System class

class System

__init__()

Default constructor

__init__(sel_str)

Constructor taking selection string as argument.

Parameters:sel_str (str) – Selection string

__init__(other_system)

Constructor taking another system.

Parameters:other_system (System) – Other system to construct from.

Note

Selections associated with the system are not copied!

num_atoms()

Returns:number of atoms in the system Return type:int

num_frames()

Returns:number of frames in the system Return type:int

select_all()

Returns:selection object for all atoms in the system Return type:Selection

select(str)

Parameters:str (string) – selection string Returns:selection object for given selection string Return type:Selection

select(ind1, ind2)

Parameters:

• ind1 (int) – first index
• ind2 (int) – last index (inclusive)

Returns:

selection object for given range of indexes

Return type:

Selection

select(l)

Parameters:l (sequence) – python list or tuple with selection indexes Returns:selection object for given indexes Return type:Selection

load(fname[, b=0[, e=-1[, skip=-1[, on_frame=None]]]])

Load any supported file format from disk (structure or trajectory)

Parameters:

• fname (string) – file to read
• b (int) – first frame to read
• e (int) – last frame to read
• skip (int) – read each n’s frame
• on_frame (callable, f(System,int)) – callable object to be called on each frame and passed current system as the first argument and the index of current frame as the second.

Usage:

# Define the callback
def callback(sys,fr):
        print sys.num_atoms(),fr

# Load structure file
sys = System('struct.pdb')
# Load trajectory with callback
sys.load('traj.xtc',on_frame=callback)

frame_dup(fr)

Duplicates given frame and adds it to the end of frame vector

frame_copy(fr1, fr2)

Copy all frame data from fr1 to fr2

frame_delete([b=0[, e=-1]])

Delete specified range of frames. If only b is supplied deletes all frames from b to the end. If only e is supplied deletes all frames from 0 to e.

Parameters:

• b (int) – first frame to delete
• e (int) – last frame to delete (inclusive)

getFrame_data(fr)

Returns:whole Frame structure from frame fr. Return type:Frame object

setFrame_data(fr, data)

Parameters:data (Frame) – Frame object to set as frame fr

getBox(fr)

Returns:Periodic box from frame fr. Return type:Periodic_box object

setBox(fr, data)

Parameters:data (Periodic_box) – box to set for frame fr

getTime(fr)

Returns:time stamp (in ps) from frame fr. Return type:float

setTime(fr, t)

Parameters:t (float) – time stamp (in ps) to set for frame fr

getXYZ(ind, fr)

Returns:XYZ coordinates of atom ind from frame fr. Return type:numpy.array(3)

setXYZ(ind, fr, coord)

Parameters:

• ind (int) – index of the atom
• fr (int) – frame to set
• coord (array-like object of dimension 3 (list, tuple, numpy.array)) – XYZ coordinates

frame_append(frame)

Parameters:frame (Frame) – Frame object to add

assign_resindex()

Assign unique resindexes. This is usually done automatically upon loading a structure from file.

atoms_dup(indexes)

Parameters:indexes (sequence) – list of tuple of atom indexes to duplicate

Warning

This method is slow due to internal convertion between Python and C++ lists!

atoms_dup(atoms, coords)

Parameters:

• atoms (sequence) – list of tuple of atoms to add
• coords (sequence) – list of tuple of atom coordinates to add

Warning

This method is slow due to internal convertion between Python and C++ lists!

wrap_all(fr[, dims=(1, 1, 1)])

Parameters:dims (array_like(3)) – dimensions to wrap

append(selection)

append(system)

Returns:selection pointing to added atoms Return type:Selection

dssp(filename)

Determines secondary structure with DSSP algorithm and writes detailed report to file

dssp()

Determines secondary structure with DSSP algorithm and returns it as a code string. The code is the same as in DSSP program:

structure	code
alphahelix	“H”
betabridge	“B”
strand	“E”
helix_3	“G”
helix_5	“I”
turn	“T”
bend	“S”
loop	“” (space)

Returns:DSSP code string

sort_by_resindex()

Sorts atoms by resindex arranging atoms with the same resindexes into contigous pieces. Could be called after atom additions or duplications.