def generate_fixed_neighbours_constraint(self, outputPath, key="sequence_number", bondMapKey="atom_name", regressive=True):
"""
generates automatically RMC++ .fnc file from a pdbParser instance.
RMC++ .cfg file atoms are ordered element wise.
Therefore .fnc atoms indexes might not be the same as the given pdb records indexes
but reordered to correspond to the .cfg file exported using convert_pdb method.
In order to get a pdb file respecting the same order as .cfg file,
one should convert the original pdb using convert_pdb then convert it back to pdb using convert method.
:Parameters:
#. outputPath (str): The RMC++ .fnc output configuration file path.
#. key (str): Any pdbParser record valid key used to split records into molecules and generate bonds.
#. bondMapKey (str): Any pdbParser record valid key used to generate bonds types.
#. regressive (bool): Insures that a bond is calculated for both atoms of the same bond.
If atom X is bonded to Y, normaly Y is in the bonds list of X, regressive insures that also X is in the bonds list of Y
"""
# get pdb records indexes element wise
elements = self.get_pdb().elements
types = set(elements)
typesIndexes = []
for t in types:
typesIndexes.extend( get_records_indexes_by_attribute_value(self.get_pdb().indexes, self.get_pdb(), "element_symbol", t) )
# get pdb
pdb = pdbParser.pdbParser()
pdb.set_name(self.get_pdb().name)
pdb.records = [self.get_pdb().records[idx] for idx in typesIndexes]
slicedPdb = pdbParser.pdbParser()
# get molecules
molecules = set(get_records_attribute_values(pdb.indexes, pdb, key))
# build bonds
centralRecord = []
connectedTo = []
for mol in molecules:
indexes = get_records_indexes_by_attribute_value(pdb.indexes, pdb, key, mol)
# build connectivity
slicedPdb.records = [pdb.records[idx] for idx in indexes]
connectivity = Connectivity(slicedPdb)
# calculate bonds
connectivity.calculate_bonds(regressive=True)
cr, ct = connectivity.get_bonds()
# map records to indexes and extend centralRecord and connectedTo
centralRecord.extend( [indexes[idx] for idx in cr] )
connectedTo.extend( [[indexes[idx] for idx in item] for item in ct] )
# get centralRecord and connectedTo in indexes order from 0 to len(pdb)
bonds = dict(zip(centralRecord,connectedTo))
# get bondsMap
bondsMapElementsKey = get_records_attribute_values(pdb.indexes, pdb, bondMapKey)
bondsMap = []
for crIdx in range(len(centralRecord)):
cr = centralRecord[crIdx]
for ct in connectedTo[crIdx]:
setted = list(set([bondsMapElementsKey[cr], bondsMapElementsKey[ct]]))
bondsMap.append( str(setted[0])+"--"+str(setted[1]) )
bondsMap = OrderedDict(zip(set(bondsMap), range(1,len(bondsMap)+1)))
# write fixed neighbours constraint file
self.__write_fnc_file__(outputPath, pdb.name, bondsMap, bondsMapElementsKey, bonds)
"""
In this test, an SDS molecule is loaded
several records manipulations, translation, rotation, orientation, ... are tested
"""
# standard distribution imports
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)
# standard libraries imports
import os
# external libraries imports
# fullrmc library imports
from pdbParser.pdbParser import pdbParser, pdbTrajectory
# visualize
traj = pdbTrajectory()
traj.set_structure('system.pdb')
time = 0
for num in sorted(
[int(item.split('.pdb')[0]) for item in os.listdir("pdbFiles")]):
pdb = os.path.join("pdbFiles", str(num) + ".pdb")
print pdb
traj.append_configuration(
pdb=pdbParser(pdb),
vectors=traj.structure.boundaryConditions.get_vectors(),
time=time)
time = time + 1
# visualize
traj.visualize()
# standard libraries imports
import time
import os
import itertools
# external libraries imports
import numpy as np
from pdbParser.pdbParser import pdbParser, pdbTrajectory
# pdbFiles
pdbFiles = [fn for fn in os.listdir("pdbFiles") if ".pdb" in fn]
generated = [int(fn.split("_")[0]) for fn in pdbFiles]
pdbFiles = [
os.path.join("pdbFiles", pdbFiles[idx]) for idx in np.argsort(generated)
]
# create trajectory
traj = pdbTrajectory()
traj.set_structure(pdbParser("thf.pdb"))
for idx in range(len(pdbFiles)):
print "loading frame %i out of %i" % (idx, len(pdbFiles))
fname = pdbFiles[idx]
pdb = pdbParser(fname)
traj.append_configuration(pdb=pdb,
vectors=pdb.boundaryConditions.get_vectors(),
time=idx)
traj.visualize()
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")
from pdbParser.pdbParser import pdbParser
from pdbParser.Utilities.Construct import AmorphousSystem
from pdbParser.Utilities.Database import __WATER__
from pdbParser.Utilities.Geometry import translate, get_center
# create pdbWATER of a single molecule of water
pdbWATER = pdbParser()
pdbWATER.records = __WATER__
pdbWATER.set_name("water")
# create amorphous water box
pdbWATER = AmorphousSystem(pdbWATER, density=1,
boxSize=[10, 10, 10]).construct().get_pdb()
# translate water box to center
translate(pdbWATER.indexes, pdbWATER, -get_center(pdbWATER.indexes, pdbWATER))
# export water box
pdbWATER.export_pdb("waterBox.pdb")
def create_fixed_neighbours_constraint(self, outputPath, map, regressive=True):
"""
generates rmc++ .fnc file from a pdbParser instance using a user-defined bonds maping.
RMC++ .cfg file atoms are ordered element wise.
Therefore .fnc atoms indexes might not be the same as the given pdb records indexes
but reordered to correspond to the .cfg file exported using convert_pdb method.
In order to get a pdb file respecting the same order as .cfg file,
one should convert the original pdb using convert_pdb then convert it back to pdb using convert method.
:Parameters:
#. outputPath (str): The RMC++ .fnc output configuration file path.
#. map (list): list of dictionary. Every dictionary must contain mapping specific keys.Valid keys are:
#. 'molecule_mapping' : Any pdbParser record valid key used to split records into molecules.
#. 'molecule_key' : the molecules in the pdb.
#. 'atoms_mapping' : Any pdbParser record valid key used to map records bonds.
#. 'bonds' : dictionary of atom keys and list of atoms bonds value.\n
::
e.g. map=[ {"molecules_mapping" : "sequence_number",
"atoms_mapping" : "atom_name",
"bonds" : {"O":["H1","H2"]} },
{"molecules_mapping" : "sequence_number",
"atoms_mapping" : "atom_name",
"bonds" : {"C":["H1","H2","H3","H4"],
"H1":["H2","H3","H4"],
"H2":["H3","H4"],
"H3":["H4"]} } ]
#. regressive (bool): Insures that a bond is calculated for both atoms of the same bond.
If atom X is bonded to Y, normaly Y is in the bonds list of X, regressive insures that also X is in the bonds list of Y
"""
assert isinstance(regressive, bool), Logger.error("regressive must be a boolean")
# check map
assert isinstance(map, (list, set, tuple)), Logger.error( "map should be a list")
map = list(map)
for m in map:
assert isinstance(m, dict), Logger.error( "map item must be python dictionary")
assert m.has_key("molecules_mapping"), Logger.error( "map item must have 'molecules_mapping' key")
assert m.has_key("atoms_mapping"), Logger.error( "map item must have 'atoms_mapping' key")
assert m.has_key("bonds"), Logger.error( "map item must have 'bonds' key")
assert isinstance(m["bonds"], dict), Logger.error( "map 'bonds' value must be a dictionary")
# create regressive bonds
if regressive:
for m in map:
for cr, values in m["bonds"].items():
for ct in values:
if m["bonds"].get(ct, None) is None:
m["bonds"][ct] = [cr]
else:
m["bonds"][ct].append(cr)
# remove redundancy
for ct in m["bonds"].keys():
m["bonds"][ct] = list(set(m["bonds"][ct]))
# get pdb records indexes element wise
elements = self.get_pdb().elements
types = set(elements)
typesIndexes = []
for t in types:
typesIndexes.extend( get_records_indexes_by_attribute_value(self.get_pdb().indexes, self.get_pdb(), "element_symbol", t) )
pdb = pdbParser.pdbParser()
pdb.set_name(self.get_pdb().name)
pdb.records = [self.get_pdb().records[idx] for idx in typesIndexes]
# build bonds
centralRecord = []
connectedTo = []
bondsMapElementsKey = [None for idx in pdb.indexes]
for m in map:
# get molecules
molecules = set(get_records_attribute_values(pdb.indexes, pdb, m["molecules_mapping"]))
for mol in molecules:
molAtomsIndexes = get_records_indexes_by_attribute_value(pdb.indexes, pdb, m["molecules_mapping"], mol)
for cr, values in m["bonds"].items():
# get central atoms index
crIdx = get_records_indexes_by_attribute_value(molAtomsIndexes, pdb, m["atoms_mapping"], cr)
assert len(crIdx)==1, "Only one central atom in molecule map bonds must be found. '%i' where found for central atom '%s'"%(len(crIdx), str(cr))
centralRecord.append(crIdx[0])
bondsMapElementsKey[crIdx[0]] = pdb.records[crIdx[0]][m["atoms_mapping"]]
# get connected atoms
ctList = []
for ct in values:
ctIdx = get_records_indexes_by_attribute_value(molAtomsIndexes, pdb, m["atoms_mapping"], ct)
assert len(ctIdx)==1, "Only one connected atom in molecule map bonds must be found. '%i' where found for connected atom '%s' in central atom '%s' in map %s"%(len(ctIdx), str(ct), str(cr), str(m["bonds"][cr]))
ctList.append(ctIdx[0])
bondsMapElementsKey[ctIdx[0]] = pdb.records[ctIdx[0]][m["atoms_mapping"]]
connectedTo.append(ctList)
# complete non-bonded atoms and create bonds dictionary
bonds = {}
for idx in pdb.indexes:
bonds[idx]=[]
for idx in range(len(centralRecord)):
bonds[centralRecord[idx]]=connectedTo[idx]
# create bondsMap
bondsMap = []
for crIdx in range(len(bonds)):
for ctIdx in bonds[crIdx]:
cr = bondsMapElementsKey[crIdx]
ct = bondsMapElementsKey[ctIdx]
assert not (cr is None or ct is None), "mapping error"
setted = list(set([cr, ct]))
bondsMap.append( str(setted[0])+"--"+str(setted[1]) )
bondsMap = OrderedDict(zip(set(bondsMap), range(1,len(bondsMap)+1)))
# write fixed neighbours constraint file
self.__write_fnc_file__(outputPath, pdb.name, bondsMap, bondsMapElementsKey, bonds)