def combine_trj_without_water(trj_names,top_names):
print "loaded TRJ: ",trj_names
print "loaded TOP: ",top_names
trj=md.load_mdcrd(trj_names[0], top_names[0]) #We load the first traj
atom_index=[] #atoms # that will be kept in the new traj
for el in trj.top.atoms: #We select the atom that are not water
if str(el.residue)[0:3]!='HOH': atom_index.append(el.index)
trj=trj.atom_slice(atom_index) #We keep only the non water atom
for trj_temp_name, top_temp_name in zip(trj_names[1:],top_names[1:]): #We concatenate the trj:
trj_temp=md.load_mdcrd(trj_temp_name, top_temp_name) # we load them
trj_temp=trj_temp.atom_slice(atom_index) # we remove water
trj.join(trj_temp) # we join them to the main trj
return(trj)
def test_ComparetoMDtraj(self):
import mdtraj as md
traj = pt.load(filename="./data/Tc5b.x",
top="./data/Tc5b.top")
m_top = md.load_prmtop("./data/Tc5b.top")
m_traj = md.load_mdcrd("./data/Tc5b.x", m_top)
m_traj.xyz = m_traj.xyz * 10 # convert `nm` to `Angstrom` unit
arr0 = pt.rmsd(traj, ref=0)
arr1 = pt.rmsd(traj, ref=0)
arr2 = pt.rmsd(traj, )
a_md0 = md.rmsd(m_traj, m_traj, 0)
aa_eq(arr0, arr1)
aa_eq(arr0, arr2)
aa_eq(arr0, a_md0)
arr0 = pt.rmsd(traj, ref=-1)
arr1 = pt.rmsd(traj, ref=-1)
a_md = md.rmsd(m_traj, m_traj, -1)
aa_eq(arr0, arr1)
aa_eq(arr0, a_md)
mask = ":3-18@CA,C"
atm = traj.top(mask)
arr0 = pt.rmsd(traj, ref=-1, mask=mask)
arr1 = pt.rmsd(traj, mask=atm.indices, ref=-1)
arr2 = pt.rmsd(traj, mask=list(atm.indices), ref=-1)
arr3 = pt.rmsd(traj, mask=tuple(atm.indices), ref=-1)
a_md = md.rmsd(m_traj, m_traj, -1, atm.indices)
aa_eq(arr0, a_md)
aa_eq(arr1, a_md)
aa_eq(arr2, a_md)
aa_eq(arr3, a_md)
fa = Trajectory(traj)
arr0 = pt.rmsd(fa, ref=-1, mask=mask)
arr1 = pt.rmsd(fa, mask=atm.indices, ref=-1)
arr2 = pt.rmsd(fa, mask=list(atm.indices), ref=-1)
arr3 = pt.rmsd(fa, mask=tuple(atm.indices), ref=-1)
a_md = md.rmsd(m_traj, m_traj, -1, atm.indices)
aa_eq(arr0, a_md)
aa_eq(arr1, a_md)
aa_eq(arr2, a_md)
aa_eq(arr3, a_md)
fa = Trajectory(traj)
mask = "!@H="
atm = fa.top(mask)
arr0 = pt.rmsd(fa, ref=4, mask=mask)
a_md = md.rmsd(m_traj, m_traj, 4, atm.indices)
# exclude 0-th frame for ref
aa_eq(arr0, a_md)
def test_ComparetoMDtraj(self):
import mdtraj as md
traj = pt.load(filename=tc5b_trajin, top=tc5b_top)
m_top = md.load_prmtop(tc5b_top)
m_traj = md.load_mdcrd(tc5b_trajin, m_top)
m_traj.xyz = m_traj.xyz * 10 # convert `nm` to `Angstrom` unit
arr0 = pt.rmsd(traj, ref=0)
arr1 = pt.rmsd(traj, ref=0)
arr2 = pt.rmsd(traj, )
a_md0 = md.rmsd(m_traj, m_traj, 0)
aa_eq(arr0, arr1)
aa_eq(arr0, arr2)
aa_eq(arr0, a_md0)
arr0 = pt.rmsd(traj, ref=-1)
arr1 = pt.rmsd(traj, ref=-1)
a_md = md.rmsd(m_traj, m_traj, -1)
aa_eq(arr0, arr1)
aa_eq(arr0, a_md)
mask = ":3-18@CA,C"
atm = traj.top(mask)
arr0 = pt.rmsd(traj, ref=-1, mask=mask)
arr1 = pt.rmsd(traj, mask=atm.indices, ref=-1)
arr2 = pt.rmsd(traj, mask=list(atm.indices), ref=-1)
arr3 = pt.rmsd(traj, mask=tuple(atm.indices), ref=-1)
a_md = md.rmsd(m_traj, m_traj, -1, atm.indices)
aa_eq(arr0, a_md)
aa_eq(arr1, a_md)
aa_eq(arr2, a_md)
aa_eq(arr3, a_md)
fa = Trajectory(traj)
arr0 = pt.rmsd(fa, ref=-1, mask=mask)
arr1 = pt.rmsd(fa, mask=atm.indices, ref=-1)
arr2 = pt.rmsd(fa, mask=list(atm.indices), ref=-1)
arr3 = pt.rmsd(fa, mask=tuple(atm.indices), ref=-1)
a_md = md.rmsd(m_traj, m_traj, -1, atm.indices)
aa_eq(arr0, a_md)
aa_eq(arr1, a_md)
aa_eq(arr2, a_md)
aa_eq(arr3, a_md)
fa = Trajectory(traj)
mask = "!@H="
atm = fa.top(mask)
arr0 = pt.rmsd(fa, ref=4, mask=mask)
a_md = md.rmsd(m_traj, m_traj, 4, atm.indices)
# exclude 0-th frame for ref
aa_eq(arr0, a_md)
def load_trj(filename, top):
try:
return md.load(filename, top=top)
except (IOError, TypeError):
pass
try:
return md.load_netcdf(filename, top=top)
except (IOError, TypeError):
pass
try:
return md.load_mdcrd(filename, top=top)
except (IOError, TypeError):
print('Trajectory format not recognized. Exiting.')
exit()
def singlepoint(topol, trajs):
energies = []
for traj in trajs:
top_file = topol
#traj = sys.argv[2] #collection of mdcrd/coordiantes
#load each frame and use it as a coordinate
#mdtraj_top = mdtraj.load_prmtop(top_file)
mdtraj_dcdfile = mdtraj.load_mdcrd(traj, top=top_file)
nframes = len(mdtraj_dcdfile)
#create a folder to store the crds
if not os.path.exists("rst7_sire_files"):
os.makedirs("rst7_sire_files")
#print("reading the mdcrd file... %s frames" %(nframes))
for framenumber in range(0, nframes):
#create a Sire system
rst_file = "rst7_sire_files/%i.rst7" % framenumber
mdtraj_dcdfile[framenumber].save_amberrst7(
"rst7_sire_files/%i.rst7" % (framenumber))
amber = Amber()
molecules, space = amber.readCrdTop(rst_file, top_file)
system = createSystem(molecules)
# Define forcefields
system = setupForcefields(system, space)
#print(framenumber , system.energy())#.value())
energies.append(system.energy().value())
#print("removing folder...")
cmd = "rm -r rst7_sire_files"
os.system(cmd)
minimum = min(energies)
new_energies = []
for val in energies:
print(val)
new_val = val - minimum
# if new_val <1000 : new_energies.append(new_val)
new_energies.append(new_val)
#print(len(new_energies))
outputenergy = open('energySinglepoint.dat', 'w')
for energy in new_energies:
outputenergy.write(str(energy) + '\n')
return [energy for energy in new_energies]
return system
if __name__ == "__main__":
energies=[]
for traj in sys.argv[2:]:
top_file = sys.argv[1] #topology file
#traj = sys.argv[2] #collection of mdcrd/coordiantes
#load each frame and use it as a coordinate
#mdtraj_top = mdtraj.load_prmtop(top_file)
mdtraj_dcdfile = mdtraj.load_mdcrd(traj,top=top_file)
nframes= len(mdtraj_dcdfile)
#create a folder to store the crds
if not os.path.exists("rst7_sire_files"):
os.makedirs("rst7_sire_files")
print("reading the mdcrd file... %s frames" %(nframes))
for framenumber in range(0, nframes):
#create a Sire system
rst_file = "rst7_sire_files/%i.rst7" % framenumber
mdtraj_dcdfile[framenumber].save_amberrst7("rst7_sire_files/%i.rst7" %(framenumber))
amber = Amber()
molecules, space = amber.readCrdTop(rst_file, top_file)
system=createSystem(molecules)
Results are plotted as a graph (interactions_frames.png) and saved as a .csv file (interactions_frames.csv)
If the script is being run on the complex using ejm_49, please use the --ejm_49 option to calculate
cation-pi interactions. This script must be used within a production simulation folder, as it reads the
Usage: python atomic_distances.py [--ejm_49]
'''
parser = argparse.ArgumentParser()
parser.add_argument("--ejm_49",
help="add cation-pi interactions for ligand ejm_49",
action="store_true")
args = parser.parse_args()
#Load trajectory
print("Loading trajectory...")
traj = md.load_mdcrd('production_short.mdcrd',
top='solvated_complex.prmtop',
stride=1)
print("Calculating atomic distances...")
#Note: See project paper for reasoning of cutoff distance used for various interactions
#Common Van Der Waals' Contacts:
#Cutoff of 4.0 angstroms used for VDW contacts
#Calculate distance between Val92 atom CG2 (sidechain C) and ligand atom C10 (pyridine) in each frame
vdw_pyridine1_val92 = traj.top.select("resid 91 and name CG2")
vdw_pyridine1_mol289 = traj.top.select("resid 288 and name C10")
vdw_pyridine1_indices = np.array(
[vdw_pyridine1_val92[0], vdw_pyridine1_mol289[0]], ndmin=2)
vdw_pyridine1 = md.compute_distances(traj, vdw_pyridine1_indices)
#Apply cutoff and only save distances within cutoff range