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Revert "Code cleanup"
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This reverts commit 2082943.
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@jlec
jlec committed Dec 9, 2015
1 parent cacaf44 commit e039c98
Showing 1 changed file with 43 additions and 51 deletions.
94 changes: 43 additions & 51 deletions rotkit.py
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Original file line number Diff line number Diff line change
@@ -1,18 +1,18 @@
"""
'''
Described at PyMOL wiki:
http://www.pymolwiki.org/index.php/rotkit
-------------------------------------------------------------------------------
Name: rotkit.py examples
Purpose: To rotate molecules easier
Name: rotkit.py examples
Purpose: To rotate molecules easier
Author: Troels Linnet
Author: Troels Linnet
Created: 30/08/2011
Copyright: (c) Troels Linnet 2011
Licence: Free
Created: 30/08/2011
Copyright: (c) Troels Linnet 2011
Licence: Free
-------------------------------------------------------------------------------
"""
'''

from __future__ import print_function

Expand All @@ -23,13 +23,7 @@


def printMat(matrix):
print(
"%s %s %s %s \n%s %s %s %s \n%s %s %s %s \n%s %s %s %s" % (
matrix[0], matrix[1], matrix[2], matrix[3], matrix[4],
matrix[5], matrix[6], matrix[7], matrix[8], matrix[9],
matrix[10], matrix[11], matrix[12], matrix[13], matrix[14], matrix[15]
)
)
print(("%s %s %s %s \n%s %s %s %s \n%s %s %s %s \n%s %s %s %s" % (matrix[0], matrix[1], matrix[2], matrix[3], matrix[4], matrix[5], matrix[6], matrix[7], matrix[8], matrix[9], matrix[10], matrix[11], matrix[12], matrix[13], matrix[14], matrix[15])))
return None


Expand All @@ -49,33 +43,33 @@ def vector(Sel1, Sel2):
PosSel1 = getxyz(Sel1)[0]
PosSel2 = getxyz(Sel2)[0]
vectorcalc = [PosSel2[0] - PosSel1[0], PosSel2[1] - PosSel1[1], PosSel2[2] - PosSel1[2]]
return vectorcalc
return(vectorcalc)


def vectoradd(Sel1, Sel2):
PosSel1 = getxyz(Sel1)[0]
PosSel2 = getxyz(Sel2)[0]
vectorcalc = [PosSel1[0] + PosSel2[0], PosSel1[1] + PosSel2[1], PosSel1[2] + PosSel2[2]]
return vectorcalc
return(vectorcalc)


def vectorstr(vector_):
return "[%s,%s,%s]" % (vector_[0], vector_[1], vector_[2])
def vectorstr(vector):
return("[%s,%s,%s]" % (vector[0], vector[1], vector[2]))


def transmat(vector_, dist=1):
mat = [1, 0, 0, 0, 0, 1, 0, 0, 0, 0, 1, 0, dist * vector_[0], dist * vector_[1], dist * vector_[2], 1]
return mat
def transmat(vector, dist=1):
mat = [1, 0, 0, 0, 0, 1, 0, 0, 0, 0, 1, 0, dist * vector[0], dist * vector[1], dist * vector[2], 1]
return(mat)


def unitvector(vector_):
vectorlen = math.sqrt(math.pow(vector_[0], 2) + math.pow(vector_[1], 2) + math.pow(vector_[2], 2))
vectordiv = [vector_[0] / vectorlen, vector_[1] / vectorlen, vector_[2] / vectorlen]
return vectordiv, vectorlen
def unitvector(vector):
vectorlen = math.sqrt(math.pow(vector[0], 2) + math.pow(vector[1], 2) + math.pow(vector[2], 2))
vectordiv = [vector[0] / vectorlen, vector[1] / vectorlen, vector[2] / vectorlen]
return(vectordiv, vectorlen)


def radangle(angle):
return math.radians(angle)
return(math.radians(angle))


def rotmat(angle, vectornorm, pointcoord):
Expand All @@ -94,8 +88,8 @@ def rotmat(angle, vectornorm, pointcoord):
(v * w * (1 - math.cos(angle)) + u * math.sin(angle)),
(math.pow(w, 2) + (math.pow(u, 2) + math.pow(v, 2)) * math.cos(angle)),
((c * (math.pow(u, 2) + math.pow(v, 2)) - w * (a * u + b * v)) * (1 - math.cos(angle)) + (a * v - b * u) * math.sin(angle)),
0, 0, 0, 1, ]
return makerotmat
(0), (0), (0), (1), ]
return(makerotmat)


def rotateline(Pos1, Pos2, degangle, molecule):
Expand All @@ -104,7 +98,7 @@ def rotateline(Pos1, Pos2, degangle, molecule):
xyz = getxyz(Pos2)[0]
rmat = rotmat(radangle(float(degangle)), uvector, xyz)
cmd.transform_selection(molecule, rmat)
return None
return(None)
cmd.extend("rotateline", rotateline)


Expand All @@ -120,9 +114,9 @@ def mutate(molecule, chain, resi, target="CYS", mutframe="1"):
# cmd.set_wizard("done")
cmd.set_wizard()
# cmd.refresh()
# ## Example in pymol
#### Example in pymol
# python
# MutList = [["5NT","A",308],["5NT","A",513],["5NT","B",513]]
#MutList = [["5NT","A",308],["5NT","A",513],["5NT","B",513]]
# for p,c,r in MutList:
# rotkit.mutate(p, chain=c, resi=r, target="CYS", mutframe=1)
# Have do mutate first before selecting, or else it only select the lase?
Expand All @@ -141,18 +135,18 @@ def toline(Pos1, Pos2, atom, molecule, dist=1):
uvector = unitvector(diffvector)[0]
move = transmat(uvector, dist)
cmd.transform_selection("%s" % molecule, move)
return None
return(None)
cmd.extend("toline", toline)


def crossprod(Vector1, Vector2):
return [Vector1[1] * Vector2[2] - Vector1[2] * Vector2[1], Vector1[2] * Vector2[0] - Vector1[0] * Vector2[2], Vector1[0] * Vector2[1] - Vector1[1] * Vector2[0]]
return([Vector1[1] * Vector2[2] - Vector1[2] * Vector2[1], Vector1[2] * Vector2[0] - Vector1[0] * Vector2[2], Vector1[0] * Vector2[1] - Vector1[1] * Vector2[0]])


def crosspoint(Pos1, crossprod_):
def crosspoint(Pos1, crossprod):
Imp1 = getxyz(Pos1)[0]
Imp2 = getxyz(crossprod_)[0]
return [Imp1[0] + Imp2[0], Imp1[1] + Imp2[1], Imp1[2] + Imp2[2]]
Imp2 = getxyz(crossprod)[0]
return([Imp1[0] + Imp2[0], Imp1[1] + Imp2[1], Imp1[2] + Imp2[2]])


def VectorToMatrix(Vector, MatColRank=4):
Expand All @@ -166,11 +160,12 @@ def VectorToMatrix(Vector, MatColRank=4):
for i in range(len(Vector)):
if i in nextrow:
rowsall.append(rowcurrent)
rowcurrent = [Vector[i]]
rowcurrent = []
rowcurrent.append(Vector[i])
else:
rowcurrent.append(Vector[i])
print(rowsall)
return numpy.matrix(rowsall)
return(numpy.matrix(rowsall))


def findMinMax(datalist, index):
Expand All @@ -183,22 +178,20 @@ def findMinMax(datalist, index):
minimum = l[index]
if l[index] > maximum:
maximum = l[index]
return minimum, maximum, datacolumn
return(minimum, maximum, datacolumn)


def createdirs(dirname):
if platform.system() == 'Windows':
new_dir = os.getcwd() + "\\%s\\" % dirname
elif platform.system() == 'Linux':
new_dir = os.getcwd() + "/%s/" % dirname
else:
raise OSError
if not os.path.exists(new_dir):
os.makedirs(new_dir)
return new_dir
Newdir = os.getcwd() + "\\%s\\" % dirname
if platform.system() == 'Linux':
Newdir = os.getcwd() + "/%s/" % dirname
if not os.path.exists(Newdir):
os.makedirs(Newdir)
return(Newdir)


def makehistogram(datalist, dataname="Histogram", datalistindex=2, nrbins=100, binrange=(0, 0)):
def makehistogram(datalist, dataname="Histogram", datalistindex=2, nrbins=100, binrange=[0, 0]):
try:
import numpy
except ImportError:
Expand All @@ -221,7 +214,6 @@ def makehistogram(datalist, dataname="Histogram", datalistindex=2, nrbins=100, b
# print DistHist
DistHistMin, DistHistMax, tmp = findMinMax(DistHist, 2)
# print DistHistMin,DistHistMax
xdelta = 1
ydelta = DistHistMax - DistHistMin
# Now write the output
fileout_write.write("#Datapoints=%s" % len(datacolumn) + "\n")
Expand Down Expand Up @@ -268,4 +260,4 @@ def makehistogram(datalist, dataname="Histogram", datalistindex=2, nrbins=100, b

fileout_write.close()
gnuplot_write.close()
return DistHist
return(DistHist)

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