Constant Field Values

Contents

org.jmol.*

  • org.jmol.adapter.readers.more.ForceFieldReader 
    Modifier and Type Constant Field Value
    private static final java.lang.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 java.lang.String secondCharOnly " AH BH AC BC "
    private static final java.lang.String specialTypes " IM IP sz az sy ay ayt "
    private static final java.lang.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 java.lang.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 java.lang.String DC_LIST "(D1) (D4) (D6) (D2) (D3) (D5)"
    private static final java.lang.String DS_LIST "(D5) (D2) (D3) (D4) (D1)"
    private static final java.lang.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 java.lang.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.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 java.lang.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.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 java.lang.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 java.lang.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 java.lang.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.Wien2kReader 
    Modifier and Type Constant Field Value
    private final java.lang.String cxyz " x y z"
  • org.jmol.dssx.DSSR1 
    Modifier and Type Constant Field Value
    private static final java.lang.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 2
    static final int CALC_TORSION 3
    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 java.lang.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 java.lang.String aaPlus "LYSN"
    private static final java.lang.String aaSp2 "ARGN;ASNN;ASNO;ASPO;GLNN;GLNO;GLUO;HISN;HISC;PHECTRPC;TRPN;TYRC"
    private static final java.lang.String aaSp21 "ARGNE;ARGNH1;ASNNH2;GLNNE2;TRPNE1;HISNE2"
    private static final java.lang.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 java.lang.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.MepCalculation 
    Modifier and Type Constant Field Value
    protected static final int E_MINUS_D 3
    protected static final int E_MINUS_D_OVER_2 1
    protected static final int ONE_OVER_D 0
    protected static final int ONE_OVER_ONE_PLUS_D 2
  • org.jmol.quantum.MOCalculation 
    Modifier and Type Constant Field Value
    private static final double CUT -50.0
    private static final double ROOT3 1.7320507764816284
  • org.jmol.quantum.NciCalculation 
    Modifier and Type Constant Field Value
    private static final double NO_VALUE 100.0
    private static final int TYPE_ALL 0
    private static final int TYPE_INTER 2
    private static final int TYPE_INTRA 1
    private static final int TYPE_LIGAND 3
  • org.jmol.quantum.NMRCalculation 
    Modifier and Type Constant Field Value
    private static final double DIPOLAR_FACTOR 1054.5717253362893
    private static final double e_charge 1.60217646E-19
    private static final double h_bar_planck 1.0545717253362894E-34
    private static final double h_planck 6.62606957E-34
    private static final double J_FACTOR 0.0167840302932219
    private static final int MAGNETOGYRIC_RATIO 1
    private static final double Q_FACTOR 2.349647144641375E8
    private static final int QUADRUPOLE_MOMENT 2
    private static final java.lang.String resource "nmr_data.txt"
  • org.jmol.quantum.QS 
    Modifier and Type Constant Field Value
    public static final java.lang.String CANONICAL_DC_LIST "DXX DYY DZZ DXY DXZ DYZ"
    public static final java.lang.String CANONICAL_DS_LIST "d0 d1+ d1- d2+ d2-"
    public static final java.lang.String CANONICAL_FC_LIST "XXX YYY ZZZ XYY XXY XXZ XZZ YZZ YYZ XYZ"
    public static final java.lang.String CANONICAL_FS_LIST "f0 f1+ f1- f2+ f2- f3+ f3-"
    public static final int DC 4
    public static final int DS 3
    public static final int FC 6
    public static final int FS 5
    public static final int GC 8
    public static final int GS 7
    public static final int HC 10
    public static final int HS 9
    public static final int IC 12
    public static final int IS 11
    private static final int MAXID 13
    public static final int P 1
    public static final int S 0
    public static final int SP 2
  • org.jmol.quantum.QuantumCalculation 
    Modifier and Type Constant Field Value
    protected static final float bohr_per_angstrom 1.8897161483764648f
  • org.jmol.shape.Axes 
    Modifier and Type Constant Field Value
    private static final float MIN_AXIS_LEN 1.5f
  • org.jmol.shape.Echo 
    Modifier and Type Constant Field Value
    private static final short COLOR 10
    private static final java.lang.String FONTFACE "Serif"
    private static final int FONTSIZE 20
  • org.jmol.shape.Frank 
    Modifier and Type Constant Field Value
    static final java.lang.String defaultFontName "SansSerif"
    static final int defaultFontSize 16
    static final java.lang.String defaultFontStyle "Plain"
    public static final int frankMargin 4
  • org.jmol.shape.Hover 
    Modifier and Type Constant Field Value
    private static final java.lang.String FONTFACE "SansSerif"
    private static final int FONTSIZE 12
    private static final java.lang.String FONTSTYLE "Plain"
  • org.jmol.shape.Mesh 
    Modifier and Type Constant Field Value
    public static final java.lang.String PREVIOUS_MESH_ID "+PREVIOUS_MESH+"
  • org.jmol.shape.MeshCollection 
    Modifier and Type Constant Field Value
    public static final java.lang.String PREVIOUS_MESH_ID "+PREVIOUS_MESH+"
  • org.jmol.shape.Shape 
    Modifier and Type Constant Field Value
    public static final float RADIUS_MAX 4.0f
  • org.jmol.shape.Sticks 
    Modifier and Type Constant Field Value
    private static final int MAX_BOND_CLICK_DISTANCE_SQUARED 100
  • org.jmol.symmetry.org.jmol.symmetry.PointGroup 
    Modifier and Type Constant Field Value
    private static final int ATOM_COUNT_MAX 100
    private static final int c2 16
    private static final int c3 17
    private static final int c4 18
    private static final int c5 19
    private static final int c6 20
    private static final int c8 22
    private static final int firstProper 14
    static final int OPERATION_IMPROPER_AXIS 2
    static final int OPERATION_INVERSION_CENTER 3
    static final int OPERATION_PLANE 0
    static final int OPERATION_PROPER_AXIS 1
    private static final int s10 10
    private static final int s12 12
    private static final int s3 3
    private static final int s4 4
    private static final int s5 5
    private static final int s6 6
    private static final int s8 8
  • org.jmol.symmetry.org.jmol.symmetry.SpaceGroup 
    Modifier and Type Constant Field Value
    private static final int NAME_HALL 5
    private static final int NAME_HM 3
    private static final int NAME_UNK 0
  • org.jmol.symmetry.org.jmol.symmetry.UnitCell 
    Modifier and Type Constant Field Value
    private static final double twoP2 19.739208802178716
  • 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 java.lang.String ALL_BUTTONS "Editor Variables Clear History State UndoRedo Close Font Help"
  • org.openscience.jmol.app.nbo.org.openscience.jmol.app.nbo.NBODialogConfig 
    Modifier and Type Constant Field Value
    protected static final java.lang.String alterHelp "ALTER IA newval (nuclear charge of atom IA)\n IA IB newval (bond length IA-IB)\n IA IB IC newval (valence angle IA-IB-IC)\n IA IB IC ID newval (dihedral IA-IB-IC-IC)\n \nExamples:\n ALTER 10 14. [change atom 10 to Si (Z = 14)]\n ALTER 2 5 1.69 [change R(5-8) bond to 1.69A]\n ALTER 1 2 3 4 180. [change 1-2-3-4 dihedral\n angle to 180 degrees]\n \nNote that \'ALTER 1 2 3 4 180.\' changes ONLYthe 1-2-3-4 dihedral (often giving unphysicaldistorted geometry). Use \'TWIST 1 2 3 4 180.\'to form a proper torsional rotamer.\n \nUse VFILE to determine which angles can besafely ALTERed. Otherwise, the coordinatesmay be re-defined, with unexpected effectson other variables."
    protected static final java.lang.String chbHelp "3CHB IA IB :Lig (form 3-center hyperbond\n IA-IB-Lig to ligand :Lig)\nExamples:\n SHOW W(:NH3)3 (normal-valent W triammine)\n 3CHB 1 2 :NH3 (hyperbonded N-W-N triad)\n SHOW H2O (water monomer)\n 3CHB 2 3 :OH2 (H-bonded water dimer)\n"
    protected static final java.lang.String clipHelp "CLIP IA IB (erase bond between IA, IB)\n \nExample:\n CLIP 1 2 [erase bond between atoms 1,2]\n \nNote that CLIP takes no account of electronicrequirements for a Lewis-compliant model."
    protected static final java.lang.String DEFAULT_PARAMS "PLOT CMO DIPOLE STERIC"
    static final int DIALOG_CONFIG 0
    static final int DIALOG_LIST -1
    static final int DIALOG_MODEL 10
    static final int DIALOG_RUN 20
    static final int DIALOG_SEARCH 40
    static final int DIALOG_VIEW 30
    protected static final java.lang.String fuseHelp "FUSE IA,IB (remove IA,IB and join the two\n \'dangling\' sites by a new bond)\n \nAllowed parameter:\n .r = ring-forming (conformational search)\n \nExamples:\n FUSE 4 12 [remove atoms 4, 12 and draw a new\n bond between resulting radical centers\n (e.g., 3-11), with no geometry change]\n FUSE.r 4 12 [similar, but a conformational\n search is performed to find the most\n suitable ring-closing geometry]\n \nNote that IA, IB must have similar valency, so\nthe resulting structure remains Lewis-compliant.\n"
    protected static final java.lang.String helpModel "NBOModel COMMAND SYNTAX\n \nCommand verbs are case-insensitive and canbe abbreviated by the leading unique characters.Arguments are separated by commas or spaces.Parameters are attached to the command verbafter a dot (viz., DRAW.ap MODEL). Argumentsand parameters are case-insensitive, exceptfor chemical formulas and group acronyms.Use \'HELP <command>\' (e.g., \'HELP SHOW\') forfurther specifics of each COMMAND type.\n \nCOMMAND(.t) arguments\n------------------------------------\nALTER IA [IB IC ID] newvalue\nCLIP IA IB\nDRAW filename\nFUSE(.R) IA IB\nHELP command\nLINK IA IB\nMUTATE IA formula\nREBOND IA symtype\nROTATE AXIS angle\nSAVE.t filename\nSHOW formula\nSWITCH IA IB\nSYMMETRY\nTRANSLATE AXIS shift\nTWIST IA IB IC ID newvalue\nUNIFY CFI1 CFI2 IA1 IB1 IA2 IB2 dist\nUSE.t filename\nVALUE IA [IB IC ID]\n3CHB IA IB :Ligand\n"
    protected static final java.lang.String linkHelp "LINK IA IB (draw a \'bond\' between atoms IA, IB)\nExamples:\n LINK 3 17 [draws a \'bond: between atoms 3-17\nNote that this command (unlike FUSE) takes no\naccount of chemical reasonability.\n"
    protected static final java.lang.String mutateHelp "MUTATE IA formula (replace atom IA by the group\n of specified chemical \'formula\',\n if both are of consistent valency)\n \nExample:\n MUTATE 4 CH3 [remove monovalent atom 4 and\n attach a methyl (CH3) radical in its\n place, preserving valence consistency]\n"
    protected static final java.lang.String rebondHelp "REBOND IA symtype (select a new Lewis valence\n isomer of \'symtype\' symmetry\n at transition metal atom IA)\n \nAllowed \'symtype\' parameters (TM species only):\n \n ML6 bonding: c3vo (\'Outer\' C3v [default])\n c3vi (\'Inner\' C3v symmetry)\n c5vo (\'Outer\' C5v symmetry)\n c5vi (\'Inner\' C5v symmetry)\n \n ML5 bonding: c4vo (\'Outer\' C4v [default])\n c4vi (\'Inner\' C4v symmetry)\n \n ML4 bonding: td (Td symmetry [default])\n c3vi (\'Inner\' C3v symmetry)\n c4v (C4v symmetry)\nExample:\n SHOW WH6 [Tungsten hexahydride, in ideal\n \'c3vo\' isomer geometry]\n REBOND 2 c5vi [reform preceding WH6 isomer\n to alternative \'inner C5v\'\n geometry at TM atom 2]\n"
    protected static final java.lang.String saveHelp "SAVE.t filename (save current model as file\n \'filename\' of type \'t\' extension)\n \nParameters: \n .v = valence coordinate VFILE ([.vfi])\n .c = cartesian coordinate CFILE (.cfi)\n .adf = ADF input file (.adf)\n .g = Gaussian input file (.gau)\n .gms = GAMESS input file (.gms)\n .jag = Jaguar input file (.jag)\n .mm = MM2 molecular mechanics file (.mm2)\n .mnd = AM1/MINDO-type input file (.mnd)\n .mp = Molpro input file (.mp)\n .nw = NWChem input file (.nw)\n .orc = Orca input file (.orc)\n .pqs = PQS input file (.pqs)\n .qc = Q-Chem input file (.qc)\nExample:\n SAVE.G job [save Gaussian-type \'job.gau\' file]\n"
    protected static final java.lang.String searchHelp " NBOSearch: COMMAND SYNTAX AND PROGRAM OVERVIEW\nPROGRAM OVERVIEW:\nFollow menu prompts through the decision tree to the keyword module and datum of interest. Each menu appears with \'Current [V-list] settings\' and a scrolling list of output values. All output lines are also echoed to an external NBOLOG$$.DAT file and error messages go to NBOERR$$.DAT for later reference.\n\nGENERAL \'M V n\' COMMAND SYNTAX:\nNBOSearch user responses generally consist of \'commands\' \n(replies to prompts)\nof the form \'M (V (n))\', where\n M (integer) = [M]enu selection from displayed items\n V (character) = [V]ariable data type to be selected\n [J](obname)\n [B](asis)\n [O](rbital number)\n [A](tom number, in context)\n [U](nit number)\n [d](onor NBO number)\n [a](cceptor NBO number, in context)\n n (integer) = [n]umber of the desired O/A/U/d/a selection\nResponses may also be of simple \'M\', \'V\', or \'Vn\' form , where\n \'M\' : selects a numbered menu choice (for current [V] choices)\n \'V\' : requests a menu of [V] choices\n \'Vn\': selects [V] number \'n\' (and current [S])\nNote that [V]-input is case-insensitive, so \'A\' (or \'a\') is interpreted as \'atom\' or \'acceptor\' according to context. Note also that \'Vn\' commands can be\ngiven in separated \'V n\' form. Although not explicitly included in each active [V]-select list, the \'H\'(elp) key is recognized at each prompt. For NRT search (only), variable [V] may also be \'R\' (for \'resonance structure\' and A\' (for \'interacting atom\'). Current A (atom) and A\' (interacting atom) values determine the current A-A\' \'bond\' selection small fractional bond order.)\n\nEXAMPLES:\n \'2 a7\' : requests menu item 2 for atom 7 (if A-select active)\n \'3 o2\' : requests menu item 3 for orbital 2 \n"
    protected static final java.lang.String showHelp "SHOW <formula> (create a molecule model from\n its \'formula\')\nSHOW <acceptor> <donor-1> <donor-2>...\n (create supramolecular model from\n radical \'acceptor\' and ligand\n \'donor-i\' formulas)\nThe chemical \'formula\' is a valid Lewis-typeline formula, similar to textbook examples.Use colons to denote multiple bonds (C::O doublebond, C:::N triple bond, etc.) and parenthesesto identify repeat units or side groups.Atomic symbols in the range H-Cf (Z = 1-98)and repetition numbers 1-9 are allowed.Chemical formula symbols are case-sensitive.\n \nLigated free radicals (with free-valent acceptorsites) can also be formed in specified hapticitymotifs with chosen molecular ligands. Radical<acceptor> and ligand <donor-i> monomers arespecified by valid line formulas, with eachligand <donor> formula preceded by a number ofcolons (:) representing the number of 2e sitesin the desired ligand denticity (such as \':NH3\'for monodentate ammine ligand, \'::NH2CH::CH2\'for bidentate vinylamine ligand, or \':::Bz\' fortridentate benzene ligand). Each such ligationsymbol may be prefixed with a stoichiometriccoefficient 2-9 for the number of ligands.\n \nIn both molecular and supramolecular formulas,valid transition metal duodectet structuresare also accepted. For d-block molecular species,the default idealized metal hybridization isomercan be altered with the REBOND command.For d-block species one can also includecoordinative ligands (:Lig), enclosed inparentheses and preceded by a colon symbol.Formal \'ylidic\' charges are allowed only foradjacent atom pairs (e.g., dative pi-bonds).\n \nModels may also be specified by using acronymsfrom a library of pre-formed species (manyat B3LYP/6-31+G* optimized level). Each suchacronym can also be used as a monovalent ligandin MUTATE commands, as illustrated below.\n \nCommon cyclic aromatic species\n Bz C6H6 benzene\n A10R2L C10H8 naphthalene\n A14R3L C14H12 anthracene\n A18R4L C18H16 tetracene\n A22R5L C22H20 pentacene\n A14R3 C14H10 phenanthrene\n A14R4 C14H12 chrysene\n A16R4 C16H10 pyrene\n A18R4 C18H12 triphenylene\n A20R5 C20H12 benzopyrene\n A20R6 C20H10 corannulene\n A24R7 C24H12 coronene\n A32R10 C32H14 ovalene\nCommon cyclic saturated species\n R6C C6H12 cyclohexane (chair)\n R6B \' \' (boat t.s.) \n R6T \' \' (twist-boat)\n R5 C5H10 cyclopentane\n R4 C4H8 cyclobutane\n R3 C3H6 cyclopropane\n RB222 [2,2,2]bicyclooctane\n RB221 [2,2,1]bicycloheptane (norbornane)\n RB211 [2,1,1]bicyclohexane\n RB111 [1,1,1]bicyclopentane (propellane)\n R5S spiropentane\n RAD adamantane\n \nCommon inorganic ligands\n acac acetylacetonate anion (bidentate)\n bipy 2,2\"\"-bipyridine (bidentate)\n cp cyclopentadienyl anion (:, ::, :::)\n dien diethylenetriamine (tridentate)\n dppe 1,2-bis(diphenylphosphino)ethane\n (bidentate)\n edta ethylenediaminetetraacetate anion\n (hexadentate)\n en ethylenediamine (bidentate)\n phen 1,10-phenanthroline (bidentate)\n tren tris(2-aminoethyl)amine (tetradentate)\n trien triethylenetetramine (tetradentate)\n \nPeptide fragments (HC::ONHCH2R)\n GLY glycine\n ALA alanine\n VAL valine\n LEU leucine\n ILE isoleucine\n PRO proline\n PHE phenylalanine\n TYR tyrosine\n TRP tryptophan\n SER serine\n THR threonine\n CYS cysteine\n MET methionine\n ASN asparagine\n GLN glutamine\n ASP aspartate\n GLU glutamate\n LYS lysine\n ARG argenine\n HIS histidine\n \nNucleic acid fragments\n NA_G guanine\n NA_C cytosine\n NA_A adenine\n NA_T thymine\n NA_U uracil\n NA_R ribose backbone fragment\n \nIn addition, the SHOW command recognizes\n\'D3H\' (trigonal bipyramid) or \'D4H\' (octahedral)\nspecies, created as SF5, SF6, respectively.\n \n(\'SHOW\' and \'FORM\' are synonymous commands.) \nMolecular examples:\n SHOW CH3C::OOH acetic acid\n SHOW CH3(CH2)4CH3 n-hexane\n SHOW WH2(:NH3)2 diammine of WH2\n SHOW NA_C cytosine\n SHOW CH4 methane\n MUTATE 3 RAD methyladamantane\n SHOW ALA alanine\n MUTATE 7 ALA ala-ala\n MUTATE 17 ALA ala-ala-ala, etc.\nSupramolecular examples:\n SHOW CH3 :H2O hydrated methyl radical\n SHOW Cr 2:::Bz dibenzene chromium\n SHOW CrCl3 2:H2O :NH3\n SHOW Cr 3::acac\n SHOW Cr ::::::edta\n"
    protected static final java.lang.String switchHelp "SWITCH IA IB [switch atoms IA, IB (and\n attached groups) to invert\n configuration at an attached\n stereocenter.]\nExample:\n SHOW ALA (L-alanine)\n SWITCH 6 7 (switch to D-alanine)\n"
    protected static final java.lang.String symHelp "SYMMETRY (determine point group)\n \nNote that exact point-group symmetry is amathematical idealization. NBOModel recognizes\'effective\' symmetry, adequate for chemicalpurposes even if actual atom positions deviateslightly (say, ~0.02A) from idealized symmetry."
    protected static final java.lang.String twistHelp "TWIST IA IB IC IC newval\n IA-IB-IC-ID angle to \'newval\')\n \nExample:\n SHOW C2H6 ethane (staggered)\n TWIST 1 2 3 4 0. ethane (eclipsed)\n"
    protected static final java.lang.String unifyHelp "UNIFY CFI-1 CFI-2 IA1 IB1 IA2 IB2 dist\n (form a complex from molecules in\n cfiles CFI-1, CFI-2, chosen to have\n linear IA1-IB1-IB2-IA2 alignment\n and IA1-IA2 separation \'dist\')\n \nCFI-1 and CFI-2 are two CFILES (previously\ncreated with SAVE.C); IA1, IB1 are two atoms\nof CFI-1 and IA2, IB2 are two atoms of CFI-2\nthat will be \'unified\' in linear IA1-IB1-IB2-IA2\narrangement, with specified IA1-IA2 \'dist\'.\n \nExample:\n SHOW H2C::O (create formaldehyde)\n SAVE.C H2CO (save H2CO.cfi)\n SHOW NH3 (create ammonia)\n SAVE.C NH3 (save NH3.cfi)\n UNIFY H2CO.cfi NH3.cfi 2 3 1 2 4.3\n (creates H-bonded complex)\n"
    protected static final java.lang.String useHelp "USE.t filename (use file \'filename\' of type \'t\'\n to initiate a modeling session)\n \n\'t\' parameters: \n .v = valence coordinate VFILE ([.vfi])\n .c = cartesian coordinate CFILE (.cfi)\n .a = NBO archive file (.47)\n .adf = ADF input file (.adf)\n .g = Gaussian input file (.gau)\n .gms = GAMESS input file (.gms)\n .jag = Jaguar input file (.jag)\n .l = Gaussian log file (.log)\n .mp = Molpro input file (.mp)\n .nw = NWChem input file (.nw)\n .orc = Orca input file (.orc)\n .pqs = PQS input file (.pqs)\n .qc = Q-Chem input file (.qc)\nExample:\n USE.G ACETIC (use Gaussian-type ACETIC.GAU\n input file to start session)\n"
  • org.openscience.jmol.app.nbo.org.openscience.jmol.app.nbo.NBODialogModel 
    Modifier and Type Constant Field Value
    private static final int ALTER 4
    private static final int CLIP 2
    protected static final int CONFIRM_SAVE 0
    protected static final int CONFIRM_VIEWOUTPUT 1
    private static final java.lang.String INPUT_FILE_EXTENSIONS ";adf;cfi;gau;gms;jag;mm2;mnd;mp;nw;orc;pqs;qc;vfi;g09;com"
    private static final java.lang.String LOAD_SCRIPT ";set zoomlarge false;zoomTo 0.5 {*} 0;"
    private static final int MUTATE 1
    protected static final int VALUE 5
  • org.openscience.jmol.app.nbo.org.openscience.jmol.app.nbo.NBODialogRun 
    Modifier and Type Constant Field Value
    private static final java.lang.String CHOOSE_DESCRIPTION "$CHOOSE Keylist - Edit lone pairs and bond orders"
  • org.openscience.jmol.app.nbo.org.openscience.jmol.app.nbo.NBODialogSearch 
    Modifier and Type Constant Field Value
    private static final int BEND_VIS 8
    private static final int CMO_VIS 9
    private static final int E2_VIS 7
    private static final int KEYWD_BAS1BAS2 11
    private static final int KEYWD_BEND 3
    private static final int KEYWD_CMO 8
    private static final int KEYWD_DIPOLE 9
    private static final int KEYWD_E2PERT 4
    private static final int KEYWD_NBO 2
    private static final int KEYWD_NLMO 5
    private static final int KEYWD_NPA 1
    private static final int KEYWD_NRT 6
    private static final int KEYWD_OPBAS 10
    private static final int KEYWD_STERIC 7
    private static final int MO_VIS 8
    private static final int NBO_VIS 7
    private static final int NLMO_VIS 7
    private static final int NPA_VIS 11
    private static final int STERIC_VIS 8
  • org.openscience.jmol.app.nbo.org.openscience.jmol.app.nbo.NBODialogView 
    Modifier and Type Constant Field Value
    protected static final int VIEW_STATE_CAMERA 3
    protected static final int VIEW_STATE_MAIN 0
    protected static final int VIEW_STATE_PLANE 1
    protected static final int VIEW_STATE_VECTOR 2
  • org.openscience.jmol.app.nbo.org.openscience.jmol.app.nbo.NBOJobQueueManager 
    Modifier and Type Constant Field Value
    private static final int QUEUE_MAX 10
  • org.openscience.jmol.app.nbo.NBOService 
    Modifier and Type Constant Field Value
    private static final int MODE_ERR -1
    static final int MODE_ERROR -1
    static final int MODE_IMAGE 88
    static final int MODE_MODEL 1
    static final int MODE_RAW 0
    static final int MODE_RUN 20
    static final int MODE_SEARCH 40
    static final int MODE_SEARCH_LIST 46
    static final int MODE_SEARCH_SELECT 47
    static final int MODE_SEARCH_VALUE 45
    static final int MODE_VIEW 30
    static final int MODE_VIEW_LIST 33
  • 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 java.lang.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 java.lang.String VERSION "JVXL.java Version 1.0"