def minimum_contact_distance(a_H, b_H, return_indices=False, strip_H=True):
"""
Calculates the minimum distance between two sets of coordinates
:param a_H: prody object of first set (rows of dist matrix)
:param b_H: prody object of second set (columns of dist matrix)
:param return_indices: boolean, whether or not to return row and column indicies of atoms with min distance in matrix
:return: minimum distance in angstroms
"""
if strip_H:
a = a_H.select('not hydrogen').getCoords()
b = b_H.select('not hydrogen').getCoords()
else:
a = a_H.getCoords()
b = b_H.getCoords()
ligand_residue_distance_matrix = prody.buildDistMatrix(a, b)
# Find minimum score in matrix
row_min_indicies = np.amin(ligand_residue_distance_matrix, axis=0)
ligand_index = np.argmin(row_min_indicies, axis=0)
residue_index = np.argmin(ligand_residue_distance_matrix, axis=0)
column_index_low = ligand_index
row_index_low = residue_index[column_index_low]
# Contact distance
if return_indices:
return ligand_residue_distance_matrix.item(
row_index_low, column_index_low), row_index_low, column_index_low
else:
return ligand_residue_distance_matrix.item(row_index_low,
column_index_low)
def set_bonds(prody_pdb):
"""Sets backbone bonds of chain based on proximity of atoms."""
bb_sel = prody_pdb.select('protein and name N C CA')
dm = pr.buildDistMatrix(bb_sel)
ind = np.where((np.tril(dm) < 1.7) & (np.tril(dm) > 0))
atom_ind = bb_sel.getIndices()
prody_pdb.setBonds([(atom_ind[i], atom_ind[j])
for i, j in zip(ind[0], ind[1])])
def set_bonds(self):
"""Sets backbone bonds of chain based on proximity of atoms, used for vdM fragment selection."""
# This needs to be for the whole protein because vdMs can reach across chains.
bb_sel = self.prody_pdb.select('protein and name N C CA')
dm = pr.buildDistMatrix(bb_sel)
ind = np.where((np.tril(dm) < 1.7) & (np.tril(dm) > 0))
atom_ind = bb_sel.getIndices()
self.prody_pdb.setBonds([(atom_ind[i], atom_ind[j])
for i, j in zip(ind[0], ind[1])])
def calcSpectrusSims(distFlucts, pdb, cutoff=10., sigma='MRSDF', **kwargs):
coords = pdb.getCoords()
n = coords.shape[0]
if distFlucts.shape != (n, n):
raise ValueError('distFlucts and atoms must have same linear '
'size (now %d and %d)' % (distFlucts.shape[0], n))
# identify atom pairs within cutoff and store relative dist. flucts
nearestNeighs = np.full((n, n), True, dtype=bool)
np.fill_diagonal(nearestNeighs, False)
if isinstance(cutoff, (int, float)):
# compute inter-atomic distances
dist = buildDistMatrix(coords)
nearestNeighs &= (dist <= cutoff)
elif cutoff is not None:
raise ValueError('cutoff must be either a number or None. '
'Got: {0}'.format(type(cutoff)))
nnDistFlucts = distFlucts[nearestNeighs]
# set the sigma parameter for the Gaussian weights
if sigma == 'MRSDF':
# sigma is computed as the average of the root distance fluctuations
# between residues within the distance cutoff, as defined in the
# SPECTRUS algorithm
sigma = np.mean(np.sqrt(nnDistFlucts))
elif sigma == 'RMSDF':
# sigma is computed as the root mean squared dist. fluctuations
# (faster to compute than MRSDF)
sigma = np.sqrt(np.mean(nnDistFlucts))
# check if sigma is a number
try:
ss = 2. * sigma**2
except:
raise ValueError('sigma must be \'MRSDF\', \'RMSDF\' or a number.')
# compute the Gaussian weights only for residue pairs
# within the distance cutoff
reducedSims = np.where(nearestNeighs, np.exp(-distFlucts / ss), 0)
np.fill_diagonal(reducedSims, 1.)
sparseSims = sparse.csr_matrix(reducedSims)
sparse.csr_matrix.eliminate_zeros(sparseSims)
return sparseSims, sigma
def pathAnalysisApp():
inp_file, out_file, sel_type, pdb_file,val_fltr, \
dis_fltr, src_res, trgt_res, num_paths\
= handle_arguments_pathAnalysisApp()
print(f"""
@> Running 'paths' app
@> Input file : {inp_file}
@> PDB file : {pdb_file}
@> Data type : {sel_type}
@> Output : {out_file}
@> Value filter : {val_fltr}
@> Distance filter: {dis_fltr}
@> Source residue : {src_res}
@> Target residue : {trgt_res}
@> Number of paths: {num_paths}""")
if (os.path.isfile(inp_file) == False):
print("@> ERROR: Could not find the correlation matrix: " + inp_file +
"!")
print(
"@> The file does not exist or it is not in the folder!\n")
sys.exit(-1)
if (os.path.isfile(pdb_file) == False):
print("@> ERROR: Could not find the pdb file: " + pdb_file + "!")
print(
"@> The file does not exist or it is not in the folder!\n")
sys.exit(-1)
##########################################################################
# Read PDB file
# TODO: This is the only place where I use Prody.
# Maybe, I can replace it with a library that only parses
# PDB files. Prody does a lot more!
selectedAtoms = parsePDB(pdb_file, subset='ca')
##########################################################################
# Read data file and assign to a numpy array
if sel_type.lower() == "ndcc":
# Check if the data type is sparse matrix
data_file = open(inp_file, 'r')
allLines = data_file.readlines()
data_file.close()
# Read the first line to determine if the matrix is sparse format
words = allLines[0].split()
# Read the 1st line and check if it has three columns
if (len(words) == 3):
ccMatrix = parseSparseCorrData(inp_file, selectedAtoms, \
Ctype=True,
symmetric=True,
writeAllOutput=False)
else:
ccMatrix = np.loadtxt(inp_file, dtype=float)
elif sel_type.lower() == "absndcc":
# Check if the data type is sparse matrix
data_file = open(inp_file, 'r')
allLines = data_file.readlines()
data_file.close()
# Read the first line to determine if the matrix is sparse format
words = allLines[0].split()
# Read the 1st line and check if it has three columns
if (len(words) == 3):
ccMatrix = np.absolute(parseSparseCorrData(inp_file, selectedAtoms, \
Ctype=True,
symmetric=True,
writeAllOutput=False))
else:
ccMatrix = np.absolute(np.loadtxt(inp_file, dtype=float))
elif sel_type.lower() == "lmi":
# Check if the data type is sparse matrix
data_file = open(inp_file, 'r')
allLines = data_file.readlines()
data_file.close()
# Read the first line to determine if the matrix is sparse format
words = allLines[0].split()
# Read the 1st line and check if it has three columns
if (len(words) == 3):
ccMatrix = parseSparseCorrData(inp_file, selectedAtoms, \
Ctype=True,
symmetric=True,
writeAllOutput=False)
else:
ccMatrix = convertLMIdata2Matrix(inp_file, writeAllOutput=False)
elif sel_type.lower() == "coeviz":
ccMatrix = np.loadtxt(inp_file, dtype=float)
elif sel_type.lower() == "evcouplings":
ccMatrix = parseEVcouplingsScores(inp_file, selectedAtoms, False)
elif sel_type.lower() == "generic":
# Check if the data type is sparse matrix
data_file = open(inp_file, 'r')
allLines = data_file.readlines()
data_file.close()
# Read the first line to determine if the matrix is sparse format
words = allLines[0].split()
# Read the 1st line and check if it has three columns
if (len(words) == 3):
ccMatrix = parseSparseCorrData(inp_file, selectedAtoms, \
Ctype=True,
symmetric=True,
writeAllOutput=False)
else:
ccMatrix = np.loadtxt(inp_file, dtype=float)
elif sel_type.lower() == "eg":
# The data type is elasticity graph
ccMatrix = parseElasticityGraph(inp_file, selectedAtoms, \
writeAllOutput=False)
else:
print(
"@> ERROR: Unknown data type: Type can only be ndcc, absndcc, lmi,\n"
)
print(
"@> coeviz or evcouplings. If you have your data in full \n"
)
print(
"@> matrix format and your data type is none of the options\n"
)
print("@> mentionned, you can set data type 'generic'.\n")
sys.exit(-1)
sourceResid = src_res
targetResid = trgt_res
distanceMatrix = buildDistMatrix(selectedAtoms)
resDict = mapResid2ResIndex(selectedAtoms)
if ((sel_type.lower() == "evcouplings") or \
(sel_type.lower() == "generic") or \
(sel_type.lower() == "eg")):
network = buildSequenceNetwork(ccMatrix, distanceMatrix, \
float(val_fltr), float(dis_fltr),\
selectedAtoms)
else:
network = buildDynamicsNetwork(ccMatrix, distanceMatrix, \
float(val_fltr), float(dis_fltr),\
selectedAtoms)
suboptimalPaths = pathAnalysis(network, \
float(val_fltr), float(dis_fltr),\
resDict[sourceResid], resDict[targetResid], \
selectedAtoms,\
int(num_paths))
out_file_full_name = out_file + "-source" + sourceResid + "-target" + targetResid + ".tcl"
writePath2VMDFile(suboptimalPaths, selectedAtoms, \
resDict[sourceResid], resDict[targetResid], \
pdb_file, out_file_full_name)
out_file_full_name = out_file + "-source" + sourceResid + "-target" + targetResid + ".pml"
writePath2PMLFile(suboptimalPaths, selectedAtoms,\
resDict[sourceResid], resDict[targetResid], \
pdb_file, out_file_full_name)
def centralityAnalysisApp():
inp_file, out_file, sel_type, pdb_file, centrality_type, value_cutoff,\
distance_cutoff = handle_arguments_centralityAnalysisApp()
print(f"""
@> Running 'analyze' app
@> Input file : {inp_file}
@> PDB file : {pdb_file}
@> Data type : {sel_type}
@> Output : {out_file}
@> Centrality : {centrality_type}
@> Value filter : {value_cutoff}
@> Distance filter: {distance_cutoff}""")
if (os.path.isfile(inp_file) == False):
print("@> ERROR: Could not find the correlation matrix: " + inp_file +
"!")
print(
"@> The file does not exist or it is not in the folder!\n")
sys.exit(-1)
if (os.path.isfile(pdb_file) == False):
print("@> ERROR: Could not find the pdb file: " + pdb_file + "!")
print(
"@> The file does not exist or it is not in the folder!\n")
sys.exit(-1)
##########################################################################
# Read PDB file
# TODO: This is the only place where I use Prody.
# Maybe, I can replace it with a library that only parses
# PDB files. Prody does a lot more!
selectedAtoms = parsePDB(pdb_file, subset='ca')
valueFilter = float(value_cutoff)
distanceFilter = float(distance_cutoff)
distanceMatrix = buildDistMatrix(selectedAtoms)
##########################################################################
# Read data file and assign to a numpy array
if sel_type.lower() == "ndcc":
# Check if the data type is sparse matrix
data_file = open(inp_file, 'r')
allLines = data_file.readlines()
data_file.close()
# Read the first line to determine if the matrix is sparse format
words = allLines[0].split()
# Read the 1st line and check if it has three columns
if (len(words) == 3):
ccMatrix = parseSparseCorrData(inp_file, selectedAtoms, \
Ctype=True,
symmetric=True,
writeAllOutput=False)
else:
ccMatrix = np.loadtxt(inp_file, dtype=float)
elif sel_type.lower() == "absndcc":
# Check if the data type is sparse matrix
data_file = open(inp_file, 'r')
allLines = data_file.readlines()
data_file.close()
# Read the first line to determine if the matrix is sparse format
words = allLines[0].split()
# Read the 1st line and check if it has three columns
if (len(words) == 3):
ccMatrix = np.absolute(parseSparseCorrData(inp_file, selectedAtoms, \
Ctype=True,
symmetric=True,
writeAllOutput=False))
else:
ccMatrix = np.absolute(np.loadtxt(inp_file, dtype=float))
elif sel_type.lower() == "lmi":
# Check if the data type is sparse matrix
data_file = open(inp_file, 'r')
allLines = data_file.readlines()
data_file.close()
# Read the first line to determine if the matrix is sparse format
words = allLines[0].split()
# Read the 1st line and check if it has three columns
if (len(words) == 3):
ccMatrix = parseSparseCorrData(inp_file, selectedAtoms, \
Ctype=True,
symmetric=True,
writeAllOutput=False)
else:
ccMatrix = convertLMIdata2Matrix(inp_file, writeAllOutput=False)
elif sel_type.lower() == "coeviz":
ccMatrix = np.loadtxt(inp_file, dtype=float)
elif sel_type.lower() == "evcouplings":
ccMatrix = parseEVcouplingsScores(inp_file, selectedAtoms, False)
elif sel_type.lower() == "generic":
# Check if the data type is sparse matrix
data_file = open(inp_file, 'r')
allLines = data_file.readlines()
data_file.close()
# Read the first line to determine if the matrix is sparse format
words = allLines[0].split()
# Read the 1st line and check if it has three columns
if (len(words) == 3):
ccMatrix = parseSparseCorrData(inp_file, selectedAtoms, \
Ctype=True,
symmetric=True,
writeAllOutput=False)
else:
ccMatrix = np.loadtxt(inp_file, dtype=float)
elif sel_type.lower() == "eg":
# The data type is elasticity graph
ccMatrix = parseElasticityGraph(inp_file, selectedAtoms, \
writeAllOutput=False)
else:
print(
"@> ERROR: Unknown data type: Type can only be ndcc, absndcc, lmi,\n"
)
print(
"@> coeviz or evcouplings. If you have your data in full \n"
)
print(
"@> matrix format and your data type is none of the options\n"
)
print("@> mentionned, you can set data type 'generic'.\n")
sys.exit(-1)
if ((sel_type.lower() == "evcouplings") or \
(sel_type.lower() == "generic") or \
(sel_type.lower() == "eg")):
network = buildSequenceNetwork(ccMatrix, distanceMatrix, \
valueFilter, distanceFilter,\
selectedAtoms)
else:
network = buildDynamicsNetwork(ccMatrix, distanceMatrix, \
valueFilter, distanceFilter,\
selectedAtoms)
if centrality_type == "all":
centralityAnalysis(network, valueFilter, distanceFilter, out_file,
"degree", selectedAtoms)
centralityAnalysis(network, valueFilter, distanceFilter, out_file,
"betweenness", selectedAtoms)
centralityAnalysis(network, valueFilter, distanceFilter, out_file,
"closeness", selectedAtoms)
centralityAnalysis(network, valueFilter, distanceFilter, out_file,
"current_flow_betweenness", selectedAtoms)
centralityAnalysis(network, valueFilter, distanceFilter, out_file,
"current_flow_closeness", selectedAtoms)
centralityAnalysis(network, valueFilter, distanceFilter, out_file,
"eigenvector", selectedAtoms)
# Community analysis is time consuming. Therefore, it will not be called by default.
# centralityAnalysis(ccMatrix, valueFilter, distanceFilter, out_file, "community",
# selectedAtoms)
else:
centralityAnalysis(network, valueFilter, distanceFilter, out_file,
centrality_type, selectedAtoms)
