def get_torsion_matrix(file_list, cgmodel, frame_start, frame_stride,
frame_end, backbone_torsion_type):
"""Internal function for reading trajectory files and computing torsions"""
# Load files as {replica number: replica trajectory}
rep_traj = {}
for i in range(len(file_list)):
if file_list[0][-3:] == 'dcd':
rep_traj[i] = md.load(file_list[i],
top=md.Topology.from_openmm(
cgmodel.topology))
else:
rep_traj[i] = md.load(file_list[i])
# Combine all trajectories, selecting specified frames
if frame_end == -1:
frame_end = rep_traj[0].n_frames
if frame_start == -1:
frame_start == frame_end
traj_all = rep_traj[0][frame_start:frame_end:frame_stride]
for i in range(len(file_list) - 1):
traj_all = traj_all.join(
rep_traj[i + 1][frame_start:frame_end:frame_stride])
# Get torsion list:
torsion_list = CGModel.get_torsion_list(cgmodel)
# Assign torsion types:
torsion_types, torsion_array, torsion_sub_arrays, n_i, i_torsion_type, torsion_dict, inv_torsion_dict = \
assign_torsion_types(cgmodel, torsion_list)
# Compute specified torsion angles over all frames:
for i in range(i_torsion_type):
if inv_torsion_dict[str(i + 1)] == backbone_torsion_type:
# Compute all torsion values in trajectory
# This returns an [nframes x n_torsions] array
torsion_val_array = md.compute_dihedrals(
traj_all, torsion_sub_arrays[str(i + 1)])
# Convert to degrees:
torsion_val_array = (180 / np.pi) * torsion_val_array
return torsion_val_array, traj_all
def calc_ramachandran(
cgmodel,
file_list,
nbin_theta=180,
nbin_alpha=180,
frame_start=0,
frame_stride=1,
frame_end=-1,
plotfile="ramachandran.pdf",
backbone_angle_type = "bb_bb_bb",
backbone_torsion_type = "bb_bb_bb_bb",
colormap="nipy_spectral",
temperature_list=None,
):
"""
Calculate and plot ramachandran plot for backbone bond bending-angle and torsion
angle, given a CGModel object and pdb or dcd trajectory.
:param cgmodel: CGModel() object
:type cgmodel: class
:param file_list: path to pdb or dcd trajectory file(s) - can be a list or single string
:type file_list: str or list(str)
:param nbin_theta: number of bins for bond-bending angle (spanning from 0 to 180 degrees)
:type nbin_theta: int
:param nbin_alpha: number of bins for torsion angle (spanning from -180 to +180 degrees)
:type nbin_alpha:
:param frame_start: First frame in trajectory file to use for analysis.
:type frame_start: int
:param frame_stride: Advance by this many frames when reading trajectories.
:type frame_stride: int
:param frame_end: Last frame in trajectory file to use for analysis.
:type frame_end: int
:param plotfile: Filename for saving torsion distribution pdf plots
:type plotfile: str
:param backbone_angle_type: particle sequence of the backbone angles (default="bb_bb_bb") - for now only single sequence permitted
:type backbone_angle_type: str
:param backbone_torsion_type: particle sequence of the backbone angles (default="bb_bb_bb_bb") - for now only single sequence permitted
:type backbone_torsion_type: str
:param colormap: matplotlib pyplot colormap to use (default='nipy_spectral')
:type colormap: str (case sensitive)
:param temperature_list: list of temperatures corresponding to file_list. If None, no subplot labels will be used.
:type temperature_list: list(Quantity())
:returns:
- hist_data ( dict )
- xedges ( dict )
- yedges ( dict )
"""
# Convert file_list to list if a single string:
if type(file_list) == str:
# Single file
file_list = file_list.split()
# Store angle, torsion values by filename for computing global colormap
ang_val_array = {}
torsion_val_array = {}
for file in file_list:
# Load in a trajectory file:
if file[-3:] == 'dcd':
traj = md.load(file,top=md.Topology.from_openmm(cgmodel.topology))
else:
traj = md.load(file)
# Select frames for analysis:
if frame_end == -1:
frame_end = traj.n_frames
traj = traj[frame_start:frame_end:frame_stride]
nframes = traj.n_frames
# Get angle list
angle_list = CGModel.get_bond_angle_list(cgmodel)
# Assign angle types:
ang_types, ang_array, ang_sub_arrays, n_i, i_angle_type, ang_dict, inv_ang_dict = \
assign_angle_types(cgmodel, angle_list)
# Set bin edges:
angle_bin_edges = np.linspace(0,180,nbin_theta+1)
angle_bin_centers = np.zeros((len(angle_bin_edges)-1,1))
for i in range(len(angle_bin_edges)-1):
angle_bin_centers[i] = (angle_bin_edges[i]+angle_bin_edges[i+1])/2
for i in range(i_angle_type):
if inv_ang_dict[str(i+1)] == backbone_angle_type:
# Compute all angle values in trajectory
# This returns an [nframes x n_angles] array
ang_val_array[file] = md.compute_angles(traj,ang_sub_arrays[str(i+1)])
# We will have different numbers of bond-bending angle and torsion angle.
# We will set a convention of omitting the last angle value.
# Convert to degrees and exclude last angle:
ang_val_array[file] = (180/np.pi)*ang_val_array[file][:,:-1]
# Reshape array:
ang_val_array[file] = np.reshape(ang_val_array[file], (nframes*(n_i[i]-1)[0],1))
# Get torsion list
torsion_list = CGModel.get_torsion_list(cgmodel)
# Assign torsion types
torsion_types, torsion_array, torsion_sub_arrays, n_j, i_torsion_type, torsion_dict, inv_torsion_dict = \
assign_torsion_types(cgmodel, torsion_list)
# Set bin edges:
torsion_bin_edges = np.linspace(-180,180,nbin_alpha+1)
torsion_bin_centers = np.zeros((len(torsion_bin_edges)-1,1))
for i in range(len(torsion_bin_edges)-1):
torsion_bin_centers[i] = (torsion_bin_edges[i]+torsion_bin_edges[i+1])/2
for i in range(i_torsion_type):
if inv_torsion_dict[str(i+1)] == backbone_torsion_type:
# Compute all torsion values in trajectory
# This returns an [nframes x n_torsions] array
torsion_val_array[file] = md.compute_dihedrals(
traj,torsion_sub_arrays[str(i+1)])
# Convert to degrees:
torsion_val_array[file] *= (180/np.pi)
# Reshape array
torsion_val_array[file] = np.reshape(torsion_val_array[file], (nframes*n_j[i][0],1))
# 2d histogram the data and plot:
hist_data, xedges, yedges = plot_2d_distribution(
file_list, torsion_val_array, ang_val_array, torsion_bin_edges, angle_bin_edges,
plotfile, colormap, xlabel='Alpha (degrees)', ylabel='Theta (degrees)', temperature_list=temperature_list)
return hist_data, xedges, yedges
def calc_2d_distribution(
cgmodel,
file_list,
nbin_xvar=180,
nbin_yvar=180,
frame_start=0,
frame_stride=1,
frame_end=-1,
plotfile="2d_hist.pdf",
xvar_name = "bb_bb_bb",
yvar_name = "bb_bb_bb_bb",
colormap="nipy_spectral",
temperature_list=None,
):
"""
Calculate and plot 2d histogram for any 2 bonded variables,
given a CGModel object and pdb or dcd trajectory.
:param cgmodel: CGModel() object
:type cgmodel: class
:param file_list: path to pdb or dcd trajectory file(s) - can be a list or single string
:type file_list: str or list(str)
:param nbin_xvar: number of bins for x bonded variable
:type nbin_xvar: int
:param nbin_yvar: number of bins for y bonded variable
:type nbin_yvar:
:param frame_start: First frame in trajectory file to use for analysis.
:type frame_start: int
:param frame_stride: Advance by this many frames when reading trajectories.
:type frame_stride: int
:param frame_end: Last frame in trajectory file to use for analysis.
:type frame_end: int
:param plotfile: Filename for saving torsion distribution pdf plots
:type plotfile: str
:param xvar_name: particle sequence of the x bonded parameter (default="bb_bb_bb")
:type xvar_name: str
:param yvar_name: particle sequence of the y bonded parameter (default="bb_bb_bb_bb")
:type yvar_name: str
:param colormap: matplotlib pyplot colormap to use (default='nipy_spectral')
:type colormap: str (case sensitive)
:param temperature_list: list of temperatures corresponding to file_list. If None, no subplot labels will be used.
:type temperature_list: list(Quantity())
:returns:
- hist_data ( dict )
- xedges ( dict )
- yedges ( dict )
"""
# Convert file_list to list if a single string:
if type(file_list) == str:
# Single file
file_list = file_list.split()
# Store angle, torsion values by filename for computing global colormap
xvar_val_array = {}
yvar_val_array = {}
# Store the reverse name of the bonded type (need to check both)
# x variable
particle_list = []
particle = ""
for c in xvar_name:
if c == '_':
particle_list.append(particle)
particle = ""
else:
particle += c
particle_list.append(particle)
particle_list_reverse = particle_list[::-1]
xvar_name_reverse = ""
for par in particle_list_reverse:
xvar_name_reverse += par
xvar_name_reverse += "_"
xvar_name_reverse = xvar_name_reverse[:-1]
# y variable
particle_list = []
particle = ""
for c in yvar_name:
if c == '_':
particle_list.append(particle)
particle = ""
else:
particle += c
particle_list.append(particle)
particle_list_reverse = particle_list[::-1]
yvar_name_reverse = ""
for par in particle_list_reverse:
yvar_name_reverse += par
yvar_name_reverse += "_"
yvar_name_reverse = yvar_name_reverse[:-1]
for file in file_list:
# Load in a trajectory file:
if file[-3:] == 'dcd':
traj = md.load(file,top=md.Topology.from_openmm(cgmodel.topology))
else:
traj = md.load(file)
# Select frames for analysis:
if frame_end == -1:
frame_end = traj.n_frames
traj = traj[frame_start:frame_end:frame_stride]
nframes = traj.n_frames
# x variable
# Determine parameter type of xvar:
n_particle_x = xvar_name.count('_')+1
if n_particle_x == 2:
# Bond
# Get bond list
bond_list = CGModel.get_bond_list(cgmodel)
# Assign bond types:
bond_types, bond_array, bond_sub_arrays, n_i, i_bond_type, bond_dict, inv_bond_dict = \
assign_bond_types(cgmodel, bond_list)
for i in range(i_bond_type):
if inv_bond_dict[str(i+1)] == xvar_name or inv_bond_dict[str(i+1)] == xvar_name_reverse:
# Compute all bond length values in trajectory
# This returns an [nframes x n_bonds] array
xvar_val_array[file] = md.compute_distances(traj,bond_sub_arrays[str(i+1)])
# Get equilibrium value:
b_eq = cgmodel.get_bond_length(bond_sub_arrays[str(i+1)][0])
# Set bin edges:
# This should be the same across all files - use heuristic from equilibrium bond length
b_min = 0.5*b_eq.value_in_unit(unit.nanometer)
b_max = 1.5*b_eq.value_in_unit(unit.nanometer)
xvar_bin_edges = np.linspace(b_min,b_max,nbin_xvar+1)
xvar_bin_centers = np.zeros((len(xvar_bin_edges)-1,1))
for i in range(len(xvar_bin_edges)-1):
xvar_bin_centers[i] = (xvar_bin_edges[i]+xvar_bin_edges[i+1])/2
xlabel = f'{xvar_name} distance ({unit.nanometer})'
elif n_particle_x == 3:
# Angle
# Get angle list
angle_list = CGModel.get_bond_angle_list(cgmodel)
# Assign angle types:
ang_types, ang_array, ang_sub_arrays, n_i, i_angle_type, ang_dict, inv_ang_dict = \
assign_angle_types(cgmodel, angle_list)
# Set bin edges:
xvar_bin_edges = np.linspace(0,180,nbin_xvar+1)
xvar_bin_centers = np.zeros((len(xvar_bin_edges)-1,1))
for i in range(len(xvar_bin_edges)-1):
xvar_bin_centers[i] = (xvar_bin_edges[i]+xvar_bin_edges[i+1])/2
for i in range(i_angle_type):
if inv_ang_dict[str(i+1)] == xvar_name or inv_ang_dict[str(i+1)] == xvar_name_reverse:
# Compute all angle values in trajectory
# This returns an [nframes x n_angles] array
xvar_val_array[file] = md.compute_angles(traj,ang_sub_arrays[str(i+1)])
# Convert to degrees:
xvar_val_array[file] *= (180/np.pi)
xlabel = f'{xvar_name} angle (degrees)'
elif n_particle_x == 4:
# Torsion
# Get torsion list
torsion_list = CGModel.get_torsion_list(cgmodel)
# Assign torsion types
torsion_types, torsion_array, torsion_sub_arrays, n_j, i_torsion_type, torsion_dict, inv_torsion_dict = \
assign_torsion_types(cgmodel, torsion_list)
# Set bin edges:
xvar_bin_edges = np.linspace(-180,180,nbin_xvar+1)
xvar_bin_centers = np.zeros((len(xvar_bin_edges)-1,1))
for i in range(len(xvar_bin_edges)-1):
xvar_bin_centers[i] = (xvar_bin_edges[i]+xvar_bin_edges[i+1])/2
for i in range(i_torsion_type):
if inv_torsion_dict[str(i+1)] == xvar_name or inv_torsion_dict[str(i+1)] == xvar_name_reverse:
# Compute all torsion values in trajectory
# This returns an [nframes x n_torsions] array
xvar_val_array[file] = md.compute_dihedrals(
traj,torsion_sub_arrays[str(i+1)])
# Convert to degrees:
xvar_val_array[file] *= (180/np.pi)
xlabel = f'{xvar_name} angle (degrees)'
# y variable
# Determine parameter type of yvar:
n_particle_y = yvar_name.count('_')+1
if n_particle_y == 2:
# Bond
# Get bond list
bond_list = CGModel.get_bond_list(cgmodel)
# Assign bond types:
bond_types, bond_array, bond_sub_arrays, n_i, i_bond_type, bond_dict, inv_bond_dict = \
assign_bond_types(cgmodel, bond_list)
for i in range(i_bond_type):
if inv_bond_dict[str(i+1)] == yvar_name or inv_bond_dict[str(i+1)] == yvar_name_reverse:
# Compute all bond length values in trajectory
# This returns an [nframes x n_bonds] array
yvar_val_array[file] = md.compute_distances(traj,bond_sub_arrays[str(i+1)])
# Get equilibrium value:
b_eq = cgmodel.get_bond_length(bond_sub_arrays[str(i+1)][0])
# Set bin edges:
# This should be the same across all files - use heuristic from equilibrium bond length
b_min = 0.5*b_eq.value_in_unit(unit.nanometer)
b_max = 1.5*b_eq.value_in_unit(unit.nanometer)
yvar_bin_edges = np.linspace(b_min,b_max,nbin_yvar+1)
yvar_bin_centers = np.zeros((len(yvar_bin_edges)-1,1))
for i in range(len(yvar_bin_edges)-1):
yvar_bin_centers[i] = (yvar_bin_edges[i]+yvar_bin_edges[i+1])/2
ylabel = f'{yvar_name} distance ({unit.nanometer})'
elif n_particle_y == 3:
# Angle
# Get angle list
angle_list = CGModel.get_bond_angle_list(cgmodel)
# Assign angle types:
ang_types, ang_array, ang_sub_arrays, n_i, i_angle_type, ang_dict, inv_ang_dict = \
assign_angle_types(cgmodel, angle_list)
# Set bin edges:
yvar_bin_edges = np.linspace(0,180,nbin_yvar+1)
yvar_bin_centers = np.zeros((len(yvar_bin_edges)-1,1))
for i in range(len(yvar_bin_edges)-1):
yvar_bin_centers[i] = (yvar_bin_edges[i]+yvar_bin_edges[i+1])/2
for i in range(i_angle_type):
if inv_ang_dict[str(i+1)] == yvar_name or inv_ang_dict[str(i+1)] == yvar_name_reverse:
# Compute all angle values in trajectory
# This returns an [nframes x n_angles] array
yvar_val_array[file] = md.compute_angles(traj,ang_sub_arrays[str(i+1)])
# Convert to degrees:
yvar_val_array[file] *= (180/np.pi)
ylabel = f'{yvar_name} angle (degrees)'
elif n_particle_y == 4:
# Torsion
# Get torsion list
torsion_list = CGModel.get_torsion_list(cgmodel)
# Assign torsion types
torsion_types, torsion_array, torsion_sub_arrays, n_j, i_torsion_type, torsion_dict, inv_torsion_dict = \
assign_torsion_types(cgmodel, torsion_list)
# Set bin edges:
yvar_bin_edges = np.linspace(-180,180,nbin_yvar+1)
yvar_bin_centers = np.zeros((len(yvar_bin_edges)-1,1))
for i in range(len(yvar_bin_edges)-1):
yvar_bin_centers[i] = (yvar_bin_edges[i]+yvar_bin_edges[i+1])/2
for i in range(i_torsion_type):
if inv_torsion_dict[str(i+1)] == yvar_name or inv_torsion_dict[str(i+1)] == yvar_name_reverse:
# Compute all torsion values in trajectory
# This returns an [nframes x n_torsions] array
yvar_val_array[file] = md.compute_dihedrals(
traj,torsion_sub_arrays[str(i+1)])
# Convert to degrees:
yvar_val_array[file] *= (180/np.pi)
ylabel = f'{yvar_name} angle (degrees)'
# Since the bonded variables may have different numbers of observables, we can use all
# combinations of the 2 parameter observables to create the histograms.
xvar_val_array_combo = {}
yvar_val_array_combo = {}
# Each array of single observables is [n_frames x n_occurances]
# x value arrays should be [xval0_y0, xval1_y0, ...xvaln_y0, ... xval0_yn, xval1_yn, xvaln_yn]
# y value arrays should be [yval0_x0, yval0_x1, ...yval0_xn, ... yvaln_x0, yvaln_x1, yvaln_xn]
for file in file_list:
n_occ_x = xvar_val_array[file].shape[1]
n_occ_y = yvar_val_array[file].shape[1]
xvar_val_array_combo[file] = np.zeros((nframes,n_occ_x*n_occ_y))
yvar_val_array_combo[file] = np.zeros_like(xvar_val_array_combo[file])
for iy in range(n_occ_y):
xvar_val_array_combo[file][:,(iy*n_occ_x):((iy+1)*n_occ_x)] = xvar_val_array[file]
for ix in range(n_occ_x):
yvar_val_array_combo[file][:,ix+iy*n_occ_x] = yvar_val_array[file][:,iy]
# Reshape arrays for histogramming:
xvar_val_array_combo[file] = np.reshape(xvar_val_array_combo[file], (nframes*n_occ_x*n_occ_y,1))
yvar_val_array_combo[file] = np.reshape(yvar_val_array_combo[file], (nframes*n_occ_x*n_occ_y,1))
# 2d histogram the data and plot:
hist_data, xedges, yedges = plot_2d_distribution(
file_list, xvar_val_array_combo, yvar_val_array_combo, xvar_bin_edges, yvar_bin_edges,
plotfile, colormap, xlabel, ylabel, temperature_list=temperature_list)
return hist_data, xedges, yedges
def calc_torsion_distribution(
cgmodel, file_list, nbins=180, frame_start=0, frame_stride=1, frame_end=-1,
plot_per_page=2, temperature_list=None, plotfile="torsion_hist.pdf"
):
"""
Calculate and plot all torsion distributions from a CGModel object and pdb or dcd trajectory
:param cgmodel: CGModel() object
:type cgmodel: class
:param file_list: path to pdb or dcd trajectory file(s)
:type file_list: str or list(str)
:param nbins: number of bins spanning the range of -180 to 180 degrees, default = 180
:type nbins: int
:param frame_start: First frame in trajectory file to use for analysis.
:type frame_start: int
:param frame_stride: Advance by this many frames when reading trajectories.
:type frame_stride: int
:param frame_end: Last frame in trajectory file to use for analysis.
:type frame_end: int
:param plot_per_page: number of subplots to display on each page (default=2)
:type plot_per_page: int
:param temperature_list: list of temperatures corresponding to file_list. If None, file names will be the plot labels.
:type temperature_list: list(Quantity())
:param plotfile: Base filename for saving torsion distribution pdf plots
:type plotfile: str
:returns:
- torsion_hist_data ( dict )
"""
# Convert file_list to list if a single string:
if type(file_list) == str:
# Single file
file_list = file_list.split()
# Get torsion list
torsion_list = CGModel.get_torsion_list(cgmodel)
# Assign torsion types
torsion_types, torsion_array, torsion_sub_arrays, n_i, i_torsion_type, torsion_dict, inv_torsion_dict = \
assign_torsion_types(cgmodel, torsion_list)
# Create dictionary for saving torsion histogram data:
torsion_hist_data = {}
# Set bin edges:
torsion_bin_edges = np.linspace(-180,180,nbins+1)
torsion_bin_centers = np.zeros((len(torsion_bin_edges)-1,1))
for i in range(len(torsion_bin_edges)-1):
torsion_bin_centers[i] = (torsion_bin_edges[i]+torsion_bin_edges[i+1])/2
file_index = 0
for file in file_list:
# Load in a trajectory file:
if file[-3:] == 'dcd':
traj = md.load(file,top=md.Topology.from_openmm(cgmodel.topology))
else:
traj = md.load(file)
# Select frames for analysis:
if frame_end == -1:
frame_end = traj.n_frames
traj = traj[frame_start:frame_end:frame_stride]
nframes = traj.n_frames
# Create inner dictionary for current file:
if temperature_list is not None:
file_key = f"{temperature_list[file_index].value_in_unit(unit.kelvin):.2f}"
else:
file_key = file[:-4]
torsion_hist_data[file_key] = {}
for i in range(i_torsion_type):
# Compute all torsion values in trajectory
# This returns an [nframes x n_torsions] array
torsion_val_array = md.compute_dihedrals(
traj,torsion_sub_arrays[str(i+1)])
# Reshape arrays and convert to degrees:
torsion_val_array = (180/np.pi)*np.reshape(torsion_val_array, (nframes*n_i[i][0],1))
# Histogram and plot results:
n_out, bin_edges_out = np.histogram(
torsion_val_array, bins=torsion_bin_edges,density=True)
torsion_hist_data[file_key][f"{inv_torsion_dict[str(i+1)]}_density"]=n_out
torsion_hist_data[file_key][f"{inv_torsion_dict[str(i+1)]}_bin_centers"]=torsion_bin_centers
file_index += 1
plot_distribution(
inv_torsion_dict,
torsion_hist_data,
xlabel="Torsion angle (degrees)",
ylabel="Probability density",
xlim=[-180,180],
figure_title="Torsion_distributions",
file_name=f"{plotfile}",
plot_per_page=plot_per_page,
)
return torsion_hist_data
