pytraj.topology.topology.Topology¶Bases: object
Attributes
angle_indices |
|
angles |
|
atom_names |
return unique atom name in Topology |
atomlist |
return a copy of atoms. If the Topology is large, this method calling |
atoms |
|
bond_indices |
|
bonds |
|
box |
|
charge |
return a copy of atom charges (numpy 1D array) |
dihedral_indices |
|
dihedrals |
|
filename |
return original filename. This is for testing purpose. |
mass |
return a copy of atom masses (numpy 1D array) |
moleculelist |
return a copy of molecules. (not much information) |
mols |
|
n_atoms |
|
n_mols |
|
n_residues |
|
n_solvents |
|
residue_names |
return unique residue names in Topology |
residuelist |
return a copy of residues |
residues |
Methods
__call__ |
intended to use with Frame indexing: atm = top('@CA‘) (for internal use) |
add_angles |
add angle for a group of 3 atoms. |
add_atom(self, Atom atom, Residue residue) |
|
add_bonds |
add bond for pairs of atoms. |
add_dihedrals |
add dihedral for a group of 4 atoms. |
atom(self, int idx) |
return an Atom based on idx. Update this Atom will update Topology. |
atom_indices(self, mask, \*args, \*\*kwd) |
return atom indices with given mask |
copy(self, \*args) |
return a copy of ‘self’ or copy from ‘other’ to ‘self’ |
from_dict(type cls, dict_data) |
internal use for serialize Topology |
has_box(self) |
|
indices_bonded_to(self, atom_name) |
return indices of the number of atoms that each atom bonds to |
is_empty(self) |
|
join(self, Topology top) |
|
load(self, string filename) |
loading Topology from filename. This is for internal use. Should pytraj.load_topology |
residue(self, int idx, bool atom=False) |
if atom is True, get full list of atoms for idx-th residue. This will be very slow |
save(self[, filename, format]) |
save to given file format (parm7, psf, ...) |
select(self, mask) |
return atom indices |
set_distance_mask_reference(self, Frame frame) |
|
set_integer_mask(self, AtomMask atm, ...) |
|
set_nobox(self) |
|
set_solvent(self, mask) |
set mask as solvent |
simplify(...) |
return a (immutable) light version of Topology for fast iterating. (experiment) |
start_new_mol(self) |
|
strip(self, mask[, copy]) |
strip atoms with given mask |
summary(...) |
basic info. This information only appears in Ipython or Python shell. |
to_dataframe(...) |
convert to pandas’ DataFrame. (experiment) |
to_dict(self) |
convert Topology to Python dict |
to_parmed(self) |
try to load to ParmEd’s Structure |
add_angles¶add angle for a group of 3 atoms.
| Parameters: | indices : 2D array_like (must have buffer interface),
|
|---|
add_atom(self, Atom atom, Residue residue)¶add_bonds¶add bond for pairs of atoms.
| Parameters: | bond_indices : 2D array_like (must have buffer interface)
|
|---|
add_dihedrals¶add dihedral for a group of 4 atoms.
| Parameters: | indices : 2D array_like (must have buffer interface),
|
|---|
angle_indices¶angles¶atom(self, int idx)¶return an Atom based on idx. Update this Atom will update Topology. Make this method private for now.
atom_indices(self, mask, *args, **kwd)¶return atom indices with given mask To be the same as cpptraj/Ambertools: we mask indexing starts from 1 but the return list/array use 0
| Parameters: | mask : str
Returns —— indices : Python array |
|---|
atom_names¶return unique atom name in Topology
atomlist¶return a copy of atoms. If the Topology is large, this method calling is every expensive. Make sure to call once and save it.
atoms¶bond_indices¶bonds¶box¶charge¶return a copy of atom charges (numpy 1D array)
copy(self, *args)¶return a copy of ‘self’ or copy from ‘other’ to ‘self’ TODO : add more doc
dihedral_indices¶dihedrals¶filename¶return original filename. This is for testing purpose.
from_dict(type cls, dict_data)¶internal use for serialize Topology
has_box(self)¶indices_bonded_to(self, atom_name)¶return indices of the number of atoms that each atom bonds to
| Parameters: | atom_name : name of the atom |
|---|
is_empty(self)¶join(self, Topology top)¶load(self, string filename)¶loading Topology from filename. This is for internal use. Should pytraj.load_topology
mass¶return a copy of atom masses (numpy 1D array)
moleculelist¶return a copy of molecules. (not much information)
mols¶n_atoms¶n_mols¶n_residues¶n_solvents¶residue(self, int idx, bool atom=False)¶if atom is True, get full list of atoms for idx-th residue. This will be very slow if atom is False, get ()
residue_names¶return unique residue names in Topology
residuelist¶return a copy of residues
residues¶save(self, filename=None, format='AMBERPARM') save to given file format (parm7, psf, ...)¶save to given file format (parm7, psf, ...)
select(self, mask)¶return atom indices
Notes
support openmp for distance-based atommask selction
Examples
>>> import pytraj as pt
>>> traj = pt.datafiles.load_tz2()
>>> atm = traj.top.select("@CA")
>>> atm
array([ 4, 15, 39, ..., 159, 173, 197])
>>> pt.rmsd(traj, mask=atm)
array([ 1.94667955e-07, 2.54596866e+00, 4.22333034e+00, ...,
4.97189564e+00, 5.53947712e+00, 4.83201237e+00])
set_distance_mask_reference(self, Frame frame)¶set_integer_mask(self, AtomMask atm, Frame frame=<???>)¶set_nobox(self)¶set_solvent(self, mask)¶set mask as solvent
simplify(self) return a (immutable) light version of Topology for fast iterating. (experiment)¶return a (immutable) light version of Topology for fast iterating. (experiment)
No writing capabibility (you should use ParmEd for Topology editing)
Examples
>>> import pytraj as pt
>>> top = pt.load_topology('data/tz2.parm7')
>>> simp_top = top.simplify()
>>> atom = simp_top.atoms[0]
>>> atom.resname
'SER'
>>> res = simp_top.residues[0]
>>> # get all atoms for 1st residue
>>> atoms = simp_top.atoms[res.first:res.last]
start_new_mol(self)¶strip(self, mask, copy=False)¶strip atoms with given mask
summary(self) basic info. This information only appears in Ipython or Python shell. It does not appear in Jupyter notebook (due to C++ stdout)¶basic info. This information only appears in Ipython or Python shell. It does not appear in Jupyter notebook (due to C++ stdout)
to_dataframe(self) convert to pandas' DataFrame. (experiment)¶convert to pandas’ DataFrame. (experiment)
to_dict(self)¶convert Topology to Python dict
to_parmed(self)¶try to load to ParmEd’s Structure
pytraj.topology.topology.ParmFile¶Bases: object
Methods
filename(self) |
|
readparm(self[, filename, top, option]) |
top : Topology instance |
writeparm(self, Topology top=<???>[, ...]) |
filename(self)¶readparm(self, filename='', top=<???>, option='') readparm(Topology top=Topology(), string filename="", "*args) Return : None (update `top`)¶top : Topology instance filename : str, output filename arglist : ArgList instance, optional
writeparm(self, Topology top=<???>, filename='default.top', ArgList arglist=<???>, format='')¶pytraj.topology.topology.SimplifiedTopology¶Bases: importlib._bootstrap.SimplifiedTopology
a lightweight Topology for fast iterating and convenient accessing atom, residue
Notes
cpptraj does not understand this class (use :class:Topology)
Attributes
atoms |
Alias for field number 0 |
residues |
Alias for field number 1 |
Methods
count(...) |
|
index((value, [start, ...) |
Raises ValueError if the value is not present. |
atoms¶Alias for field number 0
count(value) → integer -- return number of occurrences of value¶index(value[, start[, stop]]) → integer -- return first index of value.¶Raises ValueError if the value is not present.
residues¶Alias for field number 1
pytraj.topology.topology.SimplifiedAtom(name, type, element, charge, mass, index, atomic_number, resname, resid, molnum)¶Bases: importlib._bootstrap.SimplifiedAtom
Attributes
atomic_number |
Alias for field number 6 |
charge |
Alias for field number 3 |
element |
Alias for field number 2 |
index |
Alias for field number 5 |
mass |
Alias for field number 4 |
molnum |
Alias for field number 9 |
name |
Alias for field number 0 |
resid |
Alias for field number 8 |
resname |
Alias for field number 7 |
type |
Alias for field number 1 |
Methods
count(...) |
atomic_number¶Alias for field number 6
charge¶Alias for field number 3
count(value) → integer -- return number of occurrences of value¶element¶Alias for field number 2
index¶Alias for field number 5
mass¶Alias for field number 4
molnum¶Alias for field number 9
name¶Alias for field number 0
resid¶Alias for field number 8
resname¶Alias for field number 7
type¶Alias for field number 1
pytraj.topology.topology.SimplifiedResidue(name, index, first, last)¶Bases: importlib._bootstrap.SimplifiedResidue
Attributes
first |
Alias for field number 2 |
index |
Alias for field number 1 |
last |
Alias for field number 3 |
name |
Alias for field number 0 |
Methods
count(...) |
count(value) → integer -- return number of occurrences of value¶first¶Alias for field number 2
index¶Alias for field number 1
last¶Alias for field number 3
name¶Alias for field number 0