def test_superimposer_structure():
from Bio import SeqIO
from Bio.PDB import PDBParser
code = '1ptq'
fileName = testFilePath + code + '.pdb'
refStructure = PDBParser().get_structure(code, fileName)
sequences = []
with open(fileName, 'r') as f:
sequences = [r.seq for r in SeqIO.parse(f, "pdb-seqres")]
pass
ds = Distructure('test', sequences, [[
r.get_id() for r in refStructure.get_residues() if r.get_id()[0] == ' '
]])
ds.generate_primary_contacts()
ds.run()
refStructure = PDBParser().get_structure(code, fileName)
sup = Superimposer()
sup.set_structures(refStructure, ds)
return
def get_PDB_length(pdbFileLocation):
from Bio.PDB.PDBParser import PDBParser
# pdbFileLocation = '/Users/weilu/Research/database/chosen/T0869-D1.pdb'
structure = PDBParser().get_structure("a", pdbFileLocation)
return len(list(structure.get_residues()))
def launch(self) -> int:
"""Execute the :class:`ExtractResidues <utils.extract_residues.ExtractResidues>` utils.extract_residues.ExtractResidues object."""
self.io_dict['in']['input_structure_path'] = check_input_path(
self.io_dict['in']['input_structure_path'], self.out_log,
self.__class__.__name__)
self.io_dict['out']['output_residues_path'] = check_output_path(
self.io_dict['out']['output_residues_path'], self.out_log,
self.__class__.__name__)
# Setup Biobb
if self.check_restart(): return 0
self.stage_files()
# Business code
# get list of Residues from properties
list_residues = create_residues_list(self.residues, self.out_log)
# load input into BioPython structure
structure = PDBParser(QUIET=True).get_structure(
'structure', self.stage_io_dict['in']['input_structure_path'])
new_structure = []
# get desired residues
for residue in structure.get_residues():
r = {
'model': str(residue.get_parent().get_parent().get_id() + 1),
'chain': residue.get_parent().get_id(),
'name': residue.get_resname(),
'res_id': str(residue.get_id()[1])
}
if list_residues:
for res in list_residues:
match = True
for code in res['code']:
if res[code].strip() != r[code].strip():
match = False
break
if match:
new_structure.append(r)
else:
new_structure.append(r)
# if not residues found in structure, raise exit
if not new_structure:
fu.log(
self.__class__.__name__ +
': The residues given by user were not found in input structure',
self.out_log)
raise SystemExit(
self.__class__.__name__ +
': The residues given by user were not found in input structure'
)
# parse PDB file and get residues line by line
new_file_lines = []
curr_model = 0
with open(self.stage_io_dict['in']['input_structure_path']) as infile:
for line in infile:
if line.startswith("MODEL "):
curr_model = line.rstrip()[-1]
if int(curr_model) > 1: new_file_lines.append('ENDMDL\n')
new_file_lines.append('MODEL ' +
"{:>4}".format(curr_model) + '\n')
if line.startswith("ATOM"):
name = line[17:20].strip()
chain = line[21:22].strip()
res_id = line[22:27].strip()
if curr_model != 0: model = curr_model.strip()
else: model = "1"
if chain == "": chain = " "
for nstr in new_structure:
if nstr['res_id'] == res_id and nstr[
'name'] == name and nstr[
'chain'] == chain and nstr[
'model'] == model:
new_file_lines.append(line)
if int(curr_model) > 0: new_file_lines.append('ENDMDL\n')
# save new file with heteroatoms
with open(self.stage_io_dict['out']['output_residues_path'],
'w') as outfile:
for line in new_file_lines:
outfile.write(line)
self.return_code = 0
##########
# Copy files to host
self.copy_to_host()
# Remove temporal files
self.tmp_files.append(self.stage_io_dict.get("unique_dir"))
self.remove_tmp_files()
return self.return_code
