コード例 #1
0
ファイル: util.py プロジェクト: alejandrovr/htmd
def drawIsoSurface(values3d, resolution=1., plot_center=None, viewer=None):
    from htmd.vmdviewer import getCurrentViewer
    from htmd.molecule.util import writeVoxels
    # plot_center should be - molecule.get_center() + 12
    if len(values3d.shape) != 3:
        raise ValueError("Your provided a box of {} dimensions."
                         "\nThis only works with dimension of 3".format(len(values3d.shape)))
    from htmd.util import tempname
    if viewer is None:
        viewer = getCurrentViewer()
    mincoor = np.zeros(3, dtype=np.float64)
    maxcoor = np.array(values3d.shape, dtype=np.float64)
    rescoor = np.array([resolution] * 3)

    # Adjust the plotting center
    if plot_center is None:
        plot_center = maxcoor / 2.
    else:
        plot_center = np.array(plot_center)
    mincoor -= (plot_center + 0.5)  # TODO: Fix so it will work in case resolution != 1.
    maxcoor -= (plot_center + 0.5)

    outf = tempname(suffix='.cube')
    writeVoxels(values3d, outf, mincoor, maxcoor, rescoor)
    viewer.send('mol new {} type cube first 0 last -1 step 1 waitfor 1 volsets {{0 }}'.format(outf))
    viewer.send('mol modstyle 0 top Isosurface 0.75 0 2 0 1 1')
コード例 #2
0
ファイル: vmdgraphics.py プロジェクト: tonigi/htmd
    def __init__(self, xyz, color='red', radius=1):
        """ Displays a sphere in VMD.

        The function returns an instance of VMDGraphicsObject. To delete it, use the delete() method.

        Parameters
        ----------
        xyz : list
            The center of the sphere
        color : str
            Color of the sphere
        radius : float
            The radius of the sphere
        """
        super().__init__(xyz)
        #self._remember('draw materials off')
        self._remember('draw color {}'.format(color))

        self._remember('draw sphere "{} {} {}" radius {}\n'.format(
            xyz[0], xyz[1], xyz[2], radius))
        self.script.write("\n")
        self.script.write("set htmd_graphics_mol({:d}) [molinfo top]".format(
            self.n))
        cmd = self.script.getvalue()
        vmd = getCurrentViewer()
        vmd.send(cmd)
コード例 #3
0
ファイル: model.py プロジェクト: xielm12/htmd
    def viewStates(self,
                   states=None,
                   statetype='macro',
                   protein=None,
                   ligand=None,
                   viewer=None,
                   mols=None,
                   numsamples=50):
        """ Visualize macro/micro/cluster states in VMD

        Parameters
        ----------
        states : ndarray, optional
            A list of states to visualize
        statetype : ['macro','micro','cluster'], optional
            The type of state to visualize
        protein : bool, optional
            Set to True to enable pure protein system visualization
        ligand : str, optional
            Atomselection string for the ligand
        viewer : :class:`VMD <htmd.vmdviewer.VMD>` object, optional
            A viewer in which to visualize the states
        mols : ndarray, optional
            An array of :class:`Molecule <htmd.molecule.molecule.Molecule>` objects to visualize
        numsamples : int
            Number of samples (conformations) for each state.

        Examples
        --------
        >>> model = Model(data)
        >>> model.markovModel(100, 5)
        >>> model.viewStates(protein=True)

        >>> model.viewStates(ligand='resname MOL')
        """
        from htmd.config import _config
        self._integrityCheck(postmsm=(statetype != 'cluster'))

        if _config['viewer'].lower() == 'ngl':
            return self._viewStatesNGL(states, statetype, protein, ligand,
                                       mols, numsamples)

        if viewer is None:
            viewer = getCurrentViewer()
        if states is None:
            states = range(self.macronum)
        if isinstance(states, int):
            states = [states]
        if mols is None:
            mols = self.getStates(states, statetype, numsamples=numsamples)
        colors = [0, 1, 3, 4, 5, 6, 7, 9]
        for i, s in enumerate(states):
            viewer.loadMol(mols[i], name=statetype + ' ' + str(states[i]))
            if ligand is not None:
                viewer.rep('ligand',
                           sel=ligand,
                           color=colors[np.mod(i, len(colors))])
            if protein is not None:
                viewer.rep('protein')
            viewer.send('start_sscache')
コード例 #4
0
ファイル: vmdgraphics.py プロジェクト: jeiros/htmd
    def __init__(self, arr, vecMin, vecRes, color=8, isovalue=0.5):
        """ Displays an isosurface in VMD

        The function returns an instance of VMDGraphicsObject. To delete it, use the delete() method.

        Parameters
        ----------
        arr: np.ndarray
            3D array with volumetric data.
        vecMin: np.ndarray
            3D vector denoting the minimal corner of the grid
        vecRes: np.ndarray
            3D vector denoting the resolution of the grid in each dimension
        color: str
            The color to be used for the isosurface
        """
        super().__init__(arr)
        from htmd.util import tempname
        import numpy as np
        import os
        filename = tempname(suffix='.cube')
        outFile = open(filename, 'w')

        # conversion to gaussian units
        L = 1 / 0.52917725
        gauss_bin = vecRes * L
        # minCorner = 0.5*L*(vecMin - vecMax + vecRes)
        minCorner = L * (vecMin + 0.5 * vecRes)

        ngrid = arr.shape

        # write header
        outFile.write("CUBE FILE\n")
        outFile.write("OUTER LOOP: X, MIDDLE LOOP: Y, INNER LOOP: Z\n")
        outFile.write("%5d %12.6f %12.6f %12.6f\n" % (1, minCorner[0], minCorner[1], minCorner[2]))
        outFile.write("%5d %12.6f %12.6f %12.6f\n" % (ngrid[0], gauss_bin[0], 0, 0))
        outFile.write("%5d %12.6f %12.6f %12.6f\n" % (ngrid[1], 0, gauss_bin[1], 0))
        outFile.write("%5d %12.6f %12.6f %12.6f\n" % (ngrid[2], 0, 0, gauss_bin[2]))
        outFile.write("%5d %12.6f %12.6f %12.6f %12.6f\n" % (1, 0, minCorner[0], minCorner[1], minCorner[2]))

        # main loop
        cont = 0

        for i in range(ngrid[0]):
            for j in range(ngrid[1]):
                for k in range(ngrid[2]):
                    outFile.write("%13.5g" % arr[i][j][k])
                    if np.mod(cont, 6) == 5:
                        outFile.write("\n")
                    cont += 1

        outFile.close()
        vmd = getCurrentViewer()

        vmd.send('mol new {} type cube first 0 last -1 step 1 waitfor 1 volsets {{0 }}'.format(filename))
        vmd.send('mol modstyle top top Isosurface {} 0 2 0 2 1'.format(isovalue))
        vmd.send('mol modcolor top top ColorID {}'.format(color))
        vmd.send('set htmd_graphics_mol({:d}) [molinfo top]'.format(self.n))

        os.unlink(filename)
コード例 #5
0
ファイル: vmdgraphics.py プロジェクト: tonigi/htmd
    def __init__(self, text, xyz, color='red'):
        """ Displays a text in VMD.

        The function returns an instance of VMDGraphicsObject. To delete it, use the delete() method.

        Parameters
        ----------
        text : str
            The text
        xyz : list
            The position of the text
        color : str
            Color of the text
        """
        super().__init__(xyz)
        self._remember('draw materials off')
        self._remember('draw color {}'.format(color))

        self._remember('draw text "{} {} {}" "{}"\n'.format(
            xyz[0], xyz[1], xyz[2], text))
        self.script.write("\n")
        self.script.write("set htmd_graphics_mol({:d}) [molinfo top]".format(
            self.n))
        cmd = self.script.getvalue()
        vmd = getCurrentViewer()
        vmd.send(cmd)
コード例 #6
0
ファイル: util.py プロジェクト: PabloHN/htmd
def drawCube(mi, ma, viewer=None):
    from htmd.vmdviewer import getCurrentViewer
    if viewer is None:
        viewer = getCurrentViewer()

    viewer.send('draw materials off')
    viewer.send('draw color red')
    c = ''
    c += 'draw line "{} {} {}" "{} {} {}"\n'.format(mi[0], mi[1], mi[2], ma[0], mi[1], mi[2])
    c += 'draw line "{} {} {}" "{} {} {}"\n'.format(mi[0], mi[1], mi[2], mi[0], ma[1], mi[2])
    c += 'draw line "{} {} {}" "{} {} {}"\n'.format(mi[0], mi[1], mi[2], mi[0], mi[1], ma[2])

    c += 'draw line "{} {} {}" "{} {} {}"\n'.format(ma[0], mi[1], mi[2], ma[0], ma[1], mi[2])
    c += 'draw line "{} {} {}" "{} {} {}"\n'.format(ma[0], mi[1], mi[2], ma[0], mi[1], ma[2])

    c += 'draw line "{} {} {}" "{} {} {}"\n'.format(mi[0], ma[1], mi[2], ma[0], ma[1], mi[2])
    c += 'draw line "{} {} {}" "{} {} {}"\n'.format(mi[0], ma[1], mi[2], mi[0], ma[1], ma[2])

    c += 'draw line "{} {} {}" "{} {} {}"\n'.format(mi[0], mi[1], ma[2], ma[0], mi[1], ma[2])
    c += 'draw line "{} {} {}" "{} {} {}"\n'.format(mi[0], mi[1], ma[2], mi[0], ma[1], ma[2])

    c += 'draw line "{} {} {}" "{} {} {}"\n'.format(ma[0], ma[1], ma[2], ma[0], ma[1], mi[2])
    c += 'draw line "{} {} {}" "{} {} {}"\n'.format(ma[0], ma[1], ma[2], mi[0], ma[1], ma[2])
    c += 'draw line "{} {} {}" "{} {} {}"\n'.format(ma[0], ma[1], ma[2], ma[0], mi[1], ma[2])
    viewer.send(c)

    """
コード例 #7
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ファイル: model.py プロジェクト: cuzzo87/htmd
    def viewStates(self, states=None, statetype='macro', protein=None, ligand=None, viewer=None, mols=None,
                   numsamples=50, wrapsel='protein', alignsel='name CA', gui=False, simlist=None):
        """ Visualize macro/micro/cluster states in VMD

        Parameters
        ----------
        states : ndarray, optional
            A list of states to visualize
        statetype : ['macro','micro','cluster'], optional
            The type of state to visualize
        protein : bool, optional
            Set to True to enable pure protein system visualization
        ligand : str, optional
            Atom selection string for the ligand.
            See more `here <http://www.ks.uiuc.edu/Research/vmd/vmd-1.9.2/ug/node89.html>`__
        viewer : :class:`VMD <htmd.vmdviewer.VMD>` object, optional
            A viewer in which to visualize the states
        mols : ndarray, optional
            An array of :class:`Molecule <htmd.molecule.molecule.Molecule>` objects to visualize
        numsamples : int
            Number of samples (conformations) for each state.
        wrapsel : str, optional, default='protein'
            Atom selection string to use for wrapping.
            See more `here <http://www.ks.uiuc.edu/Research/vmd/vmd-1.9.2/ug/node89.html>`__
        alignsel : str, optional, default='name CA'
            Atom selection string used for aligning all frames. See to None to disable aligning.
            See more `here <http://www.ks.uiuc.edu/Research/vmd/vmd-1.9.2/ug/node89.html>`__
        simlist : numpy.ndarray of :class:`Sim <htmd.simlist.Sim>` objects
            Optionally pass a different (but matching, i.e. filtered) simlist for visualizing the states.

        Examples
        --------
        >>> model = Model(data)
        >>> model.markovModel(100, 5)
        >>> model.viewStates(protein=True)

        >>> model.viewStates(ligand='resname MOL')
        """
        from htmd.config import _config
        self._integrityCheck(postmsm=(statetype != 'cluster'))

        if _config['viewer'].lower() == 'ngl' or _config['viewer'].lower() == 'webgl':
            return self._viewStatesNGL(states, statetype, protein, ligand, mols, numsamples, gui=gui)

        if viewer is None:
            viewer = getCurrentViewer()
        if states is None:
            states = range(self.macronum)
        if isinstance(states, int):
            states = [states]
        if mols is None:
            mols = self.getStates(states, statetype, numsamples=numsamples, wrapsel=wrapsel, alignsel=alignsel, simlist=simlist)
        colors = [0, 1, 3, 4, 5, 6, 7, 9]
        for i, s in enumerate(states):
            viewer.loadMol(mols[i], name=statetype+' '+str(states[i]))
            if ligand is not None:
                viewer.rep('ligand', sel=ligand, color=colors[np.mod(i, len(colors))])
            if protein is not None:
                viewer.rep('protein')
            viewer.send('start_sscache')
コード例 #8
0
ファイル: vmdgraphics.py プロジェクト: jeiros/htmd
    def __init__(self, m, style="", preamble="", solid=False):
        """Display the convex hull of the given molecule.

        For preamble and color, see http://www.ks.uiuc.edu/Research/vmd/vmd-1.9.2/ug/node129.html

        The function returns an instance of VMDGraphicsObject. To delete it, use the delete() method.

        Parameters
        ----------
        m: Molecule
            The object of which to show the hull (only 1 frame)
        style: str
            Style for wireframe lines
        preamble: str
            Commands (material, color) to be prefixed to the output.
            E.g.: "draw color red; graphics top materials on; graphics top material Transparent".
            Note that this affects later preamble-less commands.
        solid: bool
            Solid or wireframe

        Examples
        --------
        >>> m=Molecule("3PTB")
        >>> m.view()
        >>> mf=m.copy()
        >>> mf.filter("protein ")
        >>> gh=htmd.vmdgraphics.VMDConvexHull(mf)  # doctest: +ELLIPSIS
        >>> gh.delete()
        """

        from scipy.spatial import ConvexHull

        if m.coords.shape[2] != 1:
            raise Exception("Only one frame is supported")

        cc = m.coords[:, :, 0]
        hull = ConvexHull(cc)

        super().__init__(hull)
        self.script.write(preamble + "\n")

        for i in range(hull.nsimplex):
            v1, v2, v3 = hull.simplices[i, :]
            c1s = VMDGraphicObject.tq(cc[v1, :])
            c2s = VMDGraphicObject.tq(cc[v2, :])
            c3s = VMDGraphicObject.tq(cc[v3, :])
            if solid:
                self._remember("draw triangle {:s} {:s} {:s}".format(c1s, c2s, c3s))
            else:
                self._remember("draw line {:s} {:s} {:s}".format(c1s, c2s, style))
                self._remember("draw line {:s} {:s} {:s}".format(c1s, c3s, style))
                self._remember("draw line {:s} {:s} {:s}".format(c2s, c3s, style))
                self.script.write("\n")

        self.script.write("set htmd_graphics_mol({:d}) [molinfo top]".format(self.n))
        cmd = self.script.getvalue()
        vmd = getCurrentViewer()
        vmd.send(cmd)
コード例 #9
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ファイル: model.py プロジェクト: Acellera/htmd
    def viewStates(self, states=None, statetype='macro', protein=None, ligand=None, viewer=None, mols=None,
                   numsamples=50, wrapsel='protein', alignsel='name CA', gui=False, simlist=None):
        """ Visualize macro/micro/cluster states in VMD

        Parameters
        ----------
        states : ndarray, optional
            A list of states to visualize
        statetype : ['macro','micro','cluster'], optional
            The type of state to visualize
        protein : bool, optional
            Set to True to enable pure protein system visualization
        ligand : str, optional
            Atomselection string for the ligand
        viewer : :class:`VMD <htmd.vmdviewer.VMD>` object, optional
            A viewer in which to visualize the states
        mols : ndarray, optional
            An array of :class:`Molecule <htmd.molecule.molecule.Molecule>` objects to visualize
        numsamples : int
            Number of samples (conformations) for each state.
        wrapsel : str, optional, default='protein'
            A selection to use for wrapping
        alignsel : str, optional, default='name CA'
            A selection used for aligning all frames
        simlist : simlist
            Optionally pass a different (but matching, i.e. filtered) simlist for visualizing the states.

        Examples
        --------
        >>> model = Model(data)
        >>> model.markovModel(100, 5)
        >>> model.viewStates(protein=True)

        >>> model.viewStates(ligand='resname MOL')
        """
        from htmd.config import _config
        self._integrityCheck(postmsm=(statetype != 'cluster'))

        if _config['viewer'].lower() == 'ngl':
            return self._viewStatesNGL(states, statetype, protein, ligand, mols, numsamples, gui=gui)

        if viewer is None:
            viewer = getCurrentViewer()
        if states is None:
            states = range(self.macronum)
        if isinstance(states, int):
            states = [states]
        if mols is None:
            mols = self.getStates(states, statetype, numsamples=numsamples, wrapsel=wrapsel, alignsel=alignsel, simlist=simlist)
        colors = [0, 1, 3, 4, 5, 6, 7, 9]
        for i, s in enumerate(states):
            viewer.loadMol(mols[i], name=statetype+' '+str(states[i]))
            if ligand is not None:
                viewer.rep('ligand', sel=ligand, color=colors[np.mod(i, len(colors))])
            if protein is not None:
                viewer.rep('protein')
            viewer.send('start_sscache')
コード例 #10
0
ファイル: pathplanning.py プロジェクト: jeiros/htmd
def _prepareViewer(mol, ligandsel):
    mol.view(sel='protein', style='lines', hold=True)
    mol.view(sel=ligandsel, style='licorice', hold=True)
    mol.view()

    viewer = getCurrentViewer()
    viewer.send('draw color red')
    viewer.send('color Display Background black')
    viewer.send('draw materials off')
    return viewer
コード例 #11
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ファイル: vmdgraphics.py プロジェクト: tonigi/htmd
    def __init__(self, box, color='red'):
        """ Displays a box in VMD as lines of its edges.

        The function returns an instance of VMDGraphicsObject. To delete it, use the delete() method.

        Parameters
        ----------
        box : list
            The min and max positions of the edges. Given as [xmin, xmax, ymin, ymax, zmin, zmax]
        color : str
            Color of the lines
        """
        super().__init__(box)
        xmin, xmax, ymin, ymax, zmin, zmax = box
        mi = [xmin, ymin, zmin]
        ma = [xmax, ymax, zmax]

        self._remember('draw materials off')
        self._remember('draw color {}'.format(color))

        self._remember('draw line "{} {} {}" "{} {} {}"\n'.format(
            mi[0], mi[1], mi[2], ma[0], mi[1], mi[2]))
        self._remember('draw line "{} {} {}" "{} {} {}"\n'.format(
            mi[0], mi[1], mi[2], mi[0], ma[1], mi[2]))
        self._remember('draw line "{} {} {}" "{} {} {}"\n'.format(
            mi[0], mi[1], mi[2], mi[0], mi[1], ma[2]))

        self._remember('draw line "{} {} {}" "{} {} {}"\n'.format(
            ma[0], mi[1], mi[2], ma[0], ma[1], mi[2]))
        self._remember('draw line "{} {} {}" "{} {} {}"\n'.format(
            ma[0], mi[1], mi[2], ma[0], mi[1], ma[2]))

        self._remember('draw line "{} {} {}" "{} {} {}"\n'.format(
            mi[0], ma[1], mi[2], ma[0], ma[1], mi[2]))
        self._remember('draw line "{} {} {}" "{} {} {}"\n'.format(
            mi[0], ma[1], mi[2], mi[0], ma[1], ma[2]))

        self._remember('draw line "{} {} {}" "{} {} {}"\n'.format(
            mi[0], mi[1], ma[2], ma[0], mi[1], ma[2]))
        self._remember('draw line "{} {} {}" "{} {} {}"\n'.format(
            mi[0], mi[1], ma[2], mi[0], ma[1], ma[2]))

        self._remember('draw line "{} {} {}" "{} {} {}"\n'.format(
            ma[0], ma[1], ma[2], ma[0], ma[1], mi[2]))
        self._remember('draw line "{} {} {}" "{} {} {}"\n'.format(
            ma[0], ma[1], ma[2], mi[0], ma[1], ma[2]))
        self._remember('draw line "{} {} {}" "{} {} {}"\n'.format(
            ma[0], ma[1], ma[2], ma[0], mi[1], ma[2]))
        self.script.write("\n")
        self.script.write("set htmd_graphics_mol({:d}) [molinfo top]".format(
            self.n))
        cmd = self.script.getvalue()
        vmd = getCurrentViewer()
        vmd.send(cmd)
コード例 #12
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ファイル: ffevaluate.py プロジェクト: diallobakary4/htmd
def _drawForce(start, vec):
    assert start.ndim == 1 and vec.ndim == 1
    from htmd.vmdviewer import getCurrentViewer
    vmd = getCurrentViewer()
    vmd.send("""
    proc vmd_draw_arrow {start end} {
        # an arrow is made of a cylinder and a cone
        draw color green
        set middle [vecadd $start [vecscale 0.9 [vecsub $end $start]]]
        graphics top cylinder $start $middle radius 0.15
        graphics top cone $middle $end radius 0.25
    }
    """)
    vmd.send('vmd_draw_arrow {{ {} }} {{ {} }}'.format(' '.join(map(str, start)), ' '.join(map(str, start + vec))))
コード例 #13
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ファイル: ffevaluate.py プロジェクト: alejandrovr/htmd
def _drawForce(start, vec):
    assert start.ndim == 1 and vec.ndim == 1
    from htmd.vmdviewer import getCurrentViewer
    vmd = getCurrentViewer()
    vmd.send("""
    proc vmd_draw_arrow {start end} {
        # an arrow is made of a cylinder and a cone
        draw color green
        set middle [vecadd $start [vecscale 0.9 [vecsub $end $start]]]
        graphics top cylinder $start $middle radius 0.15
        graphics top cone $middle $end radius 0.25
    }
    """)
    vmd.send('vmd_draw_arrow {{ {} }} {{ {} }}'.format(' '.join(map(str, start)), ' '.join(map(str, start + vec))))
コード例 #14
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    def __init__(self,
                 mol,
                 selection,
                 molid='top',
                 textsize=0.5,
                 textcolor='green'):
        """ Displays labels on atoms in VMD.

        Examples
        --------
        >>> from htmd.ui import *
        >>> from htmd.vmdgraphics import *
        >>> mol = Molecule('3ptb')
        >>> mol.view()
        >>> x = VMDLabels(mol, 'resid 40')
        >>> y = VMDLabels(mol, 'resid 50')
        >>> y.delete()
        >>> x.delete()
        """
        # TODO: After deleting labels it breaks. Better don't delete or fix the code
        super().__init__(None)
        print(VMDLabels.count)
        idx = mol.atomselect(selection, indexes=True)
        cmd = '''label textsize {s}
color Labels Atoms {c}
set molnum [molinfo {molid}]
set i {start}
foreach n [list {idx}] {{
    label add Atoms $molnum/$n
    label textformat Atoms $i {{%a}}
    incr i
}}'''.format(s=textsize,
             c=textcolor,
             sel=selection,
             molid=molid,
             idx=' '.join(map(str, idx)),
             start=VMDLabels.count)
        self.labelidx = list(range(VMDLabels.count,
                                   VMDLabels.count + len(idx)))
        VMDLabels.count += len(idx)
        vmd = getCurrentViewer()
        vmd.send(cmd)
コード例 #15
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    def viewStates(self, protein=None, ligand=None, nsamples=20):
        from htmd.projections.metric import _singleMolfile
        from htmd.molecule.molecule import Molecule
        from htmd.vmdviewer import getCurrentViewer
        (single, molfile) = _singleMolfile(self.data.simlist)
        if not single:
            raise RuntimeError('Can'
                               't visualize states without unique molfile')

        viewer = getCurrentViewer()
        colors = [0, 1, 3, 4, 5, 6, 7, 9]

        print('Active set includes macrostates: {}'.format(
            self.hmm.active_set))

        # dtraj = np.vstack(self.hmm.discrete_trajectories_full)
        res = self.hmm.sample_by_observation_probabilities(nsamples)
        refmol = Molecule(molfile)

        for i, s in enumerate(self.hmm.active_set):
            mol = Molecule(molfile)
            mol.coords = []
            mol.box = []
            # idx = np.where(dtraj == i)[0]
            # samples = np.random.choice(idx, 20)
            # frames = self.data.abs2sim(samples)

            frames = self.data.rel2sim(res[i])
            for f in frames:
                mol._readTraj(f.sim.trajectory[f.piece],
                              frames=[f.frame],
                              append=True)
            mol.wrap('protein')
            mol.align('protein', refmol=refmol)
            viewer.loadMol(mol, name='hmm macro ' + str(s))
            if ligand is not None:
                viewer.rep('ligand',
                           sel=ligand,
                           color=colors[np.mod(i, len(colors))])
            if protein is not None:
                viewer.rep('protein')
            viewer.send('start_sscache')
コード例 #16
0
ファイル: vmdgraphics.py プロジェクト: jeiros/htmd
    def __init__(self, box, color='red'):
        """ Displays a box in VMD as lines of its edges.

        The function returns an instance of VMDGraphicsObject. To delete it, use the delete() method.

        Parameters
        ----------
        box : list
            The min and max positions of the edges. Given as [xmin, xmax, ymin, ymax, zmin, zmax]
        color : str
            Color of the lines
        """
        super().__init__(box)
        xmin, xmax, ymin, ymax, zmin, zmax = box
        mi = [xmin, ymin, zmin]
        ma = [xmax, ymax, zmax]

        self._remember('draw materials off')
        self._remember('draw color {}'.format(color))

        self._remember('draw line "{} {} {}" "{} {} {}"\n'.format(mi[0], mi[1], mi[2], ma[0], mi[1], mi[2]))
        self._remember('draw line "{} {} {}" "{} {} {}"\n'.format(mi[0], mi[1], mi[2], mi[0], ma[1], mi[2]))
        self._remember('draw line "{} {} {}" "{} {} {}"\n'.format(mi[0], mi[1], mi[2], mi[0], mi[1], ma[2]))

        self._remember('draw line "{} {} {}" "{} {} {}"\n'.format(ma[0], mi[1], mi[2], ma[0], ma[1], mi[2]))
        self._remember('draw line "{} {} {}" "{} {} {}"\n'.format(ma[0], mi[1], mi[2], ma[0], mi[1], ma[2]))

        self._remember('draw line "{} {} {}" "{} {} {}"\n'.format(mi[0], ma[1], mi[2], ma[0], ma[1], mi[2]))
        self._remember('draw line "{} {} {}" "{} {} {}"\n'.format(mi[0], ma[1], mi[2], mi[0], ma[1], ma[2]))

        self._remember('draw line "{} {} {}" "{} {} {}"\n'.format(mi[0], mi[1], ma[2], ma[0], mi[1], ma[2]))
        self._remember('draw line "{} {} {}" "{} {} {}"\n'.format(mi[0], mi[1], ma[2], mi[0], ma[1], ma[2]))

        self._remember('draw line "{} {} {}" "{} {} {}"\n'.format(ma[0], ma[1], ma[2], ma[0], ma[1], mi[2]))
        self._remember('draw line "{} {} {}" "{} {} {}"\n'.format(ma[0], ma[1], ma[2], mi[0], ma[1], ma[2]))
        self._remember('draw line "{} {} {}" "{} {} {}"\n'.format(ma[0], ma[1], ma[2], ma[0], mi[1], ma[2]))
        self.script.write("\n")
        self.script.write("set htmd_graphics_mol({:d}) [molinfo top]".format(self.n))
        cmd = self.script.getvalue()
        vmd = getCurrentViewer()
        vmd.send(cmd)
コード例 #17
0
ファイル: util.py プロジェクト: jhprinz/htmd
def drawCube(mi, ma, viewer=None):
    from htmd.vmdviewer import getCurrentViewer
    if viewer is None:
        viewer = getCurrentViewer()

    viewer.send('draw materials off')
    viewer.send('draw color red')
    c = ''
    c += 'draw line "{} {} {}" "{} {} {}"\n'.format(mi[0], mi[1], mi[2], ma[0],
                                                    mi[1], mi[2])
    c += 'draw line "{} {} {}" "{} {} {}"\n'.format(mi[0], mi[1], mi[2], mi[0],
                                                    ma[1], mi[2])
    c += 'draw line "{} {} {}" "{} {} {}"\n'.format(mi[0], mi[1], mi[2], mi[0],
                                                    mi[1], ma[2])

    c += 'draw line "{} {} {}" "{} {} {}"\n'.format(ma[0], mi[1], mi[2], ma[0],
                                                    ma[1], mi[2])
    c += 'draw line "{} {} {}" "{} {} {}"\n'.format(ma[0], mi[1], mi[2], ma[0],
                                                    mi[1], ma[2])

    c += 'draw line "{} {} {}" "{} {} {}"\n'.format(mi[0], ma[1], mi[2], ma[0],
                                                    ma[1], mi[2])
    c += 'draw line "{} {} {}" "{} {} {}"\n'.format(mi[0], ma[1], mi[2], mi[0],
                                                    ma[1], ma[2])

    c += 'draw line "{} {} {}" "{} {} {}"\n'.format(mi[0], mi[1], ma[2], ma[0],
                                                    mi[1], ma[2])
    c += 'draw line "{} {} {}" "{} {} {}"\n'.format(mi[0], mi[1], ma[2], mi[0],
                                                    ma[1], ma[2])

    c += 'draw line "{} {} {}" "{} {} {}"\n'.format(ma[0], ma[1], ma[2], ma[0],
                                                    ma[1], mi[2])
    c += 'draw line "{} {} {}" "{} {} {}"\n'.format(ma[0], ma[1], ma[2], mi[0],
                                                    ma[1], ma[2])
    c += 'draw line "{} {} {}" "{} {} {}"\n'.format(ma[0], ma[1], ma[2], ma[0],
                                                    mi[1], ma[2])
    viewer.send(c)
    """
コード例 #18
0
ファイル: vmdgraphics.py プロジェクト: jeiros/htmd
    def __init__(self, text, xyz, color='red'):
        """ Displays a text in VMD.

        The function returns an instance of VMDGraphicsObject. To delete it, use the delete() method.

        Parameters
        ----------
        text : str
            The text
        xyz : list
            The position of the text
        color : str
            Color of the text
        """
        super().__init__(xyz)
        self._remember('draw materials off')
        self._remember('draw color {}'.format(color))

        self._remember('draw text "{} {} {}" "{}"\n'.format(xyz[0], xyz[1], xyz[2], text))
        self.script.write("\n")
        self.script.write("set htmd_graphics_mol({:d}) [molinfo top]".format(self.n))
        cmd = self.script.getvalue()
        vmd = getCurrentViewer()
        vmd.send(cmd)
コード例 #19
0
ファイル: vmdgraphics.py プロジェクト: jeiros/htmd
    def __init__(self, xyz, color='red', radius=1):
        """ Displays a sphere in VMD.

        The function returns an instance of VMDGraphicsObject. To delete it, use the delete() method.

        Parameters
        ----------
        xyz : list
            The center of the sphere
        color : str
            Color of the sphere
        radius : float
            The radius of the sphere
        """
        super().__init__(xyz)
        #self._remember('draw materials off')
        self._remember('draw color {}'.format(color))

        self._remember('draw sphere "{} {} {}" radius {}\n'.format(xyz[0], xyz[1], xyz[2], radius))
        self.script.write("\n")
        self.script.write("set htmd_graphics_mol({:d}) [molinfo top]".format(self.n))
        cmd = self.script.getvalue()
        vmd = getCurrentViewer()
        vmd.send(cmd)
コード例 #20
0
ファイル: modelhmm.py プロジェクト: alejandrovr/htmd
    def viewStates(self, protein=None, ligand=None, nsamples=20):
        from htmd.projections.metric import _singleMolfile
        from htmd.molecule.molecule import Molecule
        from htmd.vmdviewer import getCurrentViewer
        (single, molfile) = _singleMolfile(self.data.simlist)
        if not single:
            raise RuntimeError('Can''t visualize states without unique molfile')

        viewer = getCurrentViewer()
        colors = [0, 1, 3, 4, 5, 6, 7, 9]

        print('Active set includes macrostates: {}'.format(self.hmm.active_set))

        # dtraj = np.vstack(self.hmm.discrete_trajectories_full)
        res = self.hmm.sample_by_observation_probabilities(nsamples)
        refmol = Molecule(molfile)

        for i, s in enumerate(self.hmm.active_set):
            mol = Molecule(molfile)
            mol.coords = []
            mol.box = []
            # idx = np.where(dtraj == i)[0]
            # samples = np.random.choice(idx, 20)
            # frames = self.data.abs2sim(samples)

            frames = self.data.rel2sim(res[i])
            for f in frames:
                mol._readTraj(f.sim.trajectory[f.piece], frames=[f.frame], append=True)
            mol.wrap('protein')
            mol.align('protein', refmol=refmol)
            viewer.loadMol(mol, name='hmm macro ' + str(s))
            if ligand is not None:
                viewer.rep('ligand', sel=ligand, color=colors[np.mod(i, len(colors))])
            if protein is not None:
                viewer.rep('protein')
            viewer.send('start_sscache')
コード例 #21
0
 def delete(self):
     vmd = getCurrentViewer()
     for i in self.labelidx[::-1]:
         vmd.send('label delete Atoms {}'.format(i))
         VMDLabels.count -= 1
コード例 #22
0
ファイル: vmdgraphics.py プロジェクト: jeiros/htmd
 def delete(self):
     vmd = getCurrentViewer()
     vmd.send('mol delete htmd_graphics_mol({:d})'.format(self.n))