from PyQt4 import QtCore
import CCP4TaskWidget
import os, sys, re, subprocess
from Bio.SeqUtils.ProtParam import ProteinAnalysis
from Bio import SeqIO
DEVEL = False
DEVEL = True
SHOW_NOTIMPLEMENTED = True
SHOW_NOTIMPLEMENTED = False
if DEVEL:
import reload_me
class CTaskArpWarpClassic(CCP4TaskWidget.CTaskWidget):
TASKNAME = 'arp_warp_classic'
TASKVERSION = 0.0
TASKMODULE = 'test' if sys.platform.startswith('win') else 'model_building'
TASKTITLE='ARP/wARP'
DESCRIPTION='Build model (ARP/wARP classic)'
WHATNEXT = ['coot_rebuild', 'prosmart_refmac', 'edstats']
MGDISPLAYFILES = ['FPHIOUT']
def drawContents(self):
self.labels = dict()
notoggle = True
notoggle = False
folder = self.openFolder(folderFunction='inputData', title='Input Data')
self.createLine([
'label', 'Run ARP/wARP for',
'widget', 'AWA_ARP_MODE'])
self.createLine([
'subtitle', 'Select experimental data',
'Selection of anomalous data provies additional option in refinement, see below'])
self.openSubFrame(frame=[True])
self.createLine([
'message', 'XXXXX Enter input MTZ file name (HKLIN)',
'widget','AWA_FOBS'])
self.createLine([
'message', 'XXXXX Enter input MTZ file name (HKLIN)',
'widget', 'AWA_FREE'])
self.closeSubFrame()
self.createLine([
'subtitle', 'Provide model or phases for calculation of starting maps',
'Select model after molecular replacement or phases from density modification'])
self.openSubFrame(frame=[True])
self.createLine([
'message', 'XXXXX Enter input MTZ file name (HKLIN)',
'widget', 'AWA_PHINI'],
toggle = [] if notoggle else ['AWA_ARP_MODE', 'open', ['WARPNTRACEPHASES']])
self.createLine([
'message', 'XXXXX Enter name of file containing molecule coordinates (MODELIN)',
'widget', 'AWA_MODELIN'],
toggle = [] if notoggle else ['AWA_ARP_MODE', 'open', ['WARPNTRACEMODEL', 'MOLREP']])
self.closeSubFrame()
tooltip = 'To build polyalanine model unselect sequence and define the numer of residues and molecules in the AU.'
tooltip += ' Sequence is compulsory if you want to use NCS model extension and/or NCS restraints.'
self.createLine([ 'subtitle', 'Define contents of the asymmetric unit', tooltip])
self.openSubFrame(frame=[True])
self.createLine([
'message', 'Enter name of file containing the sequence (SEQIN)',
'widget','AWA_SEQIN'])
self.au_content_line = self.createLine([
'widget', 'AWA_NRES',
'label', 'residues in the sequence. Expected',
'widget', 'AWA_NMOL',
'label', 'copies in the AU'])
self.closeSubFrame()
tooltip = '(1) Use of anomalous data is only active if the experimental data contain anomalous pairs.'
tooltip += ' (2) The phases used in refinement can be the same as used for calculation of starting maps.'
self.createLine(['subtitle', 'Define phase information for refinements', tooltip])
self.openSubFrame(frame=[True])
self.createLine([
'widget', '-guiMode', 'radio', 'AWA_REF_MODE'])
self.createLine([
'message', 'XXXXX Enter input MTZ file name (HKLIN)',
'widget', 'AWA_PHREF'],
toggle = [] if notoggle else ['AWA_REF_MODE', 'open', ['AWA_HL', 'AWA_PHASED']])
self.createLine([
'message', 'XXXXX Enter name of file containing heavy atom coordinates (MODELIN)',
'widget', 'AWA_HEAVYIN'],
toggle = [] if notoggle else ['AWA_REF_MODE', 'open', ['AWA_SAD']])
line = self.createLine([
'label', 'Scattering',
'widget', 'AWA_ANO_OPTION'],
toggle = [] if notoggle else ['AWA_REF_MODE', 'open', ['AWA_SAD']])
self.createLine([
'widget', 'AWA_SCAT_LAMBDA_AWA_SAD',
'label', 'A.'],
appendLine = line,
toggle = [] if notoggle else ['AWA_ANO_OPTION', 'open', ['LAMBDA']])
self.createLine([
'label', 'for atom',
'widget', 'AWA_SCAT_ATOM',
'label', "f' =",
'widget', 'AWA_SCAT_FP_AWA_SAD',
'label', "f'' =",
'widget', 'AWA_SCAT_FDP_AWA_SAD'],
appendLine = line,
toggle = [] if notoggle else ['AWA_ANO_OPTION', 'open', ['MEASURED']])
self.closeSubFrame()
self.closeFolder()
folder = self.openFolder(folderFunction='controlParameters', title='Parameters')
self.createLine([
'subtitle', 'ARP/wARP flow parameters'])
line = self.createLine([
'message', 'Each ARP-REFMAC cycle consists of refinement with Refmac and remodelling dummy-atom substructure with ARP',
'label', 'Do',
'widget', 'AWA_BIG_CYCLES',
'label', 'macrocycles, each including',
'widget', 'AWA_SMALL_CYCLES',
'label', '.'],
toggle = [] if notoggle else ['AWA_ARP_MODE', 'hide', ['MOLREP']])
self.label_init('AWA_TOTAL_CYCLES', line, 4, 'ARP-REFMAC cycles')
self.createLine([
'label', 'Do',
'widget', 'AWA_SMALL_CYCLES',
'label', 'ARP-REFMAC cycles (NB: no autotracing in this mode)'],
toggle = [] if notoggle else ['AWA_ARP_MODE', 'open', ['MOLREP']])
self.openSubFrame(
toggle = [] if notoggle else ['AWA_ARP_MODE', 'hide', ['MOLREP']])
self.createLine([
'widget', 'AWA_USE_COND',
'label', 'Use Conditional Restraints for free atoms.'])
self.createLine([
'widget', 'AWA_FORCE_COND',
'label', 'Impose the use of Conditional Restraints for very large structures, time consuming.'])
self.createLine([
'widget', 'AWA_FAKE_DATA',
'label', 'Use Fake Data.'])
self.createLine([
'widget', 'AWA_NCS_RESTRAINTS',
'label', 'Use Non-Crystallographic Symmetry Restraints.'])
self.createLine([
'widget', 'AWA_NCS_EXTENSION',
'label', 'Use Non-Crystallographic Symmetry information to extend chains.'])
self.createLine([
'widget', 'AWA_LOOPS',
'label', 'Use Loopy to build loops between chain fragments at the end of the run.'])
self.createLine([
'widget', 'AWA_BUILD_SIDE',
'label', 'Start docking the autotraced chains to sequence after',
'widget', 'AWA_SIDE_AFTER',
'label', 'building cycles.'],
toggleFunction = [self.AWA_SEQIN_isset, ['AWA_SEQIN']])
# toggleFunction = [lambda: self.container.inputData.AWA_SEQIN.isSet(), ['AWA_SEQIN']])
self.createLine([
'widget', 'AWA_IS_SEMET',
'label', 'Sequence dock as a Se-Methionine substituted protein.'],
toggle = [] if notoggle else ['AWA_REF_MODE', 'open', ['AWA_SAD']])
self.createLine([
'widget', 'AWA_ALBE',
'label', 'Search for helices and strands before each building cycle.'])
self.createLine([
'widget', 'AWA_SKIP_BUILD',
'label', 'Skip the chain tracing for the first',
'widget', 'AWA_SKIP_CYCLES',
'label', 'building cycles.'])
self.closeSubFrame()
if SHOW_NOTIMPLEMENTED:
# NOT USED in ccp4i
self.createLine([
'widget', 'AWA_KEEP_MODEL',
'label', 'Keep the geometry of the model, do NOT convert to free atoms'],
toggle = [] if notoggle else ['AWA_ARP_MODE', 'open', ['WARPNTRACEMODEL']])
self.createLine([
'widget', 'AWA_FREEBUILD',
'label', 'Before the start of autobuilding construct new free atoms model in map'],
toggle = [] if notoggle else ['AWA_ARP_MODE', 'open', ['WARPNTRACEMODEL']])
self.createLine([
'widget', 'AWA_FLATTEN',
'label', 'Before the start of autobuilding perform density modification with DM'],
toggle = [] if notoggle else ['AWA_ARP_MODE', 'open', ['WARPNTRACEMODEL']])
if SHOW_NOTIMPLEMENTED:
self.createLine([
'widget', 'AWA_RANDTIMES',
'label', 'atomic positions during this run.'])
self.createLine([
'label', 'After cycle',
'widget', 'AWA_RAND1',
'label', 'apply',
'widget', 'AWA_RANDSHIFT1',
'label', 'A shifts and B cutoff',
'widget', 'AWA_BCUT1',
'label', '* WilsonB'],
toggle = [] if notoggle else ['AWA_RANDON11', 'hide', ['0']])
self.createLine([
'label', 'After cycle',
'widget', 'AWA_RAND2',
'label', 'apply',
'widget', 'AWA_RANDSHIFT2',
'label', 'A shifts and B cutoff',
'widget', 'AWA_BCUT2',
'label', '* WilsonB'],
toggle = [] if notoggle else ['AWA_RANDON22', 'hide', ['0']])
self.createLine([
'label', 'After cycle',
'widget', 'AWA_RAND3',
'label', 'apply',
'widget', 'AWA_RANDSHIFT3',
'label', 'A shifts and B cutoff',
'widget', 'AWA_BCUT3',
'label', '* WilsonB'],
toggle = [] if notoggle else ['AWA_RANDON33', 'hide', ['0']])
self.createLine([
'label', 'In place of autobuild cycle',
'widget', 'AWA_RAND1',
'label', 'apply',
'widget', 'AWA_RANDSHIFT1',
'label', 'A shifts and B cutoff',
'widget', 'AWA_BCUT1',
'label', '* WilsonB'],
toggle = [] if notoggle else ['AWA_RANDON1', 'hide', ['0']])
self.createLine([
'label', 'In place of autobuild cycle',
'widget', 'AWA_RAND2',
'label', 'apply',
'widget', 'AWA_RANDSHIFT2',
'label', 'A shifts and B cutoff',
'widget', 'AWA_BCUT2',
'label', '* WilsonB'],
toggle = [] if notoggle else ['AWA_RANDON2', 'hide', ['0']])
self.createLine([
'label', 'In place of autobuild cycle',
'widget', 'AWA_RAND3',
'label', 'apply',
'widget', 'AWA_RANDSHIFT3',
'label', 'A shifts and B cutoff',
'widget', 'AWA_BCUT3',
'label', '* WilsonB'],
toggle = [] if notoggle else ['AWA_RANDON3', 'hide', ['0']])
self.createLine([
'label', 'Iterate the autotracing up to',
'widget', 'AWA_MULTITRACE',
'label', 'times.'],
toggle = [] if notoggle else ['AWA_ARP_MODE', 'open', ['WARPNTRACEPHASES', 'WARPNTRACEMODEL']])
self.createLine([
'label', 'Add atoms in density above',
'widget', 'AWA_ADDATOM_SIGMA',
'label', 'sigma, and remove atoms in density below',
'widget', 'AWA_REMATOM_SIGMA',
'label', 'sigma.'])
self.createLine([
'label', 'Add and remove',
'widget', 'AWA_UP_UPDATE',
'label', 'times atoms than calculated automatically.'])
if SHOW_NOTIMPLEMENTED:
self.createLine([
'widget', 'AWA_CHECK_WILSON',
'label', 'Disable Wilson plot statistics checks.'])
self.createLine([
'subtitle', 'Refmac parameters'])
self.createLine([
'widget', 'AWA_TWIN',
'label', 'Attempt to correct for data collected from a twinned crystal.'],
toggle = [] if notoggle else ['AWA_REF_MODE', 'hide', ['AWA_SAD']])
self.createLine([
'widget', 'AWA_NCYCLES',
'label', 'cycles of refinement with REFMAC per ARP-REFMAC cycle.'])
self.createLine([
'label', 'Use phase restraints with blurring factor of',
'widget', 'AWA_PHASE_BLUR'],
toggle = [] if notoggle else ['AWA_REF_MODE', 'hide', ['AWA_REFML', 'AWA_SAD']])
self.createLine([
'widget', 'AWA_WEIGHT_MODE',
'label', 'matrix weighting for Xray / Geometry'])
self.createLine([
'label', 'Matrix weight for Xray / Geometry',
'widget', 'AWA_WMAT'],
toggle = [] if notoggle else ['AWA_WEIGHT_MODE', 'hide', ['AUTO']])
self.createLine([
'widget', 'AWA_RIDGE_RESTRAINTS',
'label', 'Jelly Body restraints'])
self.createLine([
'label', 'Use for scaling the',
'widget', 'AWA_SCALE',
'label', 'scaling model, with an',
'widget', 'AWA_SCANIS',
'label', 'scaling B factor.'])
self.createLine([
'label', 'Scaling and sigmaa calculation will be done with the',
'widget', 'AWA_REFMAC_REF_SET',
'label', 'set of reflections'],
toggleFunction = [self.AWA_FREE_isset, ['AWA_FREE']])
# toggleFunction = [lambda: self.container.inputData.AWA_FREE.isSet(), ['AWA_FREE']])
self.createLine([
'widget', 'AWA_SOLVENT',
'label', 'Solvent Mask correction'])
if SHOW_NOTIMPLEMENTED:
self.createLine([
'subtitle', 'Crystal parameters'])
self.createLine([
'label', 'Generate map in space group',
'label', 'SPACE_GROUP'])
line = self.createLine([
'label', self.container.guiParameters.AWA_CELL.get()])
self.label_init('AWA_CELL', line, 0, 'Cell: N/A')
self.createLine([
'label', 'Wilson B factor',
'label', 'WILSON_B',
'label', 'Solvent content',
'label', 'SOLVENTC'])
self.createLine([
'widget', 'AWA_EXCLUDE_RESOLUTION',
'label', 'Use reflections between',
'widget', 'AWA_EXCLUDE_RESOLUTION_MIN',
'label', 'and',
'widget', 'AWA_EXCLUDE_RESOLUTION_MAX',
'label', 'Angstrom'])
self.createLine([
'subtitle', 'Test and comparison parameters'])
self.createLine([
'widget', 'AWA_KEEP_JUNK',
'label', 'Keep intermediate files.'])
self.createLine([
'widget', 'AWA_TOGGLE_COMPTO',
'label', 'Compare with an already deposited protein for validation or testing'])
self.openSubFrame(
toggle = [] if notoggle else ['AWA_TOGGLE_COMPTO', 'open', [True]])
self.createLine([
'message', 'Enter PDB file for comparison or debugging (COMPARETO)',
'widget', 'AWA_COMPARETO'])
self.closeSubFrame()
self.createLine([
'subtitle', 'Submit a remote job at the Hamburg Cluster'])
self.createLine([
'widget', 'AWA_REMOTE_JOB',
'label', 'Submit the job for remote execution at the Hamburg cluster'],
toggle = [] if notoggle else ['AWA_ARP_MODE', 'hide', ['MOLREP']])
self.createLine([
'label', 'Remote submission is only allowed for automated model building jobs'],
toggle = [] if notoggle else ['AWA_ARP_MODE', 'hide', ['WARPNTRACEPHASES', 'WARPNTRACEMODEL']])
self.createLine([
'label', 'Your Email address',
'widget', 'AWA_USER_EMAIL'],
toggle = [] if notoggle else ['AWA_REMOTE_JOB', 'open', [True]])
self.createLine([
'label', 'Job data',
'widget', 'AWA_DATAKEEP_MODE'],
toggle = [] if notoggle else ['AWA_REMOTE_JOB', 'open', [True]])
self.closeFolder()
if self.isEditable():
self.handle_AWA_REF_MODE_changed()
self.connect(self.container.controlParameters.AWA_REF_MODE, QtCore.SIGNAL('dataChanged'), self.handle_AWA_REF_MODE_changed)
self.handle_AWA_ARP_MODE_changed()
self.connect(self.container.controlParameters.AWA_ARP_MODE, QtCore.SIGNAL('dataChanged'), self.handle_AWA_ARP_MODE_changed)
self.handle_AWA_FOBS_changed()
self.connect(self.container.inputData.AWA_FOBS, QtCore.SIGNAL('dataChanged'), self.handle_AWA_FOBS_changed)
self.handle_AWA_SEQIN_changed()
self.connect(self.container.inputData.AWA_SEQIN, QtCore.SIGNAL('dataChanged'), self.handle_AWA_SEQIN_changed)
self.handle_AWA_NMOL_changed()
self.connect(self.container.controlParameters.AWA_NMOL, QtCore.SIGNAL('dataChanged'), self.handle_AWA_NMOL_changed)
self.handle_AWA_NRES_changed()
self.connect(self.container.controlParameters.AWA_NRES, QtCore.SIGNAL('dataChanged'), self.handle_AWA_NRES_changed)
self.handle_AWA_TOTAL_CYCLES_changed()
self.handle_AWA_TOTAL_CYCLES_changed()
self.connect(self.container.controlParameters.AWA_BIG_CYCLES, QtCore.SIGNAL('dataChanged'), self.handle_AWA_TOTAL_CYCLES_changed)
self.connect(self.container.controlParameters.AWA_SMALL_CYCLES, QtCore.SIGNAL('dataChanged'), self.handle_AWA_TOTAL_CYCLES_changed)
if DEVEL:
folder = self.openFolder(folderFunction='controlParameters', title='Developer')
tooltip = 'There is a bug if you see this section'
self.createLine(['subtitle', 'Developer options', tooltip])
self.openSubFrame(frame=[True])
# reload_me_path = os.path.relpath(reload_me.__file__, os.path.join(os.environ['CCP4'], 'share'))
# self.createLine([
# 'widget', 'AWA_PRESSME',
# 'label', 'reload new code (%s)' %reload_me_path])
self.createLine([
'widget', 'AWA_MOCKYES',
'label', 'mock run using precalculated results from PSP example'])
self.createLine([
'widget', 'AWA_JSRVIEW',
'label', 'show report in jsrview'],
toggle = [] if notoggle else ['AWA_MOCKYES', 'open', [True]])
self.createLine([
'label', 'Pause for',
'widget', 'AWA_MOCKPAUSE',
'label', 'millisecond after each line read from the log file'],
toggle = [] if notoggle else ['AWA_MOCKYES', 'open', [True]])
self.closeSubFrame()
self.closeFolder()
# if self.isEditable():
# self.getWidget('AWA_PRESSME').widget.clicked.connect(self.reload_handlers)
# if DEVEL:
# def reload_handlers(self):
# reload(reload_me)
# self.getWidget('AWA_PRESSME').widget.setChecked(False)
# print 'reloaded'
# self.example()
# # A code in reload_me.py can be edited without turning off the interface and reloaded by pressing reload button.
# # When the code is debugged, just substitute functions from reload_me for corresponding functions in this file.
# def example(self):
# reload_me.example(self)
def handle_AWA_TOTAL_CYCLES_changed(self):
small = self.container.controlParameters.AWA_SMALL_CYCLES.get()
big = self.container.controlParameters.AWA_BIG_CYCLES.get()
text = 'ARP-REFMAC cycles'
if type(small) is int and type(big) is int:
text = 'ARP-REFMAC cycles (%d cycles in total)' %(small* big)
self.label_set('AWA_TOTAL_CYCLES', text)
def label_init(self, varname, line, index, default):
container = getattr(self.container.guiParameters, varname)
widget = line.layout().itemAt(index).widget()
setattr(self, 'label_' + varname, (container, widget))
text = default
if container.isSet():
value = str(container.get())
if value:
text = value
self.label_set(varname, text)
def label_set(self, varname, text):
container, widget = getattr(self, 'label_' + varname)
container.set(text)
widget.setText(text)
def handle_AWA_ARP_MODE_changed(self):
use_xyz = self.container.controlParameters.AWA_ARP_MODE == 'WARPNTRACEMODEL'
self.update_requirements(('AWA_MODELIN', 'AWA_PHINI'), ('AWA_MODELIN',) if use_xyz else ('AWA_PHINI',))
def handle_AWA_REF_MODE_changed(self):
use_ano = self.container.controlParameters.AWA_REF_MODE == 'AWA_SAD'
use_none = self.container.controlParameters.AWA_REF_MODE == 'AWA_REFML'
self.update_requirements(('AWA_HEAVYIN', 'AWA_PHREF'), ('AWA_HEAVYIN',) if use_ano else ('AWA_PHREF',) if not use_none else ())
qlt = 'As anomalous Fs' if use_ano else 'As mean Fs'
self.container.inputData.AWA_FOBS.setQualifier('guiLabel', qlt)
self.getWidget('AWA_FOBS').layout().itemAt(1).widget().setText(qlt)
def update_requirements(self, list_all, list_required):
for key in list_all:
qf = self.getWidget(key)
qcb = getattr(qf, 'jobCombo', None)
if qcb:
cdf_is_required = key in list_required
cdf_was_required = qf.model.qualifiers('mustExist')
if cdf_is_required is not cdf_was_required:
cdf = getattr(self.container.inputData, key)
cdf.setQualifier('allowUndefined', not cdf_is_required)
cdf.setQualifier('mustExist', cdf_is_required)
qcb.setItemText(qcb.findData(QtCore.QVariant(-1)), '.. must be selected' if cdf_is_required else '.. is not used')
qf.validate()
def handle_AWA_FOBS_changed(self):
type_dict = getattr(self, 'type_dict', dict(GLGL=1, KMKM=2, JQ=3, FQ=4))
obs_cdf = self.container.inputData.AWA_FOBS
obs_cdf.loadFile()
old_type = getattr(self, 'type', None)
self.type = type_dict.get(obs_cdf.fileContent.columnSignature(), None)
type_changed = self.type != old_type
old_wavelength = getattr(self, 'wavelength', None)
wavelength_list = obs_cdf.fileContent._value['wavelengths']
self.wavelength = wavelength_list[-1] if wavelength_list else None
wavelength_changed = self.wavelength != old_wavelength
cryst_data = obs_cdf.getFileContent()._value
old_symm = getattr(self, 'symm', None)
self.symm = cryst_data['spaceGroup']._value
cell_dict = cryst_data['cell']._value
old_cell = getattr(self, 'cell', [None]* 6)
cell_keys = ('a', 'b', 'c', 'alpha', 'beta', 'gamma')
self.cell = [cell_dict[key]._value for key in cell_keys]
cell_defined = sum([bool(x) for x in self.cell]) == 6
cell_label = ' '.join(["%s= %6.2d" %kv for kv in zip(cell_keys, self.cell)]) if cell_defined else 'Cell: N/A'
if SHOW_NOTIMPLEMENTED:
self.label_set('AWA_CELL', cell_label)
self.max_residue_count = getattr(self, 'max_residue_count', None)
old_max_residue_count = self.max_residue_count
if self.symm != old_symm or self.cell != old_cell:
self.max_residue_count = None
if self.type:
p = subprocess.Popen('matthews_coef', stdin=subprocess.PIPE, stdout=subprocess.PIPE, stderr=subprocess.PIPE)
p.stdin.write('cell %s\n' %' '.join([str(par) for par in self.cell]))
p.stdin.write('symm "%s"\n' %self.symm)
p.stdin.write('end\n')
out, err = p.communicate()
self.re_weight = re.compile(" The Molecular weight is estimated as: *([0-9]*\.[0-9]*) Daltons.")
result = self.re_weight.search(out)
if result:
average_weight, = result.groups()
max_weight = float(average_weight)/ 0.53
self.max_residue_count = int(max_weight/ 112.5)
if self.max_residue_count != old_max_residue_count:
self.handle_au_content_changed()
if type_changed:
obs_bg_method = getattr(self.getWidget('AWA_REF_MODE').widget, 'buttons', None)
if obs_bg_method is not None:
for obs_button in self.getWidget('AWA_REF_MODE').widget.buttons():
value = str(obs_button.objectName())
if value == 'AWA_REFML':
obs_button_none = obs_button
elif value == 'AWA_SAD':
obs_button_ano = obs_button
obs_was_ano = obs_button_ano.isEnabled()
obs_is_ano = self.type in (None, 1, 2)
if not obs_was_ano and obs_is_ano:
obs_button_ano.setEnabled(True)
elif obs_was_ano and not obs_is_ano:
if obs_button_ano.isChecked():
obs_button_none.click()
obs_button_ano.setEnabled(False)
#self.container.controlParameters.AWA_SCAT_LAMBDA_AWA_SAD.setQualifier('allowUndefined', not obs_is_ano)
self.getWidget('AWA_SCAT_LAMBDA_AWA_SAD').widget.editingFinished.emit()
if wavelength_changed:
wl_widget = self.getWidget('AWA_SCAT_LAMBDA_AWA_SAD').widget
wl_widget.setText(str(round(self.wavelength, 6)) if self.wavelength != None else '1.0')
wl_widget.editingFinished.emit()
def handle_AWA_SEQIN_changed(self):
self.mol_residue_count = None
if self.container.inputData.AWA_SEQIN.isSet():
try:
seq_records = SeqIO.parse(str(self.container.inputData.AWA_SEQIN), 'fasta')
self.mol_residue_count = sum(len(record.seq) for record in seq_records)
except:
print 'error in sequence parsing ignoorred'
nres_widget = self.getWidget('AWA_NRES').widget
nres_widget.setText(str(self.mol_residue_count) if self.mol_residue_count else '')
nres_widget.editingFinished.emit()
def handle_AWA_NRES_changed(self):
self.mol_residue_count = self.container.controlParameters.AWA_NRES._value
self.handle_au_content_changed()
def handle_au_content_changed(self):
self.mol_residue_count = getattr(self, 'mol_residue_count', None)
self.max_residue_count = getattr(self, 'max_residue_count', None)
self.molecule_count = None
if self.max_residue_count and self.mol_residue_count:
cou1 = self.max_residue_count/ (2* self.mol_residue_count)
cou2 = cou1 + 1
dif1 = 0.5 - float(self.mol_residue_count* cou1)/ self.max_residue_count
dif2 = 0.5 - float(self.mol_residue_count* cou2)/ self.max_residue_count
self.molecule_count = cou1 if abs(dif1) < abs(dif2) else cou2
nmol_widget = self.getWidget('AWA_NMOL').widget
nmol_widget.setText(str(self.molecule_count) if self.molecule_count != None else '')
nmol_widget.editingFinished.emit()
self.handle_solv_changed()
def handle_AWA_NMOL_changed(self):
self.molecule_count = self.container.controlParameters.AWA_NMOL._value
self.handle_solv_changed()
def handle_solv_changed(self):
solv_widget = self.au_content_line.layout().itemAt(3).widget()
text_solv = 'copies in the AU.'
if self.max_residue_count != None and self.mol_residue_count != None and self.molecule_count != None:
solvent = 100.0 - 100.0* float(self.mol_residue_count* self.molecule_count)/ self.max_residue_count
text_solv = 'copies in the AU and solvent content of %s%%.' %(int(solvent))
solv_widget.setText(text_solv)
def AWA_SEQIN_isset(self):
return self.container.inputData.AWA_SEQIN.isSet()
def AWA_FREE_isset(self):
return self.container.inputData.AWA_FREE.isSet()