User:Remig/plico/plicoCommon

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
#   v1.9 beta    7/24/2015 -add menu toggle
#
#   Routines and values common to all Plico suite scripts
#   Must be present in the same directory as other Plico scripts that use it
kCommon = 6
kDtolerance = 0.1
kAtolerance = 5.0
kCtolerance = 1.85
kMtolerance = 0.8
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 axis = cross(v1, v2)
    var pma = ({atomIndex=i1}.xyz + {atomIndex=i3}.xyz)/2
    var pmo = {atomIndex=i2}.xyz + {atomIndex=i2}.xyz - pma
    var pt = pmo + (axis/axis)

    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
}

# Work around - Functions returning values must be in lower case for 14.0.13
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
}

function abs( x) {
    return ((x < 0) ? -x : x)
}

# Selected must include second parameter but not the first
function set_distance_atoms( static, mobile, desired) {
    try {
        var v = mobile.xyz - static.xyz
        var dist = distance(static, 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
function set_angle_atoms( stator, pivot, rotor, toangle) {
    try {
        var v1=stator.xyz - pivot.xyz
        var v2=rotor.xyz - pivot.xyz
        var axis = cross(v1, v2) + pivot.xyz
        var curangle =  angle(stator, pivot, rotor)
        rotateselected @axis @pivot @{curangle-toangle}
    }
    catch {
    }
}
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 f = (_frameID/1000000)
    var m = (_frameID%1000000)
    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 (file=f) and (model=m))
    if ({(atomno=firstno) and (chain=gChain)
        and (file=f) and (model=m)}.atomName == "C") { # if psi
        add_sc_to_select(firstno-1, true, true, iChain)
        var a = {(atomno=@{firstno+1}) and (chain=iChain) and (file=f) and (model=m)}
        a.selected = true # add O
    }
    if ({(atomno=firstno) and (chain=iChain)
        and (file=f) and (model=m)}.atomName == "CA") {
        add_sc_to_select(firstno, true, false, iChain)
    }
    if ({(atomno=lastno) and (chain=iChain)
        and (file=f) and (model=m)}.atomName == "C") { # if psi
        add_sc_to_select(lastno-1, false, false, iChain)
    }
}

function add_sc_to_select(CAno, isAdd, addOXT, iChain) {
    var f = (_frameID/1000000)
    var m = (_frameID%1000000)
    var res = {(atomno=CaNo) and (chain=iChain) and (file=f) and (model=m)}.resno
    var scset = {(resno=res) and (chain=iChain) and (file=f)
        and (model=m) 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 f = (_frameID/1000000)
    var m = (_frameID%1000000)
    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 (file=f) and (model=m))

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

function count_collisions(rc) {
    var f = (_frameID/1000000)
    var m = (_frameID%1000000)
    var cAtoms = ({})
    for (var idx = {(file=f) and (model=m)}.min.atomIndex;
        idx <= {(file=f) and (model=m)}.max.atomIndex; idx++) {
        if ({atomIndex=idx}.size > 0) {
            var lcAtoms = (within(kCtolerance, false, {atomIndex=idx})
                and {atomIndex > idx}
                and not connected({atomIndex=idx}))
            if (lcAtoms.size > 0) {
                cAtoms = cAtoms or lcAtoms or {atomIndex=idx}
                if (rc == true) {
                    print format("Collision of idx=%d with %s", idx, lcAtoms)
                    for (var i = 1; i <= lcAtoms.size; i++) {
                        measure {atomindex=idx} ({@lcAtoms[i]})
                    }
                }
            }
        }
    }
    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
function get_atom_rcn( iResno, iChain, iName) {
    var f = (_frameID/1000000)
    var m = (_frameID%1000000)
    return {(resno=iResno) and (chain=iChain) and (atomName=iName)
        and (file=f) and (model=m)}
}

# Utility
function atom_noc( iNo, iChain) {
    var f = (_frameID/1000000)
    var m = (_frameID%1000000)
    return {(atomno=iNo) and (chain=iChain) and (atomName=iName)
        and (file=f) and (model=m)}
}

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

function plico_menu_toggle() {
    var yr = _height-25
    if ((_mouseY > (_height-25)) and (_mouseX < 240)) {
        if (gMenuMin) {
            echo @gEcho
        }
        else {
            var p = gEcho.find("|")
            if (p > 0) {
                echo @{gEcho[1][p-1]}
            }
            else {
                echo
            }
        }
        gMenuMin = !gMenuMin
    }
}

function plico_prelim(repair) {

    # Push selected
    gSelSaves = {selected}
    var f = (_frameID/1000000)
    var m = (_frameID%1000000)
    select ((file=f) and (model=m))

    # 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 ((file=f) and (model=m))
                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 (file=f) and (model=m)}
                        handle_collisions( idx)
                    }
                }
            }
            else {
                break
            }
        }
        else {
            break
        }
    } # endwhile

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

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

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

function plico_exit() {
    var p = ""
    var done = false
    if (gPlico.size > 0) {
        p = prompt(format("Exit %s?", gPlico), "Yes|No|Undo all", true)
        if (p == "Undo") {
            load plico_save.pdb
            script inline gZoom
            rotate @gRotate
            echo Tug session undone
            if (gPlicoRecord != "") {
                plico_record("load plico_save.pdb;")
            }
        }
    }
    if (p != "No") {
        unbind
        halo off
        echo
        var f = (_frameID/1000000)
        var m = (_frameID%1000000)
        select ((file=f) and (model=m))
        halo off
        star off
        color {selected} @gScheme
        draw gSCcircle DELETE
        gBusy = false
        background ECHO yellow
        gMenuMin = false
        done = true

        # Pop selected
        select gSelSaves
    }
    return done
}

function plot_o_rot( iChain) {
    var f = (_frameID/1000000)
    var m = (_frameID%1000000)
    select none
    var first = true
    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
    set echo top left
    echo "vx = phi        vy = previous psi"
}

# Prevents minimization from disrespecting planar elements
function double_bond_planars(iChain, undo) {
    for (var i = {chain=iChain}.resno.min; i <= {chain=iChain}.resno.max; i++) {
        var aa = {resno=i}.group[0]
        var bps = []
        switch (aa) {
        case 'TYR' :
        case 'PHE' :
            bps = ["CG","CD1","CD2","CE2","CE1","CZ"]
            break
        case 'HIS' :
            bps = ["CG","CD2","CE1","NE2"]
            break
        case 'TRP' :
            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
        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])
            #var a2 = {(resno=i) and (chain=iChain) and atomname=@{bps[j+1]}}
            if (undo) {
                connect @a1 @a2 single
            }
            else {
                connect @a1 @a2 double
            }
        }
        var a1 = get_atom_rcn({chain=iChain}.resno.max, iChain, "O")
        var a2 = get_atom_rcn({chain=iChain}.resno.max, iChain, "C")
        if (undo) {
            connect @a1 @a2 single
        }
        else {
            connect @a1 @a2 double
        }
    }
}

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"
    }
}

# end of plicocommon.spt

Contributors

Remig