Difference between revisions of "User:Remig/plico/plicoCommon"

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(Add double-bonding support)
(Avoid "axis," a newly reserved word)
 
(3 intermediate revisions by the same user not shown)
Line 1: Line 1:
This script contains routines used by other scripts of the Plico suite.  It must be located in the same directory as any script that uses these routines.
+
This script contains routines used by other scripts of the Plico suite.  It must be located in the same directory as any script that uses these routines.  
  
 
Copy and paste the following into a text editor and save in your scripts folder as plicoCommon.spt.
 
Copy and paste the following into a text editor and save in your scripts folder as plicoCommon.spt.
 
<pre>#  plicoCommon - Jmol script by Ron Mignery
 
<pre>#  plicoCommon - Jmol script by Ron Mignery
#  v1.8 beta    7/13/2015 -add double-bond routine
+
#  v1.12 beta    4/12/2016 -axis is now a reserved word
 
#
 
#
 
#  Routines and values common to all Plico suite scripts
 
#  Routines and values common to all Plico suite scripts
 
#  Must be present in the same directory as other Plico scripts that use it
 
#  Must be present in the same directory as other Plico scripts that use it
kCommon = 5
+
kCommon = 7
 
kDtolerance = 0.1
 
kDtolerance = 0.1
kAtolerance = 5.0
 
 
kCtolerance = 1.85
 
kCtolerance = 1.85
kMtolerance = 0.8
 
 
gMouseX = 0
 
gMouseX = 0
 
gMouseY = 0
 
gMouseY = 0
Line 21: Line 19:
 
gAltScheme = "Rasmol"
 
gAltScheme = "Rasmol"
 
gBusy = false
 
gBusy = false
 +
gEcho = ""
 +
gMenuMin = false
  
 
# Return L tetrahedron point if i1<i2<i3, else R point
 
# Return L tetrahedron point if i1<i2<i3, else R point
Line 26: Line 26:
 
     var v1 = {atomIndex=i3}.xyz - {atomIndex=i2}.xyz
 
     var v1 = {atomIndex=i3}.xyz - {atomIndex=i2}.xyz
 
     var v2 = {atomIndex=i1}.xyz - {atomIndex=i2}.xyz
 
     var v2 = {atomIndex=i1}.xyz - {atomIndex=i2}.xyz
     var axis = cross(v1, v2)
+
     var caxis = cross(v1, v2)
 
     var pma = ({atomIndex=i1}.xyz + {atomIndex=i3}.xyz)/2
 
     var pma = ({atomIndex=i1}.xyz + {atomIndex=i3}.xyz)/2
 
     var pmo = {atomIndex=i2}.xyz + {atomIndex=i2}.xyz - pma
 
     var pmo = {atomIndex=i2}.xyz + {atomIndex=i2}.xyz - pma
     var pt = pmo + (axis/axis)
+
     var pt = pmo + (caxis/caxis)
  
 
     var v = pt - {atomIndex=i2}.xyz
 
     var v = pt - {atomIndex=i2}.xyz
Line 39: Line 39:
 
}
 
}
  
# Work around - Functions returning values must be in lower case for 14.0.13
 
 
function get_trigonal_idx(i1, i2, i3, dist) {
 
function get_trigonal_idx(i1, i2, i3, dist) {
 
     var v1 = {atomIndex=i1}.xyz - {atomIndex=i2}.xyz
 
     var v1 = {atomIndex=i1}.xyz - {atomIndex=i2}.xyz
Line 51: Line 50:
  
 
     return lpt + {atomIndex=i2}.xyz
 
     return lpt + {atomIndex=i2}.xyz
}
 
 
function abs( x) {
 
    return ((x < 0) ? -x : x)
 
 
}
 
}
  
 
# Selected must include second parameter but not the first
 
# Selected must include second parameter but not the first
 +
# Static may be just a point
 
function set_distance_atoms( static, mobile, desired) {
 
function set_distance_atoms( static, mobile, desired) {
 
     try {
 
     try {
         var v = mobile.xyz - static.xyz
+
        var s = ((static.type == "point") ? static : static.xyz)       
         var dist = distance(static, mobile)
+
         var v = mobile.xyz - s
         translateSelected @{((v * (desired/dist)) - v)}
+
         var dist = distance(s, mobile)
 +
         translateSelected @{(v * (desired/dist)) - v}
 
     }
 
     }
 
     catch {
 
     catch {
Line 72: Line 69:
  
 
# Selected must include third parameter but not the first
 
# Selected must include third parameter but not the first
 +
# Stator and pivot may be just points
 
function set_angle_atoms( stator, pivot, rotor, toangle) {
 
function set_angle_atoms( stator, pivot, rotor, toangle) {
 
     try {
 
     try {
         var v1=stator.xyz - pivot.xyz
+
         var s = ((stator.type == "point") ? stator : stator.xyz)       
         var v2=rotor.xyz - pivot.xyz
+
        var p = ((pivot.type == "point") ? pivot : pivot.xyz)       
         var axis = cross(v1, v2) + pivot.xyz
+
        var v1=s - p
 +
         var v2=rotor.xyz - p
 +
         var caxis = cross(v1, v2) + p
 
         var curangle =  angle(stator, pivot, rotor)
 
         var curangle =  angle(stator, pivot, rotor)
         rotateselected @axis @pivot @{curangle-toangle}
+
         rotateselected @caxis @pivot @{curangle-toangle}
 
     }
 
     }
 
     catch {
 
     catch {
 +
        print format("unable to set_angle_atoms( stator=%s, pivot=%s, rotor=%s, toangle=%f)",
 +
            stator, pivot, rotor, toangle)
 
     }
 
     }
 
}
 
}
Line 110: Line 112:
 
# Any side atoms in the range are also selected
 
# Any side atoms in the range are also selected
 
function select_nward_idx (firstIdx, lastIdx) {
 
function select_nward_idx (firstIdx, lastIdx) {
    var f = (_frameID/1000000)
 
    var m = (_frameID%1000000)
 
 
     var firstno = ((firstIdx < 0) ? {atomIndex=lastIdx}.atomno : {atomIndex=firstIdx}.atomno)
 
     var firstno = ((firstIdx < 0) ? {atomIndex=lastIdx}.atomno : {atomIndex=firstIdx}.atomno)
 
     var lastno = ((lastIdx < 0) ? firstno : {atomIndex=lastIdx}.atomno)
 
     var lastno = ((lastIdx < 0) ? firstno : {atomIndex=lastIdx}.atomno)
Line 118: Line 118:
  
 
     select ((atomno <= firstno) and (atomno >= lastno) and (chain = iChain)
 
     select ((atomno <= firstno) and (atomno >= lastno) and (chain = iChain)
         and (file=f) and (model=m))
+
         and thisModel)
 
     if ({(atomno=firstno) and (chain=gChain)
 
     if ({(atomno=firstno) and (chain=gChain)
         and (file=f) and (model=m)}.atomName == "C") { # if psi
+
         and thisModel}.atomName == "C") { # if psi
 
         add_sc_to_select(firstno-1, true, true, iChain)
 
         add_sc_to_select(firstno-1, true, true, iChain)
         var a = {(atomno=@{firstno+1}) and (chain=iChain) and (file=f) and (model=m)}
+
         var a = {(atomno=@{firstno+1}) and (chain=iChain) and thisModel}
 
         a.selected = true # add O
 
         a.selected = true # add O
 
     }
 
     }
 
     if ({(atomno=firstno) and (chain=iChain)
 
     if ({(atomno=firstno) and (chain=iChain)
         and (file=f) and (model=m)}.atomName == "CA") {
+
         and thisModel}.atomName == "CA") {
 
         add_sc_to_select(firstno, true, false, iChain)
 
         add_sc_to_select(firstno, true, false, iChain)
 
     }
 
     }
 
     if ({(atomno=lastno) and (chain=iChain)
 
     if ({(atomno=lastno) and (chain=iChain)
         and (file=f) and (model=m)}.atomName == "C") { # if psi
+
         and thisModel}.atomName == "C") { # if psi
 
         add_sc_to_select(lastno-1, false, false, iChain)
 
         add_sc_to_select(lastno-1, false, false, iChain)
 +
    }
 +
}
 +
 +
function add_sc_to_select(CAno, isAdd, addOXT, iChain) {
 +
    var res = {(atomno=CaNo) and (chain=iChain) and thisModel}.resno
 +
    var scset = {(resno=res) and (chain=iChain) and thisModel and sidechain}
 +
    if (addOXT) {
 +
        scset = scset or get_atom_rcn(res, iChain, "OXT")
 +
    }
 +
    if (isAdd) {
 +
        select add scset
 +
    }
 +
    else {
 +
        select remove scset
 
     }
 
     }
 
}
 
}
Line 138: Line 152:
 
# Any side atoms in the range are also selected
 
# Any side atoms in the range are also selected
 
function select_cward_idx (firstIdx, lastIdx) {
 
function select_cward_idx (firstIdx, lastIdx) {
    var f = (_frameID/1000000)
 
    var m = (_frameID%1000000)
 
 
     var firstno = ((firstIdx < 0) ? gMaxNo : {atomIndex=firstIdx}.atomno)
 
     var firstno = ((firstIdx < 0) ? gMaxNo : {atomIndex=firstIdx}.atomno)
 
     var lastno = ((lastIdx < 0) ? 1 : {atomIndex=lastIdx}.atomno)
 
     var lastno = ((lastIdx < 0) ? 1 : {atomIndex=lastIdx}.atomno)
Line 162: Line 174:
  
 
     select ((atomno >= firstno) and (atomno <= lastno) and (chain = iChain)
 
     select ((atomno >= firstno) and (atomno <= lastno) and (chain = iChain)
         and (file=f) and (model=m))
+
         and thisModel)
  
 
     if ({(atomno=firstno) and (chain=iChain)
 
     if ({(atomno=firstno) and (chain=iChain)
         and (file=f) and (model=m)}.atomName == "C") { # if psi
+
         and thisModel}.atomName == "C") { # if psi
 
         add_sc_to_select(firstno-1, false, false, iChain)
 
         add_sc_to_select(firstno-1, false, false, iChain)
 
     }
 
     }
 
     if ({(atomno=lastno) and (chain=iChain)
 
     if ({(atomno=lastno) and (chain=iChain)
         and (file=f) and (model=m)}.atomName == "CA") {
+
         and thisModel}.atomName == "CA") {
 
         add_sc_to_select(lastno, true, false, iChain)
 
         add_sc_to_select(lastno, true, false, iChain)
 
     }
 
     }
 
     if ({(atomno=lastno) and (chain=iChain)
 
     if ({(atomno=lastno) and (chain=iChain)
         and (file=f) and (model=m)}.atomName == "C") { # if psi
+
         and thisModel}.atomName == "C") { # if psi
 
         add_sc_to_select(lastno-1, true, true, iChain)
 
         add_sc_to_select(lastno-1, true, true, iChain)
         var a = {(atomno=@{lastno+1}) and (chain=iChain) and (file=f) and (model=m)}
+
         var a = {(atomno=@{lastno+1}) and (chain=iChain) and thisModel}
 
         a.selected = true # add O
 
         a.selected = true # add O
 
     }
 
     }
 +
}
 +
 +
# tug.spt needed to handle collisions
 +
function to_handle_collisions( idx) {
 +
    # Load tug functions
 +
    if (kTug < 3) {
 +
        script $SCRIPT_PATH$tug.spt
 +
        if (kTug < 3) {
 +
            prompt ("A newer version of tug.SPT is required")
 +
            quit
 +
        }
 +
    }
 +
    handle_collisions( idx)
 
}
 
}
  
 
function count_collisions(rc) {
 
function count_collisions(rc) {
    var f = (_frameID/1000000)
 
    var m = (_frameID%1000000)
 
 
     var cAtoms = ({})
 
     var cAtoms = ({})
     for (var idx = {(file=f) and (model=m)}.min.atomIndex;
+
     for (var idx = {thisModel}.min.atomIndex;
         idx <= {(file=f) and (model=m)}.max.atomIndex; idx++) {
+
         idx <= {thisModel}.max.atomIndex; idx++) {
         if ({atomIndex=idx}.size > 0) {
+
         if ({atomIndex=idx} and {element!="H"}) {
 
             var lcAtoms = (within(kCtolerance, false, {atomIndex=idx})
 
             var lcAtoms = (within(kCtolerance, false, {atomIndex=idx})
                 and {atomIndex > idx}
+
                 and {atomIndex > idx} and {element!="H"}
                and not {rc}
 
 
                 and not connected({atomIndex=idx}))
 
                 and not connected({atomIndex=idx}))
             if (lcAtoms.size > 0) {
+
             if (lcAtoms) {
 
                 cAtoms = cAtoms or lcAtoms or {atomIndex=idx}
 
                 cAtoms = cAtoms or lcAtoms or {atomIndex=idx}
                 if (rc == true) {
+
                 for (var i = 1; i <= lcAtoms.size; i++) {
                     print format("Collision of idx=%d with %s", idx, lcAtoms)
+
                     print format("Collision of ({%d}) with %s", idx, lcAtoms[i])
                     for (var i = 1; i <= lcAtoms.size; i++) {
+
                     if (rc == true) {
                         measure {atomindex=idx} ({@lcAtoms[i]})
+
                         measure {atomindex=idx} {@{lcAtoms[i]}}
 
                     }
 
                     }
 
                 }
 
                 }
Line 203: Line 225:
 
     }
 
     }
 
     return cAtoms
 
     return cAtoms
}
 
 
function is_collision_in_select() {
 
    var f = (_frameID/1000000)
 
    var m = (_frameID%1000000)
 
    is = false
 
    var cAtoms = ({})
 
    var iChain = {selected}.chain
 
    for (var no = {selected}.min.atomno; no <= {selected}.max.atomno; no++) {
 
        a = {(atomno=no) and (chain=iChain) and (file=f) and (model=m)}
 
        if (a.size > 0) {
 
            is = true
 
            break
 
        }
 
    }
 
    return is
 
}
 
 
# A handy debug routine
 
function cc {
 
    print count_collisions(true)
 
 
}
 
}
  
 
# Utility
 
# Utility
 
function get_atom_rcn( iResno, iChain, iName) {
 
function get_atom_rcn( iResno, iChain, iName) {
    var f = (_frameID/1000000)
 
    var m = (_frameID%1000000)
 
 
     return {(resno=iResno) and (chain=iChain) and (atomName=iName)
 
     return {(resno=iResno) and (chain=iChain) and (atomName=iName)
         and (file=f) and (model=m)}
+
         and thisModel}
 
}
 
}
  
 
# Utility
 
# Utility
 
function atom_noc( iNo, iChain) {
 
function atom_noc( iNo, iChain) {
    var f = (_frameID/1000000)
+
     return {(atomno=iNo) and (chain=iChain) and thisModel}
    var m = (_frameID%1000000)
 
     return {(atomno=iNo) and (chain=iChain) and (atomName=iName)
 
        and (file=f) and (model=m)}
 
 
}
 
}
  
Line 247: Line 243:
 
}
 
}
  
function plico_prelim(repair) {
+
function plico_menu_toggle() {
 +
    var yr = _height-25
 +
    if ((_mouseY > (_height-25)) and (_mouseX < 300)) {
 +
        if (gMenuMin) {
 +
            echo @gEcho
 +
        }
 +
        else {
 +
            var p = gEcho.find("|")
 +
            if (p > 0) {
 +
                echo @{gEcho[1][p-1]}
 +
            }
 +
            else {
 +
                echo
 +
            }
 +
        }
 +
        gMenuMin = !gMenuMin
 +
    }
 +
    gBusy = false
 +
}
 +
 
 +
function plico_prelim(repair, backup) {
  
 
     # Push selected
 
     # Push selected
 
     gSelSaves = {selected}
 
     gSelSaves = {selected}
     var f = (_frameID/1000000)
+
     select (thisModel)
     var m = (_frameID%1000000)
+
     gBusy=false
    select ((file=f) and (model=m))
 
  
 
     # Bad idea to proceed when collisions present
 
     # Bad idea to proceed when collisions present
Line 265: Line 280:
 
             }
 
             }
 
             else if (p == "Repair") {
 
             else if (p == "Repair") {
                 select ((file=f) and (model=m))
+
                 select (thisModel)
 
                 allSet = {selected}
 
                 allSet = {selected}
 
                 gChain = "XX"
 
                 gChain = "XX"
Line 272: Line 287:
 
                     if ({atomIndex=idx}.chain != gChain) {
 
                     if ({atomIndex=idx}.chain != gChain) {
 
                         gChain = {atomIndex=idx}.chain
 
                         gChain = {atomIndex=idx}.chain
                         select {(chain=gChain) and (file=f) and (model=m)}
+
                         select {(chain=gChain) and thisModel}
                         handle_collisions( idx)
+
                         to_handle_collisions( idx)
 
                     }
 
                     }
 
                 }
 
                 }
Line 288: Line 303:
 
     gZoom = script("show zoom")
 
     gZoom = script("show zoom")
 
     gRotate = script("show rotation")
 
     gRotate = script("show rotation")
     write tugsave.pdb
+
     if (backup) {
 +
        write plico_save.pdb
 +
    }
 
     select none
 
     select none
  
Line 296: Line 313:
 
     background ECHO yellow
 
     background ECHO yellow
 
     gChain = ""
 
     gChain = ""
 +
    gMenuMin = false
 
     unbind
 
     unbind
 
}
 
}
  
# gPlicoRecord is maintained by the macro pilcoRecord
+
# gPlicoRecord is maintained by the macro plicoRecord
 
function plico_record(s) {
 
function plico_record(s) {
 
     var g = format("show file \"%s\"", gPlicoRecord)
 
     var g = format("show file \"%s\"", gPlicoRecord)
 
     var ls = script(g)
 
     var ls = script(g)
     if (ls.find("FileNotFoundException")) {
+
     if (ls.find("FileNotFoundException") > 0) {
 
         ls = ""
 
         ls = ""
 
     }
 
     }
Line 310: Line 328:
 
}
 
}
  
function plico_exit() {
+
function plico_exit(undo) {
 
     var p = ""
 
     var p = ""
 
     var done = false
 
     var done = false
     if (gPlico.size > 0) {
+
     if (gPlico) {
         p = prompt(format("Exit %s?", gPlico), "Yes|No|Undo", true)
+
         p = prompt(format("Exit %s?", gPlico),
         if (p == "Undo") {
+
            "Yes|No"+(undo ? "|Undo all" : ""), true)
             load tugsave.pdb
+
         if (p == "Undo all") {
 +
             load plico_save.pdb
 
             script inline gZoom
 
             script inline gZoom
 
             rotate @gRotate
 
             rotate @gRotate
             echo Tug session undone
+
             echo Session undone
 
             if (gPlicoRecord != "") {
 
             if (gPlicoRecord != "") {
                 plico_record("load tugsave.pdb;")
+
                 plico_record("load plico_save.pdb;")
 
             }
 
             }
 +
            reset gPlotEcho
 +
            set AnimFrameCallback NONE
 
         }
 
         }
 
     }
 
     }
Line 328: Line 349:
 
         unbind
 
         unbind
 
         halo off
 
         halo off
        echo
+
         select (thisModel)
        var f = (_frameID/1000000)
 
        var m = (_frameID%1000000)
 
         select ((file=f) and (model=m))
 
 
         halo off
 
         halo off
 
         star off
 
         star off
Line 337: Line 355:
 
         draw gSCcircle DELETE
 
         draw gSCcircle DELETE
 
         gBusy = false
 
         gBusy = false
 +
        gEcho = ""
 +
        set echo TOP LEFT
 
         background ECHO yellow
 
         background ECHO yellow
 +
        echo @gEcho
 +
        gMenuMin = false
 
         done = true
 
         done = true
  
Line 346: Line 368:
 
}
 
}
  
function plot_o_rot( iChain) {
+
function add_hydrogens(addh) {
     var f = (_frameID/1000000)
+
     delete hydrogen
    var m = (_frameID%1000000)
+
     connect {*} {*} aromatic modify
    select none
+
     if (addh) {
    var first = true
+
         calculate hydrogens
    var aNp = ({})
 
     var aCAp = ({})
 
    var aCp = ({})
 
     for (var i = {(chain=iChain) and (file=f) and (model=m)}.resno.min;
 
        i <= {(chain=iChain) and (file=f) and (model=m)}.resno.max; i++) {
 
        var aN = get_atom_rcn(i, iChain, "N")
 
        var aCA = get_atom_rcn(i, iChain, "CA")
 
        var aC = get_atom_rcn(i, iChain, "C")
 
       
 
        if (first) {
 
            first = false
 
        }
 
        else  {
 
            aN.vx = angle(aCp, aN, aCA, aC)
 
            aN.vy = angle(aNp, aCAp, aCp, aN)
 
            select ADD aN
 
        }
 
        aNp = aN
 
        aCAp = aCA
 
         aCp = aC
 
 
     }
 
     }
     plot properties vx vy resno
+
     calculate aromatic
    set echo top left
 
    echo "vx = phi        vy = previous psi"
 
 
}
 
}
  
 
# Prevents minimization from disrespecting planar elements
 
# Prevents minimization from disrespecting planar elements
 +
# and allows calculate hydrogens to place hydrogens correctly
 
function double_bond_planars(iChain, undo) {
 
function double_bond_planars(iChain, undo) {
     for (var i = {chain=iChain}.resno.min; i <= {chain=iChain}.resno.max; i++) {
+
print format("double_bond_planars(%s, %s)", iChain, undo)
 +
     for (var i = get_resno_min(iChain); i <= get_resno_max(iChain); i++) {
 
         var aa = {resno=i}.group[0]
 
         var aa = {resno=i}.group[0]
         var bps = []
+
         var bps = ["O","C"]
 
         switch (aa) {
 
         switch (aa) {
         case 'TYR' :
+
         case 'ARG' :
         case 'PHE' :
+
            bps += ["CZ","NH1"]
             bps = ["CG","CD1","CD2","CE2","CE1","CZ"]
+
            break
 +
        case 'ASN' :
 +
         case 'ASP' :
 +
             bps += ["OD1","CG"]
 +
            break
 +
        case 'GLN' :
 +
        case 'GLU' :
 +
            bps += ["OE1","CD"]
 
             break
 
             break
 
         case 'HIS' :
 
         case 'HIS' :
             bps = ["CG","CD2","CE1","NE2"]
+
             bps += ["CG","CD2","CE1","NE2"]
 +
            break
 +
        case 'PHE' :
 +
        case 'TYR' :
 +
            bps += ["CG","CD1","CD2","CE2","CE1","CZ"]
 
             break
 
             break
 
         case 'TRP' :
 
         case 'TRP' :
             bps = ["CG","CD1","CD2","CE2","CE3","CZ3","CZ2","CH2"]
+
             bps += ["CG","CD1","CD2","CE2","CE3","CZ3","CZ2","CH2"]
            break
 
        case 'GLU' :
 
        case 'GLN' :
 
            bps = ["OE1","CD"]
 
            break
 
        case 'ASP' :
 
        case 'ASN' :
 
            bps = ["OD1","CG"]
 
 
             break
 
             break
 
         case 'A' :
 
         case 'A' :
Line 419: Line 424:
 
             var a1 = get_atom_rcn( i, iChain, bps[j])
 
             var a1 = get_atom_rcn( i, iChain, bps[j])
 
             var a2 = get_atom_rcn( i, iChain, bps[j+1])
 
             var a2 = get_atom_rcn( i, iChain, bps[j+1])
            #var a2 = {(resno=i) and (chain=iChain) and atomname=@{bps[j+1]}}
 
 
             if (undo) {
 
             if (undo) {
 
                 connect @a1 @a2 single
 
                 connect @a1 @a2 single
Line 427: Line 431:
 
             }
 
             }
 
         }
 
         }
         var a1 = get_atom_rcn({chain=iChain}.resno.max, iChain, "O")
+
         var a1 = get_atom_rcn(get_resno_max(iChain), iChain, "O")
         var a2 = get_atom_rcn({chain=iChain}.resno.max, iChain, "C")
+
         var a2 = get_atom_rcn(get_resno_max(iChain), iChain, "C")
 
         if (undo) {
 
         if (undo) {
 
             connect @a1 @a2 single
 
             connect @a1 @a2 single
Line 434: Line 438:
 
         else {
 
         else {
 
             connect @a1 @a2 double
 
             connect @a1 @a2 double
 +
        }
 +
    } # endfor
 +
   
 +
    if (_version > 1402015) {
 +
        set multipleBondBananas true
 +
    }
 +
}
 +
 +
function get_resno_max( iChain) {
 +
    return {not hoh and not ligand and (chain=iChain) and thisModel}.resno.max
 +
}
 +
 +
function get_resno_min( iChain) {
 +
    return {not hoh and not ligand and (chain=iChain) and thisModel}.resno.min
 +
}
 +
 +
function plico_minimize( aset) {
 +
    try {
 +
        var savemt = useMinimizationThread
 +
        set useMinimizationThread false
 +
        var ms = minimizationSilent
 +
        set minimizationSilent true
 +
        minimize @aset
 +
       
 +
        set useMinimizationThread savemt
 +
        set minimizationSilent ms
 +
    }
 +
    catch {
 +
        print "minimization error"
 +
    }
 +
}
 +
 +
function p(s) {
 +
    print s
 +
}
 +
 +
function delete_from_array( a, item) {
 +
    for (var i = 1; i <= a.size; i++) {
 +
        if (a[i] = item) {
 +
            if (i == 1) {
 +
                a = a[i+1][0]
 +
            }
 +
            else {
 +
                a = a[1][i-1]+a[i+1][0]
 +
            }
 
         }
 
         }
 
     }
 
     }
 
}
 
}
# end of plicocommon.spt
+
 
 
# end of plicocommon.spt</pre>
 
# end of plicocommon.spt</pre>

Latest revision as of 17:08, 12 April 2016

This script contains routines used by other scripts of the Plico suite. It must be located in the same directory as any script that uses these routines.

Copy and paste the following into a text editor and save in your scripts folder as plicoCommon.spt.

#   plicoCommon - Jmol script by Ron Mignery
#   v1.12 beta    4/12/2016 -axis is now a reserved word
#
#   Routines and values common to all Plico suite scripts
#   Must be present in the same directory as other Plico scripts that use it
kCommon = 7
kDtolerance = 0.1
kCtolerance = 1.85
gMouseX = 0
gMouseY = 0
gMinNo = 1
gMaxNo = 9999
gOK = true # global return value to work around jmol *feature*
gOk2 = true # "    "
gScheme = "Jmol"
gAltScheme = "Rasmol"
gBusy = false
gEcho = ""
gMenuMin = false

# Return L tetrahedron point if i1<i2<i3, else R point
function get_tet_idx(i1, i2, i3, dist) {
    var v1 = {atomIndex=i3}.xyz - {atomIndex=i2}.xyz
    var v2 = {atomIndex=i1}.xyz - {atomIndex=i2}.xyz
    var caxis = cross(v1, v2)
    var pma = ({atomIndex=i1}.xyz + {atomIndex=i3}.xyz)/2
    var pmo = {atomIndex=i2}.xyz + {atomIndex=i2}.xyz - pma
    var pt = pmo + (caxis/caxis)

    var v = pt - {atomIndex=i2}.xyz
    var cdist = distance(pt, {atomIndex=i2})
    var factor = (dist/cdist)
    var lpt = v * factor

    return lpt + {atomIndex=i2}.xyz
}

function get_trigonal_idx(i1, i2, i3, dist) {
    var v1 = {atomIndex=i1}.xyz - {atomIndex=i2}.xyz
    var v2 = {atomIndex=i3}.xyz - {atomIndex=i2}.xyz
    var pt = {atomIndex=i2}.xyz - (v1 + v2)

    var v = pt - {atomIndex=i2}.xyz
    var cdist = distance(pt, {atomIndex=i2})
    var factor = (dist/cdist)
    var lpt = (v * factor)

    return lpt + {atomIndex=i2}.xyz
}

# Selected must include second parameter but not the first
# Static may be just a point
function set_distance_atoms( static, mobile, desired) {
    try {
        var s = ((static.type == "point") ? static : static.xyz)        
        var v = mobile.xyz - s
        var dist = distance(s, mobile)
        translateSelected @{(v * (desired/dist)) - v}
    }
    catch {
    }
}
function set_distance_idx( staticIdx, mobileIdx, desired) {
    set_distance_atoms({atomIndex=staticIdx}, {atomIndex=mobileIdx}, desired)
}

# Selected must include third parameter but not the first
# Stator and pivot may be just points
function set_angle_atoms( stator, pivot, rotor, toangle) {
    try {
        var s = ((stator.type == "point") ? stator : stator.xyz)        
        var p = ((pivot.type == "point") ? pivot : pivot.xyz)        
        var v1=s - p
        var v2=rotor.xyz - p
        var caxis = cross(v1, v2) + p
        var curangle =  angle(stator, pivot, rotor)
        rotateselected @caxis @pivot @{curangle-toangle}
    }
    catch {
        print format("unable to set_angle_atoms( stator=%s, pivot=%s, rotor=%s, toangle=%f)",
            stator, pivot, rotor, toangle)
    }
}
function set_angle_idx( statorIdx, pivotIdx, rotorIdx, toangle) {
    set_angle_atoms({atomIndex=statorIdx}, {atomIndex=pivotIdx},
        {atomIndex=rotorIdx}, toangle)
}

# Selected must include fourth parameter but not the first
function set_dihedral_atoms( stator, pivot1, pivot2, rotor, toangle) {
    try {
        var curangle =  angle(stator, pivot1, pivot2, rotor)
        rotateselected {pivot2} {pivot1} @{curangle-toangle}
    }
    catch {
    }
}
function set_dihedral_idx( statorIdx, pivot1idx, pivot2idx, rotorIdx, toangle) {
    set_dihedral_atoms({atomIndex = statorIdx}, {atomIndex = pivot1idx},
        {atomIndex = pivot2idx}, {atomIndex = rotorIdx}, toangle)
}

function angle_idx_4( a1idx, a2idx, a3idx, a4idx) {
    return angle({atomIndex=a1idx}, {atomIndex=a2idx},
        {atomIndex=a3idx}, {atomIndex=a4idx})
}

# First and last are BB atoms
# Any side atoms in the range are also selected
function select_nward_idx (firstIdx, lastIdx) {
    var firstno = ((firstIdx < 0) ? {atomIndex=lastIdx}.atomno : {atomIndex=firstIdx}.atomno)
    var lastno = ((lastIdx < 0) ? firstno : {atomIndex=lastIdx}.atomno)
    var iChain = ((firstIdx < 0)
        ? {atomIndex=lastIdx}.chain : {atomIndex=firstIdx}.chain)

    select ((atomno <= firstno) and (atomno >= lastno) and (chain = iChain)
        and thisModel)
    if ({(atomno=firstno) and (chain=gChain)
        and thisModel}.atomName == "C") { # if psi
        add_sc_to_select(firstno-1, true, true, iChain)
        var a = {(atomno=@{firstno+1}) and (chain=iChain) and thisModel}
        a.selected = true # add O
    }
    if ({(atomno=firstno) and (chain=iChain)
        and thisModel}.atomName == "CA") {
        add_sc_to_select(firstno, true, false, iChain)
    }
    if ({(atomno=lastno) and (chain=iChain)
        and thisModel}.atomName == "C") { # if psi
        add_sc_to_select(lastno-1, false, false, iChain)
    }
}

function add_sc_to_select(CAno, isAdd, addOXT, iChain) {
    var res = {(atomno=CaNo) and (chain=iChain) and thisModel}.resno
    var scset = {(resno=res) and (chain=iChain) and thisModel and sidechain}
    if (addOXT) {
        scset = scset or get_atom_rcn(res, iChain, "OXT")
    }
    if (isAdd) {
        select add scset
    }
    else {
        select remove scset
    }
}

# First and last are BB atoms
# Any side atoms in the range are also selected
function select_cward_idx (firstIdx, lastIdx) {
    var firstno = ((firstIdx < 0) ? gMaxNo : {atomIndex=firstIdx}.atomno)
    var lastno = ((lastIdx < 0) ? 1 : {atomIndex=lastIdx}.atomno)
    var iChain = ((firstIdx < 0)
        ? {atomIndex=lastIdx}.chain : {atomIndex=firstIdx}.chain)

    # If nWard anchor in range, begin selection with it
    if ((gNanchorIdx >= 0) and ({atomIndex=gNanchorIdx}.chain == iChain))  {
        var aNo = {atomIndex=gNanchorIdx}.atomno
        if (aNo > firstNo) {
            firstno = aNo
        }
    }

    # If cWard anchor in range, end selection with it
    if ((gCanchorIdx >= 0) and ({atomIndex=gCanchorIdx}.chain == iChain))  {
        var aNo = {atomIndex=gCanchorIdx}.atomno
        if (aNo < lastNo) {
            lastno = aNo
        }
    }

    select ((atomno >= firstno) and (atomno <= lastno) and (chain = iChain)
        and thisModel)

    if ({(atomno=firstno) and (chain=iChain)
        and thisModel}.atomName == "C") { # if psi
        add_sc_to_select(firstno-1, false, false, iChain)
    }
    if ({(atomno=lastno) and (chain=iChain)
        and thisModel}.atomName == "CA") {
        add_sc_to_select(lastno, true, false, iChain)
    }
    if ({(atomno=lastno) and (chain=iChain)
        and thisModel}.atomName == "C") { # if psi
        add_sc_to_select(lastno-1, true, true, iChain)
        var a = {(atomno=@{lastno+1}) and (chain=iChain) and thisModel}
        a.selected = true # add O
    }
}

# tug.spt needed to handle collisions
function to_handle_collisions( idx) {
    # Load tug functions
    if (kTug < 3) {
        script $SCRIPT_PATH$tug.spt
        if (kTug < 3) {
            prompt ("A newer version of tug.SPT is required")
            quit
        }
    }
    handle_collisions( idx)
}

function count_collisions(rc) {
    var cAtoms = ({})
    for (var idx = {thisModel}.min.atomIndex;
        idx <= {thisModel}.max.atomIndex; idx++) {
        if ({atomIndex=idx} and {element!="H"}) {
            var lcAtoms = (within(kCtolerance, false, {atomIndex=idx})
                and {atomIndex > idx} and {element!="H"}
                and not connected({atomIndex=idx}))
            if (lcAtoms) {
                cAtoms = cAtoms or lcAtoms or {atomIndex=idx}
                for (var i = 1; i <= lcAtoms.size; i++) {
                    print format("Collision of ({%d}) with %s", idx, lcAtoms[i])
                    if (rc == true) {
                        measure {atomindex=idx} {@{lcAtoms[i]}}
                    }
                }
            }
        }
    }
    return cAtoms
}

# Utility
function get_atom_rcn( iResno, iChain, iName) {
    return {(resno=iResno) and (chain=iChain) and (atomName=iName)
        and thisModel}
}

# Utility
function atom_noc( iNo, iChain) {
    return {(atomno=iNo) and (chain=iChain) and thisModel}
}

# A handy debug routine
function hi {
    hover "%D %U"
}

function plico_menu_toggle() {
    var yr = _height-25
    if ((_mouseY > (_height-25)) and (_mouseX < 300)) {
        if (gMenuMin) {
            echo @gEcho
        }
        else {
            var p = gEcho.find("|")
            if (p > 0) {
                echo @{gEcho[1][p-1]}
            }
            else {
                echo
            }
        }
        gMenuMin = !gMenuMin
    }
    gBusy = false
}

function plico_prelim(repair, backup) {

    # Push selected
    gSelSaves = {selected}
    select (thisModel)
    gBusy=false

    # Bad idea to proceed when collisions present
    while (repair) {
        var cc = count_collisions(({})).size
        if (cc > 0) {
            var p = prompt(format("%d collision%s present!\nProceed anyway?",
                cc, ((cc > 1) ? "s" : "")), "OK|Cancel|Repair", true)
            if (p == "Cancel") {
                quit
            }
            else if (p == "Repair") {
                select (thisModel)
                allSet = {selected}
                gChain = "XX"
                for (var idx = {allSet}.atomIndex.min;
                    idx <= {allSet}.atomIndex.max; idx++) {
                    if ({atomIndex=idx}.chain != gChain) {
                        gChain = {atomIndex=idx}.chain
                        select {(chain=gChain) and thisModel}
                        to_handle_collisions( idx)
                    }
                }
            }
            else {
                break
            }
        }
        else {
            break
        }
    } # endwhile

    gZoom = script("show zoom")
    gRotate = script("show rotation")
    if (backup) {
        write plico_save.pdb
    }
    select none

    gScheme = defaultColorScheme
    gAltScheme = ((gScheme == "jmol") ? "rasmol" : "jmol")
    set echo TOP LEFT
    background ECHO yellow
    gChain = ""
    gMenuMin = false
    unbind
}

# gPlicoRecord is maintained by the macro plicoRecord
function plico_record(s) {
    var g = format("show file \"%s\"", gPlicoRecord)
    var ls = script(g)
    if (ls.find("FileNotFoundException") > 0) {
        ls = ""
    }
    ls += s
    write var ls @gPlicoRecord
}

function plico_exit(undo) {
    var p = ""
    var done = false
    if (gPlico) {
        p = prompt(format("Exit %s?", gPlico),
            "Yes|No"+(undo ? "|Undo all" : ""), true)
        if (p == "Undo all") {
            load plico_save.pdb
            script inline gZoom
            rotate @gRotate
            echo Session undone
            if (gPlicoRecord != "") {
                plico_record("load plico_save.pdb;")
            }
            reset gPlotEcho
            set AnimFrameCallback NONE
        }
    }
    if (p != "No") {
        unbind
        halo off
        select (thisModel)
        halo off
        star off
        color {selected} @gScheme
        draw gSCcircle DELETE
        gBusy = false
        gEcho = ""
        set echo TOP LEFT
        background ECHO yellow
        echo @gEcho
        gMenuMin = false
        done = true

        # Pop selected
        select gSelSaves
    }
    return done
}

function add_hydrogens(addh) {
    delete hydrogen
    connect {*} {*} aromatic modify
    if (addh) {
        calculate hydrogens
    }
    calculate aromatic
}

# Prevents minimization from disrespecting planar elements
# and allows calculate hydrogens to place hydrogens correctly
function double_bond_planars(iChain, undo) {
print format("double_bond_planars(%s, %s)", iChain, undo)
    for (var i = get_resno_min(iChain); i <= get_resno_max(iChain); i++) {
        var aa = {resno=i}.group[0]
        var bps = ["O","C"]
        switch (aa) {
        case 'ARG' :
            bps += ["CZ","NH1"]
            break
        case 'ASN' :
        case 'ASP' :
            bps += ["OD1","CG"]
            break
        case 'GLN' :
        case 'GLU' :
            bps += ["OE1","CD"]
            break
        case 'HIS' :
            bps += ["CG","CD2","CE1","NE2"]
            break
        case 'PHE' :
        case 'TYR' :
            bps += ["CG","CD1","CD2","CE2","CE1","CZ"]
            break
        case 'TRP' :
            bps += ["CG","CD1","CD2","CE2","CE3","CZ3","CZ2","CH2"]
            break
        case 'A' :
        case 'G' :
        case 'DA' :
        case 'DG' :
            bps = ["N7","C8","C4","C5","N3","C2", ((aa = "A") ? "N1" : "O6"), "C6"]
            break
        case 'C' :
        case 'U' :
        case 'T' :
        case 'DC' :
        case 'DT' :
        case 'DU' :
            bps = ["C5","C6","C2","O2","C4","CZ",((aa = "C") ? "N3" : "O4")]
            break
        }
        for (var j = 1; j <= bps.size; j += 2) {
            var a1 = get_atom_rcn( i, iChain, bps[j])
            var a2 = get_atom_rcn( i, iChain, bps[j+1])
            if (undo) {
                connect @a1 @a2 single
            }
            else {
                connect @a1 @a2 double
            }
        }
        var a1 = get_atom_rcn(get_resno_max(iChain), iChain, "O")
        var a2 = get_atom_rcn(get_resno_max(iChain), iChain, "C")
        if (undo) {
            connect @a1 @a2 single
        }
        else {
            connect @a1 @a2 double
        }
    } # endfor
    
    if (_version > 1402015) {
        set multipleBondBananas true
    }
}

function get_resno_max( iChain) {
    return {not hoh and not ligand and (chain=iChain) and thisModel}.resno.max
}

function get_resno_min( iChain) {
    return {not hoh and not ligand and (chain=iChain) and thisModel}.resno.min
}

function plico_minimize( aset) {
    try {
        var savemt = useMinimizationThread
        set useMinimizationThread false
        var ms = minimizationSilent
        set minimizationSilent true
        minimize @aset
        
        set useMinimizationThread savemt
        set minimizationSilent ms
    }
    catch {
        print "minimization error"
    }
}

function p(s) {
    print s
}

function delete_from_array( a, item) {
    for (var i = 1; i <= a.size; i++) {
        if (a[i] = item) {
            if (i == 1) {
                a = a[i+1][0]
            }
            else {
                a = a[1][i-1]+a[i+1][0]
            }
        }
    }
}

# end of plicocommon.spt

Contributors

Remig