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. It also allows the user to move an entire chain to nest against another chain.
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
# v1.3 beta 2/13/2014 for Jmol 14
#
# Translate or rotate a stretch of a polypeptide against itself by mouse actions
#
var kTug = 2
var kDtolerance = 0.2
var kAtolerance = 5.0
var kCtolerance = 1.85
var kMtolerance = 0.8
var gCanchorIdx = -1
var gCanchorNo = -1
var gNanchorIdx = -1
var gNanchorNo = -1
var gCcargoIdx = -1
var gNcargoIdx = -1
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 gOkCollide = ({})
var gChain = ""
var gMinNo = 1
var gMaxNo = 9999
var gScheme = "Jmol"
var gAltScheme = "Rasmol"
var gCargoSet = ({})
var gMovingSet = ({})
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 gZoom = ""
var gRotate = ""
var gTow = FALSE
var g1dynamicIdx = -1
var g2dynamicIdx = -1
var gSCcheck = TRUE
# 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, iChain) {
while ((iNo >= 0) and (
({(atomno=iNo) and (chain=iChain)}.atomName != "N")
and ({(atomno=iNo) and (chain=iChain)}.atomName != "C")
and ({(atomno=iNo) and (chain=iChain)}.atomName != "CA"))) {
iNo--
}
return iNo
}
function getNwardBBidx (idx, iChain) {
var no = {atomIndex=idx}.atomno - 1
no = getNwardBBno( no, iChain)
return ((no >= 0) ? ({(atomno=no) and (chain=iChain)}.atomIndex) : -1)
}
function getCwardBBno (iNo, iChain) {
while ((iNo < gMaxNo) and (
({(atomno=iNo) and (chain=iChain)}.atomName != "N")
and ({(atomno=iNo) and (chain=iChain)}.atomName != "C")
and ({(atomno=iNo) and (chain=iChain)}.atomName != "CA"))) {
iNo++
}
return iNo
}
function getCwardBBidx (idx, iChain) {
var no = {atomIndex=idx}.atomno + 1
no = getCwardBBno( no, iChain)
return ((no >= 0) ? ({(atomno=no) and (chain=iChain)}.atomIndex) : -1)
}
function getScSet (scIdx, iChain) {
var scSet = ({})
var idx = getScBBidx(scIdx, iChain)
var iNo = {atomIndex=idx}.atomno + 3
for (var i = 1; i < 20; i++) {
idx = {(atomno=@{iNo+i}) and (chain=iChain)}.atomIndex
if (isBBidx(idx)) {
break
}
scSet = scSet or {atomIndex=idx}
}
return scSet
}
function getScBBidx (idx, iChain) {
var no = {atomIndex=idx}.atomno
for (; no > 0; no--) {
if ({(atomno=no) and (chain=iChain)}.atomName == "CA") {
break
}
else if ({(atomno=no) and (chain=iChain)}.atomName == "C") {
break
}
else if ({(atomno=no) and (chain=iChain)}.atomName == "N") {
break
}
else if ({(atomno=no) and (chain=iChain)}.atomName == "CB") {
no -= 3
break
}
}
return {(atomno=no) and (chain=iChain)}.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 (not isBBidx(aIDx)) {
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
var iChain = {atomIndex=fromIdx}.chain
select none
while ({(atomno=iNo) and (chain=iChain)}.atomName != "N") {
{(atomno=iNo) and (chain=iChain)}.selected = TRUE
iNo++
if (iNo > {chain=iChain}.atomno.max) {
break
}
}
}
# First and last are BB atoms
# Any side atoms in the range are also selected
function selectNwardIdx (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)
if ({(atomno=firstno) and (chain=gChain)}.atomName == "C") { # if psi
addSideChainToSelection(firstno-1, TRUE, TRUE)
{(atomno=@{firstno+1}) and (chain=iChain)}.selected = TRUE # add O
}
if ({(atomno=firstno) and (chain=iChain)}.atomName == "CA") {
addSideChainToSelection(firstno, TRUE, FALSE)
}
if ({(atomno=lastno) and (chain=iChain)}.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 selectCwardIdx (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)
if ({(atomno=firstno) and (chain=iChain)}.atomName == "C") { # if psi
addSideChainToSelection(firstno-1, FALSE, FALSE)
}
if ({(atomno=lastno) and (chain=iChain)}.atomName == "CA") {
addSideChainToSelection(lastno, TRUE, FALSE)
}
if ({(atomno=lastno) and (chain=iChain)}.atomName == "C") { # if psi
addSideChainToSelection(lastno-1, TRUE, TRUE)
{(atomno=@{lastno+1}) and (chain=iChain)}.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 cAtoms = ({})
for (var idx = {*}.min.atomIndex; idx <= {*}.max.atomIndex; idx++) {
if ({atomIndex=idx}.size > 0) {
var lcAtoms = (within(kCtolerance, FALSE, {atomIndex=idx})
and {atomIndex > idx}
and not {rc}
and not connected({atomIndex=idx}))
if (lcAtoms.size > 0) {
cAtoms = cAtoms or lcAtoms
}
}
}
return cAtoms.size
}
# Resolve collisions
function handleCollisions2( 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, gChain)}},
{atomIndex=idx} , {atomIndex=@{getNwardBBidx(idx, gChain)}}) < 100) {
continue
}
# For all local colliders
for (var c = 1; c <= lcAtoms.size; c++ ) {
var cidx = lcAtoms[c].atomIndex
# If it is with water, delete it
if (lcAtoms[c].group = "HOH") {
delete {atomIndex=cidx}
}
# else if it is with side chain not proline, fix it
else if (isSCidx(cidx) and ({atomIndex=cidx}.group != "PRO")) {
fixSCcollision2(cidx)
recollect = TRUE
# If not fixed, exit fail
if (not gOk2) {
return # early exit (break n jmol bug)
}
}
# else if it is itself a side chain not proline, fix it
else if (isSCidx(idx) and ({atomIndex=idx}.group != "PRO")) {
fixSCcollision2(idx)
recollect = TRUE
# If not fixed, exit fail
if (not gOk2) {
return # early exit (break n jmol bug)
}
}
# Else if it is with O, counter-rotate
else if (lcAtoms[c].atomName = "O") {
counterRotate2(lcAtoms[c].atomIndex,
{atomIndex=idx}.xyz, targetIdx, FALSE)
# If not fixed, exit fail
if (not gOk2) {
return # early exit (break n jmol bug)
}
}
# Else if it is itself O, counter-rotate
else if ({atomIndex=idx}.atomName = "O") {
counterRotate2(idx, lcAtoms[c].xyz, targetIdx, FALSE)
# If not fixed, exit fail
if (not gOk2) {
return # early exit (break n jmol bug)
}
}
else { # Else not fixed, exit fail
gOk2 = FALSE
return # early exit (break n jmol bug)
}
} # endfor
}
}
} # 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, gChain)}}, {atomIndex=i1},
{atomIndex=i2}, {atomIndex=i3}) + dt
}
else {
phi = angle({atomIndex=i1}, {atomIndex=i2},
{atomIndex=i3}, {atomIndex=@{getNwardBBidx(i3, gChain)}}) + dt
}
if ({atomIndex=i2}.atomno > {atomIndex=targetIdx}.atomno) {
movePt = TRUE
selectNwardIdx(i3, getCwardBBidx(targetIdx, gChain))
{atomIndex=targetIdx}.selected = TRUE
}
else {
selectCwardIdx(i2, targetIdx)
}
}
else {
if (({atomIndex=i2}.atomName="CA")) {
phi = angle({atomIndex=@{getNwardBBidx(i1, gChain)}}, {atomIndex=i1},
{atomIndex=i2}, {atomIndex=i3}) + dt
}
else {
psi = angle({atomIndex=i2}, {atomIndex=i3},
{atomIndex=i4}, {atomIndex=@{getCwardBBidx(i4, gChain)}}) + dt
}
if ({atomIndex=i2}.atomno < {atomIndex=targetIdx}.atomno) {
movePt = TRUE
selectCwardIdx(i3, getNwardBBidx(targetIdx, gChain))
{atomIndex=targetIdx}.selected = TRUE
}
else {
selectNwardIdx(i2, targetIdx)
}
}
# Relax rules if desperate
if (pass1 > 10) {
phi = -50
}
# If rotation within ramachandran limits
if ((abs(dt) >= 0.1) and
(({atomIndex=i2}.group=="GLY") or (phi < 0))) {
# 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
}
handleCollisions2( targetIdx)
if (not gOk2) {
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 docounterRotate(caPhiIdx, nIdx, cIdx, oIdx, caPsiIdx, dir, nWard) {
# Rotate psi
{atomIndex=nIdx}.selected = nWard
{atomIndex=cIdx}.selected = nWard
{atomIndex=oIdx}.selected = nward
rotateSelected {atomIndex=caPsiIdx} {atomIndex=cIdx} @{dir}
# Counter-rotate phi
{atomIndex=nIdx}.selected = not nWard
{atomIndex=cIdx}.selected = not nWard
{atomIndex=oIdx}.selected = not nward
rotateSelected {atomIndex=nIdx} {atomIndex=caPhiIdx} @{-dir}
}
function counterRotate(oIdx, dir, nWard) {
var iChain = {atomIndex=oIdx}.chain
var selsave = {selected}
var cIdx = getScBBidx(oIdx, iChain)
var nIdx = getCwardBBidx(cIdx, iChain)
var caPhiIdx = getCwardBBidx(nIdx, iChain)
var caPsiIdx = getNwardBBidx(cIdx, iChain)
if (nWard) {
nNo = {chain=iChain}.atomno.min
selectNwardIdx(caPsiIdx, {(atomno=nNo) and (chain=iChain)}.atomIndex)
}
else {
cNo = {chain=iChain}.atomno.max
selectCwardIdx(caPhiIdx, {(atomno=cNo) and (chain=iChain)}.atomIndex)
}
# Counter-rotate
docounterRotate(caPhiIdx, nIdx, cIdx, oIdx, caPsiIdx, dir, not nWard)
select selsave
}
function counterRotate2(oIdx, toPt, terminalIdx, oDrag) {
var iChain = {atomIndex=oIdx}.chain
var selsave = {selected}
var gOk2 = TRUE
var cIdx = getScBBidx(oIdx, iChain)
var nIdx = getCwardBBidx(cIdx, iChain)
var caPhiIdx = getCwardBBidx(nIdx, iChain)
var caPsiIdx = getNwardBBidx(cIdx, iChain)
var nTward = ({atomIndex=oIdx}.atomno < {atomIndex=terminalIdx}.atomno)
if (nTward) {
selectCwardIdx(cIdx, terminalIdx)
}
else {
selectNwardIdx(nIdx, terminalIdx)
}
# Until all collisions cancelled
var dir = 5
var ang = angle(toPt, {atomIndex=oIdx}, {atomIndex=cIdx})
var tcount = 0
while (oDrag or (within(kCtolerance, FALSE, {atomIndex=oIdx})
and not {atomIndex=oIdx} and not connected({atomIndex=oIdx})
and not {gOkCollide} > 0)) {
# Counter-rotate
docounterRotate(caPhiIdx, nIdx, cIdx, oIdx, caPsiIdx, dir, nTward)
var newang = angle(toPt, {atomIndex=oIdx}, {atomIndex=cIdx})
# If wrong direction once, undo and reverse
if (newang > ang) {
docounterRotate(caPhiIDx, nIdx, cIdx, oIdx, caPsiIdx, -dir, nTward)
# If first time, continue in opposite direction
dir *= -1
if (dir < 0) {
continue
}
}
if (oDrag) {
break
}
# If no go, undo and exit
tcount++
if (tcount > (360/abs(dir))) {
gOk2 = FALSE
break
}
} # endwhile
select selsave
}
# Repair proline
function repairProline(BBidx) {
var cbidx = getCBidx(BBidx)
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 repairSideChain(targetIdx, nWard) {
var idx = (nWard ? getCwardBBidx(targetIdx, gChain) : getNwardBBidx(targetIdx, gChain))
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, gChain), 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, gChain), 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(colliders[i].atomIndex,
{atomIndex=dIdx}.xyz, targetIdx, FALSE)
}
}
}
}
}
# Rebuild Cward rotors set
function tugTrackC() {
# For all bb atoms cWard of cargo
var targetIdx = gCcargoIdx
var okCount = 0
# Allow collisions with cargo
gOkCollide = gCargoSet
var tcount = 0
while (targetIdx != gCanchorIdx) {
# Step to next atom
targetIdx = getCwardBBidx(targetIdx, gChain)
# No collision with cargo allowed after two atoms placed
if (tcount == 2) {
gOkCollide = ({})
}
tcount++
# Compute targets desired coords
var c1idx = getCwardBBidx(targetIdx, gChain)
var n1idx = getNwardBBidx(targetIdx, gChain )
var n2idx = getNwardBBidx(n1Idx, gChain)
var n3idx = getNwardBBidx(n2Idx, gChain)
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, 120.0)
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 (not gOK)) {
# 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
repairSideChain(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 = gCargoSet
var tcount = 0
while (targetIdx != gNanchorIdx) {
# Step to next atom
targetIdx = getNwardBBidx(targetIdx, gChain)
# No collision with cargo allowed after two atoms placed
if (tcount == 2) {
gOkCollide = ({})
}
tcount++
# Compute targets desired coords
var n1idx = getNwardBBidx(targetIdx, gChain)
var c1idx = getCwardBBidx(targetIdx, gChain)
var c2idx = getCwardBBidx(c1idx, gChain)
var c3idx = getCwardBBidx(c2idx, gChain)
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 (not gOK)) {
# 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
repairSideChain(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, iChain) {
var scBondIdxs = array()
for (var iNo = no; iNo >= 0; iNo--) {
var ile = 0
switch ({(atomno=iNo) and (chain=iChain)}.atomName) {
case "CA" :
return scBondIdxs # Early exit since break 1 appears broken
case "CZ" :
if ({(atomno=iNo) and (chain=iChain)}.group == "TYR") {
break
}
case "CE" :
if ({(atomno=iNo) and (chain=iChain)}.group == "MET") {
break
}
case "CG1" :
if ({(atomno=iNo) and (chain=iChain)}.group == "VAL") {
break
}
if ({(atomno=iNo) and (chain=iChain)}.group == "ILE") {
ile = 1
}
case "NE" :
case "CD" :
case "SD" :
case "CG" :
case "CB" :
scBondIdxs += {(atomno=@{iNo+1+ile}) and (chain=iChain)}.atomIndex
scBondIdxs += {(atomno=@{iNo+0}) and (chain=iChain)}.atomIndex
if ({(atomno=iNo) and (chain=iChain)}.atomName%2 == "CG") {
scBondIdxs += {(atomno=@{iNo-1}) and (chain=iChain)}.atomIndex
scBondIdxs += {(atomno=@{iNo-4}) and (chain=iChain)}.atomIndex
}
else if ({(atomno=iNo) and (chain=iChain)}.atomName == "CB") {
scBondIdxs += {(atomno=@{iNo-3}) and (chain=iChain)}.atomIndex
scBondIdxs += {(atomno=@{iNo-4}) and (chain=iChain)}.atomIndex
}
else {
scBondIdxs += {(atomno=@{iNo-1}) and (chain=iChain)}.atomIndex
scBondIdxs += {(atomno=@{iNo-2}) and (chain=iChain)}.atomIndex
}
break
}
}
return scBondIdxs
}
# Drag Side Chain
function dragSC() {
var iNo = {atomIndex=gSCidx}.atomno
var iChain = {atomIndex=gSCidx}.chain
if ({atomIndex=gSCidx}.group != "PRO") {
var scBondIdxs = collectSCrotors( iNo, iChain)
var numChi = scBondIdxs.size / 4
var dist = distance({atomIndex=gSCidx}.xyz, gSCpt)
var scSet = ({})
if (gSCcheck) {
scSet = getScSet(gSCidx, iChain)
}
# 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)
if (gSCcheck) {
var colliders = (within(kCtolerance, FALSE, scSet)
and not connected(scSet) and not {scSet})
if (colliders.size > 0) {
continue
}
}
# 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=iChain)}.atomIndex
var icb = {(atomno=@{iNo-1}) and (chain=iChain)}.atomIndex
var ica = {(atomno=@{iNo-4}) and (chain=iChain)}.atomIndex
var in = {(atomno=@{iNo-5}) and (chain=iChain)}.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 iChain = {atomIndex=idx}.chain
var resno = {(atomno=iNo) and (chain=iChain)}.resno
# Get SC terminus
while (resno == {(atomno=iNo) and (chain=iChain)}.resno) {
iNo++
}
iNo--
var sc = array()
var iBno = iNo
while ({(atomno=iBno) and (chain=iChain)}.atomName != "CB") {
sc += {(atomno=iBno) and (chain=iChain)}
iBno--
}
var cbidx = {(atomno=iBno) and (chain=iChain)}.atomIndex
var scBondIdxs = collectSCrotors( iNo, iChain)
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[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
}
}
}
}
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) {
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 {
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
}
else {
gCrotors = rotors
}
}
function collectRotors() {
collectBBrotors(FALSE)
collectBBrotors(TRUE)
}
function tugSideChain(pt) {
# If destination atom defined
if (gDestAtomIdx >= 0) {
var 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=g1pivotIdx} green
color {atomIndex=g2pivotIdx} green
color @gCargoSet @gAltScheme
select {(atomIndex=gCcargoIdx) or (atomIndex=gNcargoIdx)
or (atomIndex=gCanchorIdx) or (atomIndex=gNanchorIdx)}
halo on
select {atomIndex=gDestAtomIdx}
star on
select none
}
function clearAtomIdxs() {
gCcargoIdx = -1
gNcargoIdx = -1
gCanchorIdx = -1
gNanchorIdx = -1
g1pivotIdx = -1
g2pivotIdx = -1
g1dynamicIdx = -1
g2dynamicIdx = -1
gDestAtomIdx = -1
gSCidx = -1
}
function timedOut (s) {
timeout ID"tug" OFF
prompt(s)
gBusy = FALSE
background ECHO yellow
restore state gState
select gCargoSet
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("gCcargoIdx = %d;", gCcargoIdx)
ls += format("gNcargoIdx = %d;", gNcargoIdx)
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("gOkCollide = %s;", gOkCollide)
ls += format("gChain = \"%s\";", gChain)
ls += format("gMinNo = %d;", gMinNo)
ls += format("gMaxNo = %d;", gMaxNo)
ls += format("gCargoSet = %s;", gCargoSet)
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 (not gBusy) {
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 if (not gTow) {
gOK = TRUE
timeout ID"tug" 20.0 "timedOut(\"Tug timed out\")"
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, gChain)
var in = getNwardBBidx(gCanchorIdx, gChain)
if ((ic >= 0) and
angle({atomIndex=ic}, {atomIndex=gCanchorIdx}, {atomIndex=in})
< 100.0) {
gOK = FALSE
}
}
if (gNanchorIdx >= 0) {
var ic = getCwardBBidx(gNanchorIdx, gChain)
var in = getNwardBBidx(gNanchorIdx, gChain)
if ((in >= 0) and
angle({atomIndex=ic}, {atomIndex=gNanchorIdx}, {atomIndex=in})
< 100.0) {
gOK = FALSE
}
}
}
# If too far
if (not gOK) {
timedOut("TUG TOO FAR!")
}
# Else OK
else {
select ((atomno >= gNanchorNo) and (atomno <= gCanchorNo)
and (chain = gChain))
var idx = {(atomno=@{{chain=gChain}.atomno.min})
and (chain=gChain)}.atomIndex
var ihc = 0
for (ihc = 0; ihc < 10; ihc++) {
handleCollisions2( idx)
if (countCollisions(({})) == 0) {
break
}
}
if (ihc == 10) {
var p = prompt("Unable to handle all collisions!")
restore state gState
}
}
}
select {gCargoSet}
gBusy = FALSE
background ECHO yellow
refresh
}
}
# Bound to ALT-SHIFT-LEFT-DRAG by tugEnableDrag
function tugDrag2MB() {
tugDragMB(TRUE)
}
# Bound to ALT-LEFT-DRAG by tugEnableDrag
function tugDragMB(alt) {
if (not gBusy) {
gBusy = TRUE
var dx = (40.0 * (_mouseX - gMouseX))/_width
var dy = (40.0 * (_mouseY - gMouseY))/_height
var q = quaternion()
var ptd = {@dx @dy 0}
var pt = (!q)%ptd
var axis = {0 0 0}
if (distance(pt, {0 0 0}) > 0.004) {
# If sidechain mode
if (gSCidx >= 0) {
if ({atomIndex=gSCidx}.atomName == "O") {
dir = ((abs(dx) > abs(dy))
? ((dx < 0) ? 2 : -2)
: ((dy < 0) ? 2 : -2))
counterRotate(gSCidx, dir, not alt)
}
else {
gSCcheck = not alt
tugSideChain(pt)
}
}
# Else
else {
# If new drag
if (gNewDrag) {
gNewDrag = FALSE
save state gState
}
# 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 {gCargoSet}
# If pivots defined, rotate it
if (g1pivotIdx >= 0) {
# If two pivots
if (g2pivotIdx >= 0) {
axis = {atomIndex=g2pivotIdx}
}
# Else
else {
axis = cross(pt, {0 0 0}) + {atomIndex=g1pivotIdx}.xyz
}
dir = ((abs(dx) > abs(dy))
? ((dx < 0) ? 2 : -2)
: ((dy < 0) ? 2 : -2))
rotateSelectedRecord(g1pivotIdx, axis, dir)
}
# Else translate it
else {
translateSelectedRecord(pt)
}
# If collisions
var cNotSels = (within(kCtolerance, FALSE, {selected})
and not {gMovingSet})
if ((cNotSels.size > 0) and (not alt)) {
gOk2 = TRUE
for (var i = 1; i <= cNotSels.size; i++) {
# If net collision vector same as move vector
cSels = (within(kCtolerance, FALSE, cNotSels[i]) and {selected})
for (var j = 1; j <= cSels.size; j++) {
var v1 = cNotSels[i].xyz - cSels[j].xyz
if (abs(angle(v1, {0 0 0}, pt)) < 90) {
# If tow mode
if (gTow) {
# Make a dynamic pivot
if (g1pivotIdx < 0) {
g1pivotIdx = cSels[j].atomIndex
g1dynamicIdx = cNotSels[i].atomIndex
color {atomIndex=g1pivotIdx} lightgreen
setDistanceIdx(cNotSels[i].atomIndex,
cSels[j].atomIndex,
kCtolerance + kDtolerance)
}
else if (g2pivotIdx < 0) {
g2pivotIdx = cSels[j].atomIndex
g2dynamicIdx = cNotSels[i].atomIndex
color {atomIndex=g2pivotIdx} lightgreen
setDistanceIdx(cNotSels[i].atomIndex,
cSels[j].atomIndex,
kCtolerance + kDtolerance)
}
else {
gOk2 = FALSE
}
}
else {
# Try to resolve
select cSels[j]
var idx = {(atomno=@{{chain=gChain}.atomno.min})
and (chain=gChain)}.atomIndex
handleCollisions2( idx)
}
}
} # endfor
if (not gOk2) {
break
}
} # endfor
# If unable
if (not gOk2) {
# Back off
background ECHO pink
delay 1
if (g1pivotIdx >= 0) {
rotateSelectedRecord(g1pivotIdx, axis, -a)
}
else {
translateSelectedRecord(-pt)
}
background ECHO yellow
}
}
}
# If dynamic pivotsTBD
if (g1dynamicIdx >= 0) {
var v1 = {atomIndex=g1dynamicIdx}.xyz - {atomIndex=g1pivotIdx}.xyz
if (abs(angle(v1, {0 0 0}, pt)) > 90) {
color {atomIndex=g1pivotIdx} @gAltScheme
g1pivotIdx = -1
g1dynamicIdx = -1
}
}
if (g2dynamicIdx >= 0) {
var v1 = {atomIndex=g2dynamicIdx}.xyz - {atomIndex=g2pivotIdx}.xyz
if (abs(angle(v1, {0 0 0}, pt)) > 90) {
color {atomIndex=g2pivotIdx} @gAltScheme
g2pivotIdx = -1
g2dynamicIdx = -1
}
}
gMouseX = _mouseX
gMouseY = _mouseY
}
select {gCargoSet}
gBusy = FALSE
}
}
# Bound to ALT-LEFT-DOWN by tugEnableDrag
function tugMarkMB() {
gMouseX = _mouseX
gMouseY = _mouseY
gNewDrag = TRUE
}
# Called by tugCargoMB
function tugEnableDrag() {
gEcho = "__________TUG__________|ALT-CLICK=mark block|SHIFT-CLICK=anchors" +
"|ALT-CTRL-CLICK=pivots|ALT-SHIFT-CLICK=dest atom|ALT-DRAG=move" +
"|SHIFT-ALT-DRAG=alt move|DOUBLE-CLICK=exit"
echo @gEcho
# Allow atoms to be dragged
bind "ALT-LEFT-DOWN" "tugMarkMB";
bind "ALT-LEFT-UP" "tugDragDoneMB";
bind "ALT-SHIFT-LEFT-DOWN" "tugMarkMB";
bind "ALT-SHIFT-LEFT-UP" "tugDragDoneMB";
bind "ALT-LEFT-DRAG" "tugDragMB";
bind "ALT-SHIFT-LEFT-DRAG" "tugDrag2MB";
unbind "SHIFT-LEFT-CLICK"
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";
}
# Bound to SHIFT-LEFT-CLICK by tugCargoMB
function tugAnchorMB() {
if ({atomIndex=_atomPicked}.chain == gChain) {
var aPidx = getScBBidx( _atomPicked, gChain)
var pno = {atomIndex=aPidx}.atomno
if (pno > {atomIndex=gCcargoIdx}.atomno) {
select {atomIndex=gCanchorIdx}
halo off
if (gCanchorIdx == aPidx) {
gCanchorIdx = -1
gCanchorNo = gMaxNo + 1
}
else {
gCanchorIdx = aPidx
gCanchorNo = {atomIndex=gCanchorIdx}.atomno
select {atomIndex=gCanchorIdx}
halo on
}
collectBBrotors(FALSE)
}
else if (pno < {atomIndex=gNcargoIdx}.atomno) {
select {atomIndex=gNanchorIdx}
halo off
if (gNanchorIdx == aPidx) {
gNanchorIdx = -1
gNanchorNo = gMinNo - 1
}
else {
gNanchorIdx = aPidx
gNanchorNo = {atomIndex=gNanchorIdx}.atomno
select {atomIndex=gNanchorIdx}
halo on
}
collectBBrotors(TRUE)
}
else {
towCargoMB()
}
# Get moving atoms set
gMovingSet = {((atomno < gCanchorNo) and (atomno > gNanchorNo)
and (chain=gChain))}
}
select {gCargoSet}
}
# 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 {gCargoSet}
}
}
# Bound to CTRL-LEFT-CLICK by tugCargoMB
function tugPivotMB() {
if (g1pivotIdx == _atomPicked) {
color {atomIndex=g1pivotIdx} @gScheme
if (g2pivotIdx >= 0) {
g1pivotIdx = g2pivotIdx
g2pivotIdx = -1
g2dynamicIdx = -1
}
else {
g1pivotIdx = -1
g1dynamicIdx = -1
}
}
else if (g2pivotIdx == _atomPicked) {
color {atomIndex=g2pivotIdx} @gScheme
g2pivotIdx = -1
g2dynamicIdx = -1
}
else if (g1pivotIdx >= 0) {
if (g2pivotIdx >= 0) {
color {atomIndex=g2pivotIdx} @gScheme
}
g2pivotIdx = _atomPicked
g2dynamicIdx = -1
color {atomIndex=g2pivotIdx} green
}
else {
g1pivotIdx = _atomPicked
g1dynamicIdx = -1
color {atomIndex=g1pivotIdx} green
}
select {gCargoSet}
}
# Bound to SHIFT-LEFT-CLICK by plicoTug
function towCargoMB() {
gTow = TRUE
gChain = {atomIndex=_atomPicked}.chain
gMinNo = {chain=gChain}.atomno.min
gMaxNo = {chain=gChain}.atomno.max
gCcargoIdx = -1
gNcargoIdx = -1
gCanchorIdx = -1
gCanchorNo = gMaxNo + 1
gNanchorIdx = -1
gNanchorNo = gMinNo - 1
# Highlight cargo cluster
select {chain=gChain}
gCargoSet = {selected}
gMovingSet = {selected}
setColors()
# Enable dragging
tugEnableDrag()
select {gCargoSet}
halo off
var es = gEcho.replace("anchors","mark chain")
echo @es
unbind "SHIFT-LEFT-CLICK"
bind "SHIFT-LEFT-CLICK" "_pickAtom";
bind "SHIFT-LEFT-CLICK" "+:towCargoMB";
}
# Bound to ALT-LEFT-CLICK by plicoTug
function tugCargoMB() {
# If O or movable side chain atom picked
if (({atomIndex=_atomPicked}.atomName = "O")
or (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 ({atomIndex=_atomPicked}.chain != gChain) {
if (gTow) {
select {chain=gChain}
color {selected} @gScheme
}
gChain = {atomIndex=_atomPicked}.chain
select ({atomIndex=gCcargoIdx} or {atomIndex=gNcargoIdx}
or {atomIndex=gCanchorIdx} or {atomIndex=gNanchorIdx})
halo off
gCcargoIdx = -1
gNcargoIdx = -1
gCanchorIdx = -1
gNanchorIdx = -1
}
gTow = FALSE
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, gChain)
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
}
# 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
selectNwardIdx(gCcargoIdx, gNcargoIdx)
gCargoSet = {selected}
setColors()
# Collect the rotor sets
collectRotors()
# Get moving atoms set
gMovingSet = {((atomno < gCanchorNo) and (atomno > gNanchorNo)
and (chain=gChain))}
}
# Enable dragging
tugEnableDrag()
select {gCargoSet}
}
# Top level of Tug
function plicoTug() {
# Push selected
gSelSaves = {selected}
select all
# Bad idea to proceed when collisions present
while (TRUE) {
var cc = countCollisions(({}))
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 all
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}
handleCollisions2( idx)
}
}
}
else {
break
}
}
else {
break
}
} # endwhile
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 = ("_________TUG_________|ALT-CLICK=mark block|SHIFT-CLICK=mark chain" +
"|DOUBLE-CLICK=exit")
echo @gEcho
gCrotors = array()
gNrotors = array()
clearAtomIdxs()
gChain = ""
unbind
bind "ALT-LEFT-CLICK" "_pickAtom";
bind "ALT-LEFT-CLICK" "+:tugCargoMB";
bind "SHIFT-LEFT-CLICK" "_pickAtom";
bind "SHIFT-LEFT-CLICK" "+:towCargoMB";
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
