User:Remig/plico/tug
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Tug allows the user to pull or push by mouse actions to move or rotate one part of a polypeptide against the rest by rotation on its psi and phi bonds with collision detection and restriction.
Tug is a member of the Plico suite of protein folding tools described in User:Remig/plico . It may be installed and accessed as a macro with the file:
Title=PLICO Tug Script=script <path to your scripts folder>/tug.spt;plicotug
saved as plicotug.macro in your .jmol/macros folder as described in Macro.
Copy and paste the following into a text editor and save in your scripts folder as tug.spt.
# tug - Jmol script by Ron Mignery
# v1.0 beta 2/4/2014 for Jmol 13.4
#
# These functions support protein manipulation in Jmol
var kTug = 1
var kDtolerance = 0.2
var kAtolerance = 5.0
var kCtolerance = 1.85
var kMtolerance = 0.8
var kMinRama = 2
var kCollisionLimit = 200
var gCanchorIdx = -1
var gCanchorNo = -1
var gNanchorIdx = -1
var gNanchorNo = -1
var gNanchorPidx = -1
var gCanchorXyz = {0 0 0}
var gNanchorXyz = {0 0 0}
var gNanchorPxyz = {0 0 0}
var gCcargoIdx = -1
var gNcargoIdx = -1
var gCcargoXyz = {0 0 0}
var gNcargoXyz = {0 0 0}
var gCcargoNo = -1
var gNcargoNo = -1
var gDestAtomIdx = -1
var g1pivotIdx = -1
var g2pivotIdx = -1
var gSelSaves = ({})
var gCrotors = array()
var gNrotors = array()
var gMouseX = 0
var gMouseY = 0
var gAc = ({})
var gChain = ""
var gMinNo = 1
var gMaxNo = 9999
var gScheme = "Jmol"
var gAltScheme = "Rasmol"
var gCargoAtoms = ({})
var gSeed = 23423.52
var gBusy = FALSE
var gSCidx = -1
var gSCcircle = -1
var gSCpt = {0 0 0}
var gOK = TRUE # global return value to work around jmol *feature*
var gOk2 = TRUE # " "
var gTargetPt = {0 0 0}
var gNewDrag = FALSE
var gEcho = ""
var gCountdown = 0
var gZoom = ""
var gRotate = ""
# Return L tetrahedron point if i1<i2<i3, else R point
function getTet(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
}
function getTrigonal(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) {
if (x < 0) {
x = -x
}
return x
}
function getCAmNo (iNo) {
while ((iNo > 0) and ({(atomno=iNo) and (chain=gChain)}.atomName != "CA")) {
iNo--
}
return iNo
}
function getCAmIdx (idx) {
var no = {atomIndex=idx and (chain=gChain)}.atomno
no = getCAmNo( no)
return ({(atomno=no) and (chain=gChain)}.atomIndex)
}
function getCApNo (iNo) {
while ((iNo < gMaxNo) and ({(atomno=iNo) and (chain=gChain)}.atomName != "CA")) {
iNo++
}
return iNo
}
function getCpIdx (idx) {
var no = {atomIndex=idx and (chain=gChain)}.atomno
no = getCpNo( no)
return ({(atomno=no) and (chain=gChain)}.atomIndex)
}
function getCpNo (iNo) {
while ((iNo < gMaxNo) and ({(atomno=iNo) and (chain=gChain)}.atomName != "C")) {
iNo++
}
return iNo
}
function getCApIdx (idx) {
var no = {atomIndex=idx and (chain=gChain)}.atomno
no = getCApNo( no)
return ({(atomno=no) and (chain=gChain)}.atomIndex)
}
function getCmNo (iNo) {
while ((iNo > 0) and ({(atomno=iNo) and (chain=gChain)}.atomName != "C")) {
iNo--
}
return iNo
}
function getCmIdx (idx) {
var no = {atomIndex=idx and (chain=gChain)}.atomno
no = getCmNo( no)
return ({(atomno=no) and (chain=gChain)}.atomIndex)
}
function getNmNo (iNo) {
while ((iNo > 0) and ({(atomno=iNo) and (chain=gChain)}.atomName != "N")) {
iNo--
}
return iNo
}
function getNmIdx (idx) {
var no = {atomIndex=idx and (chain=gChain)}.atomno
no = getNmNo( no)
return ({(atomno=no) and (chain=gChain)}.atomIndex)
}
function getNpNo (iNo) {
while ((iNo < gMaxNo) and ({(atomno=iNo) and (chain=gChain)}.atomName != "N")) {
iNo++
}
return iNo
}
function getNpIdx (idx) {
var no = {atomIndex=idx}.atomno
no = getNpNo( no)
return ({(atomno=no) and (chain=gChain)}.atomIndex)
}
function getCBidx (BBidx) {
var no = {atomIndex=BBidx}.atomno
var i = 1
for (; i < 5; i++) {
if ({(atomno=@{no+i}) and (chain=gChain)}.atomName == "CB") {
break
}
}
return {(atomno=@{no+i}) and (chain=gChain)}.atomIndex
}
function getOidx (BBidx) {
var no = {atomIndex=BBidx}.atomno
var i = 1
for (; i < 4; i++) {
if ({(atomno=@{no+i}) and (chain=gChain)}.atomName == "O") {
break
}
}
return {(atomno=@{no+i}) and (chain=gChain)}.atomIndex
}
function getNwardBBno (iNo) {
while ((iNo >= 0) and (
({(atomno=iNo) and (chain=gChain)}.atomName != "N")
and ({(atomno=iNo) and (chain=gChain)}.atomName != "C")
and ({(atomno=iNo) and (chain=gChain)}.atomName != "CA"))) {
iNo--
}
return iNo
}
function getNwardBBidx (idx) {
var no = {atomIndex=idx}.atomno - 1
no = getNwardBBno( no)
return ((no >= 0) ? ({(atomno=no) and (chain=gChain)}.atomIndex) : -1)
}
function getCwardBBno (iNo) {
while ((iNo < gMaxNo) and (
({(atomno=iNo) and (chain=gChain)}.atomName != "N")
and ({(atomno=iNo) and (chain=gChain)}.atomName != "C")
and ({(atomno=iNo) and (chain=gChain)}.atomName != "CA"))) {
iNo++
}
return iNo
}
function getCwardBBidx (idx) {
var no = {atomIndex=idx}.atomno + 1
no = getCwardBBno( no)
return ((no >= 0) ? ({(atomno=no) and (chain=gChain)}.atomIndex) : -1)
}
function getScBBidx (idx) {
var no = {atomIndex=idx}.atomno
for (; no > 0; no--) {
if ({(atomno=no) and (chain=gChain)}.atomName == "CA") {
break
}
else if ({(atomno=no) and (chain=gChain)}.atomName == "C") {
break
}
else if ({(atomno=no) and (chain=gChain)}.atomName == "N") {
break
}
else if ({(atomno=no) and (chain=gChain)}.atomName == "CB") {
no -= 3
break
}
}
return {(atomno=no) and (chain=gChain)}.atomIndex
}
function isBBidx(aIdx) {
var ret = FALSE
switch({atomIndex=aIdx}.atomName) {
case "N":
case "CA":
case "C":
ret = TRUE
break
}
return ret
}
function isSCidx(aIdx) {
var ret = FALSE
if (isBBidx(aIDx) == FALSE) {
ret = TRUE
switch({atomIndex=aIdx}.atomName) {
case "O":
case "CB":
ret = FALSE
break
}
}
return ret
}
function addSideChainToSelection(CAno, isAdd, addOXT) {
var iNo = CAno+3
while ({(atomno=iNo) and (chain=gChain)}.resno == {(atomno=CAno) and (chain=gChain)}.resno) {
{(atomno=iNo) and (chain=gChain)}.selected = isAdd
if ({(atomno=iNo) and (chain=gChain)}.atomName == "OXT") {
{(atomno=iNo) and (chain=gChain)}.selected = addOXT
}
iNo++
}
}
function selectAddSideChain(fromIdx) {
var iNo = {atomIndex=fromIdx}.atomno
select none
while ({(atomno=iNo) and (chain=gChain)}.atomName != "N") {
{(atomno=iNo) and (chain=gChain)}.selected = TRUE
iNo++
if (iNo > gMaxNo) {
break
}
}
}
# First and last are BB atoms
# Any side atoms in the range are also selected
function selectNward (firstIdx, lastIdx) {
var firstno = ((firstIdx < 0) ? {atomIndex=lastIdx}.atomno : {atomIndex=firstIdx}.atomno)
var lastno = ((lastIdx < 0) ? firstno : {atomIndex=lastIdx}.atomno)
select (atomno <= firstno) and (atomno >= lastno)
if ({(atomno=firstno) and (chain=gChain)}.atomName == "C") { # if psi
addSideChainToSelection(firstno-1, TRUE, TRUE)
{(atomno=@{firstno+1}) and (chain=gChain)}.selected = TRUE # add O
}
if ({(atomno=firstno) and (chain=gChain)}.atomName == "CA") {
addSideChainToSelection(firstno, TRUE, FALSE)
}
if ({(atomno=lastno) and (chain=gChain)}.atomName == "C") { # if psi
addSideChainToSelection(lastno-1, FALSE, FALSE)
}
}
# First and last are BB atoms
# Any side atoms in the range are also selected
function selectCward (firstIdx, lastIdx) {
var firstno = ((firstIdx < 0) ? gMaxNo : {atomIndex=firstIdx}.atomno)
var lastno = ((lastIdx < 0) ? 1 : {atomIndex=lastIdx}.atomno)
# If nWard anchor in range, begin selection with it
if (gNanchorIdx >= 0) {
var aNo = {atomIndex=gNanchorIdx}.atomno
if (aNo > firstNo) {
firstno = aNo
}
}
# If cWard anchor in range, end selection with it
if (gCanchorIdx >= 0) {
var aNo = {atomIndex=gCanchorIdx}.atomno
if (aNo < lastNo) {
lastno = aNo
}
}
select (atomno >= firstno) and (atomno <= lastno)
if ({(atomno=firstno) and (chain=gChain)}.atomName == "C") { # if psi
addSideChainToSelection(firstno-1, FALSE, FALSE)
}
if ({(atomno=lastno) and (chain=gChain)}.atomName == "CA") {
addSideChainToSelection(lastno, TRUE, FALSE)
}
if ({(atomno=lastno) and (chain=gChain)}.atomName == "C") { # if psi
addSideChainToSelection(lastno-1, TRUE, TRUE)
{(atomno=@{lastno+1}) and (chain=gChain)}.selected = TRUE # add O
}
}
# Selected must include second parameter but not the first
function setDistanceIdx (staticIdx, mobileIdx, desired) {
try {
var v = {atomIndex=mobileIdx}.xyz - {atomIndex=staticIdx}.xyz
var dist = distance({atomIndex=staticIdx}, {atomIndex=mobileIdx})
translateSelected @{((v * (desired/dist)) - v)}
}
catch {
}
}
# Selected must include third parameter but not the first
function setAngleIdx (statorIdx, pivotIdx, rotorIdx, toangle) {
try {
var v1={atomIndex=statorIdx}.xyz - {atomIndex=pivotIdx}.xyz
var v2={atomIndex=rotorIdx}.xyz - {atomIndex=pivotIdx}.xyz
var axis = cross(v1, v2) + {atomIndex=pivotIdx}.xyz
var curangle = angle({atomIndex=statorIdx},
{atomIndex=pivotIdx}, {atomIndex=rotorIdx})
rotateselected @axis {atomIndex = pivotIdx} @{curangle-toangle}
}
catch {
}
}
# Selected must include fourth parameter but not the first
function setDihedralIdx (stator1idx, stator2idx, rotor1idx, rotor2idx, toangle) {
try {
var a1={atomIndex = stator1idx}.xyz
var a2={atomIndex = stator2idx}.xyz
var a3={atomIndex = rotor1idx}.xyz
var a4={atomIndex = rotor2idx}.xyz
var curangle = angle(a1, a2, a3, a4)
rotateselected {a3} {a2} @{curangle-toangle}
}
catch {
}
}
function countCollisions(rc) {
var lcAtoms = ({})
for (var idx = {*}.min.atomIndex; idx <= {*}.max.atomIndex; idx++) {
lcAtoms = lcAtoms or (within(kCtolerance, FALSE, {atomIndex=idx})
and {atomIndex > idx}
and not {rc}
and not connected({atomIndex=idx}))
}
return lcAtoms.size
}
# Resolve collisions
function handleCollisions( nWard, targetIdx) {
# For all selected atoms
for (var iNo = {selected}.min.atomno; iNo <= {selected}.max.atomno; iNo++) {
var idx = {(atomno=iNo) and (chain=gchain)}.atomIndex
if ({atomindex=idx}.selected) {
# Collect local colliders
var lcAtoms = (within(kCtolerance, FALSE, {atomIndex=idx})
and not {atomIndex=idx}
and not {gOkCollide}
and not connected({atomIndex=idx}))
if (lcAtoms.size > 0) {
# Ignore kinked BB
if (isBBidx(idx) and angle({atomIndex=@{getCwardBBidx(idx)}},
{atomIndex=idx} , {atomIndex=@{getNwardBBidx(idx)}}) < 100) {
continue
}
#gCountdown--
if (gCountdown < 0) {
timedOut("Too many collsions")
}
# For all local water colliders, delete
var recollect = FALSE
for (var c = 1; c <= lcAtoms.size; c++ ) {
if (lcAtoms[c].group = "HOH") {
delete {atomIndex=@{lcAtoms[c].atomIndex}}
recollect = TRUE
}
}
# Recollect local colliders if needed
if (recollect) {
lcAtoms = (within(kCtolerance, FALSE, {atomIndex=idx})
and not {atomIndex=idx}
and not {gOkCollide}
and not connected({atomIndex=idx}))
recollect = FALSE
}
# For all local colliders
for (var c = 1; c <= lcAtoms.size; c++ ) {
# If it is with side chain not proline, fix it
var cidx = lcAtoms[c].atomIndex
if (isSCidx(cidx) and ({atomIndex=cidx}.group != "PRO")) {
fixSCcollision2(cidx)
recollect = TRUE
# If not fixed, exit fail
if (gOk2 == FALSE) {
return # early exit (break n jmol bug)
}
}
}
# Recollect local colliders if needed
if (recollect) {
lcAtoms = (within(kCtolerance, FALSE, {atomIndex=idx})
and not {atomIndex=idx}
and not {gOkCollide}
and not connected({atomIndex=idx}))
}
# For all local colliders
for (var c = 1; c <= lcAtoms.size; c++ ) {
# If it is with O, counter-rotate
if ({atomIndex=@{lcAtoms[c].atomIndex}}.atomName = "O") {
counterRotate2(idx, lcAtoms[c].atomIndex, targetIdx)
# If not fixed, exit fail
if (gOk2 == FALSE) {
return # early exit (break n jmol bug)
}
}
}
}
}
} # endfor iNo
}
# Rotate rotor set to move target atom to its proper place
function tugTrackIdx(targetIdx, targetPt, nWard, cDetect) {
gOK = FALSE
var pt = targetPt
var dist = distance(pt, {atomIndex=targetIdx}.xyz)
var rotors = (nWard ? gNrotors : gCrotors)
# For a number of passes
for (var pass1 = 0; pass1 < 20; pass1++) {
var blocked = ({})
for (var pass2 = 0; pass2 < (rotors.size/4); pass2++) {
var v1 = {atomIndex=targetIdx}.xyz - pt
# Find the most orthgonal unused rotor
var imax = 0
var smax = 0.5
for (var i = 1; i < rotors.size; i += 4) {
var i2 = rotors[i+1]
var i3 = rotors[i+2]
var i4 = rotors[i+3]
if ((i2 != targetIdx) and (i3 != targetIdx) and (i4 != targetIdx)) {
if ({blocked and {atomIndex=i2}}.count == 0) {
var v2 = {atomIndex=i3}.xyz - {atomIndex=i2}.xyz
var s = sin(abs(angle(v1, {0 0 0}, v2)))
if (s > smax) {
smax = s
imax = i
}
}
}
}
# If no more rotors, break to next full try
if (imax == 0) {
break
}
var i1 = rotors[imax+0]
var i2 = rotors[imax+1]
var i3 = rotors[imax+2]
var i4 = rotors[imax+3]
# Get dihedral of rotor with target point
var dt = angle({atomIndex=targetIdx}, {atomIndex=i2}, {atomIndex=i3}, pt)
var dh = angle({atomIndex=i1}, {atomIndex=i2}, {atomIndex=i3}, {atomIndex=i4})
if (dh == "NaN") {
dh = -50
}
var psi = dh + dt
var phi = dh + dt
# Compute resultant psi and phi
# and select from target atom to first half of rotor
var movePt = FALSE
if (nWard) {
if ({atomIndex=i2}.atomName="CA") {
psi = angle({atomIndex=@{getCwardBBidx(i1)}}, {atomIndex=i1},
{atomIndex=i2}, {atomIndex=i3}) + dt
}
else {
phi = angle({atomIndex=i1}, {atomIndex=i2},
{atomIndex=i3}, {atomIndex=@{getNwardBBidx(i3)}}) + dt
}
if ({atomIndex=i2}.atomno > {atomIndex=targetIdx}.atomno) {
movePt = TRUE
selectNward(i3, getCwardBBidx(targetIdx))
{atomIndex=targetIdx}.selected = TRUE
}
else {
selectCward(i2, targetIdx)
}
}
else {
if (({atomIndex=i2}.atomName="CA")) {
phi = angle({atomIndex=@{getNwardBBidx(i1)}}, {atomIndex=i1},
{atomIndex=i2}, {atomIndex=i3}) + dt
}
else {
psi = angle({atomIndex=i2}, {atomIndex=i3},
{atomIndex=i4}, {atomIndex=@{getCwardBBidx(i4)}}) + dt
}
if ({atomIndex=i2}.atomno < {atomIndex=targetIdx}.atomno) {
movePt = TRUE
selectCward(i3, getNwardBBidx(targetIdx))
{atomIndex=targetIdx}.selected = TRUE
}
else {
selectNward(i2, targetIdx)
}
}
# If rotation within ramachandran limits
#var ridx = 1 + (36*(((-psi\10)%180)+18)+(((phi\10)%180)+18))
if ((abs(dt) >= 0.1) and
(({atomIndex=i2}.group=="GLY") or (phi < 0))) {#kRama[ridx] >= kMinRama))) {
# If moving target point, put the target atom there
var cp = {atomIndex=targetIdx}.xyz
if (movePt) {
dt = -dt
{atomIndex=targetIdx}.xyz = pt
}
# Rotate to minimize vector ====================
rotateSelected {atomIndex=i2} {atomIndex=i3} @dt
# If collision checking
if (cDetect) {
# If collision, back off by eighths
var wasCollision = FALSE
for (var ci = 0; ci < 4; ci++) {
if (ci < 3) {
dt /= 2
}
handleCollisions( nWard, targetIdx)
if (gOk2==FALSE) {
wasCollision = TRUE
rotateSelected {atomIndex=i2} {atomIndex=i3} @{-dt}
}
else if (wasCollision) {
if (ci <3) {
rotateSelected {atomIndex=i2} {atomIndex=i3} @{dt}
}
}
else {
break
}
if (dt < 0.01) {
break
}
} # endfor
}
# If moving target point, put the target atom back
if (movePt) {
pt = {atomIndex=targetIdx}.xyz
{atomIndex=targetIdx}.xyz = cp
}
}
# If close enough, stop
if (distance(pt, {atomIndex=targetIdx}) < kDtolerance) {
gOK = TRUE
gTargetPt = pt
break
}
# Block rotor
blocked |= {atomIndex=i2}
} # endfor num rotors passes
if (gOK) {
break
}
} # endfor 10 passes
}
# Counter rotate bonds on either side of a BB O
function docounterRotate2(caPhiIDx, nIdx, cIdx, oIdx, caPsiIdx, dir, nWard) {
# Rotate phi
{atomIndex=nIdx}.selected = nWard
{atomIndex=cIdx}.selected = nWard
{atomIndex=oIdx}.selected = nWard
rotateSelected {atomIndex=caPsiIdx} {atomIndex=cIdx} @{dir}
# Counter-rotate psi
{atomIndex=nIdx}.selected = not nWard
{atomIndex=cIdx}.selected = not nWard
{atomIndex=oIdx}.selected = not nWard
rotateSelected {atomIndex=nIdx} {atomIndex=caPhiIdx} @{-dir}
}
function counterRotate2(aIdx, bIdx, targetIdx) {
var selsave = {selected}
gOk2 = TRUE
var oIdx = aIdx
var xIdx = bIdx
if ({atomIndex=bIdx}.atomName=="O") {
oIdx = bIdx
xIdx = aIdx
}
var cIdx = getScBBidx(oIdx)
var nIdx = getCwardBBidx(cIdx)
var caPhiIdx = getCwardBBidx(nIdx)
var caPsiIdx = getNwardBBidx(cIdx)
var nWard = ({atomIndex=oIdx}.atomno < {atomIndex=targetIdx}.atomno)
if (nWard) {
selectCward(cIdx, targetIdx)
}
else {
selectNward(nIdx, targetIdx)
}
# Until all collisions cancelled
var dir = 5
var ang = angle({atomIndex=xIdx}, {atomIndex=oIdx}, {atomIndex=cIdx})
var tcount = 0
while (within(kCtolerance, FALSE, {atomIndex=oIdx})
and not {atomIndex=oIdx} and not connected({atomIndex=oIdx})
and not {gOkCollide} > 0) {
# Counter-rotate
docounterRotate2(caPhiIDx, nIdx, cIdx, oIdx, caPsiIdx, dir, nWard)
var newang = angle({atomIndex=xIdx}, {atomIndex=oIdx}, {atomIndex=cIdx})
# If wrong direction once, undo and reverse
if (newang > ang) {
docounterRotate2(caPhiIDx, nIdx, cIdx, oIdx, caPsiIdx, -dir, nWard)
# If first time, continue in opposite direction
dir *= -1
if (dir < 0) {
continue
}
}
# If no go, undo and exit
tcount++
if (tcount > (360/abs(dir))) {
gOk2 = FALSE
break
}
} # endwhile
select selsave
}
# Repair proline
function repairProline(idx) {
var cbidx = getCBidx(idx)
var cbno = {atomIndex=cbidx}.atomno
var cgidx = {(atomno=@{cbno+1}) and (chain=gChain)}.atomIndex
var cdidx = {(atomno=@{cbno+2}) and (chain=gChain)}.atomIndex
var caidx = {(atomno=@{cbno-3}) and (chain=gChain)}.atomIndex
var nidx = {(atomno=@{cbno-4}) and (chain=gChain)}.atomIndex
select {atomIndex=cbidx}
setAngleIdx(nidx, caidx, cbidx, 109.5)
select {atomIndex=cdidx}
setDistanceIdx(nidx, cdidx, 1.47)
setAngleIdx(caidx, nidx, cdidx, 102.7)
setDihedralIdx(cbidx, caidx, nidx, cdidx, 16.2)
select {atomIndex=cgidx}
setDistanceIdx(cdidx, cgidx, 1.51)
setAngleIdx(nidx, cdidx, cgidx, 106.4)
setDihedralIdx(caidx, nidx, cdidx, cgidx, 16.2)
}
# Repair side chain
function plicoRepairSideChain(targetIdx, nWard) {
var idx = (nWard ? getCwardBBidx(targetIdx) : getNwardBBidx(targetIdx))
if (({atomIndex=targetIdx}.atomName == "CA")
and ({atomIndex=targetIdx}.group != "GLY")) {
var cbidx = getCBidx(targetIdx)
select none
selectAddSideChain(cbidx)
setAngleIdx(idx, targetIdx, cbidx, 110.0)
setDistanceIdx(targetIdx, cbidx, 1.5)
if ({atomIndex=targetIdx}.group != "PRO") {
var colliders = (within(kCtolerance, FALSE, {selected})
and not {atomIndex=targetIdx} and not {selected})
if (colliders.size > 0) {
if ({atomIndex=targetIdx}.group != "ALA") {
fixSCcollision2(cbidx)
}
}
}
else {
if (nWard) {
}
else {
setDihedralIdx(getNwardBBidx(idx), idx, targetIdx, cbidx, 174.2)
}
}
}
else if ({atomIndex=targetIdx}.atomName == "C") {
var oidx = getOidx(targetIdx)
select {atomIndex=oidx}
setAngleIdx(idx, targetIdx, oidx, 120.0)
setDistanceIdx(targetIdx, oidx, 1.21)
if (nWard) {
setDihedralIdx(getCwardBBidx(idx), idx, targetIdx, oidx, 0.0)
}
if ({atomIndex=idx}.group == "PRO") {
repairProline(idx)
var dNo = {atomIndex=targetIdx}.atomno + 4
var dIdx = {(atomno=dNO) and (chain=gChain)}.atomIndex
var colliders = (within(kCtolerance, FALSE, {atomIndex=dIdx})
and not connected({atomIndex=dIdx})
and not {atomIndex=dIdx})
for (var i = 1; i <= colliders.size; i++) {
if (colliders[i].atomName == "O") {
counterRotate2(dIdx, colliders[i].atomIndex, targetIdx)
}
}
}
}
}
# Rebuild Cward rotors set
function tugTrackC() {
# For all bb atoms cWard of cargo
var targetIdx = gCcargoIdx
var okCount = 0
# Allow collisions with cargo
gOkCollide = gCargoAtoms
var tcount = 0
while (targetIdx != gCanchorIdx) {
# Step to next atom
targetIdx = getCwardBBidx(targetIdx)
# No collision with cargo allowed after two atoms placed
if (tcount == 2) {
gOkCollide = ({})
}
tcount++
# Compute targets desired coords
var c1idx = getCwardBBidx(targetIdx)
var n1idx = getNwardBBidx(targetIdx)
var n2idx = getNwardBBidx(n1Idx)
var n3idx = getNwardBBidx(n2Idx)
var pt = {0 0 0}
if ({atomIndex=targetIdx}.atomName == "N") {
var oidx = getOidx(n1idx)
select {atomIndex=oidx}
# Desired target location is trigonal O
setDistanceIdx(n1idx, oidx, 1.5)
pt = getTrigonal(n2idx, n1idx, oidx, 1.37)
setDistanceIdx(n1idx, oidx, 1.21)
}
else if (({atomIndex=targetIdx}.atomName == "C")
and ({atomIndex=targetIdx}.group != "GLY")) {
# Desired target location is tetragonal CB
var cbidx = getCBidx(n1idx)
pt = getTet(n2idx, n1idx, cbidx, 1.5)
}
else { # CA (or GLY C)
# Save current target coords
var cp = {atomIndex=targetIdx}.xyz
# Set target atom at desired distance and angle
select {atomIndex=targetIdx}
setDistanceIdx(n1idx, targetIdx, 1.5)
setAngleIdx(n2idx, n1idx, targetIdx, 110.0)
if ({atomIndex=targetIdx}.atomName == "CA") {
setDihedralIdx(n3idx, n2idx, n1idx, targetIdx, 180)
}
# Record and restore target
pt = {atomIndex=targetIdx}.xyz
{atomIndex=targetIdx}.xyz = cp
}
# If target not at desired location
if (distance(pt, {atomIndex=targetIdx}) > kDtolerance) {
okCount = 0
gTargetPt = pt
var xcount = 0
gOK = FALSE
while ((xcount < 20) and (gOK == FALSE)) {
# Rotate on cWard rotor set to move it there
tugTrackIdx(targetIdx, pt, FALSE, FALSE)
#(distance(pt, {atomIndex=targetIdx}) > kMtolerance))
xcount++
}
}
else {
gOK = TRUE
okCount++
}
# If successful
if (gOK == TRUE) {
# Adust any side atoms
plicoRepairSideChain(targetIdx, FALSE)
}
# Else fail
else {
break
}
# If no movement in 4 tries, we are done
if (okCount > 3) {
break
}
} # endwhile (targetIdx != gCanchorIdx) {
}
# Rebuild Nward rotors set
function tugTrackN() {
gOK = TRUE
# For all bb atoms nWard of cargo
var targetIdx = gNcargoIdx
var okCount = 0
# Allow collisions with cargo
gOkCollide = gCargoAtoms
var tcount = 0
while (targetIdx != gNanchorIdx) {
# Step to next atom
targetIdx = getNwardBBidx(targetIdx)
# No collision with cargo allowed after two atoms placed
if (tcount == 2) {
gOkCollide = ({})
}
tcount++
# Compute targets desired coords
var n1idx = getNwardBBidx(targetIdx)
var c1idx = getCwardBBidx(targetIdx)
var c2idx = getCwardBBidx(c1idx)
var c3idx = getCwardBBidx(c2idx)
var pt = {0 0 0}
if ({atomIndex=targetIdx}.atomName == "CA") {
# Desired target location is trigonal O
var oidx = getOidx(c1idx)
select {atomIndex=oidx}
setDistanceIdx(c1idx, oidx, 1.39)
pt = getTrigonal(c2idx, c1idx, oidx, 1.41)
setDistanceIdx(c1idx, oidx, 1.21)
}
else if (({atomIndex=targetIdx}.atomName == "N")
and ({atomIndex=targetIdx}.group != "GLY")) {
# Desired target location is r-tetragonal CB
var cbidx = getCBidx(c1idx)
pt = getTet(cbidx, c1idx, c2idx, 1.5)
}
else { # C
# Save current target coords
var cp = {atomIndex=targetIdx}.xyz
# Set target atom at desired distance and angle
select {atomIndex=targetIdx}
setDistanceIdx(c1idx, targetIdx, 1.37)
setAngleIdx(c2idx, c1idx, targetIdx, 110.0)
if ({atomIndex=targetIdx}.group == "PRO") {
setDihedralIdx(c3idx, c2idx, c1idx, targetIdx, -57.0)
}
# Record and restore target
pt = {atomIndex=targetIdx}.xyz
{atomIndex=targetIdx}.xyz = cp
}
# If target not at desired location
if (distance(pt, {atomIndex=targetIdx}) > kDtolerance) {
var okCount = 0
gTargetPt = pt
var xcount = 0
gOK = FALSE
while ((xcount < 20) and (gOK == FALSE)) {
# Rotate on cWard rotor set to move it there
tugTrackIdx(targetIdx, pt, TRUE, FALSE)
#(distance(pt, {atomIndex=targetIdx}) > kMtolerance))
xcount++
}
}
else {
gOK = TRUE
okCount++
}
# If sucessful
if (gOK == TRUE) {
# Adust any side atoms
plicoRepairSideChain(targetIdx, TRUE)
}
# Else fail
else {
break
}
# If no movement in 4 tries, we are done
if (okCount > 3) {
break
}
} # endwhile (targetIdx != gNanchorIdx) {
}
# gPlicoRecord is maintained by the macro pilcoRecord
function plicoRecord(s) {
var g = format("show file \"%s\"", gPlicoRecord)
var ls = script(g)
if (ls.find("FileNotFoundException")) {
ls = ""
}
ls += s
write var ls @gPlicoRecord
}
# gPlicoRecord is maintained by the macro pilcoRecord
function translateSelectedRecord(pt) {
if (gPlicoRecord != "") {
plicoRecord(format("select %s;translateSelected %s;", {selected}, pt))
}
translateSelected @pt
}
# gPlicoRecord is maintained by the macro pilcoRecord
function rotateSelectedRecord(g1pivotIdx, axis, a) {
if (gPlicoRecord != "") {
plicoRecord(format("select %s;", {selected}))
plicoRecord(format("rotateSelected {atomIndex=%d} @%s @%s;",
g1pivotIdx, axis, a))
}
rotateSelected {atomIndex=g1pivotIdx} @axis @a
}
function collectSCrotors(no) {
var scBondIdxs = array()
for (var iNo = no; iNo >= 0; iNo--) {
var ile = 0
switch ({(atomno=iNo) and (chain=gChain)}.atomName) {
case "CA" :
return scBondIdxs # Early exit since break 1 appears broken
#break 1
case "CZ" :
if ({(atomno=iNo) and (chain=gChain)}.group == "TYR") {
break
}
case "CE" :
if ({(atomno=iNo) and (chain=gChain)}.group == "MET") {
break
}
case "CG1" :
if ({(atomno=iNo) and (chain=gChain)}.group == "VAL") {
break
}
if ({(atomno=iNo) and (chain=gChain)}.group == "ILE") {
ile = 1
}
case "NE" :
case "CD" :
case "SD" :
case "CG" :
case "CB" :
scBondIdxs += {(atomno=@{iNo+1+ile}) and (chain=gChain)}.atomIndex
scBondIdxs += {(atomno=@{iNo+0}) and (chain=gChain)}.atomIndex
if ({(atomno=iNo) and (chain=gChain)}.atomName%2 == "CG") {
scBondIdxs += {(atomno=@{iNo-1}) and (chain=gChain)}.atomIndex
scBondIdxs += {(atomno=@{iNo-4}) and (chain=gChain)}.atomIndex
}
else if ({(atomno=iNo) and (chain=gChain)}.atomName == "CB") {
scBondIdxs += {(atomno=@{iNo-3}) and (chain=gChain)}.atomIndex
scBondIdxs += {(atomno=@{iNo-4}) and (chain=gChain)}.atomIndex
}
else {
scBondIdxs += {(atomno=@{iNo-1}) and (chain=gChain)}.atomIndex
scBondIdxs += {(atomno=@{iNo-2}) and (chain=gChain)}.atomIndex
}
break
}
}
return scBondIdxs
}
# Drag Side Chain
function dragSC() {
var iNo = {atomIndex=gSCidx}.atomno
if ({atomIndex=gSCidx}.group != "PRO") {
var scBondIdxs = collectSCrotors( iNo)
var numChi = scBondIdxs.size / 4
var dist = distance({atomIndex=gSCidx}.xyz, gSCpt)
# For all rotor combinations
var dh = array()
for (var i = 0; i < numChi; i++) {
dh += angle({atomIndex=@{scBondIdxs[4+(4*i)]}},
{atomIndex=@{scBondIdxs[3+(4*i)]}},
{atomIndex=@{scBondIdxs[2+(4*i)]}},
{atomIndex=@{scBondIdxs[1+(4*i)]}})
}
for (var i = 0; i < numChi; i++) {
var rot = -120
for (var j = 0; j < 6; j++) {
rot += 60*j
selectAddSideChain(scBondIdxs[1+(4*i)])
setDihedralIdx(scBondIdxs[4+(4*i)], scBondIdxs[3+(4*i)],
scBondIdxs[2+(4*i)], scBondIdxs[1+(4*i)], rot)
var newDist = distance({atomIndex=gSCidx}.xyz, gSCpt)
# Find the best
if (newDist < dist) {
dist = newDist
for (var k = 0; k < numChi; k++) {
dh[k+1] = angle({atomIndex=@{scBondIdxs[4+(4*k)]}},
{atomIndex=@{scBondIdxs[3+(4*k)]}},
{atomIndex=@{scBondIdxs[2+(4*k)]}},
{atomIndex=@{scBondIdxs[1+(4*k)]}})
}
}
}
}
# Now set the best
for (var i = 0; i < numChi; i++) {
selectAddSideChain(scBondIdxs[1+(4*i)])
setDihedralIdx(scBondIdxs[4+(4*i)], scBondIdxs[3+(4*i)],
scBondIdxs[2+(4*i)], scBondIdxs[1+(4*i)], dh[i+1])
}
}
else { # PRO - toggle between puckers up and down
var icd = {(atomno=@{iNo+1}) and (chain=gChain)}.atomIndex
var icb = {(atomno=@{iNo-1}) and (chain=gChain)}.atomIndex
var ica = {(atomno=@{iNo-4}) and (chain=gChain)}.atomIndex
var in = {(atomno=@{iNo-5}) and (chain=gChain)}.atomIndex
select {atomIndex=gSCidx}
if (angle({atomIndex=ica}, {atomIndex=in},
{atomIndex=icd}, {atomIndex=gSCidx}) < -10.0) {
setDihedralIdx(ica, in, icd, gSCidx, 8.7)
setAngleIdx(in, icd, gSCidx, 110.0)
setDistanceIdx(icd, gSCidx, 1.5)
}
else {
setDihedralIdx(ica, in, icd, gSCidx, -29.5)
setAngleIdx(in, icd, gSCidx, 108.8)
setDistanceIdx(icd, gSCidx, 1.5)
}
}
draw gSCcircle CIRCLE {atomIndex=gSCidx} MESH NOFILL
gSCpt = {atomIndex=gSCidx}.xyz
}
# Fix side chain collisions
function fixSCcollision2(idx) {
gOk2 = FALSE
var iNo = {atomIndex=idx}.atomno
var resno = {(atomno=iNo) and (chain=gChain)}.resno
# Get SC terminus
while (resno == {(atomno=iNo) and (chain=gChain)}.resno) {
iNo++
}
iNo--
var sc = array()
var iBno = iNo
while ({(atomno=iBno) and (chain=gChain)}.atomName != "CB") {
sc += {(atomno=iBno) and (chain=gChain)}
iBno--
}
var cbidx = {(atomno=iBno) and (chain=gChain)}.atomIndex
var scBondIdxs = collectSCrotors( iNo)
var numChi = scBondIdxs.size / 4
# For all rotor combinations
for (var i = 0; i < numChi; i++) {
var rot = -120
for (var j = 0; j < 6; j++) {
rot += 60
selectAddSideChain(scBondIdxs[1+(4*i)])
#setDihedralIdx(scBondIdxs[4+(4*i)], scBondIdxs[3+(4*i)],
# scBondIdxs[2+(4*i)], scBondIdxs[1+(4*i)], rot)
setDihedralIdx(scBondIdxs[1+(4*i)], scBondIdxs[2+(4*i)],
scBondIdxs[3+(4*i)], scBondIdxs[4+(4*i)], rot)
# If no collision, exit
colliders = (within(kCtolerance, FALSE, {sc})
and not {atomIndex=cbidx} and not {sc})
# If it is with water, delete the water
for (var c = 1; c < colliders.size; c++ ) {
if (colliders[c].group = "HOH") {
delete {atomIndex=@{colliders[c].atomIndex}}
colliders = {colliders and not @{colliders[c]}}
}
}
if (colliders.size == 0) {
gOk2 = TRUE
return # Early exit since break 1 appears broken
#break 1
}
}
}
}
function isMovableSideChain(aIdx) {
var ret = (({atomIndex=aIdx}.group != "PRO")
or ({atomIndex=aIdx}.atomName == "CG"))
switch({atomIndex=aIdx}.atomName) {
case "N":
case "CA":
case "C":
case "CB":
case "O":
case "O4\'":
ret = FALSE
break
}
return ret
}
# gFreeze is maintained by the script plicoFreeze that allows the user
# to inhibit rotation on selected rotors
function isRotorAvailable(idx) {
return (gFreeze.find(idx) == 0)
}
function collectBBrotors(nWard) {
var anchorNo = (nWard
? ((gNanchorIdx >= 0) ? {atomIndex=gNanchorIdx}.atomno : gMinNo)
: ((gCanchorIdx >= 0) ? {atomIndex=gCanchorIdx}.atomno : gMaxNo))
var cargoNo = (nWard
? ((gNcargoIdx >= 0) ? {atomIndex=gNcargoIdx}.atomno
: {atomIndex=gCcargoIdx}.atomno)
: {atomIndex=gCcargoIdx}.atomno)
var rotors = array()
if (cargoNo < anchorNo) {
# If cWard cargo is C, include its psi
if ({(atomno=cargoNo) and (chain=gChain)}.atomName == "C") {
#cargoNo--
}
for (var iNo = cargoNo; iNo <= anchorNo; iNo++) {
if ({(atomno=iNo) and (chain=gChain)}.atomName == "CA") {
if (isRotorAvailable(iNo)) {
if (({(atomno=iNo) and (chain=gChain)}.group != "PRO") and (iNo > cargoNo)) { # phi
rotors += [{(atomno=@{getCmNo(iNo-1)}) and (chain=gChain)}.atomIndex,
{(atomno=@{iNo-1}) and (chain=gChain)}.atomIndex]
rotors += [{(atomno=@{iNo}) and (chain=gChain)}.atomIndex,
{(atomno=@{iNo+1}) and (chain=gChain)}.atomIndex]
}
if (iNo != (anchorNo-1)) { # psi
rotors += [{(atomno=@{iNo-1}) and (chain=gChain)}.atomIndex,
{(atomno=@{iNo}) and (chain=gChain)}.atomIndex]
rotors += [{(atomno=@{iNo+1}) and (chain=gChain)}.atomIndex,
{(atomno=@{getNpNo(iNo+2)}) and (chain=gChain)}.atomIndex]
}
}
}
}
}
else {
# If nWard cargo is C, include its phi
if ({(atomno=cargoNo) and (chain=gChain)}.atomName == "N") {
#cargoNo++
}
for (var iNo = cargoNo; iNo >= anchorNo; iNo--) {
if ({(atomno=iNo) and (chain=gChain)}.atomName == "CA") {
if (isRotorAvailable(iNo)) {
if ((iNo != (anchorNo-1)) and (iNo < cargoNo)) { # psi
rotors += [{(atomno=@{getNpNo(iNo+2)}) and (chain=gChain)}.atomIndex,
{(atomno=@{iNo+1}) and (chain=gChain)}.atomIndex]
rotors += [{(atomno=@{iNo}) and (chain=gChain)}.atomIndex,
{(atomno=@{iNo-1}) and (chain=gChain)}.atomIndex]
}
if ({(atomno=iNo) and (chain=gChain)}.group != "PRO") { # phi
rotors += [{(atomno=@{iNo+1}) and (chain=gChain)}.atomIndex,
{(atomno=@{iNo}) and (chain=gChain)}.atomIndex]
rotors += [{(atomno=@{iNo-1}) and (chain=gChain)}.atomIndex,
{(atomno=@{getCmNo(iNo-1)}) and (chain=gChain)}.atomIndex]
}
}
}
}
}
if (nWard) {
gNrotors = rotors
if (FALSE) {#DEBUG
print ("gNrotors atomnos")#DEBUG
for (var i = 1; i < gNrotors.size; i += 4) {#DEBUG
print format("%d %d %s", {atomIndex=@{gNrotors[i]}}.atomno,
{atomIndex=@{gNrotors[i+1]}}.atomno, format("%d %d",
{atomIndex=@{gNrotors[i+2]}}.atomno,
{atomIndex=@{gNrotors[i+3]}}.atomno))
}
}#DEBUG
}
else {
gCrotors = rotors
if (FALSE) {#DEBUG
print ("gCrotors atomnos")#DEBUG
for (var i = 1; i < gCrotors.size; i += 4) {#DEBUG
print format("%d %d %s", {atomIndex=@{gCrotors[i]}}.atomno,
{atomIndex=@{gCrotors[i+1]}}.atomno, format("%d %d",
{atomIndex=@{gCrotors[i+2]}}.atomno,
{atomIndex=@{gCrotors[i+3]}}.atomno))
}
}#DEBUG
}
}
function collectRotors() {
collectBBrotors(FALSE)
collectBBrotors(TRUE)
}
function tugSideChain(pt) {
# If destination atom defined
if (gDestAtomIdx >= 0) {
v = {atomIndex=gDestAtomIdx}.xyz - {atomIndex=gSCidx}.xyz
if (abs(angle({atomIndex=gDestAtomIdx}.xyz, {0 0 0}, pt)) < 90) {
pt = -v/20.0
}
else {
pt = v/20.0
}
}
gSCpt += pt
draw arrow {atomIndex=gSCidx} @gSCpt
}
function setColors() {
select all
color {selected} @gScheme
color {atomIndex=gCanchorIdx} @gAltScheme
color {atomIndex=gNanchorIdx} @gAltScheme
color {atomIndex=g1pivotIdx} green
color {atomIndex=g2pivotIdx} green
color @gCargoAtoms @gAltScheme
select {(atomIndex=gCcargoIdx) or (atomIndex=gNcargoIdx)}
halo on
select {atomIndex=gDestAtomIdx}
star on
select none
}
function clearAtomIdxs() {
gCcargoIdx = -1
gNcargoIdx = -1
gCanchorIdx = -1
gNanchorIdx = -1
g1pivotIdx = -1
g2pivotIdx = -1
gDestAtomIdx = -1
gSCidx = -1
}
function timedOut (s) {
timeout ID"tug" OFF
prompt(s)
gBusy = FALSE
background ECHO yellow
restore state gState
select gCargoAtoms
refresh
quit
}
function recordDrag() {
var ls = format("select %s;", {selected})
ls += format("gCanchorIdx = %d;", gCanchorIdx)
ls += format("gCanchorNo = %d;", gCanchorNo)
ls += format("gNanchorIdx = %d;", gNanchorIdx)
ls += format("gNanchorNo = %d;", gNanchorNo)
ls += format("gNanchorPidx = %d;", gNanchorPidx)
ls += format("gCanchorXyz = %s;", gCanchorXyz)
ls += format("gNanchorXyz = %s;", gNanchorXyz)
ls += format("gNanchorPxyz = %s;", gNanchorPxyz)
ls += format("gCcargoIdx = %d;", gCcargoIdx)
ls += format("gNcargoIdx = %d;", gNcargoIdx)
ls += format("gCcargoXyz = %s;", gCcargoXyz)
ls += format("gNcargoXyz = %s;", gNcargoXyz)
ls += format("gCcargoNo = %d;", gCcargoNo)
ls += format("gNcargoNo = %d;", gNcargoNo)
ls += format("gDestAtomIdx = %d;", gDestAtomIdx)
ls += format("g1pivotIdx = %d;", g1pivotIdx)
ls += format("g2pivotIdx = %d;", g2pivotIdx)
ls += format("gAc = %s;", gAc)
ls += format("gChain = \"%s\";", gChain)
ls += format("gMinNo = %d;", gMinNo)
ls += format("gMaxNo = %d;", gMaxNo)
ls += format("gCargoAtoms = %s;", gCargoAtoms)
ls += format("gSCidx = %d;", gSCidx)
ls += format("gSCcircle = %d;", gSCcircle)
ls += format("gSCpt = %s;", gSCpt)
ls += "collectRotors();"
ls += "tugDragDoneMB();"
plicoRecord(ls)
}
# Bound to LEFT-UP by tugEnableDrag
function tugDragDoneMB() {
if (gPlicoRecord != "") {
recordDrag()
}
# Move by rotation on rotor sets, smallest first
gBusy = TRUE
background ECHO pink
refresh
# If side chain mode
if (gSCidx >= 0) {
dragSC()
}
# Else
else {
gOK = TRUE
timeout ID"tug" 20.0 "timedOut(\"Tug timed out\")"
gCountdown = kCollisionLimit
if ((gCrotors.size < gNrotors.size) or (gNanchorIdx < 0)) {
if (gCrotors.size > 4) {
tugTrackC() # PULLSTRING MODEL
}
if (gOK and (gNrotors.size > 4)) {
tugTrackN() # PULLSTRING MODEL
}
}
else {
if (gNrotors.size > 4) {
tugTrackN() # PULLSTRING MODEL
}
if (gOK and (gCrotors.size > 4)) {
tugTrackC() # PULLSTRING MODEL
}
}
timeout ID"tug" OFF
# If anchor angles acute, fail
if (gOK == TRUE) {
if (gCanchorIdx >= 0) {
var ic = getCwardBBidx(gCanchorIdx)
var in = getNwardBBidx(gCanchorIdx)
if ((ic >= 0) and
angle({atomIndex=ic}, {atomIndex=gCanchorIdx}, {atomIndex=in})
< 100.0) {
gOK = FALSE
}
}
if (gNanchorIdx >= 0) {
var ic = getCwardBBidx(gNanchorIdx)
var in = getNwardBBidx(gNanchorIdx)
if ((in >= 0) and
angle({atomIndex=ic}, {atomIndex=gNanchorIdx}, {atomIndex=in})
< 100.0) {
gOK = FALSE
}
}
}
# If too far
if (gOK == FALSE) {
timedOut("TUG TOO FAR!")
}
# Else OK
else {
select ((atomno >= gNanchorNo) and (atomno <= gCanchorNo)
and (chain = gChain))
var idx = {atomno=@{{chain=gChain}.min.atomno}}.atomIndex
var i = 0
for (; i < 3; i++) {
handleCollisions(FALSE, idx)
if (countCollisions() == 0) {
break
}
}
if (i == 3) {
var p = prompt("Unable to handle all collisions!")
restore state gState
}
}
}
select {gCargoAtoms}
gBusy = FALSE
background ECHO yellow
refresh
}
# Bound to ALT-LEFT-DRAG by tugEnableDrag
function tugDragMB() {
if (gBusy == FALSE) {
var dx = (20.0 * (_mouseX - gMouseX))/_width
var dy = (20.0 * (_mouseY - gMouseY))/_height
var q = quaternion(script("show rotation"))
var ptd = {@dx @dy 0}
var pt = (!q)%ptd
if (distance(pt, {0 0 0}) > 0.004) {
# If sidechain mode
if (gSCidx >= 0) {
tugSideChain(pt)
}
# Else
else {
# If new drag
if (gNewDrag) {
gNewDrag = FALSE
save state gState
}
#mp = ({atomIndex=gNcargoIdx}.xyz + {atomIndex=gCcargoIdx}.xyz )/2.0
# If destination atom defined
if (gDestAtomIdx >= 0) {
var v = {atomIndex=gDestAtomIdx}.xyz - {selected}.xyz
if (abs(angle({atomIndex=gDestAtomIdx}.xyz, {0 0 0}, pt)) < 90) {
pt = -v/20.0
}
else {
pt = v/20.0
}
}
# Move the cargo
select {gCargoAtoms}
# If pivots defined, rotate it
if (g1pivotIdx >= 0) {
# If two pivots
var axis = {0 0 0}
if (g2pivotIdx >= 0) {
axis = {atomIndex=g2pivotIdx}
}
# Else
else {
axis = cross(pt, {0 0 0}) + {atomIndex=g1pivotIdx}.xyz
}
var a = ((abs(angle(pt + {atomIndex=g1pivotIdx}.xyz,
{atomIndex=g1pivotIdx}.xyz, axis)) < 90) ? -2 : 2)
#rotateSelected {atomIndex=g1pivotIdx} @axis @a
rotateSelectedRecord(g1pivotIdx, axis, a)
}
# Else translate it
else {
#translateSelected @pt
translateSelectedRecord(pt)
}
# If collisions
var aset = {((atomno < gCanchorNo) and (atomno > gNanchorNo)
and (chain=gChain))}
var ac = (within(kCtolerance, FALSE, {aset}) and not {aset}
and not connected(aset))
if (ac.size > 0) {
# Resolve them
for (var i = 1; i <= ac.size; i++) {
select ac[i]
handleCollisions()
}
# If unable
if (gOk2 == FALSE) {
# Back off
background ECHO pink
delay 1
if (g1pivotIdx >= 0) {
rotateSelectedRecord(g1pivotIdx, axis, -a)
}
else {
translateSelectedRecord(-pt)
}
background ECHO yellow
}
}
#tugDragDoneMB()
}
gMouseX = _mouseX
gMouseY = _mouseY
}
select {gCargoAtoms}
}
}
# Bound to ALT-LEFT-DOWN by tugEnableDrag
function tugMarkMB() {
gMouseX = _mouseX
gMouseY = _mouseY
gNcargoXyz = {atomIndex=gNcargoIdx}.xyz
gCcargoXyz = {atomIndex=gCcargoIdx}.xyz
gNewDrag = TRUE
}
# Called by tugCargoMB and by tugAnchorMB or tugPivotMB when cargo exists
function tugEnableDrag() {
gEcho = "ALT-CLICK=set cargo range|ALT-DRAG=move|SHIFT=set anchors|ALT-CTRL=set pivots|ALT-SHIFT=set dest atom |DOUBLE-CLICK=exit"
echo @gEcho
# Allow atoms to be dragged
bind "ALT-LEFT-DOWN" "tugMarkMB";
bind "ALT-LEFT-UP" "tugDragDoneMB";#ONCEMODE
bind "ALT-LEFT-DRAG" "tugDragMB";
}
# Bound to SHIFT-LEFT-CLICK by tugCargoMB
function tugAnchorMB() {
if ({atomIndex=_atomPicked}.chain == gChain) {
var aPidx = getScBBidx( _atomPicked)
var pno = {atomIndex=aPidx}.atomno
if (pno > {atomIndex=gCcargoIdx}.atomno) {
color {atomIndex=gCanchorIdx} @gScheme
if (gCanchorIdx == aPidx) {
gCanchorIdx = -1
gCanchorNo = gMaxNo + 1
}
else {
gCanchorIdx = aPidx
gCanchorNo = {atomIndex=gCanchorIdx}.atomno
gCanchorXyz = {atomIndex=gCanchorIdx}.xyz
color {atomIndex=gCanchorIdx} @gAltScheme
}
collectBBrotors(FALSE)
}
if (pno < {atomIndex=gNcargoIdx}.atomno) {
color {atomIndex=gNanchorIdx} @gScheme
if (gNanchorIdx == aPidx) {
gNanchorIdx = -1
gNanchorNo = gMinNo - 1
}
else {
gNanchorIdx = aPidx
gNanchorNo = {atomIndex=gNanchorIdx}.atomno
gNanchorPidx = getCwardBBidx( aPidx)
gNanchorXyz = {atomIndex=gNanchorIdx}.xyz
gNanchorPxyz = {atomIndex=gNanchorPidx}.xyz
color {atomIndex=gNanchorIdx} @gAltScheme
}
collectBBrotors(TRUE)
}
}
# Get connectors between fixed and moving part
var aset = {((atomno < gCanchorNo) and (atomno > gNanchorNo)
and (chain=gChain))}
gAc = (within(kCtolerance, FALSE, {aset}) and not {aset})
select {gCargoAtoms}
}
# Bound to ALT-SHIFT-LEFT-CLICK by tugCargoMB
function tugDestAtomMB() {
var aOk = TRUE
if ({atomIndex=_atomPicked}.chain == gChain) {
var pno = {atomIndex=_atomPicked}.atomno
if ((pno <= {atomIndex=gCcargoIdx}.atomno) and (pno >= {atomIndex=gNcargoIdx}.atomno)) {
aOk = FALSE
}
}
if (aOk) {
select {atomIndex=gDestAtomIdx}
star off
if (gDestAtomIdx == _atomPicked) {
gDestAtomIdx = -1
}
else {
gDestAtomIdx = _atomPicked
select {atomIndex=gDestAtomIdx}
star on
}
select {gCargoAtoms}
}
}
# Bound to CTRL-LEFT-CLICK by tugCargoMB
function tugPivotMB() {
if (g1pivotIdx == _atomPicked) {
color {atomIndex=g1pivotIdx} @gScheme
if (g2pivotIdx >= 0) {
g1pivotIdx = g2pivotIdx
g2pivotIdx = -1
}
else {
g1pivotIdx = -1
}
}
else if (g2pivotIdx == _atomPicked) {
color {atomIndex=g2pivotIdx} @gScheme
g2pivotIdx = -1
}
else if (g1pivotIdx >= 0) {
if (g2pivotIdx >= 0) {
color {atomIndex=g2pivotIdx} @gScheme
}
g2pivotIdx = _atomPicked
color {atomIndex=g2pivotIdx} green
}
else {
g1pivotIdx = _atomPicked
color {atomIndex=g1pivotIdx} green
}
select {gCargoAtoms}
}
# Bound to ALT-LEFT-CLICK by plicoTug
function tugCargoMB() {
if (gChain != {atomIndex=_atomPicked}.chain) {
clearAtomIdxs()
setColors()
gChain = {atomIndex=_atomPicked}.chain
}
# If movable side chain atom picked
if (isMovableSideChain( _atomPicked)) {
if (gSCidx >= 0) {
draw gSCcircle DELETE
}
if (gSCidx == _atomPicked) {
gSCidx = -1
}
else {
gSCidx = _atomPicked
gSCpt = {atomIndex=gSCidx}.xyz
draw gSCcircle CIRCLE {atomIndex=gSCidx} MESH NOFILL
}
}
else if ((gChain == "") or ({atomIndex=_atomPicked}.chain == gChain)) {
gMinNo = {chain=gChain}.atomno.min
gMaxNo = {chain=gChain}.atomno.max
if (gNanchorIdx < 0) {
gNanchorNo = gMinNo - 1
}
if (gCanchorIdx < 0) {
gCanchorNo = gMaxNo + 1
}
var aPidx = getScBBidx( _atomPicked)
gSCidx = -1
draw gSCcircle DELETE
# If existing cWard cargo picked
if (gCcargoIdx == aPidx) {
# Clear the highlight
select {atomIndex=gCcargoIdx}
halo off
# If nWard cargo exists, mark it as the cWard cargo
if (gNcargoIdx != gCcargoIdx) {
gCcargoIdx = getCpIdx(gNcargoIdx)
gCcargoNo = {atomIndex=gCcargoIdx}.atomno
}
else {
gCcargoIdx = -1
gNcargoIdx = -1
}
}
else if (gNcargoIdx == aPidx) {
select {atomIndex=gNcargoIdx}
halo off
gNcargoIdx = getNmIdx(gCcargoIdx)
gNcargoNo = {atomIndex=gNcargoIdx}.atomno
}
else if (gCcargoIdx >= 0) {
var no = {atomIndex=aPidx}.atomno
# If pick is nWard of it
if (no < {atomIndex=gCcargoIdx}.atomno) {
# If exists, clear its highlight
if (gNcargoIdx != gCcargoIdx) {
select {atomIndex=gNcargoIdx}
halo off
}
# Set new nWard cargo and highlight it
gNcargoIdx = getNmIdx(aPidx)
gNcargoNo = {atomIndex=gNcargoIdx}.atomno
}
# Else cWard
else {
# Clear its old highlight
select {atomIndex=gCcargoIdx}
if (gNcargoIdx != gCcargoIdx) {
halo off
}
# Set new cWard cargo and highlight
gCcargoIdx = getCpIdx(aPidx)
gCcargoNo = {atomIndex=gCcargoIdx}.atomno
}
}
# Else no cWard cargo
else {
# Set new cWard cargo and highlight
gCcargoIdx = getCpIdx(aPidx)
gCcargoNo = {atomIndex=gCcargoIdx}.atomno
gNcargoIdx = getNmIdx(gCcargoIdx)
gNcargoNo = {atomIndex=gNcargoIdx}.atomno
# Set default cWard anchor at cWard N
var iNo = gMaxNo
for (; iNo > 0; iNo--) {
if ({(atomno=iNo) and (chain=gChain)}.atomName == "N") {
break;
}
}
gCanchorIdx = {(atomno=iNo) and (chain=gChain)}.atomIndex
gCanchorNo = {atomIndex=gCanchorIdx}.atomno
gCanchorXyz = {atomIndex=gCanchorIdx}.xyz
}
# If any anchor now inside cargo cluster, kill it
if ({atomIndex=gCanchorIdx}.atomno <= {atomIndex=gCcargoIdx}.atomno) {
gCanchorIdx = -1
gCanchorNo = gMaxNo + 1
}
if ({atomIndex=gNanchorIdx}.atomno >= {atomIndex=gNcargoIdx}.atomno) {
gNanchorIdx = -1
gNanchorNo = gMinNo - 1
}
# Highlight cargo cluster
selectNward(gCcargoIdx, gNcargoIdx)
gCargoAtoms = {selected}
setColors()
# Collect the rotor sets
collectRotors()
# Get connectors between fixed and moving part
var aset = {((atomno < gCanchorNo) and (atomno > gNanchorNo)
and (chain=gChain))}
gAc = (within(kCtolerance, FALSE, {aset}) and not {aset})
}
# Enable dragging
tugEnableDrag()
# Bind other keys
bind "SHIFT-LEFT-CLICK" "_pickAtom";
bind "SHIFT-LEFT-CLICK" "+:tugAnchorMB";
bind "ALT-CTRL-LEFT-CLICK" "_pickAtom";
bind "ALT-CTRL-LEFT-CLICK" "+:tugPivotMB";
bind "ALT-SHIFT-LEFT-CLICK" "_pickAtom";
bind "ALT-SHIFT-LEFT-CLICK" "+:tugDestAtomMB";
select {gCargoAtoms}
}
# Top level of Tug
function plicoTug() {
set allowModelKit TRUE
set allowRotateSelected TRUE
set allowMoveAtoms TRUE
# Push selected
gSelSaves = {selected}
select all
gZoom = script("show zoom")
gRotate = script("show rotation")
write tugsave.pdb
select none
gScheme = defaultColorScheme
gAltScheme = ((gScheme == "Jmol") ? "Rasmol" : "Jmol")
set echo TOP LEFT
background ECHO yellow
gEcho = "ALT-CLICK=set cargo range"
echo @gEcho
gCrotors = array()
gNrotors = array()
clearAtomIdxs()
gChain = ""
unbind
set picking ON
bind "ALT-LEFT-CLICK" "_pickAtom";
bind "ALT-LEFT-CLICK" "+:tugCargoMB";
bind "DOUBLE" "tugExit";
}
# Bound to DOUBLE by plicoTug
function tugExit() {
var p = prompt("Exit tug?", "Yes|No|Undo", TRUE)
if (p == "Undo") {
load tugsave.pdb
script inline gZoom
rotate @gRotate
echo Tug session undone
if (gPlicoRecord != "") {
plicoRecord("load tugsave.pdb;")
}
}
if (p != "No") {
unbind
halo off
set allowMoveAtoms FALSE
echo
select all
halo off
star off
color {selected} @gScheme
draw gSCcircle DELETE
gBusy = FALSE
background ECHO yellow
# Pop selected
select gSelSaves
}
}
# End of TUG.SPT
