def _rmsd(res):
#mol is an md universe
#res,name_file_dcd,mol=args
mol = MD.Universe(pdb_file, dcd_file)
print "["+str(res)+"] Aligning Trajectory"
ref_sel = ref.selectAtoms('backbone and resid ' + str(res),'backbone and around ' + cutoff + ' (backbone and resid ' + str(res) + ')')
print ref_sel.atoms
ref_sel_str = ''
for i in list(ref_sel):
useful =str(i).split(":")[1]
ref_sel_str += '(' + useful.replace('>',' ').replace("'",'').replace(',',' and').replace('of','and') + ') or '
#ref_sel_str += "(" + useful.replace('>',' ').replace("'",'') + ') or '
ref_sel_str = ref_sel_str[:-4]
#print ref_sel_str
filenamedcd = "LA" + cutoff + "rmsd.noh.R" + str(res) + '.dcd'
MDA.rms_fit_trj(mol, ref, select=ref_sel_str, filename = filenamedcd ) #'name N and type N and resname MET resid 1 and segid P1')
output = ''
print "["+str(res)+"] Calculating RMSD for residue " + str(res) + "..." + str( 1 + range(res_beg,res_end).index(res) ) + " of " + str(res_num)
mol = MD.Universe(pdb_file, filenamedcd)
cf_timer = time.time()
atoms_mol = mol.selectAtoms("resid " + str(res) + " and not name H")
mol.trajectory[ref_frame]
atoms_ref = copy.deepcopy(mol.selectAtoms("resid " + str(res) + " and not name H").coordinates())
rmsd = []
for ts1 in mol.trajectory[0:-1:skip]:
rmsd.append(MDA.rmsd(atoms_mol.coordinates(), atoms_ref))
rmsd = numpy.array(rmsd)
numpy.savetxt(name_file_dcd + "rmsd.noh.LA" + cutoff +".%04d.txt" % res , rmsd)
os.remove(filenamedcd)
def calc_rmsd(args):
"""
input : args -> from read_traj_vmd
calculates g2(t) rmsd, and plots to file using save_plot_rmsd
"""
psffile = os.path.splitext(args.psffile)[0]
u = Universe(psffile + '.psf', args.traj)
ref_atoms = u.selectAtoms("all")
traj_atoms = u.selectAtoms("all")
frame = []
rmsd_array = []
# reference centre of mass system
ref_com = ref_atoms.centerOfMass()
ref_coordinates = ref_atoms.coordinates() - ref_com
# diff_coordinates = ref_atoms.coordinates().copy
# allocate the array for selection atom coords
traj_coordinates = traj_atoms.coordinates().copy()
for ts in u.trajectory[args.startframe:args.endframe:args.trajskip]:
# selection is updated with the time frame
x_com = traj_atoms.centerOfMass()
traj_coordinates[:] = traj_atoms.coordinates() - x_com
rmsd_value = MDrmsd.rmsd(traj_coordinates, ref_coordinates)
print "frame ", ts.frame, " rmsd ", rmsd_value
frame.append(ts.frame)
rmsd_array.append(rmsd_value)
frame = np.array(frame)
rmsd_array = np.array(rmsd_array)
save_plot_rmsd(frame, rmsd_array, psffile)
return None
def _rmsd(res):
#mol is an md universe
#res,name_file_dcd,mol=args
mol = MD.Universe(pdb_file, dcd_file)
print "[" + str(res) + "] Aligning Trajectory"
ref_sel = ref.selectAtoms(
'backbone and resid ' + str(res), 'backbone and around ' + cutoff +
' (backbone and resid ' + str(res) + ')')
print ref_sel.atoms
ref_sel_str = ''
for i in list(ref_sel):
useful = str(i).split(":")[1]
ref_sel_str += '(' + useful.replace('>', ' ').replace("'", '').replace(
',', ' and').replace('of', 'and') + ') or '
#ref_sel_str += "(" + useful.replace('>',' ').replace("'",'') + ') or '
ref_sel_str = ref_sel_str[:-4]
#print ref_sel_str
filenamedcd = "LA" + cutoff + "rmsd.noh.R" + str(res) + '.dcd'
MDA.rms_fit_trj(
mol, ref, select=ref_sel_str, filename=filenamedcd
) #'name N and type N and resname MET resid 1 and segid P1')
output = ''
print "[" + str(res) + "] Calculating RMSD for residue " + str(
res) + "..." + str(
1 + range(res_beg, res_end).index(res)) + " of " + str(res_num)
mol = MD.Universe(pdb_file, filenamedcd)
cf_timer = time.time()
atoms_mol = mol.selectAtoms("resid " + str(res) + " and not name H")
mol.trajectory[ref_frame]
atoms_ref = copy.deepcopy(
mol.selectAtoms("resid " + str(res) + " and not name H").coordinates())
rmsd = []
for ts1 in mol.trajectory[0:-1:skip]:
rmsd.append(MDA.rmsd(atoms_mol.coordinates(), atoms_ref))
rmsd = numpy.array(rmsd)
numpy.savetxt(name_file_dcd + "rmsd.noh.LA" + cutoff + ".%04d.txt" % res,
rmsd)
os.remove(filenamedcd)
pdb_file = sys.argv[1]
dcd_file = sys.argv[2]
print "Loading trajectory"
ref = MDA.Universe(pdb_file)
mol = MDA.Universe(pdb_file, dcd_file)
mol_all = mol.selectAtoms('all')
ref_all = ref.selectAtoms('all')
rmsd_list = []
if "-a" in sys.argv:
dataout = open(name_file_dcd + 'rmsd.A.txt', 'w')
for frame in mol.trajectory:
MDAaa.alignto(mol, ref, select = 'backbone', mass_weighted = True)
rmsd_list.append(MDAaa.rmsd(mol_all.coordinates(),ref_all.coordinates()))
else:
dataout = open(name_file_dcd + 'rmsd.txt', 'w')
for frame in mol.trajectory:
rmsd_list.append(MDAaa.rmsd(mol_all.coordinates(),ref_all.coordinates()))
output = ''
for i in range(len(rmsd_list)):
output += str(i) + '\t' + '%.5f' % rmsd_list[i] + '\n'
dataout.write(output)
dataout.close()
pick = 2
else:
print("fasta file irrelevant for requested operation... ignoring")
alnlis = ref.residues.resnames()
else:
alnlis = ref.residues.resnames()
for res in alnlis:
try:
refcrd = ref.selectAtoms("backbone and resid " + str(res)).coordinates()
trgcrd = trg.selectAtoms("backbone and resid " + str(res)).coordinates()
except IndexError:
print res
print alndic[res]
sys.exit()
rmsd = MDA.rmsd(refcrd, trgcrd)
if alnlis == ref.residues.resnames() or pick == 1:
print(str(res) + ' * ' + str(rmsd))
output = str(res) + ' * ' + str(rmsd) + '\n'
elif pick == 2:
print(str(alndic[res]) + ' * ' + str(rmsd))
output = str(alndic[res]) + ' * ' + str(rmsd) + '\n'
else:
if '-aln' not in sys.argv:
print("Structure from different homologs or truncated. Please insert alignment")
sys.exit()
else:
seq_dic, seq_list = bitk.fastareader(sys.argv[sys.argv.index('-aln')+1])
if bitk.threeLetter2oneLetter(ref.residues.resnames()) != seq_dic[seq_list[0]].replace('-',''):
print("input order is important. Please, make the input order coherent with the alignment file")
sys.exit()
dcd_file = sys.argv[2]
print "Loading trajectory"
ref = MDA.Universe(pdb_file)
mol = MDA.Universe(pdb_file, dcd_file)
mol_all = mol.selectAtoms('all')
ref_all = ref.selectAtoms('all')
rmsd_list = []
if "-a" in sys.argv:
dataout = open(name_file_dcd + 'rmsd.A.txt', 'w')
for frame in mol.trajectory:
MDAaa.alignto(mol, ref, select='backbone', mass_weighted=True)
rmsd_list.append(
MDAaa.rmsd(mol_all.coordinates(), ref_all.coordinates()))
else:
dataout = open(name_file_dcd + 'rmsd.txt', 'w')
for frame in mol.trajectory:
rmsd_list.append(
MDAaa.rmsd(mol_all.coordinates(), ref_all.coordinates()))
output = ''
for i in range(len(rmsd_list)):
output += str(i) + '\t' + '%.5f' % rmsd_list[i] + '\n'
dataout.write(output)
dataout.close()
selected models and it should represent the entire trajectory.
@author:JamesPino
"""
import os
import numpy as np
from MDAnalysis import *
from MDAnalysis.analysis.align import rmsd
RMSD_Matrix=np.arange(1,4239)
f=open('rmsd.txt','w')
for i in range(1,4239):
tmp_rmsd=[]
for k in range(i+1,4239):
main = Universe(str(i)+"x.pdb" )
reference=Universe(str(k)+"x.pdb" )
bb = main.selectAtoms('backbone')
A = bb.coordinates() # coordinates of main frame
cc=reference.selectAtoms('backbone')
B = cc.coordinates() # coordinates of reference frame
x = rmsd(A,B);#print>>f , i , k , x;
print i , k , x;
tmp_rmsd=np.append(tmp_rmsd,x)
for j in range(i):
tmp_rmsd=np.insert(tmp_rmsd,0,0)
RMSD_Matrix=np.column_stack((RMSD_Matrix,tmp_rmsd))
np.savetxt('RMSD_MATRIX.out',RMSD_Matrix)