pytraj.topology.topology.Topology¶Bases: object
Attributes
angle_indices |
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angles |
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atoms |
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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) |
mols |
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n_atoms |
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n_mols |
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n_residues |
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n_solvents |
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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) |
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is_empty(self) |
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join(self, Topology top) |
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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_nobox(self) |
|
set_reference(self, Frame frame) |
Set reference frame for distance-based mask |
set_solvent(self, mask) |
set mask as solvent |
simplify(self) |
return a (immutable) lightweight version of Topology for fast iterating. |
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_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 |
|---|
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)¶is_empty(self)¶join(self, Topology top)¶mass¶return a copy of atom masses (numpy 1D array)
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 ()
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_nobox(self)¶set_reference(self, Frame frame)¶Set reference frame for distance-based mask
| Parameters: | frame : Frame
|
|---|
set_solvent(self, mask)¶set mask as solvent
simplify(self)¶return a (immutable) lightweight version of Topology for fast iterating. The API is not stable.
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_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) |
|
read(self[, filename, top, option]) |
top : Topology instance |
write(self, Topology top=<???>[, filename, ...]) |
filename(self)¶read(self, filename='', top=<???>, option='') read(Topology top=Topology(), string filename="", "*args) Return : None (update `top`)¶top : Topology instance filename : str, output filename arglist : ArgList instance, optional
write(self, Topology top=<???>, filename='default.top', ArgList arglist=<???>, format='')¶pytraj.topology.topology.SimplifiedTopology¶Bases: object
EXPERIMENTAL: a lightweight Topology for fast iterating and convenient accessing atom, residue
Notes
Methods
select(self, mask) |
select(self, mask)¶