def test_run_with_StringIO_log():
stringio_file = StringIO()
with tempfolder():
run(
arg_pdbout='out.pdb',
arg_pdbin=get_fn('4lzt/4lzt_h.pdb'),
arg_logfile=stringio_file)
stringio_file.seek(0)
assert 'Summary of pdb4amber' in stringio_file.read()
def prepare_mcpb_input(structures, software_version='g09', cut_off=2.8):
"""
Get all the substructure files and prepare the MCPB.py input
"""
template = dedent("""
original_pdb master.pdb
group_name {name}
cut_off {cut_off}
ion_ids {metal_id}
ion_mol2files {metal_mol2}
naa_mol2files {residues_mol2}
frcmod_files {residues_frcmod}
large_opt 1
software_version {software_version}
""")
# First collect all files in the same master PDB
pdbfiles = [
s['pdb'] for s in structures['metals'] + structures['residues']
]
if 'pdb' in structures['protein']:
pdbfiles.append(structures['protein']['pdb'])
with open('master.unfixed.pdb', 'w') as f:
for line in fileinput(pdbfiles):
f.write(line)
# Fix residue numbering issues
pdb4amber.run(arg_pdbin='master.unfixed.pdb', arg_pdbout='master.pdb')
name = os.path.basename(os.getcwd())
with open('mcbp.in', 'w') as f:
f.write(
template.format(
name=name,
metal_id=' '.join(
map(str, range(1,
len(structures['metals']) + 1))),
metal_mol2=' '.join([s['mol2'] for s in structures['metals']]),
residues_mol2=' '.join(
[r['mol2'] for r in structures['residues']]),
residues_frcmod=' '.join(
[r['frcmod'] for r in structures['residues']]),
cut_off=cut_off,
software_version=software_version,
))
return 'mcbp.in'
def test_run_with_filename_log():
# default
logfile = 'pdb4amber.log'
with tempfolder():
run(arg_pdbout='out.pdb', arg_pdbin=get_fn('4lzt/4lzt_h.pdb'))
with open(logfile) as fh:
assert 'Summary of pdb4amber' in fh.read()
# given name
logfile = 'hello.log'
with tempfolder():
run(
arg_pdbout='out.pdb',
arg_pdbin=get_fn('4lzt/4lzt_h.pdb'),
arg_logfile=logfile)
with open(logfile) as fh:
assert 'Summary of pdb4amber' in fh.read()
def prepare_protein_amber(protein, ph=7):
"""
Prepare molecule to contain correct residues, capping groups, and so on,
using pdb4amber
Parameters
==========
molecule : chimera.Molecule
Returns
=======
pdb
"""
print('Preparing', protein.name, '...')
inpdb = protein.basename + '.unfixed.pdb'
chimera.pdbWrite([protein], protein.openState.xform, inpdb)
pdb4amber.run(arg_pdbin=inpdb,
arg_pdbout=protein.basename + '.pdb',
arg_reduce=True)
return protein.basename + '.pdb'