示例#1
0
def build(mol,
          topo=None,
          param=None,
          stream=None,
          prefix='structure',
          outdir='./build',
          caps=None,
          ionize=True,
          saltconc=0,
          saltanion=None,
          saltcation=None,
          disulfide=None,
          patches=None,
          noregen=None,
          psfgen=None,
          execute=True,
          _clean=True):
    """ Builds a system for CHARMM

    Uses VMD and psfgen to build a system for CHARMM. Additionally it allows for ionization and adding of disulfide bridges.

    Parameters
    ----------
    mol : :class:`Molecule <htmd.molecule.molecule.Molecule>` object
        The Molecule object containing the system
    topo : list of str
        A list of topology `rtf` files.
        Use :func:`charmm.listFiles <htmd.builder.charmm.listFiles>` to get a list of available topology files.
        Default: ['top/top_all36_prot.rtf', 'top/top_all36_lipid.rtf', 'top/top_water_ions.rtf']
    param : list of str
        A list of parameter `prm` files.
        Use :func:`charmm.listFiles <htmd.builder.charmm.listFiles>` to get a list of available parameter files.
        Default: ['par/par_all36_prot_mod.prm', 'par/par_all36_lipid.prm', 'par/par_water_ions.prm']
    stream : list of str
        A list of stream `str` files containing topologies and parameters.
        Use :func:`charmm.listFiles <htmd.builder.charmm.listFiles>` to get a list of available stream files.
        Default: ['str/prot/toppar_all36_prot_arg0.str']
    prefix : str
        The prefix for the generated pdb and psf files
    outdir : str
        The path to the output directory
        Default: './build'
    caps : dict
        A dictionary with keys segids and values lists of strings describing the caps of that segment.
        e.g. caps['P'] = ['first ACE', 'last CT3'] or caps['P'] = ['first none', 'last none']. 
        Default: will apply ACE and CT3 caps to proteins and none caps to the rest.
    ionize : bool
        Enable or disable ionization
    saltconc : float
        Salt concentration (in Molar) to add to the system after neutralization.
    saltanion : {'CLA'}
        The anion type. Please use only CHARMM ion atom names.
    saltcation : {'SOD', 'MG', 'POT', 'CES', 'CAL', 'ZN2'}
        The cation type. Please use only CHARMM ion atom names.
    disulfide : list of :class:`DisulfideBridge <htmd.builder.builder.DisulfideBridge>` objects
        If None it will guess disulfide bonds. Otherwise provide a list of `DisulfideBridge` objects.
    patches : list of str
        Any further patches the user wants to apply
    noregen : list of str
        A list of patches that must not be regenerated (angles and dihedrals)
        Default: ['FHEM', 'PHEM', 'PLOH', 'PLO2', 'PLIG', 'PSUL']
    psfgen : str
        Path to psfgen executable used to build for CHARMM
    execute : bool
        Disable building. Will only write out the input script needed by psfgen. Does not include ionization.

    Returns
    -------
    molbuilt : :class:`Molecule <htmd.molecule.molecule.Molecule>` object
        The built system in a Molecule object

    Example
    -------
    >>> from htmd import *
    >>> mol = Molecule("3PTB")
    >>> mol.filter("not resname BEN")
    >>> mol.renumberResidues()
    >>> molbuilt = charmm.build(mol, outdir='/tmp/build', ionize=False)  # doctest: +ELLIPSIS
    Bond between A: [serial 185 resid 42 resname CYS chain A segid 0]
                 B: [serial 298 resid 58 resname CYS chain A segid 0]...
    >>> # More complex example
    >>> topos  = ['top/top_all36_prot.rtf', './benzamidine.rtf', 'top/top_water_ions.rtf']
    >>> params = ['par/par_all36_prot_mod.prm', './benzamidine.prm', 'par/par_water_ions.prm']
    >>> disu = [DisulfideBridge('P', 157, 'P', 13), DisulfideBridge('K', 1, 'K', 25)]
    >>> molbuilt = charmm.build(mol, topo=topos, param=params, outdir='/tmp/build', saltconc=0.15, disulfide=disu)  # doctest: +SKIP
    """

    mol = mol.copy()
    _missingSegID(mol)
    _checkMixedSegment(mol)
    _checkResidueInsertions(mol)
    if psfgen is None:
        psfgen = shutil.which('psfgen', mode=os.X_OK)
        if not psfgen:
            raise FileNotFoundError(
                'Could not find psfgen executable, or no execute permissions are given. '
                'Run `conda install psfgen`.')
    if not os.path.isdir(outdir):
        os.makedirs(outdir)
    if _clean:
        _cleanOutDir(outdir)
    if topo is None:
        topo = defaultTopo()
    if param is None:
        param = defaultParam()
    if stream is None:
        stream = defaultStream()
    if caps is None:
        caps = _defaultCaps(mol)
    # patches that must _not_ be regenerated
    if noregen is None:
        noregen = ['FHEM', 'PHEM', 'PLOH', 'PLO2', 'PLIG', 'PSUL']

    alltopo = topo.copy()
    allparam = param.copy()

    # Splitting the stream files and adding them to the list of parameter and topology files
    charmmdir = path.join(home(), 'builder', 'charmmfiles')
    for s in stream:
        if s[0] != '.' and path.isfile(path.join(charmmdir, s)):
            s = path.join(charmmdir, s)
        outrtf, outprm = _prepareStream(s)
        alltopo.append(outrtf)
        allparam.append(outprm)

    #_missingChain(mol)
    #_checkProteinGaps(mol)
    if patches is None:
        patches = []
    if isinstance(patches, str):
        patches = [patches]
    allpatches = []
    allpatches += patches
    # Find protonated residues and add patches for them
    allpatches += _protonationPatches(mol)

    f = open(path.join(outdir, 'build.vmd'), 'w')
    f.write('# psfgen file generated by charmm.build\n')
    f.write('package require psfgen;\n')
    f.write('psfcontext reset;\n\n')

    # Copying and printing out the topologies
    if not path.exists(path.join(outdir, 'topologies')):
        os.makedirs(path.join(outdir, 'topologies'))
    for i in range(len(alltopo)):
        if alltopo[i][0] != '.' and path.isfile(
                path.join(charmmdir, alltopo[i])):
            alltopo[i] = path.join(charmmdir, alltopo[i])
        localname = '{}.'.format(i) + path.basename(alltopo[i])
        shutil.copy(alltopo[i], path.join(outdir, 'topologies', localname))
        f.write('topology ' + path.join('topologies', localname) + '\n')
    f.write('\n')

    _printAliases(f)

    # Printing out segments
    if not path.exists(path.join(outdir, 'segments')):
        os.makedirs(path.join(outdir, 'segments'))
    logger.info('Writing out segments.')
    segments = _getSegments(mol)
    wateratoms = mol.atomselect('water')
    for seg in segments:
        pdbname = 'segment' + seg + '.pdb'
        segatoms = mol.segid == seg
        mol.write(path.join(outdir, 'segments', pdbname), sel=segatoms)

        segwater = wateratoms & segatoms
        f.write('segment ' + seg + ' {\n')
        if np.all(segatoms ==
                  segwater):  # If segment only contains waters, set: auto none
            f.write('\tauto none\n')
        f.write('\tpdb ' + path.join('segments', pdbname) + '\n')
        if caps is not None and seg in caps:
            for c in caps[seg]:
                f.write('\t' + c + '\n')
        f.write('}\n')
        f.write('coordpdb ' + path.join('segments', pdbname) + ' ' + seg +
                '\n\n')

    # Printing out patches for the disulfide bridges
    if disulfide is None:
        disulfide = detectDisulfideBonds(mol)

    if len(disulfide) != 0:
        for d in disulfide:
            f.write('patch DISU {}:{} {}:{}\n'.format(d.segid1, d.resid1,
                                                      d.segid2, d.resid2))
        f.write('\n')

    noregenpatches = [p for p in allpatches if p.split()[1] in noregen]
    regenpatches = [p for p in allpatches if p.split()[1] not in noregen]

    # Printing regenerable patches
    if len(regenpatches) != 0:
        for p in regenpatches:
            f.write(p + '\n')
        f.write('\n')

    # Regenerate angles and dihedrals
    f.write('regenerate angles dihedrals\n')
    f.write('\n')

    # Printing non-regenerable patches
    if len(noregenpatches) != 0:
        for p in noregenpatches:
            f.write(p + '\n')
        f.write('\n')

    f.write('guesscoord\n')
    f.write('writepsf ' + prefix + '.psf\n')
    f.write('writepdb ' + prefix + '.pdb\n')
    #f.write('quit\n')
    f.close()

    if allparam is not None:
        combine(allparam, path.join(outdir, 'parameters'))

    molbuilt = None
    if execute:
        logpath = os.path.abspath('{}/log.txt'.format(outdir))
        logger.info('Starting the build.')
        currdir = os.getcwd()
        os.chdir(outdir)
        f = open(logpath, 'w')
        #call([vmd, '-dispdev', 'text', '-e', './build.vmd'], stdout=f)
        call([psfgen, './build.vmd'], stdout=f)
        f.close()
        errors = _logParser(logpath)
        os.chdir(currdir)
        if errors:
            raise BuildError(errors + [
                'Check {} for further information on errors in building.'.
                format(logpath)
            ])
        logger.info('Finished building.')

        if path.isfile(path.join(outdir, 'structure.pdb')) and path.isfile(
                path.join(outdir, 'structure.psf')):
            molbuilt = Molecule(path.join(outdir, 'structure.pdb'))
            molbuilt.read(path.join(outdir, 'structure.psf'))
        else:
            raise BuildError(
                'No structure pdb/psf file was generated. Check {} for errors in building.'
                .format(logpath))

        if ionize:
            os.makedirs(path.join(outdir, 'pre-ionize'))
            data = glob(path.join(outdir, '*'))
            for f in data:
                shutil.move(f, path.join(outdir, 'pre-ionize'))
            totalcharge = np.sum(molbuilt.charge)
            nwater = np.sum(molbuilt.atomselect('water and noh'))
            anion, cation, anionatom, cationatom, nanion, ncation = ionizef(
                totalcharge,
                nwater,
                saltconc=saltconc,
                anion=saltanion,
                cation=saltcation)
            newmol = ionizePlace(mol, anion, cation, anionatom, cationatom,
                                 nanion, ncation)
            # Redo the whole build but now with ions included
            return build(newmol,
                         topo=alltopo,
                         param=allparam,
                         stream=[],
                         prefix=prefix,
                         outdir=outdir,
                         ionize=False,
                         caps=caps,
                         execute=execute,
                         saltconc=saltconc,
                         disulfide=disulfide,
                         patches=patches,
                         noregen=noregen,
                         psfgen=psfgen,
                         _clean=False)
    _checkFailedAtoms(molbuilt)
    _recoverProtonations(molbuilt)
    return molbuilt
示例#2
0
def build(mol,
          ff=None,
          topo=None,
          param=None,
          prefix='structure',
          outdir='./build',
          caps=None,
          ionize=True,
          saltconc=0,
          saltanion=None,
          saltcation=None,
          disulfide=None,
          tleap=None,
          execute=True,
          atomtypes=None,
          offlibraries=None,
          gbsa=False,
          igb=2):
    """ Builds a system for AMBER

    Uses tleap to build a system for AMBER. Additionally it allows the user to ionize and add disulfide bridges.

    Parameters
    ----------
    mol : :class:`Molecule <htmd.molecule.molecule.Molecule>` object
        The Molecule object containing the system
    ff : list of str
        A list of leaprc forcefield files.
        Use :func:`amber.listFiles <htmd.builder.amber.listFiles>` to get a list of available forcefield files.
        Default: :func:`amber.defaultFf <htmd.builder.amber.defaultFf>`
    topo : list of str
        A list of topology `prepi/prep/in` files.
        Use :func:`amber.listFiles <htmd.builder.amber.listFiles>` to get a list of available topology files.
        Default: :func:`amber.defaultTopo <htmd.builder.amber.defaultTopo>`
    param : list of str
        A list of parameter `frcmod` files.
        Use :func:`amber.listFiles <htmd.builder.amber.listFiles>` to get a list of available parameter files.
        Default: :func:`amber.defaultParam <htmd.builder.amber.defaultParam>`
    prefix : str
        The prefix for the generated pdb and psf files
    outdir : str
        The path to the output directory
        Default: './build'
    caps : dict
        A dictionary with keys segids and values lists of strings describing the caps for a particular protein segment.
        e.g. caps['P'] = ['ACE', 'NME'] or caps['P'] = ['none', 'none']. Default: will apply ACE and NME caps to every
        protein segment.
    ionize : bool
        Enable or disable ionization
    saltconc : float
        Salt concentration to add to the system after neutralization.
    saltanion : {'Cl-'}
        The anion type. Please use only AMBER ion atom names.
    saltcation : {'Na+', 'K+', 'Cs+'}
        The cation type. Please use only AMBER ion atom names.
    disulfide : list of pairs of atomselection strings
        If None it will guess disulfide bonds. Otherwise provide a list pairs of atomselection strings for each pair of
        residues forming the disulfide bridge.
    tleap : str
        Path to tleap executable used to build the system for AMBER
    execute : bool
        Disable building. Will only write out the input script needed by tleap. Does not include ionization.
    atomtypes : list of triplets
        Custom atom types defined by the user as ('type', 'element', 'hybrid') triplets
        e.g. (('C1', 'C', 'sp2'), ('CI', 'C', 'sp3')). Check `addAtomTypes` in AmberTools docs.
    offlibraries : str or list
        A path or a list of paths to OFF library files. Check `loadOFF` in AmberTools docs.
    gbsa : bool
        Modify radii for GBSA implicit water model
    igb : int
        GB model. Select: 1 for mbondi, 2 and 5 for mbondi2, 7 for bondi and 8 for mbondi3.
        Check section 4. The Generalized Born/Surface Area Model of the AMBER manual.

    Returns
    -------
    molbuilt : :class:`Molecule <htmd.molecule.molecule.Molecule>` object
        The built system in a Molecule object

    Example
    -------
    >>> from htmd.ui import *  # doctest: +SKIP
    >>> mol = Molecule("3PTB")
    >>> molbuilt = amber.build(mol, outdir='/tmp/build')  # doctest: +SKIP
    >>> # More complex example
    >>> disu = [['segid P and resid 157', 'segid P and resid 13'], ['segid K and resid 1', 'segid K and resid 25']]
    >>> molbuilt = amber.build(mol, outdir='/tmp/build', saltconc=0.15, disulfide=disu)  # doctest: +SKIP
    """
    # Remove pdb protein bonds as they can be regenerated by tleap. Keep non-protein bonds i.e. for ligands
    mol = mol.copy()
    _removeProteinBonds(mol)

    if tleap is None:
        tleap = _findTleap()
    else:
        if shutil.which(tleap) is None:
            raise NameError(
                'Could not find executable: `{}` in the PATH. Cannot build for AMBER.'
                .format(tleap))

    if not os.path.isdir(outdir):
        os.makedirs(outdir)
    _cleanOutDir(outdir)
    if ff is None:
        ff = defaultFf()
    if topo is None:
        topo = defaultTopo()
    if param is None:
        param = defaultParam()
    if caps is None:
        caps = _defaultProteinCaps(mol)

    _missingSegID(mol)
    _checkMixedSegment(mol)

    mol = _charmmLipid2Amber(mol)

    _applyProteinCaps(mol, caps)

    f = open(os.path.join(outdir, 'tleap.in'), 'w')
    f.write('# tleap file generated by amber.build\n')

    # Printing out the forcefields
    if isinstance(ff, str):
        ff = [ff]
    for i, force in enumerate(ff):
        if not os.path.isfile(force):
            force = _locateFile(force, 'ff', tleap)
            if force is None:
                continue
        newname = 'ff{}_{}'.format(i, os.path.basename(force))
        shutil.copy(force, os.path.join(outdir, newname))
        f.write('source {}\n'.format(newname))
    f.write('\n')

    if gbsa:
        gbmodels = {
            1: 'mbondi',
            2: 'mbondi2',
            5: 'mbondi2',
            7: 'bondi',
            8: 'mbondi3'
        }
        f.write('set default PBradii {}\n\n'.format(gbmodels[igb]))

    # Adding custom atom types
    if atomtypes is not None:
        atomtypes = ensurelist(tocheck=atomtypes[0], tomod=atomtypes)
        f.write('addAtomTypes {\n')
        for at in atomtypes:
            if len(at) != 3:
                raise RuntimeError(
                    'Atom type definitions have to be triplets. Check the AMBER documentation.'
                )
            f.write('    {{ "{}" "{}" "{}" }}\n'.format(at[0], at[1], at[2]))
        f.write('}\n\n')

    # Loading OFF libraries
    if offlibraries is not None:
        offlibraries = ensurelist(offlibraries)
        for off in offlibraries:
            if not os.path.isfile(off):
                raise RuntimeError(
                    'Could not find off-library in location {}'.format(off))
            newname = 'offlib{}_{}'.format(i, os.path.basename(off))
            shutil.copy(off, os.path.join(outdir, newname))
            f.write('loadoff {}\n'.format(newname))

    # Loading frcmod parameters
    f.write('# Loading parameter files\n')
    for i, p in enumerate(param):
        if not os.path.isfile(p):
            p = _locateFile(p, 'param', tleap)
            if p is None:
                continue
        newname = 'param{}_{}'.format(i, os.path.basename(p))
        shutil.copy(p, os.path.join(outdir, newname))
        f.write('loadamberparams {}\n'.format(newname))
    f.write('\n')

    # Loading prepi topologies
    f.write('# Loading prepi topologies\n')
    for i, t in enumerate(topo):
        if not os.path.isfile(t):
            t = _locateFile(t, 'topo', tleap)
            if t is None:
                continue
        newname = 'topo{}_{}'.format(i, os.path.basename(t))
        shutil.copy(t, os.path.join(outdir, newname))
        f.write('loadamberprep {}\n'.format(newname))
    f.write('\n')

    f.write('# Loading the system\n')
    f.write('mol = loadpdb input.pdb\n\n')

    if np.sum(mol.atomtype != '') != 0:
        logger.debug('Writing mol2 files for input to tleap.')
        segs = np.unique(mol.segid[mol.atomtype != ''])
        combstr = 'mol = combine {mol'
        for s in segs:
            name = 'segment{}'.format(s)
            mol2name = os.path.join(outdir, '{}.mol2'.format(name))
            mol.write(mol2name, (mol.atomtype != '') & (mol.segid == s))
            if not os.path.isfile(mol2name):
                raise NameError(
                    'Could not write a mol2 file out of the given Molecule.')
            f.write('# Loading the rest of the system\n')
            f.write('{} = loadmol2 {}.mol2\n\n'.format(name, name))
            combstr += ' {}'.format(name)
        combstr += '}\n\n'
        f.write(combstr)

    # Write patches for disulfide bonds (only after ionizing)
    if not ionize:
        # TODO: Remove this once we deprecate the class
        from htmd.builder.builder import DisulfideBridge
        from htmd.molecule.molecule import UniqueResidueID
        if disulfide is not None and len(disulfide) != 0 and isinstance(
                disulfide[0], DisulfideBridge):
            newdisu = []
            for d in disulfide:
                r1 = UniqueResidueID.fromMolecule(
                    mol, 'resid {} and segname {}'.format(d.resid1, d.segid1))
                r2 = UniqueResidueID.fromMolecule(
                    mol, 'resid {} and segname {}'.format(d.resid2, d.segid2))
                newdisu.append([r1, r2])
            disulfide = newdisu
        # TODO: Remove up to here ----------------------

        if disulfide is not None and len(disulfide) != 0 and isinstance(
                disulfide[0][0], str):
            disulfide = convertDisulfide(mol, disulfide)

        if disulfide is None:
            logger.info('Detecting disulfide bonds.')
            disulfide = detectDisulfideBonds(mol)

        # Fix structure to match the disulfide patching
        if len(disulfide) != 0:
            torem = np.zeros(mol.numAtoms, dtype=bool)
            f.write('# Adding disulfide bonds\n')
            for d in disulfide:
                # Rename the residues to CYX if there is a disulfide bond
                atoms1 = d[0].selectAtoms(mol, indexes=False)
                atoms2 = d[1].selectAtoms(mol, indexes=False)
                mol.resname[atoms1] = 'CYX'
                mol.resname[atoms2] = 'CYX'
                # Remove (eventual) HG hydrogens on these CYS (from proteinPrepare)
                torem |= (atoms1 & (mol.name == 'HG')) | (atoms2 &
                                                          (mol.name == 'HG'))
                # Convert to stupid amber residue numbering
                uqseqid = sequenceID(
                    (mol.resid, mol.insertion, mol.segid)) + mol.resid[0]
                uqres1 = int(np.unique(uqseqid[atoms1]))
                uqres2 = int(np.unique(uqseqid[atoms2]))
                f.write('bond mol.{}.SG mol.{}.SG\n'.format(uqres1, uqres2))
            f.write('\n')
            mol.remove(torem, _logger=False)

    f.write('# Writing out the results\n')
    f.write('saveamberparm mol ' + prefix + '.prmtop ' + prefix + '.crd\n')
    f.write('quit')
    f.close()

    # Printing and loading the PDB file. AMBER can work with a single PDB file if the segments are separate by TER
    logger.debug('Writing PDB file for input to tleap.')
    pdbname = os.path.join(outdir, 'input.pdb')

    # mol2 files have atomtype, here we only write parts not coming from mol2
    # We need to write the input.pdb at the end since we modify the resname for disulfide bridges in mol
    mol.write(pdbname, mol.atomtype == '')
    if not os.path.isfile(pdbname):
        raise NameError(
            'Could not write a PDB file out of the given Molecule.')

    molbuilt = None
    if execute:
        # Source paths of extra dirs (our dirs, not amber default)
        htmdamberdir = os.path.abspath(
            os.path.join(home(), 'builder', 'amberfiles'))
        sourcepaths = [htmdamberdir]
        sourcepaths += [
            os.path.join(htmdamberdir, os.path.dirname(f)) for f in ff
            if os.path.isfile(os.path.join(htmdamberdir, f))
        ]
        extrasource = []
        for p in sourcepaths:
            extrasource.append('-I')
            extrasource.append('{}'.format(p))
        logpath = os.path.abspath(os.path.join(outdir, 'log.txt'))
        logger.info('Starting the build.')
        currdir = os.getcwd()
        os.chdir(outdir)
        f = open(logpath, 'w')
        try:
            cmd = [tleap, '-f', './tleap.in']
            cmd[1:1] = extrasource
            call(cmd, stdout=f)
        except:
            raise NameError('tleap failed at execution')
        f.close()
        errors = _logParser(logpath)
        os.chdir(currdir)
        if errors:
            raise BuildError(errors + [
                'Check {} for further information on errors in building.'.
                format(logpath)
            ])
        logger.info('Finished building.')

        if os.path.exists(os.path.join(outdir, 'structure.crd')) and \
                        os.path.getsize(os.path.join(outdir, 'structure.crd')) != 0 and \
                        os.path.getsize(os.path.join(outdir, 'structure.prmtop')) != 0:
            molbuilt = Molecule(os.path.join(outdir, 'structure.prmtop'))
            molbuilt.read(os.path.join(outdir, 'structure.crd'))
        else:
            raise BuildError(
                'No structure pdb/prmtop file was generated. Check {} for errors in building.'
                .format(logpath))

        if ionize:
            shutil.move(os.path.join(outdir, 'structure.crd'),
                        os.path.join(outdir, 'structure.noions.crd'))
            shutil.move(os.path.join(outdir, 'structure.prmtop'),
                        os.path.join(outdir, 'structure.noions.prmtop'))
            totalcharge = np.sum(molbuilt.charge)
            nwater = np.sum(molbuilt.atomselect('water and noh'))
            anion, cation, anionatom, cationatom, nanion, ncation = ionizef(
                totalcharge,
                nwater,
                saltconc=saltconc,
                anion=saltanion,
                cation=saltcation)
            newmol = ionizePlace(mol, anion, cation, anionatom, cationatom,
                                 nanion, ncation)
            # Redo the whole build but now with ions included
            return build(newmol,
                         ff=ff,
                         topo=topo,
                         param=param,
                         prefix=prefix,
                         outdir=outdir,
                         caps={},
                         ionize=False,
                         execute=execute,
                         saltconc=saltconc,
                         disulfide=disulfide,
                         tleap=tleap,
                         atomtypes=atomtypes,
                         offlibraries=offlibraries)
    tmpbonds = molbuilt.bonds
    molbuilt.bonds = []  # Removing the bonds to speed up writing
    molbuilt.write(os.path.join(outdir, 'structure.pdb'))
    molbuilt.bonds = tmpbonds  # Restoring the bonds
    return molbuilt
示例#3
0
文件: amber.py 项目: ismaelresp/htmd
def build(mol,
          ff=None,
          topo=None,
          param=None,
          prefix='structure',
          outdir='./build',
          caps=None,
          ionize=True,
          saltconc=0,
          saltanion=None,
          saltcation=None,
          disulfide=None,
          tleap='tleap',
          execute=True,
          atomtypes=None,
          offlibraries=None):
    """ Builds a system for AMBER

    Uses tleap to build a system for AMBER. Additionally it allows the user to ionize and add disulfide bridges.

    Parameters
    ----------
    mol : :class:`Molecule <htmd.molecule.molecule.Molecule>` object
        The Molecule object containing the system
    ff : list of str
        A list of leaprc forcefield files.
        Use :func:`amber.listFiles <htmd.builder.amber.listFiles>` to get a list of available forcefield files.
        Default: :func:`amber.defaultFf <htmd.builder.amber.defaultFf>`
    topo : list of str
        A list of topology `prepi` files.
        Use :func:`amber.listFiles <htmd.builder.amber.listFiles>` to get a list of available topology files.
        Default: :func:`amber.defaultTopo <htmd.builder.amber.defaultTopo>`
    param : list of str
        A list of parameter `frcmod` files.
        Use :func:`amber.listFiles <htmd.builder.amber.listFiles>` to get a list of available parameter files.
        Default: :func:`amber.defaultParam <htmd.builder.amber.defaultParam>`
    prefix : str
        The prefix for the generated pdb and psf files
    outdir : str
        The path to the output directory
        Default: './build'
    caps : dict
        A dictionary with keys segids and values lists of strings describing the caps for a particular protein segment.
        e.g. caps['P'] = ['ACE', 'NME'] or caps['P'] = ['none', 'none']. Default: will apply ACE and NME caps to every
        protein segment.
    ionize : bool
        Enable or disable ionization
    saltconc : float
        Salt concentration to add to the system after neutralization.
    saltanion : {'Cl-'}
        The anion type. Please use only AMBER ion atom names.
    saltcation : {'Na+', 'K+', 'Cs+'}
        The cation type. Please use only AMBER ion atom names.
    disulfide : list of :class:`DisulfideBridge <htmd.builder.builder.DisulfideBridge>` objects
        If None it will guess disulfide bonds. Otherwise provide a list of `DisulfideBridge` objects.
    tleap : str
        Path to tleap executable used to build the system for AMBER
    execute : bool
        Disable building. Will only write out the input script needed by tleap. Does not include ionization.
    atomtypes : list of triplets
        Custom atom types defined by the user as ('type', 'element', 'hybrid') triplets
        e.g. (('C1', 'C', 'sp2'), ('CI', 'C', 'sp3')). Check `addAtomTypes` in AmberTools docs.
    offlibraries : str or list
        A path or a list of paths to OFF library files. Check `loadOFF` in AmberTools docs.

    Returns
    -------
    molbuilt : :class:`Molecule <htmd.molecule.molecule.Molecule>` object
        The built system in a Molecule object

    Example
    -------
    >>> from htmd.ui import *
    >>> mol = Molecule("3PTB")
    >>> molbuilt = amber.build(mol, outdir='/tmp/build')  # doctest: +SKIP
    ...
    >>> # More complex example
    >>> disu = [DisulfideBridge('P', 157, 'P', 13), DisulfideBridge('K', 1, 'K', 25)]
    >>> molbuilt = amber.build(mol, outdir='/tmp/build', saltconc=0.15, disulfide=disu)  # doctest: +SKIP
    """
    # Remove pdb protein bonds as they can be regenerated by tleap. Keep non-protein bonds i.e. for ligands
    mol = mol.copy()
    _removeProteinBonds(mol)

    if shutil.which(tleap) is None:
        raise NameError(
            'Could not find executable: `{}` in the PATH. Cannot build for AMBER.'
            .format(tleap))
    if not os.path.isdir(outdir):
        os.makedirs(outdir)
    _cleanOutDir(outdir)
    if ff is None:
        ff = defaultFf()
    if topo is None:
        topo = defaultTopo()
    if param is None:
        param = defaultParam()
    if caps is None:
        caps = _defaultProteinCaps(mol)

    _missingSegID(mol)
    _checkMixedSegment(mol)
    _checkResidueInsertions(mol)

    mol = _charmmLipid2Amber(mol)

    _applyProteinCaps(mol, caps)

    f = open(os.path.join(outdir, 'tleap.in'), 'w')
    f.write('# tleap file generated by amber.build\n')

    # Printing out the forcefields
    if isinstance(ff, str):
        ff = [ff]
    for force in ff:
        f.write('source ' + force + '\n')
    f.write('\n')

    # Adding custom atom types
    if atomtypes is not None:
        atomtypes = ensurelist(tocheck=atomtypes[0], tomod=atomtypes)
        f.write('addAtomTypes {\n')
        for at in atomtypes:
            if len(at) != 3:
                raise RuntimeError(
                    'Atom type definitions have to be triplets. Check the AMBER documentation.'
                )
            f.write('    {{ "{}" "{}" "{}" }}\n'.format(at[0], at[1], at[2]))
        f.write('}\n\n')

    # Loading OFF libraries
    if offlibraries is not None:
        if not isinstance(offlibraries, list) and not isinstance(
                offlibraries, tuple):
            offlibraries = [
                offlibraries,
            ]
        for off in offlibraries:
            f.write('loadoff {}\n\n'.format(off))

    # Loading frcmod parameters
    f.write('# Loading parameter files\n')
    for p in param:
        try:
            shutil.copy(p, outdir)
            f.write('loadamberparams ' + os.path.basename(p) + '\n')
        except:
            f.write('loadamberparams ' + p + '\n')
            logger.info(
                "File {:s} not found, assuming its present on the standard Amber location"
                .format(p))
    f.write('\n')

    # Loading prepi topologies
    f.write('# Loading prepi topologies\n')
    for t in topo:
        shutil.copy(t, outdir)
        f.write('loadamberprep ' + os.path.basename(t) + '\n')
    f.write('\n')

    # Detect disulfide bridges if not defined by user
    if disulfide is None and not ionize:
        logger.info('Detecting disulfide bonds.')
        disulfide = detectDisulfideBonds(mol)

    # Fix structure to match the disulfide patching
    if not ionize and len(disulfide) != 0:
        for d in disulfide:
            # Rename the residues to CYX if there is a disulfide bond
            atoms1 = (mol.segid == d.segid1) & (mol.resid == d.resid1)
            atoms2 = (mol.segid == d.segid2) & (mol.resid == d.resid2)
            mol.resname[atoms1] = 'CYX'
            mol.resname[atoms2] = 'CYX'
            # Remove (eventual) HG hydrogens on these CYS (from proteinPrepare)
            mol.remove(atoms1 & (mol.name == 'HG'), _logger=False)
            mol.remove(atoms2 & (mol.name == 'HG'), _logger=False)

    # Printing and loading the PDB file. AMBER can work with a single PDB file if the segments are separate by TER
    logger.debug('Writing PDB file for input to tleap.')
    pdbname = os.path.join(outdir, 'input.pdb')

    # mol2 files have atomtype, here we only write parts not coming from mol2
    mol.write(pdbname, mol.atomtype == '')
    if not os.path.isfile(pdbname):
        raise NameError(
            'Could not write a PDB file out of the given Molecule.')
    f.write('# Loading the system\n')
    f.write('mol = loadpdb input.pdb\n\n')

    if np.sum(mol.atomtype != '') != 0:
        logger.debug('Writing mol2 files for input to tleap.')
        segs = np.unique(mol.segid[mol.atomtype != ''])
        combstr = 'mol = combine {mol'
        for s in segs:
            name = 'segment{}'.format(s)
            mol2name = os.path.join(outdir, '{}.mol2'.format(name))
            mol.write(mol2name, (mol.atomtype != '') & (mol.segid == s))
            if not os.path.isfile(mol2name):
                raise NameError(
                    'Could not write a mol2 file out of the given Molecule.')
            f.write('# Loading the rest of the system\n')
            f.write('{} = loadmol2 {}.mol2\n\n'.format(name, name))
            combstr += ' {}'.format(name)
        combstr += '}\n\n'
        f.write(combstr)

    # Write patches for disulfide bonds (only after ionizing)
    if not ionize and len(disulfide) != 0:
        f.write('# Adding disulfide bonds\n')
        for d in disulfide:
            # Convert to stupid amber residue numbering
            uqseqid = sequenceID(
                (mol.resid, mol.insertion, mol.segid)) + mol.resid[0]
            uqres1 = int(
                np.unique(uqseqid[(mol.segid == d.segid1)
                                  & (mol.resid == d.resid1)]))
            uqres2 = int(
                np.unique(uqseqid[(mol.segid == d.segid2)
                                  & (mol.resid == d.resid2)]))
            f.write('bond mol.{}.SG mol.{}.SG\n'.format(uqres1, uqres2))
        f.write('\n')

    f.write('# Writing out the results\n')
    f.write('saveamberparm mol ' + prefix + '.prmtop ' + prefix + '.crd\n')
    f.write('quit')
    f.close()

    molbuilt = None
    if execute:
        # Source paths of extra dirs (our dirs, not amber default)
        htmdamberdir = os.path.abspath(
            os.path.join(home(), 'builder', 'amberfiles'))
        sourcepaths = [htmdamberdir]
        sourcepaths += [
            os.path.join(htmdamberdir, os.path.dirname(f)) for f in ff
            if os.path.isfile(os.path.join(htmdamberdir, f))
        ]
        extrasource = []
        for p in sourcepaths:
            extrasource.append('-I')
            extrasource.append('{}'.format(p))
        logpath = os.path.abspath(os.path.join(outdir, 'log.txt'))
        logger.info('Starting the build.')
        currdir = os.getcwd()
        os.chdir(outdir)
        f = open(logpath, 'w')
        try:
            cmd = [tleap, '-f', './tleap.in']
            cmd[1:1] = extrasource
            call(cmd, stdout=f)
        except:
            raise NameError('tleap failed at execution')
        f.close()
        os.chdir(currdir)
        logger.info('Finished building.')

        if os.path.exists(os.path.join(outdir, 'structure.crd')) and \
                        os.path.getsize(os.path.join(outdir, 'structure.crd')) != 0 and \
                        os.path.getsize(os.path.join(outdir, 'structure.prmtop')) != 0:
            molbuilt = Molecule(os.path.join(outdir, 'structure.prmtop'))
            molbuilt.read(os.path.join(outdir, 'structure.crd'))
        else:
            raise NameError(
                'No structure pdb/prmtop file was generated. Check {} for errors in building.'
                .format(logpath))

        if ionize:
            shutil.move(os.path.join(outdir, 'structure.crd'),
                        os.path.join(outdir, 'structure.noions.crd'))
            shutil.move(os.path.join(outdir, 'structure.prmtop'),
                        os.path.join(outdir, 'structure.noions.prmtop'))
            totalcharge = np.sum(molbuilt.charge)
            nwater = np.sum(molbuilt.atomselect('water and noh'))
            anion, cation, anionatom, cationatom, nanion, ncation = ionizef(
                totalcharge,
                nwater,
                saltconc=saltconc,
                ff='amber',
                anion=saltanion,
                cation=saltcation)
            newmol = ionizePlace(mol, anion, cation, anionatom, cationatom,
                                 nanion, ncation)
            # Redo the whole build but now with ions included
            return build(newmol,
                         ff=ff,
                         topo=topo,
                         param=param,
                         prefix=prefix,
                         outdir=outdir,
                         caps={},
                         ionize=False,
                         execute=execute,
                         saltconc=saltconc,
                         disulfide=disulfide,
                         tleap=tleap,
                         atomtypes=atomtypes,
                         offlibraries=offlibraries)
    tmpbonds = molbuilt.bonds
    molbuilt.bonds = []  # Removing the bonds to speed up writing
    molbuilt.write(os.path.join(outdir, 'structure.pdb'))
    molbuilt.bonds = tmpbonds  # Restoring the bonds
    return molbuilt
示例#4
0
文件: amber.py 项目: PabloHN/htmd
def build(mol, ff=None, topo=None, param=None, prefix='structure', outdir='./', caps=None, ionize=True, saltconc=0,
          saltanion=None, saltcation=None, disulfide=None, tleap='tleap', execute=True):
    """ Builds a system for AMBER

    Uses tleap to build a system for AMBER. Additionally it allows the user to ionize and add disulfide bridges.

    Parameters
    ----------
    mol : :class:`Molecule <htmd.molecule.molecule.Molecule>` object
        The Molecule object containing the system
    ff : list of str
        A list of leaprc forcefield files. Default: ['leaprc.lipid14', 'leaprc.ff14SB', 'leaprc.gaff']
    topo : list of str
        A list of topology `prepi` files.
    param : list of str
        A list of parameter `frcmod` files.
    prefix : str
        The prefix for the generated pdb and psf files
    outdir : str
        The path to the output directory
    caps : dict
        A dictionary with keys segids and values lists of strings describing the caps of that segment.
        e.g. caps['P'] = ['ACE', 'NME']. Default: will apply ACE and NME caps to proteins and no caps
        to the rest.
    ionize : bool
        Enable or disable ionization
    saltconc : float
        Salt concentration to add to the system after neutralization.
    saltanion : {'Cl-'}
        The anion type. Please use only AMBER ion atom names.
    saltcation : {'Na+', 'K+', 'Cs+'}
        The cation type. Please use only AMBER ion atom names.
    disulfide : np.ndarray
        If None it will guess disulfide bonds. Otherwise provide a 2D array where each row is a pair of atom indexes that makes a disulfide bond
    tleap : str
        Path to tleap executable used to build the system for AMBER
    execute : bool
        Disable building. Will only write out the input script needed by tleap. Does not include ionization.

    Returns
    -------
    molbuilt : :class:`Molecule <htmd.molecule.molecule.Molecule>` object
        The built system in a Molecule object

    Example
    -------
    >>> ffs = ['leaprc.lipid14', 'leaprc.ff14SB', 'leaprc.gaff']
    >>> molbuilt = amber.build(mol, ff=ffs, outdir='/tmp/build', saltconc=0.15)
    """
    # Remove pdb bonds!
    mol = mol.copy()
    mol.bonds = []
    if shutil.which(tleap) is None:
        raise NameError('Could not find executable: `' + tleap + '` in the PATH. Cannot build for AMBER.')
    if not os.path.isdir(outdir):
        os.makedirs(outdir)
    _cleanOutDir(outdir)
    if ff is None:
        ff = ['leaprc.lipid14', 'leaprc.ff14SB', 'leaprc.gaff']
    if topo is None:
        topo = []
    if param is None:
        param = []
    if caps is None:
        caps = _defaultCaps(mol)

    _missingSegID(mol)
    _checkMixedSegment(mol)

    logger.info('Converting CHARMM membranes to AMBER.')
    mol = _charmmLipid2Amber(mol)

    #_checkProteinGaps(mol)
    _applyCaps(mol, caps)

    f = open(path.join(outdir, 'tleap.in'), 'w')
    f.write('# tleap file generated by amber.build\n')

    # Printing out the forcefields
    for force in ff:
        f.write('source ' + force + '\n')
    f.write('\n')

    # Loading TIP3P water parameters
    f.write('# Loading ions and TIP3P water parameters\n')
    f.write('loadamberparams frcmod.ionsjc_tip3p\n\n')

    # Printing out topologies
    logger.info('Writing prepi files.')
    f.write('# Loading prepi topologies\n')
    for t in topo:
        shutil.copy(t, outdir)
        f.write('loadamberprep ' + path.basename(t) + '\n')
    f.write('\n')

    # Printing and loading the PDB file. AMBER can work with a single PDB file if the segments are separate by TER
    logger.info('Writing PDB file for input to tleap.')
    pdbname = path.join(outdir, 'input.pdb')
    mol.write(pdbname)
    if not os.path.isfile(pdbname):
        raise NameError('Could not write a PDB file out of the given Molecule.')
    f.write('# Loading the system\n')
    f.write('mol = loadpdb input.pdb\n\n')

    # Printing out patches for the disulfide bridges
    '''if disulfide is None and not ionize:
        logger.info('Detecting disulfide bonds.')
        disulfide = detectDisulfideBonds(mol)

    if not ionize and len(disulfide) != 0:  # Only make disu bonds after ionizing!
        f.write('# Adding disulfide bonds\n')
        for d in disulfide:
            # Convert to stupid amber residue numbering
            uqseqid = sequenceID(mol.resid)
            uqres1 = int(np.unique(uqseqid[mol.atomselect('segid {} and resid {}'.format(d.segid1, d.resid1))]))
            uqres2 = int(np.unique(uqseqid[mol.atomselect('segid {} and resid {}'.format(d.segid2, d.resid2))]))
            # Rename the CYS to CYX if there is a disulfide bond
            mol.set('resname', 'CYX', sel='segid {} and resid {}'.format(d.segid1, d.resid1))
            mol.set('resname', 'CYX', sel='segid {} and resid {}'.format(d.segid2, d.resid2))
            f.write('bond mol.{}.SG mol.{}.SG\n'.format(uqres1, uqres2))
        f.write('\n')'''

    f.write('# Writing out the results\n')
    f.write('savepdb mol ' + prefix + '.pdb\n')
    f.write('saveamberparm mol ' + prefix + '.prmtop ' + prefix + '.crd\n')
    f.write('quit')
    f.close()

    molbuilt = None
    if execute:
        logpath = os.path.abspath('{}/log.txt'.format(outdir))
        logger.info('Starting the build.')
        currdir = os.getcwd()
        os.chdir(outdir)
        f = open(logpath, 'w')
        try:
            call([tleap, '-f', './tleap.in'], stdout=f)
        except:
            raise NameError('tleap failed at execution')
        f.close()
        os.chdir(currdir)
        logger.info('Finished building.')

        if path.getsize(path.join(outdir, 'structure.pdb')) != 0 and path.getsize(path.join(outdir, 'structure.prmtop')) != 0:
            molbuilt = Molecule(path.join(outdir, 'structure.pdb'))
            molbuilt.read(path.join(outdir, 'structure.prmtop'))
            molbuilt.bonds = []  # Causes problems in ionization mol.remove and mol._removeBonds
        else:
            raise NameError('No structure pdb/prmtop file was generated. Check {} for errors in building.'.format(logpath))

        if ionize:
            shutil.move(path.join(outdir, 'structure.pdb'), path.join(outdir, 'structure.noions.pdb'))
            shutil.move(path.join(outdir, 'structure.crd'), path.join(outdir, 'structure.noions.crd'))
            shutil.move(path.join(outdir, 'structure.prmtop'), path.join(outdir, 'structure.noions.prmtop'))
            totalcharge = np.sum(molbuilt.charge)
            nwater = np.sum(molbuilt.atomselect('water and noh'))
            anion, cation, anionatom, cationatom, nanion, ncation = ionizef(totalcharge, nwater, saltconc=saltconc, ff='amber', anion=saltanion, cation=saltcation)
            newmol = ionizePlace(molbuilt, anion, cation, anionatom, cationatom, nanion, ncation)
            # Redo the whole build but now with ions included
            return build(newmol, ff=ff, topo=topo, param=param, prefix=prefix, outdir=outdir, caps={}, ionize=False,
                         execute=execute, saltconc=saltconc, disulfide=disulfide, tleap=tleap)
    return molbuilt
示例#5
0
def build(mol,
          ff=None,
          topo=None,
          param=None,
          prefix='structure',
          outdir='./',
          caps=None,
          ionize=True,
          saltconc=0,
          saltanion=None,
          saltcation=None,
          disulfide=None,
          tleap='tleap',
          execute=True):
    """ Builds a system for AMBER

    Uses tleap to build a system for AMBER. Additionally it allows the user to ionize and add disulfide bridges.

    Parameters
    ----------
    mol : :class:`Molecule <htmd.molecule.molecule.Molecule>` object
        The Molecule object containing the system
    ff : list of str
        A list of leaprc forcefield files. Default: ['leaprc.lipid14', 'leaprc.ff14SB', 'leaprc.gaff']
    topo : list of str
        A list of topology `prepi` files.
    param : list of str
        A list of parameter `frcmod` files.
    prefix : str
        The prefix for the generated pdb and psf files
    outdir : str
        The path to the output directory
    caps : dict
        A dictionary with keys segids and values lists of strings describing the caps of that segment.
        e.g. caps['P'] = ['ACE', 'NME']. Default: will apply ACE and NME caps to proteins and no caps
        to the rest.
    ionize : bool
        Enable or disable ionization
    saltconc : float
        Salt concentration to add to the system after neutralization.
    saltanion : {'Cl-'}
        The anion type. Please use only AMBER ion atom names.
    saltcation : {'Na+', 'K+', 'Cs+'}
        The cation type. Please use only AMBER ion atom names.
    disulfide : np.ndarray
        If None it will guess disulfide bonds. Otherwise provide a 2D array where each row is a pair of atom indexes that makes a disulfide bond
    tleap : str
        Path to tleap executable used to build the system for AMBER
    execute : bool
        Disable building. Will only write out the input script needed by tleap. Does not include ionization.

    Returns
    -------
    molbuilt : :class:`Molecule <htmd.molecule.molecule.Molecule>` object
        The built system in a Molecule object

    Example
    -------
    >>> ffs = ['leaprc.lipid14', 'leaprc.ff14SB', 'leaprc.gaff']
    >>> molbuilt = amber.build(mol, ff=ffs, outdir='/tmp/build', saltconc=0.15)
    """
    # Remove pdb bonds!
    mol = mol.copy()
    mol.bonds = np.empty((0, 2), dtype=np.uint32)
    if shutil.which(tleap) is None:
        raise NameError('Could not find executable: `' + tleap +
                        '` in the PATH. Cannot build for AMBER.')
    if not os.path.isdir(outdir):
        os.makedirs(outdir)
    _cleanOutDir(outdir)
    if ff is None:
        ff = ['leaprc.lipid14', 'leaprc.ff14SB', 'leaprc.gaff']
    if topo is None:
        topo = []
    if param is None:
        param = []
    if caps is None:
        caps = _defaultCaps(mol)

    _missingSegID(mol)
    _checkMixedSegment(mol)

    logger.info('Converting CHARMM membranes to AMBER.')
    mol = _charmmLipid2Amber(mol)

    #_checkProteinGaps(mol)
    _applyCaps(mol, caps)

    f = open(path.join(outdir, 'tleap.in'), 'w')
    f.write('# tleap file generated by amber.build\n')

    # Printing out the forcefields
    if isinstance(ff, str):
        ff = [ff]
    for force in ff:
        f.write('source ' + force + '\n')
    f.write('\n')

    # Loading TIP3P water parameters
    f.write('# Loading ions and TIP3P water parameters\n')
    f.write('loadamberparams frcmod.ionsjc_tip3p\n\n')

    # Loading user parameters
    f.write('# Loading parameter files\n')
    for p in param:
        shutil.copy(p, outdir)
        f.write('loadamberparams ' + path.basename(p) + '\n')
    f.write('\n')

    # Printing out topologies
    f.write('# Loading prepi topologies\n')
    for t in topo:
        shutil.copy(t, outdir)
        f.write('loadamberprep ' + path.basename(t) + '\n')
    f.write('\n')

    # Printing and loading the PDB file. AMBER can work with a single PDB file if the segments are separate by TER
    logger.info('Writing PDB file for input to tleap.')
    pdbname = path.join(outdir, 'input.pdb')
    mol.write(pdbname)
    if not os.path.isfile(pdbname):
        raise NameError(
            'Could not write a PDB file out of the given Molecule.')
    f.write('# Loading the system\n')
    f.write('mol = loadpdb input.pdb\n\n')

    # Printing out patches for the disulfide bridges
    if disulfide is None and not ionize:
        logger.info('Detecting disulfide bonds.')
        disulfide = detectDisulfideBonds(mol)

    if not ionize and len(
            disulfide) != 0:  # Only make disu bonds after ionizing!
        f.write('# Adding disulfide bonds\n')
        for d in disulfide:
            # Convert to stupid amber residue numbering
            uqseqid = sequenceID(
                (mol.resid, mol.insertion, mol.segid)) + mol.resid[0] - 1
            uqres1 = int(
                np.unique(uqseqid[mol.atomselect(
                    'segid {} and resid {}'.format(d.segid1, d.resid1))]))
            uqres2 = int(
                np.unique(uqseqid[mol.atomselect(
                    'segid {} and resid {}'.format(d.segid2, d.resid2))]))
            # Rename the CYS to CYX if there is a disulfide bond
            mol.set('resname',
                    'CYX',
                    sel='segid {} and resid {}'.format(d.segid1, d.resid1))
            mol.set('resname',
                    'CYX',
                    sel='segid {} and resid {}'.format(d.segid2, d.resid2))
            f.write('bond mol.{}.SG mol.{}.SG\n'.format(uqres1, uqres2))
        f.write('\n')

    f.write('# Writing out the results\n')
    f.write('saveamberparm mol ' + prefix + '.prmtop ' + prefix + '.crd\n')
    f.write('quit')
    f.close()

    molbuilt = None
    if execute:
        # Source paths of extra dirs
        htmdamberdir = path.join(home(), 'builder', 'amberfiles')
        sourcepaths = [htmdamberdir]
        sourcepaths += [path.join(htmdamberdir, path.dirname(f)) for f in ff]
        extrasource = ''
        for p in sourcepaths:
            extrasource += '-I {} '.format(p)
        logpath = os.path.abspath('{}/log.txt'.format(outdir))
        logger.info('Starting the build.')
        currdir = os.getcwd()
        os.chdir(outdir)
        f = open(logpath, 'w')
        try:
            call([tleap, extrasource, '-f', './tleap.in'], stdout=f)
        except:
            raise NameError('tleap failed at execution')
        f.close()
        os.chdir(currdir)
        logger.info('Finished building.')

        if path.getsize(path.join(
                outdir, 'structure.crd')) != 0 and path.getsize(
                    path.join(outdir, 'structure.prmtop')) != 0:
            molbuilt = Molecule(path.join(outdir, 'structure.prmtop'))
            molbuilt.read(path.join(outdir, 'structure.crd'))
        else:
            raise NameError(
                'No structure pdb/prmtop file was generated. Check {} for errors in building.'
                .format(logpath))

        if ionize:
            shutil.move(path.join(outdir, 'structure.crd'),
                        path.join(outdir, 'structure.noions.crd'))
            shutil.move(path.join(outdir, 'structure.prmtop'),
                        path.join(outdir, 'structure.noions.prmtop'))
            totalcharge = np.sum(molbuilt.charge)
            nwater = np.sum(molbuilt.atomselect('water and noh'))
            anion, cation, anionatom, cationatom, nanion, ncation = ionizef(
                totalcharge,
                nwater,
                saltconc=saltconc,
                ff='amber',
                anion=saltanion,
                cation=saltcation)
            newmol = ionizePlace(mol, anion, cation, anionatom, cationatom,
                                 nanion, ncation)
            # Redo the whole build but now with ions included
            return build(newmol,
                         ff=ff,
                         topo=topo,
                         param=param,
                         prefix=prefix,
                         outdir=outdir,
                         caps={},
                         ionize=False,
                         execute=execute,
                         saltconc=saltconc,
                         disulfide=disulfide,
                         tleap=tleap)
    molbuilt.write(path.join(outdir, 'structure.pdb'))
    return molbuilt
示例#6
0
文件: amber.py 项目: Acellera/htmd
def build(mol, ff=None, topo=None, param=None, prefix='structure', outdir='./build', caps=None, ionize=True, saltconc=0,
          saltanion=None, saltcation=None, disulfide=None, tleap='tleap', execute=True):
    """ Builds a system for AMBER

    Uses tleap to build a system for AMBER. Additionally it allows the user to ionize and add disulfide bridges.

    Parameters
    ----------
    mol : :class:`Molecule <htmd.molecule.molecule.Molecule>` object
        The Molecule object containing the system
    ff : list of str
        A list of leaprc forcefield files. Default: ['leaprc.lipid14', 'leaprc.ff14SB', 'leaprc.gaff']
    topo : list of str
        A list of topology `prepi` files.
    param : list of str
        A list of parameter `frcmod` files.
    prefix : str
        The prefix for the generated pdb and psf files
    outdir : str
        The path to the output directory
        Default: './build'
    caps : dict
        A dictionary with keys segids and values lists of strings describing the caps for a particular protein segment.
        e.g. caps['P'] = ['ACE', 'NME'] or caps['P'] = ['none', 'none']. Default: will apply ACE and NME caps to every
        protein segment.
    ionize : bool
        Enable or disable ionization
    saltconc : float
        Salt concentration to add to the system after neutralization.
    saltanion : {'Cl-'}
        The anion type. Please use only AMBER ion atom names.
    saltcation : {'Na+', 'K+', 'Cs+'}
        The cation type. Please use only AMBER ion atom names.
    disulfide : np.ndarray
        If None it will guess disulfide bonds. Otherwise provide a 2D array where each row is a pair of atom indexes that makes a disulfide bond
    tleap : str
        Path to tleap executable used to build the system for AMBER
    execute : bool
        Disable building. Will only write out the input script needed by tleap. Does not include ionization.

    Returns
    -------
    molbuilt : :class:`Molecule <htmd.molecule.molecule.Molecule>` object
        The built system in a Molecule object

    Example
    -------
    >>> ffs = ['leaprc.lipid14', 'leaprc.ff14SB', 'leaprc.gaff']
    >>> molbuilt = amber.build(mol, ff=ffs, outdir='/tmp/build', saltconc=0.15)
    """
    # Remove pdb bonds!
    mol = mol.copy()
    mol.bonds = np.empty((0, 2), dtype=np.uint32)
    if shutil.which(tleap) is None:
        raise NameError('Could not find executable: `' + tleap + '` in the PATH. Cannot build for AMBER.')
    if not os.path.isdir(outdir):
        os.makedirs(outdir)
    _cleanOutDir(outdir)
    if ff is None:
        ff = ['leaprc.lipid14', 'leaprc.ff14SB', 'leaprc.gaff']
    if topo is None:
        topo = []
    if param is None:
        param = []
    if caps is None:
        caps = _defaultProteinCaps(mol)

    _missingSegID(mol)
    _checkMixedSegment(mol)

    logger.info('Converting CHARMM membranes to AMBER.')
    mol = _charmmLipid2Amber(mol)

    #_checkProteinGaps(mol)
    _applyProteinCaps(mol, caps)

    f = open(path.join(outdir, 'tleap.in'), 'w')
    f.write('# tleap file generated by amber.build\n')

    # Printing out the forcefields
    if isinstance(ff, str):
        ff = [ff]
    for force in ff:
        f.write('source ' + force + '\n')
    f.write('\n')

    # Loading TIP3P water parameters
    f.write('# Loading ions and TIP3P water parameters\n')
    f.write('loadamberparams frcmod.ionsjc_tip3p\n\n')

    # Loading user parameters
    f.write('# Loading parameter files\n')
    for p in param:
        try:
            shutil.copy(p, outdir)
            f.write('loadamberparams ' + path.basename(p) + '\n')
        except:
            f.write('loadamberparams ' + p + '\n')
            logger.info("Path {:s} not found, assuming a standard AmberTools file.".
                        format(p))
    f.write('\n')

    # Printing out topologies
    f.write('# Loading prepi topologies\n')
    for t in topo:
        shutil.copy(t, outdir)
        f.write('loadamberprep ' + path.basename(t) + '\n')
    f.write('\n')

    # Detect disulfide bonds
    if disulfide is None and not ionize:
        logger.info('Detecting disulfide bonds.')
        disulfide = detectDisulfideBonds(mol)
        if len(disulfide) != 0:
            for d in disulfide:
                # Convert to stupid amber residue numbering
                uqseqid = sequenceID((mol.resid, mol.insertion, mol.segid)) + mol.resid[0] - 1
                uqres1 = int(np.unique(uqseqid[mol.atomselect('segid {} and resid {}'.format(d.segid1, d.resid1))]))
                uqres2 = int(np.unique(uqseqid[mol.atomselect('segid {} and resid {}'.format(d.segid2, d.resid2))]))
                # Rename the CYS to CYX if there is a disulfide bond
                mol.set('resname', 'CYX', sel='segid {} and resid {}'.format(d.segid1, d.resid1))
                mol.set('resname', 'CYX', sel='segid {} and resid {}'.format(d.segid2, d.resid2))
                # Remove (eventual) HG hydrogens on these CYS (from proteinPrepare)
                mol.remove('name HG and segid {} and resid {}'.format(d.segid1, d.resid1), _logger=False)
                mol.remove('name HG and segid {} and resid {}'.format(d.segid2, d.resid2), _logger=False)

    # Printing and loading the PDB file. AMBER can work with a single PDB file if the segments are separate by TER
    logger.info('Writing PDB file for input to tleap.')
    pdbname = path.join(outdir, 'input.pdb')

    # mol2 files have atomtype, here we only write parts not coming from mol2
    mol.write(pdbname, mol.atomtype == '')
    if not os.path.isfile(pdbname):
        raise NameError('Could not write a PDB file out of the given Molecule.')
    f.write('# Loading the system\n')
    f.write('mol = loadpdb input.pdb\n\n')

    if np.sum(mol.atomtype != '') != 0:
        logger.info('Writing mol2 files for input to tleap.')
        segs = np.unique(mol.segid[mol.atomtype != ''])
        combstr = 'mol = combine {mol'
        for s in segs:
            name = 'segment{}'.format(s)
            mol2name = path.join(outdir, '{}.mol2'.format(name))
            mol.write(mol2name, (mol.atomtype != '') & (mol.segid == s))
            if not os.path.isfile(mol2name):
                raise NameError('Could not write a mol2 file out of the given Molecule.')
            f.write('# Loading the rest of the system\n')
            f.write('{} = loadmol2 {}.mol2\n\n'.format(name, name))
            combstr += ' {}'.format(name)
        combstr += '}\n\n'
        f.write(combstr)

    # Printing out patches for the disulfide bridges
    if disulfide is None and not ionize:
        logger.info('Detecting disulfide bonds.')
        disulfide = detectDisulfideBonds(mol)

    # Write patches for disulfide bonds (only after ionizing)
    if not ionize and len(disulfide) != 0:
        f.write('# Adding disulfide bonds\n')
        for d in disulfide:
            # Convert to stupid amber residue numbering
            uqseqid = sequenceID((mol.resid, mol.insertion, mol.segid)) + mol.resid[0] - 1
            uqres1 = int(np.unique(uqseqid[mol.atomselect('segid {} and resid {}'.format(d.segid1, d.resid1))]))
            uqres2 = int(np.unique(uqseqid[mol.atomselect('segid {} and resid {}'.format(d.segid2, d.resid2))]))
            f.write('bond mol.{}.SG mol.{}.SG\n'.format(uqres1, uqres2))
        f.write('\n')

    f.write('# Writing out the results\n')
    f.write('saveamberparm mol ' + prefix + '.prmtop ' + prefix + '.crd\n')
    f.write('quit')
    f.close()

    molbuilt = None
    if execute:
        # Source paths of extra dirs (our dirs, not amber default)
        htmdamberdir = path.abspath(path.join(home(), 'builder', 'amberfiles'))
        sourcepaths = [htmdamberdir]
        sourcepaths += [path.join(htmdamberdir, path.dirname(f))
                        for f in ff if path.isfile(path.join(htmdamberdir, f))]
        extrasource = []
        for p in sourcepaths:
            extrasource.append('-I')
            extrasource.append('{}'.format(p))
        logpath = os.path.abspath(os.path.join(outdir, 'log.txt'))
        logger.info('Starting the build.')
        currdir = os.getcwd()
        os.chdir(outdir)
        f = open(logpath, 'w')
        try:
            cmd = [tleap, '-f', './tleap.in']
            cmd[1:1] = extrasource
            call(cmd, stdout=f)
        except:
            raise NameError('tleap failed at execution')
        f.close()
        os.chdir(currdir)
        logger.info('Finished building.')

        if path.getsize(path.join(outdir, 'structure.crd')) != 0 and path.getsize(path.join(outdir, 'structure.prmtop')) != 0:
            molbuilt = Molecule(path.join(outdir, 'structure.prmtop'))
            molbuilt.read(path.join(outdir, 'structure.crd'))
        else:
            raise NameError('No structure pdb/prmtop file was generated. Check {} for errors in building.'.format(logpath))

        if ionize:
            shutil.move(path.join(outdir, 'structure.crd'), path.join(outdir, 'structure.noions.crd'))
            shutil.move(path.join(outdir, 'structure.prmtop'), path.join(outdir, 'structure.noions.prmtop'))
            totalcharge = np.sum(molbuilt.charge)
            nwater = np.sum(molbuilt.atomselect('water and noh'))
            anion, cation, anionatom, cationatom, nanion, ncation = ionizef(totalcharge, nwater, saltconc=saltconc, ff='amber', anion=saltanion, cation=saltcation)
            newmol = ionizePlace(mol, anion, cation, anionatom, cationatom, nanion, ncation)
            # Redo the whole build but now with ions included
            return build(newmol, ff=ff, topo=topo, param=param, prefix=prefix, outdir=outdir, caps={}, ionize=False,
                         execute=execute, saltconc=saltconc, disulfide=disulfide, tleap=tleap)
    molbuilt.write(path.join(outdir, 'structure.pdb'))
    return molbuilt
示例#7
0
文件: charmm.py 项目: leelasd/htmd
def build(mol,
          topo=None,
          param=None,
          prefix='structure',
          outdir='./',
          caps=None,
          ionize=True,
          saltconc=0,
          saltanion=None,
          saltcation=None,
          disulfide=None,
          patches=None,
          psfgen=None,
          execute=True):
    """ Builds a system for CHARMM

    Uses VMD and psfgen to build a system for CHARMM. Additionally it allows for ionization and adding of disulfide bridges.

    Parameters
    ----------
    mol : :class:`Molecule <htmd.molecule.molecule.Molecule>` object
        The Molecule object containing the system
    topo : list of str
        A list of topology `rtf` files. Default: ['top/top_all22star_prot.rtf', 'top/top_all36_lipid.rtf', 'top/top_water_ions.rtf']
    param : list of str
        A list of parameter `prm` files. Default: ['par/par_all22star_prot.prm', 'par/par_all36_lipid.prm', 'par/par_water_ions.prm']
    prefix : str
        The prefix for the generated pdb and psf files
    outdir : str
        The path to the output directory
    caps : dict
        A dictionary with keys segids and values lists of strings describing the caps of that segment.
        e.g. caps['P'] = ['first ACE', 'last CT3']. Default: will apply ACE and CT3 caps to proteins and none caps
        to the rest
    ionize : bool
        Enable or disable ionization
    saltconc : float
        Salt concentration (in Molar) to add to the system after neutralization.
    saltanion : {'CLA'}
        The anion type. Please use only CHARMM ion atom names.
    saltcation : {'SOD', 'MG', 'POT', 'CES', 'CAL', 'ZN2'}
        The cation type. Please use only CHARMM ion atom names.
    disulfide : list of :class:`DisulfideBridge <htmd.builder.builder.DisulfideBridge>` objects
        If None it will guess disulfide bonds. Otherwise provide a list of `DisulfideBridge` objects.
    patches : list of str
        Any further patches the user wants to apply
    psfgen : str
        Path to psfgen executable used to build for CHARMM
    execute : bool
        Disable building. Will only write out the input script needed by psfgen. Does not include ionization.

    Returns
    -------
    molbuilt : :class:`Molecule <htmd.molecule.molecule.Molecule>` object
        The built system in a Molecule object

    Example
    -------
    >>> charmm.listFiles()
    >>> topos  = ['top/top_all22star_prot.rtf', './benzamidine.rtf']
    >>> params = ['par/par_all22star_prot.prm', './benzamidine.prm']
    >>> molbuilt = charmm.build(mol, topo=topos, param=params, outdir='/tmp/build', saltconc=0.15)
    """
    mol = mol.copy()
    _missingSegID(mol)
    if psfgen is None:
        try:
            psfgen = shutil.which('psfgen', mode=os.X_OK)
        except:
            raise FileNotFoundError(
                'Could not find psfgen executable, or no execute permissions are given. '
                'Run `conda install psfgen`.')
    if not os.path.isdir(outdir):
        os.makedirs(outdir)
    _cleanOutDir(outdir)
    if topo is None:
        topo = _defaultTopo()
    if param is None:
        param = _defaultParam()
    if caps is None:
        caps = _defaultCaps(mol)

    #_missingChain(mol)
    #_checkProteinGaps(mol)
    if patches is None:
        patches = []
    if isinstance(patches, str):
        patches = [patches]
    # Find protonated residues and add patches for them
    patches += _protonationPatches(mol)

    f = open(path.join(outdir, 'build.vmd'), 'w')
    f.write('# psfgen file generated by charmm.build\n')
    f.write('package require psfgen;\n')
    f.write('psfcontext reset;\n\n')

    # Copying and printing out the topologies
    charmmdir = path.join(home(), 'builder', 'charmmfiles')
    for i in range(len(topo)):
        if topo[i][0] != '.' and path.isfile(path.join(charmmdir, topo[i])):
            topo[i] = path.join(charmmdir, topo[i])
        localname = '{}.'.format(i) + path.basename(topo[i])
        shutil.copy(topo[i], path.join(outdir, localname))
        f.write('topology ' + localname + '\n')
    f.write('\n')

    _printAliases(f)

    # Printing out segments
    logger.info('Writing out segments.')
    segments = _getSegments(mol)
    for seg in segments:
        pdbname = 'segment' + seg + '.pdb'
        mol.write(path.join(outdir, pdbname), sel='segid ' + seg)

        segatoms = mol.atomselect('segid {}'.format(seg))
        segwater = mol.atomselect('segid {} and water'.format(seg))

        f.write('segment ' + seg + ' {\n')
        if np.all(segatoms ==
                  segwater):  # If segment only contains waters, set: auto none
            f.write('\tauto none\n')
        f.write('\tpdb ' + pdbname + '\n')
        if caps is not None and seg in caps:
            for c in caps[seg]:
                f.write('\t' + c + '\n')
        f.write('}\n')
        f.write('coordpdb ' + pdbname + ' ' + seg + '\n\n')

    # Printing out patches for the disulfide bridges
    if disulfide is None:
        disulfide = detectDisulfideBonds(mol)

    if len(disulfide) != 0:
        for d in disulfide:
            f.write('patch DISU {}:{} {}:{}\n'.format(d.segid1, d.resid1,
                                                      d.segid2, d.resid2))
        f.write('\n')

    # Printing out extra patches
    if len(patches) != 0:
        for p in patches:
            f.write(p + '\n')
        f.write('\n')

    f.write('guesscoord\n')
    f.write('writepsf ' + prefix + '.psf\n')
    f.write('writepdb ' + prefix + '.pdb\n')
    #f.write('quit\n')
    f.close()

    if param is not None:
        _charmmCombine(param, path.join(outdir, 'parameters'))

    molbuilt = None
    if execute:
        logpath = os.path.abspath('{}/log.txt'.format(outdir))
        logger.info('Starting the build.')
        currdir = os.getcwd()
        os.chdir(outdir)
        f = open(logpath, 'w')
        #call([vmd, '-dispdev', 'text', '-e', './build.vmd'], stdout=f)
        call([psfgen, './build.vmd'], stdout=f)
        f.close()
        _logParser(logpath)
        os.chdir(currdir)
        logger.info('Finished building.')

        if path.isfile(path.join(outdir, 'structure.pdb')) and path.isfile(
                path.join(outdir, 'structure.psf')):
            molbuilt = Molecule(path.join(outdir, 'structure.pdb'))
            molbuilt.read(path.join(outdir, 'structure.psf'))
        else:
            raise NameError(
                'No structure pdb/psf file was generated. Check {} for errors in building.'
                .format(logpath))

        if ionize:
            shutil.move(path.join(outdir, 'structure.pdb'),
                        path.join(outdir, 'structure.noions.pdb'))
            shutil.move(path.join(outdir, 'structure.psf'),
                        path.join(outdir, 'structure.noions.psf'))
            totalcharge = np.sum(molbuilt.charge)
            nwater = np.sum(molbuilt.atomselect('water and noh'))
            anion, cation, anionatom, cationatom, nanion, ncation = ionizef(
                totalcharge,
                nwater,
                saltconc=saltconc,
                ff='charmm',
                anion=saltanion,
                cation=saltcation)
            newmol = ionizePlace(mol, anion, cation, anionatom, cationatom,
                                 nanion, ncation)
            # Redo the whole build but now with ions included
            return build(newmol,
                         topo=topo,
                         param=param,
                         prefix=prefix,
                         outdir=outdir,
                         ionize=False,
                         caps=caps,
                         execute=execute,
                         saltconc=saltconc,
                         disulfide=disulfide,
                         patches=patches,
                         psfgen=psfgen)
    return molbuilt
示例#8
0
文件: amber.py 项目: alejandrovr/htmd
def build(mol, ff=None, topo=None, param=None, prefix='structure', outdir='./build', caps=None, ionize=True, saltconc=0,
          saltanion=None, saltcation=None, disulfide=None, tleap=None, execute=True, atomtypes=None,
          offlibraries=None, gbsa=False, igb=2):
    """ Builds a system for AMBER

    Uses tleap to build a system for AMBER. Additionally it allows the user to ionize and add disulfide bridges.

    Parameters
    ----------
    mol : :class:`Molecule <htmd.molecule.molecule.Molecule>` object
        The Molecule object containing the system
    ff : list of str
        A list of leaprc forcefield files.
        Use :func:`amber.listFiles <htmd.builder.amber.listFiles>` to get a list of available forcefield files.
        Default: :func:`amber.defaultFf <htmd.builder.amber.defaultFf>`
    topo : list of str
        A list of topology `prepi/prep/in` files.
        Use :func:`amber.listFiles <htmd.builder.amber.listFiles>` to get a list of available topology files.
        Default: :func:`amber.defaultTopo <htmd.builder.amber.defaultTopo>`
    param : list of str
        A list of parameter `frcmod` files.
        Use :func:`amber.listFiles <htmd.builder.amber.listFiles>` to get a list of available parameter files.
        Default: :func:`amber.defaultParam <htmd.builder.amber.defaultParam>`
    prefix : str
        The prefix for the generated pdb and psf files
    outdir : str
        The path to the output directory
        Default: './build'
    caps : dict
        A dictionary with keys segids and values lists of strings describing the caps for a particular protein segment.
        e.g. caps['P'] = ['ACE', 'NME'] or caps['P'] = ['none', 'none']. Default: will apply ACE and NME caps to every
        protein segment.
    ionize : bool
        Enable or disable ionization
    saltconc : float
        Salt concentration to add to the system after neutralization.
    saltanion : {'Cl-'}
        The anion type. Please use only AMBER ion atom names.
    saltcation : {'Na+', 'K+', 'Cs+'}
        The cation type. Please use only AMBER ion atom names.
    disulfide : list of pairs of atomselection strings
        If None it will guess disulfide bonds. Otherwise provide a list pairs of atomselection strings for each pair of
        residues forming the disulfide bridge.
    tleap : str
        Path to tleap executable used to build the system for AMBER
    execute : bool
        Disable building. Will only write out the input script needed by tleap. Does not include ionization.
    atomtypes : list of triplets
        Custom atom types defined by the user as ('type', 'element', 'hybrid') triplets
        e.g. (('C1', 'C', 'sp2'), ('CI', 'C', 'sp3')). Check `addAtomTypes` in AmberTools docs.
    offlibraries : str or list
        A path or a list of paths to OFF library files. Check `loadOFF` in AmberTools docs.
    gbsa : bool
        Modify radii for GBSA implicit water model
    igb : int
        GB model. Select: 1 for mbondi, 2 and 5 for mbondi2, 7 for bondi and 8 for mbondi3.
        Check section 4. The Generalized Born/Surface Area Model of the AMBER manual.

    Returns
    -------
    molbuilt : :class:`Molecule <htmd.molecule.molecule.Molecule>` object
        The built system in a Molecule object

    Example
    -------
    >>> from htmd.ui import *  # doctest: +SKIP
    >>> mol = Molecule("3PTB")
    >>> molbuilt = amber.build(mol, outdir='/tmp/build')  # doctest: +SKIP
    >>> # More complex example
    >>> disu = [['segid P and resid 157', 'segid P and resid 13'], ['segid K and resid 1', 'segid K and resid 25']]
    >>> molbuilt = amber.build(mol, outdir='/tmp/build', saltconc=0.15, disulfide=disu)  # doctest: +SKIP
    """
    # Remove pdb protein bonds as they can be regenerated by tleap. Keep non-protein bonds i.e. for ligands
    mol = mol.copy()
    _removeProteinBonds(mol)

    if tleap is None:
        tleap = _findTleap()
    else:
        if shutil.which(tleap) is None:
            raise NameError('Could not find executable: `{}` in the PATH. Cannot build for AMBER.'.format(tleap))

    if not os.path.isdir(outdir):
        os.makedirs(outdir)
    _cleanOutDir(outdir)
    if ff is None:
        ff = defaultFf()
    if topo is None:
        topo = defaultTopo()
    if param is None:
        param = defaultParam()
    if caps is None:
        caps = _defaultProteinCaps(mol)

    _missingSegID(mol)
    _checkMixedSegment(mol)

    mol = _charmmLipid2Amber(mol)

    _applyProteinCaps(mol, caps)

    f = open(os.path.join(outdir, 'tleap.in'), 'w')
    f.write('# tleap file generated by amber.build\n')

    # Printing out the forcefields
    if isinstance(ff, str):
        ff = [ff]
    for i, force in enumerate(ff):
        if not os.path.isfile(force):
            force = _locateFile(force, 'ff', tleap)
            if force is None:
                continue
        newname = 'ff{}_{}'.format(i, os.path.basename(force))
        shutil.copy(force, os.path.join(outdir, newname))
        f.write('source {}\n'.format(newname))
    f.write('\n')

    if gbsa:
        gbmodels = {1: 'mbondi', 2: 'mbondi2', 5: 'mbondi2', 7: 'bondi', 8: 'mbondi3'}
        f.write('set default PBradii {}\n\n'.format(gbmodels[igb]))

    # Adding custom atom types
    if atomtypes is not None:
        atomtypes = ensurelist(tocheck=atomtypes[0], tomod=atomtypes)
        f.write('addAtomTypes {\n')
        for at in atomtypes:
            if len(at) != 3:
                raise RuntimeError('Atom type definitions have to be triplets. Check the AMBER documentation.')
            f.write('    {{ "{}" "{}" "{}" }}\n'.format(at[0], at[1], at[2]))
        f.write('}\n\n')

    # Loading OFF libraries
    if offlibraries is not None:
        offlibraries = ensurelist(offlibraries)
        for off in offlibraries:
            if not os.path.isfile(off):
                raise RuntimeError('Could not find off-library in location {}'.format(off))
            newname = 'offlib{}_{}'.format(i, os.path.basename(off))
            shutil.copy(off, os.path.join(outdir, newname))
            f.write('loadoff {}\n'.format(newname))

    # Loading frcmod parameters
    f.write('# Loading parameter files\n')
    for i, p in enumerate(param):
        if not os.path.isfile(p):
            p = _locateFile(p, 'param', tleap)
            if p is None:
                continue
        newname = 'param{}_{}'.format(i, os.path.basename(p))
        shutil.copy(p, os.path.join(outdir, newname))
        f.write('loadamberparams {}\n'.format(newname))
    f.write('\n')

    # Loading prepi topologies
    f.write('# Loading prepi topologies\n')
    for i, t in enumerate(topo):
        if not os.path.isfile(t):
            t = _locateFile(t, 'topo', tleap)
            if t is None:
                continue
        newname = 'topo{}_{}'.format(i, os.path.basename(t))
        shutil.copy(t, os.path.join(outdir, newname))
        f.write('loadamberprep {}\n'.format(newname))
    f.write('\n')

    f.write('# Loading the system\n')
    f.write('mol = loadpdb input.pdb\n\n')

    if np.sum(mol.atomtype != '') != 0:
        logger.debug('Writing mol2 files for input to tleap.')
        segs = np.unique(mol.segid[mol.atomtype != ''])
        combstr = 'mol = combine {mol'
        for s in segs:
            name = 'segment{}'.format(s)
            mol2name = os.path.join(outdir, '{}.mol2'.format(name))
            mol.write(mol2name, (mol.atomtype != '') & (mol.segid == s))
            if not os.path.isfile(mol2name):
                raise NameError('Could not write a mol2 file out of the given Molecule.')
            f.write('# Loading the rest of the system\n')
            f.write('{} = loadmol2 {}.mol2\n\n'.format(name, name))
            combstr += ' {}'.format(name)
        combstr += '}\n\n'
        f.write(combstr)

    # Write patches for disulfide bonds (only after ionizing)
    if not ionize:
        # TODO: Remove this once we deprecate the class
        from htmd.builder.builder import DisulfideBridge
        from htmd.molecule.molecule import UniqueResidueID
        if disulfide is not None and len(disulfide) != 0 and isinstance(disulfide[0], DisulfideBridge):
            newdisu = []
            for d in disulfide:
                r1 = UniqueResidueID.fromMolecule(mol, 'resid {} and segname {}'.format(d.resid1, d.segid1))
                r2 = UniqueResidueID.fromMolecule(mol, 'resid {} and segname {}'.format(d.resid2, d.segid2))
                newdisu.append([r1, r2])
            disulfide = newdisu
        # TODO: Remove up to here ----------------------

        if disulfide is not None and len(disulfide) != 0 and isinstance(disulfide[0][0], str):
            disulfide = convertDisulfide(mol, disulfide)

        if disulfide is None:
            logger.info('Detecting disulfide bonds.')
            disulfide = detectDisulfideBonds(mol)

        # Fix structure to match the disulfide patching
        if len(disulfide) != 0:
            torem = np.zeros(mol.numAtoms, dtype=bool)
            f.write('# Adding disulfide bonds\n')
            for d in disulfide:
                # Rename the residues to CYX if there is a disulfide bond
                atoms1 = d[0].selectAtoms(mol, indexes=False)
                atoms2 = d[1].selectAtoms(mol, indexes=False)
                mol.resname[atoms1] = 'CYX'
                mol.resname[atoms2] = 'CYX'
                # Remove (eventual) HG hydrogens on these CYS (from proteinPrepare)
                torem |= (atoms1 & (mol.name == 'HG')) | (atoms2 & (mol.name == 'HG'))
                # Convert to stupid amber residue numbering
                uqseqid = sequenceID((mol.resid, mol.insertion, mol.segid)) + mol.resid[0]
                uqres1 = int(np.unique(uqseqid[atoms1]))
                uqres2 = int(np.unique(uqseqid[atoms2]))
                f.write('bond mol.{}.SG mol.{}.SG\n'.format(uqres1, uqres2))
            f.write('\n')
            mol.remove(torem, _logger=False)

    f.write('# Writing out the results\n')
    f.write('saveamberparm mol ' + prefix + '.prmtop ' + prefix + '.crd\n')
    f.write('quit')
    f.close()

    # Printing and loading the PDB file. AMBER can work with a single PDB file if the segments are separate by TER
    logger.debug('Writing PDB file for input to tleap.')
    pdbname = os.path.join(outdir, 'input.pdb')

    # mol2 files have atomtype, here we only write parts not coming from mol2
    # We need to write the input.pdb at the end since we modify the resname for disulfide bridges in mol
    mol.write(pdbname, mol.atomtype == '')
    if not os.path.isfile(pdbname):
        raise NameError('Could not write a PDB file out of the given Molecule.')

    molbuilt = None
    if execute:
        # Source paths of extra dirs (our dirs, not amber default)
        htmdamberdir = os.path.abspath(os.path.join(home(), 'builder', 'amberfiles'))
        sourcepaths = [htmdamberdir]
        sourcepaths += [os.path.join(htmdamberdir, os.path.dirname(f))
                        for f in ff if os.path.isfile(os.path.join(htmdamberdir, f))]
        extrasource = []
        for p in sourcepaths:
            extrasource.append('-I')
            extrasource.append('{}'.format(p))
        logpath = os.path.abspath(os.path.join(outdir, 'log.txt'))
        logger.info('Starting the build.')
        currdir = os.getcwd()
        os.chdir(outdir)
        f = open(logpath, 'w')
        try:
            cmd = [tleap, '-f', './tleap.in']
            cmd[1:1] = extrasource
            call(cmd, stdout=f)
        except:
            raise NameError('tleap failed at execution')
        f.close()
        errors = _logParser(logpath)
        os.chdir(currdir)
        if errors:
            raise BuildError(errors + ['Check {} for further information on errors in building.'.format(logpath)])
        logger.info('Finished building.')

        if os.path.exists(os.path.join(outdir, 'structure.crd')) and \
                        os.path.getsize(os.path.join(outdir, 'structure.crd')) != 0 and \
                        os.path.getsize(os.path.join(outdir, 'structure.prmtop')) != 0:
            molbuilt = Molecule(os.path.join(outdir, 'structure.prmtop'))
            molbuilt.read(os.path.join(outdir, 'structure.crd'))
        else:
            raise BuildError('No structure pdb/prmtop file was generated. Check {} for errors in building.'.format(logpath))

        if ionize:
            shutil.move(os.path.join(outdir, 'structure.crd'), os.path.join(outdir, 'structure.noions.crd'))
            shutil.move(os.path.join(outdir, 'structure.prmtop'), os.path.join(outdir, 'structure.noions.prmtop'))
            totalcharge = np.sum(molbuilt.charge)
            nwater = np.sum(molbuilt.atomselect('water and noh'))
            anion, cation, anionatom, cationatom, nanion, ncation = ionizef(totalcharge, nwater, saltconc=saltconc,
                                                                            anion=saltanion, cation=saltcation)
            newmol = ionizePlace(mol, anion, cation, anionatom, cationatom, nanion, ncation)
            # Redo the whole build but now with ions included
            return build(newmol, ff=ff, topo=topo, param=param, prefix=prefix, outdir=outdir, caps={}, ionize=False,
                         execute=execute, saltconc=saltconc, disulfide=disulfide, tleap=tleap, atomtypes=atomtypes,
                         offlibraries=offlibraries)
    tmpbonds = molbuilt.bonds
    molbuilt.bonds = []  # Removing the bonds to speed up writing
    molbuilt.write(os.path.join(outdir, 'structure.pdb'))
    molbuilt.bonds = tmpbonds  # Restoring the bonds
    return molbuilt
示例#9
0
文件: charmm.py 项目: jeiros/htmd
def build(mol, topo=None, param=None, stream=None, prefix='structure', outdir='./build', caps=None, ionize=True, saltconc=0,
          saltanion=None, saltcation=None, disulfide=None, patches=None, noregen=None, psfgen=None, execute=True, _clean=True):
    """ Builds a system for CHARMM

    Uses VMD and psfgen to build a system for CHARMM. Additionally it allows for ionization and adding of disulfide bridges.

    Parameters
    ----------
    mol : :class:`Molecule <htmd.molecule.molecule.Molecule>` object
        The Molecule object containing the system
    topo : list of str
        A list of topology `rtf` files.
        Use :func:`charmm.listFiles <htmd.builder.charmm.listFiles>` to get a list of available topology files.
        Default: ['top/top_all36_prot.rtf', 'top/top_all36_lipid.rtf', 'top/top_water_ions.rtf']
    param : list of str
        A list of parameter `prm` files.
        Use :func:`charmm.listFiles <htmd.builder.charmm.listFiles>` to get a list of available parameter files.
        Default: ['par/par_all36_prot_mod.prm', 'par/par_all36_lipid.prm', 'par/par_water_ions.prm']
    stream : list of str
        A list of stream `str` files containing topologies and parameters.
        Use :func:`charmm.listFiles <htmd.builder.charmm.listFiles>` to get a list of available stream files.
        Default: ['str/prot/toppar_all36_prot_arg0.str']
    prefix : str
        The prefix for the generated pdb and psf files
    outdir : str
        The path to the output directory
        Default: './build'
    caps : dict
        A dictionary with keys segids and values lists of strings describing the caps of that segment.
        e.g. caps['P'] = ['first ACE', 'last CT3'] or caps['P'] = ['first none', 'last none']. 
        Default: will apply ACE and CT3 caps to proteins and none caps to the rest.
    ionize : bool
        Enable or disable ionization
    saltconc : float
        Salt concentration (in Molar) to add to the system after neutralization.
    saltanion : {'CLA'}
        The anion type. Please use only CHARMM ion atom names.
    saltcation : {'SOD', 'MG', 'POT', 'CES', 'CAL', 'ZN2'}
        The cation type. Please use only CHARMM ion atom names.
    disulfide : list of :class:`DisulfideBridge <htmd.builder.builder.DisulfideBridge>` objects
        If None it will guess disulfide bonds. Otherwise provide a list of `DisulfideBridge` objects.
    patches : list of str
        Any further patches the user wants to apply
    noregen : list of str
        A list of patches that must not be regenerated (angles and dihedrals)
        Default: ['FHEM', 'PHEM', 'PLOH', 'PLO2', 'PLIG', 'PSUL']
    psfgen : str
        Path to psfgen executable used to build for CHARMM
    execute : bool
        Disable building. Will only write out the input script needed by psfgen. Does not include ionization.

    Returns
    -------
    molbuilt : :class:`Molecule <htmd.molecule.molecule.Molecule>` object
        The built system in a Molecule object

    Example
    -------
    >>> from htmd import *
    >>> mol = Molecule("3PTB")
    >>> mol.filter("not resname BEN")
    >>> mol.renumberResidues()
    >>> molbuilt = charmm.build(mol, outdir='/tmp/build', ionize=False)  # doctest: +ELLIPSIS
    Bond between A: [serial 185 resid 42 resname CYS chain A segid 0]
                 B: [serial 298 resid 58 resname CYS chain A segid 0]...
    >>> # More complex example
    >>> topos  = ['top/top_all36_prot.rtf', './benzamidine.rtf', 'top/top_water_ions.rtf']
    >>> params = ['par/par_all36_prot_mod.prm', './benzamidine.prm', 'par/par_water_ions.prm']
    >>> disu = [DisulfideBridge('P', 157, 'P', 13), DisulfideBridge('K', 1, 'K', 25)]
    >>> molbuilt = charmm.build(mol, topo=topos, param=params, outdir='/tmp/build', saltconc=0.15, disulfide=disu)  # doctest: +SKIP
    """

    mol = mol.copy()
    _missingSegID(mol)
    _checkMixedSegment(mol)
    _checkResidueInsertions(mol)
    if psfgen is None:
        psfgen = shutil.which('psfgen', mode=os.X_OK)
        if not psfgen:
            raise FileNotFoundError('Could not find psfgen executable, or no execute permissions are given. '
                                    'Run `conda install psfgen`.')
    if not os.path.isdir(outdir):
        os.makedirs(outdir)
    if _clean:
        _cleanOutDir(outdir)
    if topo is None:
        topo = defaultTopo()
    if param is None:
        param = defaultParam()
    if stream is None:
        stream = defaultStream()
    if caps is None:
        caps = _defaultCaps(mol)
    # patches that must _not_ be regenerated
    if noregen is None:
        noregen = ['FHEM', 'PHEM', 'PLOH', 'PLO2', 'PLIG', 'PSUL']

    alltopo = topo.copy()
    allparam = param.copy()

    # Splitting the stream files and adding them to the list of parameter and topology files
    charmmdir = path.join(home(), 'builder', 'charmmfiles')
    for s in stream:
        if s[0] != '.' and path.isfile(path.join(charmmdir, s)):
            s = path.join(charmmdir, s)
        outrtf, outprm = _prepareStream(s)
        alltopo.append(outrtf)
        allparam.append(outprm)

    #_missingChain(mol)
    #_checkProteinGaps(mol)
    if patches is None:
        patches = []
    if isinstance(patches, str):
        patches = [patches]
    allpatches = []
    allpatches += patches
    # Find protonated residues and add patches for them
    allpatches += _protonationPatches(mol)

    f = open(path.join(outdir, 'build.vmd'), 'w')
    f.write('# psfgen file generated by charmm.build\n')
    f.write('package require psfgen;\n')
    f.write('psfcontext reset;\n\n')

    # Copying and printing out the topologies
    if not path.exists(path.join(outdir, 'topologies')):
        os.makedirs(path.join(outdir, 'topologies'))
    for i in range(len(alltopo)):
        if alltopo[i][0] != '.' and path.isfile(path.join(charmmdir, alltopo[i])):
            alltopo[i] = path.join(charmmdir, alltopo[i])
        localname = '{}.'.format(i) + path.basename(alltopo[i])
        shutil.copy(alltopo[i], path.join(outdir, 'topologies', localname))
        f.write('topology ' + path.join('topologies', localname) + '\n')
    f.write('\n')

    _printAliases(f)

    # Printing out segments
    if not path.exists(path.join(outdir, 'segments')):
        os.makedirs(path.join(outdir, 'segments'))
    logger.info('Writing out segments.')
    segments = _getSegments(mol)
    wateratoms = mol.atomselect('water')
    for seg in segments:
        pdbname = 'segment' + seg + '.pdb'
        segatoms = mol.segid == seg
        mol.write(path.join(outdir, 'segments', pdbname), sel=segatoms)

        segwater = wateratoms & segatoms
        f.write('segment ' + seg + ' {\n')
        if np.all(segatoms == segwater):  # If segment only contains waters, set: auto none
            f.write('\tauto none\n')
        f.write('\tpdb ' + path.join('segments', pdbname) + '\n')
        if caps is not None and seg in caps:
            for c in caps[seg]:
                f.write('\t' + c + '\n')
        f.write('}\n')
        f.write('coordpdb ' + path.join('segments', pdbname) + ' ' + seg + '\n\n')

    # Printing out patches for the disulfide bridges
    if disulfide is None:
        disulfide = detectDisulfideBonds(mol)

    if len(disulfide) != 0:
        for d in disulfide:
            f.write('patch DISU {}:{} {}:{}\n'.format(d.segid1, d.resid1, d.segid2, d.resid2))
        f.write('\n')

    noregenpatches = [p for p in allpatches if p.split()[1] in noregen]
    regenpatches = [p for p in allpatches if p.split()[1] not in noregen]

    # Printing regenerable patches
    if len(regenpatches) != 0:
        for p in regenpatches:
            f.write(p + '\n')
        f.write('\n')

    # Regenerate angles and dihedrals
    f.write('regenerate angles dihedrals\n')
    f.write('\n')

    # Printing non-regenerable patches
    if len(noregenpatches) != 0:
        for p in noregenpatches:
            f.write(p + '\n')
        f.write('\n')

    f.write('guesscoord\n')
    f.write('writepsf ' + prefix + '.psf\n')
    f.write('writepdb ' + prefix + '.pdb\n')
    #f.write('quit\n')
    f.close()

    if allparam is not None:
        combine(allparam, path.join(outdir, 'parameters'))

    molbuilt = None
    if execute:
        logpath = os.path.abspath('{}/log.txt'.format(outdir))
        logger.info('Starting the build.')
        currdir = os.getcwd()
        os.chdir(outdir)
        f = open(logpath, 'w')
        #call([vmd, '-dispdev', 'text', '-e', './build.vmd'], stdout=f)
        call([psfgen, './build.vmd'], stdout=f)
        f.close()
        errors = _logParser(logpath)
        os.chdir(currdir)
        if errors:
            raise BuildError(errors + ['Check {} for further information on errors in building.'.format(logpath)])
        logger.info('Finished building.')

        if path.isfile(path.join(outdir, 'structure.pdb')) and path.isfile(path.join(outdir, 'structure.psf')):
            molbuilt = Molecule(path.join(outdir, 'structure.pdb'))
            molbuilt.read(path.join(outdir, 'structure.psf'))
        else:
            raise BuildError('No structure pdb/psf file was generated. Check {} for errors in building.'.format(logpath))

        if ionize:
            os.makedirs(path.join(outdir, 'pre-ionize'))
            data = glob(path.join(outdir, '*'))
            for f in data:
                shutil.move(f, path.join(outdir, 'pre-ionize'))
            totalcharge = np.sum(molbuilt.charge)
            nwater = np.sum(molbuilt.atomselect('water and noh'))
            anion, cation, anionatom, cationatom, nanion, ncation = ionizef(totalcharge, nwater, saltconc=saltconc, ff='charmm', anion=saltanion, cation=saltcation)
            newmol = ionizePlace(mol, anion, cation, anionatom, cationatom, nanion, ncation)
            # Redo the whole build but now with ions included
            return build(newmol, topo=alltopo, param=allparam, stream=[], prefix=prefix, outdir=outdir, ionize=False, caps=caps,
                         execute=execute, saltconc=saltconc, disulfide=disulfide, patches=patches, noregen=noregen, psfgen=psfgen, _clean=False)
    _checkFailedAtoms(molbuilt)
    _recoverProtonations(molbuilt)
    return molbuilt
示例#10
0
文件: charmm.py 项目: andreubp/htmd
def build(mol, topo=None, param=None, stream=None, prefix='structure', outdir='./', caps=None, ionize=True, saltconc=0,
          saltanion=None, saltcation=None, disulfide=None, patches=None, psfgen=None, execute=True):
    """ Builds a system for CHARMM

    Uses VMD and psfgen to build a system for CHARMM. Additionally it allows for ionization and adding of disulfide bridges.

    Parameters
    ----------
    mol : :class:`Molecule <htmd.molecule.molecule.Molecule>` object
        The Molecule object containing the system
    topo : list of str
        A list of topology `rtf` files.
        Use :func:`charmm.listFiles <htmd.builder.charmm.listFiles>` to get a list of available topology files.
        Default: ['top/top_all36_prot.rtf', 'top/top_all36_lipid.rtf', 'top/top_water_ions.rtf']
    param : list of str
        A list of parameter `prm` files.
        Use :func:`charmm.listFiles <htmd.builder.charmm.listFiles>` to get a list of available parameter files.
        Default: ['par/par_all36_prot_mod.prm', 'par/par_all36_lipid.prm', 'par/par_water_ions.prm']
    stream : list of str
        A list of stream `str` files containing topologies and parameters.
        Use :func:`charmm.listFiles <htmd.builder.charmm.listFiles>` to get a list of available stream files.
        Default: ['str/prot/toppar_all36_prot_arg0.str']
    prefix : str
        The prefix for the generated pdb and psf files
    outdir : str
        The path to the output directory
    caps : dict
        A dictionary with keys segids and values lists of strings describing the caps of that segment.
        e.g. caps['P'] = ['first ACE', 'last CT3']. Default: will apply ACE and CT3 caps to proteins and none caps
        to the rest
    ionize : bool
        Enable or disable ionization
    saltconc : float
        Salt concentration (in Molar) to add to the system after neutralization.
    saltanion : {'CLA'}
        The anion type. Please use only CHARMM ion atom names.
    saltcation : {'SOD', 'MG', 'POT', 'CES', 'CAL', 'ZN2'}
        The cation type. Please use only CHARMM ion atom names.
    disulfide : list of :class:`DisulfideBridge <htmd.builder.builder.DisulfideBridge>` objects
        If None it will guess disulfide bonds. Otherwise provide a list of `DisulfideBridge` objects.
    patches : list of str
        Any further patches the user wants to apply
    psfgen : str
        Path to psfgen executable used to build for CHARMM
    execute : bool
        Disable building. Will only write out the input script needed by psfgen. Does not include ionization.

    Returns
    -------
    molbuilt : :class:`Molecule <htmd.molecule.molecule.Molecule>` object
        The built system in a Molecule object

    Example
    -------
    >>> charmm.listFiles()
    >>> topos  = ['top/top_all36_prot.rtf', './benzamidine.rtf']
    >>> params = ['par/par_all36_prot_mod.prm', './benzamidine.prm']
    >>> molbuilt = charmm.build(mol, topo=topos, param=params, outdir='/tmp/build', saltconc=0.15)
    """
    mol = mol.copy()
    _missingSegID(mol)
    if psfgen is None:
        try:
            psfgen = shutil.which('psfgen', mode=os.X_OK)
        except:
            raise FileNotFoundError('Could not find psfgen executable, or no execute permissions are given. '
                                    'Run `conda install psfgen`.')
    if not os.path.isdir(outdir):
        os.makedirs(outdir)
    _cleanOutDir(outdir)
    if topo is None:
        topo = ['top/top_all36_prot.rtf', 'top/top_all36_lipid.rtf', 'top/top_water_ions.rtf']
    if param is None:
        param = ['par/par_all36_prot_mod.prm', 'par/par_all36_lipid.prm', 'par/par_water_ions.prm']
    if stream is None:
        stream = ['str/prot/toppar_all36_prot_arg0.str']
    if caps is None:
        caps = _defaultCaps(mol)

    # Splitting the stream files and adding them to the list of parameter and topology files
    charmmdir = path.join(home(), 'builder', 'charmmfiles')
    for s in stream:
        if s[0] != '.' and path.isfile(path.join(charmmdir, s)):
            s = path.join(charmmdir, s)
        outrtf, outprm = _prepareStream(s)
        topo.append(outrtf)
        param.append(outprm)

    #_missingChain(mol)
    #_checkProteinGaps(mol)
    if patches is None:
        patches = []
    if isinstance(patches, str):
        patches = [patches]
    # Find protonated residues and add patches for them
    patches += _protonationPatches(mol)

    f = open(path.join(outdir, 'build.vmd'), 'w')
    f.write('# psfgen file generated by charmm.build\n')
    f.write('package require psfgen;\n')
    f.write('psfcontext reset;\n\n')

    # Copying and printing out the topologies
    for i in range(len(topo)):
        if topo[i][0] != '.' and path.isfile(path.join(charmmdir, topo[i])):
            topo[i] = path.join(charmmdir, topo[i])
        localname = '{}.'.format(i) + path.basename(topo[i])
        shutil.copy(topo[i], path.join(outdir, localname))
        f.write('topology ' + localname + '\n')
    f.write('\n')

    _printAliases(f)

    # Printing out segments
    logger.info('Writing out segments.')
    segments = _getSegments(mol)
    for seg in segments:
        pdbname = 'segment' + seg + '.pdb'
        mol.write(path.join(outdir, pdbname), sel='segid '+seg)

        segatoms = mol.atomselect('segid {}'.format(seg))
        segwater = mol.atomselect('segid {} and water'.format(seg))

        f.write('segment ' + seg + ' {\n')
        if np.all(segatoms == segwater):  # If segment only contains waters, set: auto none
            f.write('\tauto none\n')
        f.write('\tpdb ' + pdbname + '\n')
        if caps is not None and seg in caps:
            for c in caps[seg]:
                f.write('\t' + c + '\n')
        f.write('}\n')
        f.write('coordpdb ' + pdbname + ' ' + seg + '\n\n')

    # Printing out patches for the disulfide bridges
    if disulfide is None:
        disulfide = detectDisulfideBonds(mol)

    if len(disulfide) != 0:
        for d in disulfide:
            f.write('patch DISU {}:{} {}:{}\n'.format(d.segid1, d.resid1, d.segid2, d.resid2))
        f.write('\n')

    # Printing out extra patches
    if len(patches) != 0:
        for p in patches:
            f.write(p + '\n')
        f.write('\n')

    f.write('guesscoord\n')
    f.write('writepsf ' + prefix + '.psf\n')
    f.write('writepdb ' + prefix + '.pdb\n')
    #f.write('quit\n')
    f.close()

    if param is not None:
        _charmmCombine(param, path.join(outdir, 'parameters'))

    molbuilt = None
    if execute:
        logpath = os.path.abspath('{}/log.txt'.format(outdir))
        logger.info('Starting the build.')
        currdir = os.getcwd()
        os.chdir(outdir)
        f = open(logpath, 'w')
        #call([vmd, '-dispdev', 'text', '-e', './build.vmd'], stdout=f)
        call([psfgen, './build.vmd'], stdout=f)
        f.close()
        _logParser(logpath)
        os.chdir(currdir)
        logger.info('Finished building.')

        if path.isfile(path.join(outdir, 'structure.pdb')) and path.isfile(path.join(outdir, 'structure.psf')):
            molbuilt = Molecule(path.join(outdir, 'structure.pdb'))
            molbuilt.read(path.join(outdir, 'structure.psf'))
        else:
            raise NameError('No structure pdb/psf file was generated. Check {} for errors in building.'.format(logpath))

        if ionize:
            shutil.move(path.join(outdir, 'structure.pdb'), path.join(outdir, 'structure.noions.pdb'))
            shutil.move(path.join(outdir, 'structure.psf'), path.join(outdir, 'structure.noions.psf'))
            totalcharge = np.sum(molbuilt.charge)
            nwater = np.sum(molbuilt.atomselect('water and noh'))
            anion, cation, anionatom, cationatom, nanion, ncation = ionizef(totalcharge, nwater, saltconc=saltconc, ff='charmm', anion=saltanion, cation=saltcation)
            newmol = ionizePlace(mol, anion, cation, anionatom, cationatom, nanion, ncation)
            # Redo the whole build but now with ions included
            return build(newmol, topo=topo, param=param, prefix=prefix, outdir=outdir, ionize=False, caps=caps,
                         execute=execute, saltconc=saltconc, disulfide=disulfide, patches=patches, psfgen=psfgen)
    _checkFailedAtoms(molbuilt)
    return molbuilt