import copy,subprocess,os,uuid,time,glob
import numpy as np
from io import StringIO
import pylab as plt
from dask.distributed import as_completed
from py4xs.utils import run
    
def extract_vals(txt, dtype=float, strip=None, debug=False):
    if strip is not None:
        txt = txt.replace(strip, " ")
    sl = txt.split(" ")
    ret = []
    for ss in sl:
        try:
            val = dtype(ss)
        except:
            pass
        else:
            ret.append(val)
    return ret
    
def atsas_create_temp_file(fn, d1s, skip=0, q_cutoff=0.6):
    idx = (d1s.qgrid<=q_cutoff)
    np.savetxt(fn, np.vstack([d1s.qgrid[idx][skip:], d1s.data[idx][skip:], d1s.err[idx][skip:]]).T)
    
def atsas_autorg(fn, debug=False, path=""):
    ret = run(["autorg", fn], path).split('\n')
    #rg,drg = extract_vals(ret[0], "+/-", debug=debug)
    #i0,di0 = extract_vals(ret[1], "+/-", debug=debug)
    #n1,n2 = extract_vals(ret[2], " to ", debug=debug, dtype=int)
    #qual = extract_vals(ret[3], "%", debug=debug)
    try:
        rg,drg = extract_vals(ret[0])
        i0,di0 = extract_vals(ret[1])
        n1,n2 = extract_vals(ret[2], dtype=int)
        qual = extract_vals(ret[3], strip="%")[0]
    except:
        print("Unable to run autorg ...")
        rg,drg = 0,0
        i0,di0 = 0,0
        n1,n2 = 0,-1
        qual = 0
    
    return {"Rg": rg, "Rg err": drg, 
            "I0": i0, "I0 err": di0,
            "fit range": [n1,n2],
            "quality": qual}

def atsas_datgnom(fn, rg, first, last=None, fn_out=None, path=""):
    """ 
    """
    if fn_out is None:
        fn_out = fn.split('.')[0]+'.out'    
    options = ["-r", str(rg), "-o", fn_out, "--first", str(first)]
    if last is not None:
        options += ["--last", str(last)]
    
    # datgnom vs datgnom4, slightly different input parameters
    ret = run(["datgnom", *options, fn], path).split("\n")
    try:
        if len(ret)>1:
            # example stdout results:
            #    dmax:   50.170000000000002       Total:  0.90463013315175844     
            #    Guinier:   15.332727107179052       Gnom:   15.332431498444064   
            dmax,qual = extract_vals(ret[0])
            rgg,rgp = extract_vals(ret[1])
        else: 
            # newer version of datgnom no longer reports Dmax/Rg on stdout,
            # the .out file format is also different
            # the Rg/Dmax values used to be located at the end of the file:
            #    Total  estimate : 0.944  which is  AN EXCELLENT  solution
            #    Reciprocal space: Rg =   14.75     , I(0) =   0.5740E+01
            #    Real space: Rg =   14.74 +- 0.092  I(0) =   0.5740E+01 +-  0.2274E-01
            # in the more recent files, this info in embedded in the header
            #    Total Estimate:                      0.9546 (a EXCELLENT solution)
            #    Reciprocal space Rg:             0.1471E+02
            #    Reciprocal space I(0):           0.5733E+01
            #    Real space range:                    0.0000 to      45.9000
            #    Real space Rg:                   0.1470E+02 +-   0.1148E+00
            #    Real space I(0):                 0.5733E+01 +-   0.2619E-01
            qual = extract_vals(run(["grep", "Total Estimate", fn_out], path))[0]
            dmax = extract_vals(run(["grep", "Real space range", fn_out], path))[1]
            rgg = extract_vals(run(["grep", "Reciprocal space Rg", fn_out], path))[0]
            rgp = extract_vals(run(["grep", "Real space Rg", fn_out], path))[0]
    except:
        qual = 0
        dmax = 100
        rgg = 0
        rgp = 0
    
    return {"Dmax": dmax, "quality": qual, 
            "Rg (q)": rgg, "Rg (r)": rgp}

def read_arr_from_strings(lines, cols=[0,1,2]):
    """ assuming that any none numerical values will be ignored
        data are in multiple columns
        some columns may be missing values at the top
        for P(r), cols=[0,1,2]
        for I_fit(q), cols=[0,-1]
    """
    ret = []
    for buf in lines:
        if len(buf)<len(cols):  # empty line
            continue        
        tb = np.genfromtxt(StringIO(buf))
        if np.isnan(tb).any():   # mixed text and numbersS          J EXP       ERROR       J REG       I REG
            continue
        ret.append([tb[i] for i in cols])
    return np.asarray(ret).T

def read_gnom_out_file(fn, plot_pr=False, ax=None):
    ff = open(fn, "r")
    tt = ff.read()
    ff.close()
    
    hdr,t1 = tt.split("####      Experimental Data and Fit                     ####")
    #hdr,t1 = tt.split("S          J EXP       ERROR       J REG       I REG")
    iq, pr = t1.split("####      Real Space Data                               ####")
    #iq, pr = t1.split("Distance distribution  function of particle")
    di, dq = read_arr_from_strings(iq.rstrip().split("\n"), cols=[0,-1])
    dr, dpr, dpre = read_arr_from_strings(pr.rstrip().split("\n"), cols=[0,1,2])
    
    if plot_pr:
        if ax is None:
            plt.figure()
            ax = plt.gca()
        ax.errorbar(dr, dpr, dpre)
    
    return hdr.rstrip(),di,dq,dr,dpr,dpre

# ALMERGE   Automatically merges data collected from two different concentrations or 
#           extrapolates it to infinite dilution assuming moderate particle interactions.
#

""" version-dependent output 

$ datporod --version
datporod, ATSAS 2.8.5 (r11116)
Copyright (c) ATSAS Team, EMBL, Hamburg Outstation 2009-2018

$ datporod --help
Usage: datporod [OPTIONS] [FILE(S)]

Estimation of Porod volume. Output values are Rg, I0, estimated Volume and file name.

Known Arguments:
  FILE                       Data file

Known Options:
      --i0=<VALUE>           Forward scattering intensity
      --rg=<VALUE>           Experimental Radius of Gyration
      --first=<N>            index of the first point to be used (default: 1)
      --last=<N>             index of the last point to be used (default: s*Rg ~ 7)
  -h, --help                 Print usage information and exit
  -v, --version              Print version information and exit

Mandatory arguments to long options are mandatory for short options too.


$ datporod --version
datporod, ATSAS 3.0.1 (r12314)
Copyright (c) ATSAS Team, EMBL, Hamburg Outstation 2009-2020

$ datporod --help
Usage: datporod [OPTIONS] [FILE(S)]

Molecular weight from Porod Volume 
Output: smax (A^-1), Volume (A^3), file name

Known Arguments:
  FILE                       Data file

Known Options:
      --i0=<VALUE>           Forward scattering intensity
      --rg=<VALUE>           Experimental Radius of Gyration
      --first=<N>            index of the first point to be used (default: 1)
      --last=<N>             index of the last point to be used (default: s*Rg ~ 7)
  -h, --help                 Print usage information and exit
  -v, --version              Print version information and exit

Mandatory arguments to long options are mandatory for short options too.



datmow --version
datmow, ATSAS 2.8.5 (r11116)
Copyright (c) ATSAS Team, EMBL, Hamburg Outstation 2014-2018

$ datmow --help
Usage: datmow [OPTIONS] [FILE(S)]

Output: Q', V' (apparent Volume), V (Volume, A^3), MW (Da), file name

Known Arguments:
  FILE                       Data file

Known Options:
      --i0=<VALUE>           Forward scattering intensity
      --rg=<VALUE>           Experimental Radius of Gyration
      --rho=<VALUE>          Average protein density (default: 1.37 g/cm^-3)
  -a, --offset=<VALUE>       Offset coefficient (default: look up)
  -b, --scaling=<VALUE>      Scaling coefficient (default: look up)
  -h, --help                 Print usage information and exit
  -v, --version              Print version information and exit

Mandatory arguments to long options are mandatory for short options too.


$ datmow --version
datmow, ATSAS 3.0.1 (r12314)
Copyright (c) ATSAS Team, EMBL, Hamburg Outstation 2014-2020

$ datmow --help
Usage: datmow [OPTIONS] [FILE(S)]

Molecular weight from Apparent Volume (Fischer et al., 2010).
Output: smax (A^-1), Q', V' (apparent volume), V (Volume, A^3), MW (Da), file name

Known Arguments:
  FILE                       Data file

Known Options:
      --i0=<VALUE>           Forward scattering intensity
      --rg=<VALUE>           Experimental Radius of Gyration
      --first=<N>            index of the first point to be used (default: 1)
  -h, --help                 Print usage information and exit
  -v, --version              Print version information and exit

Mandatory arguments to long options are mandatory for short options too.


"""

def atsas_dat_tools(fn_out, path=""):
    # datporod: the used Rg, I0, the computed volume estimate and the input file name
    #
    # datvc: the first three numbers are the integrated intensities up to 0.2, 0.25 and 0.3, respectively. 
    #        the second three numbers the corresponding MW estimates
    #
    # datmow: Output: Q', V' (apparent Volume), V (Volume, A^3), MW (Da), file name
    ret = run(["datporod", fn_out], path).split('\n')
    try:
        Vv = extract_vals(ret[0])[-1]
        r_porod = {"vol": Vv}
    except:
        r_porod = {"vol": np.nan}
        print("Unable to get output from datporod ...")
    
    #ret = run(f"datvc {fn_out}").split('\n')
    #try:
    #    ii1,ii2,ii3,mw1,mw2,mw3 = extract_vals(ret[0])
    #    r_vc = {"MW": [mw1, mw2, mw3]}
    #except:
    #    print("Unable to get output from datvc ...")
    
    ret = run(["datmow", fn_out], path).split('\n')
    try:
        Qp,Vp,Vv,mw = extract_vals(ret[0])[-4:]
        r_mow = {"Q": Qp, "app vol": Vp, "vol": Vv, "MW": mw}
    except:
        r_mow = {"Q": np.nan, "app vol": np.nan, "vol": np.nan, "MW": np.nan}
        print("Unable to get output from datmow ...")

    return {"datporod": r_porod, 
            #"datvc": r_vc,  # this won't work if q_max is below 0.3 
            "datmow": r_mow}


def gen_atsas_report(d1s, ax=None, fig=None, sn=None, skip=0, q_cutoff=0.6, print_results=True, path=""):
    if ax is None:
        ax = []
        if fig is None:
            fig = plt.figure(figsize=(9,3))
        # rect = l, b, w, h
        ax.append(fig.add_axes([0.09, 0.25, 0.25, 0.6])) 
        ax.append(fig.add_axes([0.41, 0.25, 0.25, 0.6])) 
        ax.append(fig.add_axes([0.73, 0.25, 0.25, 0.6])) 
    else:
        for a in ax:
            a.clear()
    
    if sn is None:
        tfn = "processed/t.dat"
        tfn_out = "processed/t.out"
    else:
        tfn = "processed/t.dat"
        tfn_out = f"processed/{sn}.out"
    atsas_create_temp_file(tfn, d1s, skip=skip, q_cutoff=q_cutoff)

    re_autorg = atsas_autorg(tfn, path=path)
    re_gnom = atsas_datgnom(tfn, re_autorg["Rg"], first=skip+1,
                            last=len(d1s.qgrid[d1s.qgrid<=q_cutoff]), fn_out=tfn_out, path=path)
    try:
        hdr,di,dq,dr,dpr,dpre = read_gnom_out_file(tfn_out)
    except: # this would happen if gnom fails to run
        hdr,di,dq,dr,dpr,dpre = 0,0,0,0,0,0
        
    idx = (d1s.qgrid<q_cutoff)
    ax[0].semilogy(di, dq)
    ax[0].errorbar(d1s.qgrid[idx], d1s.data[idx], d1s.err[idx])
    #ax[0].yaxis.set_major_formatter(plt.NullFormatter())
    #ax[0].set_title("intensity")
    ax[0].set_xlabel(r"$q$")
    if re_autorg["Rg"]>0 and di is not None:
        axx = ax[0].twiny()
        Rg = re_autorg["Rg"] 
        I0 = re_autorg["I0"]
        n1,n2 = re_autorg["fit range"]
        qf = d1s.qgrid[n1:n2]
        gf = I0*np.exp(-(qf*Rg)**2/3)*2
        idx = (d1s.qgrid<1.5/re_autorg["Rg"])
        axx.errorbar(d1s.qgrid[idx]**2, d1s.data[idx]*2, d1s.err[idx], fmt="b.")
        axx.plot(qf*qf, gf, "k")
        axx.set_xlim(0, 3*(1.5/re_autorg["Rg"])**2)
        axx.set_xlabel(r"$q^2$", loc='right')
        locs = axx.get_xticks()
        #if len(locs>6):
        #    locs = locs[::2]
        labels = [str(t) for t in locs]
        axx.set_xticks(locs[:-2])
        axx.set_xticklabels(labels[:-2])
    
    if re_autorg["Rg"]==0:
        kratky_qm=0.3
        idx = (d1s.qgrid<kratky_qm)
        ax[1].plot(d1s.qgrid[idx], d1s.data[idx]*np.power(d1s.qgrid[idx], 2))
        ax[1].set_xlabel(r"$q$")
    else:
        kratky_qm=10./re_autorg["Rg"]
        idx = (d1s.qgrid<kratky_qm)
        ax[1].plot(d1s.qgrid[idx]*re_autorg["Rg"], d1s.data[idx]*np.power(d1s.qgrid[idx], 2))
        ax[1].set_xlabel(r"$q %times Rg$")    
    ax[1].yaxis.set_major_formatter(plt.NullFormatter())
    ax[1].set_title("kratky plot")

    ax[2].errorbar(dr, dpr, dpre)
    ax[2].yaxis.set_major_formatter(plt.NullFormatter())
    ax[2].set_title(r"$P(r)$")
    ax[2].set_xlabel(r"$r$")

    ret = atsas_dat_tools(tfn_out, path=path)
    if print_results:
        print(f"Gunier fit: quality = {re_autorg['quality']} %,", end=" ")
        print(f"I0 = {re_autorg['I0']:.2f} +/- {re_autorg['I0 err']:.2f} , ", end="")
        print(f"Rg = {re_autorg['Rg']:.2f} +/- {re_autorg['Rg err']:.2f}")
        print(f"GNOM fit: quality = {re_gnom['quality']:.2f}, Dmax = {re_gnom['Dmax']:.2f}, Rg = {re_gnom['Rg (r)']:.2f}")
        print(f"Volume estimate: {ret['datporod']['vol']:.1f} (datporod), {ret['datmow']['vol']:.1f} (MoW)")
        print(f"MW estimate: {ret['datmow']['MW']/1000:.1f} kDa (MoW)")          
    else:
        txt = f"Gunier fit: quality = {re_autorg['quality']} %, "
        txt += f"I0 = {re_autorg['I0']:.2f} +/- {re_autorg['I0 err']:.2f} , "
        txt += f"Rg = {re_autorg['Rg']:.2f} +/- {re_autorg['Rg err']:.2f}\n"
        txt += f"GNOM fit: quality = {re_gnom['quality']:.2f}, Dmax = {re_gnom['Dmax']:.2f}, Rg = {re_gnom['Rg (r)']:.2f}\n"
        txt += f"Volume estimate: {ret['datporod']['vol']:.1f} (datporod), {ret['datmow']['vol']:.1f} (MoW)\n"
        txt += f"MW estimate: {ret['datmow']['MW']/1000:.1f} kDa (MoW)"          
        return txt
              
def create_uid():
    ww,mm,dd,tt,yy = time.asctime().split(' ')
    return f"{yy}{mm}{dd}-{tt}-{str(uuid.uuid4())[:8]}"


def run_task(client, cmd, cwd, prerequire=[], shell=False, quiet=False):
    """ run cmd, in cwd
        cmd should be a list (*args), if shell is False
        when wildcards are used, shell should be Ture, and cmd is just a string
        prerequire is a list of futures that must be gathered before the cmd can run
    """
    if not quiet:
        print(f"starting job {cmd} in {cwd}")
    client.gather(prerequire)
    return client.submit(subprocess.run, cmd,
                         stdout=subprocess.PIPE,stderr=subprocess.STDOUT,
                         shell=shell, check=True, cwd=cwd, key=create_uid())
        
#server_atsas_path = "/opt/apps/ATSAS/2.8.5-0"
server_atsas_path = "/usr"

def getNSD(msg):
    # msg is the output from supcomb 
    # NSD appears to be the smalles value in the final distance column in the output
    # Read file .............................................. : t-00-1.pdb
    # Number of atoms ........................................ : 236
    # Fineness of the structure .............................. : 8.400
    # Read file .............................................. : t-01-1.pdb
    # Number of atoms ........................................ : 236
    # Fineness of the structure .............................. : 8.400
    #
    #                                Initial       Final
    #              Orientation      Distance    Distance
    #             1     1     1       1.3553      1.1500
    #             1     1    -1       1.2461      1.1552
    #             1    -1     1       1.4394      1.1577
    #             1    -1    -1       1.2884      1.1466
    #            -1     1     1       1.8763      1.5808
    #            -1     1    -1       1.9531      1.4054
    #            -1    -1     1       1.8619      1.4467
    #            -1    -1    -1       1.9294      1.4217
    #
    #                   Transformation matrix
    #         0.5193     -0.7225      0.4565     -0.9402
    #         0.0398     -0.5131     -0.8574     -6.5252
    #         0.8537      0.4634     -0.2377     -0.5459
    #         0.0000      0.0000      0.0000      1.0000
    #
    # Wrote file ............................................. : t-01-1r.pdb
    lines = msg.split("\n")
    nsd = -1
    for i in range(len(lines)):
        if lines[i].find("Distance")<0:
            continue
        vals = [float(lines[i+j+1].split(" ")[-1]) for j in range(8)]
        nsd = np.min(vals)
        break
    if nsd<0:
        raise Exception("could not find NSD")
    return nsd
    
    
def damaver(client, fns, cwd, prerequire, debug=False):
    """
    options: NOT YET IMPLEMENTED
        --symmetry=<SYMMETRY>
        --enantiomorphs=<YES|NO>
        --nbeads=<N> (damaver only)

    damaver(pdbs):
        loop over pdbi, pdbj:
            supcomb pdbi pdbj
        assemble NSD table
        discard files with nsd > Mean + 2*Standard deviation (damaver/damsel manual)
        loop over remaining pdbs pdbi, except for the ref:
            damsup pdb_ref pdbi
        damaver aligned_pdbs
        damfilt damaver.pdb
        damstart damaver.pdb    
    """

    npdb = len(fns)
    if npdb<2:
        return
    
    futures = []
    index = []
    print("calculating NSDs as models become available ...")
    #for i in range(npdb-1):
    #    for j in range(i+1, npdb):
    #        f = run_task(client,
    #                     cmd=[f"{server_atsas_path}/bin/supcomb", fns[i], fns[j], "-o", f"supcomb{i}-{j}.pdb"], 
    #                     cwd=cwd,
    #                     prerequire = [prerequire[i], prerequire[j]], quiet=True)
    #        futures.append(f)
    #        index.append([i,j])
    res_list = []
    for future,result in as_completed(prerequire, with_results=True):
        res_no = int(result.args[2][-2:]) # e.g. ['dammif', '--mode=FAST', '--prefix=t-03', '../t.out']
        res_list.append(res_no)
        print(f"model #{res_no:02d} completed ...")
        n = len(res_list)
        if n>2:
            for i in range(n-1):
                n1 = np.min([res_list[i], res_list[-1]])
                n2 = np.max([res_list[i], res_list[-1]])
                f = run_task(client,
                             cmd=[f"{server_atsas_path}/bin/supcomb", 
                                  fns[n1], fns[n2], 
                                  "-o", f"supcomb{n1}-{n2}.pdb"], 
                             cwd=cwd, quiet=True)
                futures.append(f)
                index.append([n1,n2])
    
    nsds = np.zeros([npdb, npdb])
    for i in range(len(futures)):
        i1,i2 = index[i]
        nsd = getNSD(futures[i].result().stdout.decode())
        nsds[i1][i2] = nsd
        nsds[i2][i1] = nsd
        if debug:
            print(f"NSD({i1:02d},{i2:02d}) = {nsd:.3f}")
    # average NSD for each structure
    for i in range(npdb):
        nsds[i][i] = np.average([nsds[i,j] for j in range(npdb) if j!=i])
    # damsel exclude structures with NSD-avg(NSD)>2*std
    dd = nsds.diagonal()
    if debug:
        print("averaged NSDs:", dd)
    selected = [i for i in range(npdb) if np.fabs(dd[i]-np.average(dd))<np.std(dd)*2]
    print("structures selected: ", selected)

    print("cleaning up ...")
    fns_list = [[f"{cwd}/supcomb{selected[0]}-{i}.pdb", f"{cwd}/{fns[i][:-4]}r.pdb"] for i in selected[1:]]
    futures = [client.submit(os.rename, *fns) for fns in fns_list]
    client.gather(futures)
    fn_list = client.submit(glob.glob, f"{cwd}/supcomb*-*.pdb").result()
    client.gather(client.submit(lambda x: [os.remove(x0) for x0 in x], fn_list))

    pdb_list = [fns[selected[0]]] + [f"{fns[i][:-4]}r.pdb" for i in selected[1:]]
    client.gather(run_task(client, cmd=[f"{server_atsas_path}/bin/damaver"] + pdb_list, cwd=cwd))
    client.gather(run_task(client, cmd=[f"{server_atsas_path}/bin/damfilt", "damaver.pdb"], cwd=cwd))
    client.gather(run_task(client, cmd=[f"{server_atsas_path}/bin/damstart", "damaver.pdb"], cwd=cwd))
    
    return selected
    
def model_data(client, fn, rep=10, subdir=None):
    """ repeat a bunch of dammif runs
        then run damaver on the results
    """
    
    if rep>99:
        rep = 99
    dfn = os.path.basename(fn)            # data file name
    sn = dfn[:-4]                         # sample name, strip off the .out extension from dfn
    if subdir is None:
        subdir = sn
    cwd = f"{os.path.dirname(fn)}/{subdir}"   # data file path
    if not os.path.exists(cwd):
        future = run_task(client, cmd=["mkdir", cwd], cwd="./")
        client.gather(future)
    
    dammif_cmds = [[f"{server_atsas_path}/bin/dammif", "--mode=FAST", 
                    f"--prefix={sn}-{i:02d}", f"../{dfn}"] for i in range(rep)]
    futures = [run_task(client, cmd=cmd, cwd=cwd) for cmd in dammif_cmds]
    
    print("starting damaver ...")
    damaver(client, [f"{sn}-{i:02d}-1.pdb" for i in range(rep)], cwd, futures)
    
    print("cleaning up ...") 
    # rename file to avoid future conflict
    fns = ["damaver.pdb", "damfilt.pdb", "damstart.pdb"]
    for fn in fns:
        client.gather(client.submit(os.rename, f"{cwd}/{fn}", f"{cwd}/{sn}-{fn}"))

    print("done")
import copy,subprocess,os,uuid,time,glob
import numpy as np
from io import StringIO
import pylab as plt
from dask.distributed import as_completed
from py4xs.utils import run
    
def extract_vals(txt, dtype=float, strip=None, debug=False):
    if strip is not None:
        txt = txt.replace(strip, " ")
    sl = txt.split(" ")
    ret = []
    for ss in sl:
        try:
            val = dtype(ss)
        except:
            pass
        else:
            ret.append(val)
    return ret
    
def atsas_create_temp_file(fn, d1s, skip=0, q_cutoff=0.6):
    idx = (d1s.qgrid<=q_cutoff)
    np.savetxt(fn, np.vstack([d1s.qgrid[idx][skip:], d1s.data[idx][skip:], d1s.err[idx][skip:]]).T)
    
def atsas_autorg(fn, debug=False, path=""):
    ret = run(["autorg", fn], path).split('\n')
    #rg,drg = extract_vals(ret[0], "+/-", debug=debug)
    #i0,di0 = extract_vals(ret[1], "+/-", debug=debug)
    #n1,n2 = extract_vals(ret[2], " to ", debug=debug, dtype=int)
    #qual = extract_vals(ret[3], "%", debug=debug)
    try:
        rg,drg = extract_vals(ret[0])
        i0,di0 = extract_vals(ret[1])
        n1,n2 = extract_vals(ret[2], dtype=int)
        qual = extract_vals(ret[3], strip="%")[0]
    except:
        print("Unable to run autorg ...")
        rg,drg = 0,0
        i0,di0 = 0,0
        n1,n2 = 0,-1
        qual = 0
    
    return {"Rg": rg, "Rg err": drg, 
            "I0": i0, "I0 err": di0,
            "fit range": [n1,n2],
            "quality": qual}

def atsas_datgnom(fn, rg, first, last=None, fn_out=None, path=""):
    """ 
    """
    if fn_out is None:
        fn_out = fn.split('.')[0]+'.out'    
    options = ["-r", str(rg), "-o", fn_out, "--first", str(first)]
    if last is not None:
        options += ["--last", str(last)]
    
    # datgnom vs datgnom4, slightly different input parameters
    ret = run(["datgnom", *options, fn], path).split("\n")
    try:
        if len(ret)>1:
            # example stdout results:
            #    dmax:   50.170000000000002       Total:  0.90463013315175844     
            #    Guinier:   15.332727107179052       Gnom:   15.332431498444064   
            dmax,qual = extract_vals(ret[0])
            rgg,rgp = extract_vals(ret[1])
        else: 
            # newer version of datgnom no longer reports Dmax/Rg on stdout,
            # the .out file format is also different
            # the Rg/Dmax values used to be located at the end of the file:
            #    Total  estimate : 0.944  which is  AN EXCELLENT  solution
            #    Reciprocal space: Rg =   14.75     , I(0) =   0.5740E+01
            #    Real space: Rg =   14.74 +- 0.092  I(0) =   0.5740E+01 +-  0.2274E-01
            # in the more recent files, this info in embedded in the header
            #    Total Estimate:                      0.9546 (a EXCELLENT solution)
            #    Reciprocal space Rg:             0.1471E+02
            #    Reciprocal space I(0):           0.5733E+01
            #    Real space range:                    0.0000 to      45.9000
            #    Real space Rg:                   0.1470E+02 +-   0.1148E+00
            #    Real space I(0):                 0.5733E+01 +-   0.2619E-01
            qual = extract_vals(run(["grep", "Total Estimate", fn_out], path))[0]
            dmax = extract_vals(run(["grep", "Real space range", fn_out], path))[1]
            rgg = extract_vals(run(["grep", "Reciprocal space Rg", fn_out], path))[0]
            rgp = extract_vals(run(["grep", "Real space Rg", fn_out], path))[0]
    except:
        qual = 0
        dmax = 100
        rgg = 0
        rgp = 0
    
    return {"Dmax": dmax, "quality": qual, 
            "Rg (q)": rgg, "Rg (r)": rgp}

def read_arr_from_strings(lines, cols=[0,1,2]):
    """ assuming that any none numerical values will be ignored
        data are in multiple columns
        some columns may be missing values at the top
        for P(r), cols=[0,1,2]
        for I_fit(q), cols=[0,-1]
    """
    ret = []
    for buf in lines:
        if len(buf)<len(cols):  # empty line
            continue        
        tb = np.genfromtxt(StringIO(buf))
        if np.isnan(tb).any():   # mixed text and numbersS          J EXP       ERROR       J REG       I REG
            continue
        ret.append([tb[i] for i in cols])
    return np.asarray(ret).T

def read_gnom_out_file(fn, plot_pr=False, ax=None):
    ff = open(fn, "r")
    tt = ff.read()
    ff.close()
    
    hdr,t1 = tt.split("####      Experimental Data and Fit                     ####")
    #hdr,t1 = tt.split("S          J EXP       ERROR       J REG       I REG")
    iq, pr = t1.split("####      Real Space Data                               ####")
    #iq, pr = t1.split("Distance distribution  function of particle")
    di, dq = read_arr_from_strings(iq.rstrip().split("\n"), cols=[0,-1])
    dr, dpr, dpre = read_arr_from_strings(pr.rstrip().split("\n"), cols=[0,1,2])
    
    if plot_pr:
        if ax is None:
            plt.figure()
            ax = plt.gca()
        ax.errorbar(dr, dpr, dpre)
    
    return hdr.rstrip(),di,dq,dr,dpr,dpre

# ALMERGE   Automatically merges data collected from two different concentrations or 
#           extrapolates it to infinite dilution assuming moderate particle interactions.
#

""" version-dependent output 

$ datporod --version
datporod, ATSAS 2.8.5 (r11116)
Copyright (c) ATSAS Team, EMBL, Hamburg Outstation 2009-2018

$ datporod --help
Usage: datporod [OPTIONS] [FILE(S)]

Estimation of Porod volume. Output values are Rg, I0, estimated Volume and file name.

Known Arguments:
  FILE                       Data file

Known Options:
      --i0=<VALUE>           Forward scattering intensity
      --rg=<VALUE>           Experimental Radius of Gyration
      --first=<N>            index of the first point to be used (default: 1)
      --last=<N>             index of the last point to be used (default: s*Rg ~ 7)
  -h, --help                 Print usage information and exit
  -v, --version              Print version information and exit

Mandatory arguments to long options are mandatory for short options too.


$ datporod --version
datporod, ATSAS 3.0.1 (r12314)
Copyright (c) ATSAS Team, EMBL, Hamburg Outstation 2009-2020

$ datporod --help
Usage: datporod [OPTIONS] [FILE(S)]

Molecular weight from Porod Volume 
Output: smax (A^-1), Volume (A^3), file name

Known Arguments:
  FILE                       Data file

Known Options:
      --i0=<VALUE>           Forward scattering intensity
      --rg=<VALUE>           Experimental Radius of Gyration
      --first=<N>            index of the first point to be used (default: 1)
      --last=<N>             index of the last point to be used (default: s*Rg ~ 7)
  -h, --help                 Print usage information and exit
  -v, --version              Print version information and exit

Mandatory arguments to long options are mandatory for short options too.



datmow --version
datmow, ATSAS 2.8.5 (r11116)
Copyright (c) ATSAS Team, EMBL, Hamburg Outstation 2014-2018

$ datmow --help
Usage: datmow [OPTIONS] [FILE(S)]

Output: Q', V' (apparent Volume), V (Volume, A^3), MW (Da), file name

Known Arguments:
  FILE                       Data file

Known Options:
      --i0=<VALUE>           Forward scattering intensity
      --rg=<VALUE>           Experimental Radius of Gyration
      --rho=<VALUE>          Average protein density (default: 1.37 g/cm^-3)
  -a, --offset=<VALUE>       Offset coefficient (default: look up)
  -b, --scaling=<VALUE>      Scaling coefficient (default: look up)
  -h, --help                 Print usage information and exit
  -v, --version              Print version information and exit

Mandatory arguments to long options are mandatory for short options too.


$ datmow --version
datmow, ATSAS 3.0.1 (r12314)
Copyright (c) ATSAS Team, EMBL, Hamburg Outstation 2014-2020

$ datmow --help
Usage: datmow [OPTIONS] [FILE(S)]

Molecular weight from Apparent Volume (Fischer et al., 2010).
Output: smax (A^-1), Q', V' (apparent volume), V (Volume, A^3), MW (Da), file name

Known Arguments:
  FILE                       Data file

Known Options:
      --i0=<VALUE>           Forward scattering intensity
      --rg=<VALUE>           Experimental Radius of Gyration
      --first=<N>            index of the first point to be used (default: 1)
  -h, --help                 Print usage information and exit
  -v, --version              Print version information and exit

Mandatory arguments to long options are mandatory for short options too.


"""

def atsas_dat_tools(fn_out, path=""):
    # datporod: the used Rg, I0, the computed volume estimate and the input file name
    #
    # datvc: the first three numbers are the integrated intensities up to 0.2, 0.25 and 0.3, respectively. 
    #        the second three numbers the corresponding MW estimates
    #
    # datmow: Output: Q', V' (apparent Volume), V (Volume, A^3), MW (Da), file name
    ret = run(["datporod", fn_out], path).split('\n')
    try:
        Vv = extract_vals(ret[0])[-1]
        r_porod = {"vol": Vv}
    except:
        r_porod = {"vol": np.nan}
        print("Unable to get output from datporod ...")
    
    #ret = run(f"datvc {fn_out}").split('\n')
    #try:
    #    ii1,ii2,ii3,mw1,mw2,mw3 = extract_vals(ret[0])
    #    r_vc = {"MW": [mw1, mw2, mw3]}
    #except:
    #    print("Unable to get output from datvc ...")
    
    ret = run(["datmow", fn_out], path).split('\n')
    try:
        Qp,Vp,Vv,mw = extract_vals(ret[0])[-4:]
        r_mow = {"Q": Qp, "app vol": Vp, "vol": Vv, "MW": mw}
    except:
        r_mow = {"Q": np.nan, "app vol": np.nan, "vol": np.nan, "MW": np.nan}
        print("Unable to get output from datmow ...")

    return {"datporod": r_porod, 
            #"datvc": r_vc,  # this won't work if q_max is below 0.3 
            "datmow": r_mow}


def gen_atsas_report(d1s, ax=None, fig=None, sn=None, skip=0, q_cutoff=0.6, print_results=True, path=""):
    if ax is None:
        ax = []
        if fig is None:
            fig = plt.figure(figsize=(9,3))
        # rect = l, b, w, h
        ax.append(fig.add_axes([0.09, 0.25, 0.25, 0.6])) 
        ax.append(fig.add_axes([0.41, 0.25, 0.25, 0.6])) 
        ax.append(fig.add_axes([0.73, 0.25, 0.25, 0.6])) 
    else:
        for a in ax:
            a.clear()
    
    if sn is None:
        tfn = "processed/t.dat"
        tfn_out = "processed/t.out"
    else:
        tfn = "processed/t.dat"
        tfn_out = f"processed/{sn}.out"
    atsas_create_temp_file(tfn, d1s, skip=skip, q_cutoff=q_cutoff)

    re_autorg = atsas_autorg(tfn, path=path)
    re_gnom = atsas_datgnom(tfn, re_autorg["Rg"], first=skip+1,
                            last=len(d1s.qgrid[d1s.qgrid<=q_cutoff]), fn_out=tfn_out, path=path)
    try:
        hdr,di,dq,dr,dpr,dpre = read_gnom_out_file(tfn_out)
    except: # this would happen if gnom fails to run
        hdr,di,dq,dr,dpr,dpre = 0,0,0,0,0,0
        
    idx = (d1s.qgrid<q_cutoff)
    ax[0].semilogy(di, dq)
    ax[0].errorbar(d1s.qgrid[idx], d1s.data[idx], d1s.err[idx])
    #ax[0].yaxis.set_major_formatter(plt.NullFormatter())
    #ax[0].set_title("intensity")
    ax[0].set_xlabel(r"$q$")
    if re_autorg["Rg"]>0 and di is not None:
        axx = ax[0].twiny()
        Rg = re_autorg["Rg"] 
        I0 = re_autorg["I0"]
        n1,n2 = re_autorg["fit range"]
        qf = d1s.qgrid[n1:n2]
        gf = I0*np.exp(-(qf*Rg)**2/3)*2
        idx = (d1s.qgrid<1.5/re_autorg["Rg"])
        axx.errorbar(d1s.qgrid[idx]**2, d1s.data[idx]*2, d1s.err[idx], fmt="b.")
        axx.plot(qf*qf, gf, "k")
        axx.set_xlim(0, 3*(1.5/re_autorg["Rg"])**2)
        axx.set_xlabel(r"$q^2$", loc='right')
        locs = axx.get_xticks()
        #if len(locs>6):
        #    locs = locs[::2]
        labels = [str(t) for t in locs]
        axx.set_xticks(locs[:-2])
        axx.set_xticklabels(labels[:-2])
    
    if re_autorg["Rg"]==0:
        kratky_qm=0.3
        idx = (d1s.qgrid<kratky_qm)
        ax[1].plot(d1s.qgrid[idx], d1s.data[idx]*np.power(d1s.qgrid[idx], 2))
        ax[1].set_xlabel(r"$q$")
    else:
        kratky_qm=10./re_autorg["Rg"]
        idx = (d1s.qgrid<kratky_qm)
        ax[1].plot(d1s.qgrid[idx]*re_autorg["Rg"], d1s.data[idx]*np.power(d1s.qgrid[idx], 2))
        ax[1].set_xlabel(r"$q %times Rg$")    
    ax[1].yaxis.set_major_formatter(plt.NullFormatter())
    ax[1].set_title("kratky plot")

    ax[2].errorbar(dr, dpr, dpre)
    ax[2].yaxis.set_major_formatter(plt.NullFormatter())
    ax[2].set_title(r"$P(r)$")
    ax[2].set_xlabel(r"$r$")

    ret = atsas_dat_tools(tfn_out, path=path)
    if print_results:
        print(f"Gunier fit: quality = {re_autorg['quality']} %,", end=" ")
        print(f"I0 = {re_autorg['I0']:.2f} +/- {re_autorg['I0 err']:.2f} , ", end="")
        print(f"Rg = {re_autorg['Rg']:.2f} +/- {re_autorg['Rg err']:.2f}")
        print(f"GNOM fit: quality = {re_gnom['quality']:.2f}, Dmax = {re_gnom['Dmax']:.2f}, Rg = {re_gnom['Rg (r)']:.2f}")
        print(f"Volume estimate: {ret['datporod']['vol']:.1f} (datporod), {ret['datmow']['vol']:.1f} (MoW)")
        print(f"MW estimate: {ret['datmow']['MW']/1000:.1f} kDa (MoW)")          
    else:
        txt = f"Gunier fit: quality = {re_autorg['quality']} %, "
        txt += f"I0 = {re_autorg['I0']:.2f} +/- {re_autorg['I0 err']:.2f} , "
        txt += f"Rg = {re_autorg['Rg']:.2f} +/- {re_autorg['Rg err']:.2f}\n"
        txt += f"GNOM fit: quality = {re_gnom['quality']:.2f}, Dmax = {re_gnom['Dmax']:.2f}, Rg = {re_gnom['Rg (r)']:.2f}\n"
        txt += f"Volume estimate: {ret['datporod']['vol']:.1f} (datporod), {ret['datmow']['vol']:.1f} (MoW)\n"
        txt += f"MW estimate: {ret['datmow']['MW']/1000:.1f} kDa (MoW)"          
        return txt
              
def create_uid():
    ww,mm,dd,tt,yy = time.asctime().split(' ')
    return f"{yy}{mm}{dd}-{tt}-{str(uuid.uuid4())[:8]}"


def run_task(client, cmd, cwd, prerequire=[], shell=False, quiet=False):
    """ run cmd, in cwd
        cmd should be a list (*args), if shell is False
        when wildcards are used, shell should be Ture, and cmd is just a string
        prerequire is a list of futures that must be gathered before the cmd can run
    """
    if not quiet:
        print(f"starting job {cmd} in {cwd}")
    client.gather(prerequire)
    return client.submit(subprocess.run, cmd,
                         stdout=subprocess.PIPE,stderr=subprocess.STDOUT,
                         shell=shell, check=True, cwd=cwd, key=create_uid())
        
#server_atsas_path = "/opt/apps/ATSAS/2.8.5-0"
server_atsas_path = "/usr"

def getNSD(msg):
    # msg is the output from supcomb 
    # NSD appears to be the smalles value in the final distance column in the output
    # Read file .............................................. : t-00-1.pdb
    # Number of atoms ........................................ : 236
    # Fineness of the structure .............................. : 8.400
    # Read file .............................................. : t-01-1.pdb
    # Number of atoms ........................................ : 236
    # Fineness of the structure .............................. : 8.400
    #
    #                                Initial       Final
    #              Orientation      Distance    Distance
    #             1     1     1       1.3553      1.1500
    #             1     1    -1       1.2461      1.1552
    #             1    -1     1       1.4394      1.1577
    #             1    -1    -1       1.2884      1.1466
    #            -1     1     1       1.8763      1.5808
    #            -1     1    -1       1.9531      1.4054
    #            -1    -1     1       1.8619      1.4467
    #            -1    -1    -1       1.9294      1.4217
    #
    #                   Transformation matrix
    #         0.5193     -0.7225      0.4565     -0.9402
    #         0.0398     -0.5131     -0.8574     -6.5252
    #         0.8537      0.4634     -0.2377     -0.5459
    #         0.0000      0.0000      0.0000      1.0000
    #
    # Wrote file ............................................. : t-01-1r.pdb
    lines = msg.split("\n")
    nsd = -1
    for i in range(len(lines)):
        if lines[i].find("Distance")<0:
            continue
        vals = [float(lines[i+j+1].split(" ")[-1]) for j in range(8)]
        nsd = np.min(vals)
        break
    if nsd<0:
        raise Exception("could not find NSD")
    return nsd
    
    
def damaver(client, fns, cwd, prerequire, debug=False):
    """
    options: NOT YET IMPLEMENTED
        --symmetry=<SYMMETRY>
        --enantiomorphs=<YES|NO>
        --nbeads=<N> (damaver only)

    damaver(pdbs):
        loop over pdbi, pdbj:
            supcomb pdbi pdbj
        assemble NSD table
        discard files with nsd > Mean + 2*Standard deviation (damaver/damsel manual)
        loop over remaining pdbs pdbi, except for the ref:
            damsup pdb_ref pdbi
        damaver aligned_pdbs
        damfilt damaver.pdb
        damstart damaver.pdb    
    """

    npdb = len(fns)
    if npdb<2:
        return
    
    futures = []
    index = []
    print("calculating NSDs as models become available ...")
    #for i in range(npdb-1):
    #    for j in range(i+1, npdb):
    #        f = run_task(client,
    #                     cmd=[f"{server_atsas_path}/bin/supcomb", fns[i], fns[j], "-o", f"supcomb{i}-{j}.pdb"], 
    #                     cwd=cwd,
    #                     prerequire = [prerequire[i], prerequire[j]], quiet=True)
    #        futures.append(f)
    #        index.append([i,j])
    res_list = []
    for future,result in as_completed(prerequire, with_results=True):
        res_no = int(result.args[2][-2:]) # e.g. ['dammif', '--mode=FAST', '--prefix=t-03', '../t.out']
        res_list.append(res_no)
        print(f"model #{res_no:02d} completed ...")
        n = len(res_list)
        if n>2:
            for i in range(n-1):
                n1 = np.min([res_list[i], res_list[-1]])
                n2 = np.max([res_list[i], res_list[-1]])
                f = run_task(client,
                             cmd=[f"{server_atsas_path}/bin/supcomb", 
                                  fns[n1], fns[n2], 
                                  "-o", f"supcomb{n1}-{n2}.pdb"], 
                             cwd=cwd, quiet=True)
                futures.append(f)
                index.append([n1,n2])
    
    nsds = np.zeros([npdb, npdb])
    for i in range(len(futures)):
        i1,i2 = index[i]
        nsd = getNSD(futures[i].result().stdout.decode())
        nsds[i1][i2] = nsd
        nsds[i2][i1] = nsd
        if debug:
            print(f"NSD({i1:02d},{i2:02d}) = {nsd:.3f}")
    # average NSD for each structure
    for i in range(npdb):
        nsds[i][i] = np.average([nsds[i,j] for j in range(npdb) if j!=i])
    # damsel exclude structures with NSD-avg(NSD)>2*std
    dd = nsds.diagonal()
    if debug:
        print("averaged NSDs:", dd)
    selected = [i for i in range(npdb) if np.fabs(dd[i]-np.average(dd))<np.std(dd)*2]
    print("structures selected: ", selected)

    print("cleaning up ...")
    fns_list = [[f"{cwd}/supcomb{selected[0]}-{i}.pdb", f"{cwd}/{fns[i][:-4]}r.pdb"] for i in selected[1:]]
    futures = [client.submit(os.rename, *fns) for fns in fns_list]
    client.gather(futures)
    fn_list = client.submit(glob.glob, f"{cwd}/supcomb*-*.pdb").result()
    client.gather(client.submit(lambda x: [os.remove(x0) for x0 in x], fn_list))

    pdb_list = [fns[selected[0]]] + [f"{fns[i][:-4]}r.pdb" for i in selected[1:]]
    client.gather(run_task(client, cmd=[f"{server_atsas_path}/bin/damaver"] + pdb_list, cwd=cwd))
    client.gather(run_task(client, cmd=[f"{server_atsas_path}/bin/damfilt", "damaver.pdb"], cwd=cwd))
    client.gather(run_task(client, cmd=[f"{server_atsas_path}/bin/damstart", "damaver.pdb"], cwd=cwd))
    
    return selected
    
def model_data(client, fn, rep=10, subdir=None):
    """ repeat a bunch of dammif runs
        then run damaver on the results
    """
    
    if rep>99:
        rep = 99
    dfn = os.path.basename(fn)            # data file name
    sn = dfn[:-4]                         # sample name, strip off the .out extension from dfn
    if subdir is None:
        subdir = sn
    cwd = f"{os.path.dirname(fn)}/{subdir}"   # data file path
    if not os.path.exists(cwd):
        future = run_task(client, cmd=["mkdir", cwd], cwd="./")
        client.gather(future)
    
    dammif_cmds = [[f"{server_atsas_path}/bin/dammif", "--mode=FAST", 
                    f"--prefix={sn}-{i:02d}", f"../{dfn}"] for i in range(rep)]
    futures = [run_task(client, cmd=cmd, cwd=cwd) for cmd in dammif_cmds]
    
    print("starting damaver ...")
    damaver(client, [f"{sn}-{i:02d}-1.pdb" for i in range(rep)], cwd, futures)
    
    print("cleaning up ...") 
    # rename file to avoid future conflict
    fns = ["damaver.pdb", "damfilt.pdb", "damstart.pdb"]
    for fn in fns:
        client.gather(client.submit(os.rename, f"{cwd}/{fn}", f"{cwd}/{sn}-{fn}"))

    print("done")
#rg,drg = extract_vals(ret[0], "+/-", debug=debug) #i0,di0 = extract_vals(ret[1], "+/-", debug=debug) #n1,n2 = extract_vals(ret[2], " to ", debug=debug, dtype=int) #qual = extract_vals(ret[3], "%", debug=debug) # datgnom vs datgnom4, slightly different input parameters # example stdout results: #    dmax:   50.170000000000002       Total:  0.90463013315175844 #    Guinier:   15.332727107179052       Gnom:   15.332431498444064 # newer version of datgnom no longer reports Dmax/Rg on stdout, # the .out file format is also different # the Rg/Dmax values used to be located at the end of the file: #    Total  estimate : 0.944  which is  AN EXCELLENT  solution #    Reciprocal space: Rg =   14.75     , I(0) =   0.5740E+01 #    Real space: Rg =   14.74 +- 0.092  I(0) =   0.5740E+01 +-  0.2274E-01 # in the more recent files, this info in embedded in the header #    Total Estimate:                      0.9546 (a EXCELLENT solution) #    Reciprocal space Rg:             0.1471E+02 #    Reciprocal space I(0):           0.5733E+01 #    Real space range:                    0.0000 to      45.9000 #    Real space Rg:                   0.1470E+02 +-   0.1148E+00 #    Real space I(0):                 0.5733E+01 +-   0.2619E-01 assuming that any none numerical values will be ignored         data are in multiple columns         some columns may be missing values at the top         for P(r), cols=[0,1,2]         for I_fit(q), cols=[0,-1] # empty line # mixed text and numbersS          J EXP       ERROR       J REG       I REG ###      Experimental Data and Fit                     ####") #hdr,t1 = tt.split("S          J EXP       ERROR       J REG       I REG") ###      Real Space Data                               ####") #iq, pr = t1.split("Distance distribution  function of particle") # ALMERGE   Automatically merges data collected from two different concentrations or #           extrapolates it to infinite dilution assuming moderate particle interactions. # version-dependent output   $ datporod --version datporod, ATSAS 2.8.5 (r11116) Copyright (c) ATSAS Team, EMBL, Hamburg Outstation 2009-2018  $ datporod --help Usage: datporod [OPTIONS] [FILE(S)]  Estimation of Porod volume. Output values are Rg, I0, estimated Volume and file name.  Known Arguments:   FILE                       Data file  Known Options:       --i0=<VALUE>           Forward scattering intensity       --rg=<VALUE>           Experimental Radius of Gyration       --first=<N>            index of the first point to be used (default: 1)       --last=<N>             index of the last point to be used (default: s*Rg ~ 7)   -h, --help                 Print usage information and exit   -v, --version              Print version information and exit  Mandatory arguments to long options are mandatory for short options too.   $ datporod --version datporod, ATSAS 3.0.1 (r12314) Copyright (c) ATSAS Team, EMBL, Hamburg Outstation 2009-2020  $ datporod --help Usage: datporod [OPTIONS] [FILE(S)]  Molecular weight from Porod Volume  Output: smax (A^-1), Volume (A^3), file name  Known Arguments:   FILE                       Data file  Known Options:       --i0=<VALUE>           Forward scattering intensity       --rg=<VALUE>           Experimental Radius of Gyration       --first=<N>            index of the first point to be used (default: 1)       --last=<N>             index of the last point to be used (default: s*Rg ~ 7)   -h, --help                 Print usage information and exit   -v, --version              Print version information and exit  Mandatory arguments to long options are mandatory for short options too.    datmow --version datmow, ATSAS 2.8.5 (r11116) Copyright (c) ATSAS Team, EMBL, Hamburg Outstation 2014-2018  $ datmow --help Usage: datmow [OPTIONS] [FILE(S)]  Output: Q', V' (apparent Volume), V (Volume, A^3), MW (Da), file name  Known Arguments:   FILE                       Data file  Known Options:       --i0=<VALUE>           Forward scattering intensity       --rg=<VALUE>           Experimental Radius of Gyration       --rho=<VALUE>          Average protein density (default: 1.37 g/cm^-3)   -a, --offset=<VALUE>       Offset coefficient (default: look up)   -b, --scaling=<VALUE>      Scaling coefficient (default: look up)   -h, --help                 Print usage information and exit   -v, --version              Print version information and exit  Mandatory arguments to long options are mandatory for short options too.   $ datmow --version datmow, ATSAS 3.0.1 (r12314) Copyright (c) ATSAS Team, EMBL, Hamburg Outstation 2014-2020  $ datmow --help Usage: datmow [OPTIONS] [FILE(S)]  Molecular weight from Apparent Volume (Fischer et al., 2010). Output: smax (A^-1), Q', V' (apparent volume), V (Volume, A^3), MW (Da), file name  Known Arguments:   FILE                       Data file  Known Options:       --i0=<VALUE>           Forward scattering intensity       --rg=<VALUE>           Experimental Radius of Gyration       --first=<N>            index of the first point to be used (default: 1)   -h, --help                 Print usage information and exit   -v, --version              Print version information and exit  Mandatory arguments to long options are mandatory for short options too. # datporod: the used Rg, I0, the computed volume estimate and the input file name # # datvc: the first three numbers are the integrated intensities up to 0.2, 0.25 and 0.3, respectively. #        the second three numbers the corresponding MW estimates # # datmow: Output: Q', V' (apparent Volume), V (Volume, A^3), MW (Da), file name #ret = run(f"datvc {fn_out}").split('\n') #try: #    ii1,ii2,ii3,mw1,mw2,mw3 = extract_vals(ret[0]) #    r_vc = {"MW": [mw1, mw2, mw3]} #except: #    print("Unable to get output from datvc ...") #"datvc": r_vc,  # this won't work if q_max is below 0.3 # rect = l, b, w, h # this would happen if gnom fails to run #ax[0].yaxis.set_major_formatter(plt.NullFormatter()) #ax[0].set_title("intensity") #if len(locs>6): #    locs = locs[::2] run cmd, in cwd         cmd should be a list (*args), if shell is False         when wildcards are used, shell should be Ture, and cmd is just a string         prerequire is a list of futures that must be gathered before the cmd can run #server_atsas_path = "/opt/apps/ATSAS/2.8.5-0" # msg is the output from supcomb # NSD appears to be the smalles value in the final distance column in the output # Read file .............................................. : t-00-1.pdb # Number of atoms ........................................ : 236 # Fineness of the structure .............................. : 8.400 # Read file .............................................. : t-01-1.pdb # Number of atoms ........................................ : 236 # Fineness of the structure .............................. : 8.400 # #                                Initial       Final #              Orientation      Distance    Distance #             1     1     1       1.3553      1.1500 #             1     1    -1       1.2461      1.1552 #             1    -1     1       1.4394      1.1577 #             1    -1    -1       1.2884      1.1466 #            -1     1     1       1.8763      1.5808 #            -1     1    -1       1.9531      1.4054 #            -1    -1     1       1.8619      1.4467 #            -1    -1    -1       1.9294      1.4217 # #                   Transformation matrix #         0.5193     -0.7225      0.4565     -0.9402 #         0.0398     -0.5131     -0.8574     -6.5252 #         0.8537      0.4634     -0.2377     -0.5459 #         0.0000      0.0000      0.0000      1.0000 # # Wrote file ............................................. : t-01-1r.pdb options: NOT YET IMPLEMENTED         --symmetry=<SYMMETRY>         --enantiomorphs=<YES|NO>         --nbeads=<N> (damaver only)      damaver(pdbs):         loop over pdbi, pdbj:             supcomb pdbi pdbj         assemble NSD table         discard files with nsd > Mean + 2*Standard deviation (damaver/damsel manual)         loop over remaining pdbs pdbi, except for the ref:             damsup pdb_ref pdbi         damaver aligned_pdbs         damfilt damaver.pdb         damstart damaver.pdb #for i in range(npdb-1): #    for j in range(i+1, npdb): #        f = run_task(client, #                     cmd=[f"{server_atsas_path}/bin/supcomb", fns[i], fns[j], "-o", f"supcomb{i}-{j}.pdb"], #                     cwd=cwd, #                     prerequire = [prerequire[i], prerequire[j]], quiet=True) #        futures.append(f) #        index.append([i,j]) # e.g. ['dammif', '--mode=FAST', '--prefix=t-03', '../t.out'] #{res_no:02d} completed ...") # average NSD for each structure # damsel exclude structures with NSD-avg(NSD)>2*std repeat a bunch of dammif runs         then run damaver on the results # data file name # sample name, strip off the .out extension from dfn # data file path # rename file to avoid future conflict