Uses of Class
org.jmol.adapter.smarter.AtomSetCollectionReader
Packages that use AtomSetCollectionReader
Package
Description
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Uses of AtomSetCollectionReader in org.jmol.adapter.readers.cif
Subclasses of AtomSetCollectionReader in org.jmol.adapter.readers.cifModifier and TypeClassDescriptionclass
A very simple Binary CIF file reader extention of MMCifReader extends CifReader.class
Preliminary Cif2 reader.class
A true line-free CIF file reader for CIF files.class
mmCIF files are recognized prior to class creation.class
JmolData 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.Fields in org.jmol.adapter.readers.cif declared as AtomSetCollectionReaderMethods in org.jmol.adapter.readers.cif with parameters of type AtomSetCollectionReaderModifier and TypeMethodDescriptionint
MSRdr.initialize
(AtomSetCollectionReader r, int modDim) MMCifValidationParser.set
(AtomSetCollectionReader reader) -
Uses of AtomSetCollectionReader in org.jmol.adapter.readers.molxyz
Subclasses of AtomSetCollectionReader in org.jmol.adapter.readers.molxyzModifier and TypeClassDescriptionclass
3D onlyclass
A reader for MDLI mol and sdf files.class
Minnesota 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 AtomSetCollectionReader in org.jmol.adapter.readers.more
Subclasses of AtomSetCollectionReader in org.jmol.adapter.readers.moreModifier and TypeClassDescriptionclass
A reader for various AFLOW file types.class
DCD binary trajectory file reader.class
A reader for ChemDraw binary CDX files.class
class
class
A 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 ... class
Amber Coordinate File Reader not a stand-alone reader -- must be after COORD keyword in LOAD commandclass
A reader for Amber Molecular Dynamics topology files -- requires subsequent COORD "xxxx.mdcrd" fileclass
A minimal multi-file reader for TRIPOS SYBYL mol2 files.class
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Uses of AtomSetCollectionReader in org.jmol.adapter.readers.pdb
Subclasses of AtomSetCollectionReader in org.jmol.adapter.readers.pdbModifier and TypeClassDescriptionclass
JmolData file reader, for a modified PDB formatclass
P2N file reader.class
PDB file reader.class
PQR file reader. -
Uses of AtomSetCollectionReader in org.jmol.adapter.readers.pymol
Subclasses of AtomSetCollectionReader in org.jmol.adapter.readers.pymolModifier and TypeClassDescriptionclass
PyMOL PSE (binary Python session) file reader. -
Uses of AtomSetCollectionReader in org.jmol.adapter.readers.quantum
Subclasses of AtomSetCollectionReader in org.jmol.adapter.readers.quantumModifier and TypeClassDescriptionclass
TODO: adf-2007.out causes failure reading basis functions A reader for ADF output.class
A reader for AMS output subclassing the older AdfReader.class
class
CSF file reader based on CIF idea -- fluid property fields.class
A reader for Dgrid BASISFILE data.class
class
class
class
Reader for Gaussian fchk files for vibrational modes, add Freq=(SaveNormalModes,Raman,VibRot) also allows appended freq dataclass
Reader for Gaussian 94/98/03/09 output files.class
Reader for Gaussian Wfn files -- not implemented yetclass
NBO 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 structureclass
Jaguar reader tested for the two samples files in CVS.class
A molecular structure and orbital reader for MolDen files.class
Reads Mopac 2007 GRAPHF output filesclass
General methods for reading molecular orbital data, including embedded output from the NBO program.class
A reader for NWChem 4.6 NWChem is a quantum chemistry program developed at Pacific Northwest National Laboratory.class
Reads ORCA input and output filesclass
Reader for Psi3 output files.class
A reader for Q-Chem 2.1 and 3.2 Q-Chem is a quantum chemistry program developed by Q-Chem, Inc.class
A molecular structure and orbital reader for MolDen files.class
A molecular orbital reader for WebMO files. -
Uses of AtomSetCollectionReader in org.jmol.adapter.readers.simple
Subclasses of AtomSetCollectionReader in org.jmol.adapter.readers.simpleModifier and TypeClassDescriptionclass
TRIPOS simple Alchemy reader.class
A reader for AMPAC output.class
Gaussian 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.class
FoldingAtHome json reader.class
This 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.class
Reads Ghemical ( http://www.uku.fi/~thassine/ghemical) molecular mechanics (*.mm1gp) files.class
Support for .hin, HyperChem's native file format.class
class
class
class
Mopac 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 cellclass
Reads Mopac 93, 6, 7, 2002, or 2009 output filesclass
Reads ORCA input and output filesclass
simple Tinker format requires Tinker:: prefix: load Tinker::mydata.xyz 1/2014 hansonr@stolaf.edu -
Uses of AtomSetCollectionReader in org.jmol.adapter.readers.spartan
Subclasses of AtomSetCollectionReader in org.jmol.adapter.readers.spartanModifier and TypeClassDescriptionclass
class
class
class
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Uses of AtomSetCollectionReader in org.jmol.adapter.readers.xml
Subclasses of AtomSetCollectionReader in org.jmol.adapter.readers.xmlModifier and TypeClassDescriptionclass
A crude ArgusLab .agl file Reader - http://www.planaria-software.com/ Use this reader as a template for adding new XML readers.class
A reader for CambridgeSoft CDXML files.class
An chem3d c3xml readerclass
A CML2 Reader - If passed a bufferedReader (from a file or inline string), we generate a SAX parser and use callbacks to construct an AtomSetCollection.class
class
A Molpro 2005 readerclass
An abstract class accessing MOReader -- currently just for XmlMolproReader only.class
An Odyssey xodydata readerclass
QuantumEspresso XML readerclass
A generic XML reader template -- by itself, does nothing.class
Vasp vasprun.xml readerclass
An XML reader for Materials Studio .xsd files http://accelrys.com/products/materials-studio/ Bob Hanson hansonr@stolaf.edu 6/3/09 -
Uses of AtomSetCollectionReader in org.jmol.adapter.readers.xtal
Subclasses of AtomSetCollectionReader in org.jmol.adapter.readers.xtalModifier and TypeClassDescriptionclass
class
FHI-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).class
Bilbao 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.class
CASTEP (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.class
A reader for TOPOS systre file Crystal Graph Data format.class
A reader for CrystalMaker CMDF binary/text files.class
A reader of OUT and OUTP files for CRYSTAL http://www.crystal.unito.it/class
class
class
Problems identified (Bob Hanson) -- -- Coordinates for the asymmetric unit are conventional.class
A reader for Jana M50+M40 file pairs.class
class
A (preliminary) reader for OPTIMADE resources.class
crude PWmat atom.config reader http://pwmatus.com/manualclass
A reader for SHELX output (RES) files.class
BH note: this reader was never set up to read Z-matrix structures such as benzenev4.1.fdf SIESTA http://www.icmab.es/siesta/class
http://cms.mpi.univie.ac.at/vasp/vasp/CHGCAR_file.html very simple reader of just the header information.class
http://cms.mpi.univie.ac.at/vasp/class
adjusted for AFLOW options - adding element names, environment radius on atom line http://cms.mpi.univie.ac.at/vasp/class
A reader for Wein2k DFT files.class
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Uses of AtomSetCollectionReader in org.jmol.adapter.smarter
Methods in org.jmol.adapter.smarter with parameters of type AtomSetCollectionReaderModifier and TypeMethodDescriptionint
MSInterface.initialize
(AtomSetCollectionReader r, int modDim) XtalSymmetry.set
(AtomSetCollectionReader reader) static Object
SmarterJmolAdapter.staticGetAtomSetCollection
(AtomSetCollectionReader a) Constructors in org.jmol.adapter.smarter with parameters of type AtomSetCollectionReaderModifierConstructorDescriptionAtomSetCollection
(String fileTypeName, AtomSetCollectionReader reader, AtomSetCollection[] array, Lst<?> list)