Constant Field Values

Contents

org.jmol.*

  • org.jmol.adapter.readers.more.ForceFieldReader 
    Modifier and Type Constant Field Value
    private static final String ffTypes " CA CB CC CD CE CF CG CH CI CJ CK CM CN CP CQ CR CT CV CW HA HP HC HO HS HW LP NA NB NC NT OH OS OW SH AH BH HT HY AC BC CS OA OB OE OT dw hc hi hn ho hp hs hw hscp htip ca cg ci cn co coh cp cr cs ct c3h c3m c4h c4m na nb nh nho nh+ ni nn np npc nr nt nz oc oe oh op oscp otip sc sh sp br cl ca+ ar si lp nu sz oz az pz ga ge tioc titd li+ na+ rb+ cs+ mg2+ ca2+ ba2+ cu2+ cl- br- so4 sy oy ay ayt nac+ mg2c fe2c mn4c mn3c co2c ni2c lic+ pd2+ ti4c sr2c ca2c cly- hocl py vy nh4+ so4y lioh naoh koh foh cloh beoh al CE1 CF1 CF2 CF3 CG CD2 CH1E CH2E CH3E CM CP3 CPH1 CPH2 CQ66 CR55 CR56 CR66 CS66 CT CT3 CT4 CUA1 CUA2 CUA3 CUY1 CUY2 HA HC HMU HO HT LP NC NC2 NO2 NP NR1 NR2 NR3 NR55 NR56 NR66 NT NX OA OAC OC OE OH2 OK OM OS OSH OSI OT OW PO3 PO4 PT PUA1 PUY1 SE SH1E SK SO1 SO2 SO3 SO4 ST ST2 ST2 br br- br1 cl cl- cl1 cl12 cl13 cl14 cl1p ca+ cu+2 fe+2 mg+2 zn+2 cs+ li+ na+ rb+ al4z si si4 si4c si4z ar he kr ne xe dw hi hw ca cg ci co coh cp cr cs ct ct3 na nb nh nho ni no np nt nt2 nz oa oc oh op os ot sp bt cl\' si4l si5l si5t si6 si6o si\' br ca cc cd ce cf cl cp cq cu cv cx cy ha hc hn ho hp hs na nb nc nd nh oh os pb pc pd pe pf px py sh ss sx sy hn2 ho2 cz oo oz si sio hsi osi "
    private static final String secondCharOnly " AH BH AC BC "
    private static final String specialTypes " IM IP sz az sy ay ayt "
    private static final String twoChar " al al4z ar ba2+ beoh br br- br1 ca+ ca2+ ca2c cl cl\' cl- cl1 cl12 cl13 cl14 cl1p cloh cly- co2c cs+ cu+2 cu2+ fe+2 fe2c ga ge he kr li+ lic+ lioh lp LP mg+2 mg2+ mg2c mn3c mn4c na+ nac+ naoh ne ni2c nu pd2+ rb+ si si\' si4 si4c si4l si4z si5l si5t si6 si6o sio sr2c ti4c tioc titd xe zn+2 "
  • org.jmol.adapter.readers.pdb.PdbReader 
    Modifier and Type Constant Field Value
    private static final float _8PI2_ 78.95683288574219f
    private static final String lineOptions "ATOM HETATM MODEL CONECT HELIX SHEET TURN HET HETNAM ANISOU SITE CRYST1 SCALE1 SCALE2 SCALE3 EXPDTA FORMUL REMARK HEADER COMPND SOURCE TITLE SEQADV "
    private static final int MODE_HEX 1
    private static final int MODE_HYBRID36 2
    private static final int MODE_PDB 0
    private static final float RAD_PER_DEG 0.01745329238474369f
  • org.jmol.adapter.readers.quantum.CsfReader 
    Modifier and Type Constant Field Value
    private static final byte ANUM 2
    private static final byte BFXN_ANGL 6
    private static final byte BTYPE 1
    private static final byte CHRG 3
    private static final byte COEF_INDICES 5
    private static final byte CONTRACTIONS 8
    private static final byte DIPOLE 3
    private static final byte EIG_VAL 1
    private static final byte EIG_VEC 3
    private static final byte EIG_VEC_COMPRESSED 4
    private static final byte GTO_EXP 9
    private static final byte ID -1
    private static final byte MO_OCC 2
    private static final byte NORMAL_MODE 1
    private static final byte objCls1 1
    private static final byte objCls2 3
    private static final byte objID1 2
    private static final byte objID2 4
    private static final byte PCHRG 5
    private static final byte SHELL 10
    private static final byte STO_EXP 7
    private static final byte SYM 1
    private static final byte VIB_ENERGY 2
    private static final byte XYZ 4
  • org.jmol.adapter.readers.quantum.GaussianReader 
    Modifier and Type Constant Field Value
    private static final int STD_ORIENTATION_ATOMIC_NUMBER_OFFSET 1
  • org.jmol.adapter.readers.quantum.JaguarReader 
    Modifier and Type Constant Field Value
    private static final float ROOT3 1.7320507764816284f
  • org.jmol.adapter.readers.quantum.org.jmol.adapter.readers.quantum.MopacSlaterReader 
    Modifier and Type Constant Field Value
    protected static final float MIN_COEF 9.999999747378752E-5f
  • org.jmol.adapter.readers.quantum.MOReader 
    Modifier and Type Constant Field Value
    private static final String DC_LIST "(D1) (D4) (D6) (D2) (D3) (D5)"
    private static final String DS_LIST "(D5) (D2) (D3) (D4) (D1)"
    private static final String FS_LIST "(F1) (F2) (F3) (F4) (F5) (F6) (F7)"
    protected final int HEADER_GAMESS_OCCUPANCIES 2
    protected final int HEADER_GAMESS_ORIGINAL 1
    protected final int HEADER_GAMESS_UK_MO 3
    protected final int HEADER_NONE 0
    private static final String P_LIST "(PX) (PY) (PZ)"
  • org.jmol.adapter.readers.quantum.org.jmol.adapter.readers.quantum.SlaterReader 
    Modifier and Type Constant Field Value
    private static final double _1_4pi 0.07957747154594767
  • org.jmol.adapter.readers.simple.FAHReader 
    Modifier and Type Constant Field Value
    static final String note " -- FAH:: is required for Frame files but not the Top file.\n -- automatic calculation of structure using DSSP\n -- Both files are required; three load options:\n \n LOAD FILES \"ViewerTop.json\" + \"ViewerFrame22.json\" // explicit joining to two files\n \n LOAD ViewerTop.json; \n LOAD XYZ FAH::ViewerFrame22.json // first the atoms, then the coordinates\n \n LOAD FAH::ViewerFrame22.json // just the coordinates with associated ViewerTop.json assumed present\n \n -- Subsequent calls to LOAD XYZ will replace coordinates and recalculate DSSP only.\n\n LOAD ViewerTop.json; \n LOAD XYZ FAH::ViewerFrame0.json \n delay 1.0\n LOAD XYZ FAH::ViewerFrame22.json \n \n"
  • org.jmol.adapter.readers.xtal.CastepReader 
    Modifier and Type Constant Field Value
    private static final float RAD_TO_DEG 57.295780181884766f
    private static final double TWOPI 6.283185307179586
  • org.jmol.adapter.readers.xtal.CgdReader 
    Modifier and Type Constant Field Value
    private static final String SG_ALIASES ";P2=P121;P21=P1211;C2=C121;A2=A121;I2=I121;Pm=P1m1;Pc=P1c1;Pn=P1n1;Pa=P1a1;Cm=C1m1;Am=A1m1;Im=I1m1;Cc=C1c1;An=A1n1;Ia=I1a1;Aa=A1a1;Cn=C1n1;Ic=I1c1;P2/m=P12/m1;P21/m=P121/m1;C2/m=C12/m1;A2/m=A12/m1;I2/m=I12/m1;P2/c=P12/c1;P2/n=P12/n1;P2/a=P12/a1;P21/c=P121/c1;P21/n=P121/n1;P21/a=P121/a1;C2/c=C12/c1;A2/n=A12/n1;I2/a=I12/a1;A2/a=A12/a1;C2/n=C12/n1;I2/c=I12/c1;Pm3=Pm-3;Pn3=Pn-3;Fm3=Fm-3;Fd3=Fd-3;Im3=Im-3;Pa3=Pa-3;Ia3=Ia-3;Pm3m=Pm-3m;Pn3n=Pn-3n;Pm3n=Pm-3n;Pn3m=Pn-3m;Fm3m=Fm-3m;Fm3c=Fm-3c;Fd3m=Fd-3m;Fd3c=Fd-3c;Im3m=Im-3m;Ia3d=Ia-3d;"
  • org.jmol.adapter.readers.xtal.CrystalReader 
    Modifier and Type Constant Field Value
    private static final int STATE_FREQ 6
    private static final int STATE_INPUT 1
    private static final int STATE_INPUT_FROM 2
    private static final int STATE_NONE 0
    private static final int STATE_OPT_FINAL 5
    private static final int STATE_OPT_POINT 4
    private static final int STATE_WAVEFUNCTION 3
  • org.jmol.adapter.readers.xtal.JanaReader 
    Modifier and Type Constant Field Value
    static final int CELL 5
    static final int END 35
    static final int LATT 20
    static final int NDIM 10
    static final int QI 15
    static final String records "tit cell ndim qi lat sym spg end wma"
    static final int SPG 30
    static final int SYM 25
    static final int TITLE 0
    public static final String U_LIST "U11U22U33U12U13U23UISO"
    static final int WMATRIX 40
  • org.jmol.adapter.readers.xtal.MagresReader 
    Modifier and Type Constant Field Value
    private static final int BLOCK_ATOMS 1
    private static final int BLOCK_CALC 0
    private static final int BLOCK_MAGRES 2
    private static final int BLOCK_NEW -2
    private static final int BLOCK_NONE -1
  • org.jmol.adapter.readers.xtal.ShelxReader 
    Modifier and Type Constant Field Value
    private static final String unsupportedRecordTypes ";ZERR;DISP;UNIT;LAUE;REM;MORE;TIME;HKLF;OMIT;SHEL;BASF;TWIN;EXTI;SWAT;HOPE;MERG;SPEC;RESI;MOVE;ANIS;AFIX;HFIX;FRAG;FEND;EXYZ;EXTI;EADP;EQIV;CONN;PART;BIND;FREE;DFIX;DANG;BUMP;SAME;SADI;CHIV;FLAT;DELU;SIMU;DEFS;ISOR;NCSY;SUMP;L.S.;CGLS;BLOC;DAMP;STIR;WGHT;FVAR;BOND;CONF;MPLA;RTAB;HTAB;LIST;ACTA;SIZE;TEMP;WPDB;FMAP;GRID;PLAN;MOLE;"
  • org.jmol.adapter.readers.xtal.SiestaReader 
    Modifier and Type Constant Field Value
    private static final double ACF_ANG 1.0
    private static final double ACF_BOHR 0.529177
    private static final double ACF_M 1.0E10
    private static final double ACF_NM 10.0
    private final int STATE_INPUT 1
    private final int STATE_OUTPUT 2
    private final int STATE_UNKNOWN 0
  • org.jmol.adapter.readers.xtal.Wien2kReader 
    Modifier and Type Constant Field Value
    private final String cxyz " x y z"
  • org.jmol.dssx.DSSR1 
    Modifier and Type Constant Field Value
    private static final String DSSR_PATHS "..bulges.nts_long..coaxstacks.stems.pairs.nt*..hairpins.nts_long..hbonds.atom1_id;atom2_id..helices.pairs.nt*..iloops.nts_long..isocanonpairs.nt*..junctions.nts_long..kissingloops.hairpins.nts_long..multiplets.nts_long..nonstack.nts_long..nts.nt_id..pairs.nt*..sssegments.nts_long..stacks.nts_long..stems.pairs.nt*.."
  • org.jmol.export.___Exporter 
    Modifier and Type Constant Field Value
    protected static final float degreesPerRadian 57.295780181884766f
  • org.jmol.export._ObjExporter 
    Modifier and Type Constant Field Value
    private static final boolean debug false
  • org.jmol.minimize.forcefield.org.jmol.minimize.forcefield.Calculations 
    Modifier and Type Constant Field Value
    static final int CALC_ANGLE 1
    static final int CALC_DISTANCE 0
    static final int CALC_ES 6
    static final int CALC_MAX 7
    static final int CALC_OOP 4
    static final int CALC_STRETCH_BEND 3
    static final int CALC_TORSION 2
    static final int CALC_VDW 5
    public static final double DEG_TO_RAD 0.017453292519943295
    static final double KCAL_TO_KJ 4.1868
    private static final double PI_OVER_2 1.5707963267948966
    public static final double RAD_TO_DEG 57.29577951308232
    private static final double TWO_PI 6.283185307179586
  • org.jmol.minimize.forcefield.org.jmol.minimize.forcefield.CalculationsMMFF 
    Modifier and Type Constant Field Value
    public static final int DA_D 68
    public static final int DA_DA 133
    static final double FPAR 143.9325
  • org.jmol.minimize.forcefield.org.jmol.minimize.forcefield.CalculationsUFF 
    Modifier and Type Constant Field Value
    static final double KCAL22 92.1096
    static final double KCAL332 1390.2842991599998
    static final double KCAL44 184.2192
    static final double KCAL6 25.1208
    static final double KCAL644 2696.8016159999997
    static final int PAR_D 3
    static final int PAR_HARD 9
    static final int PAR_R 0
    static final int PAR_RADIUS 10
    static final int PAR_THETA 1
    static final int PAR_U 7
    static final int PAR_V 6
    static final int PAR_X 2
    static final int PAR_XI 8
    static final int PAR_Z 5
    static final int PAR_ZETA 4
  • org.jmol.minimize.forcefield.ForceField 
    Modifier and Type Constant Field Value
    public static final int ABI_IJ 3
    public static final int ABI_JK 4
    static final int EANGLE 4
    static final int EBOND 2
    static final int EELECTROSTATIC 128
    static final int ENERGY 1
    static final int EOOP 32
    static final int ESTRBND 8
    static final int ETORSION 16
    static final int EVDW 64
    public static final int R3 0
    public static final int R4 1
    public static final int R5 2
    public static final int Raromatic 3
    public static final int TBI_AB 4
    public static final int TBI_BC 5
    public static final int TBI_CD 6
  • org.jmol.minimize.forcefield.ForceFieldMMFF 
    Modifier and Type Constant Field Value
    private static final int A4_BNDK 123
    private static final int A4_CHRG 124
    private static final int A4_SB 125
    private static final int A4_SBDEF 126
    private static final int A4_VDW 122
    private static final int KEY_BNDK 0
    private static final int KEY_OOP 6
    private static final int KEY_PBCI 0
    private static final int KEY_SBDEF 0
    private static final int KEY_VDW 0
    private static final String names "END.BCI.CHG.ANG.NDK.OND.OOP.TBN.FSB.TOR.VDW."
    private static final int TYPE_ANGLE 5
    private static final int TYPE_BNDK 546
    private static final int TYPE_BOND 3
    private static final int TYPE_CHRG 34
    private static final int TYPE_OOP 13
    private static final int TYPE_PBCI 1
    private static final int TYPE_SB 21
    private static final int TYPE_SBDEF 37
    private static final int TYPE_TORSION 9
    private static final int TYPE_VDW 17
  • org.jmol.minimize.forcefield.ForceFieldUFF 
    Modifier and Type Constant Field Value
    private static final int PT_CHARGE 5
    private static final int PT_CONNECT 6
    private static final int PT_ELEMENT 2
    private static final int TOKEN_AROMATIC 3
    private static final int TOKEN_ELEMENT_ALLYLIC 6
    private static final int TOKEN_ELEMENT_CHARGED 1
    private static final int TOKEN_ELEMENT_CONNECTED 2
    private static final int TOKEN_ELEMENT_ONLY 0
    private static final int TOKEN_ELEMENT_SP 4
  • org.jmol.minimize.forcefield.org.jmol.minimize.forcefield.MMFFAngleCalc 
    Modifier and Type Constant Field Value
    static final double CB -0.006981317007977318
  • org.jmol.minimize.forcefield.org.jmol.minimize.forcefield.MMFFDistanceCalc 
    Modifier and Type Constant Field Value
    static final double CS -2.0
    static final double CS2 2.3333333333333335
    static final double FSTRETCH 71.96625
  • org.jmol.minimize.forcefield.org.jmol.minimize.forcefield.MMFFESCalc 
    Modifier and Type Constant Field Value
    private static final double BUFF 0.05
  • org.jmol.minimize.forcefield.org.jmol.minimize.forcefield.MMFFOOPCalc 
    Modifier and Type Constant Field Value
    static final double FOOP 71.96568080495746
    static final double FOOPD 2.5120761569715815
  • org.jmol.modelsetbio.AminoMonomer 
    Modifier and Type Constant Field Value
    private static final float beta 0.296705961227417f
    private static final byte C 3
    private static final byte CA 0
    private static final byte N 2
    private static final byte O 1
    private static final byte OT 4
  • org.jmol.modelsetbio.AminoPolymer 
    Modifier and Type Constant Field Value
    private static final float maxHbondAlphaDistance 9.0f
    private static final float maxHbondAlphaDistance2 81.0f
    private static final float minimumHbondDistance2 0.25f
  • org.jmol.modelsetbio.BioExt 
    Modifier and Type Constant Field Value
    private static final String aaPlus "LYSN"
    private static final String aaSp2 "ARGN;ASNN;ASNO;ASPO;GLNN;GLNO;GLUO;HISN;HISC;PHECTRPC;TRPN;TYRC"
    private static final String aaSp21 "ARGNE;ARGNH1;ASNNH2;GLNNE2;TRPNE1;HISNE2"
    private static final String naNoH "A3;A1;C3;G3;I3"
  • org.jmol.modelsetbio.BioPolymer 
    Modifier and Type Constant Field Value
    protected static final int TYPE_AMINO 1
    protected static final int TYPE_CARBOHYDRATE 3
    protected static final int TYPE_NOBONDING 0
    protected static final int TYPE_NUCLEIC 2
  • org.jmol.modelsetbio.BioResolver 
    Modifier and Type Constant Field Value
    private static final String allCarbohydrates ",[AHR],[ALL],[AMU],[ARA],[ARB],[BDF],[BDR],[BGC],[BMA],[FCA],[FCB],[FRU],[FUC],[FUL],[GAL],[GLA],[GLC],[GXL],[GUP],[LXC],[MAN],[RAM],[RIB],[RIP],[XYP],[XYS],[CBI],[CT3],[CTR],[CTT],[LAT],[MAB],[MAL],[MLR],[MTT],[SUC],[TRE],[GCU],[MTL],[NAG],[NDG],[RHA],[SOR],[SOL],[SOE],[XYL],[A2G],[LBT],[NGA],[SIA],[SLB],[AFL],[AGC],[GLB],[NAN],[RAA]"
  • org.jmol.modelsetbio.NucleicMonomer 
    Modifier and Type Constant Field Value
    private static final byte C1P 25
    private static final byte C2 5
    private static final byte C2P 26
    private static final byte C3P 22
    private static final byte C4 7
    private static final byte C4P 27
    private static final byte C5 3
    private static final byte C5P 29
    static final byte C6 1
    private static final byte C8 10
    private static final byte H3T 20
    private static final byte H5T 18
    private static final byte N1 4
    private static final byte N2 17
    private static final byte N3 6
    private static final byte N4 14
    private static final byte N6 16
    private static final byte N7 9
    private static final byte N9 11
    private static final byte NP 15
    private static final byte O1P 23
    private static final byte O2 8
    private static final byte O2P 24
    private static final byte O2Pr 2
    private static final byte O3P 21
    private static final byte O4 12
    private static final byte O4P 28
    private static final byte O5P 19
    private static final byte O6 13
  • org.jmol.modelsetbio.PhosphorusMonomer 
    Modifier and Type Constant Field Value
    protected static final byte P 0
  • org.jmol.quantum.mo.DataAdder7F 
    Modifier and Type Constant Field Value
    static final double c0_xxz_yyz 0.6708203932499369
    static final double c1n_xxy 0.27386127875258304
    static final double c1n_yyy 0.6123724356957945
    static final double c1n_yzz 1.0954451150103321
    static final double c1p_xxx 0.6123724356957945
    static final double c1p_xyy 0.27386127875258304
    static final double c1p_xzz 1.0954451150103321
    static final double c2p_xxz_yyz 0.8660254037844386
    static final double c3n_xxy 1.0606601717798214
    static final double c3n_yyy 0.7905694150420949
    static final double c3p_xxx 0.7905694150420949
    static final double c3p_xyy 1.0606601717798214
  • org.jmol.thread.JmolThread 
    Modifier and Type Constant Field Value
    protected static final int CHECK1 1
    protected static final int CHECK2 2
    protected static final int CHECK3 3
    protected static final int FINISH -2
    protected static final int INIT -1
    protected static final int MAIN 0
  • org.jmol.viewer.binding.Binding 
    Modifier and Type Constant Field Value
    public static final int ALT 8
    public static final int BUTTON_MASK 28
    public static final int BUTTON_MODIFIER_MASK 63
    public static final int CLICK 32768
    public static final int COUNT_MASK 768
    public static final int CTRL 2
    public static final int CTRL_ALT 10
    public static final int CTRL_SHIFT 3
    public static final int DOUBLE 512
    public static final int DOWN 4096
    public static final int DRAG 8192
    public static final int LEFT 16
    public static final int MAC_COMMAND 20
    public static final int MIDDLE 8
    public static final int MODE_MASK 61440
    public static final int RIGHT 4
    public static final int SHIFT 1
    public static final int SINGLE 256
    public static final int UP 16384
    public static final int WHEEL 32

org.openscience.*

  • org.openscience.jmol.app.jmolpanel.console.AppConsole 
    Modifier and Type Constant Field Value
    public static final String ALL_BUTTONS "Editor Variables Clear History State UndoRedo Close Font Help"
  • org.openscience.jmol.app.webexport.Test 
    Modifier and Type Constant Field Value
    private static final long serialVersionUID 1L
  • org.openscience.jmol.app.webexport.WebExport 
    Modifier and Type Constant Field Value
    static final String chemappsPath "http://chemapps.stolaf.edu/jmol/jsmol"
    private static final int IN_JMOL 1
    private static final int STAND_ALONE 0
  • org.openscience.jvxl.Jvxl 
    Modifier and Type Constant Field Value
    private static final String VERSION "JVXL.java Version 1.0"