Copyright Schrodinger, LLC. All rights reserved.
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Pbc
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GeomAnalyzerBase
Base class of all geometry analyzer classes
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Distance
Calculate the distance between two atoms.
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Angle
Calculate the angle formed between three atoms.
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Torsion
Calculate the torsion formed between four atoms.
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CenterOf
N.B.: The calculated center is an unwrapped coordinate.
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Com
Class for computing averaged position weighted by atomic mass, under the
periodic boundary condition.
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Coc
Class for computing center of charge under periodic boundary
condition.
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Centroid
Class for computing centroid under periodic boundary condition.
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Gyradius
Class for computing radius of gyration under periodic boundary
condition.
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MassAvgVel
Class for computing mass-averaged velocity
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PosTrack
Class for tracking positions of selected atoms in a trajectory.
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RadiusOfGyration
Class for computing radius of gyration under periodic boundary
condition.
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CenterOfMotion
Class for computing mass-averaged velocity
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Position
Class for tracking positions of selected atoms in a trajectory.
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Ramachandran
Calculate the Phi and Psi torsions for selected atoms.
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_MaestroAnalysis
All analyzer classes whose calculations require the full-system CT
could inherit this base class, which will provide an intermediate
data that contains a trajectory frame and a full-system CT.
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PosAlign
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 ).
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RMSD
Root Mean Square Deviation from reference positions, with optional
alignment fitting.
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RMSF
Root Mean Square Fluctation from reference positions (averaged
position over the trajectory) for each atom, with optional
alignment fitting.
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LigandRMSD
Ligand Root Mean Square Deviation from reference positions, with
optional alignment fitting.
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ProteinRMSF
Root Mean Square Fluctation from reference positions (averaged
positions over the trajectory) for each residue, with optional
alignment fitting
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SecondaryStructure
Calculate the secondary-structure property for selected atoms.
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SolventAccessibleSurfaceAreaByResidue
Calculate the relative SASA broken down by residues.
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MolecularSurfaceArea
Calculate the molecular surface area.
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SolventAccessibleSurfaceArea
Calculate solvent accessible surface area for selected atoms.
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PolarSurfaceArea
Calculate polar surface area for selected atoms.
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HydrogenBondFinder
Find hydrogen bonds present between two sets of atoms.
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VolumeMapper
This class takes the coordinates of provided particles and maps them onto
a discretized grid using kernel density estimation as implemented in scipy.
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_CustomCalc
An instance of this class will store custom calculation requests (keys) and
results (values).
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GeomCalc
We use this class to batch the geometry calculations and avoid duplications.
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Positer
A class to create a positer object for use with the GeomCalc class.
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Rdf
Calculate radial distribution function (RDF) of provided selection.
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is_small_struc(atoms)
A simple API to determine whether a molecular structure is small. |
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_pos2circ(data,
pbc,
fr,
*_)
Convert a 3D vector (x, y, z) into a circular coordinate: |
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dict . Key = GID, value = a copy of the input frame
instance fr . If previous frame is available
in data , the atom coordinates are unwrapped
with respect to their coordinates in the previous frame.
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_unwrap_wrt_prevpos(data,
pbc,
fr,
*_)
Unwrap every point wrt its coordinate in the prev frame, if
available. |
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_center(data,
pbc,
fr,
*_)
Center selected particles in the simulation box, and it will automatically
make all molecules whole. |
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Nx3 numpy.ndarray
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_align_pos(pos,
fit_pos,
fit_ref_pos,
weights=None)
Align pos using transformations (rotation and
translation) derived from converting fit_pos to
fit_ref_pos . |
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dict
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_dictmap(func,
dictionary)
Map each key-value pair in a dictionary with a function
func . |
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progress_report_frame_number(i,
*_) |
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list
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analyze(tr,
analyzer,
*arg,
**kwarg)
Do analyses on the given trajectory tr , and return the
results. |
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numpy.ndarray of float s
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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 . |
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cluster(affinity_matrix)
Do clustering using the affinity propagation method. |
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