# standard libraries imports
from __future__ import print_function
import os, copy
from collections import Counter
# external libraries imports
import numpy as np
# pdbparser library imports
from pdbparser import pdbparser
from pdbparser.Utilities.Collection import get_path
from pdbparser.Utilities.Database import __ATOM__
from pdbparser.Utilities.Construct import Micelle, Sheet, Nanotube
from pdbparser.Analysis.Structure.SolventAccessibleSurfaceArea import SolventAccessibleSurfaceArea
pdbSDS = pdbparser(os.path.join(get_path("pdbparser"), "Data/SDS.pdb"))
pdbCTAB = pdbparser(os.path.join(get_path("pdbparser"), "Data/CTAB.pdb"))
PDB = Nanotube().construct().get_pdb()
PDB = Sheet().construct().get_pdb()
PDB = Micelle([pdbSDS], flipPdbs=[True, True],
positionsGeneration="symmetric").construct().get_pdb()
SASA = SolventAccessibleSurfaceArea(trajectory=PDB,
configurationsIndexes=[0],
targetAtomsIndexes=PDB.indexes,
atomsRadius='vdwRadius',
makeContiguous=False,
probeRadius=0,
resolution=0.5,
storeSurfacePoints=True,
several records manipulations, translation, rotation, orientation, ... are tested
"""
# standard distribution imports
from __future__ import print_function
import os
# pdbparser imports
from pdbparser.Utilities.Collection import get_path
from pdbparser.log import Logger
from pdbparser.pdbparser import pdbparser
from pdbparser.Utilities.Geometry import *
pdbRESULT = pdbparser()
Logger.info("loading sds molecule ...")
pdbSDS = pdbparser(os.path.join(get_path("pdbparser"), "Data", "SDS.pdb"))
INDEXES = range(len(pdbSDS.records))
# get molecule axis
sdsAxis = get_axis(INDEXES, pdbSDS)
## translate to positive quadrant
atomToOriginIndex = get_closest_to_origin(INDEXES, pdbSDS)
atom = pdbSDS.records[atomToOriginIndex]
[minX, minY,
minZ] = [atom['coordinates_x'], atom['coordinates_y'], atom['coordinates_z']]
translate(INDEXES, pdbSDS, [-1.1 * minX, -1.1 * minY, -1.1 * minZ])
Logger.info("orient molecule along [1,0,0] ...")
orient(axis=[1, 0, 0], indexes=INDEXES, pdb=pdbSDS, records_axis=sdsAxis)
sdsAxis = [1, 0, 0]
pdbRESULT.concatenate(pdbSDS)
import os
from pdbparser.pdbparser import pdbparser
from pdbparser.Utilities.Collection import get_path
from pdbparser.Utilities.Construct import AmorphousSystem
from pdbparser.Utilities.Geometry import get_satisfactory_records_indexes, translate, get_geometric_center
from pdbparser.Utilities.Modify import delete_records_and_models_records, reset_records_serial_number, reset_sequence_number_per_residue
from pdbparser.Utilities.Database import __WATER__
# read thf molecule and translate to the center
thfNAGMA = pdbparser(os.path.join(get_path("pdbparser"),"Data/NAGMA.pdb" ) )
center = get_geometric_center(thfNAGMA.indexes, thfNAGMA)
translate(thfNAGMA.indexes, thfNAGMA, -center)
# create pdbWATER
pdbWATER = pdbparser()
pdbWATER.records = __WATER__
pdbWATER.set_name("water")
# create amorphous
pdbWATER = AmorphousSystem(pdbWATER, boxSize=[40,40,40], density = 0.75).construct().get_pdb()
center = get_geometric_center(pdbWATER.indexes, pdbWATER)
translate(pdbWATER.indexes, pdbWATER, -center)
# make hollow
hollowIndexes = get_satisfactory_records_indexes(pdbWATER.indexes, pdbWATER, "np.sqrt(x**2 + y**2 + z**2) <= 10")
delete_records_and_models_records(hollowIndexes, pdbWATER)
# concatenate
thfNAGMA.concatenate(pdbWATER, pdbWATER.boundaryConditions)
# reset numbering
from __future__ import print_function
import os
import numpy as np
from pdbparser.log import Logger
from pdbparser import pdbparser
from pdbparser.Utilities.Collection import get_path
from pdbparser.Utilities.Selection import NanotubeSelection
from pdbparser.Utilities.Information import get_models_records_indexes_by_records_indexes, get_records_indexes_in_attribute_values
from pdbparser.Utilities.Modify import *
from pdbparser.Utilities.Geometry import get_principal_axis, translate, orient
# read pdb
pdbCNT = pdbparser(
os.path.join(get_path("pdbparser"), "Data/nanotubeWaterNAGMA.pdb"))
Logger.info("Define models")
# define models
define_models_by_records_attribute_value(pdbCNT.indexes, pdbCNT)
Logger.info("Getting nanotube indexes")
# get CNT indexes
cntIndexes = get_records_indexes_in_attribute_values(pdbCNT.indexes, pdbCNT,
"residue_name", "CNT")
Logger.info("Create selection")
# create selection
sel = NanotubeSelection(pdbCNT, nanotubeIndexes=cntIndexes).select()
Logger.info("Get models inside nanotube")
# construct models out of residues
import os
from pdbparser.pdbparser import pdbparser
from pdbparser.Utilities.Construct import AmorphousSystem
from pdbparser.Utilities.Collection import get_path
# create thf amorphous box
pdb = pdbparser(os.path.join(get_path("pdbparser"),"Data/Tetrahydrofuran.pdb" ))
#pdb.visualize()
#exit()
pdb = AmorphousSystem(pdb, boxSize=[48,48,48],
recursionLimit = 1000000,
insertionNumber=700,
density = 0.7,
priorities={"boxSize":True, "insertionNumber":False, "density":True}).construct().get_pdb()
pdb.export_pdb("thf.pdb")
# standard distribution imports
import os
# pdbparser imports
from pdbparser.Utilities.Collection import get_path
from pdbparser import pdbparser
from pdbparser.Utilities.Construct import AmorphousSystem
from pdbparser.Utilities.Database import __WATER__
# create pdbWATER
pdbWATER = pdbparser()
pdbWATER.records = __WATER__
pdbWATER.set_name("water")
# get pdb molecules
pdbDMPC = pdbparser(os.path.join(get_path("pdbparser"), "Data", "DMPC.pdb"))
pdbNAGMA = pdbparser(os.path.join(get_path("pdbparser"), "Data", "NAGMA.pdb"))
pdbNALMA = pdbparser(os.path.join(get_path("pdbparser"), "Data", "NALMA.pdb"))
# construct amorphous system, adding restrictions and existing micelle in universe
pdbAMORPH = AmorphousSystem(
[pdbWATER, pdbDMPC, pdbNAGMA, pdbNALMA],
boxSize=[150, 150, 150],
density=0.25,
restrictions="np.sqrt(x**2+y**2+z**2)<25").construct()
# visualize amorphous system
pdbAMORPH.get_pdb().visualize()