def write_salt_bridges(data: np.ndarray, mapping: DataFrame, mol: Molecule,
outputname: str) -> None:
"""
This function outputs the salt bridges into a VMD session
:param data: A MetricDistance object
:param mapping: A DataFrame object including the index - residue mapping
:param mol: The pdb filename.
:param outputname: The file prefix name to output the VMD session to. Example: "protein2"
:return: A file with the VMD session named outputname+"-salt-bridges.txt"
"""
f = open(outputname[:-4] + "-salt-bridges.txt", "w")
mol.reps.add(sel='protein', style='NewCartoon', color=8)
f.write(f"resid\tresid\n")
for bond in mapping[data].atomIndexes.values:
mol.reps.add(f"chain A and same residue as index {bond[0]}",
style="Licorice",
color="1")
mol.reps.add(f"chain A and same residue as index {bond[1]}",
style="Licorice",
color="0")
f.write(f"{bond[0]}\t" f"{bond[1]}\n")
vmdobject = viewer(dispdev='text')
vmdobject.loadMol(mol)
vmdobject.send("save_state " + outputname)
vmdobject.close()
f.close()
def write_clusters(g: Graph, components: PropertyArray, inputmolfile: str, outputname: str) -> None:
"""
This function prints the clusters to the terminal and outputs them
into a VMD session
:param g: A Graph object
:param outputname: The pdb filename.
:param outputname: The file name to output the VMD session to.
:return:
"""
f = open(outputname[:-4] + ".txt", "w")
mol = Molecule(f"{inputmolfile[:-4]}-chainA.pdb")
mol.reps.add(sel='protein', style='NewCartoon', color=8)
for cluster_index in range(max(components) + 1):
cluster = [i for i, x in enumerate(components) if x == cluster_index]
if len(cluster) < 2: continue
vfilt = g.new_vertex_property('bool')
for i in cluster: vfilt[i] = True
sub = GraphView(g, vfilt)
area = np.sum([g.ep.area[edge] for edge in sub.edges()])
f.write(f"Cluster index {cluster_index}:\t"
f"Residues {len(cluster)}. Total area {area} A^2.\t "
f"Number of contacts: {sub.num_edges()}.\t "
f"Contacts / Residue: {sub.num_edges() / len(cluster) }.\t "
f"Area / Residue {area / sub.num_edges()}\n") # sum reverse and inverse
resid_cluster = [g.vp.resid[i] for i in cluster]
mol.reps.add('chain A and noh and not backbone and resid %s' % ' '.join(map(str, resid_cluster)),
style="VDW", color=cluster_index)
vmdobject = viewer(dispdev='text')
vmdobject.loadMol(mol, name=inputmolfile)
vmdobject.send("save_state " + outputname)
vmdobject.close()
f.close()
def write_networks(g: Graph, components: PropertyArray, inputmolfile: str,
outputname: str) -> None:
"""
This function outputs the HH networks into a VMD session
:param g: A Graph object
:param outputname: The pdb filename.
:param outputname: The file name to output the VMD session to.
:return:
"""
f = open(outputname[:-4] + "hh-networks.txt", "w")
mol = Molecule(inputmolfile)
mol.reps.add(sel='protein', style='NewCartoon', color=8)
f.write(f"Atom index\tAtom index\tresid\tresid\n")
for network_index in range(max(components) + 1):
f.write(f"Network index {network_index}\n")
network = [i for i, x in enumerate(components)
if x == network_index] # these are the vertices
resid_network = [g.vp.resid[i]
for i in network] # these are the resids
vfilt = g.new_vertex_property('bool')
for i in network:
vfilt[i] = True
sub = GraphView(g, vfilt)
# print for each edge the atoms and resid of the two pairs
for edge in sub.edges():
f.write(f"{sub.vp.atom[edge.source()]}\t"
f"{sub.vp.atom[edge.target()]}\t"
f"{sub.vp.resid[edge.source()]}\t"
f"{sub.vp.resid[edge.target()]}\n")
mol.reps.add('chain A and noh and resid %s' %
' '.join(map(str, resid_network)),
style="Licorice",
color=network_index)
mol.reps.add('chain A and noh and resid %s' %
' '.join(map(str, resid_network)),
style="HBonds",
color=network_index)
vmdobject = viewer(dispdev='text')
vmdobject.loadMol(mol, name=inputmolfile)
vmdobject.send("save_state " + outputname)
vmdobject.close()
f.close()
def write_largest_cluster(g: Graph, inputmolfile: str, outputname: str) -> None:
"""
This function prints the clusters to the terminal and outputs them
into a VMD session
:param g: A Graph object
:param outputname: The pdb filename.
:param outputname: The file name to output the VMD session to.
:return:
"""
mol = Molecule(f"{inputmolfile[:-4]}-chainA.pdb")
mol.reps.add(sel='protein', style='NewCartoon', color=8)
l = label_largest_component(g)
sub = GraphView(g, vfilt=l)
resid_cluster = [g.vp.resid[i] for i in sub.vertices()]
mol.reps.add('chain A and noh and not backbone and resid %s' % ' '.join(map(str, resid_cluster)),
style="VDW", color=1) # red
vmdobject = viewer(dispdev='text')
vmdobject.loadMol(mol, name=inputmolfile)
vmdobject.send("save_state " + outputname)
vmdobject.close()
