Search Results for "geometry"

...New project page: https://github.com/yesint/pteros New documentation page: https://yesint.github.io/pteros/ Pteros is the C++ library for custom molecular modeling and simulations codes designed for researchers, not for C++ gurus. Provides facilities for PDB, XTC and TRR files IO, powerful selections, geometry transformations, RMSD fitting and alignment, etc.

...PhantomaJ is thus "ready to use" for most users, but advanced users can choose to modify specific parameters such as intersection mode, intensity decrease function or virtual real three dimension. In addition, adding a new "basic form" consiste for advanced users to write two short java file ( one describing the new form geometry and the other transcripting this geometry in java3D world ). PhantomaJ is the indispensable tool for who want to create phantom bank of simply an unique complexe structure very easily.

LATEST VERSION NOW LOCATED AT http://git.durrantlab.com/jdurrant/lipidwrapper As ever larger and more complex biological systems are modeled in silico, approximating physiological lipid bilayers with simple planar models becomes increasingly unrealistic. When building large-scale models of whole subcellular environments, models of lipid membranes with carefully considered, biologically relevant curvature are essential. LipidWrapper, written by Jacob Durrant in the lab of Rommie E. Amaro,...

This is an automatic spike detection program which takes account of probe geometry and produces a .mask file to be used with the new masked version of KlustaKwik. We recommend you use Python 2.6 or 2.7, e.g. a free academic version can be obtained from Entthought Python. The input files for SpiKeDeteKt are: .dat (raw data file) .probe (probe file, described below - user constructed) parameters.py (optional - otherwise it uses defaultparameters.py) SpiKeDeteKt outputs the following files: .fet.n (feature file) .mask.n (needed for using the new (masked) KlustaKwik) .clu.n (a trivial clue file where everything is put into a single cluster) .fmask.n (trial - float masks instead of binary, we are using this for testing masked KlustaKwik) .spk.n (spike file) .upsk.n (unfiltered spike waveform) .res.n (list of spike times) .xml (an xml file with all the parameters that can subsequently be used by neuroscope or klusters) .fil (highpass filtered data) .h5 (

The Protein Geometry Database hosts the development code for a flexible database for searching protein geometry, as well as a library for accessing this data for protein modeling & refinement programs.