# Uses of Class
org.jmol.adapter.smarter.AtomSetCollectionReader

Packages that use AtomSetCollectionReader
Package
Description
org.jmol.adapter.readers.cif
org.jmol.adapter.readers.molxyz
org.jmol.adapter.readers.more
org.jmol.adapter.readers.pdb
org.jmol.adapter.readers.pymol
org.jmol.adapter.readers.quantum
org.jmol.adapter.readers.simple
org.jmol.adapter.readers.spartan
org.jmol.adapter.readers.xml
org.jmol.adapter.readers.xtal
org.jmol.adapter.smarter

## Uses of AtomSetCollectionReader in org.jmol.adapter.readers.cif

Subclasses of AtomSetCollectionReader in org.jmol.adapter.readers.cif
Modifier and Type
Class
Description
`class`
`BCIFReader`
A very simple Binary CIF file reader extention of MMCifReader extends CifReader.
`class`
`Cif2Reader`
Preliminary Cif2 reader.
`class`
`CifReader`
A true line-free CIF file reader for CIF files.
`class`
`MMCifReader`
mmCIF files are recognized prior to class creation.
`class`
`MMTFReader`
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 AtomSetCollectionReader
Modifier and Type
Field
Description
`protected AtomSetCollectionReader`
MSRdr.`cr`
Methods in org.jmol.adapter.readers.cif with parameters of type AtomSetCollectionReader
Modifier and Type
Method
Description
`int`
MSRdr.`initialize(AtomSetCollectionReader r, int modDim)`
`MMCifValidationParser`
MMCifValidationParser.`set(AtomSetCollectionReader reader)`

## Uses of AtomSetCollectionReader in org.jmol.adapter.readers.molxyz

Subclasses of AtomSetCollectionReader in org.jmol.adapter.readers.molxyz
Modifier and Type
Class
Description
`class`
`Mol3DReader`
3D only
`class`
`MolReader`
A reader for MDLI mol and sdf files.
`class`
`XyzReader`
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.more
Modifier and Type
Class
Description
`class`
`AFLOWReader`
A reader for various AFLOW file types.
`class`
`BinaryDcdReader`
DCD binary trajectory file reader.
`class`
`CDXReader`
A reader for ChemDraw binary CDX files.
`class`
`ForceFieldReader`
`class`
`GromacsReader`
`class`
`JcampdxReader`
A preliminary reader for JCAMP-DX files having ##$MODELS= and ##$PEAKS= records Designed by Robert Lancashire and Bob Hanson specifications (by example here): ##$MODELS= <Models> acetophenone DSViewer 3D 0 17 17 0 0 0 0 0 0 0 0999 V2000 ...
`class`
`MdCrdReader`
Amber Coordinate File Reader not a stand-alone reader -- must be after COORD keyword in LOAD command
`class`
`MdTopReader`
A reader for Amber Molecular Dynamics topology files -- requires subsequent COORD "xxxx.mdcrd" file
`class`
`Mol2Reader`
A minimal multi-file reader for TRIPOS SYBYL mol2 files.
`class`
`TlsDataOnlyReader`

## Uses of AtomSetCollectionReader in org.jmol.adapter.readers.pdb

Subclasses of AtomSetCollectionReader in org.jmol.adapter.readers.pdb
Modifier and Type
Class
Description
`class`
`JmolDataReader`
JmolData file reader, for a modified PDB format This class also holds pseudo-static methods for spin
`class`
`P2nReader`
P2N file reader.
`class`
`PdbReader`
PDB file reader.
`class`
`PqrReader`
PQR file reader.

## Uses of AtomSetCollectionReader in org.jmol.adapter.readers.pymol

Subclasses of AtomSetCollectionReader in org.jmol.adapter.readers.pymol
Modifier and Type
Class
Description
`class`
`PyMOLReader`
PyMOL PSE (binary Python session) file reader.

## Uses of AtomSetCollectionReader in org.jmol.adapter.readers.quantum

Subclasses of AtomSetCollectionReader in org.jmol.adapter.readers.quantum
Modifier and Type
Class
Description
`class`
`AdfReader`
TODO: adf-2007.out causes failure reading basis functions A reader for ADF output.
`class`
`AmsReader`
A reader for AMS output subclassing the older AdfReader.
`class`
`BasisFunctionReader`
`class`
`CsfReader`
CSF file reader based on CIF idea -- fluid property fields.
`class`
`DgridReader`
A reader for Dgrid BASISFILE data.
`class`
`GamessReader`
`class`
`GamessUKReader`
`class`
`GamessUSReader`
`class`
`GaussianFchkReader`
Reader for Gaussian fchk files for vibrational modes, add Freq=(SaveNormalModes,Raman,VibRot) also allows appended freq data
`class`
`GaussianReader`
Reader for Gaussian 94/98/03/09 output files.
`class`
`GaussianWfnReader`
Reader for Gaussian Wfn files -- not implemented yet
`class`
`GenNBOReader`
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 structure
`class`
`JaguarReader`
Jaguar reader tested for the two samples files in CVS.
`class`
`MoldenReader`
A molecular structure and orbital reader for MolDen files.
`class`
`MopacGraphfReader`
Reads Mopac 2007 GRAPHF output files
`class`
`MOReader`
General methods for reading molecular orbital data, including embedded output from the NBO program.
`class`
`NWChemReader`
A reader for NWChem 4.6 NWChem is a quantum chemistry program developed at Pacific Northwest National Laboratory.
`class`
`OrcaReader`
Reads ORCA input and output files
`class`
`PsiReader`
Reader for Psi3 output files.
`class`
`QchemReader`
A reader for Q-Chem 2.1 and 3.2 Q-Chem is a quantum chemistry program developed by Q-Chem, Inc.
`class`
`QCJSONReader`
A molecular structure and orbital reader for MolDen files.
`class`
`WebMOReader`
A molecular orbital reader for WebMO files.

## Uses of AtomSetCollectionReader in org.jmol.adapter.readers.simple

Subclasses of AtomSetCollectionReader in org.jmol.adapter.readers.simple
Modifier and Type
Class
Description
`class`
`AlchemyReader`
TRIPOS simple Alchemy reader.
`class`
`AmpacReader`
A reader for AMPAC output.
`class`
`CubeReader`
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`
`FAHReader`
FoldingAtHome json reader.
`class`
`FoldingXyzReader`
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`
`GhemicalMMReader`
Reads Ghemical ( http://www.uku.fi/~thassine/ghemical) molecular mechanics (*.mm1gp) files.
`class`
`HyperChemReader`
Support for .hin, HyperChem's native file format.
`class`
`InputReader`
`class`
`JmeReader`
`class`
`JSONReader`
`class`
`MopacArchiveReader`
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 cell
`class`
`MopacReader`
Reads Mopac 93, 6, 7, 2002, or 2009 output files
`class`
`OrcaReader`
Reads ORCA input and output files
`class`
`TinkerReader`
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.spartan
Modifier and Type
Class
Description
`class`
`OdysseyReader`
`class`
`SpartanInputReader`
`class`
`SpartanReader`
`class`
`SpartanSmolReader`

## Uses of AtomSetCollectionReader in org.jmol.adapter.readers.xml

Subclasses of AtomSetCollectionReader in org.jmol.adapter.readers.xml
Modifier and Type
Class
Description
`class`
`XmlArgusReader`
A crude ArgusLab .agl file Reader - http://www.planaria-software.com/ Use this reader as a template for adding new XML readers.
`class`
`XmlCdxReader`
A reader for CambridgeSoft CDXML files.
`class`
`XmlChem3dReader`
An chem3d c3xml reader
`class`
`XmlCmlReader`
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`
`XmlMagResReader`
`class`
`XmlMolproReader`
A Molpro 2005 reader
`class`
`XmlMOReader`
An abstract class accessing MOReader -- currently just for XmlMolproReader only.
`class`
`XmlNmrmlReader`
A reader for the structure part of an nmrML file
`class`
`XmlOdysseyReader`
An Odyssey xodydata reader
`class`
`XmlQEReader`
QuantumEspresso XML reader
`class`
`XmlReader`
A generic XML reader template -- by itself, does nothing.
`class`
`XmlVaspReader`
Vasp vasprun.xml reader
`class`
`XmlXsdReader`
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.xtal
Modifier and Type
Class
Description
`class`
`AbinitReader`
`class`
`AimsReader`
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`
`BilbaoReader`
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`
`CastepReader`
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`
`CgdReader`
A reader for TOPOS systre file Crystal Graph Data format.
`class`
`CmdfReader`
A reader for CrystalMaker CMDF binary/text files.
`class`
`CrystalReader`
A reader of OUT and OUTP files for CRYSTAL http://www.crystal.unito.it/
`class`
`DmolReader`
`class`
`EspressoReader`
`class`
`FSGOutputReader`
A reader for JSON output from the FINDSPINGROUP program.
`class`
`GulpReader`
Problems identified (Bob Hanson) -- -- Coordinates for the asymmetric unit are conventional.
`class`
`JanaReader`
A reader for Jana M50+M40 file pairs.
`class`
`MagresReader`
`class`
`OptimadeReader`
A (preliminary) reader for OPTIMADE resources.
`class`
`PWmatReader`
crude PWmat atom.config reader http://pwmatus.com/manual
`class`
`ShelxReader`
A reader for SHELX output (RES) files.
`class`
`SiestaReader`
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`
`VaspChgcarReader`
http://cms.mpi.univie.ac.at/vasp/vasp/CHGCAR_file.html very simple reader of just the header information.
`class`
`VaspOutcarReader`
http://cms.mpi.univie.ac.at/vasp/
`class`
`VaspPoscarReader`
adjusted for AFLOW options - adding element names, environment radius on atom line http://cms.mpi.univie.ac.at/vasp/
`class`
`Wien2kReader`
A reader for Wein2k DFT files.
`class`
`XcrysdenReader`

## Uses of AtomSetCollectionReader in org.jmol.adapter.smarter

Methods in org.jmol.adapter.smarter with parameters of type AtomSetCollectionReader
Modifier and Type
Method
Description
`int`
MSInterface.`initialize(AtomSetCollectionReader r, int modDim)`
`protected void`
XtalSymmetry.FileSymmetry.`preSymmetryFinalizeMoments(AtomSetCollectionReader acr, AtomSetCollection asc, String spinFrameStr, String spinFrameExt)`
Scale the magnetic moments of magCIF and spinCIF files.
`XtalSymmetry`
XtalSymmetry.`set(AtomSetCollectionReader reader)`
`static Object`
SmarterJmolAdapter.`staticGetAtomSetCollection(AtomSetCollectionReader a)`
Constructors in org.jmol.adapter.smarter with parameters of type AtomSetCollectionReader
Modifier
Constructor
Description
``
`AtomSetCollection(String fileTypeName, AtomSetCollectionReader reader, AtomSetCollection[] array, Lst<?> list)`