********> bugfix.16
Author:   Bill Ross
Date:     5/10/95

Programs: leap

Severity: moderate

Problem:  With addIons command using ions in ions*.lib one sees:
          ContainerCenterAt(): Skipping atom w/ unknown position

Cause:    The ions in ions*.lib lack a flag indicating that they
          have positions. At the moment, there is no obvious way
          to have the code set this flag when the ions are originally
          created.

          The fix causes this flag to be set in addIons when an ion 
          consists of a single atom. The work-around below contains 
          diffs for ions*.lib for inserting the correct flags.


Fix:  Make the following change to commands.c
-------------------------------------------------------------------------
*** OLD commands.c
--- NEW commands.c
***************
*** 830,836
  	i++;
      }
  
!     VP0(( "Loading PDB file\n" ));
      uUnit = uPdbRead( fPdb, vaUnits );
  
      VarArrayDestroy( &vaUnits );

--- 830,836 -----
  	i++;
      }
  
!     VP0(( "Loading PDB file: %s\n", GsBasicsFullName )); 
      uUnit = uPdbRead( fPdb, vaUnits );
  
      VarArrayDestroy( &vaUnits );
***************
*** 4416,4422
  STRING		sTemp;
  double		dCharge, dPertCharge, dICharge1, dICharge2;
  double		dIonSize1, dIonSize2, dMinSize;
! int		iCharge, iTemp, ierr;
  VECTOR		vNewPoint, vMaxPot, vMinPot;
  RESIDUE		rRes;
  HELP		hTemp;

--- 4416,4422 -----
  STRING		sTemp;
  double		dCharge, dPertCharge, dICharge1, dICharge2;
  double		dIonSize1, dIonSize2, dMinSize;
! int		iCharge, iUnknown, iTemp, ierr;
  VECTOR		vNewPoint, vMaxPot, vMinPot;
  RESIDUE		rRes;
  HELP		hTemp;
***************
*** 4541,4547
      } 
  
      /*
!      *  Consider ion sizes.
       */
      dIonSize1 = 0.0;
      lAtoms = lLoop( uIon1, ATOMS );

--- 4540,4546 -----
      } 
  
      /*
!      *  Consider ion sizes and positions.
       */
      dIonSize1 = 0.0;
      iUnknown = 0;
***************
*** 4544,4549
       *  Consider ion sizes.
       */
      dIonSize1 = 0.0;
      lAtoms = lLoop( uIon1, ATOMS );
      for(i=0; aAtom = (ATOM)oNext(&lAtoms); i++) {
  	if ( iAtomSetTmpRadius( aAtom ) )

--- 4543,4549 -----
       *  Consider ion sizes and positions.
       */
      dIonSize1 = 0.0;
+     iUnknown = 0;
      lAtoms = lLoop( uIon1, ATOMS );
      for(i=0; aAtom = (ATOM)oNext(&lAtoms); i++) {
  	if ( iAtomSetTmpRadius( aAtom ) )
***************
*** 4550,4555
  		VP0(( "Using default radius %5.2f for ion %s\n",
  			ATOM_DEFAULT_RADIUS, sAssocName( aaArgs[1] ) ));
  	dIonSize1 = MAX( dIonSize1, dAtomTemp( aAtom ) );
      }
      if ( i > 1 ) {
  	VP0(( "Ion %s is polyatomic; multiplying max radius %5.2f by # atoms\n",

--- 4550,4557 -----
  		VP0(( "Using default radius %5.2f for ion %s\n",
  			ATOM_DEFAULT_RADIUS, sAssocName( aaArgs[1] ) ));
  	dIonSize1 = MAX( dIonSize1, dAtomTemp( aAtom ) );
+ 	if ( !bAtomFlagsSet( aAtom, ATOMPOSITIONKNOWN ) )
+ 		iUnknown++;
      }
      if ( i > 1 ) {
  	if ( iUnknown ) {
***************
*** 4552,4557
  	dIonSize1 = MAX( dIonSize1, dAtomTemp( aAtom ) );
      }
      if ( i > 1 ) {
  	VP0(( "Ion %s is polyatomic; multiplying max radius %5.2f by # atoms\n",
  		sAssocName( aaArgs[1] ), dIonSize1 ));
  	dIonSize1 *= (double) i;

--- 4554,4564 -----
  		iUnknown++;
      }
      if ( i > 1 ) {
+ 	if ( iUnknown ) {
+ 	    VP0(( "Ion %s is polyatomic and has %d atoms w/ no position\n",
+ 		sAssocName( aaArgs[1] ), iUnknown ));
+ 	    RETURN( NULL );
+ 	}
  	VP0(( "Ion %s is polyatomic; multiplying max radius %5.2f by # atoms\n",
  		sAssocName( aaArgs[1] ), dIonSize1 ));
  	dIonSize1 *= (double) i;
***************
*** 4555,4560
  	VP0(( "Ion %s is polyatomic; multiplying max radius %5.2f by # atoms\n",
  		sAssocName( aaArgs[1] ), dIonSize1 ));
  	dIonSize1 *= (double) i;
      }
      dMinSize = dIonSize1;
      if ( uIon2 ) {

--- 4562,4575 -----
  	VP0(( "Ion %s is polyatomic; multiplying max radius %5.2f by # atoms\n",
  		sAssocName( aaArgs[1] ), dIonSize1 ));
  	dIonSize1 *= (double) i;
+     } else if ( iUnknown ) {
+ 	VECTOR		vPos;
+ 
+ 	VectorDef( &vPos, 0.0, 0.0, 0.0 );
+         lAtoms = lLoop( uIon1, ATOMS );
+     	aAtom = (ATOM)oNext(&lAtoms);
+ 	AtomSetPosition( aAtom, vPos );
+ 	AtomSetFlags( aAtom, ATOMPOSITIONKNOWN );
      }
      dMinSize = dIonSize1;
      if ( uIon2 ) {
***************
*** 4559,4564
      dMinSize = dIonSize1;
      if ( uIon2 ) {
  	dIonSize2 = 0.0;
      	lAtoms = lLoop( uIon2, ATOMS );
      	for(i=0; aAtom = (ATOM)oNext(&lAtoms); i++) {
  		if ( iAtomSetTmpRadius( aAtom ) )

--- 4574,4580 -----
      dMinSize = dIonSize1;
      if ( uIon2 ) {
  	dIonSize2 = 0.0;
+ 	iUnknown = 0;
      	lAtoms = lLoop( uIon2, ATOMS );
      	for(i=0; aAtom = (ATOM)oNext(&lAtoms); i++) {
  		if ( iAtomSetTmpRadius( aAtom ) )
***************
*** 4565,4570
  			VP0(( "Using default radius %5.2f for ion %s\n",
  				ATOM_DEFAULT_RADIUS, sAssocName( aaArgs[3] ) ));
  		dIonSize2 = MAX( dIonSize2, dAtomTemp( aAtom ) );
      	}
  	if ( i > 1 ) {
  	    VP0(( 

--- 4581,4588 -----
  			VP0(( "Using default radius %5.2f for ion %s\n",
  				ATOM_DEFAULT_RADIUS, sAssocName( aaArgs[3] ) ));
  		dIonSize2 = MAX( dIonSize2, dAtomTemp( aAtom ) );
+ 		if ( !bAtomFlagsSet( aAtom, ATOMPOSITIONKNOWN ) )
+ 		    iUnknown++;
      	}
  	if ( i > 1 ) {
  	    if ( iUnknown ) {
***************
*** 4567,4572
  		dIonSize2 = MAX( dIonSize2, dAtomTemp( aAtom ) );
      	}
  	if ( i > 1 ) {
  	    VP0(( 
  		"Ion %s is polyatomic; multiplying max radius %5.2f by # atoms",
  		sAssocName( aaArgs[3] ), dIonSize2 ));

--- 4585,4595 -----
  		    iUnknown++;
      	}
  	if ( i > 1 ) {
+ 	    if ( iUnknown ) {
+ 	    	VP0(( "Ion %s is polyatomic and has %d atoms w/ no position\n",
+ 		    sAssocName( aaArgs[1] ), iUnknown ));
+ 	    	RETURN( NULL );
+ 	    }
  	    VP0(( 
  		"Ion %s is polyatomic; multiplying max radius %5.2f by # atoms",
  		sAssocName( aaArgs[3] ), dIonSize2 ));
***************
*** 4571,4576
  		"Ion %s is polyatomic; multiplying max radius %5.2f by # atoms",
  		sAssocName( aaArgs[3] ), dIonSize2 ));
  	    dIonSize2 *= (double) i;
  	}
  	dMinSize = MIN( dIonSize1, dIonSize2 );
      }

--- 4594,4607 -----
  		"Ion %s is polyatomic; multiplying max radius %5.2f by # atoms",
  		sAssocName( aaArgs[3] ), dIonSize2 ));
  	    dIonSize2 *= (double) i;
+ 	} else if ( iUnknown ) {
+ 	    VECTOR		vPos;
+ 
+ 	    VectorDef( &vPos, 0.0, 0.0, 0.0 );
+             lAtoms = lLoop( uIon1, ATOMS );
+     	    aAtom = (ATOM)oNext(&lAtoms);
+ 	    AtomSetPosition( aAtom, vPos );
+ 	    AtomSetFlags( aAtom, ATOMPOSITIONKNOWN );
  	}
  	dMinSize = MIN( dIonSize1, dIonSize2 );
      }
-------------------------------------------------------------------------

Temporary workarounds: make the following mods to ions94.lib:

8c8
<  "Cs+" "Cs" 0 1 0 1 55 1.000000
---
>  "Cs+" "Cs" 0 1 131072 1 55 1.000000
44c44
<  "K+" "K" 0 1 0 1 19 1.000000
---
>  "K+" "K" 0 1 131072 1 19 1.000000
80c80
<  "Li+" "Li" 0 1 0 1 3 1.000000
---
>  "Li+" "Li" 0 1 131072 1 3 1.000000
116c116
<  "Na+" "IP" 0 1 0 1 11 1.000000
---
>  "Na+" "IP" 0 1 131072 1 11 1.000000
152c152
<  "Rb+" "Rb" 0 1 0 1 37 1.000000
---
>  "Rb+" "Rb" 0 1 131072 1 37 1.000000

Temporary workarounds: make the following mods to ions91.lib:

9c9
<  "Cs+" "QC" 0 1 0 1 55 1.000000
---
>  "Cs+" "QC" 0 1 131072 1 55 1.000000
45c45
<  "IB" "IB" 0 1 0 1 55 1.000000
---
>  "IB" "IB" 0 1 131072 1 55 1.000000
81c81
<  "K+" "QK" 0 1 0 1 19 1.000000
---
>  "K+" "QK" 0 1 131072 1 19 1.000000
117c117
<  "Li+" "QL" 0 1 0 1 3 1.000000
---
>  "Li+" "QL" 0 1 131072 1 3 1.000000
153c153
<  "Na+" "QN" 0 1 0 1 11 1.000000
---
>  "Na+" "QN" 0 1 131072 1 11 1.000000
189c189
<  "Rb+" "QR" 0 1 0 1 37 1.000000
---
>  "Rb+" "QR" 0 1 131072 1 37 1.000000
-------------------------------------------------------------------------