Exemplo n.º 1
0
with work_manager:
    if work_manager.is_master:    
        # Process target states
        target_states = []
        if args.tstate_file:
            target_states.extend(TargetState.states_from_file(args.tstate_file, system.pcoord_dtype))
        if args.tstates:
            tstates_strio = cStringIO.StringIO('\n'.join(args.tstates).replace(',', ' '))
            target_states.extend(TargetState.states_from_file(tstates_strio, system.pcoord_dtype))
            del tstates_strio
                    
        # Process basis states
        basis_states = []
        if args.bstate_file:
            basis_states.extend(BasisState.states_from_file(args.bstate_file))
        if args.bstates:
            for bstate_str in args.bstates:
                fields = bstate_str.split(',')
                label=fields[0]
                probability=float(fields[1])
                try:
                    auxref = fields[2]
                except IndexError:
                    auxref = None
                basis_states.append(BasisState(label=label,probability=probability,auxref=auxref))
        
        if not basis_states:
            log.error('At least one basis state is required')
            sys.exit(3)
        
Exemplo n.º 2
0
        if args.tstate_file:
            target_states.extend(
                TargetState.states_from_file(args.tstate_file,
                                             system.pcoord_dtype))
        if args.tstates:
            tstates_strio = io.StringIO('\n'.join(args.tstates).replace(
                ',', ' '))
            target_states.extend(
                TargetState.states_from_file(tstates_strio,
                                             system.pcoord_dtype))
            del tstates_strio

        # Process basis states
        basis_states = []
        if args.bstate_file:
            basis_states.extend(BasisState.states_from_file(args.bstate_file))
        if args.bstates:
            for bstate_str in args.bstates:
                fields = bstate_str.split(',')
                label = fields[0]
                probability = float(fields[1])
                try:
                    auxref = fields[2]
                except IndexError:
                    auxref = None
                basis_states.append(
                    BasisState(label=label,
                               probability=probability,
                               auxref=auxref))

        if not basis_states:
    westpa.rc.process_args(args)

    system = west.rc.get_system_driver()
    data_manager = west.rc.get_data_manager()
    h5file = data_manager.we_h5filename
    try:
        os.unlink(h5file)
    except OSError as e:
        pass
    data_manager.prepare_backing()

    uv = MDAnalysis.Universe(args.template_file)

    bstate = BasisState('extsim',
                        1.0,
                        pcoord=[0.0, 0.0, 0.0, 0.0],
                        auxref=args.basis_file,
                        state_id=0)
    data_manager.create_ibstate_group([bstate])

    basis_h5 = h5py.File(args.basis_file, 'r')
    bs_norm_rmsd = basis_h5['normal_rmsd'][...]
    min_dist = basis_h5['mindist'][...]
    bs_side_chain = basis_h5['side_rmsd'][...]
    bs_ca = basis_h5['ca_rmsd'][...]
    coord_ds = basis_h5['coords']
    all_weight = basis_h5['weight'][...]
    print('Total weight of all possible structures: {}'.format(
        all_weight.sum()))
    all_pcoord = numpy.column_stack(
        [min_dist, bs_norm_rmsd, bs_ca, bs_side_chain])
Exemplo n.º 4
0
    if work_manager.is_master:
        data_manager = westpa.rc.get_data_manager()
        data_manager.open_backing(mode='a')
        sim_manager = westpa.rc.get_sim_manager()
        n_iter = data_manager.current_iteration

        assert args.mode in ('show', 'replace', 'append')
        if args.mode == 'show':

            basis_states = data_manager.get_basis_states(n_iter)
            if basis_states:
                bstate_file = sys.stdout if not args.bstate_file else open(
                    args.bstate_file, 'wt')
                bstate_file.write(
                    '# Basis states for iteration {:d}\n'.format(n_iter))
                BasisState.states_to_file(basis_states, bstate_file)

            target_states = data_manager.get_target_states(n_iter)
            if target_states:
                tstate_file = sys.stdout if not args.tstate_file else open(
                    args.tstate_file, 'wt')
                tstate_file.write(
                    '# Target states for iteration {:d}\n'.format(n_iter))
                TargetState.states_to_file(target_states, tstate_file)

        elif args.mode == 'replace':
            seg_index = data_manager.get_seg_index(n_iter)
            if (seg_index['status'] == Segment.SEG_STATUS_COMPLETE).any():
                print(
                    'Iteration {:d} has completed segments; applying new states to iteration {:d}'
                    .format(n_iter, n_iter + 1))
Exemplo n.º 5
0
with work_manager:
    if work_manager.is_master:
        data_manager = westpa.rc.get_data_manager()
        data_manager.open_backing(mode='a')
        sim_manager = westpa.rc.get_sim_manager()
        n_iter = data_manager.current_iteration
            
        assert args.mode in ('show', 'replace', 'append')
        if args.mode == 'show':
    
            basis_states = data_manager.get_basis_states(n_iter)
            if basis_states:
                bstate_file = sys.stdout if not args.bstate_file else open(args.bstate_file, 'wt')
                bstate_file.write('# Basis states for iteration {:d}\n'.format(n_iter))
                BasisState.states_to_file(basis_states, bstate_file)
            
            target_states = data_manager.get_target_states(n_iter)
            if target_states:
                tstate_file = sys.stdout if not args.tstate_file else open(args.tstate_file, 'wt')
                tstate_file.write('# Target states for iteration {:d}\n'.format(n_iter))
                TargetState.states_to_file(target_states, tstate_file)
                
        elif args.mode == 'replace':
            seg_index = data_manager.get_seg_index(n_iter)
            if (seg_index['status'] == Segment.SEG_STATUS_COMPLETE).any():
                print('Iteration {:d} has completed segments; applying new states to iteration {:d}'.format(n_iter,n_iter+1))
                n_iter += 1
            
            basis_states = []
            if args.bstate_file: