code stringlengths 3 6.57k |
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etree.SubElement(xml_residue, 'Bond', atomName1=bond[0].name, atomName2=bond[1].name) |
etree.ElementTree(root) |
etree.tostring(tree, pretty_print=True) |
decode('utf-8') |
closing(open(save_as, 'w') |
f.write(xml) |
check_atom_types(cluster, index) |
O (in Cu-O-Cu) |
O (Si-O-Si) |
unique (each atom belongs to one class and one class only) |
site(Al) |
site(Al) |
H (capping) |
NeighborList(natural_cutoffs(cluster) |
nl.update(cluster) |
get_EF_atom_indices(cluster) |
all(val not in class_H for val in nl.get_neighbors(atom.index) |
get_property_types(cluster, property_list) |
O(extra-framework) |
O(framework) |
len(whole_type_list) |
len(my_list) |
my_list.append(check_atom_types(cluster, val) |
whole_type_list.append(my_list) |
all(list(pair) |
list(permutations(my_list) |
repeated_list.append(my_list) |
_get_index_dict(type_dict, whole_type_list, index_list) |
type_dict.items() |
enumerate(whole_type_list) |
any(list(pair) |
list(permutations(items) |
temp_list.append(index_list[count]) |
get_type_index_pair(type_dict, whole_type_list, index_list) |
_get_index_dict(type_dict, whole_type_list, index_list) |
type_dict.items() |
tuple(value) |
pretty_print(my_dict) |
bond (or angle) |
bond (or angle) |
my_dict.items() |
print(key, '-->', value) |
type_index_dict.items() |
all(single_type not in type_list for single_type in exclude_atom_type) |
shortened_list.extend(index_list) |
all(list(value) |
list(permutations(type_list) |
shortened_list.extend(index_list) |
all(single_type not in type_list for single_type in exclude_atom_type) |
all(list(value) |
list(permutations(type_list) |
shortened_list.extend(index_list) |
any(list(value) |
list(permutations(type_list) |
shortened_list.extend(index_list) |
set_up_openMM_system(folder_path, cluster_tag_number, shortened_bond_list) |
PDBFile(folder_path + '/cluster_%s_labeled.pdb' % cluster_tag_number) |
list(pdb.topology.atoms() |
pdb.topology.addBond(atoms[index[0]], atoms[index[1]]) |
list(pdb.topology.bonds() |
write_xml(atoms, bonds, folder_path + '/forcefield.xml') |
ForceField(folder_path + '/forcefield.xml') |
FF.createSystem(pdb.topology) |
input (more flexible used-designed ff) |
CustomBondForce("D*(1-exp(-alpha*(r-r0) |
force.addPerBondParameter("D") |
force.addPerBondParameter("alpha") |
force.addPerBondParameter("r0") |
force.setUsesPeriodicBoundaryConditions(periodic=True) |
bond_type_index_dict.items() |
any(list(val) |
list(permutations(bond) |
force.addBond(int(bond[0]) |
int(bond[1]) |
bond_param_dict.get(my_type) |
tuple(reversed(my_type) |
force.addBond(int(bond[0]) |
int(bond[1]) |
bond_param_dict.get(my_type) |
system.addForce(force) |
HarmonicAngleForce() |
force.setUsesPeriodicBoundaryConditions(periodic=True) |
angle_type_index_dict.items() |
any(list(val) |
list(permutations(angle) |
tuple(val) |
list(angle_param_dict.keys() |
list(permutations(my_type) |
force.addAngle(int(angle[0]) |
int(angle[1]) |
int(angle[2]) |
angle_param_dict.get(type_tag[0]) |
system.addForce(force) |
assert(system.usesPeriodicBoundaryConditions() |
LangevinMiddleIntegrator(3 * kelvin, 1 / picosecond, 0.4 * picoseconds) |
Simulation(pdb.topology, system, integrator) |
simulation.context.setPositions(pdb.positions) |
simulation.context.getState(getForces=True) |
np.array(state.getForces(asNumpy=True) |
get_EF_O_index(traj) |
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