schrodinger.application.desmond.packages.analysis module¶
Classes and functions for trajectory-based analysis
Copyright Schrodinger, LLC. All rights reserved.
- class schrodinger.application.desmond.packages.analysis.GroupType(value, names=None, *, module=None, qualname=None, type=None, start=1, boundary=None)¶
Bases:
enum.Enum
Enum representing different methods to grouping method to group atoms.
Currently supported types are: - MOLECULE: Atoms are grouped by the molecule they belong to. - RESIDUE: Atoms are grouped by the residue they belong to.
- MOLECULE = 'molecule'¶
- RESIDUE = 'residue'¶
- schrodinger.application.desmond.packages.analysis.is_small_struc(atoms)¶
A simple API to determine whether a molecular structure is small.
- Parameters
atoms (
list
) – 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 triclinic cell.
- Parameters
box (
numpy.ndarray
) – 3x3 matrix whose ROWS are primitive cell vectors. For amsys.System
instance, callmsys_model.cell
to get this matrix. For atraj.Frame
instance, callfr.box
to get it. For aCms
instance, callnumpy.reshape(cms_model.box, [3, 3])
to get it.
- property box¶
- property volume¶
- property inv_box¶
- calcMinimumImage(ref_pos, pos)¶
Calculates the minimum image of a position vector
pos
relative to another position vectorref_pos
.pos
andref_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 inpos
andref_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
withnumpy.float64
elements- 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 ofto_pos
.pos
andref_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 inpos
andref_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
withnumpy.float64
elements- 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
withnumpy.float64
elements- 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.CenterOf(*args, **kwargs)¶
Bases:
schrodinger.application.desmond.packages.staf.GeomAnalyzerBase
Base class for computing averaged center of a group of atoms, with optional weights. Periodic boundary condition is taken into account.
N.B.: The calculated center is an unwrapped coordinate.
- __init__(gids: List[int], weights: Optional[List[float]] = 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.
- class schrodinger.application.desmond.packages.analysis.Com(*args, **kwargs)¶
Bases:
schrodinger.application.desmond.packages.analysis.CenterOf
Class for computing averaged position weighted by atomic mass under 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, andresults
contain alist
of unwrapped centers of mass asfloats
, onefloat
for each frame. If return_unwrapped_atompos isTrue
,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 selectiongids (
list
ofint
) – GIDs of atomsreturn_unwrapped_atompos – if
False
, return the unwrapped center. Otherwise return both unwrapped center and the unwrapped positions of the selected atoms.
Both
msys_model
andcms_model
must be previously obtained through theread_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
orgids
must be specified, but not both.
- class schrodinger.application.desmond.packages.analysis.Coc(*args, **kwargs)¶
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__
.
- class schrodinger.application.desmond.packages.analysis.Centroid(*args, **kwargs)¶
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__
.
- class schrodinger.application.desmond.packages.analysis.Vector(*args, **kwargs)¶
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)¶
- class schrodinger.application.desmond.packages.analysis.Distance(*args, **kwargs)¶
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)¶
- class schrodinger.application.desmond.packages.analysis.Angle(*args, **kwargs)¶
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
andxid1`==>`xid2
.
- class schrodinger.application.desmond.packages.analysis.Torsion(*args, **kwargs)¶
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
- class schrodinger.application.desmond.packages.analysis.PlanarAngle(*args, **kwargs)¶
Bases:
schrodinger.application.desmond.packages.staf.GeomAnalyzerBase
Calculate planar angle formed among six xids. The first three xids define the first plane and the latter three xids define the second plane. Result is a list of planar angles in degrees for the trajectory frames.
- __init__(msys_model: schrodinger.application.desmond.packages.msys.System, cms_model: schrodinger.application.desmond.cms.Cms, xid0: Union[int, schrodinger.application.desmond.packages.analysis.CenterOf], xid1: Union[int, schrodinger.application.desmond.packages.analysis.CenterOf], xid2: Union[int, schrodinger.application.desmond.packages.analysis.CenterOf], xid3: Union[int, schrodinger.application.desmond.packages.analysis.CenterOf], xid4: Union[int, schrodinger.application.desmond.packages.analysis.CenterOf], xid5: Union[int, schrodinger.application.desmond.packages.analysis.CenterOf], minangle: bool = True)¶
- Parameters
msys_model – defines the system structure and atomic mapping
cms_model – defines the system structure and atomic mapping
xid* – integer representing an aid or
CenterOf
type (Com
,Coc
,Centroid
)minangle –
True
to restrict the returned angle to the range [0, 90] degrees, treating the order of atoms defining the plane as unimportant and ignoring the directionality of the plane normals.False
to return the angle in the range [0, 180] degrees.
- class schrodinger.application.desmond.packages.analysis.FittedPlanarAngle(*args, **kwargs)¶
Bases:
schrodinger.application.desmond.packages.staf.GeomAnalyzerBase
Calculate planar angle formed among two groups of atoms, each of containing 3 or more atoms. The first list contains xids of the first group and the second list contains xids of the second group. A best-fitting plane is calculated for each group of xids. Result is a list of planar angles in degrees for the trajectory frames.
This analyzer is useful for such cases as calculating angles between two rings.
- __init__(msys_model: schrodinger.application.desmond.packages.msys.System, cms_model: schrodinger.application.desmond.cms.Cms, xids0: List[Union[int, schrodinger.application.desmond.packages.analysis.CenterOf]], xids1: List[Union[int, schrodinger.application.desmond.packages.analysis.CenterOf]], minangle: bool = True)¶
- Parameters
msys_model – defines the system structure and atomic mapping
cms_model – defines the system structure and atomic mapping
xids* – list of integers representing aid or
CenterOf
types (Com
,Coc
,Centroid
)minangle –
True
to restrict the returned angle to the range [0, 90] degrees, treating the order of atoms defining the plane as unimportant and ignoring the directionality of the plane normals.False
to return the angle in the range [0, 180] degrees.
- class schrodinger.application.desmond.packages.analysis.Gyradius(*args, **kwargs)¶
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, mass_weighted: bool = False)¶
- class schrodinger.application.desmond.packages.analysis.MassAvgVel(*args, **kwargs)¶
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
offloat
- class schrodinger.application.desmond.packages.analysis.PosTrack(*args, **kwargs)¶
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__
.
- 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(*args, **kwargs)¶
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, andresults
is alist
, and each element in thelist
is alist
: [(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, *_, **__)¶
- schrodinger.application.desmond.packages.analysis.align_pos(pos, fit_pos, fit_ref_pos, weights=None, return_trans_rot=False, allow_improper_rotation=False, is_precentered=False)¶
Align
pos
using transformations (rotation and translation) derived from convertingfit_pos
tofit_ref_pos
. Weighted Kabsch algorithm is used to obtain the transformations.- Parameters
allow_improper_rotation – If not set, only proper rotation is allowed.
is_precentered (
bool
) –True
if all position arrays, i.e.,pos
,fit_pos
, andfit_ref_pos
, have been properly centered. Note thatpos
andfit_pos
should be centered to the origin with respect toweights
.
- Returns
aligned
pos
and optionally the transformation matrices ifreturn_trans_rot
is set to beTrue
- Return type
Nx3
numpy.ndarray
ifreturn_trans
is False. Otherwise (numpy.ndarray
, (1x3numpy.ndarray
, 3x3numpy.ndarray
)) where the 1x3 array is the translation vector, and the 3x3 array is the rotation matrix. The aligned position is calculated as numpy.dot(pos - trans_vec, rot_mat).
- class schrodinger.application.desmond.packages.analysis.PosAlign(*args, **kwargs)¶
Bases:
schrodinger.application.desmond.packages.staf.CenteredSoluteAnalysis
This analyzer first centers the solute atoms. If
fit_aids
andfit_ref_pos
are provided, it further aligns the given trajectory frames: first calculate the rotation / translation transformation to fit the sub-structure defined byfit_aids
to the given geometry (fit_ref_pos
), and then apply the transformation to the coordinates of the selected atoms (aids
). The returned value is the transformed coordinates foraids
.- __init__(msys_model, cms_model, aids, fit_aids, fit_ref_pos)¶
- Parameters
fit_ref_pos (Mx3
numpy.ndarray
orNone
) – positions of reference conformer structure for translation/rotation calculation
Both
msys_model
andcms_model
must be previously obtained through theread_cms
function.
- class schrodinger.application.desmond.packages.analysis.RMSD(*args, **kwargs)¶
Bases:
schrodinger.application.desmond.packages.analysis.PosAlign
Root Mean Square Deviation with respect to reference positions, with optional alignment fitting.
See
RMSF
docstring for a detailed example (replace “RMSF” with “RMSD”).If spikes are seen, call
topo.make_glued_topology
first.- __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 structurein_place – if
True
, calculate RMSD without applying transformations onref_pos
Typically,
aids
andfit_aids
come from a common source whereasref_pos
andfit_ref_pos
come from another common source.
- class schrodinger.application.desmond.packages.analysis.RMSF(*args, **kwargs)¶
Bases:
schrodinger.application.desmond.packages.analysis.PosAlign
Per-atom Root Mean Square Fluctuation with respect to averaged position over the trajectory, with optional alignment fitting.
Example: calculate ligand RMSF with protein backbone aligned
>>> backbone_asl = 'backbone and not (atom.ele H) and not (m.n 4)' >>> backbone_aids = cms_model.select_atom(backbone_asl) >>> ligand_aids = cms_model.select_atom('ligand')
>>> # suppose the backbone reference position comes from a trajectory frame >>> backbone_gids = topo.aids2gids(cms_model, backbone_aids, include_pseudoatoms=False) >>> backbone_ref_pos = a_frame.pos(backbone_gids)
>>> ana = RMSF(msys_model, cms_model, ligand_aids, backbone_aids, backbone_ref_pos) >>> result = analysis.analyze(a_trajectory, ana)
Here result is a length N numpy array where N is the number of ligand atoms. If spikes are seen, call
topo.make_glued_topology
before any analysis:>>> topo.make_glued_topology(msys_model, cms_model)
This call will change the topology of msys_model, i.e., add ‘bonds’ for atoms that are close and belong to different molecules, using the positions in cms_model as gold standard. This change only affects position unwrapping for certain trajectory APIs such as topo.make_whole(), topo.center().
- __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 calculationin_place – if
True
, calculate RMSF without applying alignment transformations
Both
msys_model
andcms_model
must be previously obtained through theread_cms
function.
- reduce(pos_t, *_, **__)¶
Temporal average of the RMSF over the trajectory
- Return type
length N
numpy.ndarray
- class schrodinger.application.desmond.packages.analysis.LigandRMSD(*args, **kwargs)¶
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
- 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
ofint
) – Atom selections- Return type
numpy.ndarray
offloat
- class schrodinger.application.desmond.packages.analysis.ProteinSF(*args, **kwargs)¶
Bases:
schrodinger.application.desmond.packages.analysis.RMSF
Per-frame per-residue Square Fluctuation (SF) with respect to averaged positions over the trajectory, with optional alignment fitting.
It returns a tuple of (residue labels, N_frame x N_residue matrix). Each matrix entry is the mass-weighted SF averaged over the residue’s atoms.
- __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[numpy.ndarray] :return: residue tags and per-frame per-residue SF matrix
- class schrodinger.application.desmond.packages.analysis.ProteinRMSF(*args, **kwargs)¶
Bases:
schrodinger.application.desmond.packages.analysis.ProteinSF
Per-residue Root Mean Square Fluctuation with respect to averaged positions over the trajectory, with optional alignment fitting.
- reduce(pos_t, *_, **__)¶
:rtype : list[string], list[float] :return: residue tags and RMSF for each residue
- class schrodinger.application.desmond.packages.analysis.Dipole(*args, **kwargs)¶
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)¶
- class schrodinger.application.desmond.packages.analysis.AxisDirector(*args, **kwargs)¶
Bases:
schrodinger.application.desmond.packages.staf.GeomAnalyzerBase
Basis vector of 3D axis
- __init__(axis)¶
- Parameters
axis (
str
) – axis name, ‘X’, ‘Y’ or ‘Z’
- class schrodinger.application.desmond.packages.analysis.MomentOfInertia(*args, **kwargs)¶
Bases:
schrodinger.application.desmond.packages.staf.CompositeAnalyzer
Moment of inertia tensor
Result is 3x3
numpy.ndarray
- __init__(msys_model, cms_model, aids)¶
- class schrodinger.application.desmond.packages.analysis.MomentOfInertiaDirector(*args, **kwargs)¶
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
- class schrodinger.application.desmond.packages.analysis.SmartsDirector(*args, **kwargs)¶
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 ofSmartsDirector
for one frame
- class schrodinger.application.desmond.packages.analysis.SystemDipoleDirector(*args, **kwargs)¶
Bases:
schrodinger.application.desmond.packages.staf.CompositeDynamicAslAnalyzer
Direction of electric dipole moment of all the selected atoms
- class schrodinger.application.desmond.packages.analysis.DipoleDirector(*args, **kwargs)¶
Bases:
schrodinger.application.desmond.packages.analysis.SystemDipoleDirector
Dipole direction for each molecule in the selection
- class schrodinger.application.desmond.packages.analysis.LipidDirector(*args, **kwargs)¶
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’
- 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.
- schrodinger.application.desmond.packages.analysis.reduce_lipid_vec_list(n, m)¶
Calculate Legendre polynomial P2 using the inner product of n and m as the input. Return its absolute value.
- class schrodinger.application.desmond.packages.analysis.OrderParameter(*args, **kwargs)¶
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 directorvec2 – 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.
- class schrodinger.application.desmond.packages.analysis.MoleculeWiseCom(*args, **kwargs)¶
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.
- class schrodinger.application.desmond.packages.analysis.AtomicPosition(*args, **kwargs)¶
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)¶
- class schrodinger.application.desmond.packages.analysis.SecondaryStructure(*args, **kwargs)¶
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: List[int])¶
- Parameters
aids – IDs of atoms to calculate the secondary-structure property for
- reduce(results, *_, **__)¶
- class schrodinger.application.desmond.packages.analysis.SolventAccessibleSurfaceAreaByResidue(*args, **kwargs)¶
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]), where relative-SASAs has the structure of [[relative-SASA for each residue] for each frame]
- 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)¶
- Parameters
asl_center – ASL for the atoms to be centered
asl_exclude – ASL for the atoms to be excluded from centering. For example, ASL ‘protein’ could select ion and water molecules which may be too mobile for the centering.
- reduce(results, *_, **__)¶
- class schrodinger.application.desmond.packages.analysis.MolecularSurfaceArea(*args, **kwargs)¶
Bases:
schrodinger.application.desmond.packages.staf.CenteredSoluteAnalysis
Calculate the molecular surface area. The result is a single scalar number per frame.
- __init__(msys_model, cms_model, asl, grid_spacing=None)¶
- Parameters
asl (
str
) – ASL expression to select atoms whose secondary-structure property is of interest.
- class schrodinger.application.desmond.packages.analysis.SolventAccessibleSurfaceArea(*args, **kwargs)¶
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)¶
- Parameters
asl_center – ASL for the atoms to be centered
asl_exclude – ASL for the atoms to be excluded from centering. For example, ASL ‘protein’ could select ion and water molecules which may be too mobile for the centering.
- class schrodinger.application.desmond.packages.analysis.PolarSurfaceArea(*args, **kwargs)¶
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)¶
- Parameters
asl_center – ASL for the atoms to be centered
asl_exclude – ASL for the atoms to be excluded from centering. For example, ASL ‘protein’ could select ion and water molecules which may be too mobile for the centering.
- class schrodinger.application.desmond.packages.analysis.HydrogenBondFinder(*args, **kwargs)¶
Bases:
schrodinger.application.desmond.packages.staf.MaestroAnalysis
Find hydrogen bonds between two sets of atoms. The result has the structure of [[(acceptor atom ID, donor atom ID) for each H bond] for each frame].
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)¶
- Parameters
aids1 (list or None) – A list of atom indices for the first atom set. All atoms will be used if it is None.
aids2 (list or None) – A list of atom indices for the second atom set. All atoms will be used if it is None.
- class schrodinger.application.desmond.packages.analysis.HalogenBondFinder(*args, **kwargs)¶
Bases:
schrodinger.application.desmond.packages.staf.MaestroAnalysis
Find halogen bonds between two sets of atoms. The result has the structure of [[(acceptor atom ID, donor atom ID) for each bond] for each frame].
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)¶
- schrodinger.application.desmond.packages.analysis.get_ligand_fragments(lig_ct)¶
Decompose the ligand into several fragments using the murcko rules.
- Returns
ligand fragments
- Return type
list
. Each element is alist
ofint
.
- class schrodinger.application.desmond.packages.analysis.HydrophobicInter(*args, **kwargs)¶
Bases:
schrodinger.application.desmond.packages.staf.CompositeAnalyzer
Calculate hydrophobic interactions between protein and ligand, with hbonds and pi-pi interactions excluded.
The result has the structure of:
[{ 'HydrophobicResult': [`_HydrophobicInter.Result` for each interaction], 'PiPiResult': [`ProtLigPiInter.Pipi` for each interaction], 'PiCatResult': [`ProtLigPiInter.PiLCatP` or `ProtLigPiInter.PiPCatL` for each interaction], 'HBondResult': [`ProtLigHbondInter.Result` for each interaction], } for each frame]
- __init__(msys_model, cms_model, prot_asl, lig_asl, contact_cutoff=6.0, hydrophobic_search_cutoff=3.2, hbond_cutoff=2.8)¶
- class schrodinger.application.desmond.packages.analysis.HydrophobicInterFinder(*args, **kwargs)¶
Bases:
schrodinger.application.desmond.packages.staf.MaestroAnalysis
This method is adopted from the following script: mmshare/python/common/display_hydrophobic_interactions.py While a similar analyzer
HydrophobicInter
is used specifically for finding Protein-Ligand hydrophobic interactions, this method seems more general. We may want to transition using this method for detecting Protein-Ligand hydrophobic interactions.The frames are first centered on
aids1
selection.- HYDROPHOB_ASL = 'SMARTS.[#6!$([C,c][O,o])&!$([C,c][N,n]),S&^3,P,Cl,Br,I]'¶
- __init__(msys_model, cms_model, aids1, aids2, good_cutoff_ratio=1.3, bad_cutoff_ratio=0.89)¶
- Parameters
asl_center – ASL for the atoms to be centered
asl_exclude – ASL for the atoms to be excluded from centering. For example, ASL ‘protein’ could select ion and water molecules which may be too mobile for the centering.
- class schrodinger.application.desmond.packages.analysis.SaltBridgeFinder(*args, **kwargs)¶
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.The result has the structure of:
[[(anion atom, cation atom) for each bridge] for each frame]
where the atoms are
structure._StructureAtom
.- __init__(msys_model, cms_model, aids1, aids2, cutoff=5.0)¶
- Parameters
asl_center – ASL for the atoms to be centered
asl_exclude – ASL for the atoms to be excluded from centering. For example, ASL ‘protein’ could select ion and water molecules which may be too mobile for the centering.
- class schrodinger.application.desmond.packages.analysis.ProtLigPolarInter(*args, **kwargs)¶
Bases:
schrodinger.application.desmond.packages.staf.CompositeAnalyzer
Calculate polar interactions between protein and ligand, with hbonds and water bridges excluded.
The result has the structure of [{ ‘PolarResult’: [
_ProtLigSaltBridges.Result
for each bridge], ‘HBondResult’: [ProtLigHbondInter.Result
for each H bond], ‘WaterBridgeResult’: [WaterBridges.Result
for each bridge], } for each frame]- __init__(msys_model, cms_model, prot_asl, lig_asl, contact_cutoff=6.0, salt_bridge_cutoff=5.0, hbond_cutoff=2.8)¶
- class schrodinger.application.desmond.packages.analysis.MetalInter(*args, **kwargs)¶
Bases:
schrodinger.application.desmond.packages.staf.CompositeAnalyzer
Interactions between metal elements and protein/ligand atoms.
The result has the structure of [{ ‘MetalResult’: [
_MetalInter.MetalP
or_MetalInter.MetalL
for each interaction] } for each frame]- MetalP¶
alias of
schrodinger.application.desmond.packages.analysis._MetalP
- MetalL¶
alias of
schrodinger.application.desmond.packages.analysis._MetalL
- __init__(msys_model, cms_model, prot_asl, lig_asl, metal_asl=None, contact_cutoff=6.0, metal_cutoff=3.4)¶
- schrodinger.application.desmond.packages.analysis.PiPiInteraction¶
alias of
schrodinger.application.desmond.packages.analysis._PiPiInteraction
- schrodinger.application.desmond.packages.analysis.CatPiInteraction¶
alias of
schrodinger.application.desmond.packages.analysis._PiCatInteraction
- class schrodinger.application.desmond.packages.analysis.PiPiFinder(*args, **kwargs)¶
Bases:
schrodinger.application.desmond.packages.analysis._PiInteractionFinder
Find Pi-Pi interactions present between two sets of atoms, or within one set of atoms.
The result has the structure of [[
PiPiInteraction
for each interaction] for each frame]
- class schrodinger.application.desmond.packages.analysis.CatPiFinder(*args, **kwargs)¶
Bases:
schrodinger.application.desmond.packages.analysis._PiInteractionFinder
Find Cation-Pi interactions present between two sets of atoms, or within one set of atoms. With two sets of atom selections, it computes both cations in selection 1 with respect to rings in selection 2, cations in selection 2 with respect to rings in selection 1, but not within the same selection.
The result has the structure of [[
CatPiInteraction
for each interaction] for each frame]
- class schrodinger.application.desmond.packages.analysis.WatLigFragDistance(*args, **kwargs)¶
Bases:
schrodinger.application.desmond.packages.staf.CompositeAnalyzer
Distance between water oxygen atom and its closest ligand fragment, with water bridges excluded.
The result has the structure of [{ ‘LigWatResult’: [
_WatLigFragDistance.Result
for each water-ligand-fragment-pair], ‘WaterBridgeResult’: [WaterBridges.Result
for each bridge] } for each frame]- __init__(msys_model, cms_model, prot_asl, lig_asl, contact_cutoff=6.0, hbond_cutoff=2.8)¶
- class schrodinger.application.desmond.packages.analysis.ProtLigInter(*args, **kwargs)¶
Bases:
schrodinger.application.desmond.packages.staf.CompositeAnalyzer
Composition of various protein ligand interactions.
The result has the structure of [{ ‘WaterBridgeResult’: [
WaterBridges.Result
for each bridge], ‘LigWatResult’: [_WatLigFragDistance.Result
for each water-ligand-fragment-pair], ‘HBondResult’: [ProtLigHbondInter.Result
for each interaction], ‘PiPiResult’: [ProtLigPiInter.Pipi
for each interaction], ‘PiCatResult’: [ProtLigPiInter.PiLCatP
orProtLigPiInter.PiPCatL
for each interaction], ‘MetalResult’: [_MetalInter.MetalP
or_MetalInter.MetalL
for each interaction], ‘PolarResult’: [_ProtLigSaltBridges.Result
for each bridge], }]- __init__(msys_model, cms_model, prot_asl, lig_asl, metal_asl=None)¶
- Parameters
prot_asl (
str
) – ASL expression to specify protein atomslig_asl (
str
) – ASL expression to specify ligand atomsmetal_asl (
str
orNone
) – ASL expression to specify metal atoms. IfNone
, use default values.
- class schrodinger.application.desmond.packages.analysis.AmorphousCrystalInter(*args, **kwargs)¶
Bases:
schrodinger.application.desmond.packages.staf.CompositeAnalyzer
Composition of various interactions between a specified molecule and its crystal-mates.
The result has the structure of:
{'HBondResult': [number of `HydrogenBondFinder.Result` per frame], 'HalBondResult': [number of `HalogenBondFinder.Result` per frame], 'PiPiResult': [number of `PiPiFinder.Result` per frame], 'CatPiResult': [number of `CatPiFinder.Result` per frame], 'PolarResult': [number of `SaltBridgeFinder.Result` per frame] 'HydrophobResult': [number of `HydrophobicInterFinder.Result` per frame]}
- RESULT_NAMES = ['HBondResult', 'HalBondResult', 'PiPiResult', 'CatPiResult', 'PolarResult', 'HydrophobResult']¶
- __init__(msys_model, cms_model, asl)¶
Selection of molecule of interest is passed through
asl
variable. Environment selection is generated by excluding theasl
and waters.- Parameters
asl (
str
) – ASL expression to specify selection atoms
- reduce(results)¶
- class schrodinger.application.desmond.packages.analysis.VolumeMapper(*args, **kwargs)¶
Bases:
schrodinger.application.desmond.packages.staf.GeomAnalyzerBase
This class calculates the 3D histogram of selected atoms over a trajectory.
- Note: The trajectory input for this method should already be centered and
aligned on the atoms of interest. By default, 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, *_, **__)¶
- 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 ofGeomCalc.addAnalyzer
).- Parameters
tr (
list
oftraj.Frame
) – The simulation trajectory to analyzearg – 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(obj, tr, rmsd_gids, fit_gids=None)¶
Return an NxN matrix where N is the number of frames in the trajectory
tr
and the (i, j)’th entry is the RMSD between frame i and frame j. The frame-wise RMSD values are calculated for atoms specified byrmsd_gids
. Iffit_gids
is provided, the corresponding atoms are used to superimpose the two frames first.- Parameters
obj (
msys.System
orcms.Cms.glued_topology
) – connection for trjactory centeringtr (
list
oftraj.Frame
objects) – Trajectoryrmsd_gids (
list
ofint
) – GIDs of atoms for which to calculate the RMSDfit_gids (
None
or alist
ofint
) – GIDs of atoms on which to we align the structures. IfNone
, no alignment is performed.
- Return type
numpy.ndarray
offloat
- Returns
A symmetric square matrix of RMSDs
- schrodinger.application.desmond.packages.analysis.cluster(affinity_matrix) Tuple[List[int], List[int]] ¶
Use the affinity propagation method to cluster the input matrix, gradually increasing the damping factor until the algorithm converges.
The maximum number of iterations is currently hard-coded to 400. If the damping factor reaches 1.0 (which is not a valid value), the function will return empty lists for the centers and labels.
- Parameters
affinity_matrix (
numpy.ndarray
offloat
) – A square matrix of affinity/similarity values- Returns
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(*args, **kwargs)¶
Bases:
schrodinger.application.desmond.packages.staf.CompositeAnalyzer
Calculate radial distribution function (RDF, also known as g(r)) for atom or atom group selections.
In general, we need two groups of positions. The first group are the reference positions, whereas the second the distance group. The reference and distance groups can be the same.
The ‘pos_type’ parameter determines the types of positions used as reference and distance groups. When ‘pos_type’ is set to “atom”, each atom is considered individually and the ‘group_type’ parameters are ignored, meaning no grouping is performed.
However, when ‘pos_type’ is set to values other than “atom”, such as “com”, “coc”, or “centroid”, the atoms can be grouped into larger units like molecules or residues based on the ‘group_type’ parameters. In these cases, the RDF is calculated using these larger group units instead of individual atoms.
For example, if we want to calculate the RDF of the distances of water hydrogen atoms with respect to water oxygen atoms, and ‘pos_type’ is set to “atom”, each atom is considered individually. Alternatively, if ‘pos_type’ is “com” and ‘group_type’ is “MOLECULE”, atoms are grouped by their molecular identity and the center of mass of each molecule is used, thus resulting in RDF of water molecules with respect to water molecules.
- __init__(msys_model, cms_model, asl0, asl1=None, pos_type0='atom', pos_type1='atom', dr=0.1, rmax=12.0, group_type0=GroupType.MOLECULE, group_type1=GroupType.MOLECULE)¶
- Parameters
asl0 (
str
) – Atom selection for the reference groupasl1 (
str
orNone
) – Atom selection for the distance group. If it’sNone
, it will default toasl0
.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 centroidpos_type1 (
str
) – Type of positions of the distance group. Values are the same as those ofpos_type0
dr (
float
) – Bin width in the unit of Angstromsrmax (
float
) – Maximum distance in the unit in Angstroms. The RDF will be calculated untilrmax
.group_type0 (
GroupType
) – Method to use to group atoms inasl0
selection. Only used whenpos_type0
is not “atom”.group_type1 (
GroupType
) – Method to use to group atoms inasl1
selection. Only used whenpos_type1
is not “atom”.
- 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()¶
- class schrodinger.application.desmond.packages.analysis.ProtProtPiInter(*args, **kwargs)¶
Bases:
schrodinger.application.desmond.packages.staf.MaestroAnalysis
Protein-protein Pi interaction finder. The result has the structure of [{ ‘pi-pi’: [(an atom from ring1, an atom from ring2) for each interaction], ‘pi-cat’: [(an atom from ring, an atom from cation) for each interaction] } for each frame]
- __init__(msys_model, cms_model, asl)¶
- Parameters
asl (
str
) – ASL expression to select protein atoms
- class schrodinger.application.desmond.packages.analysis.ProtProtHbondInter(*args, **kwargs)¶
Bases:
schrodinger.application.desmond.packages.staf.CompositeAnalyzer
Protein-protein hydrogen bond finder.
The result has the structure of [{ ‘hbond_bb’: [(donor AID, acceptor AID) for each interaction], ‘hbond_ss’: [(donor AID, acceptor AID) for each interaction], ‘hbond_sb’: [(donor AID, acceptor AID) for each interaction], ‘hbond_bs’: [(donor AID, acceptor AID) for each interaction] } for each frame]
Here ‘b’ denotes backbone and ‘s’ sidechain.
- __init__(msys_model, cms_model, asl)¶
- class schrodinger.application.desmond.packages.analysis.ProtProtInter(*args, **kwargs)¶
Bases:
schrodinger.application.desmond.packages.staf.CompositeAnalyzer
Protein-protein interactions.
The result has the structure of:
[{ 'pi-pi': [(an atom from ring1, an atom from ring2) for each interaction], 'pi-cat': [(an atom from ring, an atom from cation) for each interaction], 'salt-bridge': [(anion atom AID, cation atom AID) for each bridge], 'hbond_bb': [(donor AID, acceptor AID) for each interaction], 'hbond_ss': [(donor AID, acceptor AID) for each interaction], 'hbond_sb': [(donor AID, acceptor AID) for each interaction], 'hbond_bs': [(donor AID, acceptor AID) for each interaction] } for each frame]
Here ‘b’ denotes backbone and ‘s’ sidechain. 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
- reduce(results, *_, **__)¶
- Parameters
results (
list
ofdict
. Its length is the number of frames.) – interactions of all frames
:rtype :
dict
:return: counts of the various interactions over the whole trajectory
- class schrodinger.application.desmond.packages.analysis.AreaPerLipid(*args, **kwargs)¶
Bases:
schrodinger.application.desmond.packages.staf.GeomAnalyzerBase
Calculate Area-Per-Lipid in from pure lipid bilayer simulation (no protein). This analyzer assumes the bilayer is symmetric – number of lipids in upper and lower leaflets are the same. To calculate area-per-lipid, get X-Y area and divides by number of lipids/2
- __init__(msys_model, cms_model, membrane_asl: str = 'membrane')¶
- Parameters
membrane_asl (
asl
) – selection to center the system along the Z-axis
- class schrodinger.application.desmond.packages.analysis.MembraneDensityProfile(*args, **kwargs)¶
Bases:
schrodinger.application.desmond.packages.staf.GeomAnalyzerBase
Calculate Density Profile along the Z axis. The results are returned in g/cm^3.
- AMU_TO_GRAM = 1.66¶
- __init__(msys_model, cms_model, membrane_asl='membrane', density_sel_asl='lipids', slice_height=1.0, z_min=- 40, z_max=40)¶
- Parameters
membrane_asl (
asl
) – selection to center the system along the Z-axisdensity_sel_asl (
asl
) – selection for density calculationslice_height (
float
) – the height of the slices to usez_min (int) – the lower limit for which density will be calculated
z_max (int) – the upper limit for which density will be calculated
- reduce(results, *_, **__)¶
Return (mean, std) density along the Z-axis
- class schrodinger.application.desmond.packages.analysis.MembraneThickness(*args, **kwargs)¶
Bases:
schrodinger.application.desmond.packages.staf.GeomAnalyzerBase
Calculate thickness of the membrane bilayer. For phospholipids a phosphate atom is often used as a proxy for each leaflet. The system is first centered along the Z-axis, and the distance betweent the <phosphates> in each leaflet is calculated.
- __init__(msys_model, cms_model, membrane_asl='membrane', proxy_asl='atom.ele P')¶
- Parameters
membrane_asl (
asl
) – selection to center the system along the Z-axisproxy_asl (
asl
) – selection of atom(s) to be used for thickness