Read PDB files and display in Gizmo

//This set of procedures will read PDB (protein database) files:
//          https://en.wikipedia.org/wiki/Protein_Data_Bank_(file_format)
//
//Jan Ilavsky, 2018
//free to use or modify, no copyright.
//      Major thanks to John Weeks who wrote most of early code when I needed it
//      Thanks to tcaus, Igor Exchange user who described the pdb file structure:
//      referecne: https://www.wavemetrics.com/forum/general/igor-does-not-recognize-decim…
//To use:
// run ReadPDBFile()    in command line.


Function ReadPDBFile()
    //      the following pdb description is from Igor user group user icaus, original reference available here:
    //      https://www.wavemetrics.com/forum/general/igor-does-not-recognize-decim…
    //
    //  start in known place...
     String NewFoldername
     setDataFolder root:
    //this is definition of way PDB locations are written
    //note that most of data I do not need, you may need to change to code to read and use atoom names and other info.
    String columnInfo = ""                  // This only works for rows starting with "ATOM"
    columnInfo+="C=1,W=6,N=keyword;"    //"ATOM" name column                                 0
    columnInfo+="C=1,W=6,N='_skip_';"   // Atom number (last column unspecified)     7
    columnInfo+="C=1,W=5,N='_skip_';"   // Atom name; last character is "alt Loc"   13
    columnInfo+="C=1,W=3,N='_skip_';"   // Residue name; starts at column 18        18
    columnInfo+="C=1,W=2,N='_skip_';"   // Chain identifier in column 22 (21=?) 21
    columnInfo+="C=1,W=4,N='_skip_';"   // Residue sequence number                      23
    columnInfo+="C=1,W=4,N='_skip_';"   // Blank stuff                                      27
    columnInfo+="C=1,W=8,N=xval;"        // Should start at column 31               31
    columnInfo+="C=1,W=8,N=yval;"            //                                                 39
    columnInfo+="C=1,W=8,N=zval;"        //                                                 47
    columnInfo+="C=1,W=6,N='_skip_';"   // Occupancy
    columnInfo+="C=1,W=6,N='_skip_';"   // Temperature info
    columnInfo+="C=1,W=11,N='_skip_';"  // Element symbol   (col 77,78)
    columnInfo+="C=1,W=2,N='_skip_';"   // Charge (col 79,80)
    //OK, now load the data...
    LoadWave/A/O/F={14,8,0}/K=2/B=columnInfo
    Wave/T xval, yval, zval
    Wave/T keyword
    //create name for future data location, unique name created from loaded file name.
     NewFoldername= UniqueName(StringFromList(0,S_FileName,"."), 11, 0)
     //remove all non ATOM lines from the waves...
    Variable count=numpnts(keyword)-1
    do
        if (strsearch(keyword[count], "ATOM", 0) <0 )
            DeletePoints count, 1, keyword, xval, yval, zval
        endif
        count-=1
    while (count >= 0 )
    //create location for centers of atoms in Gizmo and assign the positions.
    Make/O/D/n=(numpnts(xval),3) centersWave=nan
     centersWave[][0]=str2num(xval[p])
     centersWave[][1]=str2num(yval[p])
     centersWave[][2]=str2num(zval[p])
    //cleanup
    KillWaves keyword, xval, yval, zval
     //create location for data
     NewDataFolder/S $(NewFoldername)
     //move there the centers wave
     MoveWave root:centersWave, $(GetDataFolder(1))
    //now create the Gizmo, it needs to know where the data are, this is one way to tell it...
    string PathToData=GetDataFolder(1)+"centersWave"
    MakeGizmo(PathToData)
End

Function MakeGizmo(PathToData)
    string PathToData
    //will create Gizmo, I used existiing Gizmo and created recreation function.
    //these are the centers...
    Wave GizmoData=$(PathToData)
    NewGizmo/K=1/W=(83,132,981,947)
    ModifyGizmo startRecMacro=700
    ModifyGizmo scalingMode=8
    ModifyGizmo scalingOption=0
    AppendToGizmo Scatter=GizmoData,name=scatter0
    ModifyGizmo ModifyObject=scatter0,objectType=scatter,property={ scatterColorType,0}
    ModifyGizmo ModifyObject=scatter0,objectType=scatter,property={ markerType,0}
    ModifyGizmo ModifyObject=scatter0,objectType=scatter,property={ sizeType,0}
    ModifyGizmo ModifyObject=scatter0,objectType=scatter,property={ rotationType,0}
    ModifyGizmo ModifyObject=scatter0,objectType=scatter,property={ Shape,1}
    ModifyGizmo ModifyObject=scatter0,objectType=scatter,property={ size,1}
    ModifyGizmo ModifyObject=scatter0,objectType=scatter,property={ color,4.57771e-05,0.8,1.5259e-05,1}
    AppendToGizmo Axes=boxAxes,name=axes0
    ModifyGizmo ModifyObject=axes0,objectType=Axes,property={-1,axisScalingMode,1}
    ModifyGizmo ModifyObject=axes0,objectType=Axes,property={-1,axisColor,0,0,0,1}
    ModifyGizmo modifyObject=axes0,objectType=Axes,property={-1,Clipped,0}
    AppendToGizmo attribute pointSize=8, name=pointSize0
    ModifyGizmo setDisplayList=0, attribute=pointSize0
    ModifyGizmo setDisplayList=1, object=scatter0
    ModifyGizmo setDisplayList=2, object=axes0
    ModifyGizmo currentGroupObject=""
    ShowTools
    ModifyGizmo showInfo
    ModifyGizmo infoWindow={904,365,1721,662}
    ModifyGizmo showAxisCue=1
    ModifyGizmo pan={0.075688,-0.110429}
    ModifyGizmo idleEventQuaternion={-1.1184e-06,6.7395e-06,-4.52601e-06,1}
    //these next two lines scale the Gizmo axes to be 5% larger than Max atom position value.
    //*1.05 should make sure the all positions are inside, not clipped, and x,y, and z have same scale
   //(so dimensions are not distorted).
    WaveStats/Q GizmoData
    ModifyGizmo setOuterBox={-1.05*V_max,1.05*V_max,-1.05*V_max,1.05*V_max,-1.05*V_max,1.05*V_max}
end