# Copyright (C) 2002, Thomas Hamelryck (thamelry@binf.ku.dk)
# This code is part of the Biopython distribution and governed by its
# license.  Please see the LICENSE file that should have been included
# as part of this package.
 
# NACCESS interface adapted from Bio/PDB/DSSP.py
 
from __future__ import print_function
 
import os
import tempfile
import shutil
import subprocess
from Bio.PDB.PDBIO import PDBIO
from Bio.PDB.AbstractPropertyMap import AbstractResiduePropertyMap, AbstractAtomPropertyMap
 
"""Interface for the program NACCESS.
 
See: http://wolf.bms.umist.ac.uk/naccess/
 
errors likely to occur with the binary:
default values are often due to low default settings in accall.pars
- e.g. max cubes error: change in accall.pars and recompile binary
 
use naccess -y, naccess -h or naccess -w to include HETATM records
"""
 
 
def run_naccess(model, pdb_file, probe_size=None, z_slice=None,
                naccess='naccess', temp_path='/tmp/'):
 
    # make temp directory;
    tmp_path = tempfile.mkdtemp(dir=temp_path)
 
    # file name must end with '.pdb' to work with NACCESS
    # -> create temp file of existing pdb
    #    or write model to temp file
    handle, tmp_pdb_file = tempfile.mkstemp('.pdb', dir=tmp_path)
    os.close(handle)
    if pdb_file:
        pdb_file = os.path.abspath(pdb_file)
        shutil.copy(pdb_file, tmp_pdb_file)
    else:
        writer = PDBIO()
        writer.set_structure(model.get_parent())
        writer.save(tmp_pdb_file)
 
    # chdir to temp directory, as NACCESS writes to current working directory
    old_dir = os.getcwd()
    os.chdir(tmp_path)
 
    # create the command line and run
    # catch standard out & err
    command = [naccess, tmp_pdb_file]
    if probe_size:
        command.extend(['-p', probe_size])
    if z_slice:
        command.extend(['-z', z_slice])
 
    p = subprocess.Popen(command, universal_newlines=True,
                         stdout=subprocess.PIPE, stderr=subprocess.PIPE)
    out, err = p.communicate()
    os.chdir(old_dir)
 
    # get the output, then delete the temp directory
    rsa_file = tmp_pdb_file[:-4] + '.rsa'
    with open(rsa_file) as rf:
        rsa_data = rf.readlines()
    asa_file = tmp_pdb_file[:-4] + '.asa'
    with open(asa_file) as af:
        asa_data = af.readlines()
 
    shutil.rmtree(tmp_path, ignore_errors=True)
    return rsa_data, asa_data
 
 
def process_rsa_data(rsa_data):
    # process the .rsa output file: residue level SASA data
    naccess_rel_dict = {}
    for line in rsa_data:
        if line.startswith('RES'):
            res_name = line[4:7]
            chain_id = line[8]
            resseq = int(line[9:13])
            icode = line[13]
            res_id = (' ', resseq, icode)
            naccess_rel_dict[(chain_id, res_id)] = {
                'res_name': res_name,
                'all_atoms_abs': float(line[16:22]),
                'all_atoms_rel': float(line[23:28]),
                'side_chain_abs': float(line[29:35]),
                'side_chain_rel': float(line[36:41]),
                'main_chain_abs': float(line[42:48]),
                'main_chain_rel': float(line[49:54]),
                'non_polar_abs': float(line[55:61]),
                'non_polar_rel': float(line[62:67]),
                'all_polar_abs': float(line[68:74]),
                'all_polar_rel': float(line[75:80])}
    return naccess_rel_dict
 
 
def process_asa_data(rsa_data):
    # process the .asa output file: atomic level SASA data
    naccess_atom_dict = {}
    for line in rsa_data:
        atom_serial = line[6:11]
        full_atom_id = line[12:16]
        atom_id = full_atom_id.strip()
        altloc = line[16]
        resname = line[17:20]
        chainid = line[21]
        resseq = int(line[22:26])
        icode = line[26]
        res_id = (' ', resseq, icode)
        id = (chainid, res_id, atom_id)
        asa = line[54:62]               # solvent accessibility in Angstrom^2
        vdw = line[62:68]               # van der waal radius
        naccess_atom_dict[id] = asa
    return naccess_atom_dict
 
 
class NACCESS(AbstractResiduePropertyMap):
 
    def __init__(self, model, pdb_file=None,
                 naccess_binary='naccess', tmp_directory='/tmp'):
        res_data, atm_data = run_naccess(model, pdb_file,
                                         naccess=naccess_binary,
                                         temp_path=tmp_directory)
        naccess_dict = process_rsa_data(res_data)
        res_list = []
        property_dict = {}
        property_keys = []
        property_list = []
        # Now create a dictionary that maps Residue objects to accessibility
        for chain in model:
            chain_id = chain.get_id()
            for res in chain:
                res_id = res.get_id()
                if (chain_id, res_id) in naccess_dict:
                    item = naccess_dict[(chain_id, res_id)]
                    res_name = item['res_name']
                    assert (res_name == res.get_resname())
                    property_dict[(chain_id, res_id)] = item
                    property_keys.append((chain_id, res_id))
                    property_list.append((res, item))
                    res.xtra["EXP_NACCESS"] = item
                else:
                    pass
        AbstractResiduePropertyMap.__init__(self, property_dict, property_keys,
                                            property_list)
 
 
class NACCESS_atomic(AbstractAtomPropertyMap):
 
    def __init__(self, model, pdb_file=None,
                 naccess_binary='naccess', tmp_directory='/tmp'):
        res_data, atm_data = run_naccess(model, pdb_file,
                                         naccess=naccess_binary,
                                         temp_path=tmp_directory)
        self.naccess_atom_dict = process_asa_data(atm_data)
        property_dict = {}
        property_keys = []
        property_list = []
        # Now create a dictionary that maps Atom objects to accessibility
        for chain in model:
            chain_id = chain.get_id()
            for residue in chain:
                res_id = residue.get_id()
                for atom in residue:
                    atom_id = atom.get_id()
                    full_id = (chain_id, res_id, atom_id)
                    if full_id in self.naccess_atom_dict:
                        asa = self.naccess_atom_dict[full_id]
                        property_dict[full_id] = asa
                        property_keys.append((full_id))
                        property_list.append((atom, asa))
                        atom.xtra['EXP_NACCESS'] = asa
        AbstractAtomPropertyMap.__init__(self, property_dict,
                                         property_keys, property_list)
 
 
if __name__ == "__main__":
    import sys
    from Bio.PDB import PDBParser
 
    p = PDBParser()
    s = p.get_structure('X', sys.argv[1])
    model = s[0]
 
    n = NACCESS(model, sys.argv[1])
    for e in n:
        print(e)