pytraj.topology¶

class pytraj.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:

Parameters:	indices : 2D array_like (must have buffer interface), shape=(n_atoms, 3)

indices : 2D array_like (must have buffer interface),

shape=(n_atoms, 3)

add_atom(self, Atom atom, Residue residue)¶

add_bonds¶

add bond for pairs of atoms.

Parameters:

Parameters:	bond_indices : 2D array_like (must have buffer interface) shape=(n_atoms, 2)

bond_indices : 2D array_like (must have buffer interface)

shape=(n_atoms, 2)

add_dihedrals¶

add dihedral for a group of 4 atoms.

Parameters:

Parameters:	indices : 2D array_like (must have buffer interface), shape=(n_atoms, 3)

indices : 2D array_like (must have buffer interface),

shape=(n_atoms, 3)

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:

Parameters:	mask : str Atom mask Returns —— indices : Python array

mask : str

Atom mask

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

class pytraj.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='')¶

class pytraj.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

class pytraj.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

class pytraj.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