def DigestPdb(self):
""" add atoms too self and 8 neighboring cubes. points except for water ###
"""
self.pdb_water_head = pdb.Pdb() ## used for visualizations
self.pdb_water_head.AddMolecule()
if self.pdb.cryst:
self.cryst = self.pdb.cryst
print "unit cell size: ", self.cryst
else:
print "Please provide the unit-cell size in self.cryst"
num_atoms = self.pdb.NumOfAtoms()
c = 0
self.points_periodic = vtk.vtkPoints()
self.points = vtk.vtkPoints()
print "Digesting the input pdb ..."
for atom in self.pdb:
if atom.name.replace(" ","") not in ["W","WF","ROH","H1","H2","H3"] and\
( atom.GetMolNameGMX()[0]!="G" or atom.name.replace(" ","") not in ["C1","C2","C3"] ) :
self.points.InsertNextPoint(atom.pos)
for q in [-self.cryst[0], 0, self.cryst[0]]:
for p in [-self.cryst[1], 0, self.cryst[1]]:
for r in [-self.cryst[2], 0, self.cryst[2]]:
pos_aux = atom.pos + np.array([q, p, r])
self.points_periodic.InsertNextPoint(pos_aux)
self.pdb_water_head.molecules[-1].AddAtom(atom.line)
c += 1
pdb.update_progress(float(c) / num_atoms)
print "\n"
self.polydata = vtk.vtkPolyData()
self.polydata.SetPoints(self.points_periodic)
### initialize pointlocator ###
self.pointlocator = vtk.vtkPointLocator()
self.pointlocator.SetDataSet(self.polydata)
self.pointlocator.SetNumberOfPointsPerBucket(10)
self.pointlocator.BuildLocator()
def __init__(self, file_in, traj_file=False, steps_input=5):
self.color_series = vtk.vtkColorSeries()
self.color_series.SetColorScheme(
self.color_series.BREWER_SEQUENTIAL_YELLOW_ORANGE_BROWN_9
) #set the color theme
if not traj_file:
self.traj_mode = False
if file_in[-3:] == "pdb":
self.pdb = pdb.Pdb()
self.pdb.ReadFileGMX(file_in)
#self.pdb.BringToPositiveCorner()
self.marching_cubes = False
self.univ = False
elif file_in[-3:] == "gro":
self.univ = MDAnalysis.Universe(file_in)
else:
self.traj_mode = True
self.univ = MDAnalysis.Universe(file_in, traj_file)
self.univ_gro = MDAnalysis.Universe(
file_in
) #only load gro file to read coordinates and velocities from. not trajectory
self.steps = steps_input # number of steps to consider in the analysis in the whole trajectory file.
self.gauss_mean = True # in gaussian curvature case = True / in mean curvature case = False
self.test = []
self.test_lines = vtk.vtkCellArray()
self.test_points = vtk.vtkPoints()
import molar.pdb as p
import numpy as np
import random
m = p.Pdb("cernp24.pdb")
c1 = m.GetAtomByName("C2F")
c2 = m.GetAtomByName("C6F")
c3 = m.GetAtomByName("C4S")
c4 = m.GetAtomByName("C8S")
a1 = m.GetAtomByName("C2S")
a2 = m.GetAtomByName("C3S")
a3 = m.GetAtomByName("NF")
a4 = m.GetAtomByName("C1F")
a5 = m.GetAtomByName("C1F")
a6 = m.GetAtomByName("C2F")
###############
def Change(amp=10):
alpha = amp * 2 * (random.random() - 0.5)
beta = amp * 2 * (random.random() - 0.5)
gamma = amp * 2 * (random.random() - 0.5)
m.SelectBond(a2, a1)
m.RotateBond(alpha)
import molar.pdb as p
import numpy as np
import random
m = p.Pdb("cereos.pdb")
m.WriteOnFile(file_name_str="test.pdb", make_TER=False, include_CONECT=True)
import molar.pdb as pdb
import vtk
cer = pdb.Pdb()
glu = pdb.Pdb()
cer.ReadFile(
"/Users/alinar/Dropbox/The Project/MicroBio/molecule_pool/lip1.pdb")
glu.ReadFile(
"/Users/alinar/Dropbox/The Project/MicroBio/molecule_pool/glucose.pdb")
c5 = glu.GetAtomsByName("C5")[0]
o6 = glu.GetAtomsByName("O6")[0]
c6 = cer.GetAtomsByName("C6")[0]
c7 = cer.GetAtomsByName("C7")[0]
o1 = cer.GetAtomsByName("O1")[0]
h49 = cer.GetAtomsByName("H49")[0]
v1 = o6.pos - c5.pos
v2 = o1.pos - h49.pos
v_pos = c7.pos - c6.pos
trans = pdb.RotateToParallel(v2, v1)
glu.ApplyTransform(trans)
trans.Identity()
trans.Translate(o1.pos - o6.pos)
#trans.Translate(1.0 * v_pos) #fine_tune
glu.RemoveAtom(o6)
glu.ApplyTransform(trans)
cer.RemoveAtom(h49)
result = pdb.MergePdb([cer, glu])