schrodinger.application.desmond.packages.analysis module

Classes and functions for trajectory-based analysis

Copyright Schrodinger, LLC. All rights reserved.

schrodinger.application.desmond.packages.analysis.is_small_struc(atoms)

A simple API to determine whether a molecular structure is small. :type atoms: list :param atoms: A list of atoms in the structure. The atoms can be atom IDs

or atom-class instances.
class schrodinger.application.desmond.packages.analysis.Pbc(box)

Bases: object

__init__(box)

This implementation supports the general triclinic cell.

Parameters:box (numpy.ndarray) – 3x3 matrix whose ROWS are primitive cell vectors. For a msys.System instance, you can call msys_model.cell to get this matrix. For a traj.Frame instance, you can call fr.box to get it. For a Cms instance, you can call numpy.reshape(cms_model.box, [3, 3]) to get it.
box
volume
inv_box
calcMinimumImage(ref_pos, pos)

Calculates the minimum image of a position vector pos relative to another position vector ref_pos. pos and ref_pos can also be arrays of 3D vectors. In this case, they must be of the same size, and minimum images will be calculated for each element in pos and ref_pos.

Parameters:
  • ref_pos (numpy.ndarray. Either 1x3 or Nx3.) – Reference position vector(s)
  • pos (numpy.ndarray. Either 1x3 or Nx3.) – Position vector(s) of which we will calculate the minimum image.
Return type:

numpy.ndarray
Returns:

The position vector(s) of the mininum image. This function does NOT mutate any of the input vectors.
calcMinimumDiff(from_pos, to_pos)

Calculates the difference vector from from_pos to the minimum image of to_pos. pos and ref_pos can also be arrays of 3D vectors. In this case, they must be of the same size, and minimum image difference will be calculated for each element in pos and ref_pos.

Parameters:
  • from_pos (numpy.ndarray. Either 1x3 or Nx3) – Reference position vector(s)
  • to_pos (numpy.ndarray. Either 1x3 or Nx3) – Position vector(s) of which we will calculate the minimum image.
Return type:

numpy.ndarray
Returns:

The difference vector(s). This function does NOT mutate any of the input vectors.
wrap(pos)

Puts a coordinate back into the box. If the coordinate is already in the box, this function will return a new position vector that equals the original vector.

Return type:numpy.ndarray
Returns:A new position vector which is within the box. This function does NOT mutate and return the input vector pos.
isWithinCutoff(pos0, pos1, cutoff_sq)

Return True if any of pos0 and pos1 are within the cutoff distance.

Parameters:cutoff_sq (float) – = cutoff x cutoff
class schrodinger.application.desmond.packages.analysis.Vector(msys_model, cms_model, from_xid, to_xid)

Bases: schrodinger.application.desmond.packages.staf.GeomAnalyzerBase

Calculate the vector between two xids. Result is a vector for each trajectory frame.

__init__(msys_model, cms_model, from_xid, to_xid)
disableDyncalc()

Disable the execution of _dyncalc(). This is used to avoid redundant _precalc() calculations delegated in _dyncalc().

isDynamic()
class schrodinger.application.desmond.packages.analysis.Distance(msys_model, cms_model, xid0, xid1)

Bases: schrodinger.application.desmond.packages.staf.GeomAnalyzerBase

Calculate the distance between two xids. Result is a scalar (distance in Angstroms) for each trajectory frame.

__init__(msys_model, cms_model, xid0, xid1)
disableDyncalc()

Disable the execution of _dyncalc(). This is used to avoid redundant _precalc() calculations delegated in _dyncalc().

isDynamic()
class schrodinger.application.desmond.packages.analysis.Angle(msys_model, cms_model, xid0, xid1, xid2)

Bases: schrodinger.application.desmond.packages.staf.GeomAnalyzerBase

Calculate the angle formed between three xids. Result is a scalar (angle in degrees) for each trajectory frame.

__init__(msys_model, cms_model, xid0, xid1, xid2)

The angle is formed by the vectors xid1`==>`xid0 and xid1`==>`xid2.

disableDyncalc()

Disable the execution of _dyncalc(). This is used to avoid redundant _precalc() calculations delegated in _dyncalc().

isDynamic()
class schrodinger.application.desmond.packages.analysis.Torsion(msys_model, cms_model, xid0, xid1, xid2, xid3)

Bases: schrodinger.application.desmond.packages.staf.GeomAnalyzerBase

Calculate the torsion formed between four xids. Result is a scalar (dihedral angle in degrees) for each trajectory frame.

__init__(msys_model, cms_model, xid0, xid1, xid2, xid3)

The torsion is defined by the four atoms:

0 o o 3
/
/

1 o—–o 2

disableDyncalc()

Disable the execution of _dyncalc(). This is used to avoid redundant _precalc() calculations delegated in _dyncalc().

isDynamic()
class schrodinger.application.desmond.packages.analysis.PlanarAngle(msys_model, cms_model, xid0, xid1, xid2, xid3, xid4, xid5)

Bases: schrodinger.application.desmond.packages.staf.GeomAnalyzerBase

Calculate acute planar angle formed among six xids. The first three xids define the first plane and the latter three xids define the second plane.

__init__(msys_model, cms_model, xid0, xid1, xid2, xid3, xid4, xid5)

Initialize self. See help(type(self)) for accurate signature.

disableDyncalc()

Disable the execution of _dyncalc(). This is used to avoid redundant _precalc() calculations delegated in _dyncalc().

isDynamic()
class schrodinger.application.desmond.packages.analysis.CenterOf(gids, weights=None, return_unwrapped_atompos=False)

Bases: schrodinger.application.desmond.packages.staf.GeomAnalyzerBase

N.B.: The calculated center is an unwrapped coordinate.

__init__(gids, weights=None, return_unwrapped_atompos=False)
Parameters:return_unwrapped_atompos – if False, return the unwrapped center. Otherwise return both unwrapped center and the unwrapped positions of the selected atoms.
disableDyncalc()

Disable the execution of _dyncalc(). This is used to avoid redundant _precalc() calculations delegated in _dyncalc().

isDynamic()
class schrodinger.application.desmond.packages.analysis.Com(msys_model, cms_model, asl=None, gids=None, return_unwrapped_atompos=False)

Bases: schrodinger.application.desmond.packages.analysis.CenterOf

Class for computing averaged position weighted by atomic mass, under the periodic boundary condition.

Basic usage:
ana = Com(msys_model, cms_model, gids=[1, 23, 34, 5, 6]) results = analyze(tr, ana)

where tr is a trajectory, and results contain a list of unwrapped centers of mass as floats, one float for each frame. If return_unwrapped_atompos is True, results contain a list of 2-tuples: (unwrapped-center-of-mass, [unwrapped-positions-of-involved-atoms]), and each 2-tuple in the list corresponds to a trajectory frame.

__init__(msys_model, cms_model, asl=None, gids=None, return_unwrapped_atompos=False)
Parameters:
  • asl (str) – ASL expression to specify the atom selection
  • gids (list of `int`s) – GIDs of atoms
  • return_unwrapped_atompos – if False, return the unwrapped center. Otherwise return both unwrapped center and the unwrapped positions of the selected atoms.

Both msys_model and cms_model must be previously obtained through the read_cms function. They both should have the same atom coordinates and the same simulation box matrix. cms_model is used to obtain atom GIDs from ASL selection. msys_model is used to retrieve atom attribute from GIDs.

Either asl or gids must be specified, but not both.

disableDyncalc()

Disable the execution of _dyncalc(). This is used to avoid redundant _precalc() calculations delegated in _dyncalc().

isDynamic()
class schrodinger.application.desmond.packages.analysis.Coc(msys_model, cms_model, asl=None, gids=None, return_unwrapped_atompos=False)

Bases: schrodinger.application.desmond.packages.analysis.Com

Class for computing center of charge under periodic boundary condition. Pseudo atoms are included.

For each frame, the results will be the unwrapped-center-of-charge. If return_unwrapped_atompos is True, the results will be a 2-tuple: (unwrapped-center-of-charge, [unwrapped-positions-of-involved-atoms]).

__init__(msys_model, cms_model, asl=None, gids=None, return_unwrapped_atompos=False)

Refer to the docstring of Com.__init__.

disableDyncalc()

Disable the execution of _dyncalc(). This is used to avoid redundant _precalc() calculations delegated in _dyncalc().

isDynamic()
class schrodinger.application.desmond.packages.analysis.Centroid(msys_model, cms_model, asl=None, gids=None, return_unwrapped_atompos=False)

Bases: schrodinger.application.desmond.packages.analysis.CenterOf

Class for computing centroid under periodic boundary condition.

For each frame, the results will be the unwrapped centroid. If return_unwrapped_atompos is True, the results will be a 2-tuple: (unwrapped-centroid, [unwrapped-positions-of-involved-atoms]).

__init__(msys_model, cms_model, asl=None, gids=None, return_unwrapped_atompos=False)

Refer to the docstring of Com.__init__.

disableDyncalc()

Disable the execution of _dyncalc(). This is used to avoid redundant _precalc() calculations delegated in _dyncalc().

isDynamic()
class schrodinger.application.desmond.packages.analysis.Gyradius(msys_model, cms_model, asl=None, gids=None)

Bases: schrodinger.application.desmond.packages.staf.CompositeAnalyzer

Class for computing radius of gyration under periodic boundary condition.

For each frame, the result is the radius of gyration as float

__init__(msys_model, cms_model, asl=None, gids=None)

Initialize self. See help(type(self)) for accurate signature.

disableDyncalc()

Disable the execution of _dyncalc(). This is used to avoid redundant _precalc() calculations delegated in _dyncalc().

isDynamic()
class schrodinger.application.desmond.packages.analysis.MassAvgVel(msys_model, cms_model, asl=None, gids=None, return_unwrapped_atompos=False)

Bases: schrodinger.application.desmond.packages.analysis.Com

Class for computing mass-averaged velocity. The trajectory should contain velocities data.

For each frame, the result is numpy.ndarray of `float`s

__init__(msys_model, cms_model, asl=None, gids=None, return_unwrapped_atompos=False)
Parameters:
  • asl (str) – ASL expression to specify the atom selection
  • gids (list of `int`s) – GIDs of atoms
  • return_unwrapped_atompos – if False, return the unwrapped center. Otherwise return both unwrapped center and the unwrapped positions of the selected atoms.

Both msys_model and cms_model must be previously obtained through the read_cms function. They both should have the same atom coordinates and the same simulation box matrix. cms_model is used to obtain atom GIDs from ASL selection. msys_model is used to retrieve atom attribute from GIDs.

Either asl or gids must be specified, but not both.

disableDyncalc()

Disable the execution of _dyncalc(). This is used to avoid redundant _precalc() calculations delegated in _dyncalc().

isDynamic()
class schrodinger.application.desmond.packages.analysis.PosTrack(msys_model, cms_model, asl=None, gids=None)

Bases: schrodinger.application.desmond.packages.staf.GeomAnalyzerBase

Class for tracking positions of selected atoms in a trajectory. Pseudo atoms are included.

Since periodic boundary condition is assumed in the MD simulation, the atom positions are wrapped back into the simulation box when they move out of the box. The PosTrack class unwraps the atom positions with respect to their positions in the previous frame. It can be used when atom positions need to be tracked over time, such as diffusion.

__init__(msys_model, cms_model, asl=None, gids=None)

Refer to the docstring of Com.__init__.

disableDyncalc()

Disable the execution of _dyncalc(). This is used to avoid redundant _precalc() calculations delegated in _dyncalc().

isDynamic()
schrodinger.application.desmond.packages.analysis.RadiusOfGyration

alias of schrodinger.application.desmond.packages.analysis.Gyradius

schrodinger.application.desmond.packages.analysis.CenterOfMotion

alias of schrodinger.application.desmond.packages.analysis.MassAvgVel

schrodinger.application.desmond.packages.analysis.Position

alias of schrodinger.application.desmond.packages.analysis.PosTrack

class schrodinger.application.desmond.packages.analysis.Ramachandran(msys_model, cms_model, asl)

Bases: schrodinger.application.desmond.packages.analysis._Ramachandran

Calculate the Phi and Psi torsions for selected atoms.

Usage example:

ana = Ramachandran(msys_model, cms_model, ‘protein and res.num 20-30’) results = analyze(tr, ana)

where tr is a trajectory, and results is a list, and each element in the list is a list: [(phi_0, psi_0), (phi_1, psi_1),] for the corresponding trajectory frame.

__init__(msys_model, cms_model, asl)
Parameters:asl (str) – ASL expression to specify the residues
reduce(results, *_, **__)
disableDyncalc()

Disable the execution of _dyncalc(). This is used to avoid redundant _precalc() calculations delegated in _dyncalc().

isDynamic()
class schrodinger.application.desmond.packages.analysis.PosAlign(msys_model, cms_model, aids, fit_aids, fit_ref_pos)

Bases: schrodinger.application.desmond.packages.staf.CenteredSoluteAnalysis

This analyzer first aligns the geometric center of the solute atoms to that of cms_model, then calculates the rotation/translation transformation for converting the structure (fit_aids) of a centered trajectory frame to a given geometry (fit_ref_pos) and finally applies the transformation to a position array of only the selected atoms (aids).

If fit_ref_pos is not provided, perform centering.

__init__(msys_model, cms_model, aids, fit_aids, fit_ref_pos)
Parameters:fit_ref_pos (Mx3 numpy.ndarray or None) – positions of reference conformer structure for translation/rotation calculation

Both msys_model and cms_model must be previously obtained through the read_cms function.

disableDyncalc()

Disable the execution of _dyncalc(). This is used to avoid redundant _precalc() calculations delegated in _dyncalc().

isDynamic()
class schrodinger.application.desmond.packages.analysis.RMSD(msys_model, cms_model, aids, ref_pos, fit_aids=None, fit_ref_pos=None, in_place=False)

Bases: schrodinger.application.desmond.packages.analysis.PosAlign

Root Mean Square Deviation from reference positions, with optional alignment fitting.

If spikes are seen, call topo.make_glued_topology, see DESMOND-7129.

__init__(msys_model, cms_model, aids, ref_pos, fit_aids=None, fit_ref_pos=None, in_place=False)

See PosAlign for parameters.

Parameters:
  • ref_pos (Nx3 numpy.ndarray) – positions of reference conformer structure
  • in_place – if True, calculate RMSD without applying transformations on ref_pos

Typically, aids and fit_aids come from a common source whereas ref_pos and fit_ref_pos come from another common source.

disableDyncalc()

Disable the execution of _dyncalc(). This is used to avoid redundant _precalc() calculations delegated in _dyncalc().

isDynamic()
class schrodinger.application.desmond.packages.analysis.RMSF(msys_model, cms_model, aids, fit_aids, fit_ref_pos, in_place=False)

Bases: schrodinger.application.desmond.packages.analysis.PosAlign

Root Mean Square Fluctuation from reference positions (averaged position over the trajectory) for each atom, with optional alignment fitting.

If spikes are seen, call topo.make_glued_topology, see DESMOND-7129.

__init__(msys_model, cms_model, aids, fit_aids, fit_ref_pos, in_place=False)
Parameters:
  • fit_ref_pos (Mx3 numpy.ndarray) – positions of reference conformer structure for translation/rotation calculation
  • in_place – if True, calculate RMSF without applying alignment transformations

Both msys_model and cms_model must be previously obtained through the read_cms function.

reduce(pos_t, *_, **__)

Temporal average of the RMSF over the trajectory

Return type:length N numpy.ndarray
disableDyncalc()

Disable the execution of _dyncalc(). This is used to avoid redundant _precalc() calculations delegated in _dyncalc().

isDynamic()
class schrodinger.application.desmond.packages.analysis.LigandRMSD(msys_model, cms_model, aids, ref_pos, fit_aids=None, fit_ref_pos=None)

Bases: schrodinger.application.desmond.packages.analysis.PosAlign

Ligand Root Mean Square Deviation from reference positions, with optional alignment fitting. Taking conformational symmetry into account.

__init__(msys_model, cms_model, aids, ref_pos, fit_aids=None, fit_ref_pos=None)

see RMSD.__init__ for parameters

disableDyncalc()

Disable the execution of _dyncalc(). This is used to avoid redundant _precalc() calculations delegated in _dyncalc().

isDynamic()
schrodinger.application.desmond.packages.analysis.get_pdb_protein_bfactor(fsys_ct, aids)

Calculate per-residue b-factor from pdb data for the selected atoms.

Parameters:aids (list of int) – Atom selections
Return type:numpy.ndarray of float
class schrodinger.application.desmond.packages.analysis.ProteinRMSF(msys_model, cms_model, aids, fit_aids, fit_ref_pos, in_place=False)

Bases: schrodinger.application.desmond.packages.analysis.RMSF

Root Mean Square Fluctuation from reference positions (averaged positions over the trajectory) for each residue, with optional alignment fitting

__init__(msys_model, cms_model, aids, fit_aids, fit_ref_pos, in_place=False)

see RMSF.__init__ for parameters

reduce(pos_t, *_, **__)

:rtype : list[string], list[float] :return: residue tags and RMSF for each residue

disableDyncalc()

Disable the execution of _dyncalc(). This is used to avoid redundant _precalc() calculations delegated in _dyncalc().

isDynamic()
class schrodinger.application.desmond.packages.analysis.Dipole(msys_model, cms_model, aids)

Bases: schrodinger.application.desmond.packages.staf.CompositeAnalyzer

Electric dipole moment of the selected atoms, in unit of debye.

The result may not be reliable when the structure of the selected atoms are large compared to the simulation box. The unwrapping with respect to periodic boundary condition provided by CenterOf is based on circular mean and may not be adequate.

EA2DEBYE = 4.802813198
__init__(msys_model, cms_model, aids)

Initialize self. See help(type(self)) for accurate signature.

disableDyncalc()

Disable the execution of _dyncalc(). This is used to avoid redundant _precalc() calculations delegated in _dyncalc().

isDynamic()
class schrodinger.application.desmond.packages.analysis.AxisDirector(axis)

Bases: schrodinger.application.desmond.packages.staf.GeomAnalyzerBase

Basis vector of 3D axis

__init__(axis)
Parameters:axis (str) – axis name, ‘X’, ‘Y’ or ‘Z’
disableDyncalc()

Disable the execution of _dyncalc(). This is used to avoid redundant _precalc() calculations delegated in _dyncalc().

isDynamic()
class schrodinger.application.desmond.packages.analysis.MomentOfInertia(msys_model, cms_model, aids)

Bases: schrodinger.application.desmond.packages.staf.CompositeAnalyzer

Moment of inertia tensor

Result is 3x3 numpy.ndarray

__init__(msys_model, cms_model, aids)
disableDyncalc()

Disable the execution of _dyncalc(). This is used to avoid redundant _precalc() calculations delegated in _dyncalc().

isDynamic()
class schrodinger.application.desmond.packages.analysis.MomentOfInertiaDirector(msys_model, cms_model, asl)

Bases: schrodinger.application.desmond.packages.staf.CompositeDynamicAslAnalyzer

This class calculates the principal moment-of-inertia for each of the selected molecules.

Result: A list of vectors

__init__(msys_model, cms_model, asl)
disableDyncalc()

Disable the execution of _dyncalc(). This is used to avoid redundant _precalc() calculations delegated in _dyncalc().

isDynamic()
class schrodinger.application.desmond.packages.analysis.SmartsDirector(msys_model, cms_model, asl, smarts)

Bases: schrodinger.application.desmond.packages.staf.CompositeDynamicAslAnalyzer

Direction of atom pairs from SMARTS pattern. The SMARTS pattern should pick bonds, i.e., atom pairs, e.g., smarts='CC'.

Convention: The vector is pointing from the first atom to the second.

__init__(msys_model, cms_model, asl, smarts)
reduce_vec(n, m)

Calculate Legendre polynomial P2 using the inner product of n and m as the input.

Parameters:m (N’x3 numpy.array where N’ is the number of chemical bonds.) – Output of SmartsDirector for one frame
disableDyncalc()

Disable the execution of _dyncalc(). This is used to avoid redundant _precalc() calculations delegated in _dyncalc().

isDynamic()
class schrodinger.application.desmond.packages.analysis.SystemDipoleDirector(msys_model, cms_model, asl)

Bases: schrodinger.application.desmond.packages.staf.CompositeDynamicAslAnalyzer

Direction of electric dipole moment of all the selected atoms

__init__(msys_model, cms_model, asl)
disableDyncalc()

Disable the execution of _dyncalc(). This is used to avoid redundant _precalc() calculations delegated in _dyncalc().

isDynamic()
class schrodinger.application.desmond.packages.analysis.DipoleDirector(msys_model, cms_model, asl)

Bases: schrodinger.application.desmond.packages.analysis.SystemDipoleDirector

Dipole direction for each molecule in the selection

__init__(msys_model, cms_model, asl)
disableDyncalc()

Disable the execution of _dyncalc(). This is used to avoid redundant _precalc() calculations delegated in _dyncalc().

isDynamic()
class schrodinger.application.desmond.packages.analysis.LipidDirector(msys_model, cms_model, asl, tail_type)

Bases: schrodinger.application.desmond.packages.staf.CompositeAnalyzer

Direction of CH bond for carbon atoms on lipid tail

__init__(msys_model, cms_model, asl, tail_type)
Parameters:tail_type – ‘sn1’, ‘sn2’, ‘all’
disableDyncalc()

Disable the execution of _dyncalc(). This is used to avoid redundant _precalc() calculations delegated in _dyncalc().

isDynamic()
schrodinger.application.desmond.packages.analysis.reduce_vec(n, m)

Calculate Legendre polynomial P2 using the inner product of n and m as the input.

schrodinger.application.desmond.packages.analysis.reduce_vec_list(n, m)

Calculate Legendre polynomial P2 using the inner product of n and m as the input.

class schrodinger.application.desmond.packages.analysis.OrderParameter(vec1, vec2, reducer)

Bases: schrodinger.application.desmond.packages.staf.GeomAnalyzerBase

Given the director (local or global), and the descriptor (local or global), calculate the order parameter <P2> for each frame

S = 1/N sum_i ((3 * (n dot m_i)^2 -1) / 2)

Where n is the director vector and m is the descriptor vector. For example, n is the z axis and m is the electric dipole moment.

Typical usage includes
Director Descriptor result Axis Lipid avg over carbon type Axis Smarts avg over bond type Axis Dipole avg over molecule SystemDipole Dipole avg over molecule Dipole Smarts avg over bond type

To extend its functionality, implement to the GeomAnalyzerBase interface and provide the reduction rule as callable.

__init__(vec1, vec2, reducer)
Parameters:
  • vec1 – a GeomAnalyzerBase that computes director
  • vec2 – a GeomAnalyzerBase that computes descriptor

Typically both director and descriptor return Nx3 vectors for each frame, where N depends on the context. In this case, one should make sure that the orders of these vectors match. For example, if both director and descriptor give one vector per molecule, then the implementation should guarantee the molecule orders are the same in vec1() and vec2().

For axis director which returns 1x3 vector, reduction with descriptor is taken care of by numpy broadcasting. For more complicated cases where director and descriptor have incompatible dimensions, the user needs to provide special-purpose reduce function, see SmartsDirector.reduce_vec for example.

disableDyncalc()

Disable the execution of _dyncalc(). This is used to avoid redundant _precalc() calculations delegated in _dyncalc().

isDynamic()
class schrodinger.application.desmond.packages.analysis.MoleculeWiseCom(msys_model, cms_model, asl)

Bases: schrodinger.application.desmond.packages.staf.CompositeDynamicAslAnalyzer

Calculate the center-of-mass for each of the selected molecules.

Result: A list of Nx3 numpy arrays, where N is the number of molecules. Note that the array size N may vary from frame to frame if the ASL is dynamic.

__init__(msys_model, cms_model, asl)
disableDyncalc()

Disable the execution of _dyncalc(). This is used to avoid redundant _precalc() calculations delegated in _dyncalc().

isDynamic()
class schrodinger.application.desmond.packages.analysis.AtomicPosition(msys_model, cms_model, asl=None)

Bases: schrodinger.application.desmond.packages.staf.DynamicAslAnalyzer

Extract the positions of the selected atoms.

Result: A list of Nx3 numpy arrays, where N is the number of atoms. Note that the array size N may vary from frame to frame if the ASL is dynamic.

__init__(msys_model, cms_model, asl=None)
disableDyncalc()

Disable the execution of _dyncalc(). This is used to avoid redundant _precalc() calculations delegated in _dyncalc().

isDynamic()
class schrodinger.application.desmond.packages.analysis.SecondaryStructure(msys_model, cms_model, aids)

Bases: schrodinger.application.desmond.packages.staf.MaestroAnalysis

Calculate the secondary-structure property for selected atoms. The result is a list of int numbers, each of which corresponds to a selected atoms and is one of the following values:

SecondaryStructure.NONE SecondaryStructure.LOOP SecondaryStructure.HELIX SecondaryStructure.STRAND SecondaryStructure.TURN

The selected atoms can be obtained by calling the aids method.

NONE = -1
LOOP = 0
HELIX = 1
STRAND = 2
TURN = 3
__init__(msys_model, cms_model, aids)
Parameters:aids (list of `int`s) – IDs of atoms to calculate the secondary-structure property for
reduce(results, *_, **__)
disableDyncalc()

Disable the execution of _dyncalc(). This is used to avoid redundant _precalc() calculations delegated in _dyncalc().

isDynamic()
class schrodinger.application.desmond.packages.analysis.SolventAccessibleSurfaceAreaByResidue(msys_model, cms_model, asl, resolution=None)

Bases: schrodinger.application.desmond.packages.staf.MaestroAnalysis

Calculate the relative SASA broken down by residues. The values are relative to the average SASAs as given by SolventAccessibleSurfaceAreaByResidue.DIPEPTIDE_SASA.

The result is a 2-tuple: ([residue-names], [relative-SASAs]).

DIPEPTIDE_SASA = {'ACE': (115.4897, 3.5972), 'ALA': (128.7874, 4.715), 'ARG': (271.5978, 9.5583), 'ASH': (175.7041, 5.1167), 'ASN': (179.5393, 4.632), 'ASP': (173.4664, 6.9882), 'CYS': (158.1909, 5.3923), 'CYX': (99.3829, 10.7089), 'GLH': (203.2443, 6.2765), 'GLN': (208.6171, 6.5794), 'GLU': (201.466, 6.9328), 'GLY': (94.1021, 5.1977), 'HID': (208.8269, 5.9202), 'HIE': (218.799, 5.6097), 'HIP': (221.1223, 8.3364), 'HIS': (208.8269, 5.9202), 'ILE': (207.2248, 5.0012), 'LEU': (211.8823, 5.149), 'LYN': (235.5351, 6.8589), 'LYS': (242.8734, 9.351), 'MET': (218.5396, 6.9879), 'NMA': (97.3748, 4.0446), 'PHE': (243.4793, 5.9699), 'PRO': (168.783, 5.5848), 'SER': (140.6706, 4.9089), 'THR': (169.0046, 4.9049), 'TRP': (287.0895, 6.892), 'TYR': (256.8637, 6.2782), 'UNK': (189.961, 6.3732), 'VAL': (181.2543, 4.864)}
__init__(msys_model, cms_model, asl, resolution=None)

Initialize self. See help(type(self)) for accurate signature.

reduce(results, *_, **__)
disableDyncalc()

Disable the execution of _dyncalc(). This is used to avoid redundant _precalc() calculations delegated in _dyncalc().

isDynamic()
class schrodinger.application.desmond.packages.analysis.MolecularSurfaceArea(msys_model, cms_model, asl, grid_spacing=None)

Bases: schrodinger.application.desmond.packages.staf.CenteredSoluteAnalysis

Calculate the molecular surface area. The result is a single scalar number.

__init__(msys_model, cms_model, asl, grid_spacing=None)
Parameters:asl (str) – ASL expression to select atoms whose secondary-structure property is of interest.
disableDyncalc()

Disable the execution of _dyncalc(). This is used to avoid redundant _precalc() calculations delegated in _dyncalc().

isDynamic()
class schrodinger.application.desmond.packages.analysis.SolventAccessibleSurfaceArea(msys_model, cms_model, asl, exclude_asl=None, resolution=None)

Bases: schrodinger.application.desmond.packages.staf.MaestroAnalysis

Calculate solvent accessible surface area for selected atoms.

__init__(msys_model, cms_model, asl, exclude_asl=None, resolution=None)

Initialize self. See help(type(self)) for accurate signature.

disableDyncalc()

Disable the execution of _dyncalc(). This is used to avoid redundant _precalc() calculations delegated in _dyncalc().

isDynamic()
class schrodinger.application.desmond.packages.analysis.PolarSurfaceArea(msys_model, cms_model, asl, resolution=None)

Bases: schrodinger.application.desmond.packages.staf.CenteredSoluteAnalysis

Calculate polar surface area for selected atoms.

N.B.: Only O and N atoms are considered as polar atoms in this implementation.

__init__(msys_model, cms_model, asl, resolution=None)

Initialize self. See help(type(self)) for accurate signature.

disableDyncalc()

Disable the execution of _dyncalc(). This is used to avoid redundant _precalc() calculations delegated in _dyncalc().

isDynamic()
class schrodinger.application.desmond.packages.analysis.HydrogenBondFinder(msys_model, cms_model, aids1, aids2, max_dist=2.8, min_donor_angle=120.0, min_acceptor_angle=90.0, max_acceptor_angle=180.0)

Bases: schrodinger.application.desmond.packages.staf.MaestroAnalysis

Find hydrogen bonds between two sets of atoms. The result is a list of tuples, where each tuple is a pair of `schrodinger.structure._StructureAtom`s, i.e., (acceptor, donor).

Basic usage:

ana = HydrogenBondFinder(msys_model, cms_model, aids1, aids2) results = analyze(tr, ana)
__init__(msys_model, cms_model, aids1, aids2, max_dist=2.8, min_donor_angle=120.0, min_acceptor_angle=90.0, max_acceptor_angle=180.0)
disableDyncalc()

Disable the execution of _dyncalc(). This is used to avoid redundant _precalc() calculations delegated in _dyncalc().

isDynamic()
class schrodinger.application.desmond.packages.analysis.HalogenBondFinder(msys_model, cms_model, aids1, aids2, max_dist=3.5, min_donor_angle=140.0, min_acceptor_angle=90.0, max_acceptor_angle=170.0)

Bases: schrodinger.application.desmond.packages.staf.MaestroAnalysis

Find halogen bonds between two sets of atoms. The result is a list of tuples, where each tuple is a pair of `schrodinger.structure._StructureAtom`s, i.e., (acceptor, donor).

Basic usage:

ana = HalogenBondFinder(msys_model, cms_model, protein_aids, ligand_aids) results = analyze(tr, ana)
__init__(msys_model, cms_model, aids1, aids2, max_dist=3.5, min_donor_angle=140.0, min_acceptor_angle=90.0, max_acceptor_angle=170.0)
disableDyncalc()

Disable the execution of _dyncalc(). This is used to avoid redundant _precalc() calculations delegated in _dyncalc().

isDynamic()
schrodinger.application.desmond.packages.analysis.get_ligand_fragments(lig_ct)

Decompose the ligand in several fragments using the murcko rules.

Returns:ligand fragments
Return type:list. Each element is a list of `int`s.
class schrodinger.application.desmond.packages.analysis.HydrophobicInter(msys_model, cms_model, prot_asl, lig_asl, contact_cutoff=6.0, hydrophobic_search_cutoff=3.2, hbond_cutoff=2.8)

Bases: schrodinger.application.desmond.packages.staf.CompositeAnalyzer

Calculate hydrophobic interactions between protein and ligand, with hbonds and pi-pi interactions excluded.

Returns a list of dict. The length of this list is the number of frames. The dict key is ‘HydrophobicResult’, and the value is a list of _HydrophobicInter.Result, where ca_aid is the AID of alpha carbon, frag_idx is the index of ligand fragment. There are also keys of ‘PiPiResult’, ‘PiCatResult’, ‘HBondResult’ with ProtLigPiInter, ProtLigHbondInter results as values.

__init__(msys_model, cms_model, prot_asl, lig_asl, contact_cutoff=6.0, hydrophobic_search_cutoff=3.2, hbond_cutoff=2.8)

Initialize self. See help(type(self)) for accurate signature.

disableDyncalc()

Disable the execution of _dyncalc(). This is used to avoid redundant _precalc() calculations delegated in _dyncalc().

isDynamic()
class schrodinger.application.desmond.packages.analysis.SaltBridgeFinder(msys_model, cms_model, aids1, aids2, cutoff=5.0)

Bases: schrodinger.application.desmond.packages.staf.MaestroAnalysis

Find salt bridges present between two sets of atoms. This class wraps around the get_salt_bridges() function.

Return a list of tuples, where each tuple is a pair of `schrodinger.structure._StructureAtom`s, i.e., (anion atom, cation atom).

__init__(msys_model, cms_model, aids1, aids2, cutoff=5.0)

Initialize self. See help(type(self)) for accurate signature.

disableDyncalc()

Disable the execution of _dyncalc(). This is used to avoid redundant _precalc() calculations delegated in _dyncalc().

isDynamic()
class schrodinger.application.desmond.packages.analysis.ProtLigPolarInter(msys_model, cms_model, prot_asl, lig_asl, contact_cutoff=6.0, salt_bridge_cutoff=5.0, hbond_cutoff=2.8)

Bases: schrodinger.application.desmond.packages.staf.CompositeAnalyzer

Calculate polar interactions between protein and ligand, with hbonds and water bridges excluded.

Returns a list of dict. The length of this list is the number of frames. The dict key is ‘PolarResult’, and the value is a list of _ProtLigSaltBridges.Result, where prot_aid and lig_aid are the AID of the protein atom and ligand atom, polar_type is a string that denotes the side chain/backbone information, distance is the distance between the protein atom and the ligand atom. It also contains keys of ‘HBondResult’ and ‘WaterBridgeResult’ with ProtLigHbondInter and WaterBridges results as values.

__init__(msys_model, cms_model, prot_asl, lig_asl, contact_cutoff=6.0, salt_bridge_cutoff=5.0, hbond_cutoff=2.8)

Initialize self. See help(type(self)) for accurate signature.

disableDyncalc()

Disable the execution of _dyncalc(). This is used to avoid redundant _precalc() calculations delegated in _dyncalc().

isDynamic()
class schrodinger.application.desmond.packages.analysis.MetalInter(msys_model, cms_model, prot_asl, lig_asl, metal_asl=None, contact_cutoff=6.0, metal_cutoff=3.4)

Bases: schrodinger.application.desmond.packages.staf.CompositeAnalyzer

Interactions between metal elements and protein/ligand atoms.

Returns a list of dict. The length of this list is the number of frames. The dict key is ‘MetalResult’, and the value is a list of either _MetalInter.MetalP or _MetalInter.MetalL objects, where ion_aid, prot_aid and lig_aid are the AID of the ion atom, protein atom and ligand atom, ion_ele is the ion element string, distance is the distance between the ion atom and the protein/ligand atom.

MetalP

alias of _MetalP

MetalL

alias of _MetalL

__init__(msys_model, cms_model, prot_asl, lig_asl, metal_asl=None, contact_cutoff=6.0, metal_cutoff=3.4)

Initialize self. See help(type(self)) for accurate signature.

disableDyncalc()

Disable the execution of _dyncalc(). This is used to avoid redundant _precalc() calculations delegated in _dyncalc().

isDynamic()
schrodinger.application.desmond.packages.analysis.ProtLigPiInter

Compute pi-pi and pi-cation interations between protein and ligand.

Returns a list of dict. The length of this list is the number of frames. The dict keys are ‘PiPiResult’, and ‘PiCatResult’. The value is a list of ProtLigPiInter.Pipi, ProgLigPiInter.PiLCatP, or ProgLigPiInter.PiPCatL objects, where frag_idx is the index of the ligand fragment, ca_aid is the AID of alpha carbon, prot_aid and lig_aid are the AID of the protein atom and ligand atom, ring_idx is the ligand ring index, type could be ‘f2f’ or ‘e2f’, distance and angle describe the geometry of the corresponding interaction.

schrodinger.application.desmond.packages.analysis.ProtLigHalogenBondInter

Find Halogen Bonds for protein ligand interactions. Return results in a human readable format

schrodinger.application.desmond.packages.analysis.ProtLigHbondInter

Compute protein-ligand hydrogen bonds.

Returns a list of dict. The length of this list is the number of frames. The dict key is ‘HBondResult’, and the value is a list of ProtLigHbondInter.Result, where prot_aid is the AID of the protein atom, prot_type is a string that denotes the acceptor/donor, backbone/side chain information, lig_aid is the AID of ligand atom.

class schrodinger.application.desmond.packages.analysis.WatLigFragDistance(msys_model, cms_model, prot_asl, lig_asl, contact_cutoff=6.0, hbond_cutoff=2.8)

Bases: schrodinger.application.desmond.packages.staf.CompositeAnalyzer

Distance between water oxygen atom and its closest ligand fragment, with water bridges excluded.

Returns a list of dict. The length of this list is the number of frames. The dict key is ‘LigWatResult’, and the value is a list of _WatLigFragDistance.Result, where frag_idx is the index of the ligand fragment, wat_res_num is the water residue number, distance is the distance between water oxygen atom and ligand fragment centroid. It also contains the key of ‘WaterBridgeResult’ with WaterBridges results as value.

__init__(msys_model, cms_model, prot_asl, lig_asl, contact_cutoff=6.0, hbond_cutoff=2.8)

Initialize self. See help(type(self)) for accurate signature.

disableDyncalc()

Disable the execution of _dyncalc(). This is used to avoid redundant _precalc() calculations delegated in _dyncalc().

isDynamic()
schrodinger.application.desmond.packages.analysis.WaterBridges

Find water bridges between protein and ligand

Returns a list of dict. The length of this list is the number of frames. The dict key is ‘WaterBridgeResult’, and the value is a list of WaterBridges.Result, where prot_aid and lig_aid are the AID of the protein atom and ligand atom, prot_type and lig_type are strings that denotes the acceptor/donor information, wat_res_num is the water residue number.

class schrodinger.application.desmond.packages.analysis.ProtLigInter(msys_model, cms_model, prot_asl, lig_asl, metal_asl=None)

Bases: schrodinger.application.desmond.packages.staf.CompositeAnalyzer

Composition of various protein ligand interactions.

Returns a list of dict. The length of this list is the number of frames. The dict keys are ‘WaterBridgeResult’, ‘LigWatResult’, ‘HBondResult’, ‘PiPiResult’, ‘PiCatResult’, ‘MetalResult’, ‘PolarResult’.

__init__(msys_model, cms_model, prot_asl, lig_asl, metal_asl=None)
Parameters:
  • prot_asl (str) – ASL expression to specify protein atoms
  • lig_asl (str) – ASL expression to specify ligand atoms
  • metal_asl (str or None) – ASL expression to specify metal atoms. If None, use default values.
disableDyncalc()

Disable the execution of _dyncalc(). This is used to avoid redundant _precalc() calculations delegated in _dyncalc().

isDynamic()
class schrodinger.application.desmond.packages.analysis.VolumeMapper(cms_model, asl=None, aids=None, spacing=(1.0, 1.0, 1.0), length=(10.0, 10.0, 10.0), center=(0.0, 0.0, 0.0), normalize=True)

Bases: schrodinger.application.desmond.packages.staf.GeomAnalyzerBase

This class calculates the 3D histogram of selected atoms over a trajectory.

Note: The trajectory provided for this method should already be centered,
and aligned on the selection of interest. The returned histogram has origin in its central bin.
Basic usage:
ana = VolumeMapper(cms_model, ‘mol.num 1’) results = analyze(tr, ana)
__init__(cms_model, asl=None, aids=None, spacing=(1.0, 1.0, 1.0), length=(10.0, 10.0, 10.0), center=(0.0, 0.0, 0.0), normalize=True)
Parameters:asl (str) – The ASL selection for which volumetric density map will be constructed
reduce(pos_t, *_, **__)
disableDyncalc()

Disable the execution of _dyncalc(). This is used to avoid redundant _precalc() calculations delegated in _dyncalc().

isDynamic()
schrodinger.application.desmond.packages.analysis.progress_report_frame_number(i, *_)
schrodinger.application.desmond.packages.analysis.analyze(tr, analyzer, *arg, **kwarg)

Do analyses on the given trajectory tr, and return the results. The analyses are specified as one or more positional arguements. Each analyzer should satisfy the interface requirements (see the docstring of GeomCalc.addAnalyzer).

Parameters:
  • tr (list of `traj.Frame`s) – The simulation trajectory to analyze
  • arg – A list of analyzer objects
  • kwarg["progress_feedback"] (callable, e.g., func(i, fr, tr), where i is the current frame index, fr the current frame, tr the whole trajectory.) – This function will be called at start of analysis on the current frame. This function is intended to report the progress of the analysis.
Return type:

list
Returns:

For a single analyzer, this function will return a list of analysis results, and each element in the list corresponds to the result of the corresponding frame. For multiple analyzers, this function will return a list of lists, and each element is a list of results of the corresponding analyzer. If an analyzer has a reduce method, the reduce method will be called, and its result will be returned.
schrodinger.application.desmond.packages.analysis.rmsd_matrix(msys_model, tr, rmsd_gids, fit_gids)

For all pairs of frames in the trajectory tr, we first superimpose the structures from the two frames on the atoms as specified by fit_gids, and then we calculate the RMSD for atoms as specified by rmsd_gids.

Parameters:
  • tr (list of traj.Frame objects) – Trajectory
  • rmsd_gids (list of `int`s) – GIDs of atoms for which to calculate the RMSD
  • fit_gids (list of `int`s) – GIDs of atoms on which to we align the structures
Return type:

numpy.ndarray of `float`s
Returns:

A symmetric square matrix of RMSDs
schrodinger.application.desmond.packages.analysis.cluster(affinity_matrix)

Do clustering using the affinity propagation method.

Parameters:affinity_matrix (numpy.ndarray of `float`s) – A square matrix of affinity/similarity values

:rtype (list-of-int`s, `list-of-`int`s) :return: The first list is the sample indices of the clusters’ centers, the

second list is a cluster label of all samples.
class schrodinger.application.desmond.packages.analysis.Rdf(msys_model, cms_model, asl0, asl1=None, pos_type0='atom', pos_type1='atom', dr=0.1, rmax=12.0)

Bases: schrodinger.application.desmond.packages.staf.CompositeAnalyzer

Calculate radial distribution function (RDF) of provided selection.

__init__(msys_model, cms_model, asl0, asl1=None, pos_type0='atom', pos_type1='atom', dr=0.1, rmax=12.0)

This analyzer calculates the radial distribution function [RDF, also known as g(r)] of specified positions in the system.

In general, we need two groups of positions. The first group are the reference positions, whereas the second the distance group. For example, say we want to calculate the RDF of the distances of water hydrogen atoms with respect to water oxygen atoms, the first group will be all water oxygen atoms’ positions, and the second group all water hydrogen atoms’ positions. The reference and distance groups can be the same, for example, in the case of the RDF of water oxygen atoms.

Each position doesn’t have to be an atom’s position, and it could be a derived position such as the center of mass of the molecule.

Parameters:
  • asl0 (str) – Atom selection for the reference group
  • asl1 (str or None) – Atom selection for the distance group. If it’s None, it will default to asl0.
  • pos_type0 (str) – Type of positions of the reference group: “atom” : Use atom’s position directly “com” : Use molecular center of mass “coc” : Use molecular center of charge “centroid”: Use molecular centroid
  • pos_type1 (str) – Type of positions of the distance group. Values are the same as those of pos_type0
  • dr (float) – Bin width in the unit of Angstroms
  • rmax (float) – Maximum distance in the unit in Angstroms. The RDF will be calculated until rmax.
reduce(*_, **__)

Aggregates the frame-based results (histograms) and returns the final RDF results.

Return type:(list, list)
Returns:Returns the RDF (the first list), and the integral (the second list).
bins()
disableDyncalc()

Disable the execution of _dyncalc(). This is used to avoid redundant _precalc() calculations delegated in _dyncalc().

isDynamic()
class schrodinger.application.desmond.packages.analysis.ProtProtPiInter(msys_model, cms_model, asl)

Bases: schrodinger.application.desmond.packages.staf.MaestroAnalysis

Protein-protein Pi interaction finder.

Returns a dict with two keys: pi-pi and pi-cat. Values are list of 2-element `tuple`s

__init__(msys_model, cms_model, asl)
Parameters:asl (str) – ASL expression to select protein atoms
disableDyncalc()

Disable the execution of _dyncalc(). This is used to avoid redundant _precalc() calculations delegated in _dyncalc().

isDynamic()
class schrodinger.application.desmond.packages.analysis.ProtProtHbondInter(msys_model, cms_model, asl)

Bases: schrodinger.application.desmond.packages.staf.CompositeAnalyzer

Protein-protein hydrogen bond finder.

Returns a dict with four keys: hbond_bb, hbond_sb, hbond_bs, hbond_ss, b for backbone and s for sidechain. Values are list of 2-element `tuple`s (donor AID, acceptor AID).

__init__(msys_model, cms_model, asl)

Initialize self. See help(type(self)) for accurate signature.

disableDyncalc()

Disable the execution of _dyncalc(). This is used to avoid redundant _precalc() calculations delegated in _dyncalc().

isDynamic()
class schrodinger.application.desmond.packages.analysis.ProtProtInter(msys_model, cms_model, asl)

Bases: schrodinger.application.desmond.packages.staf.CompositeAnalyzer

Protein-protein interactions.

Return summary over the whole trajectory. For the same frame, results are unique up to residue level, e.g., even if there are multiple salt-bridges between residue A and B, only 1 is recorded.

__init__(msys_model, cms_model, asl)
Parameters:asl (str) – ASL expression to select protein atoms
disableDyncalc()

Disable the execution of _dyncalc(). This is used to avoid redundant _precalc() calculations delegated in _dyncalc().

isDynamic()
reduce(results, *_, **__)
Parameters:results (list of `dict`s. Its length is the number of frames.) – interactions of all frames

:rtype : dict :return: counts of the various interactions over the whole trajectory