Contents
Release 2005, March 2005
1. Introduction
- DeCipher...
- Role of analysis software in molecular modeling
- Software overview
- Substructure selection
- Data collection
- Property definition and evaluation
- Structure analysis
- Energetics analysis
- Dynamics analysis
- Property presentation
- Molecular structure and property spreadsheet
- Dynamic molecular information system
- User interface and user-software interaction
2. Theory
- Molecular properties
- Nomenclature
- Basic molecular properties
- Basic property types - scalar, vector, tensor, and reference axes:
- Atoms and atom sets
- Pseudoatoms (centroids)
- Internals
- Nonbonds
- Geometric variables
- Point
- Vector
- Plane
- Geometric functions
- Position
- Distance
- Angle
- Dihedral
- Structural functions
- Moment of inertia
- Radius of gyration
- Displacement
- Isotropic and anisotropic mean square displacement (MSD)
- B-factor
- Root mean square displacement (RMSD)
- Kinetic functions
- Linear momentum
- Center of mass velocity
- Angular momentum
- Angular velocity
- Kinetic energy
- Total kinetic energy
- Translational kinetic energy
- Rotational kinetic energy
- Vibrational kinetic energy
- Electrostatic functions: multipole moments
- Monopole
- Dipole
- Multipolar interaction energy
- Multipolar interaction forces
- Multipole calculations of DeCipher
- Potential functions
- Potential energy and forces
- Consistent valence forcefield (CVFF)
- AMBER forcefield
- The CFF forcefield (Class II forcefield)
- Energy and derivative expressions
- CFF91/CFF
- CVFF
- AMBER
- Force calculations
- Bond
- Angle
- Torsion
- Wilson out of plane
- Restraint function
- Function optimization
- High-level molecular properties
- Distribution functions
- Radial distribution functions (RadialDistFunc)
- Pair distribution functions
- Spherical and cylindrical distribution functions
- Coordination numbers
- Coordination number distribution function (CN_Distrib)
- Orientational radial distribution function (Orient_RDF)
- Spherical harmonic expansion
- Orientational pair distribution functions
- Spherical orientational distribution function
- Cylindrical orientational distribution function
- Angular distribution dunction (AngleDistFunc)
- Mean square displacement (MeanSqDisp) and diffusion coefficient
- Time correlation functions (TimeCorrFunc)
- Direct approach
- Normalized discrete time correlation functions
- Legendre polynomials Pl cosq
- Spectral density
- Diffusion coefficient
- Residency time (ResidencyTime)
3. Languages
- Introduction
- Molecular subsets
- Topological subsets
- Geometric subsets
- Three dimensional atom attributes
- Three dimensional neighborhood
- Functions and mathematical expressions in DeCipher
- Molecular properties representations
- Native functions
- Spectra
- Numerical functions
- System functions
- Geometrics
- Implicit functions
- Mathematical expressions (the "Function Spec")
- Built-in operators
- Precedence rules
- Array, vector, Ref_Axes, and tensor subscripts
- Built-in scalar functions
- Built-in constant
- Built-in vector functions
- Built-in tensor functions
- Specific built-in array functions:
- Examples (for Function Spec)
4. Command Summary
- Configurations
- Configurations/Get
- Configurations/Put
- Configurations/Record
- Configurations/Filter
- Configurations/Align
- Configurations/Color
- Configurations/Animate
- Configurations/Select
- Configurations/Tabulate
- Configurations/Delete
- Functions
- Functions/Construct_Graph
- Functions/Construct_Table
- Functions/Angles
- Functions/Dihedrals
- Functions/Dipole
- Functions/Distances
- Functions/Moment_of_Inertia
- Functions/Positions
- Functions/Radius_of_Gyration
- Functions/Numeric
- Functions/B_Factor
- Functions/Displacement
- Functions/RMSD
- Functions/Momentum
- Functions/Velocity
- Functions/Temperature
- Functions/Kinetic_Energy
- Functions/Multipolar_Energy
- Functions/Potential_Energy
- Functions/Restraint_Energy
- Functions/Non_Bond_Setup
- Functions/Optimize
- Functions/Get
- Functions/Put
- Functions/Rename
- Functions/Delete
- Functions/Info
- Spectra
- Spectra/RadialDistFunc
- Spectra/OrientRDF
- Spectra/AngleDistFunc
- Spectra/CN_Distrib
- Spectra/MeanSqDisp
- Spectra/TimeCorrFunc
- Spectra/ResidencyTime
- Geometrics
- Geometrics/Point
- Geometrics/Vector
- Geometrics/Plane
- Geometrics/Style
- Geometrics/Color
- Geometrics/Info
- SubStructure
- SubStructure/Get
- SubStructure/Put
- SubStructure/Internals
- SubStructure/NonBonds
- SubStructure/Rename
- Substructure/Delete
- Substructure/Info
- SubStructure/Plot
- Cluster
- Cluster/Construct_Graph
- Cluster/Repartition
- Cluster/Family
5. Online Tutorials
- Pilot online tutorials
A. References
B. Glossary
C. File Formats
- Multiple-file trajectory definition file
D. Units
- Electrostatic conversion factor
- Frequency conversion
E. Atom_Template Expressions
- Bond order characters
- Examples of Atom_Templates
Last updated November 22, 2003 at 02:13PM Pacific Standard Time.
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reserved.