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from promod3 import loop
from ost import io, seq
import os
# StructureDB where all data get extracted
structure_db_one = loop.StructureDB(loop.StructureDBDataType.All)
# StructureDB where we only have the default data
# (positions and sequence) plus residue depths and dihedrals.
# In order to pass the required flags, we use a bitwise or.
structure_db_two = loop.StructureDB(
loop.StructureDBDataType.ResidueDepths |
loop.StructureDBDataType.Dihedrals)
# Lets fill in some structures. It gets assumed, that all required
# data lies in the following directories.
structure_dir = "data"
prof_dir = "data"
# The naming of the files in the directories is e.g. 1CRN.pdb for
# the structure and 1CRNA.hhm for the profile.
# The structure possibly contain several chains, whereas the hhm
# file is only for that specific chain.
structure_ids = ["1CRN", "1AKI"]
chain_names = ["A", "A"]
for s_id, ch_name in zip(structure_ids, chain_names):
# Join together the data paths.
structure_path = os.path.join(structure_dir, s_id + ".pdb")
prof_path = os.path.join(prof_dir, s_id + ch_name + ".hhm")
# Let's load the structure.
structure = io.LoadPDB(structure_path).Select("peptide=True")
# And the according profile in hhm format.
prof = io.LoadSequenceProfile(prof_path)
# For simplicity we use as SEQRES the sequence from the profile.
# In this case the numbering of the structures already matches.
seqres = seq.CreateSequence(ch_name, prof.sequence)
# Add the stuff to the first StructureDB
structure_db_one.AddCoordinates(s_id, ch_name, structure,
seqres, prof)
# Add the stuff to the second StructureDB,
# No profile required here...
structure_db_two.AddCoordinates(s_id, ch_name, structure,
seqres)
# We now have two structures in both databases...
# Lets get a summary of whats actually in there
structure_db_one.PrintStatistics()
structure_db_two.PrintStatistics()
# There is no profile derived from structures assigned to
# structure_db_one yet, the memory is only allocated and set to
# zero. In structure_db_two, there'll never be stored a structure
# profile as we did not initialize it accordingly.
# However, we can still use its coordinates and residue depths to
# generate profiles!
# To demonstrate, we use our structure_db_two to derive profiles
# and set them in structure_db_one.
for i in range(structure_db_one.GetNumCoords()):
# extract all required information
bb_list = structure_db_one.GetBackboneList(i)
res_depths = structure_db_one.GetResidueDepths(i)
# generate structure profiles based on structure_db_two
prof = structure_db_two.GenerateStructureProfile(bb_list,
res_depths)
# and add it to the previously created structure_db
structure_db_one.SetStructureProfile(i, prof)
# That's it! Let's save both databases down.
# structure_db_two will use much less memory, as it contains less data.
# Sidenote: We're saving the portable version. If you intent to use
# your database only on one system, the Save / Load functions should
# be preferred, as the loading will be much faster.
structure_db_one.SavePortable("my_db_one.dat")
structure_db_two.SavePortable("my_db_two.dat")
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