def generate_ligand(self, ligsmile, outdir, outfile, flags=[]):
"""Generate ligand PDB and CIF from smile string"""
# Prepare standard settings
self._prepare_to_generate_ligand(ligsmile, outdir, outfile, flags)
# Check to see if already run, and if not, run the custom part of the object - different for each program
if os.path.exists(self.outpdb) and os.path.exists(
self.outcif) and os.path.exists(self.outlog):
if self.verbose:
print('\tLigand already generated - DOING NOTHING')
else:
cmd_line_args, std_inpt_args = self._create_program_arguments(
ligsmile, outdir, outfile, flags)
# Initialise CommandManager
self.builder = CommandManager(self.program)
# Set Command-Line Args
if cmd_line_args:
self.builder.add_command_line_arguments(cmd_line_args)
# Set Standard Input
if std_inpt_args: self.builder.add_standard_input(std_inpt_args)
# Set Parameters
self.builder.set_timeout(timeout=self.timeout)
# RUN
self.builder.run()
# Get runtime
self.runtime = self.builder.runtime
try:
# Could add postprocess here
pass
finally:
self.write_log_file()
return self.outpdb, self.outcif, self.outlog
def run_refinement_pipeline(in_mtz, ref_pdb, out_dir, program='dimple'):
"""Run refinement of the input MTZ file against a reference PDB file"""
print '*************************'
print '*** Running Pipelines ***'
print '*************************'
if program == 'dimple':
# Define output files
out_pdb = os.path.join(out_dir, 'final.pdb')
out_mtz = os.path.join(out_dir, 'final.mtz')
# Create command manager for dimple
cmd = CommandManager('dimple')
cmd.add_command_line_arguments(
['--jelly', '5', in_mtz, ref_pdb, out_dir])
else:
raise Exception("no stop that. you're doing it wrong.")
print_run_and_raise_error_maybe(cmd)
if not os.path.exists(out_pdb):
raise Failure(
'running refinement with {} has failed -- {} does not exist'.
format(program, out_pdb))
if not os.path.exists(out_mtz):
raise Failure(
'running refinement with {} has failed -- {} does not exist'.
format(program, out_mtz))
return out_pdb, out_mtz
def generate_symmetry_mates(pdbin, pdbout, sgno, cell):
"""Takes the input pdb and generates the unit cell from the point group symmetry"""
if not pdbout.endswith('.pdb'):
pdbout = pdbout + '.pdb'
if not os.path.exists(pdbin):
raise IOError('pdbin does not exist! {!s}'.format(pdbin))
if os.path.exists(pdbout):
raise Exception('pdbout already exists! {!s}'.format(pdbout))
assert isinstance(sgno,
int), 'SPACEGROUP MUST BE AN INTEGER! {!s}'.format(sgno)
assert isinstance(cell, list), 'CELL MUST BE A LIST! {!s}'.format(cell)
# Initialise Commander
PDBSET = CommandManager('pdbset')
# Set Command Arguments
PDBSET.add_command_line_arguments('XYZIN', os.path.abspath(pdbin),
'XYZOUT', os.path.abspath(pdbout))
# Set inputs
PDBSET.add_standard_input([
'SYMGEN {!s}'.format(sgno),
'CELL {!s}'.format(' '.join(map(str, cell))), 'END'
])
# run!
PDBSET.run()
if not os.path.exists(pdbout):
raise ExternalProgramError(
'PDBSET has failed to generate SYMMETRY mates. {!s}\nCOM: {!s}\nOUT: {!s}\nERR: {!s}'
.format(pdbin, PDBSET.command, PDBSET.out, PDBSET.err))
return pdbout
def create_cryst_line(pdbin, pdbout, sg, cell):
"""Adds a cryst line to pdbin"""
if not pdbout.endswith('.pdb'):
pdbout = pdbout + '.pdb'
if not os.path.exists(pdbin):
raise IOError('pdbin does not exist! {!s}'.format(pdbin))
if os.path.exists(pdbout):
raise Exception('pdbout already exists! {!s}'.format(pdbout))
# Initialise Commander
PDBSET = CommandManager('pdbset')
# Set Command Arguments
PDBSET.add_command_line_arguments('XYZIN', os.path.abspath(pdbin),
'XYZOUT', os.path.abspath(pdbout))
# Set Stdin
PDBSET.add_standard_input([
'SPACEGROUP {!s}'.format(sg),
'CELL {!s}'.format(' '.join(map(str, cell)))
])
# run!
PDBSET.run()
if not os.path.exists(pdbout):
raise ExternalProgramError(
'PDBSET has failed to create cryst line for {!s}\nOUT: {!s}\nERR: {!s}'
.format(pdbin, PDBSET.out, PDBSET.err))
return PDBSET
def create_alpha_carbon_backbone(pdbin, pdbout):
"""Takes a pdb files and removes eveything except for the alpha carbons"""
if not pdbout.endswith('.pdb'):
pdbout = pdbout + '.pdb'
if not os.path.exists(pdbin):
raise IOError('pdbin does not exist! {!s}'.format(pdbin))
if os.path.exists(pdbout):
raise Exception('pdbout already exists! {!s}'.format(pdbout))
# Initialise Commander
PDBCUR = CommandManager('pdbcur')
# Set Command Arguments
PDBCUR.add_command_line_arguments('XYZIN', pdbin, 'XYZOUT', pdbout)
# Set inputs
PDBCUR.add_standard_input(['lvatom "CA[C]:*"', 'END'])
# run!
PDBCUR.run()
if not os.path.exists(pdbout):
raise ExternalProgramError(
'PDBCUR has failed to create carbon backbone. {!s}\nOUT: {!s}\nERR: {!s}'
.format(pdbin, PDBCUR.out, PDBCUR.err))
return pdbout
def run_refinement(self,
inpdb,
inmtz,
outdir,
outfile,
incif=None,
flags=[]):
"""Run Refinement of a Structure"""
# Prepare standard settings
self._prepare_to_refine_structure(inpdb, inmtz, outdir, outfile, incif,
flags)
# Check to see if already run, and if not, run the custom part of the object - different for each program
if os.path.exists(self.outpdb) and os.path.exists(
self.outmtz) and os.path.exists(self.outlog):
if self.verbose:
print('\tRefinement already done - DOING NOTHING')
else:
if self.verbose:
print('\tRefining using {!s}.'.format(self.name))
cmd_line_args, std_inpt_args = self._create_program_arguments(
inpdb, inmtz, outdir, outfile, incif, flags)
# Initialise CommandManager
self.Refiner = CommandManager(self.program)
# Set Command-Line Args
self.Refiner.SetArguments(cmd_line_args)
# Set Standard Input
self.Refiner.SetInput(std_inpt_args)
# Set Parameters
self.Refiner.SetParameters(timeout=self.timeout)
# RUN
self.Refiner.Run()
# Calculate runtime (seconds)
self.runtime = self.Refiner.runtime
if self.verbose:
print('\tFinished refinement - post-processing structure.')
try:
# General post-process
self._standard_post_process(inpdb, inmtz, outdir, outfile,
incif, flags)
# Could add autoprocessing here...
self._post_process(inpdb, inmtz, outdir, outfile, incif, flags)
finally:
self.write_log_file()
return self.outpdb, self.outmtz, self.outlog
def extract_bfactor_statistics(pdb_file):
"""Analyse the b-factors in a pdb file and return a dictionary with all of the averages, rms deviations and Z-scores for the b-factors in a structure"""
# Create a temporary file for the output summary table and pdb_file
temp_handle, temp_path = tempfile.mkstemp(suffix='.table',
prefix='baverage_')
temp_handle2, temp_path2 = tempfile.mkstemp(suffix='.pdb',
prefix='baverage_')
BAVERAGE = CommandManager('baverage')
BAVERAGE.add_command_line_arguments('XYZIN', pdb_file, 'RMSTAB', temp_path,
'XYZOUT', temp_path2)
BAVERAGE.add_standard_input(['END'])
BAVERAGE.run()
if not os.path.exists(temp_path):
raise ExternalProgramError(
'BAVERAGE has failed to calculate b-factor summary statistics for {!s}'
.format(pdb_file))
# Process Table and Standard Out
table_contents = open(temp_path, 'r').read().split('\n')
if not table_contents:
raise ExternalProgramError(
'BAVERAGE has failed to calculate b-factor summary statistics for {!s}'
.format(pdb_file))
else:
os.remove(temp_path)
os.remove(temp_path2)
return BAVERAGE, table_contents
def run_xia2(img_dir, out_dir, method='dials', verbose=True):
"""Run xia2 on the images in img_dir, and put the results in out_dir"""
assert method in ['2d','3d','3dii','dials'], 'Invalid method provided'
assert os.path.exists(img_dir), 'Image directory does not exist'
if not os.path.exists(out_dir): os.mkdir(out_dir)
# Convert to absolute path to allow folder changing
img_dir = os.path.abspath(img_dir)
out_dir = os.path.abspath(out_dir)
# Store current directory
cur_dir = os.getcwd()
try:
# Output logfile
xia2_log = os.path.join(out_dir, 'xia2.log')
# Got to directory to run MLFSOM
os.chdir(out_dir)
xia2 = CommandManager('xia2')
xia2.add_command_line_arguments('-'+method, img_dir)
if verbose: print('Running xia2 on {}').format(img_dir)
rc = xia2.run()
if rc != 0:
print('STDOUT:')
print(xia2.output)
print('STDERR:')
print(xia2.error)
with open(xia2_log, 'a') as fh:
fh.write('==================================================>\n')
fh.write('xia2 log\n')
fh.write('==================================================>\n')
fh.write(xia2.output+'\n')
fh.write('==================================================>\n')
fh.write('xia2 errors\n')
fh.write('==================================================>\n')
fh.write(xia2.error+'\n')
fh.write('==================================================>\n')
finally:
# Change back to original directory
os.chdir(cur_dir)
return xia2
def isolate_residue(inpdb, outpdb, resname):
"""Extract the residues identified by resname using pdbcur - i.e. 'UNL'"""
PDBCUR = CommandManager('pdbcur')
PDBCUR.add_command_line_arguments('XYZIN', inpdb, 'XYZOUT', outpdb)
PDBCUR.add_standard_input(['lvresidue /*/*/({!s})'.format(resname), 'END'])
PDBCUR.run()
return PDBCUR
def __init__(self,
pdb_file,
mtz_file=None,
cif_file=None,
out_prefix=None,
**kw_args):
# Set defaults if not given
if mtz_file is None:
mtz_file = pdb_file.replace('.pdb', '.mtz')
if out_prefix is None:
out_prefix = os.path.splitext(pdb_file)[0] + '-refined'
# Main files
self.pdb_file = pdb_file
self.mtz_file = mtz_file
self.cif_file = cif_file
# Eventual output prefix
self.out_prefix = out_prefix
self.out_pdb_file = self.out_prefix + '.pdb'
self.out_mtz_file = self.out_prefix + '.mtz'
self.out_log_file = self.out_prefix + '.log'
# Validate input
assert os.path.exists(self.pdb_file)
assert os.path.exists(self.mtz_file)
assert not os.path.exists(
self.out_pdb_file), 'Output file already exists: {}'.format(
self.out_pdb_file)
assert not os.path.exists(
self.out_mtz_file), 'Output file already exists: {}'.format(
self.out_mtz_file)
# Create temporary folder for refinement
self.tmp_dir = tempfile.mkdtemp(prefix='refine-model-')
self.tmp_pre = os.path.join(self.tmp_dir, 'refine')
# Command object for refinement
self.cmd = CommandManager(self.program)
self.kw_args = kw_args
# Setup, refine and post_process
if self.auto is True:
self.run()
def phenix_find_tls_groups(pdb_file):
cmd = CommandManager('phenix.find_tls_groups')
cmd.add_command_line_arguments(pdb_file)
#cmd.print_settings()
ret_code = cmd.run()
if ret_code != 0:
print cmd.output
print cmd.error
raise Exception('Failed to determine TLS groups: {}'.format(' '.join(
cmd.program)))
regex = re.compile("refinement\.refine\.adp \{([\s\S]*?)\}")
tls_command = regex.findall(cmd.output)[0]
tls_selections = [
s.strip() for s in tls_command.split('tls =') if s.strip()
]
return tls_selections
def convert_intensities_to_amplitudes(mtzin, mtzout):
"""Takes an input mtz and converts the intensities to structure factors for model building"""
mtzobj = MtzSummary(mtzin)
# Copy data columns from new mtz file
I, SIGI = mtzobj.label.i, mtzobj.label.sigi
if not (I and SIGI):
raise LabelError('No Intensities found in {!s}'.format(mtzin))
# TODO If rfree is present, retain rfree from the reference mtz
# RFree = mtzobj.label.free
# Initialise Commander
CTRUNC = CommandManager('ctruncate')
# Set command arguments
CTRUNC.add_command_line_arguments('-mtzin', mtzin, '-mtzout', mtzout,
'-colin',
'/*/*/[{!s},{!s}]'.format(I, SIGI))
# Run!
CTRUNC.run()
if not os.path.exists(mtzout):
raise ExternalProgramError(
'CTRUNCATE has failed to convert intensities to SFs. {!s}\nOUT: {!s}\nERR: {!s}'
.format(mtzin, CTRUNC.out, CTRUNC.err))
return CTRUNC
def map_to_reference_using_symmetry(refpdb, movpdb, pdbout, conrad=5):
"""Transforms `movpdb` to the closest symmetry site to `refpdb` using csymmatch - Symmetry info must be contained in the header of the pdb file"""
if not pdbout.endswith('.pdb'):
pdbout = pdbout + '.pdb'
if not os.path.exists(refpdb):
raise IOError('refpdb does not exist! {!s}'.format(refpdb))
if not os.path.exists(movpdb):
raise IOError('movpdb does not exist! {!s}'.format(movpdb))
if os.path.exists(pdbout):
raise Exception('pdbout already exists! {!s}'.format(pdbout))
# Initialise Commander
CSYMMATCH = CommandManager('csymmatch')
# Set Command Arguments
CSYMMATCH.add_command_line_arguments('-pdbin-ref',
os.path.abspath(refpdb), '-pdbin',
os.path.abspath(movpdb), '-pdbout',
os.path.abspath(pdbout),
'-connectivity-radius', str(conrad))
# run!
CSYMMATCH.run()
if not os.path.exists(pdbout):
raise ExternalProgramError(
'CSYMMATCH has failed to map {!s} to {!s}.\nERR: {!s}'.format(
movpdb, refpdb, CSYMMATCH.err))
return pdbout
def merge_pdb_files(pdb1, pdb2, pdbout):
"""Merge two PDB Files using CCP4s pdb_merge"""
# Initialise Commander
MERGER = CommandManager('pdb_merge')
# Set command arguments
MERGER.add_command_line_arguments('xyzin1', pdb1, 'xyzin2', pdb2, 'xyzout',
pdbout)
# Set inputs
MERGER.add_standard_input('END')
# run!
MERGER.run()
return MERGER
def run(cls, script):
assert script.endswith(cls._file_type)
c = CommandManager('pymol')
c.add_command_line_arguments([
'-k', '-q', '-c', '-Q', '-s',
script[:-len(cls._file_type)] + '.log', '-r', script
])
c.run()
return c
def mask_map(mapin, maskpdb, mapout, border=1):
"""Takes mapin and masks around atoms in maskpdb"""
# Masking object
masker = CommandManager('mapmask')
# Set input files
masker.add_command_line_arguments(
['mapin', mapin, 'mapout', mapout, 'xyzin', maskpdb])
# Set stdin
masker.add_standard_input(['BORDER {!s}'.format(border), 'END'])
# Run!
masker.run()
# Report errors
if masker.process.returncode != 0:
raise RuntimeError('mapmask failed to mask map {!s}'.format(mapin))
# Return Command Managers for flexible handling of out & err
return masker
def create_asu_map(mapin, mapout):
"""Takes mapin and masks to the asymmetric unit"""
# Masking object
masker = CommandManager('mapmask')
# Set input files
masker.add_command_line_arguments(['mapin', mapin, 'mapout', mapout])
# Set stdin
masker.add_standard_input(['XYZLIM ASU', 'END'])
# Run!
masker.run()
# Report errors
if masker.process.returncode != 0:
raise RuntimeError(
'mapmask failed to create asu map from {!s}'.format(mapin))
# Return Command Managers for flexible handling of out & err
return masker
def fft_mtz_to_map(mtz_file, map_file, cols):
"""Converts an MTZ Format File to a MAP File (using fft as default)"""
# Initialise
writer = CommandManager('fft')
# Set Program Arguments
writer.add_command_line_arguments('hklin', mtz_file, 'mapout', map_file)
# Set Program Input
writer.add_standard_input(
['LABIN F1={!s} PHI={!s}'.format(cols['F'], cols['P']), 'END'])
# RUN!
writer.run()
# Check Output
if writer.process.returncode != 0:
print('\nOUT\n\n' + writer.out)
print('\nERR\n\n' + writer.err)
raise RuntimeError(
'fft failed to generate map from {!s}'.format(mtz_file))
return writer
def isolate_residue_by_res_id(inpdb,
outpdb,
chain,
resnum,
model='*',
inscode=''):
"""Isolate the residues identified by residue ids using pdbcur - i.e. '0/A/54.A/'"""
if inscode:
selection = '/{!s}/{!s}/{!s}.{!s}'.format(model, chain, resnum,
inscode)
else:
selection = '/{!s}/{!s}/{!s}'.format(model, chain, resnum)
PDBCUR = CommandManager('pdbcur')
PDBCUR.add_command_line_arguments('XYZIN', inpdb, 'XYZOUT', outpdb)
PDBCUR.add_standard_input(['lvresidue {!s}'.format(selection), 'END'])
PDBCUR.run()
return PDBCUR
def reindex_mtz_to_reference(in_mtz, out_mtz, reference_mtz, tolerance):
"""Reindex the data in one mtz to a reference mtz"""
print '**************************'
print '*** Running reindexing ***'
print '**************************'
cmd = CommandManager('pointless')
cmd.add_command_line_arguments(
['hklin', in_mtz, 'hklref', reference_mtz, 'hklout', out_mtz])
cmd.add_standard_input(['tolerance {}'.format(tolerance)])
print_run_and_raise_error_maybe(cmd)
if not os.path.exists(out_mtz):
raise Failure(
'reindexing has failed -- {} does not exist'.format(out_mtz))
def remove_residue_by_res_id(inpdb,
outpdb,
chain,
resnum,
model='*',
inscode='',
removeSolvent=False):
"""Remove the residues identified by res info using pdbcur - i.e. 'UNL'"""
if inscode:
selection = '/{!s}/{!s}/{!s}.{!s}'.format(model, chain, resnum,
inscode)
else:
selection = '/{!s}/{!s}/{!s}'.format(model, chain, resnum)
std_input = ['delresidue {!s}'.format(selection)
] + (removeSolvent) * ['delsolvent'] + ['END']
PDBCUR = CommandManager('pdbcur')
PDBCUR.add_command_line_arguments('XYZIN', inpdb, 'XYZOUT', outpdb)
PDBCUR.add_standard_input(std_input)
PDBCUR.run()
return PDBCUR
def run_coot(script, graphical=False, noguano=True):
"""Runs coot with the provided script"""
# Check that the script is valid (e.g. causes coot to exit at the end)
validate_coot_script(script)
# Stop coot droppings?
coot_flags = ['--no-guano']*(noguano)
# Run with/without graphics?
if graphical:
coot_flags.extend(['-script',script])
else:
coot_flags.extend(['--no-graphics','-s',script])
# Initialise
COOT = CommandManager('coot')
# Load arguments
COOT.add_command_line_arguments(*coot_flags)
# Run!
COOT.run()
return COOT
def get_mtz_resolution(mtz_file):
"""Gets the max resolution from the file"""
# Extract Contents of MTZ
MTZDMP = CommandManager('mtzdmp')
MTZDMP.add_command_line_arguments(mtz_file)
MTZDMP.run()
# Check for errors
if MTZDMP.process.returncode != 0:
raise RuntimeError(
'mtzdmp failed to read file {!s}:\nReturn: {!s}\nOut: {!s}'.format(
mtz_file, MTZDMP.process.returncode, MTZDMP.output))
# Search for the Column Headings
regex = re.compile('\* Resolution Range :.*\n.*\n.*\((.*)A \)\n')
matches = regex.findall(MTZDMP.output)
# Check for validity of matches
assert matches, 'No Resolution Range found in MTZFile {!s}'.format(
mtz_file)
assert len(
matches
) == 1, 'Too many matching lines found for Column Headings in MTZFile {!s}\n\t{!s}'.format(
mtz_file, matches)
# Return
return map(float, matches[0].replace(' ', '').split('-'))
def merge_cif_libraries(incifs, outcif):
"""Take a list of cifs and merge into one cif"""
assert isinstance(incifs, list), "'incifs' is not a list!"
assert len(incifs) > 1, "'incifs' must be two or more files!"
current = incifs.pop(0)
to_be_deleted = []
for additional in incifs:
# Create a file handle and path for the output
temp_handle, temp_path = tempfile.mkstemp(suffix='.lib',
prefix='libcheck_')
to_be_deleted.append(temp_path)
# Merge current and additional to temp_path
LIBCHK = CommandManager('libcheck')
LIBCHK.add_standard_input(
'_DOC N', '_FILE_L {!s}'.format(current),
'_FILE_L2 {!s}'.format(additional),
'_FILE_O {!s}'.format(temp_path.replace('.lib', '')), '_END')
LIBCHK.run()
current = temp_path
shutil.copy(current, outcif)
for file in to_be_deleted:
os.remove(file)
assert os.path.exists(outcif), 'OUTPUT CIF DOES NOT EXIST! {!s}'.format(
outcif)
return outcif
def run_mlfsom(pdb_file, res_h, out_dir='mlfsom_out', n_images=180, osc=1.0, energy=12660, verbose=True):
"""Run MLFSOM on the given file."""
ftd_pre = ['1H87.pdb', 'example.com', 'example.mat', 'mlfsom.log', 'refined.pdb', 'pristine.mtz']
assert not os.path.exists(out_dir), 'output directory already exists!'
assert os.path.exists(pdb_file)
assert isinstance(n_images, int)
# Store current directory
cur_dir = os.getcwd()
try:
# Create a temporary directory for mlfsom to run in (and go to it)
tmp_dir = tempfile.mkdtemp(prefix='mlfsom_')
mlfsom_pdb = os.path.join(tmp_dir, 'refined.pdb')
mlfsom_mtz = os.path.join(tmp_dir, 'pristine.mtz')
mlfsom_log = os.path.join(tmp_dir, 'mlfsom.log')
mlfsom_img = 'image_###.img'
# Get the mlfsom tarball and move it to the temporary directory
mlfsom_file = os.path.join(bamboo.resources.__path__[0], 'mlfsom.tar.gz')
assert os.path.exists(mlfsom_file), 'MLFSOM tarball not found'
shutil.copy(mlfsom_file, tmp_dir)
mlfsom_file = os.path.join(tmp_dir, 'mlfsom.tar.gz')
assert os.path.exists(mlfsom_file), 'MLFSOM tarball not in temporary directory'
# Untar the file
t = tarfile.open(mlfsom_file, 'r:gz')
try: t.extractall(tmp_dir)
finally: t.close()
# Delete unnecessary files
for f in ftd_pre:
fp = os.path.join(tmp_dir, f)
if os.path.exists(fp): os.remove(fp)
# Move the input files in
shutil.copy(pdb_file, mlfsom_pdb)
# Got to directory to run MLFSOM
os.chdir(tmp_dir)
# Convert the pdb_file to structure factors
ano_sfall = CommandManager('./ano_sfall.com')
ano_sfall.add_command_line_arguments(os.path.basename(mlfsom_pdb))
ano_sfall.add_command_line_arguments('energy={}'.format(energy))
ano_sfall.add_command_line_arguments('{}A'.format(res_h))
if verbose: print('Running ./ano_sfall.com on {}').format(pdb_file)
rc = ano_sfall.run()
if rc != 0:
print('STDOUT:')
print(ano_sfall.output)
print('STDERR:')
print(ano_sfall.error)
shutil.move('ideal_ano.mtz', mlfsom_mtz)
with open(mlfsom_log, 'a') as fh:
fh.write('==================================================>\n')
fh.write('ano_sfall log\n')
fh.write('==================================================>\n')
fh.write(ano_sfall.output+'\n')
fh.write('==================================================>\n')
fh.write('ano_sfall errors\n')
fh.write('==================================================>\n')
fh.write(ano_sfall.error+'\n')
fh.write('==================================================>\n')
# Run MLFSOM on the resulting mtzfile
mlfsom = CommandManager('./mlfsom.com')
mlfsom.add_command_line_arguments(mlfsom_img)
mlfsom.add_command_line_arguments('frames={}'.format(n_images))
mlfsom.add_command_line_arguments('osc={}'.format(osc))
if verbose: print('Running ./mlfsom.com on {}. This may take a while...').format(pdb_file)
rc = mlfsom.run()
if rc != 0:
print('STDOUT:')
print(mlfsom.output)
print('STDERR:')
print(mlfsom.error)
with open(mlfsom_log, 'a') as fh:
fh.write('==================================================>\n')
fh.write('mlfsom log\n')
fh.write('==================================================>\n')
fh.write(mlfsom.output+'\n')
fh.write('==================================================>\n')
fh.write('mlfsom errors\n')
fh.write('==================================================>\n')
fh.write(mlfsom.error+'\n')
fh.write('==================================================>\n')
finally:
# Change back to original directory
os.chdir(cur_dir)
# Delete temporary directory
shutil.move(tmp_dir, out_dir)
return ano_sfall, mlfsom
class BuilderObject(object):
"""Template Object for creating an Object to generate ligand restraints"""
def __init__(self, time=True, verbose=True):
self.allowed_args = allowed_builder_args
self.ligname = DEFAULT_LIGAND_NAMES[0]
# Settings
self.time = time
self.verbose = verbose
self.runtime = -1.0
self.timeout = 1800
# Custom Init
self._custom_init()
def generate_ligand(self, ligsmile, outdir, outfile, flags=[]):
"""Generate ligand PDB and CIF from smile string"""
# Prepare standard settings
self._prepare_to_generate_ligand(ligsmile, outdir, outfile, flags)
# Check to see if already run, and if not, run the custom part of the object - different for each program
if os.path.exists(self.outpdb) and os.path.exists(
self.outcif) and os.path.exists(self.outlog):
if self.verbose:
print('\tLigand already generated - DOING NOTHING')
else:
cmd_line_args, std_inpt_args = self._create_program_arguments(
ligsmile, outdir, outfile, flags)
# Initialise CommandManager
self.builder = CommandManager(self.program)
# Set Command-Line Args
if cmd_line_args:
self.builder.add_command_line_arguments(cmd_line_args)
# Set Standard Input
if std_inpt_args: self.builder.add_standard_input(std_inpt_args)
# Set Parameters
self.builder.set_timeout(timeout=self.timeout)
# RUN
self.builder.run()
# Get runtime
self.runtime = self.builder.runtime
try:
# Could add postprocess here
pass
finally:
self.write_log_file()
return self.outpdb, self.outcif, self.outlog
def _prepare_to_generate_ligand(self, ligsmile, outdir, outfile, flags):
"""Set up the generic file names"""
# Process outputfile
if '/' in outfile:
raise ValueError('outfile must be a file, not a path')
# Record Template and Outdir
self.outtemplate = os.path.join(outdir, outfile)
self.outdir = outdir
# Record Filenames
self.outpdb = self.outtemplate + '.pdb'
self.outcif = self.outtemplate + '.cif'
self.outlog = self.outtemplate + '.log'
def write_log_file(self):
"""Write the log file"""
with open(self.outlog, 'w') as logfile:
# Write out the input command
logfile.write('\nCOMMAND\n\n')
logfile.write('\n'.join(self.builder.cmd_line_args) + '\n')
logfile.write('\nINPUT\n\n')
logfile.write('\n'.join(self.builder.std_inp_lines) + '\n')
# Write out & err
logfile.write('\nSTDOUT\n\n')
logfile.write(self.builder.output)
logfile.write('\nSTDERR\n\n')
logfile.write(self.builder.error)
class _refiner(object):
program = None
auto = True
def __init__(self,
pdb_file,
mtz_file=None,
cif_file=None,
out_prefix=None,
**kw_args):
# Set defaults if not given
if mtz_file is None:
mtz_file = pdb_file.replace('.pdb', '.mtz')
if out_prefix is None:
out_prefix = os.path.splitext(pdb_file)[0] + '-refined'
# Main files
self.pdb_file = pdb_file
self.mtz_file = mtz_file
self.cif_file = cif_file
# Eventual output prefix
self.out_prefix = out_prefix
self.out_pdb_file = self.out_prefix + '.pdb'
self.out_mtz_file = self.out_prefix + '.mtz'
self.out_log_file = self.out_prefix + '.log'
# Validate input
assert os.path.exists(self.pdb_file)
assert os.path.exists(self.mtz_file)
assert not os.path.exists(
self.out_pdb_file), 'Output file already exists: {}'.format(
self.out_pdb_file)
assert not os.path.exists(
self.out_mtz_file), 'Output file already exists: {}'.format(
self.out_mtz_file)
# Create temporary folder for refinement
self.tmp_dir = tempfile.mkdtemp(prefix='refine-model-')
self.tmp_pre = os.path.join(self.tmp_dir, 'refine')
# Command object for refinement
self.cmd = CommandManager(self.program)
self.kw_args = kw_args
# Setup, refine and post_process
if self.auto is True:
self.run()
def run(self):
"""...run refinement amd export files"""
self.setup()
ret = self.refine()
self.export()
return ret
def setup(self):
raise Exception('Dummy class -- not implemented')
def refine(self):
"""...run the refinement"""
self.cmd.print_settings()
return self.cmd.run()
def export(self):
"""Copy files to output destination"""
# Find pdb file in the output folder
tmp_pdb = glob.glob(self.tmp_pre + '*.pdb')
assert tmp_pdb, 'No refined files found: {}'.format(self.tmp_dir)
tmp_pdb = tmp_pdb[0]
tmp_mtz = tmp_pdb.replace('.pdb', '.mtz')
assert os.path.exists(tmp_pdb)
assert os.path.exists(tmp_mtz)
# Copy to output folder
shutil.copy(tmp_pdb, self.out_pdb_file)
shutil.copy(tmp_mtz, self.out_mtz_file)
assert os.path.exists(self.out_pdb_file)
assert os.path.exists(self.out_mtz_file)
# Write the log to the output log file
self.cmd.write_output(self.out_log_file)
# Delete temporary directory
shutil.rmtree(self.tmp_dir)
def run(params):
# Identify any existing output directories
current_dirs = sorted(glob.glob(params.output.dir_prefix + '*'))
if not current_dirs:
next_int = 1
else:
current_nums = [
s.replace(params.output.dir_prefix, '') for s in current_dirs
]
next_int = sorted(map(int, current_nums))[-1] + 1
# Create output directory name from int
out_dir = params.output.dir_prefix + '{:04}'.format(next_int)
# Create output directory
os.mkdir(out_dir)
# Create log object
log = Log(log_file=os.path.join(
out_dir, params.output.out_prefix + '.quick-refine.log'),
verbose=params.settings.verbose)
# Report
if current_dirs:
log('Found existing refinement directories: \n\t{}'.format(
'\n\t'.join(current_dirs)))
log('')
log('Creating new output directory: {}'.format(out_dir))
# Validate input parameters
log.subheading('Validating input parameters')
assert params.input.pdb is not None, 'No PDB given for refinement'
assert params.input.mtz is not None, 'No MTZ given for refinement'
if os.path.islink(params.input.mtz):
log('Converting mtz path to real path:')
log('{} -> {}'.format(params.input.mtz,
os.path.realpath(params.input.mtz)))
params.input.mtz = os.path.realpath(params.input.mtz)
# Link input
log('Copying/linking files to refinement folder')
shutil.copy(params.input.pdb,
os.path.abspath(os.path.join(out_dir, 'input.pdb')))
rel_symlink(params.input.mtz,
os.path.abspath(os.path.join(out_dir, 'input.mtz')))
# Copy parameter file to output folder
if params.input.params:
shutil.copy(params.input.params,
os.path.abspath(os.path.join(out_dir, 'input.params')))
# Create output prefixes
output_prefix = os.path.join(out_dir, params.output.out_prefix)
log('Real output file path prefixes: {}'.format(output_prefix))
log('Link output file path prefixes: {}'.format(params.output.link_prefix))
# Create command objects
log.subheading('Preparing command line input for refinement program')
# PHENIX
if params.options.program == 'phenix':
cm = CommandManager('phenix.refine')
# Command line args
cm.add_command_line_arguments([params.input.pdb, params.input.mtz])
cm.add_command_line_arguments(
['output.prefix={}'.format(output_prefix)])
if params.input.cif:
cm.add_command_line_arguments(params.input.cif)
if params.input.params and os.path.exists(params.input.params):
cm.add_command_line_arguments([params.input.params])
# REFMAC
elif params.options.program == 'refmac':
cm = CommandManager('refmac5')
# Command line args
cm.add_command_line_arguments(
['xyzin', params.input.pdb, 'hklin', params.input.mtz])
cm.add_command_line_arguments([
'xyzout', output_prefix + '.pdb', 'hklout', output_prefix + '.mtz'
])
if params.input.cif:
for cif in params.input.cif:
cm.add_command_line_arguments(['libin', cif])
# Standard input
if params.input.params:
cm.add_standard_input(open(params.input.params).read().split('\n'))
cm.add_standard_input(['END'])
elif params.options.program == "buster":
cm = CommandManager('refine')
# Command line arguments
# inputs
cm.add_command_line_arguments(
['-p', params.input.pdb, '-m', params.input.mtz, '-d', out_dir])
if params.input.cif:
for cif in params.input.cif:
cm.add_command_line_arguments(['-l', cif])
if params.input.params:
cm.add_command_line_arguments(['-Gelly', params.input.params])
# Pass additional command line arguments?
if params.input.args:
cm.add_command_line_arguments(params.input.args)
# Report
log(str(cm))
log.bar()
log('running refinement... ({})'.format(cm.program[0]))
out = cm.run()
log.subheading('Refinement output')
if not log.verbose:
log('output written to log file ({} lines)'.format(
cm.output.count('\n')))
log('\n' + cm.output, show=False)
if out != 0:
log.subheading('Refinement Errors')
log(cm.error)
log.subheading('Post-processing output files')
if params.options.program == "buster":
log.subheading('Renaming buster output files')
shutil.move(src=os.path.join(out_dir, 'refine.pdb'),
dst=output_prefix + '.pdb')
shutil.move(src=os.path.join(out_dir, 'refine.mtz'),
dst=output_prefix + '.mtz')
# Find output files
try:
real_pdb = glob.glob(output_prefix + '*.pdb')[0]
real_mtz = glob.glob(output_prefix + '*.mtz')[0]
except:
log('Refinement has failed - output files do not exist')
log('{}: {}'.format(output_prefix + '*.pdb',
glob.glob(output_prefix + '*.pdb')))
log('{}: {}'.format(output_prefix + '*.mtz',
glob.glob(output_prefix + '*.mtz')))
raise
# List of links to make at the end of the run
link_file_pairs = [(real_pdb, params.output.link_prefix + '.pdb'),
(real_mtz, params.output.link_prefix + '.mtz')]
# Split conformations
if params.options.split_conformations:
params.split_conformations.settings.verbose = params.settings.verbose
log.subheading('Splitting refined structure conformations')
# Running split conformations
out_files = split_conformations.split_conformations(
filename=real_pdb, params=params.split_conformations, log=log)
# Link output files to top
for real_file in out_files:
link_file = params.output.link_prefix + os.path.basename(
real_file.replace(os.path.splitext(real_pdb)[0], ''))
link_file_pairs.append([real_file, link_file])
# Link output files
log.subheading('linking output files')
for real_file, link_file in link_file_pairs:
log('Linking {} -> {}'.format(link_file, real_file))
if not os.path.exists(real_file):
log('file does not exist: {}'.format(real_file))
continue
if os.path.exists(link_file) and os.path.islink(link_file):
log('removing existing link: {}'.format(link_file))
os.unlink(link_file)
if not os.path.exists(link_file):
rel_symlink(real_file, link_file)
log.heading('finished - refinement')
class FitterObject(object):
def __init__(self, time=True, verbose=True):
self.allowedArgs = allowed_fitter_args
self.preferChain = DEFAULT_OUTPUT_CHAIN[0]
# Settings
self.time = time
self.verbose = verbose
self.runtime = -1.0
self.timeout = 99999
# Custom Init
self._custom_init()
def fit_ligand(self,
ligcif,
ligpdb,
mtz,
apopdb,
outdir,
outfile,
flags=[]):
"""Fit Ligand to a structure"""
# Prepare input and output filenames
self._prepare_to_fit_ligand(ligcif, ligpdb, mtz, apopdb, outdir,
outfile, flags)
# Check to see if already run, and if not, run the custom part of the object - different for each program
if os.path.exists(self.outpdb) and os.path.exists(self.outlog):
if self.verbose:
print('\tLigand already fitted - DOING NOTHING')
self._post_process(ligcif, ligpdb, mtz, apopdb, outdir, outfile,
flags)
else:
if self.verbose:
print('\tFitting using {!s}.'.format(self.name))
cmd_line_args, std_inpt_args = self._create_program_arguments(
ligcif, ligpdb, mtz, apopdb, outdir, outfile, flags)
# Initialise CommandManager
self.Fitter = CommandManager(self.program)
# Set Command-Line Args
if cmd_line_args: self.Fitter.SetArguments(cmd_line_args)
# Set Standard Input
if std_inpt_args: self.Fitter.SetInput(std_inpt_args)
# Set Parameters
self.Fitter.SetParameters(timeout=self.timeout)
# RUN
self.Fitter.Run()
# Calculate runtime (seconds)
self.runtime = self.Fitter.runtime
try:
# Process results and generate the list of modelled ligands
if self.verbose:
print('\tFinished fitting - post-processing models.')
self._post_process(ligcif, ligpdb, mtz, apopdb, outdir,
outfile, flags)
if not self.outmodels:
raise FittingError(
'No fitted models found! Log: {!s}'.format(
self.outlog))
if not os.path.exists(self.outpdb):
# Map the model of the best ligand to the asu and check it's near to the protein
self._map_to_asu(ligcif, ligpdb, mtz, apopdb, outdir,
outfile, flags)
# Create symbolic links to the output file
self._link_output_files()
# Merge the best ligand with the apo structure
if not os.path.exists(self.mergedpdb):
self.Merger = merge_pdb_files(apopdb, self.outpdb,
self.mergedpdb)
finally:
self.write_log_file()
return self.outpdb, self.mergedpdb, self.outlog
def _prepare_to_fit_ligand(self, ligcif, ligpdb, mtz, apopdb, outdir,
outfile, flags):
"""Set up the generic file names"""
# Process outputfile
if '/' in outfile:
raise ValueError('outfile must be a file, not a path')
# Record Template and Outdir
self.outtemplate = os.path.join(outdir, outfile)
self.outdir = outdir
# Record Filenames
self.outpdb = self.outtemplate + '.lig.pdb'
self.mergedpdb = self.outtemplate + '.pdb'
self.outlog = self.outtemplate + '.log'
# Storage
self.outmodels = []
self.filtmodels = []
self.bestmodel = None
self.fittingdata = None
# Prepare custom settings
self._custom_prepare_to_fit_ligand(ligcif, ligpdb, mtz, apopdb, outdir,
outfile, flags)
return
def _map_to_asu(self, ligcif, ligpdb, mtz, apopdb, outdir, outfile, flags):
"""Map the best ligand file to the asu of the protein - pick the symmetry version with the most contacts"""
candidate = None
if self.verbose:
print('\tMapping fitted models back to the asymmetric unit.')
for model in self.outmodels:
ligand_sym_file = model.replace('.pdb', '.sym.pdb')
if os.path.exists(ligand_sym_file):
self.filtmodels.append(model)
else:
try:
# Create Cryst Line
shutil.move(model, model + '.temp.pdb')
PDBSET = create_cryst_line_from_mtz(
model + '.temp.pdb', ligand_sym_file, mtz)
# Rename the original file, then create a symmetry equivalent ligand that is close to the protein
# shutil.move(model, ligand_sym_file)
# candidate, ordered_files = map_structure_to_asu(apopdb, mtz, ligand_sym_file, model, delete_structures=True)
candidate = map_to_reference_using_symmetry(
refpdb=apopdb, movpdb=ligand_sym_file, pdbout=model)
self.filtmodels.append(candidate)
except (DistanceError, IOError) as err:
print(err)
continue
# If it gets here we have a candidate
# Break here for fast (1 model per fitter max)
# break
if not self.filtmodels:
raise FittingError('No fitted models within range of protein!')
else:
# Rename all of the filtered models
[
change_residue_chain_and_number(filtfile)
for filtfile in self.filtmodels
]
# Pick the `best` one to be the output
self.bestmodel = self.filtmodels[0]
return
def _link_output_files(self):
"""Make links to the output files"""
# Create Symlinks
os.symlink(os.path.relpath(self.bestmodel, start=self.outdir),
self.outpdb)
return
def write_log_file(self):
"""Write the log file"""
if self.verbose:
print('\tWriting fitting logfile.')
with open(self.outlog, 'w') as logfile:
if hasattr(self, 'Fitter'):
# Write out the input command
logfile.write('\nCOMMAND\n\n')
logfile.write('\n'.join(self.Fitter.command))
logfile.write('\nINPUT\n\n')
logfile.write(self.Fitter.inp)
# Write out & err
logfile.write('\nFITTER STDOUT\n\n')
logfile.write(self.Fitter.out)
logfile.write('\nFITTER STDERR\n\n')
logfile.write(self.Fitter.err)
if hasattr(self, 'Merger'):
# Write out the input command
logfile.write('\nCOMMAND\n\n')
logfile.write('\n'.join(self.Merger.command))
logfile.write('\nINPUT\n\n')
logfile.write(self.Merger.inp)
# Write out & err
logfile.write('\nMERGER STDOUT\n\n')
logfile.write(self.Merger.out)
logfile.write('\nMERGER STDERR\n\n')
logfile.write(self.Merger.err)
return
def fit_ligand(self,
ligcif,
ligpdb,
mtz,
apopdb,
outdir,
outfile,
flags=[]):
"""Fit Ligand to a structure"""
# Prepare input and output filenames
self._prepare_to_fit_ligand(ligcif, ligpdb, mtz, apopdb, outdir,
outfile, flags)
# Check to see if already run, and if not, run the custom part of the object - different for each program
if os.path.exists(self.outpdb) and os.path.exists(self.outlog):
if self.verbose:
print('\tLigand already fitted - DOING NOTHING')
self._post_process(ligcif, ligpdb, mtz, apopdb, outdir, outfile,
flags)
else:
if self.verbose:
print('\tFitting using {!s}.'.format(self.name))
cmd_line_args, std_inpt_args = self._create_program_arguments(
ligcif, ligpdb, mtz, apopdb, outdir, outfile, flags)
# Initialise CommandManager
self.Fitter = CommandManager(self.program)
# Set Command-Line Args
if cmd_line_args: self.Fitter.SetArguments(cmd_line_args)
# Set Standard Input
if std_inpt_args: self.Fitter.SetInput(std_inpt_args)
# Set Parameters
self.Fitter.SetParameters(timeout=self.timeout)
# RUN
self.Fitter.Run()
# Calculate runtime (seconds)
self.runtime = self.Fitter.runtime
try:
# Process results and generate the list of modelled ligands
if self.verbose:
print('\tFinished fitting - post-processing models.')
self._post_process(ligcif, ligpdb, mtz, apopdb, outdir,
outfile, flags)
if not self.outmodels:
raise FittingError(
'No fitted models found! Log: {!s}'.format(
self.outlog))
if not os.path.exists(self.outpdb):
# Map the model of the best ligand to the asu and check it's near to the protein
self._map_to_asu(ligcif, ligpdb, mtz, apopdb, outdir,
outfile, flags)
# Create symbolic links to the output file
self._link_output_files()
# Merge the best ligand with the apo structure
if not os.path.exists(self.mergedpdb):
self.Merger = merge_pdb_files(apopdb, self.outpdb,
self.mergedpdb)
finally:
self.write_log_file()
return self.outpdb, self.mergedpdb, self.outlog