Search Results for "format"
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Showing 10 open source projects for "format"
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Molecular Dynamics Studio
Molecular Dynamics Cell Construction
...MSI2LMP creates a LAMMPS input file based on class I or class II force fields. MSI2LMP was modified to use numerically coded force field data generated by NanoEngineer-1. The MMP file format was extended and integrated into all three software applications. http://www.nanoengineer-1.net http://www.ime.unicamp.br/~martinez/packmol/ http://lammps.sandia.gov/ -
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orbkit (Moved to Github)
A Modular Python Toolbox for Cross-Platform Post-Processing of Quantum
PLEASE NOTE ORBKIT HAS BEEN MOVED TO https://github.com/orbkit/orbkit orbkit is a parallel Python program package for post-processing wave function data extracted from output files of MOLPRO (Molden File Format), TURBOMOLE (AOMix file format), GAMESS-US, PROAIMS/AIMPAC (wfn/wfx file format), and Gaussian (Output File and Formatted Checkpoint File) output files. Futhermore, an interface to cclib, a parser for quantum chemical logfiles, is provided. If you use orbkit in your work, please cite it as follows: Gunter Hermann, Vincent Pohl, Jean Christophe Tremblay, Beate Paulus, Hans-Christian Hege, and Axel Schild, "ORBKIT: A Modular Python Toolbox for Cross-Platform Postprocessing of Quantum Chemical Wavefunction Data", J. ... -
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2DFLT
Program for Normalization, Averaging and Editing of In Situ Data Sets
...This software allows collecting individual data files from in situ experiment into one dataset. After that this data set can be visualized, edited, normalized and averaged. Resulted data can be saved as one flat file (FLT-format) which can be used for PSD/MED calculations via 2DMED software (http://sourceforge.net/projects/twodmed/?source=directory). 2DFLT specifically was written to target in situ X-ray Powder Diffraction data from synchrotron measurements. Hence it can read CHI, XYE (TOPAS), FXYE(GSAS/ GSASII) and XY- files formats. However it can read general in situ data written into individual TXT or XY – files. -
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ProtPOS
Prediction of PROTtein Preferred Orientation on a Surface
...It searches quickly for the low energy protein poses in all translational and rotational degrees of freedom of the protein with respect to the surface using particle swarm optimization. Each successful run returns the lowest energy orientation of the protein on the surface in PDB format, which is readily used for MD simulations. ProtPOS is implemented in Python, making use of the PyMOL library for generating protein conformations and calling GROMACS externally to calculate protein-surface interaction energies. https://cbbio.online/software/protpos/ -
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2DMED
Phase Sensitive Detection and Modulated Enhanced Diffraction Software
...Demodulated data can be then viewed on 2D and/or 1D plot and analyses with different tools including In Phase Plot, Maximum Amplitude Plot and Positive Pattern Plot. Demodulated data also can be saved in ASCII format for further analysis. -
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Protospacer
Rapid gRNA design and validation for CRISPR
...Protospacer then allows the user to sub-select targets from the database by gene ID, by exon/intron/UTR location, by sequence similarity, or by genomic co-ordinate. From here, users are able to evaluate potential off targeting, to export results in FASTA format or tabulated (e.g. for Microsoft Excel), and to connect to the Integrative Genomics Viewer (IGVref) and view target-sites in the context of genomic annotations, amino acid translations, and HT-Seq data (for off-target validation). We provide online video tutorials and a toy database from our main website. -
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nwbas2ecce
nwbas2ecce converts nwchem basis set files to the ECCE format
The basis sets included with ECCE have -- as far as I can tell -- not been updated for many years. In addition, many of the newer basis sets that come with nwchem aren't included, such as the def2- series. nwbas2ecce is a python script that aims to automate as much as possible of the conversion process of a nwchem basis set file into the files necessary for ECCE to included it in the basis set tool. The process isn't completely automatic, but I also believe that it shouldn't be to... -
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xyz2eps
python command line utility to print xyz-geometry to eps file format.
xyz2eps.py is an command line utility written in Python programing language which prints the geometry from xyz-file directly to the eps-file format. Originally it was designed to study the problems related to grain boundaries in graphene. -
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CellPublisher is a free, open source program to improve the navigation of biological pathways. It converts CellDesigner diagrams into fully-featured maps that live inside a browser. The navigation is based on the Google maps API.
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WebBabel is a python web application using OpenBabel to convert files from one format to another. It runs under Windows, Mac or Linux on your desktop, workstation or laptop. It uses the Jmol (or Marvin) viewer to show the structures being converted.
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