4x167_5d_20k.dcd'] start_dir = os.getcwd() all_dcds = ['4x167/run0/monte_carlo/test.dcd'] align_basis = ('((name[i] == "CA") and (segname[i] == "3H2A") and ' '(resid[i] > 105) and (resid[i] < 115))') inputs = align.inputs() inputs.path = '' inputs.goal_filter = align_basis inputs.move_filter = align_basis dimer = '/home/schowell/myData/sassieRuns/2x167_k010_s1_min.pdb' trimer = '/home/schowell/myData/sassieRuns/3x167_min.pdb' tetramer = '/home/schowell/myData/sassieRuns/c11_min.pdb' inputs.goal = inputs.ref = dimer for dcd in dimer_dcds: print 'aligning %s' % dcd inputs.move = os.path.join(start_dir, dcd) inputs.out = inputs.move.replace('.dcd', '_al.dcd') align.align(inputs) os.system('mv %s %s' % (inputs.out, inputs.move)) print '\m/ >.< \m/'
'4x167/run6/monte_carlo/4x167_5d_20k.dcd', '4x167/run7/monte_carlo/4x167_5d_20k.dcd' ] start_dir = os.getcwd() all_dcds = ['4x167/run0/monte_carlo/test.dcd'] align_basis = ('((name[i] == "CA") and (segname[i] == "3H2A") and ' '(resid[i] > 105) and (resid[i] < 115))') inputs = align.inputs() inputs.path = '' inputs.goal_filter = align_basis inputs.move_filter = align_basis dimer = '/home/schowell/myData/sassieRuns/2x167_k010_s1_min.pdb' trimer = '/home/schowell/myData/sassieRuns/3x167_min.pdb' tetramer = '/home/schowell/myData/sassieRuns/c11_min.pdb' inputs.goal = inputs.ref = dimer for dcd in dimer_dcds: print 'aligning %s' % dcd inputs.move = os.path.join(start_dir, dcd) inputs.out = inputs.move.replace('.dcd', '_al.dcd') align.align(inputs) os.system('mv %s %s' % (inputs.out, inputs.move)) print '\m/ >.< \m/'