Uses of Interface
javajs.api.GenericLineReader
Packages that use GenericLineReader
Package
Description
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Uses of GenericLineReader in javajs.api
Methods in javajs.api with parameters of type GenericLineReaderModifier and TypeMethodDescriptionGenericCifDataParser.set(GenericLineReader reader, BufferedReader br, boolean debugging) -
Uses of GenericLineReader in javajs.util
Classes in javajs.util that implement GenericLineReaderModifier and TypeClassDescriptionclassA general helper class for a variety of stream and reader functionality including: stream and byte magic-number decoding for PNG, PNGJ, ZIP, and GZIP streams various stream/reader methods, including UTF-encoded stream reading reflection-protected access to a CIF parser and ZIP toolsMethods in javajs.util with parameters of type GenericLineReaderModifier and TypeMethodDescriptionCifDataParser.set(GenericLineReader reader, BufferedReader br, boolean debugging) A Chemical Information File data parser. -
Uses of GenericLineReader in org.jmol.adapter.readers.cif
Classes in org.jmol.adapter.readers.cif that implement GenericLineReaderModifier and TypeClassDescriptionclassA very simple Binary CIF file reader extention of MMCifReader extends CifReader.classPreliminary Cif2 reader.classA true line-free CIF file reader for CIF files.classmmCIF files are recognized prior to class creation.classJmolData RCSB MMTF (macromolecular transmission format) file reader see https://github.com/rcsb/mmtf/blob/master/spec.md Note added 2024.01.19 Jose Duarte 2:03 PM (email) to MMTF-Users From July 2024 the PDB file archive will not be offered in the compressed MMTF format anymore. -
Uses of GenericLineReader in org.jmol.adapter.readers.molxyz
Classes in org.jmol.adapter.readers.molxyz that implement GenericLineReaderModifier and TypeClassDescriptionclass3D onlyclassA reader for MDLI mol and sdf files.classMinnesota SuperComputer Center XYZ file format simple symmetry extension via load command: 9/2006 hansonr@stolaf.edu setAtomCoord(atom) applySymmetryAndSetTrajectory() extended to read XYZI files (Bob's invention -- allows isotope numbers) extended to read XYZ files with fractional charges as, for example: http://www.ccl.net/cca/software/SOURCES/FORTRAN/molden/test/reacpth.xyz http://web.archive.org/web/20000120031517/www.msc.edu/msc/docs/xmol/v1.3/g94toxyz.c -
Uses of GenericLineReader in org.jmol.adapter.readers.more
Classes in org.jmol.adapter.readers.more that implement GenericLineReaderModifier and TypeClassDescriptionclassA reader for various AFLOW file types.classDCD binary trajectory file reader.classA reader for ChemDraw binary CDX files.classclassclassA preliminary reader for JCAMP-DX files having ##$MODELS= and ##$PEAKS= records Designed by Robert Lancashire and Bob Hanson specifications (by example here): ##$MODELS=acetophenone DSViewer 3D 0 17 17 0 0 0 0 0 0 0 0999 V2000 ... classAmber Coordinate File Reader not a stand-alone reader -- must be after COORD keyword in LOAD commandclassA reader for Amber Molecular Dynamics topology files -- requires subsequent COORD "xxxx.mdcrd" fileclassA minimal multi-file reader for TRIPOS SYBYL mol2 files.class -
Uses of GenericLineReader in org.jmol.adapter.readers.pdb
Classes in org.jmol.adapter.readers.pdb that implement GenericLineReaderModifier and TypeClassDescriptionclassJmolData file reader, for a modified PDB format This class also holds pseudo-static methods for spinclassP2N file reader.classPDB file reader.classPQR file reader. -
Uses of GenericLineReader in org.jmol.adapter.readers.pymol
Classes in org.jmol.adapter.readers.pymol that implement GenericLineReaderModifier and TypeClassDescriptionclassPyMOL PSE (binary Python session) file reader. -
Uses of GenericLineReader in org.jmol.adapter.readers.quantum
Classes in org.jmol.adapter.readers.quantum that implement GenericLineReaderModifier and TypeClassDescriptionclassTODO: adf-2007.out causes failure reading basis functions A reader for ADF output.classA reader for AMS output subclassing the older AdfReader.classclassCSF file reader based on CIF idea -- fluid property fields.classA reader for Dgrid BASISFILE data.classclassclassclassReader for Gaussian fchk files for vibrational modes, add Freq=(SaveNormalModes,Raman,VibRot) also allows appended freq dataclassReader for Gaussian 94/98/03/09 output files.classReader for Gaussian Wfn files -- not implemented yetclassNBO file nn reader will pull in other files as necessary acknowledgments: Grange Hermitage, Frank Weinhold upgrade to NBO 6 allows reading of resonance structures, including base structureclassJaguar reader tested for the two samples files in CVS.classA molecular structure and orbital reader for MolDen files.classReads Mopac 2007 GRAPHF output filesclassGeneral methods for reading molecular orbital data, including embedded output from the NBO program.classA reader for NWChem 4.6 NWChem is a quantum chemistry program developed at Pacific Northwest National Laboratory.classReads ORCA input and output filesclassReader for Psi3 output files.classA reader for Q-Chem 2.1 and 3.2 Q-Chem is a quantum chemistry program developed by Q-Chem, Inc.classA molecular structure and orbital reader for MolDen files.classA molecular orbital reader for WebMO files. -
Uses of GenericLineReader in org.jmol.adapter.readers.simple
Classes in org.jmol.adapter.readers.simple that implement GenericLineReaderModifier and TypeClassDescriptionclassTRIPOS simple Alchemy reader.classA reader for AMPAC output.classGaussian cube file format http://www.cup.uni-muenchen.de/oc/zipse/lv18099/orb_MOLDEN.html this is good because it is source code http://ftp.ccl.net/cca/software/SOURCES/C/scarecrow/gcube2plt.c http://www.nersc.gov/nusers/resources/software/apps/chemistry/gaussian/g98/00000430.htm distances are in Bohrs because we are reading Gaussian cube OUTPUT files not Gaussian cube INPUT files.classFoldingAtHome json reader.classThis reader is for current.xyz files generated by Folding@Home project (see http://folding.stanford.edu) I have not found a precise description of the file format.classReads Ghemical ( http://www.uku.fi/~thassine/ghemical) molecular mechanics (*.mm1gp) files.classSupport for .hin, HyperChem's native file format.classclassclassclassMopac Archive reader -- presumes "zMatrix" is really Cartesians use FILTER "NOCENTER" to NOT center atoms in unit cell use CENTROID for complete molecules with centroids within unit cell use PACKED CENTROID for complete molecules with any atoms within unit cellclassReads Mopac 93, 6, 7, 2002, or 2009 output filesclassReads ORCA input and output filesclasssimple Tinker format requires Tinker:: prefix: load Tinker::mydata.xyz 1/2014 hansonr@stolaf.edu -
Uses of GenericLineReader in org.jmol.adapter.readers.spartan
Classes in org.jmol.adapter.readers.spartan that implement GenericLineReaderModifier and TypeClassDescriptionclassclassclassclass -
Uses of GenericLineReader in org.jmol.adapter.readers.xml
Classes in org.jmol.adapter.readers.xml that implement GenericLineReaderModifier and TypeClassDescriptionclassA crude ArgusLab .agl file Reader - http://www.planaria-software.com/ Use this reader as a template for adding new XML readers.classA reader for CambridgeSoft CDXML files.classAn chem3d c3xml readerclassA CML2 Reader - If passed a bufferedReader (from a file or inline string), we generate a SAX parser and use callbacks to construct an AtomSetCollection.classclassA Molpro 2005 readerclassAn abstract class accessing MOReader -- currently just for XmlMolproReader only.classA reader for the structure part of an nmrML fileclassAn Odyssey xodydata readerclassQuantumEspresso XML readerclassA generic XML reader template -- by itself, does nothing.classVasp vasprun.xml readerclassAn XML reader for Materials Studio .xsd files http://accelrys.com/products/materials-studio/ Bob Hanson hansonr@stolaf.edu 6/3/09 -
Uses of GenericLineReader in org.jmol.adapter.readers.xtal
Classes in org.jmol.adapter.readers.xtal that implement GenericLineReaderModifier and TypeClassDescriptionclassclassFHI-aims (http://www.fhi-berlin.mpg.de/aims) geometry.in file format samples of relevant lines in geometry.in file are included as comments below modified (May 1, 2011, hansonr@stolaf.edu) to account for atom/atom_frac lines and to bring it into compliance with other load options (such as overriding file-based symmetry or unit cell parameters).classBilbao Crystallographic Database file reader see, for example, http://www.cryst.ehu.es/cryst/compstru.html Comparison of Crystal Structures with the same Symmetry Note that this reader scrapes HTML.classCASTEP (http://www.castep.org) .cell file format relevant section of .cell file are included as comments below preliminary .castep, .phonon frequency reader -- hansonr@stolaf.edu 9/2011 -- Many thanks to Keith Refson for his assistance with this implementation -- atom's mass is encoded as bfactor -- FILTER options include "q=n" where n is an integer "q={1/4 1/4 0}" "q=ALL" -- for non-simple fractions, you must use the exact form of the wavevector description: -- load "xxx.phonon" FILTER "q=(-0.083333 0.083333 0.500000) -- for simple fractions, you can also just specify SUPERCELL {a b c} where the number of cells matches a given wavevector -- SUPERCELL {4 4 1}, for example note: following was never implemented? -- following this with ".1" ".2" etc.classA reader for TOPOS systre file Crystal Graph Data format.classA reader for CrystalMaker CMDF binary/text files.classA reader of OUT and OUTP files for CRYSTAL http://www.crystal.unito.it/classclassclassA reader for JSON output from the FINDSPINGROUP program.classProblems identified (Bob Hanson) -- -- Coordinates for the asymmetric unit are conventional.classA reader for Jana M50+M40 file pairs.classclassA (preliminary) reader for OPTIMADE resources.classcrude PWmat atom.config reader http://pwmatus.com/manualclassA reader for SHELX output (RES) files.classBH note: this reader was never set up to read Z-matrix structures such as benzenev4.1.fdf SIESTA http://www.icmab.es/siesta/classhttp://cms.mpi.univie.ac.at/vasp/vasp/CHGCAR_file.html very simple reader of just the header information.classhttp://cms.mpi.univie.ac.at/vasp/classadjusted for AFLOW options - adding element names, environment radius on atom line http://cms.mpi.univie.ac.at/vasp/classA reader for Wein2k DFT files.class -
Uses of GenericLineReader in org.jmol.adapter.smarter
Classes in org.jmol.adapter.smarter that implement GenericLineReader