List of include files. Common variables. Topology file.

Include files

WHAT IF contains many INCLUDE files. (These are physically included in the Fortran 77 version). These include files contain all the common variables and parameters that WHAT IF uses. The documentation provided below is most likely not up-to-date, and is only meant to give you an impression of what to expect.
Include file:  Mainly needed for:
ANATRA.INC     Trajectory analysis
BIGINC.INC     Everywhere
CHESS.INC      Chess playing module
CMPINC.INC     
CNTINC.INC     
COMINC.INC     
CONFAC.INC     
ELMDAT.INC     
ELMINC.INC     
EPSINC.INC     
EQUFLD.INC     Chess playing module
ESPACE.INC     Anywhere where 'dynamical memory allocation' is needed
FDEVIC.INC     GL graphics
FGLINC.INC     GL graphics
FRACTI.INC     Spline option
GENINC.INC     
HB2INC.INC     Hydrogen bonds
HBONDS.INC     Hydrogen bonds
HGRINC.INC     Hydrogen bonds
INDCES.INC     Spline option
IRIGRA.INC     Graphics
MCXINC.INC     Monte Carlo procedure
MDFINC.INC     H,K,L,F file inspection
NEURON.INC     Neural network
PDBINC.INC     PDB file verification
PIRINC.INC     Obsolete sequence menu
QUALTY.INC     Packing quality control
REFINC.INC     Structure regularization
SELECT.INC     Protein selection
SPCIAL.INC     Special options
STKVLD.INC     Chess playing module
SUPPOS.INC     Three dimensional superposition
SYMANA.INC     Symmetry 
SYMDAT.INC     Symmetry
SYMINC.INC     Symmetry
TABLES.INC     Spead sheet
WALIGN.INC     New sequence manipulation menus

Common variables

The following is a list of variables used in the common blocks:
 SYMSTAT_DELETED Matrix is flagged to be deleted
 SYMSTAT_FILEF = Matrix read from file in fractional coordinates
 SYMSTAT_FILEO = Matrix read from file in orthogonal coordinates
 SYMSTAT_MTRIX = Matrix read from mtrix cards on PDB file
 SYMSTAT_SPGRP = Matrix generated by space group symmetry routine
 SYMSTAT_SYMTR = Matrix read from symtr cards on PDB file
 SYMSTAT_TRANS = Matrix has been generated by translation
 SYMSTAT_USERF = Matrix entered by user in fractional coordinates
 SYMSTAT_USERO = Matrix entered by user in orthogonal coordinates
 HB2IDN remembers whether the initialization is done
 *COOR1 saves the coordinates of the native residues temporarily
 *COOR2 saves the coordinates of the rotated residues temporarily
 ACCES1 saves the accessibility in the native form
 ACCES2 saves the accessibility in the non-native form
 ARAD stores affected donors
 ARIATA stores (1 or 2) acceptor IATs for each H atom.  
 ARIATD stores donor IATs
 ARPAAT stores potential acceptor IATs
 ARPAIS stores potential acceptor ISYMs
 ARSYMA stores (1 or 2) acceptor ISYMs for each H atom.  
 ARVALA stores (1 or 2) H-bond values for each H atom.
 ARXYZH stores fixed and flexible H-atom coordinates.
 ATDON  saves the donor number
 CURCUR stores the connections between members of the subnet
 CURR   stores the IAMB numbers for each member of the subnet
 DONAMB stores the index in the "ambiguity" arrays
 EXVAL saves the exposure value
 HB2ACB saves the connected atom numbers for each acceptor 
 HB2ACT saves the acceptor type 1-9 for all acceptors
 HB2AMB stores the number of possibilities
 HB2ANG stores the IANG within the residue
 HB2AUT stores the D-H.A look-up-table from HBOFIELD.DAT
 HB2BES stores the best scoring configuration so far
 HB2DLY number of degrees for lysine steps
 HB2DON stores the index in the array of donors for the ambiguity
 HB2DSE number of degrees for serine steps
 HB2DST stores the fixed residue
 HB2DUT stores the H...A look-up-table from HBOFIELD.DAT
 HB2DVA stores the summed-up hbond values
 HB2ERT is the same, expressed in RT units.
 HB2EXV is the expected value of a hydrogen bond to invisible water.
 HB2FAM stores the original ambiguity for the fixed residue
 HB2FIN stores the index in the HB2FFX array
 HB2FLP stores the total flip penalty
 HB2GRC stores the number of H atoms
 HB2GRP stores the group number
 HB2GRT stores the group type 
 HB2H2N stores the nearest other conformations for each conformation
 HB2IAA stores the IAA in question
 HB2IAT stores the IAT within the residue (overlayed with HB2ANG!)
 HB2LUT stores the look-up-table acceptor geometry from HBOFIELD.DAT
 HB2LYS number of possibilities for lysine+the like
 HB2MXE is the maximum energy for a Hydrogen bond
 HB2ORG stores the original angle value from CHI004
 HB2ORS stores the fixing residue
 HB2PEN stores the penalty for a residue not being in the "1" position
 HB2POS stores the position-# of the configuration under consideration
 HB2SER number of possibilities for serine+the like
 HB2TYP stores the donor type from HBOTYP (overlayed with HB2ORG!)
 HB2WHA stores the Wanted Hydrogen bond Acceptor
 HB2WHD stores the Wanted Hydrogen bond Donor
 INAD   stores the index in the array of affected donors for the ambiguity.
 INDON stores an index in the list of donors
 INPA stores the index in the array of potential acceptors
 INTT stores the index in the array of potential C-termini acceptors
 INXYZH stores indices into ARXYZH for all donors
 MAXAMB is the maximum number of ambiguities
 MAXDON is the maximum number of donor IATs we can store
 MAXFFX is the maximum number of coupled-fixed configurations
 MAXFIX is the maximum number of coupled-fixed residues
 MAXH2D is the number of H positions for water
 MAXH2N is the maximum number of neighbouring conformations for h2o
 MAXH2P is the number of H position pairs for water
 MAXHAT is the maximum number of donated H-atoms we store
 MAXHGR is the maximum number of hydrogen bond donor groups
 MAXPLU is the maximum number of positively charged 1 atom drugs
 MAXSNS is the maximum subnet size
 MAXTAD is the maximum total number of affected donors
 MAXTPA is the maximum total number of potential acceptors
 MAXWHB is the maximum number of "WANTED" hydrogen bonds.
 METPEN penalty to be added when H approaches a metal.
 NAMB1  stores the index of the last residue ambiguity
 NAMB2  stores the index of the last ambiguity
 NUAD   stores the number of affected donors for the ambiguity.
 NUDON stores the number of donors in the residue
 NUMDON stores the number of donors
 NUMFFX stores the number of coupled-fixed configurations
 NUMFIX stores the number of coupled-fixed ambiguities
 NUMHAR stores the total number of H atoms
 NUMHGR stores the number of hydrogen bond donor groups
 NUMPLU stores the number of positive one-atom drugs
 NUMTAD stores the total number of affected donors
 NUMTPA stores the number of potential acceptors
 NUMTT  stores the number of donor to TER pointers
 NUMWHB stores the number of explicitly wanted hydrogen bonds.
 NUPA stores the number of potential acceptors
 NUTT stores the number of potential acceptors C-termini acceptors
 NUXYZH stores the number of H atoms in ARXYZH for all donors
 PENGRP stores the number of C-terminal oxygen atoms
 PLUSAT remembers the IAT-s of positive charges
 TOTPEN stores the total penalty for H atoms pointing to '+'-charge.
 TOTVAL stores the total donor value
 WHBFAC is the factor used to amplify wanted hydrogen bonds
 HB2FFX stores fixed conformations
 *CELLM : CELL DIMENSION ALONG A, B, OR C AXIS
 A1NAME : AS AANAME BUT NOW NOT IN 3- BUT IN 1-LETTER CODE
 AAFREQ : FREQUENCY OF OCCURENCE OF AMINO ACIDS
 AAISOK : LOGICAL. TRUE IF THE AA WAS OK UPON READING.
 AANAME : NAMES-LIST IN WHICH AASNUM FINDS THE NAMES OF THE AA
 AAPAIR : FREQUENCY MATRIX OF PAIRS OF AMINO ACIDS
 ACCCNT    NUMBER OF TIMES AN ATOM IS AS ACCEPTOR IN A HBOND (PER ATOM)
 ACCDON : LOGICAL INDICATING WHETHER ACCESSIBILITY CALCULATION IS DONE
 ACCESS : ACCESSIBILITY FRACTION FOR ATOMS
 ACCUSD    FLAG PER ATOM FOR ACCEPTORS USED IN HBOND OR NOT
 ACDEAA : LIST OF ON-LINE DEFINED SELF-MADE AMINO ACID POINTERS
 ACONVC   COORDINATES OF CA OF CENTER OF SCREEN
 ALLGRD : ONE DIMENSIONAL INTEGER*2 ARRAY FOR EASY ALIGNMENT
 ALLMAT : ARRAY WITH ALL NEIGHBOUR MATRICES
 ALLSEQ : ARRAY CONTAINING ALL SEQUENCES
 ALPHAM : ALPHA ANGLE OF CELL
 ALREDY    ?
 ANGERA    ERROR OVER THE ACCEPTOR FOR EACH HBOND
 ANGERH    ERROR OVER THE HYDROGEN FOR EACH HBOND
 ASMEAA : NAME OF ON-LINE DEFINED SELF-MADE AMINO ACID
 ATCOLR : ALSO HERE: COLOR OF ATOM (=REFLECTION)
 ATCOLR : COLOUR PER ATOM (0-360)
 ATORAA : LOGICAL. TRUE IF ROW IS FOR ATOMS, FALSE FOR AA.
 ATPRAA : THE NUMBER OF ATOMS THAT SHOULD BE PRESENT PER RESIDUE
 ATTVAL : ARRAY WITH SCRATCH ATOM RELATED VALUES
 BETAM  : BETA ANGLE OF CELL
 BOTCNT    NUMBER OF TIMES AN ATOM IS AS DON AND ACC IN HBOND (PER ATOM)
 BOTTOM_NEURONS  NEURONS BETWEEN HIDDEN LAYER AND OUTPUT UNIT
 BPLANE   : ARRAY WITH DIRECT-ACTION RESIDUES
 BRAVAIS: Bravais type of the conventional cell
 BUTTONS  : LOGICAL ARRAY TO HOLD ON/OFF STATUS OF SCREEN BOTTOM BUTTONS
 CACA1     : CA-CA DISTANCES IN THE FIRST RANGE
 CACA2     : CA-CA DISTANCES IN THE SECOND RANGE
 CCELDIM: The 6 cell dimensions of the conventional cell
 CCLASS : CLASS of the conventional cell
 CELDIM : The 6 cell dimensions as read from the CRYST1
 CELDIMS: The 6 cell dimensions as deduced from the SCALE?
 CELFND : Valid CRYST1 card found on input?
 CELREAD: CRYST1 card read from input?
 CELTR  : Transformation to make cell input ---> conventional
 CELTRC : Transformation to make cell reduced ---> conventional
 CELTRR : Transformation to make cell input ---> reduced
 CHAINN CHAIN POINTER FOR RESIDUES
 CHARGE : ATOMIC PARTIAL CHARGES
 CHIANG : ARRAY WITH ALL CHI ANGLES FOR THE MAIN SEQUENCE 
 CHICON : POINTERS TO CONNECTED ATOMS FOR CHIANGLES
 CHIUSE : NUMBER OF USABLE CHI ANGLES PER AMINO ACID
 CLASS  : The crystal class of the cell on the CRYST1 card
 CLASS2 : The crystal class of the space group
 CLUNAM : NAMES GIVEN TO CLUSTERS
 CLUSTR : INDEX NUMBER IN MAIN SEQUENCE OF RESIDUES IN CLUSTER
 COMLST   : FULL TEXT PLUS HELP FOR OLD STYLE COMMANDS
 COMMAA : MATRIX IN 10 DEGREE STEPS FOR ALLOWED NORMAL AA PHI-PSI'S
 COMTEXT  : TEXT IN NEW-TYPE PULLDOWN MENUS
 CUTFLG : FLAG OF RESIDUES DIRECTLY BEFORE A CUT
 CYSCYS : POINTERS TO THE CYS-CYS AMINO ACIDS
 DATA_WEIGHT     WEIGHTS ON THE TEST_DATA POINTS
 DATCOL : DATABASE ATOM COLOURS
 DEBUG           DEBUG FLAG
 DEMOTX   : HELP TEXT FOR DEMOS AND DIALOG BOXES
 DGMAT  : MATRICES NEEDED TO MATCH DATABASE HITS ON THE STRUCTURE
 DGVEC  : VECTORS BELONGING WITH DGMAT
 DGWHER : CONTAINS INFO ABOUT WHERE THIS GROUP MATCHES THE STRUCTURE
 DGWVAL : WEIGHTS USED ON DGLOOP CA'S
 DIFTMP    : CA DIFFERENCES AFTER SUPPOS
 DONACD    DONOR ACCEPTOR DISTANCE FOR EACH HBOND
 DONCNT    NUMBER OF TIMES AN ATOM IS AS DONOR IN A HBOND (PER ATOM)
 DONUSD    FLAG PER ATOM FOR DONORS USED IN HBOND OR NOT
 DSTCON : DISTANCES CORRESPONDING TO THE BONDS IN MUTCON
 DUBDUB    FLAG PER ATOM FOR TWO HBONDS BETWEEN SAME DONOR AND ACCEPTOR
 DUBUSD    FLAG PER ATOM FOR DON/ACC'S FOUND IN A HBOND
 ERRUNT IS THE UNIT WHERE REAL HARD ERRORS WILL BE LOGGED
 ETERMS : ENERGY TERMS PER ATOM
 ETMNAM : NAMES OF THE ENERGY TERMS
 ETMTOT : ENERGY TERMS PER RESIDUE
 FACT1    WEIGHT ON BOND LENGTHS
 FACT2    WEIGHT ON BOND ANGLES
 FACT3    WEIGHT ON TORSION ANGLES
 FACT4    WEIGHT ON PLANARITIES
 FAMILY : POINTERS TO FIRST AND LAST AA OF FAMILY IN MAIN SEQUENCE
 FAMNAM : NAMES GIVEN TO FAMILIES
 FBRTIRI  : COORDINATES OF (CENTER OF) FBRT OBJECT
 FILCNM : CONVERTED NAMES OF THE PROTEINS IN DB (PDB 4 LETTER CODE)
 FILNMS : NAMES OF FILES TO BE USED
 FIX*   : FLAG TO DETERMINE HOW TO SET ENVELOP POINT UPON TOGGLING
 FRCCYS : USER FORCED CYS-CYS PAIRS
 FTCRDS : CA COORDINATES OF STRETCH FOR WHICH BEST FIT IS WANTED
 FUDGE3 : PRETEND THAT THERE IS A PS300
 GAMMAM : GAMMA ANGLE OF CELL
 GLYCIN : AS COMAA, BUT NOW FOR GLYCINES
 GRID   : ELECTRON DENSITY GRID POINTS (INTEGER*2)
 GRID2  : ELECTRON DENSITY GRID POINTS (REALS)
 GRID2* : SMALLER ELECTRON DENSITY MAPS (2 MAPS)
 GRPACT : (BOOLS) INDICATORS FOR ACTIVE GROUPS
 GRPHOW : (CHAR80) TELL HOW GROUPS WERE MADE
 GRPLEN : LENGTHS OF GROUPS
 GRPNT2 : SECOND POINTER ARRAY TO FIRST AA`S OF FOUND GROUPS
 GRPNT3 : THIRD POINTER ARRAY TO FIRST AA`S OF FOUND GROUPS
 GRPNT4 : FOURTH POINTER ARRAY TO FIRST AA`S OF FOUND GROUPS
 GRPNTR : POINTER ARRAY TO FIRST AA`S OF FOUND GROUPS
 HARD_LIMIT      EXTREME ABSOLUTE VALUE FOR NEURONS
 HBOCNT    NUMBER OF HYDROGEN BONDS PER ATOM
 HBOPAR : DONOR=1; ACCEPTOR=-1; BOTH OR NOTHING=0 
 HBOPOS : TRUE/FALSE FOR POSSIBLE H-BOND PARTNER PER ATOM TYPE
 HBOTYP : CLASS OF HYDROGEN BOND DONOR/ACCEPTOR
 HBOUSD    FLAG PER ATOM FOR USED IN HBOND OR NOT
 HINDX  : MILLER INDEX H
 HISTOR : ARRAY HOLDING THE HISTORY OF COMPLETED OPERATIONS
 HKLUSE : IS REFLECTION PRESENT IN MDF?
 HSTQUA  DSSP DETERMINATION FOR CENTER RESIDUE IN QUALITY CONTROL FILE
 HUEVAL   COLOUR OF VECTORS IN XMOL AND YMOL
 HYDACD    HYDROGEN ACCEPTOR DISTANCE FOR EACH HBOND
 ICOFDB : HASH TABLE FOR DRUGS IN THE ALDRUG.XYZ FILE
 IDEBUG : FLAG FOR DEBUG OUTPUT: 0 NO OUTPUT; 1 ALL OUTPUT
 IDEBUG : FLAG WHICH SETS AMOUNT OF DEBUG INFO (0=NOTHING)
 IDGSRT : INTEGER POINTER TO SORTED DGLOOP GROUP
 IDONE     : STORES THE FRAGMENTS IN THE TWO RANGES
 IH2ODB : HASH TABLE FOR WATER IN THE ALDRUG.XYZ FILE
 ILVNOW : MAP LEVEL PRESENTLY BEING CONTOURED
 INCLUDE COMMON BLOCK FOR QUALITY BOXES
 INCLUDE FILE FOR DNA REGULARIZATION
 INCLUDE FILE SPECIFIC FOR (GROMOS) TRAJECTORIES
 INDSUP    : INDICES TO MATRIX FILE NAMES
 INDTYP : PICK INDEX TYPE IN FILE 19
 INDXCA : POINTER ROW TO LOCATIONS IN CA-CA DISTANCE FILE
 INPUT_LAYER     ARRAY USED AS INPUT LAYER
 INWDTH          NUMBER OF INPUT NODES USED
 IOBJ     : ARRAY TO HOLD THE STATUS OF SG OBJECTS (ZERO=OFF)
 IPLUS  : ADDITIVE VALUE TO GO FROM USER INPUT LEVEL TO INT*2 LEVEL
 IPLVEC   LOGICAL ARRAY NEEDED FOR SENDING VECTOR LISTS TO PS300
 IRFBRT   : LOGICAL TO HOLD FBRT STATUS
 IRICC    : ARRAY TO HOLD THE STATUS OF PICK BUTTONS IN VERTICAL SCREEN MENU
 IRISFLAGS: ARRAY WITH DEVICE STATUS PARAMETERS
 IRROCK   : LOGICAL TO HOLD ROCKING STATUS
 IRSTAT   : ARRAY WITH STATUS FLAGS FOR INTER-ROUTINE COMMUNICATION
 IRSTER   : LOGICAL TO HOLD STEREO STATUS
 ISATOK : FLAG, TRUE IF THE ATOM IS OK, AND SHOULD BE CONSIDDERED
 ISET12345 : SETS OF EQUIVALENCED RESIDUES
 ISHBO1    LOGICAL IN COMMON FOR COMMUNICATION BETWEEN HBOND ROUTINES
 ISHBO2    LOGICAL IN COMMON FOR COMMUNICATION BETWEEN HBOND ROUTINES
 JUNIOR : WHAT IF JUNIOR IS BEING USED
 KINDX  : MILLER INDEX K
 LABTXT : TEXT TO BE WRITTEN NEXT TO LABELED ATOMS
 LAWDTH          WIDTH OF THE HIDDEN LAYERS
 LAYERS          NUMBER OF HIDDEN LAYERS
 LENEAA : THE GROUPSIZE OF SELF DEFINED AMINO ACIDS
 LENGTH    : LENGTH OF THE MATCHING FRAGMENT STARTING AT POSITION IAA
 LINDX  : MILLER INDEX L
 LINE   : CHARACTER*80 FOR TEMPORARY STORAGE OF CARD IMMAGES
 LLCNET : AS LOCNET, BUT NOW FOR A WHOLE SEARCH STRING
 LLCPAT : AS LOCPAT, BUT NOW FOR A WHOLE SEARCH STRING
 LOCHST DSSP DETERMINATION FOR THE RESIDUE
 LOCNEG : AS LOCNEI, BUT NOW FOR A WHOLE SEARCH STRING
 LOCNEI : AS LOCPAA, BUT NOW FOR OTHER RESIDUES (EG NEIGHBOURS)
 LOCNET : AS LOCPAT, BUT NOW FOR OTHER ATOMS (EG NEIGHBOURS)
 LOCPAA : BOOLEANS SET TO TRUE IF A CERTAIN RESIDUE SHOULD BE USED
 LOCPAT : BOOLEANS SET TO TRUE IF A CERTAIN ATOM SHOULD BE USED
 LOCPIG : AS LOCPAA, BUT NOW FOR A WHOLE SEARCH STRING
 LOGA   : POINTERS TO DOTS ON THE SURFACE
 LOOKAT    FLAG PER ATOM THAT IS LOOKED AT IN HBOND DETERMINATION
 MAPACT : SHOULD THIS MAP BE CONTOURED OR NOT
 MAPLEV : CONTOUR LEVELS OF MAPS IN REAL VALUES
 MAPMAX : HIGHEST VALUE IN MAP
 MAPMIN : LOWEST VALUE IN MAP
 MAPNAM : NAME OF MAP FILES
 MAPNOW : PRESENTLY ACTIVE MAP (=DEFAULT MAP)
 MAPNUM : NUMBER OF MAPS PRESENTLY KNOWN TO WHAT IF
 MAPORG : GRID COORDINATES OF FIRST POINT TO BE SHOWN
 MAPTXT : USER NOTES WITH THESE MAPS
 MAPTYP : 1 = INTERNAL ORTHOGONAL MAP
 MAPWID : EXTEND OF PORTION TO BE SHOWN
 MATEAA : THE MATRIX CONTAINING THE SELF DEFINED AMINO AMINO ACIDS
 MAXAA  : MAXIMAL NUMBER OF AA ALLOWED IN THE SOUP 
 MAXADB : MAXIMAL NUMBER OF RESIDUES PER SEQUENCE ALLOWED IN DATABASE
 MAXALI : MAXIMAL NUMBER OF RESIDUES PER SEQUENCE ALIGNMENT
 MAXAT  : MAXIMAL NUMBER OT ATOMS ALLOWED PER STRUCTURE 
 MAXBOX : NUMBER OF GRIDPOINTS PER SIDE OF PROPERTY/QUALITY BOXES
 MAXCCH : MAXIMAL NUMBER OF MULTI LINGUAL LINES TO BE CACHED
 MAXCLL : MAXIMAL NUMBER OF CLUSTERS
 MAXCLM : MAXIMAL NUMBER COLUMNS TO BE USED
 MAXCLU : MAXIMAL NUMBER OF AMINO ACIDS PER CLUSTERS
 MAXCMD   : MAXIMAL NUMBER OF PULL-DOWN COMMANDS
 MAXCON : MAXIMAL NUMBER OF CONNECTIVITIES IN DRUGS
 MAXCYS : MAXIMAL NUMBER OF CYSTEINES IN THE SOUP
 MAXDG  : MAXIMAL NUMBER OF DGLOOP HITS ALLOWED TO BE STORED
 MAXDG  : MAXIMALLY ALLOWED NUMBER OF DG HITS TO BE STORED
 MAXEAA : MAXIMAL NUMBER OF SELF MADE AMINO ACIDS
 MAXETM : MAXIMAL NUMBER OF ENERGY CONTRIBUTIONS PER ATOM
 MAXETM : MAXIMAL NUMBER OF ENERGY TERMS PER ATOM OR RESIDUE
 MAXFAM : MAXIMAL NUMBER OF ALLOWED FAMILIES
 MAXG10 : DIMENSION OF THE TEN VERY SMALL MAPS
 MAXG2  : DIMENSION OF THE TWO MEDIUM SIZE MAPS
 MAXG4  : DIMENSION OF THE FOUR SMALL MAPS
 MAXGR2 : DIMENSION OF EQUAL SPACE MAP IN REALS
 MAXGRD : DIMENSION OF THE MAP IN INTEGERS*2
 MAXIG  : MAXIMAL NUMBER OF RESIDUES PER SUBGROUP 
 MAXIOB   : MAXIMAL NUMBER OF SG DRAWABLE OBJECTS
 MAXITM : MAXIMAL NUMBER OF MOL-ITEMS PER MOL-OBJECT
 MAXLAB : MAXIMAL NUMBER OF LABELS VISIBLE AT THE GRAPHICS
 MAXLAY          MAXIMAL NUMBER OF HIDDEN LAYERS
 MAXLEV : MAXIMAL NUMBER OF CONTOUR LEVELS PER MAP
 MAXLLN : MAXIMAL LENGTH OF LABELS VISIBLE AT THE GRAPHICS
 MAXMAP : MAXIMAL NUMBER OF USABLE MAPS
 MAXMOL : MAXIMAL NUMBER OF MOLECULES IN THE SOUP
 MAXMOL MAXIMAL NUMBER OF NON-H2O MOLECULES IN THE SOUP
 MAXNDT          MAXIMAL NUMBER OF DATA POINTS
 MAXNEI : MAXIMAL NUMBER OF NEIGHBOURS POSSIBLE PER RESIDUE
 MAXNEU          MAXIMAL NUMBER OF NODES IN INPUT/HIDDEN LAYERS
 MAXOPT   MAXIMAL NUMBER OF OPTIONS IN A MENU
 MAXPFL : MAXIMAL LENGTH OF A PIR FILE (INCLUDING DELETIONS)
 MAXPFS : MAXIMAL NUMBER OF PIR-FILES WHAT IF KNOWS OF
 MAXPRP : MAXIMAL NUMBER OF PARAMETERS PER PARALLEL SEQUENCE
 MAXPST : MAXIMAL NUMBER OF CUT AND PASTE FLAGS
 MAXPST MAXIMAL NUMBER OF CHAIN PASTE`S
 MAXQUA  MAXIMAL VALUE IN QUALITY CONTROL FILE BEFORE SCALING
 MAXRDG : MAXIMAL NUMBER OF STEPS IN MOVIE OPTION(S)
 MAXSEQ : MAXIMAL NUMBER OF ENTRIES IN THE PROTEIN DATABASE
 MAXSP  : MAXIMAL NUMBER OF SUBGROUP ADDRESS POINTERS 
 MAXSUP : MAXIMAL NUMBER OF SUPERPOSITIONINGS WHAT IF CAN REMEMBER
 MAXSYM : Maximal number of allowed matrices
 MAXTAT : MAXIMAL NUMBER OF ATOMS THAT MOVES UPON ONE TORSION
 MAXTOR : MAXIMAL NUMBER OF TORSION ANGLES PER 'RESIDUE'
 MAXVEC : MAXIMAL NUMBER OF VECTORS ALLOWED PER GRAPHICS ITEM
 MENUPS   NUMBER OF THE PSMENU TO BE SHOWN
 MITEMS   POINTERS TO THE INSTANCES FOR MOL-ITEMS IN A MOL-OBJECT
 MITEXT   NAMES OF THE MOL-ITEMS
 MITNUM   NUMBER OF MOL-ITEMS USED PER MOL-OBJECT
 MOUSACT  : NUMBER OF THE PRESENT SET OF MOUSE ACTIONS
 MPCOLR : COLOURS FOR ALL LEVELS OF THE MAP
 MPRIME : Matrix that rotates the cell into place.
 MPRIMS : Status of the last matrix
 MUTCON : ORDER OF CONNECTIONS IN MUTROW
 MUTDAT.INC CONTAINS THE AMINO ACID NAMES ETCETERA AND
 MUTROW : ATOM NAMES STORED IN MAXTAT*CHAR*4 PER RESIDUE
 MXGDCB : TOTAL (LINEAR) SIZE OF THE GRID SPACE
 MXQBOX  MAXIMAL NUMBER OF ATOM BOXES PER BOX FILE
 MXQBSZ  DIMENSION OF ONE INDIVIDUAL BOX
 MXQIAT  TOTAL NUMBER OF POSSIBLE ATOMS (20 RES.+/- 8 ATOMS)
 MXQUAT  TOTAL NUMBER OF PACKED ATOMS
 MY_MENU  : COMMANDS IN THE PERSONAL MENU
 M_P      : MAXIMAL ATOM PICK INDEX (M_P==-MAXATM)
 N*     : NUMBER OF GRIDPOINTS IN U, V, OR W DIRECTION
 NAAFIL : NUMBER OF AMINO ACIDS PER PROTEIN
 NAMFIL : NAMES OF THE PROTEINS IN DB (PDB 4 LETTER CODE)
 NATFIL : NUMBER OF ATOMS PER PROTEIN
 NBINDB : NUMBER OF ENTRIES FOUND IN DATABASE
 NDIV*  : NUMBER OF MAP DIVISIONS IN A, B, OR C DIRECTION
 NEADST : All matrices that generate contacts less than NEADST are
 NEURONS         NEURONS BETWEEN HIDDEN LAYERS
 NEURON_FLAG     FLAGS FOR COMMUNICATION BETWEEN NEURAL NETWORK ROUTINES
 NEWCLS : Logical indicating that the conventional cell has a
 NEXT CHARACTER STRING (LABTXT) SHOULD BE MAXLLN LONG
 NMGRFN : NUMBER OF GROUPS FOUND
 NODES           ARRAY TO STORE HIDDEN NODES
 NOMAIN : FLAG THAT TELLS WHETHER THERE IS A MAIN SEQUENCE READ IN OR NOT
 NOTUNT IS FOR NOTES, INFO, STATISTICS, ETC.
 NP1    : COLUMN NUMBER OF READ COLUMN 1
 NP2    : COLUMN NUMBER OF READ COLUMN 2
 NP3    : COLUMN NUMBER OF READ COLUMN 3
 NP4    : COLUMN NUMBER OF READ COLUMN 4
 NPP    : NP1 TILL NP4
 NUMAAF : NUMBER OF AA FOUND IN SEQUENCE
 NUMAAT : NUMBER OF RESIDUES FOUND IN SOUP
 NUMAT  : MAXIMAL NUMBER OF DIFFERENT ATOM TYPES ALLOWED 
 NUMATF : NUMBER OF ATOMS PRESENT
 NUMBUF : NUMBER OF VECTORS CREATED FOR MAP
 NUMCOF : NUMBER OF COFACTORS
 NUMCYS : NUMBER OF CYS-CYS PAIRS
 NUMEAA : THE NUMBER OF SELF DEFINED AMINO ACIDS
 NUMH2O NUMBER OF SOLVENT MOLECULES IN THE SOUP
 NUMNAM : NUMBER OF AMINO ACID ACCORDING TO NOMENCLATURE
 NUMOPT   ACTUAL NUMBER OF OPTIONS
 NUMRNG NUMBER OF RESIDUES IN REQUESTED RANGE
 NUMROW : NUMBER OF HITS IN EACH ROW
 NUMSOU NUMBER OF MOLECULES IN THE SOUP
 NUMSTS    TOTAL NUMBER OF HBONDS
 NUMSUP    : NUMBER OF PRESENTLY KNOWN MATRICES
 NUMSYM : Number of available symmetry matrices
 NUMTAB : NUMBER OF TABLES IN USE
 NUMUA  : MAXIMAL NUMBER OF DIFFERENT AA ULTIMATELY ALLOWED 
 NUMUT  : OVERALL NUMBER OF ATOM TYPES FOUND SO FAR 
 NXTGRP : NUMBER OF THE NEXT FREE GROUP
 NXTROW : NUMBER OF NEXT FREE ROW
 NXTSEL NUMBER OF NEXT FREE COLUMN
 ONESA1 : RESIDUE IN ONE LETTER CODE
 ONESA3 : RESIDUE NAME IN THREE LETTER CODE
 ONESAT : ATOM TYPES FOR ATOMS PRESENT IN 4-LETTER CODE
 OPTION   OPTION SET
 ORGNAM : ORIGINAL PDB NAME IN CASE ATOMS IN ONE UNIT HAVE
 ORTMAT : OFTEN USED MATRIX FOR ORTHOGONALISATION PURPOSES
 PCKLST   COORDINATES OF LAST PICKED ATOM
 PDBUNT IS THE UNIT NUMBER WHERE ERRORS WARNINGS ETC WILL BE WRITTEN
 PIRDAT : ARRAY WITH SEQUENCES IN ONE LETTER CODE (IN ESPACE!)
 PIRFLS : FILE NAMES OF PIR FILES
 PNTAAC : POINTER TO CA'S IN ATOM TYPE ARRAYS
 PNTAAE : POINTER TO END OF AA IN ATOM TYPE ARRAYS
 PNTAAS : POINTER TO START OF AA IN ATOM TYPE ARRAYS
 POPTXT   : STATUS FLAGS FOR PULL-DOWN MENU OPTIONS
 PRESOU : MOLECULE NUMBER ON WHICH LAST PREGRO HAS RUN
 PROD   : MULTIPLIER TO GO FROM USER INPUT LEVEL TO INTEGER*2 LEVEL
 PROGRAM NEEDS TO BE RECOMPILED!! PLEASE CHECK CAREFULLY FOR PARAMETER
 PSTFLG : FLAG OF RESIDUES DIRECTLY BEFORE A PASTE
 QDONE     : STORES THE Q-RMS FOR THE MATCHED FRAGMENTS IN IDONE
 QFACTS : FIT QUALITY FACTORS FOR THE OBSERVED FITTED STRETCHES
 QFCSTR : SORTED QUALITY OF FIT FACTORS
 QUALBL  SIGNIFICANT PART OF QUALBY
 QUALBX  QUALLITY BOXES STORED AS INTEGER*2
 QUALBY  QUALITY BOXES STORED AS BYTES
 RCELDIM: The 6 cell dimensions of the reduced cell
 RECRD  : SCRATCH ARRAY TO READ COORDINATES PER AA FROM DATA BASE
 RESREF : RESOLUTION OF THIS REFLECTION (H,K,L)
 RESTYP : INTEGER REPRESENTATION OF ONESA3
 ROCKANGLE: MAXIMAL ROCKING ANGLE
 ROCKDYNOW: PRESENT ROCK ANGLE
 ROCKSPEED: ANGLE PER ROCK-STEP
 ROW123 : LOGICAL ROWS FOR STORAGE OF THE SEARCH ROWS
 ROWTXT : TEXT CREATED WITH THE ROWS
 ROWUSE : LOGICAL THAT TELLS IF THE ROW IS ON OR NOT
 SCLFND : Valid scale card found on input?
 SCLREAD: Scale card read from input?
 SECOND BLOCK IS MORE NEEDED FOR NORMAL, PAIRWISE SUPPOS
 SELCHC CONTACT CHANCE FOR AMINO ACIDS IN SELECTED PROTEINS
 SELCLM ARRAY WITH ALL COLUMNS IN IT
 SELNAM ARRAY WITH THE TITLES OF THE COLUMNS
 SELUSE ARRAY WITH FLAGS FOR USED/NON-USED COLUMNS
 SHORT_CUT       FLAG FOR SPEED PURPOSES IN CASE OF LARGE DATASETS
 SHOULD THEN ONLY BE USED IN THE MAIN PROGRAM.
 SOFT_LIMIT      PREFERRED EXTREME ABSOLUTE VALUE FOR NEURONS
 SOUADM ADMINISTRATION OF CHAIN TYPE/CONTENTS
 SOUNAM NAME OF THIS MOLECULE IN THE SOUP
 SOUPNT : POINTER FROM RESIDUE TO SOUNAM TABLE
 SOURNG RANGE OF REQUESTED RESIDUES FOR USER IO
 SPCNAM : Name of the space group
 SPCNUM : Number of the present spacegroup
 SPHRAD : CENTER AND RADIUS OF SMALLEST SPHERE AROUND THE RESIDUE
 STEP*  : STEP SIZE IN THE U, V, OR W DIRECTION
 STEP_SIZE       MAXIMAL CHANGE OF A NEURON PER TRIAL
 STNDIS   STANDARD BOND LENGTHS (PARALLEL WITH MUT***)
 SUMACC : TOTAL ACCESSIBLE SURFACE AREA PER RESIDUE
 SUPMAT    : ONE SUPERPOSITION MATRIX IN COMMON
 SUPNAM    : NAMES OF MATRIX FILES
 SUPVEC    : THE ACCOMPANYING SUPERPOSITION TRANSLATION VECTOR
 SYMAL1 : The first of the two inconsistent scale matrices
 SYMAL2 : The second of the two inconsistent scale matrices
 SYMALT : There are two inconsistent scale matrices available
 SYMGCA : If true: show only CA in mol-items created by sym
 SYMMAT : Symmetry matrices
 SYMNIN : Index of inverse transformation
 SYMSTS : The type of symmetry matrix
 SYMVEC : Translational components of symmat
 TABLEN : ARRAY WITH LENGTHS OF TABLES
 TABNAM : NAMES OF TABLES
 TABTYP : TYPE OF TABLE TO BE USED
 TABUSE : LIST OF TABLES ACTIVATED BY THE USER
 TEST_ANSWERS    DESIRED OUTPUTS (BINDING CONSTANTS)
 TEST_DATA       POINTS IN THE DATA SET
 TEST_SET_LENGTH ACTUAL NUMBER OF DATA POINTS IN DATA SET
 TOPTXT   : TEXT TO BE WRITTEN IN TOP-RIGHT CORNER OF SCREEN
 TOP_NEURONS     NEURONS BETWEEN TOP AND HIDDEN LAYER
 TORANG : ARRAY WITH ALL TOR ANGLES FOR THE MAIN SEQUENCE 
 TORCON : POINTERS TO CONNECTED ATOMS FOR TORANGLES
 TPTXLN   : FIRST INFO TEXT FOR DIALOG BOXES
 TPTXLN2  : SECOND INFO TEXT FOR DIALOG BOXES
 TRIGER : BOOLEAN TELLING WHICH REFS TO USE FOR GRAPHICS
 USE300   LOGICAL WHETHER PS300 IS ON OR NOT
 USEAT  : LOGICAL TO FLAG USAGE OF ATOMS 
 USESOU NUMBERS OF MOLECULES TO BE USED
 UVWMAT : MAP CONVERSION MATRICES
 UVWORG : ORIGIN OF THE MAPS IN FRACTIONAL COORDINATES
 V1     : VALUE FOUND IN MDF COLUMN 1
 V2     : VALUE FOUND IN MDF COLUMN 2
 V3     : VALUE FOUND IN MDF COLUMN 3
 V4     : VALUE FOUND IN MDF COLUMN 4
 VDDDON : TRUE IF VAN DER DOT FILE HAS BEEL GENERATED
 VDWRAD : VAN DER WAALS RADIUS OF ATOMS
 WARUNT WILL BE USED TO LOG WARNINGS
 WEIGHT : WEIGHT PUT ON ATOMS (TYPICAL X-RAY CRYSTALLOGRAFIC THING)
 WHAT IF CAN DEAL WITH. CHANGING ONE PARAMETER MEANS THAT THE WHOLE
 WHERIS : LOCATION (=DIRECTORY NAME) OF THE DATABASE FILES
 WIF072   FUNCTION TO CALCULATE DEPTH IN MENU TREE
 WIFFAC : INDICATES STATUS OF PROTEIN IN DATABASE
 WIFPAR : INTERNAL COUNTERS AND FLAGS (SEE PROGRAM DOCUMENTATION)
 WORKAA : AMINO ACID OF CENTER OF SCREEN
 WORKMAT  : MATRIX FOR MANIPULATING/SAVING/RESTORING VIEW MATRIX
 WORKTF : BOOLEAN FOR RESIDUE ALREADY IN WORK OR NOT
 WRKREF : THE ACTIVE COPY OF V1-4
 XBFACT : TEMPERATURE FACTORS FOR ATOMS
 XCOORD : X-COORDINATES FOR ATOMS
 XIDA   : COORDINATES OF IDENTIFIER POSITIONS AT THE SCREEN
 XMOL     COORDINATES OF START POINT OF GRAPHICS VECTOR
 XUACC  : X-COORDINATES OF DOTS AT ACCESSIBILITY CALCULATION SURFACE
 XYZ    : REAL(3) ARRAY FOR COORDINATE OPERATIONS (SCRATCH)
 XYZ1,2,3  : COORDINATES OF ALPHA CARBONS
 XYZCAS : COPY OF X,Y,Z COORDINATES OF CA'S (FOR GRAFICS MAINLY)
 YCOORD : Y-COORDINATES FOR ATOMS
 YMOL     COORDINATES OF END POINT OF GRAPHICS VECTOR
 YUACC  : Y-COORDINATES OF DOTS AT ACCESSIBILITY CALCULATION SURFACE
 ZCOORD : Z-COORDINATES FOR ATOMS
 ZUACC  : Z-COORDINATES OF DOTS AT ACCESSIBILITY CALCULATION SURFACE

Topology file

This is the description of the format of the topology file for WHAT IF. The topology file contains a number of records per entity. Entities are amino acids, co-factors, etc.

The topology file should start with N amino acids (N should be given in ICONFI.FIG, sorry). Thereafter DNA/RNA should follow, and the file should be closed with the drugs for which a topology has been user-added.

Per amino acid the following information has to be present:
 1) An asterix
 2) The name in three and 1 letter code (A4,A1 left justified)
 3) Seven constants that indicate: (Free format integers)
    1) The number of atoms (ATPRAA)
    2) The number of intra-residue bonds
    3) The number of rotable side-chain torsion angles (CHIUSE)
    4) The number of measurable torsion angles
    5) 1 -> Standard atomic coordinates are present ( 0 -> not )
    6) Standard bondlengths for the first N bonds
    7) Number of hydrogen bond 'groups'
 4) The atom names (14A4 left justified)
 5) Pairs of bonded atoms (10 pairs of integers per line, free format)
 6) Per rotable side-chain: the two atoms that define the axis followed
    by all atoms that should rotate (20 integers per line, free format)
 7) Per measurable torsion angle the four atoms (20 free format 
    integers per line; that is 5 torsion angles per line)
 8) Per atom the following information:
    1) Standard X coordinate \
    2) Standard Y coordinate |-> free formatted within columns 1-29
    3) Standard Z coordinate /
    4) T or F for hydrogen bondable or not. Fixed in column 30.
    5) + or - for donor or acceptor (blank means both possible) Fixed
       in column 31
    6) Hydrogen bond type number. Fixed column 33.
    7) Group number this donor/acceptor is member of. Fixed column 35.
 9) The standard bondlengths (one per line, free format)
10) Number of hydrogen bond groups, followed by per group ???? I5,30F5.2

Example of topology entry

*
GLU E
  15 14    3   3   1   8   1
N   CA  C   O   CB  CG  CD  OE1 OE2 1N  1CA 1CB 2CB 1CG 
2CG 
1 2  2 3  3 4  2 5  5 6  6 7  7 8  7 9  1 10 2 11
5 12 5 13 6 14 6 15  
2 5   6 7 8 9 12 13 14 15
5 6   7 8 9 14 15
6 7   8 9
1 2 5 6  2 5 6 7  5 6 7 8
  1.20131  0.84661  0.00001  T+ 1
  0.00001  0.00001  0.00001  F
 -1.25031  0.88111  0.00001  F
 -2.18531  0.66031 -0.78411  T-
 -0.05931 -0.87451  1.25831  F
  1.08171 -1.84981  1.50081  F
  0.98981 -2.68741  2.73981  F
  0.06741 -2.62371  3.53931  T  7 1
  1.97021 -3.44941  2.87091  T  7 1
  1.20131  1.84661  0.00001  F
  0.00002 -0.58204 -0.81314  F
 -0.90302 -1.40913  1.21004  F
 -0.09876 -0.26025  2.04643  F
  1.92852 -1.32051  1.55339  F
  1.12423 -2.46941  0.71704  F
1.453
1.530
1.230
1.530
1.530
1.530
1.265
1.265
    2 0.00 0.75 9.99